Journal: Pathogens

Article Title: A Novel Inhibitor against the Biofilms of Non-Tuberculous Mycobacteria

doi: 10.3390/pathogens13010040

Figure Lengend Snippet: MIC of NF1001 and SoC and other drugs on biofilms of Mabs and Mav.

Article Snippet: The following reagents in the category of other reference drugs [Bedaquiline (BDQ)] were obtained through the NIH, as HIV Reagent Program, Division of AIDS, NIAID, NIH: Bedaquiline Fumarate (BDQ) ARP-12702, contributed by Janssen Pharmaceuticals.

Techniques:

Journal: Cell reports

Article Title: Enhanced evasion of neutralizing antibody response by Omicron XBB.1.5, CH.1.1, and CA.3.1 variants

doi: 10.1016/j.celrep.2023.112443

Figure Lengend Snippet: (A and B) Syncytia-forming activity. HEK293T-ACE2 cells were co-transfected with Omicron subvariant S proteins and GFP and incubated for 30 h before (A) imaging and (B) quantifying syncytia. D614G and no S serve as positive and negative controls, respectively. Comparisons in the extent of syncytia for each variant were made against D614G, with p values indicating statistical significance. Similar results were obtained by using CaLu3 cell as target (see data in ). (C and D) Cell surface expression of S proteins. HEK293T cells used for production of pseudotyped lentiviral vectors bearing S proteins ( and ) from Omicron subvariants were fixed and surface stained for S with an anti-S1 specific antibody T62 followed by flow cytometric analyses. (C) Histogram plots of anti-S1 signals in transfected cells and (D) calculated relative mean fluorescence intensities of each subvariant by setting the value of D614G as 1. (E) S expression and processing. HEK293T cells used to produce pseudotyped vectors were lysed and probed with anti-S1, anti-S2, anti-GAPDH (loading control), or anti-p24 (HIV capsid, transfection control) antibodies; the signal for anti-GAPDH was from reblotting the membrane of anti-S1, and the signal for anti-S2 was from reblotting the membrane of anti-p24. S processing was quantified using NIH ImageJ used to determine an S1/S or S2/S ratio and normalized to D614G (D614G = 1.0). Bars in (B) and (D) represent means ± standard error. Dots represent three biological replicates from one typical experiment. Significance relative to D614G was determined using a one-way repeated measures ANOVA with Bonferroni’s multiple testing correction (n = 3). p values are displayed as ns p > 0.05 and ****p < 0.0001.

Article Snippet: Membranes were probed with anti-S1 (Sino Biological, 40591-T62; RRID:AB_2893171), anti-S2 (Sino Biological, 40590; RRID:AB_2857932), anti-p24 (NIH HIV Reagent Program, ARP-1513), and anti-GAPDH (Santa Cruz, Cat# sc-47724, RRID: AB_627678).

Techniques: Activity Assay, Transfection, Incubation, Imaging, Variant Assay, Expressing, Staining, Fluorescence, Control, Membrane

Journal: Cell reports

Article Title: Enhanced evasion of neutralizing antibody response by Omicron XBB.1.5, CH.1.1, and CA.3.1 variants

doi: 10.1016/j.celrep.2023.112443

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Membranes were probed with anti-S1 (Sino Biological, 40591-T62; RRID:AB_2893171), anti-S2 (Sino Biological, 40590; RRID:AB_2857932), anti-p24 (NIH HIV Reagent Program, ARP-1513), and anti-GAPDH (Santa Cruz, Cat# sc-47724, RRID: AB_627678).

Techniques: Infection, Recombinant, Transfection, Modification, Software, Imaging

Journal: Cells

Article Title: Identification, Quantification, and Characterization of HIV-1 Reservoirs in the Human Brain

doi: 10.3390/cells11152379

Figure Lengend Snippet: Detection of HIV DNA, HIV-mRNA, and HIV protein in uninfected HL-60 cells. We diluted uninfected control cells (HL-60) to calculate our image system’s sensitivity to detect viral reservoirs. One to ten cells were diluted in 10 3 to 10 12 HeLa cells. Then, staining for HIV DNA (top), HIV-mRNA (middle), or HIV-p24 protein (bottom) was performed to identify whether we could detect the diluted cells in the HeLa cells. The percentage of detection is indicated for 10 sample preparations for each dilution. Pellets of these cells were cut and analyzed by microscopy to identify the infected cells.

Article Snippet: The currently available antibodies are α-HIV p24 (Genetex, GTX40774, Irvine, CA, USA; NIH AIDS repository, HRP-20068, or ARP-4121), α-HIV nef (NIH AIDS repository, ARP-1124, 2949, 709), α-HIV tat (NIH AIDS repository, ARP-4672, or 466), α-HIV integrase (NIH AIDS repository, ARP-7375, or 3514), α-HIV gp120 (NIH AIDS repository, ARP-1476, 2534, 11682, or 11438), or α-HIV vpr (NIH AIDS repository, ARP-11836).

Techniques: Control, Staining, Microscopy, Infection

Journal: Cells

Article Title: Identification, Quantification, and Characterization of HIV-1 Reservoirs in the Human Brain

doi: 10.3390/cells11152379

Figure Lengend Snippet: Detection of HIV DNA, HIV-mRNA, and HIV protein in uninfected A3.01 cells. We diluted uninfected control cells (A3.01) to calculate our image system’s sensitivity to detect viral reservoirs. One to ten cells were diluted in 10 3 to 10 12 HeLa cells. Then, staining for HIV DNA (top), HIV-mRNA (middle), or HIV-p24 (bottom) was performed to identify whether we could detect the diluted cells in the HeLa cells. The percentage of detection is indicated for 10 sample preparations for each dilution. Pellets of these cells were cut and analyzed by microscopy to identify the infected cells.

Article Snippet: The currently available antibodies are α-HIV p24 (Genetex, GTX40774, Irvine, CA, USA; NIH AIDS repository, HRP-20068, or ARP-4121), α-HIV nef (NIH AIDS repository, ARP-1124, 2949, 709), α-HIV tat (NIH AIDS repository, ARP-4672, or 466), α-HIV integrase (NIH AIDS repository, ARP-7375, or 3514), α-HIV gp120 (NIH AIDS repository, ARP-1476, 2534, 11682, or 11438), or α-HIV vpr (NIH AIDS repository, ARP-11836).

Techniques: Control, Staining, Microscopy, Infection

Journal: Cells

Article Title: Identification, Quantification, and Characterization of HIV-1 Reservoirs in the Human Brain

doi: 10.3390/cells11152379

Figure Lengend Snippet: Detection of HIV DNA, HIV-mRNA, and HIV-protein in OM-10 cells. To calculate our image system’s sensitivity to detect viral reservoirs, we diluted cells with one copy of integrated HIV DNA (OM-10). One to ten cells were diluted in 10 3 to 10 12 HeLa cells. Then, staining for HIV DNA (top), HIV-mRNA (middle), or HIV-p24 (bottom) was performed to identify whether we could detect the diluted cells in the HeLa cells. The percentage of detection is indicated for 10 sample preparations for each dilution. Pellets of these cells were cut and analyzed by microscopy to identify the infected cells. These cells were not treated with reactivating agents, such as TNF-α or SAHA. Thus, detection corresponds to the baseline viral production.

Article Snippet: The currently available antibodies are α-HIV p24 (Genetex, GTX40774, Irvine, CA, USA; NIH AIDS repository, HRP-20068, or ARP-4121), α-HIV nef (NIH AIDS repository, ARP-1124, 2949, 709), α-HIV tat (NIH AIDS repository, ARP-4672, or 466), α-HIV integrase (NIH AIDS repository, ARP-7375, or 3514), α-HIV gp120 (NIH AIDS repository, ARP-1476, 2534, 11682, or 11438), or α-HIV vpr (NIH AIDS repository, ARP-11836).

Techniques: Staining, Microscopy, Infection

Journal: Cells

Article Title: Identification, Quantification, and Characterization of HIV-1 Reservoirs in the Human Brain

doi: 10.3390/cells11152379

Figure Lengend Snippet: Detection of HIV DNA, HIV-mRNA, and HIV protein in ACH-2 cells. To calculate our image system’s sensitivity to detect viral reservoirs, we diluted cells with one copy of integrated HIV DNA (ACH-2), one to ten cells into 10 3 to 10 12 HeLa cells. Then, staining for HIV DNA (top), HIV-mRNA (middle), or HIV-p24 (bottom) was performed to identify whether we could detect the diluted cells in the HeLa cells. The percentage of detection is indicated for 10 sample preparations for each dilution. Pellets of these cells were cut and analyzed by microscopy to identify the infected cells. These cells were not treated with reactivating agents such as TNF-α or SAHA. Thus, detection corresponds to the baseline viral production.

Article Snippet: The currently available antibodies are α-HIV p24 (Genetex, GTX40774, Irvine, CA, USA; NIH AIDS repository, HRP-20068, or ARP-4121), α-HIV nef (NIH AIDS repository, ARP-1124, 2949, 709), α-HIV tat (NIH AIDS repository, ARP-4672, or 466), α-HIV integrase (NIH AIDS repository, ARP-7375, or 3514), α-HIV gp120 (NIH AIDS repository, ARP-1476, 2534, 11682, or 11438), or α-HIV vpr (NIH AIDS repository, ARP-11836).

Techniques: Staining, Microscopy, Infection

Journal: Cells

Article Title: Identification, Quantification, and Characterization of HIV-1 Reservoirs in the Human Brain

doi: 10.3390/cells11152379

Figure Lengend Snippet: HIV reservoirs are organized in small clusters within the brain of HIV-infected individuals. ( A ) The image shows the detection strategy for HIV DNA, viral mRNA, and viral proteins, as well as cellular markers using 11 slice sections per tissue. The first and last sections were stained for H&E; the second section was used for a trichrome stain; the following sections were sequentially stained for DAPI, HIV DNA, HIV-mRNA, HIV protein (p24, gp120, integrase, nef, vpr, or tat), Alu repeats, or markers for astrocytes (GFAP), and microglia/macrophages (Iba-1) as indicated. ( B – G ) Confocal images show a cell cluster labeled with DAPI, containing HIV DNA, positive for microglia/macrophage markers and enlarged astrocytes, indicated by the Iba-1 protein and GFAP, respectively, and expressing HIV-p24 protein cells. Most brain tissue was negative for the viral markers (compared to ). ( H – J ) Quantification of cell clusters positive for HIV DNA in tissues obtained from uninfected brains (Un), HIV-infected brains with undetectable replication (HIV un ), HIV-infected brains with low replication (HIV low ), and HIV-infected brains with high replication (HIV high ). As a control, we used HIV encephalitic brains (HIVEs) and uninfected cases from healthy and Alzheimer’s individuals, Alz (n = 34 brains analyzed and each point corresponding to the mean of at least 3–5 different quantifications per tissue). ( H ) Corresponds to the quantification of cell clusters containing HIV DNA in the nucleus (colocalizing with DAPI and Alu repeats). ( I ) Quantification of double-positive cell clusters for HIV DNA and viral mRNA. ( J ) Quantification of cell clusters positive for HIV DNA, viral mRNA, and HIV-p24. * p ≤ 0.005 compared to uninfected conditions, # p ≤ 0.005 compared to HIV un conditions, and & p ≤ 0.005 compared to HIV un or HIV low conditions; n = 34 tissues analyzed, and 21 tissues compared to uninfected tissues, Un and Alz, n = 8 different tissues; each point represents 3–5 different areas per tissue analyzed. Bar: 8 µm.

Article Snippet: The currently available antibodies are α-HIV p24 (Genetex, GTX40774, Irvine, CA, USA; NIH AIDS repository, HRP-20068, or ARP-4121), α-HIV nef (NIH AIDS repository, ARP-1124, 2949, 709), α-HIV tat (NIH AIDS repository, ARP-4672, or 466), α-HIV integrase (NIH AIDS repository, ARP-7375, or 3514), α-HIV gp120 (NIH AIDS repository, ARP-1476, 2534, 11682, or 11438), or α-HIV vpr (NIH AIDS repository, ARP-11836).

Techniques: Infection, Staining, Labeling, Expressing, Control

Journal: Cells

Article Title: Identification, Quantification, and Characterization of HIV-1 Reservoirs in the Human Brain

doi: 10.3390/cells11152379

Figure Lengend Snippet: Quantification of myeloid and glial viral reservoirs in cortical and subcortical human brain areas. Representative confocal images of the areas analyzed for ( A ) unstained and ( B ) H&E-stained tissue. Areas detected with HIV DNA are represented in blue boxes. ( C – H ) Representative confocal images of the brain areas containing integrated HIV DNA and positive labeling for ( C ) DAPI, ( D ) HIV DNA, ( E ) HIV-mRNA, ( F ) HIV-p24, ( G ) Alu repeats, and ( H ) the merge of all colors. ( I – K ) Quantification of cells positive for ( I ) integrated HIV DNA in Macrophage/Microglia (Iba-1-positive cells) and astrocytes (GFAP-positive cells) in human tissues obtained from individuals with undetectable, low, and high systemic replication; * p ≤ 0.005 compared to uninfected conditions, # p ≤ 0.005 compared to HIV un conditions, and & p ≤ 0.005 compared to HIV un or HIV low conditions; n = 34 tissues analyzed and 21 tissues compared to uninfected tissues, Un and Alz, n = 8 different tissues; each point represents 3–5 different areas per tissue analyzed. Comparisons of the HIV-infected groups by ANOVA are described in the text and Methods Section, ( J ) integrated HIV DNA and HIV-mRNA in Macrophage/Microglia and astrocytes in human tissues obtained from individuals with undetectable, low, and high systemic replication (* p ≤ 0.005 compared to uninfected conditions and # p ≤ 0.005 compared to HIV conditions, & p ≤ 0.005), ( K ) integrated HIV DNA, HIV-mRNA, and HIV-p24 in Macrophage/Microglia and astrocytes in human tissues obtained from individuals with undetectable, low, and high systemic replication (* p ≤ 0.005 compared to uninfected conditions, # p ≤ 0.005 compared to HIV un conditions, and & p ≤ 0.005 compared to HIV un or HIV low conditions; n = 34 tissues analyzed and 21 tissues compared to uninfected tissues, Un and Alz, n = 8 different tissues; each point represents 3–5 different areas per tissue analyzed). ( L ) Quantification of cells expressing HIV-p24 in HIV and HIVE cells positive for HIV DNA (HIV DNA (+) and HIVE-DNA (+)) and negative for HIV DNA (HIV DNA (−) and HIVE-DNA (−)) (* p ≤ 0.005 compared to uninfected conditions and # p ≤ 0.005 compared to HIV DNA (+) conditions). Bar: 100 µm.

Article Snippet: The currently available antibodies are α-HIV p24 (Genetex, GTX40774, Irvine, CA, USA; NIH AIDS repository, HRP-20068, or ARP-4121), α-HIV nef (NIH AIDS repository, ARP-1124, 2949, 709), α-HIV tat (NIH AIDS repository, ARP-4672, or 466), α-HIV integrase (NIH AIDS repository, ARP-7375, or 3514), α-HIV gp120 (NIH AIDS repository, ARP-1476, 2534, 11682, or 11438), or α-HIV vpr (NIH AIDS repository, ARP-11836).

Techniques: Staining, Labeling, Infection, Expressing