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User:Ziba0916

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CACAO Spring 2017

My Annotations

StatusPageDate/TimeGO Term (Aspect)ReferenceEvidenceNotesLinks
unacceptable9HYPO:Q9HDL12017-02-05 15:17:20 CSTGO:0009405 pathogenesis (P)PMID:28132080ECO:0000314 direct assay evidence used in manual assertion

Figure 7B, fungus expressing mutant form of gene is not able to induce pathogenesis in host while fungus expressed in wild type gene is.

strains tested were Mont - 1 and (Delta)SF18 FvSNF1 protien kinase gene of Fusarium virguliforme uniprot refers to it as Fusarium solani f. sp. glycines

challenge
unacceptable9HYPO:Q9HDL12017-02-05 15:17:21 CSTGO:0044122 development of symbiont in host vascular tissue (P)PMID:28132080ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 8A,8B,and 8C, Fungus expressing wild type form of strain Mont -1 uses different types of glucose and carbon found in the vascular tissue of soybean roots to develop efficiently in contrast to its mutant strain SF18.

challenge
unacceptable9HYPO:Q9HDL12017-02-05 15:17:21 CSTGO:0044123 growth of symbiont in host vascular tissue (P)PMID:28132080ECO:0000315 mutant phenotype evidence used in manual assertion

The growth of strain Mont- 1 during fungal colonization was significant and efficient in colonizing its host’s vascular tissues when inoculated.

challenge
unacceptable9HYPO:Q9HDL12017-02-05 16:02:32 CSTGO:0015976 carbon utilization (P)28132080:28132080ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 3A, The strain Mont -1 wild type was tested against the mutant strain SF18 with various carbon sources, all of which Mont - 1 could metabolize in some amounts to survive, whereas the mutant strain SF18 was unable to utilize Xylose.

challenge
unacceptable9HYPO:Q9HDL12017-02-05 16:11:38 CSTGO:0010629 negative regulation of gene expression (P)PMID:28132080ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 4, Gene expression was non - existent in the strain ΔSF18 during galactose metabolism compared to the positive regulation in strains Mont-1 and EctSF27.

challenge
unacceptable9HYPO:Q9HDL12017-02-05 16:11:38 CSTGO:0010628 positive regulation of gene expression (P)PMID:28132080ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 5, “Expression of cell wall-degrading enzyme genes in Fvsnf1 mutant (ΔSF18) compared to the wild-type (Mont- 1), when grown in pectin, xylan or glucan.” As stated in article, with asterisks signifying major variances.

challenge
unacceptableORYSJ:Q8LRC72017-03-04 17:46:19 CSTGO:0000145 exocyst (C)PMID:28163713ECO:0000314 direct assay evidence used in manual assertion

Oryza sativa subsp. japonica (Rice), Arm repeat protein, known as osPUB3 in the paper was viewed through Fluorescence microscopy, which showed concentration of protein in the exocyst of the protoplasts in 2nd row of Fig. 3A.

SuppF3: "OsPUB2 (XP_015637531) and OsPUB3 (XP_015621922)"

challenge
acceptableORYSJ:Q75GN82017-03-04 17:46:19 CSTGO:0051865 protein autoubiquitination (P)PMID:28163713ECO:0000315 mutant phenotype evidence used in manual assertion

Organism Oryza sativa subsp. japonica (Rice), RING-type E3 ubiquitin transferase, OSPub2 (XP_015637531) "Myc-OsPUB2 and a single amino acid substitution mutant mutant Myc-OsPUB2C281A proteins were used for in vitro self-ubiquitination assay by using anti-Myc and anti-Ub antibodies” by author. In Fig. 2

challenge
unacceptableGIBZE:I1RWM52017-03-05 16:14:59 CSTGO:0009405 pathogenesis (Fusarium graminearum, GIL1 (FGSG_08701) Fig. 5C)PMID:28212314IMP: Inferred from Mutant Phenotype
challenge
acceptableORYSJ:Q8LRC72017-03-21 14:49:21 CDTGO:0000145 exocyst (C)PMID:28163713ECO:0000314 direct assay evidence used in manual assertion

