Biology Highlights 2020, Harvey Mudd College by Harvey Mudd College

B OLOGY HIGHLIGHTS 2020

Update from the Department Chair

Professor of Biology and Department Chair Eliot Bush with summer research students.

Dear Alumni, Parents and Friends of HMC Biology, I’m very happy to share our first Biology Department newsletter with you. I believe it’s been an eventful year. Among our faculty, we’ve had a number of grants funded, cumulatively totaling more than $1 million dollars (details on page 2). In addition, two of my departmental colleagues, Matina Donaldson-Matasci and Jae Hur, received tenure and will be promoted to associate professor. Congratulations and happy sabbatical to both! Our Class of 2019 graduates have gone off to pursue graduate degrees and jobs in various biology-related fields, including teaching and research. Over the course of the past year, we

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had a substantial number of students doing research in biology—45 different student researchers working either in the summer or during the academic year. One highlight I’m thrilled to share is that Emily Shimizu ’20 was awarded an Astronaut Scholarship for the 2019–2020 academic year. And of course, the COVID-19 pandemic has impacted our department greatly. Along with the rest of the College, the biology department has adapted to online classes (including labs!). Faculty have been working hard to deliver the curriculum under challenging circumstances, and I am confident in the work they’ve done. One positive impact of the pandemic is that it’s easy to connect COVID-19 to concepts we teach (like infectious disease and evolution in Bio 52), and it helps the general public

appreciate the importance of biology. We definitely look forward to having the students back on campus. Finally, thanks to all of our alumni who have shared updates with us on what they’ve been up to since they left Mudd. I enjoyed reading them, both from my own former students and from those who graduated before my time. Eliot C. Bush Chair, Department of Biology bush@hmc.edu

National Science Foundation Funds HMC Biology Research Ant Networks Matina DonaldsonMatasci, along with

collaborators at the University of York in England and George Washington University, received an NSF grant for the project, “Dynamic ant networks: How environmental constraints and ecological context shape resource transport systems.” The project aims to develop a general theory for biological networks that DonaldsonMatasci says “will emphasize how network

structure and function dynamically influence one another, and how ecological context shapes this process. Ants are a good system to study transport networks. They carry things around, food and brood, between the various nests. You can think of the nests like subway stations, and the goal is to make a system that is really good at transporting stuff/people between stations, without being too costly to maintain.” Donaldson-Matasci oversees the laboratory-experiment phase of the research. The field work will be done in the Florida Keys (led by collaborator Scott Powell, at George Washington University), where the ants are a

native species, and computational modeling will be done at the University of York, led by collaborator Elva Robinson. During the four-year project, Harvey Mudd students have opportunities to do field work in Florida, computational modeling in England and work in Donaldson-Matasci’s lab on campus. For more details on the project and to see more photos, follow Donaldson-Matasci on Twitter (@MatinaDonaldson) and read updates on the HMC Bee Lab Blog. hmcbee.blogspot.com

Evolutionary History Ran LibeskindHadas, R. Michael

Shanahan Professor of Computer Science, was awarded an NSF grant of $498,458 to support his research focusing on phylogenetic tree reconciliation and the design, analysis and empirical evaluation of algorithms leading to transformative new tools for biologists. Libeskind-Hadas studies algorithmic issues in computational biology—in particular, the problem of phylogenetic tree reconciliation,

a computational method used to reconstruct the evolutionary histories of related pairs of organisms by hypothesizing the evolutionary events that explain their incongruence. The reconciliation is a mapping of one tree onto the other that seeks to explain the evolutionary history of the pair with respect to a biological model. Funding will support six research students a year for three years, beginning summer 2020, as well as travel to conferences. It will also fund the purchase of a high-performance computer to test the algorithms and perform computational experiments. The project, “Finding Best Representative

Phylogenetic Tree Reconciliations,” seeks to develop efficient algorithms for systematically identifying a small set of the most representative MPRs. Results will be extended to deal with the larger solution spaces induced by a range of event costs and for non-binary trees. This will allow development of new software for life scientists and the ability to generalize these results to event models beyond the duplication-transfer-loss model. Libeskind-Hadas performed precursory research for this project in a previous NSFfunded project, “RUI: Algorithms and Tools for Phylogenetic Tree Reconciliation.”

the stony corals, but little is understood about these impacts on the soft corals because we don’t know how many species there are or how to tell them apart.” This project, “RUI: NSF-BSF: PurSUiT: The Indo-Pacific zooxanthellate octocorals: An integrated approach to species delimitation, phylogenetics and biogeography,” has three objectives: Combine molecular genetic analyses with high-resolution microscopy to discriminate species of soft corals collected from throughout the Indo-Pacific; examine and re-describe historical specimens housed in major museum collections to facilitate the correct assignment of names to those species; and compile the information within a publicly accessible web portal that will allow users worldwide to generate species checklists and interactive keys for identifying reef-dwelling soft corals.

