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  • Advanced Optics Lab

    The Advanced Optics Lab uses innovative optical tools, including laser-based nanotechnologies, to understand cell motility and the regulation of cell shape. We pioneered laser-based nanotechnologies, including optical tweezers, nanotracking, and laser-tracking microrheology. Applications range from physics, pharmaceutical delivery by phagocytosis (cell and tissue engineering), bacterial pathogens important in human disease and cell division.

    Other projects in the lab are related to microscopy, specifically combining fluorescence and electron microscopy to view images of the subcellular structure around proteins.

    Research Areas: optics, microscopy, physics, cellular biology, imaging, nanotechnology, drugs, tissue engineering

    Lab Website

    Principal Investigator

    Scot Kuo, Ph.D.

    Department

    Biomedical Engineering

  • Alex Kolodkin Laboratory

    Research in the Alex Kolodkin Laboratory is focused on understanding how neuronal connectivity is established during development. Our work investigates the function of extrinsic guidance cues and their receptors on axonal guidance, dendritic morphology and synapse formation and function. We have investigated how neural circuits are formed and maintained through the action of guidance cues that include semaphorin proteins, their classical plexin and neuropilin receptors, and also novel receptors. We employ a cross-phylogenetic approach, using both invertebrate and vertebrate model systems, to understand how guidance cues regulate neuronal pathfinding, morphology and synaptogenesis. We also seek to understand how these signals are transduced to cytosolic effectors. Though broad in scope, our interrogation of the roles played by semaphorin guidance cues provides insight into the regulation of neural circuit assembly and function. Our current work includes a relatively new interest in ...understanding the origins of laminar organization in the central nervous system. view more

    Research Areas: central nervous system, neural circuits, neurodevelopment, neuronal connectivity, laminar organization

    Lab Website

    Principal Investigator

    Alex Kolodkin, Ph.D.

    Department

    Neuroscience

  • Carolyn Machamer, Ph.D.

    The Machamer Lab is interested in the structure and function of the Golgi complex, an ubiquitous eukaryotic organelle that plays a central role in post-translational processing and sorting of newly synthesized proteins and lipids in the secretory pathway. One goal of our research is to understand the role of this structure in Golgi function by targeting and function of resident Golgi proteins. The other research interest in the lab is the assembly mechanism of coronaviruses, enveloped viruses that bud into Golgi compartments. We are addressing how coronaviruses target their envelope proteins to Golgi membranes, and how they interact with each other at the virus assembly site. We are also exploring how coronaviruses are exocytosed after they bud into the Golgi lumen. Our long-term goal is to understand the advantages of intracellular assembly for coronaviruses.

    Research Areas: proteomics, coronaviruses, Golgi complex, eukaryotic

    Lab Website

    Principal Investigator

    Carolyn Machamer, Ph.D.

    Department

    Cell Biology

  • Center for Research on Cardiac Intermediate Filaments

    The CRCIF was established to foster collaborative efforts aimed at elucidating the role of intermediate filaments (IFs) in the heart. Intermediate filaments constitute a class of cytoskeletal proteins in metazoan cells, however, different from actin microfilaments and tubulin microtubules, their function in cardiac cells is poorly understood. Unique from the other two components of the cytoskeleton, IFs are formed by cell type-specific proteins. Desmin is the main component of the IFs in the cardiac myocytes. We measured the consistent induction of desmin post-translational modifications (PTMs, such as phosphorylation, etc.) in various clinical and experimental models of heart failure. Therefore, one of our main focuses is to determine the contribution of desmin PTMs to the development of heart failure in different animal and clinical models.

    Active Projects:

    • Quantification of desmin PTM-forms in different forms of heart failure at the peptide level using mass spectrometry
    • F...unctional assessment of the role of desmin PTMs in heart failure development using single site mutagenesis and biophysical methods
    • Molecular characterization of desmin preamyloid oligomers using mass spectrometry, in vitro and in vivo imaging
    • Assessment of the diagnostic and pharmacological value of desmin PTMs in heart failure development
    view more

    Research Areas: heart failure, intermediate filaments

    Lab Website

    Principal Investigator

    Giulio Agnetti, Ph.D.

    Department

    Medicine

  • David Graham Lab

    The David Graham Lab studies the consequences of HIV interactions with the immune system, the resulting pathogenesis and how to sabotage these interactions. We apply advanced technologies like mass spectrometry to dissect processes at the molecular level. We are also actively involved in cardiovascular research and studies the ways proteins are organized into functional units in different cell types of the heart.

    Major projects in our lab are organized into three major areas: (1) H/SIV pathogenesis and neuropathogenesis, (2) Cardiovascular disease, and (3) High technology development

    Research Areas: immunology, mass spectrometry, HIV, cardiovascular, SIV, pathogenesis

    Principal Investigator

    David Graham, M.S., Ph.D.

