Journal: iScience

Article Title: Transposable element activation promotes neurodegeneration in a Drosophila model of Huntington's disease

doi: 10.1016/j.isci.2021.103702

Figure Lengend Snippet: Neuronal and glial expression of 128QHtt results in transposable element derepression (A) Semiquantitative RT-PCR analysis to assess the induction levels of the HD transgenic construct by elav-Gal4. cDNA was prepared from total RNA purified from HD ( elav-G4>128QHtt ) and control ( elav-G4/+ ) head tissues. The constitutive gapdh was examined as an endogenous control. (B) qRT-PCR analysis of transposable element expression in larval and adult brains of flies expressing 128QHtt in neurons ( elav-G4>128QHtt ); adult brains were analyzed at both young (0–2 days) and aged (10–12 days) time points; transcript levels were normalized to rp49 and displayed as fold change relative to flies carrying the elav-Gal4 driver with no 128QHtt transgene ( elav-G4/+ ). (C) Western blot assay of gypsy envelope protein (ENV) expression in HD larval and adult brains. GIOTTO protein was used as a loading control. Result was expressed as means for at least three independent biological replicates (∗p < 0.05; one-sample t test). (D) qRT-PCR analysis of TE expression in larval brains and adult heads isolated from 0- to 2-day-old and 10- to 12-day-old flies expressing 128QHtt with the pan-glial repo-Gal4 driver ( repo-Gal4>128QHtt ). Transcript levels were normalized to gapdh and displayed as fold change relative to flies carrying the repo-Gal4 driver with no128QHtt transgene ( repo-G4/+ ). (B and D) Bar graph represents the mean ± SEM from at least three independent experiments (∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001; unpaired t tests). Red dots indicate individual data points. The black horizontal line indicates the fold change control value, set to 1. See also .

Article Snippet: The membranes were blocked with 5% non-fat dry milk in Tris-buffered saline with Tween 20 (TBST) buffer (20 mM Tris pH 7.5, 150 mM NaCl, 0.1% Tween 20) and incubated with the following antibodies diluted in TBST: mouse anti-ENV 8E7 (1:500 , kindly provided by J. Gall), rabbit anti-GIOTTO (1:10,000 ( )), mouse anti-elav (1:500, 9F8A9 DSHB) and mouse anti-repo (1:500, 8D12 DSHB).

Techniques: Expressing, Reverse Transcription Polymerase Chain Reaction, Transgenic Assay, Construct, Purification, Quantitative RT-PCR, Western Blot, Isolation

Journal: iScience

Article Title: Transposable element activation promotes neurodegeneration in a Drosophila model of Huntington's disease

doi: 10.1016/j.isci.2021.103702

Figure Lengend Snippet:

Article Snippet: The membranes were blocked with 5% non-fat dry milk in Tris-buffered saline with Tween 20 (TBST) buffer (20 mM Tris pH 7.5, 150 mM NaCl, 0.1% Tween 20) and incubated with the following antibodies diluted in TBST: mouse anti-ENV 8E7 (1:500 , kindly provided by J. Gall), rabbit anti-GIOTTO (1:10,000 ( )), mouse anti-elav (1:500, 9F8A9 DSHB) and mouse anti-repo (1:500, 8D12 DSHB).

Techniques: Recombinant, Multiplex Assay, Gel Extraction, Picogreen Assay, SYBR Green Assay, Over Expression, Marker, CNV Assay, Software

Journal: eLife

Article Title: Epigenetic remodeling by vitamin C potentiates plasma cell differentiation

doi: 10.7554/eLife.73754

Figure Lengend Snippet:

Article Snippet: After precleared with ProteinA dynabeads (Thermo Fisher), 20 μg of chromatin was diluted to a final of 500 uL RIPA buffer (50 mM Tris–HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, 1% NP40, 0.1% SDS, and 0.5% sodium deoxycholate) and incubated with 1 μg rabbit monoclonal anti-phsopho-STAT3 (Tyr705) antibody (clone D3A7, Cell Signaling Technology) overnight at 4°C with constant rotation.

