Research

The main research activities of the Immunology, Microbiology and Virology Ph.D. Program faculty can be divided into the following general areas of emphasis.

As depicted below, faculty research is multidisciplinary and collaborative in nature; thus, many mentors are actively involved in research that spans more than one of the areas of emphasis within our training program. These research programs provide a strong environment for PhD and postdoctoral training, and provide a rich multi-disciplinary environment for our trainees to expand their tools and explore their creative ideas to address significant problems in environmental health.

  • Anti-infectives & Drug Discovery

    Anti-infectives & Drug Discovery

    Identification of new genetic targets for antimicrobial drugs, development and early-phase testing of new anti-infectives for hard-to-treat organisms such as Methicillin Resistant Staphylococcus Aureus (MRSA) and Acinetobacter baumanii, as well as TB and fungal pathogens that afflict immunocompromised persons.

    Active Research Laboratories

    • Dewhurst Lab Influenza Viruses; Virus Polymerase HIV Vaccine Development; NeuroAIDS Research
    • Dunman Lab Using S. aureus and A. baumannii as Model Organisms for Antibacterial Development and to Study Bacterial Pathogenesis
    • Haidaris Lab Infections in the immunocompromised host, mechanisms of pathogenesis, host-microbe interactions and approaches to therapy
    • Krysan Lab Antifungal Identification and Development
    • Maggirwar Lab Regulation of Neuronal Survival
    • Martinez-Sobrido Lab Evasion of the Innate Immune Response by Viruses
    • Minsoo Kim Lab Inflammation Research
    • Munger Lab Mechanisms of Pathogenic Metabolic Manipulation
    • Pavelka Lab Cell envelopes of pathogenic bacteria
  • Autoimmune Disease

    Autoimmune Disease

    A critical component of the immune system is tight regulation; ensuring appropriate termination of immune responses following pathogen clearance and avoiding the inappropriate activation of immune responses to self tissues resulting in autoimmunity.

    Active Research Laboratories

  • Biodefense

    Biodefense

    Faculty research focuses on a range of Category A, B and C Priority Pathogens. Studies include analysis of the pathogenesis of important bacterial and viral biodefense agents, comparative genomic studies on Vibrio species, genetic analysis of Francisella tularensis, analysis of immune responses to such viruses as influenza virus, Respiratory Syncytial Virus (RSV) and human arenaviruses such as Lassa and Junin, and the development and testing of new vaccines for pathogens that include human arenaviruses and influenza.

    Active Research Laboratories

    • Frelinger Lab T cell immunity to tumors and pathogens
    • Lawrence Lab Environmental signaling, immune function, and cellular development
    • Maggirwar Lab Regulation of Neuronal Survival
    • Martinez-Sobrido Lab Evasion of the Innate Immune Response by Viruses
    • Munger Lab Mechanisms of Pathogenic Metabolic Manipulation
    • Pavelka Lab Cell envelopes of pathogenic bacteria
    • Phipps Lab Antibody Production, to Lung and Cardiovascular Disease, to Ocular Diseases
    • Sant Lab Immunodominance in CD4 T Cell Responses
    • Takimoto Lab Molecular Mechanisms of Paramyxovirus Infection, Replication and Assembly
    • Ward Lab Mechanisms of Poxvirus Envelope Formation
  • Cancer

    Cancer

    Oncogenically transformed cells arise through a multistep process, and are normally subject to immune surveillance and elimination by the immune system. Cluster research focuses understanding of the immune mechanisms involved in tumor recognition and rejection, as well as fundamental mechanisms of cellular transformation and the role of microbial agents in oncogenic disease of the gastrointestinal (GI) tract. Studies include translational research aimed at improved cancer therapeutics and/or cancer vaccines, as well as studies into the basic mechanisms of cell transformation.

    Active Research Laboratories

    • Elliott Lab Phagocytic Clearance of Dying Cells: Mechanisms and Consequences
    • Frelinger Lab T cell immunity to tumors and pathogens
    • Gill Lab Microbial Pathogens and the Impact of Human Microbial Flora on Human Health and Disease
    • Lord Lab Cell Mediated Immunity to Tumors
    • Maggirwar Lab Regulation of Neuronal Survival
    • Phipps Lab Antibody Production, to Lung and Cardiovascular Disease, to Ocular Diseases
    • Robert Lab Evolution of Immune Surveillance, Tumor and Viral Immunity
  • Cell Biology

    Cell Biology

    Microbes and viruses interact with host cells to induce alterations in cellular phenotype and function, thereby subverting host cell metabolism to meet their own needs. In addition, many microbes and viruses exert effects on the host immune response, so as to evade host immune control. Knowledge of the interplay between infectious pathogens and their host cells is therefore important, in order to identify potential new targets for drug therapy and as a basis for understanding microbial pathogenesis. Research focuses on various aspects of mammalian and amphibian cell biology including, cell to cell interactions, cell cycle control, intracellular signaling, differentiation and subcellular organelles.

    Active Research Laboratories

    • Elliott Lab Phagocytic Clearance of Dying Cells: Mechanisms and Consequences
    • Fowell Lab Regulation of Immunity
    • Krysan Lab Antifungal Identification and Development
    • Lawrence Lab Environmental signaling, immune function, and cellular development
    • Minsoo Kim Lab Inflammation Research
    • Ward Lab Mechanisms of Poxvirus Envelope Formation
  • ESKAPE Pathogens, Hard-To-Treat Infections	 & Drug Resistant Organisms

    ESKAPE Pathogens, Hard-To-Treat Infections & Drug Resistant Organisms

    The ESKAPE pathogens comprise the 6 bacterial pathogens considered to be of greatest healthcare concern by the Infectious Diseases Society of America, because of their high burden of disease and frequent ability to evade currently used antibiotics. Chief among these is Staphylococcus aureus, which is the focus of several faculty laboratories, interested in establishing bacterial determinants of virulence as well as new targets for antimicrobial therapy. Other ESKAPE pathogens under investigation include Acinetobacter baumanii, Pseudomonas aeruginosa and enterobacterial species. Additional research focuses on Mycobacterium tuberculosis, as well as fungal species that a major cause of disease among medically immune suppressed persons, and polymicrobial infection.

    Active Research Laboratories

    • Dunman Lab Using S. aureus and A. baumannii as Model Organisms for Antibacterial Development and to Study Bacterial Pathogenesis
    • Gill Lab Microbial Pathogens and the Impact of Human Microbial Flora on Human Health and Disease
    • Haidaris Lab Infections in the immunocompromised host, mechanisms of pathogenesis, host-microbe interactions and approaches to therapy
    • Krysan Lab Antifungal Identification and Development
    • Pavelka Lab Cell envelopes of pathogenic bacteria
    • Schwarz Lab Bone Loss Research
  • Genetics, Genomics & Metagenomics

    Genetics, Genomics & Metagenomics

    Microbes and viruses interact with their immediate environment and in doing so alter the expression of their own genes or those of the host. Faculty study the regulation of gene expression at all levels, including global changes in bacterial gene expression in biofilms and dental caries, cytokine and gene expression changes associated with immune cell differentiation, and the comparative genomics of Vibrio cholerae species. These studies are enhanced by the University of Rochester's state of the art Functional Genomics Center, and other recent upgrades in the Core Facilities of the Medical Center.

    Active Research Laboratories

  • HIV/AIDS

    HIV/AIDS

    HIV/AIDS remains a major cause of death both in the U.S. and internationally. Faculty research on HIV/AIDS includes studies on: viral transmission and pathogenesis, including HIV-associated neurologic disease; development of novel therapeutic and preventive approaches – including new drugs and vaccines; and studies on the opportunistic pathogens that are a major cause of morbidity and mortality in persons with HIV/AIDS. The University of Rochester Center for AIDS Research provides a central hub for campus research on the virus.

    Active Research Laboratories

    • Bambara Lab Human Genome Stability, DNA Damage Response, HIV Replication & Evolution
    • Dewhurst Lab Influenza Viruses; Virus Polymerase HIV Vaccine Development; NeuroAIDS Research
    • Maggirwar Lab Regulation of Neuronal Survival
    • Munger Lab Mechanisms of Pathogenic Metabolic Manipulation
  • Immune Regulation & Immunologic Mechanisms

    Immune Regulation & Immunologic Mechanisms

    Research into immunological mechanisms includes studies in diverse research areas in immunology, including: antigen presentation and processing; B cell subsets and regulation of B cell responses; T cell activation and differentiation; T cell memory and homing; immune responses to pathogenic organisms; comparative immunology using the frog Xenopus as a model system; mechanisms of autoimmunity; and the identification and analysis of gene expression signatures associated with immune responses to infection and immunization. These varied research programs seek to dissect key regulatory events that control protective and pathogenic immune responses.

    Active Research Laboratories

    • Elliott Lab Phagocytic Clearance of Dying Cells: Mechanisms and Consequences
    • Fowell Lab Regulation of Immunity
    • Frelinger Lab T cell immunity to tumors and pathogens
    • Lawrence Lab Environmental signaling, immune function, and cellular development
    • Lord Lab Cell Mediated Immunity to Tumors
    • Minsoo Kim Lab Inflammation Research
    • Phipps Lab Antibody Production, to Lung and Cardiovascular Disease, to Ocular Diseases
    • Robert Lab Evolution of Immune Surveillance, Tumor and Viral Immunity
    • Sant Lab Immunodominance in CD4 T Cell Responses
    • Thakar Lab Delineation the effects of age, immunogenicity of the antigens, host genotype and host’s immune history using using bioinformatics, systems biology and dynamic modeling tools.
  • Molecular Basis of Microbial Pathogenesis

    Molecular Basis of Microbial Pathogenesis

    An important weapon in the battle of infectious diseases is a basic understanding of the mechanisms of pathogenesis of infectious agents and the interaction of the pathogen with the host. A major research goal of the faculty is therefore to examine the mechanisms by which pathogenic microorganisms cause disease, using an interdisciplinary approach that involves scientists trained in microbiology, virology, molecular biology, and host defense.

    Active Research Laboratories

    • Butler Lab Regulation of mRNA Expression in the Nucleus of Eukaryotic Cells
    • Dewhurst Lab Influenza Viruses; Virus Polymerase HIV Vaccine Development; NeuroAIDS Research
    • Dunman Lab Using S. aureus and A. baumannii as Model Organisms for Antibacterial Development and to Study Bacterial Pathogenesis
    • Dziejman Lab Type Three Secretion System Mediated Pathogenesis of V. cholerae
    • Fowell Lab Regulation of Immunity
    • Frelinger Lab T cell immunity to tumors and pathogens
    • Gill Lab Microbial Pathogens and the Impact of Human Microbial Flora on Human Health and Disease
    • Krysan Lab Antifungal Identification and Development
    • Martinez-Sobrido Lab Evasion of the Innate Immune Response by Viruses
    • Munger Lab Mechanisms of Pathogenic Metabolic Manipulation
    • Pavelka Lab Cell envelopes of pathogenic bacteria
    • Robert Lab Evolution of Immune Surveillance, Tumor and Viral Immunity
    • Takimoto Lab Molecular Mechanisms of Paramyxovirus Infection, Replication and Assembly
    • Thakar Lab Delineation the effects of age, immunogenicity of the antigens, host genotype and host’s immune history using using bioinformatics, systems biology and dynamic modeling tools.
    • Ward Lab Mechanisms of Poxvirus Envelope Formation
  • Respiratory Pathogens

    Respiratory Pathogens

    Interactions of respiratory pathogens with the host respiratory environment can lead to severe life-threatening infections or chronic debilitating infections that persist for years. Severe infections are often the result of synergistic interactions between bacterial and viral pathogens such as Staphylococcus aureus and Respiratory Syncytial Virus (RSV). Chronic lung infections such as Cystic Fibrosis are often polymicrobial infections of multiple bacteria, including Pseudomonas aeruginosa, Hemophilus influenzae and Staphylococcus aureus. Multiple faculty study RSV, influenza virus, Staphylococcus aureus, Pseudomonas aeruginosa, Mycobacterium tuberculosis and Pneumocystis carinii. Investigators are exploring mechanisms of virulence as well as development of vaccines.

    Active Research Laboratories

    • Dewhurst Lab Influenza Viruses; Virus Polymerase HIV Vaccine Development; NeuroAIDS Research
    • Gill Lab Microbial Pathogens and the Impact of Human Microbial Flora on Human Health and Disease
    • Pavelka Lab Cell envelopes of pathogenic bacteria
    • Takimoto Lab Molecular Mechanisms of Paramyxovirus Infection, Replication and Assembly
    • Thakar Lab Delineation the effects of age, immunogenicity of the antigens, host genotype and host’s immune history using using bioinformatics, systems biology and dynamic modeling tools.
  • Vaccine Biology

    Vaccine Biology

    Vaccines represent perhaps the most cost-effective approach to improving human health and well-being, saving tens of millions of lives each year. Moreover, the UR has an impressive track record of contributing to the development of important human vaccines, including the Hemophilus influenza b (Hib) vaccine and the recently developed Human Papillomavirus (HPV) vaccine. Research focuses on basic mechanisms involved in the generation of pathogen-specific immune responses as well as translationally-oriented studies that involve the derivation and testing of novel vaccines and/or vaccine delivery systems.

    Active Research Laboratories

    • Dewhurst Lab Influenza Viruses; Virus Polymerase HIV Vaccine Development; NeuroAIDS Research
    • Dunman Lab Using S. aureus and A. baumannii as Model Organisms for Antibacterial Development and to Study Bacterial Pathogenesis
    • Frelinger Lab T cell immunity to tumors and pathogens
    • Lord Lab Cell Mediated Immunity to Tumors
    • Martinez-Sobrido Lab Evasion of the Innate Immune Response by Viruses
    • Robert Lab Evolution of Immune Surveillance, Tumor and Viral Immunity
    • Sant Lab Immunodominance in CD4 T Cell Responses
    • Schwarz Lab Bone Loss Research
    • Thakar Lab Delineation the effects of age, immunogenicity of the antigens, host genotype and host’s immune history using using bioinformatics, systems biology and dynamic modeling tools.