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| 1 | MIWI and piRNA-mediated cleavage of messenger RNAs in mouse testes显示文摘piRNA 机械在调停以它的角色著名 transposons 的 epigenetic silencing。最近的研究建议这功能也包含导出 transposon 的抄本的指导 piRNA 的劈开。同样多 piRNAs 也看起来有能力指向多样的 mRNAs,这提起 piRNAs 可以与 siRNAs 比广泛地扮演降级的吸引人的可能性特定的 mRNAs。直接测试这个假设,我们比较了联系的老鼠 PIWI (MIWI ) 有从老鼠睾丸的试验性地识别的劈开的 mRNA 碎片的 piRNAs,和主要发生在的观察劈开地点从 5 ′ 放 10;通常认为的指向结束 piRNAs。我们也注意了强壮的偏爱因为分别地,在核苷酸的 U 和 A 残余在 piRNAs 和 mRNA 碎片放 1 和 10,由“乒乓球”类似于 piRNA 扩大的模式的特征骑车。通过由介绍的 CLIP-seq 和基因表示 MIWI-RNA 相互作用印射,我们发现许多潜在的指向 piRNA 的 mRNAs 直接与 MIWI 交往,表演在 Miwi 的睾丸提高了表达式层次催化变异的鼠标。基于记者的试金进一步揭示了在调停 piRNA 的目标压抑的为 slicer 活动和 MIWI 的装载 piRNA 能力的在 piRNAs 和 mRNA 目标和要求之间的基础配对的重要性。重要地,我们证明某些关键 piRNA 目标的那合适的周转为精子形成是必要的。一起,这些调查结果为男细菌房间开发和成熟在鼠标睾丸和它的中央要求揭示 piRNA 机械的象 siRNA 一样函数。 | Peng Zhang Jun-Yan Kang Lan-Tao GOU Jiajia Wang Yuanchao Xue Geir Skogerboe Peng Dai Da-Wei Huang Runsheng Chen Xiang-Dong Fu Mo-Fang Liu Shunmin He | 2015 | Cell Research2015，25，2： | 35 |
| 2 | A Global Identification and Analysis of Small Nucleolar RNAs and Possible Intermediate-Sized Non-Coding RNAs in Oryza sativa显示文摘积累的证据建议非编码的 RNA (ncRNAs ) 在许多真核细胞的有机体普遍、机能上地重要。在这研究,我们采用了分别和 cDNA 图书馆构造方法列在后面由的一种特殊尺寸 454 系统地介绍米饭的深定序中间尺寸的 ncRNAs。我们的分析总共导致了 1349 ncRNAs 的鉴定,包括一个未知功能的范畴的 754 新奇 ncRNAs。所有识别 ncRNAs 的染色体分发没显示出海滨偏爱,并且显示了类似于与很少染色体相关性在编码蛋白质的基因观察了那的一个模式。非常, ncRNAs 的一半被集中在附近编码区域的 5 和 3 个终点正海滨。新奇 ncRNAs 的多数是米饭特定,当 78% 小核仁的 RNA (snoRNAs ) 被保存时。双人脚踏车复制驾驶了扩大在 snoRNA 基因家庭的一半上。而且, 90% snoRNA 候选人被显示特别地生产在 2030 nt,其 80% 通常与淘金者蛋白质被联系,和 AGO1b 之间的小 RNA。总的来说,我们的调查结果在 monocot 种提供中间尺寸的非编码的 transcriptome 的一个全面看法,它将为 ncRNA 函数的深入的分析用作一个有用平台。 | Ting-Ting Liu Danmeng Zhu Wei Chen Wei Deng Hang He Guangming He Baoyan Bai Yijun Qi Runsheng Chen Xing Wang Deng | 2013 | Molecular Plant2013，6，3： | 10 |
| 3 | Genomic Features and Regulatory Roles of Intermediate-Sized Non-Coding RNAs in Arabidopsis显示文摘在染色体宽的技术的最近的进展与各种各样的尺寸 ineukaryotes 允许几千非编码的 RNA 的鉴定,其中一些进一步被显示了在许多生物进程服务重要函数。然而在 modelplant Arabidopsis,新奇中介大小的 ncRNAs (im-ncRNAs )(50 ~ 300 nt ) 很限制了信息。由与深定序的技术使用修改隔离 strategycombined,我们全球性在 Arabidopsis 识别了 838 im-ncRNAs。多于一半(58%) 是新 ncRNA 种类,主要进化分叉。有趣地,与 5-UTR-derived 小说 im-ncRNAs 注解了 protein-codinggenes 趋于高度被表示。为 intergenic im-ncRNAs,他们比得上在幼苗的 mRNAs 的平均 abundanceswere,而是子集,在开始衰老的展出显著地更低的表示离开。进一步, intergenic im-ncRNAs 被调整由类似基因并且编码蛋白质的基因的到那些的 epigenetic 机制,和 someshowed 发展地调整了表示模式。基因屏蔽显示出的大规模颠倒 down-regulationof 很多 im-ncRNAs 在 vivo 导致了明显的分子的变化或反常发展显型,在植物生长和开发显示 im-ncRNAs 的功能的重要性。一起,我们的结果证明 thatnovel Arabidopsis im-ncRNAs 发展地被调整,功能的部件在 transcriptome.Key 词发现了: | Yuqiu Wang Xuncheng Wang Wei Deng Xiuduo Fan Ting-Ting Liu Guangming He Runsheng Chen William Terzaghi Danmeng Zhu Xing Wang Deng | 2014 | Molecular Plant2014，7，3： | 9 |
| 4 | Effects of soil properties on production and bioaccumulation of methylmercury in rice paddies at a mercury mining area,China显示文摘Rice paddy soil is recognized as the hotspot of mercury(Hg) methylation, which is mainly a biotic process mediated by many abiotic factors. In this study, effects of key soil properties on the production and bioaccumulation of Hg and methylmercury(MeHg) in Hg-contaminated rice paddies were investigated. Rice and soil samples were collected from the active Hg smelting site and abandoned Hg mining sites(a total of 124 paddy fields) in the Wanshan Mercury Mine, China. Total Hg(THg) and MeHg in soils and rice grains, together with sulfur(S),selenium(Se), organic matter(OM), nitrogen(N), phosphorus(P), mineral compositions(e.g., SiO_2, Al_2O_3 and Fe_2O_3) and pH in soils were quantified. The results showed that long-term Hg mining activities had resulted in THg and MeHg contaminations in soil-rice system. The newly-deposited atmospheric Hg was more readily methylated relative to the native Hg already