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Gene Expression Levels (gene + expression_level)
Selected AbstractsNaturally Occurring Regulatory T cells (CD4+, CD25high, FOXP3+) in the Antrum and Cardia are Associated with Higher H. pylori Colonization and Increased Gene Expression of TGF-,1HELICOBACTER, Issue 4 2008Arne Kandulski Abstract Background:Helicobacter pylori causes gastric inflammation. Despite the induction of H. pylori -specific B- and T cells, the immune response is not sufficient to clear the infection. Regulatory T cells (Treg cells) suppress the activation and proliferation of antigen-specific T cells and mediate immunologic tolerance. FOXP3 was shown to be expressed in a subset of Treg cells known as ,naturally occurring Treg cells'. These cells have not been sufficiently studied in context to H. pylori -induced inflammation in human gastric mucosa. Materials and methods: The study included 76 patients stratified according to the presence of H. pylori. Gene expression levels of FOXP3, transforming growth factor (TGF)-,1, and interleukin-10 were analyzed by quantitative real-time polymerase chain reaction in biopsies from gastric antrum, corpus, and cardia. FOXP3 expression was also analyzed by immunohistochemistry. Differences in expression levels were analyzed by comprehensive statistical analyses and correlated with clinical and histomorphologic parameters. Results:H. pylori -positive patients revealed a 19- to 25-fold induction of FOXP3 transcript levels in antrum and cardia (p < .02). FOXP3 transcript levels correlated positively with inflammation (p < .04) and TGF-,1 transcript levels (p < .001). Furthermore, a positive correlation between FOXP3+ Treg cells and H. pylori colonization was demonstrated. Conclusion: This study demonstrates that H. pylori -induced gastritis is associated with a recruitment of naturally occurring FOXP3+ Treg cells that correlates with the degree of bacterial colonization and mucosal TGF-,1 expression. Together, these data support the hypothesis that naturally FOXP3+ Treg cells play a role in the lifelong persistence of H. pylori infection in humans. [source] Increasing cyclooxygenase-2 (cox-2) gene expression in the progression of Barrett's esophagus to adenocarcinoma correlates with that of Bcl-2INTERNATIONAL JOURNAL OF CANCER, Issue 4 2006Daisuke Shimizu Abstract Previous studies from our laboratory and others have suggested that increased expression of cox-2 is important in the genesis of esophageal adenocarcinoma. In vitro studies suggest that cox-2 regulates expression of the anti-apoptotic protein bcl-2, thus possibly accounting for reduced apoptosis in carcinogenesis. The aim of this study was to investigate the relationship of these 2 genes in the development of Barrett's-associated adenocarcinoma. Histologic sections from endoscopic biopsies or esophagectomy specimens were classified as non-dysplastic Barrett's (n = 30), intraepithelial neoplasia (n = 12) and adenocarcinoma (n = 48). The desired tissue was isolated by laser capture microdissection and expression levels of cox-2 and bcl-2 were measured by quantitative real-time PCR (Taqman®). Gene expression levels were compared to samples of the distal esophageal squamous epithelium (n = 55) and reflux-esophagitis (n = 25), without Barrett's or cancer. Expression of both bcl-2 and cox-2 were increased in non-dysplastic Barrett's (p = 0.0077, p = 0.0037), intraepithelial neoplasia (p = 0.0053, p = 0.0220) and adenocarcinoma (p < 0.0001, p < 0.0001) compared to squamous epithelium or reflux-esophagitis. Furthermore, there is a significant correlation between these two genes, especially in carcinoma (p < 0.0001). © 2006 Wiley-Liss, Inc. [source] AN ALDOSTERONE-RELATED SYSTEM IN THE VENTROLATERAL MEDULLA OBLONGATA OF SPONTANEOUSLY HYPERTENSIVE AND WISTAR-KYOTO RATSCLINICAL AND EXPERIMENTAL PHARMACOLOGY AND PHYSIOLOGY, Issue 1-2 2006Natasha N Kumar SUMMARY 1The actions of aldosterone include mediation of vasoconstriction, vascular fibrosis, endothelial dysfunction and sodium retention. These actions can contribute to hypertension. Recent studies implicate an abnormal aldosterone hormonal system in the brain in hypertension. However, the study of central aldosterone actions is still in its infancy, as the exact location and abundance of its components in the brain are uncertain. 2We aimed to detect components of the aldosterone cascade in the regions of the ventrolateral medulla oblongata (VLM)-containing neurons that regulate blood pressure and to see whether there are quantitative differences in these components between the spontaneously hypertensive rat (SHR) and normotensive Wistar-Kyoto (WKY) rat models. Tissues from four regions of the brainstem, namely, the rostral and caudal ventrolateral medulla (RVLM and CVLM, respectively), rostral pressor area and caudal pressor area, were examined. We measured mRNA expression of aldosterone synthase, mineralocorticoid receptor (MR1), 12-lipoxygenase (12-LO), serum- and glucocorticoid- inducible kinase and K-ras in male rats. Gene expression levels were measured using real-time reverse transcription,polymerase chain reaction. 3We detected all aldosterone components in all regions of the VLM. The K-ras levels were not significantly different in any of the regions. Expression of MR1 mRNA was lower in the RVLM of SHR (n = 5) compared with WKY rats (n = 5; t = 4.590; P = 0.002) and 12-LO mRNA levels were lower in the CVLM in SHR (n = 6) compared with WKY rats (n = 7; P = 0.04). Thus, we have shown for the first time that components of the aldosterone cascade are present in the VLM. Our results suggest that there may be a differential gene expression profile in the brainstem for genetic hypertension. [source] Diel rhythm of nitrogen and carbon metabolism in the unicellular, diazotrophic cyanobacterium Crocosphaera watsonii WH8501ENVIRONMENTAL MICROBIOLOGY, Issue 2 2010Wiebke Mohr Summary We examined the diel variation in nitrogen and carbon metabolism in Crocosphaera watsonii WH8501 at the physiological and gene expression level in order to determine the temporal constraints for N2 fixation and photosynthesis. N2 fixation and photosynthesis were restricted to the dark and light periods, respectively, during a 24 h light,dark cycle. All genes studied here except one (psbA2) showed diel variations in their expression levels. The