Welcome to BBE!
Fiona Ristic, Research Technician Assistant
Karla Vargas, Laboratory Support - Glass Wash Facility
Izabela Giriat, Research Scientist - Gradinaru Lab
Albert Zhou, Functional Genetic Technician - Parker Lab
FNU Aswini Babu, Research Technician Associate - Bronner Lab
Shelley Diamond and Her Wife Featured in a Book!
Shelley Diamond and her wife Barbara Belmont are featured in the book "Queer Power Couples: On Love and Possibility". It's a photographic celebration of queer love and excellence offering a glimpse into the journeys that led to meaningful relationships and thriving careers.
Welcome Postdocs!
Tara Chari, Pachter Lab
Orlando Chirikian, Zernicka-Goetz Lab
Sergio de la Rosa, Zernicka-Goetz Lab
Melanie Ernst, Voorhees Lab
Akash Garg, Cai Lab
Jialong Jiang, Thomson Lab
Emily Laubscher, Van Valen Lab
Andrew Perez, Guttman Lab
Tianli Qin, Bronner Lab
Morgan Schwartz, Van Valen Lab
Dan Utter, Orphan Lab
Postdoc Events
Game Night
Our postdoctoral reps organized this year's second Postdoc Game Night at Chen, and it was a FUN! The evening was alive with Indian food, music, and a variety of friendly games. Embracing the 'Engineering' in 'BBE,' teams competed to build the tallest marshmallow towers. It was a close contest, but we had a winner! Stay tuned for the 3rd Postdoc Game Night.
Please contact Emma Boxer for more information regarding Game Night. Ext. 6845, eeboxer@caltech.edu
Caltech Core Facility Event
June marked another postdoc social, featuring the second Caltech Core Facility event focused on BBE-specific Core facilities. Attended by over 120 BBE researchers, the event included poster presentations by the core facilities and engaged participants in enriching scientific discussions. Both new and veteran core facility members appreciated the event, expressing enthusiasm to join us next year.
Please contact Sayan Dutta for more information regarding the Core Facility Social. Ext. 6862, sdutta2@caltech.edu
Cool Ales Event
The June 'Cool Ales' event, organized by BBE postdoc representatives in collaboration with the Caltech Postdoc Association, was a great success! The gathering saw enthusiastic participation from postdocs across various divisions, who enjoyed a delightful array of food and drinks amidst lively conversations.
Call for BBE Postdoc Reps
BBE is looking for postdoc representatives for the 2024-25 term. Join the team and work towards building your leadership skills. If you're interested, please reach out to Stefany Nielsen (snielsen@caltech.edu) or any of the current postdoc representative: Sayan Dutta (sdutta2@caltech.edu), Pallavi Panda (ppanda@caltech.edu), and Emma Boxer (eeboxer@caltech.edu).
Please contact Stefany Nielsen, Postdoctoral and Visitor Programs Manager, for questions or additional information regarding BBE Postdocs.
BBE Spring Party 2024
The BBE Spring Party held on May 10th was a well-received educational and fun event! Faculty, postdocs, students and staff shared 3-5 minute talks about the interesting work happening in their areas.
Participants included:
- Georgia Squyres, Postdoc
- David Anderson, Faculty
- Stephen Ranson, KML
- Mackenzie Thurston, NB Grad Student
- Prashant Bhat, Postdoc
- Kate Malecek, Green Labs
- Blade Olson, BE Grad Student
- Michael Dickinson, Faculty
- David Zierler, Caltech Heritage Project
- Masami Hazu , BI Grad Student - WiBBE
After the presentations, the Alice Huang Leadership Award was announced followed by a reception.
The awardee for 2024 is Liz Ayala for unwavering support of the Biology graduate program and dedication and guidance to graduate students, faculty, and staff in the division.
Congratulations Liz!
Liz Ayala has worked at Caltech for 45+ years, in a variety of positions, primarily Option Manager for Biology but most recently as Academic Affairs Manager in BBE. She genuinely cares about staff, students and faculty and truly gives her all, working long hours if need be, to ensure all needs are met. Over the years, Liz has been supportive of countless individuals in the Caltech community and she is a terrific resource to everyone: she does not shy away from offering assistance to others outside of her own division, while asking for nothing in return.
Liz offers insightful guidance on an array of topics and is well versed on all things related to academic affairs. Her humble confidence exudes leadership and grace. Countless students have been assisted by her gentle direction and all of the BBE Options have been positively impacted by her wisdom. Her many years of service show her dedication to the Caltech community, making her a gem and role model to us all.
