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INFECTIOUS DISEASES

 
 
• Victoria Auerbuch Stone (METX) Interplay between bacterial pathogens and the mammalian innate immune system
• Phil Berman (BME) Biotechnology and Infectious Diseases
• Manel Camps (METX) Use of Random Mutagenesis for Studies of Evolution and for Therapy
• Susan Carpenter (MCD) Long Noncoding RNA and Innate Immunity
• Rebecca DuBois (BME) Structure, Function, and Engineering of Virus Proteins
• Glenn Millhauser (Chem) Remarkable Protein Structures ..... and Where They Go Wrong
• Karen Ottemann (METX) Bacterial Pathogens Sense and Respond to Host Environments
• Nader Pourmand (BME) Single Cell Analysis and Manipulation, Biosensor, Nanotechnology, DNA Sequencing
• Raquel Prado (AMS) Applications of Bayesian Analysis to Biomedical Signal Processing
• Jevgenij Raskatov (Chem) Disease-Oriented Chemical Biology
• Holger Schmidt (EE) Integrated Optofluidics: Detecting and Analyzing Single Molecules on a Chip
• Nik Sgourakis (Chem) Modelling the Structures of Protein Complexes from Sparse Experimental Data
• 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
• Christopher Vollmers (BME) Development of DNA Sequencing Tools for the Analysis of B cells
• Fitnat Yildiz (METX) Ex-vivo Survival Mechanisms of Vibrio cholerae

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 XXXBiotechnology and Infectious Diseases

Phil Berman, Dept. of Biomolecular Engineering

Professor Berman is a pioneer in the development of recombinant vaccines for AIDS and other infectious diseases. His research interests include the development of vaccines, therapeutics, and diagnostics for the prevention and treatment of infectious diseases, as well as the development of new technology for commercial production of complex recombinent glycoproteins. [More]

Berman Publications Phil Berman's Email

Prof Susan CarpenterUse of Random Mutagenesis for Studies of Evolution and for Therapy

Susan Carpenter, Molecular, Cell, & Developmental Biology

One of the most fascinating findings following the sequencing of the human genome is that less than 3% of the genome codes for protein coding exons while over 85% of the genome is actively transcribed. Long noncoding RNA (lncRNA) represent the largest class of RNA transcripts produced from the genome and to date there are 16,000 lncRNAs catalogued in Gencode. In recent years lncRNA have emerged as major regulators of chromatin remodeling, transcription and post-transcriptional regulation of gene expression in diverse biological contexts. Our goal is to understand the functions for lncRNA in inflammatory signaling pathways in macrophages and dendritic cells. [More]

Carpenter's Publications Sue Carpenter's Email

Prof Susan CarpenterUse of Random Mutagenesis for Studies of Evolution and for Therapy

Susan Carpenter, Molecular, Cell, & Developmental Biology

One of the most fascinating findings following the sequencing of the human genome is that less than 3% of the genome codes for protein coding exons while over 85% of the genome is actively transcribed. Long noncoding RNA (lncRNA) represent the largest class of RNA transcripts produced from the genome and to date there are 16,000 lncRNAs catalogued in Gencode. In recent years lncRNA have emerged as major regulators of chromatin remodeling, transcription and post-transcriptional regulation of gene expression in diverse biological contexts. Our goal is to understand the functions for lncRNA in inflammatory signaling pathways in macrophages and dendritic cells. [More]

Camps' Publications Manel Camps' 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 DuBoisStructure, Function, and Engineering of Virus Proteins

Rebecca DuBois, Biomolecular Engineering

Professor DuBois is a structural biologist studying viral surface and replication proteins. She uses her discoveries to design novel vaccines, to develop nanoscale drug delivery vehicles, and to develop antiviral therapeutics. [More]

