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User:Nfarmer91

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Spring 2013

My Annotations

StatusPageDate/TimeGO Term (Aspect)ReferenceEvidenceNotesLinks
updatedbyinstructorMOUSE:DRD22013-02-09 14:08:04 CSTGO:0045824 negative regulation of innate immune response (P)PMID:23242137ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 2 in this publication displays data that the authors found to indicate that Drd2 knockout mice were hyper-responsive with higher neuroinflammation

challenge
updatedbyinstructorCAEEL:TMC12013-02-09 14:56:37 CSTGO:0005272 sodium channel activity (F)PMID:23364694ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 4 shows sodium-sensitive cation currents in TMC-1 expressing cells indicating its role as a sodium channel. In supplementary figure 8 the authors also confirm TMC-1's localization to the plasma membrane using fluorescence imaging, further supporting the finding of its role as a sodium channel complex.

challenge
updatedbyinstructorMOUSE:CAHM12013-03-16 12:15:04 CDTGO:0050909 sensory perception of taste (P)PMID:23467090ECO:0000315 mutant phenotype evidence used in manual assertion

Through work with CALHM1 knockout mutants,it was shown (FIG. 4) that CALHM1 is involved in the taste-evoked ATP release from taste cells.

challenge
updatedbyinstructorMOUSE:CAHM12013-03-16 12:23:14 CDTGO:0005245 voltage-gated calcium channel activity (F)PMID:22711817ECO:0000314 direct assay evidence used in manual assertion

Figures 1 and 4 in this publication shwo that CALHM1 is involved in voltage-dependent gating and that the channel works with calcium.

challenge
acceptableHUMAN:DPP42013-03-16 13:25:38 CDTGO:0001618 viral receptor activity (F)PMID:23486063ECO:0000314 direct assay evidence used in manual assertion

Figure 2 shows human coronavirus-Erasmus Medical Center (hCoV-EMC) tail spike binding to DPP4 which is the event needed for viral infection, Figure 3 shows DPP4 is present on hCoV-EMC succeptible cells and figure 4 confirms DDP4 is essential for the virus infection.

challenge
acceptableMOUSE:RING22013-03-16 13:25:56 CDTGO:0007281 germ cell development (P)PMID:23486062ECO:0000315 mutant phenotype evidence used in manual assertion

In figure 1 Rnf2 is shown to regulate primordial germ cell development, as seen through the effects of Rnf2 mutants

challenge
acceptableMOUSE:TRIB12013-03-30 00:19:09 CDTGO:0045645 positive regulation of eosinophil differentiation (P)PMID:23515163ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 2: Although the proportions of B cells, T cells, dendritic cells and Ly6ChighMac1+ inflammatory monocytes were not altered between wild-type and Trib1−/− splenocytes, F4/80+Mac1+ macrophages, which also expressed Mrc1 (also called MR), Arg1 and Fizz1 (also called Retnla), were markedly reduced and Siglec-F+CCR3+ eosinophils were absent in Trib1−/− spleens (Fig. 1a and Supplementary Figs 1 and 2).

challenge
acceptableMOUSE:TRIB12013-03-30 00:19:09 CDTGO:0045659 negative regulation of neutrophil differentiation (P)PMID:23515163ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 2: Although the proportions of B cells, T cells, dendritic cells and Ly6ChighMac1+ inflammatory monocytes were not altered between wild-type and Trib1−/− splenocytes, F4/80+Mac1+ macrophages, which also expressed Mrc1 (also called MR), Arg1 and Fizz1 (also called Retnla), were markedly reduced and Siglec-F+CCR3+ eosinophils were absent in Trib1−/− spleens (Fig. 1a and Supplementary Figs 1 and 2). In contrast, the neutrophil population was increased in Trib1−/− spleens (Fig. 1a and Supplementary Fig. 3).

challenge
acceptableMOUSE:TRIB12013-03-30 00:19:09 CDTGO:0045651 positive regulation of macrophage differentiation (P)PMID:23515163ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 2: Although the proportions of B cells, T cells, dendritic cells and Ly6ChighMac1+ inflammatory monocytes were not altered between wild-type and Trib1−/− splenocytes, F4/80+Mac1+ macrophages, which also expressed Mrc1 (also called MR), Arg1 and Fizz1 (also called Retnla), were markedly reduced and Siglec-F+CCR3+ eosinophils were absent in Trib1−/− spleens (Fig. 1a and Supplementary Figs 1 and 2).

