Effectiveness of Foliar Fungicides by Timing on Hybrid Corn in Iowa

Fungicide use on hybrid corn has increased considerably in the past four growing seasons primarily due to reports of increased yields, even in the absence of disease, and higher corn prices. A number of fungicides are registered for use on corn. The objectives of this project were 1) to assess the effect of timing of application of fungicides on standability, 2) to evaluate the yield response of hybrid corn to foliar fungicide application, and 3) to discern differences, if any, between fungicide products

Effectiveness of Foliar Fungicides by Timing on Hybrid Corn

Fungicide use on hybrid corn has increased considerably in the past four growing seasons primarily due to reports of increased yields, even in the absence of disease and higher corn prices. A number of fungicides are registered for use on corn. The objectives of this project were to 1) assess the effect of timing of application of fungicides on standability, 2) evaluate the yield response of hybrid corn to foliar fungicide application, and 3) to discern differences, if any, between fungicide products

Associations of actigraphy‐assessed sleep variables with adiposity and serum cardiometabolic outcomes in emerging adults

SummaryThis study assessed associations of actigraphy‐assessed sleep with adiposity and serum cardiometabolic outcomes in emerging adults, and whether sex and race modified these associations. Data on 147 emerging adults (age = 19.4 ± 1.3 years; body mass index = 26.4 ± 7.0 kg m$^{−2}$; 59% female; 65% White) from RIGHT Track Health were used. Actigraphy‐based sleep measures included sleep duration, sleep efficiency, sleep timing midpoint, day‐to‐day sleep duration and sleep timing midpoint variability. Combined sleep duration and sleep timing behaviours were also derived (early‐bed/late‐rise, early‐bed/early‐rise, late‐bed/late‐rise, late‐bed/early‐rise). Outcomes included body mass index and BodPod‐assessed fat mass index, fasting serum leptin, C‐reactive protein, and homeostatic model assessment‐insulin resistance. Sleep duration was 5.4 h per night. We noted an inverse association between sleep duration and homeostatic model assessment‐insulin resistance. The early‐bed/early‐rise group had greater body mass index, C‐reactive protein and homeostatic model assessment‐insulin resistance compared with the early‐bed/late‐rise group (referent). Sex modified associations of sleep efficiency with C‐reactive protein; stratified results revealed positive association between sleep efficiency and C‐reactive protein in males, but not females. Race modified associations of sleep duration with body mass index and leptin, and of sleep duration variability with C‐reactive protein. Stratified analyses revealed inverse associations between sleep duration with body mass index and leptin in Black, multiracial/other race individuals only. Positive association between sleep duration variability and C‐reactive protein was noted in White individuals only. Shorter sleep duration, particularly when combined with earlier sleep timing, is associated with greater adiposity and serum cardiometabolic outcomes. Additional studies are needed to assess individual‐ and contextual‐level factors that may contribute to sex and race differences in sleep health and cardiometabolic risk in emerging adults

cis-Regulatory Changes in Kit Ligand Expression and Parallel Evolution of Pigmentation in Sticklebacks and Humans

SummaryDramatic pigmentation changes have evolved within most vertebrate groups, including fish and humans. Here we use genetic crosses in sticklebacks to investigate the parallel origin of pigmentation changes in natural populations. High-resolution mapping and expression experiments show that light gills and light ventrums map to a divergent regulatory allele of the Kit ligand (Kitlg) gene. The divergent allele reduces expression in gill and skin tissue and is shared by multiple derived freshwater populations with reduced pigmentation. In humans, Europeans and East Asians also share derived alleles at the KITLG locus. Strong signatures of selection map to regulatory regions surrounding the gene, and admixture mapping shows that the KITLG genomic region has a significant effect on human skin color. These experiments suggest that regulatory changes in Kitlg contribute to natural variation in vertebrate pigmentation, and that similar genetic mechanisms may underlie rapid evolutionary change in fish and humans

Non-linear regression models for Approximate Bayesian Computation

Approximate Bayesian inference on the basis of summary statistics is well-suited to complex problems for which the likelihood is either mathematically or computationally intractable. However the methods that use rejection suffer from the curse of dimensionality when the number of summary statistics is increased. Here we propose a machine-learning approach to the estimation of the posterior density by introducing two innovations. The new method fits a nonlinear conditional heteroscedastic regression of the parameter on the summary statistics, and then adaptively improves estimation using importance sampling. The new algorithm is compared to the state-of-the-art approximate Bayesian methods, and achieves considerable reduction of the computational burden in two examples of inference in statistical genetics and in a queueing model.Comment: 4 figures; version 3 minor changes; to appear in Statistics and Computin

Identifying the favored mutation in a positive selective sweep.

