It’s already week 6 but it dosen’t feel like it, the time has gone by in a flash. Tuesday we had the opportunity to attend a presentation given by Dr. Harish Nagaranja, who is a senior scientist at Genomatica. Genomatica is a Bioengineering company that has explored in finding renewable ways to produce chemicals for products like plastics, cosmetics, and nylon. It was cool to hear that they have found natural alternatives to nonrenewable resources. He also told us his path of becoming a research scientist. Starting out in India and moving to San Diego to do his doctorates. Then going into Genomatica as an intro research scientist and working up to senior scientist. It was interesting to hear how he got to where he is now. After the presentation were tasked to come up without poster titles. This kind of came as a shock to some of us because we thought there was a lot more time. But with only 4 weeks left its best to get started on our posters and paper now, rather than later. On Wednesday the REU cohort and Summer Scholars were invited to participate in a mentorfest. It allowed us to talk to representatives of big companies like Thermo Fisher, Illumina, Viasat, Intuit and Hunter Industries. There with our peers we networked and ask questions to mentors of the companies. On Thursday a couple of us were craving some wings so we went over to Buffalo Wild Wings and got their 75¢ wings deal. We hung out and even received an order of cheese curds by mistake. Now reaching the end of the week we are all in lab working hard to continue our research projects.
For my research we are looking into how landscape practices effect the decomposition of litter from evergreen and deciduous leaves. This week i was able to weight out super tiny sample around 10 mg int tin cups. These were then put through into a Costech CHN elemental combustion system to see how much carbon and nitrogen are in our samples. With that data we can analyze it next week to see how the 5 different sites differ in decomposition.
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WELL, WE ARE HALFWAY THERE!
Hello everyone, my name is Frank Gonzalez and I am working in Dr. Betsy Read’s lab. I can’t believe we have already been here for five weeks. They are just flying by and we are all well into our projects and looking towards our poster presentation. For these first five weeks I have been looking at three different microalgae mutants along with the wild type. I have been spending a lot of time performing lipid extractions, running it through the GC/MS, and analyzing my data to characterize the mutants based off the lipid profiles, below I included a relative percentage chart of my samples. I have also learned how to inoculate cells, perform flow cytometry to count my cells and track the amount of neutral lipids, and this week I learned how to perform a DNA extract and run my first ever gel. I did have some RNA contamination and a little shearing but that is to be expected. Besides spending our time in lab this week, we got to hear a very interesting and informative seminar about epigenetics given by Dr. Elinne Becket, participate in the annual grunion run, go on my first Californian hike, and grill out for the 4th of July. Overall my time so far here has been great and I am sure will continue to be great but over my time of being here and talking with my fellow peers I have learned that working in a lab can be hard and at times frustrating but at the same time it is so rewarding when you see the bands light up on your first gel or a unique lipid profile on one of your mutants. It makes the frustrating moments worth it. I can’t wait to see what these next five weeks have in store. So long yall! PS- peep the lab coat. For me, week 4 went by way too fast. David is definitely right, there really aren’t enough hours in the day when it comes to getting work done in the lab.
My name is Nicole DeNamur and I’m working in Dr. Becket’s lab. The overall goal of the Becket Lab is to investigate antibiotic resistance in the ocean microbiome. As a summer intern, my first goal is to come up with a non-biased way to lyse bacterial cells without fragmenting their DNA. I have been using a concoction of enzymes to do this. This past week, I’ve been focusing on using enzymes including lysozyme, mutanolysin, and lysostaphin to successfully lyse gram positive bacteria, as well as E. coli. Later in the internship, I aim to isolate mobile elements, or DNA that can move around the genome including plasmids in bacterial cells. My project relates to the overall goal of the lab because it is believed that the mechanism of antibiotic resistance is spread around the bacterial genome through these mobile elements. This week, REU students had the opportunity to tour Illumina in La Jolla where we learned about the different products and careers offered at the company. We got a behind-the-scenes look at certain sequencing systems, and learned about their manufacture and the difference between sequencer models. It was an informative and interesting tour, and I’m definitely considering applying for a job or internship there after college. Its been three weeks already, but it definitely does not feel like it. When working in the lab there are never enough hours in the day.
