S-STEM Scholar Logan Young's Blog

  Introduction     This week, a UV test was performed on Deinococcus xinjiangensis . Competent Deinococcus sonorensis  were made and a plasmid extract was done on D. sonorensis  too.  Methods     On Monday, Gram stains are performed on D. xinjiangensis  grown on three different plates: one of R2A, and two of TGY. The bacteria grown on TGY are gram-positive, while the stain done from R2A reveals contamination by Staphylococcus . Two TGY plates and two R2A plates are inoculated with D. xinjiangensis . 2 flasks of 150mL of R2A are also inoculated with D. xinjiangensis . Two R2A plates are inoculated with D. caeni . The following day, the plates inoculated with D. xinjiangensis  are tested through a gram-stain. All of the results are gram-positive. A 200mL flask of R2A is made and OD values are taken of the D. zonorensis  inoculated yesterday. On 4/24/24, three 2mL centrifuge tubes containing R2B and D. sonorensis  are centrifuged ...

  Introduction     This week was spent desiging ways to further test the UV resistance of Deinococcus xinjiangensis .  Methods    Six flasks of TGY, each containing 25uL, are prepared. Five flasks of 20 uL of R2B and one flask of 20 uL of R2A is prepared. A practice gel is done for electrophoresis. The gel contains 30mL of TAE buffer and 0.3g of agarose. Cryovials contain 2uL of the sample, 8uL of PCR water, and 2uL of the loading dye. The gel is run at 100 amps. The next day, 2 flasks of TGY and one flask of R2B are inoculated with D. xinjinangensis . They are put in the skaing incubator at 30.0 degrees Celsius. I then had a discussion with Dr. Tuohy on further avenues of research (see discussion). Gram stains are done on the flasks inoculated yesterday. However, the results are inconclusive. Aland and I design a new and simplified experimental design for the UV tests that can be easily manipulated to test for specific variables. The following day, A...

  Introduction     This week was spent making a poster for the research conference. Methods     The poster was created in PowerPoint. Michel and Aland did the majority of the work on the actual power point slide, while Evan, Carly, Madi, and I wrote the drafts for the different sections of the poster. The results of the UV Test were also examined. Results     The results of the UV test showed that Deinococcus xinjiangensis  was resistant to all levels of UV exposure so long as the bacteria were inititally incoculated in TGY. If they were inoculated on agar, they would not grow.  Discussion      There are multiple possible reasons for this, one of them being that the excess nutrient density of the TGY allowed the bacteria to build stronger cell walls compared to those grown on R2A, or that the extra nutrient density of the TGY physically blocked the UV radiaition, shielding the bacteria and thus limiting their exposure. 

  Introduction     This week we performed performed our SIM test and the UV sensitivity test on Deinococcus xinjiangensis .  Methods     On Monday, SIM media is inoculated with E. coli , Staphylococcus epidermis , and D. xinjiangensis by use of an inoculation needle. Two gram-stains are performed of D. xinjiangensisi , one of which is negative and the other is inconclusive. Two TGY plates are inoculated with D. xinjiangensis. The plates for the citrate test are checked for the presence of blue. Old SIM media from the previous week is discarded. On the following day, two gram-stains are performed on D. xinjiangensis  grown on TGY. The results of thests stains are both gram-positive. Two 300mL flasks of R2A are prepared and used to pour 20 plates, two of which are inoculated with D. xinjiangensis.  On Wednesday two gram stains are done for the R2A plates grown yesterday, which are both gram positive. The following day OD values are taken for tw...

  Week Three Introduction     This week we innoculated several medias and performed biochemical characterization tests on Deinococcus xinjiangensis .  Methods     A gram stain is done on the D. xinjiangensis . They test gram -. The plates labeled last week are innoculated with their respective bacteria species. The tubes containing SIM media are innoculated by opening the tube and passing it over a flame. The smaller tube containing the bacteria is then swabbed. The needle is then dipped into the larger tube, which is passed over the flame again and closed. The methods of using UniProt and NCBI to detect the presence and absence of genes involved in chemotaxis/mechanotaxis is then scrutinized. It is discovered that the method we had been using was unreliable. Following this, two flasks of TGY are innoculated with D. xinjiangensis.  The following day, we examine the plates for growth and inoculate the citrate plates with D. xinjiangensis . A rough draft...

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.  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 wa...