challenge
acceptableMOUSE:DAB22013-03-30 00:38:19 CDTGO:0002092 positive regulation of receptor internalization (P)PMID:23354168ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 4: While Alexa dye-coupled VEGF-A and VEGF-C were readily taken up by cultured mouse control endothelial cells, knockdown of Pard3 or Dab2 significantly decreased the perinuclear accumulation of VEGF-A and VEGF-C (Fig. 4a–c). Surface biotinylation experiments further confirmed that VEGF-C-induced internalization of VEGFR3 and VEGFR2 was impaired in Dab2 knockdown or Pard3 knockdown cells (Fig. 4d,e).

challenge
acceptableMOUSE:PARD32013-03-30 00:40:23 CDTGO:0002092 positive regulation of receptor internalization (P)PMID:23354168ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 4: While Alexa dye-coupled VEGF-A and VEGF-C were readily taken up by cultured mouse control endothelial cells, knockdown of Pard3 or Dab2 significantly decreased the perinuclear accumulation of VEGF-A and VEGF-C (Fig. 4a–c). Surface biotinylation experiments further confirmed that VEGF-C-induced internalization of VEGFR3 and VEGFR2 was impaired in Dab2 knockdown or Pard3 knockdown cells (Fig. 4d,e).

challenge
updatedbyinstructorMOUSE:NF2L22013-03-30 00:50:12 CDTGO:1902037 negative regulation of hematopoietic stem cell differentiation (P)PMID:23434824ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 2: Moreover, we found a significantly increased level of Ki-67 expression on LSKs from Nrf2−/− when compared with WT bone marrow in vivo (Fig. 2c), in concordance with the enhanced proliferation observed in vitro.

challenge

acceptable:7
unacceptable:0
requires_changes:0
flagged:0

Annotations challenged by Nfarmer91

StatusAuthor,GroupPageGO Term (Aspect)ReferenceEvidenceLinksPage history
unacceptableAyusol,
Team Viral Load Challengers
HUMAN:TRBMGO:0030195 - negative regulation of blood coagulation (P)PMID:23383040ECO:0000269 experimental evidence used in manual assertionchallengeC: 5
updatedbyinstructorAlemus,
Team Blot Blot Western Baby
HPV18:VE2GO:0044163 - host cytoskeleton (C)PMID:15020762ECO:0000314 direct assay evidence used in manual assertionchallengeC: 7
acceptableWillcoxe,
Team Legend (wait for it) DARY
ASFB7:P12GO:0019012 - virion (C)PMID:8350406ECO:0000314 direct assay evidence used in manual assertionchallengeC: 1
unacceptableAyusol,
Team Viral Load Challengers
PIG:ITIH4GO:0006953 - acute-phase response (P)PMID:23332090ECO:0000269 experimental evidence used in manual assertionchallengeC: 1
acceptableBennettv,
Team Viral Load Challengers
CXB3N:POLGGO:0042025 - host cell nucleus (C)PMID:23010168ECO:0000314 direct assay evidence used in manual assertionchallengeC: 1
unacceptableRomero.alan,
Team BTHO PubMed!
MOUSE:BADGO:0016310 - phosphorylation (P)PMID:16396982ECO:0000314 direct assay evidence used in manual assertionchallengeC: 2
unacceptableRomero.alan,
Team BTHO PubMed!
MOUSE:AKTS1GO:0016310 - phosphorylation (P)PMID:16396982ECO:0000314 direct assay evidence used in manual assertionchallengeC: 1
updatedbyinstructorRomero.alan,
Team BTHO PubMed!
MOUSE:PI3R6GO:0045582 - positive regulation of T cell differentiation (P)PMID:12707323ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 1

fixed by Nfarmer91

1 annotations fixed by Nfarmer91


Fall 2012

My Annotations

StatusPageDate/TimeGO Term (Aspect)ReferenceEvidenceNotesLinks
acceptable?2012-10-02 20:06:14 CDTGO:0001525 angiogenesis (P)PMID:22426001ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 1 references how angiogenesis is strongly enhanced in vegfr2 mutants.

challenge
acceptable?2012-10-02 19:27:59 CDTGO:0002043 blood vessel endothelial cell proliferation involved in sprouting angiogenesis (P)PMID:22426001ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 4 shows that mutant vegfr3 has an effect on the sprouting of endothelial cells

challenge
acceptableECOLI:EMRE2012-10-02 19:37:45 CDTGO:0022857 transmembrane transporter activity (F)PMID:22178925ECO:0000314 direct assay evidence used in manual assertion

