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-5,874,799,404,516,988,000 | Logo of nihpaAbout Author manuscriptsSubmit a manuscriptNIH Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
Nat Struct Mol Biol. Author manuscript; available in PMC Jul 1, 2009.
Published in final edited form as:
PMCID: PMC2615074
NIHMSID: NIHMS78951
The exosome contains domains with specific endoribonuclease, exoribonuclease and cytoplasmic mRNA decay activities
Abstract
The eukaryotic exosome is a ten subunit 3′ exoribonuclease complex responsible for many RNA processing and degradation reactions. How the exosome accomplishes this is unknown. We show that the PIN domain of Rrp44 is an endoribonuclease. The activity of the PIN domain prefers RNA with a 5′ phosphate, suggesting coordination of 5′ and 3′ processing. We also show that the endonuclease activity is important in vivo. Furthermore, the essential exosome subunit Csl4 does not contain any essential domains, but its zinc-ribbon domain is required for exosome-mediated mRNA decay. These results suggest that specific exosome domains contribute to specific functions, and that different RNAs interact with the exosome differently. The combination of an endoribonuclease and exoribonuclease activity appears to be a widespread feature of RNA degrading machines.
Virtually all RNAs are processed from longer precursors. Although the removal of 3′ extensions appears to be a simple enzymatic reaction, eukaryotic cells contain multiple endoribonucleases and 3′ exoribonucleases{Moser, 1997 #786; Mian, 1997 #787; Deutscher, 2000 #571; Zuo, 2001 #553}. These exoribonucleases can act redundantly for some reactions, but are very specific for other functions5. In addition to these RNA processing reactions that generate mature RNAs, 3′ exoribonucleases and endonucleases also carry out mRNA degradation reactions6,7 that can be an important determinant for mRNA quality control8,9. The same RNase can process some substrates and completely degrade others. It is largely unknown what determines the specificity of different RNases for their particular substrates, or for processing versus decay.
The exosome is a major 3′ exoribonuclease that is present in all eukaryotes, but whose function has been most extensively characterized in Saccharomyces cerevisiae (yeast)10,11. The yeast exosome is responsible for the 3′-end processing of stable RNAs including rRNA, snRNA, and snoRNA, and the degradation of RNAs such as the 5′ external transcribed spacer of the rRNA precursor and aberrant mRNAs that lack a stop codon or a poly(A) tail7-14.
The core exosome contains nine subunits and shows extensive structural similarity to bacterial PNPase and archaeal exosomes (Fig. 1A)15-20. These nine subunits are all essential for viability. Six subunits have an RNase PH domain, and form a ring structure in the exosome15. Although these six subunits show clear sequence and structural similarity to RNases, all six subunit in the yeast and human exosome lack important catalytic residues and are inactive21. The six PH-ring subunits can not assemble into a PH-ring in vitro, but when the three cap proteins are added, a stable core exosome can be assembled15. The crystal structure shows that each cap protein contacts two neighboring subunits of the PH-ring. These observations suggest that the cap proteins carry out an essential structural role by bridging interactions between PH domains (Fig. 4A)15. A second possible function of the cap proteins is to bind exosome substrates, since each contains three putative RNA binding domains11,20,22. Finally, a point mutation in one of the cap proteins (Csl4) disrupts the interaction between the core exosome and one of its cofactors8. The exosome requires many cofactors, and a third possible function for the cap proteins is to provide binding sites for these cofactors.
Figure 1
The N-terminal region of Rrp44 has ribonuclease activity. (a) The yeast exosome contains three layers. The exosome contains a PH-ring of 6 proteins with an RNase PH domain. Assembly and/or stability of the PH-ring requires three additional proteins that ...
Figure 4
The essential Csl4 does not contain any essential domains, but its zinc-ribbon domain is required for cytoplasmic exosome-mediated mRNA decay. (a) Rrp4 and Rrp40 make extensive contacts with two neighboring subunits of the PH-ring. Csl4 makes extensive ...
One important difference between the yeast exosome and PNPase and the archaeal exosome is that the yeast exosome contains a tenth essential subunit (Rrp44), which is homologous to bacterial RNase II (Fig. 1A+B), and is responsible for the 3′ exoribonuclease activity of the exosome21,23-26. Importantly, while Rrp44 is an essential gene, a point mutation that inactivates its exoribonuclease activity in vitro is viable21, suggesting that either the exoribonuclease activity may not be a central feature of the exosome, or the point mutant protein retains partial exoribonucleolytic activity in vivo.
The N-terminus of Rrp44 contains a CR3 domain and a PIN domain (Fig. 1B). The CR3 domain is a small domain of unknown function that contains three conserved cysteine residues. PIN domains were initially thought to have some regulatory or signaling function, but recent crystal structures of PIN domains revealed a putative active site with similarity to RNase H27,28. Indeed, some PIN domains have endoribonuclease activity, including the SMG6 protein, which is involved in nonsense-mediated decay27-32. PIN domains contain four acidic amino acid residues (Asp91, Glu120, Asp171 and Asp198 in Rrp44) and mutations in the third residue abolish activity of PIN domains in vitro and in vivo29,33,34.
In this paper we show that the Rrp44 PIN domain is an active endoribonuclease, revealing that the exosome does not only have exoribonuclease activity, but also endoribonuclease activity. Furthermore, we further characterize the functions of the cap proteins of the yeast exosome, and show that while Rrp4 and Rrp40 might have a largely structural role, Csl4 does not appear to have an important role in exosome structure, but instead appears to have specific domains that are required for specific functions.
Results
The exosome contains an endoribonuclease domain
To test whether the Rrp44 PIN domain contains endonuclease activity, we purified a truncated Rrp44 as a GST fusion from E. coli. This truncated Rrp44 contains the PIN domain, but lacks the RNB domain, and has robust nuclease activity in vitro on several RNA substrates (Fig. 1), while GST by itself does not (Fig. 1D). The activity level of the truncated Rrp44 was similar to the activity level of the full length protein (although under different conditions; Supplemental Fig. 1 online). Figure 1H shows that mutation of the third conserved acidic residue (Asp171) in the Rrp44 PIN domain abolished the endoribonuclease activity, as has been shown for some other PIN domains either in vitro or in vivo29,33,34. We conclude that the PIN domain of Rrp44 is a nuclease.
Other PIN domains and the related RNases H act as endonucleases. To test whether the Rrp44 PIN acts as an endonuclease we used 5′ or 3′ labeled substrates. An exonuclease will yield only labeled mononucleotides with one of these substrates. In contrast, the PIN domain yielded a very similar pattern of labeled oligonucleotides with each substrate showing that it is an endonuclease (Fig. 1E). Interestingly, the PIN domain was dramatically more active on substrates with a 5′ monophosphate than on substrates with a 5′ hydroxyl (Fig. 1G), which may have important implications (see discussion). As expected for an endonuclease, the PIN domain also had some activity on circular U30 (Supplemental Fig. 1B online). However, degradation of circular RNA was inefficient, probably because it lacks a free 5′ phosphate. All of these results indicate that the Rrp44 PIN domain is an active endoribonuclease, as has been shown for SMG629,32.
Either the endoribonuclease or exoribonuclease activity is sufficient for exosome function
To address whether this endonuclease activity is important for exosome function, we generated truncations and point mutants of Rrp44. C-terminal truncations that removed the RNase II homology, but left the CR3 and PIN domains, allowed for slow growth (Fig. 2A; Supplemental Fig. 2 online). Previously it was shown that a point mutation inactivating the catalytic activity of the RNB domain is viable21. The residual growth we observed upon deletion of the RNB domain rules out the possibility that the mutated RNB domain was viable due to some low level activity in vivo. Instead, our results show that exoribonuclease activity is not a critical feature of the exosome core. C-terminal truncations that also removed part of the PIN domain, or truncation from the N-terminus, did not support any growth. The smallest viable Rrp44 allele we generated includes the CR3 and PIN nuclease domains (amino acids 1-235). We conclude that the PIN domain is essential for exosome function, but we can not exclude the alternative that the PIN domain (also) functions separate from the exosome.
Figure 2
The PIN active site is important for exosome function. (a) The N-terminal region of Rrp44 is required and sufficient for viability. An rrp44Δ strain complemented by full length RRP44 on a plasmid with a URA3 marker was transformed with LEU2 plasmids ...
To further address the importance of the CR3 and PIN domains, we made point mutants in conserved residues. Mutating the three conserved cysteines of the CR3 domain caused slow growth (Fig. 2B), thus both N-terminal truncations and point mutants indicate an important role for the CR3 domain. In contrast, the D171A point mutation that inactivates the PIN domain (or mutations in the other three conserved acidic residues) does not have an obvious growth phenotype (Fig. 2C; Supplemental Fig. 3 online). However, combining the viable PIN mutations with either the viable D551N or a viable C-terminal truncation resulted in no growth (Fig. 2C and D; Supplemental Fig. 3 online). These results suggest that either active site is sufficient for viability, but simultaneous inactivation of both catalytic sites results in a non-functional exosome.
The exosome carries out both RNA processing and RNA degradation reactions. Endonuclease activity might be well-suited for processing reactions, but exonuclease activity would be more appropriate for degradation reactions. We therefore tested the hypothesis that the PIN domain of Rrp44 is sufficient for exosome-mediated RNA processing reactions, while the RNB domain is required for exosome-mediated RNA decay. Figure 3A shows that truncations lacking the RNase II homologous domain accumulate the 5′ ETS and 7S precursors to 5.8S rRNA. Similarly, 7S processing and 5′ ETS degradation intermediates accumulated due to the D551N mutation in the RNB domain. We did not observe any similar degradation or processing intermediates due to the D171A mutation in the PIN domain, and the effect of the combination of D551N with D171A appeared similar to the D551N single mutant (Fig. 3B). Thus, both degradation and processing functions of the exosome require the RNB domain. An alternative explanation for the presence of two catalytic sites is that it increases the efficiency of the overall reaction. Under this hypothesis the endo- and exonuclease domains do not have separate substrates, but both may act together on most or all exosome substrates.
Figure 3
The RNB domain of Rrp44 is required for both RNA processing and RNA degradation activities of the exosome. (a) The indicated Rrp44 truncations were expressed in a GAL::rrp44 yeast strain. RNA was isolated from cultures grown in dextrose (to inhibit ...
The essential Csl4 does not contain an essential domain
To gain further insight into the structure-function relationship of the exosome, we next focused on the function of the three “cap” proteins. The Csl4 subunit contains an N-terminal domain which resembles RPL27, a central S1 domain, and a C-terminal domain that shows structural similarity to zinc ribbons, although the zinc-coordinating residues have been mutated. In addition, the yeast Csl4 contains a 38 amino acid linker that is absent in Csl4 from humans and most other eukaryotes. The first 22 amino acid residues of this inserted sequence include ten glutamate and two aspartate residues. To test which domains of Csl4 are essential, we made several truncations. Strikingly, each of the domains could be removed, and either the RPL27-like or S1+Zn-ribbon domains are sufficient for the essential function of the exosome (Fig. 4B; Supplemental Fig. 4 online). Thus, the essential Csl4 does not appear to have an essential domain.
The other two cap proteins, Rrp4 and Rrp40 each contain an N-terminal RPL27-like domain, a central S1 domain, and a C-terminal KH domain. In contrast to Csl4, eight truncations of Rrp4 or Rrp40 each failed to complement rrp4Δ and rrp40Δ (Supplemental Fig. 5 online). Thus, the observation that the essential Csl4 does not contain any essential domains is specific for Csl4. Furthermore, the function of Rrp4 or Rrp40 could not be provided by chimeric proteins where one domain of Rrp4 was replaced by the paralogous Rrp40 domain (or vice versa), or by co-expressing two parts of Rrp4 (Supplemental Fig. 6 online). Overall, these results are consistent with Rrp4 and Rrp40 providing important bridging contacts for the PH-ring15. However, Csl4 does not appear to share this function.
The Zinc-ribbon like domain of Csl4 is required for exosome-mediated mRNA decay
Although the zinc-ribbon domain of Csl4 is not required for the essential exosome function(s), three assays each indicate that it is required for cytoplasmic exosome-mediated mRNA decay. First, PGK1-nonstop mRNA is normally rapidly degraded, but is stabilized upon inactivation of the cytoplasmic exosome (e.g. ski7Δ). The Csl4 truncation that deletes the zinc ribbon domain results in a defect similar to ski7Δ (Fig. 4C). Second, the zinc ribbon is also required for the rapid degradation of the his3-nonstop mRNA (Supplemental Fig. 7 online). Third, a role of the exosome in general mRNA decay can be monitored through synthetic lethality with dcp1-2 mutation, and this assay also indicates that the zinc ribbon of Csl4 is required for exosome-mediated mRNA decay (Supplemental Fig. 7 online). Therefore, the zinc-ribbon domain of Csl4 is not required for exosome structure or the essential exosome function(s), but is required for cytoplasmic exosome-mediated mRNA decay.
Discussion
The exosome contains an endoribonuclease activity that is stimulated by a 5′ phosphate
We show for the first time that Rrp44 contains a previously overlooked endoribonuclease domain – the PIN domain. Two observations explain why it has previously been reported that Rrp44 with a mutation in the RNB domain does not have any nuclease activity in vitro21,24. First, those assays were carried out under conditions favorable for the activity of RNB domains (i.e. Tris buffer and Mg++ ions). Under similar conditions we also failed to detect significant activity (Supplemental Fig. 1 online). Second, we observed robust endonuclease activity on truncated proteins, but much less activity on full length protein or any truncations that did not remove CSD1 (data not shown). This latter observation suggests that CSD1 and perhaps other domains of the exosome regulate the activity of the PIN domain. Nevertheless, the activity level of the truncated Rrp44 under conditions where PIN domains are generally active (i.e. HEPES buffer and Mn++ ions), was similar to the activity level of the full length protein under conditions for the RNB domain (Supplemental Fig. 1 online). This suggests that although the activity was not previously detected, it is a robust activity that is likely important in vivo under some circumstances or on some substrates that remain to be determined.
Our observation that Rrp44 needs either its endonuclease or exonuclease activity suggests that the endonuclease is active and important in vivo. Furthermore, this functional redundancy appears to be a general theme for a wide variety of RNases and is similar to that found for Rrp44 and Rrp6 in yeast21, Xrn1 and the exosome in yeast7,35, several combinations of Rex1, Rex2, Rex3, and Rrp6 in yeast5, and several exoribonuclease combinations in E. coli{Andrade, 2008 #827; Deutscher, 2000 #571}.
In the process of testing 5′ or 3′ labeled substrates in in vitro degradation reactions, we noticed that substrates with a 5′ phosphate are more rapidly degraded than substrates with a 5′ hydroxyl or circular substrates. This is analogous to what has been described for the bacterial RNase E, which prefers a 5′ monophosphate containing substrate, over a circular RNA or a linear RNA with a 5′ hydroxyl or 5′ triphosphate37. Despite this functional similarity, we have not detected any sequence similarity between Rrp44 and RNase E. The 5′ end stimulated activity of Rrp44 might have several important consequences for the substrate specificity of the endonuclease activity. First, PIN domains are part of a large group of enzymes and ribozymes that use two metal ion catalysis27-29,31. All of these enzymes generate a 5′ cleavage product with a 3′ hydroxyl, and a 3′ cleavage product with a 5′ monophosphate (reviewed in38). This cleavage mechanism suggests that the endonuclease activity of Rrp44 might cleave most primary transcripts relatively inefficient, but the 3′ cleavage product of an initial cleavage will have a 5′ phosphate and be a preferred substrate. Such preferred subsequent cleavage might ensure that RNA degradation is rapidly completed once it has been initiated. Second, many RNA species are processed both at the 5′ and 3′ end, and in most cases it is not clear how these events are coordinated. One possibility offered by our results is that 5′ end processing generates a 5′ monophosphate, which stimulates 3′ processing by the Rrp44 endonuclease. Testing these hypotheses in detail will require the identification of all, or most, of the endogenous substrates on the endonuclease activity of Rrp44.
A specific domain of the exosome core is required for specific exosome functions
The exosome contains ten different essential subunits containing 21 domains. How this structural complexity correlates with the multiple functions of the exosome is not clear. To begin to address these questions, we generated many deletions of domains, both in Rrp44 and in the three cap proteins. The cap proteins have been suggested to be important for exosome structure, by simultaneously interacting with two different PH-ring subunits. The finding that the RPL27-like domain and S1 domain of Csl4 are not both essential is inconsistent with Csl4 providing important bridging interactions between subunits of the PH-ring, since deletion of the S1 and Zn-ribbon domains results in Csl4 only interacting with Mtr3p (Fig. 4A). Conversely, deletion of the RPL27-like domain results in Csl4 only interacting with Rrp43p.
A high throughput screen previously identified transposon insertions in the essential CSL4 gene39. Surprisingly, these insertions are viable, which is explained by our observation that a severely truncated Csl4 protein is still functional. Similarly, T-DNA insertions into the Arabidopsis CSL4 gene are viable40. This observation was interpreted to mean that Csl4 is not an essential subunit of the Arabidopsis exosome, but our results suggest the alternative explanation that the T-DNA mutants produce a truncated Csl4 that retains some function.
A corollary of the conclusion that Csl4 is not important for exosome structure is that it must be functionally important. One possible model is that Csl4 provides important contacts with either an essential substrate RNA or an essential cofactor. If such an RNA or protein molecule makes contacts with both the RPL27-like domain and the S1 or Zn-ribbon domains, it might still be able to interact if either binding site is deleted, but not if both are deleted. Interestingly, some surface exposed conserved amino acid residues of the Csl4 Zn-ribbon domain that are not essential, become essential if the RPL27-like domain is deleted (Supplemental Fig. 4 online). This is consistent with these residues forming one binding site and the RPL27-like domain containing a second binding site for an exosome cofactor. Csl4 is also thought to provide the binding sites for Ski78, thus Csl4, and perhaps the other cap proteins, may provide important contacts for exosome cofactors, and thus be important for specific exosome functions.
The exosome core may have multiple ways to interact with RNA substrates
It is not clear how the exosome interacts with RNA substrates. A crystal structure of the archaeal exosome in complex with RNA19 suggests that RNA might go through the center of the PH ring as depicted in figure 1A. Our conclusion that Csl4 provides important contacts for interaction with cytoplasmic cofactors appears most consistent with the suggestion that cytoplasmic mRNA follows this route. On the other hand, it has been proposed that RNA may gain access to Rrp44 without going through the PH-ring25. The observation that the endonuclease activity is stimulated by a 5′ monophosphate indicates that Rrp44 can interact with the 5′ end of an exosome substrate. Since the 3′ exoribonuclease active site must interact with the 3′ end, Rrp44 appears to be able to interact with both ends of substrate RNAs. This is unlikely to be compatible with threading the RNA through the PH-ring. Thus our observations appear more consistent with the idea that the exosome can interact with RNA substrates in two different ways (compare fig. 1A to fig. 5). Moreover, we suggest that substrates that access Rrp44 directly might be identifiable by looking for substrates that are processed in vivo in a 5′ end dependent manner.
Figure 5
A model of how RNA might access the 5′ end stimulated endonuclease activity of Rrp44
An endoribonuclease and exoribonuclease are combined in mRNA degrading machines throughout nature
We show for the first time that the exosome contains both an endonuclease and exonuclease activity. While this is unexpected for the exosome, it is not unique in nature. It has been suggested that the archaeal exosome also contains a PIN domain41, which could provide the archaeal exosome with an endonuclease activity. Similarly, the E. coli degradosome combines the RNase E endoribonuclease with the PNPase 3′ exoribonuclease42,43, and metazoan P-bodies combine the argonaute endoribonuclease with the Xrn1 5′ exoribonuclease, and the Ccr4, Caf1, and Pan2 3′ exoribonucleases44-49. Thus, combining endoribonucleases and exoribonucleases into one RNA degrading machine is widespread in nature, which suggests that this combination offers a fundamental advantage to the cell.
Materials and methods
Strains
The strains, plasmid and oligonucleotides we used are described in detail in supplementary material (online). The heterozygous diploids RRP44/rrp44Δ, CSL4/csl4Δ, RRP4/rrp4Δ and RRP40/rrp40Δ have been described and were obtained from Open Biosystems50. We transformed each of these strains with a URA3 plasmid that encoded the corresponding wild-type exosome subunit, We sporulated the transformants and obtained haploid progeny spores by the hydrophobic spore isolation method essentially as described51. Isolated spores were germinated to generate the deletion strains complemented with the URA3 plasmid. The GAL::rrp44, GAL::csl4, GAL::rrp4 and GAL::rrp40 strains have been previously described and were obtained from Phil Mitchell and David Tollervey10,11.
Plasmids
All yeast plasmids are low copy plasmids that contain a yeast centromere and the endogenous promoter and 3′ flanking region to control expression of the exosome subunits and were verified by sequencing.
To generate C-terminal truncations, we initially PCR amplified several hundred base pairs of the 3′ flanking region of the gene of interest and cloned it into pRS41552, which contains a LEU2 marker. We then PCR amplified the promoter and desired part of the coding region, and cloned it into the plasmid described above. N-terminal truncations were generated similarly, except that the promoter was PCR amplified and cloned first, and the truncated coding region and 3′ flanking region were added in the second step.
We generated GST fusion plasmids by PCR amplifying the RRP44 coding region from the plasmids described above, digesting the PCR product with EcoRI and XhoI, and ligating into pGEX-4T-1 (GE Healthcare).
We created site-directed mutants using the QuikChange II kit (Stratagene). Each oligonucleotide also changes a restriction site. We screened putative mutants by restriction digestion and verified them by sequencing. To combine point mutations in the PIN domain of Rrp44 with the D551N mutant in the RNB domain, we digested the plasmids with each single mutant with SacI and PshAI and ligated them together. PshAI cuts at a unique site within the CSD2 domain.
Overexpression and Purification of recombinant Rrp44
Full length and truncated Rrp44 fused to GST were expressed in the Rosetta(DE3) E. coli strain. We grew cultures at 30°C in 2 liter TB medium supplemented with 200 μg/ml ampicillin and 34 μg/ml chloramphenicol to an OD600 of 1.2 and then induced expression by addition of 0.2 mM IPTG and incubation at 18°C overnight. We harvested cells by centrifugation and froze them. Cells were thawed on ice, resuspended in 30 ml PBS buffer pH 8 with 10 mM DTT and 1 mM PMSF, and lysed using the French press. We treated the crude extracts with 5 units Benzonase (Sigma) for 30 min at 0°C, clarified the extract by 30 min centrifugation at 10,000 × g, and loaded it onto a GSTrap™ FF 1 ml column (GE healthcare) equilibrated in binding buffer. We eluted proteins with a 0-10 mM glutathione gradient in 50 mM Tris-HCl pH8.5, 10 mM DTT. We pooled fractions containing the purified protein and loaded them onto a gel filtration column (Superdex 75 10/300 GL or a Superose 12 10/300 GL - GE Healthcare, depending on the protein size) in 20 mM Tris-HCl, 150 mM NaCl, 5 mM MgCl2 and 10 mM DTT buffer at pH8. We concentrated the eluted protein by centrifugation at 15 °C with Vivaspin 500 Centrifugal Concentrators (Vivaspin). We determined protein concentrations by spectrophotometry using a Nanodrop and added 50 % (v/v) glycerol to the final fractions prior storage at -20 °C.
RNase assays
RNase assays contained 100-500 nM protein, 200 nM 5′ or 3′ end labeled U30 or A30 RNA or an internally labeled 5′ETS RNA transcribed by T7 RNA polymerase, and 20 mM HEPES pH 7.5, 150 mM NaCl, 3 mM MnCl2, 1 mM DTT.
Growth assays
We performed growth assays essentially as previously described9,53. Briefly, we grew strains in appropriate liquid selection media overnight at 30°C (or 23°C for temperature-sensitive mutants). We diluted these cultures in appropriate selection media to a starting OD600 of 0.2. We grew the cultures until they reached an OD of 0.8, serially diluted them in 96-well plates by a factor of five, and spotted them onto appropriate media. We generally incubated these plates for 2-3 days at 23°C, 30°C, or 37°C. To monitor the slow growth of Rrp44 truncations, we incubated the plates for up to 20 days.
Northern blotting
Stability of PGK1-nonstop mRNA8, and 5.8S rRNA processing and 5′ETS degradation54 were assayed as previously described.
Supplementary Material
Acknowledgments
We are grateful to Todd Link and Richard Brennan for help with calculating the buried surfaces between the different domains of the cap proteins and the PH-ring and Ale Klauer for technical assistance. GAL::rrp44, GAL::csl4, GAL::rrp4, and GAL::rrp40 strains were kindly provided by Phil Mitchell (University of Sheffield) and David Tollervey (University of Edinburgh). Roy Parker, Miles Wilkinson, Michelle Steiger and members of the van Hoof and Arraiano labs gave insightful comments on the manuscript. This research was supported by the Pew Scholarship Program in the Biomedical Sciences and by the National Institutes of Health (GM069900) to A.v.H.. The University of Texas at Houston Medical School-Summer Research Program supported E.G.D and M.S.-R. The work at the ITQB was supported by Fundação para a Ciência e a Tecnologia (FCT), Portugal. A.B. was a recipient of a post-doctoral fellowship from FCT, Portugal.
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-1,051,666,083,898,471,300 | Definitions
from Wiktionary, Creative Commons Attribution/Share-Alike License.
• noun biochemistry Any enzyme that catalyses the hydrolysis of mannose glycosides.
Etymologies
Sorry, no etymologies found.
Examples
• Kuntz DA, Rose DR, Pinto BM (2005) A combined STD-NMR/molecular modeling protocol for predicting the binding modes of the glycosidase inhibitors kifunensine and salacinol to Golgi alpha-mannosidase II.
PLoS ONE Alerts: New Articles
• Activity on 4-MeUMB-Man was greater, permitting full Michaelis-Menten kinetics and allowing description of the SpGH38 as an α − mannosidase with a kcat of 1. 8±0.24 min − 1 and K.
PLoS ONE Alerts: New Articles
• Furthermore, mouse knock-outs show that mannosidase II deficient animals suffer from lupus-like auto immune diseases
PLoS ONE Alerts: New Articles
• Drosophila melanogaster Golgi alpha-mannosidase II through the structural analysis of covalent reaction intermediates.
PLoS ONE Alerts: New Articles
• Kuntz DA, Ernber B, Singh H, Moremen KW, et al. (2008) Probing the substrate specificity of Golgi alpha-mannosidase II by use of synthetic oligosaccharides and a catalytic nucleophile mutant.
PLoS ONE Alerts: New Articles
• Here we show that the Streptococcus pyogenes (M1 GAS SF370) GH38 enzyme (Spy1604; hereafter SpGH38) is an α − mannosidase with specificity for α − 1,3 mannosidic linkages.
PLoS ONE Alerts: New Articles
• Drosophila GH38 α − mannosidase II, which has been shown to be a retaining α − mannosidase that targets both α − 1,3 and α − 1,6 mannosyl linkages, an activity that enables the enzyme to process GlcNAc (Man) 5 (GlcNAc) 2 hybrid N-glycans to GlcNAc (Man) 3 (GlcNAc) 2.
PLoS ONE Alerts: New Articles
• The two enzymes, 'alpha-man' (alpha-mannosidase) and 'beta hex' (beta delta N-acetylhexosaminidase), are specifically linked to fruit softening that happens during ripening.
SciDev.Net
• One possible role for the GH38 α − mannosidase and GH84 β − GlcNAcase enzymes might therefore be in the subsequent intracellular utilization of The sequence of full length S. pyogenes α-mannosidase II, coding for SpGH38 residues
PLoS ONE Alerts: New Articles
• We have shown that The S. pyogenes ORF spy1604 encodes an α − 1,3 mannosidase that is active on disaccharides, some aryl glycosides and can also effectively deglycosylate human
PLoS ONE Alerts: New Articles
Comments
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Open Access
Genome-scale reconstruction and system level investigation of the metabolic network of Methylobacterium extorquensAM1
• Rémi Peyraud1,
• Kathrin Schneider1,
• Patrick Kiefer1,
• Stéphane Massou2, 3, 4,
• Julia A Vorholt1 and
• Jean-Charles Portais2, 3, 4Email author
BMC Systems Biology20115:189
https://doi.org/10.1186/1752-0509-5-189
Received: 6 August 2011
Accepted: 10 November 2011
Published: 10 November 2011
Abstract
Background
Methylotrophic microorganisms are playing a key role in biogeochemical processes - especially the global carbon cycle - and have gained interest for biotechnological purposes. Significant progress was made in the recent years in the biochemistry, genetics, genomics, and physiology of methylotrophic bacteria, showing that methylotrophy is much more widespread and versatile than initially assumed. Despite such progress, system-level description of the methylotrophic metabolism is currently lacking, and much remains to understand regarding the network-scale organization and properties of methylotrophy, and how the methylotrophic capacity emerges from this organization, especially in facultative organisms.
Results
In this work, we report on the integrated, system-level investigation of the metabolic network of the facultative methylotroph Methylobacterium extorquens AM1, a valuable model of methylotrophic bacteria. The genome-scale metabolic network of the bacterium was reconstructed and contains 1139 reactions and 977 metabolites. The sub-network operating upon methylotrophic growth was identified from both in silico and experimental investigations, and 13C-fluxomics was applied to measure the distribution of metabolic fluxes under such conditions. The core metabolism has a highly unusual topology, in which the unique enzymes that catalyse the key steps of C1 assimilation are tightly connected by several, large metabolic cycles (serine cycle, ethylmalonyl-CoA pathway, TCA cycle, anaplerotic processes). The entire set of reactions must operate as a unique process to achieve C1 assimilation, but was shown to be structurally fragile based on network analysis. This observation suggests that in nature a strong pressure of selection must exist to maintain the methylotrophic capability. Nevertheless, substantial substrate cycling could be measured within C2/C3/C4 inter-conversions, indicating that the metabolic network is highly versatile around a flexible backbone of central reactions that allows rapid switching to multi-carbon sources.
Conclusions
This work emphasizes that the metabolism of M. extorquens AM1 is adapted to its lifestyle not only in terms of enzymatic equipment, but also in terms of network-level structure and regulation. It suggests that the metabolism of the bacterium has evolved both structurally and functionally to an efficient but transitory utilization of methanol. Besides, this work provides a basis for metabolic engineering to convert methanol into value-added products.
Keywords
Metabolic NetworkGlyoxylateGlyoxylate CycleCentral Carbon MetabolismMethylotrophic Bacterium
Background
Methylotrophs are microorganisms able to grow on reduced C1 compounds such as methane and methanol as sole source of carbon and energy. Methylotrophy has gained increasing interest over the past decade for both basic and applied purposes, since methanol can be produced from diverse renewable sources and represents a valuable feedstock for biotechnological applications [1, 2]. Recent progress in the biochemistry, genetics, genomics, and physiology of methylotrophic bacteria has shown that methylotrophy is a phenomenon much more widespread and versatile than initially assumed [3]. The phylogenetic distribution of methylotrophy is broad and spans over a range of phyla and genera [3]. Methylotrophic bacteria are adapted to various lifestyles and ecological niches (soil, water sediments, plant roots, phyllosphere), and are involved in a number of important biological or biogeochemical processes, in particular the global carbon cycle. Methylotrophy encompasses diverse metabolic capabilities or behaviors that were used to classify them, e.g. obligate vs facultative methyltrophy, heterotrophic vs autotrophic growth, aerobic vs anaerobic metabolism. Such genetic and biochemical diversity may explain the ecological success of methylotrophs, which can represent dominant microbial populations in specific environments, e.g. plant leaves [4].
From the biochemical point of view, methylotrophy relies on specific pathways (C1 pathways) ensuring all growth requirements. Energetic requirements are enabled by dissimilation pathways, which involve a series of three basic steps: i) the oxidation of primary C1 substrates - methanol, methylamine - typically into the toxic intermediate formaldehyde, ii) the oxidation of the latter compound into formate, and iii) formate oxidation into carbon dioxide (CO2). In addition, alternative dissimilation mechanism exist in which formate is not involved. The assimilation of C1-units can be achieved by different mechanisms starting from either formaldehyde (ribulose-monophosphate pathway, RuMP), CO2 (Calvin-Benson-Bassham cycle, CBB) or methylene-tetrahydrofolate (Me-THF) + CO2 (serine cycle). Novel enzymes, biochemical mechanisms, and metabolic pathways have been discovered, resulting in a more complete description of methylotrophic pathways and their diversity. Interestingly, these findings do not modify our current view of the general organization of C1 pathways, but show that many more alternative enzymes or pathways than initially assumed carry out each of the basic steps of methylotrophy. Moreover, a growing number of newly discovered methylotrophs have been investigated, showing that different combinations of the various pathways can be found in nature, and leading to the concept of a modular metabolism [5].
Considerable progress was made in the understanding of the biochemistry and physiology of methylotrophy, and valuable insights were obtained regarding the organization and operation of central carbon metabolism [68]. However, a complete, system-level description of methylotrophy metabolism is currently lacking. The comprehensive understanding of bacterial physiology requires a detailed knowledge of the complete metabolic potential of the studied organism, but such knowledge is currently missing and no genome-scale metabolic network has been so far established for any methylotrophic bacterium. In consequence, little is currently known about the network-scale organization of methylotrophy, the specific properties of methylotrophic networks, and how the methylotrophic capacity emerges from this organization, especially in facultative representatives. Among the recently sequenced organisms, the Alphaproteobacterium Methylobacterium extorquens AM1 is a major model of methylotrophic bacteria. This facultative methylotroph is able to grow on C1- but also on multicarbon (C2-C4) compounds. Methylobacterium spp. are part of the abundant population of bacteria systematically found in the phyllosphere [4, 9], where they benefit from plant-derived methanol [10, 11]. The biochemistry, genetics, and physiology of M. extorquens AM1 has been extensively investigated, and allowed the discovery of major methylotrophic pathways, including the serine cycle [1214], the tetrahydromethanopterin (H4MPT)-dependent pathway for formaldehyde oxidation [15, 16], and of a number of novel enzymes or enzyme functions (e.g., pyrroloquinoline quinine (PQQ)-dependent methanol dehydrogenase, formaldehyde activating enzyme, methylene-H4MPT dehydrogenases coupled to pyridine nucleotides, and formyl-methanofuran hydrolase). The central metabolic pathways were progressively unraveled, and the application of novel experimental strategies - metabolic modeling, metabolic flux analysis, omics technologies - provided valuable insights into the topology and operation of central carbon metabolism [68, 17]. Finally, the pathway for methanol assimilation in M. extorquens AM1 was recently completed with the discovery of the ethylmalonyl-CoA pathway (EMCP), an alternative to the glyoxylate cycle for the synthesis of glyoxylate, which encompasses an unusual series of 12 reactions where intermediates are all Coenzyme A (CoA) esters [18, 19]. Finally, the genome of this bacterium was recently sequenced and annotated [20], providing inevitable information for genome-scale investigations.
In this work, we report on the integrated, system-level investigation of the metabolic network of the facultative methylotroph M. extorquens AM1, as a valuable model of methylotrophic bacteria. In order to obtain a comprehensive understanding of the biochemistry and physiology of this bacterium, we first evaluated its complete metabolic potential by compiling current biochemical knowledge and genome annotation data into a comprehensive genome-scale representation of the metabolic network. Then, we performed both in silico and experimental investigations to identify the subnetwork operating during methylotrophic growth, in order to analyze structurally and functionally the system-level organization of methylotrophy with an emphasis on the properties of the organization of central carbon metabolism.
Results
Metabolic network reconstruction
The genome-scale (GS) metabolic network of M. extorquens AM1 was reconstructed according to previously established guidelines [21]. The details of the process are given in material and methods and are schematically shown in Additional file 1. Briefly, the GS metabolic network was obtained by integrating relevant information collected from i) genome annotation [20], ii) published physiological, genetic and biochemical studies in M. extorquens AM1 and closely related organisms iii) biochemical information contained in databases [2224], vi) complementary investigations (biomass quantification), and intensive refinement (Additional file 2, 3). The chemical composition of M. extorquens AM1 cell was determined experimentally or taken from available literature (Table 1 and Additional file 4) and used to define the biosynthetic needs and corresponding pathways.
Table 1
Chemical content and physiological parameters of M. extorquens AM1 cells growing on methanol
Macromolecule
% Cell Dry Weight ± σ
Data source
Organism source
Protein
59.13 ± 2.11
This study
M. extorquens AM1
Carbohydrate
16.43 ± 1.09
This study
M. extorquens AM1
Rhamnose (polymer)
8.92 ± 0.92
This study
M. extorquens AM1
Glucose (polymer)
5.62 ± 0.52
This study
M. extorquens AM1
Trehalose
1.22 ± 0.20
This study
M. extorquens AM1
Glucosamine (polymer)
0.09 ± 0.67
This study
M. extorquens AM1
RNA
8.20 ± 0.68
This study
M. extorquens AM1
Fatty acid
4.95 ± 0.29
This study
M. extorquens AM1
DNA
3.00 -
Neidhart et al.; GC content: Vuilleumier et al. (2009)
E. coli
PHB
2.36 ± 0.05
This study
M. extorquens AM1
Polyamine
0.40 -
Neidhart et al.
E. coli
Carotenoid
0.023 -
Konovalova et al. (2007)
M. extorquens AM1
Intracellular metabolites
2.64 -
Kiefer et al. (2008); Guo et al. (2006); Guo et al. (2007); Vorholt et al. (1998); Crowther et al. (2008)
M. extorquens AM1
Inorganic ions
1.01 -
Neidhart et al.
E. coli
Cofactors
0.22 -
Neidhart et al.
E. coli
SUM
98.36
Physiological parameters
value ± σ
units
Data sources
Organism source
Growth rate
0.168 ± 0.003
h-1
This study
M. extorquens AM1
Specific methanol uptake rate
15.0 ± 0.25
mmol.g-1.h-1
This study
M. extorquens AM1
Specific proton production rate
0.22 ± 0.01
mmol.g-1.h-1
This study
M. extorquens AM1
Growth-associated ATP maintenance
59.81 -
mmol.g-1
Neidhart et al.
E. coli
Macromolecular building costs
26.65 -
mmol.g-1
This study
M. extorquens AM1
Non-Growth-associated ATP maintenance
9.5 -
mmol.g-1.h-1
Rokem et al. (1978)
Methylobacterium
The refined reconstruction was converted into a mathematical model using CellNetAnalyser [25] and the network was checked for self-consistency and curated to allow biosynthesis of all cell components from each of the 12 carbon sources established for M. extorquens (Additional file 5). In addition, flux balance analysis (FBA) was used to calculate the theoretical maximum growth yields for each carbon source. For methanol and succinate, the theoretical maximum growth rates could also be calculated and were in agreement with published data (Additional file 5), showing the consistency of the network with experimental observations. Last, the capability of the GS network to explain the oxidation of carbon compounds [26] was validated (Additional file 5).
The final GS network (iRP911) contained 1139 unique reactions and 977 metabolites, and was based on a gene-to-protein-to-reaction (GPR) association network that included 911 genes encoding 761 proteins (Table 2, Additional file 2, 3). The confidence in the network information was established by scoring the evidence currently available for each reaction [21]. The confidence scores ranged from 0 (lowest) to 4 (highest), with the latter being assigned to a reaction with direct evidence for both gene product function and biochemical reaction (Table 2). The average confidence score over the final network score was 2.1.
Table 2
Properties of the genome-scale (iRP911) and methylotrophic networks reconstructed for M. extorquens AM1
Properties
GS network
%
Methylotrophic network
% of GS network
Biochemically unique reactions
1139
717
62.9%
Reversible reactions
578
50.7%
340
58.8%
Metabolites
977
722
73.9%
Genes
911
706
77.5%
Enzymes
761
595
78.2%
Protein complexes
83
10.9
65
78.3%
Confidence score of reactions (GS network)
Number
%
Data sources
4
Experimental evidence for enzyme activity
54
4.7%
Biochemical data
4
Spontaneous reaction
15
3
Experimental evidence for gene function
28
2.5%
Genetic data
2
Genome annotation
856
75.2%
Genomic data
2
Evidence from physiology (Transport)
127
11.2%
Physiological data
1
Hypothetical reaction required for modeling
59
5.2%
Modeling data
2.1
Average confidence score of the network
Main features of the genome-scale metabolic network of M. extorquensAM1
M. extorquens AM1 is a facultative methylotroph able to utilize a relatively narrow range of substrates. The ability to grow on C3 and C4 organic acids - e.g. lactate, pyruvate, succinate or malate - relies on the presence of common metabolic pathways, which include the tricarboxylic acid (TCA) cycle, anaplerotic pathways, gluconeogenesis, pentose-phosphate pathway (PPP), and Entner-Doudoroff (ED) pathway (Figure 1). Growth on C1 compounds relies on specific metabolic pathways that were resolved for this bacterium in the past 50 years [5, 16]. The first step is the oxidation of primary C1 substrates - e.g. methanol - to formate via methanol dehydrogenase and the H4MPT-dependent C1 pathway. Formate is a key branch-point to trigger the flow of carbon between dissimilation and assimilation. Dissimilation is achieved by oxidation of formate into CO2. The assimilation of C1-units requires the conversion of formate into methylene tetrahydrofolate (Me-THF), since the spontaneous condensation of formaldehyde with THF was demonstrated not to be significant [7]. In the serine cycle, Me-THF is condensed with a C2 compound - generated from glyoxylate - to build C3 compounds such as 2-phosphoglycerate and phosphoenolpyruvate (PEP), which are further carboxylated to form oxaloacetate (OAA) and other C4 intermediates. The continuous operation of the serine cycle requires the operation of the recently discovered EMCP which allows glyoxylate regeneration and involves CO2 fixation. These pathways are tightly embedded into each other and the consequences of such organization will be detailed later. The C2 compounds used as carbon source enter metabolism at the level of the EMCP, from which they feed the central pathways. M. extorquens possesses also the ability to oxidize 26 additional compounds [26]. These compounds include a significant number of sugars, mainly pentoses. The reconstruction data suggest that such capability is due to the occurrence of soluble sugar dehydrogenases able to oxidize a wide range of pentoses and other sugars [27]; however, no assimilation processes were identified from the genome annotation. The reconstructed network contains a potential pathway for the utilization of two sugars (glucose and gluconate) as carbon source, although M. extorquens is not known to grow on these compounds. The identified pathway includes the periplasmic oxidation of glucose into gluconate, which could be internalized and catabolized through the pentose phosphate pathway (PPP) or the Entner-Doudoroff (ED) pathway. The glycolytic pathways are quite well established (see below) but the relevant sugar transport systems have low annotation confidence scores. Further experimental investigations will be necessary to determine whether M. extorquens possesses or not the entire enzymatic repertoire for sugar utilization.
Figure 1
Figure 1
Central carbon metabolism of M. extorquens AM1. Precursors of biomass components are labeled with an asterisk (*). Some metabolites were duplicated on the map for clearer visualization, and are indicated with ". Cofactors used as substrate or products are indicated in blue and red, respectively. GA3P, glyceraldehyde-3-phosphate; 3PG, 3-phosphoglycerate; 2PG, 2-phosphoglycerate; PEP, phosphoenol-pyruvate; OAA, oxaloacetate; 3HBCOA, 3-Hydroxy-butyryl-Coenzyme A; E4P, D-erythrose-4-phosphate; AKG, α-ketoglutarate; SED7P, sedoheptulose-7-phosphate; cyt c red: reduced cytochrome c. Dotted arrows represent uncertain reactions.
The detailed examination of the biosynthetic pathways included in the GS network indicated incomplete lipopolysaccharide (LPS) biosynthesis. The pathways for keto-deoxyoctulosonate and lipid A synthesis and assembly were found, but the genes encoding the enzymes classically involved in heptose biosynthesis and in sugar incorporation onto the lipid A were missing. These observations suggest the occurrence of an unusual LPS structure in M. extorquens AM1. Consistently, no heptose or galactose was detected from the hydrolysis of cell material (see above) though significant contents in rhamnose (8.9 ± 0.9%) and glucose (5.6 ± 0.5%) were found. The GS network also included the biosynthetic pathways for carotenoids and bacteriochlorophyll A. The biosynthetic pathway of bacteriochlorophyll was complete in addition with the presence of the enzymes of the photosystem I. Several degradation pathways are missing in the GS network of M. extorquens, including the degradation of amino acids - e.g. histidine, arginine, tyrosine - and nucleotides. This is in agreement with physiological data showing that the occurrence of these compounds in the cultivation medium did not result in detectable metabolic activity.
The GS metabolic reconstruction showed that M. extorquens possesses a respiratory chain with alternative systems for electron inputs and outputs (Additional file 6). A great variety of potential electron donors could be identified, including a significant number of soluble periplasmic dehydrogenases transferring electrons to cytochrome c, including methanol dehydrogenase, formaldehyde dehydrogenase, and the already-mentioned soluble sugar dehydrogenase. Three terminal oxidases were also present, including two ubiquinol oxidases and one cytochrome c oxidase, suggesting that M. extorquens can adapt an aerobic metabolism to different oxygen levels. Besides oxygen, nitrate might represent a potential alternative electron acceptor.
Organization of central metabolic pathways
C1 assimilation ensures the conversion of the C1-unit into precursor metabolites and involves a high number of metabolic pathways like C1 pathways, serine cycle, EMCP, TCA cycle, gluconeogenesis, anaplerotic reactions (Figure 1). They are connected by overlapping metabolites and enzyme reactions. The most central processes are interconnected cycles (serine cycle, TCA cycle) or pathways (EMCP, anaplerotic reactions). The serine cycle shares common reactions with gluconeogenesis (enolase), with the EMCP (malyl-CoA ligase, malyl-CoA lyase), with the TCA cycle (malate dehydrogenase), and with amino acid metabolism (serine hydroxymethyltransferase). The EMCP shares also reactions with the polyhydroxybutyrate (PHB) biosynthesis (acetyl-CoA C-acetyltransferase, acetoacetyl-CoA reductase), the TCA cycle (succinate dehydrogenase, fumarase), and fatty acid degradation (hydroxybutyryl-CoA (HBCOA) dehydratase, hydroxybutyryl-CoA dehydrogenase). The overall picture of M. extorquens central metabolism that emerges from these observations is an unusual series of metabolic pathways and cycles that are tightly embedded one into each other and allow operating almost as an entity. The C3 (2PG, pyruvate and PEP) and C4 (OAA and malate) intermediates play a critical role in the overall network organization. They represent the branching-points of the three main central metabolic pathways, i.e. the serine cycle, the EMCP and the TCA cycle, and of anaplerotic processes. Hence, they can be generated by different metabolic routes [28]. Accordingly, seven different reactions allow the inter-conversion of the five compounds (Figure 1). These reactions include processes inter-converting i) C3 into C3 (enolase, PEP synthase, pyruvate kinase), ii) C4 into C4 (malate dehydrogenase), iii) C3 into C4 (PEP carboxylase (PEPCL)), and iv) C4 into C3 (PEP carboxykinase (PEPCK), malic enzyme). Moreover, the C3/C4 inter-conversions include either reversible reactions (2PG/PEP and OAA/malate inter-conversion) or irreversible but opposite reactions (PEP/pyruvate and PEP/OAA inter-conversions). The result is a dense sub-network of reactions that provides alternative pathways for the same conversion [28] and the occurrence of potential substrate cycles [29].
Identification of the sub-network operating during methylotrophic growth
The functional structure of the metabolic network operating during pure methylotrophic growth conditions of M. extorquens, i.e. growth on methanol as sole source of carbon and energy, was established by determining the sub-network of the GS metabolic model that includes all the reactions operating on methanol, thereafter referred to as the 'methylotrophic network' (Additional file 1). The identification of the methylotrophic and non-methylotrophic reactions was based on both theoretical and experimental considerations, including i) physiological parameters ii) genetic and biochemical data, iii) omics data (transcriptomic, proteomic, metabolomics), and extensive refinement. The reactions were confronted against all above criteria and were included or excluded a based on multi-criterion consideration and their overall score (Additional file 7). This reduction step was also a pre-requisite for in silico analysis of the methylotrophic network. The size of the GS model was too big to apply Elementary Flux Mode (EFM) analysis, a powerful tool to analyze the functional properties of metabolic networks from their topology [30], due to computational limitation. The Additional file 1 shows the diagram of the reduction process which was carried out in the following manner:
i) Methylotrophic growth of M. extorquens
The determination of the methylotrophic network was performed here to account for conditions where M. extorquens cells were grown exponentially in a minimal medium containing methanol as the sole added source of carbon and energy, NH4Cl as nitrogen source, and mineral salts, as described in material and methods. Such growth conditions allowed three levels of reduction of the GS metabolic model. First, the processes (transport and biochemical reactions) associated with the utilization of compounds (e.g. carbon sources, nitrogen sources, etc) included in the GS network but not occurring in the medium were removed. Similarly, the pathways and transport systems associated with metabolic end-products included in the GS network but not detected experimentally during methylotrophic growth were removed. Quantitative 1H-NMR analysis of culture supernatants collected after methylotrophic growth indicated that very few by-products accumulated in the medium, and only at negligible levels, allowing the removal of 187 reactions from the GS model. It was also assumed that in exponentially-growing cells no biomass degradation occurred, resulting in a further simplification of the network by removing the biochemical pathways specifically involved in the degradation or salvage of macromolecular components. This simplification resulted in the removal of 213 biochemical reactions. Some reactions associated with macromolecule degradation could be potentially involved in other metabolic processes, such as cofactor biosynthesis or recycling of anabolic by-products. Some of these reactions - a total of 13 - appeared to be relevant for growth on methanol and were kept in the methylotrophic network.
ii) Genetic and biochemical data
Literature data were used to further substantiate the methylotrophic network. More particularly, the phenotypes of gene deletion mutants were used to support the reduction process. From currently available literature, a total of 47 genes were shown to be essential during growth on methanol. Some of these genes encode multifunctional enzymes, so that a total of 51 biochemical reactions were associated with the 47 essential genes. All monofunctional enzymes (42 reactions) were kept in the methylotrophic model. For multifunctional enzymes, it could not be determined at this stage which reaction(s) was (were) responsible for essentiality, and other considerations were applied before making a decision as regard to their inclusion or exclusion of the methylotrophic network. In total, 2 reactions were excluded from genetic data analysis.
The enzyme assays available in the literature were considered to confirm the presence of biochemical reactions during methylotrophic growth, as well as their differential activities upon non-methylotrophic condition. Additional biochemical information from in vitro assay of particular reaction like spontaneous reaction or biochemical information in other microorganisms was used to validate reaction occurrence. In total, 13 reactions were excluded from biochemical data analysis.
iii) Omics data
The next reduction step was based on the comparison of omics data - including transtriptomics [17, 31], proteomics [31], and metabolomics data [17, 3235], collected for both methylotrophic-grown and non-methylotrophic grown M. extorquens cells [17]. The molecular components corresponding to each type of omic data - e.g. protein for proteomics data - were kept in the methylotrophic network when they were identified to occur in methanol-grown cells, and/or their content was significantly higher - at least twice higher - than in non-methanol-grown cells, i.e. succinate-grown cells. The score of components identified from transcriptomics (differential expression), proteomics (spectral counting, differential expression) and metabolomics (identification) were assigned to their corresponding biochemical reactions via the GPR association. Taken together, the omics data were involved in the confirmation of the occurrence of 175 reactions, and the exclusion of 296 reactions. The final methylotrophic network contained 717 reactions and 722 metabolites, associated with 706 genes (Table 1, Additional file 7), and included approximately two thirds of the components of the GS network. To validate the topology of the methylotrophic network, non methylotrophic reactions were constrained to zero in the stoichiometric model of M. extorquens metabolism, and the reduced model was used to simulate growth performance on methanol. FBA simulations showed that the network supports a theoretical maximal growth rate of 0.20 h-1, which is consistent with experimental values [36]. Moreover, this value was close to the maximal growth rate calculated with the GS network (0.21 h-1), indicating that no significant growth capacities were lost during the reduction of the GS network and furthermore suggesting that about one-third of the total metabolic potential of the bacterium is not required for growth on methanol.
Dissimilation capabilities of the methylotrophic network
The capability of methylotrophs to use methanol as sole energy and carbon source relies on the occurrence of both dissimilatory and assimilatory pathways, which fulfill all energetic and biosynthetic requirements, respectively. The reconstruction of the metabolic network of M. extorquens gave the opportunity to analyze the (system-level) organization of the two types of processes in this model methylotroph. Elementary flux mode (EFM) analysis, a powerful tool to analyze the functionality of metabolic networks from their topology [30], and FBA simulations, were carried out. Dissimilation and assimilation processes were first analyzed separately.
Dissimilation processes were defined here as processes resulting in the net conversion of methanol into CO2 and allowing energy conservation. The main dissimilation route is known to be the stepwise oxidation of methanol to CO2 using dedicated C1 pathways [5, 15]. This process involves the periplasmic oxidation of methanol into formaldehyde, which is further oxidized to CO2 in the cytoplasm (see Figure 1). In this process one cytochrome C and two nicotinamide adenine dinucleotide (phosphate) (NAD(P)H) are released, assuming the pyridine nucleotide dependent formate dehydrogenase (FDH) operates. This 'cytoplasmic' route can fulfill both adenosine triphosphate (ATP) and redox requirements at the same time. In case cytochrome C and NADH are reoxidized by the most effective oxidative phosphorylation mechanisms, a maximal yield of 5 ATP/methanol is predicted (Table 3). The additional potential routes for methanol dissimilation within the methylotrophic network could be detailed from the in silico investigations (Table 3). A periplasmic route of formaldehyde oxidation can be predicted in case methanol-dehydrogenase-like enzyme XoxF would act together with a periplasmic formate dehydrogenase [37]. Such a route would not generate NAD(P)H and hence could only fulfill ATP requirements, albeit with reduced maximal yield (3 ATP/methanol). The network contains also other potential alternative mechanisms for the complete oxidation of methanol in which multi-carbon compounds are first generated and then completely oxidized to CO2. These processes would result from the combined action of C1 assimilation pathways (enabling the formation of multi-carbon compounds) and of catabolic pathways where multi-carbon compounds are fully oxidized to CO2 (via the TCA cycle or other decarboxylation reactions). The latter processes are the main energy conservation mechanisms upon utilization of C2 and other multi-carbon compounds, and are likely to be down-regulated during pure methylotrophic growth conditions. Nevertheless, the in silico analysis shows that the methylotrophic network contains the potential for these indirect dissimilation routes. They are however not efficient for energy conservation (Table 3) and are unlikely to operate upon methylotrophy from the energetic point of view.
Table 3
Dissimilatory processes in the methylotrophic network.
max ATP
max NADH
max NADPH
Dissimilation processes
in mol.mol(methanol)-1
MeOH - > CO2 (cytoplasmic FDH)
5
2
2
MeOH - > CO2 (periplasmic FDH)
3
0
0
MeOH + CO2 (Ser cycle) - > Acetyl-CoA - > TCA cycle - > 2 CO2
1
0.5
0.5
MeOH + n CO2 (Ser cycle + EMCP) - > other C2s, C3s, etc - > central pathways - > n+1 CO2
1
0.5
0.5
Types and number of dissimilatory EFMs detected in the methylotrophic network. For each type of dissimilation process, the theoretical maximum yields in ATP, NADH or NADPH are given.
Assimilatory processes
The consequences of the particular organization of primary C1 assimilation in M. extorquens AM1 were analyzed by examining the processes allowing the conversion of methanol into each of the 13 key carbon precursors, including C1 (Me-THF), C2 (acetyl-CoA, glycine), C3 (L-serine, pyruvate, PEP, glyceraldehyde-3-phosphate), C4 (OAA, D-erythrose-4-phosphate (E4P), 3HBCOA), C5 (α-ketoglutarate, D-ribose-5-phosphate) and C6 (D-glucose-6-phosphate (G6P)). The number of EFMs ranged from 2018 to 6576 for the various carbon precursors (Table 4, Additional file 8). The serine cycle was involved in all assimilatory EFMs except for Me-THF, which can be also generated directly in the C1 pathways. This observation was consistent with the key role of the serine cycle pathway in methanol assimilation. The EMCP was involved in 93%, 95%, and 92% of the EFMs generating Me-THF, acetyl-CoA, and (R)-3-HBCOA, respectively. For all other carbon precursors, including the serine cycle intermediate glycine and L-serine, all assimilatory EFMs required the EMCP. These data emphasize the critical role of the EMCP (12 reactions), in addition to the C1 pathways (10 reactions) and the serine cycle (9 reactions), in methanol assimilation. Hence, the initial steps of C1 assimilation require the consecutive but obligatory operation of a high number of reactions. The minimal EFM length, representing the smallest number of reactions needed to convert methanol into each carbon precursor, was calculated for each of the 13 carbon precursors. The conversion of methanol into C3 compounds required at least 50 reactions, and the minimal number of reactions required to convert methanol into E4P was 63. Even for Me-THF and acetyl-CoA, the minimal EFM lengths were high (20 and 35, respectively). These data indicated that the primary assimilation processes, ensuring the conversion of methanol into carbon precursors, is a particularly complex process in M. extorquens AM1. Despite the complexity of methanol assimilation, the carbon precursors are produced from methanol with carbon yields that are similar to that observed on glucose for species like E. coli and C. glutamicum.
Table 4
Primary assimilation processes in the methylotrophic network.
compound/precursor biosynthesis
number of carbon in precursor
number of EFMs
Max. molar-Yield
Max. carbon-Yield
Minimal EFM length
EMCP utilisation
5, 10-methylenetetrahydrofolate (Me-THF)
1
2018
1.00
1.00
20
93%
acetyl-CoA
2
2440
0.45
0.91
35
95%
glycine
2
2054
0.42
0.84
62
100%
L-serine
3
2162
0.29
0.88
62
100%
D-glyceraldehyde-3-phosphate (GA3P)
3
2592
0.27
0.81
54
100%
phosphateenolpyruvate (PEP)
3
3390
0.32
0.97
53
100%
pyruvate (PYR)
3
3065
0.33
1.00
50
100%
oxaloacetate (OAA)
4
5366
0.32
1.29
51
100%
(R)-3-hydroxybutanoyl-CoA (3HBCOA)
4
2789
0.21
0.83
37
92%
D-erythrose-4-phosphate (E4P)
4
6576
0.20
0.81
63
100%
α-ketoglutarate
5
3806
0.20
1.02
54
100%
D-ribose-5-phosphate
5
4663
0.16
0.81
61
100%
D-glucose-6-phosphate
6
2592
0.14
0.68
58
100%
Number and properties of primary assimilatory EFMs detected in the methylotrophic network. The EFMs correspond to the processes allowing the conversion of methanol into 13 key carbon precursors
Interdependencies of dissimilatory and assimilatory processes
The energetic efficiency of dissimilation processes determines the amount of energy available for assimilation and hence is a critical parameter of methylotrophic growth. The complete set of EFMs (152872) through the methylotrophic network was analyzed to investigate the relationships between dissimilation and assimilation processes. The EFMs were classified according to their biomass yields, and then to the various types of dissimilatory processes (Figure 2). In the EFM with the optimal biomass yield (0.42 g · g-1), 70% of methanol was directly oxidized via C1 pathways and the remaining was used for assimilation purposes. In a significant number of assimilatory EFMs, methanol was entirely oxidized to CO2 via the C1 pathways (Figure 2), meaning that no reduced carbon entered assimilatory pathways, and indicating that biomass could be fully generated from CO2. The highest biomass yield that could be obtained by such process was 0.283 g · g-1 (EFM number 122591). In this EFM, (Figure 3A), carbon fixation is achieved by a process involving both the EMPC and the serine cycle. The process starts in the EMCP where two glyoxylate molecules are generated from one acetyl-CoA and two CO2. The two glyoxylate molecules enter the serine cycle to produce two glycine molecules. One glycine is converted by the glycine cleavage complex into one CO2 and one Me-THF. The latter compound allows the conversion of the second glycine molecule into serine, which is used in subsequent steps of the serine cycle, allowing both the regeneration of the initial acetyl-CoA molecule and enabling - through the operation of the entire mechanism - the formation of all carbon precursors needed for biosynthetic purposes. The overall carbon balance is 2 CO2 → 1 glyoxylate. As this process requires the release of Me-THF via the glycine decarboxylase complex, it represents a distinct feature compared to the classical operation of the serine cycle. The carbon yield of the CO2-assimilation process is significantly lower than observed for methanol assimilation (40% vs 62%). The ATP needs are twice higher (7.2 vs 3.8 mol · mol(carbon assimilated)-1), and the redox needs are two to three times more elevated. Such high energetic costs can be covered by methanol oxidation, but the overall CO2 assimilation process is much less favorable than methanol assimilation. This CO2 assimilation process was not reported so far and is a direct consequence of the capability of the EMCP to ensure CO2 fixation.
Figure 2
Figure 2
Structural EMCP properties compared to ICL variant. A. EFM (#122591) with the optimal biomass yield among the EFMs where biomass carbon is derived exclusively from CO2. B. FBA simulation of optimal growth rate depending upon a fixed proportion of NADPH/NADH produced by methylene- H4MPT dehydrogenases MtdA and MtdB in EMCP and ICL-variant.
Figure 3
Figure 3
EFM analysis of the balance between dissimilation and assimilation in EMCP and ICL variants. The biomass-forming EFMs were calculated and sorted according to the biomass yield (from bottom to top, blue color scale). For each EFM, the flux through the main dissimilatory processes (see text for details) were extracted and plotted separately. Fluxes were expressed relative to the rate of methanol uptake, and were plotted using a colour-scale (black to green). First lane: cytoplasmic FDH, fdh(c); second lane: periplasmic FDH, fdh(p); third lane: TCA oxidation of acetyl-CoA, TCAc; fourth lane: other dissimilation process. A: EFMs calculated with the methylotrophic network, which contains the ethylmalonyl-CoA pathway (EMCP). B: EFMs calculated with the network variant where EMCP was replaced by the glyoxylate cycle (ICL variant).
Substitution of the ethylmalonyl-CoA pathway by the glyoxylate cycle
The recently discovered EMCP is an alternative to the classical glyoxylate cycle for the biosynthesis of glyoxylate from acetyl-CoA in organisms lacking isocitrate lyase (ICL) [18, 19, 38]. To compare the metabolic properties conferred by the EMCP with that of the glyoxylate cycle, we generated a variant of the methylotrophic network lacking the EMCP but possessing the glyoxylate cycle. This was done by setting to zero the flux from crotonyl-CoA to propionyl-CoA and by adding the ICL reaction. Malate synthase, the enzyme of the glyoxylate cycle that catalyzes the condensation of acetyl-CoA and glyoxylate into malate, was not added since M. extorquens can use a combination of two enzymes to achieve the same reaction [39], as described also in R. sphaeroids [40]. As expected, the glyoxylate cycle was essential for methanol growth and was found in all assimilatory EFMs. The maximal biomass yield predicted for the ICL variant (0.41 g · g-1) was similar to that observed for the EMCP variant yield (0.42 g · g-1). To obtain such maximal growth, the rate of methanol oxidation in the ICL variant was smaller (61% vs 70%) and the NADPH requirements lower than in the EMCP variant, showing a higher energetic efficiency of the ICL variant. In contrast to the EMCP, the ICL variant was not found to allow entire biomass formation from CO2.
To investigate the potential role of the EMCP in redox balancing, we compared the capability of the two metabolic network variants to respond to varying NADPH production levels. FBA simulations were performed where the amount of NADPH produced by the Me-H4MPT dehydrogenase MtdB [41], which can use either NADH or NADPH, was varied from 0 to 15.0 mmol · g-1 · h-1 (0 to 100% of MtdB flux). For both the EMCP and ICL variants, the absence of NADPH production in the C1 pathways can be compensated by other NADPH-production systems, the PPP or malic enzyme. The theoretical maximal growth rate increased with NADPH production until a maximum is reached, which represents the optimal balance between NADPH production and growth. Maximal growth for the EMCP variant was obtained at higher NADPH production level than the ICL variant (9.0 vs 7.7 mmol · g-1 · h-1), in agreement with the higher redox demand identified previously. The EMCP variant was able to maintain higher growth rates when the NADPH production was further increased. This capability was correlated with a significant increase of the EMCP flux. The increase in the EMCP flux was accompanied by the truncation of the serine cycle. Rather than being converted to OAA, PEP is converted into pyruvate via pyruvate kinase, which is further converted by pyruvate dehydrogenase into acetyl-CoA, which enters the EMCP. This pathway generates ATP (via pyruvate kinase) and releases NADH (via pyruvate dehydrogenase), resulting in a transhydrogenase-like mechanism where the redox equivalents are transferred from NADPH to NAD+ in addition to the transfer to CO2.
Fragility of the methylotrophic network
Robustness is an inherent property of a metabolic network and is defined as the capability of this network to operate despite one - or more - reactions are removed. The robustness of the methylotrophic network was analysed using minimal cut sets (MCSs), which correspond to minimal combinations - singlets, pairs, triplets, etc - of reactions whose removal blocks the operation of a target metabolic function [42]. The identification of all MCSs in a metabolic network allows the calculations of the fragility coefficient (FC) of each reaction. The FC of a reaction represents the probability that the metabolic system fails to achieve the target function when the reaction is removed. This approach was applied to analyze the robustness of the methylotrophic network using growth as the target metabolic function. A significant number of reactions (391) were found to have a FC of 1 and are therefore predicted to be essential (Additional file 9). Among these 391 reactions, 30% are catalyzed by multiple enzymes, indicating that enzyme redundancy is significantly used to avoid metabolic resilience in M. extorquens AM1. Most of the essential reactions (279) were found in biosynthetic pathways, which is consistent with studies performed with other organisms. The FCs of reactions found in central metabolism spanned over a wide range of values but distributed heterogeneously among metabolic pathways (Figure 4). Some processes, such as the C1- and carbohydrate pathways, and C3/C4 interconversion reactions, had low FCs and hence were predicted to be robust parts of the metabolism. Most other parts of the central metabolism had high FCs and hence were predicted to be fragile. Of the 84 reactions of the central carbon metabolism, 40 were found to be essential. The essential reactions concentrated in the primary assimilation processes (Figure 4). Most reactions of the serine cycle (67%) and of the EMCP (100%) were predicted to be essential for methylotrophic growth, indicating the assimilation processes to be highly fragile. The same observation holds true for gluconeogenesis. Because a particular reaction can be catalyzed by one or several enzymes, the essentiality of a reaction does not necessarily mean that the removal - by gene deletion - of one particular enzyme will be lethal. Among the 40 essential reactions found in central pathways, 29 were catalyzed by a single enzyme. Accordingly, 19 of these genes have been studied experimentally, and 95% of them were shown to be lethal for methylotrophic growth [43] (Additional file 10). For an essential reaction with multiple enzymes, one isoenzyme can compensate the lack of the other one(s). Genes encoding isoenzymes are therefore predicted to be not essential. However, mutant analysis showed that 4 out of 11 essential reactions with multiple enzymes found in primary assimilation processes, were encoded by gene where deletion were lethal for growth on methanol. This observation suggests that the products of these genes play an essential role during growth on methanol that cannot be compensated by the other potential enzymes catalysing the same reactions, or that they have different regulations, or both. Taken together, these data showed that the main processes of methanol assimilation are highly fragile in M. extorquens AM1. The robustness of the metabolism of M. extorquens AM1 was also calculated for a C2 compound (acetate), and for a C4 compound (succinate). The data were compared to that calculated for E. coli using the model of Klamt et al. [42, 44]. The utilization of C2 compounds like acetate relies on the EMC pathway in M. extorquens and on the glyoxylate cycle in E. coli. Interestingly, the metabolic robustness of the central metabolism upon acetate growth was calculated to be lower in the former organism compared to the latter. Upon growth on succinate, which does not rely on C1-associated pathways but on common pathways (e.g. TCA cycle) that are similar in the two organisms, metabolic robustness was calculated to be similar between the two organisms. These observations suggest that metabolic fragility in M. extorquens is mainly related to the nature and organization of C1 (& C2) pathways in this organism.
