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  • 1
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    The sequence and de novo assembly of the giant panda genome (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-12-17
    Description: Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3951497/" 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/PMC3951497/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Ruiqiang -- Fan, Wei -- Tian, Geng -- Zhu, Hongmei -- He, Lin -- Cai, Jing -- Huang, Quanfei -- Cai, Qingle -- Li, Bo -- Bai, Yinqi -- Zhang, Zhihe -- Zhang, Yaping -- Wang, Wen -- Li, Jun -- Wei, Fuwen -- Li, Heng -- Jian, Min -- Li, Jianwen -- Zhang, Zhaolei -- Nielsen, Rasmus -- Li, Dawei -- Gu, Wanjun -- Yang, Zhentao -- Xuan, Zhaoling -- Ryder, Oliver A -- Leung, Frederick Chi-Ching -- Zhou, Yan -- Cao, Jianjun -- Sun, Xiao -- Fu, Yonggui -- Fang, Xiaodong -- Guo, Xiaosen -- Wang, Bo -- Hou, Rong -- Shen, Fujun -- Mu, Bo -- Ni, Peixiang -- Lin, Runmao -- Qian, Wubin -- Wang, Guodong -- Yu, Chang -- Nie, Wenhui -- Wang, Jinhuan -- Wu, Zhigang -- Liang, Huiqing -- Min, Jiumeng -- Wu, Qi -- Cheng, Shifeng -- Ruan, Jue -- Wang, Mingwei -- Shi, Zhongbin -- Wen, Ming -- Liu, Binghang -- Ren, Xiaoli -- Zheng, Huisong -- Dong, Dong -- Cook, Kathleen -- Shan, Gao -- Zhang, Hao -- Kosiol, Carolin -- Xie, Xueying -- Lu, Zuhong -- Zheng, Hancheng -- Li, Yingrui -- Steiner, Cynthia C -- Lam, Tommy Tsan-Yuk -- Lin, Siyuan -- Zhang, Qinghui -- Li, Guoqing -- Tian, Jing -- Gong, Timing -- Liu, Hongde -- Zhang, Dejin -- Fang, Lin -- Ye, Chen -- Zhang, Juanbin -- Hu, Wenbo -- Xu, Anlong -- Ren, Yuanyuan -- Zhang, Guojie -- Bruford, Michael W -- Li, Qibin -- Ma, Lijia -- Guo, Yiran -- An, Na -- Hu, Yujie -- Zheng, Yang -- Shi, Yongyong -- Li, Zhiqiang -- Liu, Qing -- Chen, Yanling -- Zhao, Jing -- Qu, Ning -- Zhao, Shancen -- Tian, Feng -- Wang, Xiaoling -- Wang, Haiyin -- Xu, Lizhi -- Liu, Xiao -- Vinar, Tomas -- Wang, Yajun -- Lam, Tak-Wah -- Yiu, Siu-Ming -- Liu, Shiping -- Zhang, Hemin -- Li, Desheng -- Huang, Yan -- Wang, Xia -- Yang, Guohua -- Jiang, Zhi -- Wang, Junyi -- Qin, Nan -- Li, Li -- Li, Jingxiang -- Bolund, Lars -- Kristiansen, Karsten -- Wong, Gane Ka-Shu -- Olson, Maynard -- Zhang, Xiuqing -- Li, Songgang -- Yang, Huanming -- Wang, Jian -- Wang, Jun -- R01 HG003229/HG/NHGRI NIH HHS/ -- R01 HG003229-05/HG/NHGRI NIH HHS/ -- England -- Nature. 2010 Jan 21;463(7279):311-7. doi: 10.1038/nature08696. Epub 2009 Dec 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉BGI-Shenzhen, Shenzhen 518083, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20010809" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Animals ; China ; Conserved Sequence/genetics ; Contig Mapping ; Diet/veterinary ; Dogs ; Evolution, Molecular ; Female ; Fertility/genetics/physiology ; Genome/*genetics ; *Genomics ; Heterozygote ; Humans ; Multigene Family/genetics ; Polymorphism, Single Nucleotide/genetics ; Receptors, G-Protein-Coupled/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Synteny/genetics ; Ursidae/classification/*genetics/physiology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
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    High-speed graphene transistors with a self-aligned nanowire gate (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-09-03
    Description: Graphene has attracted considerable interest as a potential new electronic material. With its high carrier mobility, graphene is of particular interest for ultrahigh-speed radio-frequency electronics. However, conventional device fabrication processes cannot readily be applied to produce high-speed graphene transistors because they often introduce significant defects into the monolayer of carbon lattices and severely degrade the device performance. Here we report an approach to the fabrication of high-speed graphene transistors with a self-aligned nanowire gate to prevent such degradation. A Co(2)Si-Al(2)O(3) core-shell nanowire is used as the gate, with the source and drain electrodes defined through a self-alignment process and the channel length defined by the nanowire diameter. The physical assembly of the nanowire gate preserves the high carrier mobility in graphene, and the self-alignment process ensures that the edges of the source, drain and gate electrodes are automatically and precisely positioned so that no overlapping or significant gaps exist between these electrodes, thus minimizing access resistance. It therefore allows for transistor performance not previously possible. Graphene transistors with a channel length as low as 140 nm have been fabricated with the highest scaled on-current (3.32 mA mum(-1)) and transconductance (1.27 mS mum(-1)) reported so far. Significantly, on-chip microwave measurements demonstrate that the self-aligned devices have a high intrinsic cut-off (transit) frequency of f(T) = 100-300 GHz, with the extrinsic f(T) (in the range of a few gigahertz) largely limited by parasitic pad capacitance. The reported intrinsic f(T) of the graphene transistors is comparable to that of the very best high-electron-mobility transistors with similar gate lengths.