Oryza sativa subsp. japonica (Rice), Arm repeat protein, known as osPUB3 (XP_015621922) in the paper was viewed through Fluorescence microscopy, which showed concentration of protein in the exocyst of the protoplasts in 2nd row of Fig. 3A.

challenge
acceptableORYSJ:Q8LRC72017-03-21 14:52:45 CDTGO:0051865 protein autoubiquitination (P)PMID:28163713ECO:0000315 mutant phenotype evidence used in manual assertion

Organism Oryza sativa subsp. japonica (Rice), Arm repeat protein, "Myc-OsPUB3 (xp 015621922) and a single amino acid substitution mutant Myc-OsPUB3C280A proteins were used for in vitro self-ubiquitination assay by using anti-Myc and anti-Ub antibodies” by author. In Fig. 2

challenge
unacceptableCHICK:A0A1D5P7K72017-04-04 14:49:40 CDTGO:0030175 filopodium (C)PMID:28359843ECO:0000314 direct assay evidence used in manual assertion

Septin 7(A0A1D5P7K7) localizes specifically to the base of filopodia Fig. 3C

challenge
updatedbyinstructorCUPNH:Q0KFC82017-04-09 17:33:51 CDTGO:0043590 bacterial nucleoid (C)PMID:28389545ECO:0000314 direct assay evidence used in manual assertion

Determination of effects, c-terminal domain knock out from PHaM (Hypothetical membrane associated protein), had lead to a change in localization, fusion with the gene for the enhanced yellow fluorescent protein (eyfp). Constitutively expressed PhaMWT 182 -eYFP showed a strong 183 fluorescence in the nucleoid region of R. eutropha (Ralstonia eutropha) cells. Fig. 2A Left column

Cupriavidus necator, phaM/H16_A0141

challenge
unacceptableCUPNH:Q0KFC82017-04-09 17:52:52 CDTGO:0060187 cell pole (C)PMID:28389545ECO:0000315 mutant phenotype evidence used in manual assertion

Mutant type, PhaM∆C 191 -eYFP(Hypothetical membrane associated protein), had knocked out C-terminal domain of PhaM, which changed localization to cell poles, and areas of future septum formation when viewed from results by Imaging in bright field and/or staining with Nile red. Also showed co- localization of PhaM∆C 191 -eYFP with formed PHB granules in Ralstonia eutropha organism. Fig 2A right column.

challenge
acceptableSOLLC:ACCO12017-04-20 20:57:13 CDTGO:0005737 cytoplasm (C)PMID:28408916ECO:0000314 direct assay evidence used in manual assertion

Eight hours after abscission induction, many ACO1 gold-labeled particles (ACO1) specifically appeared in the cytoplasm of the phloem companion cells in the vascular tissues distal to the abscission zone in Solanum lycopersicum (Tomato) (Lycopersicon esculentum) shown in Fig. 2B by author.

challenge
acceptableSOLLC:ACCO12017-04-21 18:46:41 CDTGO:0009506 plasmodesma (C)PMID:28408916ECO:0000314 direct assay evidence used in manual assertion

Occasionally signals of the ACO1 gold-labeled particles (ACO1) were also seen in the plasmodesmata eight hours after the abscission in Solanum lycopersicum (Tomato) (Lycopersicon esculentum)

Fig. 2B Protein: P05116 (ACCO1_SOLLC)

challenge
unacceptableMOUSE:ANG42017-04-23 15:34:46 CDTGO:0009986 cell surface (C)PMID:28406067ECO:0000314 direct assay evidence used in manual assertion

lysozyme-treated bacteria were bound to the surface of the J774.1 cells, but were not phagocytized. Thus, RNA, the active ingredient of IC-1 cells, was not transferred into the J774.1 cells or recognized by the intracellular TLR7. Consequently, it failed to induce IL-12 production. By author, Fig. 6

Protein: Angiogenin-4 Organism: Mouse

challenge
acceptableSOLLC:ACCO12017-04-21 18:43:33 CDTGO:0009505 plant-type cell wall (C)PMID:28408916ECO:0000314 direct assay evidence used in manual assertion

Occasionally signals of the ACO1 gold-labeled particles (ACO1) was also seen in the cell walls eight hours after the abscission shown in Fig. 2B.

Protein: P05116 (ACCO1_SOLLC) Organism: Solanum lycopersicum (Tomato) (Lycopersicon esculentum)

challenge
unacceptableSOLLC:ACCO12017-04-21 19:14:08 CDTGO:0005694 chromosome (C)PMID:28408916ECO:0000314 direct assay evidence used in manual assertion

Protein: E3 ubiquitin-protein ligase pellino homolog 1

Organism: Mus musculus (Mouse) Mitotic chromosomes of non-Tg and Peli1-Tg splenocytes were spread and visualized by Giemsa staining in Fig. 1B

challenge
unacceptableSOLLC:ACCO12017-04-21 19:14:58 CDTGO:0000776 kinetochore (C)PMID:28408916ECO:0000314 direct assay evidence used in manual assertion

Protein: E3 ubiquitin-protein ligase pellino homolog 1

Organism: Mus musculus (Mouse) The graph represents the percentages of Peli1 co-localized with BubR1 at kinetochores in asynchronized or synchronized cells. By author in Fig. 2A and 2B

challenge
unacceptableMOUSE:TCL1A2017-04-22 18:29:00 CDTGO:0045821 positive regulation of glycolytic process (P)PMID:28262547ECO:0000315 mutant phenotype evidence used in manual assertion

the media of iPSCs(High-K) turned yellow faster than that of iPSCs(Low-K) (Figure 6B). This often indicates lactic acidosis resulting from enhanced glycolysis. Both glucose uptake and lactate production were higher in iPSCs(High-K) than in iPSCs(Low-K) (Figures 6C and 6D). KLF4 enhances glycolysis during the transition from iPSCs(Low-K) to iPSCs(High-K), in large part through the TCL1-AKT pathway.

P: (TCL1) O: Mouse TCL1A (TCL 1)

challenge
unacceptableMOUSE:PELI12017-04-23 16:00:54 CDTGO:0051306 mitotic sister chromatid separation (P)PMID:28410192ECO:0000315 mutant phenotype evidence used in manual assertion

The metaphase chromosome-spreading assay revealed that premature sister chromatid separation (PMSCS), a hallmark of a defective mitotic checkpoint [19, 25], was observed in approximately 18 ± 1.7% of splenocytes isolated from Peli1-Tg mice but in < 5% of control splenocytes (Figure 1B), by author.

Protein: E3 ubiquitin-protein ligase pellino homolog 1 Organism: mouse

challenge
unacceptableMOUSE:PELI12017-04-23 15:42:40 CDTGO:0048536 spleen development (P)PMID:28410192ECO:0000315 mutant phenotype evidence used in manual assertion

Protien: E3 ubiquitin-protein ligase pellino homolog 1

Organism: Mouse splenocytes were isolated from Peli1-Tg mice that displayed splenic plasmacytoid differentiation and lymphomas, and from control littermate non-Tg mice that had normal splenic features (Figure 1A, 1B) by author.

challenge
updatedbyinstructorMOUSE:PELI12017-04-23 16:07:58 CDTGO:0000778 condensed nuclear chromosome kinetochore (C)PMID:28410192ECO:0000314 direct assay evidence used in manual assertion

Protein: E3 ubiquitin-protein ligase pellino homolog 1

Organism: Mouse Immunofluorescence analyses revealed localization of Peli1 at spindle poles and kinetochores (Figure 2A).

challenge
unacceptableMOUSE:PELI12017-04-23 16:09:54 CDTGO:1905558 negative regulation of mitotic nuclear envelope disassembly (P)PMID:28410192ECO:0000314 direct assay evidence used in manual assertion

