Journal: PLOS ONE

Article Title: Machine learning-based prediction of rheumatoid arthritis with development of ACPA autoantibodies in the presence of non-HLA genes polymorphisms

doi: 10.1371/journal.pone.0300717

Figure Lengend Snippet: Basic information of the five selected SNPs in non-HLA genes.

Article Snippet: v2 , TRAF1.rs3761847 , 9 , 120927961 , A/G , C___2783640_10.

Techniques:

Journal: PLOS ONE

Article Title: Machine learning-based prediction of rheumatoid arthritis with development of ACPA autoantibodies in the presence of non-HLA genes polymorphisms

doi: 10.1371/journal.pone.0300717

Figure Lengend Snippet: Association of RA with the frequency of SNPs in PTPN22 (rs2476601), PADI4 (rs2240340), TRAF1 (rs3761847), STAT4 (rs7574865), and CD40 (rs4810485) genes.

Article Snippet: v2 , TRAF1.rs3761847 , 9 , 120927961 , A/G , C___2783640_10.

Techniques:

Journal: Oncology reports

Article Title: Overexpression of goosecoid homeobox is associated with chemoresistance and poor prognosis in ovarian carcinoma.

doi: 10.3892/or.2014.3203

Figure Lengend Snippet: Figure 3. Correlation of mRNA expression by qRT-PCR with clinicopathological parameters. (A) High expression of GSC (≥1.5-fold) was significantly associated with LN metastasis. (B) Low expression of TNFRSF10A (≤0.5-fold) and high expression of SNAI1 (≥1.5-fold) were significantly associated with distant metastasis. (C) Low expression of TRAF1 (≤0.5-fold) and high expression of E2F1 (≥2-fold), FOS (≥2-fold), TERT (≥1.5-fold) and GSC (≥1.5-fold) were significantly associated with advanced clinical stage (stages III and IV).

Article Snippet: Slides were incubated overnight at 4 ̊C with the following primary antibodies and working dilutions: TRAF1 (1:2,000; Novus Biologicals, Littleton, CO, USA), TERT (1:200; Novus Biologicals) and GSC (1:200; Abnova, Taipei, Taiwan).

Techniques: Expressing, Quantitative RT-PCR

Journal: Oncology reports

Article Title: Overexpression of goosecoid homeobox is associated with chemoresistance and poor prognosis in ovarian carcinoma.

doi: 10.3892/or.2014.3203

Figure Lengend Snippet: Figure 4. Kaplan-Meier overall survival curves. The downregulation group of TRAF1 (≤0.5-fold) and upregulation group (≥1.5-fold) of TERT, GSC, NOTCH1 and SNAI1 were associated with a significantly worse overall survival than the upregulation or downregulation group, respectively, in the ovarian serous carcinoma cases.

Article Snippet: Slides were incubated overnight at 4 ̊C with the following primary antibodies and working dilutions: TRAF1 (1:2,000; Novus Biologicals, Littleton, CO, USA), TERT (1:200; Novus Biologicals) and GSC (1:200; Abnova, Taipei, Taiwan).

Techniques:

Journal: Cell death & disease

Article Title: TRAF1 is a key mediator for hepatic ischemia/reperfusion injury.

doi: 10.1038/cddis.2014.411

Figure Lengend Snippet: Figure 1 Hepatic TRAF1 is upregulated after liver I/R injury. (a) Relative TRAF1 expression in hepatic tissues quantified by qRT-PCR at the indicated time points following ischemic onset (n = 9 per time point, *Po0.05 versus sham). (b) Western blot analysis for TRAF1 detection in protein extracts from hepatic tissues at the indicated time points following ischemic onset (left). Values were normalized to GAPDH. Right panel: quantification of TRAF1 levels (right, n = 3 per time point; the number on the bar represents the fold change). (c) Western blot analysis of TRAF1 expression in cultured hepatocytes after H/R injury (left) and the quantification of TRAF1 levels (right, n = 6 per time point, right, *Po0.05 versus sham). Data are presented as the mean ± S.D.

Article Snippet: The open reading frame (ORF) of mouse TRAF1 was purchased from OriGene (MG206422, Rockville, MD, USA) and subcloned into a pCMV6-AC-GFP shuttle vector.

Techniques: Expressing, Quantitative RT-PCR, Western Blot, Cell Culture

Journal: Cell death & disease

Article Title: TRAF1 is a key mediator for hepatic ischemia/reperfusion injury.

doi: 10.1038/cddis.2014.411

Figure Lengend Snippet: Figure 2 TRAF1 participates in the regulation of liver I/R injury. (a) Western blot analysis of TRAF1 expression in liver tissues from TRAF1-KO and WT mice. (b, h) Representative images of the areas of focal necrosis in hepatic cells of the indicated mice at different time points after I/R (left). Scale bar: 100 μm. Quantification of the necrotic areas (right; n = 8 at each time point, *Po0.05 versus WTor NTG). (c, i) Quantification of serum marker ALTand AST levels at the indicated time points after I/R (n = 8 at each time point, *Po0.05 versus sham, #Po0.05 versus I/R). (d) Schematic representation of two transgene constructs. (e) Representative images of liver I/R injury and quantification of necrotic areas (n = 8, #Po0.05 versus NTG). (f) Quantification of serum ALTand AST levels. (g) Western blot analysis of TRAF1 detection in hepatic tissues from four founder lines of TRAF1 TG mice (TG1–TG4) and NTG mice and relative TRAF1 levels in TG1–TG4 and NTG mice (the number on the bar represents the fold -change). Data are presented as the mean ± S.D.

Article Snippet: The open reading frame (ORF) of mouse TRAF1 was purchased from OriGene (MG206422, Rockville, MD, USA) and subcloned into a pCMV6-AC-GFP shuttle vector.

Techniques: Western Blot, Expressing, Marker, Construct

Journal: Cell death & disease

Article Title: TRAF1 is a key mediator for hepatic ischemia/reperfusion injury.

doi: 10.1038/cddis.2014.411

Figure Lengend Snippet: Figure 3 TRAF1 deficiency blunts the inflammatory insult induced by I/R injury. (a) Quantification of serum MPO activity at the indicated time points after I/R (n = 8 at each time point, *Po0.05 versus sham, #Po0.05 versus I/R). (b) Fluorescence staining of the indicated protein (red) and nuclei (DAPI, blue) in the hepatic cells of mice after 12 h liver I/R. Scale bar: 20 μm. (c) Quantification of the indicated protein-positive cells (n = 5–13, *Po0.05 versus WTor NTG). (d) Flow cytometry analysis of isolated cells from ischemic liver lobes stained with CD11b and either of anti-F4/80, Ly6G and Ly6C antibodies. (e, f) Quantification of the mRNA levels of TNF-α, IFNγ, IL-1β, IL-2, IL-6, and IL-10 in WTand TRAF1-KO mice, and NTG and TRAF1 TG mice, 12 h after sham surgery or I/R (n = 6 or 9, *Po0.05 versus sham, #Po0.05 versus I/R). (g, h) Quantification of the protein levels of TNF-α, IL-1β, IL-2, IL-6, and IL-10 in the peripheral blood of indicated mice 12 h after sham surgery or I/R (n = 7 or 8, *Po0.05 versus sham, #Po0.05 versus I/R). (i, j) Western blot analysis of the indicated proteins in hepatic tissues from WT/TRAF1-KO mice and NTG/TRAF1 TG mice after sham surgery or 12 h I/R (n = 6, *Po0.05 versus sham, #Po0.05 versus I/R). GAPDH served as a loading control. Data are presented as the mean ± S.D.

Article Snippet: The open reading frame (ORF) of mouse TRAF1 was purchased from OriGene (MG206422, Rockville, MD, USA) and subcloned into a pCMV6-AC-GFP shuttle vector.