Caltech Bioscience Industry Connections
Hosted by the Caltech Bioscience Industrial Partners Program (CBIPP), this event on May 17th, 2024, bridged the divisions of Biology & Biological Engineering (BBE), Chemistry & Chemical Engineering (CCE), and Engineering & Applied Science (EAS) for an evening of connection and collaboration amongst the life sciences community. The evening consisted of networking, live music by the Caltech Jazz Quartette, amazing drinks and food, and even a raffle!
This event engages students and postdocs who express an interest in pursuing careers in the life sciences. Through a series of activities and events like the Caltech Bioscience Industry Day and the winter quarter Tech Talk series, CBIPP facilitates connections between talented individuals and industry professionals. This event is open to the entire Caltech community, including alumni, as well as current CBIPP partners and interested organizations!
2024 Staff Service Awards
The 69th Annual Staff Service & Impact Awards were held on May 23rd in Beckman Auditorium. It's an annual tradition celebrating the outstanding community of staff members and the important work they do to advance the mission of the Institute.
Service awards are presented in recognition of length of service, with the first award bestowed at the 10-year mark. Congratulations to the following BBE Staff!
In appreciation of their service, the division issued embroidered jackets to the recognized BBE staff!
BBE Retreat 2024
SAVE THE DATE!
September 27th-29th
The annual BBE Retreat is a chance for BBE grad students, postdocs, research staff and faculty to share and discuss diverse research from across the division while enjoying food, music, and entertainment in a fun, family friendly event.
This year's retreat will be held at the beautiful Zachari Dunes at Mandalay Beach Resort in Oxnard.
Please register by August 9, 2024!
The class of 2024 has faced unique challenges due to the COVID-19 pandemic, so this year's event proved particularly celebratory. Graduate students relished the moment, remembering the obstacles they had to overcome during their degree programs.
At the ceremony, keynote speaker Jensen Huang, founder and CEO of NVIDIA, delivered a thoughtful address to graduates. NVIDIA, a pioneer in accelerated computing, is one of the most valuable companies in the world and is credited with inventing graphics processing units (GPUs), which have helped fuel the artificial intelligence revolution.
Excerpts taken from an article written by Julia Ehlert
Alex Burr and Chris Pukszta Recipients of the Park S. Nobel for Excellence Award
This prize recognizes undergraduate students demonstrating outstanding achievements within the Division of Biology and Biological Engineering at Caltech.
Mengyu Liu Awarded Dr. Nagendranath Reddy Biological Sciences Thesis Prize
The Reddy prize is awarded to the graduating female Ph.D. candidate in the Division of Biology and Biological Engineering who has produced the outstanding thesis in the biological sciences or bioengineering for the past year.
John Ciemniecki Awarded Lawrence L. and Audrey Ferguson Prize
The Ferguson prize is awarded to the graduating Ph.D. candidate in biology and biological engineering who has produced the outstanding doctoral thesis for the past year.
Surya Narayanan Hari and Mark Zhang Awarded 2024 Chen Institute Diversity and Inclusion Awards
Surya has a proven record of working to improve DEI at Caltech, the wider community and in STEM. Surya participates in programs that provide STEM education to local middle schools as well as mentoring Caltech students. On campus Surya is involved in a number of organizations. During his time on the Everhart Lecture series committee he recognized the underrepresentation of female scientists and successfully advocated for an additional award to be made to a female identifying scientist. As a member of Caltech's Organization of the Associated Students of the Indian Subcontinent (OASIS) club Surya has raised funds and organized religious festivals like Holi, Diwali and Ramadan. In his capacity as president of the Caltech Sovereignty club, Surya has been working to enriched Caltech's intellectual landscape by inviting speakers from diverse disciplines.
Mark has been involved in leading a number of initiatives and programs to improve DEI at Caltech. He is a key member of the BBE DEI committee. He was invited to join the committee in 2023 after his efforts to promote DEI issues at Caltech came to the attention of committee members. He compiled data concerning recent years' graduate student recruitment of URMs and suggestions for ways that Caltech can address the underrepresentation of Black, Latinx, and Native American student populations in upcoming years. He highlighted three important areas for increasing the numbers of underrepresented scientists in STEM: 1) Recruitment, 2) Retainment, and 3) Graduation and Career Placement. He has worked tirelessly to improve each of these areas for recruitment into BBE grad programs. In addition, he has overhauled the BBE DEI representatives' program (in which each lab has 1-2 representatives who initiate DEI-related activities in their lab) to institute a formal procedure in which researchers apply to be a representative.
Peiwei Chen Wins Harold M. Weintraub Graduate Student Award
Peiwei Chen, who received his PhD in biology from Caltech in June 2024, has been awarded the Harold M. Weintraub Graduate Student Award by the Fred Hutchinson Cancer Research Center. A total of 12 graduate students in the United States and abroad received the honor in 2024.
