GONUTS has been updated to MW1.31 Most things seem to be working but be sure to report problems.
Cacao
| Contributes to | GO:0006302 | double-strand break repair | PMID:21968057 | ECO:0007697 IDA: Inferred from Direct Assay | Biological Process | In Figure 3 Panel A, the graphs are showing the rate of DNA synthesis in wildtype strain of the bacteria and the strain with the knockout of ddrB gene. Both strains are allowed to grow normally as well as subjected to radiation. They used a thymidine incorporation assay to measure radioactivity and rate of DNA synthesis. There was an hour lag in DNA synthesis in cells where ddrB was knocked out, in both the irradiated and control cells. This lag was associated with a delay in fragment reassembly shown by PFGE, Panel B. But the rate of DNA synthesis and the fragment reassembly after this lag period was very similar to wildtype. This is likely evidence that DdrB is involved in a very early step of DNA double strand break repair that occurs prior to strand-annealing. | complete | |
| This annotation made on page: DEIRA:DDRB By: SRana (group Team Green B 2019) on 2019-04-14 13:52:43 CDT. | ||||||||
You must be logged in to challenge this annotation.
| Entry Type | Challenging User,Group | Time/Date | Challenge Reason | Points/Assessment | ||||||||||||||||||||||
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| Challenge | LWachhaus, Team Red B 2019 | 2019-04-15 09:53:58 CDT | The GO term used, GO:0006302 double-strand break repair, should instead be GO:0045002 double-strand break repair via single-strand annealing. The text mentions the "strong affinity of DdrB protein for single-stranded DNA" and later says "This suggests that DdrB is involved in a very early step of DNA double strand break repair preceding ESDSA associated DNA synthesis but not in annealing of the long tracts of newly synthesized single-stranded DNA required for genome reconstitution by ESDSA pathway", saying that DdrB does not anneal the newly synthesized DNA, but is used to anneal DNA preceding this region. | 2 | ||||||||||||||||||||||
| Challenge | KAtanasoff, Team Blue A 2019 | 2019-04-15 09:49:57 CDT | The "contributes to" qualifier term isn't appropriate to use for a GO annotation dealing with a biological process; instead, it's used for molecular function annotations of subunits that are part of a larger complex. Also, since the authors specifically use a [3H]thymidine incorporation assay to measure DNA synthesis, you should use a more specific ECO term for that evidence support. Finally, since the authors are comparing wild-type D. radiodurans cells to a ΔddrB mutant, you should use the IMP (Inferred from Mutant Phenotype) experimental evidence code. | 2 | ||||||||||||||||||||||
| Public Assessment | Ivanerill | 2019-04-21 14:53:48 CDT | No notes given. | Acceptable ✔ Protein ✔ Publication ✔ Qualifier ✔ Go term ✔ Evidence ✔ With/From ✔ Notes ✔ Unique/Original | ||||||||||||||||||||||
| Public Assessment | Ivanerill | 2019-04-21 13:47:55 CDT | See http://geneontology.org/docs/go-annotations/ for details on how to use qualifiers. | Requires Changes ✔ Protein ✔ Publication ✗ Qualifier ✔ Go term ✔ Evidence ✔ With/From ✔ Notes ✔ Unique/Original | ||||||||||||||||||||||
| Public Assessment | DanielRenfro | 2019-04-21 13:26:58 CDT | This annotation has been flagged because it has been edited since last assessment
| Flagged | ||||||||||||||||||||||
| Public Assessment | Ivanerill | 2019-04-18 09:40:52 CDT | See KAtanasoff challenge and http://geneontology.org/docs/go-annotations/ for details on how to use qualifiers. See LWachhaus comment and justify your use of GO term. There is a more specific ECO term for the technique reported in the paper. Look at ECO:0005008 children. | Requires Changes ✔ Protein ✔ Publication ✗ Qualifier ✗ Go term ✗ Evidence ✔ With/From ✔ Notes ✔ Unique/Original |
