Wednesday, November 30, 2016

Week 9

Hello everyone, so for week nine, it was obviously a short week because of thanksgiving, but I was able to finish up the rest of my DNA extractions. We had some food here in the lab and got to socialize some with everyone, so that was fun. I still haven't gotten all caught up yet with STEM, but at least I have gotten caught up in my other classes. The end is near and now is the time that will either make or break me. We shall see. Below is a picture of my final DNA extraction samples. I decided to do double samples to collect more data to hopefully get a more accurate depiction of which method was most effective, and also so I would have back up samples in case any went missing again.

Saturday, November 19, 2016

Week 8

Hello everyone, so this week I got into the lab and discovered that one of my DNA samples mysteriously disappeared. I had only gotten around to testing four out of the six methods that were given to us, and so with one missing, that put me at half but I decided to test the ones I had anyways. When I tested my samples, I discovered that only one of my samples was a decent sample. I think that the reason they were less than desirable was because I extracted DNA from a sample that was almost 5 days old, and they say that a young culture works best. So, I decided it was time to start all over and extract from fresh samples. So this time, I got through four samples again in a couple hours, and also doubled the extractions for each protocol, so I have a total of 8 samples to test. I plan on doing the other two samples on Monday when I get back. I also learned how to make a gel and run the nanodrop and electrophoresis.  Hopefully I won't be sick anymore by then. Trying to be optimistic even though time is running out. We will see how far I can get caught up this weekend.Below are some photos of the gel electrophoresis during set up.

Week 7

Hello everyone, I am super behind once again. I got sick last week and I thought I was getting better but I have bronchitis now so that sucks. I was only able to be in the lab for a couple hours and I think during week 7 my mentors helped me clear up some of my confusion about the assignments, although I obviously still haven't completed them. Since I am sick this weekend though, I have nothing to do other than sit in bed and try and catch up on everything so in a way it's a good thing I suppose. I also started learning about the nanodrop and gel electrophoresis, which I ran on Monday of week 8. Below is a picture of the nanodrop.

Friday, November 4, 2016

Week 6 post

Hello everyone, once again I am behind for this week, for the second week in a row, which is irritating for me. The only thing I really got accomplished was doing some more bacterial DNA extractions. I feel like I am trying to juggle way too many chaotic things in my life at one time. I am not sure if I'm the only confused one at this point or not about every aspect of life but I sure wish I could find a way to clear everything up. I have also never done anything research related until I got into this program, so I feel a little stupid. Not many things make me feel stupid but this is one of the few so it's extremely frustrating for me and makes me want to just give up, but nobody ever got anywhere in life by quitting right?
This is a picture of my DNA extractions so far. 

Friday, October 28, 2016

Week 5

Hello everyone, so this week has not been quite as productive as I wanted it to be. I have been trying to figure out classes for next semester and dealing with tests all week in my classes. But I did finally get around to starting my DNA extraction protocols, so this week has not been a total loss. I started with the boiling method of DNA extraction and just sort of went down the list testing the different methods as I went along. I still have a couple more to test, but they will have to wait until next week. My phone broke and so I was not able to take any interesting photos besides this picture of my bacteria being centrifuged, which isn't particularly enthralling.

Thursday, October 20, 2016

Week 4

Extraction of DNA from Escherichia coli
Nathan Andrew
Is it possible to extract DNA from my sample of Escherichia coli for the purpose of analyzing the DNA? I think it is possible to extract DNA from my given sample. I chose this as my research topic because I am considering a degree in Biology and this is the first step on my journey to make my final decision as to what career path I will take and expand my horizons as a scientist. I decided to do try and extract DNA from Escherichia coli to genetically analyze it. It is important to conduct research in this area because analyzing the genetics of Escherichia coli can tell us an almost infinite number of things about the bacteria. It can give us insight to its virulence and how it affects human health and disease, as well as the specific subtype. In order to be able to analyze the DNA of E. coli though, I must first be able to extract it. In order to do this, I will be experimenting using several different bacterial DNA extraction methods, such as: Boiling protocol, TE Boiling Protocol, TE Freeze and Thaw Protocol, Lysis Protocol, Meat Tenderizer Protocol, and KIT Protocol. I will then use Electrophoresis and a nanodrop spectrophotometer to determine the amount of DNA present in my sample as well as the purity.
Escherichia coli
Bacteria used for attempting DNA extraction
DNA extraction protocols
Independent variable
Methods used to extract DNA from Escherichia coli bacteria
DNA amount and purity measured by electrophoresis or nanodrop spectrophotometer
Dependent variable
Amount and purity, if any, of DNA extracted from bacteria

Works Cited
De Oliveira, C. F., Paim, T. G. da S., Reiter, K. C., Rieger, A., & D’azevedo, P. A. (2014). EVALUATION OF FOUR DIFFERENT DNA EXTRACTION METHODS IN COAGULASE-NEGATIVE STAPHYLOCOCCI CLINICAL ISOLATES. Revista Do Instituto de Medicina Tropical de São Paulo, 56(1), 29–33.

These are some of the chemicals I will be using for the DNA extraction 

Thursday, October 13, 2016

Week 3 Post

Hello everyone. So this week I spent most of my time working on my unknown bacterial identification project. Trying to keep thorough notes throughout the process has been a not so fun, but necessary challenge. I observed and recorded my bacterial colony morphology, performed a gram stain, and looked at my bacteria under the microscope to describe and record the cell morphology. Then according to the dichotomous key, I did an oxidase test, glucose fermentation, and a SIM test.  I have officially identified my bacteria to be E. Coli. I also helped Luis get caught up and showed him how to do a streak plate and explained the process of gram staining since he has never taken microbiology. So it was nice to make a new friend in the process and be able to help someone else out. Below are images of my glucose fermentation results as well as my SIM test after 24 hours of incubation.