Direct observation of the coherent nuclear response after the absorption of a photon

How molecules convert light energy to perform a specific transformation is a fundamental question in photophysics. Ultrafast spectroscopy reveals the kinetics associated with electronic energy flow, but little is known about how absorbed photon energy drives nuclear or electronic motion. Here, we used ultrabroadband transient absorption spectroscopy to monitor coherent vibrational energy flow after photoexcitation of the retinal chromophore. In the proton pump bacteriorhodopsin we observed coherent activation of hydrogen wagging and backbone torsional modes that were replaced by unreactive coordinates in the solution environment, concomitant with a deactivation of the reactive relaxation pathway

Genome-Wide Association Study of Feed Efficiency in Beef Cattle

Feed costs comprise the majority of beef production costs and feed intake has long been recognized as an economically relevant trait for beef cattle. Residual feed intake (RFI) is a function of feed intake and performance and reflects whether animals eat more or less than expected for a given level of production. The objectives of this study were to map quantitative trait loci (QTL) associated with feedlot RFI in 4 different beef cattle populations. A total of 13 significant QTL over 10 different chromosomes were detected. The identified QTL had no overlap across 4 beef cattle populations reflecting different genetic makeup of RFI across different beef populations. Further genotyping and statistical analyses are needed to find the casual mutations. Once found, knowledge of such mutations would create new opportunities for the selection of more efficient animals

Modeling Battery Performance Due To Volume Change In Porous Electrodes Due To Intercalation

The demand for energy continues to increase as the economies of developing countries become more modern and show an increased need for a reliable energy infrastructure in order to meet the increased demand associated with a large and more mobile population. An increased demand puts a strain on all sectors, however it is specifically noticeable in the transportation sector where a significant portion of the fuel utilized for transportation comes from petroleum and other fossil fuels. Recently, using alternative forms of energy for transportation has become reality, and in turn, using electricity as a transportation fuel has gained significant momentum, specifically for use in battery-only rechargeable vehicles. Significant strides have been made to improve the range, cost, and fueling times of these battery-only vehicles through the improvement of the design and control of cells, and several automobile manufacturers are releasing battery powered vehicles with price points that target the general public. New materials have also been examined in order to increase the energy densities of these batteries in order to increase the range of battery powered vehicles, and decrease the volume displacement in the vehicle powertrain. Some of the new battery electrode materials see significant expansion during cycling, which results in stress linked to capacity fade, battery failure, separator deformation, and electrolyte degradation. In order to accurately predict the behavior of complicated electrochemical devices undergoing a variety of different structural and electrochemical changes, sophisticated models that take into consideration transport processes, electrochemical phenomena, mechanical stresses, and structural deformations must be developed in order to predict the associated effects on the operation of an electrochemical system. There are many models in the literature that can predict the electrochemical performance of devices with porous electrodes under a variety of operating and design conditions, however, in many of these models, when the porosity of the porous electrode is accounted for it is assumed to be a function of current density, since the volume changes seen during the intercalation reaction can be small. However, electrodes that have been developed in recent years show battery systems that have significant volume changes during intercalation. The battery model developed here incorporates aspects of a porous electrode model that accounts for the stresses that build up in porous electrodes due to volume change in the active material. The material balances here are coupled to stress-strain relationships that are derived from rock mechanics, in which the deformation of the porous rock occurs during thermal expansion similar to the deformation of the porous electrode that occurs during intercalation. This allows for a prediction of dimensional changes and porosity changes in a porous electrode and the associated effect on battery performance

Impact of Pedigree Information and Genome Assembly Errors on Inference of SNP Haplotypes in Cattle

The impact of pedigree information and SNP location determined from either the UMD3.1 genome sequence assembly or the USDA-AIPL map on phasing accuracy were evaluated for 2 chromosomes in 2,778 parent verified Angus sire/offspring pairs. DAGPHASE (Druet and Georges, 2010), using a single generation pedigree was superior to BEAGLE software (Browning and Browning, 2007) for phasing. Results based on USDA-AIPL map are closer to expectation than those based on UMD3.1, but the difference is not significant. Recombination hotspots weredetected near 4 and 82Mb on BTA14, and near 25Mb on BTA15

Identifying Chromosomal Recombinations in Beef Cattle from Genotyped Parent-Offspring Pairs

This study investigated meiotic recombination in two breeds of cattle by comparing phased SNP haplotypes in sire-offspring pairs. The positions and number of recombination events were identified. The number of recombination events varies between individuals and is a heritable trait. A genome-wide association analysis identified quantitative trait loci (QTL) associated with variation in the number of recombination events. Regions that had more recombination events than expected were identified in both breeds, and many of these hotspots were in common. Recombination is important biologically because it is the mechanism for reassembling paternal and maternal alleles. Recombination impacts the accuracy of imputation, a commonly-used approach to infer the genotypes of some individuals based on genotypes of others

Characterization of the F94L Double Muscling Mutation in Pure- and Crossbred Limousin Animals

