Transcriptome analysis of peripheral blood mononuclear cells in human subjects following a 36 h fast provides evidence of effects on genes regulating inflammation, apoptosis and energy metabolism

There is growing interest in the potential health benefits of diets that involve regular periods of fasting. While animal studies have provided compelling evidence that feeding patterns such as alternate-day fasting can increase longevity and reduce incidence of many chronic diseases, the evidence from human studies is much more limited and equivocal. Additionally, although several candidate processes have been proposed to contribute to the health benefits observed in animals, the precise molecular mechanisms responsible remain to be elucidated. The study described here examined the effects of an extended fast on gene transcript profiles in peripheral blood mononuclear cells from ten apparently healthy subjects, comparing transcript profiles after an overnight fast, sampled on four occasions at weekly intervals, with those observed on a single occasion after a further 24 h of fasting. Analysis of the overnight fasted data revealed marked inter-individual differences, some of which were associated with parameters such as gender and subject body mass. For example, a striking positive association between body mass index and the expression of genes regulated by type 1 interferon was observed. Relatively subtle changes were observed following the extended fast. Nonetheless, the pattern of changes was consistent with stimulation of fatty acid oxidation, alterations in cell cycling and apoptosis and decreased expression of key pro-inflammatory genes. Stimulation of fatty acid oxidation is an expected response, most likely in all tissues, to fasting. The other processes highlighted provide indications of potential mechanisms that could contribute to the putative beneficial effects of intermittent fasting in humans

Comparison of analyses of the QTLMAS XIV common dataset. II: QTL analysis

Background - A quantitative and a binary trait for the 14th QTLMAS 2010 workshop were simulated under a model which combined additive inheritance, epistasis and imprinting. This paper aimed to compare results submitted by the participants of the workshop.Methods - The results were compared according to three criteria: the success rate (ratio of mapped QTL to the total number of simulated QTL), and the error rate (ratio of false positives to the number of reported positions), and mean distance between a true mapped QTL and the nearest submitted position. Results - Seven groups submitted results for the quantitative trait and five for the binary trait. Among the 37 simulated QTL 17 remained undetected. Success rate ranged from 0.05 to 0.43, error rate was between 0.00 and 0.92, and the mean distance ranged from 0.26 to 0.77 Mb. Conclusions - Our comparison shows that differences among methods used by the participants increases with the complexity of genetic architecture. It was particularly visible for the quantitative trait which was determined partly by non-additive QTL. Furthermore, an imprinted QTL with a large effect may remain undetected if the applied model tests only for Mendelian genes

Refinement of Bos taurus sequence assembly based on BAC-FISH experiments

<p>Abstract</p> <p>Background</p> <p>The sequencing of the cow genome was recently published (Btau_4.0 assembly). A second, alternate cow genome assembly (UMD2), based on the same raw sequence data, was also published. The two assemblies have been subsequently updated to Btau_4.2 and UMD3.1, respectively.</p> <p>Results</p> <p>We compared the Btau_4.2 and UMD3.1 alternate assemblies. Inconsistencies were grouped into three main categories: (i) DNA segments showing almost coincidental chromosomal mapping but discordant orientation (inversions); (ii) DNA segments showing a discordant map position along the same chromosome; and (iii) sequences present in one chromosomal assembly but absent in the corresponding chromosome of the other assembly. The latter category mainly consisted of large amounts of scaffolds that were unassigned in Btau_4.2 but successfully mapped in UMD3.1. We sampled 70 inconsistencies and identified appropriate cow BACs for each of them. These clones were then utilized in FISH experiments on cow metaphase or interphase nuclei in order to disambiguate the discrepancies. In almost all instances the FISH results agreed with the UMD3.1 assembly. Occasionally, however, the mapping data of both assemblies were discordant with the FISH results.</p> <p>Conclusions</p> <p>Our work demonstrates how FISH, which is assembly independent, can be efficiently used to solve assembly problems frequently encountered using the shotgun approach.</p

