Journal: Journal of Virology

Article Title: According to Hepatitis C Virus (HCV) Infection Stage, Interleukin-7 Plus 4-1BB Triggering Alone or Combined with PD-1 Blockade Increases TRAF1 low HCV-Specific CD8 + Cell Reactivity

doi: 10.1128/JVI.01443-17

Figure Lengend Snippet: TRAF1 expression in pentamer+/CD8+ cells. (A and B) MFI of TRAF1 in peripheral total CD8+ and pentamer+/CD8+ cells after 3 h (A) and after 10 days (B) of specific in vitro challenge, depending on the viral control. According to the MFI, TRAF1 expression was categorized as negative (Neg), dim, and high. The box plots summarize the distribution of the TRAF1 MFI in total and pentamer-binding CD8+ cells in each category. (C) Representative dot plots showing TRAF1 expression in pentamer+/CD8+ cells after 3 h and 10 days of specific in vitro challenge in patients with resolved and persistent infections. The data represent the percentage of cells in each area in reference to the number of total CD8+ and pentamer+/CD8+ cells. (D) Histograms of TRAF1 expression by pooled HCV and CMV specific pentamer+/CD8+ cells from all patients with resolved infection after treatment and persistent infection after 3 h of specific stimulation. (E) Difference in TRAF1 expression according to the MFI between NS3 pentamer+/CD8+ and total CD8+ cells from patients with PI infected by wild-type HCV NS3 or an escape variant. Bold lines, median values of the distribution; #, Mann-Whitney U test; ¤, Wilcoxon test. ○, outlier value; *, extreme value; Ag, antigen; MFI, mean fluorescence intensity; ND, not done; Negative Control, T cell labeling with the secondary antibody only; NS, nonsignificant; Pent, pentamer.

Article Snippet: The following unlabeled MAb were also used: TRAF1 rabbit anti-human immunoglobulin (clone 45D3; Cell Signaling, Boston, MA) and myeloid cell leukemia 1 protein (Mcl-1) rabbit anti-human immunoglobulin (clone Y37; Epitomics, Burlingame, CA).

Techniques: Expressing, In Vitro, Control, Binding Assay, Infection, Variant Assay, MANN-WHITNEY, Fluorescence, Negative Control, Labeling

Journal: Journal of Virology

Article Title: According to Hepatitis C Virus (HCV) Infection Stage, Interleukin-7 Plus 4-1BB Triggering Alone or Combined with PD-1 Blockade Increases TRAF1 low HCV-Specific CD8 + Cell Reactivity

doi: 10.1128/JVI.01443-17

Figure Lengend Snippet: Pilot analysis of TRAF1 expression in pentamer+/CD8+ cells from patients with resolved and persistent infections performed directly ex vivo and after 3 h of specific stimulation. Box plots (A) and representative dot plots (B) from a preliminary analysis show the level of TRAF1 expression in HCV pentamer-binding CD8+ cells determined directly ex vivo and after 3 h of specific stimulation in patients with a resolved infection after treatment and patients with persistent infection. Negative control, T cell labeling with the secondary antibody only; MFI, mean fluorescence intensity; NS, nonsignificant; st, stimulation; §, Mann-Whitney U test; ¥, Wilcoxon test.

Article Snippet: The following unlabeled MAb were also used: TRAF1 rabbit anti-human immunoglobulin (clone 45D3; Cell Signaling, Boston, MA) and myeloid cell leukemia 1 protein (Mcl-1) rabbit anti-human immunoglobulin (clone Y37; Epitomics, Burlingame, CA).

Techniques: Expressing, Ex Vivo, Binding Assay, Infection, Negative Control, Labeling, Fluorescence, MANN-WHITNEY

