Journal: Molecular cell

Article Title: Sequential Activation of Guide RNAs to Enable Successive CRISPR-Cas9 Activities

doi: 10.1016/j.molcel.2020.12.003

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Fluidigm Access Array Barcodes , Fluidigm , 101–0744.

Techniques: Recombinant, Knock-Out, DNA Extraction, Amplification, Sequencing, Plasmid Preparation, Software

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: Sequence locally, think globally: The Darwin Tree of Life Project

doi: 10.1073/pnas.2115642118

Figure Lengend Snippet: The partners in the Darwin Tree of Life Project

Article Snippet: Marine Biological Association , Sample collection (marine and littoral species); DNA barcoding; Analysis , Plymouth, UK , Nova Mieszkowska Willie Wilson.

Techniques: Sequencing

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: Sequence locally, think globally: The Darwin Tree of Life Project

doi: 10.1073/pnas.2115642118

Figure Lengend Snippet: Sequencing eukaryotic life at scale. The DToL partners have developed a cohesive end-to-end process to take organisms from the field through to publication of high-quality assembled and annotated genomes in the public domain. By collating specimen metadata and tracking information through identification, DNA barcoding, extraction, sequencing, assembly, curation, annotation, and submission, the process assures that genomes are published with rich, informative, and accurate descriptors.

Article Snippet: Marine Biological Association , Sample collection (marine and littoral species); DNA barcoding; Analysis , Plymouth, UK , Nova Mieszkowska Willie Wilson.

Techniques: Sequencing, Extraction

Journal: Journal of immunology (Baltimore, Md. : 1950)

Article Title: Early KLRG1 + but not CD57 + CD8 + T cells in Primary CMV Infection Predict Effector Function and Viral Control

doi: 10.4049/jimmunol.1900399

Figure Lengend Snippet: (A) Representative flow cytometric plots show the expression of KLRG1+ (upper panel) and CD57+ (lower panel) in total CD8+ T cells from D+R-patient during Pre-CMV and Acute CMV infection. Total CD8+ T cells were gated on live CD3+ T cells after excluding CD14+, CD16+, and CD19+ cells. (B) Cumulative data showing distributions of total KLRG1+CD8+ (left graph) and CD57+CD8+ (right graph) T cells from patients during Pre-CMV and Acute CMV infection (n=8). Statistical analysis was performed using Wilcoxon matched pair signed rank test. Also Mann-Whitney U test was performed with a two-sided and p value of less than 0.05 considered statistically significant. (C) Cumulative data shows distributions of total CD3+CD8+ T cells KLRG1+ and CD57+ for (n=23) patients during Acute CMV) infection. (D) Representative flow cytometric plots show expression of CD57+ and CD27+ on CD8+ T cells during Pre-CMV (left plot) and Acute CMV (right plot). (E) Representative flow cytometric plots showing co-expression of CD57+ and CD27+ (upper panels) or KLRG1+ and CD57+ (lower panels) on the gated population of total CD3+CD8+ T cells ex vivo from D+R-patient during Acute CMV (left plots) and Chronic CMV (right plots) infection. (F) Cumulative data graph showing frequency of total CD8+ T cells expressing phenotypic markers as labeled. PBMCs from acute CMV (orange circles) and chronic CMV (green squares) (n=14 dextramer responses) D+R-patients were stained ex vivo and analyzed by flow cytometry. (G) Representative plots show CD57+ and KLRG1+ expression on MHC class I dextramer cells and co-expression of CD57+, and CD27+ or KLRG1+ on the gated population dextramer+ cells CD3+CD8+ T cells. (H) Cumulative data graph shows proportions of total CD8+ T cells proportions of MHC class I dextramer + cells from acute CMV (n=14 dextramer responses) (orange circles) and chronic CMV (n=14 dextramer responses) (green squares) infection, expressing distinct phenotypic markers are shown.

Article Snippet: Immediately after incubation, cells were washed with the complete medium and stained with the MHC class I dextramer (Immudex, Copenhagen, Denmark) against known immunodominant CMV epitopes ( Supp.Table I ) at 25°C for 25 min.

Techniques: Expressing, Infection, MANN-WHITNEY, Ex Vivo, Labeling, Staining, Flow Cytometry

Journal: Journal of immunology (Baltimore, Md. : 1950)

Article Title: Early KLRG1 + but not CD57 + CD8 + T cells in Primary CMV Infection Predict Effector Function and Viral Control

