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Week 4/22

Introduction This week, the results for the UV test done on D. xinjiangensis were observed and a plasmid extraction was performed on D. sonorensis. Procedure The plasmid extraction was performed as follows:  -Add 600 µl of bacterial culture grown in LB medium to a 1.5 ml microcentrifuge tube  -Centrifuge the tube for 30 seconds at maximum speed and discard the supernatant -Add 600 μl of TE or water to the bacterial cell pellet and completely resuspend it -Add 100 µl of 7X Lysis Buffer to the tube and mix by inverting 4-6 times and proceed to the next step within two minutes -Add 350 µl of cold Neutralization Buffer to the sample and mix thoroughly until the sample turns yellow -Centrifuge the tube for 2-4 minutes at 11,000 – 16,000 x g -Transfer the supernatant (~900 µl) to the Zymo-Spin IIN column without disturbing the cell debris pellet -Place the column in a Collection Tube and centrifuge for 15 seconds -Discard the flow-through and place the column back into the collectio...
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Week of 3/4

Introduction Due to the Gibson assembly falling through, we have decided instead to make our project on the characterization of Deinococcus xinjiangensis through biochemical testing. The following tests will be done: Urease test: tests for presence of enzyme urease through observing for the breakdown of urea into carbon dioxide and ammonia byproducts. Indole test: tests for the presence of enzyme tryptophanase through observing for the breakdown of tryptophan into indole and pyruvate byproducts. Starch test: tests for the presence of enzyme amylase through observing for the breakdown of starch into glucose and maltose byproducts. Catalase test: Tests for the presence of enzyme catalase through observing for the breakdown of hydrogen peroxide into water and oxygen gas. Oxidase test: tests for the presence of enzyme cytochrome oxidase through observing for the breakdown of oxidase solution into water and hydrogen peroxide byproducts. Hydrogen sulfide test: tests for a bacteria’s ability...
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Week of 2/26

 Introduction This week, we performed a successful inoculation of D. aquaticus from plate to broth. The broth was used later in the week for DNA extraction using the Zyppy Plasmid Miniprep Kit. Procedure The following steps were followed to inoculate D. aquaticus from plate to broth: - A flask of appropriate size should already have media in it and be labeled with initials, date, bacteria name, and type of media. The flask should have been autoclaved and made ready for inoculation. - Gather a bunsen burner, an inoculation loop, and a plate. - Heat the inoculation loop over the bunsen burner flame to sterilize the loop, and let it cool for about 20 seconds. - Open the flask and have the lid in between your fingers underneath the loop. - Swipe the lip of the flask over the bunsen burner flame to sterilize. - Open the plate just enough to collect one colony with the inoculation loop. Close the plate. - Place the loop with the colony into the flask and sweep it around to spread the bac...
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