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User:RazMonk

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CACAO Spring 2017

My Annotations

StatusPageDate/TimeGO Term (Aspect)ReferenceEvidenceNotesLinks
updatedbyinstructorHUMAN:LN28B2017-02-14 13:56:09 CSTGO:0050779 RNA destabilization (P)PMID:18951094ECO:0000314 direct assay evidence used in manual assertion

Figure 4B: Human Lin28b (from recombinant E. coli), when added to cell extract in increasing amounts, increases the amount of uridylated pre-let-7a-1 (up-let-7a-1). Figure 4E: up-let-7a-1 shows decreased stability as compared to pre-let-7a-1. According to the authors, this indicates that "Lin28 mediates the terminal uridylation of pre-let-7 diverting the Dicer processing and irreversibly reroutes pre-let-7 into a decay pathway."

challenge
acceptableHUMAN:LN28B2017-02-14 13:56:09 CSTGO:2000627 positive regulation of miRNA catabolic process (P)PMID:18951094ECO:0000315 mutant phenotype evidence used in manual assertion

"Lin28b was identified via RNA affinity purification of Huh7 cell extracts with pre-let-7a-1"

Fig. 4b shows "in vitro uridylation of pre-let-7a-1 was carried out with purified recombinant Lin28b protein." Fig. 4e shows a quicker decay of target species, pre-let-7a-1, after uridylation by overexpressed human lin28b; up-let-7a-1 is the product of the uridylation of pre-let-7a-1 by lin28b. Called human lin28b.

challenge
acceptableHUMAN:LN28B2017-02-14 13:56:09 CSTGO:2000635 negative regulation of primary miRNA processing (P)PMID:18951094ECO:0000314 direct assay evidence used in manual assertion

"Lin28b was identified via RNA affinity purification of Huh7 cell extracts with pre-let-7a-1"

Figure S11A. Shows inhibition of Drosha processings by Lin28 in vitro "(A) In vitro processing of pri-let-7a-1, pri-let-7g and pri-miR-16-1 by Drosha with recombinant Lin28b (rLin28b) present" Called Lin28b.

challenge
acceptableMOUSE:LN28A2017-02-14 13:54:05 CSTGO:0071076 RNA 3' uridylation (P)PMID:18951094ECO:0000314 direct assay evidence used in manual assertion

Fig. 3Aa and 3Ab: When comparing Lin28a mutant with wildtype, it can be seen that Lin28a does bind the miRNA species in question, pri-let-7a. With both pri-let-7a and Lin28a present, the sharp band at pre-let-7a produced with mutant lin28a seen on the northern blot is abrogated and instead a smear can be seen in its place. In Fig. 3Ba, these species of varying lengths (cloned from HEK293T cells ectopically expressing pri-let-7a-1 and Lin28a) are sequenced showing 3' uridylation of an average of 14 U nucleotides.

Called Lin28a in paper

challenge
unacceptableMOUSE:LN28A2017-02-14 13:54:05 CSTGO:2000627 positive regulation of miRNA catabolic process (P)PMID:18951094ECO:0000315 mutant phenotype evidence used in manual assertion

"Protein knockdown was carried out against human Lin28b in Huh7 cells and mouse Lin28a in mouse ESCs" Fig. S3 shows, with knocked down mouse Lin28a, there is a marked increase in accumulation of mature let7a species.

Called mouse Lin28a in paper.

challenge
acceptableHUMAN:DHX292017-02-14 14:09:47 CSTGO:0001731 formation of translation preinitiation complex (P)PMID:23047696ECO:0000315 mutant phenotype evidence used in manual assertion

Fig. 2E: Lane 2 shows non-canonical toeprints without DHX29, and 2e lane 3 shows canonical toeprints of formation of preinitiation complex with DHX29 in the presence of all other necessary translation initiation components. Lanes 4, 5, and 6 of the same figure show non-canonical toeprints with truncated forms of DHX29

