Microbiology and Immunology

The Department of Microbiology and Immunology focuses on how pathogens cause disease and how the hosts’ immune systems discriminate between self and non-self. The juxtaposition of labs studying both sides of the host-pathogen equation provides students with the cross-fertilization of disciplines necessary to understanding these complex interactions. Given the inherent and immediate relevance of this work to human disease, the faculty in the department includes a mixture of M.D.s and Ph.D.s. Several of the faculty hold joint appointments in clinical departments and the clinical reality of the diseases being studied is never far from our minds.
       Pathogens are studied for insights into basic molecular and cellular processes and as probes of the host cell. The control of gene expression at the transcriptional, post-transcriptional and translational levels are all important areas of investigation in different systems. The response of the host cell to insult by a pathogen often gives insights into broader issues related to pathogenesis.
       On the side of the microorganism, we study the pathogenesis of viruses, bacteria and protozoan parasites. How do these organisms invade and survive in their chosen host? How do they deal with the host’s potent immune response? What properties are involved in their pathogenesis? What is responsible for latency and reactivation of infection? How can we use our results to improve prevention, diagnosis and treatment?
       On the side of the host, faculty are studying six major effector arms of the immune system: cytotoxic T-cells, helper T-cells, gamma delta T-cells, B-cells, macro-phages and natural killer cells. How are self-antigens distinguished from non-self? How are antigens processed and presented to effector cells? What cascade follows antigen presentation?
What roles do the various effector cells play in the host’s immune response to different diseases? How does tolerance arise during development and how does it breakdown in autoimmunity? And how can we interfere with this process?
       Our training program includes several graduate level courses covering principles of biological techniques, molecular parasitology, stress response, advanced immunology, animal viruses, and microbial pathogenicity. In addition, we hold biweekly seminars by invited visitors, biweekly presentations by students and postdocs on their current research, and an annual three-day retreat at a coast-side conference center with research presentations by students and postdocs from all research groups. Students also serve two quarters as teaching assistants.
 
For more information contact:
Student Services
Department of Microbiology
and Immunology
299 Campus Drive
Fairchild, D309
Stanford, CA 94305-5124
(650) 725-8541 (phone)
(650) 725-6757 (fax)
micro_immuno@lists.stanford.edu
http://cmgm.stanford.edu/micro

Faculty and their Research Interests

Manuel Amieva. Disruption of the epithelial apical-junctional complex by Helicobacter pylori CagA; targeting of H. pylori to host cell intercellular junctions, disruption of junction-mediated functions.
 
Ann Arvin. Varicella-zoster virus (VZV); molecular mechanisms of replication and pathogenesis-identification of functional domains of viral genes/promoters, roles of viral and host cell proteins in pathogenesis of VZV infection of T-cells, skin, neurons in SCIDhu model; CD4/CD8 T cell immunity to VZV; viral mechansisms of immune evasion.

Helen Blau. Molecular and cellular mechanisms that control muscle and neuronal growth; stem cell biology, differentiation, and tumorigenicity; gene therapy for angiogenesis; vector design and treatment of cardiovascular disease and cancer. Regulating stem cell fate in vitro and in vivo. Stem cell therapies. Hematopoietic and muscle stem cells. Characterizing and bioengineering stem cell niches. Nuclear reprogramming. Muscle development and disease. Drug delivery. Tracking cell behavior in vitro and in vivo.  Understanding tissue degeneration and regeneration

Matthew Bogyo. Chemical biology; Applications of chemical tools to study the function of proteases in life cycle stages of the human protozoan parasites Toxoplasma and Plasmodium falciparum.

John Boothroyd. Biology and genetics of the protozoan parasite Toxoplasma, with emphasis on protein trafficking, invasion, developmental biology and population biology.

Chang-Zheng Chen. The genetic networks controlled by regulatory RNAs, such as microRNAs and small interfering RNAs, and the roles of these RNAs in modulating the development, function and pathogenesis of vertebrate immune systems.
 
Yueh-hsiu Chien. Mechanisms underlying gamma delta T cell functions in context with the biology and pathology of the host, focusing on ligand recognition and differentiation, regulation of effector function; host response to Yersinia pseudotuberculosis infection, focusing on the adaptive immune components and the cross-talk between the adaptive and innate responses.
 
Chris Contag. Molecular mechanisms of pathogenesis and host response to insult using in vivo cellular and molecular imaging to reveal biological processes in living animal models of disease. Emphases on gene expression and cell migration in vivo.
 
