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Molecular Plant 2016年第7期9卷 1078-1081页

作者： Li, Guotian Chern, Mawsheng Jain, Rashmi Martin, Joel A. Schackwitz, Wendy S. Jiang, Liangrong Vega-Sanchez, Miguel E. Lipzen, Anna M. Barry, Kerrie W. Schmutz, Jeremy Ronald, Pamela C. Univ Calif Davis Dept Plant Pathol Davis CA 95616 USA Univ Calif Davis Genome Ctr Davis CA 95616 USA Lawrence Berkeley Natl Lab Feedstocks Div Joint BioEnergy Inst Berkeley CA 94720 USA US DOE Joint Genome Inst Walnut Creek CA 94598 USA Xiamen Univ Sch Life Sci Xiamen 361102 Peoples R China hudsonalpha inst biotechnol Huntsville AL 35806 USA Monsanto Co Chesterfield Village Campus Chesterfield MO 63017 USA

Fast-neutron （FN） irradiation has been used to create mutagen- ized collections of many plant species （Bolon et al., 2014）, FN- induced mutagenesis has clear advantages： it is an efficient means of saturating the genome, and it does not involve time- consuming plant transformation or tissue culture. In rice, most mutant collections, although highly valuable, were generated us- ing either T-DNA insertion or transposon tagging approaches that often induce mutations unlinked to the insertion and complicating analysis （Wang et al., 2013）. Another disadvantage of some of these collections is that they were created in rice varieties that are photoperiod-sensitive and often have long generation times.

关键词： mutagenesis genome valuable

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卫计委叫停基因测序的是与非

高科技与产业化 2014年第3期20卷 22-23页

作者：韩健美国hudsonalpha研究院

其实有关高通量测序产前诊断，我已经讨论过不少，可是对卫计委的突然叫停，还是有些新的感受值得和大家分享。首先，我认为叫停是对的。既然国家有相关法律，就要按照法律程序办，公司应该按照程序报批产品。虽然看上去这是一个很突然... 详细信息

其实有关高通量测序产前诊断，我已经讨论过不少，可是对卫计委的突然叫停，还是有些新的感受值得和大家分享。首先，我认为叫停是对的。既然国家有相关法律，就要按照法律程序办，公司应该按照程序报批产品。虽然看上去这是一个很突然的决定，其实也是必然。卫计委也实属无奈，他们多次交涉相关公司，两三年来一直被顶着，如果不管，一旦出事，责任就首先在国家机构。

关键词：基因测序法律程序产前诊断高通量

Trilineage Sequencing Reveals Complex TCRβTranscriptomes in Neutrophils and Monocytes Alongside T Cells

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Genomics, Proteomics & Bioinformatics 2021年第6期19卷 926-936页

作者： Tina Fuchs Kerstin Puellmann Chunlin Wang Jian Han Alexander W.Beham Michael Neumaier Wolfgang E.Kaminski institute for Clinical Chemistry University of Heidelberg Medical Faculty MannheimD-68167 MannheimGermany Aesculabor Hamburg D-22769 HamburgGermany iRepertoire Inc. HuntsvilleAL 35806USA hudsonalpha institute for biotechnology HuntsvilleAL 35806USA Department of Surgery Hospital of SiegenD-57076 SiegenGermany Ingenium digital diagnostics D-87662 KaltentalGermany

Recent findings indicate the presence of T cell receptor(TCR)-based combinatorial immune receptors beyond T cells in neutrophils and monocytes/*** this study,using a semiquantitative trilineage immune repertoire sequencing approach as well as under rigorous bioinformatic conditions,we identify highly complex TCRβtranscriptomes in human circulating monocytes and neutrophils that separately encode repertoire diversities one and two orders of magnitude smaller than that of T *** transcriptomic analyses reveal that neutrophils,monocytes,and T cells express distinct TCRβrepertoires with less than 0.1%overall trilineage repertoire *** comparison shows that in all three leukocyte lineages,the vast majority of the expressed TCRβvariants are *** also find that differentiation of monocytes into macrophages induces dramatic individual-specific repertoire shifts,revealing a surprising degree of immune repertoire plasticity in the monocyte *** results uncover the remarkable complexity of the two phagocyte-based flexible immune systems which until now has been hidden in the shadow of T cells.

