USC Dana and David Dornsife College of Letters, Arts & Sciences > Blog

July 23, 2014

Why I love my USC-WIES REU internship

Filed under: Wrigley Institute — Jessica Dutton @ 8:46 am

USC Wrigley Institutewrigley.usc.edu

By: Christine Luu

I had always heard that Research Experience for Undergraduates (REU) programs are highly competitive and only meant for college juniors and seniors. Therefore, as a freshman I felt that my chances of getting accepted to an REU program were fairly slim. Yet, during this past winter break, I applied to various summer programs anyway in order to continue conducting research, which I have become passionate about as an undergrad at Dartmouth. Even though I just finished my first year of college, I wanted to have a productive yet enjoyable summer, with an ulterior motive of increasing my self-acquired professional network—I say self-acquired because as a first-generation college student, I do not have an already family-established network of professionals to talk to. Luckily enough, by late March, my wish came true when I was accepted to the 2014 USC WIES REU program to work in Dr. David Caron’s lab!

The REU is an intensive program that consists of conducting an independent research project, and boy is it intensive! During Week 1, my mentor, Alle Lie, and I both came up with a summer project studying aquatic microorganisms. I had to learn all of the procedures over the course of only 3 days before beginning my experiments. It was definitely overwhelming, and I wasn’t sure that I would be able to complete the tasks efficiently and accordingly. I didn’t want to disappoint my mentors or myself though! Thus, through constant communication and determination, I now feel confident in my abilities to conduct independent research and carry out the experiments for my summer project. I am now largely self-sufficient and carry out most of the project myself.

In the lab making measurements to estimate growth rates of Ochromonas BG-1.

My research consists of determining how pH changes in the water affect the photosynthetic growth rate of a mixotrophic protist – Ochromonas strain BG-1 – and how prey and light availability affect the growth rate of another mixotrophic protist – Ochromonas strain CCMP-1393. These single celled organisms are important members of aquatic ecosystems, and their ability to grow and reproduce rapidly under favorable conditions allows some protists to reach high abundances in a relatively short amount of time, forming ‘blooms’ and impacting the local food web.

A preserved sample of BG-1 clumped around heat-killed bacteria (prey) under 20X magnification

The skills that I have gained and will gain through this project will definitely prove to be an integral part to my future research projects. I think that by participating in this REU right after my freshman year, it will help me decide if research is something that I see myself doing as a career and will also help me hone in on my research interests, which are still a little unclear as of now. The REU is a worthwhile experience—especially because it provides a slight glimpse of what graduate school would be like (as I have been told by several people).

Aside from my research, the Wrigley Institute’s location on Catalina Island is simply gorgeous. The sunsets always seem to leave me in awe.

Catching a Catalina sunset

The preserved land of Catalina Island gives me an amplified appreciation of nature, especially the bioluminescence and stars that shine so brightly off of each other at night. I would also add that the people that I have met here are just as amazing as the location of my summer work/home.

The REU coordinators have scheduled various events for us REUs to learn about each other research projects, and make sure we have the opportunity to network with other faculty, mentors and students. As a first generation college student, it’s rewarding in that I am able to learn about fields of research I would not have learned about if I were not here. In addition, these events allow me to meet more work/life mentors who might help open up more opportunities for me.

REU Class of 2014

For the students who are interested in research that are reading this blog, my advice for you is to step out of your comfort zone and meet as many people as you can and continue to show passion for whatever topic of research you are interested in. If opportunity doesn’t knock, you have to build a door and find the opportunities yourself, like going out and applying for REU programs. Even when chances seem very slim, take a shot and apply anyways, like I did. In my opinion, the undergraduate years are about exploring and honing in on your passions, and the only way to do so is through programs like the REU.

