OETIS Chronicle Special Edition

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OETIS Chronicle

Special Edition: Celebrating Ph.D. Graduates In this special edition of the OETIS Chronicle, we feature our most recent graduates of the Graduate School of Biomedical Sciences and share where they are now after earning their doctorate. We take a look back at what they accomplished during their time in graduate school and we wish them the best in their future endeavors!

In this issue: Alex Campos…….……………….….pg.2 Lisa Elmen………………….…...…...pg.3 Daniel Ojeda Juárez………………pg.4 Pavel Ryzhov…………………………pg.5

Alex Campos, Ph.D.

Lisa Elmen, Ph.D.

Daniel Ojeda Juárez, Ph.D.

Numana Bhat………………………..pg.6 Jessica Stupack…………...………..pg.7 Scotty Cadet………………………….pg.8 Huiyu Ren……………………..….…pg. 9

Pavel Ryzhov, Ph.D.

Scotty Cadet, Ph.D.

OETIS Chronical Special Edition

Numana Bhat, Ph.D.

Jessica Stupack, Ph.D.

Huiyu Ren, Ph.D.

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Alex Campos, Ph.D. Thesis Title: “TXNRD1 Mediated Regulation of the Wnt/β-catenin Pathway in Colorectal Cancer” Mentor: Garth Powis, Ph.D. Defense Date: September 25, 2019 Current Job Title: Postdoc at UCSD in the Cheresh lab

Alex grew up in McAllen, TX, a city steeped in both Hispanic culture and Texas pride, and was very influential for Alex’s personal development. He is the middle child of three brothers, and the son of two teachers who always stressed the importance of education and high character. Alex developed an interest in the medical field as he shadowed his uncle, a family medicine physician, during the summers and decided to follow the “pre-medicine” track for his undergraduate studies. Alex attended Trinity University (San Antonio, TX) and followed the pre-medicine track leading to a Bachelor of Science in Biochemistry and Cellular and Molecular Biology. While at Trinity, Alex was a member of the men’s soccer team, served as vice president of the university’s chemistry club, and volunteered as a math and science tutor for underprivileged high school students. Over the course of his studies, Alex became increasingly interested in therapeutic development, specifically in how new drug targets were identified and validated. Additionally, towards the end of Alex’s undergraduate studies, he was affected by the passing of two of his mentors, Joe Disque and Manuel Zamudia, from cancer-related diseases. These events led Alex to pursue opportunities in cancer-related research. After graduating from Trinity University, Alex joined the laboratory of Bryant Darnay in the Experimental Therapeutics department at the M.D. Anderson Cancer Center (MDACC) in Houston, TX as an entry-level research assistant. Alex’s time at MDACC was both rewarding and productive as his work contributed to 10 peer-reviewed publications. It was also through his experience at MDACC that enabled Alex to meet Dr.

Garth Powis, eventually following Dr. Powis to Sanford Burnham Prebys in 2013. In 2015, Alex decided to pursue a Ph.D. and enrolled in the Institute’s Graduate School of Biomedical Sciences. In Dr. Powis’ laboratory, Alex investigated how the adaptive stress response to oxidative stress enables growth, proliferation and survival advantages for colorectal cancer cells. When not working in the laboratory, Alex takes advantage of the natural beauty San Diego offers in the form of its mountains, beaches, and parks and enjoys a local craft beer and watching football games with friends.

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Lisa Elmen, Ph.D. Thesis Title: “From Disease Promotion to Therapeutics—the Multifaceted Roles of Gut Bacteria” Mentor: Scott Peterson, Ph.D. Defense Date: November 15, 2019 Current Job Title: Sr. Scientist, Microbiology at Bloom Science, Inc. Lisa was born and raised in Uppsala, Sweden, and early on had an eye towards the world beyond the Swedish borders. Her interest in cultures and languages oriented her to humanities studies in high school,

which included Latin and ancient Greek, as well as English, French and Spanish. While deciding not to pursue humanities professionally, the modern languages she started learning at this time and eventually acquired fluency in, is today a part of her everyday life in California. At university in Sweden, Lisa studied microbiology, bacterial ecology and genetics and eventually graduated with a combined degree, Master of Science in Biology. She did her master’s thesis on phage therapy, in the laboratory of Dr. Karin Carlson, Uppsala University, on the potential use of bacteriophages to combat antibiotic resistant infections.

