Computer programs for saturation properties of hydrogen

Computer programs for saturation properties of liquid and vapor hydroge

Genomic Regions Associated With Gestation Length Detected Using Whole-Genome Sequence Data Differ Between Dairy and Beef Cattle

peer-reviewedWhile many association studies exist that have attempted to relate genomic markers to phenotypic performance in cattle, very few have considered gestation length as a phenotype, and of those that did, none used whole genome sequence data from multiple breeds. The objective of the present study was therefore to relate imputed whole genome sequence data to estimated breeding values for gestation length using 22,566 sires (representing 2,262,706 progeny) of multiple breeds [Angus (AA), Charolais (CH), Holstein-Friesian (HF), and Limousin (LM)]. The associations were undertaken within breed using linear mixed models that accounted for genomic relatedness among sires; a separate association analysis was undertaken with all breeds analysed together but with breed included as a fixed effect in the model. Furthermore, the genome was divided into 500 kb segments and whether or not segments harboured a single nucleotide polymorphism (SNP) with a P ≤ 1 × 10-4 common to different combinations of breeds was determined. Putative quantitative trait loci (QTL) regions associated with gestation length were detected in all breeds; significant associations with gestation length were only detected in the HF population and in the across-breed analysis of all 22,566 sires. Twenty-five SNPs were significantly associated (P ≤ 5 × 10-8) with gestation length in the HF population. Of the 25 significant SNPs, 18 were located within three QTLs on Bos taurus autosome number (BTA) 18, six were in two QTL on BTA19, and one was located within a QTL on BTA7. The strongest association was rs381577268, a downstream variant of ZNF613 located within a QTL spanning from 58.06 to 58.19 Mb on BTA18; it accounted for 1.37% of the genetic variance in gestation length. Overall there were 11 HF animals within the edited dataset that were homozygous for the T allele at rs381577268 and these had a 3.3 day longer (P < 0.0001) estimated breeding value (EBV) for gestation length than the heterozygous animals and a 4.7 day longer (P < 0.0001) EBV for gestation length than the homozygous CC animals. The majority of the 500 kb windows harboring a SNP with a P ≤ 1 × 10-4 were unique to a single breed and no window was shared among all four breeds for gestation length, suggesting any QTLs identified are breed-specific associations

Chemical regulators of epithelial plasticity reveal a nuclear receptor pathway controlling myofibroblast differentiation

Plasticity in epithelial tissues relates to processes of embryonic development, tissue fibrosis and cancer progression. Pharmacological modulation of epithelial transitions during disease progression may thus be clinically useful. Using human keratinocytes and a robotic high-content imaging platform, we screened for chemical compounds that reverse transforming growth factor β (TGF-β)-induced epithelial-mesenchymal transition. In addition to TGF-β receptor kinase inhibitors, we identified small molecule epithelial plasticity modulators including a naturally occurring hydroxysterol agonist of the liver X receptors (LXRs), members of the nuclear receptor transcription factor family. Endogenous and synthetic LXR agonists tested in diverse cell models blocked α-smooth muscle actin expression, myofibroblast differentiation and function. Agonist-dependent LXR activity or LXR overexpression in the absence of ligand counteracted TGF-β-mediated myofibroblast terminal differentiation and collagen contraction. The protective effect of LXR agonists against TGF-β-induced pro-fibrotic activity raises the possibility that anti-lipidogenic therapy may be relevant in fibrotic disorders and advanced cancer

Double-resonant fast particle-wave interaction

In future fusion devices fast particles must be well confined in order to transfer their energy to the background plasma. Magnetohydrodynamic instabilities like Toroidal Alfv\'en Eigenmodes or core-localized modes such as Beta Induced Alfv\'en Eigenmodes and Reversed Shear Alfv\'en Eigenmodes, both driven by fast particles, can lead to significant losses. This is observed in many ASDEX Upgrade discharges. The present study applies the drift-kinetic HAGIS code with the aim of understanding the underlying resonance mechanisms, especially in the presence of multiple modes with different frequencies. Of particular interest is the resonant interaction of particles simultaneously with two different modes, referred to as 'double-resonance'. Various mode overlapping scenarios with different q profiles are considered. It is found that, depending on the radial mode distance, double-resonance is able to enhance growth rates as well as mode amplitudes significantly. Surprisingly, no radial mode overlap is necessary for this effect. Quite the contrary is found: small radial mode distances can lead to strong nonlinear mode stabilization of a linearly dominant mode.Comment: 12 pages, 11 figures; Nuclear Fusion 52 (2012