Quattrini joined the staff at the Smithsonian National Museum of Natural History, home to the world’s largest collection of coral specimens. The grant will support her work at the Smithsonian as well as provide opportunities for HMC students to join her for summer research. Over four years, the project will support three summer research positions annually (including one position earmarked for a graduate of the College’s Upward Bound program) and additional student positions during each academic year. The College will also benefit from a related NSF grant to the University of Florida, which distributed a subaward to McFadden for collaboration on a large-scale biodiversity survey of the coast of Oman. The subaward will fund one summer research position at HMC annually for three years.

Coral Reefs Harvey Mudd College was awarded an NSF grant of $839,060 to support biology professor Catherine McFadden, former HMC postdoctoral researcher Andrea Quattrini and their colleague Tel Aviv University biology professor Yehuda Benayahu in continuing their research, which addresses the issue of difficulty of distinguishing and correctly identifying octocoral species. “Most of the attention that’s been paid to coral reefs has been on stony corals, the reef builders,” says McFadden. “I work on the soft corals, which are often 50% or more of what’s living on the reefs and really important as habitat for other organisms. They are being affected by the same climate change events as

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McFadden Shares in Coral Discovery

Cathy McFadden and expedition chief scientist Erik Cordes inside the deep-sea submersible Alvin.

During her first-ever submersible dive on Aug. 23, 2018, coral reef expert and Harvey Mudd College biologist Catherine McFadden experienced a monumental moment. “We thought there might be some coral at the site, but I was expecting a fairly barren landscape of mud and rock with just some small, isolated coral colonies here and there.” Instead, McFadden and the expedition’s chief scientist Erik Cordes “landed on a massive coral reef formed by a mix of dead coral rubble and large, dense stands of living coral,” she says. The unprecedented find, approximately 160 miles off the coast of Charleston, South Carolina, revealed extensive, previously unconfirmed reefs composed of the deep-sea stony coral, Lophelia pertusa. Researchers are using the deep-sea submersible Alvin to visit previously unexplored locations, including canyons, gas seeps and coral ecosystems, in order to identify and ultimately protect sensitive habitats. During nearly eight hours in the submersible, McFadden, Cordes and pilot Bruce Strickrott viewed and sampled different coral species, including Enallopsammia, Madrepora, and octocorals (plexaurids, primnoids, Anthomastus). Lophelia was by far the most sampled coral. The Deep Search team estimates that there are approximately 85 linear miles of discontinuous Lophelia reef off the U.S. East Coast. As the Lophelia grows and dies

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over many hundreds of years, new Lophelia grows atop the old skeletons, forming 80- to 100-meter-high mound structures that stretch further than scientists had imagined. “It was really exciting to see so much coral (and no mud!),” says McFadden, the Vivian and D. Kenneth Baker Professor of Biology at Harvey Mudd College. “But the magnitude of the find didn’t really sink in until several hours into the dive when we realized we were still traveling over coral. In the course of six hours, we moved about 1.5 km and never left this reef.” “While Lophelia reefs are known to occur off the coasts of Florida to North Carolina at depths averaging 350-600 meters, the presence of these reefs at deeper depths (greater than 700 meters) and farther offshore make these newly discovered reefs unique, potentially connecting deep-sea coral habitats from the south to the north,” says biologist and NOAA web coordinator Caitlin Adams in a National Oceanic and Atmospheric Administration news release. “Connected reefs can be more resilient to environmental change, thus this extensive reef complex might help to improve the overall health of deep-sea corals off the East Coast and in the larger Atlantic ecosystem.” McFadden’s research focuses on the systematics and taxonomy of octocorals. For two weeks in August as a member of the Deep Search science team aboard R/V Atlantis, a 274-foot research vessel owned by the U.S. Navy and operated by the Woods Hole

Oceanographic Institute, McFadden collected and preserved octocorals, mussels and their associated species for molecular systematic and population genetic studies. “It’s pretty mind-blowing to know that the existence of this huge biological structure was completely unknown until now and to have been one of the first humans to visit it,” says McFadden of the Lophelia reef discovery. With funding from the National Science Foundation, McFadden’s research group at Harvey Mudd is developing next-generation sequencing-based target-enrichment methods to study phylogenetic relationships and skeletal evolution in anthozoan cnidarians (corals and sea anemones). McFadden is particularly interested in understanding species boundaries and the generation of biodiversity in shallowwater soft corals, and in recent years has focused on the coral reef communities of the South China Sea. View the blog of the Deep Search 2018 expedition by visiting: bit.ly/2V88zx1

Faculty Promotion Promotions and tenure appointments for HMC faculty were approved during the May 2019 meeting of the HMC Board of Trustees. Eliot Bush, professor and chair of the department of biology, was promoted to the rank of full professor. Bush uses computational methods to study evolution, covering a range of topics from sequence analysis to modeling. His work includes modeling the evolution of metabolism, characterizing DNA methylation patterns in insects, developing algorithms for studying substitution bias in DNA and analyzing a 30-million-year-old primate fossil. He is co-author of the book Computing for Biologists: Python Programming and Principles. His software program, xenoGI, helps researchers reconstruct the history of genomic island insertions in clades of closely related microbes.

ASF/EMILY JOURDAN

Shimizu Named Astronaut Scholar organometallic and supramolecular chemistry at HMC, the University of South Carolina, the University of Rhode Island and The Scripps Research Institute,” says Vosburg. During summer 2019, Shimizu interned at the Scripps Research Institute in Florida. Her work in the Renata Lab focused on the chemoenzymatic synthesis of peptides (molecules) gramillin C and fellutamide A. Using enzymes in this synthesis makes the process more step-efficient, says Shimizu.

Astronaut Curt Brown presents Emily Shimizu ’20 with the Astronaut Scholar Award.

Harvey Mudd College joint chemistry and biology major Emily Shimizu ’20 has been named an Astronaut Scholar for the 2019–2020 academic year by the Astronaut Scholarship Foundation. She is the 26th Harvey Mudd student to receive the honor, which includes a scholarship prize of up to $10,000 and opportunities for professional development and mentoring. “Besides the scholarship itself, I am particularly excited about the mentoring program,” Shimizu says. “The Astronaut Scholarship Foundation is a very encouraging and supportive community of scholars, who are already helping to advise me this semester as I apply to graduate school to pursue a PhD in chemistry.” Shimizu says her ASF mentor has given her guidance on graduate schools and has expanded her knowledge of career paths postgraduate school. While attending the three-day Astronaut Scholarship Foundation Innovators Weekend in August, Shimizu had the opportunity to meet other astronaut scholars and attend the Innovators Gala, which featured Apollo 16 moonwalker Charlie Duke as keynote speaker. Scholars visited the National Institutes of Health in Washington, D.C., and attended a National Science Foundation panel on future research funding opportunities, including the Graduate Research Fellowship Program. Shimizu was nominated for the Astronaut

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Scholarship by David Vosburg, professor of chemistry, who has worked with her on numerous projects during her time in his research group at HMC. Among their research projects, Vosburg has worked with Shimizu on creating a onestep process for the anesthetic lidocaine. The procedure is commonly used in dentistry

When Shimizu isn’t in the lab, she’s on the dance floor. As the president of the Claremont Colleges Ballet Company, she teaches weekly ballet classes, organizes trips to see ballet performances and performs with the club. She helped organize the annual Fast Forward student choreography showcase held in May 2019. The Astronaut Scholarship Foundation was created to ensure that the United States

am particularly excited about the mentoring program. “ IThe Astronaut Scholarship Foundation is a very encouraging and supportive community of scholars, who are already helping to advise me this semester as I apply to graduate school to pursue a PhD in chemistry. –Emily Shimizu ’20

and was featured in the fall 2019 Organic II Laboratory course at HMC. The project is being further developed by collaborators at the University of Guanajuato in Mexico, where Vosburg spent his recent sabbatical working with colleagues on developing environmentally friendly methods of producing new molecules for medicinal, agrochemical, optical and educational applications. “Emily is an enthusiastic and creative problem-solver who has significant research experience in diverse areas of organic,

would maintain its leadership in science and technology by supporting some of the very best science, technology, engineering and math college students. The Astronaut Scholarship is the largest, merit-based monetary award given in the nation to 50 science and engineering undergraduate students from colleges and universities across the country. Harvey Mudd College is one of 27 institutions—and the only non-doctorate-granting school—selected by the foundation to participate in the program.

Harvey Mudd Chem-Bio Majors Earn Best Poster Award

Lakshmi Batachari ’18 and Chris Doering ’19

Joint chemistry and biology majors Lakshmi Batachari ’18 and Chris Doering ’19 presented results of their yearlong study on how gene expression in E. coli unfolds under stress conditions, earning them Best Undergraduate Poster award at the Molecular Genetics of Bacteria and Phages meeting, the longestrunning series of molecular biology meetings. Doering, whose academic interests include molecular genetics, synthetic biology and microbiology, explains their work: “In E. coli, stress response is largely controlled by the transcription factor RpoS, a protein responsible for turning on gene expression,” he says. “Depending on the type of stress, E. coli will activate RpoS, and subsequently gene expression, to differing degrees. Our research looked into how genes respond to RpoS, what patterns of expression we see and what causes those patterns to occur. Previous work in the lab showed that some genes respond very quickly to just a small amount of RpoS (sensitive response)

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while others required large amounts to get any expression (insensitive response). Our work found that other transcription factors working with RpoS are responsible for the different types of response, and in a few cases, we identified the exact culprit.” Batachari, who now works as a lab technician at the University of California, San Diego and intends to pursue a PhD in microbiology or a related field, and Doering, who has similar PhD plans, were advised by Daniel Stoebel, associate professor of biology. Batachari and Stoebel are among the authors included on a paper published last year in the Journal of Bacteriology. That paper, “GenomeWide Transcriptional Response to Varying RpoS Levels in Escherichia coli K-12,” was the culmination of research begun in the Stoebel Lab in 2010. Students in the Stoebel Lab are on a quest to understand the consequences for the cell when some genes look one way and others look another way, and how to understand why genes

are expressed in one way or another. The E. coli global transcription regulator RpoS is the focus of work, because it allows for the integration of molecular biology, physiology and evolution. Projects include studying how RpoS levels vary across strains and environments, measuring the affect of this variation in RpoS level on the transcriptome, studying how RpoS interacts with other transcription factors to influence patterns of transcription, and exploring how the regulation of RpoS levels varies in pathogenic relatives of laboratory E. coli.

Students Tackle Healthcare Challenges at Hackathon Patients and clinicians treating rare diseases face myriad challenges. By definition, the rarity of a disease can mean that research on the condition, established protocol for diagnosis and treatment, and treatment itself are also rare. Four Harvey Mudd College students competed in the third annual Mount Sinai Health Hackathon in New York City, focusing on the theme “Rare diseases.” Sophia Cheng ’21 (mathematics and computational biology), Valerie Kwee ’19 (engineering), Victoria Marino ’20 (engineering) and Heather Wing ’21 (computer science) spent part of their fall break developing technology for at-home patient monitoring for parents with children suffering from West Syndrome, a condition characterized by infantile epileptic spasms, abnormal brain wave patterns and intellectual disability. The 48-hour multidisciplinary competition focused on creating novel technology solutions for problems in healthcare. Prior to the start of the competition, teams were given access to video interviews of patients and doctors discussing the challenges they face that involve rare disease. “We did not know which rare disease we wanted to focus on,” says Kwee, “but we did know we wanted to help monitor infantile seizures. West Syndrome just happened to be a specific rare disease with epileptic symptoms that could use the tool we created.” The students’ first task at the event was to pitch their idea to an audience and recruit people to join them in developing their device, the West Wave. “It’s a kit developed for at-home use that can collect data in real time to help doctors monitor infants with rare diseases,” says Kwee. Joined by students from other schools, employees of Mt. Sinai and an entrepreneur from Washington, D.C., the team spent Friday evening to Sunday afternoon developing prototypes and marketing pitches. “The project was challenging in that we needed to make devices that were comfortable, marketable and functioning,” Kwee says. Concealing conductive thread and flexible electrodes in a comfortable, kidfriendly beanie, the West Wave is a wearable electroencephalogram (EEG) that measures brain activity using OpenBCI (open-source, brain-computer interface platform) software and hardware. The beanie is part of a kit that

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also includes informational material on helping those with West Syndrome and an arm device that detects muscle contraction. “Our idea was to have babies wear this wireless EEG and armband when they sleep, and when there are abnormal activities detected, parents would receive an alert on their phones,” says Cheng. “We actually got a decent amount of the hardware and part of the software to work.” “The arm device uses a resistance sensor fabric that will change resistance as the material is stretched or bent,” Kwee says. “We used conductive thread to make the device comfortable for users. The armband is attached to an Arduino microcontroller that plots the changes in resistance, which corresponds to when the wearer is having a spasm and contracting their muscles.” In the end, the West Wave was not selected as a finalist in the competition. “I think all of us were disappointed, to some extent, that our project wasn’t presented the way we had wanted to,” says Cheng. “We only had three minutes to present; we had a lot of ideas and we executed a lot of them, yet we weren’t able to present them fully.” However, as biology and chemistry professor Karl Haushalter points out, “I think that the more interesting story is what they were able to create, the interdisciplinary nature of the project and the patients that it would serve.” Haushalter coordinated the team’s trip to the hackathon through a connection with the Mount Sinai medical school. “The experience was unforgettable,” says Kwee. “We were able to meet people from many trades that we likely would never have had the opportunity of meeting.” Though this team will likely not continue development of the West Wave, the project may be taken on by another group. “I really would like to continue working on it and possibly have this turned into a future Clinic project,” says Marino. “Mt. Sinai engineers were particularly interested in the product idea and will likely expand on it,” Kwee says. This was the second year that a team from Harvey Mudd competed in the Health Hackathon. “I was pleasantly surprised that other students there know about Mudd,”

says Cheng. “The presenters and the sponsor also mentioned Mudd a couple times during the introduction.” In February 2018, the team from the previous year was invited to enter its project, the Teddy Tracker, in a Shark Tank-style showcase, during which they presented a pitch to a panel of entrepreneurs and received positive feedback. The Teddy Tracker has also made it through the first round of selection for the Lemelson-MIT student prize, which honors promising student inventors. Funding for both trips came from the Shanahan StudentDirected Project Fund. “I would definitely recommend Mudd students participate in the Health Hackathon,” says Kwee, pointing out that, with the preparation that all Harvey Mudd students receive in the Core, students of any major are already equipped to participate. “I am glad I had the chance to participate in the event before I graduated,” Kwee says. “It really showed me how much I’ve learned in the past three-and-a-half years and reminded me of the impact I can make. The event helped me build confidence in myself, and I am more excited to see what the future will hold for me as an engineer.”

Sophia Cheng ’21 wears the West Wave, a wearable EEG that measures brain activity.

CRA Recognizes Computational Biology Researcher

Underwater photographs of Sinularia mesophotica (funnel-shaped morphology of colonies).

Ivy Liu ’20 was selected as a finalist in the

Computing Research Association (CRA) 2020 Outstanding Undergraduate Researcher Awards. The prestigious program recognizes undergraduates at North American colleges and universities who demonstrate outstanding potential in an area of computing research. Liu, a joint mathematical and computational biology major, is interested in developing and applying computational methods to facilitate biomedical research. “Integrating computer science with biology has allowed me to see the beauty of theoretical computer science as well as the applications of tools first-hand,” she says. Her research experience includes working with biology professor Catherine McFadden to test the feasibility of using a particular gene to differentiate species within the coral genus Sinularia; working with computer science professors Ran Libeskind-Hadas and

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Yi-Chieh (Jessica) Wu to improve a dynamic programming algorithm for phylogenetic tree reconciliation; using deep learning to predict DNA sequences related to the remodeling of epigenetic marks driven by a carcinogen with Dr. Cristian Coarfa and Dr. Cheryl Walker at Baylor College of Medicine; and working with Dr. Pavel Sumazin at Baylor College of Medicine to develop computational models to infer cell-type-specific expression from bulk tumor expression profiles. This year, Liu is conducting senior thesis research with Eliot Bush, professor and chair of the Department of Biology, developing methods to study the evolutionary history of microbes. “Through these experiences, I have found a love for computational biology, and I look forward to continuing research on fundamental problems as well as developing tools that will aid biomedical research in the long run,” she says.

computer “ Integrating science with biology has allowed me to see the beauty of theoretical computer science as well as the applications of tools first-hand. –Ivy Liu ’20

2018–2019 Biology Department Student Awards W.A. Brandenburger Biology Prize

Biology Writing Fellows

The W.A. Brandenburger Biology Prize is awarded annually to a senior biology major for outstanding performance and promise in the field of biology.

The Biology Writing Fellows are appointed annually to students who have demonstrated great prowess in the field of scientific writing. Chris Doering ’19, Camille Goldman ’19

Carissa DeRanek ’19, Camille Goldman ’19 Best Senior Thesis William K. Purves Biology Prize

The William K. Purves Biology Prize is awarded to a junior biology major who combines scholarship with some kind of breadth (intellectual, cultural, athletic or service).

The Best Senior Thesis prize is awarded annually to a senior with an outstanding research project during their capstone. Camille Goldman ’19

Callie Glanton ’20

2018–2019 Thesis Projects Christopher Doering: Control of Gene Expression Profiles Within the RPOS Regulon of E. Coli Advisor: Daniel Stoebel

Alicia Pentico: Delimiting Sinularia (Cnidaria: Anthozoa: Octocorallia) Species Using Target Capture Enrichment Of Ultraconserved Elements Advisor: Catherine McFadden / Andrea Quattrini

Camille Goldman: Effects Of Clpxp Overexpression On Drosophila Melanogaster Mitochondrial Protein Homeostasis, Physiology And Aging

Erica Quinn: Optimal Spring Stiffness In Spring-loaded Crutches Advisor: Anna Ahn

Advisor: Jae Hur

Approach

Carrie Saada: Bromodomain Protein Localization During Differentiation Between Bloodstream And Procyclic Forms Of Trypanosoma Brucei

Advisor: Stephen C. Adolph

Advisor: Danae Schulz

Katie Erickson: Evaluating The Use Of Ultraconserved Elements To Determine Species Boundaries And Population Structure In The Coral Genus Alcyonium

Liya Zhu: Establishing A High Throughput Assay Using Moclo Golden

Advisor: Catherine McFadden / Andrea Quattrini

Advisor: Daniel Stoebel

Natasha Floerke: Lizard Population Dynamics: A Meta-analysis

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Gate Cloning To Investigate The Temporal Behavior Of Rposdependent Promoters In Escherichia Coli

Alumni News Matthew Harris ’93: PhD in molecular biology

from UCSD. Four years in the Army’s Medical Service Corp working in an HIV vaccine group. Four years at startup Nanogen working on molecular diagnostics. Twelve years at Illumina working on molecular diagnostics with bead arrays and later Next Generation Sequencing. Joseph Chen ’95: I am now a faculty member

at San Francisco State University, teaching microbiology and mentoring students in research. We are investigating bacterial factors that contribute to beneficial interactions with host organisms. Lynn Nakamura ’95: My husband Dan and I

are enjoying our 12- and 8-year-old girls. Life is full including kid activities, work as a physical medicine and rehabilitation physician and finding the yoga mat whenever I can. Neil Laughlin ’96: Living in San Jose with my

Scrippsie wife and our two sons. We spend many evenings at roller hockey rinks, travel whenever possible and play a lot of board games. Professionally, I am a Silicon Valley software engineering manager. I am about to start a new role as the VP of Public Cloud Site Reliability Engineering at Salesforce in San Francisco! Rachel Donahue Beda ’97: I’ve been a practicing physician for 18 years now! After med school and residency at UW, I spent seven years working in Seattle’s level 1 trauma ER. That was followed by five years of primary care at an urban under-served community clinic. In 2015, I left that position to join a friend as co-owner of a small adult primary care clinic. We’re not happy with the current health insurance system (who is?) so we offer direct primary care: patients pay their MDs directly like a gym membership on a monthly basis in exchange for unlimited primary care. We also focus on LGBTQ folks, including genderaffirming care for trans and non-binary folks. www.imwisepatient.com. Joe Beda ’97 and I have been married for 19 years and have two kids (11 and 14). Finally, I just joined the Mudd Board of Trustees! Dan Pryma ’98: Nuclear medicine clinical

practice and radiobiology/imaging research at the University of Pennsylvania.

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Carrie (Wicklund) Wu ’98: I’m currently an associate professor of biology and director of the environmental studies program at the University of Richmond in Virginia. I’m a plant evolutionary ecologist, interested in how the environment shapes the genetic structure and evolutionary trajectory of natural populations. I earned my PhD in ecology and evolutionary biology from UC Irvine in 2005, while conducting summer research at the Rocky Mountain Biological Lab in Colorado. Following a postdoc at Duke, I joined the UR faculty in 2009. Current research themes in my lab (that involves several undergrads!) include the effect of climate change on alpine plant populations, and how invasive plants spread across the landscape. Greg Alexander ’01: I’m a registered civil/ environmental engineer but am mainly focused on air quality/goods movement issues in the L.A. basin. Recently sold my small business to an MEP design firm.

before taking my current position: associate professor of philosophy at Golden West College in Huntington Beach, California. We had two more children, Ronen (2013) and Ziva (2015) and now live in Cypress, California, with our three dogs and tortoise. Daniel Pennington ’02: I am a board-certified radiation oncologist practicing in Richmond, Virginia. A current project is getting our group set up to participate in National Cancer Institute-funded cooperative group clinical trials. Andrea (Crofut) Upton ’03: I’m an attorney, working for a technology company in the Seattle area. Erika Strandberg ’05: I

completed my PhD in biomedical informatics at Stanford in 2017 and now am executive director of strategic research initiatives in computer science at Stanford where I lead a number of programs that help external groups engage in academic research in AI and data science.

Robert Fuentes ’01: Since graduating from HMC, I earned my DVM degree from Colorado State University in 2005. I have been a practicing small-animal veterinarian in Las Vegas for the last 14 years. I am happily married with three boys and and a fourth boy on the way. Noah Levin ’02: After leaving Mudd, I married my high school sweetheart, Jenny (whom many Mudders met on her numerous visits), and then moved to Ohio to go to graduate school at Bowling Green State University where I earned a master’s in philosophy and PhD in applied philosophy. We then moved to Singapore where I taught philosophy to children using board games (and designed a few games myself) and had our first child, Talia, in 2010. I then taught at WSU for two years

Sarah Fogenburg ’06: I’m the quality assurance and regulatory affairs manager for Corning Life Sciences location in Woodland, California. My specialty is animal serum for cell culture, research, pharmaceuticals and medical devices. I also serve on the International Serum Industry Association Regulatory Committee.

Alumni News Marguerite Leeds ’06: I’m still living in Alaska and will soon receive my master’s in nursing. Erin Heyer ’07: After finishing my PhD

in RNA biochemistry at the University of Massachusetts Medical School, I took a position at Moderna Therapeutics in Cambridge. However, I jumped at the chance to postdoc at the Garvan Institute of Medical Research in Sydney, Australia—which is where I studied abroad—and have been here since September 2016 and loving it! Life in Sydney is fantastic, and my work developing novel clinical diagnostic tools using RNA sequencing is very rewarding. James Moore ’07: After earning a PhD in math at Utah and a postdoc in immunology at Emory University, I’m now working at Fred, the Fred Hutch Cancer Research Center, in Seattle. During that time, I’ve proposed mathematical models of autoimmune (dis)regulation, viral infection and evolution and the immune response to vaccines. Currently, I work as part of the HIV prevention trials network modeling team synthesizing biomedical, behavioral and epidemiological data to help end the HIV epidemic in America and abroad. Katie Mouzakis ’07: I’m an assistant

professor of biochemistry at Loyola Marymount University! I received my PhD in biochemistry from UW Madison in 2013 and went on to a tenure track position in biochemistry at Fort Lewis College in Durango,

Colorado. After several successful years there, I decided the town was a little too small for my long-term plans and career ambitions. I made a lateral move to Loyola Marymount University in August 2018. Things are going very well, and I am hoping to go up for tenure within a very short number of years. Katelyn Walker ’07: It’s been a long and winding road since I left HMC. I worked for a few years as a field biologist, got a master’s in landscape architecture and environmental planning, worked as a planner for the National Park Service and, most recently, completed a data science coding bootcamp and am now employed as a data scientist for Clarivate Analytics—working on the algorithms that underlie every scientist’s favorite database: Web of Science! While I’m no longer working directly in the biological sciences, I have such incredible appreciation for the well-rounded STEM education I got at Mudd, which has given me the background and flexibility to pursue these varied career paths. Julian Evans ’08: I’m on the faculty at Zhejiang University. I’m researching liquid crystals and colloids. My research is generally focused on the forces that define geometrical patterns within fluids. At some level it is very first principles biology. I had a recent paper on the cover of Physical Review Letters describing a many-body force which organizes droplets into a rounded superstructure. Shayni Saftler ’08: I’m a registered nurse, but

I’m moving into the field of clinical informatics, which is the ever-growing bridge between technology and healthcare. It’s data science, project management and caring for people all rolled into one. Terence Wong ’09: After graduating in 2009, I worked for two years as a research associate at Broad Institute and DFCI in Boston. In 2011, I started a PhD in the biological and biomedical sciences (BBS) program at Harvard and joined Levi Garraway’s laboratory at Broad Institute and DFCI. My dissertation research focused on using functional genomics to identify genetic vulnerabilities in different tumor types and characterizing the role of SOX10 dependency in melanoma. During this time, I was also very

HARVEY MUDD COLLEGE | BIOLOGY HIGHLIGHTS 2020

involved with the postdoc/graduate student community at Broad. In 2018, I moved to San Diego and started my current job as a Clinical Genomics Analyst at Rady Children’s Institute for Genomic Medicine, where I analyze whole genome sequencing data to make genetic diagnoses for critically ill infants.

Oksana Sergeeva ’09: Nathan Jones ’09 (physics) and I are still living in Switzerland with our 5-year-old son (Chase). I am finishing up a postdoc in cell biology at the EPFL in Lausanne. It has been a great experience living in Europe and having a French-speaking child! We have traveled all over and enjoy spending time with my grandparents in Ukraine. In 2020, we are planning our next professional step(s) so we’ll see where that takes us! Jordan (Eboreime) Williams ’09: I graduated

from the molecular and computational biology program at USC with my PhD in 2016! Shortly after I got married to my husband, Stephen, and we just had a son in March 2019. We currently live in Carlsbad, California, where I work as the West Coast field application scientist for ArcherDx, a biotech company focusing on personalized genomic testing.

Noah Atwi ’12: Graduated from LSU New Orleans School of Medicine in 2016. Currently in radiology residency at LSU New Orleans, will

Alumni News finish in 2021. Planning to do a musculoskeletal radiology fellowship. Published several radiology papers, research interest is primarily dual-energy CT.

in use. I’m in my fifth year and am planning on looking for a job in industry after finishing my PhD, sometime within the next 1.5 years. Devon Stork ’15: I’ve been working on my PhD

Hayden Hatch ’12: MD/PhD (MSTP) candidate

at Albert Einstein College of Medicine. Currently completing my PhD in the lab of Julie Secombe (departments of Genetics and Neuroscience) investigating the link between the transcriptional regulator KDM5 and intellectual disability using Drosophila as a model. Currently planning to pursue a residency in neurology with an emphasis on translational neuroscience research.

