Hello everyone. My name is Isabelle Massaro and like Antolette, I am fortunate to be one of the local California State University, San Marcos (CSUSM) students accepted into the NFS REU Research Program this summer. I am a senior here at CSUSM (with only 1 more semester left!) and am majoring in Molecular and Cellular Biology with a minor in Chemistry. As I near the end of my bachelor's degree, I plan to continue my education to pursue my passion in plant biology research.
Since I joined Dr. Escobar's molecular plant biology lab, I have gained hands-on experience working with plants. My project in the Escobar lab focuses on working with the model plant, Arabidopsis thaliana, to help characterize class III glutaredoxins (GRXs) and identify their role in plant growth and development. GRXs are small oxidoreductase enzymes that reduce disulfide bonds in target proteins. The interesting thing about class III GRXs, is that they are exclusively found in land plants, but most remain functionally uncharacterized. To help identify the biological function of these genes, we have created different transgenic plant lines that either overproduce class III glutaredoxins, or have knockout mutations in class III glutaredoxin genes. For instance, this summer I have been growing two knockout lines that have five GRX genes (AtGRXS3/4/5/7/8) inactivated and two overexpression lines that constitutively overexpresses AtGRXS8. We previously found that this cluster of class III GRXs are significantly upregulated by nitrogen in the soil, specifically in the form of nitrate. This is important because nitrogen is essential for plant growth and development and without nitrogen, plants can not produce DNA, RNA, proteins, or chlorophyll.
This summer, my main focus has been on extracting RNA from hydroponically grown transgenic plants with the end goal of sequencing the whole transcriptome using Next-Generation Sequencing (NGS). This will help identify how our GRXs influence patterns of gene expression in plants provided with nitrate as a nitrogen source. The start of the summer involved lots of tissue grinding, RNA extractions, gels for quality control, and cDNA synthesis. This week was especially exciting because we were finally able to start performing Real-Time PCR runs on all of the samples. From these results, we can identify differences in gene expression between our transgenic lines and the wildtype for some specific nitrate transporter genes in roots and shoot growth genes. These results will also help us identify the best samples to send for RNA sequencing. In addition to the molecular work that I have been doing, we have also been growing lots of plants on soil for phenotyping. This allows us to better understand how GRXs affect overall plant growth. For instance, our overexpression plants have significantly smaller shoots compared to the wildtype, which is why we hypothesize that these GRXs genes are negative regulators for shoot growth. As for phenotyping, I have been tracking flower production, weighing total shoot biomass, and imaging pavement cells. And within the next couple of weeks, we plan to complete total nitrate and protein content analyses to better understand how efficiently our transgenic plants store and utilize nitrogen. Overall this allows us to help characterize these class III GRXs and their role in plant growth and development.
At the end of the week, we were finally able to go tide pooling! Low tide this summer has been a little tricky to plan around, since it was always very early in the morning. That did not deter us though, and a group of us got up at 4:00 AM to venture out to the coast. We ending up going to Sunset Cliffs National Park and it was well worth waking up so early. This was probably one of the best tide pooling experiences I have had. We found so many neat creatures that I have never seen before. Immediately when we got there, we found an octopus hiding within the algae, which was a great start to our early tide pool adventure. After that, we also found an eel, a lobster, a beautiful red Hopkins’ rose nudibranch, a delicate brittle star, and a ginormous sea hare. And there were so many crabs, shrimps, and little isopods scurrying everywhere.
I am very grateful to be a part of such an incredible cohort this year. This summer has definitely been an amazing experience and I want to thank Dr. Sethuraman and Dr. Read for running an excellent program during these challenging times. Good luck with everyone's research project as we come to the home stretch.
Hello all! My name is Sandy Lastor (a.k.a San). I am an uprising junior at Bay Path University in Longmeadow Massachusetts. I, along with many of my colleagues, am majoring in biotechnology. I cannot express how extremely grateful I am to have the chance to travel across the country to be a part of such a wonderful program, such as the 2021 NSF REU summer program.
This summer I am a part of Dennis Kolosov's lab, where fun becomes an understatement! My six weeks being here has been such a blast. I have been able to learn new skills I never pictured myself working towards. I have met such beautiful souls that will forever mark a special place in my heart. In the lab more specifically, we are studying the epithelial physiology of caterpillars. I am inspecting the caterpillars means of secretion (i.e urination.) A great comparison would be the human kidney. This helps us learn about the organism and how much of a pest problem caterpillars really are to the economy. Caterpillars cost the U.S.A the equivalent to Argentina's yearly income in crop infestation (470 billion.) Our goal in short would be to decrease crop infestation and how we can reach our goal.
In order to study the kidney of said caterpillars, multiple rounds of troubleshooting has taken place. This week my partner and I have been dissecting multiple caterpillars in order to increase our speed to produce results in a more rapid fashion (more caterpillar tubules, more results.) With that in mind, our use for the dissection is to separate the cells into principle cells and secondary cells in order to see what exactly we are dealing with. Elastase is used as an enzyme to separate the tubules into their designated groups (principle/secondary.) Later, a percoll density gradient is used to separate principle cells from secondary cells. In addition to the separation, staining is used to differential viable cells from dead cells as well as principle from secondary.
