Journal: Retrovirology

Article Title: CCR5 interaction with HIV-1 Env contributes to Env-induced depletion of CD4 T cells in vitro and in vivo

doi: 10.1186/s12977-016-0255-z

Figure Lengend Snippet: Ablation of CCR5 usage reduces dual-tropic HIV-1 pathogenesis in PBMC infection. a Intracellular p24 staining and FACS analysis was used to quantify viral replication in infected PBMCs. Infected (p24+) CD4 T cell numbers were calculated by multiplying the percentage of (p24+) cells with total CD4 T cell numbers at each time point ( left ). RT-qPCR analysis of HIV-1 genomic RNA levels was used to measure extracellular viral replication of R3A and R3A-5/6AA in infected PBMCs ( right ). b Representative FACS Plots are presented showing CD4 and CD8 populations gated on live CD3(+) T cells in PBMC at 6 days post infection. HIV-1 fusion inhibitor T20 treatment was used as negative control. c Kinetics of CD4 T cell depletion by R3A versus R3A-5/6AA was analyzed as described in Fig. b. CD4 T cell survival are measured as %CD4 T cells in infected PBMCs relative to mock infection ( top ), or live CD4 T cell numbers ( bottom ) over time. d p24(−) and p24(+) CD4 T cell death in R3A and R3A-5/6AA infected PBMCs are quantified at 6 days post infection, as described in Fig. C. FACS plots ( left ) and graphical summary ( Right ) from a representative experiment are presented. Experimental results were repeated with PBMCs from 3 different blood donors. * p < 0.05

Article Snippet: Viremia in supernatants from infected PBMC cultures or from blood plasma of infected humanized mice was analyzed by viral RNA extraction (QIAamp viral RNA mini kit, Qiagen), and analyzed by RT-qPCR (Taqman One-Step RT-qPCR Master Mix, ABI) using the following primers and probe targeting HIV-1 Gag region: 765gagF 5′-GGTGCGAGAGCGTCAGTATTAAG-3′; 911gagR 5′-AGCTCCCTGCTTGCCCATA-3′; probe FAM-AAAATTCGGTTAAGGCCAGGGGGAAAGAA-QSY7 (TAMRA).

Techniques: Infection, Staining, Quantitative RT-PCR, Negative Control

Journal: Retrovirology

Article Title: CCR5 interaction with HIV-1 Env contributes to Env-induced depletion of CD4 T cells in vitro and in vivo

doi: 10.1186/s12977-016-0255-z

Figure Lengend Snippet: Ablation of CCR5 usage reduces pathogenesis of dual tropic HIV-1 in a humanized mouse model. a Humanized mice were infected with R3A or R3A-5/6AA as described in “ ” section. Viral replication was assessed weekly by RT-qPCR measurement of HIV-1 genomic RNA in the blood. HIV-1 infection in CD4 T cells was analyzed by intracellular p24 staining of splenocytes isolated from infected mice at 3 weeks post infection (wpi). b Total PBMCs in blood, spleen and bone marrow from infected animals were harvested at 3wpi, and CD4 T cell depletion was analyzed by FACS staining as described in Fig. b. c p24(−) and p24(+) CD4 T cell viability in R3A versus R3A-5/6AA infection in the infected animal’s spleen and bone marrow were analyzed as described in Fig. c. * p < 0.05

Article Snippet: Viremia in supernatants from infected PBMC cultures or from blood plasma of infected humanized mice was analyzed by viral RNA extraction (QIAamp viral RNA mini kit, Qiagen), and analyzed by RT-qPCR (Taqman One-Step RT-qPCR Master Mix, ABI) using the following primers and probe targeting HIV-1 Gag region: 765gagF 5′-GGTGCGAGAGCGTCAGTATTAAG-3′; 911gagR 5′-AGCTCCCTGCTTGCCCATA-3′; probe FAM-AAAATTCGGTTAAGGCCAGGGGGAAAGAA-QSY7 (TAMRA).

Techniques: Infection, Quantitative RT-PCR, Staining, Isolation

Journal: Analytical and Bioanalytical Chemistry

Article Title: Interlaboratory assessment of quantification of SARS-CoV-2 RNA by reverse transcription digital PCR

doi: 10.1007/s00216-021-03680-2

Figure Lengend Snippet: Summary of the RT-dPCR platforms and methods of the participants

Article Snippet: Laboratory 10 used one-step RT-dPCR mix of both Bio-Rad (for E gene) and Sniper (for ORF 1ab and N gene), because no positive signals were observed for E gene using Sniper’s mix but normal positive and negative signals were obtained when changing the Sniper mix to Bio-Rad mix.

Techniques:

Journal: Analytical and Bioanalytical Chemistry

Article Title: Interlaboratory assessment of quantification of SARS-CoV-2 RNA by reverse transcription digital PCR

doi: 10.1007/s00216-021-03680-2

Figure Lengend Snippet: Participants’ results for copy number concentration of SARS-CoV-2 RNA ORF 1ab gene, E gene, and N gene. Results of the five laboratories using dPCR platforms of Bio-Rad are indicated with red circle, and results of the five laboratories using other platforms with blue diamond. Solid and dashed horizontal lines indicate RV and expanded uncertainty (95% level of confidence, k = 2) of each gene

Article Snippet: Laboratory 10 used one-step RT-dPCR mix of both Bio-Rad (for E gene) and Sniper (for ORF 1ab and N gene), because no positive signals were observed for E gene using Sniper’s mix but normal positive and negative signals were obtained when changing the Sniper mix to Bio-Rad mix.

Techniques: Concentration Assay