    Department

    Molecular and Comparative Pathobiology

  • Dolores Njoku Lab

    Research in the Dolores Njoku Lab focuses on immune-mediated liver injury caused by drugs such as anti-seizure medications and antibiotics. We use an animal model to understand the pathways involved in the injury process, recognizing that this model can also uncover pathways involved with other drugs that cause similar liver injury. We hope to uncover the immunogenic epitopes, or pieces, of the proteins that trigger the autoimmune reaction and identify the key regulatory pathways involved.

    Research Areas: anesthesia, antibiotics, liver injury, liver diseases, mouse models

  • Elizabeth M. Jaffee, M.D.

    Current projects include:

    The evaluation of mechanisms of immune tolerance to cancer in mouse models of breast and pancreatic cancer. We have characterized the HER-2/neu transgenic mouse model of spontaneous mammary tumors.
    This model demonstrates immune tolerance to the HER-2/neu gene product. This model is being used to better understand the mechanisms of tolerance to tumor. In addition, this model is being used to develop vaccine strategies that can overcome this tolerance and induce immunity potent enough to prevent and treat naturally developing tumors. More recently, we are using a genetic model of pancreatic cancer developed to understand the early inflammatory changes that promote cancer development.

    The identification of human tumor antigens recognized by T cells. We are using a novel functional genetic approach developed in our laboratory. Human tumor specific T cells from vaccinated patients are used to identify immune relevant antigens that are chosen... based on an initial genomic screen of overexpressed gene products. Several candidate targets have been identified and the prevelence of vaccine induced immunity has been assessed .
    This rapid screen to identify relevant antigenic targets will allow us to begin to dissect the mechanisms of tumor immunity induction and downregulation at the molecular level in cancer patients. More recently, we are using proteomics to identify proteins involved in pancreatic cancer development. We recently identified Annexin A2 as a molecule involved in metastases.

    The analysis of antitumor immune responses in patients enrolled on vaccine studies. The focus is on breast and pancreatic cancers. We are atttempting to identify in vitro correlates of in vivo antitumor immunity induced by vaccine strategies developed in the laboratory and currently under study in the clinics.
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    Research Areas: immunology, cancer, anti-cancer drugs

    Lab Website

    Principal Investigator

    Elizabeth Jaffee, M.D.

    Department

    Oncology

  • Erika Darrah Lab

    The Erika Darrah Lab is primarily interested in the mechanisms underlying the development and progression of autoimmunity in rheumatoid arthritis (RA), with a particular focus on the peptidyl arginine deiminase (PAD) enzymes. We’re focused on understanding the development of PAD4-activating autoantibodies over time and how they contribute to the development of erosive disease. Studies are underway to determine if the newly discovered antibody is mimicking a naturally occurring PAD4 binding partner and to identify potentially pro-inflammatory effects of citrullinated proteins on effector cells of the immune system.

    Research Areas: antibodies, autoimmune diseases, peptidylarginine deiminase enzymes, rheumatoid arthritis

    Lab Website

    Principal Investigator

    Erika Darrah, Ph.D.

    Department

    Medicine

  • Foster Lab

    The Foster Lab uses the tools of protein biochemistry and proteomics to tackle fundamental problems in the fields of cardiac preconditioning and heart failure. Protein networks are perturbed in heart disease in a manner that correlates only weakly with changes in mRNA transcripts. Moreover, proteomic techniques afford the systematic assessment of post-translational modifications that regulate the activity of proteins responsible for every aspect of heart function from electrical excitation to contraction and metabolism. Understanding the status of protein networks in the diseased state is, therefore, key to discovering new therapies.

    D. Brian Foster, Ph.D., is an assistant professor of medicine in the division of cardiology, and serves as Director of the Laboratory of Cardiovascular Biochemistry at the Johns Hopkins University School of Medicine.


    Research Areas: proteomics, protein biochemistry, heart failure, cardiology, cardiac preconditioning, cardiomyopathy

    Lab Website

    Principal Investigator

    D. Brian Foster, M.Sc., Ph.D.

    Department

    Medicine

  • Green Lab

    Work in the Green Lab is centered on the ribosome. The overall fidelity of protein synthesis appears to be limited by the action of the ribosome, which is the two-subunit macromolecular machine responsible for decoding and translating messenger RNAs (mRNAs) into protein in all organisms. Our work is divided into four general project areas. The longest-standing research area concerns the interactions of eubacterial ribosomes and release factors. The goal is to understand the mechanism of action of release factors on the ribosome. A second research area involves biochemical and structure/function studies of the miRNA pathway, particularly the mechanism of action of the Argonaute proteins and their interacting factors. A third area of work in the lab is centered around regulation of eukaryotic translation, specifically in understanding the mechanism behind various mRNA quality control pathways and the interactions of proteins therein, as well as with the ribosome. The newest area of rese...arch in the lab extends our strengths in ribosome biochemistry to characterize the translation status of the cell using the ribosome profiling. We are using this technique to better understand the role of several factors involved in eukaryotic and prokaryotic translation fidelity. view more

