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User:Jkane94

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CACAO Spring 2016

Homework

Week 2

Make sure you've found at least three papers that you think would be good for CACAO. They should be about 1+ specific proteins (not RNA), and you should know what organism that protein came from. Don't worry about having a GO term yet, but it would be wise to have an idea of the component, function, and/or process the paper is showing. If you're completely at sea, start by going to PubMed and search for "Expression, purification and characterization". We'd prefer it if you added the PMIDs here, or at least email them to us, so we can look over them before class.


Week 1

Read through the following papers (accessible through the PMID links). Identify the correct figure in the paper that supports the annotation.

Edit this table & fill in the Notes (remember to save twice, save the row to the table and then save table to the page)

Page Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status

DROME:A0A0B4JCQ5

GO:0005634

nucleus

PMID:21300783[1]

C

Figure 2 shows nuclear localization of dLipin expression. Figure 2 D and E especially.

Missing: evidence

CANAL:A0A0A6Q0W8

GO:0006468

protein phosphorylation

PMID:12722181[2]

P

Figure 4 shows calmodulin inhibition of phosphorylation by beta subunits.

Missing: evidence

RAT:D4A0U6

GO:0016874

ligase activity

PMID:9600082[3]

F

Figure 2 shows DNA ligase IV activity on cohesive-ended pUC119 DNA.

Missing: evidence



My Annotations

StatusPageDate/TimeGO Term (Aspect)ReferenceEvidenceNotesLinks
unacceptableYEAST:ROT12016-02-04 17:57:56 CSTGO:0005789 endoplasmic reticulum membrane (C)PMID:16567426ECO:0000314 direct assay evidence used in manual assertion

Figure 1 E shows Rot1p is localized in the ER membrane.

challenge
acceptableSCHPO:DSK12016-02-09 12:13:42 CSTGO:0004674 protein serine/threonine kinase activity (F)PMID:26167880ECO:0000316 genetic interaction evidence used in manual assertion

Figure 5a shows Bpb1 being phosphorylated by dsk1 in a western blot.

challenge
acceptableHUMAN:SRPK22016-02-09 12:18:53 CSTGO:0004674 protein serine/threonine kinase activity (F)PMID:26167880ECO:0000316 genetic interaction evidence used in manual assertion

Figure 5b shows phosphorylation of SF1 by srpk2 in a western blot.

challenge
updatedbyinstructorHUMAN:LIF2016-02-16 19:48:59 CSTGO:0033630 positive regulation of cell adhesion mediated by integrin (P)PMID:26723254ECO:0000315 mutant phenotype evidence used in manual assertion

Figs 2,3

challenge
unacceptableHUMAN:CDK92016-02-16 20:31:00 CSTGO:0050729 positive regulation of inflammatory response (P)PMID:26859911ECO:0000314 direct assay evidence used in manual assertion

Inhibition of CDK9 lowers uptake of pro-inflammatory cytokines.

challenge
acceptableHUMAN:SRPK22016-02-16 21:08:01 CSTGO:0018105 peptidyl-serine phosphorylation (P)PMID:26167880ECO:0000316 genetic interaction evidence used in manual assertion

Figure 5b shows phosphorylation of SF1 by srpk2 in a western blot.

challenge
acceptableSCHPO:DSK12016-02-17 15:48:22 CSTGO:0018105 peptidyl-serine phosphorylation (P)PMID:26167880ECO:0000316 genetic interaction evidence used in manual assertion

Figure 5a shows Bpb1 being phosphorylated by dsk1 in a western blot.

challenge
unacceptableMEDTR:K7PEY42016-03-08 12:17:48 CSTGO:0075189 positive regulation of hyphopodium formation on or near host (P)PMID:23122845ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 1 C shows increased hyphopodia in WT and reduced in ram1-1 mutant.

challenge
updatedbyinstructorHUMAN:TOPRS2016-03-08 13:37:35 CSTGO:0005814 centriole (C)PMID:26872363ECO:0000314 direct assay evidence used in manual assertion

S3 Fig. N-TOPORS localises to the nucleus and centrioles.

Human (h)TERT-RPE1 cells were either co-transfected with V5-tagged N-TOPORS and FLAG-tagged full-length TOPORS (top panel), or with V5-tagged N-TOPORS only (middle and bottom panels). The V5-tagged artificial N-TOPORS fragment co-localised with FLAG-tagged full-length TOPORS (top panel) and endogenous TOPORS (middle panel) at nuclei of hTERT-RPE1 cells and it co-localised with pericentrin at the centrioles.

challenge
unacceptableARATH:KNAT22016-04-08 01:51:35 CDTGO:0060629 regulation of homologous chromosome segregation (P)PMID:11973272ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 4 shows incomplete chromosome segregation in mutant.

challenge
unacceptableARATH:KNAT22016-04-08 01:42:54 CDTGO:1901673 regulation of mitotic spindle assembly (P)PMID:11973272ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 5 shows faulty mitotic spindle assembly in mutant.

challenge
updatedbyinstructorHUMAN:HMGB12016-04-06 10:23:27 CDTGO:0032755 positive regulation of interleukin-6 production (P)PMID:26961863ECO:0000314 direct assay evidence used in manual assertion

Figure 1b

challenge
updatedbyinstructorHUMAN:HMGB12016-04-06 10:23:27 CDTGO:0032757 positive regulation of interleukin-8 production (P)PMID:26961863ECO:0000314 direct assay evidence used in manual assertion

Figure 5b shows increased Interleukin-8 secretion when HMGB1 is added.

challenge
updatedbyinstructorHUMAN:HMGB12016-04-06 10:23:28 CDTGO:2000343 positive regulation of chemokine (C-X-C motif) ligand 2 production (P)PMID:26961863ECO:0000314 direct assay evidence used in manual assertion

Figure 5a

challenge
acceptableHUMAN:LIF2016-04-18 01:39:08 CDTGO:0045944 positive regulation of transcription from RNA polymerase II promoter (P)PMID:26723254ECO:0000314 direct assay evidence used in manual assertion

Figure 1 shows increased integrin expression (higher levels of integrin mRNA)

challenge
acceptableHUMAN:LIF2016-04-18 01:39:08 CDTGO:0033630 positive regulation of cell adhesion mediated by integrin (P)PMID:26723254ECO:0000315 mutant phenotype evidence used in manual assertion

As shown in Fig. 2B, LIF increased the adhesion of the human trophectoderm-derived JAr cells to endometrial Ishikawa cells. On the contrary, hLA diminished the adhesion of JAr cells to LIF-stimulated Ishikawa cells. These results suggest that the enhancement of integrin αV, β3, and β5 by LIF might be associated with the adhesion of trophblast to endometrium for embryo implantation. Figure 2A shows adhesion is dependent on integrins. (hLa inhibits LIF, hence IMP)

Figure 3 uses antibodies to neutralize the integrins.

challenge
acceptableHUMAN:LIF2016-04-18 01:39:08 CDTGO:0045944 positive regulation of transcription from RNA polymerase II promoter (P)PMID:26723254ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 2A Treatment of hLA (inhibitor of LIF) clearly resulted in the reduction of ITGAV, ITGB3 and ITGB5 expression levels induced by LIF in the Ishikawa cells

challenge
updatedbyinstructorMOUSE:VEGFC2016-04-18 01:59:34 CDTGO:1902462 positive regulation of mesenchymal stem cell proliferation (P)PMID:26934950ECO:0000314 direct assay evidence used in manual assertion

Figure 2A shows increased proliferation of the MSC SG-2 cell line.

challenge
updatedbyinstructorMOUSE:VEGFC2016-04-18 01:59:34 CDTGO:0030335 positive regulation of cell migration (P)PMID:26934950ECO:0000314 direct assay evidence used in manual assertion

Figure 2B shows increased cell migration especially in the MSC SG-2 line.

challenge
updatedbyinstructorMOUSE:VEGFC2016-04-18 01:59:34 CDTGO:0045860 positive regulation of protein kinase activity (P)PMID:26934950ECO:0000314 direct assay evidence used in manual assertion

Figure 3 shows increased ERK1/2 phosphorylation.

challenge
unacceptableMOUSE:VEGFC2016-04-18 01:59:35 CDTGO:0060836 lymphatic endothelial cell differentiation (P)PMID:26934950ECO:0000314 direct assay evidence used in manual assertion

Figure 4 A and B shows increased levels of expression of genes specific to lymphatic endothelial cell, Prox1 and Lyve1.

challenge
acceptableMOUSE:VEGFC2016-04-18 01:59:35 CDTGO:0045668 negative regulation of osteoblast differentiation (P)PMID:26934950ECO:0000314 direct assay evidence used in manual assertion

Figure 4 C-F shows reduced expression of late-stage osteogenic differentiation marker genes.

challenge
unacceptableDANRE:N2F1B2016-04-18 12:12:36 CDTGO:1901342 regulation of vasculature development (P)PMID:26572615ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 2 shows nr2flb mutants have defects in vascular development.

