Hello, my name is Lakme Caceres. I would like to start off by thanking Drs. Betsy Read and Arun Sethuraman for working so hard to organize and run this REU program for us! It is difficult enough to plan a fun and educational summer, but I am sure that COVID-19 made this even more of a challenge behind the scenes.
Coming into the program I was excited and also a little nervous. After over a year of social isolation and online classes, I was weary of the transition into such an immersive experience. But after meeting the people I would be working alongside this summer, my worries were quickly assuaged. Everyone I have met in the REU and Summer Scholars programs has been friendly and eager to learn!
Week one was full of introductions to new people, places, and science! After moving into our spacious and accommodating apartments, we all got to know each other over a delicious meal of pizza, pasta, and dough balls. To kick-off the summer we met CSUSM faculty and listened to an energetic presentation on next-generation sequencing by Dr. Elinne Becket, who also happens to be my PI. The Becket lab uses genomics and ecology to study microbial antibiotic resistance in coastal environments. I will be working on a project that looks at how anthropogenic stressors influence environmentally-driven horizontal gene transfer, a large contributor to antibiotic resistance in bacteria. After just one week I had experience with preparing antibiotics, culturing and plating bacteria, and conducting MIC assays! I can tell that we are going to accomplish so much this summer.
Outside of lab we also had a lot of fun brainstorming and taking part in social events. We had an amazing time enjoying ice cream and then catching two (2!) grunions at Oceanside Pier. It took a long time for the fish to appear on the shore, but after we dug for sand crabs and enticed the grunions with Careless Whisper, I was able to catch one (Becket lab was responsible for catching both fish :D)! I also went axe throwing for the first time with my lab and Dr. Robert Iafe's lab. It was so much fun and I was stoked when I got my first bull's eye!
I had an incredible first week and I am so excited for what the rest of the summer holds. I can tell that it is going to be an invaluable experience.
Making a waterpark for the sand crabs.
Filled with trepidation, I arrived at the Pittsburgh airport at 4:00 am on June 2. Not only would this be my first flight since I was five years old, but this would be my very first time traveling further west than Ohio. Exhausted, I tried my best to drown out the chatting couples, the cackling group of old friends, and the sound of music seeping from the headphones of the passenger next to me. But I couldn’t sleep, not even a wink. I was teetering on the precipice of new experiences, and I was more than ready to fall.
I arrived at Cal State San Marcos, and the program took off like a high-speed train hurtling down the scientific track of discovery. I began working on the toxin producing cyanobacteria Microcoleus. What we wanted, more than anything, was to extract high quality RNA from our samples. However, it’s hard to achieve that goal when your samples look more and more like strawberry jelly at the passing of each day. That globular mass of cyanobacteria was producing substances that were contaminating our RNA. We tried to handle this in so many ways. The first few times our extractions didn’t work, it was a major disappointment. But, we ultimately became numb to the failure and tirelessly continued searching for a solution that would unlock the toxic secrets held in the RNA.
Bam! After eight weeks, we had our breakthrough! Our triumphant cheers were so loud that the next lab over cheered back through the closed door. We began preparing libraries of our samples and running quantitative PCR. Bursting with excitement, we were finally going to sequence our samples. Alas, another setback. Something misfired.
Such is the nature of science itself. Discovery and innovation do not exist in a linear plane and research requires failure and persistence. I understand that, now more than ever, my personality aligns with this type of work. As someone that had begrudgingly planned on going to medical school because I had no idea what else I could do with my degree, this was an awesome discovery and experience overall. Thanks to the great mentorship and work environment that I was in during the REU program, I am without a doubt applying to Ph.D. programs.
In our final week, we felt the pressure to finish our posters. Although the halls of Science Hall 2 were teeming with the anxiety of an approaching deadline, there was an underlying thread of excitement. After ten weeks of hard work, we would finally get to share the projects that had essentially become the air we were breathing for months. As we set up our posters and the room filled with visitors, the sweaty palms and nervous energy were replaced with animated passion with each new audience that arrived at our posters. The event was truly a success for each REU student personally and for the program as a whole.
Over the last ten weeks, I’ve made some great friends, explored quite a bit of southern California, received awesome mentorship, and performed meaningful research on current hot button issue. Although I am sad for the haze of a perfect summer to lift, I am invigorated and empowered moving into my last year of undergrad.
This is Allison Sullivan, signing off from summer research and signing on to a future as a scientist.
First I would like to express how grateful I am to be here... the WEATHER is fantastic compared to Las Vegas, I have been completely spoiled!!!
