Journal: Scientific Reports

Article Title: Evaluating the origin and virulence of a Helicobacter pylori cagA -positive strain isolated from a non-human primate

doi: 10.1038/s41598-018-34425-4

Figure Lengend Snippet: Impact of H . pylori infection on ES cell-derived gastric organoids. ( a ) HE staining of ES-cell derived gastric organoids infected with H . pylori for 12 hours. Scale bar: 200 µm. ( b ) Immunostaining of gastric organoids infected with H . pylori for 12 hours. “No infection” indicates that the organoid was injected with bacteria-free Brucella Broth. HP , H . pylori ; E-cad, E-cadherin. Scale bar: 10 µm.

Article Snippet: The primary antibodies used for immunostaining are: α-SMA, mouse, Sigma, A5228, 1:100; β-Catenin, rabbit, SantaCruz, sc7199, 1:100; CagA, rabbit, AUSTRAL Biologicals, HPP5003-9, 1:100; E-cadherin, mouse, BD Biosciences, 610182, 1:100; E-cadherin, goat, R&D Systems, AF648, 1:100; Gastrin, mouse, Santa Cruz, sc28302, 1:100; H . pylori , rabbit, Abcam, ab80519, 1:100; Muc5AC, mouse, Abcam, ab3649, 1:100; Muc6, mouse, Abcam, Ab49462, 1:100; Nanog, rabbit, Abcam, ab21624, 1:500; Oct3/4, mouse, Santa Cruz, sc5279, 1:500; Vimentin, goat, Santa Cruz, sc7557, 1:200; ZO-1, rabbit, Invitrogen, 617300, 1:100.

Techniques: Infection, Derivative Assay, Staining, Immunostaining, Injection, Bacteria

Journal: Arteriosclerosis, Thrombosis, and Vascular Biology

Article Title: Derivation of Endothelial Cells From Human Embryonic Stem Cells by Directed Differentiation

doi: 10.1161/atvbaha.110.204800

Figure Lengend Snippet: Figure 1. Taqman low-density array (TLDA) analysis of mRNA levels in pluri- potent hESCs and cells subjected to directed differentiation to vascular endo- thelial cells. hESCs were either main- tained under pluripotency conditions or under feeder- and serum-free monolayer-directed differentiation to vas- cular endothelial cells over 21 days. TLDA analysis was performed on extracted mRNA at different time points. A, Markers shown: pluripotency- associated mRNAs: Nanog, Oct 4, and Sox 2, with significant reduction in expression observed with progression of differentiation. B, early mesoderm mark- ers (brachyury, NKX2.5, Mesp1, and Mixl1) vascular endothelial cells (FLT-1, KDR, CD31, VE-cadherin, and CD34). Data are given as the meanSEM. * P0.05, **P0.01, and ***P0.001 vs the time-matched pluripotent sample. Supplemental Table I provides the data for complete TLDA analysis.

Article Snippet: Cells were incubated at 4°C overnight with the following antibodies: mouse IgG monoclonal anti–human OCT4 (1:200; Santa Cruz Biotechnology, Inc, Heidelberg, Germany); mouse IgG monoclonal anti–human Nanog (1:200; Abcam plc, Cambridge, England); mouse IgG monoclonal anti–human CD31 (1:100; Dako UK Ltd, Ely, England); and goat IgG polyclonal VE-cadherin (1:100; R&D Systems).

Techniques: TLDA Assay, Expressing

Journal: Arteriosclerosis, Thrombosis, and Vascular Biology

Article Title: Derivation of Endothelial Cells From Human Embryonic Stem Cells by Directed Differentiation

doi: 10.1161/atvbaha.110.204800

Figure Lengend Snippet: Figure 2. Expression of endothelial and angiogenesis-related proteins. A, FACS analysis and immunocytofluorescent staining of endothelial marker proteins. Increasing positive expression of CD31 (FL1 and far panel) and VE-cadherin (FL2 and middle panel) observed in a time-dependent manner to 21-day differen- tiation, using 4,6-diamidino-2-phenylindole (DAPI) (nuclear counterstain [blue]) (scale bar indicates 20 m). Representative scans and images from 3 independent experiments. B, Mem- brane scans of angiogenic markers in differentiated hESC-ECs (days 0, 10, 14, and 21 of differentiation). Array images are from 10-minute exposure to x-ray film. Supplemental Figure III pro- vides the corresponding densometric analysis.

Article Snippet: Cells were incubated at 4°C overnight with the following antibodies: mouse IgG monoclonal anti–human OCT4 (1:200; Santa Cruz Biotechnology, Inc, Heidelberg, Germany); mouse IgG monoclonal anti–human Nanog (1:200; Abcam plc, Cambridge, England); mouse IgG monoclonal anti–human CD31 (1:100; Dako UK Ltd, Ely, England); and goat IgG polyclonal VE-cadherin (1:100; R&D Systems).

Techniques: Expressing, Staining, Marker

Journal: Journal of Cell Science

Article Title: The gap junction protein connexin 43 controls multiple aspects of cranial neural crest cell development

doi: 10.1242/jcs.235440

Figure Lengend Snippet: Cx43 depletion decreases the number of premigratory neural crest cells in the absence of any changes in cell proliferation or cell death. Representative transverse sections taken through the midbrain and hindbrain of HH8+ to HH9 embryos after unilateral electroporation of the neural tube at HH7+ to HH8− (2ss–3ss) with either the control morpholino (MM) or Cx43 MO and immunostaining for various neural crest cell markers. In MM-treated embryos (A–A″,C–C″,E–E″,G–G″,I–I″,K–K″,M–M″), there is no decrease in the level of Cx43 in the neural tube (A′) and no change in any of the premigratory neural crest cells as identified by Pax7 (C′), Snail2 (E′), Sox10 (G′). Similarly, there are no changes in N-cadherin (I–I″), a marker of neural tube cells, cell proliferation [pHH3 (K–K″)]; or cell death [TUNEL (M–M″)]. In Cx43 MO-treated embryos (B–B″,D–D″,F–F″,H–H″,J–J″,L–L″,N–N″), however, there is obvious knockdown of Cx43 in the neural tube (B′, arrow) and also a reduction in the premigratory neural crest cell population observed after Pax7 (D′, arrow), Snail2 (F′, arrow) and Sox10 (H′, arrow) immunostaining. Interestingly, N-cadherin (J–J″) is not affected. Cx43 MO-mediated loss of Cx43 also does not seem to alter levels of either cell proliferation (L–L″) or cell death (N–N″). Additionally, in HH9 embryos, a small number of MO-positive neural crest cells begin to emerge from the neural tube (D′,F′,H′, arrowheads; neural tube indicated by dashed lines). Scale bars: 20 µm (A–K″,M–N″); 50 µm (L–L″).

Article Snippet: The following day, after washing four times for 30 min with 1× PBST, sections were incubated with appropriate secondary antibodies and incubated for 2–3 h at room temperature or overnight at 4°C [goat anti-rabbit IgG 488 or 647; Invitrogen, A11034 and Jackson ImmunoResearch, PA, USA; 111-605-003, respectively (for Cx43, Sox10, pHH3 and Snail2); goat anti-mouse IgG 1 647; Invitrogen, A21240 (for Pax7 and E-cadherin); goat anti-rat IgG; Life Technologies, MD; A21247 (for N-cadherin)].

Techniques: Electroporation, Control, Immunostaining, Marker, TUNEL Assay, Knockdown

Journal: Journal of Cell Science

Article Title: The gap junction protein connexin 43 controls multiple aspects of cranial neural crest cell development

doi: 10.1242/jcs.235440

Figure Lengend Snippet: Graphical representation of analyzed premigratory neural crest cell data after control or Cx43 MO treatment. Box and whisker plots showing the third quartile (Q3), median and first quartile (Q1) range of the data as well as data outliers. Whiskers represent minimum and maximum values. (A–C) Graphs depicting the number of premigratory, migratory and total neural crest cells (NCCs) electroporated with either the control MM or Cx43 MO normalized to the un-electroporated contralateral side for the analyzed neural crest cell markers Pax7 (A), Snail2 (B) and Sox10 (C). Asterisks denote statistically significant differences determined with un-paired Mann–Whitney (Wilcoxon) test that employed a Bonferroni correction [A, Cx43 MO premigratory NCCs (P=8.64×10−7); B, Cx43 MO premigratory NCCs (P=6.41×10−9), Cx43 MO migratory NCCs (P=0.0029), Cx43 MO Total NCCs (P=9.64×10−9); C, Cx43 MO Premigratory NCCs (P=0.0001), Cx43 MO Total NCCs (P=2.76×10−6)]. (D) Graph depicting the fluorescence intensity of N-cadherin in premigratory neural crest cells (NCCs) and the neural tube (NT) of control MM- (N=4) or Cx43 MO- (N=5) electroporated cells compared to the contralateral side.

