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The Power of Inbreeding： NGS-Based GWAS of Rice Reveals Convergent Evolution during Rice Domestication

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Molecular Plant 2016年第7期9卷 975-985页

作者： Hongru Wang Xun Xu Filipe Garrett Vieira Yunhua Xiao Zhikang Li Jun Wang rasmus nielsen Chengcai Chu State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing) Institute of Genetics and Developmental Biology Chinese Academyof Sciences Beijing 100101 China Cotlege of Life Sciences University of Chinese Academy of Sciences Beijing 100101 China BGI-Shenzhen Shenzhen 518083 China Centre for GeoGenetics University of Copenhagen 1350 Copenhagen Denmark Institute of Crop Sciences/National Key Facilities for Crop Gene Resources and Genetic Improvement Chinese Academy of Agricultural Sciences 12 SouthZhong-Guan-Cun Street Beijing 100081 China Department of Integrative Biology University of California Berkeley CA 94720 USA These authors contributed equally to this article.

Low-coverage whole-genome sequencing is an effective strategy for genome-wide association studies in hu- mans, due to the availability of large reference panels for genotype imputation. However, it is unclear whether this strategy can be utilized in other species without reference panels. Using simulations, we show that this approach is even more relevant in inbred species such as rice （Oryza sativa L.）, which are effectively haploid, allowing easy haplotype construction and imputation-based genotype calling, even without the availability of large reference panels. We sequenced 203 rice varieties with well-characterized phenotypes from the United States Department of Agriculture Rice Mini-Core Collection at an average depth of 1.5~ and used the data for mapping three traits. For the first two traits, amylose content and seed length, our approach leads to direct identification of the previously identified causal SN Ps in the major-effect loci. For the third trait, pericarp color, an important trait underwent selection during domestication, we identified a new major-effect locus. Although known loci can explain color variation in the varieties of two main subspecies of Asian domesticated rice,japonica and indica, the new locus identified is unique to another domesticated rice subgroup, aus, and together with existing loci, can fully explain the major variation in pericarp color in aus. Our discovery of a unique genetic basis of white pericarp in aus provides an example of convergent evolution during rice domestication and suggests that aus may have a domestication history independent of japonica and indica.

关键词： inbreeding GWAS rice pericarp color

Cell:研究揭示疫苗中的减毒脊髓灰质炎病毒恢复毒力机制

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现代生物医学进展 2017年第15期17卷 I0001-I0002页

作者： Adi Stern Ming Te Yeh Tal Zinger Matt Smith Caroline Wright Guy Ling rasmus nielsen Andrew Macadam Raul Andino Department of Statistics University of California Berkeley Berkeley CA 94720 USA

脊髓灰质炎（poHo，也称作小儿麻痹症）几乎被根除了。目前，大多数脊髓灰质炎爆发风险并不是来自于野外的脊髓灰质炎病毒（poliovirus），而是来自于由减毒脊髓灰质炎病毒组成的口服疫苗。这些病毒积累突变，从而允许它们在未充分接种... 详细信息

脊髓灰质炎（poHo，也称作小儿麻痹症）几乎被根除了。目前，大多数脊髓灰质炎爆发风险并不是来自于野外的脊髓灰质炎病毒（poliovirus），而是来自于由减毒脊髓灰质炎病毒组成的口服疫苗。这些病毒积累突变，从而允许它们在未充分接种的人群中传播。重新获得毒力，甚至导致疾病爆发。目前。根据一项新的研究，研究人员绘制出脊髓灰质炎病毒发生的一系列突变，

关键词：脊髓灰质炎病毒口服疫苗毒力减毒 Cen 机制研究人员麻痹症

The diploid genome sequence of an Asian individual

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The diploid genome sequence of an Asian individual

