Journal: Journal of immunological methods

Article Title: Multiparameter immunohistochemistry analysis of HIV DNA, RNA and immune checkpoints in lymph node tissue

doi: 10.1016/j.jim.2021.113198

Figure Lengend Snippet: Multiplex detection with HIV RNA and DNA probes and surface markers in LN tissue from PLWH. Representative images of LN tissue sections from a person living with HIV off ART depicting simultaneous detection of HIV DNA (red) and RNAscope (green) in combination with antibodies to CD4 (cyan), FoxP3 (white), CTLA-4 (magenta) and PD-1 (orange). (i) Whole slide scan and (ii) composite image (enlarged section of whole slide scan, white box) depicting colocalization of vDNA+ cell (arrow 1) with CD4+ T cells, PD-1 and CTLA-4 and vDNA+ and vRNA+ cell (arrow 2) with CD4+ T cells, PD-1 and CTLA-4. Representative unmixed composite images of (iii) HIV DNA and RNA and (iv) HIV DNA, RNA and CD4+ T-cells. DAPI was used for nuclear counterstain and micrographs were taken at 10× (whole slide scan) and 20 X magnifications using the Vectra™ multispectral imaging software. Scale bars are 500 μm (whole slide scan) and 20 μm. B) Images were analysed with HALO to quantify the total events (number) of HIV-1 RNA+ and/or DNA+ positive cells and denoted as total cells (DAPI+), CD4neg (CD4− FoxP3−), CD4pos (CD4+), nonTregs (CD4+FoxP3−) and Tregs (CD4+ FoxP3+) in the BCF (grey symbols) or TCZ (blue symbols) from participants off ART (closed symbol) and on ART (open symbol). C) The absolute number of HIV-1 RNA+ and/or DNA+ positive cells on total cells prior-to ART (i) and on ART (ii) and (D) the frequency of infection compared with the total amount of HTV-1 RNA+ and/or DNA+ cells is shown as log 10 for PLWH off ART (i) and on ART (ii) in TCZ and the BCF of LN. Each participant is shown by a different colour (n=7 subjects). Grey shaded area highlights people living with HIV-1 on ART. TCZ: T-cell zone; BCF: B-cell follicle. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: Rabbit monoclonal antibodies to CD4 (Cell Marque, Rocklin, CA) clone 104R-1, 1/100, high pH retrieval), mouse monoclonal antibody to FOXP3 (Abcam, Cambridge, UK), clone IgG1, 1/1000, high pH retrieval), mouse polyclonal antibody to PD-1 (Abcam, IgG1 Nat105, 1/500, low pH retrieval), mouse monoclonal antibody to CTLA-4 (MyBiosource, San Diego, CA) IgG2a/k, 1/100, high pH retrieval) were used.

Techniques: Multiplex Assay, RNAscope, Imaging, Software, Infection

Journal: bioRxiv

Article Title: Type I and Type III Interferons Differentially Shape Antiviral Defense and Epithelial Integrity at the Choroid Plexus

doi: 10.64898/2026.02.10.705109

Figure Lengend Snippet: All cerebral organoids used were 70±5 days old (A-K) . (A) Immunohistochemical staining of cerebral organoids for MAP2. (B) Immunohistochemical staining for SOX2. (C) Immunofluorescence staining for DAPI (gray), transthyretin (TTR; green), and beta tubulin III (TUBB3; red). (D) UMAP of scRNA-seq from three E5-infected and three mock-infected cerebral organoids collected at four days post infection, with annotated cell types including callosal projection neurons (CPNs), corticofugal projection neurons (CFuPNs), inhibitory interneurons (Inh_INs), excitatory neurons of unknown identity (Exc_Ukn), radial glial cells (RGCs), ribosome-high cells (Ribo), choroid plexus epithelium (ChP), intermediate progenitor cells (IPCs), and retinal epithelial cells (Ret_epi). (E) Dot plot showing expression of selected marker genes for each annotated cell type. (F) Viral titers in supernatants from cerebral organoids infected with 200 PFU of E5 virus over a five-day time course, measured by TCID50 assay and shown as log 10 TCID 50 per milliliter; the dotted line indicates the limit of detection, with data shown as mean ± standard deviation and individual organoids represented as points. (G) Proportion of cells assigned to each cluster, shown by individual sample. (H) Dot plot showing detection of E5 viral transcripts across cell clusters. (I) Dot plot showing expression of the neonatal Fc receptor (FCGRT) and β-2 microglobulin (β2M) across clusters. (J) Merged feature plot showing expression of TTR (red) and E5 viral transcripts (blue); purple indicates cells expressing both features. (K) Immunofluorescence staining of cerebral organoid sections at three days post infection for DAPI (gray), viral RNA (green), and TTR (red). Scale bars are 500 µm (A, B), 200 µm (C), and 100 µm (K). For dot plots, values are scaled such that 1 represents the highest normalized expression and 0 represents the lowest normalized expression, and dot size indicates the percentage of cells within each cluster expressing the indicated gene.

