UCSF IRACDA Scholars Program

Past Research Mentors

Mark Anderson, MD, PhD, Diabetes Center. The main research interest of the Anderson lab is to examine the genetic control of autoimmune disease susceptibility to gain a better understanding of the mechanisms by which immune tolerance can be broken. A major focus of this research effort involves the defective gene in the clinical disorder Autoimmune Polyglandular Syndrome Type 1 (APS1). The lab’s efforts have revealed unique pathways by which immune tolerance is maintained to prevent autoimmune responses. Dr. Anderson mentored Maria Mouchess.

Sergio Baranzini, PhD, Department of Neurology. The Baranzini lab is interested in the genetics and molecular mechanisms underlying complex diseases. In particular, they use a combination of wet and dry lab approaches to investigate the disease multiple sclerosis, an autoimmune disorder of the central nervous system. Work in the lab involves human genetics, immunology, molecular biology, bioinformatics and systems biology approaches. Dr. Baranzini mentored Egle Cekanaviciute.

Jody Baron, MD, PhD, Department of Medicine. The Baron lab studies mechanisms involved in the immunopathogenesis of human liver and gastrointestinal diseases, as well as the basic principles of innate and adaptive immunity to viral pathogens in general. Diseases studied include HBV and HCV-related hepatitis, cirrhosis, and hepatocellular carcinoma, Inflammatory Bowel Disease, and Tissue Fibrosis (Liver and Lung). Research in the lab includes basic science, clinical, and translational projects. Dr. Baron mentored Audra Johnson.

Esteban Burchard, MD, MPH, Department of Bioengineering and Therapeutic Sciences. The Burchard lab studies the interplay between genes and their social and physical environments to determine the root causes of asthma health disparities among different populations locally and globally. Specifically, they identify novel risk factors for asthma, then assess whether they may be generalized across all populations. They also identify risk factors associated with poor drug response to improve therapies for all populations. Dr. Burchard mentors Marquitta White.

 

Jeffrey Bush, PhD, Department of Cell and Tissue Biology. The Bush lab studies basic mechanisms by which signaling between cells coordinates morphogenesis. The Bush Lab takes approaches based in mouse genetics to understand signaling processes as they relate to development and disease. Dr. Bush mentored Dr. Zer Vue.

 

Jonah Chan, PhD, Department of Neurology. The Chan lab has a long-standing interest in fundamental glial/neuronal interactions and the molecular mechanisms that regulate myelination with the hope of promoting repair and remyelination after disease and/or injury. More importantly, the implications of this research relate specifically to the identification of new target molecules and signaling pathways in the development of potential therapeutics for demyelinating diseases. Recent findings and technical advances with both PNS and CNS glia provide a rare opportunity to characterize these target molecules and signaling pathways. Dr. Chan mentors Sonia Mayoral.

Charles Craik, PhD, Department of Pharmaceutical Chemistry. The research efforts of the Craik Lab focus primarily on the structure-function analysis of proteases and their inhibitors using a combination of genetic, biochemical and biophysical methods. Chemical biological approaches are used or are being developed to study the substrate specificity, catalytic mechanism and biological role of proteases and their macromolecular inhibitors. The genes for serine (trypsin, serine collagenase, easter, prostate specific antigen, T-cell specific granzymes, MT-SP1 and 2, KSHV protease), cysteine (cruzain, falcipain and SARS protease) and aspartyl (HIV1 & HIV2 & SIV) proteases and macromolecular inhibitors such as ecotin and single chain antibodies are manipulated and expressed in heterologous expression systems. Targeted, region specific or random substitutions are introduced recombinantly to create variants that provide insight into the structure and activity of the target protein. Dr. Craik mentored Alegra Eroy-Reveles.

Grae Davis, PhD, Department of Biochemistry and Biophysics. There are two major research objectives in Davis Lab. They are interested in understanding at a molecular level how individual cells, neurons or muscle, achieve stable levels of activity during development and throughout life. They hypothesize that each cell in the nervous system is endowed with potent homeostatic mechanisms that enable cellular activity levels to be regulated. Understanding these homeostatic mechanisms may have far-reaching implications for understanding and treating neural disease. The second major objective of the lab is to understand the cellular mechanisms that control synaptic growth in the nervous system. Understanding how neuronal and synaptic growth is normally controlled may provide the opportunity to manipulate synaptic function for the treatment of neurodegenerative disease or injury to the nervous system. Dr. Davis mentored Lani Keller.

Jaynata (Jay) Debnath, MD, Department of Pathology. Dr. Debnath’s lab studies the role and regulation of autophagy in epithelial homeostasis as well as cancer pathogenesis using in vitro and in vivo approaches. Research focuses on epithelial cell fate and tissue homeostasis, oncogenic transformation and tumor formation, and chemotherapeutic response in cancer cells. Dr. Debnath mentors Dr. Teresa Monkkonen.

 

William DeGrado, PhD, Department of Pharmaceutical Chemistry. The DeGrado lab's research focuses on small molecule and protein design as an approach to understanding macromolecule structure and function. One primary research interest is in the de novo design, in which one designs proteins beginning from first principles. The lab has also developed a number of small molecule mimics of antimicrobial host defense proteins, which show considerable promise for treating antibiotic-resistant infections. Dr. DeGrado mentored Michelle McCully and Dr. Lam-Kiu Fong.

 

Joe DeRisi, PhD, Department of Biochemistry & Biophysics. The DeRisi lab studies genomic approaches to the study of infectious disease. Specifically, they study Plasmodium falciparum, the causative agent of the most deadly form of human malaria. They are also involved in a major effort for the discovery of new viral pathogens associated with diseases of unknown etiology. Dr. DeRisi mentored Corin White.

 

Tejal Desai, PhD, Department of Physiology. Studies in the Desai laboratory focus on the design, fabrication, and use of advanced micro/nano biosystems for: cellular integration and tissue engineering; biomimetic architectures for functional biomaterials; and therapeutic drug targeting and delivery. For example, studies are being conducted to investigate the role of structural mechanics in regulating biochemical pathways, biological adhesion phenomena, cytoskeletal deformation and active cellular motility. Motivating these fundamental studies is the development of novel materials that mimic the interfacial and structural properties of natural biomaterials. Dr. Desai, together with collaborator Dr. Ophir Klein, co-mentored Kelly Chavez.

Pamela England, PhD, Department of Pharmaceutical Chemistry. One of the most amazing properties of the mammalian central nervous system is its ability to process and store information. Changes in the strength of synapses appear to underlie such learning and memory. Major research efforts in the England lab are directed towards understanding the molecular basis for this synaptic plasticity. They use a combination of synthetic organic chemistry, biochemistry, molecular biology and electrophysiology in their research. Dr. England mentored Jesse Cortez.

John Fike, PhD, Department of Neurological Surgery, Radiation Oncology, and Radiology and Principal Investigator, Brain and Spinal Injury Center. Dr. Fike's lab is involved in studies on the cellular basis of radiation injury, using both in vitro and in vivo models, which may lead to new strategies to combat this clinically significant program. Dr. Fike mentored Antiño Allen.

Li Gan, PhD, Department of Neurology and Investigator Gladstone Institute of Neurological Disease. Dr. Gan studies the molecular mechanisms behind the loss of functional neurons in neurodegenerative diseases, including Alzheimer’s disease and Frontotemporal Dementia. Her lab explores the relationship between the aging of neural circuits, the accumulation of toxic proteins and the subsequent activation of a chronic inflammatory response. Understanding how these processes become dysfunctional in neurodegeneration could lead to new therapeutic strategies to tackle Alzheimer’s disease and Frontotemporal dementia. Dr. Gan served as research mentor for Dr. Joe Udeochu.

 

Adam Gazzaley, MD, PhD, Associate Professor of Neurology, Physiology and Psychiatry, and Founding Director, Neuroscience Imaging Center at UCSF. Gazzaley Lab is a cognitive neuroscience laboratory studying the neural mechanisms of perception, attention and memory, with an emphasis on distraction and multitasking. A major focus of his research has been to expand our understanding of alterations in the aging brain that lead to cognitive decline. His most recent studies explore how we can use this knowledge to improve our attention and memory abilities. His laboratory uses the tools of human neurophysiology, including functional magnetic resonance imaging (fMRI), electroencephalography (EEG) and transcranial magnetic stimulation (TMS). Gazzaley mentored two scholars, Joaquin Anguera and Bradley Voytek.

Guo Huang, PhD, Cardiovascular Research Institute. The Huang lab's current research focuses on cardiac regeneration and repair in adult zebrafish, neonatal and adult mice, with an emphasis on the pathways that regulate resident stem cell activation and cardiac muscle cell proliferation, and with innovative and integrated approaches in engineering, single cell analysis, advanced imaging microscopy and genome manipulation technology. These new strategies to image and promote mammalian organ regeneration will provide a platform for fundamental biology discovery and could have broad and significant impact on many research areas in developmental biology and regenerative medicine. Dr. Huang mentored UCSF-IRACDA scholar Alexander Payumo.

 

Ophir Klein, PhD, Associate Professor of Orofacial Sciences at UCSF. Dr. Klein's lab focuses on the study of how teeth and other craniofacial structures form, grow, and regenerate. Specifically, they are striving to understand how adult stem cells develop and how they contribute to organ renewal. The lab is also examining the role of Sprouty genes in development, homeostasis and cancer. Klein, together with Dr. Tejal Desai, co-mentored Kelly Chavez.

Tanja Kortemme, PhD, Department of Bioengineering. Dr. Kortemme’s lab studies engineered biological systems, ranging from molecules with new functions to entire organisms. These systems change how we ask questions about the biological principles of function and fitness. The Kortemme lab aims to invent approaches to engineer new molecules that operate as predicted in biological contexts, and to utilize prediction and engineering to address fundamental questions on the relationship of molecular characteristics, cellular function and organismal fitness. The lab’s research combines concepts from computer science, physics, chemistry, mathematics, engineering and biology.​ Dr. Kortemme mentored Dr. Anum Azam Glasgow.

 

Alicia F. Lieberman, PhD, is the Irving B. Harris Endowed Chair in Infant Mental Health, Professor, Vice Chair for Academic Affairs at the UCSF Department of Psychiatry, and Director of the Child Trauma Research Project at San Francisco General Hospital. The Child Trauma Research Project (CTRP) conducts treatment outcome research and builds models of intervention for children birth to five who have experienced violence-related trauma, including exposure to domestic and community violence. Evidence-based treatment developed at CTRP is aimed at improving the parent-child relationship, at helping both parent and child better modulate their feelings, and at helping the parent understand the child’s experience so that the parent can become more effectively protective. Dr. Lieberman mentored Lisa Gutierrez-Wang.

Daniel Lim, PhD, Assistant Professor in Residence of Neurological Surgery and Director of Restorative Neurosurgery. The focus of Dr. Lim's research is on neural stem cells and neurogenesis. He is particularly interested in the molecular biology of the population of neural stem cells found in the subventricular zone. Dr. Lim was mentored Gabriel Roybal.

Martin McMahon, PhD, Helen Diller Family Comprehensive Cancer Center. Work in McMahon laboratory focuses on the role of RAS-activated signal transduction pathways in the aberrant physiology of melanoma, pancreas and lung cancer using in vivo mouse model systems and in vitro cell culture based systems. The RAS-family of GTP binding proteins transmit signals into the interior of the cell via activation of a number of cytosolic signal transduction pathways. Prominent among these is the RAF-MEK-ERK MAP kinase and the PI3'-kinase-PDK-AKT signaling pathways. Components of both of these pathways are linked to the initiation and progression of human cancer both by their association with human RAS oncogenes and by evidence of somatic mutations in BRAF, PIK3CA, AKT and PTEN that occur in a wide range of human malignancies. Dr. McMahon mentored Jillian Silva.

Melanie Ott, MD, PhD, Department of Medicine, UCSF, and Senior Investigator, Gladstone Institute of Virology and Immunology. Research in the Ott lab focuses on two pathogens—the human immunodeficiency virus (HIV-1) and the hepatitis C virus (HCV)—and how these viruses interact with the cells of a host. More specifically, her lab studies the molecular mechanisms by which HIV infects and replicates in CD4 T cells, wreaking havoc on a segment of the body’s immune system. In HCV research, they are examining ways in which HCV viral particles assemble within liver cells—in an attempt to understand the interactions between viral proteins, fat metabolism and mitochondria in these infected cells. Dr. Ott mentored Olivia Sims.

 

Katherine Pollard, PhD, Department of Epidemiology and Biostatistics and Director of the Gladstone Institute of Convergence Science. The Pollard lab develops statistical and computational methods for the analysis of massive genomic datasets. They are interested in genome evolution, in particular identifying genome sequences that differ significantly between or within species and their relationship to biomedical traits of interest. The Pollard lab pioneered the statistical phylogenetic approach for identifying Human Accelerated Regions (HARs), the fastest evolving sequences in the human genome. Dr. Pollard mentored Dr. Amber Paasch.

 

Adam Renslo, PhD, Department of Pharmaceutical Chemistry. The Renslo Lab synthesizes small molecules that can be used to better understand the biology of disease and ultimately to produce more effective therapeutics. Dr. Renslo mentors Dr. Xochina El Hilali.

 

Anita Sil, MD, PhD, Department of Microbiology and Immunology, and HHMI Early Career Scientist. Dr. Sil's research program focuses on the biology of understudied fungal pathogens through the development and application of molecular and genetic tools. The lab is looking at two key questions: First, how do cells sense temperature and make a developmental switch from the soil to the host program. And second, how does H. capsulatum, which is thought to be the most prevalent cause of fungal respiratory infections in the world, defy the innate immune response to take up residence in immunocompetent hosts? Dr. Sil mentored Chris Villalta.

Jeroen Roose, PhD, Department of Anatomy. The Roose lab studies how different Ras signals drive normal developmental processes of various cell types and organ systems and how (and why) perturbations of Ras-kinase signals cause human disease. Dr. Roose mentors Dr. Saikat Banerjee.

 

Dean Sheppard, MD, Department of Medicine, Lung Biology Center. Research in the Sheppard lab focuses on the molecular mechanisms underlying pulmonary (and other organ) fibrosis, asthma and acute lung injury. One aim of the research is to identify new therapeutic targets to ultimately improve the treatment of each of these common diseases. The work begins with basic investigation of how cells use members of the integrin family to detect, modify and respond to spatially restricted extracellular clues and how these responses contribute to the development of common lung diseases. The lab has identified important roles for these integrins in models of each common lung disease and key steps upstream and downstream of the integrins that provide potential therapeutic targets. Dr. Sheppard mentored Daud Cole.

 

Elliott Sherr, MD, PhD, Department of Neurology. Dr. Sherr and his collaborators at UCSF are studying the genetic causes of disorders of cognition and epilepsy, as well as the brain malformations associated with these disorders. Their focus is on polymicrogyria (PMG), Dandy-Walker malformation (DWM), and disorders of brain development that affect the corpus callosum (ACC/DCC).  They are studying the clinical features of these disorders to better understand the problems faced by individuals with these disorders. The goal of their research is to use a better understanding of the underlying genetic causes as a foundation to develop better treatments for these groups of patients. Dr. Sherr mentored Dorothy Jones-Davis.

Jack Taunton, PhD, Department of Cellular and Molecular Pharmacology, and HHMI Investigator. Research in the Taunton laboratory follows two intersecting trajectories: 1. a cell biology trajectory, in which they pursue a biochemical dissection of the signals that control actin assembly and force generation on the surface of cellular membranes; and 2. a chemistry trajectory, in which they synthesize small molecule tools to perturb and thereby illuminate cellular functions. They have used a structural bioinformatics approach to design ultra-specific protein kinase inhibitors. In addition, they have synthesized cotransin, a macrocyclic depsipeptide with potent anti-inflammatory activity. Biochemical and cell biological experiments have revealed its molecular target and mechanism of action. Dr. Taunton mentored Yazmin Carrasco.

 

Thea Tlsty, PhD, Department of Pathology. Dr. Tlsty's lab is studying the epigenetic and genetic alterations that confer genomic instability and fuel cancer initiation and progression. Recently the lab identified a variant subpopulation of human mammary epithelial cells (vHMEC) that express properties of premalignant lesions without any exposure of the cells to carcinogens. These variant cells exist in vivo in disease-free women. We have also demonstrated that stromal changes extend beyond a supportive role and play key functional roles in facilitating tumorigenesis. They are studying the ability of carcinoma-associated fibroblasts from human tissues to facilitate the transition to tumorigenicity in an otherwise non-tumorigenic cell population. Dr. Tlsty was mentor to past scholars Luis Estevez-Salmeron and Dr. Carlos Rodríguez.

 

Erik Ullian, PhD, Department of Opthalmology and Physiology. The Ullian laboratory is interested in the interactions between neurons and glia that are required for the proper development and function of the nervous system. To study these interactions they use a variety of techniques including purification of neurons and glia for cell culture, patch clamp recording from neurons both in culture and in slices, and gene chip and molecular techniques to look at genes and proteins that are regulated by neurons and glia. Using these techniques we have begun to identify both extrinsic signals produced by glial cells and intrinsic signals produced by neurons that regulate synapse number and function. Dr. Ullian mentored Tigwa Davis.

Valerie Weaver, PhD, UCSF Institute for Regeneration Medicine. In the Weaver lab, research focuses on several areas: (1) The role of physical force in human embryonic stem cell fate. (2) The molecular mechanism linked to JNK and SMRT pathways whereby alpha 6/beta 4 integrin activates RAC and NFkappa B to mediate apoptosis resistance in reconstituted basement generated MEC tissue structures in culture and in a transgenic mouse model. (3) The role of physical force and tissue architecture in culture and in transgenic models and clinically in the pathogenesis of therapy resistant breast cancers. Dr. Weaver mentored Jose Lopez.

Alison W. Xu, PhD, Diabetes Center and the Department of Anatomy. The Xu lab is interested in understanding how hypothalamic neurons sense and integrate peripheral adiposity signals such as leptin and insulin. Researchers are currently using a combination of mouse genetic, physiologic and real-time imaging approaches to address the following questions: 1. What are the leptin and insulin target neurons in the hypothalamus, and what are the functions of these neurons in energy balance and glucose homeostasis? 2. What are the intracellular signaling mechanisms utilized by leptin in hypothalamic neurons? 3. What are the mechanisms of hypothalamic leptin and insulin resistance? Dr. Xu mentored Jamila Newton.