Journal: NPJ biofilms and microbiomes

Article Title: Alleviation of Limosilactobacillus reuteri in polycystic ovary syndrome protects against circadian dysrhythmia-induced dyslipidemia via capric acid and GALR1 signaling.

doi: 10.1038/s41522-023-00415-2

Figure Lengend Snippet: Fig. 2 Liver transcriptome analysis of L. reuteri-treated darkness rats. Heatmaps displaying 36 highly expressed genes (a) and 76 lowly expressed genes (b) in the liver of darkness rats compared with control and DL.reuteri rats through DEG analysis using Ballgown software (| fold change | > 0.6 in the log2 ratio value, raw P < 0.05). c Top terms from GO analysis (above) and terms from KEGG analysis (below) of the 112 differential genes in the DEG analysis. The P values of GO and KEGG analyses were determined on the DAVID website. d Visualization of the top GO and KEGG terms related with lipid metabolism and circadian rhythm in the DEG analysis. e Spearman rank correlations between module eigengenes (ME) and clinical biochemical index in the WGCNA analysis (|ρ | > 0.3, *P < 0.05). f Visualization of the top GO and KEGG terms related with lipid metabolism and circadian rhythm of purple module genes (102) in the WGCNA analysis. Circle, genes; Square, KEGG terms; Hexagon, GO terms. The bigger the square or hexagon, the more genes involved. g Crosstalk among different groups of genes identified the possible target genes taking essential roles in the lipid metabolism of L. reuteri-treated darkness rats. h mRNA abundances of Galr1, Galr2, Nr1d1, Nr1d2, Insig2, Srebf1, Lxra, and Rxra in rat liver detected by qPCR. β-Actin was used as a loading control for qPCR analyses. i Serum galanin concentration detected by ELISA. Statistical analysis (h, i) was performed with one-way ANOVA followed by Newman–Keuls multiple comparison test. n = 8 per group. Data present means ± SEM. *P < 0.05, **P < 0.01.

Article Snippet: Published in partnership with Nanyang Technological University npj Biofilms and Microbiomes (2023) 47 GALR2 antibody (1:500; #26459-1-AP, Proteintech, Wuhan, China), NR1D1 antibody (1:1000, #13418 S, Cell Signaling Technology, Massachusetts, USA; 1:1000, #14506-1-AP, Proteintech), NR1D2 antibody (1:500; #13906-1-AP, Proteintech), SREBP1 antibody (1:1000; #41878, Signalway Antibody), LXRa antibody (1:1000; #ab176323, Abcam, Cambridge, UK), RXRa antibody (1:1000; #ab125001, Abcam), INSIG2 antibody (1:500; #24766-1, Proteintech), P-AKT antibody (1:1000; #4060, Cell Signaling Technology), Fig. 8 Proposed mechanisms for the amelioration of L. reuteri on dyslipidemia in circadian dysrhythmia-induced PCOS-like rats.

Techniques: Control, Software, Concentration Assay, Enzyme-linked Immunosorbent Assay, Comparison

Journal: NPJ biofilms and microbiomes

Article Title: Alleviation of Limosilactobacillus reuteri in polycystic ovary syndrome protects against circadian dysrhythmia-induced dyslipidemia via capric acid and GALR1 signaling.

doi: 10.1038/s41522-023-00415-2

Figure Lengend Snippet: Fig. 8 Proposed mechanisms for the amelioration of L. reuteri on dyslipidemia in circadian dysrhythmia-induced PCOS-like rats. Left, circadian dysrhythmia due to constant darkness resulted in dyslipidemia and reproductive hallmarks of PCOS in rats. Elevated galanin-GALR1 induced by darkness exposure functioned as an upstream factor of PI3K/AKT pathway and further suppressed NR1D1-induced SREBF1 transcription and translation, thus inducing hepatic lipid accumulation in PCOS-like rats. Right, L. reuteri supplementation ameliorated dyslipidemia and reproductive hallmarks in circadian dysrhythmia-induced PCOS-like rats. L. reuteri restructured microbiome-metabolome network in darkness rats ameliorating the abundance of Lactobacillus, Clostridium sensu stricto 1, Ruminococcaceae UCG-010, and Family XIII AD3011 group, followed by varied serum levels of cortisol, cis-9-palmitoleic acid, 13-methylmyristic acid, capric acid, and dUMP. Notably, capric acid mediated the inhibition of L. reuteri on hepatic GALR1-PI3K/AKT-NR1D1-SREBP1 pathway, which eventually alleviated dyslipidemia.

