Providence/Boston Center for Aids Research (CFAR)

Basic Sciences Core

The Basic Science Core builds and supports essential, innovative and collaborative HIV research and synergy between basic, translational, clinical, behavioral and other multidisciplinary scientists with a wide range of HIV experience, by providing laboratory, consultation and mentoring services locally, nationally and internationally

The mission of the Basic Sciences Core (BSC) is to build and support collaborative HIV research and synergy between basic, translational, clinical, behavioral, and other multidisciplinary scientists, with a focus on NIH HIV/AIDS high priority areas. A major priority of the BSC is to provide services and scientific infrastructure that extend the capacity of investigators who lack the technical expertise or laboratory resources for their research. The BSC provides expanded and flexible consultation and laboratory services to local, national and international HIV/AIDS researchers based on evolving needs, and works to significantly expand the Core user pool through outreach and education. Laboratory services are aimed at HIV quantitation and characterization using diverse analytes, and assessment of host cell responses. Specific assays include quantitative real-time PCR, antigen and antibody detection, sequence, drug resistance and phylogenetic analysis and bioinformatics. The Core also provides access to and provision of reagents, such as virus stocks, cell cultures, and other molecular virology materials. Importantly, the BSC takes an active role in all levels of mentoring and training of both new investigators and those established, who wish to expand into HIV research, and if needed also assists in generating preliminary data for grant submissions, with the goal of creating a pipeline to independent NIH funding and published research

Akiyama H, Jalloh S, Park S, Lei M, Mostoslavsky G, Gummuluru S. Expression of HIV-1 Intron-Containing RNA in Microglia Induces Inflammatory Responses. J Virol. 2020 Dec 9:JVI.01386-20. doi: 10.1128/JVI.01386-20. Epub ahead of print. PMID: 33298546.

Akiyama H, Gummuluru S. HIV-1 Persistence and Chronic Induction of Innate Immune Responses in Macrophages. Viruses. 2020 Jun 30;12(7):711. doi: 10.3390/v12070711. PMID: 32630058; PMCID: PMC7412260.

Anderson DJ, Politch JA, Cone RA, Zeitlin L, Lai SK, Santangelo PJ, Moench TR, Whaley KJ. Engineering monoclonal antibody-based contraception and multipurpose prevention technologies†. Biol Reprod. 2020 Aug 4;103(2):275-285. doi: 10.1093/biolre/ioaa096. PMID: 32607584; PMCID: PMC7401387.

Belkina AC, Azer M, Lee JJ, Elgaali HH, Pihl R, Cleveland M, Carr J, Kim S, Habib C, Hasturk H, Snyder-Cappione JE, Nikolajczyk BS. Single-Cell Analysis of the Periodontal Immune Niche in Type 2 Diabetes. J Dent Res. 2020 Jul;99(7):855-862. doi: 10.1177/0022034520912188. Epub 2020 Mar 18. PMID: 32186942; PMCID: PMC7313350.

Bharath LP, Agrawal M, McCambridge G, Nicholas DA, Hasturk H, Liu J, Jiang K, Liu R, Guo Z, Deeney J, Apovian CM, Snyder-Cappione J, Hawk GS, Fleeman RM, Pihl RMF, Thompson K, Belkina AC, Cui L, Proctor EA, Kern PA, Nikolajczyk BS. Metformin Enhances Autophagy and Normalizes Mitochondrial Function to Alleviate Aging-Associated Inflammation. Cell Metab. 2020 Jul 7;32(1):44-55.e6. doi: 10.1016/j.cmet.2020.04.015. Epub 2020 May 12. PMID: 32402267; PMCID: 7217133.

KM Byrd, CG. Beckwith, JM Garland, JE Johnson, S Aung, S Cu-Uvin, D Farmakiotis, T Flanigan, F Gillani, R Macias-Gil, M Mileno, B Ramratnam, NR Rybak, M Sanchez, K Tashima, E Mylonakis, R Kantor. SARS-CoV-2 and HIV Coinfection: Clinical Experience from Rhode Island, United States. Journal of International AIDS Society 2020; 23: e25573. PMID: 32657527. PMCID: 7357287

Eshaghi B, Alsharif N, An X, Akiyama H, Brown KA, Gummuluru S, Reinhard BM. Stiffness of HIV-1 Mimicking Polymer Nanoparticles Modulates Ganglioside-Mediated Cellular Uptake and Trafficking. Adv Sci (Weinh). 2020 Jul 29;7(18):2000649. doi: 10.1002/advs.202000649. PMID: 32999830; PMCID: PMC7509657.

He X, Eddy JJ, Jacobson KR, Henderson AJ, Agosto LM. Enhanced Human Immunodeficiency Virus-1 Replication in CD4+ T Cells Derived From Individuals With Latent Mycobacterium tuberculosis Infection. J Infect Dis. 2020 Oct 1;222(9):1550-1560. doi: 10.1093/infdis/jiaa257. PMID: 32417884; PMCID: PMC7529013.

H Ji , N Parkin, F Gao, T Denny, C Jennings, P Sandstrom, R Kantor. External quality assessment program for next generation sequencing-based HIV drug resistance testing: Logistical considerations. Viruses 2020;12:556. PMID: 32443529 PMCID: PMC7291315. 

H Ji, P Sandstrom, R Paredes, P R Harrigan, C Brumme, S Avila Ríos, M Noguera-Julian, N Parkin, R Kantor. Are we ready for NGS HIV drug resistance testing? The second ‘Winnipeg Consensus’ Symposium. Viruses 2020;12:586. PMID: 32471096 PMCID: PMC7354487

Kolluri N, Albarran N, Fan A, Olson A, Sagar M, Young A, Gomez-Marquez J, Klapperich CM. SNAPflex: a paper-and-plastic device for instrument-free RNA and DNA extraction from whole blood. Lab on a chip. 2020. Epub 2020/08/09. doi: 10.1039/d0lc00277a. PubMed PMID: 32766666.

Mostaghim A, SinhaP, Bielick C, KnudsenS, BeeramI, WhiteLF, ApovianC, SagarM, Hochberg NS. Clinical outcomes and inflammatory marker levels in patients with Covid-19 and obesity at an inner-city safety net hospital. PloS one 2020; 15(12): e0243888.

V Novitsky, JA Steingrimsson, M Howison, FS Gillani, Y Li, A Manne, J Fulton, M Spence, Z Parillo, T Marak, PA Chan, T Bertrand, U Bandy, N Alexander-Scott, CW Dunn, J Hogan, R Kantor.  Empirical Comparison of Analytical Approaches for Identifying Molecular HIV-1 Clusters. Scientific Reports 2020;10:18547. PMID: 33122765 PMCID: PMC7596705.

Olson A, Coote C, Snyder-Cappione JE, Lin N, Sagar M. HIV-1 transcription but not intact provirus levels are associated with systemic inflammation. The Journal of infectious diseases. 2020. Epub 2020/10/20. doi: 10.1093/infdis/jiaa657. PubMed PMID: 33075121.

Olson A, Basukala B, Lee S, Gagne M, Wong WW, Henderson AJ. Targeted Chromatinization and Repression of HIV-1 Provirus Transcription with Repurposed CRISPR/Cas9. Viruses. 2020 Oct 12;12(10):1154. doi: 10.3390/v12101154. PMID: 33053801; PMCID: PMC7600714.

NT Parkin, DJ Zaccaro, S Avila-Rios, M Matías-Florentino, C Brumme, G Hunt, J Ledwaba, H Ji, ER Lee, R Kantor, JL Mbisa, DF Bibby, R Paredes, M Noguera Julian, V Rivera-Amill, Y Zhang, S Zhou, R Harrigan, C Jennings. Multi-laboratory comparison of next-generation to Sanger-based sequencing for HIV-1 drug resistance genotyping. Viruses 2020;12:694.

Politch JA, Cu-Uvin S, Moench TR, Tashima KT, Marathe JG, Guthrie KM, Cabral H, Nyhuis T, Brennan M, Zeitlin L, Spiegel HML, Mayer KH, Whaley KJ, Anderson DJ. Safety, acceptability, and pharmacokinetics of a monoclonal antibody-based vaginal multipurpose prevention film (MB66): A Phase I randomized trial. PLoS Med. 2021 Feb 3;18(2):e1003495. doi: 10.1371/journal.pmed.1003495. PMID: 33534791; PMCID: PMC7857576.

Aadia I Rana , Jose R Castillo-Mancilla, Karen T Tashima, Raphael L Landovitz. Advances in Long-Acting Agents for the Treatment of HIV Infection. Drugs 2020;80:535-545. PMID 32180205; PMCID 720697.

Sagar M, Reifler K, Rossi M, Miller NS, Sinha P, White L, Mizgerd JP. Recent endemic coronavirus infection is associated with less severe COVID-19. The Journal of clinical investigation. 2020. Epub 2020/10/01. doi: 10.1172/jci143380. PubMed PMID: 32997649.

Sam SS, Rogers R, Gillani FS, Tsongalis GJ, Kraft CS, Caliendo AM. Evaluation of a Next-Generation Sequencing Metagenomics Assay to Detect and Quantify DNA Viruses in Plasma from Transplant Recipients (in press, J Mol Diagn).

Sinha P, Mostaghim A, Bielick CG, McLaughlin A, Hamer DH, Wetzler L, Bhadelia N, Fagan M, Linas BP, Assoumou SA, Ieong MH, Lin NH, Cooper ER, Brade KD, White LF, Barlam TF, Sagar M. Early administration of Interleukin-6 inhibitors for patients with severe Covid-19 disease is associated with decreased intubation, reduced mortality, and increased discharge. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases. 2020. Epub 2020/07/30. doi: 10.1016/j.ijid.2020.07.023. PubMed PMID: 32721528.

Sinha P, Jafarzadeh SR, Assoumou SA, Bielick CG, Carpenter B, Garg S, Harleen S, Neogi T, Nishio MJ, Sagar M, Sharp V, Kissin EY. The effect of IL-6 inhibitors on mortality among hospitalized COVID-19 patients: a multicenter study. The Journal of infectious diseases. 2020. Epub 2020/11/21. doi: 10.1093/infdis/jiaa717. PubMed PMID: 33216906.