S-STEM Scholar Madison Jackson's Blog

Intro     As we return to lab for the fall, we pick up exactly where we left off from the summer. With the reference gene project we've switched species to Deinococcus deserti, and with that Alex has taken time in the week inbetween to become familiarized with it. As we are officially working on the new desiccation project as well, we have been given a second species to continue our work with: Deinococcus pimensis. Over the course of the week we plated samples of both species for 24 hour, 48 hour, and 7 day desiccation.  Methods On Monday 8/19/24, a recently grown sample of deserti was gram stained to ensure no contamination before being used for inoculation. We found gram negative rods with no contaminants, so the plate was used for inoculation. A different newer plate that had left to grow over the weekend was used for starting 48hrs of desiccation to extract RNA. The 24hr and 7 day deserti, as well as the 24hr, 48hr, and 7 day pimensis were all plated the followin...

  Intro     Over the course of the summer, it was decided that we should pivot away from the AMC project and to work on something new. Our focus shifted to selection and validation of reference genes for qRT-PCR analysis in Deinococcus sonorensis under the condition of desiccation.  Method      Most of out methods changed over the course of the summer. For example, at the beginning of the project we were rehydrating our desiccated cells with water, which we later changed to a rehydration buffer to avoid essentially popping the cells.     In general the basis of the project is to desiccate cells, collect RNA from those cells (as well as a non desiccated control set), run RNA-seq on the collected RNA, identify differentially expressed genes and rank their stability through various programs, and finally validate the DEG's through qRT-PCR and qRT-PCR analysis. Our original desiccation protocol is as follows: 1.  Grow cells for 48 hrs @ 30 °C...