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• Victoria Auerbuch Stone (METX) Interplay between bacterial pathogens and the mammalian innate immune system
• Manel Camps (METX) Use of Random Mutagenesis for Studies of Evolution and for Therapy
• Phil Crews (Chem) Marine Natural Products as Potent Agents Against Human Disease
• Grant Hartzog (MCD) Examining Chromatin and Transcription in the Yeast, Saccharomyces cerevisiae
• Todd Lowe (BME) Large-scale Approaches to Study Whole-genome Archaeal Biology
• Nader Pourmand (BME) Single Cell Analysis and Manipulation, Biosensor, Nanotechnology, DNA Sequencing
• Karen Ottemann (METX) Bacterial Pathogens Sense and Respond to Host Environments
• Chad Saltikov (METX) The Role of Microbes in Arsenic Contamination of Drinking Water
• Beth Shapiro (EEB) Inferring the Evolutionary Dynamics of Species and Populations Using Genome-scale Data Sampled Over Time
• Bill Sullivan (MCD) Wolbachia host cell cycle/ cytoskeletal interactions in insects and filarial nematodes
• Fitnat Yildiz (METX) Ex-vivo Survival Mechanisms of Vibrio choleraes
• Jon Zehr (Ocean Sciences) The Roles of Microorganisms in Aquatic Ecosystems

Prof Victoria Auerbuch StoneInterplay between bacterial pathogens and the mammalian innate immune system

Victoria Auerbuch Stone , Microbiology and Environmental Toxicology

Professor Auerbuch Stone’s research interests focus on how mammalian cells recognize and respond to bacterial pathogens and how, in turn, bacterial pathogens manipulate the mammalian innate immune system. We use human pathogenic Yersinia to study the type III secretion system (T3SS), a needle-like apparatus used by dozens of pathogens, including the gut microbe Y. pseudotuberculosis and the plague agent Y. pestis, to inject effector proteins inside mammalian target cells. The T3SS is an evolutionarily ancient structure that is recognized by several mammalian innate immune receptors, leading to a host response presumably aimed at eliminating the invading pathogen. Current research in Professor Auerbuch Stone’s lab focuses on gaining a better understanding of how Yersinia regulate their T3SS, on probing the mammalian innate immune response to the Yersinia T3SS, and on discovery and characterization of small molecule inhibitors of the T3SS. [More]
Auerbuch Stone Publications Auerbuch Stone's Email

Prof Manel CampsUse of Random Mutagenesis for Studies of Evolution and for Therapy

Manel Camps, Microbiology and Environmental Toxicology

The Camps laboratory studies how random changes in genetic information (mutations) facilitate the acquisition of new biochemical activities. They couple the generation of random mutant libraries with specific selections or screens to study the functional impact of individual point mutations and to establish how genes evolve in response to selective pressure. As model systems they use extended-spectrum beta-lactamase resistance and the evolution of alterations in the substrate specificity of the demethylase ALKBH2. This work is combined (in a collaboration) with high-end computational approaches aimed at anticipating the effect of individual mutations, alone, or in combination. A separate application of random mutant library generation in vivo is the use of mutation footprints to dissect the role of individual players involved in DNA replication. Finally, the Camps laboratory is applying concepts of directed evolution to whole genomics analysis, with an emphasis on cancer. The goal of these studies is to help understand the contribution of DNA repair genes to resistance to chemotherapy and to oncogenesis. [More]

Camps' Publications Manel Camps' Email

Prof Phil CrewsMarine Natural Products as Potent Agents Against Human Disease

Phil Crews, Dept. of Chemistry and Biochemistry

A primary goal of Phillip Crews' marine natural products research is to understand the chemistry of tropical marine sponges. Using bioassay-guided isolation assists us in the discovery of natural products potent against human diseases, such as cancer or viruses. Their search for novel active compounds incorporates elements of structure elucidation, but there are other dimensions to this research, including questions in the areas of chemical ecology, marine natural products biosynthesis, and the relationship between secondary metabolite chemistry and taxonomy... [More]

Crews' Publications Phil Crews' E-Mail

Prof Grant HartzogExamining Chromatin and Transcription in the Yeast, Saccharomyces cerevisiae

Grant Hartzog, Dept. of MCD Biology

For over a century, scientists have employed yeast as a model system to understand how basic biological systems operate. Most often, the information gained from the yeast system provides us with insights into how similar processes occur in humans. Grant Hartzog's laboratory uses biochemical and genetic techniques on the yeast Saccharomyces cerevisiae to examine the role chromatin, which consists of the DNA of our genomes and the proteins that associate with the DNA, plays in gene expression and the mechanisms by which chromatin structure is manipulated to regulate transcription. The group focuses on two proteins, Spt4 and Spt5, which form a complex and appear to modulate transcription by interacting with chromatin. [More]

Prof Todd LoweLarge Scale Approaches to Study Whole-Genome Biology

Todd Lowe, Dept. of Biomolecular Engineering

Todd Lowe's research group uses a mixture of computational and experimental genomics to identify and characterize non-coding RNA (ncRNA) genes and to study the unique biology of Archaeal “extremophiles” – microbes that live at the edge of the limits of life.  His team has created several classes of non-coding RNAs gene-finders, and has created full-genome DNA microarrays for two different hyperthermophile species to study ancient forms of respiration and strategies for thermo-tolerance.  The group has also created a genome browser and functional genomics resource for all archaeal and extremophile species (archaea.ucsc.edu), now funded by the NSF. [More]