Journal: Journal of Virology

Article Title: According to Hepatitis C Virus (HCV) Infection Stage, Interleukin-7 Plus 4-1BB Triggering Alone or Combined with PD-1 Blockade Increases TRAF1 low HCV-Specific CD8 + Cell Reactivity

doi: 10.1128/JVI.01443-17

Figure Lengend Snippet: Correlation between TRAF1 expression, exhaustion phenotype, and reactivity of HCV pentamer+/CD8+ cells. Tests for TRAF1 and Mcl-1 were performed after 3 h of specific peptide stimulation, while PD-1 and CD127 were assessed directly ex vivo. (A) Correlation between TRAF1 level and CD127, PD-1, and Mcl-1 expression on pentamer+/CD8+ cells pooled from patients with persistent and resolved infections. (B) PD-1, CD127, and Mcl-1 expression on HCV pentamer+/CD8+ cells from HCV patients, according to the TRAF1 level. (C) Rates of HCV pentamer+/CD8+ cell proliferation after 10 days of specific in vitro challenge, depending on the level of TRAF1 expression. (D) Representative dot plots showing the PD-1, CD127, and Mcl-1 phenotype (as the MFI) and the expansion ability (as the percentage of pentamer-binding CD8+ cells out of the number of total CD8+ cells) according to the TRAF1 level in pentamer+/CD8+ cells. (E) Histograms of PD-1, CD127, and Mcl-1 expression on pooled pentamer+/CD8+ cells in relation to the TRAF1 level. *, Spearman correlation test; ¥, Mann-Whitney U test; negative control, T cell labeling with the nonspecific isotype antibody; ○, outlier values; LOD, limit of detection; MFI, mean fluorescence intensity.

Article Snippet: The following unlabeled MAb were also used: TRAF1 rabbit anti-human immunoglobulin (clone 45D3; Cell Signaling, Boston, MA) and myeloid cell leukemia 1 protein (Mcl-1) rabbit anti-human immunoglobulin (clone Y37; Epitomics, Burlingame, CA).

Techniques: Expressing, Ex Vivo, In Vitro, Binding Assay, MANN-WHITNEY, Negative Control, Labeling, Fluorescence

Journal: Journal of Virology

Article Title: According to Hepatitis C Virus (HCV) Infection Stage, Interleukin-7 Plus 4-1BB Triggering Alone or Combined with PD-1 Blockade Increases TRAF1 low HCV-Specific CD8 + Cell Reactivity

doi: 10.1128/JVI.01443-17

Figure Lengend Snippet: TRAF1 expression in pentamer+/CD8+ cells from resolved infection cases after interferon-free and interferon-containing regimens. Box plots (A) and representative dot plots (B) showing the level of TRAF1 expression after 3 h of antigen-specific stimulation in HCV pentamer-binding CD8+ cells from sustained virologic responders to interferon (IFN)-containing and -free regimens. MFI, mean fluorescence intensity; NS, nonsignificant; §, Mann-Whitney U test.

Article Snippet: The following unlabeled MAb were also used: TRAF1 rabbit anti-human immunoglobulin (clone 45D3; Cell Signaling, Boston, MA) and myeloid cell leukemia 1 protein (Mcl-1) rabbit anti-human immunoglobulin (clone Y37; Epitomics, Burlingame, CA).

Techniques: Expressing, Infection, Binding Assay, Fluorescence, MANN-WHITNEY

Journal: Journal of Virology

Article Title: According to Hepatitis C Virus (HCV) Infection Stage, Interleukin-7 Plus 4-1BB Triggering Alone or Combined with PD-1 Blockade Increases TRAF1 low HCV-Specific CD8 + Cell Reactivity

doi: 10.1128/JVI.01443-17

Figure Lengend Snippet: TRAF1 kinetics in pentamer+/CD8+ cells during treatment with direct-acting antivirals. Longitudinal dot plots show the peripheral ex vivo frequency, the proliferation intensity after specific in vitro challenge, the PD-1/CD127 level obtained directly ex vivo, and the level of TRAF1 expression after 3 h of specific stimulation in pentamer+/CD8+ cells from two HCV genotype 1-infected patients during treatment with direct-acting antivirals. ALT, alanine aminotransferase; EOT, end of treatment; OMB-PAR/rt/DAS+RBV, ombitasvir-paritaprevir-ritonavir-dasabuvir plus ribavirin; MFI, mean fluorescence intensity; PBL, peripheral blood lymphocyte; SOF-LED, sofosbuvir plus ledipasvir.

Article Snippet: The following unlabeled MAb were also used: TRAF1 rabbit anti-human immunoglobulin (clone 45D3; Cell Signaling, Boston, MA) and myeloid cell leukemia 1 protein (Mcl-1) rabbit anti-human immunoglobulin (clone Y37; Epitomics, Burlingame, CA).