Fred Hutch announces 2024 Harold M. Weintraub Graduate Student Award recipients
Graduate Student Chiara Berruto Named Recipient of the NSF Graduate Research Fellowship
The purpose of the NSF Graduate Research Fellowship Program (GRFP) is to help ensure the quality, vitality, and diversity of the scientific and engineering workforce of the United States. A goal of the program is to broaden participation of the full spectrum of diverse talents in STEM.
Undergraduate Student Sophia Wu Named 2024 Goldwater Scholar
Sophia Wu is one of three Caltech undergraduates that have been awarded the esteemed Goldwater Scholarship for 2024. The scholarship recognizes outstanding students and provides each recipient with $7,500 to cover tuition and expenses for each remaining year of their degree program.
"I am super grateful to be awarded the Goldwater Scholarship. This scholarship allows me to continue pursuing my passion for enzyme engineering with even greater enthusiasm and focus. I want to thank all my incredible mentors and peers who have guided and inspired me throughout my journey in science. Looking ahead, I'm excited about the potential to transform how we approach cancer treatment, making significant strides toward innovative and more effective therapies."
Ditch Day!
Another successful Ditch Day for the books, with BBE undergraduates engaging in inventive activities throughout campus.
For over a century, Caltech students have celebrated Ditch Day, an annual tradition where seniors skip school and leave behind intricate puzzles and challenges, known as "stacks," for the underclass students to solve. This year's event showcased the ingenuity, creativity, and distinctive sense of fun that epitomizes the Caltech experience.
Alexander Viloria Winnett Wins 2nd Place in the Three Minute Thesis (3MT) Competition
The Three Minute Thesis competition challenges Caltech graduate students to explain their research in an engaging and clear three-minute talk intended for a non-specialist audience. On Thursday, April 18, the Library held the annual 3MT event in the Chen Lecture Hall. Alexander Viloria Winnett (Ismagilov Lab) took the audience on a wild ride, winning second place with "The Viral Load Roller Coaster Shows Us How to Best Test for COVID-19."
Nucleate Final Pitch 2024
Nucleate is a student run non-profit organization that educates current academic trainees by helping them to translate their technologies out of their labs into a startup. The program pairs scientists with Intellectual Property (patents) with MBA students then puts the teams through a mentorship and expert workshop program to refine their strategic startup plans. The program culminates in a Final Pitch Showcase which was held on May 20th at the UCLA Ackerman Union Ballroom.
The Final Pitch showcase for the third Activator cohort had a great turnout of attendees spanning a range of sectors including venture capital, academia, biotech industry, and law. Over the course of the program, Nucleate helps graduate students and postdocs from the LA area translate their research into bioscience startups through hands-on workshops and connecting the teams to mentors across consulting, IP law, venture capital, and startups. In 3 years, the Nucleate Activator program as a whole has formed and supported a total of 143 startup teams who have raised $310M in funding to develop technologies like protein sequencing (Glyphic), drug design (Manifold Bio), and microbial fertilizer (Ivu Biologics).
This year, there was one team representing Caltech, Syntaxa, who took home the MilliporeSigma Regional High Impact Culture Award and the Genentech Regional Diversity, Equity, and Inclusion Prize!
The activator program is a great way to get hands-on knowledge of what it takes to translate a technology from the lab to the market. If you are interested in being a part of the program next year, please fill out this form: https://airtable.com/appzKKZnxEtNGSPcz/pagiDbkF6Rfmfcw5N/form
If you are interested in working on Nucleate LA leadership and coordinating events, selecting teams, and networking with the LA bioscience community, please fill out this form: https://airtable.com/appzKKZnxEtNGSPcz/pagAudCpBGj6QPdrr/form
Welcome New Grad Students!
