Journal: Cell Reports

Article Title: A High-Resolution Method for Quantitative Molecular Analysis of Functionally Characterized Individual Synapses

doi: 10.1016/j.celrep.2020.107968

Figure Lengend Snippet: Multiplexed Immunolabeling in Epoxy-Resin-Embedded Tissue after Etching and Antigen Retrieval (A) Multiple immunolabeling of an epoxy-resin-embedded section of the hippocampal CA1 area of an adult rat. Four rounds of triple labeling were performed using primary Abs raised in 3 different species (top row: mouse monoclonal IgG1; middle: rabbit polyclonal; bottom: Guinea pig polyclonal Abs). Reactions within one round were visualized with Alexa488-, Cy3-, and Cy5-coupled sAbs (all reactions are pseudocolored and shown in cyan). Boxed areas are shown at higher magnifications in panels (B 1 and B 2 ). (B 1 ) Immunolabeling for PV, Kv2.1, VGAT, and vGluT1 are present in different, nonoverlapping subcellular compartments. The vGluT1-positive terminals are only present around the PV+ IN soma but not the neighboring PC somata that are outlined by the Kv2.1 labeling. VGAT-positive terminals (cyan) surround the somata of the IN and the PCs. (B 2 ) Immunolabeling of PV, PSD95, CB1, and neuroligin-2 (NL-2). (C) Confocal images of a 200-nm-thick section of the mouse hilar region labeled for PSD95 (1 st and 3 rd rounds) and for VGAT (2 nd and 4 th rounds; both Guinea pig primary Abs). Circular ROIs were placed over PSD95-labeled glutamatergic synapses (yellow) and over VGAT-positive axons (cyan). The nonspecific background labeling (white ROI) was measured over the unlabeled neuropil. (D) Mean normalized integrated fluorescence values are plotted for 4 labeling rounds. Open symbols represent reactions from 3 mice, and the filled symbols are mean ± SD. The fluorescence in the inhibitory axons is 2.6% ± 2.4% in the 1 st and 4.6% ± 2.5% in the 3 rd rounds, similar to that measured over the excitatory synapses in the 2 nd (7.2% ± 1.1%) and 4 th (5.7% ± 2.9%) rounds. A total of 21–28 ROIs were analyzed in each condition. str. rad., stratum radiatum; str. pyr., stratum pyramidale.

Article Snippet: Rabbit polyclonal anti-N-Cadherin , Synaptic systems , Cat#363 003; RRID: AB_2620123.

Techniques: Immunolabeling, Labeling, Fluorescence

Journal: Cell Reports

Article Title: A High-Resolution Method for Quantitative Molecular Analysis of Functionally Characterized Individual Synapses

doi: 10.1016/j.celrep.2020.107968

Figure Lengend Snippet:

Article Snippet: Rabbit polyclonal anti-N-Cadherin , Synaptic systems , Cat#363 003; RRID: AB_2620123.

Techniques: Virus, Plasmid Preparation, Recombinant, Software, Microscopy

Journal: iScience

Article Title: YTHDF2-mediated circYAP1 drives immune escape and cancer progression through activating YAP1/TCF4-PD-L1 axis

doi: 10.1016/j.isci.2023.108779

Figure Lengend Snippet: The immune evasion effect of circYAP1 is dependent on PD-L1 (A) mRNA expression levels of PD-L1 were determined in HCT116 and SW480 cells after transfected with circYAP1 siRNA and circYAP1 overexpressed plasmids by RT-qPCR (n = 4 each group was made in quadruplicate, ANOVA test in right and unpaired t test in left). (B) Protein levels of PD-L1, E-cadherin, and N-cadherin were determined in HCT116 and SW480 cells after transfected with circYAP1 siRNA and circYAP1 overexpressed plasmids by western blot (C) RT-qPCR analysis of IFN-γ, TNF-α, IL-4, and Granyzm B in CD8 + T cells cocultured with circYAP1-overexpressed and si-PD-L1 SW480 cells (n = 4 each group was made in quadruplicate, ANOVA test). (D) The analysis of CRC patients OS of PD-L1 using the data of GSE39582 by BEST application ( https://rookieutopia.com/ ). (E) The correlation analysis between anti-PD-L1 treatment response and PD-L1 level by BEST application ( https://rookieutopia.com/ ). (F) The OS of PD-L1 in CRC patient treated with anti-PD1/PD-L1 by BEST application ( https://rookieutopia.com/ ). Data are expressed as mean ± standard deviation, ns p ≥ 0.05, ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001.