highest variation was seen in nifH and nifX relative transcript abundance with a factor of 3,5 × 103 between light and dark periods. Photosynthesis genes showed less variation with a maximum factor of about 500 and always had high relative transcript abundances relative to other genes. At the protein level, the photosystems appeared more stable than the nitrogenase complex over a 24 h light,dark cycle, suggesting that C. watsonii retains the ability to photosynthesize during the dark period of the diel cycle. In contrast, nitrogenase is synthesized daily and exhibits peak abundance during the dark period. Our results have implications for field studies with respect to the interpretation of environmental gene expression data. [source] A principal components regression approach to multilocus genetic association studiesGENETIC EPIDEMIOLOGY, Issue 2 2008Kai Wang Abstract With the rapid development of modern genotyping technology, it is becoming commonplace to genotype densely spaced genetic markers such as single nucleotide polymorphisms (SNPs) along the genome. This development has inspired a strong interest in using multiple markers located in the target region for the detection of association. We introduce a principal components (PCs) regression method for candidate gene association studies where multiple SNPs from the candidate region tend to be correlated. In this approach, the total variance in the original genotype scores is decomposed into parts that correspond to uncorrelated PCs. The PCs with the largest variances are then used as regressors in a multiple regression. Simulation studies suggest that this approach can have higher power than some popular methods. An application to CHI3L2 gene expression data confirms a significant association between CHI3L2 gene expression level and SNPs from this gene that has been previously reported by others. Genet. Epidemiol. 2008. © 2007 Wiley-Liss, Inc. [source] Environmental stresses induce the expression of putative glycine-rich insect cuticular protein genes in adult Leptinotarsa decemlineata (Say)INSECT MOLECULAR BIOLOGY, Issue 3 2008J. Zhang Abstract The deposition of cuticular proteins in insects usually occurs during the moulting process. Three putative glycine-rich insect cuticular proteins, Ld-GRP1 to 3, were identified and characterized from the Colorado potato beetle, Leptinotarsa decemlineata. The Ld-GRPs contained conserved GXGX and/or GGXG sequence repeats. Ld-GRP1 also contained a conserved AAPA/V motif commonly found in cuticular proteins. The transcripts of Ld-GRP1 and Ld-GRP2 were detected in the epidermal cell layer by in situ hybridization, making them putative insect cuticular proteins. The putative cuticular protein genes were highly induced by the insecticide azinphosmethyl (organophosphorous) 2,3 weeks after adult moulting. Putative cuticular protein gene expression level was higher in azinphosmethyl-resistant beetles than in susceptible beetles. Furthermore, two of the putative cuticular protein genes were highly induced by dry environmental conditions. These results suggest that the insect might increase cuticular component deposition in the adult stage in response to environmental stresses. This ability may allow the insect to adapt to new or changing environments. [source] Reference genes identified in the silkworm Bombyx mori during metamorphism based on oligonucleotide microarray and confirmed by qRT-PCRINSECT SCIENCE, Issue 5 2008Gen-Hong Wang Abstract Gene expression quantification at mRNA level is very important for post-genomic studies, as gene expression level is the reflection of the special biological function of the target gene. Methods used for gene expression quantification, such as microarray or quantitative real-time polymerase chain reaction (qRT-PCR), require stable expressed reference genes. Thus, finding suitable control genes is essential for gene quantification. In this study, a genome-wide survey of reference genes during metamorphism was performed on silkworm Bombyx mori. Twelve genes were chosen as putative reference genes based on a whole genome oligonucleotide microarray normalized by external controls. Then, qRT-PCR was employed for further validation and selection of potential reference gene candidates. The results were analyzed, and stable genes were selected using geNorm 3.4 and NormFinder software. Finally, considering factors from every aspect, translation initiation factor 4A, translation initiation factor 3 subunit 4, and translation initiation factor 3 subunit 5 (represented by sw22934, swl4876, and swl3956) were selected as reliable internal controls across the examined developmental stages, while cytoplasmic actin (sw22671), the commonly used reference gene in a previous study was shown to vary drastically throughout the examined developmental stages. For future research, we recommend the use of the geometric mean of those three stable reference genes as an accurate normalization factor for data normalization of different developmental stages during metamorphism. [source] The activities of progesterone receptor isoform A and B are differentially modulated by their ligands in a gene-selective mannerINTERNATIONAL JOURNAL OF CANCER, Issue 1 2008Joyce C.L. Leo Abstract It is known that progesterone receptor (PR) isoform A (PR-A) and isoform B (PR-B) may mediate different effects of progesterone. The objective of this study was to determine if the functions of PR isoforms also vary in response to different PR modulators (PRM). The effects of 7 synthetic PRM were tested in MDA-MB-231 cells engineered to express PR-A, PR-B, or both PR isoforms. The effects of progesterone were similar in cells expressing PR-A or PR-B in which it inhibited growth and induced focal adhesion. On the other hand, synthetic PRM modulated the activity of the PR isoforms differently. RU486, CDB4124, 17,-hydroxy CDB4124 and VA2914 exerted agonist activities on cell growth and adhesion via PR-B. Via PR-A, however, these compounds displayed agonist effect on cell growth but induced stellate morphology which was distinct from the agonist's effect. Their dual properties via PR-A were also displayed at the gene expression level: the compounds acted as agonists on cell cycle genes but exhibited antagonistic effect on cell adhesion genes. Introduction of ER, by adenoviral vector to these cells did not