Research - Genomics

The Baker Lab seeks understanding of the molecular, genetic and biochemical bases of host-microbe interactions, and investigates mechanisms of pathogen-induced host disease and disease resistance. Our experimental system to study plant-pathogen recognition and signal transduction includes a diverse plant pathogen set and Solanaceae plant hosts. We anticipate our studies will lead to new, environmentally benign strategies for durable, broad-spectrum disease resistant crops.

The Brenner Lab develops methods to characterize macromolecular function and relationships using protein and RNA sequence information, evolutionary principles, and computational methods. We also investigate how many natural mRNA transcripts are apparent targets of the nonsense-mediated mRNA decay pathway for RNA surveillance. In many instances, alternative splicing induces NMD for gene regulation.

The Bruns Lab has two central research themes: fungal ecology and evolution, with molecular systematics crucial to both. This Lab contributed some of the first sequence-based analyses of fungal evolution and developed oligonucleotide primers to the ribosomal RNA genes and spacers. These primers constitute a mainstay of fungal molecular systematics.

Research in the Buchanan Laboratory currently focuses on thioredoxin in connection with:
(1) Regulation of chloroplast enzymes. Sheng Luan (UC Berkeley) collaborates on this research.
(2) Improvement in the quality and yield of cereals. We have ongoing collaborations with several colleagues on this project: Peggy G. Lemaux (UC Berkeley); Jun Yin and his group (Henan Agricultural University, Zhengzhous, China); and William J. Hurkman and William H. Vensel (USDA Laboratory, Albany, CA).

The Cande Lab researches the mechanism of chromosome segregation during mitosis and meiosis, to understand changes in chromosome structure and behavior that lead to pairing of homologous chromosomes during meiotic prophase and their segregation at Meiosis I and II. We use three model organisms: Giardia intestinalis, Schizosaccharomyces pombe, and Zea mays. We also use a computerized light microscope workstation that records three-dimensional images of multiple cellular components in fixed and living cells.

The Coates Lab focuses on environmental microbiology: applied microbiology and bioremediation. We investigate removal of radioactive toxic metals, carcinogenic petroleum-based hydrocarbon contaminants, and toxic munitions byproducts from the environment. Recently, we identified dominant groups of bacteria that can transform perchlorate wastes into innocuous chloride, isolated and characterized more than 40 such bacteria, and identified the common biochemical pathway and genetic systems involved.

The Fischer Lab studies imprinted genes expressed from their maternal alleles in the endosperm. MET1 DNA methyltransferase methylates and silences imprinted genes. DEMETER antagonizes MET1, allowing maternal alleles to be expressed. DEMETER is a DNA glycosylase and is expressed specifically in the central cell, a maternal gamete fertilized to form the endosperm. We study how DEMETER antagonizes MET1, what restricts DEMETER expression to the central cell, how DEMETER targets imprinted genes, and the identity and function of new imprinted genes.

We study the molecular mechanisms that establish and maintain plant stem cell reservoirs. We have demonstrated that Arabidopsis stem cell maintenance requires active intercellular signaling via a spatial negative feedback loop, the CLV3-WUS pathway. We integrate genetics, molecular biology, cell biology and biochemistry to analyze the signal transduction mechanism and regulation of the pathway, and to identify additional pathway components. We use functional genomics to characterize a family of plant-specific CLV3-related signaling molecules, the CLE proteins.

The Freeling Lab researches 1) Origin of new grass genes, using maize model developmental systems and comparative grass genomics 2) Epigenetics of Mu transposons in maize and other grasses (D. Lisch). 3) Developmental genetics of the maize coleoptile, and the interaction between Knox genes (rs1, gn1 in maize, knat1, knat2 in Arabidopsis) with their negative regulatory genes (rs2/as1) 4) The meaning and uses of conserved noncoding sequences in grasses.

Cell specialization, cell communication and nonself recognition are crucial mechanisms in filamentous fungi. Neurospora crassa's experimental tractability make it a superb system to address microbial communication questions. We study communication and self-signaling mechanisms mediating hyphal fusion, and nonself recognition mechanisms resulting in programmed cell death. We use molecular biology, genetics, cell biology, genomics and bioinformatics to investigate the molecular and cellular basis of nonself recognition during the filamentous fungi lifecycle.

Our laboratory uses genetics to study plant development. We work with maize, arabidopsis, and tomato, depending on the experiment. The laboratory research falls into three categories: 1) identifying the downstream targets of the knotted1-like (knox) homeodomain transcription factors, 2) identifying genes that regulate inflorescence architecture in maize and other grasses, 3) investigating new morphological mutations.

The circadian clock is a key adaptation for life on earth, since it lets organisms coordinate internal physiological activities with daily and seasonal environmental changes. The Harmon lab investigates the plant circadian oscillator's molecular mechanism, using Arabidopsis as a model system. We apply genetic, biochemical, molecular, and genomic approaches to identify and characterize proteins contributing the plant clockworks. We seek to integrate their function into current clock models.

