Basic Sciences Core (BSC) Services

Category

Specific Services

Viral load measurement

HIV-1 RNA and/or DNA isolation

Nucleic acid extraction from plasma, whole blood, genital secretion specimens, cerebrospinal fluid (CSF), dried blood spots (DBS), Hemaspots and urine.

 

HIV-1 Viral load measurement 

Quantification of HIV-1 RNA in plasma, whole blood, genital secretion specimens, cerebrospinal fluid (CSF), dried blood spots (DBS), Hemaspots and urine.

Detection of HIV-1 DNA in whole blood, peripheral blood mononuclear cells, buffy coat samples, DBS, and genital specimens with quantitative PCR and droplet digital PCR.

 

Other viral load testing

Quantification of HBV, HCV, BKV and EBV in plasma specimens.

Quantification of CMV in plasma, genital specimens, CSF, and DBS.

Detection of sexually transmitted infections in genital secretions (vaginal lavage and semen)

Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis, Herpes simplex virus and Cytomegalovirus testing on genital specimens including tear flow, cervical vaginal lavage specimens, urine, self-collected vaginal swabs, and rectal swabs.

Genital tract specific assays

Optimization of collection of cells from cervical/vaginal lavage; viral load measurements and drug resistance testing in genital tract specimens.

 

Collection techniques for biologic specimens

Plasma, blood and plasma spots, and Hemaspots for viral load and drug resistance testing.

HIV-1 amplification, sequencing and drug resistance assays

Sanger sequencing, single genome amplification and sequencing (SGS); next generation sequencing (NGS).

Data analysis and interpretation

HIV drug resistance testing, sequence analysis, bioinformatics, phylogenetics, transmission networks.

Identification of 
HIV dependency factors (HDF)

SILAC based proteomic comparisons of HIV-1 infected subjects with high and low viral load; Characterization of identified proteins and their impact on the HIV-1 lifecycle.

Cell culture

Maintenance of varied human cell lines and performance of viral challenge experiments with p24 measurement; Assistance with creation and differentiation of pluripotent stem cells into neuronal cells; Isolation of nucleic acids and proteins from cell lines and primary patient cells.

HIV Latency studies

Droplet digital PCR assessment of intact HIV proviral DNA in peripheral blood mononuclear cells from patients or laboratory samples.

Viral stocks

Maintenance and propagation of lab adapted and primary patient viral strains

Antibody studies

Plasma and antibody assessments of neutralization and antibody dependent cellular cytotoxicity against diverse HIV strains.

Immune activation

FACS for CD8+, CD38+, and HLADR+ T cells; Cytokines assays

Laboratory consultation

Standard operating procedures for the collection, storage and shipping of specimens both nationally and internationally.

Consultation on study design with regard to testing methods and results interpretation.

Consultation on assay development to meet specific needs of investigators.

Support for clinical studies

Specimen processing; preparation of specimens for flow cytometry; specimen storage and real time distribution; experimental input and trouble-shooting; technical consultation for protocol development with an emphasis on selection of appropriate virologic assays.

Support for international studies

Training in universal precautions for all laboratory and clinical personnel; technical assistance on the setting up laboratory techniques for quantification of viral load and drug resistance testing in the resource limited setting; QA/QC of international mentored projects; consultation on the selection and performance of low tech alternatives for viral load and drug resistance testing for use in resource/ technology limited settings.

Access to data and specimens

Maintenance of repository and distribution of samples to investigators (>60,000 specimens available).

Training

Training in universal precautions for all laboratory and clinical personnel; QA/QC of all mentored projects; Training in performing rapid point-of-care HIV-1 diagnostic tests; viral load; resistance testing.

Mentoring

Scientific and career mentoring of investigators. Grant, presentation and manuscript planning and writing.