Focus Areas and Custom Option
Customized Tracks in Biomedical Sciences
Students may choose to train in general biomedical sciences or in specific focus areas outside of the structured training Tracks. Non-track students follow the core course curriculum in the first year and then choose electives tailored to their training. Such students consult with faculty advisors or a research mentor to choose electives. To facilitate advanced training opportunities in areas not directly addressed in the Genetics, Microbiology/Immunology, Molecular Cell Biology, Molecular Pathology, Molecular Pharmacology, or Physiology Training Tracks, the Biomedical Sciences faculty have also developed the focus areas described below. Selection of a focus area is not required for the customized track.
Focus Areas
Focus areas provide a nucleus of training activities around which students may plan their electives and form interactions with colleagues who share similar research interests. Current focus areas are: Anthropogeny, Bioinformatics, Cancer Biology, Developmental Biology, Endocrinology, Glycobiology , Neurobiology, Stem Cells, and Structural and Chemical Biology.
Anthropogeny
Faculty Contact: Prof. Pascal Gagneux (pgagneux@ucsd.edu)
Participating Faculty
The focus area Anthropogeny aims to provide graduate students the opportunity to specialize in transdisciplinary research and education on explaining the origins of the human phenomenon. The aim is to rectify the absence of existing training programs that provide such a broad and explicitly transdisciplinary approach "spanning the social and natural sciences" and focusing on one of the oldest questions known to humankind, namely, the origins of humans and humanity. This focus area is not a stand-alone program, but rather aims at providing graduate students who have just embarked on their graduate careers with the opportunity to interact and communicate with peers in radically different disciplines throughout the duration of their PhD projects. Such communication across disciplines from the outset is key to fostering a capacity for interdisciplinary "language" skills and conceptual flexibility.
Bioinformatics
Faculty Contact: Philip Bourne (pbourne@ucsd.edu)
Participating Faculty
The Bioinformatics focus area has emerged in response to biology becoming a data-rich discipline. Bioinformatics involves the use of computers to model and study complex biological processes (e.g. protein folding, gene expression and regulation, cellular and organismal behavior).
Bioinformatics opportunities at UCSD include over 40 faculty from several departments and the San Diego Supercomputer Center (SDSC). UCSD is home for the Protein Data Bank (PDB), a unique worldwide repository for macromolecular structure data. Improved algorithms for data modeling, sequence-sequence, sequence-structure and structure-structure alignment techniques are just some of the activities being undertaken in the program. The Bioinformatics program also participates in the Alliance for Cell Signaling (AFCS) charged with the identification and biochemical characterization of all proteins involved in cell signaling in two model organisms. The National Center for Microscopic Imaging Research (NCMIR) focuses on projects like mitochondrion reconstruction using electron tomography. The National Biomedical Computational Resource (NBCR) is a sister resource to NCMIR with investigations ranging from the electrostatics of microtubules to the modeling of integrative cardiac physiology.
Students specializing in Bioinformatics take the Biomedical Sciences core classes, specialized classes in Biological Data & Analysis Tools, Sequence Analysis, Genomic Analysis, and Statistical Methods for Bioinformatics. Students also participate in Bioinformatics Journal Club.
Cancer Biology
Faculty contact: Steve Dowdy (sdowdy@ucsd.edu)
Participating Faculty
Cancer is one of the leading causes of death in the United States. The need to train students for independent careers in cancer research is clear. The Cancer Biology focus area concentrates on understanding DNA damage and repair, cell cycle regulation, signal transduction, gene expression, cellular transformation, apoptosis, tumor biology, cell-cell and cell-matrix interactions, angiogenesis, metastasis and the deregulation that occurs during oncogenesis. The program helps train students for future careers as academic or industrial scientists interested in the underlying regulatory mechanisms controlling oncogenesis.