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July 21, 2014

Sex in the sea: Uncover the mating behavior of Giant Sea Bass

Filed under: Wrigley Institute — Jessica Dutton @ 10:01 am

USC Wrigley Institutewrigley.usc.edu

By: JR (Brian) Clark

As a Wrigley Institute Fellow this summer, my graduate research focuses on the reproductive behavior of the giant sea bass. My project has two parts: 1) describing their courting and spawning behaviors and 2) identifying their residency at spawning sites at Catalina Island.

Giant Sea Bass

The giant sea bass, Stereolepis gigas, is a part of the wreckfish family and endemic to the northeast Pacific. It is the only megacarnivore found in the southern California kelp forest, which means that these fish serve an important role in regulating and sustaining biodiversity within their ecosystem.

Unfortunately, giant sea bass are listed as critically endangered on the IUCN Red List due to extreme fishing pressure during the early 1900’s. Although sightings have become more common, we believe their numbers still have not returned to historic levels. Their courting and spawning behaviors have also not been characterized. This data, coupled with knowing how many there are and how long they stay in their spawning aggregations (groups), are important to help make proper stock assessments and predictions about their recovery.

Historic photo of sea bass fishermen

How do we study this? Along with my dive buddy Parker House (another 2014 Wrigley Institute Fellow), we are running transects using underwater scooters equipped with lasers and a camera. This allows us to accurately measure the size and count the number of giants we see on each dive at the spawning site.

JR and Parker in the field with an underwater scooter

We are also using long-term hydrophones to measure the amount of sound that they produce. This can be used as a non-invasion alternative to tagging, which also allows us to estimate their density over long periods of time.

Setting an underwater hydrophone

During dives when we come upon aggregations of giant sea bass, we take video recordings of any behavior they are exhibiting and later analyze the videos to quantify the behaviors seen.

Giant sea bass aggregation

With this study we hope to promote awareness and understand the basic biology of giant sea bass, as well as develop a non-invasive way to monitor and identify their populations.

Up close and personal with the study organism!

JR is a 2014 Wrigley Institute Summer Fellow and a graduate student at California State University, Northridge, in the Department of Biology.

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July 17, 2014

Notes from the Field – REU Program

Filed under: Wrigley Institute — Jessica Dutton @ 8:25 am

USC Wrigley Institutewrigley.usc.edu

By Yaamini Venkataraman

Week 5 of the Research Experience for Undergraduates program – how time flies. Gone are the days when us REUs would wonder about when the work would begin. Not only has the work begun, but it has also flung us into a frenzy of strict time schedules and odd sleep schedules, hours upon hours spent in the lab and of course, island fever.

My project and its scheduling has me on a short leash. I’m investigating the effects of different amounts of shade on copepods, or small marine invertebrates (think Plankton from Spongebob).

Copepod

After this week, I’ll be exposing these organisms to copper toxins and seeing if the different levels of shade change their copper tolerance. Even though I can theoretically control the amount of shade these organisms are exposed to, I can’t really control any of the variables I’m measuring — mortality, water level, temperature, salinity, pH, UV radiation and Photosynthetically Active Radiation vary throughout the day.

What does this mean for me? I have to measure these variables three times a day: 6 a.m., 1 p.m. and 6 p.m. It’s definitely not a cake walk, as essentially each variable needs to be measured for all 120 replicates (each isolated copepod), and for the large buckets of water (the simulated tidepools), they are in. Thanks to my sampling times, I get 4-5 hours of sun a day, and I have never been tanner.

But my experiment has shown me that research really is hard work. Seems obvious enough, but even the littlest thing like taking pH measurements takes up time, which can be hard to gauge if you’ve never done it before. When I first sent him my experimental protocol, outlining the tasks I would accomplish during each sampling time, my mentor Patrick made some astute observations about my workload– reminding me that if you take on too much, “you will die.” I didn’t believe him until I found myself tired after my two hours collecting data.

Sampling in the field

Although I joke around with the rest of the REUs about the buckets that have become the bane of my existence, the piles of data sheets and positive feedback from my colleagues suggest otherwise. Because when you have the opportunity to see the sunrise and sunset every single day while working on something you love, the long hours of labor are much more worth it.

Yaamini Venkataraman is an REU student and a rising junior at the University of California, San Diego, working with the USC Edmands lab studying the effects of shading on copepod mortality.

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July 15, 2014

Tracking Leopard Sharks with Underwater Vehicles

Filed under: Wrigley Institute — Jessica Dutton @ 8:00 am

USC Wrigley Institutewrigley.usc.edu

By Yukun Lin

As a Wrigley Marine Science Center Summer Fellow, my project this summer is to track leopard sharks with AUVs (Autonomous Underwater Vehicles) in Big Fisherman Cove on Catalina island.

Why track leopard sharks? They are model systems for Elasmobranchii (a subclass of fish that includes sharks), and by studying and understanding the behavior of leopard sharks, we can make inferences about other species of sharks.

To track the leopard sharks, we first tag them with an acoustic tag, which sends out a “ping” every 2 seconds. These pings are picked up by stereo hydrophones mounted below our AUVs, and are used to determine the location of the tagged shark. With the location of the sharks known, the AUV is able to follow the shark autonomously. Of course, we don’t want to end up chasing the shark around, so we program the AUVs to always keep a standoff distance from the tagged shark.

This summer, we will also be tagging leopard sharks with a new tag that clamps onto the fins of the shark. In addition to an acoustic pinger, the tag will also have a video camera, a MARG (Magnetic Angular Rate and Gravitational) sensor, and a VHF transmitter. The tags are programmed to release from the shark after a certain period of time by unclamping, allowing us to recover the tag to download data from it and also to reuse it.

The technologies that allow marine biologists to tag and track sharks were only developed in the last few decades; we hope to further develop these technologies to help marine biologists gain an even better understanding of the behavior of these animals.

 Yukun is a student at Harvey Mudd College in the Department of Computer Science, working in collaboration with Cal State University Long Beach’s Shark Lab.

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July 11, 2014

The Study of Life and Death

Filed under: Wrigley Institute — Jessica Dutton @ 8:47 am

USC Wrigley Institutewrigley.usc.edu

By Patrick Sun

“In this world nothing can be said to be certain, except death and taxes.” – Benjamin Franklin

I’m certain that somewhere, I have an economist or tax lawyer counterpart doing great work studying taxes. But as a biologist, I have the opportunity to study one of life’s great quandaries: life and death.

As a Wrigley Marine Science Center Summer Graduate Fellow, I’ve been granted the opportunity to do graduate research at the Catalina tide pools behind the Wrigley Marine Science Center this summer, studying natural fluctuations in the pools. An interesting observation my team and I have made is that these tide pools often dry up, and in the process become very unpleasant places to live. Eventually most of their inhabitants must either leave (few can) or die (most do). For perspective, one of these pools in the process of drying out has reached salinity levels 300% above normal seawater. My eyes already sting when seawater gets in them. I’m fairly certain my eyes would shrivel up and fall out (only slightly exaggerating) if they came in contact with this pool of water.

A tide pool drying out, with salinities +100 psu. White residue around the edges is salt. Small crustaceans know as copepods continue to be found alive in these pools despite the extreme environments.

Yet life continues in this harsh environment, in the form of small crustaceans called copepods. My research team and I are interested in understanding how life can continue and how long it will persist. In other terms, we are studying the process of local extinction. We also plan to document how fast life returns once these pools are refilled with seawater during the wetter seasons. In a sense, we are studying the life cycle of the tide pool.

All this talk of life and death may makes the natural world seem cold and calculating. But I believe there is a lot of love in nature (evident by this heart shaped cactus!).

Heart shaped cactus above campus

I also believe as we study the world around us, it is studying us. The other day, I had an ambassador from Bird Island visit me and examine my scientific equipment. I’m certain it was just a safety inspection. I hope I passed.

A cormorant examining our field flag.

Thanks for reading! If you have any question please let me know at patricys@usc.edu. I encourage you to continue your own exploration of life’s beautiful intricacies.

