Home About us Contact
|
Home About us Contact | ||
|
|
||
Presented Data (presented + data)
Selected AbstractsPromoter analysis of epigenetically controlled genes in bladder cancerGENES, CHROMOSOMES AND CANCER, Issue 5 2008Srinivas Veerla DNA methylation is an important epigenetic modification that regulates several genes crucial for tumor development. To identify epigenetically regulated genes in bladder cancer, we performed genome wide expression analyses of eight-bladder cancer cell lines treated with the demethylating agents 5-aza-2,-cytidine and zebularine. To identify methylated C-residues, we sequenced cloned DNA fragments from bisulfite-treated genomic DNA. We identified a total of 1092 genes that showed ,2-fold altered expression in at least one cell line; 710 showed up-regulation and 382 down-regulation. Extensive sequencing of promoters from 25 genes in eight cell lines showed an association between methylation pattern and expression in 13 genes, including both CpG island and non-CpG island genes. Overall, the methylation patterns showed a patchy appearance with short segments showing high level of methylation separated by larger segments with no methylation. This pattern was not associated with MeCP2 binding sites or with evolutionarily conserved sequences. The genes UBXD2, AQP11, and TIMP1 showed particular patchy methylation patterns. We found several high-scoring and evolutionarily conserved transcription factor binding sites affected by methylated C residues. Two of the genes, FGF18 and MMP11, that were down-regulated as response to 5-aza-2,-cytidine and zebularine treatment showed methylation at specific sites in the untreated cells indicating an activating result of methylation. Apart from identifying epigenetically regulated genes, including TGFBR1, NUPR1, FGF18, TIMP1, and MMP11, that may be of importance for bladder cancer development the presented data also highlight the organization of the modified segments in methylated promoters. This article contains supplementary material available via the Internet at http://www.interscience.wiley.com/jpages/1045-2257/suppmat. © 2008 Wiley-Liss, Inc. [source] Sperm length in sand martins Riparia riparia: a comment on Helfenstein et alJOURNAL OF AVIAN BIOLOGY, Issue 3 2009Oddmund Kleven How long is a sand martin Riparia riparia spermatozoon? In a recent study, Helfenstein et al. (2008) presented data on the intraspecific variation in sperm length, swimming speed and longevity in this species and some interesting correlations between these variables. However, the reported sperm lengths are remarkably short for the species, which casts doubts about whether sperm total length has actually been measured and how the observed relationships should be interpreted. [source] Long-Term Posttreatment Functioning Among Those Treated for Alcohol Use DisordersALCOHOLISM, Issue 2 2006Patrick R. Clifford This article summarizes the proceedings of a symposium that was organized and chaired by Patrick R. Clifford and presented at the 2005 Research Society on Alcoholism meeting in Santa Barbara, California. The aims of the presentation were to focus on the prediction and explanation of longer-term functioning following alcohol use disorders (AUD) treatment. Along these lines, Stephen A. Maisto, PhD, presented data (i.e., Project MATCH outpatient sample) on the relationship between drinking behavior in the first year following AUD outpatient treatment initiation and functioning at 3-year follow-up. Robert L. Stout, PhD, using data from the Extended Case Monitoring Study, analyzed long-term drinking patterns using shorter-term information. James R. McKay, PhD, examined the relationship between treatment services received and problem severities across a 2-year follow-up period. J. Scott Tonigan, PhD, served as the panel discussant. [source] IgA nephropathy and mesangial cell proliferation: shared global gene expression profilesNEPHROLOGY, Issue 2002Hideto SAKAI SUMMARY: It is well established that mesangial cell proliferation plays a major role in glomerular injury and progressive renal injury. the expression of a number of different genes has been reported in proliferative mesangial cells in culture. However, the relevance of these genes to renal injury in general and IgA nephropathy (IgAN) remains to be established. Assessment of gene activity on a global genome-wide scale is a fundamental and newly developed molecular strategy to expand the scope of clinical investigation from a single gene to studying all genes at once in a systematic pattern. Capitalizing on the recently developed methodology of high cDNA array hybridization, the simultaneous expression of thousands of genes in primary human proliferating mesangial cells was monitored and compared with renal tissue of IgAN. Complex [,- 33P]-labelled cDNA targets were prepared from cultured mesangial cells, remnant tissue from five IgAN renal biopsies and four nephrectomies (controls). Each target was hybridized to a high-density array of 18 326 paired target genes. the radioactive hybridization signals were analysed by phosphorimager. Approximately 8212±530 different gene transcripts were detected per target. Close to 5% (386±90 genes) were full-length mRNA human transcripts (HT) and the remainder were expressed sequence tags (EST). Using a relational database, electronic subtraction was performed and matching was carried out to allow identification of 203 HT with shared expression in proliferative mesangial cells and IgAN renal biopsies. In addition hierarchical clustering analysis was performed on the HT of IgAN and controls to establish