Outside of the lab, tons of fun activities take place as well! I would like to say my lab and I go to the beach habitually and eat yummy foods during the week! Being here for the time I have been here I have learned so much about the west coast! I also had the chance to visit the San Diego Safari and explore all kinds of animal habitats!
Carlsbad State Beach
San Diego Safari
I cannot express how fortunate I am to work in a brilliant lab and be a part of an amazing cohort of scientists! This summer is definitely one to remember.
Hello everyone! I’m Antolette Kasler. I’m a senior at California State University San Marcos majoring in Biological Sciences with a concentration in Cellular and Molecular Biology. I’m very grateful to be part of the NSF funded REU Program at CSUSM for 2021. I’m part of the Jameson Lab where we determine the role of immune cells in wound repair in type 2 diabetes and the autoimmune disease Alopecia areata. I’m in the Alopecia areata team where we look at genes that could be a possible therapeutic target for patients with Alopecia areata.
I joined Dr. Jameson’s lab spring of last year. Since then, I’ve learned how to analyze data samples of bulk RNA sequences using Galaxy, analyze data using Ingenuity Pathway Analysis (IPA) and looking at RNA sequences in the single-cell level using R programming. Due to the pandemic, most of the research work I did for Jameson Lab was virtual. I was very excited to finally be back in lab to learn hands-on work for our research this summer! Though it has only been 5 weeks, I have learned so much already. I have been trained to stain epidermal skin and look and view my prepared samples under the immunofluorescence microscope. I’ve started my very first cell line (Yay!), been trained to use Cytek’s Flow Cytometer, and many more skills that I can add to my toolbox that I will be able to use in the future.
In addition, I had the honor along with a fellow summer scholar, Albert, to escort President Neufeldt in Science Hall 1 to show her the different research labs in our building. I was very impressed with how much she genuinely cares about everyone’s research. I also was able to talk with her about the importance of research lab opportunities and experiences for students. I emphasized not only the great work that could potentially impact other people’s lives but also the amount of knowledge that I will bring with me long after I move on with my educational goals.
I’m very lucky to be a part of the Jameson Lab and I could not ask for a better PI and lab mates. Dr. Jameson truly cares about each of us and always pushes us to be better researchers. She helps us think in a way where we fully understand our research and the purpose of everything that we do. I’m also very fond of all my lab mates. Since most of us were out of the lab due to the pandemic, we have been there for each other to guide and help each other to train and navigate around the lab. We are a team and we are a family in the Jameson Lab.
Lastly, I’m very glad to have met everyone in the 2021 REU cohort this year. It’s very nice to meet brilliant researchers from different universities and get to know each of their reasons behind their passion in research. We are halfway through our summer research program, but we still have a lot of science learn and a lot of fun to experience!
Hello! My name is Haven Johansen (they/them/theirs). I am a rising senior at Western Washington University in Bellingham, WA (go Vikings), where I study Biology and am creating a second major in Reproductive Health. I am thrilled to be part of the 2021 REU Summer Scholar cohort at CSUSM.
I’m writing to you from the Becket Lab, which is a microbial genomics/ecology lab focused on the spread of antibiotic resistance (AR) in coastal microbiomes. Most of my time is spent assisting Ciara Sanders -- a graduate student in our lab -- with her thesis, which examines the rate of horizontal gene transfer of AR elements in coastal microbiomes in response to variables that will shift with the changing climate. My fellow REU labmate Lakme and I collect, filter, and bullet (preserve) seawater samples three times a week; Ciara uses these bullets in an assay she is working on, and later Lakme and I will use some of the bullets to establish community profiles of our samples through 16s rRNA sequencing. We hope that these samples, in addition to the metadata we collect each sampling day, will create a useful baseline for Ciara and for future projects in the Becket Lab; because the coastal microbiome is so complex and variable, it is helpful to ground experiments by getting to know the communities we're working with and the conditions that surround them.
This week we sampled and filtered our seawater, collected metadata, helped Ciara with her assay, delved into the bioinformatics platform we’ll use to analyze our samples, learned to isolate DNA using a DNA/RNA miniprep kit, learned to use the lab’s Qubit, and plated and cultured E. coli in an antibiotic to compare growth between two stocks and to practice sterile lab techniques. The lab’s new sequencer was delivered and its arrival was met with much fanfare. We also attended several excellent lectures and observed other protocols performed in the lab. I’ve learned that by staying observant, asking lots of questions, and carrying a notebook everywhere, I absorb a huge amount of new information in the lab every day. I feel incredibly lucky to be surrounded by so many experts and up-and-coming scientists in this field who are passionate about their work and ingest (nearly) as much coffee on a daily basis as I do.
This week was also full of post-lab mischief. We hiked Double Peak, toured White Labs, stopped by the farmer’s market, and skated at Balboa Park.
This has been an excellent experience and I look forward to our remaining six weeks in the program.
I love science!
Hello! I am Simone Henry, a rising senior at Scripps College majoring in Organismal Biology. I am from Boston, Massachusetts, but I love the southern California climate and was excited to return this summer! Outside of school and lab, I enjoy hiking and sewing my own clothes.
Everyday has had new challenges and exciting opportunities to learn. I am working under Dr. Hristova and Dr. Read studying algae. Specifically cyanobacteria. The main experiment my lab partner, Briana Vega, and I are working on is testing how varied salinity affect the growth and toxicity of a cyanobacteria, Microcoleus. Our secondary project is to classify two cyanobacteria specimens. One specimen is similar in appearance to about eight genera, so we are looking into genetic details (using gene sequencing) to give confidence to which specific genus it belongs. For the second specimen, we are working on sequencing its genome, and we have guesses to which genus it belongs because of the morphological work by Dr. Hristova. It is exciting to participate on the morphological and molecular understanding of our samples. I am fairly new to molecular lab work so this has been an incredible opportunity to learn on-the-spot theoretical and practical application.
After spending the first two weeks in the lab, we headed to Escondido Creek to collect some algal samples and get to know the natural location of the algae that we are spending these 10 weeks studying.
On Tuesday, Briana and I completed a library prep for the Chamaesiphon-similar specimen. Library prep essentially allows us to have our isolated DNA ready to be sequenced, in hopes to genetically ID our specimen. On Wednesday we tested the quantity of DNA within our library sample. On Thursday Dr. Hristova gave us a presentation summarizing what we currently know, what we don't yet know, and how we can hopefully find out the things we don't know about the unidentified specimens. Later in the day Dr. Read gave us a crash course in the program Galaxy and helped us lay out the steps we will need to take in analysis to be able to align sequences of conserved genes of the multiple genera to find which is the most similar to our sample (the first unidentified sample).
Friday, Dr. Hristova took us, with our lab technician Nate, out to La Jolla to get out of the lab a bit, as well as meet a couple of her past colleagues. We explored the Birch Aquarium and walked around the beach (picture of an very striking organism called a Velella, or a By-the-wind sailor, that we found on the beach). After some time finding anemones, crabs and isopods in the rocks on the beach, we met up with Dr. Hristova's past lab technician who is currently working at Scripps Institute and she gave us a tour of their pier (the first three pictures). It was such an honor to be able to get access to the pier and to see oceanography in the works! In the evening, the five of us met with Dr. Hristova's colleague for dinner and she gave Briana and I some invaluable tips for figuring out the process of creating a phylogenetic tree for our sample. The last picture below is the six of us out to dinner!
Here are some photos from today:
It has been an incredible first three weeks and the opportunities have been amazing. Massive thank you to Dr. Read, Dr. Hristova, Nate Kristan, and Briana Vega! I look forward to the rest of the summer!
Hi there, my name is Hannah Hausknecht-Buss! I'm from Phoenix, Arizona, but I am a biology and Spanish major currently going into my junior year at the University of San Diego. In my free time, I enjoy playing the flute and going to the beach to relax! Week 2 went by quickly, but I had tons of fun and learned so many new things. It's an understatement to say that I am ecstatic to see what the remaining time here at the CSUSM NSF REU program has to offer!
This summer, I am participating in Dennis Kolosov's lab, where we are performing research on mosquitoes and caterpillars! More specifically, I am investigating the epithelial physiology and transcriptomic response of "yellow fever" (Aedes aegypti) mosquito larvae and adults and the prevalence of voltage gated calcium ion channels present in the osmoregulatory organs (the anal papillae and Malpighian tubules). We will be testing the presence of these channels through rapid changes in salinity and blood meal feeding and I have my fingers crossed that we discover something interesting, as there isn't any pre-existing studies that are similar to what we are delving into!
To start off the week, we continued dissecting mosquito larvae so we could collect tissues (they are unbelievably small!) and prepare for an RNA extraction! We then went to check up on the "homies" (our insects) to do our weekly housekeeping and make sure they are happy and healthy. For the next couple of days, we attended a talk by Dr. Read and Dr. Sethuraman on assembling the genome and performing BlastX as well as continuing to learn UNIX coding. We also received a special talk on genomics from Dr. Mark Chaisson from USC! By the end of the week, I started dissecting adult mosquitoes, and even developed a new method for how to catch them in their cage (they are even harder to dissect than larvae, surprisingly!). Lastly, we also designed our own primers to use in PCR and created a seawater solution to use for testing rapid salinity response in our larvae.
There was a ton to do outside of lab as well! My lab group and I, as well as some fellow REU friends, spent a lot of dinners together at places like Manna Korean BBQ and Burger Bench (I highly recommend <3). Our program also met up for a Taco Thursday and I always love going to these big group events so I can see and meet new people from other lab groups! To finish off our second week, some of us headed down to La Jolla and Downtown SD to see some sea lions and walk around Balboa Park!
I am so blessed and grateful to be here! I have made some amazing new friends and everyone has been so kind. This summer will definitely be one for the books!
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!!