STD/AIDS Research Training Fellowship Program
Bacterial & Viral STD Pathogenesis & Immunology Research Track
Director: Denise A. Galloway, PhD
Overview: The Bacterial & Viral STD Pathogenesis & Immunology Research Track offers laboratory-based or
translational research on bacterial and viral STDs, including molecular epidemiology, with the goal of preparing investigators for
independent research careers working in pathogenesis, immunology, virology or bacteriology, and molecular epidemiology.
Predoctoral trainees participate in course-work and dissertation research leading to a PhD in Microbiology, Pathobiology,
Immunology, Molecular and Cellular Biology, or Pathology. Postdoctoral (PhD and MD) trainees receive rigorous focused scientific
laboratory training, with MDs working alongside PhDs. The Track Director, Dr. Galloway, is internationally recognized for her
research into the mechanisms by which HPV contributes to neoplasia.
25 Training Faculty
Galloway, Denise, PhD Track Director, Training Faculty
The overall focus of the Galloway Lab is to understand the mechanisms by which viruses, particularly HPV and human polyomaviruses,
contribute to human cancers. Research has focused on high risk HPV that are causally associated with all cervical cancers and
the majority of anogenital and oropharyngeal cancers. Additional research includes investigating whether genus beta HPVs are
involved in squamous cell skin cancers, and the role that the Merkel Cell Polyomavirus plays in Merkel Cell Carcinoma.
PhD Training Faculty
The Emerman lab studies host-cell interactions of HIV and related viruses. The goal is to understand the molecular and evolutionary
basis of virus replication and pathogenesis. The research team studies the evolution and function of host antiviral genes in order
to determine how HIV adapted to humans,and how ancient viral infections influenced the susceptibility or resistance of humans to
Frahm, Nicole, PhD, MS Training Faculty
Research centers on characterization of cellular immune responses induced by HIV-1 infection and by experimental HIV vaccines. In
her role as the Associate Director for Laboratory Science at the HIV Vaccine Trials Network, Dr. Frahm's research provides a
comprehensive overview of vaccine-induced cellular immunity including innate, T-cell, as well as B-cell responses in the periphery
and gastrointestinal tract, encompassing various vaccine platforms aimed at preventing HIV acquisition. Research involving
HIV-infected persons aims at defining immune responses associated with natural control of viral replication, including
understanding the influence of HIV sequence diversity on recognition by cytotoxic T lymphocytes.
MD Training Faculty
The Fredricks laboratory studies the human indigenous microbiota to determine how changes in microbial communities impact human
health. The team uses tools such as broad range 16S rRNA gene PCR to describe microbial diversity in human body sites with a focus
on the vaginal microbiota and the common condition bacterial vaginosis (BV). The team also studies the role of novel genital
tract bacteria in pelvic inflammatory disease, idiopathic urethritis, cervicitis, HIV acquisition and shedding, and preterm birth.
Fuller, Deborah PhD
Research is focused on the role of mucosal CD4+/CD8+ T cell responses in control of HIV infection, using the SIV model for AIDS to
investigate immune mechanisms of viral control and to design and test new vaccine approaches for prophylaxis and therapy.
Projects are driven by 3 primary hypotheses: 1. Mucosal immunity is necessary to control and prevent infection at the site of
exposure. 2. Broad specificity in the mucosal CD8 response restricts viral evolution and disables fitness of residual virus in
the gut reservoir. 3. Inflammation and immune activation influence effectiveness of prophylactic and therapeutic vaccines.
Gale, Michael, Jr., PhD
Research is aimed at understanding the innate immune processes that control virus infection and viral oncogenic potential. A major
goal is to define in molecular terms virus-host interactions that trigger and regulate innate defenses against hepatitis C virus
(HCV), HIV, influenza virus, and West Nile virus. The lab uses in vitro and in vivo models to elucidate key viral and cellular
determinants of host defense regulation to define novel therapeutic targets in anti-viral innate immune defenses and oncogenic
transformation, aiming to ultimately design strategies to augment innate immune control of these chronic viral infections and
limit malignancy progression.
Gottlieb, Geoffrey MD,
PhD Training Faculty
Dr. Gottlieb is the PI of a study in Senegal, West Africa, on the effect of antiretroviral therapy (ART) on HIV-2 disease outcomes,
emergence of drug resistance, and genital shedding. He is also involved in understanding the differences between natural history,
clinical, immunologic and virologic aspects of HIV-1 and HIV-2 infection. In addition, he has been studying the effects of dual
infection with HIV-1 and HIV-2 on disease outcomes and ART in Senegal.
Hybiske, Kevin PhD
The Hybiske laboratory is broadly interested in the interactions between intracellular pathogens and host cells. A major research
focus of the lab is to decipher the mechanisms by which the intracellular pathogen Chlamydia trachomatis
function in order to exit host cells and cause infectious disease. This pathogen has coevolved similar mechanisms to do so.
The ultimate goal is to leverage a thorough understanding of these pathogenic mechanisms as a new, unexplored therapeutic
Katzenellenbogen, Rachel, MD Training Faculty
Dr. Katzenellenbogen studies how the E6 oncoprotein of high-risk HPV 16 affects telomerase activity in cells, and specifically the
catalytic subunit of telomerase, hTERT. HPV 16E6 can increase telomerase expression through transcriptional activation of hTERT,
but HPV 16E6 also increases hTERT post-transcriptionally through its interaction with NFX1-123. NFX1-123 is an endogenous protein,
found in the cytoplasm of epithelial cells, and this protein can bind to and increase the stability of the hTERT mRNA. She is
also studying new roles for NFX1-123, HPV 16E6 and RNA processing proteins in cervical cancer, tumorigenesis, and the virus life
Koelle, David, MD
Dr. Koelle's team studies immune responses to infections, pathogen variation, and relationships of host genomics and infection
severity. Pathogens include HSV, vaccinia, Merkel cell polyoma virus and Mycobacterium tuberculosis. He uses genomic libraries
and genome-spanning ORF sets to interrogate T-cells to high definition. Candidate HSV vaccines are poised to enter phase I trials.
The team measures cellular immunity at sites of infection, such as skin, the genital tract, cornea, trigeminal ganglia, and tumor
biopsies. Mouse studies focus on vaccine immunogenicity and efficacy in the HSV-2 system. Newer initiatives include T-cell
diversity by deep sequencing, HSV genetic diversity, and long-term T-cell memory. Large numbers of T-cell tests for tuberculosis
are being run for the CDC.
Lagunoff, Michael, PhD Training Faculty
The Lagunoff lab is interested in how Kaposi's Sarcoma-associated herpesvirus KSHV alters endothelial cells to cause KS. The
team studies multiple aspects of the host-pathogen interactions with a focus on two main areas, viral induction of angiogenesis
and viral alterations in host cell metabolism, both likely critical for the formation of this highly vascularized tumor.
Lingappa, Jaisri, MD, PhD Training Faculty
The Lingappa laboratory studies viral-host interactions that promote virus assembly, and has demonstrated that during assembly
the HIV-1 capsid protein Gag progresses through an energy-dependent pathway of assembly intermediates that requires catalytic
action of at least two host enzymes, the ATP binding protein ABCE1 and the RNA helicase DDX6. This assembly pathway is initiated
when Gag co-opts a novel complex in cells that contain ABCE1, DDX6, and other proteins that may facilitate HIV-1 assembly and
packaging. Studies have led to identification of novel small molecules that inhibit replication of HIV-1 and other viruses.
Lingappa, Jairam, MD, PhD Training Faculty
Research is focused on identifying the role of host factors in modulating host susceptibility to and poor outcomes from infections.
Dr. Lingappa has used samples and data derived from recent large HIV-1 prevention clinical trials conducted in Africa to identify
genomic factors that reduce host susceptibility to HIV-1. Using technologies such as complete genome sequencing, gene expression
analysis and proteomics applied to deeply phenotyped samples, the aim is to understand the host response underlying resistance to
HIV-1 in the hope that this response could be elicited in individuals lacking specific genetic traits.
PhD Training Faculty
Dr. Lukehart has focused her research on the genetic diversity of the pathogenic treponemes, antigenic variation and molecular
pathogenesis of syphilis, and the host immune responses to Treponema pallidum. While her work is largely laboratory-based, she has conducted several clinically relevant investigations, most notably on neurosyphilis, syphilis-HIV interactions, and antibiotic
resistance in T. pallidum.
Lund, Jennifer, PhD Training Faculty
The focus of the Lund lab is on elucidating basic mechanisms of immunity in the context of virus infection. Specifically, we use a mouse
model to study how regulatory T-cells affect the anti-viral immune responses to genital HSV-2, influenza, and West Nile virus. Additionally, we
are investigating the immune correlates of protection from HIV infection using a cohort of expsed seronegative individuals, as well
as the potential immune modulatory effects of using pre-exposure prophylaxis in protection from HIV acquisition. Overall, we hope that our studies
will lead to improved clinical interventions for virus infections of public health importance.
Juliana, MD, PhD Training Faculty
Dr. McElrath is Director of the Vaccine and Infectious Disease Division, and PI of the HVTN Laboratory and Seattle VTU. She heads
the clinical infectious diseases service at the FHCRC/SCCA. Her research pursues a vaccine that will protect against HIV-1
infection and a deeper understanding of the components of immunity that control of HIV-1. She maintains a successful international
HIV vaccine laboratory program, and conducts immunological research in humans in a multicenter setting.
Mullins, James, PhD
The Mullins lab uses molecular, computational, and virus biology methods to investigate the relationship between HIV and its
human hosts, striving to understand the implications of HIV's genetic diversity on the immunopathogenesis of AIDS, with an
emphasis on acute/early infection and superinfection. The work focuses on the characterization of HIV nucleotide sequences, the
development of web tools for related computational studies, in vitro studies of the growth properties of viral isolates, host
genetic polymorphism analysis, and high-throughput analysis of cellular transcription.
Julie, PhD Training Faculty
Dr. Overbaugh's laboratory is part of a collaborative team that is pursuing translational research on the molecular epidemiology
of HIV-1 transmission. These studies, which include investigators in Seattle and Kenya, include studies of mother-to-infant
transmission, natural history studies of transmission and pathogenesis in women, and studies of virus and host factors that
contribute to transmission and disease progression in these settings. A central aspect of this work is exploring the role of
neutralizing antibodies in limiting HIV transmission and disease, including in individuals who become re-infected with HIV.
PhD Training Faculty
The Patton Laboratory utilizes several pigtailed macaque models to study C. trachomatis. Topical microbicides are also tested for effects on vaginal or rectal microflora, as well as changes in epithelial tissues and efficacy in prevention of both cervical and
rectal chlamydial infections. Second, the macaque model of pelvic inflammatory disease (PID) characterizes upper genital tract
disease resulting from ascending cervical infection. The PID model has been used to evaluate antibiotic and anti-inflammatory
treatments for existing chlamydial disease, immunologic responses to Chlamydia including Toll-like receptors, and genetic
predisposition to PID. Third, the evaluation of candidate chlamydial vaccine antigens is ongoing.
PhD Training Faculty
The Prlic lab studies conventional and innate-like T cell responses in healthy and inflamed mucosal tissues. One of our main
goals is to characterize CD4 T cell subsets in these tissues and define their intrinsic susceptibility to HIV infection.
The aim is to achieve a better understanding of the mechanisms that dictate which CD4 T cells are the initial targets of
the virus at the site of infection. In addition, the lab studies the role of mucosal-associated invariant T (MAIT) cells
in regulating inflammatory processes in the mucosal tissue. MAIT cells are a recently characterized innate-like T cell subset
that recognizes bacterial metabolites as antigen and thus represent a unique interface between host and microbiome.
Smith, Kelly D.,
MD, PhD Training Faculty
Dr. Smith's lab investigates the mucosal immune response to infectious pathogens. Much of the work has focused on Salmonella typhimurium infection, and the role of the innate immune system, specifically flagellin recognition. The team is currently
dissecting the innate immune pathways that are required for flagellin recognition, and determining how these pathways affect
mucosal infections, inflammation and the ability of the host to mount antibody responses. They are harnessing their detailed
understanding of flagellin structure and function to develop novel vaccines against broadly conserved HIV epitopes.
Donald, PhD Training Faculty
Dr. Sodora's laboratory has assessed SIV and HIV transmission and disease progression in monkeys and humans. One of the seminal
findings is that oral transmission of SIV results in entry of the virus through mucosal tissues in the mouth and esophagus and
that the virus spreads to many tissues rapidly. The overall goal of the laboratory is to compare findings from the SIV/monkey
models to what is occurring in HIV infected humans.
Stamatatos, Leonidas, PhD Training Faculty
Research aims to develop a safe, effective HIV vaccine and to investigate how HIV infection leads to AIDS. Of interest are
identifying immunological pathways that lead to development of broadly neutralizing antibodies during natural HIV infection;
exploiting these pathways for vaccine-related purposes; and understanding how HIV evolves to avoid the action of such antibodies.
Projects focus on HIV envelope structure/function relationship, B cell immunology in the context of HIV infection, HIV
evolutionary escape pathways and pathogenesis, and HIV vaccine design.
Totten, Patricia, PhD Training Faculty
Dr. Totten studies the disease syndromes, risk factors, and treatment efficacies for Mycoplasma genitalium. She also studies the repercussions of antigenic and phase variation in two surface-exposed proteins expressed by this pathogen, in studies with
persistently infected women, primate models for infection, and in vitro experiments. Finally, she is exploring the role of
potential recombination enzymes and regulatory factors leading to variation in the genes encoding these proteins and archived
copies of these genes.
Woodrow, Kim, PhD Training Faculty
The Woodrow Laboratory is focused on the applications of engineered biomaterials in mucosal infections and mucosal immunity.
Our long-term goals are to design and build multifunctional materials that will: (1) lead to novel preventative strategies for
mucosal infections, (2) program protective immune responses at mucosal sites of pathogen entry, and (3) assist studies of mucosal
infections and mucosal immunity in health and disease. These scientific goals are addressed from the perspective of fundamental
science, technology development, and translational research. We are a highly interdisciplinary group that implements knowledge
and tools from all areas of science and engineering. We strive to innovate solutions that will have the greatest impact in biomedicine
and global health technologies.
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