Article Snippet: Anti -N Cadherin Rabbit pAb , Servicebio , Cat# GB111009-100; RRID: AB_3068619.

Techniques: Expressing, Transfection, Quantitative RT-PCR, Western Blot, Standard Deviation

Journal: iScience

Article Title: YTHDF2-mediated circYAP1 drives immune escape and cancer progression through activating YAP1/TCF4-PD-L1 axis

doi: 10.1016/j.isci.2023.108779

Figure Lengend Snippet: CircYAP1 prevents YAP1 protein phosphorylation to drive PD-L1 upregulation (A) FISH-IF assay was performed to detected the colocalization of circYAP1 and YAP1 protein in CRC cells (Scale bar: 10 μm). (B) YAP1-RIP analysis of the directly binding between circYAP1 and YAP1 protein in CRC cells (n = 4 each group was made in quadruplicate, unpaired t test). (C) CircRNA pull-down assay was performed by biotin-labeled circYAP1 probes in CRC transfected circYAP1 overexpression plasmids. (D and E) Western blot and IF assays (Scale bar:10 μm) to verify changes in the proportion of YAP1 and p-YAP1 in the cytoplasm and nucleus of CRC cells after transfection with the circYAP1 overexpression plasmid. (F) RIP analysis of the circYAP1 and YAP1(Ser 127 mut) protein in CRC cells (n = 4 each group was made in quadruplicate, unpaired t test) (G and H) mRNA expression levels of PD-L1 and protein level of PD-L1, E-cadherin, and N-cadherin were determined in CRC cells after transfected with circYAP1 plasmids and si-YAP1 by RT-qPCR (n = 4 each group was made in quadruplicate, ANOVA test) and western blot. (I‒L) Proliferation, migration, and invasion abilities of HCT116 and SW480 cells were determined after transfection with circYAP1 plasmids and si-YAP1 by EDU (Scale bar: 50 μm, n = 3 each group was made in triplicate, ANOVA test), CCK8(n = 5 each group was made in quintuplicate, ANOVA test), and Transwell assays (Scale bar: 100 μm, n = 3 each group was made in triplicate, ANOVA test). Data are expressed as mean ± standard deviation, ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001, ∗∗∗∗p < 0.0001.

Article Snippet: Anti -N Cadherin Rabbit pAb , Servicebio , Cat# GB111009-100; RRID: AB_3068619.

Techniques: Phospho-proteomics, FISH/IF assay, Binding Assay, Pull Down Assay, Labeling, Transfection, Over Expression, Western Blot, Plasmid Preparation, Expressing, Quantitative RT-PCR, Migration, Standard Deviation

Journal: iScience

Article Title: YTHDF2-mediated circYAP1 drives immune escape and cancer progression through activating YAP1/TCF4-PD-L1 axis

doi: 10.1016/j.isci.2023.108779

Figure Lengend Snippet: circYAP1 promotes lung metastasis in vivo (A) Schematic diagram of the construction of a lung metastasis model in nude mice. (B) The number of lung metastasis nodules in lv-circYAP1 and lv-nc group nude mice (n = 3 mice per group, unpaired t test). (C) HE staining of lung metastatic nodules (Scale bar: 200 μm) (D, E, F, G, H) Relative protein levels of YAP1, TCF4, PD-L1, E-cadherin, and N-cadherin were detected in lung metastatic nodules by ISH (Scale bar: 200 μm). Data are expressed as mean ± standard deviation, ∗p < 0.05.

Article Snippet: Anti -N Cadherin Rabbit pAb , Servicebio , Cat# GB111009-100; RRID: AB_3068619.

