Chickasaw plum for wildlife in Oklahoma

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The Impact of Phenocopy on the Genetic Analysis of Complex Traits

A consistent debate is ongoing on genome-wide association studies (GWAs). A key point is the capability to identify low-penetrance variations across the human genome. Among the phenomena reducing the power of these analyses, phenocopy level (PE) hampers very seriously the investigation of complex diseases, as well known in neurological disorders, cancer, and likely of primary importance in human ageing. PE seems to be the norm, rather than the exception, especially when considering the role of epigenetics and environmental factors towards phenotype. Despite some attempts, no recognized solution has been proposed, particularly to estimate the effects of phenocopies on the study planning or its analysis design. We present a simulation, where we attempt to define more precisely how phenocopy impacts on different analytical methods under different scenarios. With our approach the critical role of phenocopy emerges, and the more the PE level increases the more the initial difficulty in detecting gene-gene interactions is amplified. In particular, our results show that strong main effects are not hampered by the presence of an increasing amount of phenocopy in the study sample, despite progressively reducing the significance of the association, if the study is sufficiently powered. On the opposite, when purely epistatic effects are simulated, the capability of identifying the association depends on several parameters, such as the strength of the interaction between the polymorphic variants, the penetrance of the polymorphism and the alleles (minor or major) which produce the combined effect and their frequency in the population. We conclude that the neglect of the possible presence of phenocopies in complex traits heavily affects the analysis of their genetic data

Inherited determinants of Crohn's disease and ulcerative colitis phenotypes: a genetic association study

Crohn's disease and ulcerative colitis are the two major forms of inflammatory bowel disease; treatment strategies have historically been determined by this binary categorisation. Genetic studies have identified 163 susceptibility loci for inflammatory bowel disease, mostly shared between Crohn's disease and ulcerative colitis. We undertook the largest genotype association study, to date, in widely used clinical subphenotypes of inflammatory bowel disease with the goal of further understanding the biological relations between diseases

IBD risk loci are enriched in multigenic regulatory modules encompassing putative causative genes.

GWAS have identified >200 risk loci for Inflammatory Bowel Disease (IBD). The majority of disease associations are known to be driven by regulatory variants. To identify the putative causative genes that are perturbed by these variants, we generate a large transcriptome data set (nine disease-relevant cell types) and identify 23,650 cis-eQTL. We show that these are determined by ∼9720 regulatory modules, of which ∼3000 operate in multiple tissues and ∼970 on multiple genes. We identify regulatory modules that drive the disease association for 63 of the 200 risk loci, and show that these are enriched in multigenic modules. Based on these analyses, we resequence 45 of the corresponding 100 candidate genes in 6600 Crohn disease (CD) cases and 5500 controls, and show with burden tests that they include likely causative genes. Our analyses indicate that ≥10-fold larger sample sizes will be required to demonstrate the causality of individual genes using this approach

Meta-analysis of shared genetic architecture across ten pediatric autoimmune diseases

Genome-wide association studies (GWASs) have identified hundreds of susceptibility genes, including shared associations across clinically distinct autoimmune diseases. We performed an inverse χ(2) meta-analysis across ten pediatric-age-of-onset autoimmune diseases (pAIDs) in a case-control study including more than 6,035 cases and 10,718 shared population-based controls. We identified 27 genome-wide significant loci associated with one or more pAIDs, mapping to in silico-replicated autoimmune-associated genes (including IL2RA) and new candidate loci with established immunoregulatory functions such as ADGRL2, TENM3, ANKRD30A, ADCY7 and CD40LG. The pAID-associated single-nucleotide polymorphisms (SNPs) were functionally enriched for deoxyribonuclease (DNase)-hypersensitivity sites, expression quantitative trait loci (eQTLs), microRNA (miRNA)-binding sites and coding variants. We also identified biologically correlated, pAID-associated candidate gene sets on the basis of immune cell expression profiling and found evidence of genetic sharing. Network and protein-interaction analyses demonstrated converging roles for the signaling pathways of type 1, 2 and 17 helper T cells (TH1, TH2 and TH17), JAK-STAT, interferon and interleukin in multiple autoimmune diseases

WATSEN - A Mid-IR spectrometer, humidity sensor and optical microscope to identify the subsurface water and mineralogy of Mars

Mars is currently the main focus of extra-terrestrial planetary investigation in terms of the number of surface and orbital instruments deployed there. Although several missions have scratched into the surface (most recently Phoenix) there have not been deeper measurements of the martian subsurface. Phoenix has discovered the surrounding soil to be comparable to soils found in Antarctica's Dry Valleys [1]. It seems clear from the initial results that the soil is pH alkaline (8.3 ± 0.5) [2] and that water has been involved in the formation of the soil, detected in the form of subliming ice [3]. The presence of CaCO 3 and soluble ionic species detected by TEGA and MECA [4,2] further suggests the presence of water interacting with soil at some point. Since conditions at the martian surface are unfavourable for the presence of water and potential organic signatures [5] it is necessary to look deeper into the subsurface. Recent classification of geological eras [6] suggests an early warm and wet martian environment in which phyllosilicates formed (called the Phyllosian era). Nili Fossae [7] is a region that the orbital VNIR and IR spectrometers OMEGA and CRISM [8,9] have indentified which correspond mineralogically and through crater counts to this early Phyllosian era. This location would be a prime candidate for the detection of Mars' fluvial past, with phyllosilicates detected and CRISM indentifying MgCO3 [ 10] (known to be abundant in the presence of water, CO, and an alkaline pH; all conditions hospitable for most terrestrial life)

Range Rehabilitation Enhances Cotton Rats in South Texas

During August 1961 in Kleberg County, Texas, cotton rat density was four times greater on areas planted to exotic grasses than on native rangeland, and density was six times greater on rootplowed areas. A regression model using standing crop biomass of herbaceous vegetation and percentage composition of standing crop furnished by sida, bristlegrasses, and sumpweed plus ragweed explained 81.4% of the variation in cotton rat density.This material was digitized as part of a cooperative project between the Society for Range Management and the University of Arizona Libraries.The Journal of Range Management archives are made available by the Society for Range Management and the University of Arizona Libraries. Contact [email protected] for further information.Migrated from OJS platform August 202