doi: 10.4049/jimmunol.1900399

Figure Lengend Snippet: (A) Representative flow cytometry plots from the Acute CMV showing phenotype and CMV pp65-specific proliferation in response to pp65 pooled peptides (lower panels) or medium alone (negative control) (upper panels), KLRG1+ (middle panels) and T-bet+ (right panels). (B) Representative flow plot from (A) showing KLRG1+/− and CD57+/− phenotypes in CD8+CFSElo subset (right panel). (C) Cumulative data showing CMV pp65-specific proliferation at 6 days for CD8+ T cells with respect to CD57+ (orange bars), CD57− (green bars) of CFSElo events (n=7). Bars represent median values of CFSElo events for CD57+KLRG1−, CD57+KLRG1+, CD57−KLRG1+ and CD57−KLRG1− respectively. Statistical analysis performed using Mann-Whitney U test with a two-sided and p value of less than 0.05 considered statistically significant. (D) Graphs showing frequencies of CMV-dextramer CD8+ T cells, and KLRG1+/− CD57+/− subsets in three patients during Acute-CMV, Contraction phase, and Chronic CMV infection. Samples for the contraction phase were obtained 1–2 months following clearance of acute viremia and Chronic CMV at least a year post-Acute CMV. (E) Representative flow cytometry plots of CMV dextramer proliferation in response to cognate peptide re-stimulation or medium measured at 6 days using CFSE dilution. Shown are responses during Acute-CMV and Chronic CMV and phenotypic markers CD57+ (upper left), CD27+ (upper right), KLRG1+ (lower left) and T-bet+ (lower right) plots. (F) Cumulative data from (E) showing respective phenotypes of CFSElo events in dextramer+ cells. during Acute-CMV (orange bars) and Chronic CMV (green bars). Bars represent median values of CFSElo frequencies. Statistical analysis performed using Mann-Whitney U test with a two-sided and p value of less than 0.05 considered statistically significant. NS=non-significant.

Article Snippet: Immediately after incubation, cells were washed with the complete medium and stained with the MHC class I dextramer (Immudex, Copenhagen, Denmark) against known immunodominant CMV epitopes ( Supp.Table I ) at 25°C for 25 min.

Techniques: Flow Cytometry, Negative Control, MANN-WHITNEY, Infection

Journal: Journal of immunology (Baltimore, Md. : 1950)

Article Title: Early KLRG1 + but not CD57 + CD8 + T cells in Primary CMV Infection Predict Effector Function and Viral Control

doi: 10.4049/jimmunol.1900399

Figure Lengend Snippet: (A) Cumulative distributions of KLRG1 frequency and additional six phenotypic markers expressed on the total CD8+ T cell among controllers (blue circles) (n=7) and the relapsers (red squares) (n=8) are shown (mean ± SEM). Only the KLRG1 expression exhibits the significant difference (p<0.002) between controllers and relapser as indicated. (B) Cumulative data shows frequency of KLRG1+, T-bet+, or CD57+ total CD8+ T cells among controllers (blue columns) (n=13) and relapsers (red columns) (n=10). (C) Cumulative data shows Tbet+CD8+ frequencies and (D) KLRG1+CD8+effector functions (IFN-γ+, TNF-α+, CD107a+) in controllers (blue columns) and relapsers (red columns). (E) Representative flow cytometric plot shows KLRG1+ expression on CMV-specific dextramer+CD8+ T cells. Numbers show proportion of KLRG1+ subset within the gated dextramer+CD8+ T cell in a controller (left panel) versus a relapser (right panel). (F) Cumulative distributions of KLRG1+ frequency and additional six phenotypic markers expressed on the Dextramer+CD8+ T cell among controllers (blue circles) (n=8 dextramer responses assed) and the relapsers (red squares) (n=7 dextramer responses assed) are shown (mean ± SEM). Statistical analysis performed using Mann-Whitney U test with a two-sided and p value of less than 0.05 considered statistically significant between the controller and the relapser throughout the course of statistical analyses. NS=non-significant.

Article Snippet: Immediately after incubation, cells were washed with the complete medium and stained with the MHC class I dextramer (Immudex, Copenhagen, Denmark) against known immunodominant CMV epitopes ( Supp.Table I ) at 25°C for 25 min.

Techniques: Expressing, MANN-WHITNEY

Journal: Journal of immunology (Baltimore, Md. : 1950)

Article Title: Early KLRG1 + but not CD57 + CD8 + T cells in Primary CMV Infection Predict Effector Function and Viral Control

doi: 10.4049/jimmunol.1900399

Figure Lengend Snippet: (A) Representative flow cytometry plots of CMV dextramer+CD8+ Tcells BAL cells (upper panels) and Blood (lower panels) during acute/primary CMV infection (n=6) for a panel of six markers: KLRG1+, T-bet+, CD27+, CD103+, CD69+ and CD57+ plots. (B) A cumulative data of summary of phenotypic frequency analysis of (A) showing BAL cells (orange bars) and PBMC (green bars). Statistical analysis performed using Mann-Whitney U test with a two-sided and p value of less than 0.05 considered statistically significant between the BAL and Blood compartments. NS=non-significant.

Article Snippet: Immediately after incubation, cells were washed with the complete medium and stained with the MHC class I dextramer (Immudex, Copenhagen, Denmark) against known immunodominant CMV epitopes ( Supp.Table I ) at 25°C for 25 min.

Techniques: Flow Cytometry, Infection, MANN-WHITNEY

Journal: Cell Reports Medicine

Article Title: Circulating cancer-specific CD8 T cell frequency is associated with response to PD-1 blockade in Merkel cell carcinoma

doi: 10.1016/j.xcrm.2024.101412

Figure Lengend Snippet:

Article Snippet: DNA barcode- and fluorophore-labeled HLA-I dextramers were prepared by Immudex.

Techniques: Recombinant, Staining, Multiplex Assay, Software