TRAIN Bootcamp

 January 28, 2024

Introduction

This week was an introduction to the TRAIN program for new and returning members. Lani gave a presentation about the program that included general safety information, a brief introduction into the bacteria Deinococcus, and the general expectations of the program. For example, these blog posts are required at the end of the week every Sunday detailing the work for the week and the methods and results from said work. Lani also supplied a few resources that should come in handy further into the semester, such as Google Scholar, PubMed, and BacDive. These resources should be used to gain information in order to know more about bacteria we work with here in the lab, as well as to help find information in the future for projects. Also this week was a brief introduction into making media and using the nanodrop.

Methods

The general process to making media is to follow the recipe and dilute. This week, we made TGY (tryptone, glucose, yeast) by diluting the recipe from 1 liter down to 250mL. To mix, about half of the total volume of water was added, then the tryptone, glucose, and yeast are added, followed by the rest of the water to get to 250 mL, and then tin foil is used to cover the top of the beaker, then mix thoroughly. Labels are then taped onto the side of the beaker with the initials of who made it, the date it was made, what it is, and the quantity. I was also introduced to the nanodrop this week, which is used to identify how much and what is in a given sample. To use the nanodrop, first the pedestals have to be cleaned with deionized (DI) water, then 2 uL of the blank are placed on the lower pedestal and hit blank. Clean off the pedestals again, then place 2uL of whatever sample you want to measure, and then read your results. 

Results and Discussion

This week was largely dedicated to getting to know the lab and the procedures that go on in it, and knowing about safety. Having never been in a biology setting before, I’ve never had to work with bacteria so seeing the different incubators and all of the different protocols to keep everyone safe as well as to keep samples from getting contaminated. From the procedures I’ve seen this week, much of what is done in the lab is to ensure that we know for sure what we are looking at, and that it is free of impurities because these can have a huge impact on things at such a small level. The nanodrop, for example, is specifically dedicated to measuring concentrations of proteins at a literally microscopic level, so that we can be sure of what exactly is in the sample we are working with. I look forward to learning more in the coming weeks.

Comments

Post a Comment

Popular posts from this blog

UV Exposure

  Intro Much of this week was dedicated to filling out our poster. What wasn't spent on poster work was spent on testing UV radiation tolerance again. The MRVP tests were done again and were again decided to be inconclusive. Method Method for UV exposure is exactly the same as last week, but R2A was exposed at levels of 1000, 1250, 1500, 2000, & 3000. TGY was exposed to 3000, 5000, 6000, 7000, 8000, & 9000. Results & Discussion Again, there was absolutely no growth on any of the R2A plates. The threshold is cleary far lower than we expected due to the media of R2A while, again on TGY, there was growth from the 3000 & 5000 plates. Conclusion Really all we have left moving forward is little details and pictures for the poster. All of the tests have been conducted at least once, but a few of them need to be redone still to see if we can verify a true positive/negative result. 
Read more

Week of 10/14/24-10/18/24

Image
Intro This week involved another round of RNA isolation, followed by purification and then an RNA gel and fluorometer check to ensure quality of the RNA before proceeding.  Methods Before RNA isolation, cells were rehydrated with 650uL of rehydration buffer per 100uL spot, then allowed to sit on the rocker for 15minutes at 250rpm to fully rehydrate. Kapton squares were then scraped to ensure removal of the cells, then pipetted into 1.5mL eppendorf tubes. RNA isolation procedure: 1. Resuspend fresh or frozen pellet in 800μl RNA lysis buffer and transfer the mixture to a ZR bashingbead lysis tube 2. Secure the tube on a bead beater fitted with a 2ml tube hold assembly and process. 1 min on/2 min ice repeated 5 times 3. centrifuge the tube for one minute to pellet debris 4. transfer up to 400μl of the cleared supernatant into a Zymo-Spin IICG column in a collection tube and centrifuge for one minute. Save the flow through 5. Add an equal volume of ethanol (95-100%) and mix well 6. tra...
Read more

Ref Gene Progress

Image
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...
Read more