Hello my name is Jerrika Scott and I am in Dr. Sethuraman's lab where I have been working on DNA and RNA Extractions of Hippodamia convergens, also called the convergent lady beetle, which is commonly used for biological control of aphids. We have obtained two populations of H. Convergens from Kansas City and Palomar Mountain in California. We have used fava bean plants to feed the pea aphids, Acyrthosiphon pisum which the lady beetles consume in the campus greenhouse. We collected beetles from different life stages. Then we used liquid nitrogen to freeze the lady beetles, crushed the tissue with a mortar and pestle, then used the Direct-zol RNA MiniPrep Kit from Zymo Research to extract RNA. After that, we ran RNA Gels and used a Qubit fluorometer to test the integrity of the samples, and lastly we used an Illumina Tru-Seq Protocol to build RNA Libraries for Next Generation Sequencing.
This week has been so hectic because our poster deadline was August 1st and presentations are going to be August 8th, I am so excited because this will be my first poster presentation, and we will get to show off all our hard work. Since this is our second to last week this was our last weekend together and we were able to spend some amazing quality time with each other. I am so proud of everyone because of how much progress we have made since the first day, I have had such a great time with all my lab members and mentors they have been such a great help these past few weeks. I can't wait for next week hope to see you there!!
We are fast approaching the end of our research program, so sad!
Hello, my name is Amanda Nweke and I currently work in Dr. Mothe's lab. My project is to formulate a construct to make a hypoimmunogenic stem cell using CRISPR. My research came as a result of two papers published by Harvard University and University of California San Francisco (UCSF). In both papers, hypoimmunogenic stem cells were made by knocking out HLA-A/B/C and CIITA and knocking in B2M (USCF) or PDL1, HLA-G, and CD47(Harvard). What I am currently doing now is finding if there is any MHC expression in our Gibco human induced pluripotent stem cell (hiPSC) using both PCR and a flow cytometry.
Aside from being in the lab this week, we all had the opportunity to go to various networking events and seminars. Tuesday, we visited the University of California Riverside (UCR) where Dr. Glenn Hicks gave us a tour of some the research that goes on at UCR. In the first lab we visited, the PhD students spoke on their research with bumble bees and how bacteria affects the bee population. We concluded our tour with the graduate students discussing their experience as PhD candidates at UCR. I found this discussion very useful, because a lot of times some of the graduate students “don’t keep it real” to some of the undergraduate students about some of the challenges they face in graduate school. I also found the advice they gave to us useful as well. On Wednesday, we had a poster presentation seminar hosted by both Dr. Julie Jameson and Dr. Besty Read. They gave beneficial information on how to make a scientific poster and how to effectively deliver your research to an audience. They also proposed a new way of creating a poster that pinpoints the main conclusion on the poster as the forefront of the poster. On Thursday, we went to a *NSPIRE symposium poster presentation event hosted by Dr. Robert G. Iafe. In which three guest speakers who were PhD candidates at Scripps Research Institute gave a talk about their journey to a PhD as well as the research they are currently working on at Scripps. After that, there was a poster presentation given by students from California State University San Marcos.
Almost reaching the finish line of this program and I'm truly enjoying every minute of it!
My name is Matilde Macedo and I am working in Dr. Jameson's lab which focuses on studying T cells that are involved immune diseases such as alopecia areata, and type 2 diabetes. In this lab I learn a lot of laboratory techniques such as sterilizing tools with the autoclave, working in the TC hood, and maintain cell lines. Additionally, I learn how to do epithelium preparation which consist of extracting dendric epidermal T cells (DETCs) from mice and plate them into a 96 well plate to prepare them for RNA extractions. I also learned how to do immunofluorescent staining on wounded tissues so we can visualize the t cells that are involved in wound healing.
In this program I've been working on public data analyzing the RNA of people with alopecia areata using Galaxy. In this computer program I learn how to use different tools to analyze the transcriptome which includes FASTQ, Tophat, cufflinks, and cuffdiffs. My research involves in investigating if genes signatures of DETCs in patients with alopecia areata are upregulated or downregulated. This will help us picture the influence of DETCs in this disease.
Overall my experience in this program had been amazing. In this week we attended the NSF GRFP webinar where we learned more about the program's application which can help recognize and financially support MS and PhD level research. To destress from our projects, we hiked the Iron Mountain to observe the beautiful new moon from up there. I am thankful that I get to have this experience which in turn will help me get a step further in reaching my career goals.
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.
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.