Human DHX29 transfected into E. coli

challenge
acceptableHUMAN:DHX292017-02-14 14:09:47 CSTGO:0017111 nucleoside-triphosphatase activity (F)PMID:23047696ECO:0000315 mutant phenotype evidence used in manual assertion

Fig. 7C shows NTPase activity for human DHX29. Within the paper, the protein is called DHX29 of mammalian DHX29. From fig. 1 and methods, it is said to be human DHX29

challenge
unacceptableCAEEL:ILB32017-02-14 14:17:24 CSTGO:0047484 regulation of response to osmotic stress (P)PMID:28166192ECO:0000315 mutant phenotype evidence used in manual assertion

Supplementary Figs. 1h and 1i: Shows that INS-3 is responsible for developmental arrest in response to osmotic stress. Referred to in paper as INS-3, insulin like peptide, in C. elegans.

challenge
unacceptableCAEEL:GPDH22017-02-14 14:24:08 CSTGO:0047484 regulation of response to osmotic stress (P)PMID:28166192ECO:0000315 mutant phenotype evidence used in manual assertion

Fig 2b shows that GPDH-2 is required for parental protection of progeny in response to osmotic stress (i.e. the parental protein is required to regulate response to progeny's osmotic stress). The protein is called GPDH-2 in the paper, used with the organism C. elegans

challenge
unacceptableHUMAN:DHX292017-02-14 14:39:31 CSTGO:0009615 detection of virus (P)PMID:24821782ECO:0000315 mutant phenotype evidence used in manual assertion

Fig. 2I, and J show that knockdown DHX29 expression shows a reduced production of immune response peptides IFN-β and IL-6 upon viral stimulation. The protein is referred to as DHX29 in the paper and is specifically mentioned to be human DHX29.

challenge
acceptableHUMAN:PACS22017-04-04 12:56:35 CDTGO:0032469 endoplasmic reticulum calcium ion homeostasis (P)PMID:15692567ECO:0000315 mutant phenotype evidence used in manual assertion

Human PACS-2

Fig. 3C, histamine elicited a two-fold greater increase in calcium released from the ER into the cytosol of PACS-2-depleted cells compared to PACS-1-depleted or control cells.

challenge
unacceptableHUMAN:PACS22017-04-04 13:00:40 CDTGO:0006915 apoptotic process (P)PMID:15692567ECO:0000315 mutant phenotype evidence used in manual assertion

Human PACS-2 depletion conferred a marked resistance to STS, increasing the percentage of viable cells by nearly four-fold. The antiapoptotic effects of the PACS-2 siRNA were corroborated by analyzing the STS-mediated caspase cleavage of poly-ADP-ribose polymerase (PARP) to generate p85.

challenge
updatedbyinstructorHUMAN:DHX292017-04-04 13:16:11 CDTGO:0022627 cytosolic small ribosomal subunit (C)PMID:20018725ECO:0000314 direct assay evidence used in manual assertion

Human DHX29. Figure 1: Immunofluorescence shows DHX29 was enriched in 40S fractions. A low level of DHX29 was associated with 60S and 80S ribosomes.

challenge
acceptableHUMAN:DHX292017-04-23 04:25:35 CDTGO:0042255 ribosome assembly (P)PMID:20018725ECO:0000315 mutant phenotype evidence used in manual assertion

Human DHX29. In cells with silenced DHX using shRNA, polysome profiles showed a reduction in polysomes with concomitant increases in 40S, 60S, and 80S ribosome fractions (Fig. 3B).

challenge
acceptableHUMAN:DHX292017-04-04 13:16:12 CDTGO:0008494 translation activator activity (F)PMID:20018725ECO:0000315 mutant phenotype evidence used in manual assertion

Human DHX29. In control cells, Cdc25C mRNA sedimented predominantly with heavy polysomes, whereas in DHX29-silenced cells, it was shifted to light polysomes, indicating decreased translation initiation of this mRNA (Fig. 4A). In agreement with these findings, Cdc25C protein levels decreased by more than 3-fold on DHX29 silencing (Fig. 4B).

