Journal: Cell

Article Title: Development of concurrent retinotopic maps in the fly motion detection circuit

doi: 10.1016/j.cell.2018.02.053

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Mouse Anti Connectin , DSHB , Name: Connectin C1.427.

Techniques: Recombinant, Software, Cell Culture

Journal: Cell

Article Title: A Genetically Defined Compartmentalized Striatal Direct Pathway for Negative Reinforcement

doi: 10.1016/j.cell.2020.08.032

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-MOR Immunostar 24216 Rabbit polyclonal anti-tyrosine hydroxylase Millipore AB152 Chicken polyclonal anti-GFP Aves Labs GFP1020 Rabbit polyclonal anti-RFP Rockland 600-401-379 Rabbit monoclonal anti-HA-Tag Cell Signaling 3724S Mouse monoclonal anti-Parvalbumin Millipore MAB1572 Rabbit polyclonal anti-Somatostatin-14 Peninsula Laboratories T-4103 Goat polyclonal anti-ChAT Millipore AB144P Bacterial and Virus Strains AAV8-Ef1a-fDIO-GCaMP6m Laboratory of Karl Deisseroth N/A AAVdj-hSyn-Cre OFF /Flp ON -hChR2(H134R)-eYFP Fenno et al., 2014 Addgene 55648 AAVdj-hSyn-Cre ON /Flp OFF -hChR2(H134R)-eYFP Fenno et al., 2014 Addgene 55646 AAV8-EF1a-fDIO-Cre-p2A-mCherry Laboratory of Karl Deisseroth N/A AAV5-Ef1a-DIO-hChR2(H134R)-eYFP UNC N/A AAVdj-EF1a-fDIO-eYFP UNC N/A AAV8-hSyn-DIO-KORD-IRES-Mcitrine UNC N/A AAV2/8-Ef1a-fDIO-TVA-mCherry Laboratory of Z. Josh Huang N/A retroAAV2-CBA-fDIO-Cre Vigene Biosciences N/A AAV9-CAGGS-Flex-mKate-T2A-TVA HHMI Janelia Research Campus N/A AAV9-CAGGS-Flex-mKate-T2A-N2c-G HHMI Janelia Research Campus N/A Rbv-CVS-N2c-dG-GFP HHMI Janelia Research Campus Addgene 73461 AAV8-hSyn-DIO-mCherry Addgene Addgene 50459 Experimental Models: Organisms/Strains Mouse: Tg(Drd1a-cre)FK150Gsat/Mmucd (the “D1-Cre” line) MMRRC RRID: MMRRC_029178-UCD Mouse: B6.FVB(Cg)-Tg(Adora2a-cre) KG139Gsat/Mmucd (the “A2A-Cre” line) MMRRC RRID: MMRRC_036158-UCD Mouse: Tshz1-2A-FlpO This study N/A Mouse: Frt-Stop-Frt-TdTomato He et al., 2016 N/A Mouse: Pdyn-IRES-Cre (B6.Cg-129S-Pdyn tm1.1(cre)Mjkr/LowlJ) The Jackson Laboratory JAX: 027958 Mouse: Ai14 (B6.Cg-Gt(ROSA) 26Sortm14(CAG-tdTomato)Hze/J) The Jackson Laboratory JAX: 007908 Software and Algorithms ImageJ (Fiji) software NIH https://fiji.sc/ MATLAB Mathworks https://www.mathworks.com/ GraphPad Prism 7 GraphPad Software https://www.graphpad.com/ Open in a separate window KEY RESOURCES TABLE Tshz1 labels a population of striatal direct pathway medium spiny neurons (dMSNs) Tshz1 -expressing ( Tshz1 + ) dMSNs are localized in the striosome Tshz1 + striosomal dMSNs represent punishment and drive negative reinforcement Pdyn labels another population of striosomal dMSNs mediating positive reinforcement

Techniques: Software

Journal: International endodontic journal

Article Title: Direct contact with endothelial cells drives dental pulp stem cells toward smooth muscle cells differentiation via TGF-β1 secretion.

