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Category:Team Green B 2019
|Status||Page||User||Date/Time||GO Term (Aspect)||Reference||Evidence||Notes||Links|
|DEIRA:DDRB||SRana, Team Green B 2019||2019-04-14 13:52:43 CDT||GO:0045002 double-strand break repair via single-strand annealing (P)||PMID:21968057||ECO:0001141 [3H]-thymidine incorporation assay evidence used in manual assertion|
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 [3H]Thymidine incorporation assay to measure rate of DNA synthesis. There was an increased lag phase in DNA synthesis by an hour in the knockout compared to the wildtype strain. 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. ddrB protein also has high affinity for single stranded DNA and has similar properties to E. coli SSB protein. This is likely indicates that DdrB is involved in a very early step of DNA double strand break repair that occurs prior to strand-annealing and not in annealing the newly synthesized DNA strands itself.
|CELJU:B3PDN7||CShee, Team Green B 2019||2019-03-31 11:02:19 CDT||GO:2000892 cellobiose catabolic process (P)||PMID:28118504||ECO:0001225 knockout evidence used in manual assertion|
Mutant strains with individual and combinatorial mutations were generated and growth assays were conducted to determine which genes were essential for allowing Cellvibrio japonicus to metabolize cellobiose, a disaccharide that composes cellulose. According to Figure 1A, cel3B deletion most significantly hinders growth of C. japonicus on cellobiose. Figure 2D also showed that the cel3B single mutants (triangles) had decreased cellobiose consumption and a longer lag phase compared to the wild type (circles). This shows that the gene product of cel3B, an enzyme, helps the cell use cellobiose as a carbon source.
|STRCO:CYC2||CShee, Team Green B 2019||2019-03-10 17:26:08 CDT||GO:0044550 secondary metabolite biosynthetic process (P)||PMID:12563033||ECO:0006091 functional complementation evidence used in manual assertion|
In this paper, the researchers used PCR targeting, gene replacement cassette, and transposon mutagenesis to determine whether genes cyc1 and cyc2 were both required for production of geosmin, a substance that gives soil its distinctive scent. GC-MS was used to detect geosmin production by each mutant. In Table 3, it is shown that when cyc2 is deleted, (strains J3001, J3002) there is no production of geosmin. When cyc1 is mutated using a transposon, geosmin is still produced. This indicates that cyc2, not cyc1, is required for the production of geosmin. To confirm this, the researchers reintroduced the cyc2 gene (complementation) via a vector into the strain, and geosmin production was restored.