challenge
unacceptableHUMAN:DHX292017-04-18 13:47:07 CDTGO:0008284 positive regulation of cell proliferation (P)PMID:20018725ECO:0000315 mutant phenotype evidence used in manual assertion

Human DHX29. HeLa cell proliferation was inhibited by almost 3-fold in DHX29 siRNA-silenced cells (Fig. 5A). Cell proliferation also was significantly (3-fold) inhibited by shRNA-mediated silencing of DHX29 after 4 days, compared with a nontargeting shRNA control (Fig. 5B). These results demonstrate that DHX29 is associated for cell proliferation.

challenge
acceptableARATH:ISE22017-04-04 13:32:26 CDTGO:0016554 cytidine to uridine editing (P)PMID:28346704ECO:0000315 mutant phenotype evidence used in manual assertion

ISE2 in A. thaliana. Figure 2. Loss of ISE2 compromises C-to-U RNA editing at specific sites. 6 sites known to undergo C-to-U editing are monitored, with a marked decrease in editing in cells with silenced ISE2.

challenge
acceptableARATH:ISE22017-04-04 13:32:26 CDTGO:0000373 Group II intron splicing (P)PMID:28346704ECO:0000315 mutant phenotype evidence used in manual assertion

ISE2 in A. thaliana. Figure 4. ISE2 is required for splicing of a group II intron in ycf3 transcripts. Verified using qPCR and gel electrophoresis showing an increase in the unspliced variant of the intron.

challenge
acceptableARATH:ISE22017-04-04 13:32:26 CDTGO:1901259 chloroplast rRNA processing (P)PMID:28346704ECO:0000315 mutant phenotype evidence used in manual assertion

ISE2 in A. thaliana. Figure 5. Loss of ISE2 leads to defects in rRNA processing. With silenced ISE2, aberrant forms of rRNA are visualized with gel electrophoresis when compared to overexpressed ISE2 and control cells.

challenge
acceptableHUMAN:NUP982017-04-04 13:41:14 CDTGO:0005654 nucleoplasm (C)PMID:28221134ECO:0000314 direct assay evidence used in manual assertion

Human nup98. Figure 3, immunofluorescence spectroscopy confirmed localization to the nucleoplasm.

challenge
acceptableHUMAN:DHX92017-04-04 13:44:17 CDTGO:0005654 nucleoplasm (C)PMID:28221134ECO:0000314 direct assay evidence used in manual assertion

Human DHX9. Figure 3, immunofluorescence spectroscopy shows localization to the nucleoplasm.

challenge
acceptableHUMAN:HNRPU2017-04-04 13:49:23 CDTGO:0005654 nucleoplasm (C)PMID:28221134ECO:0000314 direct assay evidence used in manual assertion

Human hnRNP U. Figure 3, immunofluorescence spectroscopy confirmed localization to the nucleoplasm.

challenge
unacceptableARATH:DNAT12017-04-16 23:42:16 CDTGO:0005777 peroxisome (C)PMID:28352967ECO:0000314 direct assay evidence used in manual assertion

AtDHNAT1 in A. thaliana; has two splice variants including At5g48950.1 (no separate UniProt ID). As predicted, the C-terminal part of At5g48950.1 could target GFP to peroxisomes (Fig. 3b), shown through GFP reporter assay

challenge
unacceptableARATH:DNAT12017-04-16 23:42:16 CDTGO:0005777 peroxisome (C)PMID:28352967ECO:0000314 direct assay evidence used in manual assertion

AtDHNAT1 in A. thaliana; has two splice variants including At3g50170.1 (no separate UniProt ID). The C-terminal part of At3g50170.1 could target GFP to peroxisomes (Fig. 5b), shown with GFP reporter assay

challenge
acceptableHUMAN:LN28B2017-04-18 13:56:44 CDTGO:2000632 negative regulation of pre-miRNA processing (P)PMID:18951094ECO:0000314 direct assay evidence used in manual assertion

"Lin28b was identified via RNA affinity purification of Huh7 cell extracts with pre-let-7a-1"

Figure S11B. Shows inhibition of Dicer processings by Lin28 in vitro "(B) In vitro processing of pre-let-7a-1, pre-let-7g and pre-miR-16-1 by Dicer with rLin28b present. "

challenge
acceptableARATH:F4JQG22017-04-23 15:08:07 CDTGO:0005654 nucleoplasm (C)PMID:28432478ECO:0000314 direct assay evidence used in manual assertion

Protein called AtU2AF65 in A. thaliana.

"As shown in Fig. 2, strong nucleoplasm GFP fluorescence was found except the dark circled area which is presumably nucleolus. We performed FRAP analysis of two areas (nucleoplasm and nucleolus). In the nucleolus area, photobleaching was done to expand the dark circled area. Fluorescence recovered rapidly after photobleaching in both areas, indicating that Arabidopsis U2AF and SF1 proteins are highly mobile nuclear proteins, like the RSZp22 protein."

challenge
acceptableARATH:F4JQG22017-04-23 15:08:07 CDTGO:0005730 nucleolus (C)PMID:28432478ECO:0000314 direct assay evidence used in manual assertion

Protein called AtU2AF65 in A. thaliana.

"As shown in Fig. 2, strong nucleoplasm GFP fluorescence was found except the dark circled area which is presumably nucleolus. We performed FRAP analysis of two areas (nucleoplasm and nucleolus). In the nucleolus area, photobleaching was done to expand the dark circled area. Fluorescence recovered rapidly after photobleaching in both areas, indicating that Arabidopsis U2AF and SF1 proteins are highly mobile nuclear proteins, like the RSZp22 protein."

challenge
acceptableARATH:A8MRI12017-04-23 15:10:00 CDTGO:0005654 nucleoplasm (C)PMID:28432478ECO:0000314 direct assay evidence used in manual assertion

Protein called AtU2AF35 in A. thaliana. "As shown in Fig. 2, strong nucleoplasm GFP fluorescence was found except the dark circled area which is presumably nucleolus. We performed FRAP analysis of two areas (nucleoplasm and nucleolus). In the nucleolus area, photobleaching was done to expand the dark circled area. Fluorescence recovered rapidly after photobleaching in both areas, indicating that Arabidopsis U2AF and SF1 proteins are highly mobile nuclear proteins, like the RSZp22 protein."

challenge
acceptableARATH:A8MRI12017-04-23 15:10:01 CDTGO:0005730 nucleolus (C)PMID:28432478ECO:0000314 direct assay evidence used in manual assertion

Protein called AtU2AF35 in A. thaliana. "As shown in Fig. 2, strong nucleoplasm GFP fluorescence was found except the dark circled area which is presumably nucleolus. We performed FRAP analysis of two areas (nucleoplasm and nucleolus). In the nucleolus area, photobleaching was done to expand the dark circled area. Fluorescence recovered rapidly after photobleaching in both areas, indicating that Arabidopsis U2AF and SF1 proteins are highly mobile nuclear proteins, like the RSZp22 protein."

challenge
acceptableARATH:Q9LU442017-04-23 15:12:26 CDTGO:0005654 nucleoplasm (C)PMID:28432478ECO:0000314 direct assay evidence used in manual assertion

Protein called AtSF1 in A. thaliana. "As shown in Fig. 2, strong nucleoplasm GFP fluorescence was found except the dark circled area which is presumably nucleolus. We performed FRAP analysis of two areas (nucleoplasm and nucleolus). In the nucleolus area, photobleaching was done to expand the dark circled area. Fluorescence recovered rapidly after photobleaching in both areas, indicating that Arabidopsis U2AF and SF1 proteins are highly mobile nuclear proteins, like the RSZp22 protein."

challenge
acceptableARATH:Q9LU442017-04-23 15:12:27 CDTGO:0005730 nucleolus (C)PMID:28432478ECO:0000314 direct assay evidence used in manual assertion