change PR-A or PR-B mediated effect of PRM radically, but it causes significant cell rounding and modified the magnitudes of the responses to PRM. The findings suggest that the activities of PR isoforms may be modulated by different PRM through gene-specific regulatory mechanisms. This raises an interesting possibility that PRM may be designed to be PR isoform and cellular pathway selective to achieve targeted therapy in breast cancer. © 2007 Wiley-Liss, Inc. [source] Differently regulated androgen receptor transcriptional complex in prostate cancer compared with normal prostateINTERNATIONAL JOURNAL OF UROLOGY, Issue 4 2005MASASHIGE KINOSHITA Abstract Background:, The coregulators of androgen receptors (AR) influence the transcriptional activity of AR. In order to better understand the mechanism of carcinogenesis in the prostate, we investigated the relationship between AR and AR coregulators in the early stage of prostate cancer. Methods:, mRNA was purified from 15 samples of prostate cancer and normal tissue and transcribed into cDNA. We screened eight AR coregulators for different gene expressions in prostate cancer, comparing these with normal tissue by a real-time polymerase chain reaction Syber green method, then quantified each component of the AR transcriptional complex by a real-time PCR hybri-probe method. The extent of gene expression similarity was compared by simple Pearson correlation coefficient analysis between prostate cancer and normal tissue. We applied a z-test to calculate significant differences between r-values. Results:, We found that the gene expression level of FHL2 decreased in prostate cancer compared with that of normal tissue and the gene expressions of PSA, AR and SMRT were not significant. The correlation coefficient analysis revealed that strong associations were found in the pairs of AR versus SMRT, AR versus FHL2 and SMRT versus FHL2 in prostate cancer, whereas similarity was found only in the pair of AR versus FHL2 in normal tissue. No association was observed between prostate-specific antigen and other genes. Conclusion:, These results demonstrate that the AR-AR coregulator relationship is different between prostate cancer and normal tissue, leading to the hypothesis that the AR transcriptional complex is regulated differently between prostate cancer and normal tissue. [source] Genotype-dependent response to carbon availability in growing tomato fruitPLANT CELL & ENVIRONMENT, Issue 7 2010MARION PRUDENT ABSTRACT Tomato fruit growth and composition depend on both genotype and environment. This paper aims at studying how fruit phenotypic responses to changes in carbon availability can be influenced by genotype, and at identifying genotype-dependent and -independent changes in gene expression underlying variations in fruit growth and composition. We grew a parental line (Solanum lycopersicum) and an introgression line from Solanum chmielewskii harbouring quantitative trait loci for fresh weight and sugar content under two fruit loads (FL). Lowering FL increased fruit cell number and reduced fruit developmental period in both genotypes. In contrast, fruit cell size was increased only in the parental line. Modifications in gene expression were monitored using microarrays and RT-qPCR for a subset of genes. FL changes induced more deployments of regulation systems (transcriptional and post-transcriptional) than massive adjustments of whole primary metabolism. Interactions between genotype and FL occurred on 99 genes mainly linked to hormonal and stress responses, and on gene expression kinetics. Links between gene expression and fruit phenotype were found for aquaporin expression levels and fruit water content, and invertase expression levels and sugar content. In summary, the present data emphasized age- and genotype-dependent responses of tomato fruit to carbon availability, at phenotypic as well as gene expression level. [source] Simultaneously detection of genomic and expression alterations in prostate cancer using cDNA microarray,THE PROSTATE, Issue 14 2008Mei Jiang Abstract BACKGROUND Prostate cancer is a common disease among men but the knowledge of the prostate carcinogenesis is still limited. METHODS cDNA microarray-based comparative genomic hybridization (CGH) and expression profiling were performed to screen the genomic and the expression changes in prostate cancer respectively. The two data were integrated to study the influence of genomic aberrations on gene expression and seek for the genes with their expression affected by the genomic aberrations. Real-time PCR was performed to evaluate the array data. RESULTS Array-based CGH detected gains at 2q, 3p/q, 5q, 6q, 8q, 9p, 10p/q, 11q, 12p, 14q, and 19p/q and losses at 1p, 2p, 4q, 6p/q, 7p, 11p/q, 12q, 17p/q, 19p/q, and Xp/q in more than 20% prostate tumors and narrowed these aberrations. For example, the gain of 8q was mapped to five minimal regions. Novel aberrations were also identified, such as loss at Xq21.33-q22.2. Expression profiling discovered the significant biological processes involved in the prostate carcinogenesis, such as exogenous antigen presentation via MHC class II and protein ubiquitination. Integration analysis revealed a weak positive correlation between genomic copy number and gene expression level. Fifty-three genes showed their expression directly affected by the genomic aberrations possibly, including more than one member of Ras superfamily and major histocompatibility complex (MHC). These genes are involved in multiple biological processes. CONCLUSIONS Integration of the CGH and expression data provided more information than separate analysis. Although the direct influence of genomic aberrations on gene expression seems weak, the influence can be extended by indirect regulation through a few directly affected genes. Because the influence can be persistent, the genes directly affected by the genomic aberrations may play key roles in the prostate carcinogenesis and are worth further analysis. Prostate 68: 1496,1509, 2008. © 2008 Wiley-Liss, Inc. [source] Persea americana (avocado): bringing ancient flowers to fruit in the genomics eraBIOESSAYS, Issue 4 2008André S. Chanderbali The avocado (Persea americana) is a major crop commodity worldwide. Moreover, avocado, a paleopolyploid, is an evolutionary "outpost" among flowering plants, representing a basal lineage (the magnoliid clade) near the origin of the flowering plants themselves. Following centuries of selective breeding, avocado germplasm has been characterized at the level of microsatellite and RFLP markers. Nonetheless, little is known beyond these general diversity estimates, and much work remains to be done to develop avocado as a major subtropical-zone crop. Among the goals of avocado improvement are to develop varieties with fruit that will "store" better on the tree, show uniform ripening and have better post-harvest storage. Avocado transcriptome sequencing, genome mapping and partial genomic sequencing will represent a major step toward the goal of sequencing the entire avocado genome, which is expected to aid in improving avocado varieties and production, as well as understanding the evolution of flowers from non-flowering seed plants (gymnosperms). Additionally, continued evolutionary and other comparative studies of flower and fruit development in different avocado strains can be accomplished at the gene expression level, including in comparison with avocado relatives, and these should provide important insights into the genetic regulation of fruit development in basal angiosperms. BioEssays 30:386,396, 2008. © 2008 Wiley Periodicals, Inc. [source] Paraoxonases role in the prevention of cardiovascular diseasesBIOFACTORS, Issue 1 2009Mira Rosenblat Abstract Increased oxidative stress is a characteristic of patients with high risk for atherosclerosis development (hypercholesterolemic, hypertensive, diabetic), and the above phenomenon was shown to be associated with attenuated antioxidative status. The increased oxidative stress in atherosclerotic patients is present in their blood, as well as in their arterial wall cells, including macrophages, the hallmark of foam cells formation during early atherogenesis. Serum high density lipoprotein (HDL)-associated paraoxonase 1 (PON1) reduces oxidative stress in lipoproteins, in macrophages, and in the atherosclerotic lesion, whereas paraoxonase 2 (PON2, which is present in tissues, but not in serum) acts as an antioxidant at the cellular and not humoral level. Both PON1 and PON2 protect against atherosclerosis development, and this phenomenon could be related to their antioxidative properties. The use of nutritional antioxidants such as vitamin E, carotenoids (lycopene and ,-carotene), and mainly polyphenols (such as those present in red wine, licorice root ethanolic extract, or in pomegranate) by atherosclerotic animals and also by cardiovascular patients, leads to a reduction in oxidative stress and to the attenuation of atherosclerosis development. These latter phenomena could be related to the nutritional antioxidants-induced increase in HDL PON1 activity (effects on gene expression, on preventing enzyme inactivation, and on increasing PON1 stability through its binding to HDL), as well as an increase in macrophage PON2 activation (at the gene expression level). © 2009 International Union of Biochemistry and Molecular Biology, Inc. [source] SERPINE1 intron polymorphisms affecting gene expression are associated with diffuse-type gastric cancer susceptibilityCANCER, Issue 18 2010Hyoungseok Ju PhD Abstract BACKGROUND: A primary inhibitor of plasminogen activators, SERPINE1 (serpin peptidase inhibitor 1, clade E, member 1, also known as plasminogen activator inhibitor type 1), is an important regulator in tumorigenesis and is highly expressed in many cancers. METHODS: Five tag single nucleotide polymorphisms (SNPs) and 1 insertion polymorphism within SERPINE1 were genotyped in 1101 unrelated Korean individuals (a case group of 612 patients with gastric cancer and a control group of 489 healthy individuals). Associations with susceptibility to diffuse-type gastric cancer (DGC) and intestinal-type gastric cancer were assessed using multivariate logistic regression analyses adjusted for age and sex. Allelic differences in the contribution to gene expression were measured using luciferase assays. RESULTS: SNP c.1162+162C>T (rs2227692) in intron 7 was associated with susceptibility to DGC but not with susceptibility to intestinal-type gastric cancer. The minor allele-carrying genotypes C/T and T/T had 1.6-fold greater odds of DGC than the C/C genotype (P = .00084). This SNP was linked to a repeat-number variation c.1162+604AAAG(11_17), a deletion (del) variation c.1162+664_1162+673del, and another SNP c.1162+859T>A (rs2070683) in intron 7 based on the sequencing of 5 patients and 5 controls. The risk haplotype of the 4 variations exhibited a 30% greater gene expression level than the nonrisk haplotype in luciferase reporter assays (P = .025). In contrast, DGC susceptibility was not associated with the c.,1969_,1968insG polymorphism (rs1799768) in the promoter, commonly known as 4G/5G, in which the minor 5G allele is less active in transcription than the major 4G allele. CONCLUSIONS: An association between SERPINE1 and DGC susceptibility was observed with 4 correlated polymorphisms in intron 7 rather than the 4G/5G polymorphism in the promoter, although all polymorphisms affected gene expression. Cancer 2010. © 2010 American Cancer Society. [source] Expression patterns of the ATM gene in mammary tissues and their associations with breast cancer survivalCANCER, Issue 9 2007Chuanzhong Ye MD Abstract BACKGROUND. The ataxia-telangiectasia mutated (ATM) gene plays a critical role in cell-cycle arrest, apoptosis, and DNA repair. However, to date, no study has directly investigated the association between ATM gene expression and breast cancer survival. METHODS. ATM gene expression levels were evaluated in tumor and adjacent normal tissue from patients diagnosed with primary breast cancer or BBD using quantitative real-time reverse transcription polymerase chain reaction (RT-PCR) assays. Cox regression models were used to evaluate the association of ATM gene expression and survival in a cohort of 471 breast cancer patients. RESULTS. In breast cancer cases, ATM expression in cancer tissues was decreased by approximately 50% compared with adjacent normal tissues from the same patients. In BBD cases, the expression level of the ATM gene was similar in benign tumor tissue and adjacent normal tissues. No apparent difference was found in ATM gene expression levels in adjacent normal tissues obtained from cancer patients or BBD controls. Compared