Association between rat decompression sickness resistance, transthyretin single nucleotide polymorphism, and expression: A pilot study

International audienceDecompression sickness (DCS) is a systemic syndrome that can occur after an environmental pressure reduction. Previously, we showed that the plasmatic tetrameric form of transthyretin (TTR) nearly disappeared in rats suffering DCS but not in asymptomatic ones. In this pilot study, we assessed whether the resistance to DCS could be associated with polymorphism of the gene of TTR. For this study, Sanger sequencing was performed on purified PCR products from the liver of 14‐week‐old male and female standard and DCS‐resistant rats ( n = 5 per group). Hepatic TTR mRNA expression was assessed by RT‐qPCR in 18–19 week‐old male and female standard and resistant rats ( n = 6 per group). There is a synonymous single nucleotide polymorphism (SNP) on the third base of codon 46 (c.138 C > T). The thymine allele was present in 90% and 100% of males and females standard, respectively. However, this allele is present in only 30% of DCS‐resistant males and females ( p = 0.0002301). In the liver, there is a significant effect of the resistance to DCS ( p = 0.043) and sex ( p = 0.047) on TTR expression. Levels of TTR mRNA were lower in DCS‐resistant animals. To conclude, DCS resistance might be associated with a SNP and a lower expression of TTR

Leaf Area Index, a good functional trait for screening genetic diversity of Winter Oil Seed Rape response to N constraint : Study of a panel of 95 genotypes

Economic competitiveness and environmental sustainability of winter oilseed rape (WOSR) depend on improvement or maintain of the crop yield under low nitrogen (N) fertilisation. Cultivars with higher N use efficiency (NUE) might be characterized (i) by higher leaf expansion and N uptake efficiency until flowering and/or (ii) by longer duration of leaf area (LAI) and photosynthetic activity, and/or (iii) by more efficient remobilisation of N reserves from source leaves to sink organs during reproductive growth phase. We investigated for a large range of WOSR genetic diversity, whether characteristics linked with changes in LAI establishment and duration could be related to high NUE (i.e. high seed yield at low N supply) or N uptake and utilisation

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

The human genome contains many thousands of long noncoding RNAs (IncRNAs). While several studies have demonstrated compelling biological and disease roles for individual examples, analytical and experimental approaches to investigate these genes have been hampered by the lack of comprehensive IncRNA annotation. Here, we present and analyze the most complete human IncRNA annotation to date, produced by the GENCODE consortium within the framework of the ENCODE project and comprising 9277 manually annotated genes producing 14,880 transcripts. Our analyses indicate that IncRNAs are generated through pathways similar to that of protein-coding genes, with similar histone-modification profiles, splicing signals, and exon /intron lengths. In contrast to protein-coding genes, however, IncRNAs display a striking bias toward two-exon transcripts, they are predominantly localized in the chromatin and nucleus, and a fraction appear to be preferentially processed into small RNAs. They are under stronger selective pressure than neutrally evolving sequences-particularly in their promoter regions, which display levels of selection comparable to protein-coding genes. Importantly, about one-third seem to have arisen within the primate lineage. Comprehensive analysis of their expression in multiple human organs and brain regions shows that IncRNAs are generally lower expressed than protein-coding genes, and display more tissue-specific expression patterns, with a large fraction of tissue-specific IncRNAs expressed in the brain. Expression correlation analysis indicates that IncRNAs show particularly striking positive correlation with the expression of antisense coding genes. This GENCODE annotation represents a valuable resource for future studies of IncRNAs

Body size and risk of colon and rectal cancer in the European Prospective Investigation into Cancer and Nutrition (EPIC)