Most approaches that capture signatures of selective sweeps in population genomics data do not identify the specific mutation favored by selection. We present iSAFE (for "integrated selection of allele favored by evolution"), a method that enables researchers to accurately pinpoint the favored mutation in a large region (∼5 Mbp) by using a statistic derived solely from population genetics signals. iSAFE does not require knowledge of demography, the phenotype under selection, or functional annotations of mutations

Genetic diversity and evolution of the human leptin locus tetranucleotide repeat

To better understand the evolutionary history of the gene region containing the multifunctional adipose tissue hormone leptin, we genotyped 1,957 individuals from 12 world populations for a highly variable tetranucleotide repeat polymorphism located 476 bp 3′ of exon 3 of the leptin gene. Common alleles shared among populations, alleles specific to geographically defined populations, and the homologous alleles in the common and pygmy chimpanzee, the gorilla and the orangutan, were sequenced to define the allelic variation at the nucleotide level. These data reveal a common set of alleles shared among world populations, presumed to have arisen from a great ape ancestral allele prior to the divergence of the major geographical subdivisions of the human population, a subset of alleles specific to populations of African ancestry and a second set of alleles that arose by tandem duplication of the core repeat unit following the separation of African and non-African populations. These findings emphasize the complex evolutionary history of this locus and raise cautions about the pooling of alleles at this locus in association studies.Universidad de Costa Rica. Instituto de Investigaciones en SaludUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias de la Salud::Instituto de Investigaciones en Salud (INISA

MIRU-VNTRplus: a web tool for polyphasic genotyping of Mycobacterium tuberculosis complex bacteria

Harmonized typing of bacteria and easy identification of locally or internationally circulating clones are essential for epidemiological surveillance and disease control. For Mycobacterium tuberculosis complex (MTBC) species, multi-locus variable number tandem repeat analysis (MLVA) targeting mycobacterial interspersed repetitive units (MIRU) has been internationally adopted as the new standard, portable, reproducible and discriminatory typing method. However, no specialized bioinformatics web tools are available for analysing MLVA data in combination with other, complementary typing data. Therefore, we have developed the web application MIRU-VNTRplus (http://www.miru-vntrplus.org). This freely accessible service allows users to analyse genotyping data of their strains alone or in comparison with a reference database of strains representing the major MTBC lineages. Analysis and comparisons of genotypes can be based on MLVA-, spoligotype-, large sequence polymorphism and single nucleotide polymorphism data, or on a weighted combination of these markers. Tools for data exploration include search for similar strains, creation of phylogenetic and minimum spanning trees and mapping of geographic information. To facilitate scientific communication, an expanding genotype nomenclature (MLVA MtbC15-9 type) that can be queried via a web- or a SOAP-interface has been implemented. An extensive documentation guides users through all application functions

In the blood: the myth and reality of genetic markers of identity

The differences between copies of the human genome are very small, but tend to cluster in different populations. So, despite the fact that low inter-population differentiation does not support a biological definition of races statistical methods are nonetheless claimed to be able to predict successfully the population of origin of a DNA sample. Such methods are employed in commercial genetic ancestry tests, and particular genetic signatures, often in the male-specific Y-chromosome or maternally-inherited mitochondrial DNA, have become widely identified with particular ancestral or existing groups, such as Vikings, Jews, or Zulus. Here, we provide a primer on genetics, and describe how genetic markers have become associated with particular groups. We describe the conflict between population genetics and individual-based genetics and the pitfalls of over-simplistic genetic interpretations, arguing that although the tests themselves are reliable, the interpretations are unreliable and strongly influenced by cultural and other social forces.</p