with patients with the lowest tertile of the ATM mRNA, patients in the upper 2 tertiles had more favorable disease-free survival (hazard ratio [HR] = 0.46, 95% confidence interval [CI]: 0.30,0.73 and HR = 0.52, 95% CI: 0.33,0.81, respectively) and overall survival (HR = 0.56, 95% CI: 0.35,0.92 and HR = 0.70, 95% CI: 0.43,1.13, respectively). CONCLUSIONS. The ATM gene expression was down-regulated in breast cancer tissues and a high ATM gene expression level in breast cancer tissue was associated with a favorable prognosis. Cancer 2007. © 2007 American Cancer Society. [source] Expression of Drug Resistance-related Genes in Head and Neck Squamous Cell Carcinoma and Normal MucosaCANCER SCIENCE, Issue 1 2000Shitau Hirata We examined the expression levels of mRNA for multidrug resistance 1 (MDR1), multidrug resistance-associated protein (MRP), human canalicular multispecific organic anion transporter (cMOAT), lung resistance-related protein (LRP), topoisomerase II,, ,(Topo II,, ,) and topoisomerase I (Topo I) genes in human head and neck squamous cell carcinoma (HNSCC) specimens and mucosa (HNM) specimens, to elucidate their roles in relation to the biological characteristics and drug resistance in vivo. Fifty-eight samples (45 head and neck carcinomas and 13 head and neck mucosa) obtained during surgical resection or biopsy from 38 patients were analyzed using the quantitative reverse transcription-polymerase chain reaction (RT-PCR) method. MDR1, MRP, LRP, Topo II,, Topo II,, and Topo I gene transcripts were detected in all the samples tested, but cMOAT mRNA was not detected in them. Comparisons of the expression levels in HNSCC with those in HNM showed that the Topo II, gene expression level was higher in HNSCC than in HNM (P=0.0298). Moreover, the Topo II, mRNA level was significantly higher in metastatic lymph node samples of HNSCC than in HNM samples (P=0.0205). There were no significant differences in the six genes' expression levels between samples exposed to platinum drugs and those not exposed to platinum drugs. These results suggest that it may be effective in anticancer therapy to use topoisomerase-targetting drugs against HNSCC, especially metastatic neck tumors, and that the expression of these genes in HNSCC is not associated with platinum drug exposure. [source] Altering the Substrate Specificity of RhlI by Directed EvolutionCHEMBIOCHEM, Issue 3 2009Pavan Kumar Reddy Kambam Abstract Reducing virulence: RhlI catalyzes the synthesis of N -butanoyl homoserine lactone (BHL), with a minor product N -hexanoyl homoserine lactone (HHL). By using directed evolution and a genetic screen, RhlI has been engineered for enhanced production of both BHL and HHL at a similar level. Quorum sensing regulates biofilm formation and virulence factor production in the human opportunistic pathogen Pseudomonas aeruginosa. We used directed evolution to engineer RhlI, an enzyme in the RhlI,RhlR quorum-sensing system of P. aeruginosa, to alter its substrate specificity and gain insight into the molecular mechanisms of quorum sensing. By using a genetic screen, we identified a mutant with improved production of RhlI's two signaling molecules, N -butanoyl- and N -hexanoyl-homoserine lactone (BHL and HHL). In particular, production of BHL has been enhanced by more than two-fold, and the synthesis of HHL has been improved from an undetectable level to a level similar to BHL; this change indicates a significant change in substrate specificity. No significant change in the gene expression level was observed. Sequence alignments suggest that the mutations are most likely to facilitate interactions between the enzyme and the two acylated ACP substrates. This work also demonstrates that the genetic screen/selection should be useful in engineering additional quorum-sensing components. [source] Impaired cardiac functional reserve in type 2 diabetic db/db mice is associated with metabolic, but not structural, remodellingACTA PHYSIOLOGICA, Issue 1 2010A. Daniels Abstract Aim:, To identify the initial alterations in myocardial tissue associated with the early signs of diabetic cardiac haemodynamic dysfunction, we monitored changes in cardiac function, structural remodelling and gene expression in hearts of type 2 diabetic db/db mice. Methods:, Cardiac dimensions and function were determined echocardiographically at 8, 12, 16 and 18 weeks of age. Left ventricular pressure characteristics were measured at 18 weeks under baseline conditions and upon dobutamine infusion. Results:, The db/db mice were severely diabetic already at 8 weeks after birth, showing elevated fasting blood glucose levels and albuminuria. Nevertheless, echocardiography revealed no significant changes in cardiac function up to 18 weeks of age. At 18 weeks of age, left ventricular pressure characteristics were not significantly different at baseline between diabetic and control mice. However, dobutamine stress test revealed significantly attenuated cardiac inotropic and lusitropic responses in db/db mice. Post-mortem cardiac tissue analyses showed minor structural remodelling and no significant changes in gene expression levels of the sarcoplasmic reticulum calcium ATPase (SERCA2a) or ,1-adrenoceptor (,1-AR). Moreover, the phosphorylation state of known contractile protein targets of protein kinase A (PKA) was not altered, indicating unaffected cardiac ,-adrenergic signalling activity in diabetic animals. By contrast, the substantially increased expression of uncoupling protein-3 (UCP3) and angiopoietin-like-4 (Angptl4), along with decreased phosphorylation of AMP-activated protein kinase (AMPK) in the diabetic heart, is indicative of marked changes in cardiac metabolism. Conclusion:, db/db mice show impaired cardiac functional reserve capacity during maximal ,-adrenergic stimulation which is associated with unfavourable changes in cardiac energy metabolism. [source] Phenotypic differences in the brains and limbs of mutant mice caused by differences of Gli3 gene expression levelsCONGENITAL ANOMALIES, Issue 2 2001Ichiro Naruse ABSTRACT, The genetic polydactyly/arhinencephaly mouse, Pdn/Pdn, exhibits severe polydactyly both in the fore-and hindlimbs, agenesis of the olfactory bulbs, corpus callosum, anterior commissure, and hydrocephalus. A candidate gene for the Pdn mouse has been speculated to be Gli3, because Pdn has been considered