Journal: Cell Death & Disease

Article Title: Preferential Fas-mediated apoptotic execution at G 1 phase: the resistance of mitotic cells to the cell death

doi: 10.1038/cddis.2012.52

Figure Lengend Snippet: FADD phosphorylation during mitotic HeLa.S-Fucci cells. Cells were arrested at the border of G 1 and S phases with a double-thymidine block, followed by release to enter S phase. Cell lysates from cells at each time point were subjected to SDS–PAGE, followed by immunoblotting with antibodies as indicated. Cyclin B and cyclin E were used for cell cycle markers of G 2 /M and G 1 /S phases, respectively

Article Snippet: Anti-caspase-3 polyclonal antibody (9662), anti-caspase-8 polyclonal antibody (9764), anti-PARP polyclonal antibody (9542), and anti-phospho-FADD (Ser-194) polyclonal antibody (2781) were obtained from Cell Signaling (Danvers, MA, USA); anti-caspase-9 monoclonal antibody (M054-3), anti-FADD monoclonal antibody (M033-3), and cyclin B1 monoclonal antibody (K0128-3) were from Medical & Biological Laboratories; anti-caspase-7/MCH-3 monoclonal antibody (610812) was from BD Biosciences (Rockville, MD, USA); anti- α -tubulin monoclonal antibody (T6074) was from Sigma (St. Louis, MO, USA); anti-cyclin E monoclonal antibody (sc-247) was from Santa Cruz Biotechnology (Santa Cruz, CA, USA).

Techniques: Phospho-proteomics, Blocking Assay, SDS Page, Western Blot

Journal: PLoS Genetics

Article Title: TENET 2.0: Identification of key transcriptional regulators and enhancers in lung adenocarcinoma

doi: 10.1371/journal.pgen.1009023

Figure Lengend Snippet: First, DNA methylation probes marking enhancer regions of interest are identified by overlapping them with both H3K27ac ChIP-seq datasets and open chromatin regions. Next, enhancer probes are classified based on their DNA methylation level in the tumor vs . normal samples and linked to the expression of genes to identify key transcriptional regulators (TRs). Using genetic alteration, Hi-C topologically associating domain (TAD), and clinical information, identified key TRs and TR-enhancer-gene networks are characterized. Additional gene expression and clinical data are used to validate findings of key TRs. Lung-related datasets used for this study are shown at left. The output from this LUAD study is indicated in the middle bottom box. The left bottom box summarizes key TENET 2.0 functions.

Article Snippet: ChIP-seq was performed on the D0, D4, and D6 AECs isolated from the 25-year-old and 62-year-old male subjects using H3K27ac antibody (Cat # 39133, Active Motif, CA, USA), as previously described [ , ].

Techniques: DNA Methylation Assay, ChIP-sequencing, Expressing, Hi-C, Gene Expression

Journal: PLoS Genetics

Article Title: TENET 2.0: Identification of key transcriptional regulators and enhancers in lung adenocarcinoma

doi: 10.1371/journal.pgen.1009023

Figure Lengend Snippet: Identification of differentially-methylated enhancer probes (A) Integrative Genomics Viewer (IGV) screenshots show 10 kb of the genomic context centered on example probes, with UCSC gene annotations (GENCODE v22) in the vicinity, the name and location of the probe, and the H3K27ac signal from AEC (normal) as well as A549 cells (LUAD cell line). The unmethylated probe shows an active enhancer region in both the AEC and A549 cells. The hypermethylated probe shows an active enhancer region found in only the AEC, indicating an enhancer that is inactive in tumors, while the hypomethylated probe displays marks in only A549 cells, indicating an enhancer that is activated in tumors. (B) Categorization of the identified enhancer probes by activity.

Article Snippet: ChIP-seq was performed on the D0, D4, and D6 AECs isolated from the 25-year-old and 62-year-old male subjects using H3K27ac antibody (Cat # 39133, Active Motif, CA, USA), as previously described [ , ].