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2965636/" 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/PMC2965636/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liao, Lei -- Lin, Yung-Chen -- Bao, Mingqiang -- Cheng, Rui -- Bai, Jingwei -- Liu, Yuan -- Qu, Yongquan -- Wang, Kang L -- Huang, Yu -- Duan, Xiangfeng -- 1DP2OD004342-01/OD/NIH HHS/ -- DP2 OD004342-01/OD/NIH HHS/ -- England -- Nature. 2010 Sep 16;467(7313):305-8. doi: 10.1038/nature09405. Epub 2010 Sep 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20811365" target="_blank"〉PubMed〈/a〉
    Keywords: Calibration ; Carbon/*chemistry ; Electric Capacitance ; Electrodes ; Electronics/*instrumentation ; Nanowires/*chemistry/ultrastructure ; Temperature ; *Transistors, Electronic
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
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    Migrastatin analogues target fascin to block tumour metastasis (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-04-16
    Description: Tumour metastasis is the primary cause of death of cancer patients. Development of new therapeutics preventing tumour metastasis is urgently needed. Migrastatin is a natural product secreted by Streptomyces, and synthesized migrastatin analogues such as macroketone are potent inhibitors of metastatic tumour cell migration, invasion and metastasis. Here we show that these migrastatin analogues target the actin-bundling protein fascin to inhibit its activity. X-ray crystal structural studies reveal that migrastatin analogues bind to one of the actin-binding sites on fascin. Our data demonstrate that actin cytoskeletal proteins such as fascin can be explored as new molecular targets for cancer treatment, in a similar manner to the microtubule protein tubulin.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2857318/" 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/PMC2857318/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Lin -- Yang, Shengyu -- Jakoncic, Jean -- Zhang, J Jillian -- Huang, Xin-Yun -- CA136837/CA/NCI NIH HHS/ -- R01 CA136837/CA/NCI NIH HHS/ -- R01 CA136837-01A1/CA/NCI NIH HHS/ -- England -- Nature. 2010 Apr 15;464(7291):1062-6. doi: 10.1038/nature08978.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology, Cornell University Weill Medical College, New York, New York 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20393565" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/metabolism ; Animals ; Antineoplastic Agents/chemistry/metabolism/pharmacology/therapeutic use ; Binding Sites/drug effects ; Breast Neoplasms/drug therapy/pathology ; Carrier Proteins/*antagonists & inhibitors/chemistry/genetics/metabolism ; Cell Line, Tumor ; Cell Movement/drug effects ; Crystallography, X-Ray ; Drug Resistance, Neoplasm/genetics ; Female ; Humans ; Lung Neoplasms/prevention & control/secondary ; Macrolides/*chemistry/metabolism/*pharmacology/therapeutic use ; Mice ; Mice, Inbred BALB C ; Mice, Inbred NOD ; Mice, SCID ; Microfilament Proteins/*antagonists & inhibitors/chemistry/genetics/metabolism ; Models, Molecular ; Mutation/genetics ; Neoplasm Invasiveness/pathology/prevention & control ; Neoplasm Metastasis/drug therapy/pathology/*prevention & control ; Piperidones/*chemistry/metabolism/*pharmacology/therapeutic use ; Protein Conformation
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
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    A hemispherical electronic eye camera based on compressible silicon optoelectronics (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-08-08