BIOLOGY
Banat Kaur Chawla, University of Cambridge, UK
Kemal Demirer, University of Michigan, Ann Arbor
Ayse Damla Durmaz, Istanbul Technical University
Kaoru Okamoto, Agnes Scott College
Benjamin Simpson, Northeastern University
Patrick Simpson, University of California, Berkeley
Hejun Tang, Nanjing Tech University
Yuqi Wang, Smith College
MD/PHDs
Santi Bhattarai-Kline (UCLA MSTP), University of California, Berkeley
Sarah Garzione (KPSOM), University of Virgina
Emily Meehan (KPSOM), University of Pittsburgh
BIOENGINEERING (BE)
Ellen Adams, Swarthmore College
Gohta Aihara, John Hopkins University
Martin Holmes, California Institute of Technology
Yunrui Lu, Dartmouth College
Matthew Ocanas, University of Texas at Austin
Anh Phung, University of Cambridge
Sandra Temgoua, Yale University
Sixiang Wang, John Hopkins University
Jiayi Yin, Stanford University
COMPUTATION AND NEURAL SYSTEMS (CNS)
Sevan Brodjian, University of Illinois, Urbana Champaign
Alexander Detkov, University of Alberta
Ruoxi Wang, University of California, San Diego
Fei Yin, University of California, San Diego
Fengqing Yu, University of Toronto
Hyoseo Yoon, Northwestern University
NEUROBIOLOGY
Ruoyi Chen, Carnegie Mellon University
Hongzhou Li, New York University Shanghai
Haoru Li, University of Science and Technology, China
Amanada Wu (NB/PhD), University of California, Los Angeles
Man Ching Sin, Cornell University
Spotlight on Procurement Drop-In Sessions
In May, Procurement launched monthly training drop-in sessions focusing on Procurement. These sessions aim to provide an open platform for Caltech customers to ask questions and gain insights into various aspects of Procurement, including Purchasing, Accounts Payable, Specialty Team, Supplier Management, Travel and P-Card.
The next sessions are scheduled for July 25th and August 15th at 10 am.
Please Contact Sue Zindle for more information or register on "My Learn" through access.caltech.edu.
PST Sneak Peek!
Crossing Over: Art and Science at Caltech, 1920–2020
A PST ART: Art & Science Collide Exhibition September 27 – December 15, 2024
This Fall, Caltech will host Crossing Over: Art and Science at Caltech, 1920–2020, an expansive public exhibition which will weave together the history of science with historical and contemporary art. How, it will ask, have science and engineering institutions like Caltech used visual culture—scientific images, art, and architecture—to construct themselves and produce discovery and invention?
The exhibition will answer this question using displays of approximately 400 objects, most drawn from the Caltech Archives and Special Collections, including rare books, paintings, drawings, photographs, scientific instruments, molecular models, and films.
Among six other installations, Chen Institute will host an optical lens sculpture by Helen Pashgian, who was an artist-in-residence at Caltech from 1969 to 1971.
Crossing Over is a part of the Getty Foundation’s major initiative PST Art: Art & Science Collide, along with JPL’s The Stars Are Calling, CaltechLive performances, and about 50 other exhibitions at Southern California art museums and other institutions.
The exhibition is a project of Caltech Library. It is directed by University Archivist Peter Collopy, curated by independent curator Claudia Bohn-Spector, and designed by architect and ArtCenter professor Tim Durfee.
More information on all installations and performances will be advertised closer to launch date.
Kavli Nanoscience Institute Celebrates 20 Years
The Kavli Nanoscience Institute, a 21st century center for science and engineering at the nanoscale, celebrated its 20th anniversary with a special symposium and a fireside chat between President Thomas F. Rosenbaum and 2022 Kavli Prize Laureate George M. Whitesides (PhD '64) from Harvard University on March 7–8, 2024.
Fisher Scientific Inventory Clearance Sale!
Fisher Scientific is pleased to inform you of an exclusive opportunity to enhance your laboratory resources at unmatched prices.
Enjoy 40-60% off select items in our Alles 181 stockroom, including Gibco cell culture media, restriction enzymes, UltraPure Water, sample prep kits, PCR enzymes, Lipofectamine, and more.
Act fast—this offer is first-come, first-served until inventory lasts.
Visit Alles 181 today to secure your purchases or contact Fisher Scientific if you have any questions.
Library News
Newly Purchased Content from Wiley
The Library recently purchased a number of reference works and electronic journal backfiles from Wiley. Relevant to BBE, they now have access to the reference source, Encyclopedia of Life Sciences. They also replaced older print editions of the following journals with electronic access:
• American Journal of Medical Genetics (1986-1995)
• Annals of Neurology (1977-1995)
• Developmental Genetics (1979-1996)
• European Journal of Immunology (1971-1995)
• Journal of Cellular Biochemistry (1985-1995)
• Journal of Neurobiology (1969-1995)
• Journal of Neuroscience Research (1975-1995)
• Molecular Reproduction & Development (pre-1996)
All of the purchased titles are turned on in their link resolver. People looking for articles in these titles should be guided straight to them. Please contact the library with any questions about this purchase, library@caltech.edu.
Need a Book that the Library does not Own?
If you ever need a book for class or for research that the library does not own, they are happy to get it for you! You can either suggest a book for purchase using this form or by emailing library@caltech.edu. You may also request the book via Docuserve (Inter-Library Loan). The Library's mission is to help you access the information resources that you need.