doi: 10.1111/iej.13943

Figure Lengend Snippet: FIGURE 5 The level of activin A and TGF-β1 in CM of dental pulp stem cell (DPSC) monoculture and HUVEC+DPSC cocultures. (a–c) Western blot analysis of the expression of p-Smad2 and Smad2 in DPSC monoculture and HUVEC+DPSC cocultures at day 3 and day 6. (d–e) ELISA analysis of the expression level of activin A and TGF-β1 in CM of DPSC monoculture and HUVEC+DPSC cocultures at the indicated time points. Data are represented as mean ± standard error (n = 3), **p < .01, ***p < .001, ****p < .0001.

Article Snippet: T- DPSCs were the DPSCs treated by recombinant human TGF- β1 (10 ng/mL) (R&D Systems) for 6 days.

Techniques: Western Blot, Expressing, Enzyme-linked Immunosorbent Assay

Journal: International endodontic journal

Article Title: Direct contact with endothelial cells drives dental pulp stem cells toward smooth muscle cells differentiation via TGF-β1 secretion.

doi: 10.1111/iej.13943

Figure Lengend Snippet: FIGURE 6 The expression of α-SMA, SM22α and Calponin in dental pulp stem cells (DPSCs) after treatment with activin A or TGF-β1. (a–d) Western blot analysis of the expression of α-SMA, SM22α and Calponin in DPSCs after treatment with activin A (25 ng/mL) for 3 and 6 days. (e–h) Western blot analysis of the expression of α-SMA, SM22α and Calponin in DPSCs after treatment with TGF-β1 (10 ng/mL) for 3 and 6 days. (i) Representative fluorescent images of DPSCs and T-DPSCs probed for α-SMA and SM22α (red), and nuclei (DAPI, blue), the scale bar represents 100 μm. (j) ELISA analysis of the TGF-β1 level in CM of HUVECs and DPSCs from monoculture and cocultures. (k) Contraction assay analysis of the contractility of DPSC, E-DPSC and T-DPSC in collagen gel. (l) The gel diameters were measured and analysed with Image J software after cells were seeded in the gels for 48 h. Data are represented as mean ± standard error (n = 3), ns = no significant difference, *p < 0.05, **p < 0.01, ***p < 0.001. HUVEC, human umbilical vascular endothelial cells.

Article Snippet: T- DPSCs were the DPSCs treated by recombinant human TGF- β1 (10 ng/mL) (R&D Systems) for 6 days.

Techniques: Expressing, Western Blot, Enzyme-linked Immunosorbent Assay, Contraction Assay, Software

Journal: International endodontic journal

Article Title: Direct contact with endothelial cells drives dental pulp stem cells toward smooth muscle cells differentiation via TGF-β1 secretion.

doi: 10.1111/iej.13943

Figure Lengend Snippet: FIGURE 7 The expression of smooth muscle cell-specific markers in HUVEC+DPSC cocultures after blocking of TGF-β1/ALK5 signalling pathway. (a) Western blot analysis of the expression of p-Smad2, Smad2, α-SMA, SM22α and Calponin in HUVEC+DPSC cocultures with or without TGF-β RI kinase inhibitor (150 nM) for 6 days. (b–f) Quantitative analysis of bands intensities in (a) with Image J. (g) Representative fluorescent images of DPSC monoculture and HUVEC+DPSC cocultures probed for α-SMA and SM22α (red), CD31 (green) and nuclei (DAPI, blue) with or without TGF-β RI kinase inhibitor (150 nM) for 6 days, the scale bar represents 100 μm. Data are represented as mean ± standard error (n = 3), *p < .05, **p < .01, ***p < .001. DPSC, dental pulp stem cell; HUVEC, human umbilical vascular endothelial cells.

Article Snippet: T- DPSCs were the DPSCs treated by recombinant human TGF- β1 (10 ng/mL) (R&D Systems) for 6 days.