Figure 1 talks about EmrE'S changes in conformation to allow substrates in.

challenge
requireschangesDROME:TRPA12012-10-02 19:49:21 CDTGO:0043052 thermotaxis (P)PMID:22139422ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 3 references differing sensitivity to warmth in TrpA1 mutants

challenge
acceptableMOUSE:FBX112012-10-02 20:04:39 CDTGO:0004842 ubiquitin-protein ligase activity (F)PMID:22113614ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 1 show that FBOX proteins were flagged and immunoblotting indicated that FBXO11 is directly involved in ubiquitin-mediated degradation of BCL6

challenge
acceptableMOUSE:SRRT2012-10-02 20:25:33 CDTGO:0050769 positive regulation of neurogenesis (P)PMID:22198669ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 2 demontrates Ars2 regulation of neurogenesis

challenge
acceptableHUMAN:PEBB2012-10-02 20:38:30 CDTGO:0000209 protein polyubiquitination (P)PMID:22190036ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 4 indicates CBF-β's role in APOBEC3G ubiquitination

challenge
acceptableMOUSE:PRGC12012-10-02 20:52:53 CDTGO:0060612 adipose tissue development (P)PMID:22237023ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 1

challenge
acceptableDROME:G9L8C42012-10-16 20:00:05 CDTGO:0009408 response to heat (P)PMID:22139422ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 4 references mutating either a cysteine (C105) or two basic residues (R113, R116) in TRPA1(A) markedly increased temperature responsiveness (Fig. 4a–c and Supplementary Figs 6 and 7). The temperatures used were from 27–37 degrees C (warming).

challenge
acceptableMOUSE:Q71F552012-10-16 20:21:53 CDTGO:0042742 defense response to bacterium (P)PMID:22801499ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 2

challenge
acceptableMOUSE:ACE22012-10-30 20:37:04 CDTGO:0015827 tryptophan transport (P)PMID:22837003ECO:0000315 mutant phenotype evidence used in manual assertion

To demonstrate that the severe colitis in Ace2 deficient mice is due to impaired tryptophan uptake, we provided tryptophan in form of a Gly-Trp dipeptide to bypass the loss of the single amino acid transporter B0AT1. Dietary dipeptidic tryptophan (a Trp+ diet) restored serum tryptophan levels (Supplementary Fig. 16a) and rescued the enhanced DSS-susceptibility of Ace2−/y mice (Fig. 2d–f; Supplementary Fig. 16b–d). Our results show that deficiency of Ace2 causes a critical impairment of local tryptophan homeostasis which alters the susceptibility to intestinal inflammation.

challenge
acceptableYEAST:MRE112012-10-30 20:52:54 CDTGO:0006302 double-strand break repair (P)PMID:22002605ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 1

To investigate a specific role for the Mre11 3′–5′ exonuclease during DNA repair in cycling cells, we challenged yeast cells with exposure to DNA damaging agents. Similar to complete abrogation of the endo/exonuclease activities (mre11-H125N), reduced Mre11 exonuclease activity (mre11-H59S) sensitized cells to the DNA alkylating agent methyl methanesulphonate (MMS) and to the topoisomerase poison camptothecin (CPT; Fig. 3).Compared to an MRE11 deletion, however, mre11-H59S and mre11-H125N are themselves far less sensitive, consistent with physical interactions within the Mre11 complex being retained (Supplementary Fig. 9). In agreement with Mre11 endonuclease activity being unaffected in mre11-H59S, and allowing redundant processing pathways, combining mre11-H59S with a deletion of EXO1 did not further sensitize cells to MMS (Supplementary Fig. 10). Together these observations indicate that the exonuclease activity of Mre11 is involved in the repair of various classes of DNA lesion.

challenge
updatedbyinstructorMOUSE:NLRP62012-11-16 03:51:45 CSTGO:0002862 negative regulation of inflammatory response to antigenic stimulus (P)PMID:22763455ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 1 depicts the NLRP6 lacking mice mutants had less damage to the liver when exposed to Listeria and Salmonella infections then did wild type mice.

