,Hi everyone! I’m Ella Caughran and I am a senior biology major with a genetics minor at University of New Hampshire. This summer I have been working in Dr. Becket’s lab which does research in coastal microbial meta-genomics. The project I am working on, along with Jenna, is sequencing RNA that has been treated with different concentrations of tetracycline (a common broad-spectrum antibiotic) for different durations of time, to see what treatments lead to the expression of mobile genetic elements. This week in lab we ran a gel of our fully prepped samples as QC, and once we got ideal results we were able to load the sequencing cartridge and begin sequencing our RNA on our in-lab iSeq! It was such a cool and unique experience to have the opportunity to actually do the sequencing ourselves in lab. The next day we got the fastq files back and begin preparing the fastqs for analysis. I then searched for databases to run our sequence data against using bowtie2 (a read alignment software) and started performing preliminary analyses. It was a very productive and exciting week in lab! Outside of lab I got the chance to go to karaoke with my lab mates, as one of our lab’s recently graduated master’s students is leaving for a PhD at Princeton (we’ll miss you, Ciara!). On Friday night I hung out with my lab mates again and had a movie night. We watched Arrival, which I would definitely recommend to anyone who hasn’t seen it. On Saturday morning, me and several of the students from the REU cohort went to La Jolla to go paddle boarding. The waves were choppy so that made it a bit tough, but it was still a ton of fun, and I even saw a leopard shark! Saturday afternoon I went up to LA for the first time with my partner who was visiting, and we hung out with a friend from back East who lives in LA now. We had super good Korean food and went to a huge flea market. I had a great time and it was so cool to experience LA, if only for a day. I can’t believe the summer is almost over. I have learned so much and, even though things didn’t always go smoothly, I am very proud of my accomplishments. I made so many friends and so many memories that I will never forget. I am so grateful to Dr. Becket, Dr. Read, my REU cohort, and my lab mates for making this experience so unforgettable!
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In 2019, Dr. Read and Dr. Hristrova went to the Anza Borrego Desert in California and discovered a desiccated stream in the San Felipe Creek of the Anza Borrego Desert. There they collected samples of desiccated cyanobacteria. Clarivel (my lab partner) and I were given the project to identify what species of cyanobacteria it is.
For the past 8 weeks, our initial goal for our project is to identify the unknown cyanobacterium from the Anza Borrego San Felipe Creek with whole genome sequencing and then to interrogate its phylogenetic history. During this time I have learned a lot of bioinformatic tools and techniques. I’ve also heard the horrors and tragedies of bioinformatics, and how important it is to maintain detailed notes of the purpose and methods used in computational analysis. With the help of Dr. Read, I was able to quickly get the hang of the programs and software really quickly, programs including Blastx, Clustal Omega, DNAdiff, etc. From learning how to code to cloning plasmids, we’ve done it all in order to identify what this cyanobacterium is. During the first few weeks of the program, we cultured the cyanobacterium in BG11 for 21 days in four different levels of salinity (25-100%). Cyanobacterium is known to be a freshwater bacteria and it was surprising to see it grow in 100% salinity. We then proceeded to manually genome annotate the strain of cyanobacterium and we were able to get results that show the whole genome sequence alignment demonstrates a 98% average identity between AB Cyanobacteria and Limnoraphis robusta. From our growing cultures we were able to practice the strategy of extracting both RNA and DNA, unfortunately extracting RNA from this particular organism is very complicated and most results were a total failure. Luckily, we were able to extract DNA. This week, after successfully extracting DNA, we proceeded to examine the concentration on the Nanodrop, and we got a really good number. This allowed us to proceed further in creating LB agar plates containing kanamycin that will be used to identify transformed cells. This whole process will allow us to create plasmids that will be shipped out for sequencing. Results are still awaiting to come back!!! Since most of the REU students, including myself, come from different states, some of us planned a weekend trip to Los Angeles, CA. The first day there, we went to the famous Santa Monica Pier. It was a dream come true, that area is so beautiful. All the shops reminded me of a calm SOHO. Later that night, we went to watch a soccer game at the Rose Bowl Stadium, where Real Madrid played against Juventus. The next day we traveled all of Hollywood, from the walk of fame, to Griffith Observatory and the Hollywood sign!!! I’ve had the time of my life these past two months!! I wish they had In-N-Out Burger back at home! Sadly it all wraps up into weeks. Hello everyone, my name is Marvin Onwukwe, and I am a rising senior at the University of Maryland Baltimore County (UMBC) majoring in Biological Sciences. I have been working under Dr. Jane Kim’s lab, investigating the genetic instability of microsatellite regions of DNA using yeast. The project I had the pleasure of working on involved performing knockouts of genes in the highly manipulable genome of yeast to investigate mutation rates of repeat sequences to gain a better understanding of the currently incurable genetic illness known as Myotonic Dystrophy type 2 and potential therapeutic treatment. Among the myriad of lab skills Dr. Kim and her work had exposed me to, I had the opportunity to develop into a more independent researcher and academic in general having had the experience of working on a project for the first time. I want to emphasize being kind to yourself especially in the first few weeks. Experiments may go wrong, equipment may be unfamiliar, and hiccups in general do happen. That is only a reflection of the fact that you are challenging yourself in a new environment. Even though perfection is ideal, don’t let it be the gateway that allows you to enjoy yourself and what you’re learning in the lab. I am excited to write to you about week 7 which happened to be the week of my 21st Birthday. That week, we were treated to a tour of the Scripps Institution of Oceanography, a world class facility dedicated to advance our understanding of the earth system and train the next generation of scientific and environmental leaders. As a department of UC San Diego, Scripps Institution of Oceanography is one of the oldest, largest, and most important centers for ocean, earth, and atmospheric research. The tour had explained how they make accurate oceanic simulations in large-scale, cleverly controlled environments among many other features. Not only are we exposed to world class facilities and quality preparation for graduate education, in California you genuinely have a higher prevalence/chance of meeting some of your favorite celebrities. On the weekend of my birthday, I had gone to downtown San Diego to celebrate, and I was elated to meet Brian Posehn on the sidewalk by chance. For any of those who watched the show Big Bang Theory, he was the geologist at Cal Tech. I would like to mention that the following week (week 8), I had the opportunity to travel to Los Angeles, which is a mere 40-minute Sprinter train from the CSUSM campus to the Oceanside Amtrak ($2.50) and a two-hour Amtrak from there to LAX union station. As part of the McNair scholars’ program at my University in Maryland I was able to join them and meet the CSUSM McNair scholars at our national conference held at the University of California, Los Angeles (UCLA) where I presented research and had tremendous networking opportunities and graduate school prep similar to the standard given at this REU experience. I couldn’t recommend this opportunity more! Here is my LinkedIn: Marvin Onwukwe Hi everyone! I am Chloe La Prairie, and I am a senior at Millikin University in Decatur, Illinois studying Biology with a pre-med concentration. This summer I have been working in Dr. Jameson’s lab conducting Neuroimmunology research! I have been studying the relationship between Gamma Delta T Cells and neurons in wound repair. During my six weeks in the lab so far, I have learned an immense amount while doing experiments. This week I conducted multiple ear peel experiments, which is where we peel apart the epidermis from the dermis of mouse ears and stain with different antibodies to look at the relationship between Gamma Delta T Cells and the neurons through the immunofluorescent microscope. We do this with wounded and non-wounded mice to examine how Gamma Delta T Cells affect wound repair. In addition to ear peels, I have also learned how to do cross sectioning cut staining and culture cell lines. When I am not in the lab, I am spending my time studying for the Medical College Admission Test which I am taking at the end of July and finishing up my applications to medical school. This week the REU students had the opportunity to go down to San Diego State University and tour several research labs. It was very interesting to see how different labs work and what other kinds of research are currently being conducted. On Saturday, we all went over to Dr. Reads house for dinner which was so much fun. Dr. Read even had homemade ice cream and crepes for us! On the weekends, I look forward to spending time with the others in the REU program, and I’ve enjoyed spending most of my weekends at the beach or the pool. I also enjoy spending time with my lab mates outside of lab, we have met up for Pizookie Nights at BJs Restaurant and walked down to the farmers market together. I look forward to learning more skills in lab that I can then take back with me to my own university where I will continue to conduct research. I am very grateful for the opportunity the REU program was given me this summer and will be sad when the summer ends. I can confidently say this is one of the best summers I have ever had! |
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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