Journal: International Journal of Molecular Sciences

Article Title: Nuclear Envelope Alterations in Myotonic Dystrophy Type 1 Patient-Derived Fibroblasts

doi: 10.3390/ijms23010522

Figure Lengend Snippet: Primary antibodies used to detect the multiple proteins analyzed by Western blotting and immunocytochemistry.

Article Snippet: Mouse monoclonal anti-nesprin-2 (MANNES2A 11A3) , Developmental Studies Hybridoma Bank , WB—0.3 μg/mL.

Techniques: Western Blot, Immunocytochemistry

Journal: TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik

Article Title: Mapping the ‘breaker’ element of the gametocidal locus proximal to a block of sub-telomeric heterochromatin on the long arm of chromosome 4S sh of Aegilops sharonensis

doi: 10.1007/s00122-015-2489-x

Figure Lengend Snippet: Fluorescence in situ hybridisation using probe UTV39 ( green ) on DAPI stained chromosomes of mitotic cells from root tip squashes of parental lines Brigand 8/2 ( a ) and Huntsman ( b ), translocation lines 12A5 ( c ), 12H3 ( d ) and deletion line 7C12 type 1 ( e ) and type 2 ( f ). Scale bar represents 10 µm

Article Snippet: The second analysis was carried out using genomic DNA from Huntsman and the Y300 translocation line 12A5 to identify further markers in the distal region of the Ae. sharonensis introgressed segment.

Techniques: Fluorescence, In Situ, Hybridization, Staining, Translocation Assay

Journal: TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik

Article Title: Mapping the ‘breaker’ element of the gametocidal locus proximal to a block of sub-telomeric heterochromatin on the long arm of chromosome 4S sh of Aegilops sharonensis

doi: 10.1007/s00122-015-2489-x

Figure Lengend Snippet: Genotypes of parental lines T. aestivum cv. Huntsman and 4DS·4DL-4S sh L translocation lines Brigand 8/2 and 8/9; translocation lines 12A5, 12H3 and the forty-eight Y300 + two Y350 whole segment translocation (WST) lines; and deletion lines 5D12, 5F8 and 7C12 type 1 using the twenty-two KASP™ markers and KASP UTV39 . ‘ H ’ represents the Huntsman allele, ‘ S ’ the Ae. sharonensis allele, ‘ S/H ’ a duplication of both S and H sequence for that marker, and ‘ del ’ the absence of an amplification product, indicative of a deletion for that marker. The phenotype for each line is represented as ‘gametocidal effect’, where the breaker element is either present ( Gc ) or absent (no Gc ). The heterochromatin block is present in every line except euploid wheat Huntsman. The sub-telomeric region proximal to the heterochromatin block is highlighted , as well as the region in which GcB maps

Article Snippet: The second analysis was carried out using genomic DNA from Huntsman and the Y300 translocation line 12A5 to identify further markers in the distal region of the Ae. sharonensis introgressed segment.

Techniques: Translocation Assay, Sequencing, Marker, Amplification, Blocking Assay

Journal: TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik

Article Title: Mapping the ‘breaker’ element of the gametocidal locus proximal to a block of sub-telomeric heterochromatin on the long arm of chromosome 4S sh of Aegilops sharonensis

doi: 10.1007/s00122-015-2489-x

Figure Lengend Snippet: Diagram representing chromosomal rearrangements caused by gamma irradiation in lines 5D12 (and 5F8—similar segregation pattern but different size deletion), 7C12, 12A5 and 12H3 and their segregation from M 1 to M 2 plants. Lines with no rearrangement in the Ae. sharonensis introgression are also represented and constituted 98 and 99.6 % of the Y300 and Y350 populations, respectively

Article Snippet: The second analysis was carried out using genomic DNA from Huntsman and the Y300 translocation line 12A5 to identify further markers in the distal region of the Ae. sharonensis introgressed segment.

Techniques: Irradiation

Journal: TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik

Article Title: Mapping the ‘breaker’ element of the gametocidal locus proximal to a block of sub-telomeric heterochromatin on the long arm of chromosome 4S sh of Aegilops sharonensis

doi: 10.1007/s00122-015-2489-x

Figure Lengend Snippet: Percentage of viable seeds in spikes of hybrid plants resulting from the backcross of deletion line 7C12 (types 1 and 2 combined) and translocation lines 12A5, 12H3 and the WST lines onto wheat cultivar Huntsman. An average percentage was calculated for each hybrid type. Three batches of plants were sown, except for the WST lines for which only two batches were sown. Percentages were adjusted according to the average spike fertility for self-pollinated parental lines for each batch to take environmental conditions into account

Article Snippet: The second analysis was carried out using genomic DNA from Huntsman and the Y300 translocation line 12A5 to identify further markers in the distal region of the Ae. sharonensis introgressed segment.

Techniques: Translocation Assay

Journal: Nature

Article Title: Mapping the T cell repertoire to a complex gut bacterial community

doi: 10.1038/s41586-023-06431-8

Figure Lengend Snippet: a, Left panel: Uniform manifold approximation and projection (UMAP) plot. These data represent three merged samples: hCom1d-colonized, hCom2d-colonized and germ-free mice. Right panel: Frequency of TCR clonotypes on the UMAP plot. Expanded TCRs (red) represent clonotypes observed in more than five cells, multiple (orange) are clonotypes found in 2–5 cells, and single (light blue) were seen in only one cell. Most of the expanded TCR clonotypes have an expression profile consistent with effector T cells, whereas naïve T cells are rich in unique (that is, non- expanded) TCR clonotypes. b, UMAP plot of intestinal immune cell clusters in each colonization condition. Immune cells were isolated from the large and small intestine from three groups of mice: hCom1d-colonized, hCom2d-colonized, and germ-free. c, Analysis of the frequency of T cell subsets in each group. The percentage of each T cell subset on the UMAP plot was calculated by the Seurat R package; fold changes compared to GF mice are shown. Colonization of germ-free mice with hCom1d and hCom2d increased pTreg, Th17, Fr4 Th and other effector T cells in the large intestine, and Th17 and other effector T cells in the small intestine. d, Analysis of expanded TCR clonotypes in each sample. Each dot represents one TCR clonotype found in multiple T cells (red, shared between effector T cells and pTreg cells; grey, effector T cell; black, pTreg). e, Differentially expressed genes in T cell subsets upon colonization with hCom1d and hCom2d. The FindMarkers function of Seurat was used to find differentially expressed genes. The two-sided non-parametric Wilcoxon rank sum test was used to calculate the adjusted p-value. White bars show mean values. Each dot represents one cell. ***p < 0.001. f, Criteria used to select TCR clonotypes for making hybridoma cells. Red genes: Upregulated by hCom1d and hCom2d colonization. Black genes: T cell subset markers.

Article Snippet: After fixation, cells were stained with combinations of the following primary antibodies in permeabilization buffer for 30 min at room temperature: Helios (22F6, BioLegend, catalogue no. 137214), T-bet (4B10, BioLegend, catalogue no. 644806), Nur77-PE (12.14, eBioscience, catalogue no. 12–5965-82), Foxp3 (FJK-16s, eBioscience, catalogue no. 25–5773-82), Nur77-purified (11C1052, LSBio, catalogue no. LS-C183978100), CD45.1 (A20, eBioscience, catalogue no. 47–0453-82), CD4 (RM4–5, BioLegend, catalogue no. 100559), CD3e (145–2C11, BioLegend, catalogue no. 100351), FR4 (12A5, BD, catalogue no. 744122), IL17A (eBio17B7, eBioscience, catalogue no. 12–7177-81), RORγt (B2D, eBioscience, catalogue no. 17–6981-82 or Q31–378, BD Bioscience, catalogue no. 562894), IFNγ (XMG1.2, BioLegend, catalogue no. 505830), PD1 (29F.1A12, BioLegend, catalogue no. 135208) and IL10 (JES3–9D7, BioLegend, catalogue no. 505010).

Techniques: Expressing, Isolation

Journal: JCI Insight

Article Title: Pregnancy dedifferentiates memory CD8 + T cells into hypofunctional cells with exhaustion-enriched programs

doi: 10.1172/jci.insight.176381

Figure Lengend Snippet: ( A–E ) Flow cytometry panel based on RNA-Seq results confirms phenotypic exhaustion in postpartum T FGS . ( A ) Radar plot presenting normalized expression of phenotypic markers (based on highest and lowest MFI for each marker expressed by T FGS and non-T FGS from all 4 experimental groups) demonstrates enhanced separation between R+P and P T FGS . ( B and C ) UMAP and FlowSOM reveal distinct clusters for R+P and P T FGS driven by phenotypic differences in TOX, EOMES, FR4, and CD73. ( D ) UMAP with heatmap overlays were generated to visualize phenotypic differences between T FGS subsets. ( E ) Expression levels of PD-1, TOX, TIGIT, and SLAMF6 by memory vs. naive T FGS from dams treated with FK506, an inhibitor of NFAT. P values were determined by 1-way ANOVA; * P < 0.05; ** P < 0.01; *** P < 0.001; **** P < 0.0001.

Article Snippet: BD Biosciences: CD90.2-BUV395 (53-2.1), CD4-BUV496 (GK1.5), CD19-BUV661 (1D3), CD11c-BUV661 (N418), F4/80-BUV661 (T45-2342), NK1.1-BUV661 (PK136), TER119-BUV661 (TER-119), CD127-BUV737 (SB/199), CD8-BUV805 (53-6.7), FR4-BV421 (12A5), CTLA4-APCR700 (UC10-4F10-11), NK1.1-eFluor450 (PK136), Ter-119-eFluor450 (Ter-119), Rorγt-BV650 (Q31-378), CD62L-BV605 (MEL-14).

Techniques: Flow Cytometry, RNA Sequencing Assay, Expressing, Marker, Generated