I am David a molecular biology student working with Dr. Rosalina Hristova and Dr. Betsy Read. We are researching the toxic cyanobacteria Phormidium which has been growing in increased numbers in northern California. It has been a really fun and interesting experience thus far working between two labs. Things have been moving fast in my lab. Week one was spent prepping, and week two marked the start of our experiment/project. This week we worked on coming up with an RNA extraction procedure that would work for the Phormidium. Every procedure we tried seemed to yield contaminated RNA. We decided on making new reagents and working with younger cultures, and that did the trick producing pure RNA. Now we will be moving forward to test the integrity of the RNA. This week we were visited by Dr. Inigo Valiente Alandi who does bioinformatics and genetics work for the San Diego Zoo Institute for Conservation Research. Inigo discussed the importance of NGS in his work to restore populations of endangered species. Inigo is currently doing research on the Northern white rhino. We were also able to talk with Inigo about his career and insights into doing research in the industry and in academic settings. Week 2 has gone by fast. I am a part of Dr. Jane Kim’s lab that is focused on genomic instability due to DNA repeats using yeast. I will admit, I was very much intimidated going in because this would be my first exposure to working in a molecular lab. Nonetheless, in just a short two weeks I have learned so much. Along with my work in the lab, the NGS REU program here has set up some very informational workshops that will benefit our projects. So far my time here has been filled with new experiences inside and outside the lab.
For the most part, week one consisted of me slowly integrating myself into lab and getting familiar with various common lab techniques. I came in with little to no lab experience, but now I have learned how to do PCR, transformations, gel purification, and so much more. I truly have learned so much in such a short period of time and I know there is still much more to learn in the weeks to come. About half way through this week I was finally let loose on my own in the lab to begin working on my project. I will be looking into chromosomal fragility caused by CCTG repeats using Next Generation Sequencing. On here there are pictures of me working with some yeast transformants and testing whether they took up a particular plasmid. I also learned how to design primers and gRNA, how cool is that? Aside from the lab, I have also learned about BLAST and its applications in a workshop done by Dr. Betsy Read. I actually did have to use BLAST this week in order to check out a gene of interest in one of the yeast strains I was using. Dr. Arun Sethuraman also gave us a seminar about population genomic analyses using Lady Beetles. I never knew just how helpful lady beetles were for agriculture, which is essential in my area (Central Valley, CA). I have never gone to any beaches in Southern California, but luckily there are some near San Marcos that are a short commute. Last weekend I went to Oceanside beach and this weekend I got to visit Carlsbad Village beach. Both are gorgeous and vibrant beaches that I highly recommend! I have definitely gotten much tanner. Week 1 of the first NSF REU Program at CSUSM was such a success and so far, has been a wonderful experience! The week began on Sunday for move in day, giving us the first chance to meet all the people we were going to be interacting with for the next ten weeks in the cohort. After moving in, all members of the cohort and the PI’s of the program got together for a dinner in order to be able to further get to know each other and be able to ask questions about the ten weeks of research ahead of us. On Monday the REU cohort, as well as other summer scholars, were lucky enough to get invited to ViaSat for a kickoff event hosted by them. This gave us a great opportunity to be able to network with more of the cohort and a few of their employees who regularly hire recent graduates. ViaSat even brought along a few employees of theirs who were CSUSM Alumni so they could tell us their journey to the company after graduation. After the event ended, we all headed back to our campus to be able to meet with our PI’s and talk about what research plan we had for the summer as well as do a few safety trainings.
On Wednesday the cohort attended a seminar on campus entitled Introduction to Next Generation Sequencing which gave us a very informative introduction into all the basics of next generation sequencing as well as the leading companies and what sequencers they produce. Throughout the week all REU students have also been working on their projects in lab. Each member of the cohort is doing some very interesting research! For example, in my lab we are focused on being able to sequence bacteria within the costal microbiome and classify any mobile elements they have within them. For this week we have started with lots of research into primer designs, the right enzymes for enzymatic lysis and we have begun making media for bacterial colonies from the ocean to grow on. My lab group was also able to take ocean samples this week so we will hopefully be able to isolate and grow the bacteria. For many others in the program they too are starting off with some basics because it is our first week of research. Some students have been shadowing grad students in their lab while they look at the influence of delta t cells on immunity in mice and others have been learning how to make filtered seawater media, inoculate cells, perform flow cytometer counts and how to prep cultures for lipid extraction in order to lead up to their project of working with a micro algae. Another is working on working on what it takes to raise different lady beetles outside of their region in order to collect an RNA sample using the Zymo Direct-zol MiniPrep Kit. So far, the first week has been filled with great networking opportunities as well as great first beginnings in our research. I can’t wait for what lies ahead for all of us! |
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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