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2011 Stanford Bio-X Fellowships

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2011 Stanford Bio-X Fellowships Bio-X fellowships 2011 The Bio-X Fellowships are made possible by various gifts in order to promote interdisciplinary research for promising scientists working on projects that bridge the gap between biology and other fields. Students are encouraged to work collaboratively with professors in different departments or schools, drawing on expertise campus-wide. NEW ADVANCES IN SCIENCE AND ENGINEERING Bio-X Fellowships Bio-X Graduate Student Fellowships 2011 Pages 2-5 Bio-X Graduate Student Fellowships 2010 Pages 6-8 Bio-X Graduate Student Fellowships 2009 Pages 9-11 Bio-X Graduate Student Fellowships 2008 Pages 12-13 Bio-X Graduate Student Fellowships 2007 Pages 14-15 Bio-X Graduate Student Fellowships 2006 Pages 16-17 Bio-X Graduate Student Fellowships 2005 Page 18 Bio-X Graduate Student Fellowships 2004 Page 18 Bio-X Postdoctoral Fellowships Page 19 Bio-X Graduate Student Fellowships 2011 Ron Alfa Jing-yu Cui Neurosciences/MSTP Electrical Engineering Professor Seung Kim (Developmental Biology) Profssor Craig Levin (Radiology) Diabetes mellitus is a chronic disease defined clinically Jing-yu is designing algorithms and systems for real- by increased blood glucose levels resulting from de- time cardiac Positron Emission Tomography (PET) for creased peripheral insulin sensitivity or impaired in non-invasive in vivo visualization of molecular signa- insulin secretion by pancreatic beta cells. While dia- tures of disease and guidance of surgical interven- betes mellitus is historically one of the oldest diseas- tions. Jing-yu applies the state-of-the-art technologies es, the complex genetics underlying the most preva- in computer graphics, optimization, and computer lent form, type-2 diabetes mellitus (T2DM), are only vision for removing motion artifacts and speeding up beginning to be elucidated. Ron’s work is directed at the imaging process by hundreds of times to enable harnessing the powerful genetics of the fruit fly, Dro- real-time visualization of molecular activities in sophila melanogaster, to study the genetics of diabetic cardiology. states. To this end, he is drawing on approaches from the neurosciences and bioengineering to study metab- Christopher Emig olism and glucose homeostasis in the fly. Bioengineering Craig Buckley Chemical Engineering Professor Stephen Quake (Bioengineering) De novo genetic material construction enables the complete programmatic control of genetic systems, paving the way for advances in biological research, Professor Alex Dunn (Chemical Engineering) molecular medicine, fuels, environmental remediation, The motor protein dynein contains a component materials, and countless industrial processes. The termed the linker that is predicted to generate the Quake lab is building a device for rapid fabrication of force that drives cytoplasmic dynein stepping along single DNA molecules to enable iterative engineering microtubules; however, its actual force-generating of biological systems. abilities have never been directly examined. Craig will use single molecule techniques to perform the first direct test of the hypothesis that the linker is the primary force generating mechanical element in dynein. If it is, he will map out the energetic surface underlying force production by tracking the linker swing in real time. These measurements will elucidate the mechanism of dynein force production and test fundamental models of motor protein biophysics. Robots from the Salisbury lab Page 2 Denitsa Milanova lows a new "multi-scale" modeling approach where Bio-X Medtronic Fellow improved macro-scale continuum models are directly Mechanical Engineering linked to micro-scale models of these molecular mechanisms. Due to its well-characterized regular and hierarchical structure, the human cornea is his target tissue. A coordinated approach between mod- Professor Annelise Barron (Bioengineering) eling and novel experimentation at different scales Most would agree that extracting accurate, quantita- combines areas of biology, chemistry, imaging, and tive diagnostic information from biological samples, applied mechanics to engineer a computational model FAST, is “difficult.” The challenging part of the analy- for direct clinical applications in refractive surgery. sis is sample preparation. The analyst must deconvo- lute a complex mixture of biological molecules into a Jack Wang clean isolate of the information-carrying molecules, Neurobiology which is hard to do quickly and requires large, expen- sive equipment. Current diagnostics rely upon fluo- rescence; however, an urgent need for rapid virus ID and viral particle counting demands a simpler analyti- cal platform. A low-cost FET (field effect transistor) Professor Ben Barres (Neurobiology) device