User:Labbeben

My Annotations

Status	Page	Date/Time	GO Term (Aspect)	Reference	Evidence	Notes	Links
acceptable	HUMAN:DDIT3	2012-04-14 12:36:53 CDT	GO:0045786 negative regulation of cell cycle (P)	PMID:22496745	ECO:0000314 direct assay evidence used in manual assertion	Figure 4 fibrosarcoma cells (HT1080) with stable expression of DDIT3morEGFP treated with tamoxifen to induce nuclear translocation show increased % of cells in G1 (see Talk page)	challenge
unacceptable	ECOLI:DNAK	2012-04-14 13:21:23 CDT	GO:0005524 ATP binding (F)	PMID:10521435	ECO:0000021 physical interaction evidence	DnaK and DnaJ bind under certain circumstances- the abstract mentions that they have been shown to be co-chaperones. Figure 1, graph 1 demonstrates binding assays using immobilized DnaK on a sensor chip. The binding of DnaK to DnaJ occurs only in the presence of ATP, and not any other form of nucleotide. While this is not a direct analysis of the ATP-binding domain, from the graph it is possible to infer that DnaK requires the presence of ATP to bind DnaJ, and that the ATP is binding to DnaK (since it was only present in solution during the process of immobilizing DnaK, not when the DnaJ was added).	challenge
updatedbyinstructor	MOUSE:SODM	2012-04-15 14:20:43 CDT	GO:0016491 oxidoreductase activity (F)	PMID:15205258	ECO:0000315 mutant phenotype evidence used in manual assertion	Figure 4 shows a Western blot that demonstrates the importance of Sod2 to the oxidation state of proteins in erythrocytes. In the progenitor stage and in both the cytosol and membranes of erythrocytes, the Sod2 -/- mutants have significantly more oxidation (here shown as darker bands, since the blot detected carbonyls resulting from reactive oxygen species activity). That Sod2 has direct oxidoreductase activity is further reinforced by the proteomics analysis in Table 2. Other proteins that might have significant oxidoreductase activity, such as Cytochrome C oxidase subunit Va, are not differentially expressed. Since the absence of Sod2 does not affect expression of these other oxidoreductases, the difference in oxidation states in the mutant is likely due to a lack of activity by Sod2 in this function, rather than as a transcription factor for other oxidoreductases.	challenge

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

Annotations challenged by Labbeben

Status	Author,Group	Page	GO Term (Aspect)	Reference	Evidence	Links	Page history

0 annotations fixed by Labbeben

My Annotations

Status	Page	Date/Time	GO Term (Aspect)	Reference	Evidence	Notes	Links
requireschanges	MYXXD:Q1D7Q3	2012-04-01 16:16:30 CDT	GO:0003677 DNA binding (F)	PMID:1539954	ECO:0000314 direct assay evidence used in manual assertion	Figure 2 demonstrates an example of one gene promoter region that FruA is able to bind to. E. coli containing a plasmid with the fruA gene was used to produce sufficient quantities of protein after induction with IPTG. 2A demonstrates that FruA was only produced after IPTG induction. The protein was then used in gel-shift assays with P32-labelled DNA, as shown in 2B. The sigma-4400 promoter region, which contains the proposed FruA binding site, forms a band that indicates binding only in the presence of IPTG-induced protein; in other words, only in the presence of FruA. The right side is another gene region from M. xanthus that does not contain the proposed FruA binding site, and acts as a negative control.	challenge

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

Annotations challenged by Labbeben

Status	Author,Group	Page	GO Term (Aspect)	Reference	Evidence	Links	Page history

0 annotations fixed by Labbeben