GCC BioTech Lab Blog Entry 2
Introduction
This week in the lab was not very busy. We hoped to innoculate plates and perform characterization tests on Deinococcus xinjiangensis, but were unable to do so. Our group also began investigating whether or not certain proteins involved in mechanotaxis and chemotaxis were present in various Deinococcus species.
This week in the lab was not very busy. We hoped to innoculate plates and perform characterization tests on Deinococcus xinjiangensis, but were unable to do so. Our group also began investigating whether or not certain proteins involved in mechanotaxis and chemotaxis were present in various Deinococcus species.
Methods
28 plates were prepared. 10 contained TGY, two contained a comibination of starch and TGY, six contained urease, and 10 contained R2A. 500 ml of TGy was heated at 350 C and poured into the TGY plates. Another TGY flask of the same volume was heated at 355 C and poured. 2g/L of strach and TGY was used to make the starch plates, while the solution for the urease test consisted of 50mL of urease in 450mL of H20 and Agar after the latter solution was heated to 350 C. After the plates were poured they were placed in the refrigerator. Next a R2B broth was prepared. 0.378g of R2B powder was dissolved in 120 mL of DI water. The plates created the day prior were labeled. Two TGY plates and two R2A plates were labelled as "Catalase D. xinjiangensis". The same was repeated twice, except that the two sets of four plates were labelled as "- catalase D roseus" and "+ catalase S. epidermus". Two TGY plates and two R2A plates were labeled as "oxidase xinxiangensis", while 1 TGY plate and 2 R2A plate sets were labelled "+ control oxidase B. subtilis" and "- control oxidase S. epidermis". One starch plate was labelled "starch xinjiangensis" and another was split down the middle with sharpie, one side being labelled "+ B. subtilis" and the other "- S. epidermis". Two Urease plates were labeled as "Urease D. xinjiangensis", two as "- control B. subtilis", and two as "+ control S.epidermis". One plate of Staphylococcus epidermis and another of Bacillus subtilis were then innoculated. None of the expiremental plates were streaked. The D. xinjiangensis just came out of freezeback, and thus cannot be innoculated. The following day, Gram stains were performed on the control plates. B. subtilis was Gram +, while the S. epidermis tested Gram -. The next day UniProt was used to determine whether or not genes involved in mechanotaxis and chemotaxis were present in various Deinococcus species. The symbol from a gene followed by the scientific name of the specific Deinococcus species. In a Google Sheets document, a "1" was placed in a cell next to the species name if the gene was present and a "0" if the gene was absent.
Results
No direct expirements were performed this week. However, the investigation on UniProt revealed several genes involved in chemotaxis and mechanitaxis were absent. Notably, cheZ and cheX appeared to be absent from most species. MCP, the methyl-accepting chemotaxis protein, was also abesnt from several species.
Discussion
No character tests were performed this week. That several important genes involved in mechanotaxis and chemotaxis are missing from Deinococcus implies that these species may be sessile. This then prompts the question of why any genes (and by extension the proteins they code for) would be present at all. In other words, why have the cheW or cheA gene if you lack the methyl-accepting chemotaxis protein needed to bind to a ligand and start the signal transduction? Several tentative hypotheses are proposed. The first is the "vestige hypothesis". According to this hypothesis, the genes involved in mechanotaxis and chemotaxis are left-overs which serve no functional purpose for the cell. Another hypothesis, the "major function hypothesis", posits that these genes perform other important functions in the cell, which explains why some genes would be lost, but others retained. Further research is needed to determine the purpose of the remnant genes.
28 plates were prepared. 10 contained TGY, two contained a comibination of starch and TGY, six contained urease, and 10 contained R2A. 500 ml of TGy was heated at 350 C and poured into the TGY plates. Another TGY flask of the same volume was heated at 355 C and poured. 2g/L of strach and TGY was used to make the starch plates, while the solution for the urease test consisted of 50mL of urease in 450mL of H20 and Agar after the latter solution was heated to 350 C. After the plates were poured they were placed in the refrigerator. Next a R2B broth was prepared. 0.378g of R2B powder was dissolved in 120 mL of DI water. The plates created the day prior were labeled. Two TGY plates and two R2A plates were labelled as "Catalase D. xinjiangensis". The same was repeated twice, except that the two sets of four plates were labelled as "- catalase D roseus" and "+ catalase S. epidermus". Two TGY plates and two R2A plates were labeled as "oxidase xinxiangensis", while 1 TGY plate and 2 R2A plate sets were labelled "+ control oxidase B. subtilis" and "- control oxidase S. epidermis". One starch plate was labelled "starch xinjiangensis" and another was split down the middle with sharpie, one side being labelled "+ B. subtilis" and the other "- S. epidermis". Two Urease plates were labeled as "Urease D. xinjiangensis", two as "- control B. subtilis", and two as "+ control S.epidermis". One plate of Staphylococcus epidermis and another of Bacillus subtilis were then innoculated. None of the expiremental plates were streaked. The D. xinjiangensis just came out of freezeback, and thus cannot be innoculated. The following day, Gram stains were performed on the control plates. B. subtilis was Gram +, while the S. epidermis tested Gram -. The next day UniProt was used to determine whether or not genes involved in mechanotaxis and chemotaxis were present in various Deinococcus species. The symbol from a gene followed by the scientific name of the specific Deinococcus species. In a Google Sheets document, a "1" was placed in a cell next to the species name if the gene was present and a "0" if the gene was absent.
Results
No direct expirements were performed this week. However, the investigation on UniProt revealed several genes involved in chemotaxis and mechanitaxis were absent. Notably, cheZ and cheX appeared to be absent from most species. MCP, the methyl-accepting chemotaxis protein, was also abesnt from several species.
Discussion
No character tests were performed this week. That several important genes involved in mechanotaxis and chemotaxis are missing from Deinococcus implies that these species may be sessile. This then prompts the question of why any genes (and by extension the proteins they code for) would be present at all. In other words, why have the cheW or cheA gene if you lack the methyl-accepting chemotaxis protein needed to bind to a ligand and start the signal transduction? Several tentative hypotheses are proposed. The first is the "vestige hypothesis". According to this hypothesis, the genes involved in mechanotaxis and chemotaxis are left-overs which serve no functional purpose for the cell. Another hypothesis, the "major function hypothesis", posits that these genes perform other important functions in the cell, which explains why some genes would be lost, but others retained. Further research is needed to determine the purpose of the remnant genes.
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