Techniques: Expressing, Blocking Assay, Western Blot

Journal: International endodontic journal

Article Title: Direct contact with endothelial cells drives dental pulp stem cells toward smooth muscle cells differentiation via TGF-β1 secretion.

doi: 10.1111/iej.13943

Figure Lengend Snippet: FIGURE 8 The expression of α-SMA, SM22α and Calponin in dental pulp stem cells (DPSCs) after blocking of TGF-β1/ALK5 signalling pathway. (a) Western blot analysis of the expression of α-SMA, SM22α and Calponin in DPSCs pretreated with TGF-β RI kinase inhibitor (150 nM) followed by treatment with E+D-CM or treated with E+D-CM supplemented with anti-TGF-β1 IgG for 6 days. (b–f) Quantitative analysis of bands intensities in (a) with Image J. (g) Representative fluorescent images of DPSC probed for α-SMA and SM22α (red), and nuclei (DAPI, blue) pretreated with TGF-β RI kinase inhibitor (150 nM) followed by treatment with E+D-CM or treated with E+D-CM supplemented with anti-TGF-β1 IgG for 6 days; the scale bar represents 100 μm. Data are represented as mean ± standard error (n = 3), ns = no significant difference, *p < .05, **p < .01, ***p < .001, ****p < .0001.

Article Snippet: T- DPSCs were the DPSCs treated by recombinant human TGF- β1 (10 ng/mL) (R&D Systems) for 6 days.

Techniques: Expressing, Blocking Assay, Western Blot

Journal: bioRxiv

Article Title: The Circadian Clock Controls Hepatic Stellate Cell Activation in Liver Fibrosis via a BMAL1/CK1ε/REV-ERBα/Transgelin Signaling Pathway

doi: 10.1101/2025.09.12.675813

Figure Lengend Snippet: A) Bmal1-Luc rhythmicity in EMS404 cells. Synchronized EMS404 Bmal1-Luc cells were treated with vehicle or TGFβ (10 ng/mL) and the bioluminescence was recorded for over 72 h. Data were analyzed using the NiteCap software for circadian parameters (inset). B) CCG expression. Time-dependent gene (upper panel, by RT-qPCR) and protein (lower panel, by WES) expression levels were measured in synchronized EMS404 cells treated or not with TGFβ (10 ng/mL). Averaged expression values (mean ± S.E.M., n=3) are shown. C) Profibrotic gene expression in EMS cells. Profibrotic gene expression levels were measured in EMS404 cells pretreated for 24 h with indicated compounds (10 µM) followed by treatment for another 24 h with additional vehicle or TGFβ (10 ng/mL) treatment. Averaged expression values (mean ± S.E.M., n=3-5) were compared for each gene using one-way ANOVA followed by Tukey’s post hoc test. D) COL1A1 protein expression in EMS cells. EMS404 cells were treated as in C) for measurement of indicated protein levels by immunoblotting. HSP90 was used as loading control. E) Contractility assay. EMS404 cells were subjected to a collagen gel contraction assay by embedding into a solidified collagen lattice and treatment with either CLK8 (10 µM), SR9011 (10 µM) or SB431542 (1 µM) in the presence or absence of TGFβ (10 ng/mL). Representative pictures of collagen disks are shown (left panel). Daily measurements of disk diameters are shown in the right panel. Averaged expression values (mean ± S.E.M., n=3) were compared for each gene using two-way ANOVA followed by Tukey’s post hoc test. *: p<0.05, **: p <0.01, ***: p<0.005, ****: p<0.001.

Article Snippet: Recombinant human TGFβ1 (#240-B-002) was from R&D Systems.

Techniques: Software, Expressing, Quantitative RT-PCR, Gene Expression, Western Blot, Control, Collagen Gel Contraction Assay

Journal: bioRxiv

Article Title: The Circadian Clock Controls Hepatic Stellate Cell Activation in Liver Fibrosis via a BMAL1/CK1ε/REV-ERBα/Transgelin Signaling Pathway

doi: 10.1101/2025.09.12.675813

Figure Lengend Snippet: EMS404 cells were pretreated for 24 h with the indicated compound, followed by an additional 24 h of treatment with the same compound in the presence of TGFβ. A) Principal component analysis (PCA) of RNA-seq data. PCA was performed on normalized gene expression values, with each point representing an individual sample. Colors indicate the eight distinct experimental conditions. B) Heatmap of averaged gene expression values (TPM). Hierarchical clustering was applied using Euclidean distance and complete linkage. C) Biological term enrichment analysis. Following DESeq2 differential expression analysis, the top 500 up- and downregulated genes were annotated using Gene Ontology Biological Process and Reactome databases. The most significantly enriched terms are shown for each comparison.

Article Snippet: Recombinant human TGFβ1 (#240-B-002) was from R&D Systems.

Techniques: RNA Sequencing, Gene Expression, Quantitative Proteomics, Comparison

Journal: bioRxiv

Article Title: The Circadian Clock Controls Hepatic Stellate Cell Activation in Liver Fibrosis via a BMAL1/CK1ε/REV-ERBα/Transgelin Signaling Pathway

doi: 10.1101/2025.09.12.675813

Figure Lengend Snippet: A) Transgelin gene expression in human fibrotic livers. TAGLN expression values were extracted from the human fibrosis sub-cohort described in , encompassing 53 non-fibrotic (F=0) and 53 fibrotic (F>2) propensity-matched liver samples. Red line: median, dotted lines: 1 st quartile. Statistical analysis was done using an unpaired two-tailed t-test. B) Transgelin gene expression in mouse fibrotic liver. Tagln expression was measured by RNAseq in mouse liver cell types after CCl 4 treatment as described in . Averaged values (n=3, mean ± S.E.M.) were compared using two-way ANOVA followed by Tukey’s post hoc test. *: p<0.05, **: p <0.01, ***: p<0.005, ****: p<0.001. C) Time-of-day expression of Tagln in mouse liver. Circadian expression of Nr1d1 , Bmal1 and Tagln was determined by RT-qPCR in livers of ad libitum -fed mice. Data were extracted from ( Zummo et al ., 2023 ). D) Tagln expression in EMS404 cells. Tagln mRNA expression was measured by RT-qPCR in EMS404 cells treated with SR9011 (10 µM), CLK8 (10 µM) or SB431542 (10 µM) in the presence or absence of TGFβ (10ng/mL). Averaged values (n=3-5, mean ± S.E.M.) were compared using one-way ANOVA followed by Tukey’s post hoc test. *: p<0.05, **: p <0.01, ***: p<0.005, ****: p<0.001. E) BMAL1 and REV-ERBα genomic binding sites. REV-ERBα and BMAL1 ChIP-Seq data from bulk mouse liver were extracted from publicly available datasets ( Bugge et al ., 2012 ; Koike et al ., 2012 ) and tracks at the Bmal1 , Nr1d1 and Tagln genomic loci were visualized using IGV.

Article Snippet: Recombinant human TGFβ1 (#240-B-002) was from R&D Systems.

Techniques: Gene Expression, Expressing, Two Tailed Test, Quantitative RT-PCR, Binding Assay, ChIP-sequencing

Journal: bioRxiv

Article Title: The Circadian Clock Controls Hepatic Stellate Cell Activation in Liver Fibrosis via a BMAL1/CK1ε/REV-ERBα/Transgelin Signaling Pathway