    Description: The human eye is a remarkable imaging device, with many attractive design features. Prominent among these is a hemispherical detector geometry, similar to that found in many other biological systems, that enables a wide field of view and low aberrations with simple, few-component imaging optics. This type of configuration is extremely difficult to achieve using established optoelectronics technologies, owing to the intrinsically planar nature of the patterning, deposition, etching, materials growth and doping methods that exist for fabricating such systems. Here we report strategies that avoid these limitations, and implement them to yield high-performance, hemispherical electronic eye cameras based on single-crystalline silicon. The approach uses wafer-scale optoelectronics formed in unusual, two-dimensionally compressible configurations and elastomeric transfer elements capable of transforming the planar layouts in which the systems are initially fabricated into hemispherical geometries for their final implementation. In a general sense, these methods, taken together with our theoretical analyses of their associated mechanics, provide practical routes for integrating well-developed planar device technologies onto the surfaces of complex curvilinear objects, suitable for diverse applications that cannot be addressed by conventional means.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ko, Heung Cho -- Stoykovich, Mark P -- Song, Jizhou -- Malyarchuk, Viktor -- Choi, Won Mook -- Yu, Chang-Jae -- Geddes, Joseph B 3rd -- Xiao, Jianliang -- Wang, Shuodao -- Huang, Yonggang -- Rogers, John A -- England -- Nature. 2008 Aug 7;454(7205):748-53. doi: 10.1038/nature07113.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18685704" target="_blank"〉PubMed〈/a〉
    Keywords: *Biomimetic Materials ; Biomimetics/*instrumentation ; Electronics/*instrumentation ; *Eye ; Humans ; Lasers ; Lighting ; Semiconductors ; Silicon/*chemistry
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
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    53BP1 facilitates long-range DNA end-joining during V(D)J recombination (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-10-22
    Description: Variable, diversity and joining (V(D)J) recombination and class-switch recombination use overlapping but distinct non-homologous end joining pathways to repair DNA double-strand-break intermediates. 53BP1 is a DNA-damage-response protein that is rapidly recruited to sites of chromosomal double-strand breaks, where it seems to function in a subset of ataxia telangiectasia mutated (ATM) kinase-, H2A histone family member X (H2AX, also known as H2AFX)- and mediator of DNA damage checkpoint 1 (MDC1)-dependent events. A 53BP1-dependent end-joining pathway has been described that is dispensable for V(D)J recombination but essential for class-switch recombination. Here we report a previously unrecognized defect in the joining phase of V(D)J recombination in 53BP1-deficient lymphocytes that is distinct from that found in classical non-homologous-end-joining-, H2ax-, Mdc1- and Atm-deficient mice. Absence of 53BP1 leads to impairment of distal V-DJ joining with extensive degradation of unrepaired coding ends and episomal signal joint reintegration at V(D)J junctions. This results in apoptosis, loss of T-cell receptor alpha locus integrity and lymphopenia. Further impairment of the apoptotic checkpoint causes propagation of lymphocytes that have antigen receptor breaks. These data suggest a more general role for 53BP1 in maintaining genomic stability during long-range joining of DNA breaks.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596817/" 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/PMC3596817/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Difilippantonio, Simone -- Gapud, Eric -- Wong, Nancy -- Huang, Ching-Yu -- Mahowald, Grace -- Chen, Hua Tang -- Kruhlak, Michael J -- Callen, Elsa -- Livak, Ferenc -- Nussenzweig, Michel C -- Sleckman, Barry P -- Nussenzweig, Andre -- R01AI074953/AI/NIAID NIH HHS/ -- Z01 BC010283-10/Intramural NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2008 Nov 27;456(7221):529-33. doi: 10.1038/nature07476. Epub 2008 Oct 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-1360, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18931658" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Apoptosis ; Chromosomal Proteins, Non-Histone ; DNA/genetics/*metabolism ; DNA Breaks ; DNA-Binding Proteins ; Gene Rearrangement, T-Lymphocyte/*genetics ; Genes, T-Cell Receptor alpha/genetics ; Genomic Instability ; Intracellular Signaling Peptides and Proteins/deficiency/genetics/*metabolism ; Lymphopenia/genetics/pathology ; Mice ; Models, Genetic ; Receptors, Antigen, T-Cell/genetics/metabolism ; *Recombination, Genetic ; Sequence Homology ; T-Lymphocytes/cytology/metabolism ; Thymus Gland/cytology
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  • 6
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    An oestrogen-receptor-alpha-bound human chromatin interactome (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-11-06
