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Biological Sciences/ Biology*
*EFFECTIVE January 1, 2008 the name of the department will change from Biological Sciences to Biology. Beginning with the entering class of 2008, the Department of Biology will award the following graduate degrees: Doctor of Philosophy in Biology and Master of Science in Biology.
Modern biological research demands an interdisciplinary approach to address the most important problems. The Department of Biological Sciences/Biology is dedicated to the study of biological questions at all levels. Current research in the department spans a broad spectrum and includes:
• Cell, Molecular, Developmental and Plant Biology: protein folding, single molecule biophysics, regulation of gene expression, cell migration, signaling, intracellular protein trafficking, cytoskeleton, cell cycle
The diverse range of interests and expertise in the department creates a challenging intellectual environment that encourages students to take innovative approaches to the study of fundamental questions in biology. In addition, Ph.D. students in biological sciences have the opportunity to gain valuable experience teaching in lecture and laboratory courses.
I. CELL, MOLECULAR,
AND PLANT BIOLOGY
II. INTEGRATIVE, ORGANISMAL AND MARINE BIOLOGY
III. ECOLOGY, EVOLUTION,
AND POPULATION BIOLOGY
For more information contact:
Faculty and their Research Interests
Cell, Molecular, Developmental and Plant Biology
Bruce S. Baker. Sex determination, sexual behavior, dosage compensation and imaginal disc development in Drosophila melanogaster, with the goal of understanding at a molecular level how these processes are brought about.
Kathryn Barton, by courtesy1. Stem cells in plants, formation of leaves and their development into flattened, polarly differentiated organs, role of small RNAs in leaf and stem cell development, embryogenesis in plants.
Dominique Bergmann. We use genetic, genomic and cell biological approaches to study how cells acquire specific fates and how those cells are patterned in a complex tissue. Our current work is focused on stomatal development as a paradigm for understanding how multiple sources of information—from cell lineage, cell-cell communication and from the environment—are integrated into the appropriate cell fate and cell proliferation responses.
Steven M. Block3. Properties of proteins or nucleic acids at the level of single macromolecules and molecular complexes. Experimental tools include laser-based optical traps (“optical tweezers”) and a variety of state-of-the-art fluorescence techniques, in conjunction with custom-built instrumentation for the nanometer-level detection of displacements and piconewton-level detection of forces.
William F. Burkholder. Our lab is interested in how bacteria monitor and coordinate cell cycle events. We are focused on identifying and characterizing signal transduction pathways used by the bacterium Bacillus subtilis to regulate cell cycle progression and development in response to chromosome status. Our goal is to understand how these pathways work mechanistically and how they contribute to normal growth, development, and genome stability.
Allan M. Campbell. Comparative molecular biology of DNA insertion by bacteriophage lambda and its relatives, analyzing the organization of the biotin operon in Escherichia coli, and the genetic control of related pathways. Phage integration is a model system for the catalysis and regulation of specific DNA rearrangements.
Martha Cyert. Cells respond to extracellular changes by activating signal transduction pathways, many of which are highly conserved. We study Ca2+-mediated signaling in a simple eukaryote, Saccharomyces cerevisiae. Using genetic, genomic, biochemical and cell biological approaches, we are examining how the Ca2+/calmodulin-regulated phosphatase, calcineurin, regulates gene expression and other cellular processes in response to environmental stress.
Guowei Fang. Our research focuses on the molecular and cellular mechanisms for mitosis and cytokinesis in normal cells and their dysregulations in cancer cells. The current focus is on the cell cycle regulatory circuits consisting of kinases and ubiquitin ligases as well as on the assembly, dynamics and function of mitotic structures, using a combination of genomic, cell biological, biochemical, and molecular genetic approaches in mammalian cells.
