Journal: Cell reports

Article Title: Differentiation of fetal hematopoietic stem cells requires ARID4B to restrict autocrine KITLG/KIT-Src signaling

doi: 10.1016/j.celrep.2021.110036

Figure Lengend Snippet:

Article Snippet: Donkey polyclonal anti-mouse IgG, horseradish Peroxidase-conjugated , Jackson ImmunoResearch Labs , Cat# 715-035-151; RRID: AB_2340771.

Techniques: Blocking Assay, Recombinant, Electron Microscopy, Plasmid Preparation, Red Blood Cell Lysis, Protease Inhibitor, SYBR Green Assay, Transfection, Gene Expression, Software, Microscopy, Irradiation, Flow Cytometry

Journal: Cell Reports Medicine

Article Title: Divergent and self-reactive immune responses in the CNS of COVID-19 patients with neurological symptoms

doi: 10.1016/j.xcrm.2021.100288

Figure Lengend Snippet:

Article Snippet: Donkey-anti-mouse Cy5 , Jackson ImmunoResearch , Cat# 715-175-151, RRID: AB_2340820.

Techniques: Virus, Plasmid Preparation, Recombinant, Over Expression, Mass Spectrometry, Software

Journal: Cell stem cell

Article Title: Differentiation of Human Pluripotent Stem Cells into Functional Lung Alveolar Epithelial Cells

doi: 10.1016/j.stem.2017.08.014

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: AffiniPure Donkey Anti-Mouse IgG (H+L), AlexaFluor 647 conjugated , Jackson Immunoresearch , Cat#715-605-150.

Techniques: Recombinant, Electron Microscopy, Lysis, Reverse Transcription, Imaging, Transfection, RNA Sequencing, Sequencing, Gene Expression, CRISPR, Software, Gentle, Membrane, Microscopy

Journal: Cell reports

Article Title: ERK1/2 interaction with DHPS regulates eIF5A deoxyhypusination independently of ERK kinase activity

doi: 10.1016/j.celrep.2024.114831

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Human eukaryotic translation initiation factor 5A-1 (residues 15–151) with N-teminal 6xHis-tag followed by TEV cleavage site in pET28-MHL for bacterial expression , Addgene , Cat#25260.

Techniques: Virus, Recombinant, Labeling, Transfection, Expressing, Software

Journal: Cell

Article Title: Human-Specific NOTCH2NL Genes Expand Cortical Neurogenesis through Delta/Notch Regulation

doi: 10.1016/j.cell.2018.03.067

Figure Lengend Snippet:

Article Snippet: AlexaFluor647 donkey anti-mouse , Jackson ImmunoResearch , Cat# 715-605-150.

Techniques: Virus, Recombinant, Knock-Out, Transfection, Magnetic Beads, Membrane, Western Blot, Imaging, Expressing, In Situ Hybridization, Plasmid Preparation, Software, Microscopy

Journal: Cell reports

Article Title: ΔNp63 drives dysplastic alveolar remodeling and restricts epithelial plasticity upon severe lung injury

doi: 10.1016/j.celrep.2022.111805

Figure Lengend Snippet:

Article Snippet: Alexa Fluor TM 488-conjugated donkey anti-mouse , Jackson Immunoresearch , Cat# 715-546-150; RRID: AB_2340849.

Techniques: Virus, Recombinant, Lysis, Magnetic Beads, Migration, Single-cell Transcriptomics, Software

Journal: Scientific Reports

Article Title: Palladin isoforms 3 and 4 regulate cancer-associated fibroblast pro-tumor functions in pancreatic ductal adenocarcinoma

doi: 10.1038/s41598-021-82937-3

Figure Lengend Snippet: Palladin iso3 & iso4 are upregulated in the fibrillar collagen-rich stroma of human PDAC. ( a ) Representative images depicting epithelial/tumoral areas (magenta) as well as stroma (cyan) areas in surgical tissue sections, pathologically defined as pancreatic cancer (PDAC) or matched normal/benign pancreas (Tumor Adjacent). The images are representative of 3 patient samples that included SMI as well as SHG assessments, while SMI alone was also conducted in 2 additional surgical sample pairs. Epithelial compartments were labeled with antibodies against pan-cytokeratin, EpCAM, and CD-70 identifying all epithelial cells including cancer cells (magenta). Stromal cell compartments were identified using anti-vimentin antibodies (cyan). Nuclei were stained using DRAQ5 dye (blue). Palladin isoforms were identified using antibodies against iso3 (clone G2; green) and iso4 (clone IE6; red). Fibrillar collagen signatures, detected via SHG, are shown in white. Yellow squares correspond to magnified regions, shown to their right, while far right column shows single colored images corresponding to the same magnified regions. Scale bars are provided for each magnification. ( b ) Evaluation of SHG generated signatures assessing straightness of collagen fibers. Values were obtained using CT-FIRE software (see “Material and methods”). Each bullet point represents a single image. Three images were acquired from each of the three paired patient samples for a total of nine images from PDAC, and nine from matching for Tumor Adjacent samples. ( c ) Quantification of the percentage coverage of iso3 or iso4 immunostaining within vimentin positive areas, relative to the total image area. Analysis was carried out using readouts generated by the SMIA-CUKIE 2.1.0 software (see “ ”). Data presented in ( c ) correspond to specimens evaluated from all 5 patients, and included a minimum of 5 images per specimen. Graphs show median with 95% CI. Mann Whitney test was used to determine statistical significance: **** p < 0.0001.

Article Snippet: Palladin (iso3 and iso 4) , Rabbit , 1:5,000 , ProteinTech.

Techniques: Labeling, Staining, Generated, Software, Immunostaining, MANN-WHITNEY

Journal: Scientific Reports

Article Title: Palladin isoforms 3 and 4 regulate cancer-associated fibroblast pro-tumor functions in pancreatic ductal adenocarcinoma

doi: 10.1038/s41598-021-82937-3

Figure Lengend Snippet: Inhibition of TGFβ1 signaling reduces CAF iso3 & iso4 expression and d-ECM alignment. ( a ) Schematic of 3D fibroblastic cell-derived ECM model used to assess assorted CAF function and/or traits. ( b ) Representative Western blot, using lysates collected at the end of ECM production, and blotted for palladin iso3 and iso4 as well as αSMA expression in vehicle vs. SB431542 treated CAFs. GAPDH served as loading control. ( c ) CAF-derived ECMs were treated during ECM production as in ( b ); shown are representative images of reconstructed confocal image stacks of human fibroblasts in 3D cultures. Images show dye-labeled nuclei in green, immunofluorescently-labeled αSMA (in red), and fibronectin (ECM in white). Scale bar: 50 microns. Last column shows pseudo-colored ECM, depicting corresponding fiber angles distribution, referenced to tone/angle bar on the right; with cyan fibers as the mode angle. Note how ECM fiber analysis of CAFs cultured in the presence of SB431542, included additional fiber color tones suggestive of broader angle distribution compared to control condition. ECM analyses of images acquired in ( c ) were conducted measuring: ECM fiber angle distributions ( d ) and percentage of ECM fibers out of total fibers at 15° from the mode angle ( e ). Data presented were derived from 6 biological replicates (n = 6) and a minimum of 5 images acquired per sample. The Mann Whitney test was used to determine statistical significance. **p = 0.0096.

Article Snippet: Palladin (iso3 and iso 4) , Rabbit , 1:5,000 , ProteinTech.

Techniques: Inhibition, Expressing, Derivative Assay, Western Blot, Control, Labeling, Cell Culture, MANN-WHITNEY

Journal: Scientific Reports

Article Title: Palladin isoforms 3 and 4 regulate cancer-associated fibroblast pro-tumor functions in pancreatic ductal adenocarcinoma

doi: 10.1038/s41598-021-82937-3

Figure Lengend Snippet: Palladin isoforms are required for CAFs to sustain a myofibroblastic cell identity. ( a ) Schematic illustrating the gRNA strategy (for CRISPR/Cas9) used to generate plasmids that target coding sequence common for both isoforms (total KD: yellow lines) or either palladin isoform (iso3 KD: green line, iso4 KD: red line). ( b ) Representative images of western blot analysis of palladin isoforms and αSMA, using GAPDH as loading controls, in CAFs at the end of ECM production. The upper panel corresponds to the upper portion of the middle panel shown at a higher exposure to highlight iso3 bands, while the middle panel clearly shows iso4. The bottom panel corresponds to αSMA and GAPDH (note that these images were cropped from images generated using the LICOR system). ( c ) Graphs corresponding to measured protein expression levels of samples as in ( b ) normalized to 1 arbitrary unit assigned for expression of the assorted protein/GAPDH in control CAF cultures. ( d ) Graphs depicting relative RT-qPCR quantification of transcripts corresponding to αSMA, iso3, and iso4 normalized to control CAFs, which were set to one arbitrary unit in each experiment. ( e ) Representative images of control vs palladin KD CAFs at the end of ECM production (selecting for substantial ECM produsing samples). Unextracted 3D cultures were subjected to indirect immunofluorescence. Images show in green, nuclei; in red, αSMA and in white, fibronectin (ECM). Pseudo-colored images depict fibronectin fiber angle distributions corresponding to tone bar on the right, showing cyan fibers as mode angle. ECM fibers of control CAFs present greater levels of cyan pseudo-colored fibers compared to palladin KD CAFs. Scale bar: 50 microns. Analyses of images acquired as in ( e ) were conducted measuring: fibronectin ECM fiber angle distributions ( f ) and percentage of ECM fibers out of total fibers at 15° from the mode angle ( g ). Data presented is derived from experimental duplicates of biological triplicates which rendered enough ECM to conduct the meassurements (n = 6). Each sample was represented by a minimum of 5 images. One Way ANOVA, Dunnett’s multiple comparison test was performed to determine statistical significance compared to control CAFs or alignment threshold * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001.

Article Snippet: Palladin (iso3 and iso 4) , Rabbit , 1:5,000 , ProteinTech.

Techniques: CRISPR, Sequencing, Western Blot, Generated, Expressing, Control, Quantitative RT-PCR, Immunofluorescence, Derivative Assay, Comparison

Journal: Scientific Reports

Article Title: Palladin isoforms 3 and 4 regulate cancer-associated fibroblast pro-tumor functions in pancreatic ductal adenocarcinoma

doi: 10.1038/s41598-021-82937-3

Figure Lengend Snippet: Guide RNAs.

Article Snippet: Palladin (iso3 and iso 4) , Rabbit , 1:5,000 , ProteinTech.

Techniques: Sequencing

Journal: Scientific Reports

Article Title: Palladin isoforms 3 and 4 regulate cancer-associated fibroblast pro-tumor functions in pancreatic ductal adenocarcinoma

doi: 10.1038/s41598-021-82937-3

Figure Lengend Snippet: List of SDS-PAGE primary antibodies.

Article Snippet: Palladin (iso3 and iso 4) , Rabbit , 1:5,000 , ProteinTech.

Techniques:

Journal: Scientific Reports

Article Title: Palladin isoforms 3 and 4 regulate cancer-associated fibroblast pro-tumor functions in pancreatic ductal adenocarcinoma

doi: 10.1038/s41598-021-82937-3

Figure Lengend Snippet: List of RNA probes.

Article Snippet: Palladin (iso3 and iso 4) , Rabbit , 1:5,000 , ProteinTech.

Techniques: Sequencing, Enzyme-linked Immunosorbent Assay

Journal: Journal of Biological Chemistry

Article Title: Activation of NF-κB by the Human T Cell Leukemia Virus Type I Tax Oncoprotein Is Associated with Ubiquitin-dependent Relocalization of IκB Kinase

doi: 10.1074/jbc.m611031200

Figure Lengend Snippet: FIGURE 1. IKK relocalizes to cellular hot spots in Jurkat cells expressing Tax and in C8166 cells. Mock-infected Jurkat (A–C), Tax-infected Jurkat (D–F), and C8166 (G–I) cells were immunostained for IKK, Tax, and nuclei. IKK was detected using RRX-conjugated donkey anti-rabbit F(ab)2 IgG, Tax was detected using Cy5-conjugated donkey anti-mouse F(ab)2 IgG, and nuclei were stained with DAPI. Tax was pseudocolored green using Zeiss LSM software. These confocal images depict the extended projection of the z stack. Bar, 10 m. This experiment was performed a minimum of three times with similar results.

Article Snippet: RRX-conjugated donkey anti-rabbit F(ab )2 IgG, Cy5-conjugated donkey anti-mouse F(ab )2 IgG, RRX-conjugated donkey anti-mouse F(ab )2 IgG, andCy5-conjugated donkey anti-rabbit F(ab )2 IgG were from Jackson Immunoresearch (West Grove, PA).

Techniques: Expressing, Infection, Staining, Software

Journal: Journal of Biological Chemistry

Article Title: Activation of NF-κB by the Human T Cell Leukemia Virus Type I Tax Oncoprotein Is Associated with Ubiquitin-dependent Relocalization of IκB Kinase

doi: 10.1074/jbc.m611031200

Figure Lengend Snippet: FIGURE 4. Tax activation of NF-B correlates with IKK relocalization to perinuclear hot spots. Mock-infected Jurkat (A–C), Tax-infected Jurkat (D–F), Tax M22-infected Jurkat (G–I), and Tax M47-infected Jurkat (J–L) were costained for IKK (A, D, G, and J) and Tax (B, E, H, and K). IKK was detected with Cy5-conjugated donkey anti-rabbit F(ab)2 IgG, and Tax was detected with RRX-conjugated donkey anti-mouse F(ab)2 IgG. Merged images with DAPI-stained nuclei are shown in C, F, I, and L. IKK was pseudocolored green using Zeiss LSM software. These confocal images depict single slices in the z stack. Bar, 5 m. This experiment was per- formed two times with similar results.

Article Snippet: RRX-conjugated donkey anti-rabbit F(ab )2 IgG, Cy5-conjugated donkey anti-mouse F(ab )2 IgG, RRX-conjugated donkey anti-mouse F(ab )2 IgG, andCy5-conjugated donkey anti-rabbit F(ab )2 IgG were from Jackson Immunoresearch (West Grove, PA).

Techniques: Activation Assay, Infection, Staining, Software

Journal: Journal of Biological Chemistry

Article Title: Activation of NF-κB by the Human T Cell Leukemia Virus Type I Tax Oncoprotein Is Associated with Ubiquitin-dependent Relocalization of IκB Kinase

doi: 10.1074/jbc.m611031200

Figure Lengend Snippet: FIGURE 5. Tax is required for IKK relocalization to cellular hot spots. Jurkat (A and B), C8166 (C and D), MT-1 (E and F), TL-OM1 (G and H), and ED40515() (I and J) cells were immunostained for IKK and nuclei. IKK was detected with RRX-conjugated donkey anti-rabbit F(ab)2 IgG, and the nuclei were stained with DAPI. Bar, 5 m. Jurkat cells were left nontreated (K and L) or were treated with PMA and ionomycin for 15 min (M and N) or 2 h (O and P). The cells were immunostained for IKK and nuclei. IKK was detected with RRX-conjugated donkey anti-mouse F(ab)2 IgG, and the nuclei were stained with DAPI. A–P depict the extended projection of the z stack. Bar, 5 m.

Article Snippet: RRX-conjugated donkey anti-rabbit F(ab )2 IgG, Cy5-conjugated donkey anti-mouse F(ab )2 IgG, RRX-conjugated donkey anti-mouse F(ab )2 IgG, andCy5-conjugated donkey anti-rabbit F(ab )2 IgG were from Jackson Immunoresearch (West Grove, PA).

Techniques: Staining

Journal: Journal of Biological Chemistry

Article Title: Activation of NF-κB by the Human T Cell Leukemia Virus Type I Tax Oncoprotein Is Associated with Ubiquitin-dependent Relocalization of IκB Kinase

doi: 10.1074/jbc.m611031200

Figure Lengend Snippet: FIGURE 6. Tax promotes IKK relocalization to the Golgi. C8166 cells were costained for IKK, Giantin, and nuclei (A–C). IKK was detected with Alexa Fluor-555-conjugated donkey anti-mouse IgG, and Giantin was detected with Cy5-conjugated donkey anti-rabbit F(ab)2 IgG. Giantin was pseudocol- ored green using Zeiss LSM software. The nuclei were stained with DAPI. The arrow in C points to a region of colocalization between IKK and Giantin. A–C depict the extended projection of the z stack. Bar, 5 m. This experiment was performed two times with similar results. C8166 cells were left untreated (D–F) or were treated with dimethyl sulfoxide (DMSO) for 2 h (G–I), nocoda- zole (10 m) for 2 h (J–L), or brefeldin A (1) for 1 h (M–O). The cells were immunostained for IKK, GM-130, and nuclei. IKK was detected with RRX- conjugated donkey anti-rabbit F(ab)2 IgG, GM-130 was detected with Cy5- conjugated donkey anti-mouse F(ab)2 IgG, and nuclei were stained with DAPI. GM-130 was pseudocolored green using Zeiss LSM software. The arrows in F, I, and L point to regions of colocalization between IKK and GM-130. D–O depict the extended projection of the z stack. Bar, 5 m.

Article Snippet: RRX-conjugated donkey anti-rabbit F(ab )2 IgG, Cy5-conjugated donkey anti-mouse F(ab )2 IgG, RRX-conjugated donkey anti-mouse F(ab )2 IgG, andCy5-conjugated donkey anti-rabbit F(ab )2 IgG were from Jackson Immunoresearch (West Grove, PA).

Techniques: Software, Staining