培育生物产业，发展绿色经济——第五届中国生物产业大会·2011基因科学与产业发展论坛

作者： Laurie Goodman Ines Hellmann Michael Inouye John Pool Karsten Kristiansen Gane Ka-Shu Wong rasmus nielsen Richard Durbin Lars Bolund Beijing Genomics Institute at Shenzhen Departments of Integrative Biology and Statistics University of CaliforniaBerkeleyCalifornia 94720USA The Wellcome Trust Sanger Institute Wellcome Trust Genome CampusHinxtonCambridge CB10 1SAUK Departments of Integrative Biology and Statistics University of CaliforniaBerkeleyCalifornia94720USA Department of Biochemistry and Molecular Biology University of Southern DenmarkOdense M DK-5230Denmark Beijing Genomics Institute at Shenzhen Shenzhen 518000China Department of Biological Sciences and Department of Medicine University of AIbertaEdmonton ABT6G 2E9Canada Insitute of Human Genetics University of AarhusAarhus DK-8000Denmark

Here we present the first diploid genome sequence of an Asian *** genome was sequenced to 36-fold average coverage using massively parallel sequencing *** aligned the short reads onto the NCBI human reference genome to 99.97%coverage,and guided by the reference genome,we used uniquely mapped reads to assemble a high-quality consensus sequence for 92%of the Asian individual's *** identified approximately 3 million single-nucleotide polymorphisms(SNPs) inside this region,of which 13.6%were not in the dbSNP *** analysis showed that SNP identification had high accuracy and consistency,indicating the high sequence quality of this *** also carried out heterozygote phasing and haplotype prediction against HapMap CHB and JPT haplotypes (Chinese and Japanese,respectively),sequence comparison with the two available individual genomes(*** and J. ***),and structural variation *** variations were considered for their potential biological *** sequence data and analyses demonstrate the potential usefulness of next-generation sequencing technologies for personal genomics.

关键词： The diploid genome sequence of an Asian individual

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SUPERKILEN

建筑技艺 2012年第2期18卷 44-49页

作者： Ondrej Tichy Jonas Lehmann Rune Hansen Jan Borgstrφm Lacin Karaoz Jonas Barre Nicklas Antoni Rasch Gabrielle Nadeau Jennifer Dahm Petersen Richard Howis Andreas Castberg Armen Menendian Jens Majdal Kaarsholm Jan Magasanik Toni Offenberger Katia Steckemetz Cristian Bohne Karoline Liedtke Jakob Fenger rasmus nielsen Bjφrnstjerne Christiansen 张岩 Superflex BIG Topotek1

正Superkilen是BIG、Topotek1和SUPERFLEX之间创造性合作的成果,从早期的概念设计到施工设计阶段的密切配合,成就了建筑、景观和艺术的完美融合。该项目是将半英里长的城市空间嵌入到丹麦种族最多样化和最具社会挑战性的一个街区中去。... 详细信息

正Superkilen是BIG、Topotek1和SUPERFLEX之间创造性合作的成果,从早期的概念设计到施工设计阶段的密切配合,成就了建筑、景观和艺术的完美融合。该项目是将半英里长的城市空间嵌入到丹麦种族最多样化和最具社会挑战性的一个街区中去。设计师们有一个总体的想法。

关键词：设计师概念设计密切配合城市空间广场设计阶段景观创造性公园多样化

Full scale amendment of a contaminated wood impregnation site with iron water treatment residues

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Frontiers of Environmental Science & Engineering 2016年第4期10卷 169-178页

作者： Sanne Skov nielsen Peter KJELDSEN rasmus JAKOBSEN Orbicon Ringstedvej 20 DK-4000 Roskilde Denmark Department of Environmental Engineering Technical University of Denmark Miljovej 113 DK-2800 Kgs. Lyngby Denmark Geological Survey of Denmark and Greenland Geological Survey of Denmark and Greenland Oster Voldgade 10 DK-1350 Copenhagen K Denmark

Iron water treatment residues （Fe-WTR） are a free by-product of the treatment of drinking water with high concentration of iron oxides and potential for arsenic sorption. This paper aims at applying Fe- WTR to a contaminated site, measuring the reduction in contaminant leaching, and discussing the design of delivery and mixing strategy for soil stabilization at field scale and present a cost-effective method of soil mixing by connnon contractor machinery. Soil contaminated by As, Cr, and Cu at an abandoned wood impregnation site was amended with 0.22% （dw） Fe-WTR. To evaluate the full scale amendment a 100 mtest site and a control site （without amendment） were monitored for 14 months. Also soil analysis of Fe to evaluate the degree of soil and Fe-WTR mixing was done. Stabilization with Fe-WTR had a significant effect on leachable contaminants, reducing pore water As by 93%, Cu by 91% and Cr by 95% in the upper samplers. Dosage and mixing of Fe-WTR in the soil proved to be difficult in the deeper part of the field, and Pire water concentrations of arsenic was generally *** water logged conditions no increase in dissolved iron or arsenic was observed in the amended soil. Our field scale amendment of contaminated soil was overall successful in decreasing leaching of As, Cr and Cu. With minor improvements in the mixing and delivery strategy, this stabilization method is suggested for use in cases, where leaching ofCu, Cr and As constitutes a risk for groundwater and freshwater.

关键词： Field experiment Iron oxide Arsenic Stabilization Wood preservation sites

亚细胞特定区域化线粒体含量是否与肌纤维类型、饮食干预有关?

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体育科学 2021年第3期41卷 34-41页

作者：耿国强梁祎珩 rasmus Jensen Joachim nielsen NielsØrtenblad 邱俊强北京体育大学北京100084 南丹麦大学丹麦欧登塞5230

目的:亚细胞特定区域化线粒体的超微结构与功能表达相关,但亚细胞特定区域下的线粒体含量与肌纤维类型及饮食干预的关系尚不清楚。研究探讨亚细胞特定区域化线粒体(肌原纤维间线粒体、肌膜下线粒体、总线粒体)的含量与不同肌纤维类型的... 详细信息

目的:亚细胞特定区域化线粒体的超微结构与功能表达相关,但亚细胞特定区域下的线粒体含量与肌纤维类型及饮食干预的关系尚不清楚。研究探讨亚细胞特定区域化线粒体(肌原纤维间线粒体、肌膜下线粒体、总线粒体)的含量与不同肌纤维类型的关系,并探究短期饮食干预对肌细胞亚细胞特定区域线粒体含量的影响。方法:招募11名无训练经历的业余锻炼者。在依次接受3种不同的短期饮食(依次为混合饮食、高脂肪+高蛋白质饮食、高碳水化合物饮食)干预后,分别进行75%最大摄氧量强度的功率自行车耐力力竭测试,在运动前、运动中每隔一个小时、运动后即刻对受试者的股外侧肌部位进行肌肉活检,根据受试者在3种不同饮食干预影响下的不同运动表现(112±22 min vs.69±18 min vs.150±30 min),每位受试者在3次测试中分别被采集3条、2条、4条,共9条肌纤维。使用体视学方法分析并计算特定亚细胞定位的线粒体含量。结果:Ⅰ型肌纤维中肌原纤维间(intermyofibrillar,IMF)、肌膜下(subsarcolemmal,SS)线粒体含量显著多于Ⅱ型肌纤维(P0.05)。结论:Ⅰ型肌纤维中线粒体总量多于Ⅱ型肌纤维,且在肌细胞微观特性视角下,亚细胞不同区域下分布的线粒体(IMF和SS线粒体),均呈现出在Ⅰ型肌纤维中的分布含量多于Ⅱ型肌纤维的状态;不同肌纤维的总线粒体含量为Z线宽度作为区分快慢肌的判断方法提供了更直接的数据支撑;不同糖原储备的短期饮食干预下,长时间亚极量运动至力竭时间有显著性差异,但运动表现的差异与亚细胞特定区域化线粒体含量无关。

关键词：线粒体含量亚细胞定位肌纤维类型饮食干预

Programmable polyketide biosynthesis platform for production of aromatic compounds in yeast

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Synthetic and Systems Biotechnology 2020年第1期5卷 11-18页

作者： Tadas Jakočiūnas Andreas K.Klitgaard Eftychia Eva Kontou Julie Bang nielsen Emil Thomsen David Romero-Suarez Kai Blin Christopher J.Petzold Jennifer W.Gin Yaojun Tong Charlotte Held Gotfredsen Pep Charusanti rasmus J.N.Frandsen Tilmann Weber Sang Yup Lee Michael K.Jensen Jay D.Keasling The Novo Nordisk Foundation Center for Biosustainability Technical University of DenmarkKgs.LyngbyDenmark Joint BioEnergy Institute EmeryvilleCAUSA Biological Systems&Engineering Division Lawrence Berkeley National LaboratoryBerkeleyCAUSA Department of Chemical and Biomolecular Engineering&Department of Bioengineering University of California BerkeleyCAUSA Center for Synthetic Biochemistry Institute for Synthetic BiologyShenzhen Institutes for Advanced TechnologiesShenzhenChina Department of Chemistry Technical University of DenmarkKgs.LyngbyDenmark Department of Biotechnology and Biomedicine Technical University of DenmarkKgs.LyngbyDenmark Department of Chemical and Biomolecular Engineering(BK21 Plus Program) Korea Advanced Institute of Science and Technology(KAIST)291 Daehak-roYuseong-guDaejeon34141Republic of Korea

To accelerate the shift to bio-based production and overcome complicated functional implementation of natural and artificial biosynthetic pathways to industry relevant organisms,development of new,versatile,bio-based production platforms is *** we present a novel yeast-based platform for biosynthesis of bacterial aromatic *** platform is based on a synthetic polyketide synthase system enabling a first demonstration of bacterial aromatic polyketide biosynthesis in a eukaryotic host.

关键词： Natural products Synthetic biology Aromatic polyketides CRISPR/Cas9 Polyketide Production platform in eukaryotes Metabolic engineering Biotechnology

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卡尔斯港文化中心

现代装饰 2014年第6期 100-103页

作者： Kim Herforth nielsen Jan Ammundsen Morten Breinholt rasmus Mφller Maria Tcacova Filip Lipinski 姜敏华 3XN建筑事务所

本案位于瑞典卡尔斯港一处面向大海的东部码头。3XN建筑事务所在此开发设计了个新文化中心和图书馆。弯曲有机形态的设计沉浸于俏皮的光的表达之中,体现出该建筑的有机形态与逻辑性。建筑分为上下两大体块,彼此之间形成位移,创建出一个... 详细信息

本案位于瑞典卡尔斯港一处面向大海的东部码头。3XN建筑事务所在此开发设计了个新文化中心和图书馆。弯曲有机形态的设计沉浸于俏皮的光的表达之中,体现出该建筑的有机形态与逻辑性。建筑分为上下两大体块,彼此之间形成位移,创建出一个面朝西北方向的低入口、一个位于东北角的露天剧场和一处可用作庇荫的阳光充足的休闲区。

关键词：文化中心建筑事务所有机形态露天剧场开发设计西北方向休闲区体量室内气候聚会场所

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大规模无创产前检测的基因组分析揭示了多个性状的遗传关联、病毒的感染模式以及中国人群的遗传历史

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科学新闻 2019年第2期 34-34页

作者： Siyang Liu Shujia Huang Fang Chen Lijian Zhao Yuying Yuan Stephen Starko Francis Lin Fang Zilong Li Long Lin Rong Liu Yong Zhang Huixin Xu Shengkang Li Yuwen Zhou Robert W.Davies Qiang Liu Robin G.Walters Kuang Lin Jia Ju Thorfinn Korneliussen Melinda A.Yang Qiaomei Fu Jun Wang Lijun Zhou Anders Krogh Hongyun Zhang Wei Wang Zhengming Chen Zhiming Cai Ye Yin Huanming Yang Mao Mao Jay Shendure 汪建 Anders Albrechtsen 金鑫 rasmus nielsen 徐讯华大基因华南理工大学深圳华大生命科学研究院

文章简介本研究分析了参与无创产前基因检测(NIPT)的141,431名中国女性的全基因组低深度测序数据。研究团队使用这些数据描绘了中国人的群体遗传特征,并探索了遗传因素与母婴健康等性状的相互关联情况。研究发现,现代中国人群等位基因... 详细信息

文章简介本研究分析了参与无创产前基因检测(NIPT)的141,431名中国女性的全基因组低深度测序数据。研究团队使用这些数据描绘了中国人的群体遗传特征,并探索了遗传因素与母婴健康等性状的相互关联情况。研究发现,现代中国人群等位基因的频率分布是古

关键词：无创产前检测感染模式基因组分析