Techniques: Dot Blot, Enzyme-linked Immunosorbent Assay, Purification, Flow Cytometry, Ligation, Sequencing, Cell Isolation, Isolation, Multiplex Assay, Recombinant, Software

Journal: Cell

Article Title: The Parkinson’s disease protein alpha-synuclein is a modulator of Processing-bodies and mRNA stability

doi: 10.1016/j.cell.2022.05.008

Figure Lengend Snippet: Key resources table

Article Snippet: BCA Protein Assay Kit , Pierce , 23225.

Techniques: Western Blot, Virus, Recombinant, Protease Inhibitor, Lysis, Magnetic Beads, Membrane, Transfection, Expressing, Bicinchoninic Acid Protein Assay, Silver Staining, In Situ, Sample Prep, Luciferase, Reporter Assay, Multiplex sample analysis, Biomarker Discovery, Marker, Generated, Software, Mass Spectrometry, Imaging

Journal: PloS one

Article Title: Kinetic analysis of mouse brain proteome alterations following Chikungunya virus infection before and after appearance of clinical symptoms.

doi: 10.1371/journal.pone.0091397

Figure Lengend Snippet: Figure 5. Western blot validations of differentially regulated proteins identified by 2D-DIGE and/or iTRAQ analyses. (A) Protein samples from each group used for proteomic analysis were minimally labeled with cyanine-3 dye. At the top, a representative protein profile of three biological replicates from brain lysates of mock (M), early (E), late paralytic (LP) and late tetanus-like (LT), separated by 10% SDS-PAGE is shown. WB with fluorescence-based methods was used to detect an overlaid fluorescent scan of the general protein patterns (Cy3 dye; green) and the specific immunoreactive proteins (FITC or Cy5 dye; red). To better visualize protein detection signals observed with each specific antibody used, corresponding cropped WB images are presented in grey levels. (B) The graphs correspond to the mean 6 S.D. of protein quantity measured by densitometry of the antigenic bands. Densitometry analyses were performed using TotalLab Quant v12.2 software (Nonlinear Dynamics), and data were normalized to levels of global protein pattern intensity. The values indicated under each graph correspond to fold changes from paired comparisons. The significance of the differential protein expression are indicated *, p,0.05; **, p,0.01; ***, p,0.001. A.U., arbitrary units. ANXA2: annexin A2; ARRB1: b-arrestin; GABRA1: c-aminobutyric acid receptor subunit alpha-1; GRASP1: GRIP-associated protein; ITGAV: integrin aV; MYPT1: myosin phosphatase target subunit 1; N-Ras: N-Ras; RABEP1: rabaptin-5; SYNGR3: synaptogyrin-3. doi:10.1371/journal.pone.0091397.g005

Article Snippet: Blots were saturated with 5% nonfat dried milk in PBS containing 0.05% (v/v) Tween 20 (PBS-T-milk) for 1 h. Western blot (WB) analyses were carried out with rabbit mono- or polyclonal antibodies directed against b-arrestin (1:5000, ARRB1, no. 4674, Cell Signaling Technology, Danvers, MA), GRIP-associated protein (1:500, GRASP1, no. sc-135681, Santa Cruz Biotechnology, Inc., Santa Cruz, CA), annexin A2 (1:100, ANXA2, no. sc-9061, Santa Cruz), integrin aV (1:100, ITGAV, no. 10179, Santa Cruz), myosin phosphatase target subunit 1 (1:100, MYPT1, no. sc25618, Santa Cruz), rabaptin-5 (1:1000, RABEP1, no. sc-15351, Santa Cruz), N-Ras (1:500, N-Ras, no. sc-519, Santa Cruz), synaptogyrin-3 (1:1000, SYNGR3, no. sc-68936, Santa Cruz), or with a goat polyclonal antibody directed against c-aminobutyric acid receptor subunit alpha-1 (1:100, GABAARa1 or GABRA1, no. sc-31045, Santa Cruz), diluted in PBS-T-milk and incubated overnight at 4uC.

