2020 Biotech Times

Biotech TimesIssue11•June2020 Marianne Hunter, Editor New DEB Student Blogs! 29 th Biotech P~l4us0 Retreat DEB INTERNSHIPS! DEB PHILANTHROPY THE BIOTECHNOLOGY PROGRAM’S ANNUAL MAGAZINE

FEATURES 03 From the Director 05 Biotech Program’s R Workshop 06 2019-20 Outreach 10 DEB Internship 11 DEB Graduates. 12 DEB Accolades 14 29th Biotechnology Retreat 16 Biotechnololgy Program Contacts 2 • Biotech Times Magazine • biotech.ucdavis.edu

FROM THE DIRECTOR Director Dr. Denneal Jamison-McClung Dear Biotech Program Community, [email protected] Needless to say, 2019 - 2020 Assistant Director Admin. has been an eventful academic Marianne Hunter year as we live through a [email protected] pivotal time in US and human history. We have all been Program Manager impacted by the COVID-19 Jacki Balderama pandemic and the on-going [email protected] struggle for racial justice in the US, acknowledging that Financial Analyst the burdens of both crises Kelly Meade have fallen disproportionately [email protected] on Black communities and underrepresented groups. Scientists and engineers are problem-solvers at heart and Program Assistant I have been very proud to witness our UC Davis colleagues, [email protected] including DEB students and faculty, pulling together 530 752-3260 and making thoughtful contributions to these dual and interwoven crises. The COVID-19/SARS-COV-2 emergency Biotech Website is new to us, though amenable to the types of technical https://biotech.ucdavis.edu/ and public health innovations we can develop through biotechnology/STEM research. Efforts to improve racial DEB Website justice been a perennial challenge for society and we are https://deb.ucdavis.edu/ fortunate to work in a campus environment with articulated Principles of Community and colleagues who can provide inspiration and resources to help us make progress. For more information on how our campus has been tackling both of these big challenges, check out the Office of Diversity, Equity and Inclusion resource pages for racial trauma and COVID-19, as well as the Office of Research resource page on SARS-CoV-2/COVID-19 research efforts. The Biotechnology Program supports Black Lives Matter and will continue to amplify the voices of our Black/African Diaspora colleagues via social media, as well as reflecting on how we can improve the overall inclusivity of our STEM training environment. In support of these goals, we are pleased to announce a new award from the University of California Hispanic Serving Institution Doctoral Diversity Initiative (UC HSI DDI) to develop the Advancing Diversity by Educating the Professors of Tomorrow (ADEPT) program, which will launch in fall 2020. Along with partners at Sacramento State University, PI Karen McDonald (Chemical Biotech Times Magazine • biotech.ucdavis.edu • 3

FROM THE DIRECTOR (Cont.) Dr. Denneal Jamison-McClung Director, Biotechnology Program Engineering) and I will be developing a mentorship cheering many DEB students in our community with and research fellowship program aimed at ensuring kind words and good advice when their doctoral a diverse pool of graduate students is well-prepared finish line seemed out of reach. In keeping with to tackle academic career paths, whether at her low-key, humble style, Marianne has requested comprehensive universities focused on undergraduate that we not make a fuss or host a digital comment teaching, or at research-intensive universities. ADEPT board to celebrate her retirement. However, I know will be biotech-focused and prepare graduate she’d be happy to hear privately from DEB faculty, students for faculty careers that include innovative students and community members who’d like to send teaching, research, entrepreneurship and public- a congratulatory note ([email protected]). Best private collaborations. wishes to Marianne on new adventures and a well- deserved retirement! As this academic year comes to a close, we would like to highlight the work of our longtime colleague Sincerely, and friend, Marianne Hunter, who will be retiring at the end of June 2020. Marianne has been an Denneal integral part of the Biotech Program for many years, making sure the “wheels of progress” have turned smoothly for our unit. Among many business skills and professional interests, Marianne stands out as an uber-technophile, programmer and digital media whiz, keeping the Biotech Program up-to-date with the latest gadgets, IT hardware/software and cutting- edge communications. She has also been a tireless advocate for graduate students and STEM diversity, 4 • Biotech Times Magazine • biotech.ucdavis.edu