doi: 10.1101/2025.09.12.675813

Figure Lengend Snippet: A,B) Transgelin expression in EMS404 cells. Tagln gene (A) and protein (B) expression was measured by RT-qPCR or WES in EMS404 cells 48 h after transfection with scrambled control or Tagln -targeting siRNA and treatment with TGFβ (10 ng/mL) for the last 24 h Averaged values (n=3-5, mean ± S.E.M.) were compared using two-way ANOVA followed by Tukey’s post hoc test. *: p<0.05, **: p <0.01, ***: p<0.005, ****: p<0.001. C) Acta2 gene expression was measured as in A). Averaged values (n=3-5, mean ± S.E.M.) were compared using two-way ANOVA followed by Tukey’s post hoc test. *: p<0.05, **: p <0.01, ***: p<0.005, ****: p<0.001. D) Contraction assay. Cells were treated as in A) for a collagen gel contraction assay as in . Means were compared as in C). NLE) Protein expression in EMS404 cells. EMS404 cells were transfected with scrambled control or Bmal1 -targeting siRNA and treated with vehicle or TGFβ (10 ng/mL) as in Supp. Fig. 1. Analysis of indicated proteins was performed by WES. F) Gene expression in EMS404 cells. Tagln expression was measured by RT-qPCR in EMS404 cells treated overnight with vehicle, TGFβ(10 ng/mL), PF670462 (10 µM) , or both compounds. Averaged values (n=3-5, mean ± S.E.M.) were compared using one-way ANOVA followed by Tukey’s post hoc test. *: p<0.05, **: p <0.01, ***: p<0.005, ****: p<0.001. G) Proposed model. A hypothetical model for the interplay between the clock and TGFβ signaling, converging on transgelin to control cell contractility, a hallmark of HSC activation, is shown. RORE: Rev-Erb/ROR Response Element; SBE: Smad Binding Element; qHSC: quiescent HSC; aHSC: activated HSC.

Article Snippet: Recombinant human TGFβ1 (#240-B-002) was from R&D Systems.

Techniques: Expressing, Quantitative RT-PCR, Transfection, Control, Gene Expression, Contraction Assay, Collagen Gel Contraction Assay, Activation Assay, Binding Assay

Journal: Cell reports

Article Title: Mild Impairment of Mitochondrial OXPHOS Promotes Fatty Acid Utilization in POMC Neurons and Improves Glucose Homeostasis in Obesity

doi: 10.1016/j.celrep.2018.09.034

Figure Lengend Snippet: (A and B) Representative confocal images (A) and quantification (B) of in situ hybridization of mRNA of AIFm1 (red) and POMC (green) and corresponding nuclear counterstaining (DAPI, blue) in the arcuate nucleus of the hypothalamus (ARH) of AIFΔPOMC and AIFfl control mice (n = 3 per genotype group). Scale bars, 50 μm.

Article Snippet: Taqman probe AIFm1 , Thermo Fisher , Mm00442545_m1.

Techniques: In Situ Hybridization, Control

Journal: Cell reports

Article Title: Mild Impairment of Mitochondrial OXPHOS Promotes Fatty Acid Utilization in POMC Neurons and Improves Glucose Homeostasis in Obesity

doi: 10.1016/j.celrep.2018.09.034

Figure Lengend Snippet: (A) Knockdown efficiency of AIFm1 mRNA expression in hypothalamic cell line N43/5 (AIF knockout [KO]) compared to control-locked nucleic acid (LNA)-treated (Control) and untreated cells (n = 4 per group).

Article Snippet: Taqman probe AIFm1 , Thermo Fisher , Mm00442545_m1.

Techniques: Knockdown, Expressing, Knock-Out, Control

Journal: Cell reports

Article Title: Mild Impairment of Mitochondrial OXPHOS Promotes Fatty Acid Utilization in POMC Neurons and Improves Glucose Homeostasis in Obesity

doi: 10.1016/j.celrep.2018.09.034

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Taqman probe AIFm1 , Thermo Fisher , Mm00442545_m1.

Techniques: Recombinant, Isolation, Enzyme-linked Immunosorbent Assay, CyQUANT Assay, Proliferation Assay, Fluorescence, RNAscope, Negative Control, Software, Control, Transferring, Patch Clamp

Journal: iScience

Article Title: Perturbation of placental protein glycosylation by endoplasmic reticulum stress promotes maladaptation of maternal hepatic glucose metabolism

doi: 10.1016/j.isci.2022.105911

Figure Lengend Snippet:

Article Snippet: Concanavalin A-biotinylated lectin , Vector Laboratories , Cat#B-1005.

Techniques: Recombinant, Plasmid Preparation, Avidin-Biotin Assay, Lysis, Isolation, Bradford Protein Assay, Labeling, SYBR Green Assay, Mutagenesis, Software