gram positive enterococcus faecalis atcc 14506 Search Results


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ATCC gram positive enterococcus faecalis atcc 14506
Gram Positive Enterococcus Faecalis Atcc 14506, supplied by ATCC, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Proteintech nr1d1
LncCplx2 expression is regulated by BMAL1. (A) ChIP-qPCR assays demonstrating enrichment of BMAL1 at the LncCplx2 promoter region in Min6 cells. RNA Polymerase II antibody and IgG serve as the positive and negative control, respectively (n = 3/2). Two different primer pairs ( LncCplx2 -P1 and LncCplx2 -P2) targeted the promoter of LncCplx2 were used for the PCR assay. IB analysis of BMAL1, <t>NR1D1</t> and E4BP4 antibody immunoprecipitation efficiency, IgG as negative control. (B) IB analysis of BMAL1 protein level in Bmal1 KO and control Min6 cells. β-Actin was used as the loading control. (C) LncCplx2 expression was analyzed by qRT-PCR in Bmal1 KO and control Min6 cells (n = 4). (D) qRT-PCR analysis of Bmal1 and LncCplx2 expression in Min6 cells expressing two shRNAs targeting Bmal1 and scrambled shRNA as control (n = 3). (E) Effects of Bmal1 overexpression on different luciferase reporter activity driven by the LncCplx2 promoter and negative control (n = 6). All the data are shown as the mean ± SEM. ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001, ∗∗∗∗p < 0.0001, using two-tailed Student's t-test and one-way ANOVA.
Nr1d1, supplied by Proteintech, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Fluka Chemical bis hexamethylene triamine fluka 14506
LncCplx2 expression is regulated by BMAL1. (A) ChIP-qPCR assays demonstrating enrichment of BMAL1 at the LncCplx2 promoter region in Min6 cells. RNA Polymerase II antibody and IgG serve as the positive and negative control, respectively (n = 3/2). Two different primer pairs ( LncCplx2 -P1 and LncCplx2 -P2) targeted the promoter of LncCplx2 were used for the PCR assay. IB analysis of BMAL1, <t>NR1D1</t> and E4BP4 antibody immunoprecipitation efficiency, IgG as negative control. (B) IB analysis of BMAL1 protein level in Bmal1 KO and control Min6 cells. β-Actin was used as the loading control. (C) LncCplx2 expression was analyzed by qRT-PCR in Bmal1 KO and control Min6 cells (n = 4). (D) qRT-PCR analysis of Bmal1 and LncCplx2 expression in Min6 cells expressing two shRNAs targeting Bmal1 and scrambled shRNA as control (n = 3). (E) Effects of Bmal1 overexpression on different luciferase reporter activity driven by the LncCplx2 promoter and negative control (n = 6). All the data are shown as the mean ± SEM. ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001, ∗∗∗∗p < 0.0001, using two-tailed Student's t-test and one-way ANOVA.
Bis Hexamethylene Triamine Fluka 14506, supplied by Fluka Chemical, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Addgene inc mutant rela 3 utr plasmid
LncCplx2 expression is regulated by BMAL1. (A) ChIP-qPCR assays demonstrating enrichment of BMAL1 at the LncCplx2 promoter region in Min6 cells. RNA Polymerase II antibody and IgG serve as the positive and negative control, respectively (n = 3/2). Two different primer pairs ( LncCplx2 -P1 and LncCplx2 -P2) targeted the promoter of LncCplx2 were used for the PCR assay. IB analysis of BMAL1, <t>NR1D1</t> and E4BP4 antibody immunoprecipitation efficiency, IgG as negative control. (B) IB analysis of BMAL1 protein level in Bmal1 KO and control Min6 cells. β-Actin was used as the loading control. (C) LncCplx2 expression was analyzed by qRT-PCR in Bmal1 KO and control Min6 cells (n = 4). (D) qRT-PCR analysis of Bmal1 and LncCplx2 expression in Min6 cells expressing two shRNAs targeting Bmal1 and scrambled shRNA as control (n = 3). (E) Effects of Bmal1 overexpression on different luciferase reporter activity driven by the LncCplx2 promoter and negative control (n = 6). All the data are shown as the mean ± SEM. ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001, ∗∗∗∗p < 0.0001, using two-tailed Student's t-test and one-way ANOVA.
Mutant Rela 3 Utr Plasmid, supplied by Addgene inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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ABclonal Biotechnology slc6a1 rabbit
LncCplx2 expression is regulated by BMAL1. (A) ChIP-qPCR assays demonstrating enrichment of BMAL1 at the LncCplx2 promoter region in Min6 cells. RNA Polymerase II antibody and IgG serve as the positive and negative control, respectively (n = 3/2). Two different primer pairs ( LncCplx2 -P1 and LncCplx2 -P2) targeted the promoter of LncCplx2 were used for the PCR assay. IB analysis of BMAL1, <t>NR1D1</t> and E4BP4 antibody immunoprecipitation efficiency, IgG as negative control. (B) IB analysis of BMAL1 protein level in Bmal1 KO and control Min6 cells. β-Actin was used as the loading control. (C) LncCplx2 expression was analyzed by qRT-PCR in Bmal1 KO and control Min6 cells (n = 4). (D) qRT-PCR analysis of Bmal1 and LncCplx2 expression in Min6 cells expressing two shRNAs targeting Bmal1 and scrambled shRNA as control (n = 3). (E) Effects of Bmal1 overexpression on different luciferase reporter activity driven by the LncCplx2 promoter and negative control (n = 6). All the data are shown as the mean ± SEM. ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001, ∗∗∗∗p < 0.0001, using two-tailed Student's t-test and one-way ANOVA.
Slc6a1 Rabbit, supplied by ABclonal Biotechnology, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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DSMZ fischer 1982
LncCplx2 expression is regulated by BMAL1. (A) ChIP-qPCR assays demonstrating enrichment of BMAL1 at the LncCplx2 promoter region in Min6 cells. RNA Polymerase II antibody and IgG serve as the positive and negative control, respectively (n = 3/2). Two different primer pairs ( LncCplx2 -P1 and LncCplx2 -P2) targeted the promoter of LncCplx2 were used for the PCR assay. IB analysis of BMAL1, <t>NR1D1</t> and E4BP4 antibody immunoprecipitation efficiency, IgG as negative control. (B) IB analysis of BMAL1 protein level in Bmal1 KO and control Min6 cells. β-Actin was used as the loading control. (C) LncCplx2 expression was analyzed by qRT-PCR in Bmal1 KO and control Min6 cells (n = 4). (D) qRT-PCR analysis of Bmal1 and LncCplx2 expression in Min6 cells expressing two shRNAs targeting Bmal1 and scrambled shRNA as control (n = 3). (E) Effects of Bmal1 overexpression on different luciferase reporter activity driven by the LncCplx2 promoter and negative control (n = 6). All the data are shown as the mean ± SEM. ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001, ∗∗∗∗p < 0.0001, using two-tailed Student's t-test and one-way ANOVA.