Article Snippet: The following day, after washing four times for 30 min with 1× PBST, sections were incubated with appropriate secondary antibodies and incubated for 2–3 h at room temperature or overnight at 4°C [goat anti-rabbit IgG 488 or 647; Invitrogen, A11034 and Jackson ImmunoResearch, PA, USA; 111-605-003, respectively (for Cx43, Sox10, pHH3 and Snail2); goat anti-mouse IgG 1 647; Invitrogen, A21240 (for Pax7 and E-cadherin); goat anti-rat IgG; Life Technologies, MD; A21247 (for N-cadherin)].

Techniques: Control, Whisker Assay, MANN-WHITNEY, Fluorescence

Journal: Breast Cancer Research : BCR

Article Title: Direct repression of MYB by ZEB1 suppresses proliferation and epithelial gene expression during epithelial-to-mesenchymal transition of breast cancer cells

doi: 10.1186/bcr3580

Figure Lengend Snippet: Antibodies used for IF, ICC, and IHC

Article Snippet: E-cadherin , Rabbit , Abcam, Cambridge, UK (cat. no. ab40772).

Techniques: Synthesized, Plasmid Preparation

Journal: Breast Cancer Research : BCR

Article Title: Direct repression of MYB by ZEB1 suppresses proliferation and epithelial gene expression during epithelial-to-mesenchymal transition of breast cancer cells

doi: 10.1186/bcr3580

Figure Lengend Snippet: Primers used in QRT-PCR

Article Snippet: E-cadherin , Rabbit , Abcam, Cambridge, UK (cat. no. ab40772).

Techniques: Sequencing

Journal: Breast Cancer Research : BCR

Article Title: Direct repression of MYB by ZEB1 suppresses proliferation and epithelial gene expression during epithelial-to-mesenchymal transition of breast cancer cells

doi: 10.1186/bcr3580

Figure Lengend Snippet: Definition of gene symbols and names used in current study

Article Snippet: E-cadherin , Rabbit , Abcam, Cambridge, UK (cat. no. ab40772).

Techniques: Binding Assay

Journal: Breast Cancer Research : BCR

Article Title: Direct repression of MYB by ZEB1 suppresses proliferation and epithelial gene expression during epithelial-to-mesenchymal transition of breast cancer cells

doi: 10.1186/bcr3580

Figure Lengend Snippet: ZEB1sh-ET cells are more epithelial, express higher MYB, and are more proliferative than SCRsh-ET controls. (A) (i) Western blotting for ZEB1 and CDH1 in PMC42-ET cells transfected with shRNA variants 1 to 4; (ii) bar graph of band intensity of the Western blot shown in (i) . (iii) Expression (MT-PCR) of EMT-related genes, ZEB1sh-ET relative to SCRsh-ET; fold expression shown. Data shown are the average of four independent biologic replicates; Student paired t test was used to determine significance (*), set at P < 0.05; error bars represent SEM. The expression of other EMT-related genes not shown in this figure is shown in Additional file , part A. (B) ZEB1sh-ET express higher MYB protein and mRNA (Additional file D) and are more proliferative (C) . (i) Percentage of ZEB1sh-ET cells in S phase as determined by BrdU staining after release from mitotic arrest with nocodazole; (ii) Growth rate as shown by the SRB growth assay. Results shown ( C , part i) are from three independent experiments; error bars represent SEM, and the repeated-measures two-way ANOVA statistical test was used to determine significance, * P < 0.05. Result shown in (ii) is one representative SRB assay, of a total of three, all of which were found to be statistically significant by the repeated-measures two-way ANOVA statistical test. Further replicates are found in Additional file B. (D) ZEB1 knockdown in MDA-MB-231 breast cancer cells: (i) characterization of ZEB1 knockdown (shRNA) MDA-MB-231 cells by QRT-PCR; (ii) immunocytochemistry showing that ZEB1 knockdown results in reexpression of E-cadherin at the cell membrane, and MYB nuclear reexpression; magnification, 400×, scale bar, 50 μm.

Article Snippet: E-cadherin , Rabbit , Abcam, Cambridge, UK (cat. no. ab40772).

Techniques: Western Blot, Transfection, shRNA, Expressing, BrdU Staining, Growth Assay, Sulforhodamine B Assay, Quantitative RT-PCR, Immunocytochemistry