Mark Davis. Mechanisms of T-lymphocyte recognition and differentiation; particular interests in T-cell receptor structure, function, thymic selection, and dynamics of cell surface molecules during T-cell recognition.
 
Stanley Falkow. Genetic and molecular mechanisms of microbial pathogenicity; Salmonella exploits caspase-1 to colonize Peyer’s patches in a murine typhoid model; OmpR regulates the two-component system SsrA-SsrB in Salmonella pathogenicity island 2.
 
Stephen J. Galli. Regulation of mast cell and basophil development, phenotype and function; roles of mast cells in innate and acquired immunity, inflammation, tissue remodeling and homeostasis, and in specific disorders such as allergy, asthma and autoimmune diseases; pathogenesis of allergic inflammation; development of new in vivo models to pursue these goals.
 
Harry Greenberg. Gene coding assignments for rotavirus; focus on the molecular determinants of virulence, host range, and immunity; cellular immunity to hepatitis C virus and mechanisms of resistance to interferon therapy, immunity to influenza.
 
Karla Kirkegaard. Molecular genetics and biochemistry of genome replication of RNA viruses and viral subversion of protein secretory apparatus during infection of human cells.
 
A.C. Matin. Drug resistance in bacteria and their biofilms; stress response under zero gravity; mechanisms of redox homoeostasis; biomolecular engineering of bacterial bioremediation capability.
 
Hugh McDevitt. Structure-function analysis of H2 and HLA-D region gene products; how these proteins regulate the immune response and predispose to autoimmunity; transgenic mice expressing TCRs specific for islet proteins; Effect on TNF and anti-TNF on TCR signaling, and on intracellular Ca++ signaling.
 
Denise Monack. Genetic and molecular mechanisms of intracellular bacterial pathogenesis. Using Salmonella and Francisella tularensis as models to study complex host-pathogen interactions; ultimate goal is understanding how Salmonella persists within certain hosts for years in the face of a robust immune response and how F. tularensis, a stealth invader, can cause a rapid, lethal infection.

Garry Nolan. Molecular virology of HIV-1 transcriptional regulation, with special emphasis on macrophage and T-cell regulators and NF-kB, IkB, and NFAT Rel components; retroviral libraries for complementation cloning of signaling molecules in apoptosis and T-cell biology; gene therapy vectors and creation of intracellular protein machines.
 
Peter Parham. Regulation of cytotoxic T-cell and natural killer cells by MHC class I polymorphisms, with an emphasis on the diversity of MHC class I in human populations and comparisons in other species.
 
Charles Prober. Conduct of seroepide-miologically based studies of HSV-2 infections, with special emphasis on gestational and neonatal infections; humoral and cellular immunologic evaluations of human hosts to determine the critical factors relevant to the acquisition and transmission of HSV-2 infections preliminary to vaccine studies; evaluation of antiviral therapies, with special emphasis on the management of herpes virus infections.
 
David Relman. Molecular and genomic features of virulence in Bordetella sp.; pathogen discovery by means of cultivation-independent molecular methods; genomic features of humans with systemic infection; ecology of human endogenous microbial communities.
 
Peter Sarnow. Molecular biology of RNA virus-host interactions; mechanism and control of internal initiation of protein synthesis in viral and cellular mRNA; roles for regulatory small RNAs, microRNAs, in regulating expression of hepatitis C viral RNA and cellular mRNAs.
 
David Schneider. Using the fruit fly, Drosophila, as a model to study innate immunity; Adaptive aspects of innate immune responses; environmental regulation of the immune system; identification of virulence mechanisms of insect pathogens. Salmonella, Streptococcal and Listeria host-pathogen interactions.
 
Gary Schoolnik. Pathogenesis of M. tuberculosis; pathogenesis of entero-pathogenic E. coli; environmental persistence of V. cholerae in environmental habitats.
 
Upinder Singh. Genetic and genomic studies of the parasite Entamoeba histolytica with an emphasis on host-pathogen interactions, disease pathogenesis, developmental biology, and global epidemiology.
 
Man-Wah Tan. Genetics and genomics dissection of host-pathogen interactions using a multipathogen C. elegans pathogenesis system; genetics and molecular analyses of signaling pathways in host innate immune response.
 
Julie Theriot. Cell biology of interactions between infectious bacteria and the human host cell actin cytoskeleton; actin-based motility of bacterial pathogens.
 
Lucy Tompkins. Molecular pathogenic studies of Helicobacter; genetic and molecular studies to characterize the host-parasite interaction with the ultimate goal of understanding gastric malignancy.