Figure 4
Figure 4
Structural fragility of the methylotrophic network. Prediction of reaction essentiality from Minimal Cut Set (MCS) analysis and comparison with experimental mutant phenotypes. The fragility coefficient (FC) calculated from MCS analysis is given for each reaction of M. extorquens central metabolism, and ranges from 0 (fully dispensable reaction) to 1 (essential reaction). Boxes next to reactions represent enzymes. Where available, the phenotype of the mutant lacking the gene encoding a particular enzyme is given by a color code (see legend). The occurrence of alternate reactions that are not displayed on the map is indicated by a star.
Distribution of metabolic fluxes during methylotrophic growth
The distribution of metabolic fluxes during methylotrophic growth was determined using 13C-metabolic flux analysis (13C-MFA). 13C-MFA was already successfully applied to M. extorquens AM1, which provided valuable insights into the operation of central pathways [8]. The novel insights such as the operation of the EMCP [19], the organization of central assimilatory pathways [17], and the biomass composition (this study) necessitates the reinvestigation of metabolic flux analysis in M. extorquens AM1 during growth on methanol. To this end, a series of 13C-methanol labeling experiments was performed, and the isotopic information was monitored by both mass spectrometry and two dimensional nuclear magnetic resonance (2D-NMR) [45] (Additional file 11, 12). Such analytical combination provides critical information for the resolution of central pathways [19]. The flux distribution obtained from these investigations is displayed in Figure 5 and listed in Additional file 13, and the fitting accuracy and sensitivity analysis are listed in Additional files 12, 13, 14 and 15. The flux data obtained in the present were significantly different from that previously published [8]. This is mainly due to the major advances made in the meantime in the description and understanding of M. extorquens metabolism, and it is now known that the size and topology - and hence the possible carbon flows - of central carbon metabolism are more complete and much different than previously assumed. For this reason they can be hardly compared.
Figure 5
Figure 5
Distribution of fluxes in the central metabolic network of M. extorquens AM1 upon methylotrophic growth. Carbon fluxes were calculated from 183 isotopomer measurements (NMR + MS data) collected during steady-state growth of M. extorquens AM1 on [13C]-methanol. Fluxes are given in mmol · g-1 · h-1, with standard deviations given below flux values. Exchange fluxes through reversible reactions are given within brackets. The width of the arrows is proportional to the flux value.
The flux data of Figure 5 indicated that 12.7 ± 0.6 mmol · g-1 · h-1 of methanol, 84% of methanol consumed (15.10 ± 0.60 mmol · g-1 · h-1), was directly oxidized to CO2 within the C1 pathways. A release of CO2 was also observed within biosynthetic pathways (2.6% of consumed methanol) and central metabolism (5.4%). The release of CO2 in central metabolism was due to substantial fluxes through malic enzyme (0.36 mmol · g-1 · h-1) and PEPCK (0.26 mmol · g-1 · h-1), but was not associated with dissimilation processes. Indeed, the TCA contributed to only 1.1% of total CO2 release and operated in an incomplete and anabolic mode. The flux of C1 assimilation via Me-THF was 2.4 ± 0.02 mmol · g-1 · h-1, which represents 16% of methanol uptake. The flux data clearly showed the central role of the serine cycle in distributing the carbon flow throughout the entire metabolic network to fulfill the requirements in carbon precursors. About 20% (0.5 mmol · g-1 · h-1) was directed towards gluconeogenesis and carbohydrate pathways, and 30% was routed to the formation of pyruvate and TCA cycle intermediates. The release of acetyl-CoA by the serine cycle was significant (1.80 mmol · g-1 · h-1). The major part (1.4 mmol · g-1 · h-1) was recycled back to the serine cycle by the EMCP, and the remaining was used for anabolic purposes. The fixation of CO2 occurring within central pathways was calculated from the difference between CO2-utilizing and CO2-releasing fluxes, and was 2.4 mmol · g-1 · h-1. This value was similar to the rate of methanol assimilation via Me-THF (2.4 mmol · g-1 · h-1). These data were consistent with the observation that 50% of the biomass carbon derived from CO2 [7, 46]. Such carbon balance can be obtained in case two molecules of glyoxylate are generated per turn of the EMCP [19], which requires that the propionyl-CoA produced in this pathway is not directly used for anabolic purposes but converted into glyoxylate. Accordingly, the replenishment of the glyoxylate pool from propionyl-CoA was almost identical to the direct release of glyoxylate within the EMCP (0.70 ± 0.02 mmol · g-1 · h-1). No flux was found through the glycine cleavage complex, indicating that the CO2 assimilation mechanism identified from EFM analysis was not operating during pure methylotrophy, for chosen cultivation conditions. Surprisingly, a glycolytic flux through the Entner-Doudoroff pathway was observed. This flux (0.08 ± 0.02 mmol · g-1 · h-1) was low compared to the rate of formate assimilation but was significant to fit the labeling data and represented about 14% of total pyruvate synthesis. This observation indicated that some carbon atoms were recycled through gluconeogenesis and glycolysis during methylotrophic growth.
The flux data provided valuable information regarding the C3/C4 pathways. The synthesis of pyruvate, which is required for various anabolic purposes, was proposed earlier to proceed via the conversion of PEP into pyruvate, via pyruvate kinase [6]. The flux data showed that pyruvate was synthesized by three different routes, including pyruvate kinase, the ED pathway and malic enzyme. The main flux was carried out by malic enzyme (0.36 vs 0.13 mmol · g-1 · h-1). Moreover PEP synthase, which catalyses the reaction opposite to pyruvate kinase, is active and its flux (0.13 mmol · g-1 · h-1) is higher than that of the latter enzyme. This observation indicated the occurrence of a substrate cycle between PEP and pyruvate due to the parallel activity of pyruvate kinase and PEP synthase, and in which 68% of pyruvate is recycled. Three additional substrate cycles were observed in this part of the metabolism. Two of them were related to C3/C4 inter-conversions: i) PEP/OAA cycling via PEPCL and PEPCK (13% of PEP recycled), and ii) PEP/malate/pyruvate cycling via PEPCL, malate dehydrogenase, malic enzyme and PEP synthase (4% of PEP recycled via malate and pyruvate). The fourth substrate cycle was observed between malate and (acetyl-CoA+glyoxylate). It relies on the reversible activity of the malyl-CoA lyase [47] and on the parallel operation of malate-CoA ligase and malyl-CoA thioesterase. Malate-CoA ligase is responsible for the release of glyoxylate and acetyl-CoA from malyl-CoA in the serine cycle. Malyl-CoA thioesterase catalyzes the opposite reaction. This enzyme is supposed to play a key role during growth on multicarbon compounds, but its activity is not expected during methylotrophic growth. Indeed, the enzyme activity is down regulated during growth in the presence of methanol [48]. However, a significant activity of this enzyme is still detected upon methanol growth [48], and represents 22% of the activity found on acetate. Such level of activity is likely to be sufficient to maintain a flux in the reaction, thereby resulting in substrate cycling. The flux data show not only that the latter cycle operates in M. extorquens AM1 during growth on methanol, but also that the extent of recycling is significant (32%). The energetic cost of metabolite recycling within the four above-mentioned processes was calculated from the flux data to be 1.3 mmol ATP · g-1 · h-1, with the most expensive one (0.8 mmol ATP · g-1 · h-1) being the malate/(acetyl-CoA+glyoxylate) cycle. The energetic cost was calculated to represent about 4% of the total production of ATP (29.3 ATP mmol · g-1 · h-1). This energetic expense might represent a tradeoff between optimal metabolic efficiency and the ability to switch metabolic modes.
The total demand in NADPH during methylotrophic growth could be calculated from the fluxes in NADPH-utilizing reactions and biomass requirements, and was 5.6 mmol · g-1 · h-1. The demand was mainly due for formate assimilation (2.3 mmol · g-1 · h-1), biosynthetic requirements (1.8 mmol · g-1 · h-1), and operation of the EMCP (1.4 mmol · g-1 · h-1). The 13C-flux data showed also that the two NADPH-forming reactions found within central carbon pathways, i.e. isocitrate dehydrogenase and G6P dehydrogenase, contributed only negligibly (below 5%) to the total NADPH production. Hence, most of NADPH is generated alongside formaldehyde oxidation. From these data it can be calculated that the production of NADPH in the C1 pathway should be 5.3 mmol · g-1 · h-1 to close the NADP balance. To evaluate the ATP balance, flux variability analysis and FBA simulations were performed in which the methylotrophic network was constrained with the 13C-flux data, biomass requirements, experimental rates of growth and methanol uptake, and maintenance energy. Because the respiratory mechanisms by which the reduced cofactors (NADH, cytochrome C) generated in the C1 pathways are not clearly established in M. extorquens the ATP cannot be firmly established from the flux data. Nevertheless, the simulations showed that, if dissimilation proceeds via the cytoplasmic, NADH-dependent route at maximal ATP efficiency (Table 3), then the total production of ATP (44 mmol · g-1 · h-1) would be in large excess compared to the requirements (29.3 mmol · g-1 · h-1).
Discussion
The genome scale metabolic network reconstructed in this work offers an integrated view of the current metabolic knowledge of the methylotrophic bacterium M. extorquens AM1. It provides new insights into the biochemistry of this organism and reveals the network-scale organization of metabolic processes as well as a first evaluation of the complete metabolic potential of this bacterium. The metabolic reconstruction allowed a detailed picture of the central carbon metabolism of the bacterium, which appears as a mosaic of common (TCA cycle, anaplerotic processes, gluconeogenesis, PPP, ED pathway) and specific (C1 pathways, serine cycle, EMCP) pathways, enabling growth on C1 and multicarbon (C2 to C4) compounds. The core of the central metabolism is organized as a highly unusual series of tightly embedded metabolic cycles that operate as an entity to achieve C1 assimilation during methylotrophic growth. The ability to assimilate C1 compounds relies on a complex metabolic machinery, in which the initial steps - from methanol to biomass precursors - require a particularly high number of reactions (e.g. at least 36 reactions to obtain acetyl-CoA). The entire process is strongly reductive and energy-consuming. Most of these reactions require enzymes and cofactors that are specific to C1 - or C2 - growth, and must be biosynthesized for the purpose of C1 or C2 utilization. Hence, the energetic costs for the biosynthesis and maintenance of this machinery are likely to be substantial for the bacteria. In addition, the network-scale analysis reveals that C1 assimilation is structurally fragile. Similarly to other metabolically specialized microorganisms [49], the core metabolism of M. extorquens is characterized by a high fraction of reactions that are essential for methylotrophic growth (almost 50%). In such networks robustness arise usually from enzyme (and genetic) redundancy, where multiple isoenzymes can catalyze essential reactions [49, 50]. The genetic or biochemical deficiency in one isoenzyme can be compensated by another one. Accordingly, the percentage of multiple genes encoding essential reactions in specialized microorganisms is much higher than in generalist - or flexible - organisms such as E. coli, B. subtilis or S. cerevisiae (> 30% vs 10% redundancy, respectively) [50]. The high degree of redundancy (28%) observed in M. extorquens confirms the specialized metabolism of this methylotroph. Furthermore, among the essential reactions with multiple genes, a significant number of particular genes were shown experimentally to be essential for growth on methanol, suggesting that the alternative gene(s) have different functions or regulations, hence are not functionally redundant. Therefore, the number of genes essential for methylotrophy is high, and the risk that a gene mutation results in loss of methylotrophic capacity is elevated. This could explain, in part, the successes in the identification of such genes in the last 2 decades [43]. The observations emerging from metabolic network analysis are highly consistent with experimental evolution experiments in which a significant number of clones collected after prolonged cultivation (1500 generations) on succinate lost their methylotrophic capacity [36]. Taken together, available data suggest that a selection pressure is required to maintain methylotrophy in M. extorquens, indicating that the bacterium encounters frequently methanol in its natural environment and that its usage provides critical advantage in terms of ecological competitiveness.
The metabolic reconstruction data indicate also that a dense network of C3/C4 inter-conversions plays a critical role as a branch-point connecting specific and common pathways. Indeed, seven reactions interconnect three C3 (2PG, PEP, pyruvate) and two C4 (malate, OAA) intermediates, thereby strongly embedding the serine cycle, the TCA cycle, anaplerotic processes, and gluconeogenesis (via 2PG). Such topology allows a wide range of alternative metabolic routes and provides metabolic flexibility. Van Dien et al. [6, 28] have emphasized the role of these processes in the metabolism of multi-carbon compounds. During growth on C4 compounds such as succinate, a functional TCA cycle is required and the generation of acetyl-CoA is ensured by pyruvate dehydrogenase. Hence, the conversion of C4 compounds into pyruvate is critical and can be achieved by redundant routes. During methylotrophic growth - in which a complete TCA does not operate -, the C3/C4 inter-conversions primarily ensure the opposite conversion of C3 intermediates into C4 intermediates in the serine cycle. They provide also alternative metabolic routes for such conversions, as observed with the significant conversion of PEP into pyruvate via PEPCL, malate dehydrogenase, and malic enzyme, though the role of this pathway is still unclear. The most striking feature is, however, the occurrence of substantial substrate cycling within the C3/C4 inter-conversions upon growth on methanol. In addition, substrate cycling was also observed between C4 (malate) and C2 (glyoxylate + acetyl-CoA), at the branch-point between the serine cycle, the TCA cycle, the EMCP and anaplerosis. Substrate cycles are resulting from the simultaneous operation of - non reversible - opposite reactions or processes, at the expense of energy. They can represent adaptation mechanisms allowing fast switching of metabolic processes [17, 29]. The nature of the substrates cycles observed predicted during methylotrophic growth indicated that the entire set of reactions starting from PEP or pyruvate to acetyl-CoA and glyoxylate are operating as a fully reversible process. As mentioned above, these processes are the branching-point of the specific - i.e. serine cycle, EMCP - and common - i.e. TCA cycle, anaplerotic processes, and gluconeogenesis - pathways. They are also the starting point of a large number of biosynthetic routes, and the entry point of the utilization pathways of all C1, C2 and C3/C4 carbon sources used by the bacterium. Taken together, these data suggest that upon pure methylotrophic growth the occurrence of substrate cycling provides flexibility between specific and common pathways, thereby allowing fast switching of the metabolism from methanol to alternative carbon substrates.
Though M. extorquens AM1 is considered to be a methylotroph but not an autotroph, the in silico investigations revealed a potential of autotrophy in this bacterium, which relies on the unique property of the EMCP to enable CO2 fixation. The CO2-fixation mode involves a cyclic operation of both the EMCP and serine cycle to generate one glyoxylate from two CO2. It can potentially operate independently of methanol assimilation in M. extorquens, but was not observed during methylotrophic growth in our investigations. Because the genome of M. extorquens contains the complete information for a photosynthetic machinery, it is tempting to speculate that this bacterium may operate in a photoautotrophic mode. However, there is currently no experimental evidence of such behavior in M. extorquens. The question of the role, benefit and conservation of this pathway in M. extorquens and other organisms is still unclear. The EMCP is more complex and energy-demanding than the glyoxylate cycle though it provides a higher carbon balance for assimilation. In photosynthetic methanol utilizers, carbon dioxide functions as an electron sink for the excess electrons in methanol [51]. It was recently proposed that CO2 fixation could represent an alternative mechanism of cofactor recycling in bacteria [52]. The potential role of the EMCP in such mechanism was recently shown from investigations of CBB mutants defective for the reductive PPP pathway in acetate-grown R. sphaeroides [53]. Our investigations show that the EMCP can potentially play such a role in M. extorquens upon methylotrophic growth. If further investigations are required to determine the actual physiological benefits of the EMCP in serine cycle methylotrophs, our investigations show that this pathway can potentially play the role of a redox-balancing mechanism or of an autotrophic pathway.
Conclusions
The unusual organization of the central carbon metabolism of M. extorquens AM1 allows efficient utilization of C1 compounds via highly specific - and fragile - pathways but is versatile enough around a flexible backbone of C2/C3/C4 inter-conversions to allow switching to other carbon sources. These observations showed that the bacterium maintains active metabolic processes that are not needed for methanol utilization but allow adaptation to other carbon sources. This hypothesis is consistent with the observation that methanol is produced by plant with methanol release in the morning [54, 55]. This work emphasizes that the metabolism of the bacterium is adapted to its lifestyle not only in terms of enzymatic equipment, but also in terms of network-level structure and regulation. It suggests that the metabolism of the bacterium is adapted both structurally and functionally to an efficient but transitory utilization of methanol. This work illustrates that the combination of GS network modeling and experimental approaches provides novel insights into the biochemistry and physiology of methylotrophic bacteria, which could be extended to obligate methylotrophs and to the comparison of serine cycle versus RuMP- and CBB-utilizing methylotrophs. Methanol is currently regarded as a highly attractive raw material for microbial bioprocesses [56]. Comprehensive, system-level understanding of methylotrophic metabolism is also expected to improve the biotechnological value of methylotrophy, and this knowledge will serve as a sound basis for a rational remodeling of existing biosynthesis routes and for the design of new synthetic pathways [1].
Methods
Network reconstruction
The genome-scale (GS) metabolic network of M. extorquens AM1 was reconstructed using procedures recommended for the generation of high-quality reconstructions [21]. The detailed procedure is given in Additional file 1. Briefly, the process of metabolic reconstruction included the following steps:
1. 1.
Generating a draft reconstruction. The genome information was extracted from the MicroScope database [57] on December 9th, 2009. Genes annotated for metabolic functions were selected and assembled with biochemical information collected from literature. The data were completed using metabolic databases - mainly Metacyc [24], KEGG [22] -. During the reconstruction process, systematic Blast and interrogation of metabolic databases were performed to refine weak - or missing - genome annotation information or new published data. In some cases this process leads to the re-annotation of genes and the publicly available annotation was corrected accordingly.
2. 2.
The reconstruction was refined from all genetic, biochemical, and physiological data available for M. extorquens and related species, metabolic (Metacyc, KEGG) and transporter (TCDB, http://www.tcdb.org/) databases, and from self-expertise on methylotrophy (Additional file 1). Metabolite information such as the name, molecular formula and metabolic database identifiers of compounds were included in the network, and refined from available metabolomics data for 157 metabolites [35]. Neutral formulas obtained from PubChem http://pubchem.ncbi.nlm.nih.gov/ were used to validate reaction stoichiometry (mass balancing) including proton balance.
3. 3.
Generation of a Gene-to-Protein-to-Reaction (GPR) association network. The GPR association was designed to describe explicitly all the relationships between molecular species and functional activities. Specific identifiers were assigned to enzymes, reactions and metabolites.
4. 4.
Gap-filling. A draft metabolic map, drawn using the software Cytoscape [58], was used as starting point for the gap filling process. Gaps were identified from stand-alone reactions or metabolites, and from missing connections in essential metabolic processes. Spontaneous reactions, and reactions or transports without associated genes in M. extorquens genome, were added according to metabolic (Metacyc, KEGG) and transport (TCDB) databases.
5. 5.
Conversion of the reconstruction into computational format. The reconstruction was loaded into the software CellNetAnalyser [25]. The consistency of the reconstructed network was evaluated from in silico investigations (modeling) and from the ability of the network to explain growth on the most studied carbon sources, namely methanol and succinate. Experimental information [26] was used to identify substrate utilization. Exchange reactions - i.e. exchange with environment - were finally added corresponding to known substrates usage and minimal medium composition.
6. 6.
Quality assessment. The quality of the reconstructed network was determined according to [21] by assigning a confidence score to each individual reaction, depending on the evidence for the presence of the reaction, with the highest score given to experimentally demonstrated reactions and the lowest score given to gap-filling reactions.
The detailed list of reactions, metabolites, and other network components, and the GPR association network are given in Additional file 2, 3. The computer model of iRP911 written in Systems Biology Markup Language (sbml) is given in the additional file 16.
Determination of the chemical composition of cells
M. extorquens AM1 was grown in fed-batch mode in mineral medium containing methanol as sole carbon and energy source, as described in [19]. For cell dry weight (CDW) determination, 30 ml of culture were centrifuged in a 50 ml falcon tube and washed with de-ionized water and dried to constant weight at 80°C. Falcon tubes were incubated for several days at 80°C prior to use. For other measurements, cells were harvested by centrifugation at 5000 g during 5 min. Cell pellets were frozen in liquid nitrogen and stored at -20°C until analysis.
i) Lipid content
whole cell hydrolysis with subsequent acid methylation of fatty acids was carried out as described in [38] with slight modifications. Cells (10-20 mg CDW) were hydrolyzed with 4 ml of 15% NaOH (w/v) in methanol/water (1:1, v/v) for 30 min at 100°C. Fatty acid methyl esters (FAMEs) were obtained by addition of 8 ml 6 M HCl/methanol (13:11, v/v) and incubation for 2.5 hrs at 80°C. An internal fatty acid standard (3 mg C15:0) was added before hydrolysis for quantification purpose. The methylation yield was measured from the addition of a FAME standard (3 mg C19:0 FAME) after the methylation step. FAMEs were extracted with 5 ml hexane/methyl-tert-butyl ether (1:1, v/v) and washed with 6 ml 1% NaOH in water (w/v). Extracted FAMEs were analyzed by gas chromatography - flame ionization detector (GC-FID) (Agilent Technologies 6850 with 7683B Series injector and FID detector) and a HP-5 column, length 30 m, I.D. 0.25 mm, film 0.25 μm (Agilent Technologies). Helium was the carrier gas with a column flow of 2.4 ml/min; detector temperature was set to 300°C, and inlet to 250°C. A temperature gradient was run from 190°C to 260°C at 5°C per min. A sample volume of 1 μl was injected with a spilt ratio of 30.
ii) Protein content
total proteins were quantified by the Biuret method [59], using bovine serum albumine (2 mg/ml) as standard. This method is independent of protein composition [60]. Cells were hydrolyzed in 0.75 ml 1N NaOH (1-2 mg/ml CDW) at 100°C for 5 min. After addition of 0.25 ml of 2.5% CuSO4 (w/v), samples were centrifuged and absorption was measured at 550 nm. The composition in amino acids of proteins was determined following hydrolysis in 6 M HCl at 110°C for 22 hours under argon samples were dried and derivatized using the AccQ-Tag™ Ultra derivatization chemistry (Waters Corp., Milford, MA, USA) according to the manufacturer's instruction. Amino acid derivatives were separated by UPLC (Waters Corp., Milford, MA, USA) using the AccQ-Tag™ Ultra standard hydrolysate conditions. Amino acid derivatives were detected by UV absorbance.
iii) Carbohydrate content
the carbohydrate content was measured after hydrolysis of the entire cell pellet. A two-step derivatization was used to convert carbohydrates into oxime trimethylsilyl derivates [61], which were analyzed by GC-FID. For glucose and rhamnose quantification, cells (1-3 mg CDW) were directly subjected to 200 μl 2 M HCl at 80°C for 4 hrs or to 4 M HCl for 16 hrs for glucosamine quantification, respectively; carbohydrates were stable under these conditions. After neutralization, 50 μl of 25 mM lactose solution was added as an internal standard. Samples were vacuum-dried and derivatized for 40 min with 150 μl 0.5 M hydroxylamine·HCl in pyridine at 80°C. After addition of 110 μl (trimethylsilyl)trifluoroacetamid (BSTFA), samples were incubated for another 20 min. Separation and quantification of the derivatives were performed by GC-FID as described under lipids except that column flow was set to 2.7 ml/min and temperature gradient was run from 160°C to 310°C with 7°C per min.
iv) Polyhydroxybutyrate (PHB) content
The measurement of the PHB content was performed according to [62, 63]. Cell pellets (3-4 mg) were lyophilized and subjected to acid methanolysis with 3% H2SO4 (v/v) in methanol/chloroform 1:1 (v/v) for 2.5 hrs at 100°C. Benzoic acid was added as an internal standard prior methanolysis. Methyl-hyroxybutyryl monomers were extracted after addition of water (20% v/v) and vigorous mixing, The organic phase was analyzed by GC-FID with a DB-WAX column, length 15 m, I.D. 0.32 mm, film 0.5 μm. Column flow was set to 1.8 ml/min, detector temperature to 270°C and inlet temperature to 240°C. A sample volume of 1 μl was injected with a split ratio of 2. Temperature gradient was run from 90°C to 230°C at 40°C/min.
v) DNA content
The DNA content was calculated from that in E. coli [64], using appropriate corrections to account for the size of M. extorquens genome and for its growth rate on methanol.
vi) RNA content
The RNA content was determined from the amount of ribose released after acidic hydrolysis (2M HCl for 2 hrs), assuming that all ribose was derived from RNA. The hydrolysis yield was determined from commercial RNA and data were corrected accordingly. Ribose was quantified as described under iii).
vii) Polyamine content
The polyamine content was calculated from that in E. coli. The occurrence of putrescine in methanol-grown M. extorquens cells was also confirmed by GC-MS-MS.
viii) Carotenoid content
Data were taken from [65]. Based on their experimentally determined chemical properties, they were assumed to be spirilloxanthin-like carotenoids.
ix) Content in intracellular metabolites
Data - which included both the nature and amounts of metabolites - were taken from [34, 35], [32, 33], [66], and [7]. The amounts of Coenzyme A thioesters were determined by P. Kiefer (unpublished data). The content in tetra-aminoptherin and related cofactors were obtained from [7, 66]. The contents in other cofactors were calculated from that in E.coli [64], using appropriate corrections.
viii) Inorganic ions
The amounts of inorganic ions were calculated from that in E.coli [64], using appropriate corrections.
The complete details of the biomass composition of M. extorquens, as they result from the above investigations or calculations, are given in Additional file 4.
Cultivation and labeling experiment
Batch cultivations (three biological replicates) of M. extorquens AM1 were carried out at 28°C in minimal medium, in a bioreactor (Infors-HT, Bottmingen, Switzerland), as described previously [19]. Cultivations carried out for the purpose of steady-state [13C]-methanol experiments were performed like in [19]. The cultivations were aerated with 5% natural labeled CO2 to remove the 13CO2 produced by the bacteria from [13C]-methanol. Under this condition, only 4.6 ± 0.4% of total CO2 was found to derive from [13C]-methanol oxidation.
In silicocalculations
The metabolic network - containing 1139 (m) reactions 977 (n) metabolites - was converted into a mathematical model corresponding to a m × n matrix defining the stoichiometric coefficient of reactions. Calculations of steady-state fluxes were performed using the software CellNetAnlyser [25] and Matlab (Mathworks, Inc.). Flux Balance Analysis (FBA) calculations were performed using various objective functions, as indicated in the text. Despite the genome annotation revealed the occurrence of a potential photosynthetic machinery, all calculations were performed assuming that no photosynthesis operated since no phototrophic behavior was reported for M. extorquens. Calculation of EFMs in the methylotrophic network was performed using the solver EFMTool [67]. They were calculated assuming no maintenance energy. To be compared with experimental data, the obtain biomass yields (Y) of the EFMs were calculated as following:
Y = μ m a x q s i × μ m a x μ i + N G A M s × 1000 M W s
With μmax: theoretical maximum growth rate (calculated to be 0.201 for the methylotrophic network from FBA simulations); μi: growth rate of the EFMi (= 0.1); qsi: substrate uptake rate of the EFMi, in mmol · g-1 · h-1; NGAMs: corresponding substrate uptake to fulfill non-growth associated maintenance energy, i.e. 1.9 mmol · g-1 · h-1; MWs: molecular weight of the substrate. Minimal cut sets [42] were calculated on the calculated EFMs, using biomass production as target function.
13C Metabolic Flux Analysis
The distribution of metabolic fluxes during methylotrophic growth was determined from 13C-labeling data collected during steady-state growth of M. extorquens on [13C]-methanol. The distribution of 13C-isotopomers in metabolites can be accurately determined by NMR or MS [45, 68, 69], alone or in combination [19]. Here the 13C-isotopomers of proteinogenic amino-acids were measured by the two methods. NMR spectra were monitored as described in [19] and LC-MS analysis were performed using Rheos 2200 HPLC system (Flux Instruments) coupled to an LTQ Orbitrap mass spectrometer (Thermo Fisher Scientific), equipped with an electrospray ionization probe and the amino acid were separated on a pHILIC column (150 × 2.0 mm, particle size 5 μm; Sequant, Umea, Sweden), following a procedure described [34]. A total of 193 isotopomer data - including 137 NMR data plus 56 MS data - were collected (Additional file 12). The metabolic network considered for flux calculations contained 65 reactions - including 7 reversible reactions - describing M. extorquens central metabolism, according to the topology of the methylotrophic network (Additional file 17). Flux calculations were performed using the software 13C-Flux [70], which uses both mass balances and carbon atom transitions to describe the metabolic. The methanol uptake rate and the requirements in biomass precursors, determined from data in Additional file 4, 11, were constrained. The confidence on the measured fluxes was determined using the sensitivity analysis module of 13C-Flux. Results were expressed as absolute fluxes in mmol.g-1.h-1 +/- standard deviations.
Declarations
Acknowledgements
We thank Philipp Christen for cultivation of M. extorquens AM1 in bioreactors. We thank Birgit Roth Zgraggen of the Functional Genomics Center Zurich for performing amino acid quantification. This work was supported by ETH Zurich, Research Grant ETH-25 08-2. The Swiss Academy of Engineering Science (SATW) and the Centre Français pour l'Accueil et les Echanges Internationaux (Egide) supported the work with a travel grant (Germaine de Staël program). The work carried out at the LISBP (Toulouse, France) was supported by the Région Midi-Pyrénées, the European Regional Development Fund (ERDF), the French Ministry for Higher Education & Research, the SICOVAL, and the Réseau RMN Midi-Pyrénées.
Authors’ Affiliations
(1)
Institute of Microbiology, ETH Zürich, Zürich, Switzerland
(2)
Université de Toulouse; INSA, UPS, INP; LISBP, Toulouse, France
(3)
INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France
(4)
CNRS, Toulouse, France
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} | 57 | cf5cd1df0ee2161e1684bdc019357275 |
5,745,347,484,987,895,000 | Format
Send to
Choose Destination
FEBS Lett. 1996 Sep 30;394(2):179-82.
Protein D2 porin of the Pseudomonas aeruginosa outer membrane bears the protease activity.
Author information
1
Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan.
Abstract
We report here our discovery that protein D2 of the outer membrane of Pseudomonas aeruginosa is a novel porin bearing protease activity. Homogeneously purified protein D2 hydrolyzed several synthetic peptides according to the Michaelis-Menten kinetics. A specific serine protease inhibitor, diisopropyl fluorophosphate (DFP), inactivated the protease activity and [3H]DFP covalently labeled protein D2. We tested the effect of two monoclonal antibodies raised against protein D2 on the protease activity. One antibody lowered the protease activity to about 20%, while the other enhanced it to about 300% of that without antibody. In addition, the fractions derived from the outer membrane of the protein D2-deficient mutants showed negligible protease activity, whereas similarly fractionated outer membrane proteins of the protein D2-positive parent strain showed strong protease activity.
PMID:
8843159
DOI:
10.1016/0014-5793(96)00945-3
[Indexed for MEDLINE]
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7,581,145,660,751,759,000 | Lineage for d3lh6b_ (3lh6 B:)
1. Root: SCOPe 2.08
2. 2923792Class d: Alpha and beta proteins (a+b) [53931] (396 folds)
3. 2998036Fold d.159: Metallo-dependent phosphatases [56299] (1 superfamily)
4 layers: alpha/beta/beta/alpha; mixed beta sheets; contains duplication
4. 2998037Superfamily d.159.1: Metallo-dependent phosphatases [56300] (13 families) (S)
different families of this superfamily are groupped in a single Pfam family, Pfam PF00149
5. 2998354Family d.159.1.7: YfcE-like [111233] (5 proteins)
6. 2998372Protein Vacuolar protein sorting 29, VPS29 [143935] (3 species)
7. 2998387Species Mouse (Mus musculus) [TaxId:10090] [143936] (6 PDB entries)
Uniprot Q9QZ88 1-182
8. 2998397Domain d3lh6b_: 3lh6 B: [305815]
automated match to d2a22b_
complexed with zn
Details for d3lh6b_
PDB Entry: 3lh6 (more details), 3 Å
PDB Description: Crystal structure of mouse VPS29 complexed with Zn2+
PDB Compounds: (B:) Vacuolar protein sorting-associated protein 29
SCOPe Domain Sequences for d3lh6b_:
Sequence; same for both SEQRES and ATOM records: (download)
>d3lh6b_ d.159.1.7 (B:) Vacuolar protein sorting 29, VPS29 {Mouse (Mus musculus) [TaxId: 10090]}
mlvlvlgdlhiphrcnslpakfkkllvpgkiqhilctgnlctkesydylktlagdvhivr
gdfdenlnypeqkvvtvgqfkiglihghqvipwgdmaslallqrqfdvdilisghthkfe
afehenkfyinpgsatgaynaletniipsfvlmdiqastvvtyvyqligddvkverieyk
ks
SCOPe Domain Coordinates for d3lh6b_:
Click to download the PDB-style file with coordinates for d3lh6b_.
(The format of our PDB-style files is described here.)
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} | 57 | cf5cd1df0ee2161e1684bdc019357275 |
4,094,355,772,225,523,000 | SET Binding Protein 1 (SETBP1) (Middle Region) antibody
Details for Product No. ABIN501780
Request Want additional data for this product?
The Independent Validation Initiative strives to provide you with high quality data. Find out more
Antigen
Synonyms SEB, C130092E12, Seb, mKIAA0437, SETBP1
Epitope
Middle Region
(2), (1)
Reactivity
Human
(16), (12), (12), (12), (12), (12), (12)
Host
Rabbit
(14), (3)
Clonality
Polyclonal
Conjugate
Un-conjugated
(1), (1), (1), (1), (1), (1), (1), (1), (1), (1), (1)
Application
Western Blotting (WB)
(10), (7), (4), (3), (2)
Pubmed 1 reference available
Catalog no. ABIN501780
Quantity 50 µg
Price
289.00 $ Plus shipping costs $45.00
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Immunogen Synthetic peptide directed towards the middle region of human SETBP1
Sequence TPRGGKRKHKPQAPAQPPQQSPPQQPLPQEEEVKAKRQRK SRGSESEVLP
Predicted Reactivity Bovine : 92 %, Horse : 92 %, Pig : 92 %, Rabbit : 92 %, Mouse : 72 %, Rat : 72 %
Characteristics This is a rabbit polyclonal antibody against SETBP1. It was validated on Western Blot using a cell lysate as a positive control.
Purification Affinity Purified
Alternative Name SETBP1
Background The function of this protein remains unknown.
Molecular Weight 170 kDa
Gene ID 26040
NCBI Accession NM_015559, NP_056374
UniProt Q9Y6X0
Research Area Cancer
Application Notes Optimal working dilutions should be determined experimentally by the investigator.
Comment
Antigen size: 1542 AA
Restrictions For Research Use only
Format Lyophilized
Reconstitution Add 50 µL of distilled water.
Concentration 1 mg/mL
Buffer PBS buffer with 2 % sucrose
Handling Advice Avoid repeated freeze-thaw cycles.
Storage -20 °C
Storage Comment For longer periods of storage, store at -20 °C
Background publications Ott, Schmidt, Schwarzwaelder et al.: "Correction of X-linked chronic granulomatous disease by gene therapy, augmented by insertional activation of MDS1-EVI1, PRDM16 or SETBP1." in: Nature medicine, Vol. 12, Issue 4, pp. 401-9, 2006 (PubMed).
Hosts (14), (3)
Reactivities (16), (12), (12), (12), (12), (12), (12)
Applications (10), (7), (4), (3), (2)
Conjugates (1), (1), (1), (1), (1), (1), (1), (1), (1), (1), (1)
Epitopes (2), (1)
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8,137,031,523,434,404,000 | What is the importance of bacteria in genetic engineering?
1 Answer | Add Yours
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bandmanjoe | Middle School Teacher | (Level 2) Senior Educator
Posted on
Always start with something small. Bacteria are single-celled organisms that have the necessary requirements for bing regarded as living organisms. They have DNA which is required for genetic engineering. Even with bacteria being small, the DNA genome is still a very large unit to try to manipulate. The next thing is, once you have performed the genetic engineering, placing the genetic sequence in the bacteriums DNA, a new cell has to be grown from the original cell. This is not a problem with bacteria, as they reproduce using a process known as binary fission. Bacteria are also expendable. Cultures of bacteria may be cultivated using appropriate incubation procedures and media. It is possible to secure a wide range of acceptable bacteria to work with at a relatively low expense. It is always important to control expenses in projects such as genetic engineering, where time and money are always controlling factors that dictate the possibility of success.
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5,810,225,747,794,452,000 | Microarray analysis of mouse brain gene expression following acute ethanol treatment
Neurochem Res. 2004 Feb;29(2):357-69. doi: 10.1023/b:nere.0000013738.06437.a6.
Abstract
Alterations in gene expression are thought to help mediate certain effects of alcohol in the brain. We have analyzed the expression of approximately 24,000 genes using oligonucleotide microarrays to examine the brain expression profiles in two strains of inbred mice, C57BL/6J and DBA/2J, following exposure to an acute dose of ethanol. Our screen identified 61 genes responding to the ethanol treatment beyond a 1.5-fold threshold, with 46 genes altered in both mouse strains and 15 altered in only one strain. Approximately 25% of the genes were selected for confirmation by reverse transcriptase polymerase chain reaction with an 87% success rate. The genes identified have roles in cell signaling, gene regulation, and homeostasis/stress response. Although some of the genes were previously known to be ethanol responsive, we have for the most part identified novel genes involved in the acute murine brain response to ethanol. Such genes have the potential to represent candidate genes in the search to elucidate the molecular pathways mediating ethanol's effects in the brain.
Publication types
• Research Support, Non-U.S. Gov't
MeSH terms
• Animals
• Brain / metabolism*
• Central Nervous System Depressants / pharmacology*
• Computer Systems
• Ethanol / pharmacology*
• Female
• Gene Expression / drug effects*
• Male
• Mice
• Mice, Inbred C57BL
• Mice, Inbred DBA
• Oligonucleotide Array Sequence Analysis*
• Reverse Transcriptase Polymerase Chain Reaction
• Species Specificity
Substances
• Central Nervous System Depressants
• Ethanol | {
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-7,854,565,439,489,891,000 | Skip to main content Skip to navigation
BUV661 Mouse Anti-Human CD11b
Product Details
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BD OptiBuild™
MAC-1A; Mac-1; ITGAM; Integrin alpha M; CR3A; CR-3 alpha; Mo1; SLEB6
Human (Tested in Development)
Mouse BALB/c IgG2a, κ
Human peripheral blood T lymphocytes
Flow cytometry (Qualified)
0.2 mg/ml
3684
AB_2874279
Aqueous buffered solution containing ≤0.09% sodium azide.
RUO
Preparation And Storage
Store undiluted at 4°C and protected from prolonged exposure to light. Do not freeze. The monoclonal antibody was purified from tissue culture supernatant or ascites by affinity chromatography. The antibody was conjugated with BD Horizon BUV661 under optimal conditions that minimize unconjugated dye and antibody.
Recommended Assay Procedures
For optimal and reproducible results, BD Horizon Brilliant Stain Buffer should be used anytime two or more BD Horizon Brilliant dyes (including BD OptiBuild Brilliant reagents) are used in the same experiment. Fluorescent dye interactions may cause staining artifacts which may affect data interpretation. The BD Horizon Brilliant Stain Buffer was designed to minimize these interactions. More information can be found in the Technical Data Sheet of the BD Horizon Brilliant Stain Buffer (Cat. No. 563794).
Product Notices
1. This antibody was developed for use in flow cytometry.
2. The production process underwent stringent testing and validation to assure that it generates a high-quality conjugate with consistent performance and specific binding activity. However, verification testing has not been performed on all conjugate lots.
3. Researchers should determine the optimal concentration of this reagent for their individual applications.
4. An isotype control should be used at the same concentration as the antibody of interest.
5. Caution: Sodium azide yields highly toxic hydrazoic acid under acidic conditions. Dilute azide compounds in running water before discarding to avoid accumulation of potentially explosive deposits in plumbing.
6. For fluorochrome spectra and suitable instrument settings, please refer to our Multicolor Flow Cytometry web page at www.bdbiosciences.com/colors.
7. Please refer to www.bdbiosciences.com/us/s/resources for technical protocols.
8. BD Horizon Brilliant Stain Buffer is covered by one or more of the following US patents: 8,110,673; 8,158,444; 8,575,303; 8,354,239.
9. BD Horizon Brilliant Ultraviolet 661 is covered by one or more of the following US patents: 8,110,673; 8,158,444; 8,227,187; 8,575,303; 8,354,239.
750064 Rev. 4
Antibody Details
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D12
The D12 monoclonal antibody specifically binds to CD11b which is also known as Integrin alpha M (Integrin αM), Mac-1 subunit alpha (Mac-1a) or complement receptor 3 alpha chain (CR3a). CD11b is encoded by ITGAM (integrin subunit alpha M) and belongs to the integrin alpha subunit gene family. CD11b is expressed as a ~165-kDa type I transmembrane glycoprotein that associates with the ~95-kDa integrin β2 (CD18) to form the heterodimeric CD11b/CD18 (αM/β2) complex which also known as Mac-1 or CR3. CD11b is expressed on monocytes, dendritic cells, granulocytes, as well as on some T cells, B cells, and NK cells. CD11b functions in cell-cell and cell-substrate interactions and is a receptor for multiple ligands including inactivated C3b (iC3b), ICAM-1 (CD54), ICAM-2 (CD102), ICAM-3 (CD50) or fibrinogen. Mac-1 regulates leucocyte adhesion and migration, as well as phagocytosis of opsonized particles.
CAUTION Binding of this CD11b antibody depends on the presence of Ca++. EDTA or ACD, as anticoagulant might affect binding. Using heparin as an anticoagulant or removal of the anticoagulant is recommended.
The antibody was conjugated to BD Horizon™ BUV661 which is part of the BD Horizon Brilliant™ Ultraviolet family of dyes. This dye is a tandem fluorochrome of BD Horizon BUV395 with an Ex Max of 348-nm and an acceptor dye with an Em Max at 661-nm. BD Horizon Brilliant BUV661 can be excited by the ultraviolet laser (355 nm) and detected with a 670/25 filter and a 630 nm LP. Due to cross laser excitation of this dye, there may be significant spillover into channels detecting APC-like emissions (eg, 670/25-nm filter).
Due to spectral differences between labeled cells and beads, using BD™ CompBeads can result in incorrect spillover values when used with BD Horizon BUV661 reagents. Therefore, the use of BD CompBeads or BD CompBeads Plus to determine spillover values for these reagents is not recommended. Different BUV661 reagents (eg, CD4 vs. CD45) can have slightly different fluorescence spillover therefore, it may also be necessary to use clone-specific compensation controls when using these reagents.
750064 Rev. 4
Format Details
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BUV661
The BD Horizon Brilliant™ Ultraviolet 661 (BUV661) Dye is part of the BD Horizon Brilliant™ Ultraviolet family of dyes. This tandem fluorochrome is comprised of a BUV395 donor with an excitation maximum (Ex Max) of 350-nm and an acceptor dye with an emission maximum (Em Max) at 660-nm. BUV661, driven by BD innovation, is designed to be excited by the ultraviolet laser (355-nm) and detected using an optical filter centered near 660-nm (e.g., 670/25 bandpass filter). The acceptor dye can be excited by the Red (628–640-nm) laser resulting in cross-laser excitation and fluorescence spillover. Please ensure that your instrument’s configurations (lasers and optical filters) are appropriate for this dye.
altImg
BUV661
Ultraviolet 355 nm
350 nm
660 nm
750064 Rev.4
Citations & References
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Development References (10)
1. Lanier LL, Phillips JH. A map of the cell surface antigens expressed on resting and activated human natural killer cells. In: Reinherz EL. Ellis L. Reinherz .. et al., ed. Leukocyte typing II. New York: Springer-Verlag; 1986:157-170.
2. Bernstein ID, Self S. Joint report of the Myeloid Section of the Second International Workshop on Human Leukocyte Differentiation Antigens. In: Reinherz EL, Haynes BF, Nadler LM, Bernstein ID, ed. Leukocyte Typing II: Human Myeloid and Hematopoietic Cells. New York, NY: Springer-Verlag; 1986:1-25.
3. Bray RA, Gottschalk LR, Landay AL, Gebel HM. Differential surface marker expression in patients with CD-16+ lymphoproliferative disorders: in vivo model for NK differentiation.. Hum Immunol. 1987; 19(2):105-15. (Biology). View Reference
4. Clement LT, Grossi CE, Gartland GL. Morphologic and phenotypic features of the subpopulation of Leu-2+ cells that suppresses B cell differentiation.. J Immunol. 1984; 133(5):2461-8. (Clone-specific: Flow cytometry, Fluorescence activated cell sorting). View Reference
5. Gebel HM, Kaizer H, Landay AL. Characterization of circulating suppressor T lymphocytes in bone marrow transplant recipients.. Transplantation. 1987; 43(2):258-63. (Biology). View Reference
6. Landay A, Gartland GL, Clement LT. Characterization of a phenotypically distinct subpopulation of Leu-2+ cells that suppresses T cell proliferative responses.. J Immunol. 1983; 131(6):2757-61. (Immunogen: Blocking, Flow cytometry, Fluorescence activated cell sorting, Immunoprecipitation, Radioimmunoassay). View Reference
7. Patarroyo M, Makgoba MW. Leucocyte adhesion to cells. Molecular basis, physiological relevance, and abnormalities.. Scand J Immunol. 1989; 30(2):129-64. (Biology). View Reference
8. Repo H, Jansson SE, Leirisalo-Repo M. Anticoagulant selection influences flow cytometric determination of CD11b upregulation in vivo and ex vivo.. J Immunol Methods. 1995; 185(1):65-79. (Clone-specific: Flow cytometry). View Reference
9. Ross GD, Cain JA, Lachmann PJ. Membrane complement receptor type three (CR3) has lectin-like properties analogous to bovine conglutinin as functions as a receptor for zymosan and rabbit erythrocytes as well as a receptor for iC3b.. J Immunol. 1985; 134(5):3307-15. (Biology). View Reference
10. Shalekoff S, Page-Shipp L, Tiemessen CT. Effects of anticoagulants and temperature on expression of activation markers CD11b and HLA-DR on human leukocytes.. Clin Diagn Lab Immunol. 1998; 5(5):695-702. (Clone-specific: Flow cytometry). View Reference
View All (10) View Less
750064 Rev. 4
Please refer to Support Documents for Quality Certificates
Global - Refer to manufacturer's instructions for use and related User Manuals and Technical data sheets before using this products as described
Comparisons, where applicable, are made against older BD Technology, manual methods or are general performance claims. Comparisons are not made against non-BD technologies, unless otherwise noted.
For Research Use Only. Not for use in diagnostic or therapeutic procedures. | {
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-8,152,358,500,890,416,000 | Phytophthora infestans (ASM14294v1)
Description
tRNA-Gln for anticodon CUG [Source:TRNASCAN_SE;Acc:tRNA-Gln]
About this transcript
This transcript has 1 exon and is associated with 28 variant alleles.
NameTranscript IDbpProteinTranslation IDBiotypeFlags
-EPrPINT0000000469372No protein-
tRNA pseudogene
Ensembl Canonical
Statistics
Exons: 1, Coding exons: 0, Transcript length: 72 bps,
Version
EPrPINT00000004693
Type
TRNA pseudogene
Annotation Method
ncRNA genes predicted using a combination of methods depending on their type. tRNAs are predicted using tRNAScan-SE, rRNAs using RNAmmer, and for all other types, using covariance models and sequences from RFAM. | {
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6,040,394,007,805,558,000 | Cart:
0
$0.00
Free Newsletter
View price in:
Biodiversity and Conservation of the Meliau Range - Arthur YC Chung
Biodiversity and Conservation of the Meliau Range - Arthur YC Chung
$16.00
Manufacturer Number: ML3766
Stock Status: In Stock
Biodiversity and Conservation of the Meliau Range
A Rain Forest in Sabah's Ultramific Belt
-------
Arthur YC Chung
An introductory account into the Meliau range noted for its ultramafic soils which, because they are poor in nutrients, support an unusual range of plants including orchids and pitcher plants. 87 pages with maps
Weight 0.4kg. Post free within Malaysia
Published by Natural History Publications Kota Kinabalu, 2006.. First edition. ISBN: 9789838121163
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} | 57 | cf5cd1df0ee2161e1684bdc019357275 |
6,377,653,504,199,208,000 | Horia I. Petrache
Learn More
Bilayer form factors obtained from x-ray scattering data taken with high instrumental resolution are reported for multilamellar vesicles of L alpha phase lipid bilayers of dipalmitoylphosphatidylcholine at 50 degrees C under varying osmotic pressure. Artifacts in the magnitudes of the form factors due to liquid crystalline fluctuations have been eliminated(More)
X-ray diffraction data taken at high instrumental resolution were obtained for EPC and DMPC under various osmotic pressures, primarily at T = 30 degrees C. The headgroup thickness DHH was obtained from relative electron density profiles. By using volumetric results and by comparing to gel phase DPPC we obtain areas AEPCF = 69.4 +/- 1.1 A2 and ADMPCF = 59.7(More)
Deuterium (H) NMR spectroscopy provides detailed information regarding the structural fluctuations of lipid bilayers, including both the equilibrium properties and dynamics. Experimental H NMR measurements for the homologous series of 1,2-diacyl-sn-glycero-3-phosphocholines with perdeuterated saturated chains (from C12:0 to C18:0) have been performed on(More)
The fundamental issue of interactions between lipid bilayers is addressed experimentally and theoretically. We report high-resolution x-ray scattering data for bilayers composed of three different kinds of phosphatidylcholine lipids. These data yield the interbilayer water spacing fluctuation s , as well as the traditional osmotic pressure P , both as(More)
Quantitative structures of the fully hydrated fluid phases of dimyristoylphosphatidylcholine (DMPC) and dilauroylphosphatidylcholine (DLPC) were obtained at 30 degrees C. Data for the relative form factors F(q(z)) for DMPC were obtained using a combination of four methods. 1), Volumetric data provided F(0). 2), Diffuse x-ray scattering from oriented stacks(More)
This study focuses on dioleoylphosphatidylcholine (DOPC) bilayers near full hydration. Volumetric data and high-resolution synchrotron x-ray data are used in a method that compares DOPC with well determined gel phase dipalmitoylphosphatidylcholine (DPPC). The key structural quantity obtained is fully hydrated area/lipid A0 = 72.2 +/- 1.1 A2 at 30 degrees C,(More)
An efficient method for extracting volumetric data from simulations is developed. The method is illustrated using a recent atomic-level molecular dynamics simulation of L alpha phase 1,2-dipalmitoyl-sn-glycero-3-phosphocholine bilayer. Results from this simulation are obtained for the volumes of water (VW), lipid (V1), chain methylenes (V2), chain terminal(More)
alpha-1 Antitrypsin (A1AT) is an abundant circulating serpin with a postulated function in the lung of potently inhibiting neutrophil-derived proteases. Emphysema attributable to A1AT deficiency led to the concept that a protease/anti-protease imbalance mediates cigarette smoke-induced emphysema. We hypothesized that A1AT has other pathobiological relevant(More)
Using x-ray diffraction and NMR spectroscopy, we present structural and material properties of phosphatidylserine (PS) bilayers that may account for the well documented implications of PS headgroups in cell activity. At 30 degrees C, the 18-carbon monounsaturated DOPS in the fluid state has a cross-sectional area of 65.3 A(2) which is remarkably smaller(More)
Starting from the glycophorin A dimer structure determined by NMR, we performed simulations of both dimer and monomer forms in explicit lipid bilayers with constant normal pressure, lateral area, and temperature using the CHARMM potential. Analysis of the trajectories in four different lipids reveals how lipid chain length and saturation modulate the(More) | {
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} | 57 | cf5cd1df0ee2161e1684bdc019357275 |
4,130,696,740,444,943,400 |
Outreach & Training
The Dishaw Lab takes outreach seriously. We are committed to communicating our multidisciplinary research, which will contribute to our understanding of host and microbe interactions in the gut and, more specifically, will help define the ecology of microbial colonization on host mucosal surfaces.
Our work is focused on training undergraduates, graduate students, and post-doctoral fellows in the cross-disciplinary field of microbial ecology and immunology.
Communicating & Mentoring
Our work is regularly presented at the international and national levels to our peers; we also present locally, often specifically to undergraduates and even at the k-12 level.
At the undergraduate level, we have specific outreach collaborations with St. Petersburg College and Eckerd College; these programs encourage rigorous honors thesis projects in a laboratory engaged in microbiological, immunological, and marine biological research on a medical campus.
Teaching & Inspring
Our collaborations to reach out to undergraduates is designed to inspire the next generation of STEM scientists and inspire some students that may even be “on the fence” about a career in science.
We also incorporate microbiome technologies in our St. Petersburg College Biotechnology Course guest lectures, take part in local science-themed activities such as the annual Saint Petersburg Science Festival, and also integrating microbial ecology modules into the USF Oceanography Camp for Girls each year of the program.
Stacks Image 517
Mya and I at the Science Festival
Stacks Image 518
Fun activities at the Science Festival
Stacks Image 519
K-12 student preparing PCR reaction
Stacks Image 520
K-12 student loading gel of his very own RFLP
Stacks Image 521
K-12 student presenting Science Fair Project done in our lab
Stacks Image 522
Reviewing biofilm results with undergrad students
Stacks Image 523
Reviewing data with students
Stacks Image 1050
Britt teaching kids about germs
Stacks Image 1052
Britt teaching kids about germs
Stacks Image 597
Oceanography Camp
Stacks Image 599
Lexi at scope with middle schooler
Stacks Image 601
Undergrad Biotech Course
Stacks Image 603
Science Festival: Phage Heroes
Stacks Image 605
Science Fest Demo
Stacks Image 607
Science Fest Demo
Stacks Image 609
Science Fest Demo
Stacks Image 738
REU students in our lab
Stacks Image 740
REU students in our lab
Stacks Image 742
REU student, Alexis, presenting her project
Stacks Image 744
REU student, Alexis, presenting her project
Stacks Image 746
Annual SPC workshop
Stacks Image 748
SPC workshop student
*This website is not an official University of South Florida website. Only the Dishaw Lab is responsible for its content. | {
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7,100,285,767,120,263,000 | Entry: PS00551
General information about the entry
Entry name [info] MOLYBDOPTERIN_PROK_1
Accession [info] PS00551
Entry type [info] PATTERN
Date [info] DEC-1991 (CREATED); NOV-1997 (DATA UPDATE); OCT-2016 (INFO UPDATE).
PROSITE Doc. [info] PDOC00392
Name and characterization of the entry
Description [info] Prokaryotic molybdopterin oxidoreductases signature 1.
Pattern [info]
[STAN]-x-[CH]-x(2,3)-C-[STAG]-[GSTVMF]-x-C-x-[LIVMFYW]-x-[LIVMA]-x(3,4)-
[DENQKHT].
Numerical results [info]
Numerical results for UniProtKB/Swiss-Prot release 2016_11 which contains 553'231 sequence entries.
Total number of hits 182 in 182 different sequences
Number of true positive hits 169 in 169 different sequences
Number of 'unknown' hits 0
Number of false positive hits 13 in 13 different sequences
Number of false negative sequences 39
Number of 'partial' sequences 1
Precision (true positives / (true positives + false positives)) 92.86 %
Recall (true positives / (true positives + false negatives)) 81.25 %
Comments [info]
Taxonomic range [info] Archaea, Prokaryotes (Bacteria)
Maximum number of repetitions [info] 1
Version [info] 1
Cross-references [info]
UniProtKB/Swiss-Prot
True positive sequences
169 sequences
DMSA_ECOLI (P18775 ), DMSA_HAEIN (P45004 ), FDHA_DESGI (Q934F5 ),
FDHA_METFO (P06131 ), FDHA_METJA (P61159 ), FDHF_ECOLI (P07658 ),
FDHL_STAA3 (Q2FEI5 ), FDHL_STAA8 (Q2FVV9 ), FDHL_STAAB (Q2YYT1 ),
FDHL_STAAC (Q5HDP9 ), FDHL_STAAM (Q931G2 ), FDHL_STAAN (Q99RW4 ),
FDHL_STAAR (Q6GEC4 ), FDHL_STAAS (Q6G711 ), FDHL_STAAW (Q7A057 ),
FDHL_STAHJ (Q4L8G8 ), FDHL_STAS1 (Q49ZN0 ), FDNGA_DESVH (Q727P3 ),
FDNG_ECOLI (P24183 ), FDOG_ECOLI (P32176 ), FDXG_HAEIN (P46448 ),
NAPA1_PHOPR (Q6LTV9 ), NAPA2_PHOPR (Q6LQJ3 ), NAPA_ACTP2 (A3N277 ),
NAPA_ACTP7 (B3H2D1 ), NAPA_ACTPJ (B0BR28 ), NAPA_ACTSZ (A6VQY7 ),
NAPA_AERHH (A0KIM1 ), NAPA_AERS4 (A4SPG7 ), NAPA_AGGAC (Q8VL02 ),
NAPA_AGRFC (Q8U7P1 ), NAPA_BORBR (Q7WIQ1 ), NAPA_BORPA (Q7W733 ),
NAPA_BORPD (A9I7M5 ), NAPA_BRADU (Q89EN5 ), NAPA_BRASB (A5ED21 ),
NAPA_BRASO (A4Z0A1 ), NAPA_BURXL (Q13I15 ), NAPA_CAMC1 (A7ZCK4 ),
NAPA_CAMC5 (A7GZP5 ), NAPA_CAMFF (A0RQ36 ), NAPA_CAMHC (A7I3Y7 ),
NAPA_CAMJ8 (A8FLJ3 ), NAPA_CAMJE (Q9PPD9 ), NAPA_CAMJJ (A1VZC8 ),
NAPA_CAMJR (Q5HV12 ), NAPA_CAMLR (B9KCQ2 ), NAPA_CITK8 (A8AE11 ),
NAPA_COLP3 (Q487G4 ), NAPA_CUPNH (P39185 ), NAPA_CUPPJ (Q46RX3 ),
NAPA_CUPTR (B3R8B4 ), NAPA_DECAR (Q47A87 ), NAPA_DINSH (A8LLY9 ),
NAPA_ECO24 (A7ZP28 ), NAPA_ECO27 (B7UFL9 ), NAPA_ECO45 (B7MFB8 ),
NAPA_ECO55 (B7LAM9 ), NAPA_ECO57 (Q8XE47 ), NAPA_ECO5E (B5YWZ7 ),
NAPA_ECO7I (B7NN18 ), NAPA_ECO81 (B7MXN6 ), NAPA_ECO8A (B7M5P6 ),
NAPA_ECOBW (C4ZU48 ), NAPA_ECODH (B1X8A2 ), NAPA_ECOHS (A8A268 ),
NAPA_ECOK1 (A1AD59 ), NAPA_ECOL5 (Q0TFN6 ), NAPA_ECOL6 (Q8CVW4 ),
NAPA_ECOLC (B1IY66 ), NAPA_ECOLI (P33937 ), NAPA_ECOLU (B7N5G7 ),
NAPA_ECOSE (B6I1A4 ), NAPA_ECOSM (B1LKV2 ), NAPA_ECOUT (Q1R9L3 ),
NAPA_EDWI9 (C5B7B9 ), NAPA_ESCF3 (B7LJU7 ), NAPA_HAEDU (Q7VPJ7 ),
NAPA_HAEI8 (Q4QNJ6 ), NAPA_HAEPS (B8F7K2 ), NAPA_HAES1 (Q0I5G9 ),
NAPA_HAHCH (Q2SGV7 ), NAPA_HELHP (Q7VJT5 ), NAPA_HISS2 (B0URQ3 ),
NAPA_LEPCP (B1Y6A6 ), NAPA_MANSM (Q65Q72 ), NAPA_METS4 (B0UCB6 ),
NAPA_NAUPA (B9L8L4 ), NAPA_NITSB (A6Q604 ), NAPA_PARPN (Q56350 ),
NAPA_PASMU (Q9CKL8 ), NAPA_PECAS (Q6D5Z2 ), NAPA_PECCP (C6DK59 ),
NAPA_PSEA7 (A6V924 ), NAPA_PSEA8 (B7UX15 ), NAPA_PSEAB (Q02IZ4 ),
NAPA_PSEAE (Q9I4G3 ), NAPA_PSEMY (A4XWM0 ), NAPA_PSEST (Q3HS05 ),
NAPA_PSEU5 (A4VJ11 ), NAPA_PSYIN (A1SWQ0 ), NAPA_RALPJ (B2UBL7 ),
NAPA_RHIME (Q92Z36 ), NAPA_RHOPB (Q21AR4 ), NAPA_RHOS4 (Q53176 ),
NAPA_SACD2 (Q21PN1 ), NAPA_SALA4 (B5EYU5 ), NAPA_SALAR (A9MJZ6 ),
NAPA_SALCH (Q57M92 ), NAPA_SALDC (B5FNQ2 ), NAPA_SALEP (B5R233 ),
NAPA_SALG2 (B5RC85 ), NAPA_SALHS (B4TAT3 ), NAPA_SALNS (B4SYT3 ),
NAPA_SALPA (Q5PI61 ), NAPA_SALPB (A9N5G2 ), NAPA_SALPC (C0Q0P2 ),
NAPA_SALPK (B5BDZ4 ), NAPA_SALSV (B4TPE6 ), NAPA_SALTI (Q8Z570 ),
NAPA_SALTY (Q8ZNH6 ), NAPA_SERP5 (A8GHJ4 ), NAPA_SHEDO (Q12P44 ),
NAPA_SHEHH (B0TSW5 ), NAPA_SHIB3 (B2TV30 ), NAPA_SHIBS (Q31Z29 ),
NAPA_SHIDS (Q32I06 ), NAPA_SHIF8 (Q0T2R8 ), NAPA_SHIFL (Q83QV0 ),
NAPA_SHISS (Q3Z001 ), NAPA_SYMTH (Q67QZ1 ), NAPA_VIBC3 (A5EZX9 ),
NAPA_VIBCB (A7N7J3 ), NAPA_VIBCH (Q9KLR4 ), NAPA_VIBCM (C3LVU3 ),
NAPA_VIBF1 (Q5E3J6 ), NAPA_VIBFM (B5FGW1 ), NAPA_VIBPA (Q87GW6 ),
NAPA_VIBTL (B7VRL0 ), NAPA_VIBVU (Q8D623 ), NAPA_VIBVY (Q7MD44 ),
NAPA_WOLSU (Q7M962 ), NAPA_YERE8 (A1JL26 ), NAPA_YERP3 (A7FG75 ),
NAPA_YERPA (Q1C5S8 ), NAPA_YERPB (B2K970 ), NAPA_YERPE (Q8ZCF3 ),
NAPA_YERPG (A9QZL3 ), NAPA_YERPN (Q1CK03 ), NAPA_YERPP (A4TMK8 ),
NAPA_YERPS (Q668I0 ), NAPA_YERPY (B1JSJ0 ), NARB_SHEFN (O33732 ),
NARB_SYNE7 (P39458 ), NARB_SYNY3 (P73448 ), NARG_BACSU (P42175 ),
NARG_ECOLI (P09152 ), NARG_HALMT (I3R9M9 ), NARG_MYCTO (P9WJQ2 ),
NARG_MYCTU (P9WJQ3 ), NARX_MYCTO (P9WJQ0 ), NARX_MYCTU (P9WJQ1 ),
NARZ_ECOLI (P19319 ), NASA_KLEOX (Q06457 ), NASC_BACSU (P42434 ),
PHSA_SALTY (P37600 ), PSRA_WOLSU (P31075 ), Y006_METJA (Q60314 ),
YNFF_ECOLI (P77783 )
» more
UniProtKB/Swiss-Prot
False negative sequences
39 sequences
AHY_PELAE (Q71EW5 ), BISC_ECOLI (P20099 ), BISC_RHOSH (P54934 ),
CLRA_IDEDE (P60068 ), DDHA_RHOSU (Q8GPG4 ), DSTOR_RHOCA (Q52675 ),
DSTOR_RHOSH (Q57366 ), FDHL_BACSU (Q795Y4 ), NAPA_DESDA (P81186 ),
NAPA_HAEIE (A5UAE1 ), NAPA_LARHH (C1D9G3 ), NAPA_MAGMG (Q93HX3 ),
NAPA_MAGSA (Q2W3T1 ), NAPA_SHEON (Q8EIJ1 ), NASA_HALMT (I3R634 ),
PCRA_DECAR (Q47CW6 ), QRCB_DESVH (Q72E84 ), SERA_THASE (Q9S1H0 ),
TORA_ECO57 (P58360 ), TORA_ECOL6 (Q8CW73 ), TORA_ECOLI (P33225 ),
TORA_PASMU (Q9CK41 ), TORA_SALTI (Q8Z2M4 ), TORA_SALTY (Q8ZKZ7 ),
TORA_SHEMA (O87948 ), TORA_SHEON (Q8EHI9 ), TORA_VIBCH (Q9KRF0 ),
TORA_VIBPA (Q87QI7 ), TORA_VIBVU (Q8D8S3 ), TORA_VIBVY (Q7MLQ2 ),
TORZ_ECO57 (P58362 ), TORZ_ECOLI (P46923 ), TORZ_HAEIN (P44798 ),
TTRA_ARCFU (O30078 ), TTRA_SALTY (Q9Z4S6 ), YJGC_BACSU (O34720 ),
YNFE_ECOLI (P77374 ), YOAE_BACSU (C0SP82 ), YYAE_BACSU (P37519 )
» more
UniProtKB/Swiss-Prot
'Partial' sequences
1 sequence
NARG_BRASZ (P85097 )
UniProtKB/Swiss-Prot
False positive sequences
13 sequences
KR510_HUMAN (Q6L8G5 ), KR511_HUMAN (Q6L8G4 ), KRA51_HUMAN (Q6L8H4 ),
KRA52_HUMAN (Q701N4 ), KRA54_HUMAN (Q6L8H1 ), KRA55_HUMAN (Q701N2 ),
KRA56_HUMAN (Q6L8G9 ), KRA57_HUMAN (Q6L8G8 ), KRA58_HUMAN (O75690 ),
KRUC_SHEEP (P26372 ), NUOG2_RHIME (P56914 ), OR59A_DROME (P81923 ),
POB3_ASHGO (Q756X6 )
» more
PDB
[Detailed view]
20 PDB
1AA6; 1FDI; 1FDO; 1H0H; 1KQF; 1KQG; 1OGY; 1Q16; 1R27; 1Y4Z; 1Y5I; 1Y5L; 1Y5N; 2IV2; 2NYA; 3EGW; 3IR5; 3IR7; 3ML1; 3O5A
» more
View entry in original PROSITE format
View entry in raw text format (no links)
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Life Science Tests Answer Key (3rd ed.)
Life Science Tests Answer Key (3rd ed.)
Answer key includes all answers for each chapter test for Life Science (3rd ed.) Page numbers are given for each answer. Format of questions include matching, multiple choice, true or false, diagram labeling, and essay.
• ISBN - 978-1-59166-478-9
• Author - BJU Press
• Copyright Year - 2007
• Edition - 3rd ed.
• Format - 3-hole punched
• Length - 136 pp.
• Grade Level - 7
• Publisher - BJU Press
228205
Life Science Tests Answer Key (3rd ed.)
$11.94Quantity
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Euchaetis
Euchaetis is a genus of eudicot in the family Rutaceae (rue family).
Taxonomy ID: 378925
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db=protein|term=txid378925[Organism:exp]|query=1|qty=2|blobid=MCID_666d49951eb9e6474a9016db|ismultiple=false|min_list=5|max_list=20|def_tree=20|def_list=|def_view=|url=/Taxonomy/backend/subset.cgi?|trace_url=/stat?