differential expression profiles of mesangial HT in IgAN and controls. Collectively the presented data constitutes a preliminary renal bioinformatics database of the transcriptional profiles in IgAN. More importantly, the information may help to speed up the discovery of genes underlying human IgAN. [source] Genomic repertoire of human mesangial cells: comprehensive analysis of gene expression by cDNA array hybridizationNEPHROLOGY, Issue 4 2000Naohiro Yano SUMMARY: Knowing when and where a gene is expressed in a cell often provides a strong clue as to its physiological role. It is estimated the human genome contains 80 000,100 000 genes. Assessment of gene activity on a global genome-wide scale is a fundamental and newly developed experimental strategy to expand the scope of biological investigation from a single gene to studying all genes at once in a systematic way. Capitalizing on the recently developed methodology of cDNA array hybridization, we monitored the simultaneous expression of thousands of genes in primary human mesangial cells. Complex ,- 33P-labelled cDNA probes were prepared from cultured mesangial cells. The probe was hybridized to a high-density array of 18 326 paired target genes. The radioactive hybridization signals were analysed by phosphorimager. Bioinformatics from public genomic databases was utilized to assign a chromosomal location of each expressed transcript. Approximately 7460 different gene transcripts were detected in mesangial cells. Close to 13% (957 genes) were full-length mRNA human transcripts (HTs), the remainder 6503 being expressed sequence tags (ESTs). Using special imaging computer software, the transcriptional level of the 957 HTs was compared with the expression of the ribosomal protein S28 (housekeeping gene). The HTs were also classified by function of the gene product and listed with information on their chromosomal loci. To allow comparison between clinical and experimental studies of gene expression, the detected human gene transcripts were cross-referenced to orthologous mouse genes. Thus, the presented data constitute a quantitative preliminary blueprint of the transcriptional map of the human mesangial cell. The information may serve as a resource for speeding up the discovery of genes underlying human glomerular diseases. The complete listing of the full-length expressed genes is available upon request via E-mail: (Abdalla_Rifai@Brown.edu). [source] Trends in suspected and recognized occupational respiratory diseases in Germany between 1970 and 2005AMERICAN JOURNAL OF INDUSTRIAL MEDICINE, Issue 7 2008V. van Kampen PhD Abstract Background Respiratory diseases represent a major proportion of occupational diseases in many countries. Little information is available about their incidences over the past several decades. Methods Based on the reports of the three German federal accident insurance agencies, the numbers of suspected and recognized cases of occupational respiratory diseases between 1970 and 2005 were collected and combined. The trends in the rates per 100,000 insured workers were calculated. Results In total, a decline in occupational respiratory diseases since 1998 could be observed. This trend is mainly based on the decrease in non-malignant respiratory diseases due to silica and obstructive airway diseases. In contrast, asbestos-induced diseases showed a leveling off or an increase (mesothelioma) during the last 10years. Conclusions Although trends in occupational disease may be influenced by several factors, the presented data indicate that prevention has been effective in reducing some ofthe most frequent occupational respiratory diseases in Germany. Am. J. Ind. Med. 51:492,502, 2008. © 2008 Wiley-Liss, Inc. [source] Quantification of alkylresorcinols in human plasma by liquid chromatography/tandem mass spectrometryRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 5 2010Alastair B. Ross Alkylresorcinols (AR) are of interest as biomarkers of wholegrain wheat and rye intake in epidemiological studies and are currently mainly measured by gas chromatography/mass spectrometry (GC/MS) after labour-intensive sample preparation including liquid-liquid extraction, solid-phase extraction (SPE) and chemical derivatization. This manuscript describes and validates an alternative approach based on normal-phase liquid chromatography/tandem mass spectrometry for the quantification of alkylresorcinols in human plasma. The method requires neither SPE nor chemical derivatization and has a shortened run time compared to GC/MS. Normal- and reversed-phase columns and various mobile phases were evaluated with and without previous SPE of the samples. Normal-phase chromatography allowed separation of AR from the interfering triacylglycerols, diacylglycerols and sterols and enabled detection of AR even without SPE of the samples. The described method has instrumental lower limits of detection in the 25,75 pg range, and lower limits of quantification in the 75,250 pg range. Pooled human plasma and 2H4 -nonadecylresorcinol (internal standard) was applied to calibrate the method in the 20,12,000,nM range. The overall method showed intra-batch precision of 8.6% and an averaged accuracy of 100.2%. Applications for diverse human plasma samples are presented and are compared with the results determined by GC/MS. Based on the presented data; this method requiring less sample preparation is suggested for further evaluation as an alternative to GC/MS for analysis of biomarkers of wholegrain wheat and rye intake in epidemiological studies. Copyright © 2010 John Wiley & Sons, Ltd. [source] | ||||||||||