Genotype imputation for the prediction of genomic breeding values in non-genotyped and low-density genotyped individuals

<p>Abstract</p> <p>Background</p> <p>There is wide interest in calculating genomic breeding values (GEBVs) in livestock using dense, genome-wide SNP data. The general framework for genomic selection assumes all individuals are genotyped at high-density, which may not be true in practice. Methods to add additional genotypes for individuals not genotyped at high density have the potential to increase GEBV accuracy with little or no additional cost. In this study a long haplotype library was created using a long range phasing algorithm and used in combination with segregation analysis to impute dense genotypes for non-genotyped dams in the training dataset (S1) and for non-genotyped or low-density genotyped individuals in the prediction dataset (S2), using the 14^th QTL-MAS Workshop dataset. Alternative low-density scenarios were evaluated for accuracy of imputed genotypes and prediction of GEBVs.</p> <p>Results</p> <p>In S1, females in the training population were not genotyped and prediction individuals were either not genotyped or genotyped at low-density (evenly spaced at 2, 5 or 10 Mb). The proportion of correctly imputed genotypes for training females did not change when genotypes were added for individuals in the prediction set whereas the number of correctly imputed genotypes in the prediction set increased slightly (S1). The S2 scenario assumed the complete training set was genotyped for all SNPs and the prediction set was not genotyped or genotyped at low-density. The number of correctly imputed genotypes increased with genotyping density in the prediction set. Accuracy of genomic breeding values for the prediction set in each scenario were the correlation of GEBVs with true breeding values and were used to evaluate the potential loss in accuracy with reduced genotyping. For both S1 and S2 the GEBV accuracies were similar when the prediction set was not genotyped and increased with the addition of low-density genotypes, with the increase larger for S2 than S1.</p> <p>Conclusions</p> <p>Genotype imputation using a long haplotype library and segregation analysis is promising for application in sparsely-genotyped pedigrees. The results of this study suggest that dense genotypes can be imputed for selection candidates with some loss in genomic breeding value accuracy, but with levels of accuracy higher than traditional BLUP estimated breeding values. Accurate genotype imputation would allow for a single low-density SNP panel to be used across traits.</p

Thermally induced magnetization dynamics of optically excited YIG/Cu/Ni81Fe19 trilayers

This is the final version of the article. Available from American Physical Society via the DOI in this record.The response of Y3Fe5O12/Cu/Ni81Fe19 trilayer structures to excitation by a femtosecond laser pulse has been studied in optical pump-probe experiments and compared with the response of Y3Fe5O12 (YIG) and Ni81Fe19 reference samples. The optical pump induces a partial demagnetization of the Ni81Fe19, a large thermal gradient within the YIG, and temperature differences across the interfaces within the sample stack. When a moderate magnetic field is applied close to normal to the sample plane, so as to quasialign the YIG magnetization with the field and cant the Ni81Fe19 magnetization from the plane, ultrafast demagnetization initiates precession of the Ni81Fe19 magnetization. The transient temperature profile within the samples has been modeled using a one-dimensional finite-element computational model of heat conduction, while the magnetization dynamics are well described by a macrospin solution of the Landau-Lifshitz-Gilbert equation. The precessional response of the Ni81Fe19 layers within the trilayers and the Ni81Fe19 reference sample are very similar for pump fluences of up to 1.5 mJ/cm2, beyond which irreversible changes to the magnetic properties of the films are observed. These results suggest that the spin Seebeck effect is ineffective in modifying the precessional dynamics of the present YIG/Cu/Ni81Fe19 samples when subject to ultrafast optical excitation.The authors gratefully acknowledge financial support from Engineering and Physical Sciences Research Council Grant No. EP/J018767/1 and an EPSRC CASE award with Dr. D. Williams of Hitachi Cambridge. H.J.M. acknowledges financial support in the form of a scholarship from “The Establishment of Martyrs of Iraq.

A phasing and imputation method for pedigreed populations that results in a single-stage genomic evaluation

<p>Abstract</p> <p>Background</p> <p>Efficient, robust, and accurate genotype imputation algorithms make large-scale application of genomic selection cost effective. An algorithm that imputes alleles or allele probabilities for all animals in the pedigree and for all genotyped single nucleotide polymorphisms (SNP) provides a framework to combine all pedigree, genomic, and phenotypic information into a single-stage genomic evaluation.</p> <p>Methods</p> <p>An algorithm was developed for imputation of genotypes in pedigreed populations that allows imputation for completely ungenotyped animals and for low-density genotyped animals, accommodates a wide variety of pedigree structures for genotyped animals, imputes unmapped SNP, and works for large datasets. The method involves simple phasing rules, long-range phasing and haplotype library imputation and segregation analysis.</p> <p>Results</p> <p>Imputation accuracy was high and computational cost was feasible for datasets with pedigrees of up to 25 000 animals. The resulting single-stage genomic evaluation increased the accuracy of estimated genomic breeding values compared to a scenario in which phenotypes on relatives that were not genotyped were ignored.</p> <p>Conclusions</p> <p>The developed imputation algorithm and software and the resulting single-stage genomic evaluation method provide powerful new ways to exploit imputation and to obtain more accurate genetic evaluations.</p

Correlations of Behavioral Deficits with Brain Pathology Assessed through Longitudinal MRI and Histopathology in the R6/2 Mouse Model of HD

Huntington's disease (HD) is caused by the expansion of a CAG repeat in the huntingtin (HTT) gene. The R6/2 mouse model of HD expresses a mutant version of exon 1 HTT and develops motor and cognitive impairments, a widespread huntingtin (HTT) aggregate pathology and brain atrophy. Despite the vast number of studies that have been performed on this model, the association between the molecular and cellular neuropathology with brain atrophy, and with the development of behavioral phenotypes remains poorly understood. In an attempt to link these factors, we have performed longitudinal assessments of behavior (rotarod, open field, passive avoidance) and of regional brain abnormalities determined through magnetic resonance imaging (MRI) (whole brain, striatum, cortex, hippocampus, corpus callosum), as well as an end-stage histological assessment. Detailed correlative analyses of these three measures were then performed. We found a gender-dependent emergence of motor impairments that was associated with an age-related loss of regional brain volumes. MRI measurements further indicated that there was no striatal atrophy, but rather a lack of striatal growth beyond 8 weeks of age. T2 relaxivity further indicated tissue-level changes within brain regions. Despite these dramatic motor and neuroanatomical abnormalities, R6/2 mice did not exhibit neuronal loss in the striatum or motor cortex, although there was a significant increase in neuronal density due to tissue atrophy. The deposition of the mutant HTT (mHTT) protein, the hallmark of HD molecular pathology, was widely distributed throughout the brain. End-stage histopathological assessments were not found to be as robustly correlated with the longitudinal measures of brain atrophy or motor impairments. In conclusion, modeling pre-manifest and early progression of the disease in more slowly progressing animal models will be key to establishing which changes are causally related. © 2013 Rattray et al

Electrical Detection of DC Spin Current Propagation Through an Epitaxial Antiferromagnetic NiO Layer

This is the author accepted manuscript. The final version is available from IEEE via the DOI in this recordA method for detecting dc spin current propagation through an epitaxial antiferromagnetic (AFM) NiO layer is presented. Spin current is generated by spin pumping from an adjoining ferromagnetic (FM) layer and detected in a non-magnetic metallic layer by the inverse spin Hall effect. Comparison is made with a YIG/Pt bilayer, where only the Pt layer is electrically conducting, but for which spin Hall magnetoresistance makes an additional contribution to the measured signal. The signal obtained from the multilayered stack containing the AFM NiO layer is found to contain additional contributions due to anisotropic magnetoresistance. By exciting the sample with out-of-plane rf magnetic field and making measurements with a static field applied at different orientations within the plane of the sample, a signal associated with the dc spin current may be identified.Engineering and Physical Sciences Research Council (EPSRC

In vivo imaging and quantitative analysis of leukocyte directional migration and polarization in inflamed tissue

Directional migration of transmigrated leukocytes to the site of injury is a central event in the inflammatory response. Here, we present an in vivo chemotaxis assay enabling the visualization and quantitative analysis of subtype-specific directional motility and polarization of leukocytes in their natural 3D microenvironment. Our technique comprises the combination of i) semi-automated in situ microinjection of chemoattractants or bacteria as local chemotactic stimulus, ii) in vivo near-infrared reflected-light oblique transillumination (RLOT) microscopy for the visualization of leukocyte motility and morphology, and iii) in vivo fluorescence microscopy for the visualization of different leukocyte subpopulations or fluorescence-labeled bacteria. Leukocyte motility parameters are quantified off-line in digitized video sequences using computer-assisted single cell tracking. Here, we show that perivenular microinjection of chemoattractants [macrophage inflammatory protein-1alpha (MIP-1alpha/Ccl3), platelet-activating factor (PAF)] or E. coli into the murine cremaster muscle induces target-oriented intravascular adhesion and transmigration as well as polarization and directional interstitial migration of leukocytes towards the locally administered stimuli. Moreover, we describe a crucial role of Rho kinase for the regulation of directional motility and polarization of transmigrated leukocytes in vivo. Finally, combining in vivo RLOT and fluorescence microscopy in Cx3CR1(gfp/gfp) mice (mice exhibiting green fluorescent protein-labeled monocytes), we are able to demonstrate differences in the migratory behavior of monocytes and neutrophils.Taken together, we propose a novel approach for investigating the mechanisms and spatiotemporal dynamics of subtype-specific motility and polarization of leukocytes during their directional interstitial migration in vivo

Effective nebulization of interferon-γ using a novel vibrating mesh.

