Non-additive QTL mapping of lactation traits in 124,000 cattle reveals novel recessive loci.

BACKGROUND: Deleterious recessive conditions have been primarily studied in the context of Mendelian diseases. Recently, several deleterious recessive mutations with large effects were discovered via non-additive genome-wide association studies (GWAS) of quantitative growth and developmental traits in cattle, which showed that quantitative traits can be used as proxies of genetic disorders when such traits are indicative of whole-animal health status. We reasoned that lactation traits in cattle might also reflect genetic disorders, given the increased energy demands of lactation and the substantial stresses imposed on the animal. In this study, we screened more than 124,000 cows for recessive effects based on lactation traits. RESULTS: We discovered five novel quantitative trait loci (QTL) that are associated with large recessive impacts on three milk yield traits, with these loci presenting missense variants in the DOCK8, IL4R, KIAA0556, and SLC25A4 genes or premature stop variants in the ITGAL, LRCH4, and RBM34 genes, as candidate causal mutations. For two milk composition traits, we identified several previously reported additive QTL that display small dominance effects. By contrasting results from milk yield and milk composition phenotypes, we note differing genetic architectures. Compared to milk composition phenotypes, milk yield phenotypes had lower heritabilities and were associated with fewer additive QTL but had a higher non-additive genetic variance and were associated with a higher proportion of loci exhibiting dominance. CONCLUSIONS: We identified large-effect recessive QTL which are segregating at surprisingly high frequencies in cattle. We speculate that the differences in genetic architecture between milk yield and milk composition phenotypes derive from underlying dissimilarities in the cellular and molecular representation of these traits, with yield phenotypes acting as a better proxy of underlying biological disorders through presentation of a larger number of major recessive impacts.

Comparison of the genetic characteristics of directly measured and Fourier-transform mid-infrared-predicted bovine milk fatty acids and proteins.

Fourier-transform mid-infrared (FT-MIR) spectroscopy is a high-throughput and inexpensive methodology used to evaluate concentrations of fat and protein in dairy cattle milk samples. The objective of this study was to compare the genetic characteristics of FT-MIR predicted fatty acids and individual milk proteins with those that had been measured directly using gas and liquid chromatography methods. The data used in this study was based on 2,005 milk samples collected from 706 Holstein-Friesian × Jersey animals that were managed in a seasonal, pasture-based dairy system, with milk samples collected across 2 consecutive seasons. Concentrations of fatty acids and protein fractions in milk samples were directly determined by gas chromatography and high-performance liquid chromatography, respectively. Models to predict each directly measured trait based on FT-MIR spectra were developed using partial least squares regression, with spectra from a random selection of half the cows used to train the models, and predictions for the remaining cows used as validation. Variance parameters for each trait and genetic correlations for each pair of measured/predicted traits were estimated from pedigree-based bivariate models using REML procedures. A genome-wide association study was undertaken using imputed whole-genome sequence, and quantitative trait loci (QTL) from directly measured traits were compared with QTL from the corresponding FT-MIR predicted traits. Cross-validation prediction accuracies based on partial least squares for individual and grouped fatty acids ranged from 0.18 to 0.65. Trait prediction accuracies in cross-validation for protein fractions were 0.53, 0.19, and 0.48 for α-casein, ß-casein, and κ-casein, 0.31 for α-lactalbumin, 0.68 for ß-lactoglobulin, and 0.36 for lactoferrin. Heritability estimates for directly measured traits ranged from 0.07 to 0.55 for fatty acids; and from 0.14 to 0.63 for individual milk proteins. For FT-MIR predicted traits, heritability estimates were mostly higher than for the corresponding measured traits, ranging from 0.14 to 0.46 for fatty acids, and from 0.30 to 0.70 for individual proteins. Genetic correlations between directly measured and FT-MIR predicted protein fractions were consistently above 0.75, with the exceptions of C18:0 and C18:3 cis-3, which had genetic correlations of 0.72 and 0.74, respectively. The GWAS identified trait QTL for fatty acids with likely candidates in the DGAT1, CCDC57, SCD, and GPAT4 genes. Notably, QTL for SCD were largely absent in the FT-MIR predicted traits, and QTL for GPAT4 were absent in directly measured traits. Similarly, for directly measured individual proteins, we identified QTL with likely candidates in the CSN1S1, CSN3, PAEP, and LTF genes, but the QTL for CSN3 and LTF were absent in the FT-MIR predicted traits. Our study indicates that genetic correlations between directly measured and FT-MIR predicted fatty acid and protein fractions are typically high, but that phenotypic variation in these traits may be underpinned by differing genetic architecture.