to be an allele of Xt whose responsible gene has been clarified to be Gli3. Recently, it has been cleared that retro-transposons are inserted into nitron 3, upstream of zinc finger domain, of the Gli3 gene in the Pdn mouse, resulting to the severe suppression of Gli3 gene expression in Pdn/Pdn embryos. Meanwhile, XtJ/XtJ mice exhibit more severe polydactyly than that of Pdn/Pdn. Arhinencephaly and microholoprosencephaly including agenesis of the olfactory bulbs, corpus callosum, anterior commissure, hippocampal commissure, habenular commissure, and posterior commissure, and moreover, the cerebral cortical plates and hippocampus are not formed in the XtJ/XtJ mice. The XtJ/XtJ mouse has a large deletion in Gli3 structural gene and shows null expression. From these corroborations, we speculated that the differences in the Gli3 gene expression levels resulted in the phenotypic differences between the Pdn/Pdn and XtJ/XtJ mice. [source] The primary cilium as a gravitational force transducer and a regulator of transcriptional noiseDEVELOPMENTAL DYNAMICS, Issue 8 2008Stephen J. Moorman Abstract Circumstantial evidence has suggested that the primary cilium might function as a gravity sensor. Direct evidence of its gravity-sensing function has recently been provided by studies of rohon beard neurons. These neurons showed changes in the variability of gene expression levels that are linked to the cyclic changes in the Earth's gravitational field due to the Sun and Moon. These cyclic changes also cause the tides. Rohon beard neurons, after the primary cilia have been selectively destroyed, no longer show changes in gene expression variability linked to the cyclic changes in Earth's gravitational field. After the neurons regrow their primary cilia, the link between variability in gene expression levels and the Earth's changing gravitational field returns. This suggests two new functions for the primary cilia, detecting the cyclical changes in the Earth's gravitational field and transducing those changes into changes in the variability (stochastic nature) of gene expression. Developmental Dynamics 237:1955,1959, 2008. © 2008 Wiley-Liss, Inc. [source] Metallothionein gene expression and protein levels in triploid and diploid oysters Crassostrea gigas after exposure to cadmium and zincENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 2 2006Véronique Marie Abstract Quantitative real-time polymerase chain reaction (PCR) was used to compare for the first time the differential expression of metallothionein (MT) isoform genes, together with biosynthesis of the total MT proteins, in the gills of triploid and diploid juvenile Pacific oyster Crassostrea gigas in response to cadmium (Cd) and zinc (Zn) exposure. Oysters were exposed to Cd (0.133 ,M), Zn (15.3 ,M), and Cd+Zn for 14 d. Results showed similar response capacities to metal exposures in the two populations. No significant difference was revealed in terms of MT gene expression, MT protein synthesis, and Cd accumulation. However, triploid oysters bioaccumulated Zn 30% less efficiently than diploid oysters. Among the three MT isoform genes, CgMT2 appeared to be more expressed than CgMT1, whereas CgMT3 appeared to be anecdotal (106 times lower than CgMT2). CgMT2 and CgMT1 gene expression levels were increased sevenfold in the presence of Cd, whereas Zn appeared to have no effect. A twofold increase in MT protein levels occurred in response to Cd exposure. Discrepancies between mRNA and protein levels suggest that in C. gigas MT are regulated at the transcriptional level, as well as at the translational level. [source] Immediate,early gene induction in hippocampus and cortex as a result of novel experience is not directly related to the stressfulness of that experienceEUROPEAN JOURNAL OF NEUROSCIENCE, Issue 7 2005Thaddeus W. W. Pace Abstract The stressful quality of an experience, as perceived by rats, is believed to be largely represented by the magnitude of a hypothalamic,pituitary,adrenal (HPA) axis response. The hippocampus may be especially important for assessing the stressfulness of psychological stressors such as novel experience. If such is the case then experience-dependent immediate,early gene expression levels within the hippocampus may parallel relative levels of HPA axis activity. We examined this prospect in rats that were placed in four different novel environments (empty housing tub, circular arena, elevated pedestal or restraint tube). Restraint and pedestal produced the largest magnitude of increased ACTH and corticosterone secretion, arena an intermediate level (Experiment 2) and tub the least magnitude of increase. We saw a very similar experience-dependent pattern of relative Fos protein, c-fos mRNA and zif268 mRNA expression in the paraventricular nucleus of the hypothalamus. However, in hippocampus (and select regions of cortex), immediate,early gene expression was associated with the exploratory potential of the novel experience rather than level of HPA axis activity; pedestal and arena elicited the greatest immediate,early gene expression, tub an intermediate level and restraint the least amount of expression. We conclude that the stressfulness of psychological stressors is not represented by the amount of immediate,early gene induction elicited in hippocampus and cortex, nor does there appear to be a general enhancing or depressive influence of acute stress on immediate,early gene induction in those brain regions. [source] Identification of differentially expressed genes in psoriasis using expression profiling approachesEXPERIMENTAL DERMATOLOGY, Issue 9 2005K. Itoh Abstract:, To identify differentially expressed genes which play causal roles in pathogenesis and maintenance for psoriasis, we used BodyMapping and introduced amplified fragment length polymorphism approaches. From the BodyMap database, we selected 2007 genes which specifically expressed in epithelial tissues. Among 2007 genes, we surveyed genes which differentially expressed in involved or uninvolved psoriatic lesional skin samples compared with atopic dermatitis, mycosis fungoides, and normal skin samples. As a result of surveying 2007 genes, 241 genes were differentially expressed only in involved psoriatic skin but not in the other samples. Hierarchical cluster analysis of gene expression profiles showed that 13 independent psoriatic-involved