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July 2, 2014

A Day in the Life – REU Research on Catalina

Filed under: Wrigley Institute — Jessica Dutton @ 8:30 am

USC Wrigley Institutewrigley.usc.edu

By Nick Fisk

I don’t think I’ll ever forget the first time I looked out at the island from the labs at the Wrigley Institute.

Two Harbors, Catalina

Who could, with a view like this?

So far, life here at WIES in the Research Experience for Undergraduates (REU) program is exceeding all my expectations. From the science to exploring Catalina, I’m having a BLAST (get it? genetics humor…) at every turn. My graduate mentor, Rohan Sachdeva with Dr. John Heidelberg‘s lab, is who I have spent the most time with since arriving on the island. It seems that the folks in charge out here did a good job pairing people with mentors and with projects, because everyone is so passionate about their research. The same holds true for me.

I guess now is as good as time as any to mention that my project is a bit different than my peers. The goal of my project is to identify and describe the activity of deep sea bacteria and archaea communities, using a metagenomic and metatranscriptomic framework. What this boils down to is a little bit of lab work (to isolate DNA and RNA) and a whole lot of computer work to get a sort of snapshot of the deep sea micro-critters. To me, this is one of the most exciting things I could be doing. It has applications in a wide range of fields, from conservation to climate change, from human health to aquaculture microbiomes, and from bioremediation to biodiversity. Of course, it hasn’t been without its hiccups (after all, science seldom goes smoothly!) but even when I mess up, I’m learning and I’m enjoying myself. It helps that my mentor is such a chill dude, too, and is always patient with me.

Deep sea microorganisms

Aren’t they just the cutest?

Of course, not all my time here has been spent on my project. Since my research doesn’t really involve any field work, my fellow REUs have invited me to help out with their various projects. I’ve gone to the beach to help collect mussels. I’ve gone to tide pools to release extra copepods. The geospatial team has invited me to go with them to geotag leopard sharks. I didn’t even have an idea of how any of these creatures even looked before arriving here. And for the record, leopard sharks are pretty darn cool. Beyond helping each other with our research projects, we find other ways to enjoy ourselves. After all, this IS the Catalina Island. We’ve gone kayaking and hiking, snorkeling and swimming. Perhaps my favorite thing is the REU ping pong tournament we have going on.

REU Ping Pong bracket

Winner plays REU Coordinator Dr. Diane Kim in a ping pong battle to the death!

I honestly thought I was going to be a bit of a loner here. Everyone’s project seemed so different than mine, and then there’s the fact that we came here from all over the nation. It probably doesn’t help that I am a bit of an oddball (as is the stereotype for bioinformatics/computer people). It makes me incredibly happy to realize that my fellow REUs both accept and embrace it. There is nothing quite like heading back from the lab after a long day of science to a group of friends like this.

REU Group

REU group trip to Hollywood

I guess science helps bring people together after all.

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June 25, 2014

A Day in the Life – REU Orientation Week

Filed under: Wrigley Institute — Jessica Dutton @ 11:33 am

USC Wrigley Institutewrigley.usc.edu

By Yaamini Venkataraman

I never fully understood the phrase “hit the ground running” until I became an REU student at the Wrigley Institute for Environmental Studies at the University of Southern California.

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REU orientation week on the USC campus

Even before I came to USC last week for our first week of the program, I found myself chatting with my mentors, Dr. Suzanne Edmands and graduate student Patrick Sun, over email in May. There were so many things that had to be decided before the program started — my project and focus for the eight-week program, how I would go about my research project and most importantly, what I would do our first week at USC. Everyone around me, from the Undergraduate Program Director Diane Kim to my mentors and another undergraduate student who had been part of the program last year, told me that the first week was critically intense.

Stuck in the middle of the quarter system with midterms, papers and final exams looming around the corner, I obviously didn’t believe them. What was so intense about orientation to research and planning a research project? Apparently everything. After the second day of the program, all eleven of us with scientific projects were running around with our mentors, learning lab techniques and collecting all of the materials we needed for our trip to the island. I had the additional challenge of completing all of my projects with Patrick by Wednesday, the third day, because he was leaving for a conference and Dr. Edmands was already out.

Strong communication is key, especially between an REU student and mentor. But since my mentor and I were not able to talk for long, problems that could have been solved with a 10 minute face-to-face conversation expanded into multiple email exchanges. This was especially the case when I started writing down my experimental methods in preparation for a presentation of my project proposal at the end of the second week. In these situations, I learned to organize the content of my emails, adding bulleted lists to aid my mentors in understanding my questions.

But the first week wasn’t all work. We got to listen to talks on interesting issues such as that by Dave Caron on harmful algal blooms, and go on a research cruise. Although the motion of the ocean was a true test of the strength of our stomachs and willpower, all us were able to learn about oceanographic equipment that measures different variables of interest like depth and light, while also getting to extract plankton from the water and view it under a microscope.

photo

Marine Microbial Ecology lecture

REU training cruise

Oceanography training cruise in the Los Angeles channel

And not everything we did was REU-related — we also took advantage of being in Los Angeles. Some of us took excursions to see Griffith Observatory at night, make a late-night In-n-Out run for the benefit of our out-of-state friends, explore the Natural History Museum and California Science Center, got out to see Hollywood and stumbled upon the Los Angeles Cultural Festival, and even went as far as the Aquarium of the Pacific in Long Beach and the Santa Monica Pier.

So although we hit the ground running, after a while we did not feel the strain on our legs and embraced the movement. As I write this, I’m enjoying the last sunlight of our first day on Catalina Island, home for the next six weeks! Personally, I feel like I’m jogging at a little bit of a slower pace. Some of it’s the island, but I’m pretty sure that it’s mainly because we really got working that first week. So yeah, we hit the ground running, but it was all in preparation for a successful research project and poster presentation. Here’s to the next seven weeks of the program, and of course that first week that got us ready for the race to the finish.

Yaamini Venkataraman is an REU student and a rising junior at the University of California, San Diego. She will be working in the USC Edmands lab with a graduate student mentor the rest of the summer, studying the effects of shading on copepod mortality.

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June 23, 2014

New Wrigley Institute Summer Blog!

Filed under: Wrigley Institute — Jessica Dutton @ 2:35 pm

USC Wrigley Institutewrigley.usc.edu

WMSC Sign

Welcome to the USC Wrigley Institute for Environmental Studies

Welcome to our new Wrigley Institute Summer Student Blog! Here, we will feature “A Day in The Life” of some of the incredible graduate and undergraduate students conducting research with us this summer. 2014 is going to be busy.

For example, we are hosting 18 stellar Wrigley Marine Science Center Fellows at Catalina Island this year. These grad students come from USC and universities across the West Coast to study a fantastic variety of environmental topics at the island. Included are two recipients of our newest fellowship: the Vicky Bertics Fellowship, which supports graduate research in coastal marine biogeochemistry.

Back on the mainland, we welcome 4 new Norma and Jerol Sonosky Fellows. These grad students from across USC’s Dornsife College all focus on research at the interface of humans and the environment. Through their studies, we are excited to learn more about society’s relationship with the natural world and sustainable paths for the future. Our International GeoBiology grads are in full swing too, zipping across research sites in California for the next several weeks and learning about the critical co-evolution of the Earth and it’s living systems.

We are also thrilled to welcome a new cohort of REU (Research Experiences for Undergraduates) students to the island. These 11 undergrads from across the country will spend 8 weeks learning about Coastal Sustainability research with USC mentors. An animation student from USC’s Division of Animation and Digital Arts will intern with the program, collaborating with science teams to find innovative new ways to communicate their research.

As you can see, the Wrigley Institute will be abuzz with activity this summer. Join us on this blog over the next few months as we introduce the students and watch their research projects unfold. Let the summer season begin!

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