Sequence-based genome-wide association study of individual milk mid-infrared wavenumbers in mixed-breed dairy cattle.

BACKGROUND: Fourier-transform mid-infrared (FT-MIR) spectroscopy provides a high-throughput and inexpensive method for predicting milk composition and other novel traits from milk samples. While there have been many genome-wide association studies (GWAS) conducted on FT-MIR predicted traits, there have been few GWAS for individual FT-MIR wavenumbers. Using imputed whole-genome sequence for 38,085 mixed-breed New Zealand dairy cattle, we conducted GWAS on 895 individual FT-MIR wavenumber phenotypes, and assessed the value of these direct phenotypes for identifying candidate causal genes and variants, and improving our understanding of the physico-chemical properties of milk. RESULTS: Separate GWAS conducted for each of 895 individual FT-MIR wavenumber phenotypes, identified 450 1-Mbp genomic regions with significant FT-MIR wavenumber QTL, compared to 246 1-Mbp genomic regions with QTL identified for FT-MIR predicted milk composition traits. Use of mammary RNA-seq data and gene annotation information identified 38 co-localized and co-segregating expression QTL (eQTL), and 31 protein-sequence mutations for FT-MIR wavenumber phenotypes, the latter including a null mutation in the ABO gene that has a potential role in changing milk oligosaccharide profiles. For the candidate causative genes implicated in these analyses, we examined the strength of association between relevant loci and each wavenumber across the mid-infrared spectrum. This revealed shared association patterns for groups of genomically-distant loci, highlighting clusters of loci linked through their biological roles in lactation and their presumed impacts on the chemical composition of milk. CONCLUSIONS: This study demonstrates the utility of FT-MIR wavenumber phenotypes for improving our understanding of milk composition, presenting a larger number of QTL and putative causative genes and variants than found from FT-MIR predicted composition traits. Examining patterns of significance across the mid-infrared spectrum for loci of interest further highlighted commonalities of association, which likely reflects the physico-chemical properties of milk constituents.

An integrative review of the evidence for Shinrin-Yoku (Forest Bathing) in the management of depression and its potential clinical application in evidence-based osteopathy.

There is growing interest in the idea of integrating Nature Therapies into the multidisciplinary management of complex conditions such as depression. Shinrin-Yoku (Forest Bathing), a practice involving spending time in a forested environment while paying attention to multi-sensory stimuli has been proposed as one such modality. The objectives of this review were to critically analyse the current evidence base on the efficacy of Shinrin-Yoku for the treatment of depression, and to examine how the findings may reflect and/or inform osteopathic principles and clinical practice. An integrative review of the evidence for Shinrin-Yoku in the management of depression published between 2009 and 2019 was conducted resulting in n = 13 peer-reviewed studies meeting inclusion criteria. Two themes emerged from the literature, the positive effect of Shinrin-Yoku on self-reported mood scores, and physiological changes arising from forest exposure. However, the methodological quality of the evidence is poor and experiments may not be generalisable. Suggestions were made for improving the research base via mixed-method studies in a biopsychosocial framework, and aspects of the research which may be applicable to evidence-based osteopathy were noted.

On the Application of Vickers Micro Hardness Testing to Isotactic Polypropylene.

