Project description:This study investigates the role of endothelial cell (EC) gene expression in the focal origin of atherosclerosis. The EC transcriptome was profiled in multiple arterial regions of normal swine. Specifically, small amounts of EC RNA were isolated from 7 athero-susceptible and 6 athero-protected regions. The number of replicates for each site varied between 4 and 8. A total of 98 samples from 76 animals were used. For each sample, linearly amplified RNA (labeled with Cy5) was co-hybridized with pooled arterial reference RNA (labeled with Cy3) onto a custom-printed porcine oligo microarray (70-mers).
Project description:The study demonstrates (i) spatial heterogeneity of endothelial responses to hypercholesterolemia in the aortic valve, (ii) that endothelial metabolism is not dysfunctional in early focal lipid insudation, and (iii) that protective endothelial pathways induced by hypercholesterolemia may initially inhibit the onset of AVS in regions most susceptible.
Project description:Female C57Bl/6J LDLr -/- mice, aged 12 weeks (n=16) and 52 weeks (n=14), were put on western-type diet for 6 weeks before perivascular bilateral collar placement in the carotid artery. RNA was isolated from the carotid artery 6 weeks after collar placement. Snap frozen carotid arteries were pooled in four subgroups of three samples per age group in order to yield a sufficient amounts of RNA. Gene expression profiles from young and old mice were compared on spotted oligonucleotide arrays containing the 22K mouse Sigma-Compugen libarary v1. A direct hybridization was used with dye swaps for each pool. Keywords: RNA expression profiling Four pools of each strain were used. Direct hybridization design. Dye swap for each pair of samples. In total 8 arrays.
Project description:A microarray analysis was performed to compare the global gene expression profile between C-CPE treated- and untreated- SKOV-3 ovarian cancer cells. SKOV-3 cells were treated with or without C-CPE for 72 hours, and total RNA was extracted and microarray was perfomed to compare the gene profiling changes between C-CPE treated- and untreated- cells. The experiment was performed in triplicate.
Project description:A microarray analysis was performed to compare the global gene expression profile between CLDN4-overexpressing (Control) and CLDN4-silencing SKOV-3 ovarian cancer cells. CLDN4 gene was knocked down by CLDN4 siRNA lentivirus. Total RNA was extracted and microarray was perfomed to compare the gene profiling changes between CLDN4-overexpressing (Control) and CLDN4-silencing cells. The experiment was performed in triplicate.
Project description:Relatively little is known about the presence and regulation of pathways involved in nutrient acquisition in the brown tide forming alga, Aureococcus anophagefferens. In this study, Long-SAGE (Serial Analysis of Gene Expression) was used to profile the A. anophagefferens transcriptome under nutrient replete (control), and nitrogen (N) and phosphorus (P) deficiency with the goal of understanding how this organism responds at the transcriptional level to varying nutrient conditions. This approach has aided A. anophagefferens genome annotation efforts and identified a suite of genes up-regulated by N and P deficiency, some of which have known roles in nutrient metabolism. Genes up-regulated under N deficiency include an ammonium transporter, an acetamidase/formamidase, and two peptidases. This suggests an ability to utilize reduced N compounds and dissolved organic nitrogen, supporting the hypothesized importance of these N sources in A. anophagefferens bloom formation. There are also a broad suite of P-regulated genes, including an alkaline phosphatase, and two 5’-nucleotidases, suggesting A. anophagefferens may use dissolved organic phosphorus under low phosphate conditions. These N- and P-regulated genes may be important targets for exploring nutrient controls on bloom formation in field populations. Aureococcus anophagefferens CCMP 1984 was obtained from the Provasoli-Guillard Center for the Culture of Marine Phytoplankton (CCMP). The cultures were grown at 18C on a 14 h:10 h light:dark cycle (140 µmol quanta m-2 s-1). Nitrogen- and phosphate-replete (883 µM NO3- and 36.3 µM PO43-) cells, –N (40 µM NO3-) cells, and –P (1 µM PO43-) cells were grown in autoclaved L1 media with no Si (Guillard and Hargraves 1993), prepared using 0.2 µm filtered Vineyard Sound seawater. Vitamins (thiamine, biotin, and B12) were sterile filtered and added to the media after autoclaving. Replete cells were harvested during mid log phase of growth, while –N and –P cells were harvested at the onset of stationary phase when N or P was depleted.
Project description:Acyl-coA synthases (ACSs) produce fatty acyl-CoAs that are used in metabolic and signaling pathways. Metazoans have a large number of ACS genes with differing expression patterns and substrate preferences, but the physiological roles of most ACS genes are unknown. Here, we focused on the C. elegans acyl CoA synthase, ACS-3, which is known to regulate fat uptake and de novo fat synthesis through the conserved nuclear hormone receptor, nhr-25. We performed microarray analysis of acs-3 mutants to elucidate the acs-3-regulated transcription program. This analysis revealed an enrichment among differentially regulated genes of those involved in lipid metabolism, pathogen and wounding responses, and sterol binding genes, among others. As the immunity genes were the most represented gene class, we performed pathogen sensitivity assays to test the phenotypic consequences of this immune gene regulation. Interestingly, acs-3 mutants were hypersensitive to the fungal pathogen D. coniospora, but only mildly sensitive to the bacterial pathogen P. aeruginosa. acs-3 mutation suppressed nhr-25 mutant sensitivity to P. aeruginosa, yet surprisingly microarray analysis of nhr-25(RNAi) animals revealed significant overlap with the acs-3 mutant transcriptome, with an enrichment of pathogen response genes. The upregulation of pathogen response genes in acs-3(ft5) mutants and following nhr-25 reduction-of-function (rf) does not appear to be due to a constitutive osmotic response or defective cuticle barrier, two potential explanations for the acs-3(ft5) and nhr-25(rf) expression of innate immunity genes in the absence of pathogen exposure. Together, these data indicate that ACS-3 promotes resistance to the fungal pathogen, D. coniospora and regulates innate immunity genes through an unknown mechanism. Potential roles for ACS-3 in innate immunity are discussed. We used two-color expression microarrays to compare the transcriptional profiles in two experimental conditions: 1) comparing wild-type (N2) L4 stage larval worms to acs-3(ft5) L4 larval mutant animals; and 2) animals grown to L4 larval stage on bacteria harboring vectors for either control or nhr-25 RNA-interference (RNAi). L4 stage was determined by morphology of the developing vulva. Three biological replicates were used for each experimental condition. Statistically significant changes in gene expression in each experimental were determined using M-bM-^@M-^\linear models for microarray dataM-bM-^@M-^] (limma).
Project description:Vasopressin/cAMP/protein kinase A (PKA) signaling phosphorylates AQP2 water channels in renal collecting ducts to reabsorb water from urine for the prevention of further water loss. Lipopolysaccharide-responsive and beige-like anchor protein (LRBA) mediates vasopressin-induced AQP2 phosphorylation; therefore LRBA is essential for urinary concentration. LRBA is identified as the PKA substrates in a mouse cortical collecting duct principal cell line (mpkCCDcl4) whose phosphorylation levels are nearly perfectly correlated with those of AQP2. Although mouse LRBA contains several consensus PKA phosphorylation sites, their phosphorylation status in response to vasopressin remain unknown. Post-translational modification analysis revealed that RRDS1607 and RRIS2189 were phosphorylated by vasopressin.
Project description:Comparative genomic hybridization analysis on advanced stage high-grade serous ovarian cancer. CGH was performed on 42 DNA isolated from microdissected advanced stage high-grade serous ovarian cancer.