Article Snippet: Published in partnership with Nanyang Technological University npj Biofilms and Microbiomes (2023) 47 GALR2 antibody (1:500; #26459-1-AP, Proteintech, Wuhan, China), NR1D1 antibody (1:1000, #13418 S, Cell Signaling Technology, Massachusetts, USA; 1:1000, #14506-1-AP, Proteintech), NR1D2 antibody (1:500; #13906-1-AP, Proteintech), SREBP1 antibody (1:1000; #41878, Signalway Antibody), LXRa antibody (1:1000; #ab176323, Abcam, Cambridge, UK), RXRa antibody (1:1000; #ab125001, Abcam), INSIG2 antibody (1:500; #24766-1, Proteintech), P-AKT antibody (1:1000; #4060, Cell Signaling Technology), Fig. 8 Proposed mechanisms for the amelioration of L. reuteri on dyslipidemia in circadian dysrhythmia-induced PCOS-like rats.

Techniques: Inhibition

Journal: Breast Cancer Research : BCR

Article Title: High expression of NR1D1 is associated with good prognosis in triple-negative breast cancer patients treated with chemotherapy

doi: 10.1186/s13058-019-1197-x

Figure Lengend Snippet: Characteristics of breast cancer patients and their NR1D1 expression level

Article Snippet: The tissue sections were then incubated for 1 h at room temperature with a primary antibody against NR1D1 (H00009572-M02, Novus Biologicals LCC, Littleton, CO, USA) diluted to a final concentration of 1:1000.

Techniques: Expressing, Biomarker Discovery, Amplification, Adjuvant

Journal: Breast Cancer Research : BCR

Article Title: High expression of NR1D1 is associated with good prognosis in triple-negative breast cancer patients treated with chemotherapy

doi: 10.1186/s13058-019-1197-x

Figure Lengend Snippet: Association of NR1D1 expression with clinical outcome in breast cancer patients. Kaplan−Meier curves for OS and DFS according to NR1D1 expression in all breast cancer patients and in breast cancer patients receiving chemotherapy. Three or two patients without OS or DFS information, respectively, were excluded from the analysis

Article Snippet: The tissue sections were then incubated for 1 h at room temperature with a primary antibody against NR1D1 (H00009572-M02, Novus Biologicals LCC, Littleton, CO, USA) diluted to a final concentration of 1:1000.

Techniques: Expressing

Journal: Breast Cancer Research : BCR

Article Title: High expression of NR1D1 is associated with good prognosis in triple-negative breast cancer patients treated with chemotherapy

doi: 10.1186/s13058-019-1197-x

Figure Lengend Snippet: Prognostic significance of NR1D1 expression in TNBC patients treated with chemotherapy. Kaplan−Meier curves for OS and DFS according to NR1D1 expression in molecular subtypes of breast cancer patients treated with chemotherapy. A patient with no subtype information was excluded from the analysis

Article Snippet: The tissue sections were then incubated for 1 h at room temperature with a primary antibody against NR1D1 (H00009572-M02, Novus Biologicals LCC, Littleton, CO, USA) diluted to a final concentration of 1:1000.

Techniques: Expressing

Journal: Breast Cancer Research : BCR

Article Title: High expression of NR1D1 is associated with good prognosis in triple-negative breast cancer patients treated with chemotherapy

doi: 10.1186/s13058-019-1197-x

Figure Lengend Snippet: Univariate analysis of OS and DFS in the TNBC patients treated with chemotherapy

Article Snippet: The tissue sections were then incubated for 1 h at room temperature with a primary antibody against NR1D1 (H00009572-M02, Novus Biologicals LCC, Littleton, CO, USA) diluted to a final concentration of 1:1000.

Techniques: Expressing, Biomarker Discovery

Journal: Breast Cancer Research : BCR

Article Title: High expression of NR1D1 is associated with good prognosis in triple-negative breast cancer patients treated with chemotherapy

doi: 10.1186/s13058-019-1197-x

Figure Lengend Snippet: Multivariate analysis of OS and DFS in the TNBC patients treated with chemotherapy

Article Snippet: The tissue sections were then incubated for 1 h at room temperature with a primary antibody against NR1D1 (H00009572-M02, Novus Biologicals LCC, Littleton, CO, USA) diluted to a final concentration of 1:1000.