Hardness is a useful measure of a material's resistance to permanent indentation; but for viscoelastic polymers, hardness data are highly dependent on the test type and the parameter set chosen. Vickers microhardness testing is used to leave small indents (<150 µm) and is shown to be applicable to polymers. A detailed investigation of the required steps for microhardness testing in isotactic polypropylene (iPP) is provided. Samples should be mounted in epoxy resin in order to maintain curing temperatures at room temperature. Mounted samples can be ground and polished in a semi-automatic polisher using graduated SiC paper (wet grinding) but progressing onto alumina suspension for polishing. Final polishing should be performed with 0.05-µm alumina suspension. The hardness measured was shown to be dependent on load and dwell time with a much greater dependency on dwell time. Strain recovery was shown to be completed after a time period equal to the dwell time. This study shows that indents can be measured thereafter, and it is recommended that they be measured within a 24 h period after the indent was created. After data fitting, the equation for hardness was shown to follow a power law with load and dwell time as the main variables. Fitting parameters were compared to those found in the literature, and it was found that parameters were significantly different to those reported elsewhere. Therefore, this study highlights the importance of calibrating on a case-by-case basis. Finally, to show the usefulness of the Vickers micro-hardness testing method, the calibrated test method was applied on iPP with additions of carbon black up to 3 wt.%. Comparisons were made with data from the literature, but the hardness data generated in our work were found to be at least twice that reported in the literature. The testing parameters were not cited in the literature: specifically, the dwell time was not provided, and this generated doubt on the usefulness of the cited data. Hence, this work is intended to serve as an exemplar of how to prepare and proceed with hardness testing of polymers.

Laser Transmission Welding of Semi-Crystalline Polymers and Their Composites: A Critical Review.

The present review provides an overview of the current status and future perspectives of one of the smart manufacturing techniques of Industry 4.0, laser transmission welding (LTW) of semi-crystalline (SC) polymers and their composites. It is one of the most versatile techniques used to join polymeric components with varying thickness and configuration using a laser source. This article focuses on various parameters and phenomena such as inter-diffusion and microstructural changes that occur due to the laser interaction with SC polymers (specifically polypropylene). The effect of carbon black (size, shape, structure, thermal conductivity, dispersion, distribution, etc.) in the laser absorptive part and nucleating agent in the laser transmissive part and its processing conditions impacting the weld strength is discussed in detail. Among the laser parameters, laser power, scanning speed and clamping pressure are considered to be the most critical. This review also highlights innovative ideas such as incorporating metal as an absorber in the laser absorptive part, hybrid carbon black, dual clamping device, and an increasing number of scans and patterns. Finally, there is presented an overview of the essential characterisation techniques that help to determine the weld quality. This review demonstrates that LTW has excellent potential in polymer joining applications and the challenges including the cost-effectiveness, innovative ideas to provide state-of-the-art design and fabrication of complex products in a wide range of applications. This work will be of keen interest to other researchers and practitioners who are involved in the welding of polymers.

The Direct 3D Printing of Functional PEEK/Hydroxyapatite Composites via a Fused Filament Fabrication Approach.

The manufacture of polyetheretherketone/hydroxyapatite (PEEK/HA) composites is seen as a viable approach to help enhance direct bone apposition in orthopaedic implants. A range of methods have been used to produce composites, including Selective Laser Sintering and injection moulding. Such techniques have drawbacks and lack flexibility to manufacture complex, custom-designed implants. 3D printing gets around many of the restraints and provides new opportunities for innovative solutions that are structurally suited to meet the needs of the patient. This work reports the direct 3D printing of extruded PEEK/HA composite filaments via a Fused Filament Fabrication (FFF) approach. In this work samples are 3D printed by a custom modified commercial printer Ultimaker 2+ (UM2+). SEM-EDX and µCT analyses show that HA particles are evenly distributed throughout the bulk and across the surface of the native 3D printed samples, with XRD highlighting up to 50% crystallinity and crystalline domains clearly observed in SEM and HR-TEM analyses. This highlights the favourable temperature conditions during 3D printing. The yield stress and ultimate tensile strength obtained for all the samples are comparable to human femoral cortical bone. The results show how FFF 3D printing of PEEK/HA composites up to 30 wt% HA can be achieved.