The Cancer Biology focus area draws on the core curriculum of the BMS program to provide a firm background in the basics of molecular and cellular biology, physiology, and pharmacology that can be applied to the study of cancer. Advanced courses in Oncogenes, Biology and Biochemistry of Cancer Cells, Biochemistry of Growth Regulation and Oncogenesis, Molecular Pathology of Cancer, and Topics in Cancer Research enhance the training experience. Cancer research laboratories at UCSD are highly active training centers for graduate and postdoctoral education. UCSD is home to the Ludwig Institute for Cancer Research and the Rebecca and John Moores UCSD Comprehensive Cancer Center. Regular research presentations and numerous seminars serve to broaden and enrich the educational experience of trainees.
Developmental Biology
Faculty contact: Sanjay Nigam (snigam@ucsd.edu)
Participating Faculty
The BMS program includes several leading scientists in developmental biology. A particular focus within this group is mechanisms of vertebrate organogenesis. Investigators use in vivo (genetic) and in vitro (organ and cell culture) approaches in order to understand developmental pathways responsible for the programming of cells to form higher order structures that have specific physiological capacities. A major theme is the application of developmental insights to human disease and tissue engineering, as well as the use of stem cells to enhance organ regenerative capacity. Research areas include kidney, breast, pituitary, brain, heart and other organs. Particular processes under study include branching morphogenesis, the transcriptional specification of cell fate, the regulatory properties of matrix molecules, and signaling pathways in the morphogenetic program. Transcriptional profiling with a variety of array based technologies, combined with sophisticated bioinformatics analysis, is being employed to define the sets of genes controlling aspects of the developmental program. The approach is thus highly interdisciplinary, involving cell and developmental biologists as well as stem cell biologists, computer scientists, physiologists, physicians and bioengineers.
Endocrinology
Faculty contact: Alexander (Sasha) Kauffman (akauffman@ucsd.edu)
Participating Faculty
Cellular communication through hormones, growth factors and neurotransmitters is the fundamental mechanism for coordinating the action of dispersed cells and tissues that comprise major physiological systems. The development and regulation tissues controlling energy balance, growth, and reproduction all rely on autocrine, paracrine and endocrine action of hormones released locally in tissues or generally into the circulation. Many human diseases and syndromes such as diabetes, cancer, infertility, obesity, and dwarfism can be attributed to disruption of normal hormone action. The Endocrinology focus area of the Biomedical Sciences program provides training in the fundamental aspects of cellular communication through hormone action. After the completion of the core curriculum, students specialize their training through advanced courses in endocrinology, cell signaling, and gene regulation. Students will be exposed to the wide range of cellular systems that are regulated by hormones. Faculty members participating in the Endocrinology focus area are drawn from a wide variety of specialties ranging from development, neuroscience, cell signaling, and cell biology. Their research is highly interdisciplinary and utilizes variety of genomic, proteomic, and animal model approaches to study various aspects of hormone action. The overall goal of the focus area is to give students the broad perspective necessary for the study of hormone action and to provide specialized training in modern molecular techniques for addressing problems at the molecular level that have a profound effect on the entire organism.
Glycobiology
Faculty contact: Jeff Esko (jesko@ucsd.edu)
Participating Faculty
The Glycobiology focus area provides training in both classic and modern glycobiology. The purpose of the training program is to facilitate education and research in the biology and chemistry of glycans, in particular those present on macromolecules. Training in glycobiology builds on biochemical and cell biological principles developed in the core curriculum. Additional specialized training includes an advanced course, Essentials of Glycobiology (BIOM 222/MED 225/CHEM 237/BGGN 236/CMM 225), which provides a current overview of fundamental facts, concepts, and methods in Glycobiology. The course is supported by the first textbook in the field co-authored by several members of the Biomedical Sciences program. Students also participate in Current Literature in Glycobiology (BIOM 246/MED 246/CMM 246), which provides a forum for discussing current papers in glycobiology research. The Glycobiology focus area co-sponsors seminars with the Department of Cellular and Molecular Medicine, the Sanford-Burnham Medical Research Institute, and the Scripps Research Institute. Students are invited to participate in the annual San Diego Glycobiology Symposium, which brings together all of the laboratories that have an interest in glycobiology from the San Diego area, the University of California system, other universities in the state, and members of the biotech community. Faculty interested in glycobiology belong to the Glycobiology Research and Training Program (GRTC) which draws from multiple programs in the La Jolla area and other UC campuses to facilitate training and research.