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-5,272,289,670,431,842,000 | The Ph.D Programme in Biotechnology session 2023 is scheduled to be held on 13th July 2023
It is notified for the information of all those candidates who have applied for Ph.D programme in Biotechnology, session 2023 under exemption i.e; having qualified UGC NET/JRF or CSIR-UGC NET/JRF/ICAR NET/SET/GATE/WoS -A / lnspire fellows with fellowships and Teacher Fellowship or any other equivalent test declared so by the UGC or M.Phil that their lnteraction with the Departmental Research Committee is scheduled to be held on 13th July 2023 at 10:30 am in the department of Biotechnology.
View | {
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1,854,348,902,721,870,600 | 2007 Competition
Year:
Team Size:
Wiki Link:
Awards:
Project Title:
Project Description:
2007
5
Purdue Biomakers 2007
Bronze Medal
Bacteria Warfare: Rock, Paper, Scissors
This year’s Purdue 2007 iGEM team will be presenting a project called “Bacteria Warfare” for this year’s competition hosted by MIT in November. The team is composed of a group of undergraduates from different majors including Biomedical Engineering, Agricultural and Biological Engineering, Biochemistry, and Chemistry. Escherichia coli (E. coli) is used to conduct the microbial warfare. The design is to use two different types of transformed E. coli. One type of E. coli produces protein that triggers the death gene of its opponent (but not for itself) which expresses the production of a protein toxin. One expresses green fluorescence protein and the other expresses red fluorescence protein so that the progression of the war between types can be easily viewed and monitored. The team decided the general topic of a bacteria warfare at the end of spring 07 and started design and construction of the warfare in summer 07. | {
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-5,973,419,313,534,264,000 | Whoops! Something went wrong.
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Microscope and Cell Observation Lab
Microscope and Cell Observation Lab
Microscope and Cell Observation Lab
Microscope and Cell Observation Lab
Microscope and Cell Observation Lab
Microscope and Cell Observation Lab
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File Type
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136 KB|3 pages
Product Description
This lab activity could be used to introduce microscope use and/or to support cell structure and function objectives. Students begin with "The Letter E" lab, a lab traditionally used to introduce students to the functions of a microscope. The lab then extends into plant and animal cell observations. Students record observations and also extend learning with enrichment questions.
Total Pages
3 pages
Answer Key
N/A
Teaching Duration
3 hours
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4,865,883,628,809,958,000 | Sequence Similarity Clusters for the Entities in PDB 1JCT
Entity #1 | Chains: A,B
Glucarate Dehydratase protein, length: 446 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 1 1 29741
95 % 9 9 1655
90 % 9 9 1689
70 % 11 11 1441
50 % 22 22 601
40 % 22 22 638
30 % 226 234 21
Instructions
In the table for each entity, view a list of similar sequences by selecting the link associated with the percentage cutoff.
View more detailed documentation on the redundancy reduction and sequence clustering procedure used by RCSB PDB. | {
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2014
Karlyshev, AV; Thacker, G; Jones, MA; Clements, MO; Wren, BW; (2014) Campylobacter jejuni gene cj0511 encodes a serine peptidase essential for colonisation. FEBS Open Bio, 4. pp. 468-72. ISSN 2211-5463 DOI: https://doi.org/10.1016/j.fob.2014.04.012
[img]
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2,135,140,752,824,712,000 | Research Associate in Field Biology
us: Research Associate in Field Biology [Non-Tenure Track | Duties: The Keith Clay lab at Indiana University is seeking a highly-motivated Research Associate to help with field work in southern Indiana related to two different projects: 1) collecting samples of ticks and mosquitoes multiple times per year from the same locations across multiple sites in south-central Indiana, funded by the IU Grand Challenge Prepared for Environmental Change project, and 2) overseeing field experiments and collections of the invasive grass, Microstegium vimineum (Japanese stiltgrass) and its fungal pathogens at Big Oaks National Wildlife Refuge ( BONWR ) near Madison, Indiana and surrounding areas funded by a grant from the USDA . Clay lab research is described at http://www.indiana.edu/~symbios/Clay_Lab/Home.html. The succ... | Minimum Requirements: B.S. or B.A. in biology, ecology, entomology, or a related field, and previous field work experience required. M.S. in biology or related field preferred. The successful applicant must be well organized and detail-oriented, with strong analytical and interpersonal skills, and be able to work effectively with minimal supervision in the filed as part of a larger research project. Additional training specific to work on these projects will be provided] / Indiana University Bloomington (IU Bloomington); Bloomington, Indiana, United States | {
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-2,336,619,899,033,724,000 | Region: CIP
Geographic Zones: Cebu Island
Survey Types: Species & Abundance, Species Only
Dates: 1/1/93 - 8/8/20
Total Surveys: 211
#Species Reported: 816
Average Species Reported on a Survey by Expert Surveyors: 97.58
Average Species Reported on a Survey by Novice Surveyors: 51.30
Survey Type: SA = Species & Abundance; SO = Species Only - How to interpret REEF data?
Expand all Collapse all
Species
%SF = Sighting Frequency; DEN = Density Score - How to interpret REEF data?
Bar length corresponds to sighting frequency
Color saturation corresponds to density score
Click + to display species image and additional information.
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4,090,482,908,325,511,700 |
2GNI
PKA fivefold mutant model of Rho-kinase with inhibitor Fasudil (HA1077)
Experimental Data Snapshot
• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.268
• R-Value Work: 0.188
• R-Value Observed: 0.192
wwPDB Validation 3D Report Full Report
This is version 1.2 of the entry. See complete history
Literature
Structural analysis of protein kinase A mutants with Rho-kinase inhibitor specificity
Bonn, S.Herrero, S.Breitenlechner, C.B.Erlbruch, A.Lehmann, W.Engh, R.A.Gassel, M.Bossemeyer, D.
(2006) J Biol Chem 281: 24818-24830
• DOI: 10.1074/jbc.M512374200
• Structures With Same Primary Citation
• PubMed Abstract:
• Controlling aberrant kinase-mediated cellular signaling is a major strategy in cancer therapy; successful protein kinase inhibitors such as Tarceva and Gleevec verify this approach. Specificity of inhibitors for the targeted kinase(s), however, is a ...
Controlling aberrant kinase-mediated cellular signaling is a major strategy in cancer therapy; successful protein kinase inhibitors such as Tarceva and Gleevec verify this approach. Specificity of inhibitors for the targeted kinase(s), however, is a crucial factor for therapeutic success. Based on homology modeling, we previously identified four amino acids in the active site of Rho-kinase that likely determine inhibitor specificities observed for Rho-kinase relative to protein kinase A (PKA) (in PKA numbering: T183A, L49I, V123M, and E127D), and a fifth (Q181K) that played a surprising role in PKA-PKB hybrid proteins. We have systematically mutated these residues in PKA to their counterparts in Rho-kinase, individually and in combination. Using four Rho-kinase-specific, one PKA-specific, and one pan-kinase-specific inhibitor, we measured the inhibitor-binding properties of the mutated proteins and identify the roles of individual residues as specificity determinants. Two combined mutant proteins, containing the combination of mutations T183A and L49I, closely mimic Rho-kinase. Kinetic results corroborate the hypothesis that side-chain identities form the major determinants of selectivity. An unexpected result of the analysis is the consistent contribution of the individual mutations by simple factors. Crystal structures of the surrogate kinase inhibitor complexes provide a detailed basis for an understanding of these selectivity determinant residues. The ability to obtain kinetic and structural data from these PKA mutants, combined with their Rho-kinase-like selectivity profiles, make them valuable for use as surrogate kinases for structure-based inhibitor design.
Related Citations:
• Protein kinase A in complex with Rho-kinase inhibitors Y-27632, Fasudil, and H-1152P: structural basis of selectivity
Breitenlechner, C.B., Gassel, M., Hidaka, H., Kinzel, V., Huber, R., Engh, R.A., Bossemeyer, D.
(2003) Structure 11: 1595
Organizational Affiliation
Group of Structural Biochemistry, German Cancer Research Center, 69120 Heidelberg.
Macromolecules
Find similar proteins by: Sequence | Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP-dependent protein kinase, alpha-catalytic subunitA350Bos taurusMutation(s): 8
Gene Names: PRKACA
EC: 2.7.11.11
Find proteins for P00517 (Bos taurus)
Explore P00517
Go to UniProtKB: P00517
Protein Feature View
( Mouse scroll to zoom / Hold left click to move )
• Reference Sequence
• Find similar proteins by: Sequence | Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
cAMP-dependent protein kinase inhibitor alphaI20N/AMutation(s): 0
Find proteins for P61925 (Homo sapiens)
Explore P61925
Go to UniProtKB: P61925
NIH Common Fund Data Resources
PHAROS P61925
Protein Feature View
( Mouse scroll to zoom / Hold left click to move )
• Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M77
Query on M77
Download CCD File
A
5-(1,4-DIAZEPAN-1-SULFONYL)ISOQUINOLINE
C14 H17 N3 O2 S
NGOGFTYYXHNFQH-UHFFFAOYSA-N
Ligand Interaction
Modified Residues 2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
AL-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
AL-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations
IDBinding Affinity (Sequence Identity %)
M77IC50: 607 nM BindingDB
M77IC50: 2452 nM BindingDB
M77IC50: 1350 nM BindingDB
M77IC50 : 2280 nM PDBBind
M77IC50: 2280 nM BindingDB
M77Ki: 2280 nM Binding MOAD
M77IC50: 1947 nM BindingDB
M77Ki: 1600 nM BindingDB
M77IC50: 7605 nM BindingDB
M77IC50: 1494 nM BindingDB
M77IC50: 541 nM BindingDB
M77IC50: 870 nM BindingDB
M77Ki: 460 nM BindingDB
M77IC50: 853 nM BindingDB
M77IC50: 893 nM BindingDB
M77IC50: 1127 nM BindingDB
Experimental Data & Validation
Experimental Data
• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.268
• R-Value Work: 0.188
• R-Value Observed: 0.192
• Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.227α = 90
b = 75.959β = 90
c = 80.396γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing
Structure Validation
View Full Validation Report
Entry History
Deposition Data
Revision History
• Version 1.0: 2006-05-23
Type: Initial release
• Version 1.1: 2008-05-01
Changes: Version format compliance
• Version 1.2: 2011-07-13
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1,244,050,577,682,159,400 | New Internationalist
Search results for Biodiversity
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Wonder and frustration: living with the animals
Mari Marcel Thekaekara’s home is on the edge of a wildlife sanctuary, which is a pleasure and a pain, as she explains.…
• Fri Jul 8 08:20:00 2016
• Rank: 100
Fuelling the debate
Its big, but its not clever the biofuel boom is threatening lives and land. .…
• Fri Jul 8 08:20:00 2016
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Corporate pollution
Africas people and environmentare suffering at the hand of foreign corporations. .…
• Fri Jul 8 08:20:00 2016
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Reality bites
If Copenhagen has proved one thing so far, its that environmental and economic issues are one and the same.…
• Fri Jul 8 08:20:00 2016
• Rank: 100
On the road from Guyana to Brazil
Nyan Storey on an inspirational trip through Guyana's rainforest and savannah.…
• Fri Jul 8 08:20:00 2016
• Rank: 100
Indigenous Groups sound the REDD Alert
I'm currently writing an article for our forthcoming issue of the New Internationalistmagazine that looks at some of the potential dangers of relying oncarbon markets for preserving forests and biodiversity. The globalcarbon market is worth $64 billion but has yet to produce much in theway of reductions in emissions. It has however delivered huge profitsto some of the world's worst polluters who have been investing heavilyin carbon trading, offsets and 'environmental services'.…
• Fri Jul 8 08:20:00 2016
• Rank: 100
Inner city orchard
In this part of the world Burnham is not a wood that moves, as inShakespeare's Scottish Play, but Burham-on-Sea, a charming littleresort on the coast nearby. Even so, Transition City Bristol reversed the usual flow last Saturday and brought trees to the city. If you looked very closely you could even see them moving.…
• Fri Jul 8 08:20:00 2016
• Rank: 100
Too much hot air
Australians are, collectively, some of theworst greenhouse gas emitters in the world. And the cows aren't helping.…
• Fri Jul 8 08:20:00 2016
• Rank: 100
Wonder Women
Women who are doing it for themselves...…
• Fri Jul 8 08:20:00 2016
• Rank: 100
Deeper into that dangerous territory
Today the UN officially launches the International Year of Forests. There's some good news, and some bad news..…
• Fri Jul 8 08:20:00 2016
• Rank: 100
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-1,174,370,763,649,009,700 | Short-review-of-cha_44562
Short-review-of-cha_44562 - Control of eukaryotic gene...
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8/17/11 Control of eukaryotic gene transcription Ground state is off – requirement for activators Promoter region usually contains many binding sites for transcription factors and enhancers Besides basal promoter elements like TATA box at -30 and CCAT box around -80, there are enhancers. Enhancers can be located far away, 5’ or 3’, or even in introns of the gene Many transcription factors are modular: DNA binding domain and activation domain (for example, yeast Gal4, lexA) DNA is packed in chromatin: DNA is wrapped around nucleosome: positivly charged proteins. How tightly DNA is bound to these proteins determines whether its regulatory regions can be bound, and whether the gene can be transcribed. The modifications of histones is therefore very important: Everything that reduces their positive charge will lead to loosened up chromatin and better accessibility of the DNA. Hyper-transcribed genes are associated with histones with a lot of modifications (methylation and acetylation)
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This note was uploaded on 08/16/2011 for the course BIOL 1361-1362 taught by Professor Any during the Spring '08 term at University of Houston.
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Severin
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Severin blocks the ends of F-actin and causes the fragmentation and depolymerization of actin filaments. This severin binds stably with actin both in a Ca(2+) dependent and a Ca(2+) independent manner.
Below are the list of possible Severin products. If you cannot find the target and/or product is not available in our catalog, please click here to contact us and request the product or submit your request for custom elisa kit production, custom recombinant protein production or custom antibody production. Custom ELISA Kits, Recombinant Proteins and Antibodies can be designed, manufactured and produced according to the researcher's specifications.
Severin
Severin ELISA Kit
Severin Recombinant
Severin Antibody
Severin blocks the ends of F-actin and causes the fragmentation and depolymerization of actin filaments. This severin binds stably with actin both in a Ca2+ dependent and a Ca2+ independent manner.
AG8 ELISA Kit
AG8 Recombinant
AG8 Antibody
Table BarTOPTable Bar
Proteins Root Name Listing
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-3,109,806,149,182,219,300 | Soil degradation as big a threat as climate change
Published by Niall Sargent on
December 5th, 2018
The widespread degradation of soil across the world is as big a threat to our existence as climate change, a leading environmentalist warned today.
Speaking at the Soils for Society conference at University College Dublin, the coordinator of the Environmental Pillar, Michael Ewing, called for greater protection of our depleted soils.
The UCD conference was held to mark World Soil Day, held annually to focus attention on soil and to advocate for the sustainable management of soil resources.
Soil degradation now affects about one-third of the global land area with widespread consequences including soil erosion, desertification, nutrient loss, and pollution.
Mr Ewing pointed to the absolute need to protect our soils if we are to have any hope of feeding a growing world population that was a mere 2.5 billion when he went to school, is now over 7 billion and is expected to reach more than 10 billion by 2050.
3rd anniversary – Sustainable Development Goals. Call to Leave No One Behind
SDGs and Soil
He told the audience that healthy soil is crucial to the delivery of the 17 Sustainable Development Goals (SDGS), such as protection for all life on land, as well as an end to human hunger and poverty on the planet.
“Soil is a vibrant living substance which is vital for life on Earth,” Mr Ewing said.
“Each and every one of us totally depends on the four or five inches of soil around the globe for our very existence and we share this space with an estimated 2 billion other species that also rely on it too.
“Looking after our precious soils as an integrated part of the delivery of the SDGs must be a priority for all governments, local, national and regional,” Mr Ewing said.
Edible soil dish to promote the People4Soil Campaign Photo: Niall Sargent
Edible soil dish to promote the 2017 People4Soil Campaign Photo: Niall Sargent
People4Soil
Mr Ewing also highlighted the People4Soil campaign last year that received great support across Ireland from citizens asking the EU for regulations to protect the soil.
“Soil has scarce protection under the law as it stands,” he warned.
“If we take a stand today, we’ll be one step closer to limiting the damage soil destruction will do to our environment, our health, and our children’s futures,” he said.
The People4Soil campaign, led in Ireland by the Environmental Pillar, received over 9,100 signatures in Ireland before last week’s deadline, smashing Ireland’s official target of 8,250.
Ireland was also the first country to reach its national quota and achieved the second highest percentage tally behind only Italy.
GROW Observatory
The GROW Observatory – a European-wide project engaging thousands of GROWers, researchers and people passionate about land and soil – is taking a lead on spotlighting the importance of soil health in Ireland.
The Irish branch of GROW is mobilising enable people to act as citizen scientists and, using low cost soil sensors, collect data that can help validate climate prediction models from satellites.
This will help to forecast the frequency and intensity of extreme climate phenomena, like droughts, floods and heatwaves, the Irish branch says.
So far, citizen scientists in the GROW Communities have deployed 2,000 soil moisture sensors in the different GROW Places, setting views to 10,000 sensors in the coming year.
This is considered to be the largest soil moisture survey conducted by citizens across Europe.
[x_author title=”About the Author”]
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Niall Sargent
Niall is the Editor of The Green News. He is a multimedia journalist, with an MA in Investigative Journalism from City University, London | {
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} | 57 | cf5cd1df0ee2161e1684bdc019357275 |
5,374,968,514,801,774,000 | Dietrich Stephan
MAGNETISM
SUCCESS
VITALS
BIRTH PLACE
N/A
“For the future, for people who don’t have ALS yet, we can envision developing a diagnostic test that would allow us to monitor individuals early, diagnose them early and put them on a to-be-developed therapy that would intervene before the pathology gets too devastating.”
- Dietrich Stephan
Dietrich Stephan is a brilliant genetic scientist who has slowly but surely moved to the forefront of the fight against deadly genetic diseases, as his work has proven instrumental in identifying genes that lead directly to such disorders as autism and even heart attacks.
MAGNETISM
Far from the cliché of a pocket protector-wearing nerd, Dietrich Stephan possesses a command of his field that most women would surely find irresistible. As someone who is actively looking to change the world, Dietrich Stephan is surely not lacking for dates or encounters with the opposite sex. He is apparently a happily married man, as evidenced by his preference to spend his Saturday nights enjoying a “quiet, romantic dinner“ with his significant other.
SUCCESS
Though still just in his 30s, Dietrich Stephan has managed to accomplish more than most of his fellow scientists and researches will be able to accomplish during their entire lives. Dietrich Stephan’s prodigious abilities have been firmly in place since his college years, with his post-college work at distinguished institutions such as Johns Hopkins University and George Washington University certainly establishing him as a force to be reckoned with in the scientific community. In addition to publishing journals and leading teams of scientists, Dietrich Stephan was recently named the Deputy Director of Discovery Research at the Translational Genomics Research Institute. He is also a chairman of the National Institutes of Health Neuroscience Microarray Consortium and is the cofounder and Chief Science Officer of the personal genomics company Navigenics.
Dietrich Stephan Biography
Though his name might not sound familiar, Dietrich Stephan has certainly established himself as one of the most promising and downright important figures within the science world. As an adolescent, however, Dietrich Stephan hardly thought of himself as anything more than just another misunderstood teenager. He took solace in J.D. Salinger’s infamous ode to existentialism Catcher in the Rye, which he read a whopping 23 times during his shaky teen years.
Dietrich Stephan’s interest in science blossomed during his high school career; when the time came to choose his post-secondary institute of learning, Dietrich Stephan settled on the well-regarded private research university Carnegie Mellon. He flourished during his tenure at the school, and eventually wound up pursuing his Ph.D. in Human Genetics at the University of Pittsburgh, with his stellar work ultimately bringing him to the attention of various scientifically oriented research laboratories.
It was the lure of studying side-by-side with the brilliant minds at Bethesda that eventually won Dietrich Stephan’s interest, as the up-and-coming scientist took on a position as a fellow within the building’s National Human Genome Research Institute. He spent the next several years hopping from one distinguished faculty appointment to the next, including stints at Johns Hopkins University and the University of Arizona.
dietrich stephan works on neurological disorders
It wasn’t until he assumed his post as director of the Neurogenomics Division of the nonprofit Translational Genomics Research Institute in Phoenix that Dietrich Stephan first attracted international attention, as it was there that the brilliant geneticist began studying how certain diseases originate within the human body. He’s devoted 15 years of his life trying to, as he says, “sift through the genetic blueprints of people with diseases versus without diseases,” which will allow scientists and doctors in the future the ability to detect such illness early on in their lifecycle.
Dietrich Stephan’s focus on neurological disorders has put him at the forefront of an effort to find cures for some of the most deadly diseases known to man, including Alzheimer’s, Parkinson’s and multiple sclerosis. Dietrich Stephan’s specific work within the realm of Amyotrophic Lateral Sclerosis (better known as ALS and Lou Gehrig’s Disease) has won accolades from the both the technological and scientific communities due to the unprecedented use of silicon chips to deconstruct certain genes and DNA sequences.
Dietrich Stephan’s impressive success rate has proved instrumental in identifying the mutations that lead to five human diseases, including prostate cancer and a form of Sudden Infant Death Syndrome. There’s little doubt that Dietrich Stephan consequently remains one of the most important figures in the fight against deadly diseases, and it certainly seems likely that his name will ultimately rank side-by-side with such well-known scientists as Marie Curie and Jonas Salk.
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4,971,853,720,844,611,000 | NZ wren DNA analysis reshapes geological theory
NZ wren DNA analysis-GeologyPage
Lyall’s wren: an extinct acanthisittid wren, infamously reported as having been both discovered and exterminated by a lighthouse-keeper’s cat. Credit: Public Domain, John Gerrard Keulemans (1842-1912)
A DNA analysis of living and extinct species of mysterious New Zealand wrens may change theories around the country’s geological and evolutionary past.
A University of Adelaide study into New Zealand’s acanthisittid wrens has provided compelling evidence that, contrary to some suggestions, New Zealand was not completely submerged under the ocean around 21 to 25 million years ago.
The acanthisittid wrens are a group of tiny, largely flightless, birds found nowhere else in the world. They are called wrens because of their similarity in appearance and behaviour to “true wrens”, but they don’t belong to the same family.
“Of the seven species living before humans arrived in New Zealand, only two now remain, the rock wren and the rifleman,” says lead author Dr Kieren Mitchell, Postdoctoral Research Associate in the University’s Australian Centre for Ancient DNA (ACAD). “Consequently, little is known about their evolution.”
Published in the journal Molecular Phylogenetics and Evolution and led by ACAD, the researchers analysed DNA from three of the extinct species along with the two living species.
The research was in collaboration with the Museum of New Zealand Te Papa Tongarewa, Canterbury Museum and the New Zealand Department of Conservation.
“Most surprisingly, we found that some of the wren species were only distantly related to each other, potentially sharing a common ancestor over 25 million years ago,” Dr Mitchell says.
“Previously, researchers have suggested that New Zealand was completely submerged 21 to 25 million years ago, which implies that all of New Zealand’s unique plants and animals must have immigrated and diversified more recently than that time.
“This theory is consistent, for instance, with what is known about the moa, where the different species all shared a common ancestor much more recently than 21 million years ago.
“But the ancient divergences we found among the wrens suggest that they have been resident in New Zealand for more than 25 million years, and possibly as long as 50 million years (when New Zealand became disconnected from the rest of Gondwana).
“As the wrens were largely very poor fliers, or even flightless, some land must have remained throughout that period.
“This has important consequences for our understanding of the evolution of New Zealand’s unique ecosystems.”
Reference:
Kieren J. Mitchell, Jamie R. Wood, Bastien Llamas, Patricia A. McLenachan, Olga Kardailsky, R. Paul Scofield, Trevor . Worthy, Alan Cooper. Ancient mitochondrial genomes clarify the evolutionary history of New Zealand’s enigmatic acanthisittid wrens. DOI: 10.1016/j.ympev.2016.05.038
Note: The above post is reprinted from materials provided by University of Adelaide.
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-155,893,852,633,146,700 | top of page
Every animal and plant on earth is part of an incredible WEB OF LIFE. But living things are disappearing all over the world, and it's a big problem. Award-winning author-illustrator Neal Layton is here to introduce the concept of biodiversity to younger readers, explaining what it is, why it's so important, and how the actions of humans are hurting it. But he's also FULL of ideas for how you can help! From building a bug hotel to growing flowers on a windowsill and eating more organic food, A World Full of Wildlife will get young readers excited about how they can make a difference to keep the web of life bursting with energy.
This brilliant non-fiction picture book is perfect for readers aged 5-7 who love nature and want to help the environment.
A World Full of Wildlife and How You Can Protect It | Neal Layton
£12.99Price
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8,493,128,143,235,871,000 | Re: Aunger vs. Pinker on Galton
From: Scott Chase ([email protected])
Date: Tue 19 Apr 2005 - 23:06:55 GMT
• Next message: Scott Chase: "Re: Aunger vs. Pinker on Galton"
--- Derek Gatherer <[email protected]> wrote:
> At 17:54 16/04/2005, you wrote:
> >Which eminent evolutionary author is correct on
> >Darwin's relation to Galton, Aunger or Pinker?
>
> I'll check. I've just written in an article I'm
> doing at the moment, that
> Galton was Darwin's cousin. That's what I've always
> believed, but I
> suppose I'd better make sure.
>
>
Bill posted a link that supports that they were hal-cousins. Unless someone can support that that Galton was Darwin's uncle I'm going to assume Aunger flubbed on this one. Coupled with his explanations of the cellular functions of ribosomes, I'm left scratching my head in amazement. I'd like your's and Chris's input into this. Maybe I didn't dive into cellular biology deep enough where the integral role of ribosomes is unmasked. I always thought that ribosomes were where mRNA is translated into peptides. I pretty sure DNA polymerases play a role in replication, but not ribosomes. I think I had brought this topic up here a while back, but want to make sure I'm not missing something this next attempt at deciphering Aunger's book. I've got the grandpappy's of neuropsych Hebb and Lashley handy, so maybe I'll be quite occupied in the near future.
BTW, has anyone gone anywhere with Lashley's notion of memory trace redupilcation? I gather that he thought the engram was non-local but still physical. His work pinted to a diffuse sort of memory trace instead of a localized engram. Hebb strats chopping away at field theories and equipotentiality stuff quite early in his monograph and starts in with the Ma Bell
(ie-switchboard) theories of synaptic connectivity.
A really interesting aside is that Jack Orbach in his
_The Neuropsychological Theories of Lashley and Hebb_ talks about (on page 5) how Hebb had used something like the Necker cube to put the organism back into S-R psychology (thus making it S-O-R). Organismic response variation to reversible figures supposedly demostrates that there's more to it than S-R behaviorism would acknowledge. Ironically isn't the Necker cube what Dawkins used as a way of getting his readers to shift focus away from the organism?
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SHI to sponsor DNA research during Celebration
Posted: June 6, 2012 - 11:04pm | Updated: June 9, 2012 - 11:03pm
Sealaska Heritage Institute will sponsor a DNA study by the Department of Anthropology, University of Pennsylvania, during Celebration 2012.
The Genographic Project: Molecular Genetic Analyses of Indigenous Populations of North America — University of Pennsylvania is being led by Principal Investigator Dr. Theodore G. Schurr, who was at Centennial Hall during Celebration June 7-9.
The goal of the study is to better understand the migration paths that early humans took as they moved from one place on earth to another place, including the time and process by which humans entered the Americas.
The institute agreed to support the study only after a thorough review of the consent form to ensure that interests of tribal members are protected, said SHI President Rosita Worl. SHI has supported DNA studies in the past because of our cultural value of “Haa Shagoon” of maintaining ties to our ancestors and obtaining knowledge for future generations, Worl said.
“What is fascinating to me about Dr. Schurr’s work is that he was able to distinguish between members of the Eagle and Raven moieties based on their mtDNA haplogroup,” said Worl, an anthropologist, who has hypothesized that the Tlingit Eagles and Ravens emerged from different populations.
Volunteers will be interviewed about their genealogy and allow a cheek swab for a DNA sample, said Schurr, an associate professor of anthropology at the University of Pennsylvania and director of the Genographic Project’s North America Regional Center.
“It’s the stories we’re able to see through the analysis of DNA, but also hear through people’s accounting of that history, and read through records, and see visibly on the ground through archaeology that really give us a very concrete sense for what’s happening, what people are experiencing, and what they’re trying to convey to us through their art, through their history and through their language,” Schurr said.
Participants’ names will be kept confidential and the DNA will be used only for this study.
Sealaska Heritage Institute is a private, nonprofit founded in 1980 to promote cultural diversity and cross-cultural understanding. The institute is governed by a Board of Trustees and guided by a Council of Traditional Scholars. Its mission is to perpetuate and enhance Tlingit, Haida, and Tsimshian cultures of Southeast Alaska.
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5,380,863,457,335,063,000 | Format
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GPC4 glypican 4 [ Homo sapiens (human) ]
Gene ID: 2239, updated on 29-Nov-2020
Summary
Official Symbol
GPC4provided by HGNC
Official Full Name
glypican 4provided by HGNC
Primary source
HGNC:HGNC:4452
See related
Ensembl:ENSG00000076716 MIM:300168
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
KPTS; K-glypican
Summary
Cell surface heparan sulfate proteoglycans are composed of a membrane-associated protein core substituted with a variable number of heparan sulfate chains. Members of the glypican-related integral membrane proteoglycan family (GRIPS) contain a core protein anchored to the cytoplasmic membrane via a glycosyl phosphatidylinositol linkage. These proteins may play a role in the control of cell division and growth regulation. The GPC4 gene is adjacent to the 3' end of GPC3 and may also play a role in Simpson-Golabi-Behmel syndrome. [provided by RefSeq, Jul 2008]
Expression
Broad expression in placenta (RPKM 22.5), kidney (RPKM 16.2) and 22 other tissues See more
Orthologs
NEW
Try the new Data Table view
Genomic context
See GPC4 in Genome Data Viewer
Location:
Xq26.2
Exon count:
9
Annotation release Status Assembly Chr Location
109.20201120 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (133300103..133415489, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (132433815..132549205, complement)
Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene RNA, U1 small nuclear 115, pseudogene Neighboring gene transcription factor Dp family member 3 Neighboring gene RNA, U6 small nuclear 203, pseudogene Neighboring gene glypican 3 Neighboring gene ribosomal protein S24 pseudogene 19
Genomic regions, transcripts, and products
Expression
• Project title: HPA RNA-seq normal tissues
• Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
• BioProject: PRJEB4337
• Publication: PMID 24309898
• Analysis date: Wed Apr 4 07:08:55 2018
Bibliography
GeneRIFs: Gene References Into Functions
What's a GeneRIF?
HIV-1 interactions
Protein interactions
Protein Gene Interaction Pubs
Tat tat Glypican 4 (GPC4) is downregulated in HIV-1 Tat and NC cotransfection of HEK 293T cells PubMed
nucleocapsid gag Glypican 4 (GPC4) is downregulated in HIV-1 Tat and NC cotransfection of HEK 293T cells PubMed
Go to the HIV-1, Human Interaction Database
Interactions
Products Interactant Other Gene Complex Source Pubs Description
General gene information
Markers
Homology
Gene Ontology Provided by GOA
Function Evidence Code Pubs
coreceptor activity involved in Wnt signaling pathway, planar cell polarity pathway NAS
Non-traceable Author Statement
more info
PubMed
protein binding IPI
Inferred from Physical Interaction
more info
PubMed
Process Evidence Code Pubs
Wnt signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed
Wnt signaling pathway, planar cell polarity pathway IEA
Inferred from Electronic Annotation
more info
cell migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed
glycosaminoglycan biosynthetic process TAS
Traceable Author Statement
more info
glycosaminoglycan catabolic process TAS
Traceable Author Statement
more info
regulation of neurotransmitter receptor localization to postsynaptic specialization membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed
regulation of presynapse assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed
regulation of protein localization to membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed
regulation of signal transduction IEA
Inferred from Electronic Annotation
more info
retinoid metabolic process TAS
Traceable Author Statement
more info
synaptic membrane adhesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed
Component Evidence Code Pubs
Golgi lumen TAS
Traceable Author Statement
more info
anchored component of presynaptic membrane IEA
Inferred from Electronic Annotation
more info
cell surface IBA
Inferred from Biological aspect of Ancestor
more info
PubMed
collagen-containing extracellular matrix IEA
Inferred from Electronic Annotation
more info
external side of plasma membrane IDA
Inferred from Direct Assay
more info
PubMed
extracellular exosome HDA PubMed
extracellular region IBA
Inferred from Biological aspect of Ancestor
more info
PubMed
glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
lysosomal lumen TAS
Traceable Author Statement
more info
nucleus HDA PubMed
plasma membrane TAS
Traceable Author Statement
more info
synapse IBA
Inferred from Biological aspect of Ancestor
more info
PubMed
General protein information
Preferred Names
glypican-4
Names
dJ900E8.1 (glypican 4)
glypican proteoglycan 4
NCBI Reference Sequences (RefSeq)
NEW Try the new Data Table view
RefSeqs maintained independently of Annotated Genomes
These reference sequences exist independently of genome builds. Explain
These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.
Genomic
1. NG_012498.1 RefSeqGene
Range
4689..120075
Download
GenBank, FASTA, Sequence Viewer (Graphics)
mRNA and Protein(s)
1. NM_001448.3NP_001439.2 glypican-4 precursor
See identical proteins and their annotated locations for NP_001439.2
Status: REVIEWED
Source sequence(s)
AL034400, AL109623
Consensus CDS
CCDS14637.1
UniProtKB/Swiss-Prot
O75487
Related
ENSP00000359864.3, ENST00000370828.4
Conserved Domains (1) summary
pfam01153
Location:26551
Glypican; Glypican
RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20201120
The following sections contain reference sequences that belong to a specific genome build. Explain
Reference GRCh38.p13 Primary Assembly
Genomic
1. NC_000023.11 Reference GRCh38.p13 Primary Assembly
Range
133300103..133415489 complement
Download
GenBank, FASTA, Sequence Viewer (Graphics)
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-981,380,252,998,125,000 | Mammalian Protein-Protein Interaction Trap (MAPPIT)
Mammalian Protein-Protein Interaction Trap (MAPPIT)
Introduction
In-depth identification of protein interaction partners is an important method for studying protein functions and positioning them in the intracellular interaction network. Over the years, various biotechnologies have been developed to meet this goal, including some methods specifically for studying post-translational modifications of mammalian proteins. Although these methods can clarify their inherent physiological context, they also have some inherent limitations.
Nowadays, these technologies have undergone many changes, providing a more appropriate environment for studying the interactions between mammalian proteins. Mammalian Protein-Protein Interaction Trap (MAPPIT) is a new type of mammalian two-hybrid system protocol based on the insights of type I cytokine receptor signal transduction, that is, activated JAK kinase can phosphorylate STAT recruitment sites in trans. The bait protein is fused with the mutant receptor chimera, and STAT target site has been eliminated from it. The prey protein is linked to a receptor fragment containing a functional STAT recruitment site. When the bait-prey interaction, the prey chimeras are phosphorylated, and the recruited STAT molecule is activated and induces the transcription of the reporter gene under the control of the STAT-responsive promoter. Compared with other similar methods, MAPPIT provides the best physiological environment, and has the comprehensive advantages of separation of interaction zone and effect zone and rapid identification of false positives.
Schematic representation of the JAK-STAT pathwayFigure 1. Schematic representation of the JAK-STAT pathway (Eyckerman, S.; et al.)
Services
Creative Proteomics has recruited many experienced technicians to provide high-quality protein-protein interaction research services to researchers all over the world. The MAPPIT system we established has been successfully applied in many studies, providing a normal physiological environment for the mammalian protein to be tested. This system ensures the correct folding of the protein and provides various necessary cofactors and regulatory proteins participating in post-translational modifications. In order to ensure the accuracy of the experiment, our technicians can also offer experimental options such as the determination of the optimal selective puromycin concentration before screening, subcloning the prey into the vector for individual testing and confirming the interaction, and reducing the expression level of the prey to reduce non-specific binding.
Flow chart of the MAPPIT screening procedureFigure 2. Flow chart of the MAPPIT screening procedure (Eyckerman, S.; et al.)
Customers can choose different technology platforms according to project requirements, or contact us directly for consultation, and our expert team will provide you with customized experimental procedures.
Highlights
• High sensitivity, versatility, and scalability
• Wide range of applications, can identify indirect interactions and instantaneous interactions
• New interaction partners can be screened
• Can clarify its normal physiological environment
Creative Proteomics is an international biotechnology company dedicated to research in molecular interactions and other related fields. The mammalian protein-protein interaction trap platform we constructed has the characteristics of high quality and efficiency, and the data obtained can be directly used for paper publication. Our one-stop service aims to save customers time and money.
Reference
1. Eyckerman, S.; et al. Design and Use of a Mammalian Protein-Protein Interaction Trap (MAPPIT). Science Signaling. 2002.
* This service is for RESEARCH USE ONLY, not intended for any clinical use. | {
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} | 57 | cf5cd1df0ee2161e1684bdc019357275 |
2,614,359,310,422,750,700 | Capitol Reef, Suturing Pigs’ Feet, And More
Don't forget to like and share! 🙂
Meeting regularly, Biology Club may be one of the most active clubs on campus, making it a perfect fit for Badgers looking to get involved. Activities are frequent and promised to excite the childhood scientist inside of everyone.
Bio Club has something for just about everyone. The club recently returned from Capitol Reef National Park where they hiked and camped, and has a “medical” style activity this week suturing pigs feet. Other Upcoming events include learning how to make wax chapstick, dissecting owl pellets, and participating in science night with the rest of the science department and finishing off with a pizza party and documentary.
Bio presidency and members go to Capitol Reef National Park. Photo courtesy of Bio Club
“Bio Club gives me an opportunity to meet other students with similar majors that I otherwise wouldn’t get to know in some of my classes being a small two year school” explains Club President. Michael Broderick. Biology Club gives the Badgers not only the ability to interact with students of similar interests outside of class, but to do so in an academic and engaging setting.
Broderick continues, stating, “Snow College doesn’t have a Pre-Med Club either, so for students wishing to pursue those interests, it doubles as a Pre-Med Club as well.” Biology covers a wide variety of studies and majors Snow students wish to continue in, making the club all the more needed and valued on campus.
Malerie Jenson, secretary of the Biology Club, loves the fact that while the club focuses on activities for everyone, there is always something interesting to learn. “We learn a LOT of cool stuff. Even at Capitol Reef, there was time taken out of the night to learn some astronomy along with the moon’s gravitational effect on Earth. During our first activity making ice cream, we watched a short documentary on the genetics of the lactose resistance gene.”
The goal of the Biology Club is to simply help students see Biology as a science that can excite and isn’t just there to fill a science credit. While physics, chemistry and other sciences are easy to get behind with crazy experiments and wild reactions, biology is usually left behind. Biology Club strives to change that and makes it both intriguing and worth while.
Jacob Clawson grew up in Orange County California where he found a passion for photography, sports and music. Utah had always been the plan after high school as generations of his family have graduated from schools across the state. He is in his second year at Snow College studying Theatre set, design and tech, hoping to one day work in Southeast Asia designing live shows. When he’s not found backstage or writing articles for newspaper he can be found working on his car, traveling or finding the best trails in Sanpete County.
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-6,568,335,686,204,569,000 | BCKDHB
TISSUE ATLAS
? »
Gene description
Branched chain keto acid dehydrogenase E1, beta polypeptide
RNA tissue category
Expressed in all.
Protein summary
Detected at High or Medium expression level in 38 of 79 analyzed normal tissue cell types.
Protein expression
Most of the normal cells showed moderate, often granular, cytoplasmic positivity. Strong staining was observed in stomach, adrenal cortex, subsets of skeletal myocytes, renal tubules and the prostate. Glial cells, Purkinje cells, myocytes and lymphoid tissues were weakly stained or negative.
Protein class
Disease related genes, Enzymes, Mitochondrial proteins, Potential drug targets, Predicted secreted proteins
Predicted localization
Secreted
Protein evidence
Evidence at protein level
Protein reliability
Supportive based on 1 antibody.
Liver
Colon
Kidney
Testis
Lymph node
Cerebral cortex
Stomach 2
RNA Protein
Expression (FPKM)
Organ system
Localization (score)
100
50
0
h
m
l
n
Liver and pancreas
Liver
Gallbladder
Pancreas
Digestive tract (GI-tract)
N/A Oral mucosa
Salivary gland
Esophagus
Stomach
Duodenum
Small intestine
Appendix
Colon
Rectum
Urinary tract (Kidney and bladder)
Kidney
Urinary bladder
Male reproductive system (Male tissues)
Testis
N/A Epididymis
Prostate
N/A Seminal vesicle
Breast and female reproductive system
N/A Breast
N/A Vagina
N/A Cervix, uterine
Endometrium
Fallopian tube
Ovary
Placenta
Skin and soft tissues
Skin
Adipose tissue
Skeletal muscle
Smooth muscle
N/A Soft tissue
Blood and immune system (Hematopoietic)
Bone marrow
Lymph node
Tonsil
Spleen
Central nervous system (Brain)
Cerebral cortex
N/A Hippocampus
N/A Lateral ventricle
N/A Cerebellum
Endocrine glands
Thyroid gland
N/A Parathyroid gland
Adrenal gland
Respiratory system (Lung)
N/A Nasopharynx
N/A Bronchus
Lung
Cardiovascular system
Heart muscle
Antibodies in assay
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} | 57 | cf5cd1df0ee2161e1684bdc019357275 |
-1,079,296,418,409,907,500 | 电话:
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ERBB3 抗体
(Receptor Tyrosine-Protein Kinase ErbB-3 (ERBB3))
This gene encodes a member of the epidermal growth factor receptor (EGFR) family of receptor tyrosine kinases. This membrane-bound protein has a neuregulin binding domain but not an active kinase domain. It therefore can bind this ligand but not convey the signal into the cell through protein phosphorylation. However, it does form heterodimers with other EGF receptor family members which do have kinase activity. Heterodimerization leads to the activation of pathways which lead to cell proliferation or differentiation. Amplification of this gene and/or overexpression of its protein have been reported in numerous cancers, including prostate, bladder, and breast tumors. Alternate transcriptional splice variants encoding different isoforms have been characterized. One isoform lacks the intermembrane region and is secreted outside the cell. This form acts to modulate the activity of the membrane-bound form. Additional splice variants have also been reported, but they have not been thoroughly characterized. [provided by RefSeq, Jul 2008].
ERBB3 抗体 (N-Term) ERBB3 抗体 (N-Term) ERBB3 抗体 (N-Term) (ABIN391949)
ERBB3 适用: 人, 小鼠 FACS, IHC (p), WB 宿主: 兔 Polyclonal RB01467 unconjugated
ERBB3 抗体 (AA 24-55) ERBB3 抗体 (AA 24-55) ERBB3 抗体 (AA 24-55) (ABIN3029524)
ERBB3 适用: 人, 小鼠 FACS, IHC, ELISA, WB 宿主: 兔 Polyclonal unconjugated
ERBB3 抗体 (AA 151-250) ERBB3 抗体 (AA 151-250) ERBB3 抗体 (AA 151-250) (ABIN681358)
ERBB3 适用: 小鼠, 大鼠 ELISA, FACS, IHC (p), WB 宿主: 兔 Polyclonal unconjugated
ERBB3 抗体 by Grade
Find ERBB3 抗体 with a specific Grade. The Grade listed below are among those available. Click on a link to go to the corresponding products.
ERBB3 抗体 by 适用
Find ERBB3 抗体 for a variety of species such as anti-Human ERBB3, anti-Rat ERBB3, anti-Mouse ERBB3. The species listed below are among those available. Click on a link to go to the corresponding products.
ERBB3 抗体 by 应用范围
Find ERBB3 抗体 validated for a specific application such as WB, ELISA, IF (p), IHC. Some of the available applications are listed below. Click on a link to go to the corresponding products.
ERBB3 抗体 by 抗体来源
Find ERBB3 抗体 with a specific 抗体来源. The 抗体来源 listed below are among those available. Click on a link to go to the corresponding products.
ERBB3 抗体 by 抗原表位
Find ERBB3 抗体 with a specific epitope. The epitopes listed below are among those available. Click on a link to go to the corresponding products.
ERBB3 抗体 by 克隆形成能力
Find available monoclonal or polyclonal ERBB3 抗体. Click on a link to go to the corresponding products.
ERBB3 抗体 by 克隆
Find ERBB3 抗体 with a specific 克隆. The 克隆 listed below are among those available. Click on a link to go to the corresponding products.
ERBB3 抗体 by 标记
Find ERBB3 抗体 with a specific conjugate such as Biotin, Alexa Fluor 488, Alexa Fluor 555. The conjugates listed below are among those available. Click on a link to go to the corresponding products.
Popular ERBB3 抗体
Product
Reactivity
Application
Validations
Cat. No.
Quantity
Datasheet
Reactivity Human, Mouse
Application FACS, IHC (p), WB
Validations
• (4)
• (5)
Cat. No. ABIN391949
Quantity 400 μL
Datasheet Datasheet
Reactivity Human, Mouse
Application FACS, IHC, ELISA, WB
Validations
• (5)
Cat. No. ABIN3029524
Quantity 0.4 mL
Datasheet Datasheet
Reactivity Mouse, Rat
Application ELISA, FACS, IHC (p), WB
Validations
• (4)
Cat. No. ABIN681358
Quantity 100 μL
Datasheet Datasheet
Reactivity Human, Mouse, Rat
Application ELISA, IF (cc), IF (p), IHC (fro), IHC (p), WB
Validations
• (4)
Cat. No. ABIN747113
Quantity 100 μL
Datasheet Datasheet
Reactivity Human, Mouse, Rat
Application ELISA, ICC, IF, IHC, WB
Validations
• (4)
Cat. No. ABIN6261585
Quantity 100 μL
Datasheet Datasheet
Reactivity Human
Application IHC (p), ELISA, WB
Validations
• (4)
Cat. No. ABIN560779
Quantity 100 μg
Datasheet Datasheet
Reactivity Mouse, Rat
Application IHC
Validations
• (3)
Cat. No. ABIN7008552
Quantity 60 μL
Datasheet Datasheet
Reactivity Human, Mouse, Rat
Application ELISA, IF (cc), IF (p), IHC (fro), IHC (p)
Validations
• (2)
• (2)
Cat. No. ABIN686767
Quantity 100 μL
Datasheet Datasheet
Reactivity Human, Rat
Application ELISA, IF (cc), IF (p), IHC (fro), IHC (p), WB
Validations
• (3)
Cat. No. ABIN800628
Quantity 100 μL
Datasheet Datasheet
Reactivity Human
Application ELISA, IF, IHC, WB
Validations
• (3)
Cat. No. ABIN7138931
Quantity 100 μL
Datasheet Datasheet
Reactivity Human
Application DB, WB
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• (5)
• (2)
Cat. No. ABIN1881314
Quantity 400 μL
Datasheet Datasheet
Reactivity Human
Application ICC, ELISA, WB
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• (2)
• (2)
Cat. No. ABIN969114
Quantity 100 μL
Datasheet Datasheet
Reactivity Human
Application IHC, ELISA, WB
Validations
• (2)
• (2)
Cat. No. ABIN969112
Quantity 100 μL
Datasheet Datasheet
Reactivity Human
Application ELISA, FACS, IF, IHC
Validations
• (3)
Cat. No. ABIN185461
Quantity 100 μg
Datasheet Datasheet
Reactivity Human
Application IF, IHC, ELISA, WB
Validations
• (3)
Cat. No. ABIN1531609
Quantity 100 μg
Datasheet Datasheet
Latest Publications for our ERBB3 抗体
Memon, Gilliver, Borre, Sundquist, Sundquist, Nexo, Sorensen: "Soluble HER3 predicts survival in bladder cancer patients." in: Oncology letters, Vol. 15, Issue 2, pp. 1783-1788, (2018) (PubMed).
Cao, Chen, Chen, Xiong: "Positive prognostic value of HER2-HER3 co-expression and p-mTOR in gastric cancer patients." in: BMC cancer, Vol. 17, Issue 1, pp. 841, (2018) (PubMed).
Zomerman, Plasschaert, Diks, Lourens, Meeuwsen-de Boer, Hoving, den Dunnen, de Bont: "Exogenous HGF Bypasses the Effects of ErbB Inhibition on Tumor Cell Viability in Medulloblastoma Cell Lines." in: PLoS ONE, Vol. 10, Issue 10, pp. e0141381, (2015) (PubMed).
Liu, Leng, Gunasekaran, Pentony, Shen, Howard, Stoops, Manchulenko, Razinkov, Liu, Fanslow, Hu, Sun, Hasegawa, Clark, Foltz, Yan: "A Novel Antibody Engineering Strategy for Making Monovalent Bispecific Heterodimeric IgG Antibodies by Electrostatic Steering Mechanism." in: The Journal of biological chemistry, (2015) (PubMed).
Sie, den Dunnen, Lourens, Meeuwsen-de Boer, Scherpen, Zomerman, Kampen, Hoving, de Bont: "Growth-factor-driven rescue to receptor tyrosine kinase (RTK) inhibitors through Akt and Erk phosphorylation in pediatric low grade astrocytoma and ependymoma." in: PLoS ONE, Vol. 10, Issue 3, pp. e0122555, (2015) (PubMed).
Cheng, Terai, Kageyama, Ozaki, McCue, Sato, Aplin: "Paracrine Effect of NRG1 and HGF Drives Resistance to MEK Inhibitors in Metastatic Uveal Melanoma." in: Cancer research, Vol. 75, Issue 13, pp. 2737-48, (2015) (PubMed).
Davies, Holmes, Lomo, Steinkamp, Kang, Muller, Wilson: "High incidence of ErbB3, ErbB4, and MET expression in ovarian cancer." in: International journal of gynecological pathology : official journal of the International Society of Gynecological Pathologists, Vol. 33, Issue 4, pp. 402-10, (2014) (PubMed).
Mimura, Shiraishi, Mueller, Izawa, Kua, So, Yong, Fujii, Seliger, Kiessling, Kono: "The MAPK pathway is a predominant regulator of HLA-A expression in esophageal and gastric cancer." in: Journal of immunology (Baltimore, Md. : 1950), Vol. 191, Issue 12, pp. 6261-72, (2013) (PubMed).
Lee, Chin, Li: "Charcot-Marie-Tooth disease-linked protein SIMPLE functions with the ESCRT machinery in endosomal trafficking." in: The Journal of cell biology, Vol. 199, Issue 5, pp. 799-816, (2012) (PubMed).
MacLeod, Elgadi, Bossi, Sankar, Pisio, Agopsowicz, Sharon, Graham, Hitt: "HER3 targeting of adenovirus by fiber modification increases infection of breast cancer cells in vitro, but not following intratumoral injection in mice." in: Cancer gene therapy, Vol. 19, Issue 12, pp. 888-98, (2012) (PubMed).
Aliases for ERBB3 抗体
erb-b2 receptor tyrosine kinase 3 (ERBB3) 抗体
v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian) (ERBB3) 抗体
erb-b2 receptor tyrosine kinase 3 (Erbb3) 抗体
c-erbB-3 抗体
c-erbB3 抗体
C76256 抗体
ErbB-3 抗体
Erbb-3 抗体
ERBB3 抗体
erbB3-S 抗体
Erbb3r 抗体
HER3 抗体
Her3 抗体
LCCS2 抗体
MDA-BF-1 抗体
nuc-ErbB3 抗体
p45-sErbB3 抗体
p85-sErbB3 抗体
p180-ErbB3 抗体
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客服 | {
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} | 57 | cf5cd1df0ee2161e1684bdc019357275 |
-1,203,702,967,426,014,700 | Lineage for d1w8bl1 (1w8b L:88-143)
1. Root: SCOP 1.73
2. 746751Class g: Small proteins [56992] (85 folds)
3. 747016Fold g.3: Knottins (small inhibitors, toxins, lectins) [57015] (19 superfamilies)
disulfide-bound fold; contains beta-hairpin with two adjacent disulfides
4. 747704Superfamily g.3.11: EGF/Laminin [57196] (7 families) (S)
5. 747705Family g.3.11.1: EGF-type module [57197] (22 proteins)
6. 747714Protein Coagulation factor VIIa [57201] (1 species)
7. 747715Species Human (Homo sapiens) [TaxId:9606] [57202] (19 PDB entries)
8. 747729Domain d1w8bl1: 1w8b L:88-143 [120717]
Other proteins in same PDB: d1w8bh1
automatically matched to d1klil_
complexed with 413, ca
Details for d1w8bl1
PDB Entry: 1w8b (more details), 3 Å
PDB Description: factor7 - 413 complex
PDB Compounds: (L:) blood coagulation factor viia
SCOP Domain Sequences for d1w8bl1:
Sequence; same for both SEQRES and ATOM records: (download)
>d1w8bl1 g.3.11.1 (L:88-143) Coagulation factor VIIa {Human (Homo sapiens) [TaxId: 9606]}
qlicvnenggceqycsdhtgtkrscrchegyslladgvsctptveypcgkipilek
SCOP Domain Coordinates for d1w8bl1:
Click to download the PDB-style file with coordinates for d1w8bl1.
(The format of our PDB-style files is described here.)
Timeline for d1w8bl1: | {
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A chronicle of a killer alga in the west: ecology, assessment, and management of Prymnesium parvum blooms (vol 764, pg 29, 2016)
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3,842,653,351,907,647,000 | There was an error in this gadget
Sunday, 12 February 2012
Sunderban
The Sundarbans (Bengali: সুন্দরবন, Shundorbôn) is the largest single block of tidal halophytic mangrove forest in the world.[1] The name Sundarban can be literally translated as "beautiful jungle" or "beautiful forest" in the Bengali language (Shundor, "beautiful" and bon, "forest" or "jungle"). The name may have been derived from the Sundari trees that are found in Sundarbans in large numbers. Alternatively, it has been proposed that the name is a corruption of Samudraban (Bengali: সমুদ্রবন Shomudrobôn "Sea Forest") or Chandra-bandhe (name of a primitive tribe). But the generally accepted view is the one associated with Sundari trees.[1]
The Sundarban forest lies in the vast delta on the Bay of Bengal formed by the super confluence of the Padma, Brahmaputra and Meghna rivers across Saiyan southern Bangladesh. The seasonally-flooded Sundarbans freshwater swamp forests lie inland from the mangrove forests on the coastal fringe. The forest covers 10,000 sq.km. of which about 6,000 are in Bangladesh.[2] It became inscribed as a UNESCO world heritage site in 1997. The Sundarbans is estimated to be about 4,110 km², of which about 1,700 km² is occupied by waterbodies in the forms of river, canals and creeks of width varying from a few meters to several kilometers.
The Sundarbans is intersected by a complex network of tidal waterways, mudflats and small islands of salt-tolerant mangrove forests. The interconnected network of waterways makes almost every corner of the forest accessible by boat. The area is known for the eponymous Royal Bengal Tiger (Panthera tigris tigris), as well as numerous fauna including species of birds, spotted deer, crocodiles and snakes. The fertile soils of the delta have been subject to intensive human use for centuries, and the ecoregion has been mostly converted to intensive agriculture, with few enclaves of forest remaining. The remaining forests, taken together with the Sundarbans mangroves, are important habitat for the endangered tiger. Additionally, the Sundarbans serves a crucial function as a protective barrier for the millions of inhabitants in and around Khulna and Mongla against the floods that result from the cyclones. The Sundarbans has also been enlisted among the finalists in the New7Wonders of Nature.
( From Wikipedia)
Big shrimp of Sundarbans
Morning delight
I am waiting
Grass flower
Morning Sunset
Reflection
Boatman
Remnants of a boat
Turning of a river
way to the village
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-2,151,371,461,198,360,800 | LSBio
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Human SMAD6 Protein (Recombinant GST) - LS-G29243
LSBio (USA Sales Only) LSBio (USA Sales Only)
206-374-1102
866-206-6909
[email protected]
Most Popular SMAD6 Proteins
Mouse SMAD6 Protein (Recombinant His + T7) (aa116-364) - LS-G14775
E. coli Expression System
His + T7
Purified / Lyophilized
Sodium Dodecyl Sulfate - Polyacrylamide Gel Electrophoresis Image
Human SMAD6 Protein (Recombinant His + T7) (aa261-495) - LS-G14776
E. coli Expression System
His + T7
Purified / Lyophilized
Sodium Dodecyl Sulfate - Polyacrylamide Gel Electrophoresis Image
Rat SMAD6 Protein (Recombinant His + T7) (aa14-211) - LS-G14778
E. coli Expression System
His + T7
Purified / Lyophilized
Sodium Dodecyl Sulfate - Polyacrylamide Gel Electrophoresis Image
Human SMAD6 Protein (Recombinant GST) - LS-G29243
Wheat Wheat Germ Extract
496 AA
GST
Purified
Sodium Dodecyl Sulfate - Polyacrylamide Gel Electrophoresis Image
100% Guaranteed
LS-G29243
Recombinant Protein
SMAD6
Human
80.96 kDa
MFRSKRSGLV RRLWRSRVVP DREEGGSGGG GGGDEDGSLG
SRAEPAPRAR EGGGCGRSEV RPVAPRRPRD AVGQRGAQGA
GRRRRAGGPP RPMSEPGAGA GSSLLDVAEP GGPGWLPESD
CETVTCCLFS ERDAAGAPRD ASDPLAGAAL EPAGGGRSRE
ARSRLLLLEQ ELKTVTYSLL KRLKERSLDT LLEAVESRGG
VPGGCVLVPR ADLRLGGQPA PPQLLLGRLF RWPDLQHAVE
LKPLCGCHSF AAAADGPTVC CNPYHFSRLC GPESPPPPYS
RLSPRDEYKP LDLSDSTLSY TETEATNSLI TAPGEFSDAS
MSPDATKPSH WCSVAYWEHR TRVGRLYAVY DQAVSIFYDL
PQGSGFCLGQ LNLEQRSESV RRTRSKIGFG ILLSKEPDGV
WAYNRGEHPI FVNSPTLDAP GGRALVVRKV PPGYSIKVFD
FERSGLQHAP EPDAADGPYD PNSVRISFAK GWGPCYSRQF
ITSCPCWLEI LLNNPR
Wheat Germ Extract
Wheat
GST
Glutathione Sepharose
Not Tested
Not Tested
50 mM Tris-HCl, pH 8.0, 10 mM reduced glutathione
Store at -80°C. Avoid freeze-thaw cycles.
For research use only.
About SMAD6
O43541 NM_005585 NP_005576.3
SMAD6 Protein, AOVD2 Protein, HSMAD6 Protein, HsT17432 Protein, SMAD 6 Protein, MADH7 Protein, Mothers against DPP homolog 6 Protein, SMAD family member 6 Protein, MAD homolog 6 Protein, MADH6 Protein
Acts as a mediator of TGF-beta and BMP antiflammatory activity. Suppresses IL1R-TLR signaling through its direct interaction with PEL1, preventing NF-kappa-B activation, nuclear transport and NF-kappa-B-mediated expression of proinflammatory genes. May block the BMP-SMAD1 signaling pathway by competing with SMAD4 for receptor-activated SMAD1-binding. Binds to regulatory elements in target promoter regions.
Sodium Dodecyl Sulfate - Polyacrylamide Gel Electrophoresis
Sodium Dodecyl Sulfate - Polyacrylamide Gel Electrophoresis
12.5% SDS-PAGE of human SMAD6 stained with Coomassie Blue
Requested From:
Date Requested: 10/19/2017
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} | 57 | cf5cd1df0ee2161e1684bdc019357275 |
-4,668,241,437,495,096,000 | Anti-DDIT4L PE
Anti-DDIT4L PE
Regulatory status
RUO
Antigen
DDIT4L
Clone
DDIT-03
Format
PE
Reactivity
Human
Application
Excitation laser
blue (488 nm)
Variant
0.1 mg
1P-725-C100
In stock
220.00 USD
0.025 mg
1P-725-C025
Delivery 1 week
110.00 USD
Variant
0.1 mg
11-261-C100
In stock
220.00 USD
0.1 mg
11-261-C100
In stock
110.00 USD
Product details
Description
References
Isotype
Mouse IgG1
Specificity
The mouse monoclonal antibody DDIT-03 recognizes DDIT4L / REDD2 protein, which belongs to intracellular stress-induced proteins involved in mediation of cell death.
Application
Application details
Flow cytometry: Recommended dilution: 1-5 μg/ml. Intracellular staining.
Reactivity
Human
Immunogen
N-terminal recombinant fragment of human DDIT4L (amino acids 2-98)
Concentration
0.1 mg/ml
Preparation
The purified antibody is conjugated with R-phycoerythrin (PE) under optimum conditions. The conjugate is purified by size-exclusion chromatography.
Formulation
Stabilizing phosphate buffered saline (PBS) solution containing 15 mM sodium azide
Storage and handling
Store in the dark at 2-8°C. Do not freeze. Avoid prolonged exposure to light. Do not use after expiration date stamped on vial label.
Exbio licence note
The product is intended For Research Use Only. Diagnostic or therapeutic applications are strictly forbidden. Products shall not be used for resale or transfer to third parties either as a stand-alone product or as a manufacture component of another product without written consent of EXBIO Praha, a.s. EXBIO Praha, a.s. will not be held responsible for patent infringement or any other violations of intellectual property rights that may occur with the use of the products. Orders for all products are accepted subject to the Term and Conditions available at www.exbio.cz. EXBIO, EXBIO Logo, and all other trademarks are property of EXBIO Praha, a.s.
Other names
DDIT4L, REDD2, Rtp801L
Antigen description
DDIT4L (DNA-damage-inducible transcript 4-like), also known as REDD2 (regulated in development and DNA damage response 2) or RTP801L is a stress-inducted protein, which was shown to mediate monocyte cell death through a reduction in thioredoxin-1 expression, and is highly expressed in atherosclerotic lesions. Stimulation of DDIT4L expression in macrophages increases oxidized LDL-induced macrophage death.
Entrez Gene ID 115265
UniProt ID Q96D03
General references:
Cuaz-Pérolin C, Furman C, Larigauderie G, Legedz L, Lasselin C, Copin C, Jaye M, Searfoss G, Yu KT, Duverger N, Nègre-Salvayre A, Fruchart JC, Rouis M.REDD2 gene is upregulated by modified LDL or hypoxia and mediates human macrophage cell death. Arterioscler Thromb Vasc Biol. 2004 Oct;24(10):1830-5.
PubMed
Corradetti MN, Inoki K, Guan KL: The stress-inducted proteins RTP801 and RTP801L are negative regulators of the mammalian target of rapamycin pathway. J Biol Chem. 2005 Mar 18;280(11):9769-72.
PubMed
Imen JS, Billiet L, Cuaz-Pérolin C, Michaud N, Rouis M: The regulated in development and DNA damage response 2 (REDD2) gene mediates human monocyte cell death through a reduction in thioredoxin-1 expression. Free Radic Biol Med. 2009 May 15;46(10):1404-10
PubMed
Variant
0.1 mg
1P-725-C100
In stock
220.00 USD
0.025 mg
1P-725-C025
Delivery 1 week
110.00 USD
Variant
0.1 mg
11-261-C100
In stock
220.00 USD
0.1 mg
11-261-C100
In stock
110.00 USD
Related products
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CloneMOPC-21
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0.1 mg
180.00 USD | {
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2,444,393,667,361,443,000 | thumbnail
Beaver dams, hydrological thresholds, and controlled floods as a management tool in a desert riverine ecosystem, Bill Williams River, Arizona
Ecohydrology
By:
,
DOI: 10.1002/eco.113
Links
Abstract
Beaver convert lotic stream habitat to lentic through dam construction, and the process is reversed when a flood or other event causes dam failure. We investigated both processes on a regulated Sonoran Desert stream, using the criterion that average current velocity is < 0.2 m s-1 in a lentic reach. We estimated temporal change in the lotic:lentic stream length ratio by relating beaver pond length (determined by the upstream lentic-lotic boundary position) to dam size, and coupling that to the dam-size frequency distribution and repeated censuses of dams along the 58-km river. The ratio fell from 19:1 when no beaver dams were present to < 3:1 after 7 years of flows favourable for beaver. We investigated the dam failure-flood intensity relationship in three independent trials (experimental floods) featuring peak discharge ranging from 37 to 65 m3 s-1. Major damage (breach ??? 3-m wide) occurred at ??? 20% of monitored dams (n = 7-86) and a similar or higher proportion was moderately damaged. We detected neither a relationship between dam size and damage level nor a flood discharge threshold for initiating major damage. Dam constituent materials appeared to control the probability of major damage at low (attenuated) flood magnitude. We conclude that environmental flows prescribed to sustain desert riparian forest will also reduce beaver-created lentic habitat in a non-linear manner determined by both beaver dam and flood attributes. Consideration of both desirable and undesirable consequences of ecological engineering by beaver is important when optimizing environmental flows to meet ecological and socioeconomic goals. ?? 2010 John Wiley & Sons, Ltd.
Additional Publication Details
Publication type:
Article
Publication Subtype:
Journal Article
Title:
Beaver dams, hydrological thresholds, and controlled floods as a management tool in a desert riverine ecosystem, Bill Williams River, Arizona
Series title:
Ecohydrology
DOI:
10.1002/eco.113
Volume
3
Issue:
3
Year Published:
2010
Language:
English
Larger Work Type:
Article
Larger Work Subtype:
Journal Article
First page:
325
Last page:
338
Number of Pages:
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5,444,126,334,875,885,000 | Sphingosine-1-phosphate-induced intracellular Ca2+ mobilization in human endothelial cells
Geun Hee Seol, Moon Y. Kim, Guo Hua Liang, Ji Aee Kim, Young Ju Kim, Seikwan Oh, Suk Hyo Suh
Research output: Contribution to journalArticlepeer-review
10 Citations (Scopus)
Abstract
The authors have studied the effect of sphingosine-1-phosphate (S1P) on Ca2+ release from intracellular stores in cultured human umbilical vein endothelial cells (HUVECs). In the presence of extracellular Ca2+, S1P increased intracellular Ca2+ concentration ([Ca2+]i) and this increase was partially inhibited by La3+ (1 μM), indicating that S1P induces Ca2+ influx from extracellular pool and Ca2+ release from intracellular stores. S1P increased [Ca2+]i concentration dependently in Ca2+-free extracellular solution. The Hill coefficient (1.7) and EC50 (420 nM) was obtained from the concentration-response relationship. When caffeine depleted Ca2+ store in the presence of ryanodine, S1P did not induce intracellular Ca2+ release. Furthermore, the Ca2+-induced Ca2+ release inhibitors ruthenium red or dantrolene completely inhibited S1P-induced intracellular Ca2+ release. S1P-induced intracellular Ca2+ release was inhibited by the phospholipase C (PLC) inhibitors neomycin and U73312, or the inositol 1,4,5-triphosphate (IP3)-gated Ca2+ channel blocker aminoethoxybiphenyl borane (2-APB). In contrast, S1P-induced intracellular Ca2+ release was not inhibited by the mitochondrial Ca2+ uptake inhibitor CCCP or the mitochondrial Ca2+ release inhibitor cyclosporin A. These results show that S1P mobilizes Ca 2+ from intracellular stores primarily via Ca2+-induced and IP3-induced Ca 2+ release and this Ca2+ mobilization is independent of mitochondrial Ca2+ stores.