skin samples clustered tightly together, reflecting highly similar expression profiles. Using the same 2007 gene set, we examined gene expression levels in five serial lesions from distal uninvolved psoriatic skin to involved psoriatic plaque. We identified seven genes such as alpha-1-microglobulin/bikunin precursor, calnexin, claudin 1, leucine zipper down-regulated in cancer 1, tyrosinase-related protein 1, Yes-associated protein 1, and unc-13-like protein (Coleonyx elegans) which show high-expression levels only in uninvolved psoriatic lesions. These seven genes, which were reported to be related to apoptosis or antiproliferation, might have causal roles in pathophysiology in psoriasis. [source] Genomic imbalances in rhabdomyosarcoma cell lines affect expression of genes frequently altered in primary tumors: An approach to identify candidate genes involved in tumor developmentGENES, CHROMOSOMES AND CANCER, Issue 6 2009Edoardo Missiaglia Rhabdomyosarcomas (RMS) are the most common pediatric soft tissue sarcomas. They resemble developing skeletal muscle and are histologically divided into two main subtypes; alveolar and embryonal RMS. Characteristic genomic aberrations, including the PAX3 - and PAX7-FOXO1 fusion genes in alveolar cases, have led to increased understanding of their molecular biology. Here, we determined the effect of genomic copy number on gene expression levels through array comparative genomic hybridization (CGH) analysis of 13 RMS cell lines, confirmed by multiplex ligation-dependent probe amplification copy number analyses, combined with their corresponding expression profiles. Genes altered at the transcriptional level by genomic imbalances were identified and the effect on expression was proportional to the level of genomic imbalance. Extrapolating to a public expression profiling dataset for 132 primary RMS identified features common to the cell lines and primary samples and associations with subtypes and fusion gene status. Genes identified such as CDK4 and MYCN are known to be amplified, overexpressed, and involved in RMS tumorigenesis. Of the many genes identified, those with likely functional relevance included CENPF, DTL, MYC, EYA2, and FGFR1. Copy number and expression of FGFR1 was validated in additional primary material and found amplified in 6 out of 196 cases and overexpressed relative to skeletal muscle and myoblasts, with significantly higher expression levels in the embryonal compared with alveolar subtypes. This illustrates the ability to identify genes of potential significance in tumor development through combining genomic and transcriptomic profiles from representative cell lines with publicly available expression profiling data from primary tumors. © 2009 Wiley-Liss, Inc. [source] Candidate glioblastoma development gene identification using concordance between copy number abnormalities and gene expression level changesGENES, CHROMOSOMES AND CANCER, Issue 10 2007Ken C. Lo Copy number abnormalities (CNAs) in tumor cells are presumed to affect expression levels of genes located in region of abnormality. To investigate this relationship we have surveyed the losses, gains and amplifications in 30 glioblastomas using array comparative genome hybridization and compared these data with gene expression changes in the same tumors using the Affymetrix U133Plus2.0 oligonucleotide arrays. The two datasets were overlaid using our in-house overlay tool which highlights concordance between CNAs and expression level changes for the same tumors. In this survey we have highlighted genes frequently overexpressed in amplified regions on chromosomes 1, 4, 11, and 12 and have identified novel amplicons on these chromosomes. Deletions of specific regions on chromosomes 9, 10, 11, 14, and 15 have also been correlated with reduced gene expression in the regions of minimal overlap. In addition we describe a novel approach for comparing gene expression levels between tumors based on the presence or absence of chromosome CNAs. This genome wide screen provides an efficient and comprehensive survey of genes which potentially serve as the drivers for the CNAs in GBM. © 2007 Wiley-Liss, Inc. [source] Stage-specific alterations of the genome, transcriptome, and proteome during colorectal carcinogenesis,GENES, CHROMOSOMES AND CANCER, Issue 1 2007Jens K. Habermann To identify sequential alterations of the genome, transcriptome, and proteome during colorectal cancer progression, we have analyzed tissue samples from 36 patients, including the complete mucosa-adenoma-carcinoma sequence from 8 patients. Comparative genomic hybridization (CGH) revealed patterns of stage specific, recurrent genomic imbalances. Gene expression analysis on 9K cDNA arrays identified 58 genes differentially expressed between normal mucosa and adenoma, 116 genes between adenoma and carcinoma, and 158 genes between primary carcinoma and liver metastasis (P < 0.001). Parallel analysis of our samples by CGH and expression profiling revealed a direct correlation of chromosomal copy number changes with chromosome-specific average gene expression levels. Protein expression was analyzed by two-dimensional gel electrophoresis and subsequent mass spectrometry. Although there was no direct match of differentially expressed proteins and genes, the majority of them belonged to identical pathways or networks. In conclusion, increasing genomic instability and a recurrent pattern of chromosomal imbalances as well as specific gene and protein expression changes correlate with distinct stages of colorectal cancer progression. Chromosomal aneuploidies directly affect average resident gene expression levels, thereby contributing to a massive deregulation of the cellular transcriptome. The identification of novel genes and proteins might deliver molecular targets for diagnostic and therapeutic interventions. © Wiley-Liss, Inc. [source] Human skin fibroblasts: From mesodermal to hepatocyte-like differentiation,HEPATOLOGY, Issue 5 2007Philippe A. Lysy The phenotypic homology of fibroblasts and mesenchymal stem cells (MSCs) has been recently described. Our study investigated the in vitro potential of human skin fibroblasts to differentiate into mesodermal (osteocyte and adipocyte) and endodermal (hepatocyte) cell lineages by comparison with human bone marrow (hBM) MSCs. The endodermal potential of fibroblasts was then