Genetic parameters of ovarian and uterine reproductive traits in dairy cows

peer-reviewedThe objective of the study was to estimate genetic parameters of detailed reproductive traits derived from ultrasound examination of the reproductive tract as well as their genetic correlations with traditional reproductive traits. A total of 226,141 calving and insemination records as well as 74,134 ultrasound records from Irish dairy cows were used. Traditional reproductive traits included postpartum interval to first service, conception, and next calving, as well as the interval from first to last service; number of inseminations, pregnancy rate to first service, pregnant within 42 d of the herd breeding season, and submission in the first 21 d of the herd breeding season were also available. Detailed reproductive traits included resumed cyclicity at the time of ultrasound examination, incidence of multiple ovulations, incidence of early postpartum ovulation, heat detection, ovarian cystic structures, embryo loss, and uterine score; the latter was a subjectively assessed on a scale of 1 (little fluid with normal uterine tone) to 4 (large quantity of fluid with a flaccid uterine tone). Variance (and covariance) components were estimated using repeatability animal linear mixed models. Heritability for all reproductive traits were generally low (0.001–0.05), with the exception of traits related to cyclicity postpartum, regardless if defined traditionally (0.07; calving to first service) or from ultrasound examination [resumed cyclicity at the time of examination (0.07) or early postpartum ovulation (0.10)]. The genetic correlations among the detailed reproductive traits were generally favorable. The exception was the genetic correlation (0.29) between resumed cyclicity and uterine score; superior genetic merit for cyclicity postpartum was associated with inferior uterine score. Superior genetic merit for most traditional reproductive traits was associated with superior genetic merit for resumed cyclicity (genetic correlations ranged from −0.59 to −0.36 and from 0.56 to 0.70) and uterine score (genetic correlations ranged from −0.47 to 0.32 and from 0.25 to 0.52). Genetic predisposition to an increased incidence of embryo loss was associated with both an inferior uterine score (0.24) and inferior genetic merit for traditional reproductive traits (genetic correlations ranged from −0.52 to −0.42 and from 0.33 to 0.80). The results from the present study indicate that selection based on traditional reproductive traits, such as calving interval or days open, resulted in improved genetic merit of all the detailed reproductive traits evaluated in this study. Additionally, greater accuracy of selection for calving interval is expected for a relatively small progeny group size when detailed reproductive traits are included in a multitrait genetic evaluation

Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcripts

An EST database has been generated for coffee based on sequences from approximately 47,000 cDNA clones derived from five different stages/tissues, with a special focus on developing seeds. When computationally assembled, these sequences correspond to 13,175 unigenes, which were analyzed with respect to functional annotation, expression profile and evolution. Compared with Arabidopsis, the coffee unigenes encode a higher proportion of proteins related to protein modification/turnover and metabolism—an observation that may explain the high diversity of metabolites found in coffee and related species. Several gene families were found to be either expanded or unique to coffee when compared with Arabidopsis. A high proportion of these families encode proteins assigned to functions related to disease resistance. Such families may have expanded and evolved rapidly under the intense pathogen pressure experienced by a tropical, perennial species like coffee. Finally, the coffee gene repertoire was compared with that of Arabidopsis and Solanaceous species (e.g. tomato). Unlike Arabidopsis, tomato has a nearly perfect gene-for-gene match with coffee. These results are consistent with the facts that coffee and tomato have a similar genome size, chromosome karyotype (tomato, n=12; coffee n=11) and chromosome architecture. Moreover, both belong to the Asterid I clade of dicot plant families. Thus, the biology of coffee (family Rubiacaeae) and tomato (family Solanaceae) may be united into one common network of shared discoveries, resources and information