Techniques: Ex Vivo, In Vitro, Expressing, Infection, Fluorescence

Journal: Journal of Virology

Article Title: According to Hepatitis C Virus (HCV) Infection Stage, Interleukin-7 Plus 4-1BB Triggering Alone or Combined with PD-1 Blockade Increases TRAF1 low HCV-Specific CD8 + Cell Reactivity

doi: 10.1128/JVI.01443-17

Figure Lengend Snippet: CD107a-mobilizing and gamma interferon (IFN-γ)-secreting HCV pentamer+/CD8+ cells according to the level of TRAF1 expression. Box plots (A) and representative dot plots (B) show the percentage of IFN-γ-secreting and CD107a-mobilizing pentamer+/CD8+ cells ex vivo and after 10 days of specific in vitro challenge, according to the TRAF1 level, among cells with a preserved expansion ability. ○, outlier value; *, extreme value. The data in each dot plot represent the percentage of positive cells out of the number of either total CD8+ cells or pentamer+/CD8+ cells. NS, nonsignificant; #, Wilcoxon test; *, Mann-Whitney U test.

Article Snippet: The following unlabeled MAb were also used: TRAF1 rabbit anti-human immunoglobulin (clone 45D3; Cell Signaling, Boston, MA) and myeloid cell leukemia 1 protein (Mcl-1) rabbit anti-human immunoglobulin (clone Y37; Epitomics, Burlingame, CA).

Techniques: Expressing, Ex Vivo, In Vitro, MANN-WHITNEY

Journal: Journal of Virology

Article Title: According to Hepatitis C Virus (HCV) Infection Stage, Interleukin-7 Plus 4-1BB Triggering Alone or Combined with PD-1 Blockade Increases TRAF1 low HCV-Specific CD8 + Cell Reactivity

doi: 10.1128/JVI.01443-17

Figure Lengend Snippet: Clinical features of recruited patients with CD8 + /pentamer + cells directly detectable ex vivo according to TRAF1 expression a

Article Snippet: The following unlabeled MAb were also used: TRAF1 rabbit anti-human immunoglobulin (clone 45D3; Cell Signaling, Boston, MA) and myeloid cell leukemia 1 protein (Mcl-1) rabbit anti-human immunoglobulin (clone Y37; Epitomics, Burlingame, CA).

Techniques: Ex Vivo, Expressing, Infection

Journal: Journal of Virology

Article Title: According to Hepatitis C Virus (HCV) Infection Stage, Interleukin-7 Plus 4-1BB Triggering Alone or Combined with PD-1 Blockade Increases TRAF1 low HCV-Specific CD8 + Cell Reactivity

doi: 10.1128/JVI.01443-17

Figure Lengend Snippet: TRAF1 regulation by IL-7 and TGF-β1 in pentamer+/CD8+ cells. (A) Levels of TRAF1 expression in pentamer+/CD8+ cells after β-galactosidase (β-Gal), IL-7, and TGF-β1 treatments in vitro. Box plots summarize the distribution of the level of TRAF1 expression in each category. (B) Representative dot plots and histograms showing TRAF1 levels in pentamer+/CD8+ cells after IL-7, TGF-β1, and β-galactosidase treatments in vitro. (C) In selected patients with PI, the dynamics of the TGF-β1 levels in PBL culture supernatants between day 2 and day 9 of NS3-specific in vitro challenge, according to cell expansion status. (Top) Global variation in TGF-β1 levels; (bottom) individual variation in TGF-β1 levels. Box plots summarize the distribution of either the absolute value or the relative variation in the TGF-β1 level in each category. (D) (Left) Serum TGF-β1 level in patients with persistent infection and resolved infection after treatment. Box plots represent the distribution of the TGF-β1 levels in each group. (Right) Correlation between the serum TGF-β1 level and TRAF1 expression in HCV pentamer+/CD8+ cells after 3 h of specific stimulation. (E) Serum TGF-β1 concentration according to the TRAF1 phenotype of HCV pentamer+/CD8+ cells after 3 h specific stimulation. Box plots summarize the distribution of the TGF-β1 level in every group. ¤, Wilcoxon test; #, Mann-Whitney U test; ¥, Spearman correlation test; ○, outlier value; MFI, mean fluorescence intensity.