Non-additive association analysis using proxy phenotypes identifies novel cattle syndromes.

Mammalian species carry ~100 loss-of-function variants per individual1,2, where ~1-5 of these impact essential genes and cause embryonic lethality or severe disease when homozygous3. The functions of the remainder are more difficult to resolve, although the assumption is that these variants impact fitness in less manifest ways. Here we report one of the largest sequence-resolution screens of cattle to date, targeting discovery and validation of non-additive effects in 130,725 animals. We highlight six novel recessive loci with impacts generally exceeding the largest-effect variants identified from additive genome-wide association studies, presenting analogs of human diseases and hitherto-unrecognized disorders. These loci present compelling missense (PLCD4, MTRF1 and DPF2), premature stop (MUS81) and splice-disrupting (GALNT2 and FGD4) mutations, together explaining substantial proportions of inbreeding depression. These results demonstrate that the frequency distribution of deleterious alleles segregating in selected species can afford sufficient power to directly map novel disorders, presenting selection opportunities to minimize the incidence of genetic disease.

Osteoblasts response to microstructured and nanostructured polyimide film, processed by the use of silica bead microlenses.

The surface of polyimide films was modified by the use of silica microspheres as microlenses to focus radiation emitted by an excimer laser. The resultant surface had both microstructures and nanostructures. Physical and chemical characterization was performed by atomic force and Fourier transform-infrared microscopy. Laser processing resulted in surfaces that had similar roughness but different component frequencies. Chemical changes were not observed with the techniques used. The response of osteoblasts to the surface was assayed by measuring their metabolic activity and the enzyme alkaline phosphatase activity, after 24 hours of growth. Cytoskeleton and expression were both investigated. Metabolic activity was similar on treated and untreated samples. Total cell number and size were increased on microstructured polymer, where specific structures were observed (protrusions). Adhesion was noted, and the actin cytoskeleton showed normal morphology. Cells on nanostructured samples had a diffuse actin network and less mature adhesions as compared with the control. FROM THE CLINICAL EDITOR: Polyimide films with microstructure and nanostructure surface elements were studied from the standpoint of osteoblast response. Total cell number and size were increased on microstructured polymer and protrusions were also observed. Adhesion was noted and the actin cytoskeleton exhibited normal morphology. Cells on nanostructured samples had a diffuse actin network and less mature adhesions.

Understanding turbulent free-surface vortex flows using a Taylor-Couette flow analogy.

Free-surface vortices have long been studied to develop an understanding of similar rotating flow phenomena observed in nature and technology. However, a complete description of its turbulent three-dimensional flow field still remains elusive. In contrast, the related Taylor-Couette flow system has been well explicated which classically exhibits successive instability phases manifested in so-called Taylor vortices. In this study, observations made on the turbulent free-surface vortex revealed distinguishable, time-dependent "Taylor-like" vortices in the secondary flow field similar to the Taylor-Couette flow system. The observations were enabled by an original application of 2D ultrasonic Doppler velocity profiling complemented with laser induced fluorescence dye observations. Additional confirmation was provided by three-dimensional numerical simulations. Using Rayleigh's stability criterion, we analytically show that a wall bounded free-surface vortex can indeed become unstable due to a centrifugal driving force in a similar manner to the Taylor-Couette flow. Consequently, it is proposed that the free-surface vortex can be treated analogously to the Taylor-Couette flow permitting advanced conclusions to be drawn on its flow structure and the various states of free-surface vortex flow stability.

Sequence-based Association Analysis Reveals an MGST1 eQTL with Pleiotropic Effects on Bovine Milk Composition.

