S-Stem Scholar Jaira Munoz Zavala's Blog

On Saturday, February 8th, we worked did a second DNA with Sample 14.  These are the results of the DNA isolation done on 2/7/20. The results were not good, so we decided to do another DNA isolation of Sample 14.  We decided to use another kit different from last time. This one was the DNeasy UltraClean Microbial Kit. The steps in this kit were different from the Wizard Plus SV Miniprep. We continue using the same culture from Friday, thus now it was a 48hrs. We have used this kit multiple times. We usually repeat the first step (centrifuge 1.8 ml of microbial culture in order to have a pellet), However, this time we only worked with 1.8 ml instead of 5.4. We worked with only one bacteria culture, so we had to balance it with the same tubes but with distilled water instead.  These were the results of this DNA Isolation:

This is the fourth week. Today we worked with sample 14 from the previous experiments. Sample 14 is Deinococcus Pimensis. The bacteria were inoculated from a new bacteria colony. We worked with a 24hrs culture. On Tuesday 2/4/20, a gel was done with the DNA samples from last week. This is the gel with the ladder, samples 1, 7, 8, 14 and the blank (in that order). Sample 14 did not show results.  PICTURE CREDIT: CHAD ALBERT. First, we did a Gram Stain with sample 14 We used the "Wizard Plus S.V. Miniprep DNA Purification System" for A1330. This was the first time we used this type of miniprep. It was faster than the other miniprep we used before. Also, we were able to have more DNA.  Note: We didn't do nanodrop today. 

On Saturday of the third week, we finished doing DNA isolation for the rest of the DNA samples and prepared them for PCR. The samples we worked on were Sample 14 (Pimensis) and Sample 10 (Indicus). When we did the Nanodrop for these bacteria DNA, the results were not good for Indicus (they were negative). Here are the results: As a result, we only prepared the PCR tubes for samples 1,7,8 and 14. We pipetted 5 microliters of these DNA samples into the PCR tubes that were already prepared. Also, we pipetted 5 microliters of autoclaved distilled water for the blank : After the PCR tubes were ready, they were placed into the DNA amplifier for 1 hour and a half.

In the third week, we did DNA isolation, so we could do a PCR on the next day. The bacteria that was used for this DNA isolation was the one that was inoculated on January 24th.  There were eight samples of bacteria (1, 7, 8, 10, 11, 14, 17, 20). On Tuesday, January 24th, Gram Stains were with this bacteria in order to see if they were not contaminated. Samples 11, 17 and 20 were contaminated. We performed DNA isolation on samples 1, 7 and 8 on this day. Sample 1 was Aquaticus  Sample 7 was Gobiensis Sample 8 was Grandis Unfortunately, I did not take pictures while we did them, but here is a picture of the results: 

In the second week of the Spring semester (Saturday), we did a fluorescent gram stain for the first time. First, we were taught how the microscope worked with a slide that was already prepared.  Then we learned to prepare the Gram Stains. In the end, we saw the results.    We practiced how to place the slides in the microscope.  After we learned how to placed them, we looked at this slide that was already prepared. Also, Chad taught us how to placed them in the microscope. We were taught the different images we can get with this microscope. We looked at the different lights the microscope used. Also, we looked at all the options that the screen showed us. These are the pictures that I took. I was amazed by how the bacteria looked like a p hysiographic world map. Then we started to do a Fluorescent Gram Stain for the first time. The process was longer than the other Gram Stain we usually do. Results:

In the second week of the Spring semester, we worked with some bacteria colonies in Petri dishes and learn some basics about the automated fluorescence microscopy. Agar and TGY First, we inoculated some of the bacteria from the Petri dish to flasks with TGY.                                             We didn't use metal loops this time, so there was no need to use the Bunsen Burner. Instead, we used disposable loops (to avoid any type of cross-contamination from one bacteria to another).  We learned how to inoculate from Agar to Broth (we knew from Broth to Agar).  "I'll have a different post explaining this in detail"                                         There were 8 different bacteria. Each one of us worked in either one or two of them.  In order to avoid contamination, we were away from the person who was working with the Petri dish at that moment. After a person was done, the same person cleaned the area, and then the next pe