Techniques: Western Blot, Multiplex sample analysis, Labeling, SDS Page, Fluorescence, Software, Expressing

Journal: Nature Communications

Article Title: Investigational eIF2B activator DNL343 modulates the integrated stress response in preclinical models of TDP-43 pathology and individuals with ALS in a randomized clinical trial

doi: 10.1038/s41467-025-63031-y

Figure Lengend Snippet: a Schematic depicting the ISR pathway, including kinases mediating the phosphorylation of eIF2α, and activation of eIF2B by DNL343. b Confocal microscopy images showing induced expression of GFP-TDP-43 FL and GFP-TDP-43 (86-414) variant in H4 cells increased immunoreactivity of ATF4 (anti-ATF4, red) compared to GFP control. This ATF4 signal was reduced with 1 µM DNL343 treatment. Scale bar: 20 µm. c Quantification of ATF4 immunoreactivity in ( b ) from n = 3 (GFP Control) or 4 biological replicates (GFP-TDP-43 variants). a.u.: arbitrary units. d ECLIA-based assay result demonstrating elevated ATF4 protein levels with induced expression of GFP-TDP-43 FL and GFP-TDP-43 (86-414) , compared to GFP control cells. Pre-treatment with DNL343 reduced ATF4 protein levels in each cell line ( n = 6 biological replicates). e Volcano plot of differentially regulated genes in H4 cells induced with GFP-TDP-43 FL compared to GFP control. Representative ISR genes with significant expression changes are labeled as red (upregulation) or blue (downregulation) and insignificant genes as gray. Significance cutoff, adjusted p -value < 0.05. f Volcano plot of differentially regulated genes in H4 cells induced with GFP-TDP-43 (86-414) compared to GFP control. Representative ISR genes are labeled as in ( e ). Significance cutoff, adjusted p -value < 0.05. g Gene set enrichment analysis (GSEA) plot for ISR gene comparing truncated GFP-TDP-43 (86-414) from GFP control expressing cells. h Volcano plot of differentially regulated genes 24 hours after DNL343 treatment in H4 cells induced with GFP-TDP-43 (86-414) . The same set of representative ISR genes from ( e ) and ( f ) are labeled. All data are shown as mean ± SEM ( c , d ). Statistical significance was determined with one-way ANOVA, with Tukey’s multiple comparison, ns P > 0.05. Source data are provided in Source Data file.

Article Snippet: A non-competitive sandwich immunoassay employing a biotinylated CREB-2 (ATF4) mAb (Santa Cruz Biotechnology, #sc-390063 LS) as capture and a SULFO TAG labeled (ruthenylated) anti-ATF4 pAb (Proteintech, #10835-1-AP) for detection was used to quantify levels of ATF4 protein.

Techniques: Phospho-proteomics, Activation Assay, Confocal Microscopy, Expressing, Variant Assay, Control, Labeling, Comparison

Journal: Nature Communications

Article Title: Investigational eIF2B activator DNL343 modulates the integrated stress response in preclinical models of TDP-43 pathology and individuals with ALS in a randomized clinical trial

doi: 10.1038/s41467-025-63031-y

Figure Lengend Snippet: a Experimental design of acute DN9058 dosing of rNLS8 transgenic mice. All animals were fed Dox-containing diet until 8 weeks of age, including non-transgenic (nTg) controls, single transgenic (sTg) controls and double transgenic (rNLS8) mice, then Dox was removed from their diet except for group 6 (double transgenic (rNLS8) on Dox for two additional weeks). On 13th and 14th day off Dox, indicated groups were dosed with DN9058 by oral gavage at 50 mg/kg per animal weight. b - c Quantification of p-eIF2α normalized to loading control eIF2α ( b ) and ATF4 level normalized to GAPDH ( c ) from Supplementary Fig. and j ( n = 8 sTg Control or 12 rNLS8 mice). Data are shown as fold-changes relative to vehicle-treated control mice. d Transcriptional fold change of pre-selected ISR genes in rostral cortex of indicated mouse line ( n = 7 (nTg Ctrl), 8 (rNLS8 Dox), 9 (sTg Ctrl) and 12 (rNLS8) mice). Data are shown as mean ± SEM ( b − d ). Statistical significance was determined with Kruskal-Wallis test with Dunn’s multiple comparisons ( b ), ordinary One-way ANOVA with Tukey’s multiple comparison ( c , d ). Source data are provided in Source Data file.

Article Snippet: A non-competitive sandwich immunoassay employing a biotinylated CREB-2 (ATF4) mAb (Santa Cruz Biotechnology, #sc-390063 LS) as capture and a SULFO TAG labeled (ruthenylated) anti-ATF4 pAb (Proteintech, #10835-1-AP) for detection was used to quantify levels of ATF4 protein.

Techniques: Transgenic Assay, Control, Comparison

Journal: Nature Communications

Article Title: Investigational eIF2B activator DNL343 modulates the integrated stress response in preclinical models of TDP-43 pathology and individuals with ALS in a randomized clinical trial

doi: 10.1038/s41467-025-63031-y

Figure Lengend Snippet: a Experimental design of chronic DN9058 dosing for 6 weeks off dox (WOD). DN9058 was formulated at 50 mg/kg per chow for the chronic administration to the indicated conditions. b - c Quantification of p-eIF2α normalized to loading control eIF2α ( b ) and ATF4 level normalized to GAPDH ( c ) from Supplementary Fig. and j, respectively ( n = 8 (sTg Control), 10 (rNLS8 Veh), and 13 (rNLS8 DN9058) mice). Data are shown as fold-changes relative to vehicle-treated control mice. d - e Transcript level changes of pre-selected ISR genes ( d ) and ISR genes indicated in later stage of the disease ( e ) in rostral cortex ( n = 9 (sTg Control), 10 (rNLS8 Dox), 11 (rNLS8 Veh), and 16 (rNLS8 DN9058) mice). f Time (weeks) to show clasping for individual rNLS8 mice that demonstrated the clasping phenotype ( n = 13 (Veh) and 18 (DN9058) mice). g Plasma NfL concentration at baseline (0 WOD), 2, 4, and 6 WOD in rNLS8 mice ( n = 11 (Veh) and 16 (DN9058) mice). The same figure legend for rNLS8 + Veh (yellow) and rNLS8 + DN9058 (orange) is shared with panel ( f ). Source data are provided in Source Data file. Data are shown as mean ± SEM ( b − e ) and individual values overlayed on violin plot ( f , g ). Statistical significance was determined with Kruskal-Wallis test with Dunn’s multiple comparisons ( b , c ), ordinary One-way ANOVA with Tukey’s multiple comparison ( d , e ), Two-tailed Mann-Whitney test ( f ), and Two-way ANOVA with multiple comparisons ( g ).

Article Snippet: A non-competitive sandwich immunoassay employing a biotinylated CREB-2 (ATF4) mAb (Santa Cruz Biotechnology, #sc-390063 LS) as capture and a SULFO TAG labeled (ruthenylated) anti-ATF4 pAb (Proteintech, #10835-1-AP) for detection was used to quantify levels of ATF4 protein.

Techniques: Control, Clinical Proteomics, Concentration Assay, Comparison, Two Tailed Test, MANN-WHITNEY

Journal: Nature Communications

Article Title: Investigational eIF2B activator DNL343 modulates the integrated stress response in preclinical models of TDP-43 pathology and individuals with ALS in a randomized clinical trial

doi: 10.1038/s41467-025-63031-y

Figure Lengend Snippet: a − d ATF4 protein ( a ) and CHAC1 gene ( b ) expression in ex vivo stimulated PBMCs from healthy participants. ATF4 protein ( c ) and CHAC1 gene ( d ) expression in ex vivo stimulated PBMCs from ALS participants. PBMCs were freshly isolated from participants in each dose group shown at the times indicated and analyzed by either ECLIA ( a , c ) or multiplex qPCR ( b , d ). Values shown as median (IQR = interval from the first to the third quartile, shown as error bars) percent change from baseline. For MAD healthy participants ATF4 protein, n = 12, 6, 7, 7, 7, 6 participants for placebo, 45 mg, 100 mg, 145 mg, 200 mg and 260 mg groups respectively; CHAC1 gene, n = 11, 6, 7, 5, 7, 6 participants for placebo, 45 mg, 100 mg, 145 mg, 200 mg and 260 mg groups respectively. For ALS participants ATF4 protein, n = 6, 7, 6 participants for placebo, 100 mg, and 200 mg groups respectively; CHAC1 gene, n = 5, 7, 6 participants for placebo, 100 mg, 200 mg groups respectively through Day 28 for each dose group. e Heat map depicting relative change from baseline for a panel of ISR genes. Gene expression measured by multiplex qPCR in freshly isolated ex vivo stimulated PBMCs from ALS patients in each dose group. Values grouped based on median percent change from baseline and genes rank ordered based on percent change from baseline at Day 28 in the highest dose cohort (200 mg). f Percent change from baseline in CSF GDF-15 protein concentration at Day 28 in ALS participants, n = 9, 8, 8 participants for placebo, 100 mg, 200 mg groups respectively per group. Data are shown as box plot with individual percent change values overlayed. The middle line of the boxplot displays the median, the lower and upper limits of the box display the first and third quartiles, and the whiskers extend to the largest and smallest values. Source data are provided in Source Data file.

Article Snippet: A non-competitive sandwich immunoassay employing a biotinylated CREB-2 (ATF4) mAb (Santa Cruz Biotechnology, #sc-390063 LS) as capture and a SULFO TAG labeled (ruthenylated) anti-ATF4 pAb (Proteintech, #10835-1-AP) for detection was used to quantify levels of ATF4 protein.

Techniques: Expressing, Ex Vivo, Isolation, Multiplex Assay, Gene Expression, Protein Concentration

Journal: iScience

Article Title: Metabolic nuclear receptors coordinate energy metabolism to regulate Sox9 + hepatocyte fate

doi: 10.1016/j.isci.2021.103003

Figure Lengend Snippet: PPARα activation promotes proliferation of Sox9 + hepatocytes, and FXR suppresses proliferation of Sox9 + hepatocytes after CCl 4 -induced chronic liver injury in Sox9-Cre ERT2 ; Rosa26-mTmG mice (A) Schematic diagram showing mTom/mGFP reporter gene expression in the absence and presence of tamoxifen (TAM)-inducible Cre-mediated recombination. (B) Sox9-Cre ERT2 ; Rosa26-mTmG mice were intraperitoneally injected with a single dose of tamoxifen once per day for three days before treatment. The Sox9-Cre ERT2 ; Rosa26-mTmG mice were received intraperitoneal paraffin oil injection (control group) or CCl 4 injection twice per week for four weeks and these mice were orally gavaged with either Veh, GW7647, or GW4064 four times a week for four weeks. BrdU was injected twice per day for two days before sacrifice. (C) GFP(Sox9)/Hnf4α double staining was performed. Graphs show percentages of GFP + Hnf4α + cell (n = 5). Scale bar represents 20μm. (D) GFP(Sox9)/BrdU double staining was performed. Arrowheads depict the asymmetric division. Graphs show percentages of GFP + BrdU + cell (n = 5). Scale bar represents 20μm. Data are expressed as means ± SD. Comparisons between multiple groups were performed using ordinary one-way ANOVA with the Dunnett's multiple comparison test. Significant difference is presented at the levels of ∗p < 0.05 and ∗∗p < 0.01.

