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Microarray System (microarray + system)
Selected AbstractsGene expression profile analysis of regenerating liver after portal vein ligation in rats by a cDNA microarray systemLIVER INTERNATIONAL, Issue 3 2004Y Nagano Abstract: Aims: We assessed changes in gene expression of hypertrophied liver after portal vein ligation (PL) in a test group of rats compared to a control group, which had the same size liver but no PL. Methods: The portal veins of the left and median lobes in the test group were ligated in an initial operation. Four days after the PL, the liver volume of the posterior caudate lobe (5%) increased two-fold and comprised 10% of the liver. A 90% hepatectomy was then performed, leaving only the hypertrophied posterior caudate lobe, and leaving the normal anterior and posterior caudate lobes (10%) in the control (sham) group. A comparison of the expression profiles between two groups was performed using cDNA microarrays and the hepatic ATP level was measured. Results: The survival rate for the PL group was significantly higher than for the sham group at 4 days after the hepatectomy (56.3% and 26.7%, P<0.05). Gene expression of cyclin D1, proliferating cell nuclear antigen, cyclin A and B was upregulated, and the cyclin-dependent kinase inhibitor was downregulated. Increases were observed in: (i) pyruvate dehydrogenase, the tricarboxylic acid cycle cycle regulator, (ii) acyl-CoA dehydrogenase, the oxidation regulator, and (iii) cytochrome oxidases, the oxidative phosphorylation regulator. Hepatic ATP concentration after hepatectomy was better maintained in the PL group than in the sham group (0.48±0.01 ,mol/ml vs. 0.33±0.01 ,mol/ml, P<0.05). Conclusion: The regenerating liver increased tolerance for extended hepatectomy compared to normal liver. It is believed that this is because the induced rapid regeneration of the remaining liver after hepatectomy increases ATP metabolism. [source] Surface plasmon resonance imaging protein arrays for analysis of triple protein interactions of HPV, E6, E6AP, and p53PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 7 2006Hyeon-Su Ro Abstract We have developed a surface plasmon resonance (SPR)-based protein microarray to study protein,protein interactions in a high-throughput mode. As a model system, triple protein interactions have been explored with human papillomaviral E6 protein, tumor suppressor p53, and ubiquitin ligase E6AP. Human papillomavirus (HPV) is known to be a causative agent of cervical cancer. Upon infection, the viral E6 protein forms a heterotrimeric protein complex with p53 and E6AP. The formation of the complex eventually results in the degradation of p53. In the present study, a GST-fused E6AP protein was layered onto a glutathione (GSH)-modified gold chip surface. The specific binding of GST-E6AP protein onto the gold chip surface was facilitated through the affinity of GST to its specific ligand GSH. The interacting proteins (E6 and/or p53) were then spotted. Detection of the interaction was performed using a SPR imaging (SPRI) technique. The resulting SPRI intensity data showed that the protein,protein interactions of E6AP, E6, and p53 were detected in a concentration-dependent manner, suggesting that the SPRI-based microarray system can be an effective tool to study protein,protein interactions where multiple proteins are involved. [source] DNA microarray analyses of the effects of dietary proteinsBIOFACTORS, Issue 1-4 2004Hisanori Kato Abstract Dietary proteins and amino acids serve not only as a building block for body components but also as regulators of a variety of body functions. A great many of the functions of ingested proteins, their peptide fragments, and amino acids have been characterized and some have been brought to practical application. Using a GeneChip DNA microarray system, we first compared the gene expression profiles among rats fed on 12% casein, 12% gluten, and protein-free diets for one week. The results revealed that a few hundred genes in the liver and muscle were up- or down-regulated by more than two-fold after feeding of the gluten or the protein-free diet. Interesting findings included the induction of genes for synthesis and catabolism of cholesterol by gluten feeding. In addition, we performed a study to examine the effect of the consumption of an enzymatically produced, hypoallergenic wheat flour on gene expression profiles in rats. The results confirmed the safety of this novel food product. [source] ,B-crystallin: A novel p53-target gene required for p53-dependent apoptosisCANCER SCIENCE, Issue 12 2009Gou Watanabe The p53 protein is a transcription factor that trans -activates various genes in response to DNA-damaging stress. To search for new p53-target genes, we applied a cDNA microarray system using two independent p53-inducible cell lines, followed by in silico analysis to detect p53 response elements. Here, we report on crystallin alpha B gene (CRYAB), which encodes ,B-crystallin, and is one of the genes directly trans -activated by p53. We confirmed it is directly transcribed by p53 using promoter analysis, deletion reporter assay, ChIP assay and EMSA. ,B-crystallin is also upregulated in a p53-dependent manner and binds to the DNA-binding domain of p53. Overexpression of ,B-crystallin increased p53 protein and, in contrast, repression of ,B-crystallin decreased p53 protein. Interestingly, both overexpression and repression of ,B-crystallin reduced p53-dependent apoptosis. In conclusion, we identified that ,B-crystallin was a novel p53-target gene and required for p53-dependent apoptosis using two independent p53-inducible cell lines. This is the first report associating p53 directly with a heat shock protein through trans -activation and physical interaction. (Cancer Sci 2009; 100: 2368,2375) [source] Identification of cold-inducible downstream genes of the Arabidopsis DREB1A/CBF3 transcriptional factor using two microarray systemsTHE PLANT JOURNAL, Issue 6 2004Kyonoshin Maruyama Summary The transcriptional factor DREB/CBF (dehydration-responsive element/C-repeat-binding) specifically interacts with the dehydration-responsive element (DRE)/C-repeat (CRT) cis -acting element (A/GCCGAC) and controls the expression of many stress-inducible genes in Arabidopsis. Transgenic plants overexpressing DREB1A showed activated expression of many stress-inducible genes and improved tolerance to not only drought, salinity, and freezing but also growth retardation. We searched for downstream genes in transgenic plants overexpressing DREB1A using the full-length cDNA microarray and Affymetrix GeneChip array. We confirmed candidate genes selected by array analyses using RNA gel blot and identified 38 genes as the DREB1A downstream genes, including 20 unreported new downstream genes. Many of the products of these genes were proteins known to function against stress and were probably responsible for the stress tolerance of the transgenic plants. The downstream genes also included genes for protein factors involved in further regulation of signal transduction and gene expression in response to stress. The identified genes were classified into direct downstream genes of DREB1A and the others based on their expression patterns in response to cold stress. We also searched for conserved sequences in the promoter regions of the direct downstream genes and found A/GCCGACNT in their promoter regions from ,51 to ,450 as a consensus DRE. The recombinant DREB1A protein bound to A/GCCGACNT more efficiently than to A/GCCGACNA/G/C. [source] | |||||||||||||