in soils, which could be responsible for the elevated MeHg levels in soils and rice grains around the active artificial Hg smelting site. The MeHg concentrations in soils and rice grains showed a significantly negative relationship with soil N/Hg, S/Hg and OM/Hg ratio possibly due to the formation of low-bioavailability Hg–S(N)–OM complexes in rhizosphere. The Hg–Se antagonism undoubtedly occurred in soil-rice system, while its role in bioaccumulation of MeHg in the MeHg-contaminated rice paddies was minor. However, other soil properties showed less influence on the production and bioaccumulation of MeHg in rice paddies located at the Wanshan Mercury Mine zone. | Deliang Yin Tianrong He Runsheng Yin Lingxia Zeng | 2018 | Journal of Environmental Sciences2018，30，6： | 8 |
| 5 | Integrated transcriptomic and metabolomic analyses of a wax deficient citrus mutant exhibiting jasmonic acid-mediated defense against fungal pathogens显示文摘Naturally,resistant crop germplasms are important resources for managing the issues of agricultural product safety and environment deterioration.We found a spontaneous mutant of‘Newhall’navel orange(Citrus sinensis Osbeck)(MT)with broad-spectrum protections against fungal pathogens in the orchard,postharvest-storage,and artificial inoculation conditions.To understand the defense mechanism of MT fruit,we constructed a genome-scale metabolic network that integrated metabolome and transcriptome datasets.The coordinated transcriptomic and metabolic data were enriched in two sub-networks,showing the decrease in very long chain fatty acid(by 41.53%)and cuticular wax synthesis(by 81.34%),and increase in the synthesis of jasmonic acid(JA)(by 95.23%)and JA-induced metabolites such as 5-dimethylnobietin(by 28.37%)in MT.Furthermore,cytological and biochemical analyses confirmed that the response to fungal infection in MT was independent of wax deficiency and was correlated with the levels of jasmonates,and the expression of plant defensin gene PDF1.2.Results of exogenous application of MeJA and JA inhibitors such as propyl gallate proved that JA-mediated defense contributes to the strong tolerance against pathogens in MT.Our results indicated that jasmonate biosynthesis and signaling are stimulated by the fatty acid redirection of MT,and participate in the tolerance of pathogenic fungi. | Yizhong He Jingwen Han Runsheng Liu Yuduan Ding Jinqiu Wang Li Sun Xiaoming Yang Yunliu Zeng Weiwei Wen Juan Xu Hongming Zhang Xiang Yan Zhaoxing Chen Zuliang Gu Hong Chen Huanqing Tang Xiuxin Deng Yunjiang Cheng | 2018 | Horticulture Research2018，5，1： | 8 |
| 6 | A draft sequence of the rice (Oryza sativa ssp. indica) genome显示文摘The sequence of the rice genome holds fundamental information for its biology, including physiology, genetics, development, and evolution, as well as information on many beneficial phenotypes of economic significance. Using a 'whole genome shotgun' approach, we have pro-duced a draft rice genome sequence of Oryza sativa ssp. in-dica, the major crop rice subspecies in China and many other regions of Asia. The draft genome sequence is constructed from over 4.3 million successful sequencing traces with an accumulative total length of 2214.9 Mb. The initial assembly of the non-redundant sequences reached 409.76 Mb in length, based on 3.30 million successful sequencing traces with a total length of 1797.4 Mb from an indica variant cultivar 93-11, giving an estimated coverage of 95.29% of the rice genome with an average base accuracy of higher than 99%. The coverage of the draft sequence, the randomness of the sequence distribution, and the consistency of BIG-ASSEM-BLER, a custom-designed software package | YU Jun, HU Songnian, WANG Jun,LI Songgang WONG Ka-Shu Gane, LIU Bin,DENG