Genomic profiling of CHEK2*1100delC-mutated breast carcinomas

Background: CHEK2*1100delC is a moderate-risk breast cancer susceptibility allele with a high prevalence in the Netherlands. We performed copy number and gene expression profiling to investigate whether CHEK2*1100delC breast cancers harbor characteristic genomic aberrations, as seen for BRCA1 mutated breast cancers. Methods: We performed high-resolution SNP array and gene expression profiling of 120 familial breast carcinomas selected from a larger cohort of 155 familial breast tumors, including BRCA1, BRCA2, and CHEK2 mutant tumors. Gene expression analyses based on a mRNA immune signature was used to identify samples with relative low amounts of tumor infiltrating lymphocytes (TILs), which were previously found to disturb tumor copy number and LOH (loss of heterozygosity) profiling. We specifically compared the genomic and gene expression profiles of CHEK2*1100delC breast cancers (n = 14) with BRCAX (familial non-BRCA1/BRCA2/CHEK2*1100delC mutated) breast cancers (n = 34) of the luminal intrinsic subtypes for which both SNP-array and gene expression data is available. Results: High amounts of TILs were found in a relatively small number of luminal breast cancers as compared to breast cancers of the basal-like subtype. As expected, the

Circumstellar disks and planets. Science cases for next-generation optical/infrared long-baseline interferometers

We present a review of the interplay between the evolution of circumstellar disks and the formation of planets, both from the perspective of theoretical models and dedicated observations. Based on this, we identify and discuss fundamental questions concerning the formation and evolution of circumstellar disks and planets which can be addressed in the near future with optical and infrared long-baseline interferometers. Furthermore, the importance of complementary observations with long-baseline (sub)millimeter interferometers and high-sensitivity infrared observatories is outlined.Comment: 83 pages; Accepted for publication in "Astronomy and Astrophysics Review"; The final publication is available at http://www.springerlink.co

Characterization of the behavior of carotenoids from pitanga (Eugenia uniflora) and buriti (Mauritia flexuosa) during microemulsion production and in a dynamic gastrointestinal system

Uncommon tropical fruits are emerging as raw-material for new food products with health benefits. This work aimed at formulating and processing microemulsions from pitanga (Eugenia uniflora) and buriti (Mauritia flexuosa) fruits, since they are very rich in carotenoids (particularly lycopene and -carotene), in order to encapsulate and increase carotenoids bioaccessibility. Pitanga and buriti microemulsions were produced by applying a direct processing (high-speed homogenization at 15,000 rpm and ultrasound with 20 kHz probe at 40% amplitude) of the whole pulp together with surfactant (Tween 80 or Whey Protein Isolate at 2%) and corn oil (5%). All treatments (HSHUS for 04, 40, 44, 48 minmin) applied were able to increase the amount of carotenoid released. However, the processing also decreased the total amount of carotenoids in the whole pulp of studied fruits. The impact of processing during microemulsion production was not severe. The overall data suggest that the presence of surfactant and oil during processing may protect the carotenoids in fruits and microemulsions. Final recovery of total carotenoids, after passing the samples through a dynamic gastrointestinal system that simulates the human digestion, was higher for microemulsions than for whole pulps. High losses of total carotenoids in buriti and -carotene and lycopene in pitanga occurred during jejunum and ileum phases. The present work confirms that it is possible to increase -carotene and lycopene bioaccessibility from fruits by directly processing microemulsions (p<0.01).This work was supported by the São Paulo Research Foundation—FAPESP through research funding [Grant #2015/15507-9] and Ph.D. scholarship for Paulo Berni [Grant #2014/15119-6] and a Research Internships Abroad (BEPE) support [Grant #2016/13355-0]. The author Ana C. Pinheiro is recipient of a fellowship from the Portuguese Foundation for Science and Technology (FCT) [Grant SFRH/BPD/101181/2014]info:eu-repo/semantics/publishedVersio

Utility of whole-genome sequence data for across-breed genomic prediction

Background: Genomic prediction (GP) across breeds has so far resulted in low accuracies of the predicted genomic breeding values. Our objective was to evaluate whether using whole-genome sequence (WGS) instead of low-density markers can improve GP across breeds, especially when markers are pre-selected from a genome-wide association study (GWAS), and to test our hypothesis that many non-causal markers in WGS data have a diluting effect on accuracy of across-breed prediction. Methods: Estimated breeding values for stature and bovine high-density (HD) genotypes were available for 595 Jersey bulls from New Zealand, 957 Holstein bulls from New Zealand and 5553 Holstein bulls from the Netherlands. BovineHD genotypes for all bulls were imputed to WGS using Beagle4 and Minimac2. Genomic prediction across the three populations was performed with ASReml4, with each population used as single reference and as single validation sets. In addition to the 50k, HD and WGS, markers that were significantly associated with stature in a large meta-GWAS analysis were selected and used for prediction, resulting in 10 prediction scenarios. Furthermore, we estimated the proportion of genetic variance captured by markers in each scenario. Results: Across breeds, 50k, HD and WGS markers resulted in very low accuracies of prediction ranging from − 0.04 to 0.13. Accuracies were higher in scenarios with pre-selected markers from a meta-GWAS. For example, using only the 133 most significant markers in 133 QTL regions from the meta-GWAS yielded accuracies ranging from 0.08 to 0.23, while 23,125 markers with a − log10(p) higher than 7 resulted in accuracies of up 0.35. Using WGS data did not significantly improve the proportion of genetic variance captured across breeds compared to scenarios with few but pre-selected markers. Conclusions: Our results demonstrated that the accuracy of across-breed GP can be improved by using markers that are pre-selected from WGS based on their potential causal effect. We also showed that simply increasing the number of markers up to the WGS level does not increase the accuracy of across-breed prediction, even when markers that are expected to have a causal effect are included

Determinants of participation in a longitudinal two-stage study of the health consequences of the Chornobyl nuclear power plant accident

<p>Abstract</p> <p>Background</p> <p>The determinants of participation in long-term follow-up studies of disasters have rarely been delineated. Even less is known from studies of events that occurred in eastern Europe. We examined the factors associated with participation in a longitudinal two-stage study conducted in Kyiv following the 1986 Chornobyl nuclear power plant accident.</p> <p>Methods</p> <p>Six hundred child-mother dyads (300 evacuees and 300 classmate controls) were initially assessed in 1997 when the children were 11 years old, and followed up in 2005–6 when they were 19 years old. A population control group (304 mothers and 327 children) was added in 2005–6. Each assessment point involved home interviews with the children and mothers (stage 1), followed by medical examinations of the children at a clinic (stage 2). Background characteristics, health status, and Chornobyl risk perceptions were examined.</p> <p>Results</p> <p>The participation rates in the follow-up home interviews were 87.8% for the children (88.6% for evacuees; 87.0% for classmates) and 83.7% for their mothers (86.4% for evacuees and 81.0% for classmates). Children's and mothers' participation was predicted by one another's study participation and attendance at the medical examination at time 1. Mother's participation was also predicted by initial concerns about her child's health, greater psychological distress, and Chornobyl risk perceptions. In 1997, 91.2% of the children had a medical examination (91.7% of evacuees and 90.7% of classmates); in 2005–6, 85.2% were examined (83.0% of evacuees, 87.7% of classmates, 85.0% of population controls). At both times, poor health perceptions were associated with receiving a medical examination. In 2005–6, clinic attendance was also associated with the young adults' risk perceptions, depression or generalized anxiety disorder, lower standard of living, and female gender.</p> <p>Conclusion</p> <p>Despite our low attrition rates, we identified several determinants of selective participation consistent with previous research. Although evacuee status was not associated with participation, Chornobyl risk perceptions were strong predictors of mothers' follow-up participation and attendance at the medical examinations. Understanding selective participation offers valuable insight for future longitudinal disaster studies that integrate psychiatric and medical epidemiologic research.</p

Within- and across-breed genomic prediction using whole-genome sequence and single nucleotide polymorphism panels

International audienceBackground Currently, genomic prediction in cattle is largely based on panels of about 54k single nucleotide polymorphisms (SNPs). However with the decreasing costs of and current advances in next-generation sequencing technologies, whole-genome sequence (WGS) data on large numbers of individuals is within reach. Availability of such data provides new opportunities for genomic selection, which need to be explored.MethodsThis simulation study investigated how much predictive ability is gained by using WGS data under scenarios with QTL (quantitative trait loci) densities ranging from 45 to 132 QTL/Morgan and heritabilities ranging from 0.07 to 0.30, compared to different SNP densities, with emphasis on divergent dairy cattle breeds with small populations. The relative performances of best linear unbiased prediction (SNP-BLUP) and of a variable selection method with a mixture of two normal distributions (MixP) were also evaluated. Genomic predictions were based on within-population, across-population, and multi-breed reference populations.ResultsThe use of WGS data for within-population predictions resulted in small to large increases in accuracy for low to moderately heritable traits. Depending on heritability of the trait, and on SNP and QTL densities, accuracy increased by up to 31 %. The advantage of WGS data was more pronounced (7 to 92 % increase in accuracy depending on trait heritability, SNP and QTL densities, and time of divergence between populations) with a combined reference population and when using MixP. While MixP outperformed SNP-BLUP at 45 QTL/Morgan, SNP-BLUP was as good as MixP when QTL density increased to 132 QTL/Morgan.ConclusionsOur results show that, genomic predictions in numerically small cattle populations would benefit from a combination of WGS data, a multi-breed reference population, and a variable selection method