Techniques: Activity Assay, Fluorescence, Staining, Flow Cytometry, Isolation, Western Blot, Control

Journal: Cell death & disease

Article Title: TRAF1 is a key mediator for hepatic ischemia/reperfusion injury.

doi: 10.1038/cddis.2014.411

Figure Lengend Snippet: Figure 4 TRAF1 mediates I/R-induced cell death. (a, b) Quantification of TUNEL-positive cells of WTand TRAF1 KO (a), and NTG and TRAF1 TG (b) mice after 12 h I/R (n = 7–13, *Po0.05 versus WTor NTG). (c, d, e, g) Western blot analysis of the indicated proteins in the hepatic tissues of WT/TRAF1 KO (c, e) and NTG/TRAF1 TG (d, g) mice after sham surgery or 12 h I/R injury. The right panels indicate the quantification of these proteins (n = 6, *Po0.05 versus sham, #Po0.05 versus I/R). Data are presented as the mean ± S.D. (f, h) Release of cytochrome c (Cyt C) from mitochondria into the cytoplasm of hepatic cells from WT/TRAF1 KO (f) and NTG/TRAF1 TG (h) mice. LDH and COX II are shown as the internal markers for cytoplasm and mitochondria, respectively. LDH, lactate dehydrogenase; COX II, cytochrome c oxidase subunit II

Article Snippet: The open reading frame (ORF) of mouse TRAF1 was purchased from OriGene (MG206422, Rockville, MD, USA) and subcloned into a pCMV6-AC-GFP shuttle vector.

Techniques: TUNEL Assay, Western Blot

Journal: Cell death & disease

Article Title: TRAF1 is a key mediator for hepatic ischemia/reperfusion injury.

doi: 10.1038/cddis.2014.411

Figure Lengend Snippet: Figure 5 TRAF1 is a modulator of hepatocyte survival after H/R. (a) Western blot analysis of TRAF1 expression in cultured hepatocytes infected with the indicated adenovirus (left) and the quantification of TRAF1 normalized to GAPDH. (n = 4, *Po0.05 versus AdshRNA, #Po0.05 versus AdGFP). (b) Cell viability, LDH release and DNA fragmentation of hepatic cells isolated from WT/TRAF1 KO and NTG/TRAF1 TG mice at the indicated time points after H/R. (n = 11 or 12 for each time point, *Po0.05 versus Basal, #Po0.05 versus H/R). (c) Cell viability, LDH release and DNA fragmentation of primary hepatocytes infected with AdshRNA/AdshTRAF1 and AdGFP/AdTRAF1 at the indicated time points after H/R (n = 12 for each time point, *Po0.05 versus Basal, #Po0.05 versus H/R). (d, e) Western blot analysis of apoptosis-related protein levels in cells infected with the indicated adenoviral vectors for 48 h and subjected to H/R for 6 h. Right panel: quantification of protein levels (n = 6, *Po0.05 versus AdshRNA or AdGFP control, #Po0.05 versus AdshRNA or AdGFP H/R). Data are presented as the mean ± S.D.

Article Snippet: The open reading frame (ORF) of mouse TRAF1 was purchased from OriGene (MG206422, Rockville, MD, USA) and subcloned into a pCMV6-AC-GFP shuttle vector.

Techniques: Western Blot, Expressing, Cell Culture, Infection, Isolation, Control

Journal: Cell death & disease

Article Title: TRAF1 is a key mediator for hepatic ischemia/reperfusion injury.

doi: 10.1038/cddis.2014.411

Figure Lengend Snippet: Figure 6 TRAF1 regulates the regenerative capacity of the liver. (a, b) Fluorescence staining of PCNA (red) and nuclei (DAPI, blue) in the hepatic cells of WT/TRAF1 KO (a) and NTG/TRAF1 TG (b) after sham surgery or 24 h liver I/R. Scale bar: 20 μm. The right panels demonstrate the quantification of PCNA-positive cells (n = 10–20, *Po0.05 versus WT/NTG). (c, d) Quantification of the mRNA levels of PCNA, cyclin D, and cyclin E in WT/TRAF1 KO (c) and NTG /TRAF1 TG (d) mice after sham surgery or 24 h liver I/R (n = 9, *Po0.05 versus sham, #Po0.05 versus I/R). Data are presented as the mean ± S.D. (e, f) Western blot analysis of the levels of PCNA and cyclin E in hepatic cells of WT and TRAF1 KO (e) and NTG and TRAF1 TG (f) mice after sham operation or 12 h liver I/R. Right panel: quantification of protein levels (n = 6, *Po0.05 versus sham, #Po0.05 versus I/R). Data are presented as the mean ± S.D.

Article Snippet: The open reading frame (ORF) of mouse TRAF1 was purchased from OriGene (MG206422, Rockville, MD, USA) and subcloned into a pCMV6-AC-GFP shuttle vector.

Techniques: Fluorescence, Staining, Western Blot

Journal: Cell death & disease

Article Title: TRAF1 is a key mediator for hepatic ischemia/reperfusion injury.

doi: 10.1038/cddis.2014.411

Figure Lengend Snippet: Figure 7 TRAF1 has an important role in the activation of the ASK1-MKK4–JNK signaling pathway. (a, b) Western blot analysis (left) and quantification (right) of the levels of the indicated proteins in the hepatic tissues of WT/TRAF1 KO (a) and NTG/TRAF1 TG (b) mice after sham surgery or 12 h liver I/R (n = 6, *Po0.05 versus sham, #Po0.05 versus I/R). (c, d) Western blot analysis (left) and quantification (right) of the levels of the indicated proteins in hepatocytes infected with the indicated adenovirus for 48 h and subjected to H/R for 6 h (n = 6, *Po0.05 versus AdshRNA or AdGFP control, #Po0.05 versus AdshRNA or AdGFP H/R). GAPDH served as an internal control. Data are presented as the mean ± S.D.

Article Snippet: The open reading frame (ORF) of mouse TRAF1 was purchased from OriGene (MG206422, Rockville, MD, USA) and subcloned into a pCMV6-AC-GFP shuttle vector.

Techniques: Activation Assay, Western Blot, Infection, Control

Journal: Cell death & disease

Article Title: TRAF1 is a key mediator for hepatic ischemia/reperfusion injury.

doi: 10.1038/cddis.2014.411

Figure Lengend Snippet: Figure 8 TRAF1 function is ASK1-dependent during liver I/R injury. (a) Co-immunoprecipitation of TRAF1 and ASK1 from HepG2 cells transfected with Myc-tagged TRAF1 and Flag-tagged ASK1. The lysates were immunoprecipitated with anti-Myc (left) or anti-Flag (right) antibody and analyzed by immunoblotting as indicated. (b) The interaction of endogenous TRAF1 and ASK1 detected by co-immunoprecipitation. (c) Schematic representation of the TRAF1 and ASK1 deletion mutants. (d, f) Mapping of the ASK1-binding region of TRAF1. HepG2 cells were transfected with Flag-tagged ASK1 and Myc-tagged TRAF1 mutants or control vector. The lysates were immunoprecipitated with anti-Myc (d) or anti-Flag (f) antibody and immunoblotted with the indicated antibodies. (e, g) Mapping of the TRAF1-binding region of ASK1. HepG2 cells were transfected with Myc-tagged TRAF1 and Flag-tagged ASK1 mutants or control vector. The lysates were immunoprecipitated with anti-Flag (e) or anti-Myc (g) antibody and immunoblotted as indicated. (h) Colocalization of full-length (1–409 aa) or truncated (1–187 aa) EGFP-TRAF1 and mCherry-ASK1 in the cytoplasm of HepG2 cells. (i) ASK1-CFP and full-length (1–409 aa) or truncated (1–187 aa) TRAF1-YFP fluorescence with excitation/emission at 457/485 nm (top) and 514/535 nm (bottom). (j) The average efficiency after photobleaching is indicative of the FREToccurring between ASK1-CFP and TRAF1-YFP (n = 4, #Po0.05). (k) Quantification of cell viability and LDH release of cultured hepatocytes infected with AdGFP, AdTRAF1, or an Ad-mutant harboring a mutant TRAF1-domain and subjected to H/R for 12 h (n = 12, NS, not significant). (l, m) Quantification of cell viability and LDH release of primary hepatocytes isolated from WT/TRAF1 KO (l) and NTG/TRAF1 TG mice (m) infected with AdGFP, AdASK1 and Addn-ASK1 and subjected to H/R for 12 h (n = 12, NS, not significant)

Article Snippet: The open reading frame (ORF) of mouse TRAF1 was purchased from OriGene (MG206422, Rockville, MD, USA) and subcloned into a pCMV6-AC-GFP shuttle vector.