Techniques: Expressing

Journal: Nature communications

Article Title: Circadian clock molecule REV-ERBα regulates lung fibrotic progression through collagen stabilization.

doi: 10.1038/s41467-023-36896-0

Figure Lengend Snippet: Fig. 1 | Decreased REV-ERBα protein abundance and increased protein levels of COL1A1 and LOX in IPF lungs compared to healthy control. Healthy control and IPF formalin fixed-paraffin embedded (FFPE) lung samples were purchased from Origene Inc. Healthy controls contained 100% normal lung architecture with 85% alveoli surface area. IPF patient samples contained at least 50% lesion surface area. The protein abundance of REV-ERBα, COL1A1, and LOX were visualized and

Article Snippet: Sections were then blocked with 10% normal goat serum and incubated with anti-COL1A1 (1:100, NBP1-30054, Novus Biologicals), anti-Lox (1:100, NB100-2527, Novus Biologicals), anti-Col4A1 (1:200, ab227616, Abcam), and anti-Rev-erbα (1:100, NBP1-84931, Novus Biologicals) at 4 °C overnight.

Techniques: Quantitative Proteomics, Control

Journal: Nature communications

Article Title: Circadian clock molecule REV-ERBα regulates lung fibrotic progression through collagen stabilization.

doi: 10.1038/s41467-023-36896-0

Figure Lengend Snippet: Fig. 4 | Rev-erbα agonist (SR9009) treatment helped to reduce the collagen overexpression occurred in bleomycin induced lung fibrosis. C57BL/6J WT mice (equal number of male and female mice) were dosed with bleomycin for 14 days, and SR9009 was given via i.p. injection at a dose of (100 mg/kg) daily. a The body weights and the survival rate was monitored until day 14 post-injury (n = 8–12 mice per group). b Lungs were harvested, and H&E staining was performed to identify the injured area percentage (n = 8 mice per group). c RNA was isolated, and gene expression analysis was conducted using nCounter Fibrosis panel via nCounter SPRINT Profiler, and transcripts levels were normalized and visualized by nSolver. The dysregulated genes focused on collagen dynamics and ECM remodeling were

Article Snippet: Sections were then blocked with 10% normal goat serum and incubated with anti-COL1A1 (1:100, NBP1-30054, Novus Biologicals), anti-Lox (1:100, NB100-2527, Novus Biologicals), anti-Col4A1 (1:200, ab227616, Abcam), and anti-Rev-erbα (1:100, NBP1-84931, Novus Biologicals) at 4 °C overnight.

Techniques: Over Expression, Injection, Staining, Isolation, Gene Expression

Journal: Nature communications

Article Title: Circadian clock molecule REV-ERBα regulates lung fibrotic progression through collagen stabilization.

doi: 10.1038/s41467-023-36896-0

Figure Lengend Snippet: Fig. 5 | IAV induced lung injury and profibrotic responses exaggerated in Rev- erbα Het mice compared to WT mice. WT and Rev-erbα Het mice were infected (103 PFU/mouse) with IAV or PBS control for 15 days. a Body weights were mon- itored during infection, and virus-specific antibodies in serum were detected by ELISA (n = 5–19 mice per group, *p < 0.05, **p < 0.01, ***p < 0.01 vs. IAV infected WT mice). b During sacrifice, lung mechanics (resistance, compliance, and elastance) were measured. (n = 3–4 mice per group). c H&E stained lung sections were used to analyze the injured area induced by IAV infection. Regions within the black squares were shown with ×20 magnification (n = 4–6 mice per group). Data were shown as

Article Snippet: Sections were then blocked with 10% normal goat serum and incubated with anti-COL1A1 (1:100, NBP1-30054, Novus Biologicals), anti-Lox (1:100, NB100-2527, Novus Biologicals), anti-Col4A1 (1:200, ab227616, Abcam), and anti-Rev-erbα (1:100, NBP1-84931, Novus Biologicals) at 4 °C overnight.

Techniques: Infection, Control, Virus, Enzyme-linked Immunosorbent Assay, Staining

Journal: Nature communications

Article Title: Circadian clock molecule REV-ERBα regulates lung fibrotic progression through collagen stabilization.

doi: 10.1038/s41467-023-36896-0

Figure Lengend Snippet: Fig. 7 | IAV infection induced dysregulation of profibrotic progression exa- cerbated in Rev-erbα Het mice. WT and Rev-erbα Het mice (equal number of male and female) infected (103 PFU/mouse) with IAV for 15 days, and lungs were sepa- rated for RNA/protein isolation, or fixed with 10% formalin for FFPE sections. a The protein abundance of COL1A2, VIM and activated LOX were measured by western blot. Representative blot images were shown. Different targets were run on the same membrane: COL1A2, VIM and activated LOX were probed in the same membrane and β-ACTIN was used as an endogenous control (n = 5–6 mice per group). b The localizations of COL1A1 and LOX were determined by

Article Snippet: Sections were then blocked with 10% normal goat serum and incubated with anti-COL1A1 (1:100, NBP1-30054, Novus Biologicals), anti-Lox (1:100, NB100-2527, Novus Biologicals), anti-Col4A1 (1:200, ab227616, Abcam), and anti-Rev-erbα (1:100, NBP1-84931, Novus Biologicals) at 4 °C overnight.

Techniques: Infection, Isolation, Quantitative Proteomics, Western Blot, Membrane, Control

Journal: Current Issues in Molecular Biology

Article Title: Loss of Melanopsin (OPN4) Leads to a Faster Cell Cycle Progression and Growth in Murine Melanocytes

doi: 10.3390/cimb43030101

Figure Lengend Snippet: Primers, sequences, and access numbers.

Article Snippet: Cells were washed and incubated overnight in PER1 (ABCAM, USA, ab136451, 1:200), BMAL1 (ABCAM, ab93806, 1:200), or REV-ERBα (Novus Biological, Minneapolis, Minnesota, USA, NBP2-19574, 1:200) antibodies in Perm/Wash buffer.

Techniques:

Journal: Current Issues in Molecular Biology

Article Title: Loss of Melanopsin (OPN4) Leads to a Faster Cell Cycle Progression and Growth in Murine Melanocytes

doi: 10.3390/cimb43030101

Figure Lengend Snippet: PER1, BMAL1, and REV-ERBα protein evaluation using specific antibodies in flow cytometry in Opn4 WT and Opn4 KO melanocytes. ( A , D , G ) Representative gates of PER1-, BMAL1-, and REV-ERBα-stained cells; ( B , E , H ) percentage of positive cells for a given protein; ( C , F , I ) median intensity fluorescence (MIF). ( n = 4–6). * p < 0.05. ** p < 0.01.

Article Snippet: Cells were washed and incubated overnight in PER1 (ABCAM, USA, ab136451, 1:200), BMAL1 (ABCAM, ab93806, 1:200), or REV-ERBα (Novus Biological, Minneapolis, Minnesota, USA, NBP2-19574, 1:200) antibodies in Perm/Wash buffer.

Techniques: Flow Cytometry, Staining, Fluorescence

Journal: Animals : an Open Access Journal from MDPI

Article Title: The Distribution, Expression Patterns and Functional Analysis of NR1D1 and NR4A2 in the Reproductive Axis Tissues of the Male Tianzhu White Yak

doi: 10.3390/ani11113117

Figure Lengend Snippet: Localization of NR1D1 and NR4A2 proteins in adult male yak (4 years old) HPG tissues. ( A1 – F1 ), Localization of NR1D1 protein in adult male yak HPG tissues. ( A2 – F2 ), Localization of NR4A2 protein in adult male yak HPG tissues. ( A3 – F3 ), The negative control of adult male yak HPG tissues. NC, neurogliocyte (100×). The box in the lower left corner is a partial enlarged view (400×). A, adenohypophysis; N, neurohypophysis; P, pituicyte; AC, acidophilic cells; BC, basophilic cells; CC, chromophobe cells; NF, nerve fibers; ST, seminiferous tubule; MC, myoid cells; LC, interstitial cells; SC, spermatogonium; PS, primary spermatocyte; S, spermatozoon; DET, ductuli efferentes testis; B, basal cells; PC, principal cells; SM, smooth muscle cells; CT, connective tissue; DE, ductus epididymidis.

Article Snippet: The membranes were incubated at 4 °C overnight with rabbit monoclonal anti-NR1D1 (1:300), anti-NR4A2 (1:300), and anti-β-actin (1:4000, Bioss, Beijing, China) primary antibodies.

