35 research outputs found

    Genome bioinformatic analysis of nonsynonymous SNPs

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    Background: Genome-wide association studies of common diseases for common, low penetrance causal variants are underway. A proportion of these will alter protein sequences, the most common of which is the non-synonymous single nucleotide polymorphism (nsSNP). It would be an advantage if the functional effects of an nsSNP on protein structure and function could be predicted, both for the final identification process of a causal variant in a disease-associated chromosome region, and in further functional analyses of the nsSNP and its disease-associated protein. Results: In the present report we have compared and contrasted structure-and sequence-based methods of prediction to over 5500 genes carrying nearly 24,000 nsSNPs, by employing an automatic comparative modelling procedure to build models for the genes. The nsSNP information came from two sources, the OMIM database which are rare (minor allele frequency, MAF, 0.05, have no known link to a disease. For over 40% of the nsSNPs, structure-based methods predicted which of these sequence changes are likely to either disrupt the structure of the protein or interfere with the function or interactions of the protein. For the remaining 60%, we generated sequence-based predictions. Conclusion: We show that, in general, the prediction tools are able distinguish disease causing mutations from those mutations which are thought to have a neutral affect. We give examples of mutations in genes that are predicted to be deleterious and may have a role in disease. Contrary to previous reports, we also show that rare mutations are consistently predicted to be deleterious as often as commonly occurring nsSNPs.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

    Effect of childbirth on the course of Crohn's disease; results from a retrospective cohort study in the Netherlands

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    Contains fulltext : 95846.pdf (publisher's version ) (Open Access)BACKGROUND: Pregnant women with Crohn's disease needs proper counselling about the effect of pregnancy and childbirth on their disease. However, Literature about the effect of childbirth on Crohn's disease is limited. This study examined the effect of childbirth on the course of Crohn's disease and especially perianal Crohn's disease. METHODS: This is a retrospective cohort study which was performed in a tertiary level referral hospital in the Netherlands. From the IBD database, female patients aged 18-80 years in 2004 were selected. Data analysis took place in the years 2005 and 2006. Eventually, 114 women with at least one pregnancy after the diagnosis of Crohn's disease were eligible for the study. Differences between groups were analyzed using Wilcoxon Mann Whitney tests and Chi-square analysis with 2 x 2 or 2 x 3 contingency tables. Two-tailed values were used and p values < 0.05 were considered statistically significant. RESULTS: 21/114 women (18%) had active luminal disease prior to pregnancy, with significantly more pregnancy related complications compared to women with inactive luminal disease (Odds ratio 2.8; 95% CI 1.0 - 7.4). Caesarean section rate was relatively high (37/114, 32%), especially in patients with perianal disease prior to pregnancy compared to women without perianal disease (Odds ratio 4.6; 95% CI 1.8 - 11.4). Disease progression after childbirth was more frequent in patients with active luminal disease prior to pregnancy compared to inactive luminal disease (Odds ratio 9.7; 95% CI 2.1 - 44.3). Progression of perianal disease seems less frequent after vaginal delivery compared with caesarean section, in both women with prior perianal disease (18% vs. 31%, NS) and without prior perianal disease (5% vs 14%, NS). There were no more fistula-related complications after childbirth in women with an episiotomy or second degree tear. CONCLUSION: A relatively high rate of caesarean sections was observed in women with Crohn's disease, especially in women with perianal disease prior to pregnancy. A protective effect of caesarean section on progression of perianal disease was not observed. However, this must be interpreted carefully due to confounder effect by indication for caesarean section

    Regulation of Adipocyte 11β-Hydroxysteroid Dehydrogenase Type 1 (11β-HSD1) by CCAAT/Enhancer-Binding Protein (C/EBP) β Isoforms, LIP and LAP

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    11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1) catalyses intracellular regeneration of active glucocorticoids, notably in liver and adipose tissue. 11β-HSD1 is increased selectively in adipose tissue in human obesity, a change implicated in the pathogenesis of metabolic syndrome. With high fat (HF)-feeding, adipose tissue 11β-HSD1 is down-regulated in mice, plausibly to counteract metabolic disease. Transcription of 11β-HSD1 is directly regulated by members of the CCAAT/enhancer binding protein (C/EBP) family. Here we show that while total C/EBPβ in adipose tissue is unaltered by HF diet, the ratio of the C/EBPβ isoforms liver-enriched inhibitor protein (LIP) and liver-enriched activator protein (LAP) (C/EBPβ-LIP:LAP) is increased in subcutaneous adipose. This may cause changes in 11β-HSD1 expression since genetically modified C/EBPβ(+/L) mice, with increased C/EBPβ-LIP:LAP ratio, have decreased subcutaneous adipose 11β-HSD1 mRNA levels, whereas C/EBPβΔuORF mice, with decreased C/EBPβ-LIP:LAP ratio, show increased subcutaneous adipose 11β-HSD1. C/EBPβ-LIP:LAP ratio is regulated by endoplasmic reticulum (ER) stress and mTOR signalling, both of which are altered in obesity. In 3T3-L1 adipocytes, 11β-HSD1 mRNA levels were down-regulated following induction of ER stress by tunicamycin but were up-regulated following inhibition of mTOR by rapamycin. These data point to a central role for C/EBPβ and its processing to LIP and LAP in transcriptional regulation of 11β-HSD1 in adipose tissue. Down-regulation of 11β-HSD1 by increased C/EBPβ-LIP:LAP in adipocytes may be part of a nutrient-sensing mechanism counteracting nutritional stress generated by HF diet