    Description: Genomes are organized into high-level three-dimensional structures, and DNA elements separated by long genomic distances can in principle interact functionally. Many transcription factors bind to regulatory DNA elements distant from gene promoters. Although distal binding sites have been shown to regulate transcription by long-range chromatin interactions at a few loci, chromatin interactions and their impact on transcription regulation have not been investigated in a genome-wide manner. Here we describe the development of a new strategy, chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) for the de novo detection of global chromatin interactions, with which we have comprehensively mapped the chromatin interaction network bound by oestrogen receptor alpha (ER-alpha) in the human genome. We found that most high-confidence remote ER-alpha-binding sites are anchored at gene promoters through long-range chromatin interactions, suggesting that ER-alpha functions by extensive chromatin looping to bring genes together for coordinated transcriptional regulation. We propose that chromatin interactions constitute a primary mechanism for regulating transcription in mammalian genomes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774924/" 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/PMC2774924/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fullwood, Melissa J -- Liu, Mei Hui -- Pan, You Fu -- Liu, Jun -- Xu, Han -- Mohamed, Yusoff Bin -- Orlov, Yuriy L -- Velkov, Stoyan -- Ho, Andrea -- Mei, Poh Huay -- Chew, Elaine G Y -- Huang, Phillips Yao Hui -- Welboren, Willem-Jan -- Han, Yuyuan -- Ooi, Hong Sain -- Ariyaratne, Pramila N -- Vega, Vinsensius B -- Luo, Yanquan -- Tan, Peck Yean -- Choy, Pei Ye -- Wansa, K D Senali Abayratna -- Zhao, Bing -- Lim, Kar Sian -- Leow, Shi Chi -- Yow, Jit Sin -- Joseph, Roy -- Li, Haixia -- Desai, Kartiki V -- Thomsen, Jane S -- Lee, Yew Kok -- Karuturi, R Krishna Murthy -- Herve, Thoreau -- Bourque, Guillaume -- Stunnenberg, Hendrik G -- Ruan, Xiaoan -- Cacheux-Rataboul, Valere -- Sung, Wing-Kin -- Liu, Edison T -- Wei, Chia-Lin -- Cheung, Edwin -- Ruan, Yijun -- 1U54HG004557-01/HG/NHGRI NIH HHS/ -- R01 HG004456/HG/NHGRI NIH HHS/ -- R01 HG004456-01/HG/NHGRI NIH HHS/ -- R01 HG004456-02/HG/NHGRI NIH HHS/ -- R01 HG004456-03/HG/NHGRI NIH HHS/ -- R01HG003521-01/HG/NHGRI NIH HHS/ -- R01HG004456-01/HG/NHGRI NIH HHS/ -- U54 HG004557/HG/NHGRI NIH HHS/ -- U54 HG004557-01/HG/NHGRI NIH HHS/ -- U54 HG004557-02/HG/NHGRI NIH HHS/ -- U54 HG004557-03/HG/NHGRI NIH HHS/ -- U54 HG004557-04/HG/NHGRI NIH HHS/ -- England -- Nature. 2009 Nov 5;462(7269):58-64. doi: 10.1038/nature08497.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19890323" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cell Line ; Chromatin/*genetics/*metabolism ; Chromatin Immunoprecipitation ; Cross-Linking Reagents ; Estrogen Receptor alpha/*metabolism ; Formaldehyde ; Genome, Human/*genetics ; Humans ; Promoter Regions, Genetic/genetics ; Protein Binding ; Reproducibility of Results ; Sequence Analysis, DNA ; Transcription, Genetic ; Transcriptional Activation
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  • 7
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    Structural insights into mechanisms of the small RNA methyltransferase HEN1 (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-10-09
    Description: RNA silencing is a conserved regulatory mechanism in fungi, plants and animals that regulates gene expression and defence against viruses and transgenes. Small silencing RNAs of approximately 20-30 nucleotides and their associated effector proteins, the Argonaute family proteins, are the central components in RNA silencing. A subset of small RNAs, such as microRNAs and small interfering RNAs (siRNAs) in plants, Piwi-interacting RNAs in animals and siRNAs in Drosophila, requires an additional crucial step for their maturation; that is, 2'-O-methylation on the 3' terminal nucleotide. A conserved S-adenosyl-l-methionine-dependent RNA methyltransferase, HUA ENHANCER 1 (HEN1), and its homologues are responsible for this specific modification. Here we report the 3.1 A crystal structure of full-length HEN1 from Arabidopsis in complex with a 22-nucleotide small RNA duplex and cofactor product S-adenosyl-l-homocysteine. Highly cooperative recognition of the small RNA substrate by multiple RNA binding domains and the methyltransferase domain in HEN1 measures the length of the RNA duplex and determines the substrate specificity. Metal ion coordination by both 2' and 3' hydroxyls on the 3'-terminal nucleotide and four invariant residues in the active site of the methyltransferase domain suggests a novel Mg(2+)-dependent 2'-O-methylation mechanism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, Ying -- Ji, Lijuan -- Huang, Qichen -- Vassylyev, Dmitry G -- Chen, Xuemei -- Ma, Jin-Biao -- GM074252/GM/NIGMS NIH HHS/ -- R01 GM074840/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Oct 8;461(7265):823-7. doi: 10.1038/nature08433.