Techniques: Negative Control

Journal: Animals : an Open Access Journal from MDPI

Article Title: The Distribution, Expression Patterns and Functional Analysis of NR1D1 and NR4A2 in the Reproductive Axis Tissues of the Male Tianzhu White Yak

doi: 10.3390/ani11113117

Figure Lengend Snippet: Localization of NR1D1 and NR4A2 in adult yak (4 years old) testis and epididymis tissues using IF staining. ( A – D ), localization of NR1D1 and NR4A2 in adult yak testis, caput epididymis, corpus epididymis and cauda epididymis, respectively (100×). ( a – d ), The amplification results of local structures in yak testis, caput epididymis, corpus epididymis and cauda epididymis, respectively (400×). ST, seminiferous tubule; MC, myoid cells; LC, interstitial cells; SC, spermatogonium; S, spermatozoon; DET, ductuli efferentes testis; B, basal cells; PC, principal cells; SM, smooth muscle cells; CT, connective tissue; DE, ductus epididymidis.

Article Snippet: The membranes were incubated at 4 °C overnight with rabbit monoclonal anti-NR1D1 (1:300), anti-NR4A2 (1:300), and anti-β-actin (1:4000, Bioss, Beijing, China) primary antibodies.

Techniques: Staining, Amplification

Journal: Animals : an Open Access Journal from MDPI

Article Title: The Distribution, Expression Patterns and Functional Analysis of NR1D1 and NR4A2 in the Reproductive Axis Tissues of the Male Tianzhu White Yak

doi: 10.3390/ani11113117

Figure Lengend Snippet: The expression levels of NR1D1 and NR4A2 mRNA and proteins in adult yak (4 years old) HPG tissues. ( A , B ), The expression of NR1D1 and NR4A2 mRNA, respectively, in yak HPG tissues, measured using qPCR. ( C , D ), The expression of NR1D1 and NR4A2 protein, respectively, in yak HPG tissues, measured using Western blot. ( E , F ), The IOD values of NR1D1 and NR4A2 proteins in yak HPG tissues, respectively. The expression levels of NR1D1 and NR4A2 mRNA and protein in the hypothalamus were used as the controls. The expression of β-actin was used as an endogenous control. **, represent extremely significant difference vs. control ( p < 0.01).

Article Snippet: The membranes were incubated at 4 °C overnight with rabbit monoclonal anti-NR1D1 (1:300), anti-NR4A2 (1:300), and anti-β-actin (1:4000, Bioss, Beijing, China) primary antibodies.

Techniques: Expressing, Western Blot

Journal: Animals : an Open Access Journal from MDPI

Article Title: The Distribution, Expression Patterns and Functional Analysis of NR1D1 and NR4A2 in the Reproductive Axis Tissues of the Male Tianzhu White Yak

doi: 10.3390/ani11113117

Figure Lengend Snippet: Expression patterns of NR1D1 and NR4A2 mRNA and protein in yak testicular tissues in animals of different ages. ( A , B ), The expression of NR1D1 and NR4A2 mRNA, respectively, in yak testicular tissues from animals of different ages, detected using qPCR. ( C , D ), The expression of NR1D1 and NR4A2 protein, respectively, detected using Western blot in yak reproductive axis tissues. ( E , F ), The IOD value of NR1D1 and NR4A2 protein, respectively, in testicular tissues from yaks of different ages. The expression levels of NR1D1 and NR4A2 mRNA and protein in testicular tissues of 2-year-old yaks were used as controls. The expression of β-actin was used as an endogenous control. *, represent significant difference vs. control ( p < 0.05), **, represent extremely significant difference vs. control ( p < 0.01). Y, Year; ns, represent NO significant difference.

Article Snippet: The membranes were incubated at 4 °C overnight with rabbit monoclonal anti-NR1D1 (1:300), anti-NR4A2 (1:300), and anti-β-actin (1:4000, Bioss, Beijing, China) primary antibodies.

Techniques: Expressing, Western Blot

Journal: Animals : an Open Access Journal from MDPI

Article Title: The Distribution, Expression Patterns and Functional Analysis of NR1D1 and NR4A2 in the Reproductive Axis Tissues of the Male Tianzhu White Yak

doi: 10.3390/ani11113117

Figure Lengend Snippet: GO and pathway prediction of yak NR1D1 and NR4A2 in reproductive hormone metabolism. ( A ), Network of GO terms and associated proteins in reproductive hormone metabolism. ( B ), Network of pathways and associated proteins in reproductive hormone metabolism.

Article Snippet: The membranes were incubated at 4 °C overnight with rabbit monoclonal anti-NR1D1 (1:300), anti-NR4A2 (1:300), and anti-β-actin (1:4000, Bioss, Beijing, China) primary antibodies.

Techniques: