Journal: mBio

Article Title: Citrobacter rodentium Infection Induces Persistent Molecular Changes and Interferon Gamma-Dependent Major Histocompatibility Complex Class II Expression in the Colonic Epithelium

doi: 10.1128/mbio.03233-21

Figure Lengend Snippet: Changes to the cellular composition of the crypt. (A, C, G, and K) Temporal measurements of CCH (A), the crypt PCNA + zone (C), goblet cell density (G), and CHGB-positive cell density (K). Each point represents the mean for an individual mouse. *, P < 0.0.5; ****, P < 0.0001 (by one-way ANOVA with Dunnett’s posttest for multiple comparisons to the control group [uninfected {UI} mice]). (B and L) Representative distal colonic sections showing temporal changes in the crypt PCNA + zone (B) and CHGB-positive cell density (L). Bars = 50 μm (B) or 100 μm (L). (D and F) Average Log 2 FC values of selected significantly changed (FDR of <0.05 by one-way ANOVA) proteins involved in cell proliferation and cIEC metabolic changes (D) and cIEC markers (F). DSC, deep secretory cell. In panel F, “−ve” indicates that proteins are negative regulators of terminal differentiation into the specified cell type. (E, I, and J) qRT-PCR of the indicated mRNAs isolated from cIECs. Each point represents an individual mouse. *, P < 0.05; **, P < 0.01 (by one-way ANOVA with Dunnett’s posttest for multiple comparisons to the control group [uninfected mice]). For panels G and J, square data points were identified as outliers and not included in the statistical analysis. (H) z scores of selected protein abundances across the entire C. rodentium infection time course (4 to 48 DPI). Means ± standard errors of the means (SEM) are shown.

Article Snippet: The following primary antibodies were used: rabbit polyclonal anti‐ C. rodentium antibody (1:50) (Statens Serum Institute, Copenhagen, Denmark), mouse anti-PCNA antibody (1:500) (catalog number ab29; Abcam), and rabbit anti-CHGB antibody (1:50) (catalog number 14968-1-AP; Proteintech).

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

Journal: Contemporary Oncology

Article Title: Histological characterisation and prognostic evaluation of 62 gastric neuroendocrine carcinomas

doi: 10.5114/wo.2016.61852

Figure Lengend Snippet: List of antibodies used in immunohistochemistry

Article Snippet: Monoclonal, rabbit anti-human Chromogranin A (Clone: SP12) , 1: 100 , Thermo Fisher Scientific, Fremont, CA, USA.

Techniques:

Journal: bioRxiv

Article Title: Chromatin Remodelling in Damaged Intestinal Crypts Orchestrates Redundant TGFβ and Hippo Signalling to Drive Regeneration

doi: 10.1101/2024.08.30.610472

Figure Lengend Snippet: a) Representative images of Clu-tdTom;Lgr5-GFP organoids treated with TGFβ1 (200 pM) and 4-OHT (schematic), with Paneth, Enteroendocrine and Goblet cells identified by staining for Lyz1, ChgA, and Muc2 (red), respectively. Scale bars, 10 µm (Crypt view) and 50 µm (complete organoid). Red arrows indicate cells of interest. b) Schematic (top) and representative IF images (bottom) of control and 5-FU-treated (20 µM; 24 h) Lgr5-GFP expressing organoids. Scale bar, 10 µm (Crypts), 50 µm (whole organoids). c) Schematic (top) and brightfield images (bottom) showing organoid morphology following a 24-hour pulse of 5-FU (20 µM) and after 2 successive passages. Scale bar, 10 µm. d) Expression of ISC signature genes in organoids treated with 5-FU (20 µM; 48 h) quantified by RT-qPCR and normalized to Ywhaz expression. Bars indicate mean ± S.E.M of three independent experiments performed in triplicate. Unpaired, two-tailed t-test; ***p<0.001 e) Expression of revSC signature genes in organoids treated with 5-FU (20 µM; 48 h), quantified by RT-qPCR, and normalized to Ywhaz expression. Bars indicate mean ± S.E.M of three independent experiments performed in triplicate. Unpaired, two-tailed t-test; ***p<0.001 f) Clu-CreERT2;lsl-tdTom;Lgr5-GFP organoids treated with 5-FU (20 µM) and 4-OHT (top) as indicated (Schematic), and lineage-traced offspring visualized after damage, as indicated. Scale bars, 10 µm.

Article Snippet: The following primary antibodies were used: rabbit anti-lysozyme (Dako, #2230, 1:1,000), rabbit anti-Muc2 (Santa Cruz, #sc-15334, 1:300), rabbit anti-Olfm4 (Cell Signaling, #66479, 1:300), rabbit anti-ChgA (Abcam, #ab85554, 1:250), goat anti-GFP (Abcam, #ab5450, 1:1000), chicken anti-GFP (Abcam, #ab13970; 1:1000) Rabbit anti-ki67(Abcam, #ab15580), Anti-CD326 (Biolegend, #118205), Rabbit anti-Smad2/3 (Cell Signaling, #8685S, 1:300), Rabbit anti-pSmad2 (Cell signaling, #18338, 1:200), Rabbit anti-Smad7 (Abcam, #ab216428; 1:100).

Techniques: Staining, Control, Expressing, Quantitative RT-PCR, Two Tailed Test