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California Institute of Technology Division of Biology and Biological California Institute of Technology Division of Biology and Biological Engineering Annual Report 2016 Introduction Annual Report | Biology and Biological Engineering | 2016 Introduction The annual report for Caltech's Division of Biology and Biological Engineering (BBE) presents major research accomplishments of faculty, students, and staff during the previous academic year. This report covers October 1, 2015 to September 30, 2016. Front Cover Illustration Expression of the APETALA3 Gene in Young Arabidopsis Flowers Maximum intensity projection of a confocal z-stack of an Arabidopsis inflorescence expressing a fluorescent reporter for the APETALA3 gene (green). Plasma membranes were stained with propidium iodide (purple). APETALA3 controls the formation of petals and stamens. Credit: Nathanael Prunet and Elliot Meyerowitz Inside Back Cover Illustration A Clear Look at Chronic Infection MiPACT-HCR, a tissue clearing technique designed for bacterial retention and identification, was applied to a sputum sample from a cystic fibrosis patient. Confocal microscopy of cleared sputum revealed that Streptococcus (green) aggregated around host cells stained with WGA lectin (orange). DAPI staining (blue) shows host cell nuclei. Credit: Will DePas, Dianne Newman, Viviana Gradinaru, and Ruth Starwalt-Lee Back Cover Illustration Painting the Heart with Virally Delivered Fluorescent Proteins The Gradinaru lab and BI CLOVER center are part of a NIH SPARC-funded, multi-center effort to map the cardiac nervous system using viral vectors and tissue clearing. The image shows expression of three fluorescent proteins in cardiac myocytes and neurons that innervate the heart (thin axonal processes can be seen running diagonally across the image). The genes for the three fluorescent proteins were delivered to the heart by a mixture of novel adeno-associated virus (AAV) vectors injected into the vasculature. Image credit: Credit: Ben Deverman and Viviana Gradinaru News, Events, and People Annual Report | Biology and Biological Engineering | 2016 Press Releases 6 Annual Retreat 12 Ferguson Prize 14 Professorial Awards and Honors 15 Seminars 16 Named Lectures 23 News, Events, and People Annual Report | Biology and Biological Engineering | 2016 Symposiums 24 Current Graduate Students 33 Graduating Class of 2016 35 Financial Support and Donors 38 Faculty and Research Staff 41 Division Staff 46 Biology and Biological Engineering Faculty Research Updates 47 News, Events, and People Annual Report | Biology and Biological Engineering | 2016 Biology and Biological Engineering Facilities 230 Press Releases Annual Report | Biology and Biological Engineering | 2016 09/27/2016 Infections in Plain View Caltech researchers can now image bacterial infections in 3D by rendering cystic fibrosis mucus transparent. Dianne Newman, Viviana Gradinaru, Will DePasd 09/26/2016 Postdoc Named L'Oréal USA For Women in Science Fellow Moriel Zelikowsky is a neuroscientist with a passion for diversity in STEM fields. Moriel Zelikowsky, David Anderson 09/22/2016 Aravin and Hoelz Named HHMI Faculty Scholars The program is a new partnership between the Howard Hughes Medical Institute, the Simons Foundation, and the Bill & Melinda Gates Foundation. Alexei Aravin, André Hoelz 09/21/2016 Newman and Orphan Named MacArthur Fellows The "no strings attached" fellowships award $625,000 over five years. Dianne Newman, Victoria Orphan 09/15/2016 In the Light of Evolution Students reflect on experiences in a biannual evolution course which culminates in a trip to the Galápagos Islands. Rob Phillips, Victoria Orphan 09/01/2016 Multitasking Protein Keeps Immune System Healthy Caltech researchers have shed light on the 3-D structure of a protein crucial to immune system function. Pamela Bjorkman, Beth Stadtmueller 08/18/2016 Analyzing a Worm's Sleep New research from Caltech finds three chemicals that collectively work together to induce sleep in the roundworm C. elegans. Paul Sternberg, Ravi Nath 08/05/2016 Hushing the X Chromosome A new study highlights the role of DNA's three-dimensional structure in silencing genes. Mitch Guttman, Chun-Kan Chen 07/15/2016 Team of Proteins Works Together to Turn on T Cells Press Releases Annual Report | Biology and Biological Engineering | 2016 Scientists are learning how cells make the decision to become T cells. Ellen Rothenberg, Hao Yuan Kueh, Mary Yui, Shirley Pease, Jingli Zhang, Sagar Damle, George Freedman, Sharmayne Siu, Michael Elowitz 06/24/2016 Scientists Transform Lower-Body Cells into Facial Cartilage Researchers have discovered a “gene circuit” that can alter the fate of cells, turning them into ones that make cartilage. Marianne Bronner 06/13/2016 Dietary Fiber and Microbes Change the Gel That Lines Our Gut The Caltech study is the first to look at the structure of the mucus gel lining our gut and how it morphs in the presence of other substances naturally found in the gut. Rustem Ismagilov 05/20/2016 Oka Receives McKnight Award Yuki Oka, assistant professor of biology, will receive the 2016 McKnight Scholars Award. Yuki Oka, Kai Zinn, Thanos Siapas 05/18/2016 A Feeling Touch Caltech biologist Richard Andersen is working to incorporate a sense of touch into the neural prosthetics he has been helping develop for years—devices implanted in the brain that allow a paralyzed patient to manipulate a robotic arm. Richard Andersen 05/06/2016 When Beneficial Bacteria Knock But No One is Home Probiotic therapies hold promise for the treatment of intestinal disorders, but Caltech researchers reveal why they may not work for all patients. Sarkis Mazmanian, Hiutung Chu 05/03/2016 Seven from Caltech Elected to National Academy of Sciences Three faculty members and four alumni have been elected to the National Academy of Sciences. Ray Deshaies 04/21/2016 American Academy of Arts and Sciences Elects Two from Caltech Hirosi Ooguri and Rob Phillips have been elected as members of the American Academy of Arts and Sciences. Rob Phillips 04/20/2016 Press Releases Annual Report | Biology and Biological Engineering | 2016 Mapping Neurons to Improve the Treatment of Parkinson's Caltech researchers have mapped out a circuit of neurons that is responsible for motor impairment— such as difficulty walking—in patients with Parkinson's disease. Viviana Gradinaru, Cheng Xiao 04/13/2016 Midnight Blue: A New System for Color Vision A newly discovered mechanism of color vision in mice might help answer why the dimly lit night sky has a bluish cast. Markus Meister 03/23/2016 Living—and Giving—the Caltech Dream In appreciation for the opportunities Caltech afforded him, professor, vice provost, and alumnus Mory Gharib is paying it forward, supporting new generations of Caltech graduate students through an endowed fellowship fund. Mory Gharib 03/17/2016 An Up-Close View of Bacterial "Motors" In two recent papers, Caltech biologists use state-of-the-art imaging to study the machinery necessary for cell motility. Grant Jensen, Yi-Wei Chang 03/11/2016 Learning to Program Cellular Memory Combining synthetic biology approaches with time-lapse movies, a team led by Caltech biologists has determined how some proteins shape a cell's ability to remember particular states of gene expression. Michael Elowitz, Lacramioara Bintu, John Yong, 03/10/2016 Rothenberg Wins Feynman Prize The 2016 Richard P. Feynman Prize for Excellence in Teaching has been awarded to Ellen Rothenberg, the Albert Billings Ruddock Professor of Biology. Ellen Rothenberg 03/02/2016 Caltech Bioethics Forum: HeLa Cells in the Lab A panel of Caltech faculty examines the ethics of using Henrietta Lacks’s cells along with issues of privacy, informed consent, and who profits from the technologies her cells engendered. David Baltimore, Ellen Rothenberg, Barbara Wold, Changhuei Yang 02/24/2016 Gradinaru and Benardini Receive Presidential Early Career Awards Viviana Gradinaru and James Benardini have been named as recipients of the 2016 Presidential Early Career Award for Scientists and Engineers. Viviana Gradinaru Press Releases Annual Report | Biology and Biological Engineering | 2016 02/18/2016 Studying Memory's 'Ripples' Caltech neuroscientists have looked inside brain cells as they undergo the intense bursts of neural activity known as "ripples" that are thought to underlie memory formation. Thanos Siapas, Brad Hulse, Evgueniy Lubenov 02/17/2016 A Gene That Helps Regulate Sleep Sleep is still a mysterious process that is difficult to study in vertebrate animals. By conducting a genetic screen in zebrafish, biologist David Prober and his colleagues have identified a gene that seems to serve as nature's stimulant. David Prober, Cindy Chiu, Jason Rihel 02/04/2016 Geobiologist Honored by National Academy of Sciences Lori Dajose Dianne Newman has been awarded the National Academy of Sciences Award in Molecular Biology. Dianne Newman, David Baltimore 02/02/2016 Rosens Recharge Support for Bioengineering Caltech board chair emeritus and longtime Compaq chairman Benjamin M. (Ben) Rosen (BS ’54) and his wife, Donna, have made a bequest commitment to advance scientific exploration at the intersection of biology and engineering. 02/01/2016 Delivering Genes Across the Blood-Brain Barrier Caltech biologists have developed a vector capable of noninvasive delivery of genetic cargo throughout the adult central nervous system. Viviana Gradinaru, Paul Patterson, Ben Deverman 01/11/2016 A Healthy Start Explore the origins of Caltech's joint MD/PhD programs, which have helped dozens of students develop expertise in both basic science and clinical
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