关键词： Monocyte Neutrophil T cell TCRβtranscriptome Next-generation sequencing

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不做实验的老板和不拼刺刀的将军

科技导报 2010年第5期28卷 124-124页

作者：韩健美国hudsonalpha研究院

经常听到学生抱怨．说老板（国内更习惯叫导师）自己不做实验，脱离现实，没有水平。还说“研究生的目的就是把老板培养成院士”，好像只有那些亲手做实验的老板才真正有本事，值得佩服。

关键词：老板实验刺刀研究生

Integrative genomics reveals paths to sex dimorphism in Salix purpurea L

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Horticulture Research 2021年第1期8卷 2305-2318页

作者： Brennan Hyden Craig H.Carlson Fred E.Gouker Jeremy Schmutz Kerrie Barry Anna Lipzen Aditi Sharma Laura Sandor Gerald A.Tuskan Guanqiao Feng Matthew S.Olson Stephen P.DiFazio Lawrence B.Smart Horticulture Section School of Integrative Plant ScienceCornell UniversityCornell AgriTechGenevaNYUSA Floral and Nursery Plants Research Unit US National ArboretumUnited States Department of AgricultureAgricultural Research ServiceBeltsvilleMDUSA United States Department of Energy Joint Genome InstituteBerkeleyCAUSA hudsonalpha institute for biotechnology HuntsvilleALUSA The Center for Bioenergy Innovation Oak Ridge National LaboratoryOak RidgeTNUSA Department of Biology Texas Tech UniversityLubbockTXUSA Department of Biology West Virginia UniversityMorgantownWVUSA

Sex dimorphism and gene expression were studied in developing catkins in 159 F 2 individuals from the bioenergy crop Salix purpurea,and potential mechanisms and pathways for regulating sex development were *** expression,eQTL,bisulfite sequencing,and network analysis were used to characterize sex dimorphism,detect candidate master regulator genes,and identify pathways through which the sex determination region(SDR)may mediate sex *** genes are presented as candidates for master regulators of sex,supported by gene expression and network *** include genes putatively involved in hormone signaling,epigenetic modification,and regulation of *** analysis revealed a suite of transcription factors and genes involved in secondary metabolism and floral development that were predicted to be under direct control of the sex determination ***,data from bisulfite sequencing and small RNA sequencing revealed strong differences in expression between males and females that would implicate both of these processes in sex dimorphism *** data indicate that the mechanism of sex determination in Salix purpurea is likely different from that observed in the related genus *** further demonstrates the dynamic nature of SDRs in plants,which involves a multitude of mechanisms of sex determination and a high rate of turnover.

关键词： purpurea metabolism likely

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读者之声

科技导报 2010年第5期28卷 124-124页

作者：韩健盖鑫磊美国hudsonalpha研究院加州大学戴维斯分校空气质量研究中心

本刊“读者之声”栏目着力反映科研一线人员的声音，尤其欢迎您对《科技导报》刊登的学术论文及其他文章进行评论．同时也欢迎您将您身边发生的吸引人的故事或您的一个经历，以300～500的文字写信给我们。本刊将努力把它办成大家的园地... 详细信息

本刊“读者之声”栏目着力反映科研一线人员的声音，尤其欢迎您对《科技导报》刊登的学术论文及其他文章进行评论．同时也欢迎您将您身边发生的吸引人的故事或您的一个经历，以300～500的文字写信给我们。本刊将努力把它办成大家的园地。下面是本栏目内容的建议：

关键词：栏目内容故事读者征集学术论文

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给“精准医疗”泼点儿冷水

中国战略新兴产业 2015年第15期 93-93页

作者：韩健美国hudsonalpha生物科技研究院

今年初,美国总统奥巴马宣布启动"精准医疗计划",预计将于2016年向相关机构共提供2.15亿美元,用于资助"精准医疗"方面的科学研究和创新发展。"精准医疗"实际上就是"个体化医疗"的一个新提法:指给所有人在正确的时间用上正确的药。不过,... 详细信息

今年初,美国总统奥巴马宣布启动"精准医疗计划",预计将于2016年向相关机构共提供2.15亿美元,用于资助"精准医疗"方面的科学研究和创新发展。"精准医疗"实际上就是"个体化医疗"的一个新提法:指给所有人在正确的时间用上正确的药。不过,因为是美国总统奥巴马提出的,而且还在提出的时候给出了一定的政府投入,所以就有了品牌,有了影响力,似乎也有了"理论根据",国内一窝蜂地涌上去拥抱这个概念,大会小会

关键词：精准美国提法总统美利坚合众国北美洲医疗基因组测序冷水

Dissect the rice immune system using a whole-genome sequenced mutant population

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Dissect the rice immune system using a whole-genome sequence...

Dissect the rice immune system using a whole-genome sequenced mutant population

第十九届中国作物学会学术年会

作者：沙干 Rashmi Jain Juan Zhao Xiaojing Kong Qiping Sun Lei Yang Jerry Jenkins Mawsheng Chern Joel A.Martin Feng Xing Weibo Xie Qiang Li Liang Guo Rod A.Wing Jeremy Schmutz Pamela C.Ronald 李国田 College of Plant Science and Technology Huazhong Agricultural University Department of Plant Pathology University of California Joint Bioenergy institute Lawrence Berkeley National Laboratory U.S.Department of Energy Joint Genome institute hudsonalpha institute for biotechnology National Key Laboratory of Crop Genetic Improvement National Center of Plant Gene Research (Wuhan) Huazhong Agricultural University Arizona Genomics institute School of Plant Sciences University of Arizona BIO5 institute School of Plant Sciences University of Arizona

Background: The availability of thousands of sequenced rice genomes from diverse varieties and accessions provides a rich genetic resource for in-depth exploration in rice function genomics. One drawback to these collections is that most of these rice varieties have long life cycles, and/or low transformation efficiencies, which limits their usefulness as model organisms for biological studies. In contrast, the rice variety Kitaake has a rapid life cycle(9 weeks seed to seed) and is easy to transform and propagate. For these reasons, Kitaake has emerged as a model for studies of diverse monocotyledonous species. Results: We report the de novo genome sequencing and analysis of an early flowering Geng/japonica variety KitaakeX. Our KitaakeX sequence assembly contains 377.6 Mb, consisting of 33 scaffolds(476 contigs) with a contig N50 of 1.4 Mb. Complementing the assembly are detailed gene annotations of 35,594 protein coding genes. To further facilitate rice research, we generated and sequenced a fast-neutron-induced mutant population. We sequenced 1,504 mutant lines at 45-fold coverage and identified 91,513 mutations affecting 32,307 genes, i.e., 58% of all rice genes. To facilitate public access to this genetic resource, we established an open access database called KitBase that provides access to sequence data and seed stocks. We have screened this mutant population for lines altered in plant immunity and identified multiple mutant candidates. One of them named rbl1 showed enhanced resistance to the rice blast fungus Magnaporthe oryzae. We cloned the target gene that is involved in phospholipid biosynthesis and plasma membrane integrity. RBL1 is mainly located in endoplasmic reticulum(ER). Lipidomics assays show that the phosphatidylinositol(PI) level is significantly reduced in the rbl1 mutant. We have used RNA-seq assays to analyze genes with altered expression levels and identified multiple downstream candidate genes, including receptor-like cytoplasmic kinases(

关键词： Rice Kitaake Lesion mimic mutant Blast resistance Lipidomics

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Whole-genome sequences shed light on the demographic history and contemporary genetic erosion of free-ranging jaguar(Panthera onca) populations

中国植物病理学会2019年学术年会

作者： Li Guotian Sha Gan Jain Rashmi Jenkins Jerry Shu Shengqiang Chern Mawsheng Copetti Dario Xing Feng Xie Weibo Wing Rod A Schmutz Jeremy Ronald Pamela C State Key Laboratory of Agricultural Microbiology and College of Plant Science and Technology Huazhong Agricultural University Department of Plant Pathology University of California Joint BioEnergy institute Lawrence Berkeley National Laboratory U.S.Department of Energy Joint Genome institute Arizona Genomics institute School of Plant SciencesUniversity of Arizona National Key Laboratory of Crop Genetic Improvement National Center of Plant Gene ResearchHuazhong Agricultural University hudsonalpha institute for biotechnology

Rice provides food for more than half of the world’s population and also serves as a model for studies of other monocotyledonous ***,we report the de novo genome sequencing and analysis of an early flowering Geng/japonica variety KitaakeX,which completes its life cycle in 9 *** KitaakeX sequence assembly contains 377.6 Mb,consisting of 33 scaffolds（476 contigs） with a contig N50 of 1.4 *** the assembly are detailed gene annotations of 35 594 protein coding *** high-quality genome of the model rice plant KitaakeX will accelerate rice functional *** further facilitate rice research,we generated and sequenced a fast-neutron-induced mutant population in *** sequenced 1 504 mutant lines at 45-fold coverage and identified 91 513 mutations affecting 32 307 genes,i.e.,58% of all rice *** detected an average of 61 mutations per *** types include single-base substitutions,deletions,insertions,inversions,translocations,and tandem *** observed a high proportion of loss-of-function *** facilitate public access to this genetic resource,we established an open access database called KitBase that provides access to sequence data and seed *** have screened this mutant population for lines altered in plant immunity and identified multiple mutant *** on these mutants will be presented.

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Journal of Genetics and Genomics 2022年第1期49卷 77-80页

作者： Gustavo P.Lorenzana Henrique V.Figueirò Jeremy Johnson Elinor Karlsson Ronaldo G.Morato Dênis A.Sana Laury Cullen Joares A.May Jr. Edsel A.Moraes Jr. Daniel L.Z.Kantek Leandro Silveira William J.Murphy Oliver A.Ryder Eduardo Eizirik Pontiﬁcal Catholic University of Rio Grande do Sul PUCRS.School of Health and Life SciencesPorto AlegreRS 90619Brazil Christopher B.Kaelin Gregory S.Barsh HudsonAlpha Institute for BiotechnologyHuntsvilleAL 35806USA Vertebrate Genome Biology Broad InstituteCambridgeMA 02142USA CENAP/ICMBio AtibaiaSP 12952Brazil PPG Biologia Animal Instituto de Bioci^enciasUFRGSPorto AlegreRS 90650Brazil instituto de Pesquisas Ecol ogicas Teodoro SampaioSP 19280Brazil UniSul TubarãoSC 88704Brazil Instituto Prò-CarnivorosAtibaiaSP 12945Brazil instituto Biotr opicos DiamantinaMG39100Brazil Estacão Ecologica de Taiamã ICMBioCaceresMT 78200Brazil instituto Onca-pintada-Jaguar Conservation Fund MineirosGO 75830Brazil Texas A&M University College StationTX 77843USA San Diego Zoo institute for Conservation Research San DiegoCA 92027USA Pontiﬁcal Catholic University of Rio Grande do Sul PUCRS.School of Health and Life SciencesPorto AlegreRS 90619Brazil Instituto Pr o-Carni¬vorosAtibaiaSP 12945Brazil Centro Regional del Bajio INECOLP atzcuaroMIC61600Mexico Smithsonian Conservation Biology institute WashingtonDC20008USA

Whole-genome sequences provide massive amounts of data that can illuminate many aspects of a species’biology and evolutionary history,as well as valuable information for conservation *** is particularly important for large carnivores,whose large area requirements and typical low densities make them prone to undergo rapid genetic erosion(*** of runs of homozygosity,Diez del Molino et al.,2018;Leroy et al.,2018)in the face of habitat loss and human *** such species is the jaguar(Pan-thera onca),the largest extant felid in the Americas,whose range has already declined by>50%and some of whose remaining popu-lations have been severely impacted by human-induced habitat frag-mentation(De La Torre et al.,2018).

关键词： Whole habitat erosion