2019 R WORKSHOP BIOTECH PROGRAM’S R WORKSHOP This workshop was The Biotechnology Program offered a new course last summer, designed for graduate Introduction to R for Life Scienrtists and Engineers. This class was students (DEB and non- co-taught by Dr. Denneal Jamison-McClung and DEB student Don Gibson. DEB) who are new to programming and data This interactive instructor-led environment allowed participants to analysis using R. become familiar with basic concepts including reading data into R, basic statistics (e.g. average, std. deviation, ANOVA), exploration of data types and data frames, and graphing/use of ggplot2. After completion, particpants were able to perform basic statistical analyses and could plot their data using R. Biotech Times Magazine • biotech.ucdavis.edu • 5

2019 - 2020 BIOTECH SYSTEM OUTREACH The BioTech SYSTEM regional Alonna Wright, Tiffany (Yue) Expanding Horizons K-14 education consortium was Zhang. Research STEM-Talks founded in 2005 and serves as High School E-Mentoring the primary outreach arm of the Research STEM-Talks Elementary School STEM Fairs Biotechnology Program. DEB Several times per quarter in winter students continue to be generous and spring, we host high school “DEB students continue in sharing their love of science students, teachers and parents for to be generous in and engineering with kids and a seminar on biotech basics and sharing their love communities in the region. several ~5 minute “STEM-Talks” of science and Though we were not able to host given by DEB volunteers. This is a engineering with kids our annual Picnic Day experiments win-win educational activity, with and communities in or the Teen Biotech Challenge our visitors getting a look at the the region” Awards event during spring latest biotech-related research and quarter due to the pandemic lock- DEB students getting a chance to down, we still reached hundreds perfect their sci comm skills for of middle and high school kids general audiences. After the STEM- during fall quarter 2019 and winter Talks, DEB volunteers take small quarter 2020. Sincere thanks to the groups on a brief campus walking volunteers who helped with the tour to the Coffee House and outreach events described below! answer questions about research, grad school and UC Davis. Please note that we’ve recently retired the external BioTech Though we were not able to host SYSTEM website and have visitors during spring quarter 2020 established a site farm page for due to COVID-19 lockdown, we still this effort: https://biotech.ucdavis. reached ~130 high school visitors edu/biotech-system. this academic year. STEM-Talks covered a wide variety of STEM Expanding Your Horizons 2019 topics, including biofortification DEB volunteers were in great form of crops, bovine genomics and at the Expanding Your Horizons GWAS, environmental toxicology event held at Sacramento State (PCB persistence), reducing University on November 2, 2019. livestock emissions of greenhouse The one-day science and math gasses, measuring cell autophagy, conference is tailored to inspire nanomedicine to treat joint middle school girls to consider injuries, trogocytosis or “cell training and careers in STEM. This nibbling” by infectious amoebae, fall, we hosted a biotech careers protein structural chemistry, booth and hands-on demos for and plant synthetic biology and ~200 participants. 2019 EYH metabolic engineering. Volunteers: Hannah Brinkman, 6 • Biotech Times Magazine • biotech.ucdavis.edu

Top Left: Nitin highlighted his research in understanding cell autophagy Bottom Left: Tiffany Zhang and Alonna Wright explained genetic engineering and industrial enzymes in bioprocessing while the students performed an experiment with chymosin and non-fat milk to make “cheese”. Right Photo: Hannah Brinkman hosted a personal genomics activity at EYH2019 • November 8, 2019 – South San Francisco Unified Kawakita, Hyunsoo Gloria Kim, Director Emerita School District (Genentech sponsored, ~50 Judy Kjelstrom, Mirko Ledda, Sharon Lee, Yixing Lu, students and teachers): Nitin Sai Beesabathuni, Linda Ma, Kasey Markel, Lucas McKinnon, Jessica Ellen Lai, Lucas McKinnon and Rene Suleiman Mizzi, Alan Nguyen, Saghi Nojoomi, Beatriz Pereira, • February 21, 2020 – Sheldon HS (~50 students and Kevin Pham, Peter Sariano, Sara Sukenik, Rene teachers): Amanda Agosto Ramos, Marcus Deloney, Suleiman, Tina Truong, Lei Wei, Toni West, Sydney Anna Naranjo and Rene Suleiman Wyatt, Phoebe Yam, Cody Yothers and Kelly Zacanti. • March 13, 2020 – Vanden HS (~30 students and teachers): Sambid Adhikari, Cody Bekkering and (Note: Tracking participation in off-campus efforts Bianca Yaghoobi can be spotty, so if you are a DEB student who volunteered for e-mentoring, but do not see your High School E-Mentoring name listed, please let us know so that we can Sheldon High School Biotech Academy organized make the correction.) an eight-week e-mentoring program to link their senior students with biotech researchers in the Elementary School STEM Fairs region. DEB students, alumni and administrators Once again, DEB volunteers helped out with hands- comprise a large chunk of the mentors who offer on demos for the Smythe Academy of Arts and advice on developing professional skills and share Sciences Community Science Night in Sacramento academic “helpful hints” for successfully navigating on October 24, 2019, organized by teacher Deanna higher education. DEB-affiliated mentors during Kigar. Many thanks to the Rodrigues lab members winter quarter 2020 included: who hosted the DEB tables at the event: Rachel Glory Bui, Lizbeth Camacho, Takeyah Campbell, Danielson, Alexandra Gulachenski, Jonathan Lin, Savannah Conlon, Anna Cowie, Sonny Elizaldi, and Jordan Sayre. Shea Feeney, Dayn Godinez, Jake Gonzales, Jake Gonzales, Eduardo Gonzalez, Noah Goshi, Naomi Hamada, Michelle Hu, Jessica Huang, Ryan Biotech Times Magazine • biotech.ucdavis.edu • 7

BIOTECH SYSTEM OUTREACH (CONT.) Ellen Lai led a GWAS activity to illustrate the main points in her STEM-Talk. Rene opted for a white board talk and regaled the group with her work in the Ralston Lab to fight global diarrheal disease caused by Entamoeba RT: Amanda Agosto Ramos, a first year gradu- ate student, shares about her previous research experiences, journey to grad school, and interests in plant synthetic biology and metabolic pathway engineering. TEEN BIOTECH CHALLENGE Teen Biotech Challenge 2020 was the final year for was unfortunately cancelled due to the COVID-19 this popular website design competition. Launched pandemic. Though we were unable to provide a final in 2005, TBC grew to reach ~300-350 California high awards event, the contest did take place (distance school students at ~15 schools each year. Funded learning!) and final entries were judged by the primarily by industry sponsorship and in-kind following DEB/campus volunteers: Annabel Alonso donation of work through our program. TBC has (post-doc, Winey Lab), Glory Bui, Laney Casella, Jonas served as important regional activity to connect high Calsbeek, Amber Flores, Angelica Guercio, Jessica school biotech teachers and students to the university. Huang, Hyunsoo Gloria Kim, Sharon Lee, Yulong Liu, We have hosted an on-site TBC awards event at UC Yixing Lu, Shiaki Minami, Sichong Peng, Gabrielle Davis from contest inception until 2020, when it Rossidivito, Eric Stevens, Lei Wei and Phoebe Yam. 8 • Biotech Times Magazine • biotech.ucdavis.edu