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19812675" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Arabidopsis/*enzymology/genetics ; Arabidopsis Proteins/*chemistry/genetics/*metabolism ; Biocatalysis ; Catalytic Domain ; Crystallography, X-Ray ; Magnesium/metabolism ; Methylation ; Methyltransferases/*chemistry/*metabolism ; Models, Biological ; Models, Molecular ; Protein Structure, Tertiary ; RNA/genetics/*metabolism ; RNA-Binding Proteins/chemistry/metabolism ; S-Adenosylhomocysteine/chemistry/metabolism ; Structure-Activity Relationship ; Substrate Specificity
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 8
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    Structure of the formate transporter FocA reveals a pentameric aquaporin-like channel (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-11-27
    Description: FocA is a representative member of the formate-nitrite transporter family, which transports short-chain acids in bacteria, archaea, fungi, algae and parasites. The structure and transport mechanism of the formate-nitrite transporter family remain unknown. Here we report the crystal structure of Escherichia coli FocA at 2.25 A resolution. FocA forms a symmetric pentamer, with each protomer consisting of six transmembrane segments. Despite a lack of sequence homology, the overall structure of the FocA protomer closely resembles that of aquaporin and strongly argues that FocA is a channel, rather than a transporter. Structural analysis identifies potentially important channel residues, defines the channel path and reveals two constriction sites. Unlike aquaporin, FocA is impermeable to water but allows the passage of formate. A structural and biochemical investigation provides mechanistic insights into the channel activity of FocA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Yi -- Huang, Yongjian -- Wang, Jiawei -- Cheng, Chao -- Huang, Weijiao -- Lu, Peilong -- Xu, Ya-Nan -- Wang, Pengye -- Yan, Nieng -- Shi, Yigong -- England -- Nature. 2009 Nov 26;462(7272):467-72. doi: 10.1038/nature08610.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Ministry of Education Protein Science Laboratory, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19940917" target="_blank"〉PubMed〈/a〉
    Keywords: Aquaporins/*chemistry/metabolism ; Crystallography, X-Ray ; Escherichia coli/chemistry/genetics/metabolism ; Escherichia coli Proteins/*chemistry/genetics/metabolism ; Formates/metabolism ; Liposomes/chemistry/metabolism ; Membrane Transport Proteins/*chemistry/genetics/metabolism ; Models, Molecular ; Molecular Mimicry ; Mutation ; Permeability ; Protein Structure, Quaternary ; Structure-Activity Relationship ; Water/analysis/metabolism
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  • 9
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    The carbon balance of terrestrial ecosystems in China (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-04-28
    Description: Global terrestrial ecosystems absorbed carbon at a rate of 1-4 Pg yr(-1) during the 1980s and 1990s, offsetting 10-60 per cent of the fossil-fuel emissions. The regional patterns and causes of terrestrial carbon sources and sinks, however, remain uncertain. With increasing scientific and political interest in regional aspects of the global carbon cycle, there is a strong impetus to better understand the carbon balance of China. This is not only because China is the world's most populous country and the largest emitter of fossil-fuel CO(2) into the atmosphere, but also because it has experienced regionally distinct land-use histories and climate trends, which together control the carbon budget of its ecosystems. Here we analyse the current terrestrial carbon balance of China and its driving mechanisms during the 1980s and 1990s using three different methods: biomass and soil carbon inventories extrapolated by satellite greenness measurements, ecosystem models and atmospheric inversions. The three methods produce similar estimates of a net carbon sink in the range of 0.19-0.26 Pg carbon (PgC) per year, which is smaller than that in the conterminous United States but comparable to that in geographic Europe. We find that northeast China is a net source of CO(2) to the atmosphere owing to overharvesting and degradation of forests. By contrast, southern China accounts for more than 65 per cent of the carbon sink, which can be attributed to regional climate change, large-scale plantation programmes active since the 1980s and shrub recovery. Shrub recovery is identified as the most uncertain factor contributing to the carbon sink. Our data and model results together indicate that China's terrestrial ecosystems absorbed 28-37 per cent of its cumulated fossil carbon emissions during the 1980s and 1990s.