We are interested in epigenetic mechanisms that generate and maintain heritable phenotypic variation. Paramutation is one such mechanism in which the regulation of one allele is heritably altered through interactions with its homologous partner. We use genetic and molecular analyses in Zea mays to understand the paramutation process and the genomic features on which it operates. These studies provide novel insights regarding chromosome organization, evolution and gene function.

The Jackson Lab researches how viruses elicit plant diseases, and devises mechanisms for disease control in transgenic plants. We work with three viruses: a plus sense monopartite RNA virus, tomato bushy stunt virus; a plus sense tripartite RNA virus, barley stripe mosaic virus; and a minus strand plant rhabdovirus, sonchus yellow net virus. We use genetic and biochemical analysis to investigate replication and movement of these viruses and to determine virus-host interactions culminating in disease.

We study structural and functional characterization of bacterial microcompartments and of proteins involved in photoprotection in photosynthetic organisms.

We study Amt and Rh proteins, which appear to be membrane channels for hydrated gases. They are the only two members of their superfamily. The Amt proteins are channels for ammonium. The Rh proteins, of Rh blood group substance fame, appear to be channels for carbon dioxide (probably H2CO3). We focus on the physiological roles of Rh and Amt proteins in the green alga Chlamydomonas reinhardtii. We continue collaborations to determine the structures of bacterial enhancer-binding proteins, which regulate transcription by the sigma54 holoenzyme form of RNA polymerase.

The research objectives of the Lemaux Lab include the development and use of genetic transformation systems for monocotyledonous species, such as Triticum aestivum, Zea mays, Avena sativa, Hordeum vulgare, Oryzae sativa, Festuca spp., Dactylis glomerata, and Poa pratensis. Our long-term objective is to use transformed cereals to explore basic biological questions as well as to understand and improve crop characteristics.

Our research group studies aspects of epiphytic bacteria that live on healthy plants' surfaces, emphasizing bacteria active in ice nucleation, causing frost damage to plants. We also study plant pathogenic bacteria that inhabit plant surfaces before infection. We use molecular genetic and ecological approaches to study how epiphytic bacteria interact with other microorganisms on plants, and with the plants on which they live. We seek to better understand adaptations epiphytic bacteria have evolved to exploit this unique habitat.

We study how plants perceive and respond to extracellular signals by modifying their developmental and physiological programs. Our studies have identified a new molecular network for calcium signal transduction in plants. Downstream of these early signaling events, plants respond to environmental signals by regulating the biochemical processes including those in the chloroplasts. We focus on the new regulators for the biogenesis of the photosynthetic complexes (bioenergy conversion) and for starch metabolism (biomass production).

We study the photosynthesis of plants, microalgae, cyanobacteria, and photosynthetic bacteria. Approaches include biophysics and biochemistry of the process, molecular biology and genetics of the organisms, and scale ups for product generation. Applied aspects include diverting the flow of photosynthesis to generate high-value compounds instead of the normally produced sugars. Products of interest are biofuels, feedstock for the synthetic chemistry industry and neutraceuticals. Our trademark is product generation directly from photosynthesis, bypassing the need to harvest and process the respective biomass.

Photosynthetic organisms have evolved multiple mechanisms to cope with excessive light. We seek to identify and dissect these processes by isolating algal and plant mutants. We use a diverse set of techniques, including genetics, physiology, biochemistry, and molecular biology, focused on one particular species, Chlamydomonas reinhardtii, a unicellular green alga. We study the cellular processes involved in coping with reactive oxygen species produced in excessive light.

The cells of higher plants are encased by a wall, a sophisticated, highly complex material consisting mainly of various polysaccharides and polyphenols. The Pauly lab uses a synthetic biology approach whereby all necessary components of the biosynthetic machinery of cross-linking glycans and pectins are identified. To achieve this goal we use various genetic approaches including forward, reverse, and chemical genetics with the model organism Arabidopsis, but also maize as a grass species.

We seek to enhance the efficiency of plant transformation, by developing high frequency DNA integration to expedite functional analysis, precise DNA integration into known genome locations for more predictable gene expression, and removal of DNA no longer needed after gene transfer. We also characterize genes that confer plant metal tolerance, and research ways to get rid of gossypol in cottonseed, e.g. engineering the breakdown of gossypol in the seed.

We research molecular mechanisms by which light regulates gene expression in plants, focusing on the phytochromes family of photoreceptors. The photoreceptor molecule acts as a biological switch that upon perception of the light signal, triggers changes in transcription detectable within 5 minutes of stimulus. We recently developed a novel light-switchable gene promoter system potentially usable in any light-accessible eukaryotic cell system for rapid, conditional induction or repression of expression.

We isolate pure populations of Caulobacter swarmer cells and observe many parameters during their synchronous cell cycle progress including fluorescent protein localization, DNA content, and global transcriptional patterns. The sequenced Caulobacter genome expedites genetic manipulations and lets us search comprehensively for genes affecting processes of interest. We also pursue in vitro studies to determine how biochemical properties of individual regulatory proteins contribute to cell cycle progression and cellular asymmetry.

Research in the Specht lab centers on the processes and patterns involved in the evolution and diversification of plants, especially the monocots. We use a phylogenetic framework to test hypotheses of morphological evolution and to analyze temporal and spatial patterns of plant speciation. We emphasize use of systematics in comparative biology. We focus on the evolution of development, comparative genomics and the genetics of interspecies interactions.

We seek to obtain a genetic, bio-chemical, and cell biological understanding of the mechanisms that enable gram-negative plant pathogens to cause disease on plants, and that allow plants to counteract bacterial pathogens.

The Sung laboratory investigates the mechanism that represses flowering, whereby enabling vegetative growth and expanding life span. We focus on the epigenetic mechanism that maintains the silencing of flower homeotic genes by the PcG protein complex. We also take a phylogenetic approach to study the origin and evolution of the EMF proteins, as well as their function in early emerging plants. The long term goal is to understand their contribution in the evolution of plant development and generation of diverse morphology.

Vitamin B12 is essential to most animals but is synthesized only by certain prokaryotes. Using genetic, biochemical, and bioinformatics approaches, we are investigating three areas related to vitamin B12 in bacteria: 1) the biosynthesis of 5,6-dimethylbenzimidazole (DMB), the least understood component of B12; 2) the function of B12 in the symbiotic interaction between the nitrogen-fixing bacterium Sinorhizobium meliloti and its plant host, alfalfa, and 3) the structure and function of novel B12-like compounds found in nature

We study the pattern and process of fungal evolution, both to understand the process and to make fungi the best models for evolutionary biology. We focus on the key evolutionary event that forms the tree of life: speciation. Recently we have documented species divergences, compared phylogenetic and biological species recognition, addressed the timing of species divergence, and evaluated selection acting on potentially adaptive genes. Now, we are using genetics and genomics to find genes that maintain species and facilitate adaptation.

The Terry Lab researches how to improve the efficiency with which plants remove and detoxify toxic metals and metalloids like Arsenic, Chromium, Lead, Selenium, Mercury, and Cadmium from contaminated soil, sediments, and water. For example, many plant species detoxify Chromium (VI), a very toxic form of the element, to essentially non-toxic Chromium (III). Some plants can also convert toxic forms of Selenium, e.g., selenate and selenite, to volatile but non-toxic dimethylselenide.

We research the molecular mechanism of auxin action, using auxin-inducible genes as probes. We isolated novel, interacting proteins that bind to the auxin responsive domains, and constructed Arabidopsis transgenic lines for isolating mutants responsible for transcriptional activation by auxin. We also research ACC synthase gene expression regulation. We use some ACS genes as molecular probes to study signal transduction pathways responsible for auxin inducibility of ACC synthase gene expression.

My Lab couples predictive biochemistry and analytical chemistry with forward and reverse genetics and genomics to discover small molecules and their biosynthetic pathways which alter defense-related regulatory pathways resulting in large-scale transcriptional changes and redirection of plant cellular metabolism. We use biochemical, molecular, theoretical and informatic approaches to analyze these molecules at cellular and organismic levels. We study the evolution of their biosynthesis, their regulation, and functional roles.

My Lab has two projects underway 1) studying Agrobacterium-specific proteins and their molecular mechanisms responsible for producing a DNA-protein complex capable of plant cell transformation, and 2) researching Plasmodesmata structure.

Our goal is to understand how components of eukaryotic chromatin interrelate and integrate to regulate transcriptional activity. We combine genetics and biochemistry with genomics and computational analysis to study DNA methylation, deposition of histone variants, chromatin associated proteins and nucleosome remodeling.

Associates of the Department

We work on algorithm development for homolog identification, multiple sequence alignment, phylogenetic tree construction, protein fold prediction, identification of domain boundaries (and novel domains), and detection of key amino acids, such as catalytic or binding pocket residues. We integrate phylogenetic tree construction and subfamily identification into our protein structure and function prediction methods, to enable us to infer the changes produced in protein function and structure over the evolution of a protein superfamily.

We research two facets of development in the fruiting bacterium Myxococcus xanthus. The first concerns cell-cell communication and signal transduction; the second concerns the regulation of gene expression during cellular morphogenesis and development. Myxococcus exhibits complexity of multicellular behavior and morphogenetic development unusual among prokaryotes. We apply sophisticated genetic and molecular biological techniques to examine these processes.