Journal: BioMed Research International

Article Title: Gene Profiling of Bone around Orthodontic Mini-Implants by RNA-Sequencing Analysis

doi: 10.1155/2015/538080

Figure Lengend Snippet: Differentially expressed genes associated with growth factors.

Article Snippet: WISP2 , WNT1-inducible-signaling pathway protein 2 , Cf02702369_g1 , 1 w , 3.11 , 1.65.

Techniques: Binding Assay, Histone Deacetylase Assay

Journal: BioMed Research International

Article Title: Gene Profiling of Bone around Orthodontic Mini-Implants by RNA-Sequencing Analysis

doi: 10.1155/2015/538080

Figure Lengend Snippet: Differentially expressed genes associated with osteogenesis.

Article Snippet: WISP2 , WNT1-inducible-signaling pathway protein 2 , Cf02702369_g1 , 1 w , 3.11 , 1.65.

Techniques:

Journal: BioMed Research International

Article Title: Gene Profiling of Bone around Orthodontic Mini-Implants by RNA-Sequencing Analysis

doi: 10.1155/2015/538080

Figure Lengend Snippet: Real-time polymerase chain reaction (PCR) validation.

Article Snippet: WISP2 , WNT1-inducible-signaling pathway protein 2 , Cf02702369_g1 , 1 w , 3.11 , 1.65.

Techniques: Real-time Polymerase Chain Reaction, Biomarker Discovery

Journal: PLoS ONE

Article Title: Mitogen-Activated Protein Kinases Regulate Susceptibility to Ventilator-Induced Lung Injury

doi: 10.1371/journal.pone.0001601

Figure Lengend Snippet: (A) The pattern of 103 differentially expressed genes is displayed. The gene expression profile of controls and animals subjected to mechanical ventilation (10 ml/kg, 8 hours) is compared. Confirmed genes: growth arrest and DNA-damage-inducible protein-45alpha ( gadd45α ), WNT1 inducible signaling pathway protein 2 ( wisp2 ), activating transcription factor 4 ( atf4 ) and mmp8 are highlighted. red = upregulation, blue = downregulaton, yellow = null expression. Big columns represent wild-type control, wild-type ventilated, jnk1 −/− control and jnk1 −/− ventilated mice. Small columns show the gene expression profile of one animal. Each row represents one gene. Gene symbols are shown on right side of the panel. For complete gene names please refer to . (B) Microarray and confirmatory TaqMan RT-PCR expression profile of gadd45α , wisp2 , atf4 and mmp8 genes. The increased expression gadd45α following ventilation was identified by microarray and verified with RT-PCR. Jnk1 −/− mice had a higher expression of gadd45α after ventilation than wild-type mice. Wisp2 expression was decreased in both wild-type and jnk1 −/− mice following mechanical ventilation. RT-PCR confirmed the microarray findings. Microarray results showed that atf4 gene was regulated only in jnk1 −/− mice and RT-PCR verified this finding. Mmp8 showed increased expression with ventilation on microarray and with RT-PCR verification, which was similar in both wild-type and jnk1 −/− mice. *represents significant differences between control and ventilated animals, †represents significant difference between wild-type ventilated and jnk1 −/− ventilated mice.

Article Snippet: Commercially available Assay-on-Demand primer probe sets (Applied Biosystems, Inc.) were used for Gadd45α (Mm00432802_m1), for Wisp2 (Mm01247817_m1) for Atf4 (Mm00515324_m1) and for Mmp8 (Mm00772335_m1).

Techniques: Gene Expression, Expressing, Control, Microarray, Reverse Transcription Polymerase Chain Reaction

Journal: iScience

Article Title: Nuclear respiratory factor-1 negatively regulates TGF-β1 and attenuates pulmonary fibrosis

doi: 10.1016/j.isci.2021.103535

Figure Lengend Snippet: Pro-fibrotic and anti-fibrotic response in lungs of BLM treated mice (A) Immunoblot of lung extracellular fibrosis proteins Fn1 and Vim and epithelial marker E-cad during BLM-induced lung fibrosis. (B–D) Scatterplots of densitometry analysis of Fn1, Vim, and E-cad at 7 d post-BLM. (E) Immunoblot of lung nuclear proteins CCN5, Smad7, and phosphorylated Smad2 and 3 as targets for Smad7 during BLM-induced lung fibrosis. (F–I) Scatterplots of densitometry analysis of CCN5, pSmad2, pSmad3, and Smad7 at 7 d. N = 6 in each group and data expressed as mean ± SD. ∗P < 0.05 compared with the ReCORM and iCORM group, †P < 0.05 ReCORM + BLM vs BLM group.

Article Snippet: For overexpression, HO-1 TrueORF (Origene, MR203944), NRF-1 TrueORF (Origene, MG208550), or CCN5 (Origene, RC204636) was used with FuGENE-HD (Promega, E2311).

Techniques: Western Blot, Marker

Journal: iScience

Article Title: Nuclear respiratory factor-1 negatively regulates TGF-β1 and attenuates pulmonary fibrosis

doi: 10.1016/j.isci.2021.103535

Figure Lengend Snippet: Human lung fibroblast (MRC5) cells are protected from BLM induced- αSMA expression by ReCORM (A) MRC5 were exposed to 5 μg/mL BLM with or without ReCORM (50 μM) for 96 h. Cells were stained with MitoTracker green for mitochondrial mass and αSMA for fibrosis, presented as red wrinkle fluorescence (arrow). Nuclei stained with DAPI (blue). Images analyzed by confocal microscopy. Scale bar is 25 μm. (B) MRC5 cells exposed to BLM with or without ReCORM (50 μM) for 96 h. MRC5 cells’ total protein was examined for the levels of pro-fibrotic proteins, αSMA, Vimentin, pSmad2, and pSmad3, and the anti-fibrotic proteins, CCN5 and SMAD7 by using immunoblotting. (C–H) Scatterplots of densitometry analysis of αSMA, VIM, CCN5, and SMAD7 normalized to tubulin while pSmads normalized to total Smads. (I) Scatterplots for mtDNA lesions in MRC5. MtDNA lesions increased significantly in BLM treated cells, but the lesions decreased by ReCORM treatment. All experiments were performed in quadruplicate, representative data are shown. N = 4 in each group and data expressed as mean ± SD (∗P < 0.05 compared with ReCORM and iCORM treated groups, †P < 0.05 ReCORM + BLM groups).

Article Snippet: For overexpression, HO-1 TrueORF (Origene, MR203944), NRF-1 TrueORF (Origene, MG208550), or CCN5 (Origene, RC204636) was used with FuGENE-HD (Promega, E2311).

Techniques: Expressing, Staining, Fluorescence, Confocal Microscopy, Western Blot

Journal: iScience

Article Title: Nuclear respiratory factor-1 negatively regulates TGF-β1 and attenuates pulmonary fibrosis

doi: 10.1016/j.isci.2021.103535

Figure Lengend Snippet: Bioinformatics analysis of mouse and human promoter regions of CCN5 and SMAD7 . The corresponding sequences between human and mouse were aligned by rVISTA 2.0. The degree of interspecies conservation of the DNA within the 5′-UTR segment is represented by the histogram. CNS (interspecies conservation more than 75%) is emphasized in red (A) Conserved NRF-1, motifs on the human and mouse CCN5 gene were identified using the Genomatox and DNAsis database, and are displayed with red stripes above the histograms. (B) ChIP for occupancy of NRF1 on CCN5 promoters in BLM treated mouse lung with or without ReCORM. (C) ChIP assays assessing DNA enrichment by NRF1 on CCN5 promoters in human lung fibroblasts incubated with BLM, with or without ReCORM. (D) Human and mouse Smad7 promoter sequences were aligned and scanned for NRF-1 conserved motifs. Conservation plot diagrams are shown for each region, with conserved NRF1 sites displayed with red stripes above the histograms. (E) NRF-1 occupancy on Smad7 promoter in BLM treated mouse lung with or without ReCORM and assessed by ChIP assay and displayed as histogram. (F) NRF-1 occupancy on SMAD7 promoter in BLM treated MRC5 with or without ReCORM and assessed by ChIP assay and displayed as histogram. Values along the abscissa indicate positions of DNA regions amplified by qPCR. Green and blue bars depict significant DNA enrichment after ReCORM at positions indicated. Values represent the means ± SEM of independent experiments performed in triplicate. ∗P < 0.05 compared ReCORM with the iCORM group. †P < 0.05 ReCORM + BLM vs BLM groups).

Article Snippet: For overexpression, HO-1 TrueORF (Origene, MR203944), NRF-1 TrueORF (Origene, MG208550), or CCN5 (Origene, RC204636) was used with FuGENE-HD (Promega, E2311).

Techniques: Incubation, Amplification

Journal: iScience

Article Title: Nuclear respiratory factor-1 negatively regulates TGF-β1 and attenuates pulmonary fibrosis

doi: 10.1016/j.isci.2021.103535

Figure Lengend Snippet: Human lung fibroblasts (MRC5) and BLM induction of fibrotic markers (A and B) MRC5 cells transduced with sh-HO-1 or sh-NRF1 to silence these genes were then exposed to BLM for 18 h. Transcripts for CCN5 or SMAD7 were determined as seen in scatterplots. (C and D) Immunoblot of cells transfected with NS-ShRNA or ShRNA targeting NRF-1 (Sh-NRF-1). (E and F) ReCORM inhibits TGFβ1 signaling dependent on HO1 and NRF-1. MRC5 cells transduced with sh-HO-1 or sh-NRF1 to silence these genes were then exposed to TGFβ1for 18 h. Transcripts for HO-1 or NRF1 were determined as seen in scatterplots. (G) Responsiveness of overexpression or silencing of CCN5 with and without ReCORM to TGFβ1 induction of α-SMA mRNA levels in MRC5 cells. (H) Responsiveness to overexpression or silencing of NRF-1 with and without ReCORM to TGF-β induction of α-SMA mRNA levels in MRC5 cells. All experiments in quadruplicate representative data are shown. Quantitative data expressed as mean ± SD. ∗P < 0.05 ReCORM vs iCORM or †P < 0.05 ReCORM + BLM or ReCORM + TGFβ1 vs BLM or TGFβ1 groups.

Article Snippet: For overexpression, HO-1 TrueORF (Origene, MR203944), NRF-1 TrueORF (Origene, MG208550), or CCN5 (Origene, RC204636) was used with FuGENE-HD (Promega, E2311).

Techniques: Transduction, Western Blot, Transfection, shRNA, Over Expression

Journal: iScience

Article Title: Nuclear respiratory factor-1 negatively regulates TGF-β1 and attenuates pulmonary fibrosis

doi: 10.1016/j.isci.2021.103535

Figure Lengend Snippet:

Article Snippet: For overexpression, HO-1 TrueORF (Origene, MR203944), NRF-1 TrueORF (Origene, MG208550), or CCN5 (Origene, RC204636) was used with FuGENE-HD (Promega, E2311).

Techniques: Recombinant, Software, TUNEL Assay