Techniques: In Vivo, Staining, Standard Deviation

Journal: iScience

Article Title: YTHDF2-mediated circYAP1 drives immune escape and cancer progression through activating YAP1/TCF4-PD-L1 axis

doi: 10.1016/j.isci.2023.108779

Figure Lengend Snippet:

Article Snippet: Anti -N Cadherin Rabbit pAb , Servicebio , Cat# GB111009-100; RRID: AB_3068619.

Techniques: Recombinant, Virus, CCK-8 Assay, Transfection, SYBR Green Assay, In Vitro, In Situ, Hybridization, Cell Isolation, Chromatin Immunoprecipitation, Immunoprecipitation, Isolation, Negative Control, Plasmid Preparation, Software, Modification

Journal: Journal of Oral Biology and Craniofacial Research

Article Title: Cadherin switching in oral squamous cell carcinoma: A clinicopathological study

doi: 10.1016/j.jobcr.2023.05.001

Figure Lengend Snippet: Photomicrograph of peri-coronal normal epithelial tissue (A) H & E stained section x200. (B) anti- E cadherin stain reaction mainly localized at the basal and supra-basal cell layer. Avidin–biotin-complex (ABC) x200. (C) negative staining of normal epithelium by anti N-cadherin staining ABC x200.

Article Snippet: Anti-E-cadherin antibody (Biogenex, USA, Clone 36, anti-rabbit monoclonal), Anti-N-cadherin antibody (Biogenex, USA, Clone EPR1792Y, anti-rabbit monoclonal), and An avidin–biotin-complex universal kit (ABC Elite Kit, Vector, Burlingame, CA, USA) were used in the current study.

Techniques: Staining, Avidin-Biotin Assay, Negative Staining

Journal: Journal of Oral Biology and Craniofacial Research

Article Title: Cadherin switching in oral squamous cell carcinoma: A clinicopathological study

doi: 10.1016/j.jobcr.2023.05.001

Figure Lengend Snippet: photomicrograph of OSCC in different grades of OSCC: (A, D, G) well differentiated OSCC. (B, E, H) moderately differentiated OSCC. (C, F, I) poorly differentiated OSCC. (A, B, C) H&E staining x100. (D, E, F) E-cadherin staining ABC x200. (G, H, I) N-cadherin staining ABC x200.

Article Snippet: Anti-E-cadherin antibody (Biogenex, USA, Clone 36, anti-rabbit monoclonal), Anti-N-cadherin antibody (Biogenex, USA, Clone EPR1792Y, anti-rabbit monoclonal), and An avidin–biotin-complex universal kit (ABC Elite Kit, Vector, Burlingame, CA, USA) were used in the current study.

Techniques: Staining

Journal: Journal of Oral Biology and Craniofacial Research

Article Title: Cadherin switching in oral squamous cell carcinoma: A clinicopathological study

doi: 10.1016/j.jobcr.2023.05.001

Figure Lengend Snippet: Relation between histopathological grades of OSCC and cadherin switching.

Article Snippet: Anti-E-cadherin antibody (Biogenex, USA, Clone 36, anti-rabbit monoclonal), Anti-N-cadherin antibody (Biogenex, USA, Clone EPR1792Y, anti-rabbit monoclonal), and An avidin–biotin-complex universal kit (ABC Elite Kit, Vector, Burlingame, CA, USA) were used in the current study.

Techniques:

Journal: Journal of Oral Biology and Craniofacial Research

Article Title: Cadherin switching in oral squamous cell carcinoma: A clinicopathological study

doi: 10.1016/j.jobcr.2023.05.001

Figure Lengend Snippet: Correlation between cadherin switching and histopathological grades of OSCC.

Article Snippet: Anti-E-cadherin antibody (Biogenex, USA, Clone 36, anti-rabbit monoclonal), Anti-N-cadherin antibody (Biogenex, USA, Clone EPR1792Y, anti-rabbit monoclonal), and An avidin–biotin-complex universal kit (ABC Elite Kit, Vector, Burlingame, CA, USA) were used in the current study.