Kristin Briney specializes in helping scientists navigate information resources and in managing research data. You may contact her at briney@caltech.edu.
Join the monthly BBE Library Newsletter to learn more about Library news, events, and resources.
Mikhail Shapiro Selected as Fulbright U.S. Scholar for France
Mikhail Shapiro, the Max Delbrück Professor of Chemical Engineering and Medical Engineering, has been awarded the Fulbright-Tocqueville Distinguished Chair Award by the Franco-American Fulbright Commission. The award will support Shapiro's ongoing research and teaching at two institutions in France, ESPCI Paris – PSL and Inserm, during the 2024–25 academic year while he is on sabbatical from Caltech.
Bil Clemons and Ned Ruby Elected into Academy of Arts and Sciences
William M. (Bil) Clemons, Jr., the Arthur and Marian Hanisch Memorial Professor of Biochemistry, and Edward (Ned) Ruby, faculty associate in the Division of Biology and Biological Engineering, have been elected to the American Academy of Arts and Sciences, an honorary society founded in 1780 by John Adams, John Hancock, and others.
Clemons has been on the faculty at Caltech since 2005, specializing in structural biology. He earned his PhD from the University of Utah in 2000, researching under the supervision of Nobel Prize winner in Chemistry Venki Ramakrishnan. There, Clemons worked to determine the atomic-level structure of a small ribosomal subunit, helping to elucidate how proteins are made and the mechanism of antibiotics. Clemons next spent four years as a Damon Runyon Cancer Research Fellow at Harvard Medical School using X-ray crystallography to characterize the universal protein translocation channel.
Ruby, who is associated with Carnegie Institute for Science and Caltech, has done research on beneficial bacterial–host interactions for the past 40 years, and brought his lab to the Caltech campus in 2022 as part of Carnegie Science's move to Pasadena.
Alumna Doris Tsao Receives the Kavli Prize in Neuroscience
Alumna Doris Tsao (BS '96), now professor at UC Berkeley, is a recipient of the 2024 Kavli Prize in Neuroscience. She shares the prize with longtime collaborators Nancy Kanwisher of MIT and Winrich Freiwald of The Rockefeller University for their discovery of a specialized system within the brain to recognize faces.
Newest Cohort of Leadership Chairs and Named Professorships Announced
Leadership Chair
Viviana Gradinaru, Lois and Victor Troendle Professor of Neuroscience and Biological Engineering, Allen V. C. Davis and Lenabelle Davis Leadership Chair, Richard N. Merkin Institute for Translational Research, Director, Center for Molecular and Cellular Neuroscience, Director, Richard N. Merkin Institute for Translational Research
Named Professorships
Michael B. Elowitz, Roscoe Gilkey Dickinson Professor of Biology and Bioengineering, Investigator, Howard Hughes Medical Institute
Niles A. Pierce, John D. and Catherine T. MacArthur Professor of Applied and Computational Mathematics and Bioengineering, Executive Officer for Biology and Biological Engineering
Mikhail Shapiro, Max Delbrück Professor of Chemical Engineering and Medical Engineering Investigator, Howard Hughes Medical Institute
"Inherited Traits and the Molecules of Life"
A Reception to Celebrate the History of Genetics Research at Caltech
A new artistic display created by David Zierler in collaboration with David Glover, depicting the story of Caltech and genetics, from T.H. Morgan and the origins of the Division of Biology, to the Recombinant DNA Revolution and the birth of biotechnology is now displayed on the second floor of Parson-Gates.
A reception was held in May featuring opening remarks by Dr. Dave Tirrell followed by Dr. David Baltimore, who reflected on his personal appreciation of the Institute’s leadership in this field, which goes back to the 1950s.
An Indepth Look - Caltech Heritage Project
In 2022 President Rosenbaum asked David Zierler, the director of the Caltech Heritage Project, to design a new display to be featured in the four glass display cases on the second floor of Parsons-Gates. Drawing on his collaborations with Professor David Glover, Zierler decided that a history of genetics research at Caltech would be the ideal topic.
After two years of research and art design, the displays are now completed and available for viewing. The presentation begins with the origins of the Division of Biology at Caltech in 1928 (for its first eight years, there was no formal biology program at the Institute), and the recruitment of Thomas Hunt Morgan from Columbia and the relocation of the famous “Fly Room” to Caltech.
The panels go on to document how Caltech quickly became a world-leading center in genetics research, with the transition from the classical to the molecular age, with highlights that include the work Institute luminaries including George Beadle, Linus Pauling, Max Delbrück, and Ed Lewis, among others. The displays explain Caltech’s leading role in orienting genetics research toward the search for life beyond Earth, and for helping to create the revolution in recombinant DNA and the resulting launch in biotechnology.
The displays also feature the numerous Nobel Prize Laureates whose research in genetics and association with Caltech underscore the Institute’s leading role in science, along with 3D printings of a Drosophila Melanogaster (the common fruit fly), a Bacteriophage virus, and a DNA double helix, courtesy of the Institute’s TechLab.
The display presentation concludes with an artistic presentation of current and emeritus BBE faculty engaged in genetics research, which conveys that this is an ongoing story, and that the field has benefited by a diversification both of the research itself and the professors who continue to lead and redefine the field.
David Zierler, Caltech Heritage Project Director and Senior Strategist.
Debunking a Decades-Long Misconception about the Origin of the Vertebrate Sympathetic Nervous System - Bronner ("Neural crest origin of sympathetic neurons at the dawn of vertebrates" Nature, April 17)
How Insects Control Their Wings: The Mysterious Mechanics of Insect Flight - Dickinson ("Machine learning reveals the control mechanics of an insect wing hinge" Nature, April 17)
Birds Overcome Brain Damage to Sing Again - Lois ("Unsupervised restoration of a complex learned behavior after large-scale neuronal perturbation" Nature Neuroscience, April 29)
Genes Spatially Organize for Efficient mRNA Splicing - Guttman ("Genome organization around nuclear speckles drives mRNA splicing efficiency" Cell, May 8)
Fetal Cells Can Be Traced Back to the First Day of Embryonic Development - Zernicka-Goetz ("The first two blastomeres contribute unequally to the human embryo" Cell, May 13)
Brain-Machine Interface Device Predicts Internal Speech in Second Patient - Andersen ( "Representation of internal speech by single neurons in human supramarginal gyrus" Nature Human Behaviour, May 13)
A Window into the Brain - Andersen, Shapiro ("Functional ultrasound imaging of human brain activity through an acoustically transparent cranial window" Science Translational Medicine, May 29)
A New CRISPR-Driven Technology for Gene Drive in Plants - Hay, Oberhofer ("Cleave and Rescue gamete killers create conditions for gene drive in plants" Nature Plants, June 17)
Beetles Conquered Earth by Evolving Their Own Biochemical Laboratory - Parker ("The genomic and cellular basis of biosynthetic innovation in rove beetles" Cell, June 17)
Center for Evolutionary Science (CES)
Please mark your calendars for EVOxZANKOU seminar days featuring talks by professors and postdocs on evolution-related research while enjoying Zankou Chicken! September 12, October 3, and December 12.
For updates, please visit the CES website. If you would like to give a talk at an upcoming EVOxZANKOU Seminar, please sign up HERE!
Subscribe to the Center for Evolutionary Science’s email newsletter! You’ll be the first to know about all sorts of exciting things they have planned! Subscribe HERE.
Please contact Leah Bieltvedt, Evolution Center Program Administrator, for additional CES information; lbieltve@caltech.edu, ext. 2684
There's a lot going at KML. Check out their latest Newsletter!
If you would like to receive the latest news from KML, please join the mailing list by emailing kml-info@caltech.edu to sign up.
Please contact Stephen Ranson with questions regarding KML. sranson@caltech.edu, Ph. (949) 675-2159
Office of Environmental, Health, and Safety
How to Perform a Comprehensive Risk Assessment for AI Applications in Synthetic Biology
by Leyma P. De Haro, Ph.D., RBP, Assistant Biosafety Officer
Are you working on a project at the intersection of artificial intelligence and synthetic biology? Maybe you are using large language models (LLMs) to design new genes or leveraging AI-driven tools to enhance the efficiency of CRISPR-Cas9 targeting. While AI is revolutionizing productivity and innovation in synthetic biology, conducting a thorough risk assessment is important before embarking on a new project. But do you know where to start and how to perform a comprehensive risk assessment for AI applications in synthetic biology? I have developed several tools to guide you through this process (https://www.liebertpub.com/doi/full/10.1089/apb.2023.0031).
A Step-by-Step Guide to Biosecurity Risk Assessment for AI in Synthetic Biology
- Understand the Application and Context: Identify the specific AI applications and synthetic biology experiments involved. Use Table 1 to guide you through this identification process.
- Identify Potential Risks: Define or categorize the relevant risks in synthetic biology applications using Table 1.
- Assess Vulnerabilities and Threats of AI Technology: Using Table 2, identify applicable vulnerabilities or threats of the AI system.
- Evaluate AI System's Maturity and Automation Level: Use Table 3 to assess the AI system's maturity (emerging, current, obsolete, etc.) and Table 4 to evaluate its level of automation. This will help you understand potential risks and the degree of human oversight required.
- Determine Consequences and Risk Levels: Use Table 5 to determine potential consequences if risks materialize. Using the definitions in Table 6, assign a risk level (low, moderate, high) to each potential consequence based on its severity and probability of occurrence. Map the risk on a "likelihood versus consequences" chart using Figure 1.
- Develop and Implement Mitigation Strategies: Develop strategies to mitigate or manage each identified risk. Implement and integrate these strategies into the project's overall risk management plan.
- Monitor and Review: Continuously monitor the AI system and its interaction with synthetic biology applications for emerging risks or changes in the risk profile. Regularly review and update the risk assessment based on changes in the AI system, regulatory landscape, or new relevant information.
Following these steps ensures that your innovative projects at Caltech remain secure and responsibly managed. If you have any questions or would like to discuss, please reach out, and I will be happy to nerd out about AI with you.
Please contact Leyma De Haro with questions or concerns regarding Lab Safety. ldeharo@caltech.edu, Ext. 2427
Autoclaves in Chen and Broad Up and Running!
New autoclaves are fully operational in Chen B155E, 224Q, 265E, 324N, 384 and Broad 140, 344. We want you and your lab mates to use them! Be sure to have the proper training before using them.
Please contact Jesse Flores for additional information. Ext. 3641, floresj@caltech.edu
Green Labs Update
Green Labs Has Three Exciting New Adventures This Quarter!
Firstly, Green Labs is calling for presenters for Lightning Talks on September 20th. Green Labs is inviting labs to give 3-minute lightning talks highlighting sustainable initiatives their lab has implemented, or would like to implement, in their labs. Furthermore, we have some exciting updates to share about the first year of our sustainable pilot programs, including a year-long study comparing samples kept in -70˚C vs. -80˚C! We are providing food, drinks, a raffle, sustainable giveaways for attendees, and providing RocketBooks (sustainable notebooks) to our presenters. If you would like to attend or present at this event, please use the link here to RSVP!
Secondly, we have a new Instagram, so please follow us! Our first few posts have focused on the Spring Clean Event, for which we made a ton of resources, including our inventory sheets, chore maintenance schedule guides and chore checklists, recycling guides, and more! If you want to check out more photos of lab cleanups, check out our Spring Clean Event webpage.
Thirdly, in addition to Green Labs representatives Kate Malecek and Jaasiel Alvarez presenting on behalf of our group at the May 10th BBE Spring Event, we have several ongoing pilot programs, studies, monthly meetings, and are celebrating Green Labs Certified Labs! Green Labs Certification takes less than 30 minutes, but there are huge benefits. Your lab will even be awarded a brag-worthy plaque to post outside your lab, and your lab will also gain access to special deals and events, along with free energy-efficiency stickers for lab equipment, recycling bins, and recycling signage for your lab spaces, and exclusive educational tools. Certify your lab today!
Green Labs is a volunteer driven group working towards making labs more sustainable. If you are interested in volunteering, or if you have any questions, please email greenlabsinfo@caltech.edu, or sign up for meetings and/or mailing list!
Millard and Muriel Jacobs Genetics and Genomics Laboratory
The Millard and Muriel Jacobs Genetics and Genomics Laboratory (MMJGGL) provides genomic services to Caltech scientists and offers both short and long read sequencing using Illumina NextSeq2000 and Oxford Nanopore MinION platforms.
Recent improvements to MMJGGL workflows include the transition to XLEAP-SBS chemistry used on the Illumina NextSeq2000. XLEAP-SBS is a fundamentally new sequencing by synthesis (SBS) chemistry engineered for increased speed, greater fidelity, and more robustness. It introduces re-engineered fluorophore-coupled nucleotides with new blocks, linkers and dyes. The X-nucleotides have high heat resistance, are 50x more stable in solution and 500x more stable lyophilized, display 3 times faster block cleavage and reduce phasing/prephasing errors by more than 50%. XLEAP-SBS features a tailored X-polymerase engineered to incorporate X-nucleotides 3 times faster and with higher fidelity than the polymerase used in standard SBS.
XLEAP-SBS was first introduced on the NextSeq2000 platform with the release of P4 kits in May 2024. With output of up to 540 GB and 1.8 billion paired end reads, the P4 flowcell enables large-scale applications previously not optimally supported by NextSeq2000, such as deep single cell multiomics studies. In addition to higher output, greater accuracy, and faster run times, the new P4 kits offer a dramatic decrease in sequencing costs of more than 40% compared to the previous cheapest NextSeq2000 option, the non-XLEAP P3, with price per GB as low as $12 (300 cycle kit) and price per M paired end reads ranging from $1.6 to $3.6, depending on read length.
In June 2024, XLEAP-SBS chemistry was also launched on smaller P1/P2/P3 flowcells enabling run time improvements, higher accuracy and cost reduction compared to non-XLEAP kits. With 14 kit configurations and read lengths from 1x 50 bp to 2 x 300 bp, NextSeq2000 with XLEAP-SBS now offers broad platform utility with flexibility to expand application and scale efficiently.
Nanopore sequencing has undergone significant changes in recent months as well. The latest R10.4.1 flowcells in combination with the new K14 chemistry deliver simplex reads of Q20+ accuracy and are compatible with duplex reads, with data from both strands of the DNA molecule combined for single molecule accuracies of ~Q30. The K14 chemistry also offers higher yields compared to previous chemistry iterations. Together with the recent price decrease for sequencing consumables by Oxford Nanopore, this further increases the affordability of long-read sequencing. The latest neural network-based basecalling models are capable of accurately detecting base modification in both DNA and RNA from the native nanopore signal without the need for special library preparation procedures. Currently, detection of 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), N4-methylcytosine (4mC) and N6-methyladenosine (6mA) is supported for DNA, and N6-methyladenosine (6mA) and pseudouridine (pseU) for RNA. With increased interest in long-read sequencing on campus, MMJGGL is exploring possibilities of expanding Nanopore services by adding additional sequencing capacity and implementing new workflows, such as target enrichment or depletion of unwanted regions using adaptive sampling.
In addition to providing sequencing services, MMJGGL hosts a number of instruments that are available to Caltech researchers. These include Agilent 2100 Bioanalyzer, Qubit fluorometer, Nanodrop ND-1000 spectrophotometer and Agilent G2565 Microarray Scanner. In the coming weeks, we will be expanding the shared equipment pool by adding Thermo Fisher ViiA 7 and Roche LightCycler 480 II Real-Time PCR instruments. The shared equipment is reserved using the Clustermarket booking system and is free to use.
MMJGGL is located in the Kerckhoff Laboratory building, rooms 102-108.
For any questions about our services and pricing, please contact the Laboratory director, Igor Antoshechkin: email: igor.antoshechkin@caltech.edu, phone: (626) 395-5913
Please Welcome Professor Tejada to Kerckhoff!
Professor Julia Tejada is a paleobiologist that applies stable isotope methods to answer an array of ecological, physiological, and evolutionary questions. Her research program lies at the intersection of paleontology, organismal biology, systematics, and geochemistry, and integrates laboratory experiments and expeditionary fieldwork in understudied settings, like western Amazonia, Central Andes, and coastal areas of Peru.
Professor Tejada's main interests involve the characterization of the ecological evolution of vertebrates and ecosystems in the Neotropics (with a special focus on the Amazon rainforest), and understanding the physiological processes underlying stable isotope variation across organisms. A protagonist organism in her research are sloths, whose morphological and physiological oddities make them an interesting study system to test some of the truisms established on other more "traditional" mammals.
The Tejada lab occupies spaces on the second floor of Kerckhoff. The art on the lab walls depicts the megafauna that inhabited Los Angeles over the last 50,000 years, during the last Pleistocene ice age. This includes a mammoth, a sabre-tooth cat, and a giant ground sloth. It also pays homage to Chester Stock (1892-1950), a Caltech paleontologist and the second Chair of the GPS Division. He played a crucial role in the early excavations and research of La Brea Tar Pits fauna and other fossil vertebrates from Southern California and Northern Mexico. The illustrations on the walls are from one of his publications.
When Chester Stock passed away in 1950, Caltech decided not to continue this line of research. The money from selling his paleontological collection was used to start the geochemistry option. It’s come full circle now, as Professor Tejada combines both paleontology and geochemistry in her research.
Lunch and Learn Seminar - Optimizing Controls for Flow - July 16, 12:00-1:00pm, Kerckhoff 101 (Please RSVP)
Chen Institute Ice Cream Social - August 23, 4:00pm, Chen Sunken Zen Garden
EVOxZANKOU Seminar - September 12, 12:00-1:15pm - Chen 130
BBE Retreat - September 27-29, Zachari Dunes at Mandalay Beach Resort, Oxnard
All upcoming events can be found on the BBE Calendar (login required)
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Photo Credits: Jaasiel Alvarez, Igor Antoshechkin, Lauren Breeyear, Caltech, Tsui-Fen Chou, Sayan Dutta, Green Labs, Liz Hughes, Katie Fisher, Joan Sullivan, Kenya Zeigler,