Curiosity and a sense of adventure brought Lisa to the U.S. and in 2007 she joined Dr. Rolf Bodmer’s lab at Sanford Burnham Prebys as Lab Manger. She gained valuable research experience, studying cardiac disease and aging with Drosophila as a model system. Inspired by the problem-solving challenges and the creative nature of scientific research, she decided to pursue a Ph.D. degree and to return to work on microorganisms. In 2014, Lisa enrolled in the Institute’s Graduate School of Biomedical Sciences and joined Dr. Scott Peterson’s lab to do research in the relatively new and very exciting field of the human microbiome, with focus on the influence of intestinal bacteria on cancer. Lisa is an enthusiastic cook and pastry chef, and believes that the best conversations, in any language, are had around a good dinner with family and friends. Her interest in food overlaps with her research, in the sense that diet is the strongest determinant of the composition of gut bacteria, which in turn, greatly influences overall health. Her French-Swedish-American family enjoys cooking and entertaining, travelling internationally and locally, and spending time on San Diego beaches. Graduate school was a great learning experience that allowed Lisa to grow personally as well as scientifically, and she is very grateful for all the amazing support she received from family, friends and colleagues. OETIS Chronical Special Edition

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Daniel Ojeda Juárez, Ph.D. Thesis Title: “Lipocalin-2 Mediates Neuronal Damage and Behavioral Deficits in HIV-induced Brain Injury” Mentor: Marcus Kaul, Ph.D. Defense Date: January 24, 2020 Current Job Title: Postdoc at UCSD in the School of Medicine, Department of Pathology

Daniel was born and raised in the southern state of Oaxaca, Mexico. Growing up he had a passion for medicine and biology, and by high school, Daniel was already determined to pursue an academic career in science. To accomplish his goal, Daniel knew that obtaining a Ph.D. abroad would open a plethora of opportunities and connections that would be instrumental in accomplishing his dreams. His focus and determination earned him an opportunity to study abroad in high school - the Rotary Youth Study Abroad Program awarded him with a scholarship to study in Cedar Springs, Michigan. Daniel got accepted to the California State University, Fresno. During this time, Daniel took his first steps as a scientist and simultaneously joined two research laboratories. He studied microbiology using

bio-informatics and genetics to study bees and their gut bacteria in Dr. Quinn McFrederik’s laboratory. In addition, he studied the effects of insecticides on breast cancer under the supervision of Dr. Jason Bush. He was also selected to take part in a Partnership Program between Fresno State and then Sanford Burnham Cancer Center, supported by the National Cancer Institute in the laboratory of Dr. Guy Salvesen. During this internship, Daniel fell in love with San Diego and decided to apply to the Ph.D. program at Sanford Burnham Prebys. After graduating Magna Cum Laude with a Bachelor’s of Science in Biology and minors in Chemistry and Japanese, Daniel started his Ph.D. in Biomedical Sciences. In 2015, he joined the laboratory of Dr. Marcus Kaul to study HIV-induced brain injury. At the end of his second year, Daniel followed Dr. Kaul and his laboratory to the University of California, Riverside to complete his Ph.D. studies. All these experiences have been a great learning experience that allowed Daniel to grow personally as well as scientifically. He is very grateful for all the support he received from his family, friends and colleagues both in San Diego and in Riverside.

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Pavel Ryzhov, Ph.D. Thesis Title: “Structural Studies of Bcl-2 Family Proteins in Lipid Bilayers” Mentor: Francesca Marassi, Ph.D. Defense Date: February 12, 2020 Current Job Title: Application Scientist at Applied Photophysics

Pavel Ryzhov was born in Nizhny Novgorod, Russia, into a multi-generational family of physicians, fully expecting to continue in his parents’ and relatives’ footsteps. After finishing high school with a focus on

medicine-related subjects that included Latin language, advanced biology and chemistry classes in 2010, he left Russia to pursue undergraduate education in the U.S. He obtained an Associate in Sciences in Biology and Physics from San Diego Mesa College in 2013 where he assumed multiple leadership roles in the Pre-Med/Pharm Club, which he transformed into a Chapter of the American Medical Student Association and established a scholarship for pre-medical students on campus. However, during that time, his curiosity in the natural sciences, in particular molecular biology, developed. He studied at the Bonn-Rhein-sieg University of Applied Sciences in Rheinbach, Germany, where he joined an undergraduate degree program in Applied Biology. During the next two and a half years, Pavel’s

passion for learning more about protein structure grew and for his Bachelor Thesis project he joined the laboratory of Prof. Jane Clarke at the University of Cambridge, UK. He spent the last few months of his program there and defended his thesis analyzing protein folding pathways. During his last year of undergraduate studies, Pavel applied for Ph.D. programs and immediately after graduation in Germany in 2016, he joined Sanford Burnham Prebys’ Graduate School of Biomedical Sciences. In the laboratory of Prof. Francesca M. Marassi he studied Bcl-2 family proteins and their structure-function relationship using NMR spectroscopy. Over the next few years, his curiosity remained one of the main drivers and allowed him to overcome many experimental and personal challenges. As part of his Ph.D. experience, Pavel learned a great deal about the big picture of where biomedical discoveries fall in the complex landscape of treatment of patients, which developed into his hobby of staying up-to-date with the latest news in healthcare, pharmaceutical industry and life sciences. He started sharing them with his network as part of his Biofilm News YouTube channel and plans to continue growing his skills in science communication.