RT: Anna Naranjo describes her research into sus- tainable livestock production and how to use life cycle assessments to improve food systems. LFT: Sambid Adhikari talks about the importance of protein pu- rification and structural characterization for designing enzymes, therapeutics and other useful proteins in biotechnology.plant synthetic biology and metabolic pathway engineering. RT: Cody Bekkering outlines the crop breeding and engineering strategies for biofortification and improved human nutrition.engineering. First place TBC2020 Websites: Agricultural Biotechnology: Pranav Walimbe, Pranav Environmental Biotechnology and Planetary Mittal, Arsh Koneru Ansari (Folsom HS – Canty), Health: Parneet Kaur (Sheldon HS – Brennan), Biofuels: Biosensors: The Optimum Crop Monitor https:// pranav1077.wixsite.com/biosensors An Emerging Source of Energy https://parneetk2207. wixsite.com/mysite Computational Biology & Genomics: Melanie Molecular Tools: Hannah Velez (Sheldon HS – Cecil), Nguyen (Sheldon HS – Kosney), Precision Medicine: Rewriting the Blueprint https://hannahvelez13. Care for the Individual https://nguyenmel03.wixsite. wixsite.com/mysite com/precision Regenerative Medicine & Biomedical Engineering: Drug Discovery & Biomanufacturing: Naomi Kaitlynn Le (Sheldon – Brennan), Wound Healing Ferrer (Sheldon HS – Cecil), Fighting Cancers with and Cicatrization: Repairing the Human Body https:// Virotherapy https://naomijannae099.wixsite.com/ kaitlynnthuyle.wixsite.com/woundhealing fighting-all-cancers (Grand Prize Winner) Biotech Times Magazine • biotech.ucdavis.edu • 9

DEB INTERNSHIPS MIC 282 IS A REQUIREMENT FOR ALL DEB STUDENTS One of the most unique and rewarding experiences that DEB students have during training is the professional internship. The internship is a required course graded by DEB Chair, Prof. Abhaya Dandekar and coordinated by DEB Director, Dr. Denneal Jamison-McClung. DEB Internships that occurred since the fall of 2019 are listed below: 10X Genomics, Pleasanton, CA: Lisa Johnson (nee Cohen) 23andMe: Akhila Bettadapur Amyris, Inc, Emeryville, CA: Stephen Bolus Atul Parikh’s Lab - Cross College: Daniel Lewis BioMarin Regulatory Affairs, Novato, CA: Prema Karunanithi CA State University: Lucas McKinnon California Safe Soil, LLC, McClellan, CA: Oscar Munoz DEB instructor - R course: Don Gibson Genentech, SF: Sukriti Gakhar, Allison Hsiah, Chandrima Majumdar, Shanaya Shah, Xiaoxiao Yang, Yihui Zhu Gilead (Regulatory Affairs), Oceanside, CA: Kelly Zacanti iBio CMO, Bryan, TX : Kantharakorn Macharoen Mills College (Oakland) instructor of Bio181 (Immunology): Riley Allen Phase Genomics, Seattle WA: Maika Malig Regeneron Pharmaceuticals, Inc, Tarrytown NY: Alireza Tafazzol Roche, Pleasanton, CA: Amirhossain Bolandparvaz STEM Center Coordinator at American River College, Los Rios Community College District, Sacramento CA: Javier Garcia Takeda Pharmaceuticals in Cambridge, MA: Johnathon Li TechAccel, LLC: Katherine Murphy UC Davis Institute for Food & Agricultural Literacy (IFAL) and Science Says!: Jacklyn Woods (nee Whitehead) LFT: Genentech campus in San Francisco 10 • Biotech Times Magazine • biotech.ucdavis.edu

DEB GRADS! Congratulations go out to our DEB graduates! Below is PI) a list of DEB students who graduated since summer of Hannah Petrik, PhD in Biochemistry, Molecular, Cellular 2019. & Developmental Biology (Aiming Yu, PI) Betsy Alford, PhD in Plant Pathology (Doug Cook, PI) Marc Pollack, PhD in Microbiology (Bryce Falk, PI) Riley Allen, PhD in Biomedical Engineering (Jamal Anita Rajamani, PhD in Biomedical Engineering Lewis, PhD) Sima Asadi, PhD in Chemical Engineering (William (Anthony Passerini, PI) Ristenpart, PI) Shanaya Shah, PhD in Biochemistry, Molecular, Cellular Katherine Beglinger, PhD in Biochemistry, Molecular, Cellular & Developmental Biology (Chris Fraser, PI) & Developmental Biology (Wolf-Dietrich Heyer, PI) Stephen Bolus, PhD in Plant Pathology (Jorge David Silberstein, PhD in Chemical Engineering (Karen Dubcovsky, PI) Nicole Coggins, PhD in Molecular, Cellular & Integrative McDonald, PI) Physiology (David Segal & Luis Carvajal-Carmona, PIs) Alireza Tafazzol, PhD in Biomedical Engineering (Yong Shea Feeney, PhD in Biochemistry, Molecular, Cellular & Developmental Biology (Katherine Ralston, PI) Duan, PI) Michael Fong, PhD in Biomedical Engineering (Dominik Sana Vaziri, PhD in Computer Science (Sharon Aviran, Haudenschild, PI) Sukriti Gakhar, PhD in Chemical Engineering (Marjorie PhD) Longo, PI) Yaxin Wang, PhD in Plant Biology (John Yoder, PI) Donald Gibson, PhD in Integrative Genomics & Genetics Jacklyn Woods (nee Whitehead), PhD in Biomedical (Siobhan Halloran, PI) Shawn Higdon, PhD in Plant Biology (Alan Bennett, PI) Engineering (Kent Leach, PI) Allison Hsia, PhD in Biomedical Engineering (Blaine Yongao (Mary) Xiong, PhD in Chemical Engineering Christianson, PI) Lisa Johnson (nee Cohen), PhD in Molecular, Cellular (Karen McDonald, PI) and Integrative Physiology (Titus Brown, PI) Britt Yazel, PhD in Neurosciences (Lee Miller, PI) Prema Karunanithi, PhD in Biochemistry, Molecular, Cellular & Developmental Biology (Philipp Zerbe, PI) Daniel Lewis, PhD in Integrative Genomics & Genomics (Cheemeng Tan, PI) Johnathon Li, PhD in Animal Biology (Dietmar Kueltz, PI) Alice Martinic, PhD in Nutritional Biology (Carolyn Slupsky, PI) Lauren Matelski, PhD in Immunology (Pam Lein, Pi) Lucas McKinnon, PhD in Plant Biology (Steven Theg, PI) Jared Nigg, PhD in Microbiology (Bryce Falk, PI) Jennifer Nill, PhD in Chemical Engineering (Tina Jeoh, Biotech Times Magazine • biotech.ucdavis.edu • 11

DEB STUDENT ACCOLADES Lft Top: Claire Shaw Rt Top: Marwa Zafarullah Bottom: Ellen Lai Next Page: Morgan Matson & Noah Siegel DEB STUDENTS’ 1. UC Davis Grad Slam Finalists ACCOLADES ARE included three DEB students. REGULARLY PUBLISHED They were: ON THE BIOTECH PROGRAM’S SOCIAL MEDIA OUTLETS Ellen Lai from the Integrative CHECK US OUT! Genetics & Genomics grad group presentation was on Why are cows so 12 • Biotech Times Magazine • biotech.ucdavis.edu lame? Claire Shaw, an Animal Biology graduate student gave her Grad Slam presentation on Meet Your Microbiome. Morgan Matson hails from the Chemistry grad group and her presentation was on Zap! Electrifying Bacteria for a Better Future.

2. DJ Darwin Bandoy is helping with science-based COVID-19 policy development and public education in the Philippines via participation on the University of the Philippines Pandemic Response Team. If you are the recipient of an award, For an explanation of his forecast model COVID- prestigious fellowship or other type of 19 in the Philippines, watch his short video honor - let us know. We’d love to brag HERE. This model employs an SIR model with about you on our social media outlets! reproductive number computed from incidence data in the Philippines. 3. Congrats to Marwa Zafarullah 5. Noah Siegel winning a NIH who recently won the UC Davis research supplement to study Emmy Werner and Stanley the lung microbiome Noah Jacobsen Fellowship. Marwa is a Ph.D. student in the Integrative Genetics and Genomics Graduate Group, Her research investigates the pathology of a rare neurodegenerative disease Siegel, was awarded a research supplement from @NIH to called Fragile X- Associated Tremor/Ataxia promote diversity in health research! Noah Syndrome (FXTAS). She is also a Keller Pathway Fellowship alumna. researches the lung #microbiome. That’s right, LUNG. He’s characterizing bacteria’s contributions to infant lung development after antibiotic treatment 4. Congratulations to Jackie Woods who was named the 2019 BME Outstanding Graduate Student. Jackie is from the Leach lab and her research is working to uncover and direct cell signaling within MSC spheroids for tissue repair. Biotech Times Magazine • biotech.ucdavis.edu • 13

2020 BIOTECH TRAINING RETREAT THIS WAS THE BIOTECHNOLOGY PROGRAM’S TWENTY NINTH ANNUAL TRAINING RETREAT! L ast March, the UC Davis Biotechnology Poster Winners: Program held their 29th Annual 1st Place - Morgan Matson, Chemistry Grad Biotechnology Training Retreat. We Group, in the Atsumi Lab presented “Electrical- were pleased to see the Genome Center Biological Hybrid System for Co2 Reduction in fill up with attendees, many of them presented Escherichia coli”. posters, gave STEM Talks or presentations on their 2nd Place - Mary Xiong, Chemical Engineering companies or professional journeys. Grad Group, in the McDonald/Nandi Lab talked about “Development and Characterizations of STEM Talk Winners: a Plant-Recombinant Therapeutic for Bone Loss 1st Place - Nitin Beesabathuni, Chemical During Space Missions”. Engineering Grad Group, in the Shah Lab gave A big thank you goes out to our industry and a talk on “An Engineering Approach to Measure campus partners who gave excellent talks. It Autophagy”. was also great to have our alums come back to present to the next generation of DEB students, 2nd Place - Yixing Lu, Food Science Grad Group, in we are very proud of them! the Nitin Lab presented on “Customizable Future The presenters were: Supplements: Matrix Effect on Bioaccessibility of Gian Oddone (DEB Alum): Research Manager Encapsulated Micronutrients”. Fermentation, Novozymes Cole Pearson: Group Leader Invertebrate Pest Audience Favorite - Angela Zhang, Chemistry Biology, Marrone Bio Innovations Grad Group, in the Atsumi Lab discussed“Microbial Production of Human Breast Milk Sugars”. 14 • Biotech Times Magazine • biotech.ucdavis.edu

Top: STEM Talk & Poster Presenters Rt Top: Genome Center Anita Rajamani (DEB Alum): Business Analyst, Lifescience Dynamics Limited Juan P Sanchez (DEB Alum): Sr. Environmental Scientist with the CA Dept. of Pesticide Regulation Zane Starkewolfe (DEB Alum): Associate Director New Venture Resources, Venture Catalyst, UCD It was also great to have our alums come back to present to the next generation of DEB students, we are very proud of them! ” Biotech Times Magazine • biotech.ucdavis.edu • 15

BIOTECHNOLOGY PROGRAM CONTAC TS Dr. Denneal Jamison-McClung - Director [email protected] Jacki Balderama - Program Manager [email protected] Kelly Meade - Financial Analyst [email protected]