Background: Body weight and body mass index (BMI) are positively related to risk of colon cancer in men, whereas weak or no associations exist in women. This discrepancy may be related to differences in fat distribution between sexes or to the use of hormone replacement therapy (HRT) in women. Methods: We used multivariable adjusted Cox proportional hazards models to examine the association between anthropometric measures and risks of colon and rectal cancer among 368 277 men and women who were free of cancer at baseline from nine countries of the European Prospective Investigation Into Cancer and Nutrition. All statistical tests were two-sided. Results: During 6.1 years of follow-up, we identified 984 and 586 patients with colon and rectal cancer, respectively. Body weight and BMI were statistically significantly associated with colon cancer risk in men (highest versus lowest quintile of BMI, relative risk [RR] = 1.55, 95% confidence interval [CI] = 1.12 to 2.15; P trend =.006) but not in women. In contrast, comparisons of the highest to the lowest quintile showed that several anthropometric measures, including waist circumference (men, RR = 1.39, 95% CI = 1.01 to 1.93; P trend = .001; women, RR = 1.48, 95% CI = 1.08 to 2.03; P trend = .008), waist-to-hip ratio (WHR; men, RR = 1.51, 95% CI = 1.06 to 2.15; P trend = .006; women, RR = 1.52, 95% CI = 1.12 to 2.05; P trend = .002), and height (men, RR = 1.40, 95% CI = 0.99 to 1.98; P trend = .04; women, RR = 1.79, 95% CI = 1.30 to 2.46; P trend <.001) were related to colon cancer risk in both sexes. The estimated absolute risk of developing colon cancer within 5 years was 203 and 131 cases per 100 000 men and 129 and 86 cases per 100 000 women in the highest and lowest quintiles of WHR, respectively. Upon further stratification, no association of waist circumference and WHR with risk of colon cancer was observed among postmenopausal women who used HRT. None of the anthropometric measures was statistically significantly related to rectal cancer. Conclusions: Waist circumference and WHR, indicators of abdominal obesity, were strongly associated with colon cancer risk in men and women in this population. The association of abdominal obesity with colon cancer risk may vary depending on HRT use in postmenopausal women; however, these findings require confirmation in future studies. © 2006 Oxford University Press

The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression

The human genome contains many thousands of long noncoding RNAs (lncRNAs). While several studies have demonstrated compelling biological and disease roles for individual examples, analytical and experimental approaches to investigate these genes have been hampered by the lack of comprehensive lncRNA annotation. Here, we present and analyze the most complete human lncRNA annotation to date, produced by the GENCODE consortium within the framework of the ENCODE project and comprising 9277 manually annotated genes producing 14,880 transcripts. Our analyses indicate that lncRNAs are generated through pathways similar to that of protein-coding genes, with similar histone-modification profiles, splicing signals, and exon/intron lengths. In contrast to protein-coding genes, however, lncRNAs display a striking bias toward two-exon transcripts, they are predominantly localized in the chromatin and nucleus, and a fraction appear to be preferentially processed into small RNAs. They are under stronger selective pressure than neutrally evolving sequences-particularly in their promoter regions, which display levels of selection comparable to protein-coding genes. Importantly, about one-third seem to have arisen within the primate lineage. Comprehensive analysis of their expression in multiple human organs and brain regions shows that lncRNAs are generally lower expressed than protein-coding genes, and display more tissue-specific expression patterns, with a large fraction of tissue-specific lncRNAs expressed in the brain. Expression correlation analysis indicates that lncRNAs show particularly striking positive correlation with the expression of antisense coding genes. This GENCODE annotation represents a valuable resource for future studies of lncRNAs.This work has been carried out under grants RD07/0067/0012, BIO2006-03380, and CSD2007-00050 from the Spanish Ministry of Science, grant SGR-1430 from the Catalan Government, grants 1U54HG004557-01 and 1U54HG004555-01 from the National Institutes of Health, and INBISCIII from Instituto de Salud Carlos III and FEDER. This research project has been cofinanced by the European Commission, within the 7th Framework Programme, Grant Agreement KBBE-2A-222664 (‘‘Quantomics’’). C.N. is financed by the Plan Nacional BFU2008-00419. G.B. is supported by the La Caixa Ph.D. progra