Original languageEnglish
Pages (from-to)263-269
Number of pages7
JournalEndothelium: Journal of Endothelial Cell Research
Volume12
Issue number5-6
DOIs
Publication statusPublished - 2005 Sep
Externally publishedYes
Keywords
• Ca-induced Ca release
• Human umbilical vein endothelial cells
• IP-induced Ca release
• Sphingosine-1-phosphate
ASJC Scopus subject areas
• Physiology
• Cell Biology
Fingerprint
Dive into the research topics of 'Sphingosine-1-phosphate-induced intracellular Ca2+ mobilization in human endothelial cells'. Together they form a unique fingerprint.
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2,010,129,954,828,924,400 | AWRA Philadelphia
American Water Resources Association
• Home
• Nature-Based Living Shorelines for Coastal Resilience and Cleaner Water
Nature-Based Living Shorelines for Coastal Resilience and Cleaner Water
• 12 May 2021
• 12:00 PM - 1:00 PM
• ONLINE: https://us02web.zoom.us/j/82958865536
• 57
Registration
(depends on selected options)
Base fee:
Registration is closed
Nature-Based Living Shorelines for Coastal Resilience and Cleaner Water
Danielle Kreeger, Ph.D.
ABSTRACT:
Most people understand the importance of wetlands, submerged vegetation and shellfish beds for clean water, carbon capture, essential fish habitat, and flood protection. Unfortunately, the abundance and condition of most of these habitats are in decline. The traditional management goal of restoring habitats to past conditions is being replaced by a new paradigm that promotes nature-based, engineered tactics to promote coastal and estuarine resilience to climate change. Living shorelines are an example of a nature-based restoration tactic that aims to stem the erosion and degradation of these coastal habitats by taking advantage of the structural and function properties of the biota themselves. The presentation will show examples of local living shoreline projects and monitoring data to quantify ecosystem service outcomes. Where appropriate and with sustained investment, living shorelines represent an ecologically beneficial alternative to traditional restoration and shoreline armoring that can help sustain key ecosystem services in the face of development and climate change.
SPEAKER BIOS:
Dr. Danielle Kreeger is a shellfish and wetland ecologist with more than 30 years of experience working as a research scientist and educator. She currently serves as Science Director for the Partnership for the Delaware Estuary and Associate Research Professor at The Academy of Natural Sciences of Drexel University.
http://www.delawareestuary.org/dr-danielle-kreeger
http://drexel.edu/coas/academics/departments-centers/bees/faculty/
Engineers:
This seminar does qualify for 1.0 Professional Development Hour (PDH). A Certificate of Attendance will be available for AWRA-PMAS members only. The meeting price for non-members who wish to receive a Certificate of Attendance for the PDH is $10.00 ($3.00 for meeting + $7.00 for certificate).
Please note: Presentation is to be given through Zoom at the link below. PDH's will be issued through PDFs. Please allow extra time to register through Zoom and get software set up. Presentation will start at noon. Early participants will be in a Waiting Room until noon. Participants must email [email protected] to request PDH Certificate after the event.
Presentation at https://us02web.zoom.us/j/82958865536
Thank you!
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9,049,404,758,022,999,000 | Atlas of Genetics and Cytogenetics in Oncology and Haematology
Home Genes Leukemias Solid Tumors Cancer-Prone Deep Insight Case Reports Journals Portal Teaching
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LOX (lysyl oxidase)
Written2009-02Sheri FT Fong, Keith SK Fong, Katalin Csiszar
John A. Burns School of Medicine, University of Hawaii, 1960 East West Road, Biomed T415, Honolulu, HI 96822, USA
(Note : for Links provided by Atlas : click)
Identity
Other alias
HGNC (Hugo) LOX
LocusID (NCBI) 4015
Atlas_Id 41191
Location 5q23.1 [Link to chromosome band 5q23]
Location_base_pair Starts at 122063195 and ends at 122078501 bp from pter ( according to hg19-Feb_2009) [Mapping LOX.png]
Local_order FTMT - SRFBP1 - LOX - ZNF474 - SNCAIP
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
CORO7-PAM16 (16p13.3) / LOX (5q23.1)LOX (5q23.1) / LOC642852 (21q22.3)
DNA/RNA
Figure 1. Lysyl oxidase gene structure. Exons are depicted as boxes separated by intron sequences (solid lines). The size of each exon and intron is shown in base pairs, above (exons) and below (introns) of the gene, respectively. The exons shaded in red encode amino acids sequences that are conserved in all lysyl oxidase family members. The exon shaded in blue contains the 3' UTR sequence.
Description The LOX gene is composed of seven exons and six introns, distributed through approximately 14.5 kb of genomic DNA (Hamalainen et al., 1993; Boyd et al., 1995). Three transcripts of sizes 2.0 kb, 3.8 kb and 4.8 kb are produced (Mariani et al., 1992), as a consequence of differential use of several polyadenylation signals within the 3' UTR (Boyd et al., 1995). There is a heritable restriction fragment length polymorphism within a PstI restriction site in the first exon (Csiszar et al., 1993). Three additional polymorphisms were also identified: Ala75Ala, Arg103Pro, Arg158Gln (Kaneda et al., 2004). There are no microsatellites within the LOX gene, but three have been described in the LOX gene locus within 20 kb and 5 kb centromeric, and 7 kb telomeric to the LOX gene (Csiszar et al., 2002). The 5' region of LOX also contains a CpG island which extends into exon 1 (Kaneda et al., 2002; Kaneda et al., 2004).
Transcription The rat LOX promoter contains a metal-response element, a hypoxia-response element, an antioxidant-response element, at least four positive regulatory segments and 2 negative regulatory segments. Multiple transcriptional start sites have been described (Gao et al., 2007).
The regulation of LOX gene expression has been described in different tissues and cells from several species, and has revealed multiple complex mechanisms that regulate the expression and activity of LOX. Many of these effectors are reviewed in Csiszar, 2001, and encompass cytokines and growth factors, such as fibroblast growth factor, basic fibroblast growth factor, insulin-like growth factor-1, interferon-gamma and transforming growth factor-beta; hormones and mediators, such as testosterone, progestin and prostaglandin E2; signaling molecules, such as cAMP, interferon regulatory factor-1 and ras; and drugs, such as adriamycin, bleomycin and hydralazine. Additional effectors have since been described, including follicle stimulating hormone (Slee et al., 2001; Harlow et al., 2003), hyperosmotic solution (Omori et al., 2002), secretory leukocyte protease inhibitor (Zhang et al., 2002), interleukin-1alpha (Rae et al., 2004), cigarette smoke condensate (Chen et al., 2005; Gao et al., 2005), tumor necrosis factor-alpha (Rodriguez et al., 2008), granulocyte macrophage colony-stimulating factor (Weissen-Plenz et al., 2008), hyaluronan with insulin-like growth factor-1 (Kothapalli and Ramamurthi, 2008) and parathyroid hormone (Lowry et al., 2008).
LOX expression is promoted in MCF-7 breast cancer cells by contact with fibroblast-conditioned media, collagen I matrix conditioned by fibroblasts (Kirschmann et al., 2002), and in HK-2 renal proximal tubule cells co-cultured with HMEC-1 microvascular endothelial cells (Aydin et al., 2008).
LOX expression is also induced by hypoxia. Hypoxia-inducible factor-1alpha (HIF-1alpha) stimulates LOX mRNA transcription (Erler et al., 2006; Higgins et al., 2007). LOX expression in hypoxia can be modulated by pH (Sorensen et al., 2007). The recruitment of HIF-1alpha to the LOX promoter is potentiated by Notch, which also increases Snail-1 expression (Sahlgren et al., 2008).
Transcription of the LOX gene is also affected by the methylation status of its CpG island (Kaneda et al., 2002; Kaneda et al., 2004).
Pseudogene No known pseudogene.
Protein
Figure 2. Lysyl oxidase protein structure. All members of the lysyl oxidase family of proteins share two highly conserved domains: a unique copper-binding (Cu) domain containing four histidines, shaded in red; and a cytokine-receptor like (CRL) domain similar to type I cytokine receptors, shaded in green. The predicted signal sequence is shaded in purple. The BMP-1 cleavage site, shaded in yellow, is noted by the arrow.
Description The lysyl oxidase transcript encodes for a 417-amino acid protein, including a signal peptide of 21 amino acids (Hamalainen et al., 1991; Mariani et al., 1992). Removal of the signal sequence and N-glycosylation within the propeptide region produces a 50 kDa proenzyme (Trackman et al., 1992). Incorporation of copper is thought to occur either in the endoplasmic reticulum or in the Golgi in prior to and independently of glycosylation (Kosonen et al., 1997). After secretion into the extracellular space, the mature, non-glycosylated 32 kDa protein (Trackman et al., 1992) is generated by proteolytic cleavage of the propeptide region between Gly-168 and Asp-169 by C-proteinase (Cronshaw et al., 1995), encoded by the bone morphogenic protein-1 (BMP-1), and the related tolloid-like-1 and -2 (Kessler et al., 1996; Uzel et al., 2001). LOX may also be a substrate of human meprin, an astacin-like metallopeptidase belonging to the same subfamily as BMP-1 and mammalian tolloid (Ambort et al., 2008).
Expression As LOX is necessary for the assembly and tensile strength and mechanical stability of collagen fibrils, and for the assembly and repetitive and reversible deformation of elastin, it is highly expressed in tissues containing fibrillar collagen and/or elastic fibers. These include skin, lung, cartilage, the cardiovascular system and the fibrous laminia propria in the small intestine. LOX was also detected in the liver, kidney, stomach, retina, and brain (Hayashi et al., 2004). In the eye, LOX has been identified in the vitreous, iris/ciliary body, lens, choroid/retinal pigment epithelium and retina (Coral et al., 2008). LOX has also been described in the mesencephalon, corpus callosum, cerebral cortex and cerebellum of the brain (Laczko et al., 2007).
Protein expression of LOX may be influenced by microRNAs. The 3' UTR of LOX mRNA contains a binding site for mir-145, which is down-regulated in many cancers (Dalmay and Edwards, 2006).
Localisation LOX has been classically characterized as an extracellular matrix enzyme (Kagan and Trackman, 1991). However, less is known about intracellular LOX. The LOX protein has been localized within the nuclei of various cells and tissues (Li et al., 1997; Hayashi et al., 2004; Li et al., 2004), and retains its catalytic activity inhibited by beta-aminopropionitrile (bAPN) (Li et al., 1997). Nuclear LOX has been shown to originate from extracellular LOX that enters the cytosol and concentrates within the nucleus (Nellaiappan et al., 2000). Histones have been reported as substrates for lysyl oxidase (Kagan et al, 1983; Giampuzzi et al, 2003), and transfection of LOX yielded less tightly packed chromatin (Mello et al., 1995). Electron microscopy confirmed association of LOX with condensed chromatin in the nucleus (Kagan and Li, 2003).
In addition to its nuclear localization, LOX has also been identified in the cytoplasm of numerous cells and tissues (Wakasaki and Ooshima, 1990; Kobayashi et al., 1994; Hayashi et al., 2004; Jansen and Csiszar, 2007). This cytoplasmic LOX was localized to cytoskeletal filaments and microtubule networks (Wakasaki and Ooshima, 1990; Guo et al., 2007).
The propeptide of LOX (LOX-PP), which has been described to have a different function than the LOX enzyme, differs in its localization compared to the active LOX enzyme, and is dependent on cell stage. LOX-PP, which is generated extracellularly, is able to reenter the cells. In differentiating osteoblasts, both LOX-PP and LOX enzyme localized to the cytoplasm associated with tubulin and the microtubule network, while in proliferating osteoblasts, LOX-PP localized perinuclearly in the Golgi complex and endoplasmic reticulum while LOX enzyme was mainly in the nucleus (Guo et al., 2007).
Function Lysyl oxidase oxidizes peptidyl lysine and hydroxylysine residues in collagen and lysine residues in elastin to produce peptidyl alpha-aminoadipic-delta-semialdehydes. These aldehyde residues can spontaneously condense with vicinal peptidyl aldehydes or with epsilon-amino groups of peptidyl lysine to form the covalent cross-links that stabilize and insolubilize several fibrillar collagen types and elastin fibers (reviewed in Lucero and Kagan, 2006). This catalytic reaction can be irreversibly inhibited by bAPN, a specific inhibitor that binds to the active site of LOX (Tang et al., 1983). Semicarbazide is a partial inhibitor of LOX (Mercier et al., 2007), as is 2-mercaptopyridine-N-oxide, although it acts through a different mechanism than bAPN (Anderson et al., 2007). Pathological concentrations of homocysteine also inhibit LOX activity (Raposa et al., 2004). The activity of LOX in the extracellular matrix may be coordinated by its interaction with fibronectin (Fogelgren et al, 2005).
The critical nature of LOX enzyme activity was demonstrated in the LOX "knockout" mouse, which expires immediately after birth due to rupture of the aorta and diaphragm from incomplete cross-linking of elastin (Maki et al., 2002; Hornstra et al., 2003). Local administration of LOX resulted in inhibition of abdominal aortic aneurysm development in a mouse model (Yoshimura et al., 2006). LOX is also essential for development of the distal and proximal airways, and alveolarization in the lungs (Maki et al., 2005), and is increased in preterm lamb lungs compared to full-term (Bland et al., 2007). In zebrafish, LOX is critical for notochord formation and muscle development (Anderson et al., 2007; Gansner et al., 2007; Reynaud et al., 2008), a process that may involve the fibrillin-2 gene or alpha1 chain of type VIII collagen (Gansner et al., 2008; Gansner and Gitlin, 2008). In sea urchins, inhibition of LOX caused developmental arrest at the mesenchymal blastula state (Butler et al., 1987), and in Xenopus laevis, LOX was shown to antagonize p21-Ha-Ras-induced and progesterone-dependent oocyte maturation (Di Donato et al., 1997).
LOX also has a role in cell differentiation. LOX was identified as an early marker in adipocyte differentiation responsive to retinoic acid (Dimaculangan et al., 1994). Increased LOX may affect osteoblastic differentiation through cross-link formation in the surrounding collagen matrix (Kaku et al., 2007; Turecek et al., 2008). LOX may also modulate cartilage growth (Asanbaeva et al., 2008).
Alterations in LOX expression were observed in development and aging of the skin, as well as physiological and pathological processes of the skin, including wound healing, fibrosis, hypertrophic scarring, keloids, and scleroderma (reviewed in Szauter et al., 2005). Inhibition of LOX activity resulted in inhibition of skin graft contraction in a human skin model (Harrison et al., 2006) Decreased LOX expression was noted in pelvic organ prolapse (Klutke et al., 2008), in pregnant mouse vagina and cervix compared to non-pregnant and post-partum tissues (Drewes et al., 2007), in proliferative diabetic retinopathy and rhegmatogenous retinal detachment (Coral et al., 2008), and early atherosclerosis (reviewed in Rodriguez et al., 2008). Induction of LOX was reported in inflamed oral tissue (Trackman et al., 1998) and gingival atrophy from experimental occlusal hypofunction (Ishida et al., 2008); rheumatoid arthritis (Kaufmann et al., 2003); inflammatory bowel disease (Rivera et al., 2006); liver stiffness preceding liver fibrosis (Georges et al., 2007); fibrosis of the liver (reviewed in Kagan, 1994), lung (Counts et al., 1981; Almassian et al., 1991; Peyrol et al., 1997), kidney (Di Donato et al., 1997; Goto et al., 2005; Higgins et al., 2007), oral submucosa (reviewed in Tilakaratne et al., 2006) and heart (Lopez et al., 2008; Sivakumar et al., 2008; Spurney et al., 2008; Urashima et al., 2008); systemic sclerosis (Meyringer et al., 2007); amyotrophic lateral sclerosis (Malaspina et al., 2001; Li et al., 2004); senile plaque development in Alzheimer's and non-Alzheimer's dementia (Gilad et al., 2005) and stromal reactions in cancer, which are described in more detail below.
Besides collagen and elastin, other substrates have been identified for LOX. The oxidation of lysine residues in basic fibroblast growth factor (bFGF) caused covalent crosslinking of bFGF monomers to form dimers and higher order oligomers, leading to reduced mouse fibroblast proliferation (Li et al., 2003). LOX also oxidizes the platelet-derived growth factor (PDGF) receptor beta, which increases its binding affinity for PDGF-BB and decreases the turnover of PDGF receptor beta signal transduction pathway (Lucero et al., 2008). LOX also interacts with mature transforming growth factor-beta (TGF-b). LOX and TGF-b colocalize to mineral associated bone matrix, and LOX was able to suppress TGF-b1-induced Smad3 phosphorylation (Atsawasuwan et al., 2008).
LOX has been shown to regulate the promoters of collagen III (COL3A1) and elastin (Giampuzzi et al., 2000; Oleggini et al., 2007; Lelievre et al., 2008). LOX also interacts with histones H1 and H2, and may be able to modulate the condensation status of chromatin to affect transcription of other genes as well (Giampuzzi et al., 2003).
LOX has chemokinetic and chemotactic effects on human blood monocytes (Lazarus et al., 1995), a predominantly chemotactic effect on rat vascular smooth muscle cells and mouse embryonic fibroblasts (Li et al., 2000; Lucero et al., 2008), and has been demonstrated to regulate breast cancer cell migration and adhesion and astrocytoma migration through a hydrogen-peroxide mediated mechanism (Payne et al., 2005; Laczko et al., 2007). The same mechanism may also play a role in the promotion of normal breast epithelial cell proliferation and migration by the interaction of LOX and hormone placental lactogen (PL), although PL is not a substrate for LOX (Polgar et al., 2007). The catalytic domain of LOX is able to interact with Snail-1 in vitro, a transcription factor crucial to EMT (Peinado et al., 2005). LOX is responsible for increased migratory ability of renal tubular epithelial cells induced by hypoxia (Higgins et al., 2007). Smooth muscle migration may be modulated through the interaction with VE-statin/egfl7 to inhibit LOX enzyme activity (Lelievre et al., 2008). LOX also interacts and oxidizes PDGF receptor beta to modulate chemokine activity (Lucero et al., 2008).
LOX also has multiple roles in cancer, including its opposing effect on ras-transformation, tumor suppression, stromal reaction in cancer, and the promotion of cancer cell adhesion, migration, invasion and metastases, and these are described in more detail in the following sections.
Homology In the human lysyl oxidase protein family, there are five members, named LOX, LOXL1, LOXL2, LOXL3 and LOXL4. They all contain a lysine tyrosylquinone (LTQ), the only mammalian cofactor derived from the cross-linking of two amino acid side chains (reviewed in Anthony, 1996), and which is unique to the LOX family. The other highly conserved motif that is unique to the LOX family is the copper-binding domain, which contains four histidines (Krebs and Krawetz, 1993). All LOX family members also contain a cytokine receptor-like (CRL) domain, which has part of the consensus sequence of Class 1 cytokine receptors (Bazan, 1990). LOX has closest homology to LOXL1, and both seem to be found exclusively in vertebrates.
Mutations
Note Despite the implication of LOX in many diseases and disorders, including inflammation and inflammatory diseases, fibrosis of distinct organs and fibrotic disorders, and cancer promotion and progression, there are only sparse reports of any mutations or epigenetic alterations in the LOX gene.
Epigenetics The CpG island of LOX was described to be methylated in 27% of a primary gastric cancer panel. Silencing of LOX expression by methylation was also observed in gastric, colon, lung and ovarian cancer cell lines (Kaneda et al., 2002, Kaneda et al., 2004). Our group has also noted increase in LOX expression following treatment with the demethylating agent, 5-aza-2'-deoxycytidine, in breast cancer cell lines (unpublished data). Methylation is thought to be the mechanism of LOX suppression after ras-transformation (Contente et al., 1999).
Somatic Loss of heterozygosity has been documented in colon and gastric cancers. In 42 colon tumors informative for the microsatellites flanking the LOX gene, 38% demonstrated loss of heterozygosity (Csiszar et al., 2002). In gastric cancer, 33% of 27 informative tumors demonstrated loss of heterozygosity (Kaneda et al., 2004).
Somatic mutations of the LOX gene have been documented in colon cancer and possibly, an ovarian cancer cell line. One nonsense mutation that affected codon 332, a 3' rearrangement affecting exons 5-7, and six 5' intragenic alterations or deletions, were detected out of the 8 colon tumors that demonstrated both loss of heterozygosity and reduced LOX expression (Csiszar et al., 2002). Of 96 gastric cancer samples and 58 gastric, lung, colon, ovarian and pancreatic cancer cell lines, only one somatic mutation or rare polymorphism was found in an ovarian cancer cell line: Ala147Gly (Kaneda et al., 2004).
The polymorphism Arg158Glu is associated with earlier clinical stage, lower tumor grade and decreased lymph node metastases in oral squamous cell carcinomas. The polymorphism also did not induce anchorage independent growth as did the wild type LOX (Shieh et al., 2007).
As point mutations and deletions appear to be infrequent, the loss of LOX expression may be due to a combination of the more frequent loss of heterozygosity and epigenetic regulation. Indeed, some gastric cancers demonstrated biallelic methylation or loss of heterozygosity of one allele with methylation of the other allele (Kaneda et al., 2004).
Implicated in
Note
Entity Tumor suppression, stromal reactions and cancer progression
Note Due to its multiple functions both extracellularly and intracellularly, lysyl oxidase has been implicated in several processes in the tumorigenic pathway, in many different cancer types and stages. These are addressed separately below.
Entity Inhibition of ras transformation
Note
• Tumor suppression
A putative tumor suppressor gene named the ras recision gene (rrg) was discovered to be greatly reduced in NIH 3T3 cells transformed by LTR-c-H-ras, and re-expressed in revertant cells, despite retaining high levels of ras expression (Contente et al., 1990). Analysis of rrg cDNA revealed that it was lysyl oxidase (Kenyon et al., 1991; Mariani et al., 1992), and the expression of LOX in revertant ras-transformed cells was confirmed by other investigators (Krzyzosiak et al., 1992; Hajnal et al., 1993; Friedman et al., 1997), and in other cell lines such as v-Ki-ras-transformed mouse osteoblastic cells (Shibanuma et al., 1993), EJ-ras-transformed rat fibroblasts (Oberhuber et al., 1995) and c-Ha-ras-transformed human osteosarcoma cell line (Csiszar et al., 1996), and transformed enterocytes (Sagiv et al., 2007). Ras-transformed NIH 3T3 cells transfected with rrg were non-tumorigenic in athymic mice (Contente et al., 1990), and anchorage independence of transformed cells was dependent on down-regulation of rrg (Hajnal et al., 1993). Even in a non-transformed normal rat kidney fibroblast cell line (NRK-49F), down-regulation of LOX was able to induce a oncogenic phenotype accompanied by p21ras activation, phosphorylation of c-jun and up-regulation of beta-catenin and cyclin D1 (Giampuzzi et al., 2001; Giampuzzi et al., 2003; Giampuzzi et al., 2005). The initial loss of LOX expression with ras transformation is thought to be due to methylation (Contente et al., 1999).
This counter-effect of ras by LOX was confirmed by the ability of LOX to inhibit ras-induced meiotic maturation downstream of the ras-MEK1-Erk2 pathway in normal Xenopus laevis oocytes, an action that was blocked by bAPN, a selective inhibitor of LOX enzyme activity (DiDonato et al., 1997). In ras-transformed NIH 3T3 cells, LOX was able to partially inhibit MEK kinase activity, but was more potent against PI3K and Akt kinases and blocked membrane localization of Akt and PDK1, preventing activation of NF-kB (Jeay et al., 2003).
It was determined that the 18 kD propeptide domain of LOX (LOX-PP), released during proteolytic cleavage to mature LOX, not LOX enzyme activity, was responsible for inducing phenotypic reversion. LOX-PP inhibited ras-transformation, anchorage independent growth and migration of fibroblasts, lung and pancreatic cancer cells (Palakumbura et al., 2004; Wu et al., 2007), and invasive phenotype of Her-2/neu breast cancer (Min et al., 2007). LOX-PP is thought to inhibit ras signaling via Akt and ERK pathways, the expression and activity of downstream effectors NF-kB, Bcl-2 and cyclin D1, and EMT (Min et al., 2007; Wu et al., 2007). LOX-PP inhibits primary rat aorta smooth muscle cell proliferation, DNA synthesis, MMP-9 mRNA expression and TNF-a stimulated Erk 1 / Erk 2 activation (Hurtado et al., 2008). LOX-PP has also been described to attenuate fibronectin-stimulated activation of FAK and its downstream activation of p130Cas, leading to inhibition of fibronectin-stimulated cell migration (Zhao et al., 2009).
•
Entity Basal and squamous cell carcinoma
Note
• Tumor suppression
Lysyl oxidase expression was present in the basal and spinous layers of the epidermis, but absent in basal and squamous cell carcinomas. Silencing of LOX expression in the human keratinocyte cell line, HaCaT, by transfection with anti-sense LOX, induced invasive ability as demonstrated by invasion of the dermis in a skin equivalent model (Bouez et al., 2006).
• Stromal reactions in cancer
In the stromal reactions around basal and squamous cell carcinoma foci, LOX protein expression indicated the fibrillar reaction and discriminated the tumor-stroma interface of late densely organized desmoplasia (Bouez et al., 2006).
•
Entity Bone cancer
Note
• Tumor suppression
Treatment of human osteosarcoma cells with suramin, an anti-cancer agent, caused decreased proliferation and upregulation of LOX and genes involved in osteoblast differentiation (Buchinger et al., 2008).
• Promotion of tumor progression, invasion and/or metastasis
Mututally subtractive RNA fingerprinted demonstrated up-regulation of LOX in the osteosarcoma cell line, MG63, compared to absent expression in normal osteoblasts (Fuchs et al., 2000). In five closely related murine osteosarcoma cell lines derived from the same tumor, LOX mRNA expression was elevated, but varied, and did not strictly correspond with collagen mRNA levels, insoluble collagen accumulation or LOX enzyme activity (Uzel et al., 2000).
•
Entity Brain cancer
Note
• Promotion of tumor progression, invasion and/or metastasis
LOX was found to be highly expressed in a panel of glioblastoma cell lines (Ross et al., 2000). Gene expression profiling of gliomas identified over-expressed lysyl oxidase as part of a molecular signature indicative of invasion, and associated with higher-grade tumors that are strongly correlated with poor patient survival (Freije et al., 2004). LOX protein expression was increased in glioblastoma and astrocytoma tissues, and in invasive U343 and U251 cultured astrocytoma cells. LOX was shown to be responsible for astrocytoma cell migration and FAK and paxillin phosphorylation (Laczko et al., 2007).
•
Entity Breast cancer
Note
• Tumor suppression
LOX-PP is able to attenuate fibronectin-stimulated activation of FAK and its downstream activation of p130Cas, leading to inhibition of fibronectin-stimulated breast cancer cell migration (Zhao et al., 2008).
LOX mRNA expression was down-regulated in invasive breast cancer tumor vasculature compared to normal vasculature, indicating that LOX may be involved in regulating tumor vasculature plasticity (Parker et al., 2004).
• Stromal reactions in cancer
LOX could be detected at the invasion front of infiltrating breast tumors, but decreased in late stromal reactions and disappeared from the stroma of invading ductal carcinomas (Peyrol et al., 1997).
• Promotion of tumor progression, invasion and/or metastasis
LOX mRNA was demonstrated to be up-regulated in the invasive and metastatic cell lines, MDA-MB-231 and Hs578T, compared to the poorly-invasive and non-metastatic cell lines, MCF-7 and T47D, as well as in more aggressive breast cancer cell lines and distant metastatic tissues compared with primary cancer tissues (reviewed in Payne et al., 2007; Nagaraja et al., 2006; Mbeunkui et al., 2007). Transfection of MDA-MB-231 and Hs578T with antisense LOX, resulted in repression of invasive ability. Treatment of MDA-MB-231 and Hs578T with bAPN also inhibited invasive ability as well as cell migration and adhesion. Conversely, transfection of MCF-7 with LOX increased cell invasiveness, migration and adhesion (reviewed in Payne et al., 2007).
Focal adhesion kinase (FAK) and src kinase were decreased with bAPN treatment and increased with LOX transfection. Hydrogen peroxide, a by-product of LOX activity, was necessary for FAK activity in hypoxic cells and src activation. In addition, inhibition of LOX was associated with increased Rho activity, and decreased Rac and Cdc42 activity. LOX was determined to promote p130Cas phosphorylation and formation of the p130Cas/Crk/DOCK180 signaling complex that would increase Rac-GTP, decrease actin stress fiber formation and increase formation of lamellipodium (reviewed in Payne et al., 2007). Intense staining of extracellular LOX was observed at the leading edge of MDA-MB-231 cells grown on collagen, localizing along the hairlike fibers protruding from the cell surface, accompanied by remodeling of the actin cytoskeleton, and increased formation of stress fibers and focal adhesion (Erler et al., 2006). Cell migration may also be influenced by the interaction of LOX with placental lactogen (Polgar et al., 2007), a protein implicated in breast cancer and associated with increased incidence of lymph node metastases (Latham et al., 2001). Cell invasion, migration and adhesion may also involve interaction between LOX and fibronectin (Fogelgren et al., 2005).
LOX mRNA expression was determined to be regulated by HIF-1 through a hypoxia-responsive element in the LOX promoter. Increased LOX expression was found in hypoxic patients, and was associated with negative estrogen receptor status (ER-), decreased overall survival in ER- patients and node-negative patients who did not receive adjuvant systemic treatment, and shorter metastasis-free survival in ER- patients and node negative patients (Erler et al., 2006; Helleman et al., 2008). Another study found LOX expression to only correlate with tumor hypoxia in primary breast cancers, thus LOX expression may not be stimulated by hypoxia in later stages of tumor progression (Postovit et al., 2008).
Intratumoral administration of bAPN resulted in growth inhibition of tumors formed by orthotopic injection of the 13 762NF cell line into rats (reviewed in Chvapil, 2005). Orthotopic injection of either MDA-MB-231 cells transfected with LOX shRNA, or MDA-MB-231 cells followed by treatment with bAPN or LOX antibody (which also inhibited LOX activity), demonstrated fewer or no lung metastasis, respectively, and no liver metastasis. Increased in vitro invasive ability of MDA-MB-231 under hypoxic/anoxic conditions, was repressed by inhibition of extracellular catalytically active LOX by treatment with LOX antisense oligos, bAPN, LOX antibody, LOX shRNA or an extracellular copper chelator (Erler et al., 2006).
In an computational model of oxidative stress in vascular smooth muscle cells, lysyl hydroxylase, syk tyrosine kinase and osteopontin, markers of breast cancer cell growth, migration, invasion and metastases, were identified as behavioral predictors of lysyl oxidase (Johnson et al., 2007).
•
Entity Cervical cancer
Note
• Promotion of tumor progression, invasion and/or metastasis
SiHa cervical cancer cells demonstrated increased invasion in vitro under hypoxic/anoxic conditions, that was repressed by inhibition of extracellular catalytically active LOX by treatment with LOX antisense oligos, bAPN, LOX antibody, LOX shRNA or an extracellular copper chelator (Erler et al., 2006).
•
Entity Choriocarcinoma
Note
• Tumor suppression
Choriocarcinoma cell lines BeWo and JEG-3 had decreased levels of lysyl oxidase activity (Kuivaniemi et al., 1986). JEG-3 was also shown to have decreased LOX mRNA expression (Hamalainen et al., 1995).
•
Entity Colon cancer
Note
• Tumor suppression
Reduced LOX mRNA levels were described in a colon cancer cell line panel, two of which (HCT-116, Colo205) demonstrated complete methylation of the LOX promoter and loss of LOX expression. Treatment of HCT-116 cells with 5-aza-dC induced gain of LOX expression (Kaneda et al., 2004). Significant loss of heterozygosity or allelic imbalance was reported in colon cancer, and a panel of colon cancer samples was noted to have reduced LOX mRNA levels. Somatic mutations emcompassing one nonsense mutation that affected codon 332, a 3' rearrangement affecting exons 5-7, and six 5' intragenic alterations or deletions, were detected out of the 8 colon tumors that demonstrated both loss of heterozygosity and reduced LOX expression (Csiszar et al., 2002).
•
Entity Esophageal cancer
Note
• Tumor suppression
Reduced lysyl oxidase mRNA expression was observed in esophageal cancers, and was further reduced in tumors with lymph node metastasis (He et al., 2002).
•
Entity Fibrosarcoma
Note
• Tumor suppression
Fibrosarcoma cell lines 8387 and HT-1080 had decreased levels of lysyl oxidase activity (Kuivaniemi et al., 1986). HT-1080 was also shown to have decreased LOX mRNA expression (Hamalainen et al., 1995).
•
Entity Gastric cancer
Note
• Tumor suppression
Reduced expression rate of lysyl oxidase mRNA was observed in gastric cardiac and gastric cancers, and was further reduced in tumors with lymph node metastasis (He et al., 2002). Reduced LOX mRNA expression was described in a gastric cancer cell line panel, four of which (KATOIII, MKN28, MKN74, AGS) demonstrated complete methylation of the LOX promoter and loss of LOX expression which was reversed upon treatment with 5-aza-dC. Transfection of LOX into the gastric cancer cell lines, MKN28 and KATOIII, resulted in decreased numbers of colonies in soft agar, reduced number of anchorage-dependent colonies, and smaller tumors after injection into nude mice (Kaneda et al., 2004).
•
Entity Head and neck squamous cell carcinoma (HNSCC)
Note
• Tumor suppression
Reduced LOX mRNA levels were noted in HNSCC cell lines and tissues. In the tissues, there was also a negative correlation between LOX levels and UICC- or T-stage of the tumor (Rost et al., 2003).
In oral squamous cell carcinoma cultured cells, LOX expression was highest in precancerous lesions. LOX overexpression induced reduced migration and invasion, with lower LOX expression associated with increased neck lymph node metastasis (Shieh et al., 2007).
• Stromal reactions in cancer
Increased levels of LOX protein were distributed in the stromal reactions of squamous cell carcinomas, directly adjacent to invading epithelial cells. The increased expression was less than the up-regulation seen in oral submucous fibrosis (Trivedy et al., 1999).
• Promotion of tumor progression, invasion and/or metastasis
In oral squamous cell carcinoma, LOX mRNA expression was upregulated compared to normal mucosa (Ziober et al., 2006). In head and neck squamous cell carcinomas, increased LOX expression was found in association with CA-IX, a marker of hypoxia, and was associated with decreased cancer specific survival, decreased overall survival and lower metastasis-free survival (Erler et al., 2006; Le et al., 2007).
•
Entity Lung cancer
Note
• Tumor suppression
Reduced LOX mRNA expression was described in a lung cancer cell line panel, one of which (VRMC-LCD) demonstrated complete methylation of the LOX promoter and loss of LOX expression which was reversed upon treatment with 5-aza-dC (Kaneda et al., 2004). The epigenetic modulation of LOX was supported by the induction of LOX expression by 5-aza-dC in non-small cell lung cancer cell lines (Shames et al., 2006).
In bronchogenic carcinoma tissues, LOX mRNA expression levels in Stage I, II and IV were 161%, 83% and 47% of normal adjacent lung tissue, respectively, with a similar pattern of reduction in LOX protein expression (Woznick et al., 2005). Microarray analysis demonstrated decreased LOX mRNA expression in primary lung adenocarcinoma tissues and lung cancer cell lines compared to normal lung tissues and lung cells (Wu et al., 2007).
• Stromal reactions in cancer
In the fibrous stromal reaction typically seen in non-small cell adenocarcinoma, strong LOX expression was observed with the fibrillar reaction (mainly collagens type I and III, fibronectin and elastic fibers), and discriminated the tumor-stroma interface of late densely organized desmoplasia. In the microfibrillar angiogenic stromal reaction seen with small cell carcinoma and neuroendocrine carcinoma, there was slight LOX expression, co-localized with type I collagen that was a minor component of the stroma (mainly laminin and fibrillin), and increased LOX expression in the thickened alveolar septa adjacent to the progression front. In the pseudostromal reaction seen with non-sclerosing broncho-alveolar carcinoma, LOX stained the thickened septa (fibronectin and numerous elastic fibers) edged by tumor cells (Peyrol et al., 2000).
• Promotion of tumor progression, invasion and/or metastasis
Repression of TGFbRII by siRNA in the lung carcinoma cell line H23, was associated with increased number of invasive cells and increased levels of LOX mRNA (Borczuk et al., 2005).
•
Entity Melanoma
Note
• Tumor suppression
The melanoma cell line G-361 had decreased levels of lysyl oxidase activity (Kuivaniemi et al., 1986).
• Promotion of tumor progression, invasion and/or metastasis
LOX mRNA expression was demonstrated to be absent in poorly invasive cutaneous and uveal melanoma cell lines (A375P and OCM-1A), and highly expressed in highly invasive cutaneous and uveal melanoma cell lines (C8161, M619, C918) (Kirschmann et al., 2002). B16F-10 melanoma cells treated with beta-carotene had decreased LOX mRNA expression, and with Biophytum sensitivum or amentoflavone had decreased motility, invasion, in vivo metastasis and decreased LOX mRNA expression in lung metastases (Guruvayoorappan and Kuttan, 2007; Guruvayoorappan and Kuttan, 2008; Guruvayoorappan and Kuttan, 2008).
•
Entity Multiple endocrine neoplasia (MEN)
Note
• Tumor suppression
Lysyl oxidase mRNA expression was repressed in NIH 3T3 cells expressing either RET-MEN2A or RET-MEN2B mutant proteins (Watanabe et al., 2002).
•
Entity Ovarian cancer
Note
• Tumor suppression
Evaluation of an ovarian cancer cell line panel revealed reduced LOX mRNA levels, three of which (RMUG-L, RTSG, TYK-nu) demonstrated complete methylation of the LOX promoter and loss of LOX expression (Kaneda et al., 2004).
•
Entity Pancreatic cancer
Note
• Tumor suppression
Reduced levels of LOX mRNA was noted in a pancreatic cancer cell line panel (Kaneda et al., 2004). Microarray analysis demonstrated decreased LOX mRNA expression in primary pancreatic tumor tissues and cell lines compared to normal pancreatic tissues and cultured cells (Wu et al., 2007).
•
Entity Prostate cancer
Note
• Tumor suppression
LOX was detected by differential display PCR in primary vs. metastatic prostate cancer cells following TGF-b1 stimulation. LOX was detectable in more primary prostate tumor-derived cell lines than metastasis-derived cell lines, indicating that reduced LOX mRNA levels may be an acquired feature of the metastatic phenotype in cultured cells. Immunohistochemistry showed progressive reduction of lysyl oxidase expression with the transition from normal prostate epithelium to malignant prostate epithelium to metastatic tumors in both human and mouse tissues (Ren et al., 1998).
• Promotion of tumor progression, invasion and/or metastasis
LOX mRNA expression was demonstrated to be absent in a poorly invasive rat prostate cancer cell line, compared to highly invasive rat prostate cancer cell lines (Kirschmann et al., 2002). In tissues, LOX mRNA was upregulated in prostate cancer compared to benign prostatic hypertrophy, correlated with Gleason score, and associated with both high grade and short time to recurrence (Lapointe et al., 2004; Stewart et al., 2008). LOX mRNA is upregulated in the PC-3 prostate cancer cell line cultured under hypoxic conditions (Stewart et al., 2009).
•
Entity Renal cell carcinoma (RCC)
Note
• Promotion of tumor progression, invasion and/or metastasis
Up-regulation of LOX mRNA expression was detected in RCC cell lines and tissues (Ross et al., 2000; Stassar et al., 2001). Clear cell RCC also demonstrated LOX up-regulation (Takahashi et al., 2001). Indeed, LOX overexpression appeared preferentially in clear cell RCC compared to mixed clear and granular, granular, oxyphil, tubulopapillary, and chromophobe RCC/ontocytomas (Stassar et al., 2001; Young et al., 2001). In clear cell RCC, smoking was associated with allelic imbalances at chromosome 5q23.1, where the LOX gene is localized, and may involve duplication of the gene (Korenaga et al., 2005).
•
Entity Rhabdomyosarcoma
Note
• Tumor suppression
Rhabdomyosarcoma cell lines RD and A-204 had decreased levels of lysyl oxidase activity (Kuivaniemi et al., 1986). RD was also shown to have decreased LOX mRNA expression (Hamalainen et al., 1995).
•
Breakpoints
Note None involving the LOX gene.
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Citation
This paper should be referenced as such :
Fong, SFT ; Fong, KSK ; Csiszar, K
LOX (lysyl oxidase)
Atlas Genet Cytogenet Oncol Haematol. 2010;14(1):15-28.
Free journal version : [ pdf ] [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/LOXID41191ch5q23.html
External links
Nomenclature
HGNC (Hugo)LOX 6664
Cards
AtlasLOXID41191ch5q23
Entrez_Gene (NCBI)LOX 4015 lysyl oxidase
AliasesAAT10
GeneCards (Weizmann)LOX
Ensembl hg19 (Hinxton)ENSG00000113083 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000113083 [Gene_View] ENSG00000113083 [Sequence] chr5:122063195-122078501 [Contig_View] LOX [Vega]
ICGC DataPortalENSG00000113083
TCGA cBioPortalLOX
AceView (NCBI)LOX
Genatlas (Paris)LOX
WikiGenes4015
SOURCE (Princeton)LOX
Genetics Home Reference (NIH)LOX
Genomic and cartography
GoldenPath hg38 (UCSC)LOX - chr5:122063195-122078501 - 5q23.1 [Description] (hg38-Dec_2013)
GoldenPath hg19 (UCSC)LOX - 5q23.1 [Description] (hg19-Feb_2009)
GoldenPathLOX - 5q23.1 [CytoView hg19] LOX - 5q23.1 [CytoView hg38]
ImmunoBaseENSG00000113083
Mapping of homologs : NCBILOX [Mapview hg19] LOX [Mapview hg38]
OMIM153455 617168
Gene and transcription
Genbank (Entrez)AF039291 AI351010 AI536895 AK297709 AK298781
RefSeq transcript (Entrez)NM_001178102 NM_001317073 NM_002317
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)LOX
Alternative Splicing GalleryENSG00000113083
Gene ExpressionLOX [ NCBI-GEO ] LOX [ EBI - ARRAY_EXPRESS ] LOX [ SEEK ] LOX [ MEM ]
Gene Expression Viewer (FireBrowse)LOX [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets] [Normal Tissue Atlas] [carcinoma Classsification] [NCI60]
GenevestigatorExpression in : [tissues] [cell-lines] [cancer] [perturbations]
BioGPS (Tissue expression)4015
GTEX Portal (Tissue expression)LOX
Human Protein AtlasENSG00000113083-LOX [pathology] [cell] [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP28300 [function] [subcellular_location] [family_and_domains] [pathology_and_biotech] [ptm_processing] [expression] [interaction]
NextProtP28300 [Sequence] [Exons] [Medical] [Publications]
With graphics : InterProP28300
Splice isoforms : SwissVarP28300
PhosPhoSitePlusP28300
Domaine pattern : Prosite (Expaxy)LYSYL_OXIDASE (PS00926)
Domains : Interpro (EBI)Lysyl_oxidase Lysyl_oxidase_CS
Domain families : Pfam (Sanger)Lysyl_oxidase (PF01186)
Domain families : Pfam (NCBI)pfam01186
Conserved Domain (NCBI)LOX
DMDM Disease mutations4015
Blocks (Seattle)LOX
SuperfamilyP28300
Human Protein Atlas [tissue]ENSG00000113083-LOX [tissue]
Peptide AtlasP28300
HPRD01087
IPIIPI00002802 IPI00978057 IPI01013884 IPI00965456
Protein Interaction databases
DIP (DOE-UCLA)P28300
IntAct (EBI)P28300
FunCoupENSG00000113083
BioGRIDLOX
STRING (EMBL)LOX
ZODIACLOX
Ontologies - Pathways
QuickGOP28300
Ontology : AmiGOosteoblast differentiation regulation of protein phosphorylation protein-lysine 6-oxidase activity protein-lysine 6-oxidase activity protein-lysine 6-oxidase activity copper ion binding protein binding collagen binding extracellular region extracellular region collagen trimer extracellular space extracellular space cell nucleus cellular protein modification process heart development regulation of gene expression regulation of striated muscle tissue development regulation of transforming growth factor beta receptor signaling pathway peptidyl-lysine oxidation peptidyl-lysine oxidation extracellular matrix organization collagen fibril organization bone mineralization lung development extracellular matrix platelet-derived growth factor receptor-beta signaling pathway ascending aorta development descending aorta development wound healing response to drug regulation of apoptotic process protein kinase B signaling regulation of megakaryocyte differentiation muscle cell cellular homeostasis elastic fiber assembly blood vessel morphogenesis response to steroid hormone muscle fiber development cell chemotaxis connective tissue development DNA biosynthetic process regulation of receptor binding regulation of bone development cellular response to chemokine regulation of platelet-derived growth factor receptor-beta signaling pathway
Ontology : EGO-EBIosteoblast differentiation regulation of protein phosphorylation protein-lysine 6-oxidase activity protein-lysine 6-oxidase activity protein-lysine 6-oxidase activity copper ion binding protein binding collagen binding extracellular region extracellular region collagen trimer extracellular space extracellular space cell nucleus cellular protein modification process heart development regulation of gene expression regulation of striated muscle tissue development regulation of transforming growth factor beta receptor signaling pathway peptidyl-lysine oxidation peptidyl-lysine oxidation extracellular matrix organization collagen fibril organization bone mineralization lung development extracellular matrix platelet-derived growth factor receptor-beta signaling pathway ascending aorta development descending aorta development wound healing response to drug regulation of apoptotic process protein kinase B signaling regulation of megakaryocyte differentiation muscle cell cellular homeostasis elastic fiber assembly blood vessel morphogenesis response to steroid hormone muscle fiber development cell chemotaxis connective tissue development DNA biosynthetic process regulation of receptor binding regulation of bone development cellular response to chemokine regulation of platelet-derived growth factor receptor-beta signaling pathway
REACTOMEP28300 [protein]
REACTOME PathwaysR-HSA-2243919 [pathway]
NDEx NetworkLOX
Atlas of Cancer Signalling NetworkLOX
Wikipedia pathwaysLOX
Orthology - Evolution
OrthoDB4015
GeneTree (enSembl)ENSG00000113083
Phylogenetic Trees/Animal Genes : TreeFamLOX
HOGENOMP28300
Homologs : HomoloGeneLOX
Homology/Alignments : Family Browser (UCSC)LOX
Gene fusions - Rearrangements
Fusion : FusionGDB8142
Fusion : Fusion_HubCORO7-PAM16--LOX LOX--LOC642852 LOX--SH3GL1 P12--LOX
Fusion : QuiverLOX
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerLOX [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)LOX
dbVarLOX
ClinVarLOX
1000_GenomesLOX
Exome Variant ServerLOX
ExAC (Exome Aggregation Consortium)ENSG00000113083
GNOMAD BrowserENSG00000113083
Varsome BrowserLOX
Genetic variants : HAPMAP4015
Genomic Variants (DGV)LOX [DGVbeta]
DECIPHERLOX [patients] [syndromes] [variants] [genes]
CONAN: Copy Number AnalysisLOX
Mutations
ICGC Data PortalLOX
TCGA Data PortalLOX
Broad Tumor PortalLOX
OASIS PortalLOX [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICLOX [overview] [genome browser] [tissue] [distribution]
Somatic Mutations in Cancer : COSMIC3DLOX
Mutations and Diseases : HGMDLOX
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch LOX
DgiDB (Drug Gene Interaction Database)LOX
DoCM (Curated mutations)LOX (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)LOX (select a term)
intoGenLOX
NCG5 (London)LOX
Cancer3DLOX(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM153455 617168
Orphanet
DisGeNETLOX
MedgenLOX
Genetic Testing Registry LOX
NextProtP28300 [Medical]
TSGene4015
GENETestsLOX
Target ValidationLOX
Huge Navigator LOX [HugePedia]
snp3D : Map Gene to Disease4015
BioCentury BCIQLOX
ClinGenLOX
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD4015
Chemical/Pharm GKB GenePA30427
Clinical trialLOX
Miscellaneous
canSAR (ICR)LOX (select the gene name)
HarmonizomeLOX
DataMed IndexLOX
Probes
Litterature
PubMed205 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineLOX
EVEXLOX
GoPubMedLOX
iHOPLOX
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed
Search in all EBI NCBI
© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Wed Mar 11 18:16:12 CET 2020
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For comments and suggestions or contributions, please contact us
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1,131,085,097,824,307,600 | NLM Logo
Forkhead Box Protein O1 MeSH Descriptor Data 2023
MeSH Heading
Forkhead Box Protein O1
Tree Number(s)
D12.776.260.950.249.250
D12.776.930.977.249.250
Unique ID
D000071161
RDF Unique Identifier
http://id.nlm.nih.gov/mesh/D000071161
Scope Note
A forkhead box transcription factor that is a major target of INSULIN signaling and regulator of metabolic homeostasis in response to OXIDATIVE STRESS. It binds to the insulin RESPONSE ELEMENT (IRE) and the related Daf-16 family binding element (DBE). Its activity is suppressed by insulin and it also regulates OSTEOBLAST proliferation, controls bone mass, and skeletal regulation of GLUCOSE metabolism. It promotes GLUCONEOGENESIS in HEPATOCYTES and regulates gene expression in ADIPOSE TISSUE. It is also an important CELL DEATH regulator. Chromosomal aberrations involving the FOXO1 gene occur in RHABDOMYOSARCOMA.
Entry Term(s)
FOXO1 Protein
Forkhead in Rhabdomyosarcoma Protein
Registry Number
0
Previous Indexing
Forkhead Transcription Factors (2006-2016)
Public MeSH Note
2017
History Note
2017
Date Established
2017/01/01
Date of Entry
2016/07/08
Revision Date
2016/02/26
Forkhead Box Protein O1 Preferred
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} | 57 | cf5cd1df0ee2161e1684bdc019357275 |
1,364,991,416,479,698,700 | Header
UZH-Logo
Maintenance Infos
Epidemiology of fishborne trematodiasis in Kazakhstan
Sultanov, A; et al; Torgerson, P R (2014). Epidemiology of fishborne trematodiasis in Kazakhstan. Acta Tropica, 138:60-66.
Statistics
Citations
Altmetrics
Downloads
40 downloads since deposited on 06 Aug 2014
13 downloads since 12 months
Detailed statistics
Additional indexing
Item Type:Journal Article, refereed, original work
Communities & Collections:05 Vetsuisse Faculty > Chair in Veterinary Epidemiology
Dewey Decimal Classification:570 Life sciences; biology
610 Medicine & health
Language:English
Date:2014
Deposited On:06 Aug 2014 15:13
Last Modified:05 Apr 2016 18:00
Publisher:Elsevier
ISSN:0001-706X
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.1016/j.actatropica.2014.04.030
Download
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Content: Accepted Version
Filetype: PDF
Size: 439kB
View at publisher
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} | 57 | cf5cd1df0ee2161e1684bdc019357275 |
-6,682,085,433,225,969,000 |
Overview
• Product name
• Description
Rabbit polyclonal to CD160
• Host species
Rabbit
• Tested applications
Suitable for: WB, IHC-Pmore details
• Species reactivity
Reacts with: Mouse, Rat, Human
• Immunogen
Synthetic peptide within Human CD160 aa 80-122 conjugated to Keyhole Limpet Haemocyanin (KLH). The exact sequence is proprietary.
Sequence:
KRDPGIDGVGEISSQLMFTISQVTPLHSGTYQCCARSQKSGIR
Database link: O95971
• Positive control
• Rat kidney tissue lysates; Human cervical carcinoma and Rat brain tissues.
Properties
Applications
Our Abpromise guarantee covers the use of ab202845 in the following tested applications.
The application notes include recommended starting dilutions; optimal dilutions/concentrations should be determined by the end user.
Application Abreviews Notes
WB 1/200. Predicted molecular weight: 20 kDa.
IHC-P 1/100 - 1/500.
Target
• Function
Receptor showing broad specificity for both classical and non-classical MHC class I molecules.
• Tissue specificity
Expressed in spleen, peripheral blood, and small intestine. Expression is restricted to functional NK and T cytotoxic lymphocytes.
• Sequence similarities
Contains 1 Ig-like V-type (immunoglobulin-like) domain.
• Cellular localization
Cell membrane.
• Information by UniProt
• Database links
• Alternative names
• BY55 antibody
• BY55_HUMAN antibody
• CD160 antibody
• CD160 antigen [Precursor] antibody
• CD160 antigen antibody
• CD160 delta Ig antibody
• CD160 molecule antibody
• CD160 transmembrane isoform antibody
• FLJ46513 antibody
• Natural killer cell receptor BY55 antibody
• Natural killer cell receptor, immunoglobulin superfamily member antibody
• NK1 antibody
• NK28 antibody
see all
Images
• All lanes : Anti-CD160 antibody (ab202845) at 1/200 dilution
Lane 1 : Rat brain tissue lysate
Lane 2 : Rat kidney tissue lysate
Secondary
All lanes : Goat Anti-Rabbit IgG Antibody (H+L), HRP Conjugated at 1/3000 dilution
Predicted band size: 20 kDa
Observed band size: 27 kDa
why is the actual band size different from the predicted?
12% Gel.
• Immunohistochemical analysis of formalin-fixed paraffin-embedded Human cervical carcinoma tissue labeling CD160 with ab202845 at 1/200 dilution, followed by conjugation to the secondary antibody and DAB staining.
• Immunohistochemical analysis of formalin-fixed paraffin-embedded Rat brain tissue labeling CD160 with ab202845 at 1/200 dilution followed by conjugation to the secondary antibody and DAB staining.
References
ab202845 has not yet been referenced specifically in any publications.
Customer reviews and Q&As
There are currently no Customer reviews or Questions for ab202845.
Please use the links above to contact us or submit feedback about this product.
Please note: All products are "FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES"
For licensing inquiries, please contact [email protected]
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} | 57 | cf5cd1df0ee2161e1684bdc019357275 |
-6,201,620,393,852,680,000 | OriGene Technologies, Inc.
Search:
Left ProductsProducts divider ServicesServices divider technologyTechnology divider researchResearch divider TechsupportTechSupport divider AboutAbout Right
Home TrueClone Cdkn1a Clone
Cdkn1a (NM_007669) Mouse cDNA Clone
Specifications Citations (0) Clones of Other Species Product Documents
SKU Description Price Availibility*
MC200171 Cdkn1a (untagged) - Mouse cyclin-dependent kinase inhibitor 1A (P21) (Cdkn1a), transcript variant 1, (10ug), BC002043, 10ug $185 In Stock
TF81001 TurboFectin, High performance Transfection reagent (1ml/vial) $420 In Stock
Add to Shopping Cart
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OriGene Data
Vector:pCMV6-Kan/Neo Insert Size: 480 Restriction Site: RsrII-NotI
Sequence Data: Fully Sequenced ORF
OTI Disclaimer: Our molecular clone sequence data has been matched to the reference identifier above as a point of reference. Note that the complete sequence of our molecular clones may differ from the sequence published for this corresponding reference, e.g., by representing an alternative RNA splicing form or single nucleotide polymorphism (SNP).
Product Components: The cDNA clone is shipped in a 2-D bar-coded Matrix tube as dried plasmid DNA. The package also includes 100 pmols of both the corresponding 5' and 3' vector primers in separate vials. Every lot of primer is tested to provide clean sequencing of OriGene TrueClones.
Reference Data
RefSeq: BC002043, NP_031695
RefSeq Size: 727 RefSeq ORF: 480
Synonyms : CAP20; CDKI; Cdkn1; CIP1; mda6; P21; p21Cip1; p21WAF; SDI1; Waf1
LocusID: 12575 Cytogenetic: 17 A3.3|17 15.12 cM
Summary: Interacts with MKRN1. Interacts with PSMA3. Interacts with PCNA. Component of the ternary complex, cyclin D-CDK4-CDKN1A. Interacts (via its N-terminal domain) with CDK4; the interaction promotes the assembly of the cyclin D-CDK4 complex, its nuclear translocation and promotes the cyclin D-dependent enzyme activity of CDK4. Binding to CDK2 leads to CDK2/cyclin E inactivation at the G1-S phase DNA damage checkpoint, thereby arresting cells at the G1-S transition during DNA repair (By similarity). Interacts with HDAC1; the interaction is prevented by competitive binding of C10orf90/FATS to HDAC1 facilitating acetylation and protein stabilization of CDKN1A/p21. Interacts with PIM1. [UniProtKB/Swiss-Prot Function]
* Delivery time is an estimate in business days. Occasional delays may occur due to unforeseen complexities in the preparation of your construct. International customers may expect an additional 1-2 weeks in shipping
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All Products by: Title | Price | Category | Popularity | Best Sellers Topselling Products by: Title | Price | Category | Popularity | Favorites
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1,089,804,869,570,412,200 | Secondary transport of metalcitrate complexes: The CitMHS family
Joshua J. Lensbouer, Robert P. Doyle
Research output: Contribution to journalReview articlepeer-review
18 Scopus citations
Abstract
Primary and secondary transport of citrate has been extensively studied in pathogenic and non-pathogenic bacteria. Primary transporters of citrate complexed with metal ions, particularly Fe, have also garnered attention, with the fec system of E. coli being a classic example. In contrast, little is known about secondary transporters of metalcitrate complexes. Recently, a family of proteins responsible for secondary metalcitrate transport in bacteria was discovered and designated as the CitMHS transporter family. Several members have been functionally characterized to date and serve as the foundation for understanding this family. Three subfamilies have been categorized, depending on the main metal ion transported. These subfamilies are the Mg2citrate transporter, the Ca2citrate transporter, and the Fe 3citrate transporter. Each subfamily is believed to be substrate-selective due to the metalcitrate complexes being abundantly present in their environment and/or the ability of the complex to be metabolized by the organism. The implication of this family in the pathogenic access to Fe, information about transcriptional control, putative structure, predicted family members, members characterized to date and potential use in bioremediation are discussed.
Original languageEnglish (US)
Pages (from-to)453-462
Number of pages10
JournalCritical Reviews in Biochemistry and Molecular Biology
Volume45
Issue number5
DOIs
StatePublished - Oct 2010
Keywords
• Metal-citrate
• Streptomyces
• integral membrane
• iron
• secondary transport
ASJC Scopus subject areas
• Biochemistry
• Molecular Biology
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-3,515,884,016,341,274,000 | Native Canine C-Reactive Protein/CRP
Hersteller Cell Sciences
Kategorie
Typ Proteins
Specific against Canine
Menge 0.5 mg
Host Canine
ArtNr CS-CRC113B
eClass 6.1 34160400
eClass 9.0 42020190
Lieferbar
Description
C-Reactive Protein (CRP) is a pentameric serum protein belonging to the pentraxin family that is comprised of five identical ca. 23kDa subunits. It is a positive acute phase reactant , the levels of which increase modestly in dogs (1.5-2 fold) in response to inflammation, tissue injury or disease.
Formulation
Liquid in 0.05 M Tris buffer containing 0.15 M Sodium Chloride + 0.002 M Calcium Chloride + 0.02% Sodium Azide, pH 8.0. Precaution: Sodium azide is a poisonous and hazardous substance which should be handled by trained staff only.
Source
Dog Serum
Purity
>96% by SDS-PAGE
Menge: 0.5 mg
Lieferbar: In stock
Listenpreis: 1.654,05 €
Preis: 1.654,05 €
lieferbar
Vergleichen
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Fragen zum Produkt?
Schließen | {
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2,012,981,203,044,508,700 | Skip to ContentGo to accessibility pageKeyboard shortcuts menu
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Microbiology
17.2 Chemical Defenses
Microbiology17.2 Chemical Defenses
Menu
Table of contents
1. Preface
2. 1 An Invisible World
1. Introduction
2. 1.1 What Our Ancestors Knew
3. 1.2 A Systematic Approach
4. 1.3 Types of Microorganisms
5. Summary
6. Review Questions
1. Multiple Choice
2. Fill in the Blank
3. Short Answer
4. Critical Thinking
3. 2 How We See the Invisible World
1. Introduction
2. 2.1 The Properties of Light
3. 2.2 Peering Into the Invisible World
4. 2.3 Instruments of Microscopy
5. 2.4 Staining Microscopic Specimens
6. Summary
7. Review Questions
1. Multiple Choice
2. Fill in the Blank
3. Short Answer
4. Critical Thinking
4. 3 The Cell
1. Introduction
2. 3.1 Spontaneous Generation
3. 3.2 Foundations of Modern Cell Theory
4. 3.3 Unique Characteristics of Prokaryotic Cells
5. 3.4 Unique Characteristics of Eukaryotic Cells
6. Summary
7. Review Questions
1. Multiple Choice
2. True/False
3. Fill in the Blank
4. Short Answer
5. Critical Thinking
5. 4 Prokaryotic Diversity
1. Introduction
2. 4.1 Prokaryote Habitats, Relationships, and Microbiomes
3. 4.2 Proteobacteria
4. 4.3 Nonproteobacteria Gram-Negative Bacteria and Phototrophic Bacteria
5. 4.4 Gram-Positive Bacteria
6. 4.5 Deeply Branching Bacteria
7. 4.6 Archaea
8. Summary
9. Review Questions
1. Multiple Choice
2. True/False
3. Fill in the Blank
4. Short Answer
5. Critical Thinking
6. 5 The Eukaryotes of Microbiology
1. Introduction
2. 5.1 Unicellular Eukaryotic Parasites
3. 5.2 Parasitic Helminths
4. 5.3 Fungi
5. 5.4 Algae
6. 5.5 Lichens
7. Summary
8. Review Questions
1. Multiple Choice
2. Fill in the Blank
3. Short Answer
4. Critical Thinking
7. 6 Acellular Pathogens
1. Introduction
2. 6.1 Viruses
3. 6.2 The Viral Life Cycle
4. 6.3 Isolation, Culture, and Identification of Viruses
5. 6.4 Viroids, Virusoids, and Prions
6. Summary
7. Review Questions
1. Multiple Choice
2. True/False
3. Fill in the Blank
4. Short Answer
5. Critical Thinking
8. 7 Microbial Biochemistry
1. Introduction
2. 7.1 Organic Molecules
3. 7.2 Carbohydrates
4. 7.3 Lipids
5. 7.4 Proteins
6. 7.5 Using Biochemistry to Identify Microorganisms
7. Summary
8. Review Questions
1. Multiple Choice
2. True/False
3. Matching
4. Fill in the Blank
5. Short Answer
6. Critical Thinking
9. 8 Microbial Metabolism
1. Introduction
2. 8.1 Energy, Matter, and Enzymes
3. 8.2 Catabolism of Carbohydrates
4. 8.3 Cellular Respiration
5. 8.4 Fermentation
6. 8.5 Catabolism of Lipids and Proteins
7. 8.6 Photosynthesis
8. 8.7 Biogeochemical Cycles
9. Summary
10. Review Questions
1. Multiple Choice
2. True/False
3. Matching
4. Fill in the Blank
5. Short Answer
6. Critical Thinking
10. 9 Microbial Growth
1. Introduction
2. 9.1 How Microbes Grow
3. 9.2 Oxygen Requirements for Microbial Growth
4. 9.3 The Effects of pH on Microbial Growth
5. 9.4 Temperature and Microbial Growth
6. 9.5 Other Environmental Conditions that Affect Growth
7. 9.6 Media Used for Bacterial Growth
8. Summary
9. Review Questions
1. Multiple Choice
2. Matching
3. Fill in the Blank
4. Short Answer
5. Critical Thinking
11. 10 Biochemistry of the Genome
1. Introduction
2. 10.1 Using Microbiology to Discover the Secrets of Life
3. 10.2 Structure and Function of DNA
4. 10.3 Structure and Function of RNA
5. 10.4 Structure and Function of Cellular Genomes
6. Summary
7. Review Questions
1. Multiple Choice
2. True/False
3. Matching
4. Fill in the Blank
5. Short Answer
6. Critical Thinking
12. 11 Mechanisms of Microbial Genetics
1. Introduction
2. 11.1 The Functions of Genetic Material
3. 11.2 DNA Replication
4. 11.3 RNA Transcription
5. 11.4 Protein Synthesis (Translation)
6. 11.5 Mutations
7. 11.6 How Asexual Prokaryotes Achieve Genetic Diversity
8. 11.7 Gene Regulation: Operon Theory
9. Summary
10. Review Questions
1. Multiple Choice
2. True/False
3. Fill in the Blank
4. Short Answer
5. Critical Thinking
13. 12 Modern Applications of Microbial Genetics
1. Introduction
2. 12.1 Microbes and the Tools of Genetic Engineering
3. 12.2 Visualizing and Characterizing DNA, RNA, and Protein
4. 12.3 Whole Genome Methods and Pharmaceutical Applications of Genetic Engineering
5. 12.4 Gene Therapy
6. Summary
7. Review Questions
1. Multiple Choice
2. True/False
3. Fill in the Blank
4. Short Answer
5. Critical Thinking
14. 13 Control of Microbial Growth
1. Introduction
2. 13.1 Controlling Microbial Growth
3. 13.2 Using Physical Methods to Control Microorganisms
4. 13.3 Using Chemicals to Control Microorganisms
5. 13.4 Testing the Effectiveness of Antiseptics and Disinfectants
6. Summary
7. Review Questions
1. Multiple Choice
2. True/False
3. Fill in the Blank
4. Short Answer
5. Critical Thinking
15. 14 Antimicrobial Drugs
1. Introduction
2. 14.1 History of Chemotherapy and Antimicrobial Discovery
3. 14.2 Fundamentals of Antimicrobial Chemotherapy
4. 14.3 Mechanisms of Antibacterial Drugs
5. 14.4 Mechanisms of Other Antimicrobial Drugs
6. 14.5 Drug Resistance
7. 14.6 Testing the Effectiveness of Antimicrobials
8. 14.7 Current Strategies for Antimicrobial Discovery
9. Summary
10. Review Questions
1. Multiple Choice
2. True/False
3. Fill in the Blank
4. Short Answer
5. Critical Thinking
16. 15 Microbial Mechanisms of Pathogenicity
1. Introduction
2. 15.1 Characteristics of Infectious Disease
3. 15.2 How Pathogens Cause Disease
4. 15.3 Virulence Factors of Bacterial and Viral Pathogens
5. 15.4 Virulence Factors of Eukaryotic Pathogens
6. Summary
7. Review Questions
1. Multiple Choice
2. Fill in the Blank
3. Short Answer
4. Critical Thinking
17. 16 Disease and Epidemiology
1. Introduction
2. 16.1 The Language of Epidemiologists
3. 16.2 Tracking Infectious Diseases
4. 16.3 Modes of Disease Transmission
5. 16.4 Global Public Health
6. Summary
7. Review Questions
1. Multiple Choice
2. Matching
3. Fill in the Blank
4. Short Answer
5. Critical Thinking
18. 17 Innate Nonspecific Host Defenses
1. Introduction
2. 17.1 Physical Defenses
3. 17.2 Chemical Defenses
4. 17.3 Cellular Defenses
5. 17.4 Pathogen Recognition and Phagocytosis
6. 17.5 Inflammation and Fever
7. Summary
8. Review Questions
1. Multiple Choice
2. Matching
3. Fill in the Blank
4. Short Answer
5. Critical Thinking
19. 18 Adaptive Specific Host Defenses
1. Introduction
2. 18.1 Overview of Specific Adaptive Immunity
3. 18.2 Major Histocompatibility Complexes and Antigen-Presenting Cells
4. 18.3 T Lymphocytes and Cellular Immunity
5. 18.4 B Lymphocytes and Humoral Immunity
6. 18.5 Vaccines
7. Summary
8. Review Questions
1. Multiple Choice
2. Matching
3. Fill in the Blank
4. Short Answer
5. Critical Thinking
20. 19 Diseases of the Immune System
1. Introduction
2. 19.1 Hypersensitivities
3. 19.2 Autoimmune Disorders
4. 19.3 Organ Transplantation and Rejection
5. 19.4 Immunodeficiency
6. 19.5 Cancer Immunobiology and Immunotherapy
7. Summary
8. Review Questions
1. Multiple Choice
2. Matching
3. Fill in the Blank
4. Short Answer
5. Critical Thinking
21. 20 Laboratory Analysis of the Immune Response
1. Introduction
2. 20.1 Polyclonal and Monoclonal Antibody Production
3. 20.2 Detecting Antigen-Antibody Complexes
4. 20.3 Agglutination Assays
5. 20.4 EIAs and ELISAs
6. 20.5 Fluorescent Antibody Techniques
7. Summary
8. Review Questions
1. Multiple Choice
2. Fill in the Blank
3. Short Answer
4. Critical Thinking
22. 21 Skin and Eye Infections
1. Introduction
2. 21.1 Anatomy and Normal Microbiota of the Skin and Eyes
3. 21.2 Bacterial Infections of the Skin and Eyes
4. 21.3 Viral Infections of the Skin and Eyes
5. 21.4 Mycoses of the Skin
6. 21.5 Protozoan and Helminthic Infections of the Skin and Eyes
7. Summary
8. Review Questions
1. Multiple Choice
2. Fill in the Blank
3. Short Answer
4. Critical Thinking
23. 22 Respiratory System Infections
1. Introduction
2. 22.1 Anatomy and Normal Microbiota of the Respiratory Tract
3. 22.2 Bacterial Infections of the Respiratory Tract
4. 22.3 Viral Infections of the Respiratory Tract
5. 22.4 Respiratory Mycoses
6. Summary
7. Review Questions
1. Multiple Choice
2. Fill in the Blank
3. Short Answer
4. Critical Thinking
24. 23 Urogenital System Infections
1. Introduction
2. 23.1 Anatomy and Normal Microbiota of the Urogenital Tract
3. 23.2 Bacterial Infections of the Urinary System
4. 23.3 Bacterial Infections of the Reproductive System
5. 23.4 Viral Infections of the Reproductive System
6. 23.5 Fungal Infections of the Reproductive System
7. 23.6 Protozoan Infections of the Urogenital System
8. Summary
9. Review Questions
1. Multiple Choice
2. Fill in the Blank
3. Short Answer
4. Critical Thinking
25. 24 Digestive System Infections
1. Introduction
2. 24.1 Anatomy and Normal Microbiota of the Digestive System
3. 24.2 Microbial Diseases of the Mouth and Oral Cavity
4. 24.3 Bacterial Infections of the Gastrointestinal Tract
5. 24.4 Viral Infections of the Gastrointestinal Tract
6. 24.5 Protozoan Infections of the Gastrointestinal Tract
7. 24.6 Helminthic Infections of the Gastrointestinal Tract
8. Summary
9. Review Questions
1. Multiple Choice
2. Fill in the Blank
3. Short Answer
4. Critical Thinking
26. 25 Circulatory and Lymphatic System Infections
1. Introduction
2. 25.1 Anatomy of the Circulatory and Lymphatic Systems
3. 25.2 Bacterial Infections of the Circulatory and Lymphatic Systems
4. 25.3 Viral Infections of the Circulatory and Lymphatic Systems
5. 25.4 Parasitic Infections of the Circulatory and Lymphatic Systems
6. Summary
7. Review Questions
1. Multiple Choice
2. Fill in the Blank
3. Short Answer
4. Critical Thinking
27. 26 Nervous System Infections
1. Introduction
2. 26.1 Anatomy of the Nervous System
3. 26.2 Bacterial Diseases of the Nervous System
4. 26.3 Acellular Diseases of the Nervous System
5. 26.4 Fungal and Parasitic Diseases of the Nervous System
6. Summary
7. Review Questions
1. Multiple Choice
2. Matching
3. Fill in the Blank
4. Short Answer
5. Critical Thinking
28. A | Fundamentals of Physics and Chemistry Important to Microbiology
29. B | Mathematical Basics
30. C | Metabolic Pathways
31. D | Taxonomy of Clinically Relevant Microorganisms
32. E | Glossary
33. Answer Key
1. Chapter 1
2. Chapter 2
3. Chapter 3
4. Chapter 4
5. Chapter 5
6. Chapter 6
7. Chapter 7
8. Chapter 8
9. Chapter 9
10. Chapter 10
11. Chapter 11
12. Chapter 12
13. Chapter 13
14. Chapter 14
15. Chapter 15
16. Chapter 16
17. Chapter 17
18. Chapter 18
19. Chapter 19
20. Chapter 20
21. Chapter 21
22. Chapter 22
23. Chapter 23
24. Chapter 24
25. Chapter 25
26. Chapter 26
34. Index
Learning Objectives
By the end of this section, you will be able to:
• Describe how enzymes in body fluids provide protection against infection or disease
• List and describe the function of antimicrobial peptides, complement components, cytokines, and acute-phase proteins
• Describe similarities and differences among classic, alternate, and lectin complement pathways
In addition to physical defenses, the innate nonspecific immune system uses a number of chemical mediators that inhibit microbial invaders. The term “chemical mediators” encompasses a wide array of substances found in various body fluids and tissues throughout the body. Chemical mediators may work alone or in conjunction with each other to inhibit microbial colonization and infection.
Some chemical mediators are endogenously produced, meaning they are produced by human body cells; others are produced exogenously, meaning that they are produced by certain microbes that are part of the microbiome. Some mediators are produced continually, bathing the area in the antimicrobial substance; others are produced or activated primarily in response to some stimulus, such as the presence of microbes.
Chemical and Enzymatic Mediators Found in Body Fluids
Fluids produced by the skin include examples of both endogenous and exogenous mediators. Sebaceous glands in the dermis secrete an oil called sebum that is released onto the skin surface through hair follicles. This sebum is an endogenous mediator, providing an additional layer of defense by helping seal off the pore of the hair follicle, preventing bacteria on the skin’s surface from invading sweat glands and surrounding tissue (Figure 17.8). Certain members of the microbiome, such as the bacterium Propionibacterium acnes and the fungus Malassezia, among others, can use lipase enzymes to degrade sebum, using it as a food source. This produces oleic acid, which creates a mildly acidic environment on the surface of the skin that is inhospitable to many pathogenic microbes. Oleic acid is an example of an exogenously produced mediator because it is produced by resident microbes and not directly by body cells.
A micrograph and diagram both show a large hair follicle (a vase-shaped pocket) with a hair projecting out past the epidermis. On the side of the hair follicle is the sebaceous gland, which is a lumpy structure.
Figure 17.8 Sebaceous glands secrete sebum, a chemical mediator that lubricates and protect the skin from invading microbes. Sebum is also a food source for resident microbes that produce oleic acid, an exogenously produced mediator. (credit micrograph: Micrograph provided by the Regents of University of Michigan Medical School © 2012)
Environmental factors that affect the microbiota of the skin can have a direct impact on the production of chemical mediators. Low humidity or decreased sebum production, for example, could make the skin less habitable for microbes that produce oleic acid, thus making the skin more susceptible to pathogens normally inhibited by the skin’s low pH. Many skin moisturizers are formulated to counter such effects by restoring moisture and essential oils to the skin.
The digestive tract also produces a large number of chemical mediators that inhibit or kill microbes. In the oral cavity, saliva contains mediators such as lactoperoxidase enzymes, and mucus secreted by the esophagus contains the antibacterial enzyme lysozyme. In the stomach, highly acidic gastric fluid kills most microbes. In the lower digestive tract, the intestines have pancreatic and intestinal enzymes, antibacterial peptides (cryptins), bile produced from the liver, and specialized Paneth cells that produce lysozyme. Together, these mediators are able to eliminate most pathogens that manage to survive the acidic environment of the stomach.
In the urinary tract, urine flushes microbes out of the body during urination. Furthermore, the slight acidity of urine (the average pH is about 6) inhibits the growth of many microbes and potential pathogens in the urinary tract.
The female reproductive system employs lactate, an exogenously produced chemical mediator, to inhibit microbial growth. The cells and tissue layers composing the vagina produce glycogen, a branched and more complex polymer of glucose. Lactobacilli in the area ferment glycogen to produce lactate, lowering the pH in the vagina and inhibiting transient microbiota, opportunistic pathogens like Candida (a yeast associated with vaginal infections), and other pathogens responsible for sexually transmitted diseases.
In the eyes, tears contain the chemical mediators lysozyme and lactoferrin, both of which are capable of eliminating microbes that have found their way to the surface of the eyes. Lysozyme cleaves the bond between NAG and NAM in peptidoglycan, a component of the cell wall in bacteria. It is more effective against gram-positive bacteria, which lack the protective outer membrane associated with gram-negative bacteria. Lactoferrin inhibits microbial growth by chemically binding and sequestering iron. This effectually starves many microbes that require iron for growth.
In the ears, cerumen (earwax) exhibits antimicrobial properties due to the presence of fatty acids, which lower the pH to between 3 and 5.
The respiratory tract uses various chemical mediators in the nasal passages, trachea, and lungs. The mucus produced in the nasal passages contains a mix of antimicrobial molecules similar to those found in tears and saliva (e.g., lysozyme, lactoferrin, lactoperoxidase). Secretions in the trachea and lungs also contain lysozyme and lactoferrin, as well as a diverse group of additional chemical mediators, such as the lipoprotein complex called surfactant, which has antibacterial properties.
Check Your Understanding
• Explain the difference between endogenous and exogenous mediators
• Describe how pH affects antimicrobial defenses
Antimicrobial Peptides
The antimicrobial peptides (AMPs) are a special class of nonspecific cell-derived mediators with broad-spectrum antimicrobial properties. Some AMPs are produced routinely by the body, whereas others are primarily produced (or produced in greater quantities) in response to the presence of an invading pathogen. Research has begun exploring how AMPs can be used in the diagnosis and treatment of disease.
AMPs may induce cell damage in microorganisms in a variety of ways, including by inflicting damage to membranes, destroying DNA and RNA, or interfering with cell-wall synthesis. Depending on the specific antimicrobial mechanism, a particular AMP may inhibit only certain groups of microbes (e.g., gram-positive or gram-negative bacteria) or it may be more broadly effective against bacteria, fungi, protozoa, and viruses. Many AMPs are found on the skin, but they can also be found in other regions of the body.
A family of AMPs called defensins can be produced by epithelial cells throughout the body as well as by cellular defenses such as macrophages and neutrophils (see Cellular Defenses). Defensins may be secreted or act inside host cells; they combat microorganisms by damaging their plasma membranes. AMPs called bacteriocins are produced exogenously by certain members of the resident microbiota within the gastrointestinal tract. The genes coding for these types of AMPs are often carried on plasmids and can be passed between different species within the resident microbiota through lateral or horizontal gene transfer.
There are numerous other AMPs throughout the body. The characteristics of a few of the more significant AMPs are summarized in Table 17.3.
Characteristics of Selected Antimicrobial Peptides (AMPs)
AMP Secreted by Body site Pathogens inhibited Mode of action
Bacteriocins Resident microbiota Gastrointestinal tract Bacteria Disrupt membrane
Cathelicidin Epithelial cells, macrophages, and other cell types Skin Bacteria and fungi Disrupts membrane
Defensins Epithelial cells, macrophages, neutrophils Throughout the body Fungi, bacteria, and many viruses Disrupt membrane
Dermcidin Sweat glands Skin Bacteria and fungi Disrupts membrane integrity and ion channels
Histatins Salivary glands Oral cavity Fungi Disrupt intracellular function
Table 17.3
Check Your Understanding
• Why are antimicrobial peptides (AMPs) considered nonspecific defenses?
Plasma Protein Mediators
Many nonspecific innate immune factors are found in plasma, the fluid portion of blood. Plasma contains electrolytes, sugars, lipids, and proteins, each of which helps to maintain homeostasis (i.e., stable internal body functioning), and contains the proteins involved in the clotting of blood. Additional proteins found in blood plasma, such as acute-phase proteins, complement proteins, and cytokines, are involved in the nonspecific innate immune response.
Micro Connections
Plasma versus Serum
There are two terms for the fluid portion of blood: plasma and serum. How do they differ if they are both fluid and lack cells? The fluid portion of blood left over after coagulation (blood cell clotting) has taken place is serum. Although molecules such as many vitamins, electrolytes, certain sugars, complement proteins, and antibodies are still present in serum, clotting factors are largely depleted. Plasma, conversely, still contains all the clotting elements. To obtain plasma from blood, an anticoagulant must be used to prevent clotting. Examples of anticoagulants include heparin and ethylene diamine tetraacetic acid (EDTA). Because clotting is inhibited, once obtained, the sample must be gently spun down in a centrifuge. The heavier, denser blood cells form a pellet at the bottom of a centrifuge tube, while the fluid plasma portion, which is lighter and less dense, remains above the cell pellet.
Acute-Phase Proteins
The acute-phase proteins are another class of antimicrobial mediators. Acute-phase proteins are primarily produced in the liver and secreted into the blood in response to inflammatory molecules from the immune system. Examples of acute-phase proteins include C-reactive protein, serum amyloid A, ferritin, transferrin, fibrinogen, and mannose-binding lectin. Each of these proteins has a different chemical structure and inhibits or destroys microbes in some way (Table 17.4).
Some Acute-Phase Proteins and Their Functions
C-reactive protein Coats bacteria (opsonization), preparing them for ingestion by phagocytes
Serum amyloid A
Ferritin Bind and sequester iron, thereby inhibiting the growth of pathogens
Transferrin
Fibrinogen Involved in formation of blood clots that trap bacterial pathogens
Mannose-binding lectin Activates complement cascade
Table 17.4
The Complement System
The complement system is a group of plasma protein mediators that can act as an innate nonspecific defense while also serving to connect innate and adaptive immunity (discussed in the next chapter). The complement system is composed of more than 30 proteins (including C1 through C9) that normally circulate as precursor proteins in blood. These precursor proteins become activated when stimulated or triggered by a variety of factors, including the presence of microorganisms. Complement proteins are considered part of innate nonspecific immunity because they are always present in the blood and tissue fluids, allowing them to be activated quickly. Also, when activated through the alternative pathway (described later in this section), complement proteins target pathogens in a nonspecific manner.
The process by which circulating complement precursors become functional is called complement activation. This process is a cascade that can be triggered by one of three different mechanisms, known as the alternative, classical, and lectin pathways.
The alternative pathway is initiated by the spontaneous activation of the complement protein C3. The hydrolysis of C3 produces two products, C3a and C3b. When no invader microbes are present, C3b is very quickly degraded in a hydrolysis reaction using the water in the blood. However, if invading microbes are present, C3b attaches to the surface of these microbes. Once attached, C3b will recruit other complement proteins in a cascade (Figure 17.9).
The classical pathway provides a more efficient mechanism of activating the complement cascade, but it depends upon the production of antibodies by the specific adaptive immune defenses. To initiate the classical pathway, a specific antibody must first bind to the pathogen to form an antibody-antigen complex. This activates the first protein in the complement cascade, the C1 complex. The C1 complex is a multipart protein complex, and each component participates in the full activation of the overall complex. Following recruitment and activation of the C1 complex, the remaining classical pathway complement proteins are recruited and activated in a cascading sequence (Figure 17.9).
The lectin activation pathway is similar to the classical pathway, but it is triggered by the binding of mannose-binding lectin, an acute-phase protein, to carbohydrates on the microbial surface. Like other acute-phase proteins, lectins are produced by liver cells and are commonly upregulated in response to inflammatory signals received by the body during an infection (Figure 17.9).
A diagram outlining the three complement pathways. At the top is the invading pathogen. Two antibodies bind to an antigen on the surface of the pathogen. C1 binds to the antigen-antibody complex. This is labeled the classic pathway. C1 causes C2 and C4 to be cut into two pieces. Parts of C2 and C4 bind together to form C3 convertase. The alternate pathway also leads to C3 convertase but does so directly. C3 convertase then cuts C3 in two and one of these binds to C3 convertase. The resulting enzyme is called C5 convertase. C5 convertase lyses C5 into two pieces. One of the C5 pieces joins other complement proteins (C6, C7, C8 and C9) to create a pore through the membrane of the invading cell. This pore kills the cell. Endogenous proteins on the host cell protect the host membrane from the complement proteins.
Figure 17.9 The three complement activation pathways have different triggers, as shown here, but all three result in the activation of the complement protein C3, which produces C3a and C3b. The latter binds to the surface of the target cell and then works with other complement proteins to cleave C5 into C5a and C5b. C5b also binds to the cell surface and then recruits C6 through C9; these molecules form a ring structure called the membrane attack complex (MAC), which punches through the cell membrane of the invading pathogen, causing it to swell and burst.
Although each complement activation pathway is initiated in a different way, they all provide the same protective outcomes: opsonization, inflammation, chemotaxis, and cytolysis. The term opsonization refers to the coating of a pathogen by a chemical substance (called an opsonin) that allows phagocytic cells to recognize, engulf, and destroy it more easily. Opsonins from the complement cascade include C1q, C3b, and C4b. Additional important opsonins include mannose-binding proteins and antibodies. The complement fragments C3a and C5a are well-characterized anaphylatoxins with potent proinflammatory functions. Anaphylatoxins activate mast cells, causing degranulation and the release of inflammatory chemical signals, including mediators that cause vasodilation and increased vascular permeability. C5a is also one of the most potent chemoattractants for neutrophils and other white blood cells, cellular defenses that will be discussed in the next section.
The complement proteins C6, C7, C8, and C9 assemble into a membrane attack complex (MAC), which allows C9 to polymerize into pores in the membranes of gram-negative bacteria. These pores allow water, ions, and other molecules to move freely in and out of the targeted cells, eventually leading to cell lysis and death of the pathogen (Figure 17.9). However, the MAC is only effective against gram-negative bacteria; it cannot penetrate the thick layer of peptidoglycan associated with cell walls of gram-positive bacteria. Since the MAC does not pose a lethal threat to gram-positive bacterial pathogens, complement-mediated opsonization is more important for their clearance.
Cytokines
Cytokines are soluble proteins that act as communication signals between cells. In a nonspecific innate immune response, various cytokines may be released to stimulate production of chemical mediators or other cell functions, such as cell proliferation, cell differentiation, inhibition of cell division, apoptosis, and chemotaxis.
When a cytokine binds to its target receptor, the effect can vary widely depending on the type of cytokine and the type of cell or receptor to which it has bound. The function of a particular cytokine can be described as autocrine, paracrine, or endocrine (Figure 17.10). In autocrine function, the same cell that releases the cytokine is the recipient of the signal; in other words, autocrine function is a form of self-stimulation by a cell. In contrast, paracrine function involves the release of cytokines from one cell to other nearby cells, stimulating some response from the recipient cells. Last, endocrine function occurs when cells release cytokines into the bloodstream to be carried to target cells much farther away.
Cytokines are molecular messengers. In autocrine signaling the same cell secretes and receives cytokine signals. The diagram shows a single cell releasing molecules and having the molecules bind to receptors on its surface. In paracrine signaling cytokine signals are secreted to a nearby cell. The diagram shows a cell labeled secreting cell secreting cytokines. A nearby cell has receptors for the molecules. In endocrine signaling cytokine signals are secreted to the circulatory system and travel to distant cells. The diagram shows the secreting cell secreting cytokines; the cytokines then travel through a blood vessel and bind to receptors on a distant cell.
Figure 17.10 Autocrine, paracrine, and endocrine actions describe which cells are targeted by cytokines and how far the cytokines must travel to bind to their intended target cells’ receptors.
Three important classes of cytokines are the interleukins, chemokines, and interferons. The interleukins were originally thought to be produced only by leukocytes (white blood cells) and to only stimulate leukocytes, thus the reasons for their name. Although interleukins are involved in modulating almost every function of the immune system, their role in the body is not restricted to immunity. Interleukins are also produced by and stimulate a variety of cells unrelated to immune defenses.
The chemokines are chemotactic factors that recruit leukocytes to sites of infection, tissue damage, and inflammation. In contrast to more general chemotactic factors, like complement factor C5a, chemokines are very specific in the subsets of leukocytes they recruit.
Interferons are a diverse group of immune signaling molecules and are especially important in our defense against viruses. Type I interferons (interferon-α and interferon-β) are produced and released by cells infected with virus. These interferons stimulate nearby cells to stop production of mRNA, destroy RNA already produced, and reduce protein synthesis. These cellular changes inhibit viral replication and production of mature virus, slowing the spread of the virus. Type I interferons also stimulate various immune cells involved in viral clearance to more aggressively attack virus-infected cells. Type II interferon (interferon-γ) is an important activator of immune cells (Figure 17.11).
A cell with viruses inside it releases signals labeled interferons. The interferons travel to 3 different cells. The interferon signals neighboring uninfected cells to destroy RNA and reduce protein synthesis. The interferon signals neighboring infected cells to undergo apoptosis. The interferon also activates immune cells.
Figure 17.11 Interferons are cytokines released by a cell infected with a virus. Interferon-α and interferon-β signal uninfected neighboring cells to inhibit mRNA synthesis, destroy RNA, and reduce protein synthesis (top arrow). Interferon-α and interferon-β also promote apoptosis in cells infected with the virus (middle arrow). Interferon-γ alerts neighboring immune cells to an attack (bottom arrow). Although interferons do not cure the cell releasing them or other infected cells, which will soon die, their release may prevent additional cells from becoming infected, thus stemming the infection.
Inflammation-Eliciting Mediators
Many of the chemical mediators discussed in this section contribute in some way to inflammation and fever, which are nonspecific immune responses discussed in more detail in Inflammation and Fever. Cytokines stimulate the production of acute-phase proteins such as C-reactive protein and mannose-binding lectin in the liver. These acute-phase proteins act as opsonins, activating complement cascades through the lectin pathway.
Some cytokines also bind mast cells and basophils, inducing them to release histamine, a proinflammatory compound. Histamine receptors are found on a variety of cells and mediate proinflammatory events, such as bronchoconstriction (tightening of the airways) and smooth muscle contraction.
In addition to histamine, mast cells may release other chemical mediators, such as leukotrienes. Leukotrienes are lipid-based proinflammatory mediators that are produced from the metabolism of arachidonic acid in the cell membrane of leukocytes and tissue cells. Compared with the proinflammatory effects of histamine, those of leukotrienes are more potent and longer lasting. Together, these chemical mediators can induce coughing, vomiting, and diarrhea, which serve to expel pathogens from the body.
Certain cytokines also stimulate the production of prostaglandins, chemical mediators that promote the inflammatory effects of kinins and histamines. Prostaglandins can also help to set the body temperature higher, leading to fever, which promotes the activities of white blood cells and slightly inhibits the growth of pathogenic microbes (see Inflammation and Fever).
Another inflammatory mediator, bradykinin, contributes to edema, which occurs when fluids and leukocytes leak out of the bloodstream and into tissues. It binds to receptors on cells in the capillary walls, causing the capillaries to dilate and become more permeable to fluids.
Check Your Understanding
• What do the three complement activation pathways have in common?
• Explain autocrine, paracrine, and endocrine signals.
• Name two important inflammation-eliciting mediators.
Clinical Focus
Part 2
To relieve the constriction of her airways, Angela is immediately treated with antihistamines and administered corticosteroids through an inhaler, and then monitored for a period of time. Though her condition does not worsen, the drugs do not seem to be alleviating her condition. She is admitted to the hospital for further observation, testing, and treatment.
Following admission, a clinician conducts allergy testing to try to determine if something in her environment might be triggering an allergic inflammatory response. A doctor orders blood analysis to check for levels of particular cytokines. A sputum sample is also taken and sent to the lab for microbial staining, culturing, and identification of pathogens that could be causing an infection.
• Which aspects of the innate immune system could be contributing to Angela’s airway constriction?
• Why was Angela treated with antihistamines?
• Why would the doctor be interested in levels of cytokines in Angela’s blood?
Jump to the next Clinical Focus box. Go back to the previous Clinical Focus box.
Table 17.5 provides a summary of the chemical defenses discussed in this section.
Chemical Defenses of Nonspecific Innate Immunity
Defense Examples Function
Chemicals and enzymes in body fluids Sebum from sebaceous glands Provides oil barrier protecting hair follicle pores from pathogens
Oleic acid from sebum and skin microbiota Lowers pH to inhibit pathogens
Lysozyme in secretions Kills bacteria by attacking cell wall
Acid in stomach, urine, and vagina Inhibits or kills bacteria
Digestive enzymes and bile Kill bacteria
Lactoferrin and transferrin Bind and sequester iron, inhibiting bacterial growth
Surfactant in lungs Kills bacteria
Antimicrobial peptides Defensins, bacteriocins, dermcidin, cathelicidin, histatins, Kill bacteria by attacking membranes or interfering with cell functions
Plasma protein mediators Acute-phase proteins (C-reactive protein, serum amyloid A, ferritin, fibrinogen, transferrin, and mannose-binding lectin) Inhibit the growth of bacteria and assist in the trapping and killing of bacteria
Complements C3b and C4b Opsonization of pathogens to aid phagocytosis
Complement C5a Chemoattractant for phagocytes
Complements C3a and C5a Proinflammatory anaphylatoxins
Cytokines Interleukins Stimulate and modulate most functions of immune system
Chemokines Recruit white blood cells to infected area
Interferons Alert cells to viral infection, induce apoptosis of virus-infected cells, induce antiviral defenses in infected and nearby uninfected cells, stimulate immune cells to attack virus-infected cells
Inflammation-eliciting mediators Histamine Promotes vasodilation, bronchoconstriction, smooth muscle contraction, increased secretion and mucus production
Leukotrienes Promote inflammation; stronger and longer lasting than histamine
Prostaglandins Promote inflammation and fever
Bradykinin Increases vasodilation and vascular permeability, leading to edema
Table 17.5
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7,328,599,852,048,407,000 | Fermer
C3E Newsletter
The Centre of Chemical Ecology publishes once or twice a year a newsletter which covers a range of topics such as research highlights (recent publications), new research projects, organizational changes (e.g. new appointments), events and all kinds of other relevant news pertaining to the Centre (e.g. awards).
The newsletter is not printed on paper, but is spread as a PDF-document via email to the interested parties. You can subscribe by sending an email with subscription C3E newsletter in the subject line to Thomas Degen. Past and present issues can also be downloaded from this webpage.
2016
C3E_Newsletter_2016_185x262.jpg
2015
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3,391,487,941,688,459,000 | Ying-Ju Lin,China Medical University Taiwan,Immunology,Biochemistry,Diseases
Profile - Ying-Ju Lin
Ying-Ju Lin
Publications: 31 | Citations: 91
Fields: ImmunologyBiochemistryDiseases
View FAQ about top research areas and Fields of study
Collaborated with 106 co-authors from 2003 to 2011 | Cited by 425 authors
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Publications (31)
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-6,594,806,976,494,560,000 | biosynthesis
Also found in: Dictionary, Thesaurus, Encyclopedia, Wikipedia.
Related to biosynthesis: Purine biosynthesis
biosynthesis
[bi″o-sin´thĕ-sis]
creation of a compound by physiologic processes in a living organism. adj., adj biosynthet´ic.
Miller-Keane Encyclopedia and Dictionary of Medicine, Nursing, and Allied Health, Seventh Edition. © 2003 by Saunders, an imprint of Elsevier, Inc. All rights reserved.
bi·o·syn·the·sis
(bī'ō-sin'thĕ-sis),
Formation of a chemical compound by enzymes, either in the organism (in vivo) or by fragments or extracts of cells (in vitro).
Synonym(s): biogenesis (2)
Farlex Partner Medical Dictionary © Farlex 2012
biosynthesis
(bī′ō-sĭn′thĭ-sĭs)
n.
Formation of a chemical compound by a living organism. Also called biogenesis.
bi′o·syn·thet′ic (-thĕt′ĭk) adj.
bi′o·syn·thet′i·cal·ly adv.
The American Heritage® Medical Dictionary Copyright © 2007, 2004 by Houghton Mifflin Company. Published by Houghton Mifflin Company. All rights reserved.
biosynthesis
Bodywork
A proprietary form of spiritual bodywork, which
combines features of bioenergetics and Reichian therapy. Developed by a David Boadella, “Bosynthesis” is based on the belief that 3 currents of energy flow through the body, arising from the embryonal germ cell layers, the ectoderm, the mesoderm and the endoderm. It posits that stresses began in utero affect emotions in later life and interrupt the flow of energy; the intent of the system is to reintegrate the flow of energy, by breathing techniques, emotional centring, grounding the posture, and shaping of experience through verbal communication and eye contact.
Cell biology
Synthesis of biomolecules by a living system.
Pharmacology
See Combinatorial biosynthesis.
Physiology
The production of proteins, lipids and carbohydrates by enzyme activity and physiologic processes within an organism; the synthesis of chemical compounds by enzymatic processes in living organisms.
Segen's Medical Dictionary. © 2012 Farlex, Inc. All rights reserved.
biosynthesis
Pharmacology See Combinatorial biosynthesis.
McGraw-Hill Concise Dictionary of Modern Medicine. © 2002 by The McGraw-Hill Companies, Inc.
bi·o·syn·the·sis
(bī'ō-sin'thĕ-sis)
Formation of a chemical compound by enzymes, either in the organism (in vivo) or by fragments or extracts of cells (in vitro).
Synonym(s): biogenesis (2) .
Medical Dictionary for the Health Professions and Nursing © Farlex 2012
biosynthesis
the process by which more complex molecules are formed from simpler ones by living organisms, e.g. PHOTOSYNTHESIS.
Collins Dictionary of Biology, 3rd ed. © W. G. Hale, V. A. Saunders, J. P. Margham 2005
Biosynthesis
The manufacture of materials in a biological system.
Mentioned in: Porphyrias
Gale Encyclopedia of Medicine. Copyright 2008 The Gale Group, Inc. All rights reserved.
bi·o·syn·the·sis
(bī'ō-sin'thĕ-sis)
Formation of a chemical compound by enzymes, either in the organism (in vivo) or by fragments or extracts of cells (in vitro).
Synonym(s): biogenesis (2) .
Medical Dictionary for the Dental Professions © Farlex 2012
References in periodicals archive ?
Forward-looking information in this news release includes statements about: developing a proprietary biosynthesis manufacturing technology for the production of pharmaceutical-grade cannabinoids as well as a pipeline of medications targeting diseases with high unmet medical needs; Mr.
Carnitine biosynthesis is a function of multiple tissues with the last reaction involving the hydroxylation of [gamma]-butyrobetaine to carnitine by [gamma]-BBH occurring in liver.
Candidate Genes Involved in Phenolic Compounds Biosynthesis of Sophorae Radix.
These variables are related to seven metabolic pathways, including TCA cycle, ubiquinone and other terpenoid quinone biosyntheses, N-glycan biosynthesis, other glycan degradation, glycosaminoglycan degradation, and glycosylphosphatidylinositol (GPI) anchor biosynthesis and glycosphingolipid biosynthesis-ganglioseries.
During the biosynthesis procedure, functional groups of herbal materials reduce metal ions and play the capping roles as well.
Microbial biosynthesis of auxins was stimulated due to application of L-TRP results in enhanced plant growth (Zahir et al., 2004; Khalid et al., 2006; Parthiban et al., 2016).
lactiflora (Jia et al., 2008) and the accumulation of avonoids is determined by a series of genes in the avonoids biosynthesis pathway (Nakatsuka et al., 2005).
(2017) analyzed the genes involved in dendrobine biosynthesis in Dendrobium nobile Lindl., and they found 30 Unigenes encoding proteins were possibly related to the biosynthesis of dendrobine sesquiterpene backbone; MF23 might stimulate dendrobine biosynthesis by regulating the expressions of genes involved in the mevalonate (MVA) pathway and postmodification enzymes might play a major role in dendrobine biosynthesis [19].
Ex vivo whole blood stimulation for the biosynthesis of 5-LO products was performed as previously reported [20].
Typical morphologies produced via biosynthesis include cubes, hexagons, pentagons, rods, spheres, triangles, and wires [34, 93].
KEYWORDS: Westiellopsis sp., Chroococcus minor Oscillatoria sancta, Biosynthesis of Ag-nanoparticles, AFM, UVChroococcus minor, nanoparticles, UV-Visible spectrometer.
Statins inhibit CoQ10 and "heme A" biosynthesis, compounds required for ATP generation and mitochondrial maintenance and repair. | {
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3,981,802,132,395,769,300 | Navigation Links
Rabbit Anti-Human PVRL2 Polyclonal Antibody, Unconjugated from Proteintech Group, Inc.
...
... Disrupts biological cells for DNA isolation. ... well plates (includes 96 well plate ... lysis across the entire plate length ... Can be used for soil, ...
... Chicken polyclonal to LYZL6 ( ... Antigen: Synthetic ... DYKSYSENLC HVDCQD , corresponding to amino ... Entrez Gene ID: ...
Drugs and NO-drug Rat Anti-conjugated Acetyl Salicylic Acid Polyclonal Antibody...
Biology Products:
(Date:6/22/2016)... On Monday, the Department of Homeland Security (DHS) issued ... the Biometric Exit Program. The Request for Information (RFI), ... that CBP intends to add biometrics to confirm when ... , in order to deter visa overstays, to ... Logo - http://photos.prnewswire.com/prnh/20160622/382209LOGO ...
(Date:6/16/2016)... , June 16, 2016 ... size is expected to reach USD 1.83 billion ... Grand View Research, Inc. Technological proliferation and increasing ... applications are expected to drive the market growth. ... , The development of advanced multimodal ...
(Date:6/9/2016)... 2016 Paris Police Prefecture ... security solution to ensure the safety of people and operations ... the major tournament Teleste, an international technology group ... announced today that its video security solution will be utilised ... up public safety across the country. The system roll-out is ...
Breaking Biology News(10 mins):
(Date:6/23/2016)... June 23, 2016 Houston Methodist Willowbrook ... Cy-Fair Sports Association to serve as their official ... Houston Methodist Willowbrook will provide sponsorship support, athletic ... with association coaches, volunteers, athletes and families. ... Cy-Fair Sports Association and to bring Houston Methodist ...
(Date:6/23/2016)... -- The Biodesign Challenge (BDC), a university competition that asks ... systems and biotechnology, announced its winning teams at the ... York City . The teams, chosen ... MoMA,s Celeste Bartos Theater during the daylong summit. Keynote ... of architecture and design, and Suzanne Lee , ...
(Date:6/23/2016)... (PRWEB) , ... June 23, 2016 , ... STACS DNA ... Technical Leader at the Arkansas State Crime Laboratory, has joined STACS DNA as a ... STACS DNA team,” said Jocelyn Tremblay, President and COO of STACS DNA. “In further ...
(Date:6/23/2016)... , June 23, 2016 Blueprint Bio, a company ... to the medical community, has closed its Series A ... Nunez . "We have received a commitment ... capital we need to meet our current goals," stated ... us the runway to complete validation on the current ...
Breaking Biology Technology: | {
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8,993,410,610,167,910,000 |
製品の概要
• 製品名Anti-HP1 alpha antibody
HP1 alpha 一次抗体 製品一覧
• 製品の詳細
Rabbit polyclonal to HP1 alpha
• アプリケーション適用あり: WB, ICC/IFmore details
• 種交差性
交差種: Human
交差が予測される動物種: Sheep, Rabbit, Horse, Cow, Dog, Pig, Rhesus monkey, Gorilla, Loxodonta Africana (African bush elephant)
• 免疫原
Synthetic peptide corresponding to Human HP1 alpha aa 179-191.
Sequence:
CEDAENKEKETAKS
Database link: P45973
• ポジティブ･コントロール
• MCF7 extract
製品の特性
関連製品
アプリケーション
Our Abpromise guarantee covers the use of ab123101 in the following tested applications.
The application notes include recommended starting dilutions; optimal dilutions/concentrations should be determined by the end user.
アプリケーション Abreviews 特記事項
WB 1/1000 - 1/3000. Predicted molecular weight: 21 kDa.
ICC/IF 1/200 - 1/1000.
ターゲット情報
• 機能Component of heterochromatin that recognizes and binds histone H3 tails methylated at 'Lys-9' (H3K9me), leading to epigenetic repression. In contrast, it is excluded from chromatin when 'Tyr-41' of histone H3 is phosphorylated (H3Y41ph). Can interact with lamin-B receptor (LBR). This interaction can contribute to the association of the heterochromatin with the inner nuclear membrane. Involved in the formation of functional kinetochore through interaction with MIS12 complex proteins.
• 配列類似性Contains 2 chromo domains.
• 翻訳後修飾Phosphorylation of HP1 and LBR may be responsible for some of the alterations in chromatin organization and nuclear structure which occur at various times during the cell cycle (By similarity). Phosphorylated during interphase and possibly hyper-phosphorylated during mitosis.
Ubiquitinated.
• 細胞内局在Nucleus. Chromosome. Chromosome > centromere. Component of centromeric and pericentromeric heterochromatin. Associates with chromosomes during mitosis. Associates specifically with chromatin during metaphase and anaphase.
• Information by UniProt
• 参照データベース
• 別名
• Antigen p25 antibody
• CBX5 antibody
• CBX5_HUMAN antibody
• CG8409 antibody
• Chromobox 5 antibody
• Chromobox homolog 5 (HP1 alpha homolog, Drosophila) antibody
• Chromobox homolog 5 antibody
• Chromobox protein homolog 5 antibody
• Epididymis luminal protein 25 antibody
• HEL25 antibody
• Heterochromatin protein 1 alpha antibody
• Heterochromatin protein 1 antibody
• Heterochromatin protein 1 homolog alpha antibody
• HP1 alpha antibody
• HP1 alpha homolog antibody
• HP1 antibody
• HP1A antibody
• HP1Hs alpha antibody
• Su(var)205 antibody
see all
Anti-HP1 alpha antibody 画像
• Anti-HP1 alpha antibody (ab123101) at 1/1000 dilution + MCF7 extract
Predicted band size : 21 kDa
Anti-HP1 alpha antibody (ab123101) 使用論文
ab123101 has not yet been referenced specifically in any publications.
Product Wall
There are currently no Abreviews or Questions for ab123101.
Please use the links above to contact us or submit feedback about this product.
Please note: All products are "FOR RESEARCH USE ONLY AND ARE NOT INTENDED FOR DIAGNOSTIC OR THERAPEUTIC USE" | {
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} | 57 | cf5cd1df0ee2161e1684bdc019357275 |
1,544,141,558,170,493,000 | Biology
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Biology
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} | 57 | cf5cd1df0ee2161e1684bdc019357275 |
-4,108,138,215,851,179,500 | Proteomic applications of automated GPCR classification
Davies, Matthew N. and Gloriam, David E. and Secker, Andrew D. and Freitas, Alex A. and Mendao, Miguel and Timmis, Jon and Flower, Darren R. (2007) Proteomic applications of automated GPCR classification. Proteomics, 7 (16). pp. 2800-2814. ISSN 1615-9853. (doi:10.1002/pmic.200700093) (The full text of this publication is not currently available from this repository. You may be able to access a copy if URLs are provided)
The full text of this publication is not currently available from this repository. You may be able to access a copy if URLs are provided. (Contact us about this Publication)
Official URL
http://dx.doi.org/10.1002/pmic.200700093
Abstract
The G-protein coupled receptor (GPCR) superfamily fulfils various metabolic functions and interacts with a diverse range of ligands. There is a lack of sequence similarity between the six classes that comprise the GPCR superfamily. Moreover, most novel GPCRs found have low sequence similarity to other family members which makes it difficult to infer properties from related receptors. Many different approaches have been taken towards developing efficient and accurate methods for GPCR classification, ranging from motif-based systems to machine learning as well as a variety of alignment-free techniques based on the physiochemical properties of their amino acid sequences. This review describes the inherent difficulties in developing a GPCR classification algorithm and includes techniques previously employed in this area.
Item Type: Article
Uncontrolled keywords: data mining, classification, bioinformatics alignment; bioinformatics; classification; GPCR; tools
Subjects: Q Science > QA Mathematics (inc Computing science) > QA 76 Software, computer programming,
Divisions: Faculties > Science Technology and Medical Studies > School of Computing > Applied and Interdisciplinary Informatics Group
Depositing User: Mark Wheadon
Date Deposited: 24 Nov 2008 18:04
Last Modified: 19 May 2014 16:00
Resource URI: https://kar.kent.ac.uk/id/eprint/14555 (The current URI for this page, for reference purposes)
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-1,963,252,915,867,334,000 | English español
Please use this identifier to cite or link to this item: http://hdl.handle.net/10261/115741
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Title
Novel polymorphic microsatellites for the red-legged partridge ( Alectoris rufa ) and cross-species amplification in Alectoris graeca
AuthorsGonzález, Elena G. ; Castilla, Aurora M. ; Zardoya, Rafael
KeywordsGame bird
Hybridization
Microsatellite
Red-legged partridge
Rock partridge
Issue Date2005
PublisherJohn Wiley & Sons
CitationMolecular Ecology Notes 5(2): 449-451 (2005)
AbstractThe red-legged partridge, Alectoris rufa, is an endemic species of the southwestern Mediterranean, and the most popular game bird in the Iberian Peninsula. A total of 27 microsatellite loci was isolated from an enriched genomic library of A. rufa. Six perfect GT microsatellites were characterized and optimized in 45 individuals of A. rufa. All loci revealed high levels of polymorphism with a number of alleles that ranged from three to 13. Observed heterozygosity ranged from 0.2 to 0.6. Cross-species amplification showed that all loci were also polymorphic in rock partridge, Alectoris graeca. The new markers will be useful in determining hybridization between both species of Alectoris.
Publisher version (URL)http://dx.doi.org/10.1111/j.1471-8286.2005.00960.x
URIhttp://hdl.handle.net/10261/115741
DOIhttp://dx.doi.org/10.1111/j.1471-8286.2005.00960.x
ISSN1471-8278
E-ISSN1471-8286
Appears in Collections:(MNCN) Artículos
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} | 57 | cf5cd1df0ee2161e1684bdc019357275 |
-6,699,619,857,965,456,000 | UC SPARK - University of Canterbury - New Zealand
Professor Jack Heinemann
Biological Sciences
Fields of Research
• Microbial genetics and evolution
• Horizontal gene transfer
• Risk assessment especially of genetically modified organisms
• Academic freedom and role of critic and conscience of society
• Cartagena Protocol on Biosafety
• Conflicts of interest in research
• Sustainable agriculture
• Project management
• Antibiotic resistance
• Science, technology and tertiary sector policies including funding
Researcher Summary
Research interests include the genetics and molecular biology of single-celled bacteria, phage and some eukaryotic microorganisms, horizontal gene transfer, particularly conjugation, effects of stress, particularly induced by antibiotics and agrochemicals, evolution and risk assessment, influence of language on science and eugenics. Specific interests are the biochemical and genetic characterization of horizontal gene transfer (particularly as it relates to the evolution of virulence and antibiotic resistance in microbes and the risks of genetically modified/engineered organisms) and yeast, bacteria and the test of evolutionary theories.
Subject Area: Disciplines
Research Groups
Future Research
• Particular ongoing emphasis on how antibiotic resistance evolves and persists, role of toxin-anti-toxin systems in the evolution of fundamental cellular reactions, and in recruiting vectors of horizontal (lateral) gene transfer.
Key Methodologies
• genetic engineering, molecular biology, microbial genetics, genotoxicity
Research/Scholarly/Creative Works
• Coray DS., Kurenbach B. and Heinemann JA. (2017) Exploring the parameters of post-segregational killing using heterologous expression of secreted toxin barnase and antitoxin barstar in an Escherichia coli case study. Microbiology 163(2): 122-130. http://dx.doi.org/10.1099/mic.0.000395. (Journal Article)
• Coray DS., Kurenbach B. and Heinemann JA. (2017) Exploring the parameters of post-segregational killing using heterologous expression of secreted toxin barnase and antitoxin barstar in an Escherichia coli case study.. Microbiology 163(2): 122-130. http://dx.doi.org/10.1099/mic.0.000395. (Journal Article)
• Coray DS., Wheeler NE., Heinemann JA. and Gardner PP. (2017) Why so narrow: Distribution of anti-sense regulated, type I toxin-antitoxin systems compared with type II and type III systems. RNA Biology 14(3): 275-280. http://dx.doi.org/10.1080/15476286.2016.1272747. (Journal Article)
• Heinemann JA. (2016) Expert scientific opinion on the status of certain new techniques of genetic modification under Directive 2001/18/EC.Commissioned by Greenpeace. (Report)
• Heinemann JA. (2015) Statement of primary evidence for hearings on GMO provisions in the Auckland Unitary Plan and Whangarei and Far North District Plans.Commissioned by Whangarei and Auckland District Councils. (Report)
• Heinemann JA. (2015) Statement of rebuttal evidence for hearings on GMO provisions in the Auckland Unitary Plan and Whangarei and Far North District Plans.Commissioned by Whangarei and Auckland District Councils. https://hearings.aupihp.govt.nz/hearings. (Report)
• Heinemann JA., Agapito-Tenfen SZ. and Kurenbach B. (2015) Response to "A 28-day oral toxicity evaluation of small interfering RNAs and a long double-stranded RNA targeting vacuolar ATPase in mice.". Regulatory Toxicology and Pharmacology 71(3): 599-600. http://dx.doi.org/10.1016/j.yrtph.2015.02.003. (Journal Article)
• Hilbeck A., Binimelis R., Defarge N., Steinbrecher R., Székács A., Wickson F., Antoniou M., Bereano PL., Clark EA. and Hansen M. (2015) No scientific consensus on GMO safety. Environmental Sciences Europe 27(1) http://dx.doi.org/10.1186/s12302-014-0034-1. (Journal Article)
• Kurenbach B., Marjoshi D., Amábile-Cuevas CF., Ferguson GC., Godsoe W., Gibson P. and Heinemann JA. (2015) Sublethal exposure to commercial formulations of the herbicides dicamba, 2,4-dichlorophenoxyacetic acid, and Glyphosate cause changes in antibiotic susceptibility in Escherichia coli and Salmonella enterica serovar Typhimurium. mBio 6(2) http://dx.doi.org/10.1128/mBio.00009-15. (Journal Article)
• Heinemann JA., Massaro M., Coray DS. and Agapito-Tenfen SZ. (2014) Reply to comment on sustainability and innovation in staple crop production in the US Midwest. International Journal of Agricultural Sustainability http://dx.doi.org/10.1080/14735903.2014.939843. (Journal Article)
• Heinemann JA., Massaro M., Coray DS., Agapito-Tenfen SZ. and Wen JD. (2014) Sustainability and innovation in staple crop production in the US Midwest. International Journal of Agricultural Sustainability 12(1): 71-88. http://dx.doi.org/10.1080/14735903.2013.806408. (Journal Article)
• Heinemann JA. (2013) Affidavit to the High Court of New Zealand (1 of 2) for case: The Sustainability Council of New Zealand Trust v The Environmental Protection Authority.High Court of New Zealand. 17pp. (Report)
• Heinemann JA. (2013) Affidavit to the High Court of New Zealand (2 of 2) for case: The Sustainability Council of New Zealand Trust v The Environmental Protection Authority.High Court of New Zealand. 22pp. (Report)
• Heinemann JA. (2013) Food and chemical toxicology.. Food and Chemical Toxicology 53: 442. (Journal Article)
• Heinemann JA. (2013) Keep the pause button on GM pressed. The Hindu. [Newspaper]. (Other)
• Heinemann JA. (2013) The truth about GMOs. Boston Review. (Discussion/Working Paper)
• Heinemann JA. (2013) Genetic engineering and biotechnology for food security and for climate change mitigation and adaptation: potential and risks. In United Nations (Ed.), Wake Up Before It Is Too Late - Make Agriculture Truly Sustainable Now For Food Security In A Changing Climate: 203-218. New York: United Nations Conference on Trade and Development. http://unctad.org/en/PublicationsLibrary/ditcted2012d3_en.pdf. (Chapter)
• Heinemann JA., Agapito-Tenfen SZ. and Carman JA. (2013) A comparative evaluation of the regulation of GM crops or products containing dsRNA and suggested improvements to risk assessments. Environment International 55: 43-55. http://dx.doi.org/10.1016/j.envint.2013.02.010. (Journal Article)
• Hilbeck A., Lebrecht T., Vogel R., Heinemann JA. and Binimelis R. (2013) Farmer's choice of seeds in four EU countries under different levels of GM crop adoption. Environmental Sciences Europe 25(1) http://dx.doi.org/10.1186/2190-4715-25-12. (Journal Article)
• Quist D., Heinemann JA., Myhr AI., Aslaksen I. and Funtowicz S. (2013) Hungry for innovation in a world of food: Pathways from GM crops to agroecology. In Gee D (Ed.), Late Lessons from Early Warnings (2nd ed.): 29. Cophenhagen: EEA. (Chapter)
• Bigwood T., Hudson JA., Cooney J., McIntyre L., Billington C., Heinemann JA. and Wall F. (2012) Inhibition of Listeria monocytogenes by Enterococcus mundtii isolated from soil. Food Microbiology 32(2): 354-360. http://dx.doi.org/10.1016/j.fm.2012.07.015. (Journal Article)
• Coray DS., Heinemann JA., Tyrer PC. and Keenan JI. (2012) Human lactoferrin increases Helicobacter pylori internalisation into AGS cells. World Journal of Microbiology and Biotechnology 28(5): 1871-1880. http://dx.doi.org/10.1007/s11274-011-0984-z. (Journal Article)
• Heinemann JA. (2012) Affidavit.Greenpeace. (Report)
• Heinemann JA. (2012) Briefing on Suggestions on How to Apply International Safety Testing Guidelines for Genetically Modified Organisms.Commissioned by Supreme Court of India. (Report)
• Heinemann JA. (2012) Evaluation of risks from creation of novel RNA molecules in genetically engineered wheat plants and recommendations for risk assessment.Safe Food Institute, Australia. Commissioned by Safe Food Institute. 16. http://www.inbi.canterbury.ac.nz/. (Report)
• Heinemann JA. (2012) Should NZ Grow GM Crops? New Zealand Herald. (Discussion/Working Paper)
• Heinemann JA. (2012) Suggestions on how to apply international safety testing guidelines for genetically modified organisms.Centre for Integrated Research in Biosafety (INBI). 33pp. (Report)
• Heinemann JA., Dobson R. and Walker S. (2012) Serological evaluation of sheep.Confidential. 5pp. (Report)
• Rankin DJ., Turner LA., Heinemann JA. and Brown SP. (2012) The coevolution of toxin and antitoxin genes drives the dynamics of bacterial addiction complexes and intragenomic conflict. Proceedings of the Royal Society B: Biological Sciences 279(1743): 3706-3715. http://dx.doi.org/10.1098/rspb.2012.0942. (Journal Article)
• Romero-Suarez S., Jordan B. and Heinemann JA. (2012) Isolation and characterization of bacteriophages infecting Xanthomonas arboricola pv. juglandis, the causal agent of walnut blight disease. World Journal of Microbiology and Biotechnology 28(5): 1917-1927. http://dx.doi.org/10.1007/s11274-011-0992-z. (Journal Article)
• Bigot B., Lee WJ., McIntyre L., Wilson T., Hudson JA., Billington C. and Heinemann JA. (2011) Control of Listeria monocytogenes growth in a ready-to-eat poultry product using a bacteriophage. Food Microbiology 28(8): 1448-1452. http://dx.doi.org/10.1016/j.fm.2011.07.001. (Journal Article)
• Heinemann J. and Wickson F. (2011) Genetic modification: Strong opinions continue to fuel the GM foods debate locally as well as globally. Food Australia 63(12): 14-17. (Journal Article)
• Heinemann JA. (2011) How the world looks to a gene. Monte Verita, Switzerland: Understanding and managing ecological novelty: Towards an integrative framework of the socio-ecological risks of novel organisms, 4-9 Sep 2011 (Conference Contribution - Other)
• Heinemann JA. (2011) Potential and risks of genetic engineering and biotechnology related to assuring food security under the challenges of climate change mitigation and adaptation.Commissioned by United Nations Conference on Trade and Development. (Report)
• Heinemann JA., Kurenbach B. and Bleyendaal N. (2011) Evaluation of horizontal gene transfer monitoring experiments conducted in New Zealand between 2004 and 2009. Journal of Organic Systems 6(1): 3-19. (Journal Article)
• Heinemann JA., Kurenbach B. and Quist D. (2011) Molecular profiling - a tool for addressing emerging gaps in the comparative risk assessment of GMOs. Environment International 37(7): 1285-1293. http://dx.doi.org/10.1016/j.envint.2011.05.006. (Journal Article)
• Cooper TF., Paixão T. and Heinemann JA. (2010) Within-host competition selects for plasmidencoded toxin-antitoxin systems. Proceedings of the Royal Society B: Biological Sciences 277(1697): 3149-3155. http://dx.doi.org/10.1098/rspb.2010.0831. (Journal Article)
• Heinemann J. (2010) Are some scientists just taking the cis out of genetic engineering? Pt I. Sciblog.co.nz (NZ Royal Society). (Other)
• Heinemann J. (2010) Are some scientists just taking the cis out of genetic engineering? Pt II. Sciblog.co.nz (NZ Royal Society). (Other)
• Heinemann J. (2010) Is genetic engineering just like breeding? Sciblog.co.nz (NZ Royal Society). (Other)
• Heinemann JA. (2010) Agriculture at a crossroads - beyond IAASTD. Zurich, Switzerland: Tropentag 2010. World food system: A contribution from Europe, 14-16 Sep 2010 (Conference Contribution - Other)
• Heinemann JA. (2010) Summary of analysis of dossier from Mahyco et al. in support of their claims of safety of fruit and shoot borer tolerant brinjal.Third World Network. Commissioned by Third World Network. (Report)
• Calvo G., Fonte M., Heinemann J., Ishii-Eiteman M., Jiggins J., Leakey R. and Plencovich C. (2009) Towards sustainable agriculture. UNESCO-SCOPE-UNEP Policy Brief Series Policy Brief 8: 6pp. Paris: UNESCO, SCOPE, UNEP. (Other)
• Gurib-Fakim A., Smith L., Acikgoz N., Avato P., Bossio D., Ebi K., Gonçalves A., Heinemann JA., Herrmann TM. and Padgham J. (2009) Options to Enhance the Impact of AKST on Development and Sustainability Goals. In McIntyre BD; Herren HR; Wakhungu J; Watson RT (Ed.), Agriculture at a Crossroads: International Assessment of Agricultural Knowledge, Science and Technology for Development Global Report: 377-440. Washington D.C.: Island Press. (Chapter)
• Heinemann J. (2009) Report on animals exposed to GM ingredients in animal feed.Commissioned by Commerce Commission of New Zealand. 49pp. (Report)
• Heinemann J., Abate T., Hilbeck A. and Murray D. (2009) Biotechnology in 'Agriculture at a Crossroads: IAASTD Synthesis Report'.Commissioned by FAO, GEF, UNDP, UNEP, UNESCO, the World Bank, WHO. 40-45. (Report)
• Heinemann JA. (2009) Biotechnology supervised by Darwin. Melbourne, Australia: Evolution: The experience, 8-13 Feb 2009 (Conference Contribution - Other)
• Heinemann JA. (2009) Bt brinjal part one and Bt brinjal part two.Commissioned by Minister for the Environment, India. (Report)
• Heinemann JA. (2009) Hope not Hype. The future of agriculture guided by the International Assessment of Agricultural Knowledge, Science and Technology for Development. Penang: Third World Network. 160pp. (Authored Book)
• Heinemann JA. (2009) More on Bt Cotton. Economic and Political Weekly 44(40) (Journal Article)
• Heinemann JA., Coray D. and Keenan J. (2009) Intra- and inter-species horizontal gene transfer inside human tissue culture cells. Christchurch, New Zealand: ComBio 2009, 6-10 Dec 2009 (Conference Contribution - Other)
• Bigwood T., Hudson JA., Billington C., Carey-Smith GV. and Heinemann JA. (2008) Phage inactivation of foodborne pathogens on cooked and raw meat. Food Microbiology 25(2): 400-406. http://dx.doi.org/10.1016/j.fm.2007.11.003. (Journal Article)
• Filutowicz M., Burgess R., Gamelli RL., Heinemann JA., Kurenbach B., Rakowski SA. and Shankar R. (2008) Bacterial conjugation-based antimicrobial agents. Plasmid 60(1): 38-44. http://dx.doi.org/10.1016/j.plasmid.2008.03.004. (Journal Article)
• Heinemann J. (2008) Desert grain. Ecologist -London and Wadebridge then Slinfold then London- 38(9): 22-24. (Other)
• Heinemann JA. (2008) MOP4 side event. Bonn, Germany. (Oral Presentation)
• Heinemann JA. (2008) Emerging GMOs and Biosafety Considerations. Beijing, China: International Biosafety Forum - Workshop 3, 1 Sep 2008 (Conference Contribution - Other)
• Heinemann JA. (2008) Gene flow: Assessing environmental risks and identifying biosafety research need. Beijing, China: International Biosafety Forum - Workshop 3, 24-26 Sep 2008 (Conference Contribution - Other)
• Heinemann JA. and Kurenbach B. (2008) Special threats to the agroecosystem from the combination of genetically modified crops and glyphosate. : 8pp. Third World Network. [Briefing Paper]. (Other)
• Heinemann JA., Kurenbach B., Feng S. and Ferguson G. (2008) The molecular biology of the biggest and the smallest human ecosystems: from the size of a cell to a planet. Dartmouth University, NH, USA. (Oral Presentation)
• Kiers ET., Leakey RRB., Izac AM., Heinemann JA., Rosenthal E., Nathan D. and Jiggins J. (2008) Ecology: Agriculture at a crossroads. The Scientific monthly 320(5874): 320-321. http://dx.doi.org/10.1126/science.1158390. (Journal Article)
• Heinemann JA. (2007) A typology of the effects of (trans)gene flow on the conservation and sustainable use of genetic resources.Commissioned by Commission on Genetic Resources for Food and Agriculture. 100pp. (Report)
• Heinemann JA. (2007) Letter to the editor. Environmental and Planning Law Journal 24(3): 157-160. (Journal Article)
• Heinemann JA. and Goven J. (2007) The Social Context of Drug Discovery and Safety Testing. In Amábile-Cuevas CF (Ed.), Antimicrobial Resistance in Bacteria: 179-196. Norfolk: Horizon Bioscience. (Chapter)
• Silby MW., Ferguson GC., Billington C. and Heinemann JA. (2007) Localization of the plasmid-encoded proteins TraI and MobA in eukaryotic cells. Plasmid 57(2): 118-130. http://dx.doi.org/10.1016/j.plasmid.2006.08.006. (Journal Article)
• Tsuei AC., Carey-Smith GV., Hudson JA., Billington C. and Heinemann JA. (2007) Prevalence and numbers of coliphages and Campylobacter jejuni bacteriophages in New Zealand foods. International Journal of Food Microbiology 116(1): 121-125. http://dx.doi.org/10.1016/j.ijfoodmicro.2006.12.028. (Journal Article)
• Carey-Smith GV., Billington C., Cornelius AJ., Hudson JA. and Heinemann JA. (2006) Isolation and characterization of bacteriophages infecting Salmonella spp.. FEMS Microbiology Letters 258(2): 182-186. http://dx.doi.org/10.1111/j.1574-6968.2006.00217.x. (Journal Article)
• Chowdhury PR. and Heinemann JA. (2006) The general secretory pathway of Burkholderia gladioli pv. agaricicola BG164R is necessary for cavity disease in white button mushrooms. Applied and Environmental Microbiology 72(5): 3558-3565. http://dx.doi.org/10.1128/AEM.72.5.3558-3565.2006. (Journal Article)
• Cretenet M., Goven J., Heinemann JA., Moore B. and Rodriguez-Beltran C. (2006) Submission on the DAR for Application A549 Food Derived from High-Lysine Corm LY038: to permit the use in food of high-lysine corn. : 100pp. http://www.inbi.canterbury.ac.nz/. (Other)
• Cretenet M., Goven JA., Heinemann JA., Moore B. and Rodriguez-Beltran C. (2006) Submission to Food Standards Australia/New Zealand on A549 High Lysine Corn Draft Assessment Recommendation. : 99. (Other)
• Heineman JA. and Terry S. (2006) Submission to Codex Alimentarius Commission on Recombinant DNA Plants Modified for Nutritional or Health Benefits. : 4. (Other)
• Heinemann JA. (2006) Submission on the IAR for APPLICATION A580 FOOD DERIVED FROM AMYLASE-MODIFIED CORN LINE 3272. : 2. (Other)
• Heinemann JA., Rosén H., Savill M., Burgos-Caraballo S. and Toranzos GA. (2006) Environment arrays: A possible approach for predicting changes in waterborne bacterial disease potential. Environmental Science and Technology 40(23): 7150-7156. http://dx.doi.org/10.1021/es060331x. (Journal Article)
• Willms AR., Roughan PD. and Heinemann JA. (2006) Static recipient cells as reservoirs of antibiotic resistance during antibiotic therapy. Theoretical Population Biology 70(4): 436-451. http://dx.doi.org/10.1016/j.tpb.2006.04.001. (Journal Article)
• Cooper TF. and Heinemann JA. (2005) Selection for plasmid post-segregational killing depends on multiple infection: Evidence for the selection of more virulent parasites through parasite-level competition. Proceedings of the Royal Society B: Biological Sciences 272(1561): 403-410. http://dx.doi.org/10.1098/rspb.2004.2921. (Journal Article)
• Heinemann JA. and Bungard RA. (2005) Horizontal Gene Transfer. In Meyers RA (Ed.), Encyclopedia of Molecular Cell Biology and Molecular Medicine, Volume 6: 223-243. Weinheim: Wiley-VCH. (Chapter)
• Heinemann JA. and Traavik T. (2005) Erratum: Problems in monitoring horizontal gene transfer in field trials of transgenic plants (Nature Biotechnology (2005) 22 (1105-1109)). Nature Biotechnology 23(4): 488. (Journal Article)
• Heinemann JA., Goven J., Gerrard JA., Moore B., Beltran C., Cretenet M., Bohn T. and Traavik T. (2005) Submission to Food Standards Australia/New Zealand on A549 High Lysine Corn. http://www.nzige.canterbury.ac.nz/. (Other)
• Moore B., Goven J. and Heinemann J. (2005) Terminator vista [1]. New Scientist 185(2492): 30. (Other)
• Amábile-Cuevas CF. and Heinemann JA. (2004) Shooting the messenger of antibiotic resistance: Plasmid elimination as a potential counter-evolutionary tactic. Drug Discovery Today 9(11): 465-467. http://dx.doi.org/10.1016/S1359-6446(03)02989-1. (Journal Article)
• Anker P., Zajac V., Lyautey J., Lederrey C., Dunand C., Lefort F., Mulcahy H., Heinemann J. and Stroun M. (2004) Transcession of DNA from bacteria to human cells in culture: A possible role in oncogenesis. Annals of the New York Academy of Sciences 1022: 195-201. http://dx.doi.org/10.1196/annals.1318.030. (Journal Article)
• Bland MV., Ismail S., Heinemann JA. and Keenan JI. (2004) The action of bismuth against Helicobacter pylori mimics but is not caused by intracellular iron deprivation. Antimicrobial Agents and Chemotherapy 48(6): 1983-1988. http://dx.doi.org/10.1128/AAC.48.6.1983-1988.2004. (Journal Article)
• Davison J., Heinemann JA., Traavik T., Nielsen KM. and Townsend J. (2004) Monitoring horizontal gene transfer [3] (multiple letters). Nature Biotechnology 22(11): 1349-1350. (Journal Article)
• Heinemann JA. (2004) Scientific advice received by the Committee on PCR and the Lot 9114 test results.Commissioned by Local Government and Environment Select Committee. (Report)
• Heinemann JA. (2004) Submission to Food Standards Australia New Zealand on application A524 Food Derived from Herbicide-Tolerant Wheat MON 71800. (Other)
• Heinemann JA. (2004) Challenges to regulating the industrial gene: Views inspired by the New Zealand experience. In Dew K; Fitzgerald R (Ed.), Challenging Science: Science and Society Issues in New Zealand (1st ed.): 240-257. Palmerston North: Dunmore Press. (Chapter)
• Heinemann JA. (2004) Horizontal transfer of genes between microorganisms. In Lederberg J (Ed.), Desk Encyclopedia of Microbiology: 580-588. London: Elsevier, Ltd. (Chapter)
• Heinemann JA. and Billington C. (2004) How do genomes emerge from genes? ASM News- American Society for Microbiology 70(10): 464-471. (Journal Article)
• Heinemann JA. and Goven J. (2004) Submission to the Ministry of Foreign Affairs and Trade on the question of ratifying the Cartagena Protocol on Biosafety. (Other)
• Heinemann JA. and Traavik T. (2004) Problems in monitoring horizontal gene transfer in field trials of transgenic plants. Nature Biotechnology 22(9): 1105-1109. http://dx.doi.org/10.1038/nbt1009. (Journal Article)
• Heinemann JA. and Traavik T. (2004) Reply to Monitoring horizontal gene transfer from transgenic plants to bacteria. Nature Biotechnology 22: 1349-1350. (Journal Article)
• Heinemann JA. (2003) Evaluation of scientific data supplied to the Parliamentary Local Government and Environment Select Committee investigating "Corngate".Commissioned by Local Government and Environment Select Committee. (Report)
• Heinemann JA. (2003) Is horizontal gene transfer the Cinderella of genetics? NZ BioScience 12(2): 18-20. (Journal Article)
• Heinemann JA. (2003) To the Education and Science Committee call for submissions on the New Organisms and Other Matters Bill. (Other)
• Heinemann JA. and Silby M. (2003) Horizontal gene transfer and the selection of antibiotic resistance. In Amábile-Cuevas CF (Ed.), Multiple Drug Resistant Bacteria: 161-178. San Diego: Horizon Scientific Press. (Chapter)
• Heinemann JA., Buchanan LN., Silby MW., Ferguson GC. and Billington C. (2003) (2003, Sept). "Physiology of Interkingdom Gene Transfer". ICAAC: Chicago, USA. Chicago, USA: ICAAC. (Oral Presentation)
• Billington C., Giddens S., Bean D. and Heinemann JA. (2002) Effects of stress mutation on barriers to interkingdom horizontal gene transfer. Bergen Norway: BAGECO-7 Symposium on bacterial genetics and ecology, 1 Jun 2002 (Conference Contribution - Other)
• Billington C., Silby MW. and Heinemann JA. (2002) Conjugative proteins TraI and MobA localise to yeast and human nuclei. Queenstown, New Zealand: Queenstown International Molecular Biology Meeting, 1 Sep 2002 (Conference Contribution - Other)
• Ferguson C. and Heinemann JA. (2002) Intracellular Mating. Queenstown, New Zealand: Queenstown International Molecular Biology Meeting, 1 Sep 2002 (Conference Contribution - Other)
• Ferguson GC. and Heinemann JA. (2002) Recent history of trans-kingdom conjugation. In Syvanen M; Kado CI (Ed.), Horizontal Gene Transfer (2nd ed.): 3-17. London and San Diego: Academic Press. (Chapter)
• Ferguson GC., Heinemann JA. and Kennedy MA. (2002) Gene transfer between Salmonella enterica serovar Typhimurium inside epithelial cells. Journal of Bacteriology 184(8): 2235-2242. http://dx.doi.org/10.1128/JB.184.8.2235-2242.2002. (Journal Article)
• Ferguson GC., Heinemann JA. and Kennedy MA. (2002) Gene Transfer between Salmonella enterica Serovar Typhimurium inside Epithelial Cells. Journal of Bacteriology 1848(April 15): 2235-2242. (Journal Article)
• Heinemann JA. (2002) (2002, November). "Up to the minute status of horizontal gene transfer". NZMS: Christchurch, NZ. Christchurch, NZ: NZMS, 01 Jan 2001. (Oral Presentation)
• Heinemann JA. (2002) Are DNA sequences too simple as intellectual property? Reply to Gene patents: are they socially acceptable monopolies - essential for drug discovery? Drug Discovery Today 7: 23-24. (Journal Article)
• Heinemann JA. (2002) Bacterial Resistance to Antimicrobials (Review). Drug Discovery Today 714: 758. (Journal Article)
• Heinemann JA. (2002) Genetic scientists under siege: What next? NZ Microbiology 6: 15-17. (Journal Article)
• Heinemann JA. (2002) Submission To the Finance Select Committee on the Hazardous Substances and New Organisms (Genetically Modified Organisms) Amendment Bill/Inquiry. (Other)
• Heinemann JA. (2002) Submission To the Ministry of Science Research and Technology on the Public Discussion Paper “New Zealand Biotechnology Strategy”. http://www.nzige.canterbury.ac.nz/. (Other)
• Heinemann JA. (2002) Submission to the New Zealand Environmental Risk Management Authority on AgResearch Application GMD01194. http://www.nzige.canterbury.ac.nz/. (Other)
• Newman AL., Billington C. and Heinemann JA. (2002) Protein localisation to mitochondria. Queenstown, New Zealand: Queenstown International Molecular Biology Meeting, 1 Sep 2002 (Conference Contribution - Other)
• Siefkes-Boer HJ., Heinemann JA. and Kennedy MA. (2002) Bacterial conjugation using modified transfer proteins as testing method for mediating DNA transfer to yeast mitochondria. Queenstown, New Zealand: Queenstown International Molecular Biology Meeting, 1 Sep 2002 (Conference Contribution - Other)
• Weld R. and Heinemann JA. (2002) Antibiotic-induced pseudolysogeny. Bergen, Norway: Bageco-6, 6th International Congress on Bacterial Genetics and Ecology, 1 Jan 2002 (Conference Contribution - Other)
• Weld R. and Heinemann JA. (2002) Horizontal transfer of proteins between species: part of the big picture or just a genetic vignette? In Kado CI; Syvanen M (Ed.), Horizontal Gene Transfer (2nd ed.): 51-62. London and San Diego: Academic Press. (Chapter)
• Weld R., Heinemann J. and Eady C. (2002) Transient GFP expression in Nicotiana plumbaginifolia suspension cells following co-cultivation with Agrobacterium tumefaciens: the role of gene silencing, cell death and T-DNA loss. Plant Mol. Biol 45: 377-385. (Journal Article)
• Weld RJ., Bicknell RA., Heinemann JA. and Eady CC. (2002) Ds transposition mediated by transient transposase expression in Heiracium aurantiacum. Plant Cell, Tissue and Organ Culture 69(1): 45-54. http://dx.doi.org/10.1023/A:1015017218982. (Journal Article)
• Heinemann JA. (2001) (2001, January). "How antibiotics cause antibiotic resistance". International Symposium on Drug Discovery and Development: Bangalore, India. Bangalore, India: International Symposium on Drug Discovery and Development, 01 Sep 1999. (Oral Presentation)
• Heinemann JA. (2001) Alternative vs. conventional medicines: a clash of culture or of science? N.Z. Coll. Midwiv. J 24: 23-25. (Journal Article)
• Heinemann JA. (2001) The fate of students within our hands. N.Z. Educ. Rev Jan 12: 7. (Journal Article)
• Weld R., Heinemann J. and Eady C. (2001) Transient GFP expression in Nicotiana plumbaginifolia suspension cells: The role of gene silencing, cell death and T-DNA loss. Plant Molecular Biology 45(4): 377-385. http://dx.doi.org/10.1023/A:1010798625203. (Journal Article)
• Weld RJ., Downs C., Butts C. and Heinemann JA. (2001) Optimising Animal Health and Growth with Phage. In PaMS client confidential report 01-1, Commissioned by Leiner Davis Gelatin NZ. (Report)
• Adams B. and Heinemann JA. (2000) Antibacterial viruses and antibacterial agents: a one-two punch? N.Z. Medical J 113: 107. (Journal Article)
• Cooper TF. and Heinemann JA. (2000) Postsegregational killing does not increase plasmid stability but acts to mediate the exclusion of competing plasmids. Proceedings of the National Academy of Sciences 97(23): 12643-12648. http://dx.doi.org/10.1073/pnas.220077897. (Journal Article)
• Cooper TF. and Heinemann JA. (2000) Transfer of conjugative plasmids and bacteriophage λ occurs in the presence of antibiotics that prevent de novo gene expression. Plasmid 43(2): 171-175. http://dx.doi.org/10.1006/plas.1999.1450. (Journal Article)
• Ferguson GC., Heinemann JA. and Kennedy MA. (2000) Gene transfer between Salmonella typhimurium inside cultured human cells. Cairns, Australia: Joint Australian/New Zealand Microbiology Society Meeting, 1 Jul 2000 (Conference Contribution - Other)
• Gunn A. and Heinemann JA. (2000) Stealth antibiotic resistance. N.Z. Medical J 113: 107. (Journal Article)
• Heinemann JA. (2000) Complex effects of DNA gyrase inhibitors on bacterial conjugation. Journal of biochemistry, molecular biology, and biophysics : JBMBB : the official journal of the Federation of Asian and Oceanian Biochemists and Molecular Biologists (FAOBMB) 4(3): 165-177. (Journal Article)
• Heinemann JA. (2000) How can we build a 'knowledge economy' if research is handcuffed? Nature: New biology 406(6791): 13. (Journal Article)
• Heinemann JA. and Roughan PD. (2000) New hypotheses on the material nature of horizontally mobile genes. Annals of the New York Academy of Sciences 906: 169-186. (Journal Article)
• Weld R. and Heinemann JA. (2000) Antibiotic-induced pseudolysogeny: Implications for Antibiotic/Phage Combination Therapy. Montreal, Canada: Millenial Phage Biology Meeting, 1 Jan 2000 (Conference Contribution - Other)
• Cooper TF. and Heinemann JA. (1999) Plasmid post segregational killing: benefitting from the death of wayward daughters. Queenstown, New Zealand: Queenstown International Molecular Biology Meeting, 1 Aug 1999 (Conference Contribution - Other)
• Heinemann JA. (1999) "The genes crawl in the genes crawl out, into your stomach and out your mouth". Circulating Nucleic Acids in Plasma/Serum: Anice, France. Anice, France: Circulating Nucleic Acids in Plasma/Serum, 01 Aug 1999. (Oral Presentation)
• Heinemann JA. (1999) Looking sideways at the evolution of replicons. In Syvanen M; Kado C (Ed.), Horizontal Gene Transfer: 11-24. London: International Thomson Publishing. (Chapter)
• Heinemann JA., Cooper TF. and Ferguson GC. (1999) (1999, August). "One small pop for prokaryotes, one big bang for medicine". Queenstown International Molecular Biology Meeting: Queenstown, NZ. Queenstown NZ: Queenstown International Molecular Biology Meeting, 01 May 2000. (Oral Presentation)
• Weld RJ., Heinemann JA. and Eady CC. (1999) Transient gene expression following co-cultivation with Agrobacterium tumefaciens. Rotorua, New Zealand: Thirteenth Biennial Meeting of the New Zealand Branch of the International Association for Plant Tissue Culture, 1 Jan 1999 (Conference Contribution - Other)
• Heinemann JA. (1998) Superbugs: by killing them we have made them stronger. N.Z. Sci. Monthly 9: 6-8. (Journal Article)
• Weld R., Heinemann JA., Bicknell RA. and Eady CC. (1998) Transient transposase expression in Hieracium aurantiacum following co-cultivation with Agrobacterium tumefaciens. Queenstown, New Zealand: Eighth Annual Queenstown Molecular Biology Meeting, 1 Jan 1998 (Conference Contribution - Other)
• Heinemann JA. (1997) Assessing the risk of interkingdom DNA transfer. Nordic Seminar an Antibiotic Resistance Marker Genes and Transgenic Plants: 17-28. Oslo: Norwegian Biotechnology Board. (Chapter)
• Singh KK. and Heinemann JA. (1997) Yeast plasmids.. : 113-130. (Chapter)
• Heinemann JA. (1996) MD's and PhD's: Differences in pay. ASM News- American Society for Microbiology 62(5): 234-235. (Journal Article)
• Heinemann JA., Scott HE. and Williams M. (1996) Doing the conjugative two-step: Evidence of recipient autonomy in retrotransfer. Genetics 143(3): 1425-1435. (Journal Article)
• Heinemann JA., Ankenbauer RG. and Horecka J. (1994) Isolation of a conditional suppressor of leucine auxotrophy in Saccharomyces cerevisiae. Microbiology 140(1): 145-152. (Journal Article)
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• Heinemann JA. and Ankenbauer RG. (1993) Retrotransfer of IncP piasmid R751 from Escherichia coli maxicells: evidence for the genetic sufficiency of self‐transferable plasmids for bacterial conjugation. Microbiological sciences 10(1): 57-62. http://dx.doi.org/10.1111/j.1365-2958.1993.tb00903.x. (Journal Article)
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• Heinemann JA. and Sprague GF. (1989) Bacterial conjugative plasmids mobilize DNA transfer between bacteria and yeast. Nature: New biology 340(6230): 205-209. (Journal Article) | {
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-3,531,881,685,793,948,700 | @article {Shchur724815, author = {Vladimir Shchur and Jesper Svedberg and Paloma Medina and Russ Corbett-Detig and RASMUS Nielsen}, title = {On the distribution of tract lengths during adaptive introgression}, elocation-id = {724815}, year = {2019}, doi = {10.1101/724815}, publisher = {Cold Spring Harbor Laboratory}, abstract = {Admixture is increasingly being recognized as an important factor in evolutionary genetics. The distribution of genomic admixture tracts, and the resulting effects on admixture linkage disequilibrium, can be used to date the timing of admixture between species or populations. However, the theory used for such prediction assumes selective neutrality despite the fact that many famous examples of admixture involve natural selection acting for or against admixture. In this paper, we investigate the effects of positive selection on the distribution of tract lengths. We develop a theoretical framework that relies on approximating the trajectory of the selected allele using a logistic function. By numerically calculating the expected allele trajectory, we also show that the approach can be extended to cases where the logistic approximation is poor due to the effects of genetic drift. Using simulations, we show that the model is highly accurate under most scenarios. We use the model to show that positive selection on average will tend to increase the admixture tract length. However, perhaps counter-intuitively, conditional on the allele frequency at the time of sampling, positive selection will actually produce shorter expected tract lengths. We discuss the consequences of our results in interpreting the timing of the introgression of EPAS1 from Denisovans into the ancestors of Tibetans.}, URL = {https://www.biorxiv.org/content/early/2019/08/05/724815}, eprint = {https://www.biorxiv.org/content/early/2019/08/05/724815.full.pdf}, journal = {bioRxiv} } | {
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7,489,940,850,307,226,000 | Iodine and Hydrogen Ions
To make a complex topic simple – iodine is a metallic element that can be electrically active and it helps stabilize water and hydrogen ions in a electrically active form. The combination of iodine and water in ionic form can create changes in protein structure more rapidly than regular enzymatic chemical reactions. The combination can effect DNA and mitochondria which helps explain why iodine is so important to infant development and energy levels throughout life.
Iodine is known as the mineral used in the thyroid hormone which is essential for energy metabolism but it is also essential for mitochondria which produce energy within every cell.
For more details: Tensegrity #6: Hydrogen Bonding Networks in Water, by Dr. Jack Kruse, a neurosurgeon, jackkruse.com.
Iodine & Proton Tunneling in Tadpole Development:
• Providing iodine allows normal development of frog tadpoles even when they are missing normal pituitary or thyroid gland function which typically would disrupt the loss of their tail and growth of legs. (Accelerated Metamorphosis of Frog Tadpoles by Injections of Extract of Anterior Lobe Pituitary Gland and the Administration of Iodinepdf)
• A video with a simple explanation of proton tunneling (positive hydrogen ions are a single positive proton, the negative electron likely remains with the oxygen atom of a water molecule), and the role proton tunneling may help a tadpole change into a four legged frog is available in a video: How do tadpoles change into frogs: The secrets of quantum physics. Spark.
• Early stages of human development is somewhat similar to the changes seen in a frog tadpole. Between weeks four to seven of human fetal development the fertilized egg changes from a sphere shaped ball of cells into a tadpole type shape and then eventually into more of a human infant shape. (fetal development)
• Early miscarriages in human pregnancy may be more of a risk if the woman is low in iodine levels. (Iodine status in women after early miscarriages in the Czech Republic, endocrine-abstracts.org)
• Apathy, depression, slightly or significantly reduced cognitive skills, feeling cold in normal room temperatures, constipation, and sparse hair growth may all be symptoms of iodine deficiency in addition to increased risk for miscarriage in early pregnancy. Food sources and symptoms of deficiency for iodine and selenium are available here: Iodine & Thyroid, effectivecare.info)
Humans need iodine, we are water based creatures, 60-70% water, and it is electrically stabilized and made more chemically efficient by iodine. We grow rapidly during infancy and childhood however we continue to perform rapid electrical reactions in all of our mitochondria in all of our cells, every day of our lives. Loss of mitochondria function has been linked to many chronic illnesses and with aging.
We need iodine because the water within our brain cells and other cells need iodine and the hydrogen ion rich plasma of our mitochondria need iodine. Quantum proton tunneling saves energy, – it is how the sun works too.
/Disclaimer: This information is provided for educational purposes within the guidelines of fair use. While I am a Registered Dietitian this information is not intended to provide individual health guidance. Please see a health professional for individual health care purposes./ | {
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8,162,938,948,873,233,000 | BookDepository.com
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Biosciences on the Internet
$75.42
Explains how to use the Internet to find the information in the field of bioscience. This book shows readers how to access the information they need on the Internet and make the most efficient and effective use of their time online.
Biosciences on the Internet
$75.42
Explains how to use the Internet to find the information in the field of bioscience. This book shows readers how to access the information they need on the Internet and make the...
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Search hundreds of online stores that deliver to Sydney, Brisbane, Melbourne, Canberra, Perth, and all over Australia and find the best offers for Biosciences on the Internet book. Only on ShopMania you can find the lowest Biosciences on the Internet prices available, learn about the latest discounts and compare books deals. Here you can browse through the Biosciences on the Internet photo gallery, find out all about its features and specs and read the product reviews and user comments from our community. | {
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2,180,136,999,633,707,000 | Home » Blog posts » Harmful algal blooms
Tag: Harmful algal blooms
Puget Sound’s growing nutrient problem
First there was “The Blob” that fed last year’s massive algae bloom in the Pacific Ocean. Now there is another monster getting our attention. You might call it “The slime that ate Lake Erie.” The incredible images of Lake Erie’s expanding blanket of green show the familiar effect of nutrient pollution. Nutrients such as phosphorous … | {
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-8,360,123,179,088,261,000 | Arctic post
The conservation of biodiversity in the Arctic was discussed at the meeting of Project Office for Arctic Development (PORA) discussion club. The online conference was attended by the representatives of research centers for northern studies, protected areas, and private biodiversity conservation projects. More than 21,000 species inhabit in the Arctic. Climate change and human activity can cause serious consequences for the biodiversity of the Far North. In this regard, the importance of programs, projects and strategies aimed at conserving the Arctic ecosystem and its species is growing. During the discussion, the ongoing biodiversity conservation projects in the Arctic zone of Russia, their results and prospects, as well as partnership opportunities for their implementation were considered.
“The topic of biodiversity is important for the Arctic Council, where Russia chairs in 2021-2023. During the period of “freezing” the interaction with other member countries in the Council, Russia intends to work on implementing the chairmanship program based on its national interests in the region. Under these conditions, the role of contacts between the Arctic regions of our country is growing, and the need to strengthen cooperation between them on the priority issues of the Arctic agenda, including biodiversity conservation, is updated. In this regard, I would like to highlight the role of research centers, universities, competence centers and public organizations. In this context, the contribution of interregional interaction formats is also in demand, among which we can highlight the activities of the Northern Forum, the Arctic Council observer, the Secretariat of which is located in Yakutsk,” emphasized Nikolay Korchunov, Ambassador-at-Large of the Ministry of Foreign Affairs of the Russian Federation, Chair of the Senior Arctic Officials of the Arctic Council.
In particular, the approved projects of the Northern Forum aimed at developing cooperation in the field of environmental protection and biodiversity conservation were noted, including Environmental Monitoring, Wildlife Management, State of the Environment and Emergency Response. Within the Environment Program, cooperation has been established on such projects as Development of Protected Areas, Brown Bear Populations Management, and Youth Eco-Forum.
Northern Sustainable Development Form, held annually at the end of September, regularly discusses the issues of environmental protection, protected areas development, and biodiversity conservation and enrichment. The annual campaign for the conservation of rare and endangered species has gained popularity and become the NSDF traditional event.
The holding of the PORA discussion club will be the first stage in creating a report in which it is planned to present the best biodiversity conservation practices in the regions of the Russian Arctic, the Russian Chairmanship in the Arctic Council press office explained.
Source: Arctic Post | {
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} | 57 | cf5cd1df0ee2161e1684bdc019357275 |
-6,741,346,503,519,196,000 | Regulation of pyruvate kinase by 6-phosphogluconate in isolated hepatocytes. Academic Article uri icon
abstract
• Isolated liver parenchymal cells from rats fed a 65% sucrose diet for 14 days were incubated in the presence and absence of 10(-6) M glucagon. The pyruvate kinase obtained from homogenates of the glucagon-treated cells displayed and increased Ks 0.5 for phosphoenolpyruvate (P-enolpyruvate), as well as an increased Ka 0.5 for 6-phosphogluconate (6-P-gluconate), compared to pyruvate kinase from untreated cells. Additionally, glucagon treatment decreased the maximal stimulation of pyruvate kinase by 6-P-gluconate by approximately two-thirds and decreased the Hill coefficient value of pyruvate kinase for 6-P-gluconate from 1.76 to 1.56. 6-Aminonicotinamide, an inhibitor of 6-P-gluconate dehydrogenase, increased 6-P-gluconate levels in isolated liver parenchymal cells three- to sevenfold, depending on the substrates present. The flux of P-enolpyruvate through pyruvate kinase was increased from 18 to 40% in these preparations and was highly correlated with the increase in 6-P-gluconate levels. The results suggest that 6-P-gluconate could regulate pyruvate kinase activity in the intact liver parenchymal cell. Furthermore, the activator would be of greatest importance in the lipogenic animal.
published proceedings
• Am J Physiol
author list (cited authors)
• Smith, S. B., & Freedland, R. A.
citation count
• 15
complete list of authors
• Smith, SB||Freedland, RA
publication date
• March 1981 | {
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} | 57 | cf5cd1df0ee2161e1684bdc019357275 |
7,721,781,146,494,650,000 |
Title : Lipid raft microdomain compartmentalization of TC10 is required for insulin signaling and GLUT4 translocation.
Pub. Date : 2001 Aug 20
PMID : 11502760
1 Functional Relationships(s)
Download
Sentence
Compound Name
Protein Name
Organism
1 Recent studies indicate that insulin stimulation of glucose transporter (GLUT)4 translocation requires at least two distinct insulin receptor-mediated signals: one leading to the activation of phosphatidylinositol 3 (PI-3) kinase and the other to the activation of the small GTP binding protein TC10. Guanosine Triphosphate insulin receptor Homo sapiens | {
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5,051,902,848,965,603,000 | Dissertation/Thesis Abstract
Using transcriptomics to identify targets of eyeless and signaling pathways in Drosophila eye development
by Ewongkem, Nfonsam Landry, Ph.D., New Mexico State University, 2012, 253; 3579915
Abstract (Summary)
Tissue-specific transcription factors cooperate with signaling pathways to promote specification, in part by co-regulating transcription. The Drosophila melanogaster Pax6 homolog Eyeless forms a complex, incompletely understood regulatory network with signaling pathways to control eye-specific gene expression. I employed mRNAseq and microarray approaches to identify targets co-regulated by Eyeless and Hedgehog, Decapentaplegic or Notch signals, to further understand the Drosophila eye network. The gene encoding the neprilysin family peptidase ‘Abnormally blistered and morphologically misshapen eyes’ Abams and the Drosophila class II ‘Myosin heavy chain' protein, Mhc, were expressed at higher levels in the eye tissues versus wing tissues, and were highly expressed in eye tissues in response to Ey+N. Thus, both abams and Mhc were predicted to have roles in eye development. Whereas wild type eyes have a regular array of ommatidia interspersed with regularly occurring sensory bristles, using RNA interference (RNAi), I showed that reduction of abams function resulted in smaller eyes that consisted of patches of individual ommatidia surrounded by numerous bristles. Photoreceptor development was disrupted when abams function was reduced in eye precursors. Loss of function analyses and RNAi of Mhc revealed disruptions in the eye lattice and the mis-positioning of photoreceptor nuclei within the eye precursor epithelium. My results suggest that Abams is involved in cell-cell signaling while Mhc regulates cell morphology and/or cell-cell adhesion during eye development. Transcription factor binding site (BS) analyses using computational modeling revealed ≥94 other candidate genes as potential direct targets of Ey or Ey+Hh, Dpp or N. These included genes with already known roles in Drosophila eye development, as well as genes with unknown function, thus providing potential new directions to pursue to further understand the mechanism of interaction between Ey and Hh, Dpp or Notch during Drosophila eye development. Given the similarity between D. melanogaster and vertebrate eye development, further study of Abams and Mhc in Drosophila eye development will provide novel insights into our understanding of eye development in D. melanogaster and humans.
Indexing (document details)
Advisor: Curtiss, Jennifer
Commitee:
School: New Mexico State University
School Location: United States -- New Mexico
Source: DAI-B 75/07(E), Dissertation Abstracts International
Source Type: DISSERTATION
Subjects: Genetics, Bioinformatics, Developmental biology
Keywords: Drosophila melanogaster, Eye development, Eyeless, Paxb, Signaling pathways, Transcriptomics
Publication Number: 3579915
ISBN: 9781303839573
Copyright © 2019 ProQuest LLC. All rights reserved. Terms and Conditions Privacy Policy Cookie Policy
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6,381,694,421,315,299,000 | Isolation and Differentiation of Xenopus Animal Cap Cells
Takashi Ariizumi1, Shuji Takahashi1, Te‐chuan Chan2, Yuzuru Ito3, Tatsuo Michiue1, Makoto Asashima3
1 University of Tokyo, Tokyo, Japan, 2 Japan Science and Technology Agency, Tokyo, Japan, 3 Organ Development Research Laboratory, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan
Publication Name: Current Protocols in Stem Cell Biology
Unit Number: Unit 1D.5
DOI: 10.1002/9780470151808.sc01d05s9
Online Posting Date: April, 2009
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Abstract
Xenopus is used as a model animal for investigating the inductive events and organogenesis that occur during early vertebrate development. Given that they are easy to obtain in high numbers and are relatively large in size, Xenopus embryos are excellent specimens for performing manipulations such as microinjection and microsurgery. The animal cap, which is the area around the animal pole of the blastula, is destined to form the ectoderm during normal development. However, these cells retain pluripotentiality and upon exposure to specific inducers, the animal cap can differentiate into neural, mesodermal, and endodermal tissues. In this sense, the cells of the animal cap are equivalent to mammalian embryonic stem cells. In this unit, the isolation and differentiation of animal cap cells, the so‐called animal cap assay, is described. Useful methods for analyzing the mechanism of animal cap differentiation at the molecular level are also described. Curr. Protoc. Stem Cell Biol. 9:1D.5.1‐1D.5.31. © 2009 by John Wiley & Sons, Inc.
Keywords: animal cap; pluripotency; activin; retinoic acid; induction; organogenesis; Xenopus laevis
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Table of Contents
• Introduction
• Basic Protocol 1: Animal Cap Assay
• Support Protocol 1: Obtaining Fertilized Eggs and Membrane Removal
• Support Protocol 2: In Vitro Fertilization and Rapid Removal of the Jelly Coat
• Support Protocol 3: Preparation of Micromanipulation Tools
• Alternate Protocol 1: Multiple Treatments of Animal Caps for Kidney and Pancreas Induction
• Alternate Protocol 2: Dissociation/Reaggregation of Animal Caps for Heart Induction
• Basic Protocol 2: Microinjection of mRNA for Animal Cap Assay
• Support Protocol 4: Histological Examination of Animal Cap Explants
• Support Protocol 5: RT‐PCR for Analyzing Gene Expression in Animal Cap Cells
• Support Protocol 6: Immunohistochemistry of the Induced Animal Cap Cells
• Support Protocol 7: Whole‐Mount In Situ Hybridization
• Reagents and Solutions
• Commentary
• Literature Cited
• Figures
• Tables
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Materials
Basic Protocol 1: Animal Cap Assay
Materials
• Blastula embryos at developmental stages 8 or 9 (Fig. )
• Steinberg's solution (SS; see recipe)
• 0.1% (w/v) bovine serum albumin in SS (pH 7.4; 0.1% BSA‐SS)
• Test solutions (e.g., such as activin and fibroblast growth factor dissolved in 0.1% BSA‐SS)
• Operating dishes, transfer pipets, and tungsten needles (see protocol 4)
• Low‐adhesion, 24‐well tissue culture plate (Sumitomo Bakelite, cat. no. MS‐80240)
• 20° to 22°C incubator
Support Protocol 1: Obtaining Fertilized Eggs and Membrane Removal
Materials
• hCG dissolved in saline (0.9% NaCl) at a concentration of 2000 U/ml
• Fully mature male and female frogs (Xenopus laevis or X. borealis)
• Steinberg's solution (SS; see recipe)
• Dejelling solution (CSS): 4.5% (w/v) cysteine‐HCl in SS (pH 7.8), prepare fresh
• Sterilized 1‐ml syringe with 26‐G needle
• 10‐ to 15‐liter container
• Thin plastic card
• Large‐bore pipet (∼5‐mm diameter)
• Sterilized beakers (100‐ml)
• Operating dishes, transfer pipets, and two pairs of watchmaker's forceps (see protocol 4)
Support Protocol 2: In Vitro Fertilization and Rapid Removal of the Jelly Coat
Materials
• Fully mature male and hCG‐primed female frogs (Xenopus laevis)
• Anesthetic: 0.1% (w/v) ethyl 3‐aminobenzoate methanesulfonate salt (Tricaine/MS222; Sigma) in tap water (not distilled water)
• DeBoer's solution (DB; see recipe)
• FBS
• Dejelling solution: 1% (w/v) sodium thioglycollate in SS (pH 6.0)
• 1 M NaOH
• Steinberg's solution (SS; see recipe)
• Surgical board
• Forceps
• Scissors
• 60‐mm dishes
• 15‐ml conical tubes
• Pasteur pipets with tipfused by a flame
Support Protocol 3: Preparation of Micromanipulation Tools
Materials
• Late‐blastula embryos at developmental stage 9 (Fig. )
• 0.1% (w/v) BSA in SS, pH 7.4 (0.1% BSA‐SS; see recipe for SS)
• Retinoic acid stock solution (10−2 M): 3 mg all‐trans retinoic acid (Sigma, cat. no. R2625) dissolved in 1 ml DMSO or ethanol
• Test solution 1: 10 µl retinoic acid stock solution plus 990 µl of 10 ng/ml activin in 0.1% BSA‐SS
• Test solution 2: 100 ng/ml activin in 0.1% BSA‐SS
• Test solution 3: 10 µl retinoic acid plus 990 µl of 0.1% BSA‐SS
• Operating dishes, transfer pipets, and two pairs of watchmaker's forceps (see protocol 4)
• Low‐adhesion, 24‐well tissue culture plate (Sumitomo Bakelite, cat. no. MS‐80240)
• 20°C incubator
Alternate Protocol 1: Multiple Treatments of Animal Caps for Kidney and Pancreas Induction
Materials
• Mid‐blastula embryos at developmental stage 8 (Fig. )
• Steinberg's solution (SS; see recipe)
• 0.1% (w/v) bovine serum albumin in SS, pH 7.4 (0.1% BSA‐SS)
• 0.1% (w/v) BSA in Ca2+/Mg2+‐free SS, pH 7.4 (0.1% BSA‐CMFSS)
• Activin solution: 100 ng/ml activin dissolved in 0.1% BSA‐SS
• Operating dishes, transfer pipets, and tungsten needles (see protocol 4)
• Low‐adhesion, 96‐well tissue culture plates with concave (U‐shaped)‐well bottoms (Sumitomo Bakelite, cat. no. MS‐30960)
Alternate Protocol 2: Dissociation/Reaggregation of Animal Caps for Heart Induction
• Synthetic RNA of interest
• 5% (w/v) Ficoll in SS
• In vitro fertilized eggs (see protocol 3)
• Steinberg's solution (SS; see recipe)
• Glass needles
• Microloader tip (Eppendorf, cat. no. 5242 956.003)
• Microinjection capillary (e.g., Narishige G‐1)
• Micromanipulator (e.g., Marzhauser MM33) and support base (Drummond Scientific)
• Microinjector (e.g., PLI‐100/‐90 Pico‐Injector, Harvard/Medical Systems)
• Microscope
• Air compressor (e.g., oil‐free BEBICON, Hitachi or N 2 gas cylinder)
• 60‐mm glass dishes
• Stainless‐steel mesh
• Pasteur pipets
• Hair loop or polished forceps
• 6‐well plates, optional
Basic Protocol 2: Microinjection of mRNA for Animal Cap Assay
Materials
• Animal cap explants
• Steinberg's solution (SS; see recipe)
• Bouin's solution: 15 ml picric acid, 5 ml formalin, 1 ml acetic acid, prepare fresh
• 70% ethanol
• Xylene
• Paraffin
• Delafield's hematoxylin solution (Sigma, cat. no. 03971)
• Eosin Y solution (Sigma, cat. no. HT 110216)
• Canada balsam (Sigma, cat. no. 03984)
• Special basket, consisting of a glass tube (1 cm × 1 cm) with the bottom covered with a nylon mesh (148‐µm grids)
• Paraffin molds
• 56° to 58°C paraffin oven
• Heated wide‐bore pipet
• Microtome
• Glass microscope slides
• 45°C oven
• Coverslips
Support Protocol 4: Histological Examination of Animal Cap Explants
Materials
• Animal caps
• ISOGEN RNA purification reagent (Nippon Gene)
• Chloroform
• 2‐Propanol
• 70% (v/v) ethanol, RNase‐free
• RNase‐free water
• Oligo(dT) 15 (Roche cat. no. 814‐270)
• 0.1 M DTT
• dNTP mixture (2.5 mM each)
• Ribonuclease inhibitor (Takara)
• Superscript II reverse transcriptase and buffer (Invitrogen cat. no. 18064‐022)
• ExTaq polymerase and 10× ExTaq buffer (Takara cat. no. RR001A)
• Specific primer sets for detecting target genes (10 pmol/µl each)
• 200‐µl micropipettor
• 1.5‐ml tubes
• Spectrophotometer
• 1.5‐ml microcentrifuge tubes
• 42°, 60°, and 70°C heating blocks
• 200‐µl PCR tubes
• Thermal cycler
Support Protocol 5: RT‐PCR for Analyzing Gene Expression in Animal Cap Cells
Materials
• Induced animal caps
• Fixation solution: 4% (w/v) paraformaldehyde in PBS (see recipe)
• 25%, 55%, 75%, and 100% methanol
• Bleaching solution (see recipe)
• PBT: 0.1% (v/v) Triton X‐100 in PBS (see recipe for PBS)
• Blocking solution (see recipe)
• Primary antibody
• Secondary antibody, alkaline phosphatase (AP)–conjugated
• AP reaction buffer (see recipe)
• Color solution: 4.5 µg/ml NBT, 3.5 µg/ml BCIP in AP reaction buffer
• Screw‐cap glass vial
• Incline shaker
• Dish
• Aluminum foil
• Fluorescent light source
• Pasteur pipet
Support Protocol 6: Immunohistochemistry of the Induced Animal Cap Cells
Materials
• Plasmid containing target clone
• Appropriate restriction enzyme
• Phenol/chloroform
• 100% ethanol
• RNase‐free water
• T3 RNA polymerase (Roche cat. no. 1031163), T7 RNA polymerase (Roche cat. no. 881767), or SP6 RNA polymerase (Roche cat. no. 810274) and 10× transcription buffer
• Dig RNA labeling mix (Roche cat. no. 1277073)
• RNase inhibitor (Takara cat. no. 2310A)
• DNase I (Invitrogen cat. no. 18068‐015)
• Stop solution (see recipe)
• Hydrolysis buffer (see recipe)
• 3 M sodium acetate, pH 5.2
• MEMFA (see recipe)
• 50% and 75% ethanol in RNase‐free water
• 25% ethanol in PTw
• PTw (see recipe)
• 10 µg/ml Proteinase K (see recipe)
• 0.1 M TEA (see recipe)
• 4% PFA (see recipe)
• Hybridization buffer (see recipe)
• 0.2× and 2× SSC (see recipes)
• RNase in 2× SSC (see recipe)
• MAB (see recipe)
• MAB+BR (see recipe)
• MAB+BR+SS (see recipe)
• Anti‐digoxigenin‐AP, Fab fragment (Roche cat. no. 1093274)
• AP buffer (see recipe)
• BM Purple (Roche cat. no. 1442074)
• 70% and 100% methanol
• Bleaching solution (see recipe)
• Spectrophotometer
• 37° and 60°C water bath
• 5‐ml screw‐cap glass vial
• Pipet
• Mild shaker
• Hybridization incubator
• 24‐well plate
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Figures
Literature Cited
Literature Cited
Ariizumi, T. and Asashima, M. 1994. In vitro control of the embryonic form of Xenopus laevis by activin A: Time and dose‐dependent inducing properties of activin‐treated ectoderm. Develop. Growth Differ. 36:499‐507.
Ariizumi, T., Sawamura, K., Uchiyama, H., and Asashima, M. 1991a. Dose‐ and time‐dependent mesoderm induction and outgrowth formation by activin A in Xenopus laevis. Int. J. Dev. Biol. 35:407‐414.
Ariizumi, T., Moriya, N., Uchiyama, H., and Asashima, M. 1991b. Concentration‐dependent inducing activity of activin A. Roux's Arch. Dev. Biol. 200:230‐233.
Ariizumi, T., Kinoshita, M., Yokota, C., Takano, K., Fukuda, K., Moriyama, N., Malacinski, G.M., and Asashima, M. 2003. Amphibian in vitro heart induction: A simple and reliable model for the study of vertebrate cardiac development. Int. J. Dev. Biol. 47:405‐410.
Asashima, M., Michiue, T., and Kurisaki, A. 2008. Elucidation of the role of activin in organogenesis using a multiple organ induction system with amphibian and mouse undifferentiated cells in vitro. Develop. Growth Differ. 50:S35‐S45.
Green, J.B. and Smith, J.C. 1990. Graded changes in dose of a Xenopus activin A homologue elicit stepwise transitions in embryonic cell fate. Nature 347:337‐338.
Green, J.B., New, H.V., and Smith, J.C. 1992. Responses of embryonic Xenopus cells to activin and FGF are separated by multiple dose thresholds and correspond to distinct axes of the mesoderm. Cell 71:731‐739.
Harland, R.M. 1991. In situ hybridization: An improved whole‐mount method for Xenopus embryos. Methods Cell Biol. 36:685‐695.
Kay, B.K. and Peng, H.B., eds. 1991. Methods in Cell Biology. Xenopus laevis: Practical Use in Cell and Molecular Biology. Academic Press, San Diego, California.
Kobayashi, H., Michiue, T., Yukita, A., Danno, H., Sakurai, K., Fukui, A., Kikuchi, A., and Asashima, M. 2005. Novel Daple‐like protein positively regulates both the Wnt/beta‐catenin pathway and the Wnt/JNK pathway in Xenopus. Mech. Dev. 122:1138‐1153.
Moriya, H., Uchiyama, H., and Asashima, M. 1993. Induction of pronephric tubules by activin and retinoic acid in presumptive ectoderm of Xenopus laevis. Develop. Growth Differ. 35:123‐128.
Moriya, N., Komazaki, S., Takahashi, S., Yokota, C., and Asashima, M. 2000. In vitro pancreas formation from Xenopus ectoderm treated with activin and retinoic acid. Develop. Growth Differ. 42:593‐602.
Nieuwkoop, P.D. 1969. The formation of mesoderm in urodelan amphibians, Pt. 1: Induction by the endoderm. Roux' Arch. Entwicklungsmech. Org. 162:341‐373.
Nieuwkoop, P.D. and Faber, J. 1967. Normal Table of Xenopus laevis (Daudin). North‐Holland Publishing, Amsterdam.
Sambrook, J. and Russell, D.W. 2001. Molecular Cloning. Cold Spring Harbor Laboratory Press. Cold Spring Harbor, New York.
Sive, H.L., Grainger, R.M., and Harland, R.M. 2000. Early development of Xenopus laevis. Cold Spring Harbor Laboratory Press. Cold Spring Harbor, New York.
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7,951,242,056,097,700,000 | Skip to main content
Fecal pollution events reconstructed and sources identified using a sediment bag grid
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ABSTRACT:
Conventional microbiological surveys, relying on periodic sampling of the water column, were unable to identify sources of fecal contamination at a local beach in North Vancouver, B.C., Canada. Many sources of human and/or animal wastes to the cove were evident (for example, storm sewers, animal feces on the beach, urban streams, discharges from boats, leaking sanitary sewers) but it was not possible to identify any one source as the cause of the pollution by sampling the water column since the contaminant source was likely episodic (that is, discharging for only brief periods). It was unlikely that any conventional sampling survey would coincide with a pollution event and thereby reveal a pattern of contamination. As a result, a novel sampling strategy was devised using sediment bags (porous bags filled with sand) suspended from buoys and deployed in a grid pattern around the beach. The sand in these bags accumulated fecal bacteria during pollution events and retained them long enough so that they could be analyzed during weekly sampling surveys; in this way, the true pattern of the pollution plume was documented and the source was revealed. Results from an analysis of the sediment bag grid indicated that storm sewers were the principal contaminant sources. The subsequent clean-up was inexpensive compared with other proposed remedies (for example, diversion of urban creeks, replacement of sanitary sewers).
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Keywords: analysis; fecal bacteria; microbiology; oceans; sampling
Document Type: Research Article
Publication date: 01 September 1994
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Published as: Sewage Works Journal, 1928 - 1949; Sewage and Industrial Wastes, 1950 - 1959; Journal Water Pollution Control Federation, 1959 - Oct 1989; Research Journal Water Pollution Control Federation, Nov 1989 - 1991; Water Environment Research, 1992 - present.
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-251,323,144,599,507,740 |
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4. all of these
D
MCQ. Excess amino acids are stored as
1. seeds
2. stem tubers
3. proteins
4. corms
C
MCQ. Fats do not help in
1. dark stage of photosynthesis
2. storage
3. developing new protoplasm in leaves
4. cellular respiration
A
MCQ. Proteins help in
1. developing new protoplasm in leaves
2. cellular respiration
3. providing energy to the body
4. providing minerals for digestion
A | {
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} | 57 | cf5cd1df0ee2161e1684bdc019357275 |
6,275,337,137,707,318,000 | Assays
Flask3-64x64 In vitro knock down of Rab5
ID: 99
Assay type: Rnai
Technology type: Technology type
Investigation: 1 hidden item
Study: In vitro knock down of Rab5
Scales: Cell and Liver
No description specified
Created: 28th Feb 2014 at 11:11 Last updated: 11th Jan 2016 at 15:18
Flask3-64x64 in vivo fluorescence analysis of LNP-siRNA-Alexa647
ID: 78
Assay type: Rnai
Technology type: fluorescence
Investigation: 1 hidden item
Study: Image-based analysis of lipid nanoparticle-medi...
Scales: Liver lobule and Liver
No description specified
Created: 6th Dec 2013 at 12:06 Last updated: 11th Jan 2016 at 15:18
Flask3-64x64 In vivo LNP injections
ID: 100
Assay type: Rnai
Technology type: Technology type
Investigation: 1 hidden item
Study: In vivo Rab5 knock down
Contributor: Konstantina Diamantara
Projects: A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato...
Organisms: Not Specified
SOPs: SOP In vivo LNP injections-Marino Zerial MPI-CBG
Data files: No Data files
Scales: Cell, Intercellular and Liver
No description specified
Created: 28th Feb 2014 at 12:36 Last updated: 11th Jan 2016 at 15:18
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7,938,998,638,810,449,000 | Difference between revisions of "Biostatistics 666: Power of Genomewide Association Studies"
From Genome Analysis Wiki
Jump to: navigation, search
(Lecture Notes)
(Lecture Notes)
Line 5: Line 5:
== Lecture Notes ==
== Lecture Notes ==
[[Media:666.2010.01.pdf|Slides in PDF Format]]
+
[[666.2010.01_-_Power_of_Genomewide_Studies.pdf |Slides in PDF Format]]
== Recommended Reading ==
== Recommended Reading ==
Skol el al (2006) Joint analysis is more efficient than replication based analysis for two-stage genomewide association studies. ''Nature Genetics'' '''38''':209-13
Skol el al (2006) Joint analysis is more efficient than replication based analysis for two-stage genomewide association studies. ''Nature Genetics'' '''38''':209-13
Latest revision as of 04:28, 1 November 2017
Objective
This lecture discusses power calculations in the context of genomewide association studies. It also introduces the concept of two stage designs and the tradeoffs between replication based and two stage analyses. The "Winner's Curse" makes a brief cameo appearance.
Lecture Notes
Slides in PDF Format
Recommended Reading
Skol el al (2006) Joint analysis is more efficient than replication based analysis for two-stage genomewide association studies. Nature Genetics 38:209-13 | {
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-9,092,855,872,590,607,000 | WoRMS banner
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WoRMS taxon details
Checked: verified by a taxonomic editorKudoa thyrsites (Gilchrist, 1924)
AphiaID: 120491
Classification: Biota > Checked: verified by a taxonomic editorAnimalia (Kingdom) > Checked: verified by a taxonomic editorCnidaria (Phylum) > Unreviewed: has not been verified by a taxonomic editorMyxozoa (Class) > Unreviewed: has not been verified by a taxonomic editorMyxosporea (Subclass) > Checked: verified by a taxonomic editorMultivalvulida (Order) > Checked: verified by a taxonomic editorKudoidae (Family) > Unreviewed: has not been verified by a taxonomic editorKudoa (Genus) > Checked: verified by a taxonomic editorKudoa thyrsites (Species)
Status accepted
Rank Species
Parent Unreviewed: has not been verified by a taxonomic editorKudoa Meglitsch, 1947
Source basis of record Karlsbakk, E. (2001). Myxozoa, in: Costello, M.J. et al. (Ed.) (2001). European register of marine species: a check-list of the marine species in Europe and a bibliography of guides to their identification. Collection Patrimoines Naturels, 50: pp. 80-84 (look up in IMIS[details]
Environment marine
Distribution
From other sources
North Atlantic Ocean
Unreviewed: has not been verified by a taxonomic editorEuropean waters (ERMS scope) [details]
Unreviewed: has not been verified by a taxonomic editorNorth West Atlantic [details]
Links Unreviewed: has not been verified by a taxonomic editorTo Biodiversity Heritage Library (2 publications)
Unreviewed: has not been verified by a taxonomic editorTo Encyclopedia of Life
Unreviewed: has not been verified by a taxonomic editorTo GenBank (86 nucleotides; 12 proteins)
Unreviewed: has not been verified by a taxonomic editorTo PESI
LSID urn:lsid:marinespecies.org:taxname:120491
Taxonomic
Edit history
Date action by
2004-12-21 15:54:05Z created Karlsbakk, Egil
[Taxonomic tree] [Occurrence map] [Google] [Google scholar] [Google images]
Citation: WoRMS (2015). Kudoa thyrsites (Gilchrist, 1924). Accessed through: World Register of Marine Species at http://www.marinespecies.org/aphia.php?p=taxdetails&id=120491 on 2015-11-28
Creative Commons License The webpage text is licensed under a Creative Commons Attribution 4.0 License
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-2,506,189,734,144,973,300 | Advanced search
Start date
Betweenand
Study of the influence of signaling Toll-Like Receptors (TLRs) and the gene MyD88 on olfactry epithelium neuronal regeneration
Grant number: 11/13134-0
Support Opportunities:Scholarships in Brazil - Doctorate (Direct)
Effective date (Start): January 01, 2012
Effective date (End): August 31, 2014
Field of knowledge:Biological Sciences - Biochemistry - Molecular Biology
Principal Investigator:Isaias Glezer
Grantee:Umberto Crisafulli
Host Institution: Instituto de Química (IQ). Universidade de São Paulo (USP). São Paulo , SP, Brazil
Associated research grant:07/53732-8 - Post-lesion cell regeneration in the nervous system and functional aspects of genes linked to innate immune response, AP.JP
Associated scholarship(s):12/21854-5 - Investigation of insulin degrading enzyme (IDE) regulatory role in olfactory sensory neurons regeneration, BE.EP.DD
Abstract
The Nervous System (NS) is essential for animal interaction with theenvironment. However, lesions in the mammalian CNS are usually irreversible due to its limited regenerative capacity. The regenerative process that follows injury recruits cells of the immune system, which is also the case for brain lesions. Immune cells mediate the innate immune response through activation of receptors that detect molecular Pathogen-Associated Molecular Patterns (PAMPs). Among these receptors, the Toll-Like Receptor (TLR) family engages major defense mechanism upon PAMPs detection. TLRs are associated with intracellular adapter molecules that trigger gene expression of inflammatory signals for the neutralization and elimination of pathogens, as well as the restoration and modification of the injured tissue. Our studies indicate that TLR signaling components slow the neuroregeneration of the murine Olfactory Epithelium (OE). For a better understanding of the mechanisms involved, we will characterize the gene expression profile related to better nerve regeneration. In addition, we will analyze the impact of strategies for TLRs activation or interference through bone marrow chimerism, the use of peptide agonists or inhibitors and also by means of antiinflammatory therapies, which can help define if the use of these compounds is applicable in case of OE injury. (AU)
News published in Agência FAPESP Newsletter about the scholarship:
Articles published in other media outlets (0 total):
More itemsLess items
VEICULO: TITULO (DATA)
VEICULO: TITULO (DATA)
Scientific publications
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
CRISAFULLI, UMBERTO; XAVIER, ANDRE M.; DOS SANTOS, FABIANA B.; CAMBIAGHI, TAVANE D.; CHANG, SEO Y.; PORCIONATTO, MARIMELIA; CASTILHO, BEATRIZ A.; MALNIC, BETTINA; GLEZER, ISAIAS. Topical Dexamethasone Administration Impairs Protein Synthesis and Neuronal Regeneration in the Olfactory Epithelium. FRONTIERS IN MOLECULAR NEUROSCIENCE, v. 11, . (09/04437-9, 07/53732-8, 16/24471-0, 11/13134-0, 09/52047-5, 13/07937-8)
Academic Publications
(References retrieved automatically from State of São Paulo Research Institutions)
CRISAFULLI, Umberto. Influence of innate immune signaling and dexamethasone (DEX) administration on the degeneration and neororegeneration of the olfactory epithelium (OE). 2015. Doctoral Thesis - Universidade de São Paulo (USP). Conjunto das Químicas (IQ e FCF) (CQ/DBDCQ) São Paulo.
Please report errors in scientific publications list by writing to: [email protected]. | {
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} | 57 | cf5cd1df0ee2161e1684bdc019357275 |
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• Software
• Open Access
BSPAT: a fast online tool for DNA methylation co-occurrence pattern analysis based on high-throughput bisulfite sequencing data
BMC Bioinformatics201516:220
https://doi.org/10.1186/s12859-015-0649-2
• Received: 11 February 2015
• Accepted: 6 June 2015
• Published:
Abstract
Background
Bisulfite sequencing is one of the most widely used technologies in analyzing DNA methylation patterns, which are important in understanding and characterizing the mechanism of DNA methylation and its functions in disease development. Efficient and user-friendly tools are critical in carrying out such analysis on high-throughput bisulfite sequencing data. However, existing tools are either not scalable well, or inadequate in providing visualization and other desirable functionalities.
Results
In order to handle ultra large sequencing data and to provide additional functions and features, we have developed BSPAT, a fast online tool for bisulfite sequencing pattern analysis. With a user-friendly web interface, BSPAT seamlessly integrates read mapping/quality control/methylation calling with methylation pattern generation and visualization. BSPAT has the following important features: 1) instead of using multiple/pairwise sequence alignment methods, BSPAT adopts an efficient and widely used sequence mapping tool to provide fast alignment of sequence reads; 2) BSPAT summarizes and visualizes DNA methylation co-occurrence patterns at a single nucleotide level, which provide valuable information in understanding the mechanism and regulation of DNA methylation; 3) based on methylation co-occurrence patterns, BSPAT can automatically detect potential allele-specific methylation (ASM) patterns, which can greatly enhance the detection and analysis of ASM patterns; 4) by linking directly with other popular databases and tools, BSPAT allows users to perform integrative analysis of methylation patterns with other genomic features together within regions of interest.
Conclusion
By utilizing a real bisulfite sequencing dataset generated from prostate cancer cell lines, we have shown that BSPAT is highly efficient. It has also reported some interesting methylation co-occurrence patterns and a potential allele-specific methylation case. In conclusion, BSPAT is an efficient and convenient tool for high-throughput bisulfite sequencing data analysis that can be broadly used.
Keywords
• DNA methylation
• Bisulfite sequencing analysis
• Methylation co-occurrence patterns
• Allele-specific methylation
Background
As one type of epigenetic events, DNA methylation plays an important role in gene regulation and during normal development [1]. Abnormal DNA methylation patterns in CpG dinucleotides have been shown to be associated with human diseases such as cancer [2]. Analysis of DNA methylation patterns is of great importance in understanding the mechanism of DNA methylation and its functions during development [3].
Many technologies have been developed to systematically acquire DNA methylation information [4]. Bisulfite sequencing is one of the most popular methods, which uses bisulfite treated DNA samples to obtain single nucleotide methylation status. For example, ultra-deep bisulfite sequencing is designed to sequence a limited number of loci but with an extreme high coverage [5, 6], which makes analysis of methylation co-occurrence patterns feasible. Reduced representation bisulfite sequencing (RRBS) uses restriction enzymes to select regions of high CpG content in a genome for sequencing [7, 8]. Whole genome bisulfite sequencing (WGBS) provides an unbiased assay of methylation information across the genome [9].
Along with the generation of bisulfite sequencing data, many bisulfite sequencing data analysis tools have been proposed in recent years. Among them, QUMA [10], BISMA [11] and BiQ Analyzer [12] are earlier tools for bisulfite sequencing data analysis that have been widely adopted. However, none of the tools can handle large datasets with ultra-high read coverages or a large number of targeted regions, which are increasingly common in real data analysis. For example, QUMA web server limits the maximum number of bisulfite sequence reads per request to 400. Similarly for BISMA, the number of sequences that can be uploaded is limited to 400. The upload files size is limited to 10 MB. Even for later tools such as BiQ Analyzer HT [13] that were designed specifically for processing large datasets, their performance still cannot keep up with the throughput of data generation, mainly because they utilized a global sequence alignment algorithm. The alignment strategy also limits its usage on very small genomic regions.
More recently, some newer tools such as Bismark [14] and BS-Seeker [15] have utilized more efficient mapping tools with modifications for bisulfite sequencing data. Therefore they can effectively handle larger datasets, especially those generated by next-generation sequencing (NGS) technologies [16]. However, the primary focus of these tools is to perform sequence read map and to call methylation status at each site. Other functionalities in downstream pattern analysis and visualization are limited. Furthermore, most existing tools provide little if any functions in analyzing methylation co-occurrence patterns, nor in correlating methylation patterns with mutations. Investigating such patterns may provide further insights in distinguishing different cancer subtypes [17], in revealing mechanisms of cancer development [18], and in detecting allele-specific methylation.
In this paper, we present a web application service named BSPAT for Bisulfite Sequencing Pattern Analysis Tool, which takes advantage of Bismark’s read alignments and methylation calling functionalities, and provides further quality control, co-occurrence pattern analysis, simple allele specific methylation analysis, visualization and integration with other databases and tools. In addition to the web service, the source code of the tool is also made available, which enables advanced users to deploy BSPAT on their own machines for dedicated analysis of large volume of data without uploading them to our own server. We have applied BSPAT on a real dataset generated from two prostate cancer cell lines and one normal prostate epithelial cell line. Results have shown some interesting methylation co-occurrence patterns that are different in different cell lines. A potential allele specific methylation case is also observed. We have also compared the performance of BSPAT with a popular tool BiQ Analyzer HT [13]. Results show that BSPAT is much faster, uses less memory, and generates more results for visualization and further analysis.
Implementation
BSPAT is designed to analyze bisulfite sequencing data for regions with extreme high read depths so that DNA methylation co-occurrence patterns can be reliably measured. It can accept reads from multiple regions and multiple experiments, which are then mapped to reference sequences by calling Bismark [14]. Based on mapping results, methylation status of a read at each CpG site is called and patterns of co-occurrence are reported. Mutations are called based on the number of reads with mismatches at each nucleotide.
Characteristics
Comparing with existing tools, BSPAT has several important features: 1) The methylation pattern analysis features provided by most existing tools focus on either an overall methylation status of a CpG rich region or methylation level of each CpG site. Although the detailed single read methylation patterns may be presented, the significant co-occurrence patterns are not summarized. 2) BSPAT also provides a feature to automatically discover potential allele-specific DNA methylation co-occurrence patterns in a targeted region. 3) By utilizing a sequence mapping approach instead of sequence alignment algorithms, BSPAT is much faster than existing tools, as demonstrated in Result section. 4) BSPAT implements an easy to use integrated workflow and visualizes results in multiple formats.
Workflow
The workflow of BSPAT is shown in Fig. 1. It mainly consists of two stages: mapping stage and analysis stage. We discuss both of them in details in this subsection. For sequence reads generated from bisulfite sequencing projects, BSPAT accepts both FASTA and FASTQ format as its inputs (Fig. 1 a) for mapping. Four different types of quality scores (i.e.,phred33, phred64, solexa and solexa1.3) for FASTQ format are supported. Reads from multiple experiments can be uploaded at the same time. Each experiment can consist of one or more genomic regions. A utility script is also provided to extract data from multiplex experiments. BSPAT also requires users to provide a reference sequence file using FASTA format, which can consist of reference sequences from all the regions/experiments. Because the program uses a mapping strategy instead of an alignment strategy, it assumes read lengths are smaller than the lengths of reference sequences. The design of BSPAT is mainly for targeted sequencing data, where the regions sequenced are known a priori. Therefore, users should provide reference sequences of targeted regions, not the whole human genome, to speed up the mapping and analysis. To obtain genome coordinates of these regions for the analysis stage, BSPAT calls Blat service hosted by UCSC Genome Browser [19, 20] to automatically acquire the genome coordinates of reference sequences. Three versions of genome assemblies (i.e., hg38, hg19, hg18) are supported currently. The top Blat result for each region, which in general represents the true region, will be selected for use in the analysis step. To map bisulfite converted sequence reads to reference regions, BSPAT relies on another program Bismark (Fig. 1 b), which actually calls Bowtie [21] to perform the mapping. The mapping step takes the majority of execution time. BSPAT allows up to three mismatches in the seed region of each read but gaps are not allowed. Reads with low mapping qualities are discarded. Users will be notified by email (if provided) when the mapping result is ready. A unique identifier is assigned to each executed job and users can use that number to retrieve the results. The webpage will also be refreshed when the result is ready, which provides some summary information about the mapping result, the genomic coordinates of the targeted regions, and a link to the detailed results generated from Bismark.
Fig. 1
Fig. 1
Workflow of BSPAT. a Example of input sequence reads in FASTQ format. b Sequence reads are mapped to the reference. c For a given targeted region, only reads that cover all CpG sites in the region are considered in generating co-occurrence patterns. d) Methylation patterns and mismatch information at single read level. e Visualization of results in three different formats. 1) DNA Methylation co-occurrence patterns in text format. ‘@@’ represents a methylated CpG site; ‘**’ represents an unmethylated CpG site; ‘-’ represents a non-CpG context nucleotide; a mismatch is represented by the variant allele at the position. 2) Graphical representation of methylation co-occurrence patterns with genomic coordinate information. A black circle represents a methylated CpG site and a white one represents an unmethylated CpG site. The last row represents the proportion of methylated reads to the total number of reads at each site. The colored circles show methylation rates from low (green) to high (red). Variant allele in each pattern is represented by a blue bar. 3) Methylation patterns are shown as a UCSC Genome Browser custom track
Based on mapping results, BSPAT not only summarizes the methylation level at each CpG site, more importantly, it examines methylation co-occurrence patterns of CpG sites in close proximity. BSPAT does so in several steps. First, low quality reads will be filtered out based on user-defined parameters such as bisulfite conversion rate and sequence identity. Second, in order to view co-occurrence patterns, a user needs to specify a window by providing its genomic coordinates. If no such window is given, BSPAT uses a default window of size 70 bps starting at the first CpG site of the reference sequence. Only reads that cover all the CpG sites in the view window will be considered in generating co-occurrence patterns (Fig. 1 c). For each read, the methylation status at all CpG sites covered by the read is regarded as its methylation signature or a pattern (Fig. 1 d.) Then, all reads with the same signature will be grouped into a methylation co-occurrence pattern and the number of all such reads is the support of the pattern.
Given the noisy nature of data, in general, only prevalent patterns with enough support are meaningful/significant. To filter out random patterns, users can use a simple fraction threshold (i.e., the percentage of the number of reads supporting a pattern over the number of all reads). In addition, BSPAT provides a simple Z-score like statistic to measure the significance of a pattern. Basically, it assumes all CpG sites in the region are independently methylated with a probability of 0.5. Therefore, for k CpG sites in a region, there are 2 k different patterns each with equal probability of 1/2 k . Any patterns with frequencies that are significantly greater than this probability are potentially important. However, the assumption may not hold in reality in the sense that the total number of reads in the region may not be sufficiently large relative to the total number of CpG sites, and methylation status of nearby CpG sites may be correlated. Therefore, instead of this probability, we actually define the baseline probability p 0 as one over the number of observed patterns in the data, to better reflect dependencies among methylated CpG sites in close proximity. Assume \(\hat {p}\) is the percentage of reads supporting a pattern and n is the total number of reads. Then one can utilize the one-sample Z-test for proportions to assess the significance of each pattern, with the alternative hypothesis H 1: \(\hat {p} > p_{0}\). The Z-score can be calculated based on Equation (1), where the numerate represents the difference between the observed frequency and the expected frequency, and the denominator is the estimated standard deviation under the binomial distribution. If the p-value corresponding to the Z-score is smaller than a predefined threshold, the co-occurrence pattern is treated as significant. All significant patterns will be shown in the results in the descending order of their significance.
$$ Z = \frac{\hat{p} - p_{0}}{\sqrt{\frac{\hat{p}(1-\hat{p})}{n}}} $$
(1)
In order to assess potential allele-specific methylation patterns, BSPAT first needs to discover mutations from mapping reads. In the current implementation, it simply defines a mutation as a mismatch that is supported by an excessive number of reads, using a user-defined threshold. When a mutation exists, BSPAT naturally separates all reads into two groups: reads with the reference allele and reads with the mutated allele. For each group, BSPAT assesses the methylation level at each CpG site and assigns all CpG sites into three categories based on the proportion of methylated reads covering the sites: low methylation level (≤ 20 % reads are methylated), high methylation level (≥ 80 % reads are methylated), and intermediate level (otherwise). If the two groups corresponding to the two alleles have at least one CpG site where their methylation levels are in two different categories and the actual difference of their methylation proportions is larger than 20 %, BSPAT regards the region as a potential allele specific methylation region. Then within each group, BSPAT further generates methylation co-occurrence pattens by grouping reads with the same methylation signature.
When BSPAT finishes the analysis, it visualizes significant methylation co-occurrence patterns and allele specific methylation patterns in three different formats including text format (Fig. 1e1), graph (PNG or EPS) format (Fig. 1e2), and a format that can be loaded directly to UCSC Genome Browser [22] as a custom track (Fig. 1e3). In addition, When a mutation coincides with an existing SNP in the dbSNP database [23], a link to that SNP is provided.
Implementation details
BSPAT was developed mainly in Java/JSP and hosted in Apache Tomcat Server. To fully utilize computation resources that may be available to users, BSPAT also supports a multiple-thread mode. In this case, each experiment is executed using a separate thread, therefore it can greatly speed up the analysis. The single-thread or multiple-thread mode can be configured when users deploy the code locally. The performance improvement using multi-threads is discussed in Result section.
Results and discussion
To test the functions and performance of BSPAT, we have performed analysis based on a real bisulfite amplicon sequencing dataset as well as a simulated dataset based on the real dataset. The real dataset consists of three prostate related cell lines (DU145, LNCaP, PrEC), each with 24 genomic regions. DU145 and LNCaP are prostate cancer cell lines. PrEC is normal prostate epithelial cell line. Genomic DNA from each cell line was bisulfite treated. The bisulfite treated DNA was PCR amplified using primers specific for the 24 regions of interest. PCR products for all 24 amplicons were pooled for each cell line and used for subsequent Illumina next-gen sequencing library construction. To enable multiplexing, a uniquely indexed adapter was used for each cell line during library preparation. The final library for each cell line was pooled together in equal molar ratios before sequencing on one lane of Illumina GAIIx. The average length of a region is about 127 bps with the total length of all regions 3020 bps. The whole dataset contains about half million reads with read length varying from 69 to 80 bps after trimming the library index and PCR primers. With default mapping parameters (maximum permitted mismatches = 2), 93.88 % reads were mapped uniquely to the reference sequences, with an average read depth of 18,886. The unmapped reads (6.12 %) were all with low quality scores or with gaps. Default parameters were used in performing pattern analysis (e.g., bisulfite conversion rate 0.95, sequence identity 0.9, p-value 0.05 and mutation threshold 0.2). By examining the results, we have found some interesting patterns that are potentially biologically important, which will be discussed here. More thorough analysis of the dataset will be presented elsewhere.
DNA methylation co-occurrence pattern analysis
Unlike overall methylation patterns that summarize methylation levels at each individual CpG site, methylation co-occurrence patterns can reveal rich information that could be biologically important. For example, Fig. 2 a shows the methylation patterns in gene CYP1B1 region for two cell lines DU145 and LNCaP. Although the overall methylation patterns are similar in these two cell lines, the significant methylation co-occurrence patterns are different, with DU145 showing a single significant pattern while LNCaP showing two additional patterns. The diversity may be due to the existence of sub-categories in LNCaP samples. Also, because the number of reads covering this region is extremely high, simply sorting and displaying all reads (as some other tools do) is not helpful in this case. In contrast, significant co-occurrence patterns give a clear and direct view of the methylation patterns. This is best illustrated in another example in the downstream region of gene HIST1H4D. There are two significant methylation co-occurrence patterns in DU145 cell line, while all CpG sites are completely methylated in one and all CpG sites are totally unmethylated in the other (Fig. 2 b). This suggests that the partially methylation status in those CpG sites are likely caused by mixture of fully methylated and unmethylated reads [24]. Some other methylation co-occurrence patterns reveal possibly correlated methylation among neighboring CpG sites. Two examples are shown in Fig. 2 c and d for genes TLX3 and NPR3, respectively. For TLX3, methylation status of the first and the last CpG sites seems correlated, while for NPR3, the methylation status of the first and the third CpG sites seems correlated. By using a simple contingency table based on the read count of each pattern, we can calculate the significance level of such dependency based on a χ 2 statistics. The p-values for the two cases are 0.0046 and <0.0001, respectively. The observation supports the general notation that nearby CpG sites may be methylated together, but the biological mechanism of this dependence needs further investigation.
Fig. 2
Fig. 2
Examples of DNA methylation co-occurrence patterns. a DU145 and LNCaP cell lines have different significant methylation co-occurrence patterns in region CYP1B1. b Two distinct co-occurrence patterns (one all sites are methylated while the other all cites are unmethylated) in the downstream region of HIST1H4D of DU145 cell line. Examples of correlated partially methylated CpG sites in a region in the upstream of TLX3 from PrEC cell line (c) and in the NPR3 region from LNCaP (d). For all sub-panels, coordinates used are based on hg18. Because not all reads belong to a significant pattern, the sum of percentages of all significant patterns (on the right hand side of each pattern) is not necessarily 100 %
Potential ASM detection
From pattern analysis results, we have found a potential allele specific methylation pattern in PAX6 region, as shown in Fig. 3. The mutation identified is at the third CpG site, which is also reported in dbSNP as SNP rs4440995. The nucleotide in the reference sequence is G and the variant allele is A. We first notice that in LNCaP cell line, the overall methylation levels of reads with the reference allele and reads with the variant allele are significantly different (Fig. 3 a). Further investigation based on co-occurrence patterns shows that the reference allele is associated with hypermethylation while the variant allele is associated with hypomethylation (Fig. 3 b). We further examined the mutation and co-occurrence patterns in the other two cell lines in this region (Fig. 3 c and d). Both alleles in the normal cell line (PrEC) are the reference allele while both alleles in DU145 cell line are the variant allele. The association between alleles and methylation co-occurrence patterns are different from those observed in LNCaP cell line: the variant allele in DU145 exhibits hypermethylation patterns while the reference allele in PrEC exhibits hypomethylation patterns.
Fig. 3
Fig. 3
An allele specific methylation example near PAX6. a Potential allele-specific methylation patterns were discovered in LNCaP cell line near gene PAX6. The first row is the overall methylation level associated with the reference allele. The second row is the overall methylation level associated with the variant allele (indicated by the blue bar). Significant methylation co-occurrence patterns in LNCaP (b), in DU145 (c), and in PrEC (d) for the same region. Coordinates used here are based on hg18
There are several possibilities to explain the observation. First, PrEC is a normal cell line and has intact machinery to maintain normal methylation pattern, which is largely not methylated. This locus may be free of methylation in all normal prostate cells. In cancer cell lines, when methylation becomes abnormal, this locus gets methylated to achieve some desirable function, and the reference allele has a higher chance of becoming methylated (in LNCaP). Another possibility is the reference allele in LNCaP is in linkage disequilibrium with something that needs to be methylated here in order to achieve desirable effects. For example, the reference allele in LNCaP is linked to a wild-type protein that needs to be silenced. The SNP is linked to mutant protein already inactive. In DU145, both alleles are variant alleles and need to be silenced. Further studies and experiments are needed to confirm which hypothesis is true.
Efficiency
To evaluate the efficiency of BSPAT on larger datasets, we have generated a simulated dataset by replicating the reads from the original data multiple times (2X, 5X, 10X, see Table 1), and compared its performance with a state-of-the-art tool called BiQ Analyzer HT. BiQ Analyzer HT is a standalone program written in Java that was developed specifically for high-throughput bisulfite sequencing data. It performs read alignments and can visualize methylation level at each CpG site and methylation status of each read. But unlike BSPAT, it does not generate methylation co-occurrence patterns. BiQ Analyzer HT can only take FASTA format input files and BSPAT can take both FASTA and FASTQ formats. We have compared the memory usage and time needed to perform the analysis by BSPAT and by BiQ Analyzer HT. All experiments were executed on the same computer with 4-core 3GHz CPU and 12 GB memory. BiQ Analyzer HT was executed in command line interface with JVM heap setting:-Xmx12g. The same JVM heap parameter was used in the Tomcat Server which hosts BSPAT. BiQ Analyzer HT can only run in the single-thread mode. We have tested BSPAT using both single-thread and multiple-thread modes (3 threads for 3 cell lines in the experiments).
Table 1
Sizes of datasets used in the experiments
Read count
File size (MB)
FASTA
FASTQ
1X
482,791
67
134
2X
965,582
134
268
5X
2,413,955
335
670
10X
4,827,910
670
1,340
Figure 4 shows that BSPAT is much faster than BiQ Analyzer HT under all settings. When using the same setting,i.e., the same FASTA format input and both using the single-thread mode, BSPAT is about 3 to 4 times faster than BiQ Analyzer HT. When using the multi-thread mode, BSPAT is about 6 to 7 times faster than BiQ Analyzer HT. The time for BSPAT using FASTQ is almost the same as the time it used for FASTA. When using BSPAT as a web service, the memory usage does not have any influence on end users. However users can deploy BSPAT in their own server. In this case, BSPAT still have less peak memory usage than BiQ Analyzer HT (Fig. 5). Comparing with BiQ Analyzer HT, single-thread BSPAT used about half of its memory. Multi-thread BSPAT utilized more memory than the single-thread version, but it was still less than the memory usage of BiQ Analyzer HT. In summary, BSPAT provides more features and has better performance than BiQ Analyzer HT both in terms of running time and memory usage.
Fig. 4
Fig. 4
Efficiency comparison of BSPAT and BiQ Analyzer HT (referred as BiQ HT here) using different settings. BSPAT outperformed BiQ HT in all cases. BSPAT can accept FASTA or FASTQ format and run in single or multi-thread mode. All experiments were run on the same computer with quite background. For BSPAT, the Tomcat Server did not host any other applications
Fig. 5
Fig. 5
Peak memory usage comparison of BSPAT and BiQ Analyzer HT (referred as BiQ HT here) using different settings. BSPAT used less memory than BiQ HT in all cases. Here the peak memory usage of BSPAT was measured by monitoring the memory usage of Tomcat Server. For smaller datasets, the majority memory usage of BSPAT was by Tomcat Server itself. So there are no significant differences using single-thread or multiple-thread for 1X dataset
Conclusion
In this paper, we have presented BSPAT, a web application for methylation pattern analysis based on bisulfite sequencing data. BSPAT capitalizes on ultra deep sequence data in targeted regions to automate the n of methylation co-occurrence patterns and allele specific methylation. The implementation is efficient and also provides great flexibilities in parameter settings. Visualization of result patterns and integration with Genome Browser allow users to examine other genomic features in the same regions together. For our future work, we will refine mutation calling by combining prior information on genetic variations and more advanced variation calling algorithms. Furthermore, we will extend BSPAT to handle non-human bisulfite sequencing data.
Availability and requirements
Project name: BSPATProject home page: http://cbc.case.edu/BSPAT Project source code: https://github.com/lancelothk/BSPAT Operating system: LinuxProgramming language: JavaOther requirements: Java 1.7 or higher, Tomcat 7.0 or higher, and Bismark, Perl (required by Bismark) and Bowtie (required by Bismark).License: GPL v3Any restrictions to use by non-academics: None
Abbreviations
BSPAT:
Bisulfite sequencing pattern analysis
ASM:
Allele-specific methylation
RRBS:
Reduced representation bisulfite sequencing
WGBS:
Whole genome bisulfite sequencing
NGS:
Next-generation sequencing
Declarations
Acknowledgements
This work was supported in part by the National Science Foundation [III1162374], the National Institutes of Health [DC012380, and CA154356 to A.T.]. We thank Drs. Yaomin Xu and Bo Hu for helpful discussions.
Authors’ Affiliations
(1)
Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, 44106, Ohio, USA
(2)
Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, 44195, Ohio, USA
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} | 57 | cf5cd1df0ee2161e1684bdc019357275 |
-7,312,117,752,185,839,000 | TRMT1
ProteinTRMT1
NCBI GeneID55621
ClassTF
Protein SequenceTRMT1
Binding logo
MatrixPosition Weight Matrix
Binding Motifs
CATTAATCAGCATT
GCTTTCAGAAATCC
CAAATGAAATTCATTTGG
TGAATTCATTTTCCAAAGCA
TTAATGGGAAATTTG
GAAAACAGTTTGTTCTCT
TGACCTAGAGGTGAAAGGC
TTTCATTAGAAGATGAAGCA
TGGCTGGCTTCCCAG
GAATTTAGTGCTTGTGAAAA
TGTTTCATAAAGCTG
TGAATAA
TTTAAGGTGGC
GCTGCAG
CCGGACATAACG
TCAAGGACG
AACCACAG
GGGGACCCCCAT
TGCTCCAAGAACAGC
GCTCACAAGCTAATTT
TTTCCCATTGG
AAAGTTAACTTT
TTCCCGAGGG
TGACGGTACAG
TTTCCTGTCCAAA
CTGACTTGATT
GCCAGACAGACAGAT
When we calculated the concensus sequences for proteins, we also considered the spacer between two repeated motif sequences.
Click the motif sequence to find the spacer sequence
[Home][Download] | {
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} | 57 | cf5cd1df0ee2161e1684bdc019357275 |
2,661,952,002,560,514,600 | Reactome: A Curated Pathway Database
SUMO is proteolytically processed
Stable Identifier
R-HSA-3065679
Type
Pathway
Species
Homo sapiens
Compartment
Locations in the PathwayBrowser
Summation
SUMO1, 2, and 3 are initially expressed as propeptides containing extra residues at the C-terminus. (SUMO1 has 4 residues, SUMO2 has 2 residues, and SUMO3 has 11 residues,) SENP1, 2, and 5 are endoproteases that process the precursors to produce the mature peptides (reviewed in Wang and Dasso 2009, Wilkinson and Henley 2010, Hannoun et al. 2010, Gareau and Lima 2010). SENP1 processes SUMO1 with greater efficiency than SUMO2 or SUMO3. SENP2 and SENP5 process SUMO2 with greater efficiency than SUMO1 or SUMO3 (Gong and Yeh 2006, Mikolajczyk et al. 2007). SENP1 shuttles between the cytosol and nuceoplasm and is predominantly nuclear (Bailey and O'hare 2004, Kim et al. 2005). SENP2 also shuttles (Itahana et al. 2006) and is mainly located on nucleoplasmic filaments of the nuclear pore complex (Hang and Dasso 2002, Zhang et al. 2002). SENP5 is located mostly in the nucleolus (Di Bacco et al. 2006, Gong and Yeh 2006).
Literature References
Participants
Participant Of
Orthologous Events
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749,772,556,453,720,200 | Ancient Phoenicians Left Genetic Markers Around Mediterranean
The ancient Phoenicians may be largely forgotten, but they're not gone.
Rome destroyed the Phoenicians' greatest city — Carthage — centuries ago, but new genetic studies indicate that as many as one in 17 men living in communities around the Mediterranean may be descended from these ancient mariners.
Originating from what is now Lebanon, the Phoenicians were early seafarers and traders who spread their culture, including a love for the color purple, to North Africa, Spain and other countries around the region.
But they seemed to fade from history after their main colony, Carthage, was defeated in a series of wars with Rome.
• Click here to visit FOXNews.com's Archaeology Center.
• Click here to visit FOXNews.com's Natural Science Center.
Researchers led by Chris Tyler-Smith of the Wellcome Trust Sanger Institute in England were able to locate a genetic marker for the Phoenicians on the male-only Y chromosome.
First they studied references in the Bible and by Greek and Roman writers to determine where there had been Phoenician cities and colonies.
Then the researchers compared the genes of residents in those areas to those of people living in other Mediterranean communities which had not been Phoenician settlements.
They were able to find differences on the Y chromosome that occurred only in the Phoenician-settled areas, affecting more than 6 percent of the population there.
"When we started, we knew nothing about the genetics of the Phoenicians. All we had to guide us was history: We knew where they had and hadn't settled. But this simple information turned out to be enough, with the help of modern genetics, to trace a vanished people," Tyler-Smith said in a statement.
Added Daniel Platt, of IBM's Computational Biology Center: "The results are important because they show that the Phoenician settlement sites are marked by a genetic signature distinct from any that might have been left by other trading and settlement expansions through history, or which may have emerged by chance. This proves that these settlements, some of which lasted hundreds of years, left a genetic legacy that persists to modern times."
While it wasn't part of their study, the researchers said they also saw genetic indications of the spread of the Greeks around the Mediterranean.
They suggested similar studies may be able to trace the genetic influence of the army of Alexander the Great in Asia and India, the Mongol invasion of Europe and the spread of the Vikings.
The findings are being published online Thursday by the American Journal of Human Genetics. The work was supported by National Geographic and IBM's Genographic Project, an effort to research the history of human migration. | {
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6,073,958,758,325,333,000 | Increases in soil organic carbon sequestration can reduce the global warming potential of long-term liming to permanent grassland
A - Papers appearing in refereed journals
Fornara, D. A., Steinbeiss, S., Mcnamara, N. P., Gleixner, G., Oakley, S., Poulton, P. R., Macdonald, A. J. and Bardgett, R. D. 2011. Increases in soil organic carbon sequestration can reduce the global warming potential of long-term liming to permanent grassland. Global Change Biology. 17 (5), pp. 1925-1934.
AuthorsFornara, D. A., Steinbeiss, S., Mcnamara, N. P., Gleixner, G., Oakley, S., Poulton, P. R., Macdonald, A. J. and Bardgett, R. D.
Abstract
The application of calcium- and magnesium-rich materials to soil, known as liming, has long been a foundation of many agro-ecosystems worldwide because of its role in counteracting soil acidity. Although liming contributes to increased rates of respiration from soil thereby potentially reducing soils ability to act as a CO(2) sink, the long-term effects of liming on soil organic carbon (C(org)) sequestration are largely unknown. Here, using data spanning 129 years of the Park Grass Experiment at Rothamsted (UK), we show net C(org) sequestration measured in the 0-23 cm layer at different time intervals since 1876 was 2-20 times greater in limed than in unlimed soils. The main cause of this large C(org) accrual was greater biological activity in limed soils, which despite increasing soil respiration rates, led to plant C inputs being processed and incorporated into resistant soil organo-mineral pools. Limed organo-mineral soils showed: (1) greater C(org) content for similar plant productivity levels (i.e. hay yields); (2) higher 14C incorporation after 1950s atomic bomb testing and (3) lower C : N ratios than unlimed organo-mineral soils, which also indicate higher microbial processing of plant C. Our results show that greater C(org) sequestration in limed soils strongly reduced the global warming potential of long-term liming to permanent grassland suggesting the net contribution of agricultural liming to global warming could be lower than previously estimated. Our study demonstrates that liming might prove to be an effective mitigation strategy, especially because liming applications can be associated with a reduced use of nitrogen fertilizer which is a key cause for increased greenhouse gas emissions from agro-ecosystems.
Keywordsbiodiversity conservation; Ecology; Environmental Sciences
Year of Publication2011
JournalGlobal Change Biology
Journal citation17 (5), pp. 1925-1934
Digital Object Identifier (DOI)doi:10.1111/j.1365-2486.2010.02328.x
Open accessPublished as non-open access
FunderMarie Curie Outgoing Fellowship
NERC - Natural Environment Research Council
Funder project or codeSEF
Centre for Biofuels and Climate Change (BCC)
PublisherWiley
ISSN1354-1013
Permalink - https://repository.rothamsted.ac.uk/item/8q704/increases-in-soil-organic-carbon-sequestration-can-reduce-the-global-warming-potential-of-long-term-liming-to-permanent-grassland
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1,670,321,720,942,905,600 | Harvard Catalyst Profiles
Contact, publication, and social network information about Harvard faculty and fellows.
Login and Edit functionaility are currrently unavailable.
Gregory Crosby, M.D.
Concepts
This page shows the publications Gregory Crosby has written about Mutation, Missense.
Connection Strength
0.035
1. NMDA-R1 antisense oligodeoxynucleotides modify formalin-induced nociception and spinal c-Fos expression in rat spinal cord. Pharmacol Biochem Behav. 2004 Sep; 79(1):183-8.
View in: PubMed
Score: 0.035
Connection Strength
The connection strength for concepts is the sum of the scores for each matching publication.
Publication scores are based on many factors, including how long ago they were written and whether the person is a first or senior author.
Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541. | {
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9,160,436,020,486,594,000 | Home > Products > Human MicroRNA Agomir/Antagomir >
MIRacle™ hsa-miR-454-3p miRNA Agomir/Antagomir
Product Name
MIRacle™ hsa-miR-454-3p miRNA Agomir/Antagomir
Price Get Quote
Cat.No
AM1060
Species
Human
Size/Quantity
2 OD, 4 OD, 50 OD (size by request, 1 OD corresponds to 33 ug)
Shipping Info
Room Temperature
Storage
-20°C / -80°C
Description
MicroRNA: hsa-miR-454-3p
Accession Number: MIMAT0003885
Mature Sequence: UAGUGCAAUAUUGCUUAUAGGGU
hsa-miR-454-3p are small non-coding RNAs of 20-22 nucleotides, typically excised from 60-110 nucleotide foldback RNA precursor structures. miRNAs are involved in crucial biological processes, including development, differentiation, apoptosis, and proliferation, through imperfect pairing with target messenger RNAs (mRNAs) of protein-coding genes and the transcriptional or post-transcriptional regulation of their expression. Click here to browse detailed information about hsa-miR-454-3p in miRBase.
What is MicroRNA Agomir/Antagomir?
MicroRNA Agomir is a special-labeled and chemically modified double-stranded small RNA that mimics the endogenous miRNA to regulate the biological function of the target gene. MicroRNA Antagomir is an especially chemically modified miRNA antagonist. It strongly competes with mature miRNAs in the body to prevent the complementary pairing of miRNAs and their target genes, thereby inhibiting miRNAs from functioning.
Why choose hsa-miR-454-3p miRNA Agomir/Antagomir from AcceGen?
AcceGen has extended experience in MicroRNA Agomir/Antagomir synthesis services that cover all human, mouse, and rat miRNAs in the current miRBase. Compared to standard miRNA mimics and inhibitors, AcceGen miRNA agomir and antagomir are more resistant to degradation, thus having a lasting effect: minimum for 1 week, up to 5-6 weeks. These products can be used in in vitro or in vivo miRNA functional studies.
Recommended Medium And Supplement
Citation Guide
When you publish your research, please cite our product as "AcceGen Biotech Cat.# XXX-0000". In return, we’ ll give you a $100 coupon. Simply click here and submit your paper’ s PubMed ID (PMID).
Label
FAM, CY3, CY5, etc. (optional)
Application
For research use only
Key Features
*cover all human, mouse, and rat miRNAs listed in miRBase
*higher stability/inhibitory effects in vivo and in vitro
*more stable, easier to pass the cell membrane and tissue gap
*purified and ready-to transfect cells/be administered by injection, inhalation, feeding
*less reagent use amount with longer effect time
Component
hsa-miR-454-3p Agomir and/or Antagomir (Product Form: Dry Powder)
Agomir N.C and/or Antagomir N.C (optional)
Product Type
microRNA Agomir/Antagomir
Product Image AcceGen Frozen Cells & Cell Lines AcceGen Frozen Cells & Cell Lines
Tech Document
MIRacle™ Agomir Product Manual
MIRacle™ Antagomir Product Manual
MSDS-AcceGen MicroRNA Agomir
MSDS-AcceGen MicroRNA Antagomir
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8,903,570,357,689,263,000 |
Anti-Histone H3 (citrulline R2 + R8 + R17) antibody - ChIP Grade (ab5103)
Overview
• Product name
Anti-Histone H3 (citrulline R2 + R8 + R17) antibody - ChIP Grade
See all Histone H3 primary antibodies
• Description
Rabbit polyclonal to Histone H3 (citrulline R2 + R8 + R17) - ChIP Grade
• Host species
Rabbit
• Specificity
ab5103 detects a 17 kDa band in single lane Western Blot. Peptide inhibition in Western Blot hasn't been processed. Modification specificity is determined by Peptide Array. ab5103 binds strongly to Histone H3 citrulline 2 + 8 + 17 peptide.
• Tested applications
Suitable for: ICC/IF, PepArr, IHC-Fr, Flow Cyt, ChIP/Chip, WB, ChIPmore details
• Species reactivity
Reacts with: Mouse, Rat, Rabbit, Cow, Human, Monkey
Predicted to work with: a wide range of other species
• Immunogen
Synthetic peptide corresponding to Human Histone H3 aa 1-100 (citrulline R2 + R8 + R17) conjugated to Keyhole Limpet Haemocyanin (KLH). Also SwissProt: P84243, Q71DI3, Q16695, Q6NXT2.
Database link: P68431
(Peptide available as ab32876)
• Positive control
• This antibody gave a positive signal in HL60 Whole Cell Lysate - DMSO and Calcium Ionophore treated. In WB ab5103 only recognizes human or bovine histone H3 when PADI4 and calcium are added.
• General notes
Abcam recommended secondaries - Goat Anti-Rabbit HRP (ab205718) and Goat Anti-Rabbit Alexa Fluor® 488 (ab150077).
See other anti-rabbit secondary antibodies that can be used with this antibody.
Properties
• Form
Liquid
• Storage instructions
Shipped at 4°C. Store at +4°C short term (1-2 weeks). Upon delivery aliquot. Store at -20°C or -80°C. Avoid freeze / thaw cycle.
• Storage buffer
pH: 7.40
Preservative: 0.02% Sodium azide
Constituent: PBS
Batches of this product that have a concentration < 1mg/ml may have BSA added as a stabilising agent. If you would like information about the formulation of a specific lot, please contact our scientific support team who will be happy to help.
• Concentration information loading...
• Purity
Immunogen affinity purified
• Clonality
Polyclonal
• Isotype
IgG
• Research areas
Applications
Our Abpromise guarantee covers the use of ab5103 in the following tested applications.
The application notes include recommended starting dilutions; optimal dilutions/concentrations should be determined by the end user.
Application Abreviews Notes
ICC/IF Use at an assay dependent concentration. PubMed: 20733033
PepArr Use a concentration of 0.2 - 0.02 µg/ml.
IHC-Fr Use at an assay dependent concentration.
Flow Cyt Use at an assay dependent concentration.
ab171870 - Rabbit polyclonal IgG, is suitable for use as an isotype control with this antibody.
ChIP/Chip Use at an assay dependent concentration.
WB Use a concentration of 1 µg/ml. Detects a band of approximately 17 kDa (predicted molecular weight: 15 kDa).
Abcam recommends using 3-5% milk as the blocking agent
We recommend Goat Anti-Rabbit IgG H&L (HRP) (ab97051) secondary antibody.
ChIP Use at an assay dependent concentration.
Target
• Function
Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.
• Sequence similarities
Belongs to the histone H3 family.
• Developmental stage
Expressed during S phase, then expression strongly decreases as cell division slows down during the process of differentiation.
• Post-translational
modifications
Acetylation is generally linked to gene activation. Acetylation on Lys-10 (H3K9ac) impairs methylation at Arg-9 (H3R8me2s). Acetylation on Lys-19 (H3K18ac) and Lys-24 (H3K24ac) favors methylation at Arg-18 (H3R17me).
Citrullination at Arg-9 (H3R8ci) and/or Arg-18 (H3R17ci) by PADI4 impairs methylation and represses transcription.
Asymmetric dimethylation at Arg-18 (H3R17me2a) by CARM1 is linked to gene activation. Symmetric dimethylation at Arg-9 (H3R8me2s) by PRMT5 is linked to gene repression. Asymmetric dimethylation at Arg-3 (H3R2me2a) by PRMT6 is linked to gene repression and is mutually exclusive with H3 Lys-5 methylation (H3K4me2 and H3K4me3). H3R2me2a is present at the 3' of genes regardless of their transcription state and is enriched on inactive promoters, while it is absent on active promoters.
Methylation at Lys-5 (H3K4me), Lys-37 (H3K36me) and Lys-80 (H3K79me) are linked to gene activation. Methylation at Lys-5 (H3K4me) facilitates subsequent acetylation of H3 and H4. Methylation at Lys-80 (H3K79me) is associated with DNA double-strand break (DSB) responses and is a specific target for TP53BP1. Methylation at Lys-10 (H3K9me) and Lys-28 (H3K27me) are linked to gene repression. Methylation at Lys-10 (H3K9me) is a specific target for HP1 proteins (CBX1, CBX3 and CBX5) and prevents subsequent phosphorylation at Ser-11 (H3S10ph) and acetylation of H3 and H4. Methylation at Lys-5 (H3K4me) and Lys-80 (H3K79me) require preliminary monoubiquitination of H2B at 'Lys-120'. Methylation at Lys-10 (H3K9me) and Lys-28 (H3K27me) are enriched in inactive X chromosome chromatin.
Phosphorylated at Thr-4 (H3T3ph) by GSG2/haspin during prophase and dephosphorylated during anaphase. Phosphorylation at Ser-11 (H3S10ph) by AURKB is crucial for chromosome condensation and cell-cycle progression during mitosis and meiosis. In addition phosphorylation at Ser-11 (H3S10ph) by RPS6KA4 and RPS6KA5 is important during interphase because it enables the transcription of genes following external stimulation, like mitogens, stress, growth factors or UV irradiation and result in the activation of genes, such as c-fos and c-jun. Phosphorylation at Ser-11 (H3S10ph), which is linked to gene activation, prevents methylation at Lys-10 (H3K9me) but facilitates acetylation of H3 and H4. Phosphorylation at Ser-11 (H3S10ph) by AURKB mediates the dissociation of HP1 proteins (CBX1, CBX3 and CBX5) from heterochromatin. Phosphorylation at Ser-11 (H3S10ph) is also an essential regulatory mechanism for neoplastic cell transformation. Phosphorylated at Ser-29 (H3S28ph) by MLTK isoform 1, RPS6KA5 or AURKB during mitosis or upon ultraviolet B irradiation. Phosphorylation at Thr-7 (H3T6ph) by PRKCBB is a specific tag for epigenetic transcriptional activation that prevents demethylation of Lys-5 (H3K4me) by LSD1/KDM1A. At centromeres, specifically phosphorylated at Thr-12 (H3T11ph) from prophase to early anaphase, by DAPK3 and PKN1. Phosphorylation at Thr-12 (H3T11ph) by PKN1 is a specific tag for epigenetic transcriptional activation that promotes demethylation of Lys-10 (H3K9me) by KDM4C/JMJD2C. Phosphorylation at Tyr-42 (H3Y41ph) by JAK2 promotes exclusion of CBX5 (HP1 alpha) from chromatin.
Monoubiquitinated by RAG1 in lymphoid cells, monoubiquitination is required for V(D)J recombination (By similarity). Ubiquitinated by the CUL4-DDB-RBX1 complex in response to ultraviolet irradiation. This may weaken the interaction between histones and DNA and facilitate DNA accessibility to repair proteins.
• Cellular localization
Nucleus. Chromosome.
• Information by UniProt
• Database links
• Alternative names
• H3 histone family member E pseudogene antibody
• H3 histone family, member A antibody
• H3/A antibody
• H31_HUMAN antibody
• H3F3 antibody
• H3FA antibody
• Hist1h3a antibody
• HIST1H3B antibody
• HIST1H3C antibody
• HIST1H3D antibody
• HIST1H3E antibody
• HIST1H3F antibody
• HIST1H3G antibody
• HIST1H3H antibody
• HIST1H3I antibody
• HIST1H3J antibody
• HIST3H3 antibody
• histone 1, H3a antibody
• Histone cluster 1, H3a antibody
• Histone H3 3 pseudogene antibody
• Histone H3.1 antibody
• Histone H3/a antibody
• Histone H3/b antibody
• Histone H3/c antibody
• Histone H3/d antibody
• Histone H3/f antibody
• Histone H3/h antibody
• Histone H3/i antibody
• Histone H3/j antibody
• Histone H3/k antibody
• Histone H3/l antibody
see all
Images
• Chromatin immunoprecipitation using ab5103 on the pS2 promoter. Times are after stimulation by estrogen (Ul).
• All lanes : Anti-Histone H3 (citrulline R2 + R8 + R17) antibody - ChIP Grade (ab5103) at 0.2 µg/ml
Lane 1 : HL60 whole cell lysate (negative control)
Lane 2 : HL60 whole cell lysate + DMSO (solvent control)
Lane 3 : HL60 whole cell lysate + DMSO + Calcium Ionophore (positive control)
Lysates/proteins at 20 µg per lane.
Secondary
All lanes : Goat anti Rabbit IR680 at 1/10000 dilution
Performed under reducing conditions.
Predicted band size: 15 kDa
Observed band size: 17 kDa
why is the actual band size different from the predicted?
Loading Control: GAPDH
This blot was produced using a 4-12% Bis-tris gel under the MES buffer system. The gel was run at 200V for 35 minutes before being transferred onto a Nitrocellulose membrane at 30V for 70 minutes. The membrane was then blocked for an hour using Licor blocking buffer before being incubated with ab5103 overnight at 4°C. Antibody binding was detected using Goat anti Rabbit IR680 secondary at a 1:10,000 dilution for 1hr at room temperature and then imaged using the Licor Odyssey CLx.
• ab5103 staining Histone H3 (citrulline 2 + 8 + 17) in Mouse bone marrow cells by Immunocytochemistry/ Immunofluorescence. Cells were fixed in formaldehyde and permeabilized in 0.1% Triton X-100 prior to blocking in 5% Goat serum for 2 hours at 25°C. The primary antibody was diluted 1/250 in PBS and incubated with the sample for 12 hours at 4°C. The secondary antibody was Alexa Fluor® 488-conjugated Goat anti-Rabbit polyclonal, diluted 1/500.
Nuclei were counterstained blue with DAPI.
See Abreview
• All batches of ab5103 are tested in Peptide Array against peptides to different Histone H3 modifications. Six dilutions of each peptide are printed on to the Peptide Array in triplicate and results are averaged before being plotted on to a graph. Results show strong binding to Histone H3 - citrulline 2 + 8 + 17 peptide (ab32876), indicating that this antibody specifically recognises the Histone H3 - citrulline 2 + 8 + 17 modifications.
ab32876 - Histone H3 - citrulline 2 + 8 + 17
ab17566 - Histone H3 - unmodified
• Rabbit polyclonal to Histone H3 (citrulline 2 + 8 + 17) used at 1/2000 dilution, after blocking with TBST 5% BSA. Purified histones run out with approximately 250 ng of each histone.
Lanes 1-3 contain Histone H3 (250 ng per lane)
Lane 1: PADI4 + Calcium
Lane 2: H3 + PADI4
Lane 3: H3 + PADI4 + Calcium
Lanes 4-5 contain bulk histones (250 ng per lane)
Lane 4: PADI4
Lane 5: PADI4 + Calcium
Lane 6: MCF7 cell extract
Lane 7: MCF7 cell extract (HA-PADI4)
Secondary antibody : anti-rabbit HRP from Sigma.
In WB ab5103 only recognizes human or bovine histone H3 when PADI4 and calcium are added.
• ICC/IF image of ab5103 stained human HeLa cells. The cells were PFA fixed (10 min), permabilised in TBS-T (20 min) and incubated with the antibody (ab5103, 1µg/ml) for 1h at room temperature. 1%BSA / 10% normal goat serum / 0.3M glycine was used to quench autofluorescence and block non-specific protein-protein interactions. The secondary antibody (green) was Alexa Fluor® 488 goat anti-rabbit IgG (H+L) used at a 1/1000 dilution for 1h. Alexa Fluor® 594 WGA was used to label plasma membranes (red). DAPI was used to stain the cell nuclei (blue).
• All lanes : Anti-Histone H3 (citrulline R2 + R8 + R17) antibody - ChIP Grade (ab5103) at 1 µg/ml
Lane 1 : HL60 (Human Caucasian promyelocytic leukaemia) DMSO and Calcium Ionophore treated Whole Cell Lysate with with 5% BSA
Lane 2 : HL60 (Human Caucasian promyelocytic leukaemia) DMSO and Calcium Ionophore treated Whole Cell Lysate with with 5% milk
Lane 3 : HL60 (Human Caucasian promyelocytic leukaemia) DMSO and Calcium Ionophore treated Whole Cell Lysate with with 3% milk
Lysates/proteins at 10 µg per lane.
Secondary
All lanes : Goat Anti-Rabbit IgG H&L (HRP) (ab97051) at 1/10000 dilution
Developed using the ECL technique.
Performed under reducing conditions.
Predicted band size: 15 kDa
Observed band size: 17 kDa why is the actual band size different from the predicted?
Exposure time: 30 seconds
Abcam recommends using milk as the blocking agent. Abcam welcomes customer feedback and would appreciate any comments regarding this product and the data presented above .
Blots were developled with Goat Anti-Rabbit IgG H&L (HRP) (ab97051) secondary antibody
References
This product has been referenced in:
• Fetz AE et al. Localized Delivery of Cl-Amidine From Electrospun Polydioxanone Templates to Regulate Acute Neutrophil NETosis: A Preliminary Evaluation of the PAD4 Inhibitor for Tissue Engineering. Front Pharmacol 9:289 (2018). Read more (PubMed: 29643810) »
• Pircher J et al. Cathelicidins prime platelets to mediate arterial thrombosis and tissue inflammation. Nat Commun 9:1523 (2018). Read more (PubMed: 29670076) »
See all 130 Publications for this product
Customer reviews and Q&As
1-10 of 23 Abreviews or Q&A
Abcam guarantees this product to work in the species/application used in this Abreview.
Application
Western blot
Sample
Mouse Cell lysate - whole cell (RAW 264.7 cells)
Gel Running Conditions
Reduced Denaturing (4-20%)
Loading amount
25 µg
Specification
RAW 264.7 cells
Blocking step
Milk as blocking agent for 1 hour(s) and 30 minute(s) · Concentration: 5% · Temperature: RT°C
Abcam user community
Verified customer
Submitted Jun 07 2018
Application
Immunocytochemistry/ Immunofluorescence
Sample
Mouse Cell (macrophage cell line)
Permeabilization
Yes - 0.1% Triton in PBS for 5 min
Specification
macrophage cell line
Blocking step
Serum as blocking agent for 30 minute(s) · Concentration: 1% · Temperature: RT°C
Fixative
Paraformaldehyde
Abcam user community
Verified customer
Submitted Jun 04 2018
Application
Immunohistochemistry (Frozen sections)
Sample
Mouse Cell (Lung)
Permeabilization
Yes - Triton 0.1%
Specification
Lung
Blocking step
BSA as blocking agent for 2 hour(s) and 0 minute(s) · Concentration: 3% · Temperature: 37°C
Fixative
Zinc fixative
Abcam user community
Verified customer
Submitted Jul 26 2017
Application
ELISA
Sample
Human Serum (EDTA Plasma Samples)
Specification
EDTA Plasma Samples
Blocking step
BSA as blocking agent for 1 hour(s) and 0 minute(s) · Concentration: 1% · Temperature: 21°C
Type
Direct
Herr Dr. Thomas Scherz
Verified customer
Submitted Apr 28 2017
Application
Western blot
Sample
Human Cell lysate - whole cell (MCF-7, Hep G2)
Gel Running Conditions
Reduced Denaturing
Loading amount
25 µg
Specification
MCF-7, Hep G2
Blocking step
Milk as blocking agent for 1 hour(s) and 0 minute(s) · Concentration: 10% · Temperature: 25°C
Abcam user community
Verified customer
Submitted Aug 19 2016
Application
Immunohistochemistry (Formalin/PFA-fixed paraffin-embedded sections)
Sample
Mouse Tissue sections (Kidney)
Antigen retrieval step
Heat mediated - Buffer/Enzyme Used: 10 mM Citrate
Permeabilization
No
Specification
Kidney
Blocking step
Serum as blocking agent for 1 hour(s) and 0 minute(s) · Concentration: 10% · Temperature: 4°C
Fixative
Paraformaldehyde
Abcam user community
Verified customer
Submitted Oct 06 2015
Application
Western blot
Sample
Mouse Tissue lysate - whole (Kidney)
Gel Running Conditions
Reduced Denaturing (4-12%)
Loading amount
20 µg
Specification
Kidney
Blocking step
Milk as blocking agent for 1 hour(s) and 0 minute(s) · Concentration: 5% · Temperature: 25°C
Dr. Wesley Konsavage
Verified customer
Submitted Oct 05 2015
Application
Western blot
Loading amount
15 µg
Gel Running Conditions
Reduced Denaturing
Sample
Mouse Cell lysate - whole cell (hepatocytes)
Specification
hepatocytes
Blocking step
Milk as blocking agent for 1 hour(s) and 0 minute(s) · Concentration: 5% · Temperature: 23°C
Abcam user community
Verified customer
Submitted Dec 26 2014
Answer
The image shown using PADI4 and Calcium on our datasheet is copied from 2004 Cell paper by Kouzarides’ lab.
This experiment was not actually performed in the abcam labs and therefore I’m afraid that I can’t add much clarification to what’s already described in the original paper:
http://www.ncbi.nlm.nih.gov/pubmed/15339660?dopt=Abstract
It looks that left-hand side and middle panels are in-vitro modification of H3 using purified recomb PADI4 that deposits the cit-modification and active only in the presence of Ca++
Left-hand side panel is overexpression of PADI4 in MCF7 cells.
“The Cit-H3 antibody http://www.sciencedirect.com/science/article/pii/S0092867404007998#FIG3 was raised against a peptide corresponding to the tail of H3 with citrulline present in the place of R2, R8, and R17 http://www.sciencedirect.com/science/article/pii/S0092867404007998#FIG3. http://www.sciencedirect.com/science/article/pii/S0092867404007998#FIG3 shows that the Cit-H3 antibody recognizes the faster migrating deiminated H3, which is generated when PADI4 is incubated with H3. No reactivity is observed with unmodified H3 http://www.sciencedirect.com/science/article/pii/S0092867404007998#FIG3 or with other histones treated by PADI4 http://www.sciencedirect.com/science/article/pii/S0092867404007998#FIG3. Use of this antibody in Western blots indicates that H3 has virtually undetectable levels of citrulline in cultured MCF-7 cells (http://www.sciencedirect.com/science/article/pii/S0092867404007998#FIG3, lane 1). However, when PADI4 is overexpressed in these cells, detection of deiminated H3 by the Cit-H3 antibody increases substantially (http://www.sciencedirect.com/science/article/pii/S0092867404007998#FIG3, lane 2). These results confirm that endogenous H3 tail arginine residues are deiminated by the action of PADI4.”
Experimental Procedures
In Vitro Reactions
GST.PADI4 constructs were expressed at 30°C in 2TY media in 0.1 mM IPTG from pGEX6p and purified using glutathione-Sepharose resin. Deimination reactions were carried out using bead-bound enzyme in 50 mM HEPES [pH 7.5], 2 mM DTT, and 10 mM CaCl2 at 30°C. Substrates were bulk calf thymus histones (Sigma), purified calf thymus histone H3 (Roche), recombinant histone H3 and tailless histone H3 lacking residues 1–26, and various peptides. Peptides described in the manuscript were synthesized by Graham Bloomberg at the University of Bristol.
GST.CARM1 was expressed and purified as above. GST.CARM1 was eluted using 50 mM reduced glutathione then dialyzed against 10% glycerol in PBS. Methylation reactions were carried out in 5% glycerol, PBS with [3H]S-adenosyl-L-methionine. CARM1 peptide reactions were bound to p81 cation exchange membrane (Whatman), washed with 50 mM carbonate buffer [pH 9.2], and incorporated radioactivity measured by scintillation counting http://www.sciencedirect.com/science/article/pii/S0092867404007998#BIB3.
HEK293 and MCF-7 cells were maintained in Dulbecco's modified Eagle's medium (DMEM, Gibco-BRL) supplemented with 10% fetal calf serum (FCS, Gibco-BRL) at 37°C and 5% CO2. Cells were transfected with pcDNA3.HA.PADI4 using FuGENE transfection reagent (Roche) according to the manufacturer's instructions. 48 hr posttransfection cells were lysed in 50 mM HEPES [pH 7.5], 2 mM DTT, 150 mM NaCl, 0.5% NP-40, and HA.PADI4 was immunoprecipitated using an anti-HA antibody (Abcam ab9110). Immunoprecipitated bead-bound protein was washed with lysis buffer and reactions carried in vitro out as above. Whole-cell extracts were made by lysing MCF-7 cells in RIPA buffer (50 mM Tris [pH 8.0], 150 mM NaCl, 1% NP-40, 0.5% deoxycholate).
Antibodies
Polyclonal α-PADI4 was raised by immunizing a rabbit with purified GST-PADI4 then affinity purifying the antibody from whole serum with GST-PADI4 http://www.sciencedirect.com/science/article/pii/S0092867404007998#BIB11. Polyclonal α-modified citrulline was purchased from Upstate (Cat.no.17-347) and the modification of membrane bound citrulline carried out according to the supplier's instructions. The monoclonal antibody recognizing context-independent monomethyl arginine was purchased from Abcam (ab415), as was the antibody against dimethyl R17 of H3 (ab8284). The polyclonal citH3 antibody was raised in collaboration with Abcam (ab5103) by immunizing a rabbit with a peptide of the sequence ACitTKQTACitKSTGGKAPCitKQLA and purifying the antibody against the same peptide. The monoclonal antibody against RNA polymerase II was purchased from Covance (Cat. no. MMS-126R-500).
Read More
Answer
HeLa Cells:
For 3.5 x 10e6 HeLa cells per plate, we pool 2 plates per falcon tube (in about 16ml PBS). We then centrifuge the cells @ 4°C for 5mins at 3000rpm. The PBS is then aspirated off and the cells re-suspended into 2.8ml of ChIP lysis buffer and incubated on ice for 10mins. Sonicate after these 10mins.
Sonication:
We never use ethanol, just ice cold water. It is important though that there is no ice in the water. We use a Bioruptor with probes. The cells are sonicated for 40mins at intervals of 5mins, changing the water in between each 5min sonication. The 5min sonication is 30secs sonication and then 30sec rest (5 times).
There is no real answer to avoiding foaming during sonication as the lysis buffer can cause this. What I would recommend though, is to check for foaming/bubbles in between the 5min sonications and if there are bubbles etc, transfer the supernatant to a new tube, leaving the bubbles/foam behind - this tends to work.
Read More
1-10 of 23 Abreviews or Q&A
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1,715,492,206,527,159,600 |
製品の概要
法規制情報
製品の詳細
• 由来
Recombinant
• 由来
Baculovirus
• アミノ酸配列
• 生物種
Human
特性
Our Abpromise guarantee covers the use of ab82241 in the following tested applications.
The application notes include recommended starting dilutions; optimal dilutions/concentrations should be determined by the end user.
• アプリケーション
SDS-PAGE
Western blot
• 精製度
> 95 % SDS-PAGE.
ab82241 is greater than 95% homogeneous based on SDS-PAGE analysis, purified by affinity and FPLC chromatography.
• 製品の状態
Liquid
• Concentration information loading...
前処理および保存
• 保存方法および安定性
Shipped on dry ice. Upon delivery aliquot and store at -80ºC. Avoid freeze / thaw cycles.
Preservative: None
Constituents: 20% Glycerol, 20mM Tris Cl, 100mM Potassium chloride, 1mM DTT, 0.2mM EDTA, pH 8.0
関連情報
• 別名
• AI132454
• B cell CLL/lymphoma 10
• B cell lymphoma/leukemia10
• B-cell CLL/lymphoma 10
• B-cell leukemia/lymphoma 10
• B-cell lymphoma/leukemia 10
• Bcl 10
• Bcl-10
• Bcl10
• BCL10_HUMAN
• c E10
• c-E10
• C81403
• CARD containing apoptotic signaling protein
• CARD containing molecule enhancing NF kappa B
• CARD containing molecule enhancing NF kB
• CARD containing molecule enhancing NF-kB
• CARD containing molecule enhancing NFkB
• CARD containing proapoptotic protein
• CARD like apoptotic protein
• CARD-containing apoptotic signaling protein
• CARD-containing molecule enhancing NF-kappa-B
• CARD-containing proapoptotic protein
• CARD-like apoptotic protein
• CARMEN
• Caspase recruiting domain containing protein
• caspase-recruiting domain-containing protein
• cCARMEN
• cE 10
• cE10
• CED 3/ICH 1 prodomain homologous E10 like regulator
• CED-3/ICH-1 prodomain homologous E10-like regulator
• CED3/ICH1 prodomain homologous E10 like regulator
• Cellular E10
• Cellular homolog of vCARMEN
• Cellular-E10
• CIPER
• CLAP
• hCLAP
• Mammalian CARD containing adapter molecule E10
• Mammalian CARD-containing adapter molecule E10
• mE 10
• mE10
• R-RCD1
see all
• 機能
Promotes apoptosis, pro-caspase-9 maturation and activation of NF-kappa-B via NIK and IKK. May be an adapter protein between upstream TNFR1-TRADD-RIP complex and the downstream NIK-IKK-IKAP complex. Is a substrate for MALT1.
• 組織特異性
Ubiquitous.
• 関連疾患
Note=A chromosomal aberration involving BCL10 is recurrent in low-grade mucosa-associated lymphoid tissue (MALT lymphoma). Translocation t(1;14)(p22;q32). Although the BCL10/IgH translocation leaves the coding region of BCL10 intact, frequent BCL10 mutations could be attributed to the Ig somatic hypermutation mechanism resulting in nucleotide transitions.
Note=Defects in BCL10 are involved in various types of cancer.
• 配列類似性
Contains 1 CARD domain.
• 翻訳後修飾
Phosphorylated. Phosphorylation results in dissociation from TRAF2 and binding to BIRC2/c-IAP2.
• 細胞内局在
Cytoplasm > perinuclear region. Membrane raft. Appears to have a perinuclear, compact and filamentous pattern of expression. Also found in the nucleus of several types of tumor cells. Colocalized with DPP4 in membrane rafts.
• Information by UniProt
参考文献
ab82241 has not yet been referenced specifically in any publications.
レビューと Q&A
There are currently no Customer reviews or Questions for ab82241.
Please use the links above to contact us or submit feedback about this product.
Please note: All products are "FOR RESEARCH USE ONLY AND ARE NOT INTENDED FOR DIAGNOSTIC OR THERAPEUTIC USE"
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1,586,240,835,307,885,800 | Changes related to "MEG"
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7,929,286,700,507,377,000 | TEX9 antibody
Principal name
TEX9 antibody
Alternative names for TEX9 antibody
Testis-expressed sequence 9 protein
SwissProt ID
Q8N6V9 (Human), Q9D845 (Mouse)
Gene ID
374618 (TEX9)
Available reactivities
Can (Canine), Hu (Human), Ms (Mouse), Rt (Rat), Ze (Zebrafish), Bov (Bovine), Eq (Equine), GP (Guinea Pig), Por (Porcine), Rb (Rabbit)
Available hosts
Rabbit, Mouse
Available applications
Western blot / Immunoblot (WB), Paraffin Sections (P), Flow Cytometry (F)
Background of TEX9 antibody
Transient overexpression lysate of testis expressed 9 (TEX9)
9 Item(s)
per page
Primary Antibodies
Catalog No. Host Iso. Clone Pres. React. Applications
TEX9 antibody
Host: Rabbit; Target Name: TEX9; Sample Tissue: 721_B Whole cell lysates; Antibody Dilution: 1.0 ug/ml Rabbit IgG Purified Bov, Can, Eq, GP, Hu, Ms, Por, Rb, Rt, Ze WB
50 µg / €325.00
OriGene Technologies, Inc.
TEX9 antibody
WB Suggested Anti-TEX9 Antibody Titration: 0.2-1 ug/ml; ELISA Titer: 1:312500; Positive Control: Human brain Rabbit IgG Purified Can, Eq, GP, Hu, Ms, Por, Rb, Rt, Ze WB
50 µg / €325.00
OriGene Technologies, Inc.
TEX9 (N-term) antibody
TEX9 antibody (N-term) (AP54223PU-N) immunohistochemistry analysis in formalin fixed and paraffin embedded human testis carcinoma followed by peroxidase conjugation of the secondary antibody and DAB staining. This data demonstrates the use of the TEX9 antibody (N-term) for immunohistochemistry. Clinical relevance has not been evaluated. Rabbit Ig Aff - Purified Hu F, P, WB
0.4 ml / €370.00
Acris Antibodies GmbH
TEX9 antibody
TEX9 Mouse Hu WB
0.5 mg / €1,400.00
Abnova Taiwan Corp.
TEX9 antibody
Human Brain; WB Suggested Anti-TEX9 Antibody Titration: 0.2-1 ug/ml. ELISA Titer: 1:312500. Positive Control: Human brain; TEX9 antibody - middle region (ARP55896_P050) in Human Brain cells using Western Blot Rabbit Aff - Purified Can, Hu, Ms, Rt, Ze WB
50 µg / €350.00
AVIVA Systems Biology
TEX9 antibody
Western Blot: TEX9 Antibody [NBP1-56553] - This Anti-TEX9 antibody was used in Western Blot of Fetal Brain tissue lysate at a concentration of 1ug/ml. Rabbit Aff - Purified Hu, Ms, Rt WB
50 µg / €440.00
Novus Biologicals Inc.
TEX9 antibody
Immunohistochemistry-Paraffin: TEX9 Antibody [NBP1-86249] - Immunohistochemical staining of human testis shows strong cytoplasmic positivity in cells in seminiferus ducts. Rabbit IgG Aff - Purified Hu P, WB
0.1 ml / €500.00
Novus Biologicals Inc.
Proteins & Growth Factors
Catalog No. Species Pres. Purity Source
TEX9
TEX9 Human > 80 %
Preparation: Recombint protein was captured through anti-DDK affinity column followed by conventiol chromatography steps.
Purity Detail: > 80% as determined by SDS-PAGE and Coomassie blue staining.
HEK293 cells
20 µg / €680.00
OriGene Technologies, Inc.
Lysates
Catalog No.
TEX9 overexpression lysate
TEX9 overexpression lysate
0.1 mg / €280.00
OriGene Technologies, Inc.
9 Item(s)
per page
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} | 57 | cf5cd1df0ee2161e1684bdc019357275 |
4,520,840,022,178,849,000 | Online GK Series
This site is dedicated to the aspirants of competitive exams SSC, UPSC, Railways, Postal Assistants, Bank, GATE and NET
Biogeography - GK Questions and Answers for competitive exams on Geography | page-6
Questions
26 Which of the following soils is very hard to cultivate ?
A Alluvial
B Black
C Red
D Sandy
Answer: Option [C]
27 Which soil is formed by deposition of silt brought by rivers ?
A Black
B Alluvial
C Red
D Pod
Answer: Option [B]
28 Which of the following soils is most suitable for cultivation of cereals ?
A Alluvial soils
B Red soils
C Laterite soils
D Pod soils
Answer: Option [A]
29 Which of the following soils is most suitable for cultivation of cotton ?
A Red
B Clayey
C Alluvial
D Regur
Answer: Option [D]
30 Which of the following types of soils have a marked capacity to retain water ?
A Desert soil
B Laterite soil
C Regur soil
D Pod soil
Answer: Option [C]
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-664,272,718,462,887,700 | August 2015
Table of Contents - PeerJ (Biology Articles)
August 20, 2015
3 citations
513 downloads
2,084 views
, ,
https://doi.org/10.7717/peerj.1193 PubMed 26312184
August 20, 2015
1 citation
275 downloads
1,835 views
,
https://doi.org/10.7717/peerj.1166 PubMed 26312176
August 13, 2015
1 citation
585 downloads
1,782 views
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https://doi.org/10.7717/peerj.1153 PubMed 26339538
August 4, 2015
3 citations
397 downloads
2,588 views
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https://doi.org/10.7717/peerj.1137 PubMed 26290793
August 4, 2015
8 citations
442 downloads
2,059 views
, , , , , ,
https://doi.org/10.7717/peerj.1119 PubMed 26290787
I told my colleagues that PeerJ is a journal where they need to publish if they want their paper to be published quickly and with the strict peer review expected from a good journal.
Sohath Vanegas,
PeerJ Author
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2,746,556,283,014,553,000 | Feeds:
Posts
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Posts Tagged ‘Cell Biology’
Biologists Wondered—How Old are Cells in an Organism?
Reporter: Irina Robu, PhD
Scientists form Salk Institute discovered that the mouse brain, live and pancreas contain populations of cells and proteins with extremely long lifespans with some as old as neurons. The research was published in Cell Metabolism on June 6, 2019. The general idea is that most neurons in the brain do not divide during adulthood and experience a long lifespan and age-related decline. Yet, due to limitations the lifespan of cells outside of the brain was difficult to determine.
However, the researchers knew very well that neurons are not replaced during the lifespan, they used them as control to compare other non-dividing cells. The team used an electron isotope labeling with hybrid imaging method to visualize and quantify cell and protein age and turnover in the brain, pancreas and liver in the young and old rodent models.
To confirm that their method is correct, the scientist determined first the age of the neurons and then realized that the cells that line blood vessels, endothelial cells were as old as neurons. According to this research, it means that some non-neuronal cells do not replicate themselves throughout the lifespan. The pancreas, the organ responsible for maintaining blood sugar levels and secreting digestive enzymes showed cells of all ages. Still, some beta cells, replicate during the lifetime and are relatively young, while others do not divide and were long lived. Yet, delta cells found in stomach do not divide at all.
Unlike other type of cells, the liver cells have the capacity to regenerate during adulthood. The researchers expected to observe young liver cells, however the majority of liver cells were found to be as old as the animal, while the cells that line blood vessels and stellate like cells, another liver type cell were short lived.
But on the molecular level, a selection of long-lived cells contains protein complexes displaying age mosaicism. Due to the modern visualizing technologies, scientists were able to pinpoint the age of the cells and their supra-molecular complexes precisely. The ultimate goal to determining the age of the cells and sub-cellular structures is to provide insights into cell maintenance and repair mechanism and utilize these mechanisms to prevent or delay old age-linked decline of organs with limited cell regeneration.
SOURCE
https://www.salk.edu/news-release/how-old-are-your-organs-to-scientists-surprise-organs-are-a-mix-of-young-and-old-cells/
Read Full Post »
First Haploid Human Stem Cells
Reported: Irina Robu, PhD
Most of the cells in our body are diploid, which indicate they carry two sets of chromosomes—one from each parent. So far, scientists have only succeeded in generating haploid embryonic stem cells—which comprise a single set of chromosomes in non-human mammals such as mice, rats and monkeys. Nevertheless, scientists have tried to isolate and duplicate these haploid ESCs in humans, which would allow them to work with one set of human chromosomes as opposed to a mixture from both parents.
Scientists from Hebrew from The Hebrew University of Jerusalem, Columbia University Medical Center (CUMC) and The New York Stem Cell Foundation Research Institute (NYSCF) were successful in generating a new type of embryonic stem cells that has a single copy of the human genome, instead of two copies which is typically found in normal stem cells.
This landmark was finally obtained by Ido Sagi, working as a PhD student at the Hebrew University of Jerusalem which was successful in isolating and maintaining haploid embryonic stem cells in humans. Unlike in mice, these haploid stem cells were capable to differentiate into various cell types such as brain, heart and pancreas, although holding a single set of chromosomes. Sagi and his advisor, Prof. Nissim Benvenisty showed that this new human stem cell type will play an important role in human genetic and medical research. This new human cell type cell type will aid in understanding human development and it will make genetic screening simpler and more precise, by examining a single set of chromosomes.
Based on this research, the Technology Transfer arm of the Hebrew University, started a new company New Stem, which is developing a diagnostic kit for predicting resistance to chemotherapy treatments. By gathering a broad library of human pluripotent stem cells with various genetic makeups and mutations. The company is planning to use this kit for personalized medication and future therapeutic and reproductive products.
SOURCE
https://medicalxpress.com/news/2017-06-haploid-human-stem-cells-medical.html#jCp
Other related articles published in this Open Access Online Scientific Journal include the following:
Ido Sagi – PhD Student @HUJI, 2017 Kaye Innovation Award winner for leading research that yielded the first successful isolation and maintenance of haploid embryonic stem cells in humans.
Reporter: Aviva Lev-Ari, PhD, RN
Ido Sagi – PhD Student @HUJI, 2017 Kaye Innovation Award winner for leading research that yielded the first successful isolation and maintenance of haploid embryonic stem cells in humans.
Read Full Post »
Cellular Guillotine Created for Studying Single-Cell Wound Repair
Reporter: Irina Robu, PhD
Using the century-old cutting method, it would take a researcher five hours to cut 100 cells, and by the time they were done, the cells they cut first would be well on their way to healing.
In an effort to comprehend how a single cell heal, mechanical engineer Sing Tand developed a microscopic guillotine that proficiently cuts cells into two.
Tang, who is an assistant professor of mechanical engineering at Stanford University knew that finding a way to competently slice the cell in two could lead to engineering self-healing materials and machines. In order, to efficiently slice a cell in two he developed a tool that could cut 150 cells in just over 2 minutes, and the cuts were much more standardized and synchronized in the stage of their repair process. They attained this rate by creating a scaled-up version of their tool with eight identical parallel channels that run simultaneously. Being able to efficiently study cell healing could eventually help scientists study and treat a variety of human diseases such as cancer and neurodegenerative diseases. Prior to Tang’s cellular guillotine, scientists used to slice cells by hand under a microscope using a glass needle which is a method that can lead to errors.
Tang’s method can be the Holy Grail of engineering self-healing materials and machines.
SOURCE
http://news.stanford.edu/2017/06/26/stanford-scientists-create-cellular-guillotine-studying-single-cell-wound-repair/
Read Full Post »
Nanostraws Developed at Stanford Sample a Cell’s Contents without Damage
Reporter: Irina Robu, PhD
Cells within our bodies change over time and divide, with thousands of chemical reactions happening within cell daily. Nicholas Melosh, Associate Professor of Materials Science and Engineering, developed a new, non-destructive system for sampling cells with nanoscale straws which could help uncover mysteries about how cells function.
Currently, cells are sampled via lysing which ruptures the cell membrane which means that it can’t ever be sampled again. The sample system that Dr. Melosh invented banks on, on tiny tubes 600 times smaller than a strand of hair that allow researchers to sample a single cell at a time. The nanostraws penetrate a cell’s outer membrane, without damaging it, and draw out proteins and genetic material from the cell’s salty interior.
The Nanostraw sampling technique, according to Melosh, will knowingly impact our understanding of cell development and could result to much safer and operational medical therapies because the technique allows for long term, non-destructive monitoring. The sampling technique could also inform cancer treatments and answer questions about why some cancer cells are resistant to chemotherapy while others are not. The sampling platform on which the nanostraws are grown is tiny, similar to the size of a gumball. It’s called the Nanostraw Extraction (NEX) sampling system, and it was designed to mimic biology itself.
The goal of developing this technology was to make an impact in medical biology by providing a platform that any lab could build.
SOURCE
http://news.stanford.edu/2017/02/20/minuscule-nanostraws-sample-cells-contents-without-damage
Read Full Post »
Spermatogenic Defects in Sex Reversed Mice
Reporter and Curator: Dr. Sudipta Saha, Ph.D.
“Sex reversed” (Sxr) is an inherited form of sex reversal that causes XX and XO mice to develop as phenotypically normal males. Adult XYSxra mice exhibit varying degrees of spermatogenic deficiency but are usually fertile, while XOSxra mice have severe spermatogenic failure and are always sterile. The present quantitative spermatogenic analysis reports when these anomalies first appear during puberty. The results demonstrate that in XYSxra mice there was increased degeneration of pachytene spermatocytes and, to a lesser extent, meiotic metaphase stages. On average, there were only one-half the number of spermatids compared with the XY controls. The defect in XOSxra mice appeared a little later, with an almost complete arrest and degeneration during the meiotic metaphases.
A minority of XYSxra mice are sterile, and these may have testes as small as those from XOSxra mice. Adult XOSxra mice have consistently small testes and are invariably sterile. The reported results document the testicular defects in XYSxra and XOSxra testes as they first arise during puberty. The only other quantitative data on XYSxra and XOSxra spermatogenesis are for adult mice. A previous report described XYSxra testes as being a “mosaic” of normal and defective spermatogenesis. Recently a more extensive analysis was carried out of adult XYSxra and XOSxra testes. Once again there is good agreement with the present results in that the spermatogenic failure in XYSxra testes was predominantly between pachytene and diplotene, while in XOSxra testes the block was predominantly during the meiotic metaphases. To explain the spermatogenic anomalies in XYSxra and XOSxra testes, Burgoyne and Baker (1984) invoked the “meiotic pairing site” hypothesis of Miklos (1974). The other notable feature of the present study was the demonstration that the testicular deficiency is manifested earlier (with respect to age and spermatogenic stage) in XYSxra testes than in XOSxra testes. Krzanowska (1989) recently reported increased levels of X-Y univalence in pubertal XY males. So, it is suggested that this reduced efficiency of X-Y pairing at puberty that leads to the increased incidence of diploid spermatids in pubertal XYSxra males and to the presence of diploid spermatids in pubertal XY males. The other feature of pubertal XYSxra testes that deserves mention is the increase in the number of differentiating spermatogonia.
The conclusion is that most of the spermatogenic deficiencies in XYSxra and XOSxra testes can be explained in terms of the “meiotic pairing site” hypothesis, which links spermatogenic failure with sex chromosome univalence during meiosis. In XYSxra testes a variable proportion of pachytene spermatocytes have the X and Y unpaired, and the elimination of these cells explains the variable reduction in testis size and fertility. In XOSxra testes all spermatocytes have a univalent sex chromosome, accounting for the almost total spermatogenic block in these mice. It is suggested that the affected spermatocytes are eliminated earlier in XYSxra testes than in XOSxra testes, because two univalent sex chromosomes have more unpaired sites than the univalent X alone.
References:
Sutcliffe M. J., Darling S. M., Burgoyne P. S. (1991) Spermatogenesis in XY, XYSxra and XOSxra Mice: A quantitative analysis of spermatogenesis throughout puberty. Molecular Reprod. Dev. 30(2), 81–89.
Burgoyne P. S., Baker T. G. (1984) Meiotic pairing and gametogenic failure. In CW Evans and HG Dickinson (eds): “Controlling Events in Meiosis (38th Symp SOC Exp Biol).” Cambridge Company of Biologists, pp 349-362.
Miklos G. L. G. (1974) Sex-chromosome pairing and male fertility. Cytogen. Cell Genet. 13, 558-577.
Krzanowska H (1989) X-Y chromosome dissociation in mouse strains differing in efficiency of spermatogenesis: Elevated frequency of univalents in pubertal males. Gamete. Res. 23, 357-365.
Read Full Post »
3D “Squeeze” Helps Adult Cells Become Stem Cells
Reported by: Irina Robu, PhD
Scientists based at Ecole Polytechnique Fédérale de Lausanne led by Matthias Lutolf have been engineering 3D extracellular matrices—gels. These scientists report that they have developed a gel that boosts the ability of normal cells to revert into stem cells by simply “squeezing” them.
The detail of the scientists’ work appeared in Nature Materials, January 11, 2015 in an article entitled, “Defined three-dimensional microenvironments boost induction of pluripotency.” According to the authors they find that the physical cell confinement imposed by the 3D microenvironment boosts reprogramming through an accelerated mesenchymal-to-epithelial transition and increased epigenetic remodeling. They concluded that 3D microenvironmental signals act synergistically with reprogramming transcription factors to increase somatic plasticity.
The researchers discovered that they could reprogram the cells faster and more efficiently by simply adjusting the composition, hence the stiffness and density of the surrounding gel. As a result, the gel exerts different forces on the cells, “squeezing” them.
The scientists propose that the 3D environment is key to this process, generating mechanical signals that work together with genetic factors to make the cell easier to transform into a stem cell. The technique can be applied to a large number of cells to produce stem cells on an industrial scale.
Source
http://www.genengnews.com/gen-news-highlights/3d-squeeze-helps-adult-cells-become-stem-cells/81252223/
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brown adipocyte protein CIDEA promotes lipid droplet fusion
Larry H. Bernstein, MD, FCAP, Curator
LPBI
The brown adipocyte protein CIDEA promotes lipid droplet fusion via a phosphatidic acid-binding
Parker, Nicholas T Ktistakis, Ann M Dixon, Judith Klein-Seetharaman, Susan Henry, Mark Christian Dirk Dormann, Gil-Soo Han, Stephen A Jesch, George M Carman, Valerian Kagan, et al.
eLife 2015;10.7554/eLife.07485 http://dx.doi.org/10.7554/eLife.07485
Maintenance of energy homeostasis depends on the highly regulated storage and release of triacylglycerol primarily in adipose tissue and excessive storage is a feature of common metabolic disorders. CIDEA is a lipid droplet (LD)-protein enriched in brown adipocytes promoting the enlargement of LDs which are dynamic, ubiquitous organelles specialized for storing neutral lipids. We demonstrate an essential role in this process for an amphipathic helix in CIDEA, which facilitates embedding in the LD phospholipid monolayer and binds phosphatidic acid (PA). LD pairs are docked by CIDEA trans-complexes through contributions of the N-terminal domain and a C-terminal dimerization region. These complexes, enriched at the LD-LD contact site, interact with the cone-shaped phospholipid PA and likely increase phospholipid barrier permeability, promoting LD fusion by transference of lipids. This physiological process is essential in adipocyte differentiation as well as serving to facilitate the tight coupling of lipolysis and lipogenesis in activated brown fat.
Evolutionary pressures for survival in fluctuating environments that expose organisms to times of both feast and famine have selected for the ability to efficiently store and release energy in the form of triacyclglycerol (TAG). However, excessive or defective lipid storage is a key feature of common diseases such as diabetes, atherosclerosis and the metabolic syndrome (1). The organelles that are essential for storing and mobilizing intracellular fat are lipid droplets (LDs) (2). They constitute a unique cellular structure where a core of neutral lipids is stabilized in the hydrophilic cytosol by a phospholipid monolayer embedding LD-proteins. While most mammalian 46 cells present small LDs (<1 Pm) (3), white (unilocular) adipocytes contain a single giant LD occupying most of their cell volume. In contrast, brown (multilocular) adipocytes hold multiple LDs of lesser size, increasing the LD surface/volume ratio which facilitates the rapid consumption of lipids for adaptive thermogenesis (4).
The exploration of new approaches for the treatment of metabolic disorders has been stimulated by the rediscovery of active brown adipose tissue (BAT) in adult humans (5, 6) and by the induction of multilocular brown-like cells in white adipose tissue (WAT) (7). The multilocular morphology of brown adipocytes is a defining characteristic of these cells along with expression of genes such as Ucp1. The acquisition of a unilocular or multilocular phenotype is likely to be controlled by the regulation of LD growth. Two related proteins, CIDEA and CIDEC promote LD enlargement in adipocytes (8-10), with CIDEA being specifically found in BAT. Together with CIDEB, they form the CIDE (cell death-inducing DFF45-like effector) family of LD-proteins, which have emerged as important metabolic regulators (11).
Different mechanisms have been proposed for LD enlargement, including in situ neutral lipid synthesis, lipid uptake and LD-LD coalescence (12-14). The study of CIDE 62 proteins has revealed a critical role in the LD fusion process in which a donor LD progressively transfers its content to an acceptor LD until it is completely absorbed (15). However, the underlying mechanism by which CIDEC and CIDEA facilitate the interchange of triacylglycerol (TAG) molecules between LDs is not understood. In the present study, we have obtained a detailed picture of the different steps driving this LD enlargement process, which involves the stabilization of LD pairs, phospholipid binding, and the permeabilization of the LD monolayer to allow the transference of lipids.
CIDEA expression mimics the LD dynamics observed during the differentiation of brown adipocytes
Phases of CIDEA activity: LD targeting, LD-LD docking and LD growth
A cationic amphipathic helix in C-term drives LD targeting
The amphipathic helix is essential for LD enlargement
LD-LD docking is induced by the formation of CIDEA complexes
CIDEC differs from CIDEA in its dependence on the N-term domain
CIDEA interacts with Phosphatidic Acid
PA is required for LD enlargement
The Cidea gene is highly expressed in BAT, induced in WAT following cold exposure (46), and is widely used by researchers as a defining marker to discriminate brown or brite adipocytes from white adipocytes (7, 28). As evidence indicated a key role in the LD biology (47) we have characterized the mechanism by which CIDEA promotes LD enlargement, which involves the targeting of LDs, the docking of LD pairs and the transference of lipids between them. The lipid transfer step requires the interaction of CIDEA and PA through a cationic amphipathic helix. Independently of PA-binding, this helix is also responsible for anchoring CIDEA in the LD membrane. Finally, we demonstrate that the docking of LD pairs is driven by the formation of CIDEA complexes involving the N-term domain and a C-term interaction site.
CIDE proteins appeared during vertebrate evolution by the combination of an ancestor N-term domain and a LD-binding C-term domain (35). In spite of this, the full process of LD enlargement can be induced in yeast by the sole exogenous expression of 395 CIDEA, indicating that in contrast to SNARE-triggered vesicle fusion, LD fusion by lipid transference does not require the coordination of multiple specific proteins (48). Whereas vesicle fusion implicates an intricate restructuring of the phospholipid bilayers, LD fusion is a spontaneous process that the cell has to prevent by tightly controlling their phospholipid composition (23). However, although phospholipid-modifying enzymes have been linked with the biogenesis of LDs (49, 50), the implication of phospholipids in physiologic LD fusion processes has not been previously described.
Complete LD fusion by lipid transfer can last several hours, during which the participating LDs remain in contact. Our results indicate that both the N-term domain and a C-term dimerization site (aa 126-155) independently participate in the docking of LD pairs by forming trans interactions (Fig. 7). Certain mutations in the dimerization sites that do not eliminate the interaction result in a decrease on the TAG transference efficiency, reflected on the presence of small LDs docked to enlarged LDs. This suggests that in addition to stabilizing the LD-LD interaction, the correct conformation of the 409 CIDEA complexes is necessary for optimal TAG transfer. Furthermore, the formation of stable LD pairs is not sufficient to trigger LD fusion by lipid transfer. In fact, although LDs can be tightly packed in cultured adipocytes, no TAG transference across neighbour LDs is observed in the absence of CIDE proteins (15), showing that the phospholipid monolayer acts as a barrier impermeable to TAG. Our CG-MD simulations indicate that certain TAG molecules can escape the neutral lipid core of the LD and be integrated within the aliphatic chains of the phospholipid monolayer. This could be a transition state 416 prior to the TAG transference and our data indicates that the docking of the amphipathic helix in the LD membrane could facilitate this process. However, the infiltrated TAGs in LD membranes in the presence of mutant helices, or even in the absence of docking, suggests that this is not enough to complete the TAG transference.
To be transferred to the adjacent LD, the TAGs integrated in the hydrophobic region of the LD membrane should cross the energy barrier defined by the phospholipid polar heads, and the interaction of CIDEA with PA could play a role in this process, as suggested by the disruption of LD enlargement by the mutations preventing PA-binding (K167E/R171E/R175E) and the inhibition of CIDEA after PA depletion. The minor effects observed with more conservative substitutions in the helix, suggests that the presence of positive charges is sufficient to induce TAG transference by attracting anionic phospholipids present in the LD membrane. PA, which requirement is indicated by our PA-depletion experiments, is a cone-shaped anionic phospholipid which could locally destabilize the LD monolayer by favoring a negative membrane curvature incompatible with the spherical LD morphology (51). Interestingly, while the zwitterion PC, the main component of the monolayer, stabilizes the LD structure (23), the negatively charged PA promote their coalescence (29). This is supported by our CD-MD results which resulted in a deformation of the LD shape by the addition of PA. We propose a model in which the C-term amphipathic helix positions itself in the LD monolayer and interacts with PA molecules in its vicinity, which might include trans interactions with PA in the adjacent LD. The interaction with PA disturbs the integrity of the phospholipid barrier at the LD-LD interface, allowing the LD to LD transference of TAG molecules integrated in the LD membrane (Fig. 7). Additional alterations in the LD composition could be facilitating TAG transference, as differentiating adipocytes experience a reduction in saturated fatty acids in the LD phospholipids (52), and in their PC/PE ratio (53) which could increase the permeability of the LD membranes, and we previously observed that a change in the molecular structures of TAG results in an altered migration pattern to the LD surface (32).
