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  • 11
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    Insights into hominid evolution from the gorilla genome sequence (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-03-09
    Description: Gorillas are humans' closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago. In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303130/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303130/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scally, Aylwyn -- Dutheil, Julien Y -- Hillier, LaDeana W -- Jordan, Gregory E -- Goodhead, Ian -- Herrero, Javier -- Hobolth, Asger -- Lappalainen, Tuuli -- Mailund, Thomas -- Marques-Bonet, Tomas -- McCarthy, Shane -- Montgomery, Stephen H -- Schwalie, Petra C -- Tang, Y Amy -- Ward, Michelle C -- Xue, Yali -- Yngvadottir, Bryndis -- Alkan, Can -- Andersen, Lars N -- Ayub, Qasim -- Ball, Edward V -- Beal, Kathryn -- Bradley, Brenda J -- Chen, Yuan -- Clee, Chris M -- Fitzgerald, Stephen -- Graves, Tina A -- Gu, Yong -- Heath, Paul -- Heger, Andreas -- Karakoc, Emre -- Kolb-Kokocinski, Anja -- Laird, Gavin K -- Lunter, Gerton -- Meader, Stephen -- Mort, Matthew -- Mullikin, James C -- Munch, Kasper -- O'Connor, Timothy D -- Phillips, Andrew D -- Prado-Martinez, Javier -- Rogers, Anthony S -- Sajjadian, Saba -- Schmidt, Dominic -- Shaw, Katy -- Simpson, Jared T -- Stenson, Peter D -- Turner, Daniel J -- Vigilant, Linda -- Vilella, Albert J -- Whitener, Weldon -- Zhu, Baoli -- Cooper, David N -- de Jong, Pieter -- Dermitzakis, Emmanouil T -- Eichler, Evan E -- Flicek, Paul -- Goldman, Nick -- Mundy, Nicholas I -- Ning, Zemin -- Odom, Duncan T -- Ponting, Chris P -- Quail, Michael A -- Ryder, Oliver A -- Searle, Stephen M -- Warren, Wesley C -- Wilson, Richard K -- Schierup, Mikkel H -- Rogers, Jane -- Tyler-Smith, Chris -- Durbin, Richard -- 062023/Wellcome Trust/United Kingdom -- 075491/Z/04/Wellcome Trust/United Kingdom -- 077009/Wellcome Trust/United Kingdom -- 077192/Wellcome Trust/United Kingdom -- 077198/Wellcome Trust/United Kingdom -- 089066/Wellcome Trust/United Kingdom -- 090532/Wellcome Trust/United Kingdom -- 095908/Wellcome Trust/United Kingdom -- 15603/Cancer Research UK/United Kingdom -- 202218/European Research Council/International -- A15603/Cancer Research UK/United Kingdom -- G0501331/Medical Research Council/United Kingdom -- G0701805/Medical Research Council/United Kingdom -- HG002385/HG/NHGRI NIH HHS/ -- U54 HG003079/HG/NHGRI NIH HHS/ -- WT062023/Wellcome Trust/United Kingdom -- WT077009/Wellcome Trust/United Kingdom -- WT077192/Wellcome Trust/United Kingdom -- WT077198/Wellcome Trust/United Kingdom -- WT089066/Wellcome Trust/United Kingdom -- Medical Research Council/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Howard Hughes Medical Institute/ -- Intramural NIH HHS/ -- England -- Nature. 2012 Mar 7;483(7388):169-75. doi: 10.1038/nature10842.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22398555" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Evolution, Molecular ; Female ; Gene Expression Regulation ; *Genetic Speciation ; Genetic Variation/genetics ; Genome/*genetics ; Genomics ; Gorilla gorilla/*genetics ; Humans ; Macaca mulatta/genetics ; Molecular Sequence Data ; Pan troglodytes/genetics ; Phylogeny ; Pongo/genetics ; Proteins/genetics ; Sequence Alignment ; Species Specificity ; Transcription, Genetic
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 12
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    Analysis of the bread wheat genome using whole-genome shotgun sequencing (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-11-30
    Description: Bread wheat (Triticum aestivum) is a globally important crop, accounting for 20 per cent of the calories consumed by humans. Major efforts are underway worldwide to increase wheat production by extending genetic diversity and analysing key traits, and genomic resources can accelerate progress. But so far the very large size and polyploid complexity of the bread wheat genome have been substantial barriers to genome analysis. Here we report the sequencing of its large, 17-gigabase-pair, hexaploid genome using 454 pyrosequencing, and comparison of this with the sequences of diploid ancestral and progenitor genomes. We identified between 94,000 and 96,000 genes, and assigned two-thirds to the three component genomes (A, B and D) of hexaploid wheat. High-resolution synteny maps identified many small disruptions to conserved gene order. We show that the hexaploid genome is highly dynamic, with significant loss of gene family members on polyploidization and domestication, and an abundance of gene fragments. Several classes of genes involved in energy harvesting, metabolism and growth are among expanded gene families that could be associated with crop productivity. Our analyses, coupled with the identification of extensive genetic variation, provide a resource for accelerating gene discovery and improving this major crop.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3510651/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3510651/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brenchley, Rachel -- Spannagl, Manuel -- Pfeifer, Matthias -- Barker, Gary L A -- D'Amore, Rosalinda -- Allen, Alexandra M -- McKenzie, Neil -- Kramer, Melissa -- Kerhornou, Arnaud -- Bolser, Dan -- Kay, Suzanne -- Waite, Darren -- Trick, Martin -- Bancroft, Ian -- Gu, Yong -- Huo, Naxin -- Luo, Ming-Cheng -- Sehgal, Sunish -- Gill, Bikram -- Kianian, Sharyar -- Anderson, Olin -- Kersey, Paul -- Dvorak, Jan -- McCombie, W Richard -- Hall, Anthony -- Mayer, Klaus F X -- Edwards, Keith J -- Bevan, Michael W -- Hall, Neil -- B/J004588/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/E004725/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/G012865/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/G013004/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/G013985/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/G024650/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/H022333/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- G0900753/Medical Research Council/United Kingdom -- G0900753(91100)/Medical Research Council/United Kingdom -- England -- Nature. 2012 Nov 29;491(7426):705-10. doi: 10.1038/nature11650.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Genome Research, University of Liverpool, Liverpool L69 7ZB, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23192148" target="_blank"〉PubMed〈/a〉
    Keywords: Brachypodium/genetics ; *Bread ; Chromosomes, Plant/genetics ; Crops, Agricultural/genetics ; DNA, Complementary/genetics ; DNA, Plant/genetics ; Evolution, Molecular ; Genes, Plant/genetics ; Genome, Plant/*genetics ; Genomics ; Multigene Family/genetics ; Oryza/genetics ; Polymorphism, Single Nucleotide/genetics ; Polyploidy ; Pseudogenes/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Triticum/classification/*genetics ; Zea mays/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 13
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    Objected-oriented remote sensing image classification method based on geographic ontology model (2016)
    Institute of Physics (IOP)
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    Publication Date: 2016-11-22
    Description: Nowadays, with the development of high resolution remote sensing image and the wide application of laser point cloud data, proceeding objected-oriented remote sensing classification based on the characteristic knowledge of multi-source spatial data has been an important trend on the field of remote sensing image classification, which gradually replaced the traditional method through improving algorithm to optimize image classification results. For this purpose, the paper puts forward a remote sensing image classification method that uses the he characteristic knowledge of multi-source spatial data to build the geographic ontology semantic network model, and carries out the objected-oriented classification experiment to implement urban features classification, the experiment uses protégé software which is developed by Stanford University in the United States, and intelligent image analysis software—eCognition software as the experiment platform, uses hyperspectral image and Lidar...
    Print ISSN: 1755-1307
    Electronic ISSN: 1755-1315
    Topics: Geography , Geosciences , Physics
    Published by Institute of Physics (IOP)
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  • 14
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    Structural basis of outer membrane protein insertion by the BAM complex (2016)
    Nature Publishing Group (NPG)
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    Publication Date: 2016-02-24
    Description: All Gram-negative bacteria, mitochondria and chloroplasts have outer membrane proteins (OMPs) that perform many fundamental biological processes. The OMPs in Gram-negative bacteria are inserted and folded into the outer membrane by the beta-barrel assembly machinery (BAM). The mechanism involved is poorly understood, owing to the absence of a structure of the entire BAM complex. Here we report two crystal structures of the Escherichia coli BAM complex in two distinct states: an inward-open state and a lateral-open state. Our structures reveal that the five polypeptide transport-associated domains of BamA form a ring architecture with four associated lipoproteins, BamB-BamE, in the periplasm. Our structural, functional studies and molecular dynamics simulations indicate that these subunits rotate with respect to the integral membrane beta-barrel of BamA to induce movement of the beta-strands of the barrel and promote insertion of the nascent OMP.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gu, Yinghong -- Li, Huanyu -- Dong, Haohao -- Zeng, Yi -- Zhang, Zhengyu -- Paterson, Neil G -- Stansfeld, Phillip J -- Wang, Zhongshan -- Zhang, Yizheng -- Wang, Wenjian -- Dong, Changjiang -- G1100110/1/Medical Research Council/United Kingdom -- WT106121MA/Wellcome Trust/United Kingdom -- England -- Nature. 2016 Mar 3;531(7592):64-9. doi: 10.1038/nature17199. Epub 2016 Feb 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK. ; Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK. ; Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK. ; Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical College, Xuzhou 221004, China. ; Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu 610064, China. ; Laboratory of Department of Surgery, the First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, Guangdong 510080, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26901871" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Outer Membrane Proteins/*chemistry/*metabolism ; Crystallography, X-Ray ; Escherichia coli/*chemistry ; Escherichia coli Proteins/*chemistry/*metabolism ; Lipoproteins/chemistry/metabolism ; Models, Molecular ; Molecular Dynamics Simulation ; Movement ; Multiprotein Complexes/*chemistry/*metabolism ; Periplasm/metabolism ; Protein Binding ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Rotation
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 15
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    Impacts of sectoral emissions in China and the implications: air quality, public health, crop production, and economic costs (2018)
    Institute of Physics (IOP)
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    Publication Date: 2018-07-28
    Description: China has experienced considerable economic losses from a severe deterioration in air quality. To solve this, a comprehensive understanding of the impacts and sources of air pollution is necessary. This study aimed to quantify the environmental and human health impacts of PM 2.5 and O 3 pollution from the six major emission-producing sectors in China. We utilized a chemical transport model to simulate the air quality impacts engendered by sectoral emissions. The consequent impacts on public health and crop production, as well as the corresponding collateral economic costs, were quantified by concentration-response functions. The results show that the sectoral emissions in 2010 caused approximately 1 143 000 (95% confidence interval (CI): 168 000–1 796 000) premature mortalities and a 20 035 (95% CI: 6776–32 166) Gg crop production loss. Of the six sectors, the industrial sector was the largest contributor of air pollution, accounting for 36% of the total impa...
    Print ISSN: 1748-9318
    Electronic ISSN: 1748-9326
    Topics: Biology , Energy, Environment Protection, Nuclear Power Engineering
    Published by Institute of Physics (IOP)
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  • 16
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    Stochastic parameterization for light absorption by internally mixed BC/dust in snow grains for application to climate models (2014)
    Wiley
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    Publication Date: 2014-06-03
    Description: A stochastic approach has been developed to model the positions of BC/dust internally mixed with two snow-grain types: hexagonal plate/column (convex) and Koch snowflake (concave). Subsequently, light absorption and scattering analysis can be followed by means of an improved geometric-optics approach coupled with Monte Carlo photon tracing to determine BC/dust single-scattering properties. For a given shape (plate, Koch snowflake, spheroid, or sphere), the action of internal mixing absorbs substantially more light than external mixing. The snow-grain shape effect on absorption is relatively small, but its effect on asymmetry factor is substantial. Due to a greater probability of intercepting photons, multiple inclusions of BC/dust exhibit a larger absorption than an equal-volume single inclusion. The spectral absorption (0.2 – 5  μ m) for snow grains internally mixed with BC/dust is confined to wavelengths shorter than about 1.4  μ m, beyond which ice absorption predominates. Based on the single-scattering properties determined from stochastic and light absorption parameterizations and using the adding/doubling method for spectral radiative transfer, we find that internal mixing reduces snow albedo substantially more than external mixing and that the snow-grain shape plays a critical role in snow albedo calculations through its forward scattering strength. Also, multiple inclusion of BC/dust significantly reduces snow albedo as compared to an equal-volume single sphere. For application to land/snow models, we propose a two-layer spectral snow parameterization involving contaminated fresh snow on top of old snow for investigating and understanding the climatic impact of multiple BC/dust internal mixing associated with snow grain metamorphism, particularly over mountain/snow topography.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 17
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    Quantum chemical calculation of imidization mechanism of polyamic acid (2018)
    Institute of Physics (IOP)
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    Publication Date: 2018-02-03
    Description: In this paper, the imidization mechanism of polyamic acid to prepare polyimide has been studied by the density functional theory (DFT) method. Our results have shown that the imidization would proceed via two different reaction paths. The activation barrier via hydrogen transfer to closer carboxylate oxygen in the COOH is 220.35 kJ/mol while the activation barrier via hydrogen transfer to hydroxyl oxygen in the COOH is 220.70 kJ/mol. Both reaction paths would run in the actual thermal imidization process with closer high activation barriers. The high energy barrier interpreted the fact that additional energy or catalyst is usually needed during imidization. Moreover, the intrinsic imidization mechanism indicated is critical to further improve the imidization process.
    Print ISSN: 1757-8981
    Electronic ISSN: 1757-899X
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Published by Institute of Physics (IOP)
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  • 18
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    Selective Life-Long Skeletal Myofiber – Targeted VEGF Gene Ablation Impairs Exercise Capacity in Adult Mice (2015)
    Wiley
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    Publication Date: 2015-07-24
    Description: ABSTRACT Exercise is dependent on adequate oxygen supply for mitochondrial respiration in both cardiac and locomotor muscle. To determine whether skeletal myofiber VEGF is critical for regulating exercise capacity, independent of VEGF function in the heart, ablation of the VEGF gene was targeted to skeletal myofibers (skmVEGF-/-) during embryogenesis (∼ E9.5), leaving intact VEGF expression by all other cells in muscle. In adult mice, VEGF levels were decreased in the soleus (by 65%), plantaris (94%), gastrocnemius (74%), EDL (99%) and diaphragm (64%) (p 〈 0.0001, each muscle). VEGF levels were unchanged in the heart. Treadmill speed (WT 86  ± 4 cm/sec., skmVEGF-/- 70 ± 5 cm/sec., p = 0.006) and endurance (WT 78 ± 24 min., skmVEGF-/- 18 ± 4 min., p = 0.0004) were severely limited in skmVEGF-/- mice in contrast to minor effect of conditional skmVEGF gene deletion in the adult. Body weight was also reduced (WT 22.8 ± 1.6 g, skmVEGF-/-, 21.1 ± 1.5, p = 0.02), but the muscle mass/body weight ratio was unchanged. The capillary/fiber ratio was lower in skmVEGF-/- plantaris (WT 1.51 ± 0.12, skmVEGF-/- 1.16 ± 0.20, p = 0.01), gastrocnemius (WT 1.61 ± 0.08, skmVEGF-/- 1.39 ± 0.08, p = 0.01), EDL (WT 1.36 ± 0.07, skmVEGF-/- 1.14 ± 0.13, p = 0.03) and diaphragm (WT 1.39 ± 0.18, skmVEGF-/- 0.79 ± 0.16, p = 0.0001) but, not in soleus. Cardiac function (heart rate, maximal pressure, maximal dP/dt, minimal dP/dt,) in response to dobutamine was not impaired in anesthetized skmVEGF-/- mice. Isolated soleus and EDL fatigue times were 16% and 20% (p 〈 0.02) longer, respectively, in skmVEGF-/- mice than the WT group. These data suggest that skeletal myofiber VEGF expressed during development is necessary to establish capillary networks that allow maximal exercise capacity. This article is protected by copyright. All rights reserved
    Electronic ISSN: 1097-4652
    Topics: Biology , Medicine
    Published by Wiley
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  • 19
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    Mechanical properties of gutta-percha sulfide modified asphalt (2017)
    Institute of Physics (IOP)
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    Publication Date: 2017-01-24
    Description: Gutta-percha is the isomer of caoutchouc and can be used to enhance the performance of asphalt. In this paper, the produce proceedings of gutta-percha sulfide and gutta-percha sulfide modified asphalt are introduced. The performance indices of gutta-percha sulfide modified asphalt samples with different proportions are examined based on laboratory tests and the optimum ratio of gutta-percha and sulfur is decided.The micromechanism, temperature sensitivity, high and low temperature properties and viscoelasticity of the polymer modified asphalt are analyzed to discuss the modified mechanism and to decide the optimal polymer content. Low temperature bending tests are carried out to verify the low temperature performance of gutta-percha sulfide modified asphalt mixture. Research results showed that gutta-percha sulfide modified asphalt has good low temperature performance and a promising application prospect in the cold regions.
    Print ISSN: 1757-8981
    Electronic ISSN: 1757-899X
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Published by Institute of Physics (IOP)
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  • 20
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    Design and interaction mechanism of ligand targeted with folate receptor α and β (2017)
    Wiley
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    Publication Date: 2017-06-01
    Description: Four compounds 1 to 4 (folic acid, methotrexate and 2 dyes) were used to interact with folate receptor (FR)α and FRβ. The interaction structures and binding energies of the bound complexes were investigated. In order to analyze the differences between FRα and FRβ complexes, the details of the weak intermolecular interactions were analyzed, and the frontier orbital properties of the FR complexes were studied by a dispersion complemented density functional tight-binding method. By comparing the different interaction properties of the 4 compounds with FRα and FRβ, the basic strategies for design of novel compound targeted with FR subtype were suggested. Further, a novel compound with high selectively with FRα based on compound 3 was designed to illustrate our conclusion. These data should be helpful for the design of novel molecules with extreme discerningly with FRα and FRβ. The variety of interaction models between ligands and FRα or FRβ was studied. By the difference between FRα and FRβ complexes, a novel compound with high selectively with FRα was designed, which will improve the recognition accuracy of the tumor cell and the efficiency of targeted drug delivery systems.
    Print ISSN: 0894-3230
    Electronic ISSN: 1099-1395
    Topics: Chemistry and Pharmacology , Physics
    Published by Wiley
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