This week I learned how to digest Malpighian tubules from Trichoplusia ni (a species of caterpillars) while waiting for our purchased insect medium to arrive. These tubules help scientists understand Trichoplusia ni osmoregulatory and excretory system. Along with digestion, I began to prepare for cell culture, which involved autoclaving my materials and sterilizing an area in the lab. Cell culture in this lab has never been done before so I am a bit nervous, but excited to be a part of this process!
After our field work, we visited Julian to feast on their famous pies before heading back to campus. Later that day, I attended a Mentor Fest with other interns where I had the opportunity to listen and ask questions related to the science field and potential career paths. Although many of them are not in job positions I am interested in, it was fulfilling to hear their life journeys and the endless advice they had to offer. Gaining perspectives of people in the working field was such a motivating and reassuring experience. I am truly grateful for the opportunity as it helped me decide on my plans post undergraduate school.
It has been great getting to hang out with the amazing REU and Summer Scholar interns. I can't believe we are halfway through the internship already! There is still a lot I want to learn at CSUSM and places I want to adventure to with the other interns. We have a lot of ideas that I hope we get to do before the end of summer. But I am going to make the most out it and enjoy it all <3
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Hey y’all! My name is Jenna Archambeau and I am a rising senior at American University in Washington, DC. I study biochemistry and statistics, which I have been able to apply here at CSUSM for next-generation sequencing and bioinformatics! For this summer, I have been working with Dr. Elinne Becket in her microbial genomics lab. We work with coastal water metagenomes to get a better understanding of horizontal gene transfers in response to tetracycline, which we hypothesize to have an impact on community antibiotic resistance. This week I have been assisting others in the lab on their projects. Last week, Ella (another REU student in Dr. Becket’s lab) and I troubleshooted the protocol for our RNA Library Prep because the samples contain RNA from both eukaryotes and prokaryotes. We are hoping to isolate our mRNA from bacteria, so we need to eliminate ribosomal RNA from the eukaryotes and prokaryotes. Depleting rRNA from both sources turned out to be more difficult than expected, so we had to consult with various biotech companies to figure out our best option moving forward. It was nerve racking to make all of the technical support calls; however, it was rewarding to get more pieces to the puzzle. While waiting for our supplies to come in, I have been helping other students in the lab with their projects. On Tuesday, we went out to Scripps Pier to take ocean water samples for one of our graduate students. I enjoy field work because seeing the environment we are studying makes our lab goals more tangible. The rest of the week I have been developing both dry lab and wet lab skills by working on code and DNA extraction. Though I have used R and CommandLine previously, it has been a welcome challenge to explore new pipelines and applications of these resources. It was fascinating to learn how many different ways you can manipulate the code to get results that are relevant and significant toward your research question. Lastly, I conducted a DNA extraction experiment from Vibrio bacterial cells for the first time. I had a lot of fun with the experiment, as you can tell from the picture. Outside of the lab, I have made a lot of great memories with my fellow REU students. This weekend, we celebrated our long weekend for the Fourth of July together by hanging out by the pool, going to the beach, and playing laser tag. I’m hoping to explore more beaches (maybe learn surfing?) and experience everything Southern California has to offer during my time here. It’s been amazing to connect with others, both inside and outside of the lab, and I look forward to what’s next to come in the next six weeks!!
REU DR. Read’s lab This week I successfully extracted genomic DNA and RNA from the cultures I grew up in the past two weeks. There are some practical goals in my research project. One is performing all the processes of DNA and RNA extraction sterilely to avoid any contaminations. The second one is extracting genomic DNA. To do so, DNA should not be sheared in anyway. With that being said I was not able to use pipetting methods to transfer my DNA content which can be challenging sometimes. Also, I had to use a new method to pellet the algae instead of centrifuging it. This week, Dr. Read; my mentor, decided to use a filtration method instead of spinning the cells. It was meow first-time using filtration method to get the cells out of their cultures. Although it took about two hours to filter all the cells, I am so happy that the method worked and I could extract the DNA and RNA from my samples. The ultimate goal of this project I am working on is to understand the algae’s characteristics in genomic level. I also started to help Dr. Read with another project which I found very interesting. I started to inject gas chromatography and mass spectrometry samples in GC-MS machine. The samples are from different specious such as Emiliania huxleyi. In this project we would like to identify the components of Emiliania huxleyi’s lipids at a molecular level. I started to learn how to work with the machine and the software program which is being used to operate the machine. I would like to thank my great mentor Dr. Read for conveying her expertise to me passionately and being willing to teach and help all the time. Bioinformatics In our Wednesday bioinformatic meeting I learn a lot in many ways. This week we started to use new tools in Kbase website such as Kaijo. We also started to analyze the FASTQC results from the previous weeks. I believe our bioinformatic meetings are very important for one main reason and that is the necessity of bioinformatics in our filed of work. We pretty much know how to practically generate the data that we think can be helpful for our research project. However, understanding the generated data and making biological sense out of them is what bioinformatics does, and it can be quite challenging. This week we have to analyze some of the generated data with different tools in Kbase website and present them in our next week bioinformatics meeting. Next week I will run agarose gels for my extracted DNA and RNA and I can’t wait to see what the results are. I am also looking forward to present the table that we generated for results section of our manuscript in our bioinformatics meeting. Activities Beside work which was so exciting, I had a great week in terms of the fun activities that we all did. First of all, I celebrated my birthday with my REU colleagues at our pool. It was a great party and we all enjoyed the pool in on a sunny Saturday. Before that some of my REU friends distracted me for a day to arrange a surprise birthday which they did a great job doing that. In the middle of the week I got a chance to visit Thermo Fisher’s Carlsbad site for the second time. This time I went with a group of CSUSM students who are mostly looking for job immidiently or sometime soon. It was great meeting both graduated and senior peers in a different setting than collage. Next week are going to a field trip to Anza-Borrego desert state park, which I’ve been waiting for a long time. |
Watch this space for weekly updates!Every week, one of our CSUSM NSF REU students will post their blurb, summarizing their week, and chronicling our program. AuthorWrite something about yourself. No need to be fancy, just an overview. Archives
August 2023
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