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Numana Bhat, Ph.D. Thesis Title: “Regnase-1 is Essential for B Cell Homeostasis to Prevent Autoimmunity” Mentor: Robert C. Rickert, Ph.D. Defense Date: April 22, 2020 Current Job Title: Postdoc at the La Jolla Institute for Immunology

Numana was born in the beautiful, snowy valley of Kashmir. She went to her first biology class when she

was a year old as she tagged along with her mother to college, who was majoring in biology at the time. She grew to be naturally inclined to enjoying reading and watching TV shows about science, especially the ones with animals and wildlife. In school, she loved working on science projects the most, and was also fortunate to have been taught by amazing science teachers.

She later went to college in her hometown at the University of Kashmir to earn a bachelor’s degree in biology and chemistry and obtained her master’s in clinical biochemistry from the same university. She then joined the Ph.D. program in UMass Medical school, Worcester, Massachusetts and worked in Kate Fitzgerald’s laboratory before moving to San Diego to be with her husband who was a postdoc at the Scripps Research Institute. The time in the Fitzgerald Lab was a formative experience where she began developing critical scientific thinking and appreciation for cutting edge science and learned the importance of teamwork. In San Diego, she worked in the lab of Dr. Sumit Chanda at Sanford Burnham Prebys for some time before joining the Sanford Burnham Prebys graduate program in Dr. Robert Rickert’s laboratory. Her Ph.D. thesis work resulted in the discovery of the role of Regnase-1 as molecular brakes in antibody producing cells, preventing autoimmunity in mice. Dr. Rickert's expectations, mentoring style, and encouragement further strengthened her desire to become an independent scientist. She values her time at Sanford Burnham Prebys for her professional growth and for having met great friends in San


After finishing her Ph.D., she joined the La Jolla Institute for Immunology for her postdoctoral training with Shane Crotty to study immune responses to viral infections and vaccines. Her current research is focused on understanding how a specialized subset of T cells enables antibody secreting B cells to effectively counter viral infections and to generate humoral responses upon vaccination.

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Jessica Stupack, Ph.D. Thesis Title: “Novel Roles for the Alzheimer’s Disease Risk Factor SORLA in

Neurite Outgrowth, Regeneration, and Synaptic Protection” Mentor: Timothy Huang, Ph.D. Defense Date: August 14, 2020 Current Job Title: Senior Research Associate at Vertex Pharmaceuticals

Jessica was born in Winnipeg, Manitoba Canada in May of 1992. After a few years of playing in the snow, she and her family relocated to San Diego, California, where her dad had taken a job at Scripps Research Institute. Growing up in Rancho Penasquitos and attending Westview High School, she played competitive soccer as a goalkeeper and played recreational basketball whenever she wasn’t playing soccer. Jessica attended University of California, San Diego. As part of Warren College, she majored in biology with a focus on neuroscience. During her time at UCSD, she worked as a lab assistant in Dr. David Schlaepfer’s lab at the Moore’s Cancer Center; the lab specialized in Focal-Adhesion Kinase function in gynecological cancers.

After UCSD, Jessica started working at Vertex Pharmaceuticals with Amy Turnbull and Mike Liu, investigating Huntingtin protein deficits in Huntington’s disease. Jessica also worked at Vertex as a Research Assistant investigating patient mutation impacting Cystic Fibrosis. Jessica then transferred to Sanford Burnham Prebys 2015 to join the lab of Dr. Huaxi Xu as a graduate student. After working on a project related to Tauopathy in Traumatic Brain Injury, she pursued her research project establishing novel roles for SORLA under the guidance of Dr. Timothy Huang. Jessica enjoys painting, weightlifting, hiking, playing guitar, and playing with her dogs Nellie and Stella in her spare time. Jessica recently received her American citizenship 25 short years after moving to San Diego.

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Scotty Cadet, Ph.D. Thesis Title: “Mannose Supplement and SGK1 Attenuation Enhance EGFR-