    GW8510 Increases Insulin Expression in Pancreatic Alpha Cells through Activation of p53 Transcriptional Activity

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    Background: Expression of insulin in terminally differentiated non-beta cell types in the pancreas could be important to treating type-1 diabetes. Previous findings led us to hypothesize involvement of kinase inhibition in induction of insulin expression in pancreatic alpha cells. Methodology/Principal Findings: Alpha (αTC1.6) cells and human islets were treated with GW8510 and other small-molecule inhibitors for up to 5 days. Alpha cells were assessed for gene- and protein-expression levels, cell-cycle status, promoter occupancy status by chromatin immunoprecipitation (ChIP), and p53-dependent transcriptional activity. GW8510, a putative CDK2 inhibitor, up-regulated insulin expression in mouse alpha cells and enhanced insulin secretion in dissociated human islets. Gene-expression profiling and gene-set enrichment analysis of GW8510-treated alpha cells suggested up-regulation of the p53 pathway. Accordingly, the compound increased p53 transcriptional activity and expression levels of p53 transcriptional targets. A predicted p53 response element in the promoter region of the mouse Ins2 gene was verified by chromatin immunoprecipitation (ChIP). Further, inhibition of Jun N-terminal kinase (JNK) and p38 kinase activities suppressed insulin induction by GW8510. Conclusions/Significance: The induction of Ins2 by GW8510 occurred through p53 in a JNK- and p38-dependent manner. These results implicate p53 activity in modulation of Ins2 expression levels in pancreatic alpha cells, and point to a potential approach toward using small molecules to generate insulin in an alternative cell type.Chemistry and Chemical BiologyMolecular and Cellular Biolog

    Methane production as a result from rumen fermentation in cattle calculated by using the IPCC-GPG tier 2 method

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    Following the IPCC GPG Guidelines the enteric fermentation emission is calculated as a percentage of the gross energy intake in cattle feedstuffs. The energy consumption for maintenance, activity, growth, lactation and pregnancy is described in detail. Combining this with the average rations for cattle the methane emissions are calculated. The report presents for the period 1990-2002 for all cattle categories the methane emission resulting from enteric fermentation.Volgens de IPCC-GPG methode wordt de methaanemissie berekend als percentage van de door het dier opgenomen bruto energie met het voer. Het rapport beschrijft in detail de benodigde energie voor onderhoud, activiteit, groei, lactatie en dracht. Met behulp van de rantsoenen van het Nederlandse rundvee wordt vervolgens de bruto energie opname berekend. Het rapport presenteert voor de volledige periode 1990-2002 voor alle rundveecategorieen de methaanemissie als gevolg van pensfermentatie

    Methane production as a result from rumen fermentation in cattle calculated by using the IPCC-GPG tier 2 method

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    Is tevens verschenen als FIS rapport FS 04 12, Feed Innovation Services, Aarle-Rixtel. Verder is het als engelstalig rapport verschenen onder nummer RIVM 680125005.Alleen digitaal beschikbaarVolgens de IPCC-GPG methode wordt de methaanemissie berekend als percentage van de door het dier opgenomen bruto energie met het voer. Het rapport beschrijft in detail de benodigde energie voor onderhoud, activiteit, groei, lactatie en dracht. Met behulp van de rantsoenen van het Nederlandse rundvee wordt vervolgens de bruto energie opname berekend. Het rapport presenteert voor de volledige periode 1990-2002 voor alle rundveecategorieen de methaanemissie als gevolg van pensfermentatie.Following the IPCC GPG Guidelines the enteric fermentation emission is calculated as a percentage of the gross energy intake in cattle feedstuffs. The energy consumption for maintenance, activity, growth, lactation and pregnancy is described in detail. Combining this with the average rations for cattle the methane emissions are calculated. The report presents for the period 1990-2002 for all cattle categories the methane emission resulting from enteric fermentation.SenterNovem Utrech
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