challenge
unacceptableDANRE:N2F1B2016-04-18 12:12:36 CDTGO:0072358 cardiovascular system development (P)PMID:26572615ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 2 shows nr2flb mutants have defects in vascular development.

challenge
acceptableDANRE:N2F1B2016-04-18 12:12:36 CDTGO:0035476 angioblast cell migration (P)PMID:26572615ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 5 shows decrease ISV angioblast cell migration in nr2f1b mutants.

challenge
updatedbyinstructorYEAST:GET32016-04-12 03:28:48 CDTGO:1990507 ATP-independent chaperone mediated protein folding (P)PMID:23203805ECO:0000314 direct assay evidence used in manual assertion

Figure 7: Influence of Get3 on the aggregation behavior of citrate synthase (CS)."It is of note that addition of either 2 mM ATP or ADP reproducibly reduced the holdase activity of Get3, implying that Get3 acts most efficiently on these clients in the absence of nucleotides (Fig. 7D)"

challenge
acceptableMOUSE:LRP52016-04-19 03:00:15 CDTGO:0061304 retinal blood vessel morphogenesis (P)PMID:27031698ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 1 shows loss of Lrp5 causes retinal hypovascularization and neovascularization in all stages of mouse development. Figure 5 also shows restoring Lrp5 in endothelial cells rescues retinal vascular defect.

challenge
acceptableRAT:PTN12016-04-19 03:17:45 CDTGO:0030061 mitochondrial crista (C)PMID:18583343ECO:0000314 direct assay evidence used in manual assertion

Figure 2 shows immunogold labeling of PTP-1B in isolated brain mitochondria. Figure 2A shows PTP-1B in the electron dense areas of the mitochondria, associated with the cristae.

challenge
acceptableRAT:PTN12016-04-19 03:17:45 CDTGO:0005759 mitochondrial matrix (C)PMID:18583343ECO:0000314 direct assay evidence used in manual assertion

Figure 2 shows immunogold labeling of PTP-1B in isolated brain mitochondria. Figure 2A shows PTP-1B in the electron dense areas of the mitochondria, associated with the matrix.

challenge
updatedbyinstructorRAT:SRC2016-04-19 03:22:41 CDTGO:0038083 peptidyl-tyrosine autophosphorylation (P)PMID:18583343ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 5 shows src autophosphorylation of src involving its own tyrosine amino acid residues.

challenge
unacceptableRAT:LYN2016-04-19 03:33:46 CDTGO:0005758 mitochondrial intermembrane space (C)PMID:27087918ECO:0000314 direct assay evidence used in manual assertion

IDA Figure 11 shows immunogold detection of lyn in rat brain mitrochondrial intermembrane space.

challenge
unacceptableRAT:HCK2016-04-19 03:41:26 CDTGO:0043525 positive regulation of neuron apoptotic process (P)PMID:27053350ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 6 D shows decreased levels of caspase-3 and p53 (signals apoptotic process) when hck expression is eliminated using hck siRNA.

challenge
unacceptableHUMAN:PKD12016-04-19 05:07:08 CDTGO:0030155 regulation of cell adhesion (P)PMID:25947155ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 3 shows Polycystin-1 regulates cell adhesion to the substrate.

challenge
unacceptableRAT:LYN2016-04-25 15:10:23 CDTGO:0044290 mitochondrial intracristal space (C)PMID:27087918ECO:0000314 direct assay evidence used in manual assertion

Figure 11 shows immunogold detection of lyn in rat brain mitrochondrial cristal lumen (intracristal space).

challenge

acceptable:12
unacceptable:12
requires_changes:0
flagged:0

Annotations challenged by Jkane94

StatusAuthor,GroupPageGO Term (Aspect)ReferenceEvidenceLinksPage history
unacceptableTracy.Pham,
Team Espresso my genes
HUMAN:BIRC1GO:0006954 - inflammatory response (P)PMID:21874021ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 2
unacceptableCaleb.N.Laney,
Team Grapes of Staph
VIBF1:Q5E614GO:0007165 - signal transduction (P)PMID:14507383ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 1
unacceptableKassandra.Kompelien,
Team The Jackson 5
STRR6:Q8DNW9GO:0098635 - protein complex involved in cell-cell adhesion (C)PMID:23341464ECO:0000314 direct assay evidence used in manual assertionchallengeC: 2