Targeted Therapy” Mentor: Garth Powis, Ph.D. Defense Date: March 5, 2021 Current Job Title: Senior Scientist at ImmunityBio Scotty was born in New York City, NY to parents who immigrated from Haiti and France. Scotty is the youngest of his family and has an older sister and an older brother. Growing up, Scotty traveled often with his family to Haiti to help build classrooms for children in Port-au-Prince. Scotty benefited from his experiences in Haiti and understood

at a very young age the value of education. Scotty graduated from Loyola University Chicago with a B.S. degree in Molecular and Cellular Biology. Throughout his undergraduate studies, Scotty developed an interest in scientific research at Argonne National Laboratory and Northwestern University in the Chicago Area. After graduating, Scotty went on to the National Institute on Aging at the National Institutes of Health (NIH) in Baltimore, MD, where he helped make important discoveries of several pluripotent factors for somatic cell reprogramming and stem cell maintenance in the laboratory of Dr. Minoru Ko. Following his fellowship at the NIH, Scotty joined the Pluripotent Stem Cell Innovation Center at Lonza Biopharma in Walkersville, MD, and helped develop clinically relevant cell culture products to enable pluripotent stem cell

therapy applications in regenerative medicine. While at Lonza, Scotty was recruited to the University of WisconsinMadison (UW-Madison) by Dr. Patricia Keely. Scotty continued his interest in the applications and technologies of stem cells at UW-Madison in the laboratory of Dr. Tim Kamp. Dr. Keely also became a close mentor to Scotty, but later succumbed to pancreatic cancer in 2017. After this unfortunate experience at UW-Madison, Scotty changed his thesis work at Sanford Burnham Prebys in 2018 to understand the events leading to drug resistance which cause relapse in cancer patients. Scotty identified that a novel mechanism for drug resistance in cancer is due to the decrease of several DNA repair enzymes that are responsible for error-free homologous recombination. He showed this occurs through a hypoxia-mediated metabolic switch that shunts mannose into glycolysis away from glycan synthesis and protein N-glycosylation resulting in incomplete protein folding in the endoplasmic reticulum and selective proteasomal degradation of DNA repair proteins. Scotty is a Senior Scientist at ImmunityBio where he leads efforts in translational medicine to find novel biomarkers on tumor cells and enhance immuno-oncology approaches. As part of his role, Scotty leads a neutralizing antibody assay development to test a thermal stable COVID-19 booster vaccine to meet the gaps of a stable vaccine in developing countries with limited freezers. Scotty is an avid football fan and supports his English Club, Chelsea. When Scotty is not watching Chelsea play, he is enjoying the beaches, mountains, and vineyards in southern California with his wife, a Senior Scientist at Aspen Neuroscience.

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Huiyu Ren, Ph.D. Thesis Title: “Discovery of Novel Cancer Therapeutics by Targeting the ULK1/2 Autophagy Initiation Complex” Mentor: Nicholas Cosford, Ph.D. Defense Date: March 28, 2021 Current Job Title: Senior Scientist at AbbVie

Huiyu was born and raised in Xinzhou, a city known for its hot springs and coal resources in northern China. She went to the neighboring city, Taiyuan, for high school, during which she developed a strong interest in biology. Huiyu moved to Beijing for college and majored in Biological Sciences from the China Agricultural University. During the first semester of her sophomore year, she got a chance to work in the laboratory of Dr. Ning Li, where she used transgenic mice to study the transport of human IgGs by the neonatal Fc receptor across the blood-milk barrier, to build a foundation for the development of a mammary gland bioreactor. She learned various experiments and methods which are invaluable for her career as a biologist. After that, Huiyu performed her thesis research in Peking University under the mentorship of Dr.

Min Fang. Using a small molecule probe, she focused on dissecting the crosstalk between the two major forms of cell death, apoptosis and necrosis. Huiyu graduated in 2014 with a bachelor’s degree from Peking University before joining the Sanford Burnham Prebys Graduate School of Biomedical Sciences. She joined the laboratory of Dr. Nicholas Cosford, who focuses on small molecule drug discovery and the investigation of intracellular pathways using chemical biology approaches. During her graduate studies, Huiyu’s research optimized small molecule inhibitors of the autophagy initiating kinases, ULK1 and ULK2, to provide a novel strategy to treat cancer. She devised a platform for ULK1/2 inhibitor screening with colleagues and discovered ULK1/2 inhibitors with improved inhibitory potency and oral bioavailability. Her work also contributed to the identification of a lead inhibitor that was licensed to a pharmaceutical company for clinical development, and this inhibitor is promising to be a drug that benefits cancer patients.

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Office of Education, Training, & International Services Diane M. Klotz, Ph.D. Director Associate Dean, Administration & Professional Development Megan Elyamani Program Coordinator, OETIS Education & Training Nisha A. Cavanaugh, Ph.D. Associate Director, Career Development & Postdoctoral Programs Paula Checchi, Ph.D. Program Manager, Recruitment, Outreach & Achievement

Angelica Rocha, Ph.D. Assistant Director, Institutional Research & Academic Planning

International Services Mitchell Furumoto, MS.Ed. Manager, International Services

Susie Bolor Senior International Advisor

Leadership Support Guy Salvesen, Ph.D. Faculty Advisor, Graduate Education & Postdoctoral Training

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Doug Battista Chief Human Resources Officer Human Resources

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