Yajun, DAI Li, ZHOU Yan,ZHANG Xiuqing, CAO Mengliang, LIU Jing,SUN Jiandong , TANG Jiabin, CHEN Yanjiong,HUANG Xiaobing, LIN Wei, YE Chen, TONG Wei,CONG Lijuan, GENG Jianing, HAN Yujun, LI Lin,LI Wei, HU Guangqiang, HUANG Xiangang,LI Wenjie, LI Jian, LIU Zhanwei, LI Long,LIU Jianping, Ql Qiuhui, LIU Jinsong, LI Li,WANG Xuegang, LU Hong, WU Tingling,ZHU Miao, Nl Peixiang, HAN Hua, DONG Wei,REN Xiaoyu, FENG Xiaoli, GUI Peng,LI Xianran, WANG Hao, XU Xin, ZHAI Wenxue,XU Zhao, ZHANG Jinsong, HE Sijie,ZHANG Jianguo, XU Jichen, ZHANG Kunlin,ZHENG Xianwu, DONG Jianhai, ZENG Wanyong,TAO Lin, CHEN Xuewei, HE Jun, LIU Daofeng,TIAN Wei, TIAN Chaoguang, XIA Hongai,LI Gang, GAO Hui, LI Ping, CHEN Wei ,WANG Xudong, ZHANG Yong, HU Jianfei,WANG Jing, LIU Song, YANG Jian,ZHANG Guangyu, XIONG Yuqing, LI Zhijie,MAO Long, ZHOU Chengshu, ZHU Zhen,CHEN Runsheng, HAO Bailin,ZHENG Weimou, CHEN Shouyi, QUO Wei,LI Guojie, LIU Siqi, HUANG Guyang,TAO Ming, WANG Jian, ZHU Lihuang,YUAN Longping& YANG HuanmingBeijing Genomics Institute/Center of Genomics & Bioinformatics, Chinese Academy of Sciences, Beijing 101300, China Hangzhou Genomics Institute/Institute of Bioinformatics of Zhejiang University/Key Laboratory of Bioinformatics of Zhejiang Province, Hangzhou 310007, China Institute of Genetics, Chinese Academy of Sciences, Beijing 100101, China National Hybrid Rice R & D Center, Changsha 410125, China Laboratory of Bioinformatics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China College of Life Sciences, Peking University, Beijing 100871, China Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 1Q0080, China Digital China Ltd., Beijing 100080, China Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China Medical College, Xi’an Jiaotong University, Xi’an 710061, ChinaThese authors contributed equally to this work.Corresponding author.Corresponden | 2001 | Chinese Science Bulletin2001，46，23： | 6 |
| 7 | An experimental study on metal precipitation driven by fluid mixing: implications for genesis of carbonate-hosted lead–zinc ore deposits显示文摘A type of carbonate-hosted lead–zinc(Pb–Zn)ore deposits, known as Mississippi Valley Type(MVT)deposits, constitutes an important category of lead–zinc ore deposits. Previous studies proposed a fluid-mixing model to account for metal precipitation mechanism of the MVT ore deposits, in which fluids with metal-chloride complexes happen to mix with fluids with reduced sulfur, producing metal sulfide deposition. In this hypothesis, however, the detailed chemical kinetic process of mixing reactions, and especially the controlling factors on the metal precipitation are not yet clearly stated. In this paper, a series of mixing experiments under ambient temperature and pressure conditions were conducted to simulate the fluid mixing process, by titrating the metal-chloride solutions, doping withor without dolomite, and using NaHS solution. Experimental results, combined with the thermodynamic calculations, suggest that H_2S, rather than HS^-or S^(2-),dominated the reactions of Pb and/or Zn precipitation during the fluid mixing process, in which metal precipitation was influenced by the stability of metal complexes and the pH. Given the constant concentrations of metal and total S in fluids, the pH was a primary factor controlling the Pb and/or Zn metal precipitation. This is because neutralizing or neutralized processes for the ore-forming fluids can cause instabilities of Pb and/or Zn chloride complexes and re-distribution of sulfur species, and thus can facilitate the hydrolysis of Pb and Zn ions and precipitation of sulfides. Therefore, a weakly acidic to neutral fluid environment is most favorable for the precipitation of Pb and Zn sulfides associated with the carbonate-hosted Pb–Zn deposits. | Yan Zhang Runsheng Han Xing Ding Junjie He Yurong Wang | 2019 | Acta Geochimica2019，38，2： | 4 |
| 8 | Cep57, a NEDDl-binding pericentriolar material component, is essential for spindle pole integrity显示文摘 | Qixi Wu Runsheng He Haining Zhou Albert CH Yu Bo Zhang Junlin Teng Jianguo Chen | 2012 | Cell Research2012，22，9： | 2 |
| 9 | SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling显示文摘Small proteins specifically refer to proteins consisting of less than 100 amino acids translated from small open reading frames(s ORFs),which were usually missed in previous genome annotation.The significance of small proteins has been revealed in current years,along with the discovery of their diverse functions.However,systematic annotation of small proteins is still insufficient.Sm Prot was specially developed to provide valuable information on small proteins for scientific community.Here we present the update of Sm Prot,which emphasizes reliability of translated s ORFs,genetic variants in translated s ORFs,disease-specific s ORF translation events or sequences,and remarkably increased data volume.More components such as non-ATG translation initiation,function,and new sources are also included.Sm Prot incorporated638,958 unique small proteins curated from 3,165,229 primary records,which were computationally predicted from 419 ribosome profiling(Ribo-seq)datasets or collected from literature and other sources from 370 cell lines or tissues in 8 species(Homo sapiens,Mus musculus,Rattus norvegicus,Drosophila melanogaster,Danio rerio,Saccharomyces cerevisiae,Caenorhabditis elegans,and Escherichia coli).In addition,small protein families identified from human microbiomes were also collected.All datasets in Sm Prot are free to access,and available for browse,search,and bulk downloads at http://gffzz47cba05b3f0c4ad7hcccqk9n65npb6quq.ffgz.tsg.suse.edu.cn/SmProt/. | Yanyan Li Honghong Zhou Xiaomin Chen Yu Zheng Quan Kang Di Hao Lili Zhang Tingrui Song Huaxia Luo Yajing Hao Runsheng Chen Peng Zhang Shunmin He | 2021 | Genomics, Proteomics & Bioinformatics2021，19，4： | 1 |
| 10 | Application of wind-profiling radar data to the analysis of dust weather in the Taklimakan Desert显示文摘 | Minzhong Wang Wenshou Wei Zheng Ruan Qing He Runsheng Ge | 2013 | Environmental Monitoring and Assessment2013，，6： | 1 |
| 11 | Metallogenic Regularities and Deposit Type of Rich(Ge-Ag)-Zn-Pb Deposits in the Sichuan-Yunnan-Guizhou Triangle(SYGT)Area,China显示文摘1 Introduction The well-known1 Sichuan-Yunnan-Guizhou Triangle(SYGT)area of poly-metallic Zn-Pb deposits,southwest China is located at the south-western margin of the Yangtze Block in the transition area of the Tethys Belt and the Circum-Pacific Metallogenic Belt,and is composed of the Northeastern Yunnan。 | HAN RunSheng WANG Feng ZHANG Yan ZHOU Gaoming HE Jiaojiao | 2017 | Acta Geologica Sinica(English Edition)2017，91，S1： | 1 |
| 12 | Application of wind-profiling radar data to the analysis of dust weather in the Taklimakan Desert显示文摘 | Minzhong Wang Wenshou Wei Zheng Ruan Qing He Runsheng Ge | 2013 | Environmental Monitoring and Assessment2013，，6： | 1 |
| 13 | Genome-wide identification and characterization of thaumatin-like protein family genes in wheat and analysis of their responses to Fusarium head blight infection显示文摘Thaumatin-like proteins (TLPs) play potential roles in plant resistance to various diseases. Identifying TLPs is neces-sary to determine their function and apply them to plant disease resistance. However, limited information is available about TLP-family genes in wheat, especially regarding their responses to Fusarium species, which cause Fusarium head blight in wheat. In this study, we conducted a comprehensive genome-wide survey of TLP genes in wheat and identified 129 TLP genes in the wheat genome, which were unevenly distributed on 21 wheat chromosomes, with 5A containing the highest number. Phylogenetic analysis showed that these 129 wheat TLP genes together with 24 Arabidopsis TLPs were classified into 7 groups based on the protein sequences. We systematically analyzed the genes in terms of their sequence characterization, chromosomal locations, exon-intron distribution, duplication (tandem and segmental) events and expression profiles in response to Fusarium infection. Furthermore, we analyzed differen-tially expressed TLP genes based on publicly available RNA-seq data obtained from a resistant near isogenic wheat line at different time points after Fusarium graminearum inoculation. Then, the expression of 9 differentially expressed TLP genes was confirmed by real-time PCR, and these 9 genes were all upregulated in the resistant Sumai 3 variety, which was generally consistent with the RNA-seq data. Our results provide a basis for selecting candidate wheat TLP genes for further studies to determine the biological functions of the TLP genes in wheat. | Runsheng Ren Xinli Zhou Xu Zhang Xin Li Pingping Zhang Yi He | 2022 | Food Production, Processing and Nutrition2022，4，1： | 0 |
| 14 | Exploring noncoding variants in genetic diseases:from detection to functional insights显示文摘Previous studies on genetic diseases predominantly focused on protein-coding variations, overlooking the vast noncoding regions in the human genome. The development of high-throughput sequencing technologies and functional genomics tools has enabled the systematic identification of functional noncoding variants. These variants can impact gene expression, regulation, and chromatin conformation, thereby contributing to disease pathogenesis. Understanding the mechanisms that underlie the impact of noncoding variants on genetic diseases is indispensable for the development of precisely targeted therapies and the implementation of personalized medicine strategies. The intricacies of noncoding regions introduce a multitude of challenges and research opportunities. In this review, we introduce a spectrum of noncoding variants involved in genetic diseases, along with research strategies and advanced technologies for their precise identification and in-depth understanding of the complexity of the noncoding genome. We will delve into the research challenges and propose potential solutions for unraveling the genetic basis of rare and complex diseases. | Ke Wu Fengxiao Bu Yang Wu Gen Zhang Xin Wang Shunmin He Mo-Fang Liu Runsheng Chen Huijun Yuan | 2024 | Journal of Genetics and Genomics2024，51，2： | 0 |
| 15 | Tectono-geochemical Characteristics at the level 1584m in Huize Zinc-Lead Deposit,Yunnan Province显示文摘1 Introduction The Huize Zn-Pb district is located in the tectonic composite position,became one of the important production areas of zinc,lead and germanium in China.In the Huize lead-zinc deposit,the interlayer faults are | Jiaojiao He Runsheng Han Peng Wu | 2017 | Acta Geologica Sinica(English Edition)2017，91，S1： | 0 |
| 16 | Quantitative Analysis of Mineralization-Alteration Index about the Huize Lead-zinc district in Northeast Yunnan, China显示文摘1 Introduction The super-large Huize lead-zinc ore district is one of the most representative lead-zinc deposits in Northeastern Yunnan poly-metallic deposit concentration district.So far,studies(Liu and Lin,1999;Han et al.,2007)on the type of deposits like the Huize lead-zinc deposit,focused on deposit genesis,the sources of metallogenic materials, | ZHANG Xiaopei HAN Runsheng ZHAO Dong QIU Wenlong HE Jiaojiao CUI Junhao | 2017 | Acta Geologica Sinica(English Edition)2017，91，S1： | 0 |
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