explored in vivo in a mouse model of liver injury. Fibroblasts were able to acquire osteocyte and adipocyte phenotypes as assessed by cytochemistry and gene expression analyses. After exposure to a specific differentiation cocktail, these cells presented hepatocyte-like morphology and acquired liver-specific markers on protein and gene expression levels. Furthermore, these fibroblast-derived hepatocyte-like cells (FDHLCs) displayed the ability to store glycogen and synthesize small amounts of urea. By gene expression analysis, we observed that fibroblasts remained in a mesenchymal-epithelial transition state after hepatocyte differentiation. Moreover, FDHLCs lost their hepatocyte-like phenotype after dedifferentiation. In vivo, human fibroblasts infused directly into the liver of hepatectomized severe combined immunodeficient (SCID) mice engrafted in situ and expressed hepatocyte markers (albumin, alpha-fetoprotein, and cytokeratin 18) together with the mesodermal marker fibronectin. Despite lower liver-specific marker expression, the in vitro and in vivo differentiation profile of fibroblasts was comparable to that of mesenchymal-derived hepatocyte-like cells (MDHLCs). In conclusion, our work demonstrates that human skin fibroblasts are able to display mesodermal and endodermal differentiation capacities and provides arguments that these cells share MSCs features both on the phenotypic and functional levels. (HEPATOLOGY 2007;46:1574,1585.) [source] Characteristics of hepatocellular carcinoma in a murine model of alpha-1-antitrypsin deficiencyHEPATOLOGY RESEARCH, Issue 6 2010Nancy Y. Marcus Aim:, Individuals with homozygous (ZZ) alpha-1-antitrypsin (,1AT) deficiency are at an increased risk for liver damage, cirrhosis and hepatocellular carcinoma (HCC). The transgenic PiZ mouse, expressing the human ,1AT mutant Z gene, is a valuable model for this disease. We studied PiZ mice in order to identify and characterize mechanisms involved in the development of HCC. Methods:, Tumor incidence and histology were studied, gene expression levels were surveyed with microarrays, RNA quantified with quantitative real time polymerase chain reaction and protein levels determined with immunoblots and immunohistochemistry. Results:, By 16,19 months of age, approximately 69% of the PiZ mice had developed tumors. HCC was present with no evidence of benign adenomas as pre-cancerous lesions. Tumors showed abnormal mitochondria, variable levels of steatosis, globular inclusions of ,1AT mutant Z protein and metastases. PiZ mice that subsequently developed liver tumors had higher serum levels of ,1AT mutant Z protein than those that did not develop tumors. Cyclin D1, a cell cycle protein, was upregulated in PiZ livers without tumors compared to Wt. cFOS, a component of AP-1 that may be involved in transforming cells and MCAM, an adhesion molecule likely involved in tumorigenesis and metastases, were elevated in tumors compared with livers without tumors. Conclusion:, In the PiZ model, many of the histological characteristics of HCC recapitulated features seen in human HCC, whether from individuals with homozygous ZZ liver disease or from unrelated causes in individuals that were not homozygous ZZ. The accumulation of mutant Z protein altered the regulation of several genes driving proliferation and tumorigenesis. [source] Cholesterol homeostasis markers are localized to mouse hippocampal pyramidal and granule layersHIPPOCAMPUS, Issue 8 2010Chris M. Valdez Abstract Changes in brain cholesterol homeostasis are associated with multiple diseases, such as Alzheimer's and Huntington's; however, controversy persists as to whether adult neurons produce their own cholesterol, or if it is outsourced to astrocytes. To address this issue, we analyzed 25 genes most immediately involved in cholesterol homeostasis from in situ data provided by the Allen Brain Mouse Atlas. We compared the relative mRNA expression in the pyramidal and granule layers, populated with neurons, with the rest of the hippocampus which is populated with neuronal processes and glia. Comparing the expression of the individual genes to markers for neurons and astrocytes, we found that cholesterol homeostasis genes are preferentially targeted to neuronal layers. Therefore, changes in gene expression levels might affect neuronal populations directly. © 2010 Wiley-Liss, Inc. [source] Molecular determinants of irinotecan efficacyINTERNATIONAL JOURNAL OF CANCER, Issue 10 2006Daniel Vallböhmer Abstract Molecular markers predicting the efficacy of CPT-11 based chemotherapies in patients with colorectal cancer (CRC) are unknown. Therefore, we investigated whether mRNA levels of drug targets (Topoisomerase I, TS), enzymes involved in 5-FU metabolism (DPD), in angiogenesis (EGFR, IL-8, VEGF) and in DNA-repair/drug detoxification (ERCC1, GST-P1) are associated with the clinical outcome of patients with CRC treated with first-line CPT-11 based chemotherapy. Thirty three patients with metastatic CRC were included in the study. Intratumoral gene expression levels were assessed from paraffin-embedded tissue samples, using laser capture microdissection and quantitative Real-Time PCR. Complete response was observed in 1 patient, partial response in 12 patients, stable disease in 13 patients and progressive disease in 6 patients. Response was inevaluable for 1 patient. Patients with complete response or partial response were classified as responders, while patients with stable disease or progressive disease were classified as nonresponders. High intratumoral mRNA levels of EGFR, ERCC1 and GSPT-P1 were each significantly associated with response to CPT-11 based chemotherapy. Recursive partitioning analysis showed that mRNA levels of EGFR and ERCC1 are primarily responsible for delineating responders from nonresponders. Also, the combination of high intratumoral gene expression levels of both EGFR and ERCC1 was significantly associated with progression-free survival. The mRNA levels of EGFR had a significant correlation with expression levels of ERCC1, GST-P1 and VEGF. This small retrospective study suggests that gene expression levels of EGFR, ERCC1 and GST-P1 may be useful in predicting the clinical outcome of patients with metastatic CRC treated with first-line CPT-11 based chemotherapy. © 2006 Wiley-Liss, Inc. [source] | ||||||||||||||||||||||||||||||||||