Article Snippet: Tissue sections were stained with hematoxylin and eosin (H&E) or processed for immunohistochemistry using antibodies against AQP1 (Abcam, ab15080), MAP2 (Abcam, ab183830), SOX2 (Cell Signaling Technology, 14962), and ZO-1 (Abcam, ab221547) (see Supplemental Table 6).

Techniques: Immunohistochemical staining, Staining, Immunofluorescence, Infection, Expressing, Marker, Virus, TCID50 Assay, Standard Deviation

Journal: bioRxiv

Article Title: Type I and Type III Interferons Differentially Shape Antiviral Defense and Epithelial Integrity at the Choroid Plexus

doi: 10.64898/2026.02.10.705109

Figure Lengend Snippet: (A–K) Tg32 and Tg32 Ifnlr1⁻/⁻ mice were intracranially inoculated with 1,000 PFU of E5 at postnatal day three and monitored through viral clearance (∼17 days post infection). (A) Viral titers in Tg32 and Tg32 Ifnlr1⁻/⁻ mice at 2 and 14 days post infection, measured by TCID50 assay and shown as log 10 TCID50 per milliliter; the dotted line indicates the limit of detection. Data are shown as mean ± standard deviation with individual animals represented as points. (B) Body length of mock- and E5-infected Tg32 and Tg32 Ifnlr1⁻/⁻ mice, shown as box-and-whisker plots with individual animals represented as points; statistical significance was assessed by unpaired t test (**** p < 0.0001; * p = 0.0169). (C) Head-to-body length ratio of mock- and E5-infected Tg32 and Tg32 Ifnlr1⁻/⁻ mice; no significant differences were detected by unpaired t test. (D) Representative H&E-stained whole-brain sections from mock- and E5-infected Tg32 and Tg32 Ifnlr1⁻/⁻ mice; the red asterisk indicates an enlarged ventricle. (E) Quantification of ventricular area in mock- and E5-infected Tg32 and Tg32 Ifnlr1⁻/⁻ mice, shown as mean ± standard deviation with individual animals represented as points. (F) Percentage of mock- and E5-infected Tg32 and Tg32 Ifnlr1⁻/⁻ mice exhibiting ventricular enlargement. (G) Representative H&E-stained sections and serial sections immunohistochemically stained for SOX2 from an E5-infected Tg32 mouse with ventricular enlargement and an E5-infected Tg32 Ifnlr1⁻/⁻ mouse; the boxed region indicates the area shown at higher magnification. (H) Quantification of SOX2-positive cells lining the ventricular wall in mock-and E5-infected Tg32 and Tg32 Ifnlr1⁻/⁻ mice; statistical significance was assessed by unpaired t test (p = 0.0477). (I) Representative RNAscope images showing viral RNA (vRNA; green) and the ependymal marker Foxj1 (red) in Tg32 and Tg32 Ifnlr1⁻/⁻ mice at two days post infection; the dashed box indicates the region shown at higher magnification. (J) Quantification of the percentage of infected ependymal cells, shown as mean ± standard deviation with individual ventricles represented as points; no significant differences were detected by unpaired t test. (K) Representative RNAscope images showing vRNA (green) and Ifit1 (red) in Tg32 and Tg32 Ifnlr1⁻/⁻ mice at two days post infection; the dashed box indicates the region shown at higher magnification. Values in the lower left corner indicate total Ifit1 signal intensity. High-magnification images in (I) and (K) are pseudocolored white and brightness adjusted to enhance visibility. Scale bars: 2.5 mm (D), 1 mm and 50 µm (G), and 100 µm (I, K).