Wolf Frommer, by courtesy1. Focus: Transport/signaling across the plasma membrane (sugars, amino acids). Tools: FRET-based nanosensors for imaging metabolites in living organisms using confocal fluorescence microscopy; Sensor optimization by computational design; RNAi to modify cellular functions. Goals: Identify unknown sugar effluxers from liver or plant cells; study regulatory networks. Model systems: yeast, mammalian cell cultures and Arabidopsis.
Judith Frydman. The mechanism of protein folding has become a central problem in biology. We wish to understand the pathways and regulation of protein folding in eukaryotic cells. Knowledge of how proteins actually fold in the cell should eventually provide the basis for controlling protein function under normal conditions and during abnormal conditions of environmental stress and disease.
Or Gozani. Research in the Gozani lab aims to understand how alterations in chromatin structure are sensed and transduced to effect diverse biological outcomes, and how disruption in these mechanisms can lead to pathologic states. Questions are addressed utilizing a combination of biochemical, molecular and cell biological approaches.
Arthur R. Grossman, by courtesy1. How photosynthetic organisms acclimate to their environment and adjust the physiology of the cell. Effects of light are studied in cyanobacteria. Effects of changes in nutrients such as sulphur and phosphorus are studied in mutant green algae and cyanobacteria which are unable to acclimate to nutrient limitation.
Philip C. Hanawalt. Philip Hanawalt discovered repair replication of DNA, the major process by which all living cells deal with damage to their genetic material. His research group studies the mechanisms by which living cells maintain their genomes in the face of endogenous DNA damage and environmental radiations and chemical carcinogens.
Patricia P. Jones. Genetic, cellular, and molecular mechanisms that regulate adaptive immune responses (the antigen-specific responses carried out by B and T lymphocytes, unique to vertebrates), and innate immune responses (responses present in both invertebrates and vertebrates triggered by microbial components).
Ron R. Kopito. Cellular mechanisms which monitor protein biogenesis and ensure that only properly folded and assembled proteins are deployed within the cell. Genetic biochemical and cell biological approaches are used to identify the machinery involved in recognizing and destroying misfolded proteins.
Sharon R. Long. Molecular, genetic, and biochemical techniques are used to study how Rhizobium cells recognize and form nodules on their plant hosts. The association is highly specific and involves complex transcriptional and cellular responses by both the bacterium and eukaryotic host.
Liqun Luo. We use molecular genetics to understand the logic of neural circuit organization and assembly in fruit flies and mice. For additional information, see
Susan K. McConnell. How individual neurons know where they should sit in the brain and with which neurons they should form specific axonal connections. Identify and characterize the progenitor cells that give rise to neuron and the processes by which young neurons locate their correct targets among hundreds of thousands of other neurons in the brain.
Mary Beth Mudgett. Molecular and cellular basis of microbial pathogenesis and plant disease resistance. Early protein signaling events occurring between the leaf pathogens Pseudomonas syringae and Xantho-monas campestris and their plant hosts Lycopersicum esculentum and Arabidopsis thaliana.
W. James Nelson10. Our research objectives are to understand cellular mechanisms involved in development and maintenance of cell polarity. Recent studies indicate that development of epithelial cell polarity is a multistage process requiring instructive extracellular cues (eg. cell-cell and cell-substratum contact) and reorganization of proteins in the cytoplasm and on the plasma membrane. Once established, polarity is maintained by targeting and retention of proteins to functionally distinct apical and basal-lateral plasma membrane domains.
Carla J. Shatz11. The major goal of research in the Shatz Laboratory is to discover cellular and molecular mechanisms that transform early fetal and neonatal brain circuits into mature connections, and in particular to determine the extent to which neural function during critical periods of development is needed for these circuits to tune up into adult patterns of connectivity.
Kang Shen. We are interested in understanding how synapses are formed, the final step in wiring a nervous system. In particular, the molecular mechanisms underlying synaptic specify: how neurons recognize each other and how they make decisions about forming synapses between contacting neurites during development. We use molecular, genetic and cell biological tools to study this question in the nematode, C. elegans, which has a very simple nervous system containing only 302 neurons and approximately 6000 synapses.
Michael A. Simon. We use genetic and biochemical approaches to study three areas of developmental biology; planar cell polarity (PCP) in epithelial cells, control of cell shape, motility and the actin cytoskeleton by Src family protein tyrosine kinases, and control of cell fate specification by receptor tyrosine kinases.
Robert D. Simoni. The nature of cellular membranes using a broad range of techniques, from molecular biology and biochemistry to cell biology. We continue to analyze the role of cholesterol in biological membranes, as well as the genetic mechanisms by which cholesterol production is regulated. This study has direct clinical relevance to the problems of atherosclerosis and heart disease.
Chris R. Somerville. My laboratory employs the small mustard Arabidopsis thaliana as a model species for plant molecular genetics. My research is focused on understanding how the polysaccharides in plant cell walls are synthesized and assembled into the final structure.
Alfred M. Spormann, by courtesy7. Molecular mechanisms of microbial degradation of unusual organic compounds, for example organic pollutants. Also the molecular mechanism of gliding motility in bacteria.
Tim Stearns. The central question in our work is how cells accurately segregate their genome at each cell division. The work is focused on the centrosome, a unique organelle at the center of the cell that organizes the cytoskeleton and serves as a site for integration of cellular signals. We use the tools of cell biology, genetics, and biochemistry in systems ranging from yeast to human cells to understand how the centrosome duplicates once per cell cycle, and how centrosome defects are involved in the genome instability that is observed in many types of cancer.
Virginia Walbot. Our laboratory studies the behavior of MuDR/Mu transposons of maize to answer fundamental questions about transposon regulation and plant development. Without a fixed body size, how do plant cells cease division and how are Mu element excisions restricted to the final cell divisions? Plants lack a germ line, but a few floral cells differentiate to undergo meiosis - why does Mu transposition outcome change in pre-meiotic cells?
Zhiyong Wang, by courtesy1. Steroid responses mediated by a receptor kinase in Arabidopsis thaliana using molecular genetics and proteomics.
Irving L. Weissman, by courtesy6. Developmental biology, self-renewal, homing and functions of the cells that make up blood-forming and immune systems.
Charles Yanofsky8. Studies are focused on two major problems: 1) Determining the features of the attenuation regulatory mechanism used by E. coli to control transcription of the degradative tryptophanase operon; 2) Determining the features of the transcriptional and translational regulatory mechanisms controlling expression of operons concerned with tryptophan biosynthesis in B. subtilis. Both studies are revealing novel features of gene regulation.
Integrative, Organismal and Marine Biology
Barbara A. Block2. The Block lab investigates endothermy in fish including cellular, ecological and evolutionary physiology. Cellular basis for endothermic metabolism. Research at sea is focused on understanding the movements and physiological ecology of tunas and billfishes to gain insight into the selective advantage of endothermy in fish and habitat utilization.
Anthony De Tomaso2. Using a combination of genetic, genomic, and cell-biological approaches, we are studying the phenomenon of self/non-self recognition in a primitive chordate organism, Botryllus schlosseri. This interaction links together a number of disparate fields, including immunology, stem-cell, developmental, and evolutionary biology, and also has ecological consequences. Several unique aspects of the Botryllus life history make it a novel, experimentally accessible model organism to ask pertinent questions in these distinct disciplines.
Mark W. Denny2. Mechanical design of intertidal organisms. This subject is studied at many different levels of organization, from the molecular, through the material, structural, and organismal, to the ecological.
David Epel2. How development takes place in the marine environment, especially how embryos resist the effects of such environmental stresses as ultraviolet radiation, pathogens and natural and man-made toxins. How can the oocyte or the few-celled embryo protect itself from pathogens such as bacteria, ultraviolet radiation, or the effects of toxins, both natural and manmade?
Russell D. Fernald. In the course of evolution, two of the strongest selective forces in nature, light and sex, have left their mark on living organisms. I am interested in how the evolution and function of the nervous system reflects these events. In the visual system, we are studying how eyes evolved. In the reproductive system, we have identified a collection of cells in the brain containing gonodotropin releasing hormone (GnRH) that respond to changes in the social conditions by changing size.
William F. Gilly2. Mechanisms involved in the cellular regulation of properties, density, and spatial distribution of voltage-gated Na and K channels and of ionotropic glutamate receptors cloned from the squid nervous system and expressed in frog oocytes and insect cells.
H. Craig Heller. Neurobiology of sleep, circadian rhythms, regulation of body temperature, mammalian hibernation, and human exercise physiology. Dr. Heller is co-director of the Center for Sleep and Circadian Neurobiology. The Center fosters multidisciplinary approaches and collaborations that will help us understand the neural mechanisms controlling arousal states and arousal state transitions, the function of sleep, and the neural mechanisms of circadian rhythms. Research on human exercise physiology focuses on the effects of body temperature on physical conditioning and performance.
Fiorenza Micheli2. We are investigating how coastal marine assemblages are shaped through the interplay of physical factors and biological interactions, and examining how much of the observed variation in these assemblages can be attributed to human impacts on the marine environment. http://www.stanford.edu/group/MicheliLab/
Stephen R. Palumbi2. We study genetics, evolution, conservation, population biology and systematics in a wide variety of marine organisms. Primary focus is the use of molecular genetic techniques in conservation, including identification of dolphin and whale products in commercial markets. Also, molecular evolution of reproductive isolation and its influence on speciation.
Robert M. Sapolsky. How a neuron dies during aging or following various neurological insults; how such neuron death can be accelerated by stress; the design of gene therapy strategies to protect endangered neurons from neurological disease.
Mark J. Schnitzer3. In vivo fluorescence optical imaging and electrophysiological studies of the mammalian brain towards understanding biophysical aspects of learning and memory. We are developing and applying novel imaging approaches such as multiphoton fluorescence endoscopy for examining individual neurons and dendrites, with emphasis on experiments in awake behaving animals.
George N. Somero2. We study how changes in protein sequence and gene expression enable organisms to succeed in diverse marine environments, including the Antarctic ocean and rocky intertidal habitats. By comparing homologous proteins from animals adapted to different temperatures, we have shown that only minor differences in habitat temperature are sufficient to favor evolutionary changes. Abilities to shift gene expression adaptively in response to environmental change vary among species and may be critical in setting tolerance limits.
Stuart H. Thompson2. Signal transduction mechanisms in neurons with the goal of better understanding how neurons process information. Signal cascades initiated by G-protein coupled receptors and regional specialization of function in neurons and the role that localized clusters of ion channels play in the processing of information by the cell.
Ecology and Evolutionary Biology
Joseph A. Berry, by courtesy1. Physiological means by which plants adapt to environmental stress and climactic change, and photosynthetic mechanisms used by higher plants and algaes to fix carbon dioxide.
Carol L. Boggs. We are exploring how environmental variation affects life-history traits, population structure and dynamics, and species interactions in ecological and evolutionary time, using Lepidoptera. Current interests include (1) how resource allocation strategies interact with foraging and life history in variable environments to affect fitness and population dynamics; (2) the ecological and evolutionary dynamics of small populations, including population re-introductions; and (3) invasion biology, particularly the evolutionary and ecological effects of non-native species’ invasion into co-evolved systems.
Gretchen C. Daily4. Forecasting changes in biodiversity and the delivery of ecosystem services, quantifying the return on alternative conservation investments, oriented around opportunities for biodiversity conservation in human-dominated landscapes.
Rodolfo Dirzo. My current work on conservation biology emphasizes the need of complementing the traditional interests of the conservation of taxa with the increasingly needed conservation of ecological processes. Most of my tropical work is carried out in Mexico and Central Amazonia.
Paul R. Ehrlich. Conservation biology; ecology, evolution, and behavior of natural populations (especially of butterflies); human ecology and evolution.
Marcus W. Feldman. Evolution of complex genetic systems that can undergo both natural selection and recombination. Human demographic studies, particularly of the sex ratio. Human molecular evolution. The evolution of learning as one interface between modern methods in artificial intelligence and models of biological processes, including communication. The interaction of biological and cultural evolution, for example in the spread of food plant domestication across Europe, and the transmission of learned behaviors in contemporary groups.
Christopher B. Field. Ecosystem responses to interacting global changes, controls on the carbon and energy balance of natural ecosystems, and ecology and biogeochemistry at the global scale.
Deborah M. Gordon. We study how ant colonies are organized, how colonies interact with their neighbors, and use of genetic markers to measure reproductive success and gene flow in harvester ants.
Elizabeth A. Hadly. Evolution and ecology of animal populations over the last two million years, especially focusing on the last 10,000 years. We sequence DNA collected from subfossils from locations in North and South America.
Richard G. Klein9. Researches the archeological and fossil evidence for the evolution of human behavior. He has done fieldwork in Spain and especially in South Africa, where has excavated ancient sites and analyzed the excavated materials since 1969. He has focused on the behavioral changes that allowed anatomically modern Africans to spread to Eurasia about 50,000 years ago, where they swamped or replaced the Neanderthals and other non-modern Eurasians.
Harold A. Mooney. Harold Mooney has demonstrated that convergent evolution takes place in the properties of different ecosystems that are subject to comparable climates, and has pioneered in the study of the allocation of resources in plants. Research in his laboratory is currently centered on the study of the impact of enhanced CO2 on ecosystem structure and function.
Dmitri A. Petrov. To study the role of mutational biases in evolution, we have been using defunct transposable elements to estimate mutational biases in different organisms. Evolution of mitochondrial DNA insertions into the nuclear genome, the evolution of introns and intergenic regions, and experimental evolution of gene regulation.
Terry L. Root, by courtesy4. Research interests include: ecological analyses of the distribution and abundance patterns of species on a continent-wide scale; examining the physiological constraints on the distribution of wintering birds; influence of global warming on the biogeography of species; large-scale geographic examinations of the structure and composition of communities; applying quantitative problems; analyzing the ecological causes of rarity and commonness; and women’s attrition rate out of academics.
Joan Roughgarden5. We study the relationship between evolutionary biology and ecology using a combination of theoretical ecology and field studies. We use mathematical descriptions of evolution of community structure and population dynamics and we study Anolis lizards in the Caribbean and barnacles in California.
Stephen H. Schneider4. Climatic change, global warming, economic implications of global warming mitigation strategies, food/climate and other environmental/science public policy issues, public understanding of science, ecological implications of climatic change, climatic modeling of paleoclimates and of human impacts on climate, e.g., carbon dioxide “greenhouse effect” or environmental consequences of nuclear war.
Shripad Tuljapurkar. Dynamics and evolution of human and natural populations. Sensitivity and extinction dynamics in the presence of disturbance, population aging and age structural transitions, evolution of senescence.
Peter M. Vitousek. Nutrient cycling in tropical and temperate forests. Regulation of cycling of nitrogen, phosphorus, and several other nutrients by using chemical analysis of soil, water, and gas samples from field sites. The biogeochemistry of indigenous agriculture, biological invasion by exotic species, and sources of elements during long-term soil and ecosystem development in the Hawaiian Islands.
Ward B. Watt. Developing evolutionary theory from mechanistic viewpoints. Using techniques ranging from biochemistry, DNA sequencing, and wind-tunnel flight biophysics to field ecology and mathematical population genetics, we study biochemical and physiological mechanisms of genetic variation, ecological niche structure as the source of natural-selective pressures, and the resulting patterns of evolution of metabolic organization.
1. Carnegie Institution of Washington