Techniques:

Journal: Journal of Oral Biology and Craniofacial Research

Article Title: Cadherin switching in oral squamous cell carcinoma: A clinicopathological study

doi: 10.1016/j.jobcr.2023.05.001

Figure Lengend Snippet: Photomicrograph showing OSCC in lymphnodes (A) H & E staining x100. (B) E-cadherin staining ABC ×100 shows weak staining. (C, D) N-cadherin staining ABC ×100 shows intense staining.

Article Snippet: Anti-E-cadherin antibody (Biogenex, USA, Clone 36, anti-rabbit monoclonal), Anti-N-cadherin antibody (Biogenex, USA, Clone EPR1792Y, anti-rabbit monoclonal), and An avidin–biotin-complex universal kit (ABC Elite Kit, Vector, Burlingame, CA, USA) were used in the current study.

Techniques: Staining

Journal: Journal of Oral Biology and Craniofacial Research

Article Title: Cadherin switching in oral squamous cell carcinoma: A clinicopathological study

doi: 10.1016/j.jobcr.2023.05.001

Figure Lengend Snippet: N and E-cadherin gene expression in different OSCC cell cultures.

Article Snippet: Anti-E-cadherin antibody (Biogenex, USA, Clone 36, anti-rabbit monoclonal), Anti-N-cadherin antibody (Biogenex, USA, Clone EPR1792Y, anti-rabbit monoclonal), and An avidin–biotin-complex universal kit (ABC Elite Kit, Vector, Burlingame, CA, USA) were used in the current study.

Techniques: Gene Expression

Journal: PLoS ONE

Article Title: Enhanced Expression of Integrin αvβ3 Induced by TGF-β Is Required for the Enhancing Effect of Fibroblast Growth Factor 1 (FGF1) in TGF-β-Induced Epithelial-Mesenchymal Transition (EMT) in Mammary Epithelial Cells

doi: 10.1371/journal.pone.0137486

Figure Lengend Snippet: Starved MCF10A cells were treated with or without 5 ng/ml TGF-β1 in the absence or presence of 50 ng/ml FGF1 for 48 h. A , Cell lysates were applied for Western blotting with the indicated antibodies. GAPDH and total ERK1/2 were used as a loading control. B , Total RNA was extracted and revers transcribed to cDNA. N-cadherin and vimentin, Snail1 and Snail2 expressions were assessed by real-time RT-PCR. C , Cell lysates were applied for Western blotting with the indicated antibodies. D , Matrigel invasion assay was performed on MCF10A cells following treatment with 5 ng/ml TGF-β1 in the presence or absence of FGF1. E , Conditioned media were applied for gelatin zymography and MMP2 activity were assessed by gelatin digestion in the gel. F , MCF12A cells were starved and treated with or without 5 ng/ml TGF-β1 in the absence or presence of 50 ng/ml FGF1 for 48 h. Western blotting was performed with the indicated antibodies. Data represent the mean ± S.E. (n = 3; *, p < 0.05). Bands intensity was measured by densitometry.

Article Snippet: Rabbit anti-N-cadherin (YS) was Immuno-Biological Laboratories (Gunma, Japan); mouse anti-E-cadherin (4A2C7) was Invitrogen (Carlsbad, CA); rabbit anti-ERK1/2 (137F5), rabbit anti-phospho ERK1/2 (D13.14.4E), rabbit anti-phospho Smad2, mouse anti-MMP9 (D603H), mouse anti-PAI-1 (D9C4) were from Cell Signaling Technology (Danvers, MA); rabbit anti-FGFR1 (C-15), mouse anti-integrin β3 (SAP), mouse-integrin αV (P2W7), mouse anti-GAPDH (0411) were from Santa Cruz Biotechnology (Santa Cruz, CA); rabbit anti- FGFR2 was from Sigma; mouse anti-MMP2 (42-5D11) was from Daiichi fine chemical (Toyama, Japan).

Techniques: Western Blot, Quantitative RT-PCR, Invasion Assay, Zymography, Activity Assay

Journal: Cell Proliferation

Article Title: The impact of dynamic caudal type homeobox 2 expression on the differentiation of human trophoblast lineage during implantation

doi: 10.1111/cpr.13729

Figure Lengend Snippet:

Article Snippet: Rabbit anti‐N‐cadherin , GeneTex , GTX1217345 , 1:500.

Techniques: