Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.

Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. `Morex' was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).Peer reviewe

A chromosome conformation capture ordered sequence of the barley genome

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Genome-wide DNA polymorphism in the indica rice varieties RGD-7S and Taifeng B, revealed by whole genome re-sequencing

Next-generation sequencing technologies provide opportunities to understand the genetic variation even in the closely related cultivars. We performed the whole genome resequencing of two elite indica rice varieties RGD-7S and Taifeng B, whose F1 progeny showed hybrid weakness and hybrid vigor when they were grown in the early- and late-cropping seasons, respectively. Approximate 150 million 100-bp pair-end reads were generated, which covered about 86% of rice (Oryza sativa L. Japonica. cv. Nipponbare) reference genome. A total of 2,758,740 polymorphic sites including 2,408,845 SNPs and 349,895 InDels were detected in RGD-7S and Taifeng B, respectively. Applying stringent parameters, we identified 961,791SNPs and 46,640 InDels between RGD-7S and Taifeng B (RGD-7S/Taifeng B). The density of DNA polymorphisms was 256.8 SNPs and 12.5 InDels per 100 kb for RGD-7S/Taifeng B. Copy number variations (CNVs) were also investigated. In RGD-7S, 1,989 of 2,727 CNVs were overlapped in 218 genes, and 1,231 of 2,010 CNVs were annotated in 175 gene in Taifeng B. In addition, we verified a subset of InDels in the interval of hybrid weakness genes Hw3 and Hw4, and obtained some polymorphic InDel markers, which will provide a sound foundation for cloning hybrid weakness genes. Analysis of genomic variations will also contribute to understanding the genetic basis of hybrid weakness and heterosis.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

The biological effect of recombinant humanized collagen on damaged skin induced by UV-photoaging: An in vivo study

The application of medical devices to repair skin damage is clinically accepted and natural polymer enjoys an important role in this field, such as collagen or hyaluronic acid, etc. However, the biosafety and efficacy of these implants are still challenged. In this study, a skin damage animal model was prepared by UV-photoaging and recombinant humanized type III collagen (rhCol III) was applied as a bioactive material to implant in vivo to study its biological effect, comparing with saline and uncrosslinked hyaluronic acid (HA). Animal skin conditions were non-invasively and dynamically monitored during the 8 weeks experiment. Histological observation, specific gene expression and other molecular biological methods were applied by the end of the animal experiment. The results indicated that rhCol III could alleviate the skin photoaging caused by UV radiation, including reduce the thickening of epidermis and dermis, increase the secretion of Collagen I (Col I) and Collagen III (Col III) and remodel of extracellular matrix (ECM). Although the cell-material interaction and mechanism need more investigation, the effect of rhCol III on damaged skin was discussed from influence on cells, reconstruction of ECM, and stimulus of small biological molecules based on current results. In conclusion, our findings provided rigorous biosafety information of rhCol III and approved its potential in skin repair and regeneration. Although enormous efforts still need to be made to achieve successful translation from bench to clinic, the recombinant humanized collagen showed superiorities from both safety and efficacy aspects

Responses of the Carbon Storage and Sequestration Potential of Forest Vegetation to Temperature Increases in Yunnan Province, SW China

The distribution of forest vegetation and forest carbon sequestration potential are significantly influenced by climate change. In this study, a map of the current distribution of vegetation in Yunnan Province was compiled based on data from remote sensing imagery from the Advanced Land Observing Satellite (ALOS) from 2008 to 2011. A classification and regression tree (CART) model was used to predict the potential distribution of the main forest vegetation types in Yunnan Province and estimate the changes in carbon storage and carbon sequestration potential (CSP) in response to increasing temperature. The results show that the current total forest area in Yunnan Province is 1.86 × 107 ha and that forest covers 48.63% of the area. As the temperature increases, the area of forest distribution first increases and then decreases, and it decreases by 11% when the temperature increases from 1.5 to 2 °C. The mean carbon density of the seven types of forest vegetation in Yunnan Province is 84.69 Mg/ha. The total carbon storage of the current forest vegetation in Yunnan Province is 871.14 TgC, and the CSP is 1100.61 TgC. The largest CSP (1114.82 TgC) occurs when the temperature increases by 0.5 °C. Incremental warming of 2 °C will sharply decrease the forest CSP, especially in those regions with mature coniferous forest vegetation. Semi-humid evergreen broad-leaved forests were highly sensitive to temperature changes, and the CSP of these forests will decrease with increasing temperature. Warm-hot coniferous forests have the greatest CSP in all simulation scenarios except the scenario of a 2 °C temperature increase. These results indicate that temperature increases can influence the CSP in Yunnan Province, and the largest impact emerged in the 2 °C increase scenario

Genetic Control over mtDNA and Its Relationship to Major Depressive Disorder

Summary Control over the number of mtDNA molecules per cell appears to be tightly regulated, but the mechanisms involved are largely unknown. Reversible alterations in the amount of mtDNA occur in response to stress suggesting that control over the amount of mtDNA is involved in stress-related diseases including major depressive disorder (MDD). Using low-coverage sequence data from 10,442 Chinese women to compute the normalized numbers of reads mapping to the mitochondrial genome as a proxy for the amount of mtDNA, we identified two loci that contribute to mtDNA levels: one within the TFAM gene on chromosome 10 (rs11006126, p value = 8.73 × 10−28, variance explained = 1.90%) and one over the CDK6 gene on chromosome 7 (rs445, p value = 6.03 × 10−16, variance explained = 0.50%). Both loci replicated in an independent cohort. CDK6 is thus a new molecule involved in the control of mtDNA. We identify increased rates of heteroplasmy in women with MDD, and show from an experimental paradigm using mice that the increase is likely due to stress. Furthermore, at least one heteroplasmic variant is significantly associated with changes in the amount of mtDNA (position 513, p value = 3.27 × 10−9, variance explained = 0.48%) suggesting site-specific heteroplasmy as a possible link between stress and increase in amount of mtDNA. These findings indicate the involvement of mitochondrial genome copy number and sequence in an organism’s response to stress

Synthesis of Co‐Doped MoS 2

Internal magnetic moments induced by magnetic dopants in MoS2 monolayers are shown to serve as a new means to engineer valley Zeeman splitting (VZS). Specifically, successful synthesis of monolayer MoS2 doped with the magnetic element Co is reported, and the magnitude of the valley splitting is engineered by manipulating the dopant concentration. Valley splittings of 3.9, 5.2, and 6.15 meV at 7 T in Co-doped MoS2 with Co concentrations of 0.8%, 1.7%, and 2.5%, respectively, are achieved as revealed by polarization-resolved photoluminescence (PL) spectroscopy. Atomic-resolution electron microscopy studies clearly identify the magnetic sites of Co substitution in the MoS2 lattice, forming two distinct types of configurations, namely isolated single dopants and tridopant clusters. Density functional theory (DFT) and model calculations reveal that the observed enhanced VZS arises from an internal magnetic field induced by the tridopant clusters, which couples to the spin, atomic orbital, and valley magnetic moment of carriers from the conduction and valence bands. The present study demonstrates a new method to control the valley pseudospin via magnetic dopants in layered semiconducting materials, paving the way toward magneto-optical and spintronic devices.Accepted versio

Regulation of Toll-like receptor–mediated inflammatory response by complement in vivo

Toll-like receptors (TLRs) and complement are 2 components of innate immunity that are critical for first-line host defense and elicitation of adaptive immune responses. Many pathogen-associated molecular patterns activate both TLR and complement, but whether and how these 2 systems, when coactivated in vivo, interact with each other has not been well studied. We demonstrate here a widespread regulation of TLR signaling by complement in vivo. The TLR ligands lipopolysacharride (TLR4), zymosan (TLR2/6), and CpG oligonucleotide (TLR9) caused, in a complement-dependent manner, strikingly elevated plasma interleukin-6 (IL-6), tumor necrosis factor α (TNF-α), and IL-1β, and/or decreased plasma IL-12 levels in mice deficient in the membrane complement inhibitor decay-accelerating factor (DAF). A similar outcome was observed in wild-type mice cotreated with the TLR ligands and cobra venom factor, a potent complement activator. The regulatory effect of complement on TLR-induced cytokine production in vivo was mediated by the anaphylatoxin receptors C5aR and C3aR. Additionally, changes in lipopolysaccharide (LPS)–induced cytokine production in DAF-deficient mice correlated with increased mitogen-activated protein kinase and nuclear factor-κB activation in the spleen. These results reveal a strong interaction between complement and TLR signaling in vivo and suggest a novel mechanism by which complement promotes inflammation and modulates adaptive immunity