Journal: Oncotarget

Article Title: Immunohistochemical profiling of receptor tyrosine kinases, MED12, and TGF-βRII of surgically resected small cell lung cancer, and the potential of c-kit as a prognostic marker

doi: 10.18632/oncotarget.14410

Figure Lengend Snippet: Distribution of RTKs, MED12, and TGF-βRII stratified by IHC total score in SCLC tumors as shown in Figure 2 (n=125)

Article Snippet: Rabbit anti-human polyclonal MED12 antibody (NB100-2357, Novus Biologicals, Littleton, CO, USA), rabbit anti-human polyclonal TGF-βRII antibody (NB100-91994, Novus Biologicals), rabbit anti-human polyclonal c-kit antibody (A4502, Dako, Glostrup, Denmark), rabbit anti-human polyclonal HER2 antibody (A0485, Dako), rabbit anti-human monoclonal c-Met antibody (EP1454Y, Abcam, Cambridge, UK), rabbit anti-human monoclonal VEGFRII antibody (#2479, CST, Danvers, MA, USA), mouse anti-human monoclonal EGFR antibody (31G7, Nichirei Biosciences, Tokyo, Japan), and mouse anti-human monoclonal ALK antibody (5A4, ab17127, Abcam) were used as first antibodies.

Techniques:

Journal: Oncotarget

Article Title: Immunohistochemical profiling of receptor tyrosine kinases, MED12, and TGF-βRII of surgically resected small cell lung cancer, and the potential of c-kit as a prognostic marker

doi: 10.18632/oncotarget.14410

Figure Lengend Snippet: Univariate analysis of the association between molecular expression and OS (n=107)

Article Snippet: Rabbit anti-human polyclonal MED12 antibody (NB100-2357, Novus Biologicals, Littleton, CO, USA), rabbit anti-human polyclonal TGF-βRII antibody (NB100-91994, Novus Biologicals), rabbit anti-human polyclonal c-kit antibody (A4502, Dako, Glostrup, Denmark), rabbit anti-human polyclonal HER2 antibody (A0485, Dako), rabbit anti-human monoclonal c-Met antibody (EP1454Y, Abcam, Cambridge, UK), rabbit anti-human monoclonal VEGFRII antibody (#2479, CST, Danvers, MA, USA), mouse anti-human monoclonal EGFR antibody (31G7, Nichirei Biosciences, Tokyo, Japan), and mouse anti-human monoclonal ALK antibody (5A4, ab17127, Abcam) were used as first antibodies.

Techniques: Expressing

Journal: Cell Reports

Article Title: Specific Roles of XRCC4 Paralogs PAXX and XLF during V(D)J Recombination

doi: 10.1016/j.celrep.2016.08.069

Figure Lengend Snippet: Accumulation of 53BP1 DDR Foci and Impaired Igk Rearrangement in Paxx −/− Xlf −/− pro-B Cells (A) Representative 3D projections of 53BP1 immunostaining conducted on ABLki-treated v-abl pro–B cells. (B) Percentage of v-abl pro–B cells harboring 1, 2, or >2 53BP1 foci 65 hr post ABLki treatment. Data represent mean ± SEM from three independent experiments with one or two independent cell lines for each genotype. See also . (C) Schematic of the Igk locus with position of primers (arrows) used to assay coding joint (CJ) and hybrid joint (HJ) formation during inversional IgkV 6-23 -J 1 rearrangement. (D) Semiquantitative nested PCR analysis of IgkV 6-23 -J 1 coding joints (CJ) and hybrid joints (HJ) from indicated v-abl pro-B cell lines treated for 72h with ABLki. Il-2 gene PCR was used as a loading control.

Article Snippet: Immunofluorescence was performed after 30 min blocking in 2.5% BSA/10% goat serum/0.1% Tween-20/PBS, with a primary antibody against 53BP1 (NB100-304SS, 1:600 dilution, Novus Biologicals) and a secondary goat-anti-rabbit antibody (Alexa Fluor 594, 1:900 dilution; Life Technologies) in blocking solution for 1 hr each at RT.

Techniques: Immunostaining, Nested PCR, Control

Journal: Animal Models and Experimental Medicine

Article Title: Bilateral carotid‐jugular arteriovenous graft implantation in an ovine model is safe and durable for facilitation of arteriovenous graft innovation

doi: 10.1002/ame2.70096

Figure Lengend Snippet: Representative imaging of explanted AV grafts. The images include scanning electron microscopy (SEM) in the first column, immunohistochemisty (IHC) in the second column, and hematoxylin and eosin (H&E) staining in the third column. The IHC imaging includes DAPI staining (dark blue) for cell nuclei and CD31 staining (magenta) for endothelial cell junctions, which when observed in the characteristic circular ring‐like staining pattern as seen here, suggests the presence of endothelial cells. Column 3 demonstrates patent sections of graft on the left and occluded sections of the graft on the right. The image on the far‐right side of the figure demonstrates the graft sectioning technique relative to its orientation with “1” corresponding to the venous anastomosis, “2” corresponding to graft mid‐segment, and “3” corresponding to the arterial anastomosis.

Article Snippet: Samples were then incubated with mouse anti‐sheep CD31 antibody (NB100‐65900, Novus Biologicals; 1:50 in 1% BSA/PBS) at 4°C overnight.

Techniques: Imaging, Electron Microscopy, Staining

Journal: Frontiers in Microbiology

Article Title: Comparative analysis of absent in melanoma 2-inflammasome activation in Francisella tularensis and Francisella novicida

doi: 10.3389/fmicb.2023.1188112

Figure Lengend Snippet: Mitophagy is induced upon Francisella tularensis LVS infection. (A) Western blot analysis of uninfected and BMDMs infected with F . tularensis LVS or Francisella novicida (MOI 100). Lysates were collected 6 h post-infection and subjected to SDS-PAGE, then blotted for PINK1, LC3 I/II, and β-Actin. F-PINK1, full-length PINK1, and C-PINK1, cleaved PINK1. A representative blot out of three is shown. (B) Relative LC3II/LC3I expression was quantitated from three blots. The p values were determined using one-way ANOVA. ** p < 0.01.

Article Snippet: The membrane was incubated overnight at 4°C with primary antibodies diluted in 5% Bovine Serum Albumin (BSA) against PINK1 (Novus Biologicals, United States), LC3A/B, and β-actin (Cell Signaling Technology, United States).

Techniques: Infection, Western Blot, SDS Page, Expressing

Journal: bioRxiv

Article Title: A comprehensive genetic catalog of human double-strand break repair

doi: 10.1101/2024.08.03.606369

Figure Lengend Snippet: (A) Effect of GET3 on overall editing efficiency at TKOv3 Cut 2 in RPE1- Cas9 TKOv3-NT cells. Experiments carried out as in . Two GET3 -/- clones are tested. n = 12 for WT and 4 for GET3 -/- clones. Error bars show ±SD. Statistical analysis was performed using One-way ANOVA. (B) Cas9 cutting efficiency at TKOv3 Cut site 2 estimated by qPCR. Primers annealing at both sides of the cut site are used to determine the percentage of cut molecules 6h after gRNA transfection in the indicated cell lines. Amplification levels were normalized to the endogenous gene GREB1. n = 6, error bars show ±SD. Statistical analysis was performed using One-way ANOVA. (C) 53BP1 foci number per cell 12h after transfection with a multi-target gRNA (1.5 nM) in the indicated cell lines. Data shows foci count of two independent replicates merged. Statistical analysis was performed using One-way ANOVA. (D) Heatmap showing indel frequency variation (Log2 fold change) in the three cut sites of the screen for the reduced editing efficiency gene cluster . Two insertion events in the TKOv3 Cut site 2 that are consistently reduced or increased across most knockouts in this group are marked with a blue and a red triangle, respectively. (E) Frequency of +2 (left) and +1 (right) nucleotide insertions, relative to the overall editing efficiency, after transfection with the TKOv3 Cut site 2 gRNA in RPE1- Cas9 TKOv3 GET 3 -/- clones compared to wild type cells. Experiments carried out as in . n = 12 for WT and 4 for GET3 -/- clones. Error bars show ±SD. Statistical analysis was performed using One-way ANOVA. (F) Variation in the frequency of +1 and +2 nucleotide insertions produced after transfection with decreasing concentrations (2-fold serial dilutions from our standard gRNA final concentration, 12 nM) of gRNA targeting TKOv3 Cut site 2 in RPE1- Cas9 TKOv3-NT Cells. n = 3, error bars show ±SD. (G) In-vitro Cas9 DNA cleavage assay showing differential gRNA mismatch tolerance. Schematic representation of the two constructs containing Cut site 1 and 2 sequence either unedited or including the most common +1 nucleotide insertion outcome observed in the screen data (left) (see Methods). Agarose gel showing digestion of the constructs with increasing concentrations of Cas9 ribonucleoparticle bearing gRNA targeting either Cut site 1 or 2 (right).

Article Snippet: Samples were permeabilized with PBS 0.5% Triton for 15 min, blocked in 5% BSA in PBS and stained with anti-53BP1 primary antibody (1:500, 5% BSA PBS, Novus NB100-304, Rabbit) for 1 hour at room temperature, and secondary antibody coupled to Alexa Fluor 488 (1:1000, 5% BSA PBS, Invitrogen A11008, goat).

Techniques: Clone Assay, Transfection, Amplification, Produced, Concentration Assay, In Vitro, DNA Cleavage Assay, Construct, Sequencing, Agarose Gel Electrophoresis