that obviates fluorescence and operates with Degeneration of the nerve fibers, or axons, is a pivot- minimal sample prep requirements will enable a rapid al event and a major determinant of clinical outcome medical response to emerging infectious diseases. in many neurodegenerative diseases; however, the mechanisms that regulate this process remain largely Patricia Ortiz-Tello unclear. Remarkably, expression of a mutant protein Genetics (WldS) significantly delays axon degeneration from many neurological insults. Through a series of genetic, biochemical and proteomic approaches, Jack propos- es to understand how this protein is able to exert such a profound neuro-protective effect. The goals of Professor Carlos D. Bustamante (Genetics) his research are to understand the molecular mecha- Preeclampsia, a disorder that complicates 3-8% of nisms of axon degeneration and to identify therapeu- pregnancies worldwide, occurs at 2-3 fold higher tic targets to prevent axon loss following neurological prevalence at higher altitudes – most likely due to the injuries and diseases. hypoxic environment. Interestingly, the prevalence remains low in populations that are indigenous to Jongmin Kim high altitude. The Bustamante lab hypothesizes that Bio-X SIGF populations that have adapted to living in a hypoxic Bruce and Elizabeth Dunlevie Fellow environment have acquired adaptations that may Chemical and Systems Biology confer protection against preeclampsia. Such adapta- tions may have imprinted a molecular signature in the genome, which they can recognize by looking at the Professor Margaret Fuller (Developmental Biology) genomic patterns of the population. They aim to Most of our tissues are constantly replenished by disentangle the underlying genetic mechanism of this tissue specific adult stem cells. The goal of Jongmin’s clinical consequence of human evolution. research is to understand how the switch from prolif- eration to differentiation in adult stem cell lineages is Steven J. Petsche regulated. He has developed an in vivo differentiation Mechanical Engineering system that can trigger proliferating progenitor cells to synchronously differentiate in the male germ line of fruit flies. By employing this differentiation assay, he will identify genes critical for the switch and will determine how those genes are regulated. Under- Professor Peter M. Pinsky (Mechanical Engineering) standing this switch will be important in regenerative As a result of advances in imaging and experimenta- medicine and cancer therapy. tion at small scales, the molecular mechanisms that give rise to the mechanical properties of human con- nective tissue can be better understood. Steven fol- Page 3 Paul Lebel for neurological disorders as well as improve how Bio-X SIGF neural prosthetics decode the brain’s motor activity. Applied Physics Daniel Newburger Bio-X SIGF Morgridge Family Fellow Professor Zev Bryant (Bioengineering) Biomedical Informatics Paul’s goal is to further our mechanistic understand- ing of molecular motors by capturing single molecule microscopy data at unprecedented bandwidth and Profs. Serafim Batzoglou (Computer Science) and resolution. He has developed an imaging and data Hanlee Ji (Oncology) acquisition system to track gold nanoparticles as Each year more than three hundred thousand people precise probes of length and twist of single DNA develop colorectal cancer (CRC) due to inherited molecules at more than 20,000 frames per second. genetic risk factors. Identifying the germline muta- Their lab exploits the resolution of this technique as a tions responsible for CRC susceptibility in affected tool to study various systems: they observe individual families dramatically improves preventative care and torque-generating steps of a single ATP-powered clinical outcome, but the vast majority of these muta- enzyme as it winds up DNA and measure the basic tions remain uncharacterized. In order to identify physical properties of DNA itself under applied ten- these unknown mutations, Daniel will help develop sion and torque. Additionally, through independent machine learning algorithms for evaluating genomic collaborations with Professors Stephen Quake and data from high-throughput DNA sequencing technol- Jody Puglisi, he is developing nanoparticle-based as- ogies. They hope this work will provide genetic find- says for high-throughput condition screening and real- ings that immediately inform clinical intervention and time dynamics of translating ribosomes. that it will illuminate new aspects of CRC pathogene- sis. Mark Longo Bio-X SIGF Ruth Sommese Morgridge Family Fellow Bio-X SIGF Biology Paul Berg Fellow Biochemistry Profs. Ward Watt (Biology) and Jay McClelland (Psychology) Professor James Spudich (Biochemistry) In the course of Mark’s research in evolutionary In the United States,
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