During LD fusion by lipid transfer, the pressure gradient experienced by LDs favors TAG flux from small to large LDs (15). However, the implication of PA, a minor component of the LD membrane, could represent a control mechanism, as it is plausible that the cell could actively influence the TAG flux direction by differently regulating the levels of PA in large and small LDs, which could be controlled by the activity of enzymes such as AGPAT3 and LIPIN-1J (13, 30). This is a remarkable possibility, as a switch in the favored TAG flux direction could promote the acquisition of a multilocular phenotype and facilitate the browning of WAT (24). Interestingly, Cidea mRNA is the LD protein- encoding transcript that experiences the greatest increase during the cold-induced process by which multilocular BAT-like cells appear in WAT (24). Furthermore, in BAT, cold exposure instigates a profound increase in CIDEA protein levels that is independent of transcriptional regulation (54). The profound increase in CIDEA is coincident with elevated lipolysis and de novo lipogenesis that occurs in both brown and white adipose tissues after E-adrenergic receptor activation (55). It is likely that CIDEA has a central role in coupling these processes to package newly synthesized TAG in LDs for subsequent lipolysis and fatty acid oxidation. Importantly, BAT displays high levels of glycerol kinase activity (56, 57) that facilitates glycerol recycling rather than release into the blood stream, following induction of lipolysis (58), which occurs in WAT. Hence, the reported elevated glycerol released from cells depleted of CIDEA (28) is likely to be a result of decoupling lipolysis from the ability to efficiently store the products of lipogenesis in LDs and therefore producing a net increase in detected extracellular glycerol. This important role of CIDEA is supported by the marked depletion of TAG in the BAT of Cidea null mice following overnight exposure to 4 °C (28) and our findings that CIDEA-dependent LD enlargement is maintained in a lipase negative yeast strain.
Cidea and the genes that are required to facilitate high rates of lipolysis and lipogenesis are associated with the “browning” of white fat either following cold exposure (46) or in genetic models such as RIP140 knockout WAT (59). The induction of a brown- like phenotype in WAT has potential benefits in the treatment and prevention of metabolic disorders (60). Differences in the activity and regulation of CIDEC and CIDEA could also be responsible for the adoption of unilocular or multilocular phenotypes. In addition to their differential interaction with PLIN1 and 5, we have observed that CIDEC is more resilient to the deletion of the N-term than CIDEA, indicating that it may be less sensitive to regulatory posttranslational modifications of this domain. This robustness of CIDEC activity together with its potentiation by PLIN1, could facilitate the continuity of the LD enlargement in white adipocytes until the unilocular phenotype is achieved. In contrast, in brown adipocytes expressing CIDEA the process would be stopped at the multilocular stage for example due to post-translational modifications that modulate the function or stability of the protein or alteration of the PA levels in LDs.
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Early Diagnosis
Reporter: Stephen J. Williams, Ph.D.
This post contains a curation of all Early Diagnosis posts on this site as well as a curation of the Early Detection Research Network.
Early Research Detection Network (EDRN)
Welcome to EDRN
The Early Detection Research Network (EDRN), an initiative of the National Cancer Institute (NCI), brings together dozens of institutions to help accelerate the translation of biomarker information into clinical applications and to evaluate new ways of testing cancer in its earliest stages and for cancer risk.
Getting Started…
Check out the EDRN Highlights — a listing of our accomplishments and milestones.
► Scientific Components ► For Public, Patients, Advocates
► Collaborative Opportunities (how to join EDRN) ► For Researchers
Highlights
Highlights of the accomplishments of the Early Detection Research Network.
A brief list of major EDRN-developed assays that have been adapted for clinical use is described in the table below:
Detection/Biomarker Assay Discovery Refine/Adapt for Clin Use Clinical Validation Clinical Translation
Blood proPSA FDA approved
Urine PCA3 FDA approved
OVA1™ for Ovarian Cancer FDA approved
ROMA Algorithm for CA125 and HE4 Tests for Pelvic Mass Malignancies FDA approved
Blood/DCP and AFP-L3 for Hepatocellular Carcinoma FDA approved
Blood GP73 Together with AFP-L3 used for monitoring cirrhotic patients for HCC in China
MiPS (Mi Prostate Score Urine test), Multiplex analysis of T2-ERG gene fusion, PCA3 and serum PSA In CLIA Lab
FISH to detect T2S:Erg fusion for Prostate Cancer In CLIA Lab
GSTP1 methylation for repeat biopsies in prostate cancer In CLIA Lab
Mitochondrial deletion for detection of prostate cancer In CLIA Lab
Somalogic 12-marker panel for Lung Cancer In CLIA Lab
80-gene panel for Lung Cancer In CLIA Lab
Vimentin Methylation Marker for Colon Cancer In CLIA Lab
Galectin-3 ligand for detection of adenomas and colon cancer In CLIA Lab
8-gene panel for Barrett’s Esophagus In CLIA Lab
SOPs for Blood (Serum, Plasma), Urine, Stool Frequently used by biomarker research community
EDRN Pre/Validation Specimen Reference Sets (specimens from well characterized and matched cases and controls from specific disease spectra) Frequently used by biomarker research community
Since its inception in 1999 EDRN has achieved several key milestones, summarized below:
1998 through 2000: Inception and Inauguration of EDRN
2001 to 2003: Meeting the Challenges to Harness and Share Emerging Scientific Knowledge
• EDRN Second Report, Translational Research to Identify Early Cancer and Cancer Risk, October 2002, http://edrn.nci.nih.gov/docs.) published.
• EDRN joined the Gordon Research Conferences to co-host the New Frontiers in Cancer detection and Diagnosis in 2002.
• Guidelines Set for Studies Measuring Biomarker Predictive Power Journal of National Cancer Institute (Vol. 93, No. 14, July 18, 2001).
• EDRN Associate Membership Program Initiated: This novel approach to make EDRN inclusive has been extremely successful. EDRN has now more than 120 Associate Members who are significantly contributing to EDRN efforts in biomarker discovery, development and validation.
2003 to 2004: Network Surges Ahead in Real-time
• Collaborative Discovery and Validation Projects: More than 100 collaborative projects spanned the various organ sites. These projects are monitored through the EDRN’s electronic System Information System (eSIS).
• EDRN Virtual Specimen Bank and Validation Management System Launched: The EDRN Virtual Specimen Bank, also known as ERNE knowledge system, was deployed to 10 institutions in early 2003, allowing a common web-based query to search for available specimens across the EDRN Clinical Epidemiology and Validation Centers https://ginger.fhcrc.org/edrn/imp/GateServlet?pwd. VSIMS was created to allow multiple studies to be administered efficiently by minimizing development time with standardization of information and data management across multiple activities and research sites. This system encompasses all the security features of Food and Drug Administration (FDA)-required auditing systems.
• Partnership on the Plasma Proteome Project (PPP) Initiative of the Human Proteome Organization (HUPO): PPP project was initiated to evaluate multiple technology platforms, develop bioinformatic tools and standards for protein identification, and create a database of the plasma proteome. The entire study was published in the August issue of the journal Proteomics August 2005, Volume 4 (4), pp 1045-1450.
2005 to 2008: An Investment in Prevention
• In late 2006, EDRN’s Program for Rapid, Independent Diagnostic Evaluation (PRIDE), was established (http://grants.nih.gov/grants/guide/notice-files/NOT-CA-07-003.html ) as an administrative means to assist extramural investigators in successfully conducting cross-laboratory validation of biomarkers. Ten applications have been reviewed and five are being supported.
• EDRN underwent external reviews in 2007 and 2008.
• The Canary Foundation, Palo Alto, CA signed a Memorandum of Understanding with EDRN, NCI on supporting prostate cancer surveillance network of investigators from seven institutions. The tissue and serum will be collected during a three-year period and will be made available to extramural scientists for discovery and validation research.
• The Lustgarten Foundation, N.Y., funded 6 institutions to generate monoclonal antibodies and associated hybridoma cell lines for pancreatic cancer antigens (biomarkers) identified by EDRN and non-EDRN investigators. These resources will be stored at the NCI-Frederick Facility for distribution to extramural investigators.
2009 to 2011: Realizing Investment for Clinical Use
• Two biomarker tests approved by FDA and two IVDs pending FDA review.
• Six biomarker tests offered by CLIA labs.
• One biomarker test approved for clinical use outside the USA
A Curation of Posts on Early Detection of Cancer and Other Early Detection Networks is Included Below
BRCA 1 and 2 and Early Detection of Cancer
Early Detection of Prostate Cancer: American Urological Association (AUA) Guideline
Mechanism involved in Breast Cancer Cell Growth: Function in Early Detection & Treatment
Warning signs may lead to better early detection of ovarian cancer
Cancer Detection
Biomarker tool development for Early Diagnosis of Pancreatic Cancer: Van Andel Institute and Emory University
China, India, and Russia account for 46% of all new cancer cases globally, as well as 52% of cancer-related mortality per 4/2014 Lancet Oncology article
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New Generation of Platinated Compounds to Circumvent Resistance
Curator/Writer: Stephen J. Williams, Ph.D.
Resistance to chemotherapeutic drugs continues to be a major hurdle in the treatment of neoplastic disorders, irregardless if the drug is a member of the cytotoxic “older” drugs or the cytostatic “newer” personalized therapies like the tyrosine kinase inhibitors. For the platinatum compounds such as cisplatin and carboplatin, which are mainstays in therapeutic regimens for ovarian and certain head and neck cancers, development of resistance is often regarded as the final blow, as new options for these diseases have been limited.
Although there are many mechanisms by which resistance to platinated compounds may develop the purpose of this posting is not to do an in-depth review of this area except to refer the reader to the book Ovarian Cancer and just to summarize the well accepted mechanisms of cisplatin resistance including:
• Decreased cellular cisplatin influx
• Increased cellular cisplatin efflux
• Increased cellular glutathione and subsequent conjugation, inactivation
• Increased glutathione-S-transferase activity (GST) and subsequent inactivation, conjugation
• Increased γ-GGT
• Increased metallothionenes with subsequent conjugation, inactivation
• Increased DNA repair: increased excision repair
• DNA damage tolerance: loss of mismatch repair (MMR)
• altered cell signaling activities and cell cycle protein expression
Williams, S.J., and Hamilton, T.C. Chemotherapeutic resistance in ovarian cancer. In: S.C. Rubin, and G.P. Sutton (eds.), Ovarian Cancer, pp.34-44. Lippincott, Wilkins, and Williams, New York, 2000.
Also for a great review on clinical platinum resistance by Drs. Maritn, Hamilton and Schilder please see the following Clinical Cancer Research link here.
This curation represents the scientific rationale for the development of a new class of platinated compounds which are meant to circumvent mechanisms of resistance, in this case the loss of mismatch repair (MMR) and increased tolerance to DNA damage.
An early step in the production of cytotoxicity by the important anticancer drug cisplatin and its analog carboplatin is the formation of intra- and inter-strand adducts with tumor cell DNA 1-3. This damage triggers a cascade of events, best characterized by activation of damage-sensing kinases (reviewed in 4), p53 stabilization, and induction of p53-related genes involved in apoptosis and cell cycle arrest, such as bax and the cyclin-dependent kinase inhibitor p21waf1/cip1/sdi1 (p21), respectively 5,6. DNA damage significantly induces p21 in various p53 wild-type tumor cell lines, including ovarian carcinoma cells, and this induction is responsible for the cell cycle arrest at G1/S and G2/M borders, allowing time for repair 7,8. DNA lesions have the ability of to result in an opening of chromatin structure, allowing for transcription factors to enter 56-58. Therefore the anti-tumoral ability of cisplatin and other DNA damaging agents is correlated to their ability to bind to DNA and elicit responses, such as DNA breaks or DNA damage responses which ultimately lead to cell cycle arrest and apoptosis. Therefore either repair of such lesions, the lack of recognition of such lesions, or the cellular tolerance of such lesions can lead to resistance of these agents.
resistmech2
Mechanisms of Cisplatin Sensitivity and Resistance. Red arrows show how a DNA lesion results in chemo-sensitivity while the beige arrow show common mechanisms of resistance including increased repair of the lesion, effects on expression patterns, and increased inactivation of the DNA damaging agent by conjugation reactions
mechPtresistance
Increased DNA Repair Mechanisms of Platinated Lesion Lead to ChemoResistance
DNA_repair_pathways
Description of Different Types of Cellular DNA Repair Pathways. Nucleotide Excision Repair is commonly up-regulated in highly cisplatin resistant cells
Loss of Mismatch Repair Can Lead to DNA Damage Tolerance
dnadamage tolerance
In the following Cancer Research paper Dr. Vaisman in the lab of Dr. Steve Chaney at North Carolina (and in collaboration with Dr. Tom Hamilton) describe how cisplatin resistance may arise from loss of mismatch repair and how oxaliplatin lesions are not recognized by the mismatch repair system.
Cancer Res. 1998 Aug 15;58(16):3579-85.
The role of hMLH1, hMSH3, and hMSH6 defects in cisplatin and oxaliplatin resistance: correlation with replicative bypass of platinum-DNA adducts.
Abstract
Defects in mismatch repair are associated with cisplatin resistance, and several mechanisms have been proposed to explain this correlation. It is hypothesized that futile cycles of translesion synthesis past cisplatin-DNA adducts followed by removal of the newly synthesized DNA by an active mismatch repair system may lead to cell death. Thus, resistance to platinum-DNA adducts could arise through loss of the mismatch repair pathway. However, no direct link between mismatch repair status and replicative bypass ability has been reported. In this study, cytotoxicity and steady-state chain elongation assays indicate that hMLH1 or hMSH6 defects result in 1.5-4.8-fold increased cisplatin resistance and 2.5-6-fold increased replicative bypass of cisplatin adducts. Oxaliplatin adducts are not recognized by the mismatch repair complex, and no significant differences in bypass of oxaliplatin adducts in mismatch repair-proficient and -defective cells were found. Defects in hMSH3 did not alter sensitivity to, or replicative bypass of, either cisplatin or oxaliplatin adducts. These observations support the hypothesis that mismatch repair defects in hMutL alpha and hMutS alpha, but not in hMutS beta, contribute to increased net replicative bypass of cisplatin adducts and therefore to drug resistance by preventing futile cycles of translesion synthesis and mismatch correction.
The following are slides I had co-prepared with my mentor Dr. Thomas C. Hamilton, Ph.D. of Fox Chase Cancer Center on DNA Mismatch Repair, Oxaliplatin and Ovarina Cancer.
edinborough2mmrtranslesion1
Multiple Platinum Analogs of Cisplatin (like Oxaliplatin )Had Been Designed to be Sensitive in MMR Deficient Tumors
edinborough2diffptanalogs
mmroxaliplatin
edinborough2ptanalogsresist
edinborough2relresistptanalogsdifflines
edinborough2msimlmh2refract
edinborough2gogoxaliplatintrial
Please see below video on 2015 Nobel Laureates and their work to elucidate the celluar DNA repair mechanisms.
Clinical genetics expert Kenneth Offit gives an overview of Lynch syndrome, a genetic disorder that can cause colon (HNPCC) and other cancers by defects in the MSH2 DNA mismatch repair gene. (View Video)
References
1. Johnson, S. W. et al. Relationship between platinum-DNA adduct formation, removal, and cytotoxicity in cisplatin sensitive and resistant human ovarian cancer cells. Cancer Res 54, 5911-5916 (1994).
2. Eastman, A. The formation, isolation and characterization of DNA adducts produced by anticancer platinum complexes. Pharmacology and Therapeutics 34, 155-166 (1987).
3. Zhen, W. et al. Increased gene-specific repair of cisplatin interstrand cross-links in cisplatin-resistant human ovarian cancer cell lines. Molecular and Cellular Biology 12, 3689-3698 (1992).
4. Durocher, D. & Jackson, S. P. DNA-PK, ATM and ATR as sensors of DNA damage: variations on a theme? Curr Opin Cell Biol 13, 225-231 (2001).
5. el-Deiry, W. S. p21/p53, cellular growth control and genomic integrity. Curr Top Microbiol Immunol 227, 121-37 (1998).
6. Ewen, M. E. & Miller, S. J. p53 and translational control. Biochim Biophys Acta 1242, 181-4 (1996).
7. Gartel, A. L., Serfas, M. S. & Tyner, A. L. p21–negative regulator of the cell cycle. Proc Soc Exp Biol Med 213, 138-49 (1996).
8. Chang, B. D. et al. p21Waf1/Cip1/Sdi1-induced growth arrest is associated with depletion of mitosis-control proteins and leads to abnormal mitosis and endoreduplication in recovering cells. Oncogene 19, 2165-70 (2000).
9. Davies, N. P., Hardman, L. C. & Murray, V. The effect of chromatin structure on cisplatin damage in intact human cells. Nucleic Acids Res 28, 2954-2958 (2000).
10. Vichi, P. et al. Cisplatin- and UV-damaged DNA lure the basal transcription factor TFIID/TBP. Embo J 16, 7444-7456 (1997).
11. Xiao, G. et al. A DNA damage signal is required for p53 to activate gadd45. Cancer Res 60, 1711-9 (2000).
Other articles in this Open Access Journal on ChemoResistance Include:
Cancer Stem Cells as a Mechanism of Resistance
An alternative approach to overcoming the apoptotic resistance of pancreatic cancer
Mutation D538G – a novel mechanism conferring acquired Endocrine Resistance causes a change in the Estrogen Receptor and Treatment of Breast Cancer with Tamoxifen
Can IntraTumoral Heterogeneity Be Thought of as a Mechanism of Resistance?
Nitric Oxide Mitigates Sensitivity of Melanoma Cells to Cisplatin
Heroes in Medical Research: Barnett Rosenberg and the Discovery of Cisplatin
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Cancer Stem Cells as a Mechanism of Resistance
Curator: Stephen J. Williams, Ph.D.
The cancer stem-cell hypothesis proposes the existence of a subset of cells within a heterogeneous tumor cell population that have stem-cell like properties [1], and may be essential for the progression and metastases of epithelial malignancies, by providing a reservoir of cells that self-renew and differentiate into the bulk of the tumor [2]. The stem-cell hypothesis implies that similar genetic regulatory pathways might define critical stem-cell like functions, such as self-renewal and pluripotency, in both normal and cancer stem-cells. Indeed, cancer stem-cells have been identified in many tumor types, such as breast [3], pancreas [4] and ovarian [5], based on screening with cellular markers typically found in normal stem-cells such as CD44, ALDH1, and CD133 (reviewed in [2]). A number of studies have suggested that the expression of these stem-cell markers is correlated with poor prognosis [6-9]. The ability to identify and isolate these populations may have a significant impact on design of individualized therapies.
Great general posts and good review on this site about Cancer Stem Cells, their markers, and ability to target them with chemotherapy can be seen here.
In Focus: Identity of Cancer Stem Cells
In Focus: Targeting of Cancer Stem Cells
Stem Cells and Cancer
However, there has been growing acknowledgement of the ability of cancer stem cell populations to resist the cytotoxic effects of most chemotherapeutic agents, including cisplatin, topoisomerase inhibitors, DNA damaging agents, and even tyrosine kinase inhibitors (TKI). Indeed, some feel that intrinsic resistance to cytotoxic drugs may be a biological feature of cancer stem cells.
Definitions:
Acquired resistance: a resistance to a particular drug which results following continued exposure to said drug. Can take days (in cases of some TKIs) or months to develop. Acquired resistant cells lines are developed by exposure to increasing drug concentration over a time period (either intermittent exposure or continuous exposure)
Intrinsic resistance: a pre-existing resistance usually termed refractory where cancer cells THAT HAVE NOT BEEN EXPOSED to drug, do not respond to initial drug exposure. Can be seen experimentally in panels of unrelated cancer cells lines isolated from untreated patients which show no cytotoxicity to drug exposure in vitro.
Below is one of the first reports which described the drug resistant phenotype of cancer stem cells in an in vivo (mouse) model of breast cancer with videos.
Cancer Res. 2008 May 1;68(9):3243-50. doi: 10.1158/0008-5472.CAN-07-5480.
Cancer stem cells contribute to cisplatin resistance in Brca1/p53-mediated mouse mammary tumors.
Shafee N1, Smith CR, Wei S, Kim Y, Mills GB, Hortobagyi GN, Stanbridge EJ, Lee EY.
Author information
Abstract
The majority of BRCA1-associated breast cancers are basal cell-like, which is associated with a poor outcome. Using a spontaneous mouse mammary tumor model, we show that platinum compounds, which generate DNA breaks during the repair process, are more effective than doxorubicin in Brca1/p53-mutated tumors. At 0.5 mg/kg of daily cisplatin treatment, 80% primary tumors (n = 8) show complete pathologic response. At greater dosages, 100% show complete response (n = 19). However, after 2 to 3 months of complete remission following platinum treatment, tumors relapse and become refractory to successive rounds of treatment. Approximately 3.8% to 8.0% (mean, 5.9%) of tumor cells express the normal mammary stem cell markers, CD29(hi)24(med), and these cells are tumorigenic, whereas CD29(med)24(-/lo) and CD29(med)24(hi) cells have diminished tumorigenicity or are nontumorigenic, respectively. In partially platinum-responsive primary transplants, 6.6% to 11.0% (mean, 8.8%) tumor cells are CD29(hi)24(med); these populations significantly increase to 16.5% to 29.2% (mean, 22.8%; P < 0.05) in platinum-refractory secondary tumor transplants. Further, refractory tumor cells have greater colony-forming ability than the primary transplant-derived cells in the presence of cisplatin. Expression of a normal stem cell marker, Nanog, is decreased in the CD29(hi)24(med) populations in the secondary transplants. Top2A expression is also down-regulated in secondary drug-resistant tumor populations and, in one case, was accompanied by genomic deletion of Top2A. These studies identify distinct cancer cell populations for therapeutic targeting in breast cancer and implicate clonal evolution and expansion of cancer stem-like cells as a potential cause of chemoresistance.
Please Watch Videos
Below is a curation of talks and abstracts from the 2015 Annual AACR Meeting in Philadelphia, PA.
The Talk by Dr. Cheresh is an example of this school of thought; that inducing cancer cell stemness can result in development of drug resistance, in this case to a TKI. (For a press release on this finding see here.)
SY27-04: Induction of cancer stemness and drug resistance by EGFR blockade
Tuesday, Apr 21, 2015, 12:00 PM -12:15 PM
David A. Cheresh. UCSD Moores Cancer Center, La Jolla, CA
SY27-04
Presentation Title: Induction of cancer stemness and drug resistance by EGFR blockade
Presentation Time: Tuesday, Apr 21, 2015, 12:00 PM -12:15 PM
Abstract Body: Tumor drug resistance is often accompanied by genetic and biological changes in the tumor cell population reflecting the acquisition of a stem-like state. However, it is not clear whether cancer therapies select for the growth of drug resistance cancer stem cells and/or directly induce the reprograming of tumor cells to a cancer stem-like, drug resistance state. We provide evidence that breast, pancreas and lung carcinomas in the presence of prolonged exposure to EGFR inhibitors undergo an epigenetic reprogramming resulting in a drug resistant stem-like tumor population expressing the cell surface marker CD61 (b3 integrin). In fact, CD61 in the context of KRAS, is necessary and sufficient to account for drug resistance, tumor initiation, self-renewal and expression of the pluripotent genes Oct 4 and Nanog. Once expressed, CD61 in the unligated state recruits KRAS to the plasma membrane leading to the activation of RalB, TBK1 and c-Rel driving both stemness and EGFR inhibitor resistance. Pharmacological targeting this pathway with drugs such as bortezomib or revlimid not only reverses stemness but resensitizes these epithelial tumors to EGFR inhibition. This epigenetic pathway can also be initiated by range of cellular stresses found within the tumor microenvironment such as hypoxia, nutrient deprivation, low pH, and oxidative stress. In normal tissues CD61 is induced during tissue remodeling and repair. For example, CD61 was found to be critical for mammary gland remodeling during pregnancy and as a mediator of pathological neovascularization. Together these findings reveal a stress-induced epigenetic pathway characterized by the upregulation of CD61 that promotes the remodeling of normal tissues but in tumors contributes to EGFR inhibitor resistance and tumor progression.
http://cancerres.aacrjournals.org/gca?gca=canres%3B75%2F15_Supplement%2F4&gca=canres%3B75%2F15_Supplement%2F6&gca=canres%3B75%2F15_Supplement%2F19&gca=canres%3B75%2F15_Supplement%2F24&gca=canres%3B75%2F15_Supplement%2F48&gca=canres%3B75%2F15_Supplement%2F54&gca=canres%3B75%2F15_Supplement%2F57&gca=canres%3B75%2F15_Supplement%2F88&gca=canres%3B75%2F15_Supplement%2F90&gca=canres%3B75%2F15_Supplement%2F97&allch=&submit=Go
Selected Abstracts
1. Abstract 1
2. Molecular and Cellular Biology – Poster Presentations – Proffered Abstracts – Poster Presentations – Cell Death Mechanisms: Abstract 4: ABT-263 is effective in a subset of non-small cell lung cancer cell lines
• Aoi Kuroda,
• Keiko Ohgino,
• Hiroyuki Yasuda,
• Junko Hamamoto,
• Daisuke Arai,
• Kota Ishioka,
• Tetsuo Tani,
• Shigenari Nukaga,
• Ichiro Kawada,
• Katsuhiko Naoki,
• Kenzo Soejima,
• and Tomoko Betsuyaku
Cancer Res August 1, 2015 75:4; doi:10.1158/1538-7445.AM2015-4
1. Abstract 2
2. Molecular and Cellular Biology – Poster Presentations – Proffered Abstracts – Poster Presentations – Cell Death Mechanisms: Abstract 6: Quantitative assessment of BCL-2:BIM complexes as a pharmacodynamic marker for venetoclax (ABT-199)
• Sha Jin,
• Paul Tapang,
• Donald J. Osterling,
• Wenqing Gao,
• Daniel H. Albert,
• Andrew J. Souers,
• Joel D. Leverson,
• Darren C. Phillips,
• and Jun Chen
Cancer Res August 1, 2015 75:6; doi:10.1158/1538-7445.AM2015-6
1. Molecular and Cellular Biology – Poster Presentations – Proffered Abstracts – Poster Presentations – Cell Death Mechanisms: Abstract 24: The phosphorylation of p53 at serine 46 is essential to induce cell death through palmdelphin in response to DNA damage
• Nurmaa Khund Dashzeveg and
• Kiyotsugu Yoshida
Cancer Res August 1, 2015 75:24; doi:10.1158/1538-7445.AM2015-24
1. Abstract 5
2. Molecular and Cellular Biology – Poster Presentations – Proffered Abstracts – Poster Presentations – Cell Signaling in Cancer 1: Abstract 48: Identification of a novel binding protein playing a critical role in HER2 activation in lung cancer cells
• Tomoaki Ohtsuka,
• Masakiyo Sakaguchi,
• Katsuyoshi Takata,
• Shinsuke Hashida,
• Mototsugu Watanabe,
• Ken Suzawa,
• Yuho Maki,
• Hiromasa Yamamoto,
• Junichi Soh,
• Hiroaki Asano,
• Kazunori Tsukuda,
• Shinichiro Miyoshi,
• and Shinichi Toyooka
Cancer Res August 1, 2015 75:48; doi:10.1158/1538-7445.AM2015-48
1. Abstract 1 of 10Molecular and Cellular Biology / Poster Presentations – Proffered Abstracts / Poster Presentations – Cell Death Mechanisms
Abstract 4: ABT-263 is effective in a subset of non-small cell lung cancer cell lines
Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA
Rationale:
ABT-263 (Navitoclax) is one of the BH3 mimetics targeting anti-apoptotic B-cell lymphoma-2 (Bcl-2) family proteins such as Bcl-2, Bcl-XL, and Bcl-w, thereby inducing apoptosis. It has been reported that the response to ABT-263 is associated with expressions of myeloid cell leukemia-1 (Mcl-1), an anti-apoptotic protein. Given its effectiveness as a single agent in preclinical studies, ABT-263 is currently being evaluated in clinical trials for small cell lung cancer (SCLC) and leukemia. However, the efficacy of ABT-263 in non-small cell lung cancer (NSCLC) has not been fully evaluated. We examined the effect of ABT-263 on cell proliferation of NSCLC cell lines and investigated the underlying mechanisms.
Methods:
The following 9 NSCLC cell lines were examined: SK-LU-1, A549, H358, Calu3, H3122, H1975, H460, H441, and BID007. The effects of ABT-263 in NSCLC cell lines were evaluated by MTS assay. Apoptosis was examined by flowcytometry using staining for annexin V and propidium iodide (PI), and also western blotting for cleaved PARP. Quantitative RT-PCR was carried out to assess the mRNA expression levels of anti-apoptotic genes and pro-apoptotic genes. Immunoprecipitation and western blotting were performed to compare the levels of anti-apoptotic and pro-apoptotic proteins between the sensitive and resistant cell lines. In addition, knockdown of Mcl-1 was performed by siRNA.
Results:
By screening 9 NSCLC cell lines using MTS assay, we found Calu3 and BID007were sensitive to ABT-263. We also confirmed that apoptosis was induced only in the ABT-263 sensitive lines but not in the ABT-263 resistant cell lines after ABT-263 treatment. However, the expression levels of Bcl-2 family proteins, including Mcl-1, did not differ significantly among the ABT-263 sensitive and resistant cell lines. Unlike the results in previous reports regarding SCLC, Mcl-1 was not decreased in the sensitive cell lines. The ABT-263 resistant cell lines became sensitive to ABT-263 after knockdown of Mcl-1 by siRNA, while the ABT-263 sensitive cell lines maintained the same sensitivity.
Conclusion:
We found that Calu3 and BID007 were sensitive to ABT-263. In the sensitive NSCLC cell lines, ABT-263 induces apoptosis irrespective of Mcl-1 expression levels.
Citation Format: Aoi Kuroda, Keiko Ohgino, Hiroyuki Yasuda, Junko Hamamoto, Daisuke Arai, Kota Ishioka, Tetsuo Tani, Shigenari Nukaga, Ichiro Kawada, Katsuhiko Naoki, Kenzo Soejima, Tomoko Betsuyaku. ABT-263 is effective in a subset of non-small cell lung cancer cell lines. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4. doi:10.1158/1538-7445.AM2015-4
• ©2015 American Association for Cancer Research.
1. Abstract 2 of 10Molecular and Cellular Biology / Poster Presentations – Proffered Abstracts / Poster Presentations – Cell Death Mechanisms
Abstract 6: Quantitative assessment of BCL-2:BIM complexes as a pharmacodynamic marker for venetoclax (ABT-199)
Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA
The BCL-2-selective inhibitor venetoclax (ABT-199) binds with high affinity to the BH3-binding groove of BCL-2, thereby competing for binding with the BH3-only protein BIM (Souers et al., 2013). Venetoclax is currently being evaluated in clinical trials for CLL, AML, multiple myeloma and NHL. To facilitate these studies, we developed and validated a 384-well electrochemiluminescent ELISA (MSD, Gaithersburg, MD,USA) that quantifies expression of BCL-2, BCL-XL, and MCL-1protein alone or in complex with BIM. We subsequently quantified expression of BCL-2 and BCL-2:BIM complexes in 16 hematologic tumor cell lines. We found the EC50 of venetoclax in these tumor cell lines to correlate strongly with baseline BCL-2:BIM complex levels. This correlation was superior to the correlation between venetoclax EC50 and absolute BCL-2 expression. We also applied the assay to measure disruption of BCL-2:BIM complexes in vivo. Treatment of the Non-Hodgkin’s Lymphoma (NHL) xenograft model SU-DHL-4 with a BCL-2-selective inhibitor resulted in disruption of tumor BCL-2:BIM complexes that aligned with serum and tumor concentrations of inhibitor. Collectively, these data demonstrate that quantifying BCL-2:BIM complexes offers an accurate means of assessing target engagement by venetoclax and, potentially, predicting its efficacy. The utility of this assay is currently being assessed in clinical trials.
Citation Format: Sha Jin, Paul Tapang, Donald J. Osterling, Wenqing Gao, Daniel H. Albert, Andrew J. Souers, Joel D. Leverson, Darren C. Phillips, Jun Chen. Quantitative assessment of BCL-2:BIM complexes as a pharmacodynamic marker for venetoclax (ABT-199). [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 6. doi:10.1158/1538-7445.AM2015-6
• ©2015 American Association for Cancer Research.
1. Abstract 3 of 10Molecular and Cellular Biology / Poster Presentations – Proffered Abstracts / Poster Presentations – Cell Death Mechanisms
Abstract 19: Antitumor activity of selective inhibitors of XPO1/CRM1-mediated nuclear export in diffuse malignant peritoneal mesothelioma: the role of survivin
Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA
Survivin, which is highly expressed and promotes cell survival in diffuse malignant peritoneal mesothelioma (DMPM), exclusively relies on the nuclear exportin 1 (XPO1/CRM1) to be released in the cytoplasm and perform its anti-apoptotic function. Here, we explored the efficacy of selective inhibitors of nuclear export (SINEs) in patient-derived DMPM preclinical models. Exposure to individual SINE (KPT-251, KPT-276, KPT-330) was able to induce a time- and dose-dependent inhibition of the growth of two DMPM cell lines without affecting normal cell proliferation. Such a cell growth inhibition was preceded by a decline in the nuclear XPO1/CRM1 levels and an increase in the nuclear accumulation of its cargo proteins p53 and p21, which led to a cell cycle arrest at G1-phase. Our results also indicated that survivin is an essential component of the downstream signaling pathway of XPO1/CRM1 inhibition in DMPM cells. In fact, in both cell lines, exposure to SINEs led to a time-dependent reduction of cytoplasmic survivin levels and, after an initial survivin nuclear accumulation, also to a progressive decrease in the nuclear protein abundance, through the ubiquitin-proteasomal degradation pathway, leading to the complete depletion of total survivin levels. In both DMPM cell models, according to survivin anti-apoptotic activity, drug-induced reduction of cytoplasmic survivin levels correlated with the onset of caspase-dependent apoptosis. We further observed that SINEs can be combined with other survivin inhibitors, such as the survivin suppressant YM155 to achieve enhanced growth inhibition in DMPM cells. Initial in vivo experiments with orally administered KPT-251, KPT-276 and the orally available, clinical stage KPT-330 (selinexor) indicated that each compound was able to significantly reduce the growth of early-stage subcutaneous DMPM xenografts. Interestingly, additional experiments carry out with selinexor demonstrated that the compound was also able to inhibit the growth of late-stage subcutaneous DMPM xenografts in nude mice. Most importantly, oral administration of selinexor to SCID mice reduced the growth of orthotopic DMPM xenografts, which properly recapitulate the dissemination pattern in the peritoneal cavity of human DMPM and, for this reason, represent a valuable model for investigating novel therapeutic approaches for the disease. Consistent with an important role of survivin as a determinant of anti-cancer activity of SINE compounds, a reduction of the protein expression was observed in tumor specimens obtained from selinexor treated mice. Overall, our results (i) demonstrate a marked efficacy of SINEs in DMPM preclinical models, which is, at least in part, dependent on the interference with survivin intracellular distribution and function, and (ii) suggest SINE-mediated XPO1/CRM1 inhibition as a novel therapeutic option for the disease.
Citation Format: Nadia Zaffaroni, Michelandrea De Cesare, Denis Cominetti, Valentina Doldi, Alessia Lopergolo, Marcello Deraco, Paolo Gandellini, Yosef Landesman, Sharon Friedlander, Michael G. Kauffman, Sharon Shacham, Marzia Pennati. Antitumor activity of selective inhibitors of XPO1/CRM1-mediated nuclear export in diffuse malignant peritoneal mesothelioma: the role of survivin. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 19. doi:10.1158/1538-7445.AM2015-19
• ©2015 American Association for Cancer Research.
1. Abstract 4 of 10Molecular and Cellular Biology / Poster Presentations – Proffered Abstracts / Poster Presentations – Cell Death Mechanisms
Abstract 24: The phosphorylation of p53 at serine 46 is essential to induce cell death through palmdelphin in response to DNA damage
Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA
Tumor suppressor p53 plays a pivotal role in cell cycle arrest, DNA repair, and apoptosis in response to DNA damage. Promoter selectivity of p53 depends mainly on post-translational modification. Notably, the apoptotic function of p53 is related to its phosphorylation at serine-46 (ser46) to promote pro-apoptotic genes. However, little is known about the pro-apoptotic genes induced by Ser46 phosphorylation. Our research achieved to investigate the pro-apoptotic genes induced by p53 in a phospho-ser46-specific manner using microarray and ChIP sequencing in human cancer cell lines. As a result, palmdelphin (PALMD), an isoform of paralemmin protein, was strongly elicited from the phosphorylation of ser46. The mRNA and protein expression of PALMD increased only in wild type p53 transfected cells, but not in ser46-mutated cells. Importantly, PALMD moved to the nucleus in response to DNA damage and the apoptotic function of PALMD was tightly exerted with localization into nucleus. Interestingly, down-regulation of PALMD by siRNA resulted in necroptosis-like cell death through ATP depletion. Moreover, we found vimentin as a PALMD interacting protein and the depletion of vimentin increased PALMD level to accelerate apoptosis. These results demonstrate that p53 regulates cell death fate (apoptosis or necroptosis-like cell death) through promoting PALMD expression in a phospho-ser46-specific manner in response to DNA damage.
Citation Format: Nurmaa Khund Dashzeveg, Kiyotsugu Yoshida. The phosphorylation of p53 at serine 46 is essential to induce cell death through palmdelphin in response to DNA damage. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 24. doi:10.1158/1538-7445.AM2015-24
• ©2015 American Association for Cancer Research.
1. Abstract 5 of 10Molecular and Cellular Biology / Poster Presentations – Proffered Abstracts / Poster Presentations – Cell Signaling in Cancer 1
Abstract 48: Identification of a novel binding protein playing a critical role in HER2 activation in lung cancer cells
Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA
Human epidermal growth factor receptor 2 (HER2) is a member of epidermal growth factor receptor (EGFR) family. Previous studies have revealed that many kinds of malignant tumors have genetic mutations or amplification of HER2, indicating that HER2 alterations are oncogenic. Many kinds of HER2 targeted therapies are effective to HER2 positive tumors, but those treated tumors often get resistance to drugs. Thus, to elucidate HER2 related pathway in cancer biology is important to develop new therapeutic strategy for cancers.
Recently, we newly identified a protein X (a temporary name) as a novel binding protein to HER2 with immunoprecipitation and following LC-Ms/Ms analysis. The protein generally expressed in lung and breast cancers at remarkable level.
We constructed plasmid vectors carrying wild type HER2 and gene X. These vectors were simultaneously introduced to HEK293T cells to examine the binding ability of protein X and HER2 as well as the effect of gene X on HER2-mediated signal-transduction pathway. The approach clearly showed that the expression of gene X, resulted in phosphorylation of HER2 and subsequent activation of oncogenic effector molecules.
We next constructed several kinds of gene X-truncated variants and subjected to the binding assay to look for the binding domain of gene X to HER2. The analysis showed that N-terminal head domain of gene X was essential for the HER2 binding. This domain has an ability to induce HER2 phosphorylation and subsequent activation of the effector kinase, ERK.
In conclusion, we found that gene X is a novel binding protein to HER2 and has a role in HER2 activation.
Citation Format: Tomoaki Ohtsuka, Masakiyo Sakaguchi, Katsuyoshi Takata, Shinsuke Hashida, Mototsugu Watanabe, Ken Suzawa, Yuho Maki, Hiromasa Yamamoto, Junichi Soh, Hiroaki Asano, Kazunori Tsukuda, Shinichiro Miyoshi, Shinichi Toyooka. Identification of a novel binding protein playing a critical role in HER2 activation in lung cancer cells. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 48. doi:10.1158/1538-7445.AM2015-48
• ©2015 American Association for Cancer Research.
1. Abstract 6 of 10Molecular and Cellular Biology / Poster Presentations – Proffered Abstracts / Poster Presentations – Cell Signaling in Cancer 1
Abstract 54: Ezrin enhances signaling and nuclear translocation of the epidermal growth factor receptor in non-small cell lung cancer cells
Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA
The cytoskeletal cross linker protein ezrin is a member of the ezrin-radixin-moesin (ERM) family and plays important roles not only in cell motility, cell adhesion, and apoptosis, but also in various cell-signaling pathways. Ezrin interacts with EGFR in the cell membrane and involves in cell motility events, but little is known about the effects of this interaction on the EGFR signaling pathway. We investigated the role of Ezrin in EGFR signaling and nuclear trafficking in non-small cell lung cancer (NSCLC) cell lines. The ligand induced interaction between Ezrin and EGFR was evaluated by immunoprecipitation (IP) and immunofluorescence (IF) in H292 and A549 cells. Ezrin levels were reduced using siRNA in these two cell lines. Downstream signaling protein phosphorylation and nuclear localization of EGFR were detected after EGF treatment. Expressions of nuclear EGFR target genes were evaluated by qPCR. Endogenous Ezrin was found in a complex with EGFR in IP and IF. When Ezrin protein expression was inhibited, phosphorylation levels of EGFR at Y1068, Y1101 and Y845 were reduced as well as phosphorylation levels of downstream signaling pathway proteins ERK and STAT3. Cell fractionation revealed that EGFR nuclear translocation after EGF treatment significantly reduced in Ezrin-knockdown cells. Further, mRNA levels of EGFR target genes AuroraK-A, COX2, Cyclin D1 and iNOS were decreased in Ezrin-knockdown A549 cells. Small molecule ezrin inhibitors showed strong synergy with EGFR inhibitors in cytotoxicity assays. These results suggest that Ezrin has a role as an enhancer in the EGFR pathway and targeting ezrin may potentiate anti-EGFR based therapies in NSCLC.
Citation Format: Yasemin Saygideger Kont, Haydar Celik, Hayriye V. Erkizan, Tsion Minas, Jenny Han, Jeffrey Toretsky, Aykut Uren. Ezrin enhances signaling and nuclear translocation of the epidermal growth factor receptor in non-small cell lung cancer cells. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 54. doi:10.1158/1538-7445.AM2015-54
• ©2015 American Association for Cancer Research.
1. Abstract 7 of 10Molecular and Cellular Biology / Poster Presentations – Proffered Abstracts / Poster Presentations – Cell Signaling in Cancer 1
Abstract 57: Substrates of protein kinase C drive cell rac1-dependent motility
Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA
This laboratory has identified and/or characterized substrates of PKC that upon phosphorylation give rise to motility, an aspect of metastasis. By use of the traceable kinase method, we discovered that alpha-tubulin and Cdc42 effector protein-4 (CEP4) are PKC substrates. Phosphorylation of alpha-tubulin stimulates its incorporation into microtubules (MTs), consequently increasing the stability and prolonged growth of MTs and leading to the activation of the small GTPase Rac1. CEP4 undergoes phosphorylation by PKC that results in its release from Cdc42, whereupon CEP4 binds a guanine nucleotide exchange factor (GEF) that in turn activates Rac1 GTPase. These results imply that Rac1 acts as a node in pathways driven by phosphorylated PKC substrates. Since translocation of IQGAP to the membrane is known to be promoted by Rac1, a role is explored in non-transformed human MCF-10A cells that express a specific phospho-mimetic mutant substrate. In addition, the phospho-mimetic mutant for each substrate expressed in human metastatic MDA-MB-231 cells produces different morphologies in 3-D growth assays. This research is being supported by NIH CA125632.
Citation Format: Susan A. Rotenberg, Xin Zhao, Shatarupa De. Substrates of protein kinase C drive cell rac1-dependent motility. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 57. doi:10.1158/1538-7445.AM2015-57
• ©2015 American Association for Cancer Research.
1. Abstract 8 of 10Molecular and Cellular Biology / Poster Presentations – Proffered Abstracts / Poster Presentations – Deregulation of Gene Expression in Prostate Cancer and Sarcoma
Abstract 88: The Nkx3.1 homeobox gene maintains prostatic identity while its loss leads to prostate cancer initiation
Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA
Background
Maintenance of epithelial cell identity is tightly coordinated by tissue-specific gene expression programs, which are often deregulated during tumorigenesis. The homeodomain-containing transcription factor, Nkx3.1, is a key regulator of normal prostatic development and is frequently lost at early stages of prostate cancer initiation. In this study, we aim to elucidate detailed mechanisms governing Nkx3.1-driven maintenance of prostate identity and how deregulation of such can lead to prostate tumorigenesis.
Models and Methods
We evaluated the consequences of Nkx3.1 loss or gain of function in vivo using genetically-engineered mouse models and cell-recombination assays. RNA sequencing was performed to generate gene expression profiles, which were analyzed using Gene Set Enrichment analysis (GSEA), and validated by quantitative real-time PCR. In parallel, protein expression was assessed by immunofluorescence and western blot. Immunoprecipitation (IP) and chromatin-immunoprecipitation (ChIP) assays were performed using RWPE1 prostate epithelial cells.
Results
Here, we show that loss of function of Nkx3.1 leads to the progressive down-regulation of a prostate-specific gene expression program and to aberrant expression of genes that are not typically expressed in the prostate epithelium. Conversely, gain of function of Nkx3.1 in non-prostatic epithelium leads to the acquisition of a prostate-like morphology and expression of prostate-related genes. Our findings indicate that the underlying mechanism by which Nkx3.1 promotes prostatic identity is via epigenetic regulation of gene expression. In particular, we show that Nkx3.1 interacts with the histone methyl-transferase complex G9a/Glp. Finally, we demonstrate that this interaction is necessary for maintenance of prostate identity in vivo and that Nkx3.1 and G9a cooperate to control expression of genes that coordinate prostatic epithelial integrity.
Conclusions
Our results suggest that Nkx3.1 promotes prostatic identity by interacting with histone modifying enzymes to coordinate the expression of prostate-specific genes and that the loss of this function results in a failure to maintain prostate identity associated with early stages of prostate tumorigenesis.
Citation Format: Clémentine Le Magnen, Aditya Dutta, Cory Abate-Shen. The Nkx3.1 homeobox gene maintains prostatic identity while its loss leads to prostate cancer initiation. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 88. doi:10.1158/1538-7445.AM2015-88
• ©2015 American Association for Cancer Research.
1. Abstract 9 of 10Molecular and Cellular Biology / Poster Presentations – Proffered Abstracts / Poster Presentations – Deregulation of Gene Expression in Prostate Cancer and Sarcoma
Abstract 90: K63-linked JARID1B ubiquitination by TRAF6 contributes to aberrant elevation of JARID1B in prostate cancer
Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA
Aberrant elevation of JARID1B and histone H3 Lys4 trimethylations (H3K4me3) is frequently observed in many diseases including prostate cancer (PCa), yet the mechanisms on the regulations of JARID1B and H3K4me3 through epigenetic modifications still remain poorly understood. In this study we performed immunohistochemistry staining, immunofluorescence imaging, immunoprecipitation, shRNA and Western blotting analysis in mouse embryonic fibroblasts (MEFs), mouse models, and cultured human prostate cancer cells. As a result, we discovered that SKP2 modulates JARID1B and H3K4me3 levels in vitro in PTEN null prostate cancer cells and in vivo in Pten/Trp53 mouse models. We demonstrated that levels of SKP2, JARID1B and H3K4me3 are strikingly elevated in vitro and in vivo when both PTEN and P53 are inactivated. Importantly, SKP2 inactivation resulted in a reduction of cell growth, cell migration and malignant transformation of Pten/Trp53 double null MEFs, and further restrained prostate tumorigenesis of Pten/Trp53 mutant mice. Mechanistically, JARID1B is ubiquitinated by E3 ligase TRAF6 through the K63-linkage in prostate cancer cells. Interestingly, SKP2 contributes to JARID1B ubiquitination machinery as a non-E3 ligase regulator by decreasing TRAF6-mediated ubiquitination of JARID1B. SKP2 deficiency resulted in an increase of JARID1B ubiquitination and in turn a reduction of H3K4me3, and induced senescence through JARID1B accumulation in nucleoli of PCa cells and prostate tumors of mice. Furthermore, we showed that the aberrant levels of SKP2, JARID1B, and H3K4me3 are associated with malignant features of castration-resistant prostate cancer (CRPC) in mice. Overall, our findings reveal a novel network of SKP2- JARID1B, and targeting SKP2 and JARID1B may be a potential strategy for PCa control.
Citation Format: Wenfu Lu, Shenji Liu, Bo Li, Yingqiu Xie, Christine Adhiambo, Qing Yang, Billy R. Ballard, Keiichi I. Nakayama, Robert J. Matusik, Zhenbang Chen. K63-linked JARID1B ubiquitination by TRAF6 contributes to aberrant elevation of JARID1B in prostate cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 90. doi:10.1158/1538-7445.AM2015-90
• ©2015 American Association for Cancer Research.
1. Abstract 10 of 10Molecular and Cellular Biology / Poster Presentations – Proffered Abstracts / Poster Presentations – Histone Methylation and Acetylation
Abstract 97: CARM1 preferentially methylates H3R17 over H3R26 through a random kinetic mechanism
Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA
CARM1 (PRMT4) is a type I arginine methyltransferase involved in the regulation of transcription, pre-mRNA splicing, cell cycle progression and the DNA damage response. Overexpression of CARM1 has been implicated in breast, prostate, and colorectal cancers. Since CARM1 appears to be a good target for the development of therapies against these cancers, we studied the substrate specificity and kinetic mechanism of the full-length human enzyme. CARM1 has been shown to methylate both residues R17 and R26 of histone H3. Substrate specificity was examined by testing CARM1 activity with several H3-based peptide substrates using a radiometric assay. Comparison of kcat/KM values reveal that methylation of H3R17 is preferred over H3R26. An R17/R26K peptide produced 8-fold greater kcat/KM value compared to the corresponding R17K/R26 peptide. These effects are KM-driven as kcat values remain relatively constant for the peptides tested. Shortening the peptide at the C-terminus by 5 amino acid residues greatly reduced the specificity (16-24-fold), demonstrating the contribution of distal residues to substrate binding. In contrast, adding residues to the N-terminus of the shortened peptide had a negative effect on activity. CARM1 displays little preference for monomethylated over unmethylated H3R17 (2-5-fold by kcat/KM) suggesting that it operates through a distributive mechanism. Previous crystallographic studies with mouse CARM1 showed that part of the substrate binding groove was formed by cofactor binding, thereby suggesting an ordered kinetic mechanism (Yue et al., EMBO J., 2007). Our results from dead-end and product inhibition studies performed with human CARM1, however, are consistent with a random kinetic mechanism. SAH and sinefungin demonstrate competitive inhibition with respect to SAM and produced noncompetitive inhibition patterns with respect to peptide. Both dimethylated R17 product peptide and dead-end R17K peptide exhibited noncompetitive inhibition patterns with respect to SAM. Furthermore, binding of SAM and peptide substrates were shown to be independent of each other in initial velocity experiments where both substrates were varied. Together, these results elucidate the kinetic mechanism of CARM1 and highlight elements important for binding affinity.
Citation Format: Suzanne L. Jacques, Katrina P. Aquino, Jodi Gureasko, P Ann Boriack-Sjodin, Robert A. Copeland, Thomas V. Riera. CARM1 preferentially methylates H3R17 over H3R26 through a random kinetic mechanism. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 97. doi:10.1158/1538-7445.AM2015-97
• ©2015 American Association for Cancer Research.
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7. Ginestier C, Hur MH, Charafe-Jauffret E, Monville F, Dutcher J, Brown M, Jacquemier J, Viens P, Kleer CG, Liu S et al: ALDH1 is a marker of normal and malignant human mammary stem cells and a predictor of poor clinical outcome. Cell Stem Cell 2007, 1(5):555-567.
8. Dontu G: Breast cancer stem cell markers – the rocky road to clinical applications. Breast Cancer Res 2008, 10(5):110.
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Read Full Post »
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7,814,443,153,231,085,000 | Atlas of Chick Development - 3rd Edition - ISBN: 9780123849519, 9780123849526
Atlas of Chick Development
3rd Edition
Authors: Ruth Bellairs Mark Osmond
eBook ISBN: 9780123849526
Hardcover ISBN: 9780123849519
Imprint: Academic Press
Published Date: 2nd June 2014
Page Count: 692
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Description
The Atlas of Chick Development, Third Edition, a classic work covering all major event of chick development, is extensively updated with new and more detailed photographs, enlargements showing regions of special-interest and complexity, and new illustrations. The revised text and expanded illustrative material describe the intricate changes that take place during development, together with accounts of recent experimental and molecular research that has transformed our understanding of morphogenesis.
These wide-ranging updates make this book an essential resource for developmental biologists, geneticists, molecular biologists, poultry scientists, biochemists, immunologists, and other life scientists who use the chick embryo as their research model. Individuals joining this burgeoning area, ignited by the increased insight into events surrounding organ and tissue differentiation, will find this a valuable tool to help grow a basic knowledge of morphogenesis.
Key Features
• Remains the established standard—the only book providing a comprehensive description of chick development from fertilization to hatching
• Contains more than 750 photographs and illustrations, including 410 labelled histological sections and 85 new high-quality plates, showing the major anatomical events from the earliest stages to 13 days of incubation
• Includes more than 200 labelled and detailed scanning electron micrographs, showing various tissues in great detail
• Leads the reader to important reviews on aspects of this rapidly moving field, along with extensive and updated references
Readership
Developmental biologists and embryologists, molecular biologists, cell biologists, poultry scientists, students and teachers of developmental biology
Table of Contents
• Preface to First Edition
• Preface to Second Edition
• Preface to Third Edition
• Note on Plates
• Glossary
• Some Highlights in the History of Chick Embryology
• Chapter 1. The Hen’s Egg and its Formation
• The Reproductive Tract of the Hen
• The Oviduct
• The Ovulation Cycle in the Laying Hen
• The Vitelline Membrane (Perivitelline Layer)
• Transport of Materials Across the Vitelline Membrane
• Albumen and the Chalazae
• The Egg Shell and its Formation
• The Laid Egg
• Chapter 2. Techniques
• ‘Milking’ Hens
• Storage of Eggs
• Incubation
• Stages of Development
• Labelling Techniques
• Culture Techniques
• Grafting and Transplants
• IN Ovo Techniques
• Preparation of Serial Sections
• Instruments
• Common Abnormalities
• Chapter 3. Early Stages
• Fertilization and Pre-Laying
• Normal Tables
• The Early Post-Laying Stages
• Gastrulation Movements
• Ingression and Cell Migration Away from the Primitive Streak
• Chapter 4. Establishment of the Embryonic Body
• Head Process and Regression
• The Tailbud
• Neural Induction
• Formation of the Neural Plate and Neural Tube
• Regionalization of the Neural Tissue
• Formation of the Notochord and Somites
• The Lateral Plate Mesoderm and the Intermediate Mesoderm
• The Neural Crest
• Chapter 5. External Appearance and Polarity
• Face
• Origin of the Limbs
• Growth of the Embryo
• Apoptosis
• Polarity: Symmetry and Asymmetry
• Chapter 6. Heart, Blood Vessels and Lymphatics
• Heart
• Primary and Secondary Heart Fields
• The Blood Vessels
• Embryonic Blood Vessels
• The Venous System
• The Endothelial and Haemopoietic Stem Cells
• The Lymphatics
• Chapter 7. Urino-Genital System
• The Urinary System
• The Genital System
• Chapter 8. Gut, Coelom and Respiratory System
• Early Stages
• The Intestines
• The Coelom, Mesenteries and Respiratory System
• The Respiratory Tract
• Chapter 9. Nervous System
• The Brain
• Histology of the Spinal Cord and Development of the Fibre Tracts
• Spinal Nerves
• The Cranial Nerves and Ganglia
• The Autonomic Nervous System
• Organs of Special Sense
• Chapter 10. Skeleton and Muscles
• Skeleton
• The Muscles
• Chapter 11. The Integument
• The Feathers
• The Periderm
• Beak and Claws
• The Comb
• The Uropygial Gland
• Pigmentation
• Innervation and Sensory Receptors in the Integument
• Chapter 12. Endocrine Glands
• The Pituitary Gland
• The Thyroid Gland
• The Parathyroid Glands
• The Adrenal Glands
• The Pancreas
• The Gonads
• Gut Endocrine Cells
• Chapter 13. Extra-Embryonic Membranes
• The Yolk Sac
• The Amnion and Chorion
• The Chorioallantoic Membrane
• Photographic Plates
• Appendices. Normal Tables
• Appendix I. Normal Table of Eyal-Giladi and Kochav (1975)
• Appendix II. Normal Table of Hamburger and Hamilton (1951; 1992)
• Appendix III. Additional Normal Tables
• References
• Index
Details
No. of pages:
692
Language:
English
Copyright:
© Academic Press 2014
Published:
Imprint:
Academic Press
eBook ISBN:
9780123849526
Hardcover ISBN:
9780123849519
About the Author
Ruth Bellairs
BSc (hons) in Zooloy, University of Birmingham UK 1947
PhD in Zoology (Embryology), University of London 1951, supervised by Sir Gavin deBeer and Michael Abercrombie.
Apart from brief periods in Anatomy Department, Cambridge and Department of Biology, St Bartholomew’s Hospital Medical School, academic posts have all been at UCL (University College London). Retired 1991 as Emeritus Professor in Embryology.
Research predominantly on early chick embryos concerned mainly with problems of tissue interaction, gastrulation and segmentation.
Founder member of Embryologists’ Club, the predecessor of BSDB (British Society of Developmental Biology). Served on several editorial boards, including JEEM (now Development) and Anatomy and Embryology.
Publications: approximately 120, including 2 books, 5 edited books.
Affiliations and Expertise
University College London, UK
Mark Osmond
Affiliations and Expertise
University College London, UK
Reviews
"...concisely summarize the development of the different body systems and sections of the chick embryo. Readers are clearly directed to figures within the text and to the plates throughout the chapters." --Javima
"...an updated version of the only available publication dedicated to the chick embryo...an essential reference text for developmental biologists and geneticists." --Nicole A. Theodosiou, Bowdin College, In Vitro Cell Development Biology | {
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-5,706,805,792,777,893,000 | NR1D1 (REV-ERBA) represses gene expression
Stable Identifier
R-HSA-1368071
Type
Pathway
Species
Homo sapiens
Compartment
Locations in the PathwayBrowser
Summation
REV-ERBA binds DNA elements very similar to those bound by the transcription activator RORA. RORAREV-ERBA bound to DNA and heme recruits the corepressors NCoR and HDAC3 to repress transcription. Thus REV-ERBA and RORA appear to compete to repress or activate genes, repectively.
Participants
Participant Of
hasEvent
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Reviewed
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} | 57 | cf5cd1df0ee2161e1684bdc019357275 |
-1,760,539,108,420,513,800 | Calabria Elisa
From Bioblast
(Redirected from Calabria E)
Jump to: navigation, search
e-COST MitoEAGLE
e-COST MitoEAGLE countries
MitoGlobal
MitoEAGLE
News and Events BEC 2020.1 Mitochondrial physiology About COST Action MitoEAGLE Working Groups MitoEAGLE Summit 2020 Obergurgl AT Short-Term Scientific Missions Inclusiveness Target Countries Management Committee Members
MiPsociety
COST Action CA15203 MitoEAGLE
Evolution-Age-Gender-Lifestyle-Environment: mitochondrial fitness mapping
Calabria Elisa
MitoPedia topics: EAGLE
COST: Member
COST WG4: WG4 COST Mentor: Mentor
Vice Chair - Management Committee MitoEAGLE
Name Calabria Elisa, PhD
ORCID ID
Institution
Elisa Calabria
Department of Neurological and Movement Sciences,
University of Verona, IT
Address Via Felice Casorati 43, 37131
City Verona
State/Province
Country Italy
Email [email protected]
Weblink
O2k-Network Lab IT Verona Calabria E
Labels:
Publications
PublishedReference
BEC 2020.1 doi10.26124bec2020-0001.v12020Gnaiger Erich et al ― MitoEAGLE Task Group (2020) Mitochondrial physiology. Bioenerg Commun 2020.1. doi:10.26124/bec:2020-0001.v1.
MitoEAGLE blood cells 12020Åsander Frostner Eleonor*, Aburel Oana M*, Avram Vlad F*, Calabria Elisa, Castelo Rueda Maria Paulina*, Chamkha Imen*, Čižmárová Beata, Danila Maria-Daniela*, Doerrier Carolina*, Eckert Gunter P*, Ehinger Johannes K, Elmer Eskil*, Garcia-Souza Luiz F*, Gnaiger Erich*, Hoppel Florian*, Karabatsiakis Alexander*, Keppner Gloria, Kidere Dita*, Krako Jakovljević Nina, Labieniec-Watala Magdalena*, Lelcu Theia*, Micankova Petra, Michalak Slawomir*, Molina Anthony JA*, Pavlovic Kasja, Pichler Irene*, Piel Sarah, Rousar Tomas, Rybacka-Mossakowska Joanna, Schartner Melanie, Siewiera Karolina*, Silaidos Carmina*, Sjövall Fredrik*, Sobotka Ondrej*, Sumbalova Zuzana*, Swiniuch Daria, Vernerova Andrea*, Volani Chiara*, Vujacic-Mirski Ksenija*, Watala Cezary* (2020) Interlaboratory guide to mitochondrial respiratory studies with peripheral blood mononuclear cells and platelets. - Updated: 2020-03-06 - *Confirmed
Calabria 2019 Front Neurosci2019Calabria Elisa, Scambi Ilaria, Bonafede Roberta, Schiaffino Lorenzo, Peroni Daniele, Potrich Valentina, Capelli Carlo, Schena Federico, Mariotti Raffaella (2019) ASCs-exosomes recover coupling efficiency and mitochondrial membrane potential in an in vitro model of ALS. Front Neurosci 13:1070.
Gnaiger 2019 MitoFit Preprint Arch2019Gnaiger E, Aasander Frostner E, Abdul Karim N, Abdel-Rahman EA, Abumrad NA, Acuna-Castroviejo D, Adiele RC, et al (2019) Mitochondrial respiratory states and rates. MitoFit Preprint Arch doi:10.26124/mitofit:190001.v6.
Chabi 2019 MitoFit Preprint Arch EA2019Chabi Béatrice, Ost M, Gama-Perez P, Dahdah N, Lemieux H, Holody CD, Carpenter RG, Tepp K, Puurand M, Kaambre T, Dubouchaud H, Cortade F, Pesta D, Calabria E, Casado M, Fernandez-Ortiz M, Acuña-Castroviejo D, Villena JA, Grefte S, Keijer J, O'Brien K, Sowton A, Murray AJ, Campbell MD, Marcinek DJ, Nollet E, Wüst R, Dayanidhi S, Gnaiger E, Doerrier C, Garcia-Roves PM (2019) Generating reference values on mitochondrial respiration in permeabilized muscle fibers. MitoFit Preprint Arch doi:10.26124/mitofit:ea19.MitoEAGLE.0001.
Hoppel 2019 Front Physiol2019Hoppel F, Calabria E, Pesta D, Kantner-Rumplmair W, Gnaiger E, Burtscher M (2019) Physiological and pathophysiological responses to ultramarathon running in non-elite runners. Front Physiol 10:1300.
Tam 2016 Eur J Appl Physiol2016Tam E, Bruseghini P, Calabria E, Sacco LD, Doria C, Grassi B, Pietrangelo T, Pogliaghi S, Reggiani C, Salvadego D, Schena F, Toniolo L, Verratti V, Vernillo G, Capelli C (2016) Gokyo Khumbu/Ama Dablam Trek 2012: effects of physical training and high-altitude exposure on oxidative metabolism, muscle composition, and metabolic cost of walking in women. Eur J Appl Physiol 116:129-44.
Abstracts
PublishedReference
Doerrier 2020 PaduaMuscleDays Poster2020Doerrier C, Gama-Perez P, Chabi B, Ost M, Distefano G, Pesta D, Dahdah N, Lemieux H, Holody C, Carpenter RG, Tepp K, Puurand M, Kaambre T, Dubouchaud H, Cortade F, Calabria E, Casado M, Fernandez-Ortiz M, Acuna-Castroviejo D, Villena JA, Grefte S, Keijer J, O'Brien K, Sowton A, Murray AJ, Campbell MD, Marcinek DJ, Nollet E, Wuest R, Dayanidhi S, Soendergaard SD, Chroeis KM, Gonzalez-Franquesa A, Goodpaster BH, Coen PM, Larsen S, Gnaiger E, Garcia-Roves PM (2020) Commitment to reproducibility in mitochondrial respiration studies with permeabilized muscle fibers. PaduaMuscleDays.
Garcia-Roves 2019 MiPschool Coimbra2019
Pablo Garcia-Roves
Generating reference values on mitochondrial respiration in permeabilized muscle fibers.
Calabria 2019 MiPschool Coimbra2019
Elisa Calabria
Investigating mitochondrial function in blood cells by high-resolution respirometry: contribution to an interlaboratory study. MitoEAGLE WG4.
Chabi 2019 MiP20192019
Béatrice Chabi
Generating reference values on mitochondrial respiration in permeabilized muscle fibers.
Garcia-Roves 2018 MiP2018b2018
Pablo Garcia-Roves
Generating mitochondrial respirometry reference values from permeabilized mouse soleus muscle fibers. Working Group 2 report. Garcia-Roves_Presentation
Calabria 2017 MiP20172017
Elisa Calabria
Age and frailty related changes in PBMCs mitochondrial function and whole body physiology.
Calabria 2017 Abstract MITOEAGLE Barcelona2017
COST Action MITOEAGLE
Age and frailty related changes in PBMCs mitochondrial function and whole body physiology.
Calabria 2017 MiP2017 WG42017
Calabria Elisa
PBMCS purification and mitochondrial function assay: monitoring preparative steps and comparison of protocols.
Sumbalova 2016b Abstract MitoFit Science Camp 20162016Human blood cells: isolation and HRR.
Hoppel 2015 Abstract MiP20152015Effects of ultramarathon performance on mitochondrial respiration in human platelets.
Calabria 2014 Abstract IOC962014Calabria E (2014) High-intensity interval training (HIT) in aging: changes in cardiovascular fitness and cardiometabolic risk factors. Mitochondr Physiol Network 19.11.
Co-chair - Management Committee MitoEAGLE
MitoEAGLE Short-Term Scientific Mission
Work Plan summary
To Whom it may concern, I’m applying for a STSM to sustain my participation to the MITOEAGLE workshop organized in Lund for the manuscript from WG4 - Blood Cells, concerning procedures for mitochondrial respiratory studies with blood cells accompanied by data. My contribute to the development of the article is based on research experience and data collected about the physiological activity of mitochondria in PBMCs. During the period May 27th - May 31st dedicated to the Short-Term-Scientific-Mission MITOEAGLE the working plan will be focused on the contribution to a joint publication relevant to the themes of Mitoeagle WG4, and will follow the workflow proposed by the organizers WG 4 blood cell workshop and retreat - Lund University. In particular the contribute will be on the development and refinement of the Innsbruck-Poznan-Lund Manuscript, a manuscript concerning standard operating procedures for mitochondrial respirometry with PMBCs and PLTs. On May 27th we will introduce ourselves and we will organize working subgroups. On May 28th we will start organizing information, data and writing. On My 29th we will develop the manuscript and in the second part of the day we will have an open discussion about procedures for separation of cells, storage, counting, cell viability and purity of cell fraction. On May 30th on the basis of the themes emerged during discussion further work will be done on the manuscript and we will fix timelines, actions and responsibilities. On May 31st further work on the manuscript based on the last decisions taken. This STSM is expected to strengthen collaborations with other groups working on blood cells, to consolidate data and finalize the realization of a joint publication aimed to harmonize protocols and procedures for handling and analyzing mitochondria of PBMCs and PLTs.
Participated at
Visiting scientist in the Oroboros O2k-Laboratory
O2k-Network
Elisa Calabria: Visiting scientist at the Oroboros O2k-Laboratory
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} | 57 | cf5cd1df0ee2161e1684bdc019357275 |
-2,334,950,999,231,397,000 |
Matt Good
Matthew Good, PhD
Assistant Professor
Department of Cell and Developmental Biology
[email protected]
1142 BRB II/III
Visit the lab website here
The Good laboratory is interested in how cells sense and regulate their dimensions and in mechanisms that control the spatial organization and insulation of biochemical reactions within a cell. We focus gene expression regulation and principles of organelle assembly in model systems ranging from cultured cells to blastula embryos.
Matt Good Cell Cover.jpg
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