Einstein-Montefiore Center for AIDS Research

Einstein-Montefiore Center for AIDS Research

Einstein-Montefiore CFAR Virology Core Director: Dr. Ganjam V. Kalpana, Ph.D. Overarching Goal To provide CFAR Investigators with the appropriate support, training and access for the most relevant and cutting-edge approaches to rapidly and efficiently support their virology research programs. Virology Core Aims Providing the Infrastructure, reagents, assays and technologies to enable basic and translational researchers to Investigate HIV Infection, pathogenesis and therapy;

Performing cellular and molecular assays characterizing HIVlnfection to support clinical and translational investigators engaged in patient-based studies of HIV/AIDS patients; and Providing training to investigators In a wide range of cellular and molecular assays used in the study of HIV pathogenesis. Maintaining a central repository of molecular clones of infectious HIV, viral isolates, reporter HIV clones and HIV reporter cells lines as well as HIV-based expression vectors. Virology Core Training Programs Measurement of p24 antigen by ELISA Co-culture, quantification and sequence analysis of HIV from PBMCs Determining the viral titers, infectious units (i.u.) and m.o.i. of HIV using reporter cell lines Real-time PCR for quantification of HIV RNA and cellular gene expression

Application of advanced virological techniques to analyze all stages of HIV-1 replication-including entry, reverse transcription, nuclear localization, integration, transcription, assembly and particle production. Virological Core Services

HIV culture and isolation HIV p24 antigen capture assay Repository of titered primary HIV isolates HIV-1 neutralization assays Quantitative HIV-1 DNA and RNA measurements HIV and cellular RNA quantification by real-time qPCR Determination of viral tropism. Reporter virus entry assay. HIV sequence analysis. Patient sample processing and storage. Immunosorting of control and HIV-infected cellular subpopulations. Measurement of serum HCV antibody and plasma HCV virus

levels. Molecular Biological Core Services Routine o o o o Custom vector and plasmid design and construction Provision and expression of reporter and full-length molecular clones of viruses of many clades Site-directed mutagenesis Large-scale expression of recombinant HIV, human or other pathogen proteins

Advanced o o o o o o Lentiviral vector construction and preparation of virus particles RNA interference analysis Genetic and biochemical systems to study protein-protein interactions Chromatin immunoprecipitation (ChIP) techniques FRET-based BLam assay (beta-Lactamase based assay) Heteroduplex mobility assay (HMA)

Expansion of Core Activities and Innovation The core (in collaboration with ATRP program) purchased a new Applied Biosystem qPCR machine to facilitate the demand for use of this assay in studying HIV-1 infection. Core is developing methods to carry out microRNA analysis in HIV-1 infected samples. In collaboration with Epigenomics and Genomics Center, the core is planning to optimize the methods for RNA/microRNA-seq, ChIP-seq and Affymatrix techniques. Consultation for the developing and carrying out these techniques will be provided for CFAR users. Expansion of Core Activities and

Innovation In collaboration with Bronx WHIS (PI: Dr. Anastos) and the Einsteins Microbicide program (PI: Dr. Herold), CFAR has purchased an Abbott m2000 machine M200sp Sample preperation station M2000rt RT-PCR machine Expansion of Core Activities and

Innovation Abbot m2000 Provides automation for sample preparation and real time PCR. Ideal for using a variety of clinical samples and allows the use of bar coded tubes, creates an efficient workflow, minimizes errors and contamination. Barcoded Laboratory Tubes, Precision Pipetting-no manual mixing or

manipulation, Open Mode-Flexible protocol for various sample types and volumes Efficient Sample Extraction--Flexible throughput options of 24 to 96 samplesallows isolation of nucleic acids, RNA or DNA from variety of samples (serum, plasma) based on the magnetic bead method. Samples are prepared automatically and loaded onto 96 well plates and sealed for transfer to PCR machine. Expansion of Core Activities and Innovation --- continued Abbot m2000 currently being used for HIV-1 viral load assays (range 40 to 10,000,000 copies/mL). Can be used for other clinical applications. Other viral loadsHCV, HBV Detection of cellular transcripts-biomarkers, depending on the availability of the kit to use in the Abbott

machine. Expansion of Core Activities and Innovation --- continued echnical InnovationsAlpha Technology AlphaLISA-instead of p24 ELISA Various enzymatic- Kinase Assays Protein-protein interactions A reduced number of assay steps---no washing steps. Automated---good for adopting to HTS Versatilemeasure large biomolecules (up to 2000 kDa) or

weak interactions (mM). Proposed Activities for Next Project Period The Core will expand its sequencing activities for molecular characterization of clinical isolates Expansion of virological support for WIHS studies Expansion of support to carry out epigenetic (methylation and ChIP assays) and microRNA analysis during HIV-1 pathogenesis Expand service to include support of protein production Accomplishments Over the past 5 years, we have contributed to data in

31 publications In the past year we have supported studies by 32 NlH-funded investigators. We have expanded the Core services In response to the needs of Investigators including developing highly cost-effective lab-developed assays.

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