The Plant Biology program at Stanford University provides opportunities to receive graduate education in a wide range of subjects from global ecology to molecular genetics. The program is centered in the Department of Biological Sciences. Many of the Carnegie faculty also have appointments in the Department of Biological Sciences and participate in teaching and advising graduate students. The Department of Biological Sciences offfers an extensive series of advanced courses in topics of relevance to graduate studies in plant biology. The research interests of the Stanford faculty with interests in plant biology are listed below. For additional information about graduate studies see Plant Cell and Molecular Biology, a Graduate Program at Stanford University.

Dominique Bergmann

We use genetic, genomic and cell biological approaches to study cell fate acquisition, focusing on cases where cell fate is correlated with asymmetric cell division. Generating the full complement of functional cell types requires coordinating the production of cells with the specification programs that distinguish one cell type from another. Asymmetric cell division, in which one cell divides to create daughter cells that differ in size, location, cellular components or fate, is extensively used in the development of animals. In development of the epidermis in the model plant Arabidopsis thaliana, the specification and distribution of stomatal guard cells also requires oriented cell divisions. By studying stomatal development, one can explore how cells choose to initiate asymmetric divisions, how cells establish an internal polarity that can be translated into an asymmetric cell division, and how cells interpret external cues to align their divisions relative to the polarity of the whole tissue. Moreover, approaching these questions in a plant system is likely to reveal new solutions to the problem of balancing the robust specification of cell types with the ability to change development in the face of injury or environmental change. Our current research is focused on three areas. (1) Regulation of cell fate by MAP kinase signaling; (2)Pattern formation and its reliance on cell communication to regulate division polarity; (3) Identification of positive regulators of stomatal formation.

Sharon Long

Studies on the mechanisms by which bacteria of the genus Rhizobium infect legume plants and establish a nitrogen-fixing symbiosis in root nodules. Members of the group have identified bacterial genes for early nodulation and characterized chemical signal exchange leading to recognition and differentiation by bacteria and plants. The group uses diverse approaches from genomics to cell biology as means to study root nodule development and its regulation.

Hal Mooney

Research is currently centered on the study of the impact of enhanced carbon dioxide on ecosystem structure and function, in collaboration with the Carnegie Institution, Dept. of Plant Biology, and Stanford's Jasper Ridge Biological Preserve.

Mary Beth Mudgett

Research is focused in two areas. One is the study of the initial interactions of bacterial pathogens with plant cells. To grow in the plant, bacteria need to sense their environment and to induce genes required for infection. A primary locus induced in Gram-negative bacteria is the Hrp locus. The Hrp gene locus encodes the bacterial type III machinery required for the secretion and translocation of effector proteins to the plant cell. The goals in this area are to: (1) determine how specific type III effector proteins are delivered to the plant cell, (2) to identify the plant substrates for type III effector proteins, and (3) to elucidate the molecular mechanism used by these effectors to suppress plant host defenses.
The second area of study is to molecularly and biochemically dissect the host surveillance mechanisms in plants. Single plant resistance genes that have evolved to recognize bacteria expressing type III effector genes often control the genetic basis of plant resistance to bacterial pathogens. The major goals in this area of research are: (1) to identify how plant cells perceive type III effector proteins and (2) to identify how resistance proteins function to initiate the molecular signaling events controlling plant defense responses. email mudgett@stanford.edu

Peter Vitousek

Experimental and comparative studies of nutrient cycling in tropical and temperate forests. Demonstrated that biological invasions by exotic species can alter ecosystem-level properties in the areas they invade. His laboratory is at the forefront of efforts to understand nutrient cycling in forest ecosystems, and is now working towards understanding interactions between components of global change and terrestrial ecosytems. Field studies are currently underway in Hawaii on gradients of volcanic sites from young lava to old rainforests, from sea level to treeline, from very wet forests to deserts, and on natural tropical forests and cleared lands. His research group determines the regulation of cycling of nitrogen, phosphorus, and several other nutrients by using chemical analysis of soil, water, and gas samples from field sites. The laboratory is also following biological invasion by exotic species, soil development, and the mutual influence of soil and vegetation following volcanic eruptions.

Virginia Walbot

Studies in mutator transposon family of maize. Focus is on developmental regulation of transposition. MuDR/Mu transposons increase mutation frequency 50-100 fold in maize:  they are the most aggressive DNA transposons characterized in any organism.  MuDR/Mu elements transpose late in development, with a different molecular outcome in strictly somatic cells and in cells that are pre-germinal or gametophytic.  We are analyzing the multiple molecular mechanisms that confer developmental timing and differential transpositional outcome to MuDR/Mu elements.  These studies are aimed at defining host processes that are instrumental in regulating organ growth (the decision of when to stop cell division within an organ, which confers late timing) and in the fundamental switch between somatic and germinal cells in flowers (a developmental decision that impacts the outcome of Mu transposition).   RescueMu, a genetically engineered transposon suitable for plasmid rescue, and other transgenic maize lines containing individual cDNAs encoded by MuDR are being used to define the precise requirements for somatic and germinal transposition.  RescueMu is also used in high throughput genomics research to tag, clone, and sequence maize genes; see http://zmdb.iastate.edu for details.  Epigenetically silenced Mu elements can be reactivated by UV-B radiation; this observation has sparked new experiments on the impact of UV-A and UV-B on maize.  Currently we are using microarrays to uncover additional pathways beyond DNA repair and flavonoid synthesis that are stimulated by UV exposure.  Because we use anthocyanin pigmentation as one of our primary assays for transposon behavior, we are also studying the deposition of this pigment.  We are particularly interested in the mechanism of vacuolar sequestration as this determines when the pigment becomes a cell autonomous marker. 

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