Organism: mouse

Protein:E3 ubiquitin-protein ligase pellino homolog 1 Peli1 overexpressing cells showed severe delays in the metaphase-to-anaphase transition compared to control cells. (B) Average time from mitotic onset (nuclear envelope breakdown) to anaphase of Peli1 overexpressing cells or control cells (control cells, n = 24; Myc-Peli1-transfected cells, n = 20).

challenge
unacceptableMOUSE:TCL1A2017-04-23 16:35:15 CDTGO:0008283 cell proliferation (P)PMID:28262547ECO:0000315 mutant phenotype evidence used in manual assertion

Although the AKT pathway is involved in cell proliferation and survival (Manning and Cantley, 2007), iPSCs(Low-K) and iPSCs(High-K), which differ in AKT activity (Figures 5A and 5B), showed unexpectedly similar rates of cell proliferation (Figure 6A), by author.

Mouse TCL1A (TCL 1) EC: IMP

challenge

acceptable:6
unacceptable:18
requires_changes:0
flagged:0

Annotations challenged by Ziba0916

StatusAuthor,GroupPageGO Term (Aspect)ReferenceEvidenceLinksPage history
updatedbyinstructorCRoss2008,
Team Dank Genes
MOUSE:GBRDGO:0030424 - axon (C)PMID:25339733ECO:0000314 direct assay evidence used in manual assertionchallengeC: 5

fixed by Cherylrood
unacceptableMCGU2014,
Team Lily Whale
MOUSE:TCTPGO:0007026 - negative regulation of microtubule depolymerization (P)PMID:26802898ECO:0000314 direct assay evidence used in manual assertionchallengeC: 1
unacceptableLoganMcCurry,
Team Gene String
SCHPO:YPT2GO:0051286 - cell tip (C)PMID:27082518ECO:0000314 direct assay evidence used in manual assertionchallengeC: 1
unacceptableMCGU2014,
Team Lily Whale
ORYSI:A0A165TZX1GO:0006979 - response to oxidative stress (P)PMID:24534105ECO:0000316 genetic interaction evidence used in manual assertionchallengeC: 1
unacceptableSStone15,
Team Lily Whale
MOUSE:TCL1AGO:0090324 - negative regulation of oxidative phosphorylation (P)PMID:28262547ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 2
updatedbyinstructorSarahCouv,
Team Lily Whale
MLVMS:GAGGO:0120026 - host cell uropod (C)PMID:24965475ECO:0000314 direct assay evidence used in manual assertionchallengeC: 1

fixed by Ziba0916
unacceptableSarahCouv,
Team Lily Whale
MOUSE:P63GO:0005634 - nucleus (C)PMID:22035303ECO:0000314 direct assay evidence used in manual assertionchallengeC: 5
updatedbyinstructorMCGU2014,
Team Lily Whale
BRARP:M4D425GO:0048450 - floral organ structural organization (P)PMID:25314222ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 5

fixed by Ziba0916
unacceptableMCGU2014,
Team Lily Whale
BRANA:NLTP1GO:0008283 - cell population proliferation (P)PMID:25314222ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 5
unacceptableSStone15,
Team Lily Whale
MOUSE:FABP5GO:0048144 - fibroblast proliferation (P)PMID:23722546ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 1
updatedbyinstructorMCGU2014,
Team Lily Whale
YEAST:TRM1GO:0004809 - tRNA (guanine-N2-)-methyltransferase activity (F)PMID:2426253ECO:0000315 mutant phenotype evidence used in manual assertionchallengeC: 6

fixed by TheBockster
updatedbyinstructorSStone15,
Team Lily Whale
HPV16:VE4GO:0030430 - host cell cytoplasm (C)PMID:15767402ECO:0000314 direct assay evidence used in manual assertionchallengeC: 4

fixed by TheBockster
acceptableMCGU2014,
Team Lily Whale
SCHPO:LEM2GO:0034506 - chromosome, centromeric core domain (C)PMID:27451393ECO:0000314 direct assay evidence used in manual assertionchallengeC: 4

2 annotations fixed by Ziba0916


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