Lowe Publications Todd Lowe's Email

Prof Karen OttemannHow Bacterial Pathogens Sense and Respond to Host Environments

Karen Ottemann, Dept. of Microbiology and Environmental Toxicology

Professor Karen Ottemann's laboratory investigates how bacteria translate chemical and physical cues in their host environment into pathogenic outcomes. Mistakes in sensation and subsequent gene expression by bacteria may result in their elimination by the host immune response or peristaltic flow. Elucidation of such processes will hopefully lead to identification of anti-bacterial drug targets. Ottemann is particularly interested in the role of outer membrane proteins and chemotaxis associated with the bacterium Helicobacter pylori. This pathogen infects some 3 billion humans and can lead to serious disease, including ulcers and cancer. [More]

Ottemann Publications Karen Ottemann's Email

Prof Nader PourmandSingle Cell Analysis and Manipulation, Biosensor, Nanotechnology, DNA Sequencing

Nader Pourmand, Dept. of Biomolecular Engineering

The Pourmand lab develops new tools and technologies that integrate biology, electronics, and nanofabrication for the detection and study of genes and proteins. These tools are specifically designed to increase the speed and lower the cost of sample analysis. The lab directs particular attention to the development of medically relevant technology, such as instruments for single cell analysis. Pourmand is also Director of Genome Technology Center. [More]

Pourmand Publications Nader Pourmand's Email

Prof Chad SaltikovThe Role of Microbes in Arsenic-Contamination of Drinking Water

Chad Saltikov Dept. of Microbiology and Environmental Toxicology

By converting the chemical form of arsenic found in the soil, naturally occurring microbes have been shown to exacerbate arsenic contamination of ground water, resulting in serious health crises in Asia and Latin America. Professor Chad Saltikov investigates the molecular biology of these microbial processes. Data from his laboratory will help devise strategies that can be used to ameliorate contamination of drinking water. [More]

Saltikov Publications Chad Saltikov's Email

Prof Beth ShapiroInferring the Evolutionary Dynamics of Species and Populations Using Genome-scale Data Sampled Over Time

Beth Shapiro, Dept. of Ecology and Evolutionary Biology

The Shaprio lab combines temporal and genetic data to identify periods of growth, decline, dispersal, and replacement in populations. Recent statistical innovations have made it possible to co-estimate molecular rates, demographic histories and phylogenetic relationships in populations that can be sampled through time. While large mammals fall into this category (when ancient samples are available) by far the richest source of these data are RNA viruses, whose fast rate of mutation makes it easy to see evolution happening over only a few years. [More]

Shapiro Publications Beth Shapiro's Email

Prof Bill SullivanWolbachia Host Cell Cycle/Cytoskeletal Interactions in Insects and Filarial Nematodes

Bill Sullivan, Dept. of MCD Biology

Among bacterial endosymbionts, the interaction between Wolbachia and their insect hosts is one of the most successful. Wolbachia are gram-negative, obligate, intracellular bacteria, carried by millions of arthropod and nematode hosts worldwide. It was recently discovered that Wolbachia maintain an obligate symbiotic relationship with pathogenic nematodes and are the causative agent of Elephantiasis and African River-blindness, neglected diseases afflicting over 200 million globally. The Sullivan lab uses a combination of molecular genetic, cellular and biochemical approaches to define the mechanisms by which Wolbachia interacts with the host cytoskeleton and influences the host cell cycle. In addition, they are engaged in high-throughput cell-based screens, using automated microscpy to identify new potent anti-Wolbachia compounds for combating Elephantiasis and River-blindness. [More]

Sullivan's Publications Bill Sullivan's E-Mail

Prof Fitnat YildizEx-vivo Survival Mechanisms Used by Vibrio cholerae between Epidemics

Fitnat Yildiz, Dept. of Microbiology and Environmental Toxicology

Ex-vivo Survival Mechanisms used by Vibrio cholerae between Epidemics: Fitnat Yildiz's laboratory investigates signaling and regulatory networks of Vibrio cholerae, the causative agent of the Asiatic cholera. She and her colleagues are particularly interested in those mechanisms that allow the pathogen to adapt to changes in its habitat. The bacteria's ability to survive in different growth modes in aquatic environments is closely linked to seasonal epidemics of cholera. Yildiz's laboratory is attempting to identify and characterize genes and processes associated with phase variations of the pathogen. Their results will be useful for prediction and control of epidemics of this devastating disease. [More]

Yildiz Publications Fitnat Yildiz's E-Mail

Prof Jon ZehrCell Cycle, Cytoskeleton and Pathogenesis

Jon Zehr, Dept. of Ocean Sciences

Microbes play critical roles in the cycling of organic matter and in the biogeochemical cycles of nutrients and trace elements. Many studies involve the nitrogen cycle, with an emphasis on biological nitrogen fixation. Nitrogen fixation is an important source of biologically available nitrogen in the world's oceans. Using molecular biology approaches, including the polymerase chain reaction (PCR) and reverse-transcriptase PCR, novel nitrogen fixing cyanobacteria have been discovered in the North Pacific. Zehr's interests include the fundamental basis for the distribution of microorganisms and genetic information in the environment. Many microorganisms in the environment cannot be easily cultivated, and thus cultivation-independent approaches are needed in order to study biodiversity and biocomplexity of microbial populations. Zehr's laboratory studies the patterns of distribution of genes and genomes in aquatic systems ranging from the open ocean, to estuaries and freshwater lakes. [More]

Zehr's Publications Jon Zehr's E-Mail

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