Article Snippet: Tissue sections were stained with hematoxylin and eosin (H&E) or processed for immunohistochemistry using antibodies against AQP1 (Abcam, ab15080), MAP2 (Abcam, ab183830), SOX2 (Cell Signaling Technology, 14962), and ZO-1 (Abcam, ab221547) (see Supplemental Table 6).

Techniques: Infection, TCID50 Assay, Standard Deviation, Whisker Assay, Staining, RNAscope, Marker

Journal: bioRxiv

Article Title: Type I and Type III Interferons Differentially Shape Antiviral Defense and Epithelial Integrity at the Choroid Plexus

doi: 10.64898/2026.02.10.705109

Figure Lengend Snippet: Uninfected control Tg32 and Tg32 Ifnlr1-/- mice were injected with saline at postnatal day 3 and monitored over time. A) Representative images of H&E-stained sections and serial sections IHC-stained for SOX2 from mock Tg32 and Tg32 Ifnlr1-/- mice at 17 days post injection. Scale bars are 1 mm and 50 μm for (A) .

Article Snippet: Tissue sections were stained with hematoxylin and eosin (H&E) or processed for immunohistochemistry using antibodies against AQP1 (Abcam, ab15080), MAP2 (Abcam, ab183830), SOX2 (Cell Signaling Technology, 14962), and ZO-1 (Abcam, ab221547) (see Supplemental Table 6).

Techniques: Control, Injection, Saline, Staining

Journal: Cell Reports Medicine

Article Title: Outer radial glia promotes white matter regeneration after neonatal brain injury

doi: 10.1016/j.xcrm.2025.101986

Figure Lengend Snippet:

Article Snippet: Rabbit polyclonal anti-Sox2 , Cell Signaling , Cat# 2748; RRID: AB_823640.

Techniques: Virus, Plasmid Preparation, Recombinant, RNAscope, Blocking Assay, Staining, Knock-Out, In Situ, Multiplex Assay, Sequencing, Software

Journal: Cell Reports Medicine

Article Title: Outer radial glia promotes white matter regeneration after neonatal brain injury

doi: 10.1016/j.xcrm.2025.101986

Figure Lengend Snippet:

Article Snippet: Mouse monoclonal anti-Sox2 , Santa Cruz , Cat# sc-365823; RRID: AB_10842165.

Techniques: Virus, Plasmid Preparation, Recombinant, RNAscope, Blocking Assay, Staining, Knock-Out, In Situ, Multiplex Assay, Sequencing, Software

Journal: eLife

Article Title: Pituitary stem cells produce paracrine WNT signals to control the expansion of their descendant progenitor cells

doi: 10.7554/eLife.59142

Figure Lengend Snippet:

Article Snippet: Antibody , Anti-SOX2 (Goat Polyclonal) , Immune Systems Ltd , GT15098, RRID: AB_2195800 , IF(1:200).

Techniques: Isolation, Sequencing, RNAscope, Positive Control, Negative Control, Recombinant, Staining, Software

Journal: Cell Reports Medicine

Article Title: Outer radial glia promotes white matter regeneration after neonatal brain injury

doi: 10.1016/j.xcrm.2025.101986

Figure Lengend Snippet:

Article Snippet: For double staining using anti-Sox2 and anti-Ki67 antibodies, sequential immunostaining was performed with AffiniPure Fab Fragment Donkey Anti-mouse IgG (H + L) (Jackson ImmunoResearch Laboratories, Inc.) was used.

Techniques: Virus, Plasmid Preparation, Recombinant, RNAscope, Blocking Assay, Staining, Knock-Out, In Situ, Multiplex Assay, Sequencing, Software