Fischer 1982, supplied by DSMZ, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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ABclonal Biotechnology slc6a11 rabbit
LncCplx2 expression is regulated by BMAL1. (A) ChIP-qPCR assays demonstrating enrichment of BMAL1 at the LncCplx2 promoter region in Min6 cells. RNA Polymerase II antibody and IgG serve as the positive and negative control, respectively (n = 3/2). Two different primer pairs ( LncCplx2 -P1 and LncCplx2 -P2) targeted the promoter of LncCplx2 were used for the PCR assay. IB analysis of BMAL1, <t>NR1D1</t> and E4BP4 antibody immunoprecipitation efficiency, IgG as negative control. (B) IB analysis of BMAL1 protein level in Bmal1 KO and control Min6 cells. β-Actin was used as the loading control. (C) LncCplx2 expression was analyzed by qRT-PCR in Bmal1 KO and control Min6 cells (n = 4). (D) qRT-PCR analysis of Bmal1 and LncCplx2 expression in Min6 cells expressing two shRNAs targeting Bmal1 and scrambled shRNA as control (n = 3). (E) Effects of Bmal1 overexpression on different luciferase reporter activity driven by the LncCplx2 promoter and negative control (n = 6). All the data are shown as the mean ± SEM. ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001, ∗∗∗∗p < 0.0001, using two-tailed Student's t-test and one-way ANOVA.
Slc6a11 Rabbit, supplied by ABclonal Biotechnology, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Proteintech anti rev erba
LncCplx2 expression is regulated by BMAL1. (A) ChIP-qPCR assays demonstrating enrichment of BMAL1 at the LncCplx2 promoter region in Min6 cells. RNA Polymerase II antibody and IgG serve as the positive and negative control, respectively (n = 3/2). Two different primer pairs ( LncCplx2 -P1 and LncCplx2 -P2) targeted the promoter of LncCplx2 were used for the PCR assay. IB analysis of BMAL1, <t>NR1D1</t> and E4BP4 antibody immunoprecipitation efficiency, IgG as negative control. (B) IB analysis of BMAL1 protein level in Bmal1 KO and control Min6 cells. β-Actin was used as the loading control. (C) LncCplx2 expression was analyzed by qRT-PCR in Bmal1 KO and control Min6 cells (n = 4). (D) qRT-PCR analysis of Bmal1 and LncCplx2 expression in Min6 cells expressing two shRNAs targeting Bmal1 and scrambled shRNA as control (n = 3). (E) Effects of Bmal1 overexpression on different luciferase reporter activity driven by the LncCplx2 promoter and negative control (n = 6). All the data are shown as the mean ± SEM. ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001, ∗∗∗∗p < 0.0001, using two-tailed Student's t-test and one-way ANOVA.
Anti Rev Erba, supplied by Proteintech, used in various techniques. Bioz Stars score: 92/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Proteintech anti rev erbα nridi antibody
ROR inhibition modulates host circadian clock factors and HIV-1 replication (A) U-2 OS cells stably expressing luciferase under control of the Bmal1 promoter (Bmal1-luc) were synchronized followed by treatment with GSK805. Luminescence was measured at 30 min intervals (mean ± S.E.M., n = 3, raw data in <xref ref-type=Figure S9 B). Amplitude reduction compared to UT: 36.1% for 3 μM, 63.9% for 10 μM (FFT-NLLS analysis, BioDare2). Synchronized parental U-2 OS cells were treated with GSK805 (10 μM) and harvested at 4 h intervals, followed by RNA extraction and qPCR detection of Bmal1 transcripts relative to a B2M housekeeper (mean ± S.E.M., n = 3). (B) Jurkat cells stably expressing Bmal1-luc were treated with GSK805 for 24 h, and luciferase activity quantified (mean ± S.E.M., n = 3, Kruskal-Wallis ANOVA). Jurkat cells were treated with GSK805 (20 μM), with BMAL1 and β-actin protein expression assessed by western blotting (representative of n = 3). (C) CD8-depleted PBMCs were activated for 3 days with anti-CD3/CD28, treated with GSK805 (2.5 μM) for 7 days, followed by RNA extraction, and qPCR detection of Bmal1, Rev-erbα, Per1, or Cry2 RNA levels relative to a B2M housekeeper (mean ± S.E.M., n = 4–5, Mann-Whitney test). (D) U-2 OS cells infected with NL4.3-luc VSV-G were synchronized, treated with GSK805 (10 μM) and luciferase activity measured at 30 min intervals (mean ± S.E.M., n = 3, normalized to peak) or cells harvested at 4 h intervals, followed by qPCR detection of HIV-1 Gag RNA relative to a B2M housekeeper (mean ± S.E.M., n = 3, raw data in Figure S9 C). (E) Jurkat cells or activated CD8-depleted PBMCs were infected with NL4.3-luc VSV-G, treated with GSK805 for 24 h and luciferase quantified as a readout of HIV-1 replication (mean ± S.E.M, n = 3–4, Kruskal-Wallis ANOVA). (F) Activated CD8-depleted PBMCs were spinoculated for 2 h with patient-derived HIV-1 (transmitted founder virus clone CH185) and cultured with GSK805 for 7 days, followed by qPCR detection of HIV-1 Gag RNA relative to B2M housekeeper (mean ± S.E.M., n = 3, Kruskal-Wallis ANOVA). All data are expressed relative to UT control. " width="250" height="auto" />
Anti Rev Erbα Nridi Antibody, supplied by Proteintech, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Cell Signaling Technology Inc nr1d1 antibody
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 log 2 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 , <t>Nr1d1</t> , 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.
Nr1d1 Antibody, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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LncCplx2 expression is regulated by BMAL1. (A) ChIP-qPCR assays demonstrating enrichment of BMAL1 at the LncCplx2 promoter region in Min6 cells. RNA Polymerase II antibody and IgG serve as the positive and negative control, respectively (n = 3/2). Two different primer pairs ( LncCplx2 -P1 and LncCplx2 -P2) targeted the promoter of LncCplx2 were used for the PCR assay. IB analysis of BMAL1, NR1D1 and E4BP4 antibody immunoprecipitation efficiency, IgG as negative control. (B) IB analysis of BMAL1 protein level in Bmal1 KO and control Min6 cells. β-Actin was used as the loading control. (C) LncCplx2 expression was analyzed by qRT-PCR in Bmal1 KO and control Min6 cells (n = 4). (D) qRT-PCR analysis of Bmal1 and LncCplx2 expression in Min6 cells expressing two shRNAs targeting Bmal1 and scrambled shRNA as control (n = 3). (E) Effects of Bmal1 overexpression on different luciferase reporter activity driven by the LncCplx2 promoter and negative control (n = 6). All the data are shown as the mean ± SEM. ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001, ∗∗∗∗p < 0.0001, using two-tailed Student's t-test and one-way ANOVA.

Journal: Molecular Metabolism

Article Title: Long non-coding RNA LncCplx2 regulates glucose homeostasis and pancreatic β cell function

doi: 10.1016/j.molmet.2024.101878

Figure Lengend Snippet: LncCplx2 expression is regulated by BMAL1. (A) ChIP-qPCR assays demonstrating enrichment of BMAL1 at the LncCplx2 promoter region in Min6 cells. RNA Polymerase II antibody and IgG serve as the positive and negative control, respectively (n = 3/2). Two different primer pairs ( LncCplx2 -P1 and LncCplx2 -P2) targeted the promoter of LncCplx2 were used for the PCR assay. IB analysis of BMAL1, NR1D1 and E4BP4 antibody immunoprecipitation efficiency, IgG as negative control. (B) IB analysis of BMAL1 protein level in Bmal1 KO and control Min6 cells. β-Actin was used as the loading control. (C) LncCplx2 expression was analyzed by qRT-PCR in Bmal1 KO and control Min6 cells (n = 4). (D) qRT-PCR analysis of Bmal1 and LncCplx2 expression in Min6 cells expressing two shRNAs targeting Bmal1 and scrambled shRNA as control (n = 3). (E) Effects of Bmal1 overexpression on different luciferase reporter activity driven by the LncCplx2 promoter and negative control (n = 6). All the data are shown as the mean ± SEM. ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001, ∗∗∗∗p < 0.0001, using two-tailed Student's t-test and one-way ANOVA.

Article Snippet: The membranes were incubated with primary antibodies against Tubulin (Proteintech, 66031-1-Ig), DDX1 (Proteintech, 11357-1-AP), SETD8 (Abcam, ab111691), HistoneH3 (Invitrogen, PA5-16183), CPLX2 (Proteintech, 18149-1-AP), BMAL1 (Invitrogen, PA1-46118), E4BP4 (Proteintech, 11773-1-AP), NR1D1 (Proteintech, 14506-1-AP), EZH2 (Invitrogen, 36-6300), and β-actin (Sigma Aldrich, A1978), followed by the appropriate HRP-conjugated secondary antibodies (Proteintech, SA00001-2/SA00001-1), and protein expression was detected with enhanced luminescence reagents (GE Healthcare, RPN2106).

Techniques: Expressing, ChIP-qPCR, Negative Control, Immunoprecipitation, Control, Quantitative RT-PCR, shRNA, Over Expression, Luciferase, Activity Assay, Two Tailed Test

ROR inhibition modulates host circadian clock factors and HIV-1 replication (A) U-2 OS cells stably expressing luciferase under control of the Bmal1 promoter (Bmal1-luc) were synchronized followed by treatment with GSK805. Luminescence was measured at 30 min intervals (mean ± S.E.M., n = 3, raw data in <xref ref-type=Figure S9 B). Amplitude reduction compared to UT: 36.1% for 3 μM, 63.9% for 10 μM (FFT-NLLS analysis, BioDare2). Synchronized parental U-2 OS cells were treated with GSK805 (10 μM) and harvested at 4 h intervals, followed by RNA extraction and qPCR detection of Bmal1 transcripts relative to a B2M housekeeper (mean ± S.E.M., n = 3). (B) Jurkat cells stably expressing Bmal1-luc were treated with GSK805 for 24 h, and luciferase activity quantified (mean ± S.E.M., n = 3, Kruskal-Wallis ANOVA). Jurkat cells were treated with GSK805 (20 μM), with BMAL1 and β-actin protein expression assessed by western blotting (representative of n = 3). (C) CD8-depleted PBMCs were activated for 3 days with anti-CD3/CD28, treated with GSK805 (2.5 μM) for 7 days, followed by RNA extraction, and qPCR detection of Bmal1, Rev-erbα, Per1, or Cry2 RNA levels relative to a B2M housekeeper (mean ± S.E.M., n = 4–5, Mann-Whitney test). (D) U-2 OS cells infected with NL4.3-luc VSV-G were synchronized, treated with GSK805 (10 μM) and luciferase activity measured at 30 min intervals (mean ± S.E.M., n = 3, normalized to peak) or cells harvested at 4 h intervals, followed by qPCR detection of HIV-1 Gag RNA relative to a B2M housekeeper (mean ± S.E.M., n = 3, raw data in Figure S9 C). (E) Jurkat cells or activated CD8-depleted PBMCs were infected with NL4.3-luc VSV-G, treated with GSK805 for 24 h and luciferase quantified as a readout of HIV-1 replication (mean ± S.E.M, n = 3–4, Kruskal-Wallis ANOVA). (F) Activated CD8-depleted PBMCs were spinoculated for 2 h with patient-derived HIV-1 (transmitted founder virus clone CH185) and cultured with GSK805 for 7 days, followed by qPCR detection of HIV-1 Gag RNA relative to B2M housekeeper (mean ± S.E.M., n = 3, Kruskal-Wallis ANOVA). All data are expressed relative to UT control. " width="100%" height="100%">

Journal: iScience

Article Title: Molecular components of the circadian clock regulate HIV-1 replication

doi: 10.1016/j.isci.2023.107007

Figure Lengend Snippet: ROR inhibition modulates host circadian clock factors and HIV-1 replication (A) U-2 OS cells stably expressing luciferase under control of the Bmal1 promoter (Bmal1-luc) were synchronized followed by treatment with GSK805. Luminescence was measured at 30 min intervals (mean ± S.E.M., n = 3, raw data in Figure S9 B). Amplitude reduction compared to UT: 36.1% for 3 μM, 63.9% for 10 μM (FFT-NLLS analysis, BioDare2). Synchronized parental U-2 OS cells were treated with GSK805 (10 μM) and harvested at 4 h intervals, followed by RNA extraction and qPCR detection of Bmal1 transcripts relative to a B2M housekeeper (mean ± S.E.M., n = 3). (B) Jurkat cells stably expressing Bmal1-luc were treated with GSK805 for 24 h, and luciferase activity quantified (mean ± S.E.M., n = 3, Kruskal-Wallis ANOVA). Jurkat cells were treated with GSK805 (20 μM), with BMAL1 and β-actin protein expression assessed by western blotting (representative of n = 3). (C) CD8-depleted PBMCs were activated for 3 days with anti-CD3/CD28, treated with GSK805 (2.5 μM) for 7 days, followed by RNA extraction, and qPCR detection of Bmal1, Rev-erbα, Per1, or Cry2 RNA levels relative to a B2M housekeeper (mean ± S.E.M., n = 4–5, Mann-Whitney test). (D) U-2 OS cells infected with NL4.3-luc VSV-G were synchronized, treated with GSK805 (10 μM) and luciferase activity measured at 30 min intervals (mean ± S.E.M., n = 3, normalized to peak) or cells harvested at 4 h intervals, followed by qPCR detection of HIV-1 Gag RNA relative to a B2M housekeeper (mean ± S.E.M., n = 3, raw data in Figure S9 C). (E) Jurkat cells or activated CD8-depleted PBMCs were infected with NL4.3-luc VSV-G, treated with GSK805 for 24 h and luciferase quantified as a readout of HIV-1 replication (mean ± S.E.M, n = 3–4, Kruskal-Wallis ANOVA). (F) Activated CD8-depleted PBMCs were spinoculated for 2 h with patient-derived HIV-1 (transmitted founder virus clone CH185) and cultured with GSK805 for 7 days, followed by qPCR detection of HIV-1 Gag RNA relative to B2M housekeeper (mean ± S.E.M., n = 3, Kruskal-Wallis ANOVA). All data are expressed relative to UT control.

Article Snippet: Samples were precleared with Protein A agarose beads (Millipore), immunoprecipitated with anti-BMAL1 antibody (abcam, Ab3350), anti-REV-ERBα (NRIDI) antibody (Proteintech, 14506-I-AP), anti-RORC antibody (eBioscience, AFKJS-9) or rabbit IgG (Sigma, NI01) and precipitated with Protein A agarose beads.

Techniques: Inhibition, Stable Transfection, Expressing, Luciferase, Control, RNA Extraction, Activity Assay, Western Blot, MANN-WHITNEY, Infection, Derivative Assay, Virus, Cell Culture

Differential binding of REV-ERBα and RORC to the HIV-LTR at different circadian times (A) Consensus plot showing the conservation of nucleotides in position 121 to 126 of 1266 HIV-1 sequences deposited in the Los Alamos Database (coordinates are from the HXB2 reference). Bases of coding strand are displayed which correspond to the nucleotides ‘AGGTCA’ on the antisense strand, thereby representing the ROR response element (RORE) ‘RGGTCA’. Conservation is reflected by the height of the bases (y axis 0–100%). (B) Jurkat cells were transfected with reporter constructs of HIV-1 subtypes A-G, followed by GSK2981278 treatment (40 μM) and LTR activity measured by quantifying luciferase activity 24h later (mean ± S.E.M., n = 4, Mann-Whitney test). (C) Location of the RORE in the 5′ HIV-LTR of NL4.3 strain; base pairs (bp) are shown relative to the transcriptional start site (TSS). Model where ROR and REV-ERBα compete for binding to the HIV-LTR which can be tested by chromatin immunoprecipitation (ChIP). RORC binding to the HIV-LTR was shown by Wiche Salinas et al. (D) Jurkat cells were infected with NL4.3-luc VSV-G for 24 h, and chromatin extracts immunoprecipitated with anti-REV-ERBα or rabbit IgG as a negative control. Fold enrichment of binding to the RORE in either the HIV-LTR or the Bmal1 promoter was quantified by qPCR and is shown compared to the IgG control (mean ± S.E.M., n = 4, Mann-Whitney test). (E) Jurkat cells were infected with NL4.3-luc VSV-G followed by treatment with GSK805 (10 μM) for 24 h. Fold enrichment of REV-ERBα binding to the HIV-LTR RORE or the Bmal1 promoter was compared between untreated and GSK805-treated cells (mean ± S.E.M., n = 4–6, Mann-Whitney test). (F) U-2 OS cells were infected with HIV-1 NL4.3-luc VSV-G for 24 h followed by serum shock synchronization for 1 h. 24 h (CT0), and 36 h (CT12) post-synchronization cells were harvested, and chromatin extracts immunoprecipitated with REV-ERBα antibody, RORC antibody, or rabbit IgG as a negative control. Fold enrichment of binding to either the RORE in the HIV-LTR or to the Bmal1 promoter as a positive control was quantified by qPCR, normalized to non-specific IgG binding and shown as fold change of binding (mean ± S.E.M., n = 4, Mann-Whitney test). (G) Model where RORC binding to the HIV-LTR promotes HIV-1 replication, and REV-ERBα binding supresses viral replication at different circadian times resulting in rhythmic HIV-1 replication. See related <xref ref-type=Figure S7 . All data are expressed relative to the control cells. " width="100%" height="100%">

Journal: iScience

Article Title: Molecular components of the circadian clock regulate HIV-1 replication

doi: 10.1016/j.isci.2023.107007

Figure Lengend Snippet: Differential binding of REV-ERBα and RORC to the HIV-LTR at different circadian times (A) Consensus plot showing the conservation of nucleotides in position 121 to 126 of 1266 HIV-1 sequences deposited in the Los Alamos Database (coordinates are from the HXB2 reference). Bases of coding strand are displayed which correspond to the nucleotides ‘AGGTCA’ on the antisense strand, thereby representing the ROR response element (RORE) ‘RGGTCA’. Conservation is reflected by the height of the bases (y axis 0–100%). (B) Jurkat cells were transfected with reporter constructs of HIV-1 subtypes A-G, followed by GSK2981278 treatment (40 μM) and LTR activity measured by quantifying luciferase activity 24h later (mean ± S.E.M., n = 4, Mann-Whitney test). (C) Location of the RORE in the 5′ HIV-LTR of NL4.3 strain; base pairs (bp) are shown relative to the transcriptional start site (TSS). Model where ROR and REV-ERBα compete for binding to the HIV-LTR which can be tested by chromatin immunoprecipitation (ChIP). RORC binding to the HIV-LTR was shown by Wiche Salinas et al. (D) Jurkat cells were infected with NL4.3-luc VSV-G for 24 h, and chromatin extracts immunoprecipitated with anti-REV-ERBα or rabbit IgG as a negative control. Fold enrichment of binding to the RORE in either the HIV-LTR or the Bmal1 promoter was quantified by qPCR and is shown compared to the IgG control (mean ± S.E.M., n = 4, Mann-Whitney test). (E) Jurkat cells were infected with NL4.3-luc VSV-G followed by treatment with GSK805 (10 μM) for 24 h. Fold enrichment of REV-ERBα binding to the HIV-LTR RORE or the Bmal1 promoter was compared between untreated and GSK805-treated cells (mean ± S.E.M., n = 4–6, Mann-Whitney test). (F) U-2 OS cells were infected with HIV-1 NL4.3-luc VSV-G for 24 h followed by serum shock synchronization for 1 h. 24 h (CT0), and 36 h (CT12) post-synchronization cells were harvested, and chromatin extracts immunoprecipitated with REV-ERBα antibody, RORC antibody, or rabbit IgG as a negative control. Fold enrichment of binding to either the RORE in the HIV-LTR or to the Bmal1 promoter as a positive control was quantified by qPCR, normalized to non-specific IgG binding and shown as fold change of binding (mean ± S.E.M., n = 4, Mann-Whitney test). (G) Model where RORC binding to the HIV-LTR promotes HIV-1 replication, and REV-ERBα binding supresses viral replication at different circadian times resulting in rhythmic HIV-1 replication. See related Figure S7 . All data are expressed relative to the control cells.

Article Snippet: Samples were precleared with Protein A agarose beads (Millipore), immunoprecipitated with anti-BMAL1 antibody (abcam, Ab3350), anti-REV-ERBα (NRIDI) antibody (Proteintech, 14506-I-AP), anti-RORC antibody (eBioscience, AFKJS-9) or rabbit IgG (Sigma, NI01) and precipitated with Protein A agarose beads.

Techniques: Binding Assay, Transfection, Construct, Activity Assay, Luciferase, MANN-WHITNEY, Chromatin Immunoprecipitation, Infection, Immunoprecipitation, Negative Control, Control, Positive Control

HIV-1 host factors are regulated by the circadian clock (A) Expression of 90 HIV-1 host proteins was analyzed using the Circa database, and 43% of genes identified as cycling in humans. (B) BMAL1-regulated genes, REV-ERBα-regulated genes, and RORC-regulated genes were compared with host factors known to alter HIV-1 replication. (C) HOMER (Hypergeometric Optimization of Motif EnRichment tool ) was used to analyze -1kb promoter regions of HIV-1 host factors and identified gene promoters encoding E-box motifs or ROR response elements (ROREs). (D) Jurkat cells were treated with GSK2981278 (40 μM) or GSK805 (20 μM) for 24 h, cells were lysed, RNA was extracted, and gene expression analyzed via qPCR (mean ± S.E.M., n = 4, Mann-Whitney test). (E) Gene ontology (GO) cellular components analysis where each node represents an enriched GO term. Related GO terms are connected by lines, where thickness reflects the percentage of overlapping genes. See related <xref ref-type=Figure S8 . " width="100%" height="100%">

Journal: iScience

Article Title: Molecular components of the circadian clock regulate HIV-1 replication

doi: 10.1016/j.isci.2023.107007

Figure Lengend Snippet: HIV-1 host factors are regulated by the circadian clock (A) Expression of 90 HIV-1 host proteins was analyzed using the Circa database, and 43% of genes identified as cycling in humans. (B) BMAL1-regulated genes, REV-ERBα-regulated genes, and RORC-regulated genes were compared with host factors known to alter HIV-1 replication. (C) HOMER (Hypergeometric Optimization of Motif EnRichment tool ) was used to analyze -1kb promoter regions of HIV-1 host factors and identified gene promoters encoding E-box motifs or ROR response elements (ROREs). (D) Jurkat cells were treated with GSK2981278 (40 μM) or GSK805 (20 μM) for 24 h, cells were lysed, RNA was extracted, and gene expression analyzed via qPCR (mean ± S.E.M., n = 4, Mann-Whitney test). (E) Gene ontology (GO) cellular components analysis where each node represents an enriched GO term. Related GO terms are connected by lines, where thickness reflects the percentage of overlapping genes. See related Figure S8 .

Article Snippet: Samples were precleared with Protein A agarose beads (Millipore), immunoprecipitated with anti-BMAL1 antibody (abcam, Ab3350), anti-REV-ERBα (NRIDI) antibody (Proteintech, 14506-I-AP), anti-RORC antibody (eBioscience, AFKJS-9) or rabbit IgG (Sigma, NI01) and precipitated with Protein A agarose beads.

Techniques: Expressing, Gene Expression, MANN-WHITNEY

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 log 2 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.

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: 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 log 2 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: The nonspecific binding sites of membrane were blocked and incubated with diluted GALR1 antibody (1:500; #47567, Signalway Antibody, Maryland, USA), 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), T-AKT antibody (1:1000; #4691, Cell Signaling Technology), P-ERK antibody (1:1000; #4370, Cell Signaling Technology) and T-ERK antibody (1:1000; #4695, Cell Signaling Technology) at 4°C for overnight.

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

mRNA and protein abundances of NR1D1, NR1D2, INSIG2, SREBP1, LXR, and RXR after NR1D1 knockdown or NR1D2 knockdown ( a , b ) as well as NR1D1 overexpression or NR1D2 overexpression ( c , d ) in HepG2 cells. a , c Left, representative images of western blot were shown. Right, immunoreactive bands were densitometrically quantified. b , d mRNA abundance detected by qPCR was presented. e mRNA and protein abundances of NR1D1, NR1D2, INSIG2, SREBP1, LXR, RXR, P-ERK, T-ERK, P-AKT, and T-AKT after galanin treatment (#1179, Tocris Bioscience, Bristol, UK) at the concentration of 0, 50, 150, and 300 pg/mL for 24 h in HepG2 cells. Left, representative images of western blot were shown. Right, immunoreactive bands were densitometrically quantified (above); mRNA abundance detected by qPCR was presented (below). f mRNA and protein abundances of GALR1, GALR2, NR1D1, NR1D2, INSIG2, SREBP1, LXR, RXR, P-ERK, T-ERK, P-AKT and T-AKT after GALR1 knockdown or GALR2 knockdown and further treatment with 300 pg/mL galanin for 24 h in HepG2 cells. g mRNA and protein abundances of GALR1, GALR2, NR1D1, NR1D2, INSIG2, SREBP1, LXR, RXR, P-ERK, T-ERK, P-AKT, and T-AKT after GALR1 overexpression or GALR2 overexpression in HepG2 cells. h mRNA and protein abundances of NR1D1, NR1D2, INSIG2, SREBP1, LXR, RXR, P-ERK, T-ERK, P-AKT, and T-AKT after treatment with(out) 300 pg/mL galanin, with(out) 10 μM LY294002 (#19-142, Sigma-Aldrich, St. Louis, USA) and with(out) 20 μM PD98059 (#19-143, Sigma-Aldrich). i mRNA and protein abundances of GALR1, NR1D1, NR1D2, INSIG2, SREBP1, LXR, RXR, P-AKT, and T-AKT after GALR1 overexpression and further treatment with 10 μM LY294002 in HepG2 cells. GAPDH or β-ACTIN were used as loading controls for western blot and qPCR analyses. Representative Oil Red O staining and Nile Red staining after the induction of oleic acid and palmitic acid (OPA) and treatment with 300 pg/mL galanin for 24 h ( j ) or NR1D1 siRNA ( k ) in HepG2 cells. Left, representative images were shown. Right, intensity was quantified. Blots and images are representative. Statistical analysis was performed with unpaired Student’s t-test or one-way ANOVA followed by Newman–Keuls multiple comparison test. Data present means ± SEM from 3 to 5 experiments. * P < 0.05, ** P < 0.01, *** P < 0.001 against si-NC cells or against Vec-NC cells or against control cells; # P < 0.05, ## P < 0.01 against si-GALR2 cells or against PD98059 cells or against Vec-GALR1 cells.

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: mRNA and protein abundances of NR1D1, NR1D2, INSIG2, SREBP1, LXR, and RXR after NR1D1 knockdown or NR1D2 knockdown ( a , b ) as well as NR1D1 overexpression or NR1D2 overexpression ( c , d ) in HepG2 cells. a , c Left, representative images of western blot were shown. Right, immunoreactive bands were densitometrically quantified. b , d mRNA abundance detected by qPCR was presented. e mRNA and protein abundances of NR1D1, NR1D2, INSIG2, SREBP1, LXR, RXR, P-ERK, T-ERK, P-AKT, and T-AKT after galanin treatment (#1179, Tocris Bioscience, Bristol, UK) at the concentration of 0, 50, 150, and 300 pg/mL for 24 h in HepG2 cells. Left, representative images of western blot were shown. Right, immunoreactive bands were densitometrically quantified (above); mRNA abundance detected by qPCR was presented (below). f mRNA and protein abundances of GALR1, GALR2, NR1D1, NR1D2, INSIG2, SREBP1, LXR, RXR, P-ERK, T-ERK, P-AKT and T-AKT after GALR1 knockdown or GALR2 knockdown and further treatment with 300 pg/mL galanin for 24 h in HepG2 cells. g mRNA and protein abundances of GALR1, GALR2, NR1D1, NR1D2, INSIG2, SREBP1, LXR, RXR, P-ERK, T-ERK, P-AKT, and T-AKT after GALR1 overexpression or GALR2 overexpression in HepG2 cells. h mRNA and protein abundances of NR1D1, NR1D2, INSIG2, SREBP1, LXR, RXR, P-ERK, T-ERK, P-AKT, and T-AKT after treatment with(out) 300 pg/mL galanin, with(out) 10 μM LY294002 (#19-142, Sigma-Aldrich, St. Louis, USA) and with(out) 20 μM PD98059 (#19-143, Sigma-Aldrich). i mRNA and protein abundances of GALR1, NR1D1, NR1D2, INSIG2, SREBP1, LXR, RXR, P-AKT, and T-AKT after GALR1 overexpression and further treatment with 10 μM LY294002 in HepG2 cells. GAPDH or β-ACTIN were used as loading controls for western blot and qPCR analyses. Representative Oil Red O staining and Nile Red staining after the induction of oleic acid and palmitic acid (OPA) and treatment with 300 pg/mL galanin for 24 h ( j ) or NR1D1 siRNA ( k ) in HepG2 cells. Left, representative images were shown. Right, intensity was quantified. Blots and images are representative. Statistical analysis was performed with unpaired Student’s t-test or one-way ANOVA followed by Newman–Keuls multiple comparison test. Data present means ± SEM from 3 to 5 experiments. * P < 0.05, ** P < 0.01, *** P < 0.001 against si-NC cells or against Vec-NC cells or against control cells; # P < 0.05, ## P < 0.01 against si-GALR2 cells or against PD98059 cells or against Vec-GALR1 cells.

Article Snippet: The nonspecific binding sites of membrane were blocked and incubated with diluted GALR1 antibody (1:500; #47567, Signalway Antibody, Maryland, USA), 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), T-AKT antibody (1:1000; #4691, Cell Signaling Technology), P-ERK antibody (1:1000; #4370, Cell Signaling Technology) and T-ERK antibody (1:1000; #4695, Cell Signaling Technology) at 4°C for overnight.

Techniques: Over Expression, Western Blot, Concentration Assay, Staining

a Timeline depicting the treatments of darkness, L. reuteri , and M617 in different groups of the M617-treated rat model ( n = 6 per group). b Body weight changes. c Representative Oil Red O staining of liver. Scale bar: 50 μm and 25 μm. d Left to right, serum concentrations of TG, CHOL, HDL-C, LDL-C, and NEFA detected by ELISA. e mRNA abundances of Nr1d1 and Srebf1 in rat liver. f Protein abundances of NR1D1 and SREBP1 in rat liver. Left, representative images of western blot were shown. Right, immunoreactive bands were densitometrically quantified. g Timeline depicting the treatments of darkness and M40 in different groups of the M40-treated rat model ( n = 8 per group). h Body weight changes. i Representative Oil Red O staining of liver. Scale bar: 50 μm and 25 μm. j Left to right, serum concentrations of TG, CHOL, HDL-C, LDL-C, and NEFA detected by ELISA. k mRNA abundances of Nr1d1 and Srebf1 in rat liver. l Protein abundances of NR1D1 and SREBP1 in rat liver. Left, representative images of western blot were shown. Right, immunoreactive bands were densitometrically quantified. GAPDH or β-Actin were used as loading controls for western blot and qPCR analyses. Statistical analysis was performed with one-way ANOVA followed by Newman–Keuls multiple comparison test. Data present means ± SEM. * P < 0.05, ** P < 0.01.

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: a Timeline depicting the treatments of darkness, L. reuteri , and M617 in different groups of the M617-treated rat model ( n = 6 per group). b Body weight changes. c Representative Oil Red O staining of liver. Scale bar: 50 μm and 25 μm. d Left to right, serum concentrations of TG, CHOL, HDL-C, LDL-C, and NEFA detected by ELISA. e mRNA abundances of Nr1d1 and Srebf1 in rat liver. f Protein abundances of NR1D1 and SREBP1 in rat liver. Left, representative images of western blot were shown. Right, immunoreactive bands were densitometrically quantified. g Timeline depicting the treatments of darkness and M40 in different groups of the M40-treated rat model ( n = 8 per group). h Body weight changes. i Representative Oil Red O staining of liver. Scale bar: 50 μm and 25 μm. j Left to right, serum concentrations of TG, CHOL, HDL-C, LDL-C, and NEFA detected by ELISA. k mRNA abundances of Nr1d1 and Srebf1 in rat liver. l Protein abundances of NR1D1 and SREBP1 in rat liver. Left, representative images of western blot were shown. Right, immunoreactive bands were densitometrically quantified. GAPDH or β-Actin were used as loading controls for western blot and qPCR analyses. Statistical analysis was performed with one-way ANOVA followed by Newman–Keuls multiple comparison test. Data present means ± SEM. * P < 0.05, ** P < 0.01.

Article Snippet: The nonspecific binding sites of membrane were blocked and incubated with diluted GALR1 antibody (1:500; #47567, Signalway Antibody, Maryland, USA), 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), T-AKT antibody (1:1000; #4691, Cell Signaling Technology), P-ERK antibody (1:1000; #4370, Cell Signaling Technology) and T-ERK antibody (1:1000; #4695, Cell Signaling Technology) at 4°C for overnight.

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

a Multiomics correlation networks of all variables for the faecal microbiome (green), faecal metabolome (purple) and serum metabolome (yellow) within control rats (left), darkness rats (middle), and DL.reuteri rats (right). Vertices indicate omics variables, and lines indicate a significant Spearman’s rank correlation coefficient at |ρ | > 0.8 and P < 0.05. Red connections indicate positive correlation, and blue connections show negative correlations. b Procrustes analyses of faecal microbiome versus faecal metabolome (above) and of faecal metabolome versus serum metabolome (below). c Spearman correlation network between target faecal metabolites (circle) and target serum metabolites (square) ( P < 0.05). The color of each metabolite was determined by their correlations with target genera ( P < 0.05): Pink, Lactobacillus ; Blue, Clostridium sensu stricto 1 ; Green, Ruminococcaceae UCG-010 ; Yellow, Family XIII AD3011 group . d Spearman rank correlations between target serum metabolites and mRNA expression of Galr1 , Nr1d1 , and Srebf1 in rat liver (* P < 0.05, ** P < 0.01, *** P < 0.001). e Timeline depicting the treatments of darkness, L. reuteri , and capric acid in different groups of the capric acid-treated rat model ( n = 6 per group). f Body weight changes. g Left to right, serum concentrations of TG, CHOL, HDL-C, LDL-C, and NEFA detected by ELISA. h Representative Oil Red O staining of liver. Scale bar: 50 μm and 25 μm. i mRNA abundances of Galr1 , Nr1d1, and Srebf1 in rat liver. β-Actin was used as a loading control for qPCR analyses. Statistical analysis ( g , i ) was performed with one-way ANOVA followed by Newman–Keuls multiple comparison test. Data present means ± SEM. * P < 0.05, ** P < 0.01.

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: a Multiomics correlation networks of all variables for the faecal microbiome (green), faecal metabolome (purple) and serum metabolome (yellow) within control rats (left), darkness rats (middle), and DL.reuteri rats (right). Vertices indicate omics variables, and lines indicate a significant Spearman’s rank correlation coefficient at |ρ | > 0.8 and P < 0.05. Red connections indicate positive correlation, and blue connections show negative correlations. b Procrustes analyses of faecal microbiome versus faecal metabolome (above) and of faecal metabolome versus serum metabolome (below). c Spearman correlation network between target faecal metabolites (circle) and target serum metabolites (square) ( P < 0.05). The color of each metabolite was determined by their correlations with target genera ( P < 0.05): Pink, Lactobacillus ; Blue, Clostridium sensu stricto 1 ; Green, Ruminococcaceae UCG-010 ; Yellow, Family XIII AD3011 group . d Spearman rank correlations between target serum metabolites and mRNA expression of Galr1 , Nr1d1 , and Srebf1 in rat liver (* P < 0.05, ** P < 0.01, *** P < 0.001). e Timeline depicting the treatments of darkness, L. reuteri , and capric acid in different groups of the capric acid-treated rat model ( n = 6 per group). f Body weight changes. g Left to right, serum concentrations of TG, CHOL, HDL-C, LDL-C, and NEFA detected by ELISA. h Representative Oil Red O staining of liver. Scale bar: 50 μm and 25 μm. i mRNA abundances of Galr1 , Nr1d1, and Srebf1 in rat liver. β-Actin was used as a loading control for qPCR analyses. Statistical analysis ( g , i ) was performed with one-way ANOVA followed by Newman–Keuls multiple comparison test. Data present means ± SEM. * P < 0.05, ** P < 0.01.

Article Snippet: The nonspecific binding sites of membrane were blocked and incubated with diluted GALR1 antibody (1:500; #47567, Signalway Antibody, Maryland, USA), 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), T-AKT antibody (1:1000; #4691, Cell Signaling Technology), P-ERK antibody (1:1000; #4370, Cell Signaling Technology) and T-ERK antibody (1:1000; #4695, Cell Signaling Technology) at 4°C for overnight.

Techniques: Expressing, Enzyme-linked Immunosorbent Assay, Staining

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.

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: 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: The nonspecific binding sites of membrane were blocked and incubated with diluted GALR1 antibody (1:500; #47567, Signalway Antibody, Maryland, USA), 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), T-AKT antibody (1:1000; #4691, Cell Signaling Technology), P-ERK antibody (1:1000; #4370, Cell Signaling Technology) and T-ERK antibody (1:1000; #4695, Cell Signaling Technology) at 4°C for overnight.

Techniques: Inhibition