Techniques: Immunoprecipitation, Transfection, Western Blot, Binding Assay, Control, Plasmid Preparation, Fluorescence, Cell Culture, Infection, Mutagenesis, Isolation

Journal: Digital Chinese Medicine

Article Title: Mechanism of Yishen Tonglong Decoction inhibiting TLR4/p38 MAPK/NF-κB signaling pathway against prostate cancer via upregulating miR-145-5p

doi: 10.1016/j.dcmed.2023.02.008

Figure Lengend Snippet: Figure 6 Effects of miR-145-5p and YSTLD on TLR4/p38 MAPK/NF-κB signaling pathway and mRNA expression of apoptosis-related genes in prostate cancer PC-3 cells A − I, the relative expression levels of miR-145-5p, p38 MAPK, p65 NF-κB, TLR4, Bax, Bcl-2, caspase3, TNF-α, and TRAF1 in prostate cancer PC-3 cells of each group. *P < 0.05.

Article Snippet: 2.2 Drugs and reagents Phosphate buffered solution (PBS) buffer (GIBCO, USA); Roswell Park Memorial Institute (RPMI) 1640 medium (Procell Life Science & Technology Co., Ltd., China); fetal bovine serum (GIBCO, USA); trypsin (GIBCO, USA); 0.25% prote-sin-EDTA (GIBCO, USA); miR-145-5p antibody (Proteintech, USA); p38 MARK antibody (Proteintech, USA); p65 NF-κB antibody (Proteintech, USA); caspase3 antibody (Proteintech, USA); TNF-α antibody (Proteintech, USA); Bax antibody (Proteintech, USA); Bcl2 antibody (Proteintech, USA); TRAF1 antibody (Proteintech, USA); Cell Counting Kit-8 (CCK8) assay kit (Proteintech, USA); fluorescent secondary antibody IgG (Proteintech, USA); RNA extraction kit (Bioflux, USA); reverse transcription kit (Promega, USA); 2 × Taq PCR Master mix (NovoTech, Slovakia); PureLink RNA Mini Kit (TFS, USA).

Techniques: Expressing

Journal: Digital Chinese Medicine

Article Title: Mechanism of Yishen Tonglong Decoction inhibiting TLR4/p38 MAPK/NF-κB signaling pathway against prostate cancer via upregulating miR-145-5p

doi: 10.1016/j.dcmed.2023.02.008

Figure Lengend Snippet: Figure 7 Effects of YSTLD on TLR4/p38 MAPK/NF-κB signaling pathway and protein expression of apoptosis- related genes in prostate cancer PC-3 cells A, YSTLD on p38 MAPK, p65 NF-κB, TLR4, caspase3, and TRAF1 protein expression in prostate cancer PC-3 cells. B − F, p38 MAPK, p65 NF-κB, caspase3, TLR4, and TRAF1 protein ex- pression levels in prostate cancer PC-3 cells of each group. *P < 0.05.

Article Snippet: 2.2 Drugs and reagents Phosphate buffered solution (PBS) buffer (GIBCO, USA); Roswell Park Memorial Institute (RPMI) 1640 medium (Procell Life Science & Technology Co., Ltd., China); fetal bovine serum (GIBCO, USA); trypsin (GIBCO, USA); 0.25% prote-sin-EDTA (GIBCO, USA); miR-145-5p antibody (Proteintech, USA); p38 MARK antibody (Proteintech, USA); p65 NF-κB antibody (Proteintech, USA); caspase3 antibody (Proteintech, USA); TNF-α antibody (Proteintech, USA); Bax antibody (Proteintech, USA); Bcl2 antibody (Proteintech, USA); TRAF1 antibody (Proteintech, USA); Cell Counting Kit-8 (CCK8) assay kit (Proteintech, USA); fluorescent secondary antibody IgG (Proteintech, USA); RNA extraction kit (Bioflux, USA); reverse transcription kit (Promega, USA); 2 × Taq PCR Master mix (NovoTech, Slovakia); PureLink RNA Mini Kit (TFS, USA).

Techniques: Expressing