Novel coding genetic variants of the GBP1 gene in wild and domestic pigs (Sus scrofa)

The interferon-induced guanylate-binding protein 1 gene (GBP1) plays an important role in host defense against viral, bacterial and protozoan infections. To explore novel genetic variants in this gene, we re-sequenced a 587-bp fragment spanning the exon 2 of the GBP1 gene in a sample panel consisting of 34 wild boars and 59 local domestic pigs from three geographic regions (China, Iberian Peninsula, and Central Europe) and 12 individuals of three commercial breeds (Pietrain, Landrace, and Large White). In a final 543-bp sequence fragment, there were 14 single nucleotide polymorphisms (SNPs), of which five were coding (three novel mutations). A total of 19 haplotypes were reconstructed and most haplotypes were shared by two or more sample groups. Those shared haplotypes revealed a clear signature of genetic introgression from Chinese domestic pigs into European domestic pigs. In addition, there were six haplotypes with frequencies below 1%, but none of them were present in the three commercial breeds (Pietrain, Landrace, and Large White). Although a limited number of individuals and breeds were analyzed, the absence of rare alleles (or haplotypes) in the commercial breeds is an indication that a significant proportion of genetic diversity in domestic species is not present in commercial breeds. This study demonstrated the potential to find sufficient genetic variation for population genetic analyses of demography versus selection, in functional candidate genes of domestic pigs and wild boars worldwide

Sex-Biased Gene Flow Among Elk in the Greater Yellowstone Ecosystem

We quantified patterns of population genetic structure to help understand gene flow among elk populations across the Greater Yellowstone Ecosystem. We sequenced 596 base pairs of the mitochondrial control region of 380 elk from eight populations. Analysis revealed high mitochondrial DNA variation within populations, averaging 13.0 haplotypes with high mean gene diversity (0.85). The genetic differentiation among populations for mitochondrial DNA was relatively high (FST = 0.161; P = 0.001) compared to genetic differentiation for nuclear microsatellite data (FST = 0.002; P = 0.332), which suggested relatively low female gene flow among populations. The estimated ratio of male to female gene flow (mm/mf = 46) was among the highest we have seen reported for large mammals. Genetic distance (for mitochondrial DNA pairwise FST) was not significantly correlated with geographic (Euclidean) distance between populations (Mantel’s r = 0.274, P = 0.168). Large mitochondrial DNA genetic distances (e.g., FST . 0.2) between some of the geographically closest populations (,65 km) suggested behavioral factors and/or landscape features might shape female gene flow patterns. Given the strong sex-biased gene flow, future research and conservation efforts should consider the sexes separately when modeling corridors of gene flow or predicting spread of maternally transmitted diseases. The growing availability of genetic data to compare male vs. female gene flow provides many exciting opportunities to explore the magnitude, causes, and implications of sex-biased gene flow likely to occur in many species

Development and validation of the health literacy environment scale for Chinese hospitals from patients’ perspective

IntroductionWhile the research on improving individual health literacy by promoting individual skills and abilities is increasing, less attention has been paid to the complexities of the healthcare environment that may influence patients’ ability to access, understand, and apply health information and health services to make health decisions. This study aimed to develop and validate a Health Literacy Environment Scale (HLES) that is suitable for Chinese culture.MethodsThis study was conducted in two phases. First, using the Person-Centered Care (PCC) framework as a theoretical framework, initial items were developed by using the existing health literacy environment (HLE) related measurement tools, literature review, qualitative interviews, and the researcher’s clinical experience. Second, scale development was based on two rounds of Delphi expert consultation and a pre-test conducted with 20 hospitalized patients. Using 697 hospitalized patients from three sample hospitals, the initial scale was developed after item screening and its reliability and validity were evaluated.ResultsThe HLES comprised 30 items classified into three dimensions as follows: interpersonal (11 items), clinical (9 items), and structural (10 items) dimensions. The Cronbach’s α coefficient of the HLES was 0.960 and the intra-class correlation coefficient was 0.844. The confirmatory factor analysis verified the three-factor model after allowing for the correlation of five pairs of error terms. The goodness-of-fit indices signified a good fit for the model (χ2/df = 2.766, RMSEA = 0.069, RMR = 0.053, CFI = 0.902, IFI = 0.903, TLI = 0.893, GFI = 0.826, PNFI = 0.781, PCFI = 0.823, PGFI = 0.705). The item-content validity index ranged from 0.91 to 1.00, and the scale-content validity index was 0.90.ConclusionThe HLES had good reliability and validity and provides a patient perspective tool for evaluating HLE and a new perspective for improving health literacy in China. That is, healthcare organizations make it easier for patients to access, understand, and use health information and service. Further studies about the validity and reliability of HLE should include other districts and different tiers or types of healthcare organizations

Legacies of domestication, trade and herder mobility shape extant male zebu cattle diversity in South Asia and Africa

All tropically adapted humped cattle (Bos indicus or 'zebu'), descend from a domestication process that took place >8,000 years ago in South Asia. Here we present an intercontinental survey of Y-chromosome diversity and a comprehensive reconstruction of male-lineage zebu cattle history and diversity patterns. Phylogenetic analysis revealed that all the zebu Y-chromosome haplotypes in our dataset group within three different lineages: Y3A, the most predominant and cosmopolitan lineage; Y3B, only observed in West Africa; and Y3C, predominant in South and Northeast India. The divergence times estimated for these three Zebu-specific lineages predate domestication. Coalescent demographic models support either de novo domestication of genetically divergent paternal lineages or more complex process including gene flow between wild and domestic animals. Our data suggest export of varied zebu lineages from domestication centres through time. The almost exclusive presence of Y3A haplotypes in East Africa is consistent with recent cattle restocking in this area. The cryptic presence of Y3B haplotypes in West Africa, found nowhere else, suggests that these haplotypes might represent the oldest zebu lineage introduced to Africa ca. 3,000 B.P. and subsequently replaced in most of the world. The informative ability of Interspersed Multilocus Microsatellites and Y-specific microsatellites to identify genetic structuring in cattle populations is confirmed

Colossal optical anisotropy from atomic-scale modulations

In modern optics, materials with large birefringence ({\Delta}n, where n is the refractive index) are sought after for polarization control (e.g. in wave plates, polarizing beam splitters, etc.), nonlinear optics and quantum optics (e.g. for phase matching and production of entangled photons), micromanipulation, and as a platform for unconventional light-matter coupling, such as Dyakonov-like surface polaritons and hyperbolic phonon polaritons. Layered "van der Waals" materials, with strong intra-layer bonding and weak inter-layer bonding, can feature some of the largest optical anisotropy; however, their use in most optical systems is limited because their optic axis is out of the plane of the layers and the layers are weakly attached, making the anisotropy hard to access. Here, we demonstrate that a bulk crystal with subtle periodic modulations in its structure -- Sr9/8TiS3 -- is transparent and positive-uniaxial, with extraordinary index n_e = 4.5 and ordinary index n_o = 2.4 in the mid- to far-infrared. The excess Sr, compared to stoichiometric SrTiS3, results in the formation of TiS6 trigonal-prismatic units that break the infinite chains of face-shared TiS6 octahedra in SrTiS3 into periodic blocks of five TiS6 octahedral units. The additional electrons introduced by the excess Sr subsequently occupy the TiS6 octahedral blocks to form highly oriented and polarizable electron clouds, which selectively boost the extraordinary index n_e and result in record birefringence ({\Delta}n > 2.1 with low loss). The connection between subtle structural modulations and large changes in refractive index suggests new categories of anisotropic materials and also tunable optical materials with large refractive-index modulation and low optical losses.Comment: Main text + supplementar

Giant Modulation of Refractive Index from Correlated Disorder

Correlated disorder has been shown to enhance and modulate magnetic, electrical, dipolar, electrochemical and mechanical properties of materials. However, the possibility of obtaining novel optical and opto-electronic properties from such correlated disorder remains an open question. Here, we show unambiguous evidence of correlated disorder in the form of anisotropic, sub-angstrom-scale atomic displacements modulating the refractive index tensor and resulting in the giant optical anisotropy observed in BaTiS3, a quasi-one-dimensional hexagonal chalcogenide. Single crystal X-ray diffraction studies reveal the presence of antipolar displacements of Ti atoms within adjacent TiS6 chains along the c-axis, and three-fold degenerate Ti displacements in the a-b plane. 47/49Ti solid-state NMR provides additional evidence for those Ti displacements in the form of a three-horned NMR lineshape resulting from low symmetry local environment around Ti atoms. We used scanning transmission electron microscopy to directly observe the globally disordered Ti a-b plane displacements and find them to be ordered locally over a few unit cells. First-principles calculations show that the Ti a-b plane displacements selectively reduce the refractive index along the ab-plane, while having minimal impact on the refractive index along the chain direction, thus resulting in a giant enhancement in the optical anisotropy. By showing a strong connection between correlated disorder and the optical response in BaTiS3, this study opens a pathway for designing optical materials with high refractive index and functionalities such as a large optical anisotropy and nonlinearity.Comment: 24 pages, 3 figure

Exome-wide DNA capture and next generation sequencing in domestic and wild species

<p>Abstract</p> <p>Background</p> <p>Gene-targeted and genome-wide markers are crucial to advance evolutionary biology, agriculture, and biodiversity conservation by improving our understanding of genetic processes underlying adaptation and speciation. Unfortunately, for eukaryotic species with large genomes it remains costly to obtain genome sequences and to develop genome resources such as genome-wide SNPs. A method is needed to allow gene-targeted, next-generation sequencing that is flexible enough to include any gene or number of genes, unlike transcriptome sequencing. Such a method would allow sequencing of many individuals, avoiding ascertainment bias in subsequent population genetic analyses.</p> <p>We demonstrate the usefulness of a recent technology, exon capture, for genome-wide, gene-targeted marker discovery in species with no genome resources. We use coding gene sequences from the domestic cow genome sequence (<it>Bos taurus</it>) to capture (enrich for), and subsequently sequence, thousands of exons of <it>B. taurus</it>, <it>B. indicus</it>, and <it>Bison bison </it>(wild bison). Our capture array has probes for 16,131 exons in 2,570 genes, including 203 candidate genes with known function and of interest for their association with disease and other fitness traits.</p> <p>Results</p> <p>We successfully sequenced and mapped exon sequences from across the 29 autosomes and X chromosome in the <it>B. taurus </it>genome sequence. Exon capture and high-throughput sequencing identified thousands of putative SNPs spread evenly across all reference chromosomes, in all three individuals, including hundreds of SNPs in our targeted candidate genes.</p> <p>Conclusions</p> <p>This study shows exon capture can be customized for SNP discovery in many individuals and for non-model species without genomic resources. Our captured exome subset was small enough for affordable next-generation sequencing, and successfully captured exons from a divergent wild species using the domestic cow genome as reference.</p

Unconventional Charge-density-wave Order in a Dilute d-band Semiconductor

Electron-lattice coupling effects in low dimensional materials give rise to charge density wave (CDW) order and phase transitions. These phenomena are critical ingredients for superconductivity and predominantly occur in metallic model systems such as doped cuprates, transition metal dichalcogenides, and more recently, in Kagome lattice materials. However, CDW in semiconducting systems, specifically at the limit of low carrier concentration region, is uncommon. Here, we combine electrical transport, synchrotron X-ray diffraction and optical spectroscopy to discover CDW order in a quasi-one-dimensional (1D), dilute d-band semiconductor, BaTiS3, which suggests the existence of strong electron-phonon coupling. The CDW state further undergoes an unusual transition featuring a sharp increase in carrier mobility. Our work establishes BaTiS3 as a unique platform to study the CDW physics in the dilute filling limit to explore novel electronic phases

How immunogenetically different are domestic pigs from wild boars: a perspective from single-nucleotide polymorphisms of 19 immunity-related candidate genes.

The coexistence of wild boars and domestic pigs across Eurasia makes it feasible to conduct comparative genetic or genomic analyses for addressing how genetically different a domestic species is from its wild ancestor. To test whether there are differences in patterns of genetic variability between wild and domestic pigs at immunity-related genes and to detect outlier loci putatively under selection that may underlie differences in immune responses, here we analyzed 54 single-nucleotide polymorphisms (SNPs) of 19 immunityrelated candidate genes on 11 autosomes in three pairs of wild boar and domestic pig populations from China, Iberian Peninsula, and Hungary. Our results showed no statistically significant differences in allele frequency and heterozygosity across SNPs between three pairs of wild and domestic populations. This observation was more likely due to the widespread and long-lasting gene flow between wild boars and domestic pigs across Eurasia. In addition, we detected eight coding SNPs from six genes as outliers being under selection consistently by three outlier tests (BayeScan2.1, FDIST2, and Arlequin3.5). Among four non-synonymous outlier SNPs, one from TLR4 gene was identified as being subject to positive (diversifying) selection and three each from CD36,IFNW1, and IL1B genes were suggested as under balancing selection. All of these four non-synonymous variants were predicted as being benign by PolyPhen-2. Our results were supported by other independent lines of evidence for positive selection or balancing selection acting on these four immune genes (CD36, IFNW1, IL1B, and TLR4). Our study showed an example applying a candidate gene approach to identify functionally important mutations (i.e., outlier loci) in wild and domestic pigs for subsequent functional experiments