Natasha Parikh ’14: In May 2019, I completed my PhD in cognitive neuroscience at Duke University. My dissertation focused on understanding how people with varying levels of anxiety regulate the emotions evoked by negative memories, and it was funded by the DoD’s National Defense Science and Engineering Graduate (NDSEG) Fellowship. I’m now completing a teaching postdoc at Harvard University, developing and teaching three new courses for the psychology department and furthering my research in affective neuroscience. In my free time, I’ve been enjoying singing in various choirs, rock climbing and fostering cats!

at Harvard Medical School. I am jointly advised by Ethan Garner and George Church, and my PhD project is getting nonstandard amino acids working in Bacillus subtilis. I believe I’m on track to defend in April, graduate in May. We’ll see if that happens. After grad school, I plan to join a small biotech company, though I’m not sure which one yet! Arthur Chang ’16: I am a first-year medical student at the University of Illinois at Chicago College of Medicine. I am also involved in their co-curricular Innovation Medicine (IMED) program. The first year of IMED consists of a industry-sponsored project (similar to HMC Clinic), in which medical students form interdisciplinary teams with students from bioengineering, marketing and design to tackle a healthcare-related problem. Between Mudd and med school, I completed my master’s program in applied life sciences at KGI.

Beverly Yeh ’14: I am a recent Teach for

Bryan Visser ’13: Hopefully wrapping up my PhD in biomedical sciences at Baylor College of Medicine in Houston, Texas. I’m developing a novel and simple method to measure DNA supercoiling in vivo. I’m doing this to discover patterns of supercoiling in E. coli and then relating them replication fork collapse and chromosome segregation. Megan Wheeler ’13: I am nearing the end of a PhD at Arizona State University working on social and ecological drivers of plant community dynamics in cities. My work is primarily in urban ecology, and I’ve been experimenting with a combination of methods from the social sciences and field ecology. I’ve also designed and am teaching my first class on quantitative methods for ecologists, digging back to my first programming experiences at Mudd and how bio professors were able to help me make connections between quantitative skills and biological questions. I don’t see many Mudders out in Phoenix, but I’m planning a move up to the Bay Area when I’m done and hope to do some reconnecting then!

HARVEY MUDD COLLEGE | BIOLOGY HIGHLIGHTS 2020

America alum, and I have continued to teach middle school math in my placement district. Prior to Teach for America, I taught English in Fukui Prefecture, Japan on the JET Program. My journey after graduation has been unlike many Mudders’ paths, and I do not regret a bit of it!

Mary May ’15: I’m currently a graduate student at Harvard in Dan Kahne’s lab studying a protein machine that builds the outer membrane of gram negative bacteria. Our lab is interested in studying how the outer membrane is made and how we can design and discover new inhibitors of outer membrane biogenesis to target these bacteria that are inherently resistant to many clinical antibiotics

Samuel Woodman ’16: Since graduating, I’ve been working as a contractor at the NOAA Southwest Fisheries Science Center doing both coding/data analysis and fieldwork. I built an R Shiny tool for creating ensembles of species distribution model predictions (Woodman et al. 2019 - doi.org/10.1111/2041-210X.13283), and am currently part of a team assessing the risk of whale entanglement in fishing gear off the U.S. West Coast. I also spent two, fivemonth field seasons at Cape Shirreff, Antarctica, collecting and analyzing data related to pinniped and seabird reproduction, foraging ecology, growth, abundance and distribution, and survival. My other projects

Alumni News have included collecting data for sea lion diet studies and creating tools to analyze data collected during research cruises and aerial surveys. Rachael Kretsch ’18: I just completed my

master’s in science and security at King’s College London! After a year of fun in London and lots of reading and writing about science from an international security perspective, I am happily back in lab in California starting my PhD in biophysics at Stanford. Bella Lee ’18: I work at an early stage

biotechnology company called A2 Biotherapeutics in Agoura Hills, California. Our focus is on innovation of novel peptide-

HARVEY MUDD COLLEGE | BIOLOGY HIGHLIGHTS 2020

MHC immunotherapies for cancer as well as other immune diseases. On the side, I volunteer as a trilingual medical scribe at a free clinic. In addition, this past year I received my 200-hour yoga teacher certificate, and I teach class weekly in my office. Concurrently, I applied to MST programs (medical scientist training programs, or MD/PhD) this cycle. I look forward to returning to school in 2020 to earn a medical degree, where I’m hoping to specialize in hematology/oncology and earn a graduate degree in molecular immunology. Jacob Rosalsky ’18: I moved to the Bay Area have been working at 23andMe as a site reliability engineer directly supporting both the research and therapeutics teams.

Annalise Schweickart ’18: I am currently a PhD student at Cornell’s Medical School in NYC! I work with large medical datasets that include information about patients’ genes, proteins and other important biomolecules. I take these datasets and turn them into biological networks that I can then statistically analyze to look for pathways or processes that may be involved in disease. Currently, I am focusing on diabetes and Alzheimer’s disease for my studies, but I am excited to expand my work into the field of cancer. When I’m not coding at my research computer, I like to attend talks about what is new in computational biology and explore the big city!