Research Program

Daniel Malamud

Bill Abrams

Paul Corstjens

Haiteng Deng

David Levy

Joan Phelan

Michael Poles

Zhiwei Wu

Linqi Zhang

Susan Zolla-Pazner

Malamud Research Group

Pathogenesis of infectious diseases and oral-based diagnostics

Our laboratory focuses on HIV pathogenesis and on the development of point-of-care diagnostic systems utilizing oral samples.

Point Detection of Pathogens in Oral Samples 

We are developing a novel diagnostic system that utilizes samples oral fluid detected with novel Up-converting Phosphor reporters for use in the diagnosis of multiple infectious diseases. Central to this project is a microfluidic technology platform that permits simultaneous analysis of viral and/or bacterial antigens and nucleic acids, as well as antibodies to these pathogens. The project focuses on HIV, but is applicable to detection of any infectious agent. Currently available tests require a considerable period of time between sample acquisition and test results. If a sample could be diagnosed on-site an individual could be counseled immediately and appropriate therapy initiated. Our goal is to develop an assay capable of detecting multiple pathogens and antibodies to the pathogens, performed on-site in less than 1 hour using an oral sample.

Inhibition of HIV Infectivity

Oral transmission of HIV infection is a rare event.  Salivary proteins have been implicated in this protection.  We have identified a salivary glycoprotein (gp340) that agglutinates bacteria and also demonstrates potent anti-HIV activity.  Gp340 is a member of the Scavenger Receptor Cysteine Rich (SRCR) superfamily, known to exist in secreted and membrane bound forms. The goal is to understand the mechanism of inhibition of HIV infection by gp340, and then use this information to design novel anti-HIV therapeutic agents. Gp-340 appears to be an excellent candidate for study in that the molecule targets a highly conserved Env region and blocks infectivity in all M-tropic and T-tropic HIV-1 strains tested. Therapeutic agents to be developed may be directly derived from gp-340 or could involve the synthesis of glycopeptides and/or the design of mimetics based on the identified active structure.

Crosstalk among oral & gastrointestinal soluble innate factors,
HIV and Microbes

This project, involving 4 collaborating research teams, will analyze soluble members of the innate immune system known to interact with both HIV and bacteria.  Using a cohort of HIV infected antiretroviral naïve subjects, oral and gastrointestinal samples will be characterized before and during administration of antiretroviral therapy.  The goal is to understand the characteristics that contribute to “resistance” of infection in the oral cavity as compared to the remainder of the GI track.

Return to Top

Wu Research Group

The Center for Public Health Research (CPHR) of Nanjing University is a newly formed research institution aimed to deal with public health challenges for the newmillennium. The center has a dual interest on epidemiology/public health and a basic biomedical research. Initially the center will focus on viral and bacterial infectious diseases as well as auto-immune and immunodeficiency diseases. The center is funded by a dedicated state fund and has been awarded a number of major research grants from the Ministry of Sciences and Technology (MOST). The CPHR has received funding for China's first HIV/AIDS program project.

Return to Top

Proteomics Resource Center
Haiteng Deng, Ph.D., Director

The Proteomics Resource Center of the Rockefeller University is a state of the art biochemical analysis and synthesis center. Proteomic analysis using both mass spectrometric and Edman degradation sequencing techniques as well as peptide synthesis are routinely performed in the facility. Basic research within the center is focused on the development of more sensitive microanalytical techniques and enhanced biopolymer synthesis strategies.

Return to Top

Levy Research Group

Our research broadly concerns the replication and pathogenesis of HIV-1 seeking fundamental insights that will inform development of novel therapeutics and vaccines.  Primarily through experimental approaches which allow single cell analysis of HIV-1 replication, we conduct investigations into the evolution of HIV-1 through genetic recombination, the influence of multiple infection on HIV-1 replication, and the role of unintegrated HIV-1 DNA in the natural history of HIV-1 and the immune response to the virus.

Recombination
The extraordinarily rapid diversification of HIV-1 presents perhaps the most important obstacle to the development of vaccines and improved antiviral therapeutics. HIV-1 employs two distinct but inter-related processes, mutation and recombination, to generate diversity. Our work has demonstrated that HIV-1 recombination proceeds at an exceptionally high rate as the  result of two factors: First, multiple infection of cells occurs more frequently than previously thought, and second, the frequency at which recombination itself occurs is also higher than previously known and is highly cell-type dependent. Currently we are investigating factors which influence the process of recombination, such as the role of HIV-1 RNA secondary structure and of cellular differentiation.

Multiple Infection
A necessary precondition for HIV-1 recombination to create new genetic diversity is for a cell to become infected with two or more divergent viruses. There are several other consequences of multiple infection of cells that are important to the natural history of HIV-1, including altered pathogenicity of infected cells, potentially increased virus production, virus-virus cooperation or virus-virus antagonism, and increased repertoire of viral antigens presented to the immune system.  Through our single cell approaches, we are investigating these important factors in HIV-1 replication and pathogenesis.

HIV-1 unintegrated DNA
After reverse transcription, which generates a single cDNA genome from each infecting virus, this cDNA seeks to integrate into the host cell’s chromosomal DNA. This integrated provirus serves as the template for the generation of new virions.  However, it is well documented that in vivo, up to 99% of all HIV-1 DNA remains unintegrated, resulting in non-productive infection. Our recent work is demonstrating that this unintegrated DNA (uDNA) does substantially contribute to the natural history and the immune response to HIV-1. Under certain circumstances, uDNA can complete its replication cycle, and  through recombination, contribute to the overall diversity of HIV-1.

Cytotoxic T cells (CTL)
In collaboration with Dr. Paul Goepfert, U. Alabama at Birmingham, and Dr. Otto Yang, UCLA, we are investigating the role of uDNA-directed gene expression in the recognition and elimination of HIV-1 infected cells by CTL. Through the use of antigen-specific T cell clones, and in the future, through the application of these studies to natural responses from HIV-1 infected individuals, we are gaining import insights into the connections between the HIV-1 replication cycle and immunity against HIV-1.

Modeling studies
In collaboration with Dr. Dominik Wodarz, UC Irvine, and Dr. Igor Rouzine, we are applying what we are learning from each of the above studies to the development of quantitative models of HIV-1 replication, pathogenesis and the immune response to HIV-1.

Return to Top

Zhang Research Group

HIV-1 Pathogenesis

A better understanding of the dynamics of HIV-1 replication in vivo has provided an important rationale for early and aggressive treatment. Combination antiretroviral therapy can suppress HIV-1 replication in HIV positive individuals to the extent that the virus is undetectable. However, a major obstacle to HIV-1 elimination is replication-competent virus found to reside latently within resting memory CD4+ lymphocytes. Our studies focus on residual viral replication, as well as the decay of the latent reservoir, in patients who had been HIV negative for ~2-3 years while on combination therapy. Virologic and immunologic characterization of these patients has provided significant insights into the pathogenesis of HIV-1 infection.

The role of the thymus in HIV/SIV infection before and after treatment with combination therapy

The thymus plays a crucial role in the development of T lymphocytes during ontogeny and is believed to have a significant impact on T lymphocyte regeneration in adults. Autopsy studies of HIV-1-infected humans or SIV-infected macaques demonstrate infection and altered histopathology of the thymus. Our studies are addressing critical factors in the capacity for immune reconstitution by the thymus during HIV/SIV pathogenesis.

Genotypic and Phenotypic Diversity of HIV

HIV-1 exists as a divergent swarm of viral quasi-species both in infected individuals and in different geographic locations. This diversity poses tremendous difficulties for the human immune system and an enormous benefit to the virus. We seek to better understand the mechanisms and consequences of this diversity to facilitate the design of therapeutic strategies.

Generation of replication-competent single-cycle simian immunodeficiency virus (SIV) for potential vaccine studies

Development of an effective anti-HIV vaccine is of vital importance to prevent HIV infection and to reduce the spread of AIDS. Although a number of vaccines have been developed, the majority carry intrinsic properties which render these vaccines either ineffective or potentially risky. Our goal is to develop an effective anti-HIV vaccine by exploring a novel strategy that allows viral infection to undergo a single replication cycle. This approach would prevent the potential risk associated with inactivated whole virus vaccine and live attenuated virus vaccine, and at the same time, preserve the conformational integrity of infecting viral particles that are important to generate a protective immune response.

Return to Top

Zolla-Pazner Group

HIV Vaccines, Human immunity to tuberculosis, Human Monoclonal Antibody Production

Susan Zolla-Pazner is a biologist who has devoted her professional life to areas of Immunology where basic research intersects with the needs of modern medicine. By 1981, Dr. Zolla-Pazner had an established reputation for studying the immune systems of individuals with cancer. At that time, she was asked to consult on several patients who had an unusual type of tumor. These patients were the first patients to be seen with a new form of Kaposi's sarcoma, a tumor related to the disease which, only later, became known as AIDS. In the two decades since, Dr. Zolla-Pazner has authored nearly 250 scientific papers on AIDS and related illnesses. She collaborates actively with researchers arount the world and has support through the National Institutes of Health, the Department of Veterans Affairs, and the Bill and Melinda Gates Foundation for her studies to develop an AIDS vaccine and to train students and health care professionals from India, Cameroon, and China in the prevention, diagnosis, and treatment of AIDS and tuberculosis.

Return to Top