    Research Areas: biochemistry, genomics, ribosome, RNA

  • Haughey Lab: Neurodegenerative and Neuroinfectious Disease

    Dr. Haughey directs a disease-oriented research program that address questions in basic neurobiology, and clinical neurology. The primary research interests of the laboratory are:

    1. To identify biomarkers markers for neurodegenerative diseases including HIV-Associated Neurocognitive Disorders, Multiple Sclerosis, and Alzheimer’s disease. In these studies, blood and cerebral spinal fluid samples obtained from ongoing clinical studies are analyzed for metabolic profiles through a variety of biochemical, mass spectrometry and bioinformatic techniques. These biomarkers can then be used in the diagnosis of disease, as prognostic indicators to predict disease trajectory, or as surrogate markers to track the effectiveness of disease modifying interventions.
    2. To better understand how the lipid components of neuronal, and glial membranes interact with proteins to regulate signal transduction associated with differentiation, motility, inflammatory signaling, survival, and neuronal excitab...ility.
    3. To understand how extracellular vesicles (exosomes) released from brain resident cells regulate neuronal excitability, neural network activity, and peripheral immune responses to central nervous system damage and infections.
    4. To develop small molecule therapeutics that regulate lipid metabolism as a neuroprotective and restorative strategy for neurodegenerative conditions.
    view more

    Research Areas: multiple sclerosis, PTSD, HAND, HIV

    Lab Website

    Principal Investigator

    Norman Haughey, Ph.D.

    Department

    Neurology
    Neurosurgery

  • Heng Zhu Lab

    The Zhu lab is focused on characterizing the activities of large collection of proteins, building signaling networks for better understanding the mechanisms of biological processes, and identifying biomarkers in human diseases and cancers. More specifically, our group is interested in analyzing protein posttranslational modifications, and identifying important components involved in transcription networks and host-pathogen interactions on the proteomics level, and biomarkers in human IBD diseases.

    Research Areas: inflammatory bowel disease, biomarkers, cancer

  • J. Marie Hardwick Laboratory

    Our research is focused on understanding the basic mechanisms of programmed cell death in disease pathogenesis. Billions of cells die per day in the human body. Like cell division and differentiation, cell death is also critical for normal development and maintenance of healthy tissues. Apoptosis and other forms of cell death are required for trimming excess, expired and damaged cells. Therefore, many genetically programmed cell suicide pathways have evolved to promote long-term survival of species from yeast to humans. Defective cell death programs cause disease states. Insufficient cell death underlies human cancer and autoimmune disease, while excessive cell death underlies human neurological disorders and aging. Of particular interest to our group are the mechanisms by which Bcl-2 family proteins and other factors regulate programmed cell death, particularly in the nervous system, in cancer and in virus infections. Interestingly, cell death regulators also regulate many other cel...lular processes prior to a death stimulus, including neuronal activity, mitochondrial dynamics and energetics. We study these unknown mechanisms.

    We have reported that many insults can trigger cells to activate a cellular death pathway (Nature, 361:739-742, 1993), that several viruses encode proteins to block attempted cell suicide (Proc. Natl. Acad. Sci. 94: 690-694, 1997), that cellular anti-death genes can alter the pathogenesis of virus infections (Nature Med. 5:832-835, 1999) and of genetic diseases (PNAS. 97:13312-7, 2000) reflective of many human disorders. We have shown that anti-apoptotic Bcl-2 family proteins can be converted into killer molecules (Science 278:1966-8, 1997), that Bcl-2 family proteins interact with regulators of caspases and regulators of cell cycle check point activation (Molecular Cell 6:31-40, 2000). In addition, Bcl-2 family proteins have normal physiological roles in regulating mitochondrial fission/fusion and mitochondrial energetics to facilitate neuronal activity in healthy brains.
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    Research Areas: cell death

  • Jeffry Corden Laboratory

    Jeffry Corden's lab is using genetic and biochemical approaches to investigate the functional role of the C-terminal domain (CTD) in the biogenesis of mRNA. We use both yeast and mammalian systems to conduct research.

    A major effort in the lab is directed at studies of proteins that bind the CTD. Using the yeast two-hybrid approach, we've identified a family of proteins that interact with the CTD. These proteins are similar to the serine/arginine-rich proteins involved in pre-mRNA splicing. A current focus of the laboratory is to determine how these proteins function in mRNA biogenesis and how CTD phosphorylation regulates this function. Other research in our lab investigates the mechanism by which RNA sequences in the nascent transcript trigger Pol II termination.

    Research Areas: biochemistry, C-terminal domain (CTD), genomics, yeast, RNA

    Principal Investigator

    Jeffry Corden, Ph.D.

    Department

    Molecular Biology and Genetics

  • Kalina Hristova Lab

    The Kalina Hristova Lab investigates the structure and assembly of biological membranes. Our team conducts research on the structural and thermodynamic principles that enable membrane protein folding and signal transduction across biological membranes. Part of our work has involved developing new tools to study the structure of thermally disordered fluid membranes and the energetics of biomolecular interactions in biological membranes. Through our studies, we have established a better understanding of the physical principles behind complex biological processes and the mechanisms of disease development in humans.

    Research Areas: membranes, proteins, biology

    Principal Investigator

    Kalina Hristova, Ph.D.

    Department

    Biomedical Engineering

  • Katherine Wilson Lab

    Research in the Wilson Lab focuses on three components of nuclear lamina structure: lamins, LEM-domain proteins (emerin), and BAF.

    These three proteins all bind each other directly, and are collectively required to organize and regulate chromatin, efficiently segregate chromosomes and rebuild nuclear structure after mitosis. Mutations in one or more of these proteins cause a variety of diseases including Emery-Dreifuss muscular dystrophy (EDMD), cardiomyopathy, lipodystrophy and diabetes, and accelerated aging.

    We are examining emerin's role in mechanotransduction, how emerin and lamin A are regulated, and whether misregulation contributes to disease.

    Research Areas: cell biology, Emery-Dreifuss muscular dystrophy (EDMD), accelerated aging, chromatin, diabetes, genomics, emerin, nuclear lamina, lipodystrophy, cardiomyopathy

    Principal Investigator

    Katherine Wilson, Ph.D.

    Department

    Cell Biology

  • Landon King Lab

    The Landon King Lab studies aquaporins water-specific membrane channel proteins. We hope to understand how these proteins contribute to water homeostasis in the respiratory tract and how their expression or function may be altered in disease states.

    Research Areas: respiratory system, proteomics, aquaporins

    Principal Investigator

    Landon King, M.D.

    Department

    Medicine

  • Mark Donowitz Lab

    Research in the Mark Donowitz Lab is primarily focused on the development of drug therapy for diarrheal disorders, intestinal salt absorption and the proteins involved including their regulation, and the use of human enteroids to understand intestinal physiology and pathophysiology. We study two gene families initially recognized by this laboratory: mammalian Na/H exchangers and the subgroup of PDZ domain containing proteins present in the brush border of epithelial cells called NHERF family. A major finding is that NHE3 exists simultaneously in different sized complexes in the brush border, which change separately as part of signal transduction initiated by mimics of the digestive process. Relevance to the human intestine is being pursued using mini-human intestine made from Lgr5+ stems cells made from intestinal biopsies and measuring function via two-photon microscopy.

    Research Areas: gastrointestinal system, gastroenterology, pathophysiology, diarrhea, drugs, physiology

    Lab Website

    Principal Investigator

    Mark Donowitz, M.D.

    Department

    Medicine

  • Mass Spectrometry Core

    The Mass Spectrometry Core identifies and quantifies proteins that change expression in well-characterized protein fractions from cancerous cells or tissues. This includes identifying and quantifying changes in binding partners and post-translational modifications. Column chromatography and gel electrophoresis-based one and two-dimensional separations of protein complexes coupled to mass spectrometry are used. Techniques such as difference gel electrophoresis (DIGE), isobaric tag for relative and absolute quantitation (iTRAQ) and 18O-labeling as well as non-labeling methods (MudPit, multi-dimensional protein identification technology) are available for quantifying relative differences in protein expression and post-translational modifications. We developed methods to detect post-translational modifications such as LCMS methods to accurately determine the intact mass of proteins, selective fluorescent labeling of S-nitrosothiols (S-FLOS) to detect nitrosated cysteines in proteins, and i...on mapping methods to map post-translational modifications that produce a signature mass or mass difference when the modified peptide is fragmented. view more

    Research Areas: mass spectrometry, proteomics, cancer

  • Michael Caterina Lab

    The Michael Caterina Lab studies the biological functions and biophysical characteristics of a group of ion channel proteins of the transient receptor potential vanilloid (TRPV) family--TRPV1, TRPV2, TRPV3 and TRPV4.

    These channels can be activated by warm or painfully hot temperatures, as well as by many nonthermal stimuli. Our lab is dissecting the biological contributions of these channels to thermosensory and nonthermosensory processes in both neuronal and nonneuronal cells. The goal of their research is to more broadly understand the biological and pathophysiological basis of chronic pain.

    Research Areas: biophysics, biochemistry, proteomics, inflammation, pain

    Lab Website

    Principal Investigator

    Michael Caterina, M.D., Ph.D.

    Department

    Neurosurgery

  • Michael Matunis Lab

    Research in the Michael Matunis Lab focuses on the SUMO family of small ubiquitin-related proteins. We study the covalent conjugation of SUMOs to other cellular proteins, which regulates numerous processes needed for cell growth and differentiation, and which, when defective, can lead to conditions such as cancer, neurodegenerative disease and diabetes.

    Research Areas: SUMO proteins, neurodegenerative diseases, cellular biology, proteomics, cancer, diabetes, malaria

    Principal Investigator

    Michael Matunis, Ph.D.

    Department

    Cell Biology

  • Miho Iijima Laboratory

    The Miho Iijima Laboratory works to make a further connection between cells' signaling events and directional movement. Our researchers have identified 17 new PH domain-containing proteins in addition to 10 previously known genes in the Dictyostelium cDNA and genome database. Five of these genes contain both the Dbl and the PH domains, suggesting these proteins are involved in actin polymerization. A PTEN homologue has also been identified in Dictyostelium that is highly conserved with the human gene. We are disrupting all of these genes and studying their roles in chemotaxis.

    Research Areas: cell biology, chemotaxis, genomics

    Lab Website

    Principal Investigator

    Miho Iijima, M.S., Ph.D.

    Department

    Cell Biology

  • O'Rourke Lab

    The O’Rourke Lab uses an integrated approach to study the biophysics and physiology of cardiac cells in normal and diseased states.

    Research in our lab has incorporated mitochondrial energetics, Ca2+ dynamics, and electrophysiology to provide tools for studying how defective function of one component of the cell can lead to catastrophic effects on whole cell and whole organ function. By understanding the links between Ca2+, electrical excitability and energy production, we hope to understand the cellular basis of cardiac arrhythmias, ischemia-reperfusion injury, and sudden death.

    We use state-of-the-art techniques, including single-channel and whole-cell patch clamp, microfluorimetry, conventional and two-photon fluorescence imaging, and molecular biology to study the structure and function of single proteins to the intact muscle. Experimental results are compared with simulations of computational models in order to understand the findings in the context of the system as a whole....

    Ongoing studies in our lab are focused on identifying the specific molecular targets modified by oxidative or ischemic stress and how they affect mitochondrial and whole heart function.

    The motivation for all of the work is to understand
    • how the molecular details of the heart cell work together to maintain function and
    • how the synchronization of the parts can go wrong

    Rational strategies can then be devised to correct dysfunction during the progression of disease through a comprehensive understanding of basic mechanisms.

    Brian O’Rourke, PhD, is a professor in the Division of Cardiology and Vice Chair of Basic and Translational Research, Department of Medicine, at the Johns Hopkins University.
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    Research Areas: biophysics, ischemia-reperfusion injury, imaging, electrophysiology, cardiovascular, arrhythmia, physiology, sudden cardiac death, molecular biology, cardiac cells

    Lab Website

    Principal Investigator

    Brian O'Rourke, Ph.D.

    Department

    Medicine

  • Paul Worley Lab

    The Paul Worley Lab examines the molecular basis of learning and memory. In particular, we cloned a set of immediate early genes (IEGs) that are rapidly transcribed in neurons involved in information processing, and that are essential for long term memory. IEG proteins can directly modify synapses and provide insight into cellular mechanisms that support synapse-specific plasticity.

    Research Areas: synaptic plasticity, neurons, memory, learning, immediate early genes

    Lab Website

    Principal Investigator

    Paul Worley, M.D.

    Department

    Neuroscience

  • Retrovirus Laboratory

    Research in the Retrovirus Laboratory focuses on the molecular virology and pathogenesis of lentivirus infections. In particular, we study the simian immunodeficiency virus (SIV) to determine the molecular basis for the development of HIV CNS, pulmonary and cardiac disease.

    Research projects include studies of viral molecular genetics and host cell genes and proteins involved in the pathogenesis of disease. We are also interested in studies of lentivirus replication in macrophages and astrocytes and their role in the development of disease. These studies have led us to identify the viral genes that are important in neurovirulence of SIV and the development of CNS disease including NEF and the TM portion of ENV. The mechanisms of the action of these proteins in the CNS are complex and are under investigation. We have also developed a rapid, consistent SIV/macaque model in which we can test the ability of various antiviral and neuroprotective agents to reduce the severity of CNS and ...pulmonary disease. view more

    Research Areas: HIV, genomics, pulmonology, SIV, cardiology, lentivirus

    Principal Investigator

    Janice Clements, Ph.D.

    Department

    Molecular and Comparative Pathobiology

  • Ronald Schnaar Lab

    The Ronald Schnaar Lab is involved in the rapidly expanding field of glycobiology, which studies cell surface glycans, lectins, and their roles in cell physiology.

    Current projects in our lab study include (1) Glycans and glycan-binding proteins in inflammatory lung diseases, (2) Ganglioside function in the brain, and (3) HIV-Tat and HIV-associated neurocognitive disorders.

    Research Areas: cell physiology, HIV, neurocognitive disorders, glycobiology

  • Rong Li Lab

    Research in the Rong Li Lab aims to better understand the fundamental laws that regulate the behavior and interactions of cellular systems. Our team is currently examining how cells consolidate their damaged proteins and prevent them from spreading freely — work aimed at understanding how to better treat diseases such as Alzheimer’s and ALS. We are also applying insights gained through basic research to better understand diseases such as cancer and polycystic kidney disease.

    Research Areas: cell biology, ALS, kidney diseases, cancer, cellular dynamics, molecular biology, Alzheimer's disease

    Lab Website

    Principal Investigator

    Rong Li, M.S., Ph.D.

    Department

    Cell Biology

  • Saraswati Sukumar Lab

    Our lab is focused on using comprehensive gene expression, methylation and sequencing and metabolomics analysis to identify alterations in breast cancer, and exploiting these for early detection and therapy. Among deferentially expressed genes, our lab has focused on the HOX genes. HOX genes are intimately involved in the development of resistance to both chemotherapy and to agents targeting the estrogen receptor. Our work explores the alternate pathways that are activated by HOX proteins leading to this resistance and novel treatments to overcome resistance in both tissue culture and xenograft models. In addition, epigenetically silenced genes and a metabolic reprogramming in tumors also trigger novel early detection and therapeutic strategies. We are testing the utility of differentiation therapy through reactivating RAR-beta in breast cancer using histone deacetylase inhibitors with great success. Also, we are targeting enzymes involved in gluconeogenesis and glycolysis with small ...molecule FDA-approved antimetabolites to achieve antitumor effects. view more

    Research Areas: breast cancer, genetics

    Lab Website

    Principal Investigator

    Saraswati Sukumar, Ph.D.

    Department

    Oncology

  • Sean Taverna Laboratory

    The Taverna Laboratory studies histone marks, such as lysine methylation and acetylation, and how they contribute to an epigenetic/histone code that dictates chromatin-templated functions like transcriptional activation and gene silencing. Our lab uses biochemistry and cell biology in a variety of model organisms to explore connections between gene regulation and proteins that write and read histone marks, many of which have clear links to human diseases like leukemia and other cancers. We also investigate links between small RNAs and histone marks involved in gene silencing.

    Research Areas: biochemistry, histone marks, cell biology, leukemia, cancer, epigenetics, eukaryotic cells, gene silencing, RNA

  • Seth Blackshaw Lab

    The Seth Blackshaw Lab uses functional genomics and proteomics to rapidly identify the molecular mechanisms that regulate cell specification and survival in both the retina and hypothalamus. We have profiled gene expression in both these tissues, from the start to the end of neurogenesis, characterizing the cellular expression patterns of more than 1,800 differentially expressed transcripts in both tissues. Working together with the lab of Heng Zhu in the Department of Pharmacology, we have also generated a protein microarray comprised of nearly 20,000 unique full-length human proteins, which we use to identify biochemical targets of developmentally important genes of interest.

    Research Areas: retina, central nervous system, biochemistry, hypothalamus, proteomics, genomics

    Lab Website

    Principal Investigator

    Seth Blackshaw, Ph.D.

    Department

    Neuroscience

  • Shanthini Sockanathan Laboratory

    The Shanthini Sockanathan Laboratory uses the developing spinal cord as our major paradigm to define the mechanisms that maintain an undifferentiated progenitor state and the molecular pathways that trigger their differentiation into neurons and glia. The major focus of the lab is the study of a new family of six-transmembrane proteins (6-TM GDEs) that play key roles in regulating neuronal and glial differentiation in the spinal cord. We recently discovered that the 6-TM GDEs release GPI-anchored proteins from the cell surface through cleavage of the GPI-anchor. This discovery identifies 6-TM GDEs as the first vertebrate membrane bound GPI-cleaving enzymes that work at the cell surface to regulate GPI-anchored protein function. Current work in the lab involves defining how the 6-TM GDEs regulate cellular signaling events that control neuronal and glial differentiation and function, with a major focus on how GDE dysfunction relates to the onset and progression of disease. To solve the...se questions, we use an integrated approach that includes in vivo models, imaging, molecular biology, biochemistry, developmental biology, genetics and behavior. view more

    Research Areas: glia, biochemistry, neurons, imaging, developmental biology, genomics, spinal cord, behavior, molecular biology

    Lab Website

    Principal Investigator

    Shanthini Sockanathan, D.Phil.

    Department

    Neuroscience

  • Shigeki Watanabe Lab

    Research in the Shigeki Watanabe Lab focuses on the cellular and molecular characterizations of rapid changes that occur during synaptic plasticity. Our team is working to determine the composition and distribution of proteins and lipids in the synapse as well as understand how the activity alters their distribution. Ultimately, we seek to discover how the misregulation of protein and lipid compositions lead to synaptic dysfunction. Our studies make use of cutting-edge electron microscopy techniques in combination with biochemical and molecular approaches.

    Research Areas: microscopy, cell biology, proteins, lipids, molecular biology

    Lab Website

    Principal Investigator

    Shigeki Watanabe, Ph.D.

    Department

    Cell Biology

  • Solomon Snyder Laboratory

    Information processing in the brain reflects communication among neurons via neurotransmitters. The Solomon Snyder Laboratory studies diverse signaling systems including those of neurotransmitters and second messengers as well as the actions of drugs upon these processes. We are interested in atypical neurotransmitters such as nitric oxide (NO), carbon monoxide (CO), and the D-isomers of certain amino acids, specifically D-serine and D-aspartate. Our discoveries are leading to a better understanding of how certain drugs for Parkinson's disease and Hungtington's disease interact with cells and proteins. Understanding how other second messengers work is giving us insight into anti-cancer therapies.

    Research Areas: Huntington's disease, amino acids, neurotransmitters, brain, cancer, nitric oxide, drugs, carbon monoxide, Parkinson's disease, nervous system

  • Steven Claypool Lab

    Research in the Claypool Lab is focused on defining how lipids and membrane proteins interact to establish and maintain normal mitochondrial function and how derangements in this complex relationship result in pathophysiology. We have demonstrated that yeast lacking tafazzin recapitulates all of the phospholipid abnormalities observed in human patients and many of the mitochondrial defects.

    Another major project in our lab focuses on the mitochondrial ADP/ATP carrier that is required for oxidative phosphorylation. Researchers are studying how these novel interactions help establish normal mitochondrial function, the biochemical details of these associations, and whether disturbances in these assemblies can contribute to mitochondrial dysfunction.

    Research Areas: biochemistry, proteomics, lipids, yeast, mitochondria, oxidative phosphorylation

    Lab Website

    Principal Investigator

    Steven Claypool, Ph.D.

    Department

    Physiology

  • Susan Michaelis Lab

    The Michaelis Laboratory's research goal is to dissect fundamental cellular processes relevant to human health and disease, using yeast and mammalian cell biology, biochemistry and high-throughput genomic approaches. Our team studies the cell biology of lamin A and its role in the premature aging disease Hutchinson-Gilford progeria syndrome (HGPS). Other research focuses on the core cellular machinery involved in recognition of misfolded proteins. Understanding cellular protein quality control machinery will ultimately help researchers devise treatments for protein misfolding diseases in which degradation is too efficient or not enough.

    Research Areas: biochemistry, cell biology, protein folding, lamin A, aging, genomics, Hutchinson-Gilford progeria syndrome, yeast

    Principal Investigator

    Susan Michaelis, Ph.D.

    Department

    Cell Biology

  • Tamara O'Connor Lab

    The O'Connor Lab studies the molecular basis of infectious disease using Legionella pneumophila pathogenesis as a model system.

    We are looking at the network of molecular interactions acting at the host-pathogen interface. Specifically, we use L. pneumophila pathogenesis to examine the numerous mechanisms by which an intracellular bacterial pathogen can establish infection, how it exploits host cell machinery to accomplish this, and how individual proteins and their component pathways coordinately contribute to disease.

    We are also studying the role of environmental hosts in the evolution of human pathogens. Using genetics and functional genomics, we compare and contrast the repertoires of virulence proteins required for growth in a broad assortment of hosts, how the network of molecular interactions differs between hosts, and the mechanisms by which L. pneumophila copes with this variation.

    Research Areas: infectious disease, Legionella pneumophila, genomics, pathogenesis, molecular biology

    Principal Investigator

    Tamara O'Connor, Ph.D.

    Department

    Biological Chemistry

  • The Burns Lab

    Our research laboratory studies the roles mobile DNAs play in human disease. Our group was one of the first to develop a targeted method for amplifying mobile DNA insertion sites in the human genome, and we showed that these are a significant source of structural variation (Huang et al., 2010). Since that time, our group has continued to develop high throughput tools to characterize these understudied sequences in genomes and to describe the expression and genetic stability of interspersed repeats in normal and malignant tissues. We have developed a monoclonal antibody to one of the proteins encoded for by Long INterspersed Element-1 (LINE-1) and showed its aberrant expression in a wide breadth of human cancers (Rodi? et al., 2014). We have demonstrated acquired LINE-1 insertion events during the evolution of metastatic pancreatic ductal adenocarcinoma and other gastrointestinal tract tumors (Rodi? et al., 2015). We have major projects focused on studying functional consequences of inh...erited sequence variants, and exciting evidence that these predispose to cancer risk and other disease phenotypes. Our laboratory is using a combination of genome wide association study (GWAS) analyses, custom RNA-seq analyses, semi-high throughput gene expression reporter assays, and murine models to pursue this hypothesis. view more

    Research Areas: cancer, DNA, malignant tumors

    Lab Website

    Principal Investigator

    Kathleen Burns, M.D., Ph.D.

    Department

    Pathology

  • The Sun Laboratory

    The nervous system has extremely complex RNA processing regulation. Dysfunction of RNA metabolism has emerged to play crucial roles in multiple neurological diseases. Mutations and pathologies of several RNA-binding proteins are found to be associated with neurodegeneration in both amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). An alternative RNA-mediated toxicity arises from microsatellite repeat instability in the human genome. The expanded repeat-containing RNAs could potentially induce neuron toxicity by disrupting protein and RNA homeostasis through various mechanisms.

    The Sun Lab is interested in deciphering the RNA processing pathways altered by the ALS-causative mutants to uncover the mechanisms of toxicity and molecular basis of cell type-selective vulnerability. Another major focus of the group is to identify small molecule and genetic inhibitors of neuron toxic factors using various high-throughput screening platforms. Finally, we are also highly i...nterested in developing novel CRISPR technique-based therapeutic strategies. We seek to translate the mechanistic findings at molecular level to therapeutic target development to advance treatment options against neurodegenerative diseases. view more

    Research Areas: ALS, neurodegeneration, RNA

    Lab Website

    Principal Investigator

    Shuying Sun, Ph.D.

    Department

    Pathology

  • Tom Woolf Lab

    The Tom Woolf Lab studies the quarter of the genome devoted to membrane proteins. This rapidly growing branch of bioinformatics, which includes computational biophysics, represents the main research direction of our group. We aim to provide insight into critical issues for membrane systems. In pursuit of these goals, we use extensive computer calculations to build an understanding of the relations between microscopic motions and the world of experimental measurements. Our calculations use our own Beowulf computer cluster as well as national supercomputer centers. An especially strong focus has been on the computed motions of proteins and all-atom models of the lipid bilayers that mediate their influence. To compute these motions, we use the molecular dynamics program CHARMM. We hope to use our understanding of the molecular motions for the prediction of membrane protein structures using new computational methods.

    Research Areas: proteomics, genomics, bioinformatics, computational biophysics

    Lab Website

    Principal Investigator

    Thomas Woolf, Ph.D.

    Department

    Physiology

  • Urban Lab

    The Urban Lab studies rhomboid proteases--a class of enzymes that cut proteins to initiate signaling between cells as a form of communication that organizes embryo development. Current studies in the lab focus on the biophysics of how these enzymes function inside the cell membrane, where it's hard for catalysis to take place. Because rhomboid intramembrane proteolysis plays a central role in malaria infection and Parkinson's disease pathogenesis, these studies may have therapeutic implications.

    Research Areas: enzymes, cell biology, membrane biophysics, structural biology, synthetic chemistry, malaria, Parkinson's disease, rhomboid proteases

  • Wei Dong Gao Lab

    Work in the Wei Dong Gao Lab primarily focuses on heart failure and defining molecular and cellular mechanisms of contractile dysfunction. We use molecular biology and proteomic techniques to investigate the changes that myofilament proteins undergo during heart failure and under drug therapy. We're working to determine the molecular nature of nitroxyl (HNO) modification of tropomyosin.

    Research Areas: heart disease, contractile dysfunction, heart failure, cardiovascular diseases, molecular biology

  • William B. Guggino Lab

    Work in the William B. Guggino Lab focuses on the structure of the cystic fibrosis transmembrane conductance regulator (CFTR) and water channels; the molecular structure of transport proteins in epithelial cell membranes; and gene therapies to treat cystic fibrosis (CF) patients. We are also working to identify CF’s specific defect in chloride channel regulation. One recent study showed that insulin-like growth factor 1 (IGF-1) enhances the protein expression of CFTR.

    Research Areas: cell biology, cystic fibrosis, kidney diseases, gene therapy, ion channels

    Lab Website

    Principal Investigator

    William Guggino, Ph.D.

    Department

    Physiology

  • Zachara Lab

    Elevation of O-GlcNAc levels modulates numerous pathways in a manner consistent with increased cell survival, including the expression of heat shock proteins. The Zachara Lab's goal is to understand the O-GlcNAc regulated stress response, how this can be manipulated to improve patient outcome and how this response is misregulated in disease.

    Research Areas: stress response, proteomics, O-GlcNAc, heat shock proteins

    Lab Website

    Principal Investigator

    Natasha Zachara, Ph.D.

    Department

    Biological Chemistry

  • Zhaozhu Qiu Laboratory

    Ion channels are pore-forming membrane proteins gating the flow of ions across the cell membrane. Among their many functions, ion channels regulate cell volume, control epithelial fluid secretion, and generate the electrical impulses in our brain. The Qiu Lab employs a multi-disciplinary approach including high-throughput functional genomics, electrophysiology, biochemistry, and mouse genetics to discover novel ion channels and to elucidate their role in health and disease.

    Research Areas: ion channel, neurological disease, electrophysiology, functional genomics, sensory neuroscience

    Lab Website

    Principal Investigator

    Zhaozhu Qiu, Ph.D.

    Department

    Neuroscience
    Physiology

  • Zhu Lab

    The Zhu lab is focused on characterizing the activities of large collection of proteins, building signaling networks for better understanding the mechanisms of biological processes, and identifying biomarkers in human diseases and cancers.

    More specifically, our group is interested in analyzing protein posttranslational modifications, and identifying important components involved in transcription networks and host-pathogen interactions on the proteomics level, and biomarkers in human IBD diseases.

    Research Areas: proteomics, biomarkers, cancer, genomics, protein chip, signaling networks

    Principal Investigator

    Heng Zhu, Ph.D.

    Department

    Pharmacology and Molecular Sciences

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