challenge
updatedbyinstructorMOUSE:NLRP62012-11-16 04:05:42 CSTGO:0043124 negative regulation of I-kappaB kinase/NF-kappaB cascade (P)PMID:22763455ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 3 gives evidence that NLRP6 lacking mutant mice failed to downregulate phospho-IkappaB resulting in more NF-kappaB activation while in the wild type mice production of phospho-IkappaB peaked at 60 minutes and went down after durring Listeria infections

challenge
updatedbyinstructorMOUSE:NLRP62012-11-16 04:09:13 CSTGO:0070373 negative regulation of ERK1 and ERK2 cascade (P)PMID:22763455ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 3 indicates that NLRP6 lacking mutant mice had significantly increased ERK1/ERK2 levels while in the wild types the levels were significantly less in Listeria infections.

challenge
unacceptableSHIFL:OSPF2012-11-16 04:40:41 CSTGO:0075132 negative regulation by symbiont of host protein kinase-mediated signal transduction (P)PMID:22820255ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 1 indicates the ability of OspF to be specifically targeted to different scaffold complexes (such as yeast osmolarity scaffold Pbs2) where it can inhibit MAPK activity and prevent growth.

challenge
acceptableMOUSE:SHAN22012-11-18 14:55:13 CSTGO:0051968 positive regulation of synaptic transmission, glutamatergic (P)PMID:22699619ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 2 shows that in Shank2 lacking mutant mice there was reduced synaptic transmission compared to the wild type mice suggesting that Shank2 is a positive regulator of the hippocampal glutamatergic synaptic transmission.

challenge
acceptableMOUSE:BCL22012-11-18 15:17:32 CSTGO:0010506 regulation of autophagy (P)PMID:22258505ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 2 shows that in the BCL2 mutant mice exercise and starvation induced autophagy were blocked

challenge
updatedbyinstructorMOUSE:HSP722012-11-18 15:49:31 CSTGO:0032781 positive regulation of ATPase activity (P)PMID:22495301ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 2 shows that Hsp72 binding improves sarcoplasmic/endoplasmic reticulum Ca2+ -ATPase function in mice with muscular dystrophy

challenge
updatedbyinstructorMOUSE:FFAR42012-11-18 16:08:14 CSTGO:0045444 fat cell differentiation (P)PMID:22343897ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 2 suggests that in GPR120 deficient mice there was increased adipogenesis (fat cell differentiation) resulting in obesity.

challenge

acceptable:13
unacceptable:1
requires_changes:1
flagged:0

Annotations challenged by Nfarmer91

StatusAuthor,GroupPageGO Term (Aspect)ReferenceEvidenceLinksPage history
unacceptableCourtney.kast,
Team Team
HUMAN:KDM1AGO:0070076 - histone lysine demethylation (P)PMID:18440794ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 3
unacceptableAriana.brovarenko,
Team Honey Badgers
STRCO:GCH1GO:0003934 - GTP cyclohydrolase I activity (F)PMID:12000953ECO:0000314 direct assay evidence used in manual assertionchallengeC: 2
requireschangesPaige.stump,
Team Team
ECOLI:PBP2GO:0009252 - peptidoglycan biosynthetic process (P)PMID:2681889ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 3
unacceptablePaige.stump,
Team Team
HUMAN:MYD88GO:0002224 - toll-like receptor signaling pathway (P)PMID:3409161ECO:0000314 direct assay evidence used in manual assertionchallengeC: 2
unacceptablePaige.stump,
Team Team
ECOLX:SULAGO:0009273 - peptidoglycan-based cell wall biogenesis (P)PMID:3343033ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 2
updatedbyinstructorLindsay.wargelin,
Team Roll Tide
ECOLI:CSRAGO:0017148 - negative regulation of translation (P)PMID:17526692ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 1
requireschangesLindsay.wargelin,
Team Roll Tide
HUMAN:CDK5GO:0006468 - protein phosphorylation (P)PMID:21499257ECO:0000314 direct assay evidence used in manual assertionchallengeC: 2
unacceptableHannah smalley,
Team Gene Simmons
YEAST:MRE11GO:0010780 - meiotic DNA double-strand break formation involved in reciprocal meiotic recombination (P)PMID:7625279ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 1
unacceptableSarahtheriault,
Team Gene Simmons
MOUSE:TDRD1GO:0005515 - protein binding (F)PMID:22996915ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 1
acceptableChelsea.jenney,
Team DC2
MOUSE:MOXD1GO:0016020 - membrane (C)PMID:15337741ECO:0000255 match to sequence model evidence used in manual assertionchallengeC: 1

0 annotations fixed by Nfarmer91

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