CACAO Phage Hunters 2018
My Annotations
| Status | Page | Date/Time | GO Term (Aspect) | Reference | Evidence | Notes | Links |
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| updatedbyinstructor | BPT4:TOPS | 2018-03-04 22:59:37 CST | GO:0009330 DNA topoisomerase complex (ATP-hydrolyzing) (C) | PMID:6296073 | ECO:0000315 mutant phenotype evidence used in manual assertion | In figure 7, gp60 was replaced with a mutant version, amE429 or amE594, and then the protein complex was eluted and run through a gel. Lanes 1-3 are gels of increasingly concentrated fractions of amE492 infected cells. Lane 4 uses the same fraction as lane 3, but eluted with .1M potassium phosphate buffer, as a control for the buffer. Lane 5 is the same fraction as lane 3, but eluted with .3M potassium phosphate buffer. Lane 6 is the same as lane 5, but with .5M potassium phosphate buffer. Lane 6 has the standards for the three proteins in topoisomerase, p39, p52, and p60. Lanes 8 and 9 are the same as lanes 5 and 6, respectively, but using amE594 as the mutant gene 60 instead of amE429. In lanes 5 and 8, p60 is absent (due to the mutation) and p39 is also absent. P52 is evident, meaning it was able to be eluted by the .3M buffer. In lanes 6 and 9, p60 is again absent as is p52, since it had already been eluted out. P39 is evident, as it was eluted out of fraction by .5M buffer. Since both proteins were eluted out by different concentrations of buffer, they were not bound together, which differs from past research that proves them bound together in complex. Therefore, p60 must be capable of binding them together without any conformational change of p39 or p52(both proteins' identities were confirmed after experiment).
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| updatedbyinstructor | 9VIRU:A0A088FLK9 | 2018-03-17 18:09:40 CDT | GO:0051715 cytolysis in other organism (P) | PMID:26375388 | ECO:0000314 direct assay evidence used in manual assertion | In figure 3, T. thermophilus was exposed to different concentrations of Ts2631 endolysin. At 5 minute intervals, for 40 minutes, the number of cells still alive was found by measuring OD600. According to the graph, no matter what concentration of endolysin was added, a significant number of cells died compared to cell death in the control. At the 35 minute mark, all concentration amounts showed over 50% cell death. This means that the endolysin from Ts2631 phage causes the death of the host cell.
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| acceptable | BPT4:DNLI | 2018-03-18 21:02:28 CDT | GO:0003909 DNA ligase activity (F) | PMID:16302964 | ECO:0000314 direct assay evidence used in manual assertion | In figure 2, single stranded DNA was mixed with T4 DNA ligase and oligonucleotides. In 2A, it was amplified using PCR. The resulting products were run through a gel. Lanes 1 and 6 were used as controls, either missing the ligase or the oligonucleotides. Lanes 3-5 showed the results from the PCR. The smear corresponds with the DNA ligase binding sequences of DNA to the experimental ssDNA, making the DNA longer and so the bands would have a larger masses. Figure 2B shows this better, as RCA was used to amplify the ssDNA, which is better to use for circular DNA. Distinct bands were seen due to this better fitting technique. The larger masses of the circular DNA also supports the fact that the DNA ligase can bind DNA ends together.
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| acceptable | STRCO:TOP1 | 2018-03-31 15:29:17 CDT | GO:0007059 chromosome segregation (P) | PMID:23913317 | ECO:0000315 mutant phenotype evidence used in manual assertion | In figure 4, a wild type S. coelicolor (M145)and two examples of a mutant S. coelicolor without TopA proteins (PS01) were stained to show organization of cell walls (blue) and DNA (red) during sporulation. In the mutant cells, both the DNA and cell wall showed no order, as the red and blue colors were smeared throughout the cell. This meant that there is no chromosome condensing or separating. But in the wild type, the DNA is packed between evenly spaced cell walls. This means that, in the presence of TopA, chromosomes were condensed and segregated into different segments along the cell, ready for sporulation.
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| acceptable | BPPRD:ENLYS | 2018-04-14 18:14:26 CDT | GO:0033922 peptidoglycan beta-N-acetylmuramidase activity (F) | PMID:7925454 | ECO:0000314 direct assay evidence used in manual assertion | In figure 3, samples of cell walls were combined with the enzyme P15, hydrolyzed with HCl, and chromatographed on a column. Eluted fractions were then tested for radioactivity. Only the sample with [3H]muramicitol was seen only in the tubes with P15 and cell walls, not in any of the control. This meant that P15 bound to [3H]muramicitol and hydrolyzed it, which would lead to cell death. It had previously been discovered that adding p15 to a tube of E. coli would decrease the turbidity of the tube by killing the cells. Figure 3 was just to show the nature of the cells' death.
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