BACKGROUND: Interferon gamma (IFN-γ) is a clinically relevant immunomodulatory cytokine that has demonstrated significant potential in the treatment and management of respiratory diseases such as tuberculosis and pulmonary fibrosis. As with all large biomolecules, clinical translation is dependent on effective delivery to the disease site and delivery of IFN-γ as an aerosol offers a logical means of drug targeting. Effective localization is often hampered by instability and a lack of safe and efficient delivery systems. The present study sought to determine how effectively IFN-γ can be nebulized using two types of vibrating mesh nebulizer, each with differing mesh architectures, and to investigate the comparative efficiency of delivery of therapeutically active IFN-γ to the lungs. METHODS: Nebulization of IFN-γ was carried out using two different Aerogen vibrating mesh technologies with differing mesh architectures. These technologies represent both a standard commercially available mesh type (Aerogen Solo®) and a new iteration mesh (Photo-defined aperture plate (PDAP®). Extensive aerosol studies (aerosol output and droplet analysis, non-invasive and invasive aerosol therapy) were conducted in line with regulatory requirements and characterization of the stability and bioactivity of the IFN-γ post-nebulization was confirmed using SDS-PAGE and stimulation of Human C-X-C motif chemokine 10 (CXCL 10) also known as IFN-γ-induced protein 10KDa (IP 10) expression from THP-1 derived macrophages (THP-1 cells). RESULTS: Aerosol characterization studies indicated that a significant and reproducible dose of aerosolized IFN-γ can be delivered using both vibrating mesh technologies. Nebulization using both devices resulted in an emitted dose of at least 93% (100% dose minus residual volume) for IFN-γ. Characterization of aerosolized IFN-γ indicated that the PDAP was capable of generating droplets with a significantly lower mass median aerodynamic diameter (MMAD) with values of 2.79 ± 0.29 μm and 4.39 ± 0.25 μm for the PDAP and Solo respectively. The volume median diameters (VMD) of aerosolized IFN-γ corroborated this with VMDs of 2.33 ± 0.02 μm for the PDAP and 4.30 ± 0.02 μm for the Solo. SDS-PAGE gels indicated that IFN-γ remains stable after nebulization by both devices and this was confirmed by bioactivity studies using a THP-1 cell model in which an alveolar macrophage response to IFN-γ was determined. IFN-γ nebulized by the PDAP and Solo devices had no significant effect on the key inflammatory biomarker cytokine IP-10 release from this model in comparison to non-nebulized controls. Here we demonstrate that it is possible to combine IFN-γ with vibrating mesh nebulizer devices and facilitate effective aerosolisation with minimal impact on IFN-γ structure or bioactivity. CONCLUSIONS: It is possible to nebulize IFN-γ effectively with vibrating mesh nebulizer devices without compromising its stability. The PDAP allows for generation of IFN-γ aerosols with improved aerodynamic properties thereby increasing its potential efficiency for lower respiratory tract deposition over current technology, whilst maintaining the integrity and bioactivity of IFN-γ. This delivery modality therefore offers a rational means of facilitating the clinical translation of inhaled IFN-γ

Characterization of stochastic orders by L-functionals

Random variables may be compared with respect to their location by comparing certain functionals ad hoc, such as the mean or median, or by means of stochastic ordering based directly on the properties of the corresponding distribution functions. These alternative approaches are brought together in this paper. We focus on the class of L-functionals discussed by Bickel and Lehmann (1975) and characterize the comparison of random variables in terms of these measures by means of several stochastic orders based on iterated integrals, including the increasing convex orde

Alternative patterns of sex chromosome differentiation in Aedes aegypti (L).

BACKGROUND: Some populations of West African Aedes aegypti, the dengue and zika vector, are reproductively incompatible; our earlier study showed that divergence and rearrangements of genes on chromosome 1, which bears the sex locus (M), may be involved. We also previously described a proposed cryptic subspecies SenAae (PK10, Senegal) that had many more high inter-sex FST genes on chromosome 1 than did Ae.aegypti aegypti (Aaa, Pai Lom, Thailand). The current work more thoroughly explores the significance of those findings. RESULTS: Intersex standardized variance (FST) of single nucleotide polymorphisms (SNPs) was characterized from genomic exome capture libraries of both sexes in representative natural populations of Aaa and SenAae. Our goal was to identify SNPs that varied in frequency between males and females, and most were expected to occur on chromosome 1. Use of the assembled AaegL4 reference alleviated the previous problem of unmapped genes. Because the M locus gene nix was not captured and not present in AaegL4, the male-determining locus, per se, was not explored. Sex-associated genes were those with FST values ≥ 0.100 and/or with increased expected heterozygosity (H exp , one-sided T-test, p < 0.05) in males. There were 85 genes common to both collections with high inter-sex FST values; all genes but one were located on chromosome 1. Aaa showed the expected cluster of high inter-sex FST genes proximal to the M locus, whereas SenAae had inter-sex FST genes along the length of chromosome 1. In addition, the Aaa M-locus proximal region showed increased H exp levels in males, whereas SenAae did not. In SenAae, chromosomal rearrangements and subsequent suppressed recombination may have accelerated X-Y differentiation. CONCLUSIONS: The evidence presented here is consistent with differential evolution of proto-Y chromosomes in Aaa and SenAae