Neurobiology
Faculty contacts: Joseph Gleeson (jogleeson@ucsd.edu) and Binhai Zheng (binhai@ucsd.edu)
Participating Faculty
The Neurobiology focus area builds on an extremely vibrant and interactive neurosciences community within UCSD Medical School. Understanding how the brain develops and functions is considered by many to be one of the great scientific frontiers. How the billions of neurons are generated, migrate, differentiate, and interconnect to form the trillions of synaptic connections that characterize higher mammalian brain is one of the great mysteries of science. The areas of Neurobiology research represented within the Biomedical Sciences program include study of geneticetiologies of neurological disease, molecular neuroendocrinology, transcriptional and epigenetic regulation of neuronal function, and synaptic and intracellular signaling. Faculty active in the Neurobiology focus area are drawn from nine basic science and clinical departments within the School of Medicine, and a conscious effort is made to promote interaction among different research groups and to develop a multi-disciplinary approach to teaching.
BMS students specializing in Neurobiology will take the core Biomedical Sciences graduate courses, and specialized courses related to neuroscience. Additionally, there are weekly Neuroscience Seminars from prominent visiting scholars and journal clubs to complement laboratory experiences.
Stem Cells
Faculty contact: Sylvia Evans (syevans@ucsd.edu)
Participating Faculty
A stem cell is a cell that can give rise to identical daughter cells or differentiated cells that perform different functions. Stem cells are described by their power to differentiate more widely, as with pluripotent embryonic stem cells or in ways restricted to the organ from which they derive, for example, in the blood-forming system in the bone marrow.
The Stem Cell research focus investigates the variable presence of stem cells in the developing embryo and in various organs; the identification, purification and properties of stem cells; possible and actual uses of stem cells in animal models of diseases; possible and actual uses in clinical application to an organ system or disease state.
Many human diseases and syndromes such as diabetes, cancer, heart failure, congenital and acquired neurodegeneration and others can be better understood and possibly treated by application of results from stem cell research. The Stem Cell focus area of the Biomedical Sciences program provides training in the fundamental aspects of stem cell basic biology, bioengineering, and biomedicine.
Students bring their individual background and experience to courses, journal club exchanges, and laboratory projects applying their education, skills and interests to emphatically multi-disciplinary basic or applied research projects. Faculty members participating in the Stem Cell focus area are drawn from a wide variety of specialties including neurobiology, medicine, embryology, development, neuroscience, cell signaling, cell biology, bioinformatics, and engineering. Their research is highly interdisciplinary and utilizes variety of genomic, cellular, animal model, and in vitro approaches to study various aspects of stem cells at the level of molecular, cellular, tissue and organ regeneration and differentiation. The overall goal of the focus area is to give students the broad perspective necessary for the design and application of stem cell experimental studies to basic and applied problems in biology.
Structural and Chemical Biology
Faculty contact: Susan Taylor (staylor@ucsd.edu)
Participating Faculty
The Structural and Chemical Biology focus area provides training in macromolecular structure and function, chemical and molecular recognition, and small molecule design. X-ray crystallography, NMR, mass spectrometry, and computational approaches are used to understand protein folding, macromolecular interactions, and protein dynamics. Researchers in this area benefit from the resources at the San Diego Supercomputer Center (SDSC). UCSD is also home for the Protein Data Bank (PDB), a unique worldwide repository for macromolecular structure data. There is a strong, highly interactive, and highly interdisciplinary program that spans many departments from Physics, Chemistry and Biochemistry, Pharmacology, and Bioengineering as well as the Salk Institute.
Students specializing in Structural and Chemical Biology take the Biomedical Sciences core curriculum, specialized classes in Molecular Structure, Biological Data & Analysis Tools, and Biophysical Methods for Analyzing Structure and Dynamics.