Genomic regions associated with muscularity in beef cattle differ in five contrasting cattle breeds

peer-reviewedBackground Linear type traits, which reflect the muscular characteristics of an animal, could provide insight into how, in some cases, morphologically very different animals can yield the same carcass weight. Such variability may contribute to differences in the overall value of the carcass since primal cuts vary greatly in price; such variability may also hinder successful genome-based association studies. Therefore, the objective of our study was to identify genomic regions that are associated with five muscularity linear type traits and to determine if these significant regions are common across five different breeds. Analyses were carried out using linear mixed models on imputed whole-genome sequence data in each of the five breeds, separately. Then, the results of the within-breed analyses were used to conduct an across-breed meta-analysis per trait. Results We identified many quantitative trait loci (QTL) that are located across the whole genome and associated with each trait in each breed. The only commonality among the breeds and traits was a large-effect pleiotropic QTL on BTA2 that contained the MSTN gene, which was associated with all traits in the Charolais and Limousin breeds. Other plausible candidate genes were identified for muscularity traits including PDE1A, PPP1R1C and multiple collagen and HOXD genes. In addition, associated (gene ontology) GO terms and KEGG pathways tended to differ between breeds and between traits especially in the numerically smaller populations of Angus, Hereford, and Simmental breeds. Most of the SNPs that were associated with any of the traits were intergenic or intronic SNPs located within regulatory regions of the genome. Conclusions The commonality between the Charolais and Limousin breeds indicates that the genetic architecture of the muscularity traits may be similar in these breeds due to their similar origins. Conversely, there were vast differences in the QTL associated with muscularity in Angus, Hereford, and Simmental. Knowledge of these differences in genetic architecture between breeds is useful to develop accurate genomic prediction equations that can operate effectively across breeds. Overall, the associated QTL differed according to trait, which suggests that breeding for a morphologically different (e.g. longer and wider versus shorter and smaller) more efficient animal may become possible in the future

The organic geochemistry of ancient sediments, part II

Chemical analysis of sediment and oil hydrocarbon content by gas chromatography and mass spectrometry to establish inception period of bio-organic evolutio

Genomic Regions Associated With Skeletal Type Traits in Beef and Dairy Cattle Are Common to Regions Associated With Carcass Traits, Feed Intake and Calving Difficulty

Linear type traits describing the skeletal characteristics of an animal are moderately to strongly genetically correlated with a range of other performance traits in cattle including feed intake, reproduction traits and carcass merit; thus, type traits could also provide useful insights into the morphological differences among animals underpinning phenotypic differences in these complex traits. The objective of the present study was to identify genomic regions associated with five subjectively scored skeletal linear traits, to determine if these associated regions are common in multiple beef and dairy breeds, and also to determine if these regions overlap with those proposed elsewhere to be associated with correlated performance traits. Analyses were carried out using linear mixed models on imputed whole genome sequence data separately in 1,444 Angus, 1,129 Hereford, 6,433 Charolais, 8,745 Limousin, 1,698 Simmental, and 4,494 Holstein-Friesian cattle, all scored for the linear type traits. There was, on average, 18 months difference in age at assessment of the beef versus the dairy animals. While the majority of the identified quantitative trait loci (QTL), and thus genes, were both trait-specific and breed-specific, a large-effect pleiotropic QTL on BTA6 containing the NCAPG and LCORL genes was associated with all skeletal traits in the Limousin population and with wither height in the Angus. Other than that, little overlap existed in detected QTLs for the skeletal type traits in the other breeds. Only two QTLs overlapped the beef and dairy breeds; both QTLs were located on BTA5 and were associated with height in both the Angus and the Holstein-Friesian, despite the difference in age at assessment. Several detected QTLs in the present study overlapped with QTLs documented elsewhere that are associated with carcass traits, feed intake, and calving difficulty. While most breeding programs select for the macro-traits like carcass weight, carcass conformation, and feed intake, the higher degree of granularity with selection on the individual linear type traits in a multi-trait index underpinning the macro-level goal traits, presents an opportunity to help resolve genetic antagonisms among morphological traits in the pursuit of the animal with optimum performance metrics.</p