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Piao, Shilong -- Fang, Jingyun -- Ciais, Philippe -- Peylin, Philippe -- Huang, Yao -- Sitch, Stephen -- Wang, Tao -- England -- Nature. 2009 Apr 23;458(7241):1009-13. doi: 10.1038/nature07944.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology, College of Urban and Environmental Science, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China. slpiao@pku.edu.cn〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19396142" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere/chemistry ; Biomass ; Carbon/analysis/*metabolism ; Carbon Dioxide/analysis/chemistry/metabolism ; China ; *Ecosystem ; Forestry/history ; Fossil Fuels/*history ; History, 20th Century ; Soil/analysis ; Trees/metabolism
    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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  • 10
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    Natural allelic variation underlying a major fitness trade-off in Arabidopsis thaliana (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-06-04
    Description: Plants can defend themselves against a wide array of enemies, from microbes to large animals, yet there is great variability in the effectiveness of such defences, both within and between species. Some of this variation can be explained by conflicting pressures from pathogens with different modes of attack. A second explanation comes from an evolutionary 'tug of war', in which pathogens adapt to evade detection, until the plant has evolved new recognition capabilities for pathogen invasion. If selection is, however, sufficiently strong, susceptible hosts should remain rare. That this is not the case is best explained by costs incurred from constitutive defences in a pest-free environment. Using a combination of forward genetics and genome-wide association analyses, we demonstrate that allelic diversity at a single locus, ACCELERATED CELL DEATH 6 (ACD6), underpins marked pleiotropic differences in both vegetative growth and resistance to microbial infection and herbivory among natural Arabidopsis thaliana strains. A hyperactive ACD6 allele, compared to the reference allele, strongly enhances resistance to a broad range of pathogens from different phyla, but at the same time slows the production of new leaves and greatly reduces the biomass of mature leaves. This allele segregates at intermediate frequency both throughout the worldwide range of A. thaliana and within local populations, consistent with this allele providing substantial fitness benefits despite its marked impact on growth.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3055268/" 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/PMC3055268/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Todesco, Marco -- Balasubramanian, Sureshkumar -- Hu, Tina T -- Traw, M Brian -- Horton, Matthew -- Epple, Petra -- Kuhns, Christine -- Sureshkumar, Sridevi -- Schwartz, Christopher -- Lanz, Christa -- Laitinen, Roosa A E -- Huang, Yu -- Chory, Joanne -- Lipka, Volker -- Borevitz, Justin O -- Dangl, Jeffery L -- Bergelson, Joy -- Nordborg, Magnus -- Weigel, Detlef -- F23-GM65032-1/GM/NIGMS NIH HHS/ -- GM057171/GM/NIGMS NIH HHS/ -- GM057994/GM/NIGMS NIH HHS/ -- GM073822/GM/NIGMS NIH HHS/ -- GM62932/GM/NIGMS NIH HHS/ -- R01 GM062932/GM/NIGMS NIH HHS/ -- R01 GM062932-08/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Jun 3;465(7298):632-6. doi: 10.1038/nature09083.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20520716" target="_blank"〉PubMed〈/a〉
    Keywords: *Alleles ; Ankyrins/genetics/metabolism ; Arabidopsis/*genetics/growth & development/metabolism/microbiology ; Arabidopsis Proteins/genetics/metabolism ; Biomass ; Gene Expression Regulation, Plant ; Genes, Plant ; Genetic Fitness/*genetics ; Genetic Variation/*genetics ; Genome-Wide Association Study ; Molecular Sequence Data ; Phenotype ; Plant Diseases/genetics/microbiology ; Plant Leaves/anatomy & histology/genetics/growth & development/parasitology ; Quantitative Trait Loci
    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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