0 annotations fixed by Jkane94

Spring 2016 Grade

Inning Credits Notes

Final grade

  • Acceptable: 12
  • Fixed Through Challenges: 0
  • Total: 12


CACAO Fall 2015

My Annotations

StatusPageDate/TimeGO Term (Aspect)ReferenceEvidenceNotesLinks
updatedbyinstructorHUMAN:TPX22015-09-29 20:52:44 CDTGO:0007020 microtubule nucleation (P)PMID:26414402ECO:0000314 direct assay evidence used in manual assertion

Fig 6.b, and Fig 6.c shows microtuble nucleation by TPX2

challenge
acceptablePLAF7:Q8IDZ82015-10-27 20:53:58 CDTGO:0061077 chaperone-mediated protein folding (P)PMID:23326533ECO:0000314 direct assay evidence used in manual assertion

Figure 2 shows pf-cpn20 folding denatured malate dehydrogenase.

challenge
unacceptableHUMAN:Q96FC32015-11-02 17:34:43 CSTGO:0008017 microtubule binding (F)PMID:26414402ECO:0000314 direct assay evidence used in manual assertion

Fig. 2 C-F show TPX2 binding along tubulin.

challenge
updatedbyinstructorHUMAN:TPX22015-11-02 17:42:43 CSTGO:0007026 negative regulation of microtubule depolymerization (P)PMID:26414402ECO:0000314 direct assay evidence used in manual assertion

Fig 3f shows reduced depolymerization activity with TPX2.

challenge
updatedbyinstructor9CAUD:Q3V5F22015-11-10 20:07:05 CSTGO:0017116 single-stranded DNA-dependent ATP-dependent DNA helicase activity (F)PMID:26277776ECO:0000314 direct assay evidence used in manual assertion

Figure 7, "helicase activity could only be detected on the forked substrate". Figure 5 A also shows that there was only helicase activity seen with ssDNA for gp43-1

challenge

acceptable:1
unacceptable:1
requires_changes:0
flagged:0

Annotations challenged by Jkane94

StatusAuthor,GroupPageGO Term (Aspect)ReferenceEvidenceLinksPage history
updatedbyinstructorChristin3sheets,
Team Hardy Weinburgers
STAA8:Q2G0W2GO:0045838 - positive regulation of membrane potential (P)PMID:25448817ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 5

fixed by Sandyl 27
updatedbyinstructorChristin3sheets,
Team Hardy Weinburgers
STAA8:Q2G0W2GO:0005887 - integral component of plasma membrane (C)PMID:25448817ECO:0000250 sequence similarity evidence used in manual assertionchallengeC: 2

fixed by Kaylamichbrown
acceptableMadstidham1,
Team G-nomes
CHICK:FGF8GO:0045944 - positive regulation of transcription by RNA polymerase II (P)PMID:12006981ECO:0000316 genetic interaction evidence used in manual assertionchallengeC: 2
updatedbyinstructorVvg0009,
Team Hardy Weinburgers
MOUSE:STK4GO:1904237 - positive regulation of substrate-dependent cell migration, cell attachment to substrate (P)PMID:19073936ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 1
updatedbyinstructorMxb5379,
Team PSU 2
ECOLI:MCP2GO:0051286 - cell tip (C)PMID:19547746ECO:0000314 direct assay evidence used in manual assertionchallengeC: 1
updatedbyinstructorChristin3sheets,
Team Hardy Weinburgers
BACSU:MRPFGO:0036376 - sodium ion export across plasma membrane (P)PMID:11004162ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 1

fixed by Jkane94
updatedbyinstructorChristin3sheets,
Team Hardy Weinburgers
BACSU:CIMHGO:0015531 - citrate:proton symporter activity (F)PMID:11566984ECO:0000314 direct assay evidence used in manual assertionchallengeC: 1

1 annotations fixed by Jkane94


Grade as of 4 Dec

  • 2 Total
  • 1 Accepted
  • 1 Through Challenges
  • NTRs


What do the icons mean in the status column?

assessment icons.jpg

References

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  1. Ugrankar, R et al. (2011) Lipin is a central regulator of adipose tissue development and function in Drosophila melanogaster. Mol. Cell. Biol. 31 1646-56 PubMed GONUTS page
  2. Zelada, A et al. (2003) cDNA cloning, biochemical and phylogenetic characterization of beta- and beta'-subunits of Candida albicans protein kinase CK2. Yeast 20 471-8 PubMed GONUTS page
  3. Nagaki, S et al. (1998) Non-histone chromosomal proteins HMG1 and 2 enhance ligation reaction of DNA double-strand breaks. Biochem. Biophys. Res. Commun. 246 137-41 PubMed GONUTS page