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User:ADPowell

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CACAO Spring 2019

My Annotations

StatusPageDate/TimeGO Term (Aspect)ReferenceEvidenceNotesLinks
acceptableCAUVC:DIVJ2019-02-05 14:30:54 CSTGO:0000160 phosphorelay signal transduction system (P)PMID:16176121ECO:0001202 in vitro protein kinase assay evidence used in manual assertion

Cell cycle regulator

Figure 5C-D Ten-second time point phosphotransfer profile of DivJ demonstrating phosphorylation of PleD and DivK Caulobacter vibrioides

challenge
unacceptableBORBG:C5J4822019-02-05 21:28:17 CSTGO:0004867 complement binding (F)PMID:26808924ECO:0001269 surface plasmon resonance evidence used in manual assertion

C1r binding protein. Figure 5A-E shows C1r binding to BBK32 Full-length and the C-terminal of BBK32 through surface plasmon resonance assays. Far Western blot analysis was used to confirm this interaction.

Waiting on new GO term - Complement component C1r binding. Borrelia burgdorferi

challenge
unacceptableBORBU:O508352019-02-12 16:18:37 CSTGO:0048519 negative regulation of biological process (P)PMID:26808924ECO:0001258 spectrophotometry evidence used in manual assertion

Figure 4A-C shows use of classical pathway (CP)-mediated hemolysis assays using absorbance to measure cell lysis. Performed with BBK32 N-terminal, C-termainl, and full-length protein

Waiting on new GO term Borrelia burgdorferi

challenge
acceptableYERPE:YOPM2019-04-09 16:16:56 CDTGO:1990001 inhibition of cysteine-type endopeptidase activity involved in apoptotic process (P)PMID:27911947ECO:0007183 protein expression level evidence based on western blot used in manual assertion

Figure 2D shows Western Blot data showing decreased pro-Caspase-1 and IL-1B, the inactive form of Caspase-1 that plays a role in Pyrin Inflammasome activation and the inactive form of IL-1B that is activated by Caspase-1, respectively, in the YopM mutants. This is indicative of more activation of Caspase-1 and IL-1B in the absence of YopM, which implies increased Pyrin Inflammasome activation. The figure also shows increased IL-1B in the YopM mutant, which inversely corresponds with the IL-1B protein expression data.

Yersinia pests

challenge
acceptableYERPE:O687042019-03-19 15:46:56 CDTGO:1900226 negative regulation of NLRP3 inflammasome complex assembly (P)PMID:27911947ECO:0005581 enzyme-linked immunoabsorbent assay evidence used in manual assertion

Figure 3E,G YopK mutants showed a sharp increase in IL-1B production in 3E. 3G shows the independence of this effect on Pyrin, but its dependence on NLRP3/NLRC4 pathway.

Yersinia pestis

challenge
acceptableYERPS:YOPB2019-03-26 15:44:08 CDTGO:0042536 negative regulation of tumor necrosis factor biosynthetic process (P)PMID:9535085ECO:0000335 substance quantification evidence

CL:0000235 occurs in human macrophages. Figure 1B shows J774A.1 macrophages were infected with Yersinia pseudotuberculosis strains both able and unable to secrete full-length translocon YopB for 1 hour. Levels of TNF-alpha in media were quantified, with YopB mutants consistently producing twofold more TNF-alpha.

Yersinia pseudotuberculosis

A0A0N9NJG3 should be the protein ID. This is described as an Uncharacterized protein, I chose this protein designation because there is no YopB for Yersinia pseudotuberculosis.

challenge
updatedbyinstructorYERPS:YOPJ2019-03-26 15:52:44 CDTGO:0042536 negative regulation of tumor necrosis factor biosynthetic process (P)PMID:9535085ECO:0000335 substance quantification evidence

Figure 3b shows that strain YP25, defective for secretion of effector YopJ, had increased macrophage TNF-alpha production after J774A.1 macrophages were infected with Yersinia pseudotuberculosis strains both able and unable to secrete YopJ.

Yersinia pseudotuberculosis accuring in human macrophages.

challenge
updatedbyinstructorYERPU:A0A0N9NCU62019-03-26 16:00:08 CDTGO:1903753 negative regulation of p38MAPK cascade (P)PMID:9535085ECO:0000279 qualitative western immunoblotting evidence used in manual assertion

CL:0000235 occurs in human macrophages. Figure 6 shows J774A.1 macrophages infected with Yersinia pseudotuberculosis strains both able and unable to secrete full-length translocon YopJ for 1 hour, and protein samples were taken to be analyzed by immunoblotting with anti-P38, indicating down-regulation of P38 by YopJ.

Yersinia pseudotuberculosis

challenge
updatedbyinstructorYERPU:A0A0N9NCU62019-03-26 16:04:05 CDTGO:0046329 negative regulation of JNK cascade (P)PMID:9535085ECO:0000279 qualitative western immunoblotting evidence used in manual assertion

CL:0000235 occurs in human macrophages. Figure 6c shows J774A.1 macrophages were infected with Yersinia pseudotuberculosis strains both able and unable to secrete full-length translocon YopJ for 1 hour. Cell lysates were taken for immunoblotting with a phosphospecific anti-JNK antibody. Blotting showed YopJ down regulated JNK in macrophages.

Yersinia pseudotuberculosis

challenge
acceptableYERPU:A0A0N9NCT82019-04-09 21:45:42 CDTGO:0030254 protein secretion by the type III secretion system (P)PMID:8112310ECO:0007042 epifluorescence microscopy evidence used in manual assertion

Figure 7 panels C and D show epifluorescence microscopy images of YopE localization in HeLa cells infected with the yopD mutant YPIII(pIB15) (Yersinia pseudotuberculosis serotype III). YopE was shown to not be dispersed throughout HeLa cells in YopD mutants in this imaging, indicating that YopD plays a role in the secretion of YopE.

challenge
unacceptableRABIT:LBP2019-04-09 22:06:53 CDTGO:0032760 positive regulation of tumor necrosis factor production (P)PMID:2402637ECO:0007070 crystal violet staining evidence used in manual assertion

Figure 2 A shows cytolytic activity of TNF pooled from cell-free supernatants from cultures of peritoneal exudate macrophages (PEM) with and without LPS binding protein (LBP) after being stimulated with LPS from E. coli. Although this TNF is being isolated from media, indicating it might be secreted, it is more logical to assume that LBP plays a role in TNF production rather than in the process of its secretion. L929 cells were incubated with purified TNF from PEM cell-free media, stained with crystal violet, and analyzed using spectrophotometry.

challenge
updatedbyinstructorYERPU:A0A3G5IPC52019-04-10 19:52:27 CDTGO:0044164 host cell cytosol (C)PMID:8112310ECO:0005804 immunofluorescence evidence used in manual assertion

Figure 5 shows the localization of the YopE protein to the host cytosol. Indirect immunofluorescence was used to visualize this localization in HeLa cells transfected with Yersinia pseudotuberculosis (serotype III did not have YopE protein listed). Used broader evidence code because indirect immunofluorescence microscopy was not a term.

challenge
unacceptableYERPU:A0A0N9NCT82019-04-10 19:52:28 CDTGO:0044164 host cell cytosol (C)PMID:8112310ECO:0005804 immunofluorescence evidence used in manual assertion

Figure 5 shows the localization of the YopE protein to the host cytosol. Indirect immunofluorescence was used to visualize this localization in HeLa cells transfected with Yersinia pseudotuberculosis (serotype III did not have YopE protein listed). Used broader evidence code because indirect immunofluorescence microscopy was not a term.

challenge
acceptableYERPE:A0A3N4BLC72019-04-11 00:15:57 CDTGO:0030254 protein secretion by the type III secretion system (P)PMID:23357388ECO:0007122 in vitro assay evidence used in manual assertion

Figure S1A shows the dependence on RfaL in the presence of calcium for secretion of late-phase type III secretion system proteins in Yersinia pestis through secretion assays followed by western blotting using anti YopD (early T3SS protein) and YopE (late T3SS protein) in WT, RfaL mutant, and RfaL complemented strains. YopD is still secreted in RfaL mutant in the absence of calcium, but to a lesser extent.

submitted a new term request for an evidence code describing secretion assays - waiting on term.

challenge

acceptable:6
unacceptable:4
requires_changes:0
flagged:0