The mammary gland is a prolific lipogenic organ, synthesising copious amounts of triglycerides for secretion into milk. The fat content of milk varies widely both between and within species, and recent independent genome-wide association studies have highlighted a milk fat percentage quantitative trait locus (QTL) of large effect on bovine chromosome 5. Although both EPS8 and MGST1 have been proposed to underlie these signals, the causative status of these genes has not been functionally confirmed. To investigate this QTL in detail, we report genome sequence-based imputation and association mapping in a population of 64,244 taurine cattle. This analysis reveals a cluster of 17 non-coding variants spanning MGST1 that are highly associated with milk fat percentage, and a range of other milk composition traits. Further, we exploit a high-depth mammary RNA sequence dataset to conduct expression QTL (eQTL) mapping in 375 lactating cows, revealing a strong MGST1 eQTL underpinning these effects. These data demonstrate the utility of DNA and RNA sequence-based association mapping, and implicate MGST1, a gene with no obvious mechanistic relationship to milk composition regulation, as causally involved in these processes.

Functionally reciprocal mutations of the prolactin signalling pathway define hairy and slick cattle.

Lactation, hair development and homeothermy are characteristic evolutionary features that define mammals from other vertebrate species. Here we describe the discovery of two autosomal dominant mutations with antagonistic, pleiotropic effects on all three of these biological processes, mediated through the prolactin signalling pathway. Most conspicuously, mutations in prolactin (PRL) and its receptor (PRLR) have an impact on thermoregulation and hair morphology phenotypes, giving prominence to this pathway outside of its classical roles in lactation.

Effect of functionalized micropatterned PLGA on guided neurite growth.

When coaptation is not possible in the repair of nerve injuries, a bridge of biomaterial scaffold provides a structural support for neuronal cell growth and guides nerve regeneration. Poly(lactide-co-glycolide) (PLGA) scaffolds have been widely investigated for neural tissue engineering applications. In order to investigate guided neurite growth, we have fabricated micropatterns on PLGA films using laser ablation methods. The micropatterned PLGA films were coated with collagen type I or laminin peptide (PPFLMLLKGSTR) to promote axon growth. Micropatterned PLGA films provide a guidance effect on both early stage neurite outgrowth and elongation. Small (5 microm) grooves showed more statistically significant parallel neurite growth compared with larger size grooves (10 microm). Micropatterned PLGA films coated with laminin peptide showed more parallel neurite growth compared with those coated with collagen type I. Primary neurite number and total neurite length per cell decreased on micropatterned PLGA films compared with the controls. Neurites showed a preference for growth in the microgrooves rather than on the spaces. This study indicates that surface micropatterned structures with conjugated functional molecules can be used to guide neurite growth.

Religiosity as a public good.

Public Goods can be seen as one important way in which societies sustain themselves over time. These are part of the puzzle of the development of political order. Public goods like the rule of law are non-substractable and non-excludable . For economists the classic textbook examples are national defense and police protection. In this paper I argue that religiosity can function like police protection, a means of sustaining order through fear of punishment from a transcendent source. As a means of reducing defection from social norms it has a role to play as a public good. But religion cannot at the same time be seen as the source of such norms or dissention will undermine the very order that punishment seems to reinforce.

Comparison of cell interactions with laser machined micron- and nanoscale features in polymer.

Control of cell responses to artificial surfaces is a research goal for much of the biomaterials community. The role that the micron scale topography of a surface can play in controlling cell responses has been well documented and recent advances in nanofabrication techniques have lead to an interest in cells' responses to submicron-scale surface features. The study described here compares the relative influences that nanoscale and micron-scale features exert on cells by examining cytoskeletal organisation. Micron-scale structures were generated on the polyamide Kapton using a 193 nm ArF Excimer laser, at 400 mJ/cm2 fluence. Nanoscale features were generated on Kapton using the excimer laser with a phase mask. Osteoblasts were seeded onto surfaces for 24 h, then the cell membranes were detergent-extracted, and the cells were applied with a primary antibody to actin and a colloidal gold-conjugated secondary antibody. Samples to be examined using the confocal were mounted in glycerol, those for electron microscopy were carbon-coated. The organisation of actin was examined on micron- and nano-scale structures by scoring sections for order of branching and angles of branching to relate changes in the cytoskeleton relative to the control. Although there was a strong influence of micron-scale structures, the cytoskeleton of cells on the nanoscale structures were similar to the controls.