Pathway analysis comparison using Crohn's disease genome wide association studies

<p>Abstract</p> <p>Background</p> <p>The use of biological annotation such as genes and pathways in the analysis of gene expression data has aided the identification of genes for follow-up studies and suggested functional information to uncharacterized genes. Several studies have applied similar methods to genome wide association studies and identified a number of disease related pathways. However, many questions remain on how to best approach this problem, such as whether there is a need to obtain a score to summarize association evidence at the gene level, and whether a pathway, dominated by just a few highly significant genes, is of interest.</p> <p>Methods</p> <p>We evaluated the performance of two pathway-based methods (Random Set, and Binomial approximation to the hypergeometric test) based on their applications to three data sets of Crohn's disease. We consider both the disease status as a phenotype as well as the residuals after conditioning on IL23R, a known Crohn's related gene, as a phenotype.</p> <p>Results</p> <p>Our results show that Random Set method has the most power to identify disease related pathways. We confirm previously reported disease related pathways and provide evidence for IL-2 Receptor Beta Chain in T cell Activation and IL-9 signaling as Crohn's disease associated pathways.</p> <p>Conclusions</p> <p>Our results highlight the need to apply powerful gene score methods prior to pathway enrichment tests, and that controlling for genes that attain genome wide significance enable further biological insight.</p

Genomic Structure of and Genome-Wide Recombination in the Saccharomyces cerevisiae S288C Progenitor Isolate EM93

The diploid isolate EM93 is the main ancestor to the widely used Saccharomyces cerevisiae haploid laboratory strain, S288C. In this study, we generate a high-resolution overview of the genetic differences between EM93 and S288C. We show that EM93 is heterozygous for >45,000 polymorphisms, including large sequence polymorphisms, such as deletions and a Saccharomyces paradoxus introgression. We also find that many large sequence polymorphisms (LSPs) are associated with Ty-elements and sub-telomeric regions. We identified 2,965 genetic markers, which we then used to genotype 120 EM93 tetrads. In addition to deducing the structures of all EM93 chromosomes, we estimate that the average EM93 meiosis produces 144 detectable recombination events, consisting of 87 crossover and 31 non-crossover gene conversion events. Of the 50 polymorphisms showing the highest levels of non-crossover gene conversions, only three deviated from parity, all of which were near heterozygous LSPs. We find that non-telomeric heterozygous LSPs significantly reduce meiotic recombination in adjacent intervals, while sub-telomeric LSPs have no discernable effect on recombination. We identified 203 recombination hotspots, relatively few of which are hot for both non-crossover gene conversions and crossovers. Strikingly, we find that recombination hotspots show limited conservation. Some novel hotspots are found adjacent to heterozygous LSPs that eliminate other hotspots, suggesting that hotspots may appear and disappear relatively rapidly

Polygenic transmission disequilibrium confirms that common and rare variation act additively to create risk for autism spectrum disorders

Autism spectrum disorder (ASD) risk is influenced by common polygenic and de novo variation. We aimed to clarify the influence of polygenic risk for ASD and to identify subgroups of ASD cases, including those with strongly acting de novo variants, in which polygenic risk is relevant. Using a novel approach called the polygenic transmission disequilibrium test and data from 6,454 families with a child with ASD, we show that polygenic risk for ASD, schizophrenia, and greater educational attainment is over-transmitted to children with ASD. These findings hold independent of proband IQ. We find that polygenic variation contributes additively to risk in ASD cases who carry a strongly acting de novo variant. Lastly, we show that elements of polygenic risk are independent and differ in their relationship with phenotype. These results confirm that the genetic influences on ASD are additive and suggest that they create risk through at least partially distinct etiologic pathways

What determines cell size?

AbstractFirst paragraph (this article has no abstract) For well over 100 years, cell biologists have been wondering what determines the size of cells. In modern times, we know all of the molecules that control the cell cycle and cell division, but we still do not understand how cell size is determined. To check whether modern cell biology has made any inroads on this age-old question, BMC Biology asked several heavyweights in the field to tell us how they think cell size is controlled, drawing on a range of different cell types. The essays in this collection address two related questions - why does cell size matter, and how do cells control it

Condenação ao abate em bovinos devido a lesões parasitárias e seu impacto econômico em estabelecimentos do Sistema Federal de Inspeção no Brasil e no Sistema Estadual de Inspeção no Rio Grande do Sul

Slaughter condemnations are important sources of information on cattle health. The incidence of bovine parasitic diseases is still very high in Brazil. These diseases, in addition to causing harm to the animals health, are neglected zoonotic diseases in several parts of world. The study analysed not only the Carcass losses, but also the economic damage resulting from slaughter condemnations due to parasitic causes. Cattle slaughter data from the Brazilian Ministry of Agriculture, Livestock and Supply (MAPA), over the period of 2012 to 2015 and data from the Secretary of Livestock and Irrigation of the state of Rio Grande do Sul (SEAPI-RS) were analyzed between 2014 and 2018.The number of organs and carcasses condemned was multiplied by the respective values (in Brazilian Real) obtained from slaughterhouses and subsequently converted into dollars. Brazilian analysis in SIF (Federal Inspection System) establishments showed that more than 1.2 million organs (3,884,505 kg) and 20,000 carcasses (4,547,718 kg) were condemned only due to parasitic causes during post-mortem inspection. In Rio Grande do Sul, in state inspection establishments, more than 1.7 million organs (8,210,559 kg) and 5,000 carcasses (1,243,200 kg) were condemned. These data are alarming and support the need for public policies to control these parasitic diseases.Condenações durante o abate são importantes fontes de informação sobre a sanidade dos rebanhos. Ainda são altas as incidências de doenças parasitárias, as quais trazem consequências à saúde dos animais, são zoonoses e têm sua importância negligenciada em diversos países. O estudo objetivou quantificar não apenas as perdas encontradas, mas o prejuízo econômico resultante das condenações ao abate por causas parasitárias. Para isso foram analisados dados de abate de bovinos do Ministério da Agricultura Pecuária e Abastecimento, no período de 2012 a 2015, e dados da Secretaria da Agricultura Pecuária e Irrigação, do estado do Rio Grande do Sul, no período de 2014 a 2018. A quantidade de órgãos e carcaças condenados foi multiplicada pelos respectivos valores (em Reais), obtidos da indústria frigorífica e, posteriormente, convertidos para dólar. A análise brasileira de estabelecimentos com SIF (Serviço de Inspeção Federal) mostrou que mais de 1,2 milhão de órgãos (3.884.505 kg) e 20 mil carcaças (4.547.718 kg) foram condenados devido a causas parasitárias durante a inspeção. No estado do Rio Grande do Sul, nos estabelecimentos de inspeção estadual, foram condenados mais de 1,7 milhão de órgãos (8.210.559 kg) e 5 mil carcaças (1.243.200 kg). Os dados são alarmantes e ressaltam a necessidade de políticas públicas para controlar estas parasitoses

Non Destructive Characterization of Cortical Bone MicroDamage by Nonlinear Resonant Ultrasound Spectroscopy

The objective of the study was to evaluate the ability of a nonlinear ultrasound technique, the so-called nonlinear resonant ultrasound spectroscopy (NRUS) technique, for detecting early microdamage accumulation in cortical bone induced by four-point bending fatigue. Small parallelepiped beam-shaped human cortical bone specimens were subjected to cyclic four-point bending fatigue in several steps. The specimens were prepared to control damage localization during four-point bending fatigue cycling and to unambiguously identify resonant modes for NRUS measurements. NRUS measurements were achieved to follow the evolution of the nonlinear hysteretic elastic behavior during fatigue-induced damage. After each fatigue step, a small number of specimens was removed from the protocol and set apart to quantitatively assess the microcrack number density and length using synchrotron radiation micro-computed tomography (SR-µCT). The results showed a significant effect of damage steps on the nonlinear hysteretic elastic behavior. No significant change in the overall length of microcracks was observed in damaged regions compared to the load-free control regions. Only an increased number of shortest microcracks, those in the lowest quartile, was noticed. This was suggestive of newly formed microcracks during the early phases of damage accumulation. The variation of nonlinear hysteretic elastic behavior was significantly correlated to the variation of the density of short microcracks. Our results suggest that the nonlinear hysteretic elastic behavior is sensitive to early bone microdamage. Therefore NRUS technique can be used to monitor fatigue microdamage progression in in vitro experiments.BONUS_07BLAN019