DuBois Publications Rebecca Dubois' E-Mail

 


xxxRemarkable Protein Structures... and Where They Go Wrong in Disease

Glenn Millhauser, Department of Chemistry

In modern biochemistry, structural determination is essential for understanding the function of biomolecules. Scientists in Glenn Millhauser's laboratory use peptide synthesis, nuclear magnetic resonance spectroscopy (NMR), and electron paramagnetic spin resonance spectroscopy (EPR) to examine the structure and analyze the function of proteins that have been implicated in several debilitating diseases. This includes the prion protein, which is responsible for mad cow disease and the related human affliction, Creutzfeldt-Jakob disease. They have also examined a novel signaling molecule, called AGRP, which is involved in energy balance and metabolic pathologies, such as diabetes and obesity. [More]
Millhauser Publications Glenn Millhauser's E-Mail

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 Biomolucular 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 Pourmand's Email

Prof Raquel PradoApplications of Bayesian Analysis to Biomedical Signal Processing

Raquel Prado, Dept. of Applied Mathematics and Statistics

Dr. Prado is a statistician whose research deals with sophisticated Bayesian time series methods to analyze complex and large-dimensional data that arise in various biomedical applications. She is currently working on developing statistical models and computational tools for the analysis of brain signals that are recorded in clinical and non-clinical neuroscience studies, such as electroencephalograms, fMRI data, and magnetoencephalograms. [More]

Prado Publications Raquel Prado 's Email

Prof. Jevgenij A. RaskatovDisease-Oriented Chemical Biology

Jevgenij A. Raskatov, Dept. of Chemistry and Biochemistry

Raskatov draws inspiration from aging-related medicinally challenging questions, which are becoming increasingly pressing as life expectancy continues to rise (the cancer/inflammation interface is of specific interest). Raskatov's lab identifies biomolecular signaling nodes that are sufficiently well-understood at the molecular level, so that a biology problem can be translated into a chemistry problem. As chemists, their goal is to synthesize molecules and study their properties by means of NMR spectroscopy (1), crystallography (2) and DFT computation (3). Molecular scaffolds that show initial promise are tested in relevant biological systems both in cell culture (4) and in vivo (5). [More]

Raskatov Publications Jevgenij Raskatov's Email

Prof Holger SchmidtIntegrated Optofluidics: Detecting and Analyzing Single Molecules on a Chip

Holger Schmidt, Dept. of Electrical Engineering

Optofluidics describes the combination of optics and microfluidics and holds great promise for novel devices for biomedical instrumentation, analytical chemistry and other fields that deal with liquid analytes. A highly desirable extension of optofluidics is to use integrated optics to replace the bulky microscopy analysis that is still commonly in use. This would allow development of a fully planar, fully integrated lab on a chip. We are using optofluidic approaches for early infectious disease and cancer detection and genome analysis. [More]

Schmidt Publications Holger Schmidt's Email

Prof Nik SgourakisModelling the Structures of Protein Complexes from Sparse Experimental Data

Nik Sgourakis, Dept. of Chemistry and Biochemistry

Research in the Sgourakis lab focuses on elucidating the structures of important protein complexes involved in Immune recognition of viruses, bacterial secretion and neurodegeneration. Determining the structural basis of protein-protein interactions and self-assembly will help clarify fundamental biological mechanisms and facilitate the design of novel therapeutics. To achieve this, structure-based modelling at sufficient resolution is required. The Sgourakis lab is developing and implementing new tools based on Nuclear Magnetic Resonance spectroscopy and complementary sources of experimental data alongside advanced computational sampling methods. The integration of a range of experimental and computational approaches enables structural studies of proteins and their complexes at high resolution. [More]
Sgourakis Publications Nik Sgourakis' 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 Christopher VollmersDNA Sequencing Tools for the Analysis of B cells

Christopher Vollmers, Dept. of Biomolecular Engineering

Our adaptive immune systems is highly efficient in protecting us from the most diverse intruders. B cells are an essential part of the adaptive immune system. Each B cell uniquely rearranges its genome several times to produce an unique antibody. Until very recently, the analysis of B cell populations circulating in the periphery at any given time was labor intensive and low throughput. The Vollmers lab focuses on developing DNA sequencing tools to analyze B cells on a population and single cell level. [More]

Vollmers' Publications Christopher Vollmers' 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
 

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