Journal: Apoptosis

Article Title: Molecular mechanism underlying differential apoptosis between human melanoma cell lines UACC903 and UACC903(+6) revealed by mitochondria-focused cDNA microarrays

doi: 10.1007/s10495-008-0231-8

Figure Lengend Snippet: Consistent RNA levels measured by microarray and qRT-PCR. ( a ) Relative RNA ratios of 10 genes, each at 3 time points, between UACC903 and UACC903(+6) cell lines measured by microarrays. ( b ) Relative RNA levels of the same 10 genes, each at the same 3 time points, measured by qRT-PCR. The ‘+’ sign indicates P < 0.05, and the ‘*’ indicates P < 0.01 for a pair within measurement. Out of these 30 gene-and-time-point comparisons, 28 (93.3%) are consistent between these two types of measurements, including 21 (70%) with agreement in both change (down, no, or up) and P -value, and 7 (23.3%) consistent with the changes but not with P -value (underlined). Two (6.7%) was inconsistent and included BAK1 at 0-h time point and MCL1 at 3-h time point (arrowhead)

Article Snippet: TaqMan probes and primers for glyceraldehyde-3-phosphate dehydrogenase (GAPDH, 4352934E); Fanconi anemia complementation group D2 (FANCD2, Hs00276992_m1); DEAH (Asp-Glu-Ala-His) box polypeptide 16 (DHX16, Hs00374356_m1); adenosylmethionine decarboxylase 1 (AMD1, Hs00750876_s1); BCL2-like 1 (BCL2L1, Hs99999146_m1); uracil-DNA glycosylase (UNG, Hs00422172_m1); Fas TNF receptor superfamily member 6 (FAS, Hs00531110_m1); BCL2-antagonist/killer 1 (BAK1, Hs00832876_g1); caspase 3 apoptosis-related cysteine peptidase (CASP3, Hs00234387_m1); protein phosphatase 2 catalytic subunit alpha isoform (PPP2CA, Hs00427259_m1); and myeloid cell leukemia sequence 1 (MCL1, Hs03043898_m1) were purchased from Applied Biosystems.

Techniques: Microarray, Quantitative RT-PCR

Journal: Apoptosis

Article Title: Molecular mechanism underlying differential apoptosis between human melanoma cell lines UACC903 and UACC903(+6) revealed by mitochondria-focused cDNA microarrays

doi: 10.1007/s10495-008-0231-8

Figure Lengend Snippet: Western blots and quantification. ( a ) Western blot of cell lysate from UACC903(+6) and UACC903 cell lines before (0) and at 1.5-, 3-, 6-, and 12-h after the UV treatment, using the antibodies against BAK1, BCL2L1, FAS, MCL1 and GAPDH proteins. GAPDH was used as a control for loading error. ( b ) Bar graph for the quantitative comparison among protein expression levels. The signal intensities of a protein band and its surrounding background were scanned from images derived from two independent Western experiments for each protein and quantified by using Scanalytics IPLAB 3.6 (Rockville, MD). The resultant background-subtracted values of protein expression were normalized to those of GAPDH and then plotted as the relative protein levels for each protein at each time point in each cell line with or without UV treatment

Article Snippet: TaqMan probes and primers for glyceraldehyde-3-phosphate dehydrogenase (GAPDH, 4352934E); Fanconi anemia complementation group D2 (FANCD2, Hs00276992_m1); DEAH (Asp-Glu-Ala-His) box polypeptide 16 (DHX16, Hs00374356_m1); adenosylmethionine decarboxylase 1 (AMD1, Hs00750876_s1); BCL2-like 1 (BCL2L1, Hs99999146_m1); uracil-DNA glycosylase (UNG, Hs00422172_m1); Fas TNF receptor superfamily member 6 (FAS, Hs00531110_m1); BCL2-antagonist/killer 1 (BAK1, Hs00832876_g1); caspase 3 apoptosis-related cysteine peptidase (CASP3, Hs00234387_m1); protein phosphatase 2 catalytic subunit alpha isoform (PPP2CA, Hs00427259_m1); and myeloid cell leukemia sequence 1 (MCL1, Hs03043898_m1) were purchased from Applied Biosystems.

Techniques: Western Blot, Expressing, Derivative Assay

Journal: BMC Genomics

Article Title: Transcriptomic profiles of aging in purified human immune cells

doi: 10.1186/s12864-015-1522-4

Figure Lengend Snippet: Age-associated expression pattern for the Bcl-2 family and other key autophagy genes suggest autophagy declines with age. The ‘black’ co-expression network module gene - MCL1 (circle), and other key genes (diamonds) encoding autophagy machinery and autophagy inhibitors/activators (related to the Bcl-2 family and the PI3K/AKT signaling pathway) are shown, with edges representing previously characterized protein-protein interactions (STRING v9.05). Color denotes the direction and significance resulting from the association of age and gene expression in 1,264 CD14+ human monocyte samples, adjusting for race, sex, study site, and residual cell contamination with other cell types.

Article Snippet: Blots were blocked in non-fat dry milk and incubated with antibodies to Mcl1 (Santa Cruz Biotechnology, Santa Cruz, CA) (clone S-19, 1:500 dilution), MRPS12 (Proteintech Group, Chicago, Il) (rabbit polyclonal, catalog #15225-1-AP, 1:333 dilution), and GAPDH (Ablabs, Vancouver, British Columbia) (clone ga1r, 1:3000 dilution) overnight at 4°C.

Techniques: Expressing, Protein-Protein interactions, Gene Expression

Journal: BMC Genomics

Article Title: Transcriptomic profiles of aging in purified human immune cells

doi: 10.1186/s12864-015-1522-4

Figure Lengend Snippet: Co-expression network modules associated with chronological age. Six mutually exclusive gene network modules with coordinate gene expression profiles associated with chronological age were identified in 1,264 monocyte samples (using WGCNA), ranging in size from 3 to 1,466 genes. For each module (x-axis), the partial correlation between age and the module eigengene is shown (y-axis); covariates included race, sex, site of data collection, and residual sample contamination with non-targeted cells. Below each module is the number of genes assigned to the module, and the direction of expression association with age; network modules discussed in further detail include the ‘black’ module (containing three genes: MCL1, TSC22D3, and CEBPD ), and the ‘blue’ and ‘turquoise’ modules (which were significantly enriched with age-related pathways shown in Table ). The significance of the module eigengene association with age is denoted as: * p < 0.008 (Bonferroni adjusted significance threshold for testing six modules, alpha = 0.05), and ** p ≤ 1x10 −6 .

Article Snippet: Blots were blocked in non-fat dry milk and incubated with antibodies to Mcl1 (Santa Cruz Biotechnology, Santa Cruz, CA) (clone S-19, 1:500 dilution), MRPS12 (Proteintech Group, Chicago, Il) (rabbit polyclonal, catalog #15225-1-AP, 1:333 dilution), and GAPDH (Ablabs, Vancouver, British Columbia) (clone ga1r, 1:3000 dilution) overnight at 4°C.

Techniques: Expressing, Gene Expression

Journal: Cancer cell

Article Title: Synthetic Lethality of Combined Bcl-2 Inhibition and p53 Activation in AML: Mechanisms and Superior Antileukemic Efficacy

doi: 10.1016/j.ccell.2017.11.003

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Antibodies for immunoblotting were purchased from the following sources: p53 (sc-126), MDM2 (sc-5304), Bcl-2 (sc-7382), Mcl-1 (sc-819), Puma (sc-28226), ERK (sc-1647), N-Ras (sc-31) and GSK3 (sc-7291) from Santa Cruz Biotechnology (Dallas, TX, USA); pERK (T202/Y204, 4370), pMEK (S217/S221, 9121), MEK (4694), AKT (2920), pAKT(S473, 9271), pGSK3 (S21/S9, 8566), PARP-1 (9542), Bim (2819), Bak (12105), caspase-3 (9664), caspase-9 (9508), pMcl-1 (T163, 14765), B-Raf (9433), pB-Raf (S445, 2696), JNK (9252) and pJNK (T183Y185, 9255) from Cell Signaling Technology; Bax (B8554) and β-Actin (A2228) from Sigma-Aldrich; Noxa (ab13654) and pMcl-1 (T163S159, ab111574) from Abcam; p21 (OP64) from EMD Millipore (Darmstadt, Germany).

Techniques: Recombinant, Imaging, Staining, Mutagenesis, Transfection, shRNA, Negative Control, Plasmid Preparation, Software, In Vivo Imaging, Microscopy, Flow Cytometry