Article Snippet: Samples were fixed and permeabilized, saturated, and processed for immunostaining with primary antibody Sox9(1:100 dilution Millipore, AB5535)/Hnf4α(1:100 dilution Abcam, ab41898), Sox9(1:100 dilution)/BrdU(1:100 dilution), GFP(1:200 dilution Proteintech, 50430-2-AP)/Hnf4α(1:100 dilution), GFP(1:200 dilution)/BrdU(1:200 dilution), GFP(1:200 dilution)/Ck19(1:200 dilution Servicebio, GB12197), Ck19(1:200 dilution Abcam ab52625)/BrdU(1:200 dilution), GFP(1:200 dilution)/Notch1(1:100 dilution Santa Cruz, sc-376403).

Techniques: Activation Assay, Expressing, Injection, Double Staining

Journal: iScience

Article Title: Metabolic nuclear receptors coordinate energy metabolism to regulate Sox9 + hepatocyte fate

doi: 10.1016/j.isci.2021.103003

Figure Lengend Snippet: PPARα activation increases differentiation of Sox9 + hepatocytes, and FXR activation promotes self-renewal of Sox9 + hepatocytes in Sox9-Cre ERT2 ; Rosa26-mTmG mice The model of CCl 4 -induced chronic liver injury in Sox9-Cre ERT2 ; Rosa26-mTmG mice that was described in Figure 6 B. (A) GFP(Sox9)/CK19 staining was performed in the indicated groups. Graphs show percentages of GFP + CK19 + cells (n = 5). Scale bar represents 20μm. (B) GFP(Sox9)/Notch1 staining was performed in the indicated groups. Scale bar represents 20μm. (C) Hepatic expression levels of Cpt1a were determined by QRT-PCR analysis (n = 5). (D) Hepatic expression levels of PDK4 were determined by QRT-PCR analysis (n = 5). (E) ATP concentration measurements of liver samples (n = 5). Data are expressed as means ± SD. Comparisons between multiple groups were performed using ordinary one-way ANOVA with the Dunnett's multiple comparison test. Significant difference is presented at the levels of ∗p < 0.05 and ∗∗p < 0.01.

Article Snippet: Samples were fixed and permeabilized, saturated, and processed for immunostaining with primary antibody Sox9(1:100 dilution Millipore, AB5535)/Hnf4α(1:100 dilution Abcam, ab41898), Sox9(1:100 dilution)/BrdU(1:100 dilution), GFP(1:200 dilution Proteintech, 50430-2-AP)/Hnf4α(1:100 dilution), GFP(1:200 dilution)/BrdU(1:200 dilution), GFP(1:200 dilution)/Ck19(1:200 dilution Servicebio, GB12197), Ck19(1:200 dilution Abcam ab52625)/BrdU(1:200 dilution), GFP(1:200 dilution)/Notch1(1:100 dilution Santa Cruz, sc-376403).

Techniques: Activation Assay, Staining, Expressing, Quantitative RT-PCR, Concentration Assay

Journal: iScience

Article Title: Metabolic nuclear receptors coordinate energy metabolism to regulate Sox9 + hepatocyte fate

doi: 10.1016/j.isci.2021.103003

Figure Lengend Snippet: PPARα induces proliferation and differentiation of Sox9+ hepatocytes by enhancing OXPHOS, and FXR promote self-renewal of Sox9 + hepatocytes by increasing glycolysis and inhibiting OXPHOS (A) GFP + primary mouse hepatocytes were stained with BrdU. Scale bar represents 20μm. The morphology of mitochondria in GFP + hepatocytes. Scale bar represents 1μm. (B) GFP + primary mouse hepatocytes were stained with Notch1. Scale bar represents 20μm. (C) ATP concentration, O 2 consumption and Glycolysis measurements of primary mouse hepatocytes. Data are expressed as means ± SD. Comparisons between multiple groups were performed using ordinary one-way ANOVA with the Dunnett's multiple comparison test. Significant difference is presented at the levels of ∗p < 0.05 and ∗∗p < 0.01

Article Snippet: Samples were fixed and permeabilized, saturated, and processed for immunostaining with primary antibody Sox9(1:100 dilution Millipore, AB5535)/Hnf4α(1:100 dilution Abcam, ab41898), Sox9(1:100 dilution)/BrdU(1:100 dilution), GFP(1:200 dilution Proteintech, 50430-2-AP)/Hnf4α(1:100 dilution), GFP(1:200 dilution)/BrdU(1:200 dilution), GFP(1:200 dilution)/Ck19(1:200 dilution Servicebio, GB12197), Ck19(1:200 dilution Abcam ab52625)/BrdU(1:200 dilution), GFP(1:200 dilution)/Notch1(1:100 dilution Santa Cruz, sc-376403).

Techniques: Staining, Concentration Assay

Journal: iScience

Article Title: Metabolic nuclear receptors coordinate energy metabolism to regulate Sox9 + hepatocyte fate

doi: 10.1016/j.isci.2021.103003

Figure Lengend Snippet:

Article Snippet: Samples were fixed and permeabilized, saturated, and processed for immunostaining with primary antibody Sox9(1:100 dilution Millipore, AB5535)/Hnf4α(1:100 dilution Abcam, ab41898), Sox9(1:100 dilution)/BrdU(1:100 dilution), GFP(1:200 dilution Proteintech, 50430-2-AP)/Hnf4α(1:100 dilution), GFP(1:200 dilution)/BrdU(1:200 dilution), GFP(1:200 dilution)/Ck19(1:200 dilution Servicebio, GB12197), Ck19(1:200 dilution Abcam ab52625)/BrdU(1:200 dilution), GFP(1:200 dilution)/Notch1(1:100 dilution Santa Cruz, sc-376403).

Techniques: Recombinant, Detection Assay, Cell Based Assay, Electrophoretic Mobility Shift Assay, Plasmid Preparation, Staining, Multiplex Assay, Mutagenesis, Software, Microscopy

Journal: Journal of Inflammation Research

Article Title: Adiponectin Ameliorates Hyperglycemia-Induced Retinal Endothelial Dysfunction, Highlighting Pathways, Regulators, and Networks

doi: 10.2147/jir.s358594

Figure Lengend Snippet: Figure 4 (A–C) Canonical pathways by IPA core analysis. (A) Histogram displays the most relevant canonical pathways (p <0.05) involved in the response of HRMECs cells to APN treatment. The rank was based on the log p-value, the ratio of genes of the dataset compared to the knowledge base of IPA. See supplementary tables for details. (B) Bars display the values of Z- activation of the most relevant canonical pathways. (C) Network displays the HMGB1 pathway cascade and involves the downstream genes that are differentially expressed; downregulated as the green color and upregulated as red color, labeled with values of fold changes, and their role in biological process. Abbreviations: A, activation; p, phosphorylation; e, expression; c, causative to; and PP, protein-binding. See legends for details.

Article Snippet: In addition, an aliquot of each supernatant was assayed in duplicate as per the manufacturer’s instruction for IL-8, TNF-α, and IL-Iβ using the human cytokine multiplex immunoassay kit (HADK2MAG-61) from Millipore (Merck Millipore, Billerica, MA, USA) as published previously.16 Western Blot Proteins were extracted using RIPA buffer, and the protein concenteration was evaluated using BCA assay then resolved on 10% Bis-Tris gels (NuPAGE, Novex, Thermo Fischer), transferred to PVDF membrane, and immunoblotted using Primary antibodies HMGB1 (sc-548457), AdipoR1 (sc-518030), and AdipoR2 (sc-514045)(purchased from Santa Cruz, Germany), and SOD2 (cst#13141), and Beta-Actin (cst#3700) (purchased from cell signaling, USA).

Techniques: Activation Assay, Labeling, Phospho-proteomics, Expressing, Protein Binding

Journal: Developmental cell

Article Title: Canonical Wnt5b signaling directs outlying Nkx2.5+ mesoderm into pacemaker cardiomyocytes

doi: 10.1016/j.devcel.2019.07.014

Figure Lengend Snippet: Key Resources Table

Article Snippet: Chicken anti-GFP antibody , Aves Labs , Cat# GFP-1020.

Techniques: Recombinant, In Situ, RNAscope, Multiplex Assay, SYBR Green Assay, Software