Research interests: The role marine microalgae play in biogeochemical cycling, with particular emphasis on the scales of temporal and spatial variability of microalgal biomass, productivity, and ecology. Also of interest is the genetic and biochemical basis for regulation of phytoplankton productivity and nutrient utilization.

Microbes studied: Phaeocystis antarctica, Nitzschia sp., Fragillariopsis sp., Synechocystis sp., Prochlorococcus sp., natural phytoplankton and ice algal communities

Research topics: metabolism, genomics, gene expression, evolution, environment, biogeochemistry, ecology, photosynthesis

Research interests: Molecular basis of phototaxis in cyanobacteria; signal transduction networks; typeIV pilus mediated motility; comparative and functional genomics in cyanobacteria

Microbes studied: Synechocystis sp., Anabaena sp., Synechococcus sp.

Research topics: genetics, genomics, gene regulation, evolution, photosynthesis, environment

Research interests: Responses of microbial communities to environmental change, control of microbial biodiversity, role of trophic interactions in microbial communities, application of molecular tools to the study of microbial ecology, theoretical microbial ecology and evolution, natural microbial communities.

Microbes studied Escherichia coli, coliphage, nitrifying bacteria, denitrifying bacteria, methanotrophic bacteria, natural microbial communities.

Research topics: genetics, genomics, plant-microbe interactions, host-pathogen interaction, biofilm, ecology, evolution, environment,biogeochemistry

Research interests: We are putting all of our current effort into studies of the obligate intracellular parasite, Toxoplasma gondii. This is a member of the protozoan phylum Apicomplexa which includes the causative agent of malaria and coccidiosis. Toxoplasma is perhaps the most wide-spread parasite on earth with infection being possible in almost any warm-blooded animal and with prevalence rates in many regions being extremely high (e.g., ~75% of adult humans in France are infected). Our interests are in the novel aspects of Toxoplasma biology. We approach these issues through a combination of genetics and cell and molecular biology. The specific questions we are focusing on are:
(i) how does Toxoplasma attach to and invade almost any eukaryotic cell it encounters?
(ii) how does the parasite nurture itself within the parasitophorous vacuole it creates inside the host cell?
(iii) how does Toxoplasma manipulate the immune response of the host to achieve a chronic infection?
(iv) how are proteins destined for novel organelles specifically targeted?
(v) what are the signals and mechanisms that control gene expression during development from the chronic "bradyzoite" form to the active "tachyzoite" stage?
(vi) what are the physiological differences between these two developmental forms?
(vii) do different strains of Toxoplasma cause different disease outcomes in humans and, if so, can we exploit this to manage the disease better?

Microbes studied: Toxoplasma gondii. (a protozoan parasite of humans and many other warm-blooded animals).

Research topics:genetics, recombination, genomics, gene regulation, metabolism, symbiosis, development, differentiation, cell cycle, ecology, environment, parasites

There are three relatively diverse programs of research in the laboratory, united by the focus on modern molecular genetics and genomics. One of these programs focuses on the cell biology of budding yeast, (Saccharomyces cerevisiae). Another focuses on the genetics of common human diseases. The third is on the organization, analysis and storage of biological information, which, with rapid advance of genome sequencing, has flooded the scientific community. The yeast cell biology studies concentrate on the structure and function of the cytoskeletion, whose component proteins are virtually all highly conserved among all eukaryotes. The laboratory has for many years studied the genetics of actin and the tubulins and their many protein ligands, using a great variety of technologies, including systematic scanning mutagenesis, genetic tests for gene and protein interaction, and light and electron microscopy. A major feature of recent studies is the extensive use of microarray hybridization technology, part of an extensive collaboration with Prof. P. O. Brown (Department of Biochemistry). Together we study yeast gene expression, deriving information about the genes associated with many cellular process, ranging from basic metabolism and the cell cycle to meiosis and sporulation.

Microbes studied: Saccharomyces cerevisiae

Research topics: Genetics, Yeast, Cytoskeleton, DNA Polymorphisms, Linkage

Research Interests: 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.

Microbes studied: Bacillus subtilis

Research topics: Cell cycle, Development, Gene Regulation, Genetics

Research Interests: Our primary current interest is in the evolution of biological diversity. The system under study is the site-specific integration of bacteriophage DNA into the bacterial chromosome. We are examining the molecular basis of site specificity in natural relatives of coliphage lambda, as well as diversity in their regulatory programs governing expression of the integrase genes.

Microbes studied: Escherichia coli and its phages, especially phage 21 and defective phage e14.

Research Interests: 1) RNA decay as a genetic control mechanism. Mechanisms and signals that regulate RNA stability in bacteria and eukaryotes are being studied. 2) Genetics of antibiotic resistance. The developmentally complex antibiotic producing genus Streptomyces is a source of plasmid-borne antibiotic resistance genes found in pathogenic bacteria. We are studying mechanisms that control the formation, evolution, and replication of linear plasmids in Streptomyces and the signals that regulate the conjugal transfer of plasmids among bacteria. 3) Bioinformatic analysis of microarray data. GABRIEL (Genetic Analysis By Rules Incorporating Expert Logic), a novel system of computer programs, incorporates expert knowledge into rules and uses algorithms capable of analyzing genetic data and explaining the basis for decisions.

Microbes studied: E. coli, Streptomyces species.

Research topics:genetics, genomics, gene regulation, host-pathogen interaction, development, differentiation, cell cycle

Research interests: microbial community ecology and functional stability, gene expression and its control, process kinetics, fate of persistent contaminants. Microbes studied: Pseudomanas stutzeri KC, Shewanella oneidensis MR1

Research topics: microbially-mediated dechlorination and defluorination, metal reduction, incomplete denitrification, community analysis, community ecology.

Research interests: We study the role of Ca2+ dependent signaling in yeast, especially roles of the Ca2+ calmodulin regulated phosphatase, calcineurin. In response to stress, calcineurin dephosphorylates the Crz1p transcription factor causing its nuclear localization and activation of gene expression. Other roles and substrates of calcineurin and mechanisms of Ca2+ signaling are also studied.

Microbes studied: Saccharomyces cerevisiae

Research topics: genetics, genomics, gene regulation

Our laboratory is focused on the development and application of molecular biology, manipulative genetics to a variety of problems. As model organisms, we generally use Saccharomyces cerevisiae and Arabidopsis thaliana. We are studying the replication of artificial yeast chromosomes and are investigating the effect of spacing of the origins of replication on chromosomal stability. We have identified several Saccharomyces cerevisiae isolates that grow at much higher temperatures than is typical for and have discovered that some of these strains show pathogenic traits and show proliferation in a mouse. We are developing novel methods for identifying all of the "pathogenic" genes. In a separate project we are developing technologies that will allow rapid DNA sequencing and are sequencing several yeast chromosomes. We are developing new methods that will allow us to identify all essential genes under certain growth conditions in the yeast genome by a single hybridization to a large array of oligonucleotide on a chip. We are also exploring the use of enzymes such as dominant lethal mutants of recA to solve a number of technical problems.

Microbes studied: Saccharomyces cerevisiae

Research topic: Genetics, Vaccines, Molecular Biology, Virology, Leprosy, Biochemistry, Arabidopsis, DNA, Yeast

Research Interests: Marine microbial biology. Physiology, biochemistry, ecology and evolution of marine microbes. Marine biogeochemical cycles. Microbial evolution and ecology. Genomic approaches in environmental microbiology.

Only a very small percentage of naturally occurring microbes can be readily cultured and studied using standard cultivation techniques. This a serious impediment for microbial characterization. Our lab is investing significant effort in developing and app lying culture-independent methods to identify, quantify, and characterize naturally occurring marine microbes. Our approach consists of melding field and laboratory intensive efforts. Our focus is on the marine environment Ì­åö planktonic bacteria and archaea, sediment dwelling microorganisms, and metazoan symbionts can all be more thoroughly characterized using cultivation-independent approaches. Our approach combines traditional, biochemical, genomic and ecological methods to better understand and characterize naturally occurring microbes in the world around us.

The primary focus of our research is to understand how bacterial agents cause infection and disease. We examine the genetic and molecular basis of microbial pathogenicity in several model systems. We also investigate the natural history of infectious diseases by looking at the molecular organization of the genetic material of pathogens in endemic and epidemic settings. Our research techniques range from model infection of animals and cultured human cells to the cloning and sequencing of specific bacterial genes.

Microbes studied: Salmonella species, Helicobacter pylori

Research topics: Bacterial pathogenesis; eukaryotic cell invasion; cell biology of bacterial-host cell interaction

Research interests: Microbial mediated redox dynamics of iron and trace elements in soils and sediments; biofilm development on mineral surfaces and their impacts on contaminant retention.

Microbes studied: Shewanella putrefaciens, Shewanella alga, Desulfovibrio vulgaris, Bacillus sp.

Research topics: biofilm, metabolism, environment, bioremediation, biogeochemistry

Research interests: Genomics; acclimation of photosynthetic organisms to environmental conditions; Photoperception and signal transduction; Acquisition and utilization of nutrients.

Microbes and photosynthetic organisms studied: Synechocystis Pcc6803, Porchlorococcus ProMed4, Prochlorococcus 9313, Chlamydomans reinhardtii, Saccharomycetes cerevisiae, arabidopsis thaliana

Research topics: genomics genetics, gene regulation, metabolism, photosynthesis, environment

Studies the mechanisms by which living cells maintain their genomes in the face of endogenous DNA damage and environmental radiations and chemical carcinogens.

Research Topics: genetics, recombination, gene regulation, DNA repair

How are genes regulated to construct a developmental program? How do signals received from other cells change the program and coordinate it for organized multicellular development? The approach taken by our laboratory group to answer these questions utilizes biochemisty and genetics; genetics to isolate mutants that have particular defects in development and biochemistry to determine the molecular basis of the defects. Microbe studied: Myxococcus xanthus Research topics: Cell interactions, gene regulation, molecular genetics, morphogenesis, signal transduction, quorum sensing, microbial genetics, cell motility, signal molecules, biochemistry of development, microbial development, swarming, developmental biology, microbiology

Research interests: Environmental sensing and response mechanisms, metabolic engineering of antibiotic production.

Microbes studied: Streptomyces bacteria.

Research topics: genomics, gene regulation, metabolism

Research interests:protein engineering, natural product biosynthesis.

Microbes studied:E. coli, Streptomyces coelicolor

Reseach topics: structure-function of poyketide synthases, structure-function of prolyl endopeptidases

Research interests: Cell signaling between symbionts and host plants; genetics and functional genomics of Rhizobium; symbiotic nitrogen fixation; gene expression

Microbes studied:Sinorhizobium meliloti, other Rhizobium

Reseach topics: genetics, genomics, gene regulation, plant-microbe interaction, symbiosis, developmetn, differentiation, cell cycle

Research interests: Bacterial stress response to identify targets for therapeutic intervention. Transcriptomic and proteomic studies on resistance genes of bacterial biofilms. Multidrug resistance pumps. Molecular approaches to bioremediation with concentration on chromate and the use of starvation promoters. DNA shuffling to evolve proteins with superior capacity for chromate and prodrug reduction. Sigma factors and post-transcriptional regulation.

Microbes studied: Escherichia coli, Pseudomonas putida, Staphylococci, Bacillus subtilis, Helicobacter pylori, Streptococci

Research topics: Stress response, Antibiotic resistance, MDR, Biofilms, Genomics, Bioremediation, Prodrug cancer chemotherapy, Gene expression

Studies of biogeochemical process in terrestrial and aquatic ecosystems, with a special emphasis on the mechanisms and regulation of nitrogen cycling processes. Her research questions focus on the response of ecosystems to anthropogenic influences, including fertilization, atmospheric nitrogen deposition, and changes in moisture. Her approach utilizes measurements of fluxes, identification of controlling processes, estimation of microbial activity through measures of enzyme potentials, istope labelling, and isotope dilution, and identification of microbial communities at relatively coarse scales. Matson particiates in multi-disciplinary and interdisciplinary studies of socioeconomics and ecosystem change.

Research interests: Genetic regulatory networks; Systems biology; Functional genomics; Cell-cycle regulation; Modeling and simulations of genetic regulatory networks; Cross-species genomics

Microbes studied: Caulobacter crescentus

Research topics: genetics, genomics, gene regulation, development, differentiation, cell cycle, evolution, bioremediation, biogeochemistry

Research interests: Molecular and biochemical basis of plant-pathogen interactions, cell-to-cell communication, bacterial type III protein secretion, type III effector function, plant disease resistance, plant localized cell death.

Microbes studied: Pseudomonas syringae, Xanthomonas campestris

Research topics: plant-microbe interaction, host-pathogen interaction, genetics, genomics, signal transduction.

Research interests: Infection as a cause of chronic disease, gastrointestinal neoplasms, interactions among microbial agents within the human host, epidemiology of diarrheal diseases and foodborne diseases stomach neoplasms, esophageal neoplasms, epidemiology, diarrhea, gastroenteritis, transmission.

Microbes studied: Helicobacter pylori (predominantly). To a lesser extent, intestinal helminths, Chlamydia pneumonia, other helicobacters, and Mycobacterium tuberculosis

Research topics: biofilm 

Research interests: Microbial processes in the global biogeochemical cycle, methane production in wetlands, nitrogen cycling in coastal systems, sulfate reduction in the geological record using S istopes

Microbes studied: natural microbial communities (methanogens, methane oxidizers, nitrifiers, denitrifieers, sulfate reducers)

Research topics: biogeochemistry, photosynthesis, environment, ecology

Research interests: Genetics and biology of fungi. Meiosis and ascus development. Cytogenetics. Genome organization. Natural populations. Speciation. Meiotic drive.

Microbes studied:Neurospora and related euascomycetes.

Research topics: genetics, recombination, development, differentiation, evolution, ecology.

Research interests: human microbial ecology; community genomics of human endogenous microflora; development and application of novel methods for pathogen discovery; genomics of host-microbe interaction

Microbes studied: Cultivation-resistant microbes, Bordetella species

Research topics: genomics, host-pathogen interaction, ecology

Research interests:, Association of proteins at liquid and solid interfaces; surface reactivity of enzymes; aggregation and association phenomena of polyphenols and proteins; metabolic engineering

Microbes studied: Bacillus subtilis; E.  coli; Streptomyces aureofaciens; Saccharomyces cerevisiae

Research topics: recombination, metabolism, biofilm

Our laboratory has been studying the unusual mechanism of translation initiation by internal ribosome entry in certain viral and cellular mRNA molecules. In the conventional ?scanning mechanism? of translation initiation, which operates on most mRNA molecules, 40S subunits are recruited at or near the 5? end of the mRNA. Subsequently, the 40S ribosomal subunits are predicted to scan the mRNA in a 5' to 3' direction until the first AUG codon is encountered as start site for protein synthesis. However, certain viral and cellular mRNAs, notably encoding proto-oncogenes and regulatory genes, contain long 5? noncoding regions with multiple AUG codons. Thus, the translation initiation rate in these mRNAs is predicted to be low according to the scanning model; alternatively, other translation initiation mechanisms may operate to ensure efficient translation. Indeed, some of such mRNAs with long leaders contain internal ribosome entry sites which can bind ribosomes directly. Much of our work has been focussing on the mechanism and prevalence of internal ribosome binding. Specifically, we are addressing the following questions: Which cellular and viral mRNAs can be translated by internal ribosome binding? What are the cellular gene products that mediate internal ribosome binding? Is internal initiation regulated in the cell? What is the molecular basis for designating a given AUG codon as start site codon?

Microbe studied: S. cerevisiae

Research topics: Virus-host interactions, translational control, RNA viruses, hepatitis C virus, picornavirus, Drosophila RNA viruses, nuclear-cytoplasmic trafficking, internal ribosome entry, reinitiation, cDNA microarray display, cell cycle arrest, S. cerevisiae, de novosynthesis of viruses, nucleolin, proto-oncogene mRNAs, gene knock out, RNA-protein interactions, RNA structure, frameshifting

Structure-function analysis of bacterial adhesion proteins and toxins; design and synthesis of synthetic antigens; immunobiology of human Papillomaviruses

Microorganisms studied: Vibrio cholerae, Mycobacterium tuberculosis, enteropathogenic E. coli

Research topics: Infectious Diseases, Protein, Molecular Biology, Vaccines, Bacteria, Genetics, AIDS, Geographic Medicine

A basic question in developmental biology involves the mechanisms used to generate the three-dimensional organization of a cell from a one-dimensional genetic code. Our goal is to define these mechanisms using both molecular genetics and biochemistry. The developmental program by which a single cell proceeds to a fully-developed organism involves cell divisions that yield dissimilar daughter cells. The characteristics that differentiate one daughter cell from the other result from differential transcription and subcellular positioning of regulatory and structural proteins. How this is brought about remains one of the most fundamental questions of developmental biology. To approach this question, we are studying a bacterial cell, whose simple life cycle is focused on the generation of asymmetry in the predivisional cell. We are using full genome sequence and microarray technology to identify the genetic circuitry that controls the cell cycle in a bacterial cell with 3767 genes. Dynamic protein localization, phosphorelay signaling cascades, and spatially and temporally controlled proteolysis are overlayed on the transcription network that controls cell cycle progression and cell differentiation.

Microorganism studied: Caulobacter crescentus

Research topics: Developmental biology, Caulobacter, mRNA, protein

Research Interests: plant-pathogen interactions, host susceptibility factors, basal host resistance mechanisms, pathogen-induced hypersensitive necrosis response

Microbes Studied: powdery mildew fungi  Erysiphe cichoracearum and Blumeria graminis f. sp. hordei

Research topics: genetics, genomics, host-pathogen interaction, plant-microbe interaction

Research interests: Microbial community intereactions, Metabolic and signaling cell-cell interactions,  Molecular evolution of biofilm microbes; Microbe-mineral interactions; Molecular mechanisms of degradation of environmental pollutants, Photosynthetic hydrogen production.

Microbes studied: Shewanella oneidensis,  Caulobacter crescentus, Azoarcus species, Vibrio cholerae, Xanthobacter, Dehalococcoidesand natural microbial communities.

Research topics: biofilm, metabolism, genomics, gene expression, evolution, environment, bioremediation, biogeochemistry, ecology 

The general research interest of this laboratory is the molecular basis of cell motility. We have three specific research interests, the molecular basis of energy transduction that leads to ATP-driven myosin movement on actin, the biochemical basis of the regulation of actin and myosin interaction and their assembly states, and the roles these proteins play in vivo, in cell movement and changes in cell shape. We work on two experimental systems: contraction of mammalian muscle and chemotaxis of Dictyostelium discoideum cells. Each of these systems has its special advantages. Skeletal muscle has the most highly organized contractile apparatus of any cell type, and the chemistry and biochemistry of muscle actin and myosin are most advanced.

Microorganism studied: Dictyostelium discoideum

Research topics: Dictyostelium discoideum, molecular motors, myosin, cell motility, muscle contraction, protein structure and function, cell biology, cell development

We study the organization and regulation of the microtubule cytoskeleton, and the relationship between the cell cycle and the cytoskeleton. Microtubules are polymers assembled from alpha-tubulin and beta-tubulin subunits, and are an essential element of the cytoskeleton. Microtubules are polar polymers, acting as directional tracks for the many motor proteins that move along them. Microtubules and motors move vesicles and organelles, and make up the spindle, which segregates chromosomes in mitosis and meiosis. How do cells organize microtubules into complex structures like the mitotic spindle? One of the keys is the centrosome, a unique organelle that nucleates microtubule polymerization from free subunits. How does the centrosome nucleate microtubule polymerization, how does the centrosome Ì°åÂhold onÌ°å¨ to one end of the microtubule, and how is the copy number of the centrosome controlled by the cell cycle such that it is present at one copy per cell?

Microbe studied: Saccharomyces cereviseae

Research topics: microtubules, tubulin, centrosome, cell cycle, mitosis, cell division, chromosome segregation, cell biology, genetics, yeast, frog, cancer, genomics, checkpoints, folding, human, proteomics, cytoskeleton,

Research interests: Cell-free protein synthesis, protein expression and folding, biodesulfurization, metabolic engineering, conversion of sunlight into hydrogen

Microbes studied: E.coli, Rhodococcus sp., Synechocystis sp, Clostirium pasteurainum

Research topics: cell-free protein synthesis, metabolic engineering, transcription, translation, protein folding.

Research interests: Actin-based motility by intracellular bacterial pathogens; Protein polymerization in cell organization and movement; Establishment and maintenance of bacterial polarity; Quantitative videomicroscopy, image and motion analysis

Microbes studied: Listeria monocytogenes, Shigella flexneri, Escherichia coli (clinical and laboratory strains)

Research topics: host-pathogen interaction, differentiation, cell cycle, genomics, metabolism, evolution

Molecular and cellular basis of pathogenicity of Helicobacter pylori infection and the relationship to gastric malignancy. We are studying the interaction between Helicobacter pylori, the causative agent of peptic ulcers and gastric cancer, and gastric epithelial cells. We have identified bacterial genes associated with inducing IL-8, an inflammatory cytokine, and with gastric inflammation. Genes encoded by a pathogenicity island in H. pylori comprise a secretory apparatus that secretes bacterial CagA protein into target gastric epithelial cells. CagA is phosphorylated on tyrosine residues by host cell kinases and is associated with signal transduction and changes in the cytoskeleton and motility. Cells that have received CagA develop an elongated phenotype and become motile. Current studies in the laboratory using DNA microarrays coupled with cell biology methods have shown that H. pylori are intimately associated with cellular junctions in polarized epithelial cells, specifically with junctional proteins, including Zo1, a claudin. We are also employing DNA microarrays to study the molecular epidemiology and evolution of H. pylori strains and also to examine the host cell response to infection by transcriptional profiling. These investigations are focused on understanding the complex interaction between H. pylori and the stomach in which both partners participate in producing disease.

Microbes studied: Helicobacter pylori

Keywords: Bacterial pathogenesis, genetics, cell biology, molecular epidemiology, hospital epidemiology

Research interests: Gene regulation, metabolism, transcription attenuation, gene and protein evolution

Microbes studied: Escherichia coli; Bacillus subtilis

Research topics: genetics, genomics, gene regulation, metabolism, evolution