The objective of this study was to investigate the nature of the effect of the F94L variant in the myostatin (MSTN) gene on economic traits in Limousin and Limousin-Angus crossbred animals in the context of genomic analyses using Illumina BovineSNP50 Bead chip genotypes

Accuracy of direct genomic breeding values for nationally evaluated traits in US Limousin and Simmental beef cattle

BACKGROUND: In national evaluations, direct genomic breeding values can be considered as correlated traits to those for which phenotypes are available for traditional estimation of breeding values. For this purpose, estimates of the accuracy of direct genomic breeding values expressed as genetic correlations between traits and their respective direct genomic breeding values are required. METHODS: We derived direct genomic breeding values for 2239 registered Limousin and 2703 registered Simmental beef cattle genotyped with either the Illumina BovineSNP50 BeadChip or the Illumina BovineHD BeadChip. For the 264 Simmental animals that were genotyped with the BovineHD BeadChip, genotypes for markers present on the BovineSNP50 BeadChip were extracted. Deregressed estimated breeding values were used as observations in weighted analyses that estimated marker effects to derive direct genomic breeding values for each breed. For each breed, genotyped individuals were clustered into five groups using K-means clustering, with the aim of increasing within-group and decreasing between-group pedigree relationships. Cross-validation was performed five times for each breed, using four groups for training and the fifth group for validation. For each trait, we then applied a weighted bivariate analysis of the direct genomic breeding values of genotyped animals from all five validation sets and their corresponding deregressed estimated breeding values to estimate variance and covariance components. RESULTS: After minimizing relationships between training and validation groups, estimated genetic correlations between each trait and its direct genomic breeding values ranged from 0.39 to 0.76 in Limousin and from 0.29 to 0.65 in Simmental. The efficiency of selection based on direct genomic breeding values relative to selection based on parent average information ranged from 0.68 to 1.28 in genotyped Limousin and from 0.51 to 1.44 in genotyped Simmental animals. The efficiencies were higher for 323 non-genotyped young Simmental animals, born after January 2012, and ranged from 0.60 to 2.04. CONCLUSIONS: Direct genomic breeding values show promise for routine use by Limousin and Simmental breeders to improve the accuracy of predicted genetic merit of their animals at a young age and increase response to selection. Benefits from selecting on direct genomic breeding values are greater for breeders who use natural mating sires in their herds than for those who use artificial insemination sires. Producers with unregistered commercial Limousin and Simmental cattle could also benefit from being able to identify genetically superior animals in their herds, an opportunity that has in the past been limited to seed stock animals

Biosimilar infliximab use in paediatric IBD

Background Biosimilar infliximab became available in the UK in 2015. Paediatric experience to date on its use is limited. We prospectively evaluated the safety and efficacy of biosimilar infliximab (Remsima) in two paediatric gastroenterology networks in patients with inflammatory bowel disease. Methods Prospective clinical data were collected from laboratory reports, electronic patient records and case notes of 40 patients starting Remsima for the first time. Disease activity scores together with blood and stool biomarkers were used to assess response. Results Our data set highlights that Remsima was associated with a significant clinical and biochemical improvement (p<0.01 or less for all parameters assessed) in Crohn’s disease post induction. There were no significant safety issues noted. The total cost saving was £47 800, representing a 38% reduction from originator. Conclusion We found that biosimilar infliximab is as effective as originator infliximab and its use is associated with significant cost savings

Community-wide correlations between species richness, abundance and population genomic diversity in a freshwater biodiversity hotspot

Understanding patterns of diversity across macro (e.g. species-level) and micro (e.g. molecular-level) scales can shed light on community function and stability by elucidating the abiotic and biotic drivers of diversity within ecological communities. We examined the relationships among taxonomic and genetic metrics of diversity in freshwater mussels (Bivalvia: Unionidae), an ecologically important and species-rich group in the southeastern United States. Using quantitative community surveys and reduced-representation genome sequencing across 22 sites in seven rivers and two river basins, we surveyed 68 mussel species and sequenced 23 of these species to characterize intrapopulation genetic variation. We tested for the presence of species diversity–abundance correlations (i.e. the more-individuals hypothesis, MIH), species-genetic diversity correlations (SGDCs) and abundance-genetic diversity correlations (AGDCs) across all sites to evaluate relationships between different metrics of diversity. Sites with greater cumulative multispecies density (a standardized metric of abundance) had a greater number of species, consistent with the MIH hypothesis. Intrapopulation genetic diversity was strongly associated with the density of most species, indicating the presence of AGDCs. However, there was no consistent evidence for SGDCs. Although sites with greater overall densities of mussels had greater species richness, sites with higher genetic diversity did not always exhibit positive correlations with species richness, suggesting that there are spatial and evolutionary scales at which the processes influencing community-level diversity and intraspecific diversity differ. Our work reveals the importance of local abundance as indicator (and possibly a driver) of intrapopulation genetic diversity