Techniques: Methylation, Activity Assay

Journal: PLoS Genetics

Article Title: TENET 2.0: Identification of key transcriptional regulators and enhancers in lung adenocarcinoma

doi: 10.1371/journal.pgen.1009023

Figure Lengend Snippet: (A) Shown are three examples of lung cancer-specific enhancers linked to CENPA, FOXM1, or MYBL2 in LUAD. IGV screenshots show 10 kb of the genomic context centered on example probes, with GENCODE v22-annotated UCSC genes in the vicinity, the name and location of the probe, and the H3K27ac signal from normal AEC as well as lung tumor A549 cells. These hypomethylated probes show H3K27ac marks in A549 cells, indicating enhancers active in LUAD but not normal lung tissue. (B) Kaplan-Meier survival plots comparing differences in survival between samples with the highest and lowest quartiles of methylation of the enhancer probe.

Article Snippet: ChIP-seq was performed on the D0, D4, and D6 AECs isolated from the 25-year-old and 62-year-old male subjects using H3K27ac antibody (Cat # 39133, Active Motif, CA, USA), as previously described [ , ].

Techniques: Methylation

Journal: PLoS Genetics

Article Title: TENET 2.0: Identification of key transcriptional regulators and enhancers in lung adenocarcinoma

doi: 10.1371/journal.pgen.1009023

Figure Lengend Snippet: Volcano plots showing gene expression changes after knocking down (A) FOXM1 or (B) MYBL2 or (C) Double (both FOXM1 and MYBL2). The knocked down genes (FOXM1 or MYBL2) are highlighted by a green or purple box, respectively. (D) Heatmap displaying fold change expression of significantly downregulated genes in the vicinity of cancer-specific enhancers associated with poor patient survival after FOXM1 (light blue) or MYBL2 (orange) or double (green) knockdown; log2(fold change) were plotted from dark blue to dark red (see ). Genes shown represent potential target genes within 1 Mb of CENPA/FOXM1/MYBL2-linked enhancers whose activation is significantly associated with poor patient survival. Expression of the gene TK1 is highlighted by the red arrow. (E) Diagram of A549 H3K27ac mark overlapping the MYBL2-linked probe cg09580922 and its potential target gene TK1 (see ). (F) Kaplan-Meier survival plot comparing differences in survival between LUAD tumor samples with the highest and lowest quartiles of cg09580922 methylation. (G) Kaplan-Meier survival plot comparing differences in survival between LUAD tumor samples with the highest and lowest quartiles of TK1 expression.

Article Snippet: ChIP-seq was performed on the D0, D4, and D6 AECs isolated from the 25-year-old and 62-year-old male subjects using H3K27ac antibody (Cat # 39133, Active Motif, CA, USA), as previously described [ , ].

Techniques: Gene Expression, Expressing, Knockdown, Activation Assay, Methylation

Journal: Animals : an Open Access Journal from MDPI

Article Title: Mitochonic Acid 5 Increases Ram Sperm Quality by Improving Mitochondrial Function during Storage at 4 °C

doi: 10.3390/ani14030368

Figure Lengend Snippet: Effect of MA-5 on mitochondrial energy in liquid storage at 4 °C. ( A ) Western blot analysis of MT-ND1 and MT-ND6 in ram sperm. ( B ) Impact of MA-5 on MT-ND1 activity in ram sperm. Values are presented as means ± standard deviations (SDs). The mitochondrial production of proteins with MA-5 and its effect on mitochondrial function were assessed ( n = 3). Different letters within a line denote significant differences ( p < 0.05), determined through a one-way ANOVA and Dunnett’s test, relative to the medium without MA-5. ( C ) The impact of MA-5 on MT-ND6 activity in ram sperm. Values are specified as means ± standard deviations (SDs). The mitochondrial production of proteins with MA-5 and its effect on mitochondrial function were evaluated ( n = 3). Different letters within a line signify significant differences ( p < 0.05), as determined by a one-way ANOVA and Dunnett’s test, compared to the medium without MA-5.

Article Snippet: Primary antibodies, including anti-mitochondrial NADPH dehydrogenase subunit 1 (anti-MT-ND1; 1973-1-AP, Proteintech, Rosemont, IL, USA), anti-mitochondrial NADPH dehydrogenase subunit 6 (anti-MT-ND6; bs-3955R; Bioss, Inc., Boston, MA, USA), and anti-α-tubulin (2148; Cell Signaling Technology, Inc., Danvers, MA, USA), were diluted to 1:1000 in 5% bovine serum albumin in TBS-Tween and applied overnight at 4 °C.

Techniques: Western Blot, Activity Assay