The purpose of the Molecular Biology Core is to assist the HIVRAD program in characterizing the epitopes recognized by MAbs and polyclonal human and monkey antisera that target QNEs. The main role of this Core will be to generate DNA and protein reagents needed by the other projects and the Viral Immunology Core.
The Specific Aims are : 1) To design and produce plasmids expressing chimeric and mutant HIV-1 Envs for epitope mapping studies and for viral neutralization assays in Projects 1, 2 and 4. 2) To generate monomeric WT gp120 and gp140 proteins, and soluble monomers and trimers that express QNEs. These proteins will be used for binding and adsorption studies in Projects 1, 2 and 4, and as immunogens in Project 3. These studies willl be guided by results of epitope mapping experiments obtained from Projects 1, 2 and 4. 3) To generate infectious SHIV pseudotypes and infectious mutant SHIVs with variant Envs that express QNEs. Fragments of the SHIV Env will be cloned into appropriate vectors to facilitate mutagenesis experiments, and the complete SHIV Env-Rev genes will be subcloned into the pcDNA 3.1 vector to generate viral pseudotype. These will be used to allow efficient construction of Env mutants and chimeras and for the generation of viral pseudotypes for the characterization of functional activity of the mutant SHIV Envs. QNEs defined in Projects 1 and 2 will be introduced into the SHIV1157ip Env for characterization of their infectivity in monkey blood PBMCs and their neutralization sensitivity. Ultimately, mutant SHIV Envs will be introduced in the SHIV1157ip proviral backbone to generate infectious SHIVs expressing QNEs for invivo studies described in Project 3. 4) To isolate and characterize escape mutant Envs from infected macaques. The evolution of Env sequence in the infected animals will be investigated during the course of infection to follow the anti-QNEs neutralizing responses and identify viral escape mutants. Envs will be cloned and escape mutants will be identified by neutralization assays (Viral Immunology core).

Public Health Relevance

The goal of this HIVRAD program is to define and characterize new bnAbs that target QNEs. The molecular biology core will play a primordial role in providing molecular reagents to the other projects and the viral immunology core. The availability of a centralized facility will increase the efficiency and improve the uniformity of reagents and subsequent data.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Research Program Projects (P01)
Project #
Application #
Study Section
Special Emphasis Panel (ZAI1-RB-A)
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Medicine & Dentistry of NJ
United States
Zip Code
Salomon, Aidy; Krachmarov, Chavdar; Lai, Zhong et al. (2014) Specific sequences commonly found in the V3 domain of HIV-1 subtype C isolates affect the overall conformation of native Env and induce a neutralization-resistant phenotype independent of V1/V2 masking. Virology 448:363-74
Derdeyn, Cynthia A; Moore, Penny L; Morris, Lynn (2014) Development of broadly neutralizing antibodies from autologous neutralizing antibody responses in HIV infection. Curr Opin HIV AIDS 9:210-6
Moore, Penny L; Sheward, Daniel; Nonyane, Molati et al. (2013) Multiple pathways of escape from HIV broadly cross-neutralizing V2-dependent antibodies. J Virol 87:4882-94
Murphy, Megan K; Yue, Ling; Pan, Ruimin et al. (2013) Viral escape from neutralizing antibodies in early subtype A HIV-1 infection drives an increase in autologous neutralization breadth. PLoS Pathog 9:e1003173
Wibmer, Constantinos Kurt; Bhiman, Jinal N; Gray, Elin S et al. (2013) Viral escape from HIV-1 neutralizing antibodies drives increased plasma neutralization breadth through sequential recognition of multiple epitopes and immunotypes. PLoS Pathog 9:e1003738
Sethi, Anurag; Tian, Jianhui; Derdeyn, Cynthia A et al. (2013) A mechanistic understanding of allosteric immune escape pathways in the HIV-1 envelope glycoprotein. PLoS Comput Biol 9:e1003046
Moore, Penny L; Gray, Elin S; Sheward, Daniel et al. (2011) Potent and broad neutralization of HIV-1 subtype C by plasma antibodies targeting a quaternary epitope including residues in the V2 loop. J Virol 85:3128-41
Gray, Elin S; Madiga, Maphuti C; Hermanus, Tandile et al. (2011) The neutralization breadth of HIV-1 develops incrementally over four years and is associated with CD4+ T cell decline and high viral load during acute infection. J Virol 85:4828-40
Krachmarov, Chavdar; Lai, Zhong; Honnen, William J et al. (2011) Characterization of structural features and diversity of variable-region determinants of related quaternary epitopes recognized by human and rhesus macaque monoclonal antibodies possessing unusually potent neutralizing activities. J Virol 85:10730-40