Protein called AtSF1 in A. thaliana. "As shown in Fig. 2, strong nucleoplasm GFP fluorescence was found except the dark circled area which is presumably nucleolus. We performed FRAP analysis of two areas (nucleoplasm and nucleolus). In the nucleolus area, photobleaching was done to expand the dark circled area. Fluorescence recovered rapidly after photobleaching in both areas, indicating that Arabidopsis U2AF and SF1 proteins are highly mobile nuclear proteins, like the RSZp22 protein."

challenge
unacceptableARATH:Q9LU442017-04-23 15:20:15 CDTGO:0006913 nucleocytoplasmic transport (P)PMID:28432478ECO:0000314 direct assay evidence used in manual assertion

Protein called AtSF1 in A. thaliana. "As shown in Fig. 5, the GFP fluorescence of all these proteins in nuclei was strongly reduced during the course of cytoplasmic photobleaching. … These results demonstrate that AtU2AF35, AtU2AF65, and AtSF1 are nucleocytoplasmic shuttling proteins"

challenge
unacceptableARATH:A8MRI12017-04-23 15:20:22 CDTGO:0006913 nucleocytoplasmic transport (P)PMID:28432478ECO:0000314 direct assay evidence used in manual assertion

Protein called AtU2AF35 in A. thaliana. "As shown in Fig. 5, the GFP fluorescence of all these proteins in nuclei was strongly reduced during the course of cytoplasmic photobleaching. … These results demonstrate that AtU2AF35, AtU2AF65, and AtSF1 are nucleocytoplasmic shuttling proteins"

challenge
unacceptableARATH:F4JQG22017-04-23 15:20:27 CDTGO:0006913 nucleocytoplasmic transport (P)PMID:28432478ECO:0000314 direct assay evidence used in manual assertion

Protein called AtU2AF65 in A. thaliana.

"As shown in Fig. 5, the GFP fluorescence of all these proteins in nuclei was strongly reduced during the course of cytoplasmic photobleaching. … These results demonstrate that AtU2AF35, AtU2AF65, and AtSF1 are nucleocytoplasmic shuttling proteins"

challenge

acceptable:21
unacceptable:11
requires_changes:0
flagged:0

Annotations challenged by RazMonk

StatusAuthor,GroupPageGO Term (Aspect)ReferenceEvidenceLinksPage history
updatedbyinstructorSeannash,
Team Voldemort
PORGN:A0A0E2LMN8GO:0044011 - single-species biofilm formation on inanimate substrate (P)PMID:17020544ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 3
updatedbyinstructorCRoss2008,
Team Dank Genes
MOUSE:GBRDGO:0030424 - axon (C)PMID:25339733ECO:0000314 direct assay evidence used in manual assertionchallengeC: 5

fixed by Cherylrood
acceptableCSears,
Team Girl, you trypsin
HUMAN:INSRGO:0002092 - positive regulation of receptor internalization (P)PMID:25401701ECO:0000314 direct assay evidence used in manual assertionchallengeC: 1
updatedbyinstructorSarahCouv,
Team Lily Whale
DROME:CDK1GO:0045169 - fusome (C)PMID:27170181ECO:0000314 direct assay evidence used in manual assertionchallengeC: 2

fixed by SarahCouv
updatedbyinstructorSarahCouv,
Team Lily Whale
DROME:DDX6GO:0005783 - endoplasmic reticulum (C)PMID:16256742ECO:0000314 direct assay evidence used in manual assertionchallengeC: 2

fixed by SarahCouv
unacceptableSarahCouv,
Team Lily Whale
DROME:Q9VB05GO:0005813 - centrosome (C)PMID:25635693ECO:0000314 direct assay evidence used in manual assertionchallengeC: 1
acceptableMCGU2014,
Team Lily Whale
SCHPO:LEM2GO:0034506 - chromosome, centromeric core domain (C)PMID:27451393ECO:0000314 direct assay evidence used in manual assertionchallengeC: 4

0 annotations fixed by RazMonk

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