Article Snippet: The following unlabeled MAb were also used: TRAF1 rabbit anti-human immunoglobulin (clone 45D3; Cell Signaling, Boston, MA) and myeloid cell leukemia 1 protein (Mcl-1) rabbit anti-human immunoglobulin (clone Y37; Epitomics, Burlingame, CA).

Techniques: Expressing, In Vitro, Infection, Concentration Assay, MANN-WHITNEY, Fluorescence

Journal: Biology of reproduction

Article Title: Tumor necrosis factor stimulates matrix metalloproteinase 9 secretion from cultured human chorionic trophoblast cells through TNF receptor 1 signaling to IKBKB-NFKB and MAPK1/3 pathway.

doi: 10.1095/biolreprod.109.082578

Figure Lengend Snippet: FIG. 2. mRNA and protein expression of TNF, TNF receptors (TNFRs), TNFR relatives, and effects of TNF and TNFRs on expression of TNFRSF1A, TRAF1, and TRAF2 protein expression in chorion trophoblast cells. A) mRNA expression (1, TNF; 2, TNFRSF1A; 3, TNFRSF1B; 4, TRAF1; 5, TRAF2; 6, TRADD; 7, FADD; 8, RIPK1). Analysis of the real-time PCR is shown (top); each bar represents the relative amounts of ACTB. Representative RT-PCR analysis is also shown (bottom). B) Protein expression (TNFRSF1A, TNFRSF1B, TRAF1, TRAF2, and ACTB) by Western blot analysis. C) Effects of TNF on TRAF1, TRAF2, and TNFRSF1A protein expression at different time points. D) Effects of TNFRs and inhibitors on TRAF1 and TRAF2 protein expression. Cells were preincubated with neutralizing antibodies as indicated for 1 h and then treated with TNF for 18 h. Cell proteins were harvested, and protein production was analyzed by Western blotting. Examples of Western blots are shown for one of three different experiments in each group.

Article Snippet: Mouse monoclonal TNFRSF1A, TNFRSF1B, TRAF1, TRAF2, phosphoMAPK1/3, and MAPK1/3 antibodies were from Santa Cruz Biotechnology; rabbit polyclonal RELA (p65) antibody was from eBioscience.

Techniques: Expressing, Real-time Polymerase Chain Reaction, Reverse Transcription Polymerase Chain Reaction, Western Blot

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

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: Brain and Behavior

Article Title: Tetrandrine alleviates inflammation and neuron apoptosis in experimental traumatic brain injury by regulating the IRE1α/JNK/CHOP signal pathway

doi: 10.1002/brb3.2786

Figure Lengend Snippet: The inflammation and IRE1α/JNK/CHOP signal pathway inhibitory effects of tetrandrine (TET) on traumatic brain injury (TBI) mouse model were reversed by Anisomycin. (a) TNF‐α, NF‐κB, and TRAF1 expression in the hippocampus was evaluated by enzyme‐linked immunosorbent assay (ELISA) assay. (b) TdT‐mediated dUTP nick‐end labeling (TUNEL) staining was used to detect apoptosis. (c) GADD34, PERK, p‐PERK, IRE1α, CHOP, JNK, and p‐JNK expression in the hippocampus was determined by western blot. (d) The expression of Caspase 3 and Caspase 12 was detected by immunofluorescence. * p < .05 versus control group, # p < .05 versus vehicle group, & p < .05 versus TET group

Article Snippet: According to the instruction of the manufacturer, enzyme‐linked immunosorbent assay (ELISA) kits (TNF‐α, CSB‐E11987r; NF‐κB, CSB‐E13148r; CUSABIO, China; TRAF1, E02T0901, BLUE GENE, China) were used to detect the concentration of TNF‐α, NF‐κB, and TRAF1 in the hippocampal homogenate of each mouse.

Techniques: Expressing, Enzyme-linked Immunosorbent Assay, End Labeling, TUNEL Assay, Staining, Western Blot, Immunofluorescence, 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 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: 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: