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The role of genomic structural variation in the genetic improvement of polyploid crops 预览
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作者 Sarah-Veronica Schiessl Elvis Katche +2 位作者 Elizabeth Ihien Harmeet Singh Chawla Annaliese S. Mason 《作物学报:英文版》 CAS CSCD 2019年第2期127-140,共14页
Many of our major crop species are polyploids,containing more than one genome or set of chromosomes.Polyploid crops present unique challenges,including difficulties in genome assembly,in discriminating between multipl... Many of our major crop species are polyploids,containing more than one genome or set of chromosomes.Polyploid crops present unique challenges,including difficulties in genome assembly,in discriminating between multiple gene and sequence copies,and in genetic mapping,hindering use of genomic data for genetics and breeding.Polyploid genomes may also bemore prone to containing structural variation,such as loss of gene copies or sequences (presence–absence variation) and the presence of genes or sequences inmultiple copies (copynumber variation).Although the two main types of genomic structural variation commonly identified are presence–absence variation and copy-number variation,we propose that homeologous exchanges constitute a third major form of genomic structural variation in polyploids.Homeologous exchanges involve the replacement of one genomic segment by a similar copy from another genome or ancestrally duplicated region,and are known to be extremely common in polyploids.Detecting all kinds of genomic structural variation is challenging,but recent advances such as optical mapping and long-read sequencing offer potential strategies to help identify structural variants even in complex polyploid genomes.All three major types of genomic structural variation (presence–absence,copy-number,and homeologous exchange) are now known to influence phenotypes in crop plants,with examples of flowering time,frost tolerance,and adaptive and agronomic traits.In this review,we summarize the challenges of genome analysis in polyploid crops,describe the various types of genomic structural variation and the genomics technologies and data that can be used to detect them,and collate information produced to date related to the impact of genomic structural variation on crop phenotypes.We highlight the importance of genomic structural variation for the future genetic improvement of polyploid crops. 展开更多
关键词 Presence–absence VARIATION Copy-number VARIATION Homeologous exchanges Genome structure PAN-GENOME
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Plant Genome Editing Database (PGED): A Call for Submission of Information about Genome-Edited Plant Mutants
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作者 Yi Zheng Ning Zhang +1 位作者 Gregory B. Martin Zhangjun Fei 《分子植物:英文版》 SCIE CAS CSCD 2019年第2期127-129,共3页
Recent advances in genome editing technologies, particularly CRISPR/Cas, enable the alteration of DNA sequences to produce deletions, insertions, and substitutions in genes (Jaganathan et al., 2018), as well as large ... Recent advances in genome editing technologies, particularly CRISPR/Cas, enable the alteration of DNA sequences to produce deletions, insertions, and substitutions in genes (Jaganathan et al., 2018), as well as large or entire chromosome deletions in the genomes of plants and animals (Zhou et al., 2014;Adikusuma et al., 2017). 展开更多
关键词 PLANT GENOME EDITING DATABASE (PGED) Genome-Edited PLANT MUTANTS
Structural variation during dog domestication: insights from gray wolf and dhole genomes
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作者 Guo-Dong Wang Xiu-Juan Shao +14 位作者 Bing Bai Junlong Wang Xiaobo Wang Xue Cao Yan-Hu Liu Xuan Wang Ting-Ting Yin Shao-Jie Zhang Yan Lu Zechong Wang Lu Wang Wenming Zhao Bing Zhang Jue Ruan Ya-Ping Zhang 《国家科学评论:英文版》 CSCD 2019年第1期110-122,共13页
Several processes like phenotypic evolution, disease susceptibility and environmental adaptations, which fashion the domestication of animals, are largely attributable to structural variations(SVs) in the genome.Here,... Several processes like phenotypic evolution, disease susceptibility and environmental adaptations, which fashion the domestication of animals, are largely attributable to structural variations(SVs) in the genome.Here, we present high-quality draft genomes of the gray wolf(Canis lupus) and dhole(Cuon alpinus) with scaffold N50 of 6.04 Mb and 3.96 Mb, respectively. Sequence alignment comprising genomes of three canid species reveals SVs specific to the dog, particularly 16 315 insertions, 2565 deletions, 443 repeats, 16 inversions and 15 translocations. Functional annotation of the dog SVs associated with genes indicates their enrichments in energy metabolisms, neurological processes and immune systems. Interestingly, we identify and verify at population level an insertion fully covering a copy of the AKR1 B1(Aldo-Keto Reductase Family 1 Member B) transcript. Transcriptome analysis reveals a high level of expression of the new AKR1 B1 copy in the small intestine and liver, implying an increase in de novo fatty acid synthesis and antioxidant ability in dog compared to gray wolf, likely in response to dietary shifts during the agricultural revolution. For the first time, we report a comprehensive analysis of the evolutionary dynamics of SVs during the domestication step of dogs. Our findings demonstrate that retroposition can birth new genes to facilitate domestication, and affirm the importance of large-scale genomic variants in domestication studies. 展开更多
关键词 DOG DOMESTICATION GENOME assembly structural variation GRAY WOLF dhole
福建省2015年本地登革热病例的病原学特征 预览
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作者 张拥军 吴生根 +3 位作者 王金章 游丽斌 阚乃鹏 翁育伟 《中国人兽共患病学报》 CAS CSCD 北大核心 2019年第1期28-33,共6页
目的 分析2015年福建省本地登革热病例部分登革病毒流行株的基因组序列,调查相关病毒株之间的遗传联系,为福建省登革热防控提供病原学证据。方法 采集急性期患者血清,实时荧光RT-PCR检测登革病毒RNA,阳性者分离病毒,扩增病毒基因组并测... 目的 分析2015年福建省本地登革热病例部分登革病毒流行株的基因组序列,调查相关病毒株之间的遗传联系,为福建省登革热防控提供病原学证据。方法 采集急性期患者血清,实时荧光RT-PCR检测登革病毒RNA,阳性者分离病毒,扩增病毒基因组并测序,以病毒全长编码区序列进行种系发生分析。结果 2015年福建省先后出现登革1型(DENV1)和登革2型病毒(DENV2)引起的本地暴发疫情,共发生4起聚集性病例,报告41例。分离到DENV1毒株9株,DENV2毒株8株。种系发生分析显示,9株DENV1高度相似,同属于基因1型(G1),提示其共同的输入来源可能为斯里兰卡;而8株DENV2病毒虽然同属于大都市基因型,却分为差异较大的两簇,表明莆田与福州两地疫情相关毒株的遗传关联度较低,可能分别来自马来西亚和印度。结论 2015年共出现4起聚集性本地登革热疫情,部分患者病毒分离株的病原学特征表明,福建省2015年本地登革热暴发疫情存在多个输入来源。 展开更多
关键词 登革热 病原学 基因组 序列分析
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小黑杨基因组的初步组装及SSR信息分析 预览
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作者 周玉敏 王遂 +2 位作者 刘轶 李开隆 由香玲 《植物研究》 CAS CSCD 北大核心 2019年第1期156-160,共5页
小黑杨是人们以小叶杨和欧洲黑杨为亲本培育出的杂交种,兼具双亲生长速度快、抗性强的优点。本研究通过二代测序技术,对小黑杨进行全基因组测序,初步组装出小黑杨基因组,并以此为基础,识别分析其SSR序列,为小黑杨品种划分、表型性状关... 小黑杨是人们以小叶杨和欧洲黑杨为亲本培育出的杂交种,兼具双亲生长速度快、抗性强的优点。本研究通过二代测序技术,对小黑杨进行全基因组测序,初步组装出小黑杨基因组,并以此为基础,识别分析其SSR序列,为小黑杨品种划分、表型性状关联等提供参考。结果表明,共组装得到了366876条总计368.96Mbp的contig序列;对其中不小于2000bp的21788条的非冗余contig进行SSR分析,共识别出18111条SSR序列,其中一、二、三核苷酸重复基序较多。对得到的SSR序列设计引物,共得到12838对引物,供今后实验使用。 展开更多
关键词 小黑杨 基因组 SSR
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Genome editing opens a new era of genetic improvement in polyploid crops 预览
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作者 Qamar U. Zaman Chao Li +1 位作者 Hongtao Cheng Qiong Hu 《作物学报:英文版》 CAS CSCD 2019年第2期141-150,共10页
Sequence-specific nucleases (SSN) that generate double-stranded DNA breaks (DSBs) in genes of interest are the key to site-specific genome editing in plants.Genome editing has developed into one method of reducing und... Sequence-specific nucleases (SSN) that generate double-stranded DNA breaks (DSBs) in genes of interest are the key to site-specific genome editing in plants.Genome editing has developed into one method of reducing undesirable traits in crops by the induction of knockout mutations.Different SSN-mediated genome-editing systems,including LAGLIDADG homing endonucleases or meganucleases,zinc-finger nucleases,transcription activator-like effector nucleases and clustered regularly interspaced short palindromic repeats,are emerging as robust tools for introducing functional mutations in polyploid crops including citrus,wheat,cotton,soybean,rapeseed,potato,grapes,Camelina sativa,dandelion,and tobacco.The approach utilizes knowledge of biological mechanisms for targeted induction of DSBs and their error-prone repair,allowing highly specific changes at designated genome loci.In this review,we briefly describe genome-editing technologies and their application to genetic improvement of polyploid crops. 展开更多
关键词 GENOME EDITING CRISPR SITE-SPECIFIC MUTAGENESIS POLYPLOID Crop improvement
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水产生物基因组研究进展与趋势 预览
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作者 郑先虎 匡友谊 +4 位作者 吕伟华 栾培贤 孙志鹏 鲁翠云 孙效文 《水产学报》 CAS CSCD 北大核心 2019年第1期15-35,共21页
本文综述了水产生物基因组研究相关技术的发展历程和关键技术的应用。以二代测序技术的出现为分界点,首先回顾了早期水产养殖生物在遗传学和分子生物学方面的研究结果,以及为开展全基因组测序所做的相关基础研究,然后重点介绍了二代测... 本文综述了水产生物基因组研究相关技术的发展历程和关键技术的应用。以二代测序技术的出现为分界点,首先回顾了早期水产养殖生物在遗传学和分子生物学方面的研究结果,以及为开展全基因组测序所做的相关基础研究,然后重点介绍了二代测序技术应用于水产生物全基因组测序和经济性状遗传基础解析的研究进展,最后展望了水产生物基因组研究发展趋势。水产生物经济性状遗传机制高度复杂,从全基因组角度阐明其遗传机制仍有很多难题,但基因决定性状是生物学法则之一,探索这一过程的奥秘引人入胜。 展开更多
关键词 水产生物 基因组 下一代测序
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甘蓝型油菜基因组与花色遗传研究进展 预览
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作者 朱吉风 张俊英 +5 位作者 杨立勇 蒋美艳 江建霞 李延莉 王伟荣 周熙荣 《作物研究》 2019年第1期77-81,85共6页
加强甘蓝型油菜花色研究对指导油菜花色育种利用具有重要意义。从甘蓝型油菜遗传图谱构建、花色种类与来源、花色遗传研究以及基因定位等方面进行了综述,指出了油菜花色研究中存在的几点障碍及甘蓝型油菜基因组与花色遗传的研究方向。
关键词 甘蓝型油菜 基因组 花色 遗传
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系统评估X射线损伤修复交叉互补基因1多态性位点与冠心病相关性的Meta分析 预览
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作者 吴旭庭 王阳 +1 位作者 王镇波 陈刚 《安徽医药》 CAS 2019年第4期637-641,共5页
目的系统地评估X射线损伤修复交叉互补基因1(XRCC 1)Arg399Gln和Arg194Trp多态性位点与冠状动脉粥样硬化性心脏病(coronary artery disease,CAD)易感性关联。方法检索PubMed、Google学术、万方和CNKI数据库,筛得XRCC 1基因Arg399Gln和Ar... 目的系统地评估X射线损伤修复交叉互补基因1(XRCC 1)Arg399Gln和Arg194Trp多态性位点与冠状动脉粥样硬化性心脏病(coronary artery disease,CAD)易感性关联。方法检索PubMed、Google学术、万方和CNKI数据库,筛得XRCC 1基因Arg399Gln和Arg194Trp多态性与CAD易感性关联的病例对照研究。采用Stata 12.0数据计算软件对获得的各项研究数据进行分析统计,并对数据可靠性、发表偏倚等进行评估。结果纳入8项病例对照研究,包含病例组3 093例,对照组2 799例。Meta分析结果提示,XRCC 1基因Arg399Gln多态性位点与CAD易感性呈显著正相关(M比W:OR=1.153,95%CI:1.025~1.296,P=0.017;MM比WW:OR=1.514,95%CI:1.129~2.031,P=0.006;MM比MW+WW:OR=1.472,95%CI:1.110~1.953,P=0.007)。在以种族为依据的亚组分析中发现,XRCC 1基因Arg399Gln多态性位点增加了亚洲人群CAD的发病风险。此外,研究还发现XRCC 1基因Arg194Trp多态性位点在MM比WW和MM比MW+WW模型下与CAD发病风险呈显著正相关(MM比WW:OR=1.393,95%CI:1.048~1.850,P=0.022;MM比MW+WW:OR=1.499,95%CI:1.143~1.966,P=0.003)。在以种族为依据的亚组分析中,研究发现携带有XRCC 1基因Arg194Trp多态性的亚洲人群易患CAD。结论XRCC 1基因Arg399Gln和Arg194Trp多态性位点与CAD易感性显著相关,可作为该疾病诊断和筛查的潜在靶点。 展开更多
关键词 冠状动脉疾病 动脉粥样硬化 基因组 染色体结构变异 META分析 X射线损伤修复交叉互补基因1
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Short hairpin RNA-mediated knockdown of nuclear factor erythroid 2-like 3 exhibits tumor-suppressing effects in hepatocellular carcinoma cells 预览
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作者 Miao-Mei Yu Yue-Hua Feng +2 位作者 Lu Zheng Jun Zhang Guang-Hua Luo 《世界胃肠病学杂志:英文版》 SCIE CAS 2019年第10期1210-1222,共13页
BACKGROUND Hepatocellular carcinoma(HCC) is one of the most common malignant tumors with high mortality-to-incidence ratios. Nuclear factor erythroid 2-like 3(NFE2 L3), also known as NRF3, is a member of the cap ‘n’... BACKGROUND Hepatocellular carcinoma(HCC) is one of the most common malignant tumors with high mortality-to-incidence ratios. Nuclear factor erythroid 2-like 3(NFE2 L3), also known as NRF3, is a member of the cap ‘n’ collar basic-region leucine zipper family of transcription factors. NFE2 L3 is involved in the regulation of various biological processes, whereas its role in HCC has not been elucidated.AIM To explore the expression and biological function of NFE2 L3 in HCC.METHODS We analyzed the expression of NFE2 L3 in HCC tissues and its correlation with clinicopathological parameters based on The Cancer Genome Atlas(TCGA) data portal. Short hairpin RNA(shRNA) interference technology was utilized to knock down NFE2 L3 in vitro. Cell apoptosis, clone formation, proliferation, migration,and invasion assays were used to identify the biological effects of NFE2 L3 in BEL-7404 and SMMC-7721 cells. The expression of epithelial-mesenchymal transition(EMT) markers was examined by Western blot analysis.RESULTS TCGA analysis showed that NFE2 L3 expression was significantly positively correlated with tumor grade, T stage, and pathologic stage. The qPCR and Western blot results showed that both the mRNA and protein levels of NFE2 L3 were significantly decreased after shRNA-mediated knockdown in BEL-7404 and SMMC-7721 cells. The shRNA-mediated knockdown of NFE2 L3 could induce apoptosis and inhibit the clone formation and cell proliferation of SMMC-7721 and BEL-7404 cells. NFE2 L3 knockdown also significantly suppressed the migration, invasion, and EMT of the two cell lines.CONCLUSION Our study showed that shRNA-mediated knockdown of NFE2 L3 exhibited tumor-suppressing effects in HCC cells. 展开更多
关键词 Nuclear factor ERYTHROID 2-like 3 Hepatocellular carcinoma The Cancer Genome Atlas Short HAIRPIN RNA Epithelial-mesenchymal transition
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Development of a Haploid-Inducer Mediated Genome Editing System for Accelerating Maize Breedi ng
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作者 Baobao Wang Lei Zhu +5 位作者 Binbin Zhao Yongping Zhao Yurong Xie Zhigang Zheng Yaoyao Li Haiyang Wang 《分子植物:英文版》 SCIE CAS CSCD 2019年第4期597-602,共6页
Crop breeding aims to generate pure in bred lines with multiple desired traits. Doubled haploid (DH) and genome editing using CRISPR/Cas9 are two powerful game-changing technologies in crop breeding. However, both of ... Crop breeding aims to generate pure in bred lines with multiple desired traits. Doubled haploid (DH) and genome editing using CRISPR/Cas9 are two powerful game-changing technologies in crop breeding. However, both of them still fall short for rapid generation of pure elite lines with integrated favorable traits. Here, we report the development of a Haploid-Inducer Mediated Genome Editing (IMGE) approach, which utilizes a maize haploid inducer line carrying a CRISPR/Cas9 cassette targeting for a desired agronomic trait to pollinate an elite maize in bred line and to generate genome-edited haploids in the elite maize background. Homozygous pure DH lines with the desired trait improvement could be generated within two generations, thus bypassing the lengthy procedure of repeated crossing and backcrossing used in conventional breeding for integrating a desirable trait into elite commercial backgrounds. 展开更多
关键词 maize doubled HAPLOIDS (DH) CRSIPR/Cas9 haploid-inducer mediated genome EDITING (IMGE) crop breeding
基于Roche 454 GS FLX高通量测序的叶城沙蜥基因组微卫星特征分析 预览
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作者 宋琪 刘金龙 郭宪光 《四川动物》 北大核心 2019年第1期62-67,共6页
叶城沙蜥Phrynocephalus axillaris是我国特有的一种小型爬行动物,广泛分布于新疆塔里木盆地、吐鲁番-哈密盆地和甘肃敦煌盆地。本研究利用Roche 454 GS FLX高通量测序技术进行叶城沙蜥微卫星位点筛选,获得了91 190条高质量序列。用Krai... 叶城沙蜥Phrynocephalus axillaris是我国特有的一种小型爬行动物,广泛分布于新疆塔里木盆地、吐鲁番-哈密盆地和甘肃敦煌盆地。本研究利用Roche 454 GS FLX高通量测序技术进行叶城沙蜥微卫星位点筛选,获得了91 190条高质量序列。用Krait搜索微卫星位点,共得到1~6个碱基重复类型的完美型微卫星序列29 890个。不同类型微卫星中,单碱基重复类型数目最多,有14 630个,占总数的48. 95%,其次是二碱基,约占28. 60%,四碱基、三碱基、五碱基和六碱基分别占10. 73%、10. 48%、0. 92%和0. 32%。二碱基微卫星中AC重复类型数量最多,三碱基、四碱基、五碱基和六碱基中分别是ATC、AAAT、AAAAT和AATCCC。叶城沙蜥完美型微卫星中数量最多的11种重复拷贝类型分别为C、A、AC、AG、AAAT、ATC、AT、AAT、ATAG、AGG和AAC。本研究深化了对叶城沙蜥基因组的了解,并为以后开发和筛选大量高质量微卫星标记提供了数据支持,也为利用微卫星标记研究叶城沙蜥种群遗传结构和谱系地理模式奠定了基础。 展开更多
关键词 叶城沙蜥 基因组序列 微卫星 分布
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高通量测序平台发展及在临床分子诊断中的应用与展望
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作者 童永清 李艳 《中华检验医学杂志》 CAS CSCD 北大核心 2019年第2期73-76,共4页
高通量测序又称下一代测序(NGS),是一种新型的遗传学筛查和诊断技术,它的不断革新加速了人们对遗传学标志物及疾病分子机制的认识,特别是针对复杂遗传性疾病。NGS技术的发展,特别是靶向基因组测序、全基因组外显子组测序以及全基因组测... 高通量测序又称下一代测序(NGS),是一种新型的遗传学筛查和诊断技术,它的不断革新加速了人们对遗传学标志物及疾病分子机制的认识,特别是针对复杂遗传性疾病。NGS技术的发展,特别是靶向基因组测序、全基因组外显子组测序以及全基因组测序项目的出现,NGS在临床已经应用到检测单核苷酸变性以及结构重排和拷贝数变异,监测循环肿瘤DNA,并分析先前对标准生物信息学算法进行管理所挑战的基因组区域等。 展开更多
关键词 高通量核苷酸序列分析 分子诊断技术 DNA拷贝数变异 循环肿瘤DNA 基因组
Pathogenic Characterization and Full Length Genome Sequence of a Reassortant Infectious Bursal Disease Virus Newly Isolated in Pakistan
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作者 Altaf Hussain Tiantian Wu +15 位作者 Hui Li Linjin Fan Kai Li Li Gao Yongqiang Wang Yulong Gao Changjun Liu Hongyu Cui Qing Pan Yanping Zhang Asim Aslam Khan Muti-Ur-Rehman Muhammad Munir Salman Latif Butt Xiaomei Wang Xiaole Qi 《中国病毒学:英文版》 CAS CSCD 2019年第1期102-105,共4页
Dear Editor,Infectious bursal disease (IBD) is one of the most important diseases of the poultry. The IBD virus (IBDV), a nonenveloped virus belonging to the Birnaviridae family with a genome consisting of two segment... Dear Editor,Infectious bursal disease (IBD) is one of the most important diseases of the poultry. The IBD virus (IBDV), a nonenveloped virus belonging to the Birnaviridae family with a genome consisting of two segments of double-stranded RNA (segments A and B), targets B lymphocytes of bursa of Fabricious leading to immunosuppression. In Pakistan,poultry farming is the second biggest industry and IBD is the second biggest disease threating the poultry sector.However. 展开更多
关键词 In PATHOGENIC CHARACTERIZATION and Full LENGTH Genome Sequence of a REASSORTANT Infectious Bursal Disease Virus NEWLY ISOLATED in Pakistan
球孢白僵菌基因组候选效应子的预测与分析 预览
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作者 罗梅 董章勇 +1 位作者 林进添 林桂文 《核农学报》 CAS CSCD 北大核心 2019年第4期680-686,共7页
球孢白僵菌(Beauveria bassiana)是一种广泛应用的生防菌株,效应子在其对寄主昆虫侵染过程中发挥着重要作用。为高通量地筛选球孢白僵菌的效应子,本研究根据球孢白僵菌全基因组信息,利用SignalP、TMHMM、TargetP和Protcomp等生物信息学... 球孢白僵菌(Beauveria bassiana)是一种广泛应用的生防菌株,效应子在其对寄主昆虫侵染过程中发挥着重要作用。为高通量地筛选球孢白僵菌的效应子,本研究根据球孢白僵菌全基因组信息,利用SignalP、TMHMM、TargetP和Protcomp等生物信息学软件和预测程序对球孢白僵菌中10 364个蛋白序列进行分泌蛋白预测。结果表明,共分析到940个分泌蛋白,包含了185个碳水化合物活性酶家族蛋白。其中碳水化合物结合模块(CBM) 40个,碳水化合物酯酶(CE) 23个,糖苷水解酶(GH) 92个,糖基转移酶(GT) 4个,多糖裂解酶(PL) 2个,辅助功能酶(AA) 24个。进一步将上述分泌蛋白与胞外酶数据库进行比对分析、半胱氨酸含量分析、多个串联重复序列分析、病原寄主互作数据库进行比对及剔除大于300个氨基酸序列的蛋白,共获得18个候选效应子,其中11个为功能未知的假定蛋白,其余为胞外蛋白、细胞壁蛋白、几丁质酶蛋白等。本研究结果为进一步探究效应子在病原菌与昆虫寄主中的互作奠定了理论基础,并为其他病原菌效应子的预测及分析提供了技术参考。 展开更多
关键词 球孢白僵菌 效应子 全基因组 生物信息学
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子宫内膜异位症的遗传学发病机制研究进展 预览
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作者 曹现岭 孙振高(审校) 《国际生殖健康/计划生育杂志》 CAS 2019年第1期67-70,82共5页
子宫内膜异位症(EMs)严重影响育龄期女性的健康和生活质量。EMs临床表现多样,大多数女性表现为慢性非周期性盆腔痛、痛经和不孕等,但是EMs的具体发病机制尚不完全清楚。研究发现,EMs在患者一级亲属和单卵双胞胎中发病率较高,EMs的发病... 子宫内膜异位症(EMs)严重影响育龄期女性的健康和生活质量。EMs临床表现多样,大多数女性表现为慢性非周期性盆腔痛、痛经和不孕等,但是EMs的具体发病机制尚不完全清楚。研究发现,EMs在患者一级亲属和单卵双胞胎中发病率较高,EMs的发病风险中高达51%是遗传导致的,提示遗传因素在EMs的发生中发挥重要作用。近年来通过全基因组关联分析(GWAS)和其他技术的应用,发现炎症相关基因、细胞色素家族相关基因和癌前病变相关基因等与EMs的发生、发展有着密切关系。为进一步了解EMs的遗传学发病机制,现就近年来该领域研究进展进行综述。 展开更多
关键词 基因组 多态性 单核苷酸 细胞色素P450酶系统 DNA甲基化 白细胞介素12
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Functional diversifications of GhERF1 duplicate genes after the formation of allotetraploid cotton^FA
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作者 Chunxiao Liu TianZhen Zhang 《植物学报:英文版》 SCIE CAS CSCD 2019年第1期60-74,共15页
Whole genome duplication,a prevalent forceof evolution in plants,results in massive genome restructuring in different organisms.Roles of the resultant duplicated genes are poorly understood,both functionally and evolu... Whole genome duplication,a prevalent forceof evolution in plants,results in massive genome restructuring in different organisms.Roles of the resultant duplicated genes are poorly understood,both functionally and evolutionarily.In the present study,differentially expressed ethylene responsive factors(GhERF1s),anchored on Chr-A07 and Chr-D07,were isolated from a highγielding cotton hybrid(XZM2)and its parents.The GhERF1 was located in the B3 subgroup of the ethylene responsive factors subfamily involved in conferring tolerance to abiotic stress.Nucleotide sequence analysis of 524 diverse accessions,together with quantitative real-time polymerase chain reaction analysis,elucidated that de-functionalization of GhERF1-7A occurred due to one base insertion following trait loci and association mapping analyses highlighted a role for GhERF1-7A in conferring high boll number per plant in modern cotton cultivars.Overexpression of GhERF1-7A in transgenic Arabidopsis resulted in a substantial increase in the number of siliques and total seed yield.Neo-functionalization of GhERF1-7A was also observed in modern cultivars rather than in races andfor landraces,further suppo此ing its role in the development of high-yielding cotton cultivars.Both de-and neofunctionalization occurred in one of the duplicate genes,thus providing new genomic insight into the evolution of allotetraploid cotton species. 展开更多
关键词 COTTON WHOLE GENOME DUPLICATION
基于高通量技术的SFTS病毒基因组测序方法的建立
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作者 俞维维 孙逸 +4 位作者 颜浩 姚文武 楼秀玉 茅海燕 张严峻 《中华实验和临床病毒学杂志》 CAS CSCD 2019年第1期89-94,共6页
目的建立一种基于高通量测序技术的发热伴血小板减少综合征病毒(severe fever with thrombocytopenia syndrome virus,SFTS)基因组的测序方法。方法提取SFTS病毒核酸,分别采用随机引物和oligo(dT)磁珠特异性抓取核酸的方法,优化扩增和... 目的建立一种基于高通量测序技术的发热伴血小板减少综合征病毒(severe fever with thrombocytopenia syndrome virus,SFTS)基因组的测序方法。方法提取SFTS病毒核酸,分别采用随机引物和oligo(dT)磁珠特异性抓取核酸的方法,优化扩增和纯化条件并建库,利用二代测序仪检测病毒核酸序列。结果3株病毒采用两种方法测序结果差距较大,利用随机引物建库法获得的数据测序深度和覆盖度明显低于oligo(dT)磁珠抓取建库法。采用oligo(dT)磁珠抓取建库的方法,可对提取的核酸大于300ng的毒株进行测序,3株病毒测序深度都在900以上,覆盖度均超过99%,与NCBI上数据匹配度在90%以上。结论利用oligo(dT)磁珠抓取SFTS病毒核酸的方法进行建库,建立了基于二代测序平台的SFTS病毒基因组检测方法。 展开更多
关键词 发热伴血小板减少综合征病毒 文库构建 高通量测序 基因组
Molecular Epidemiology of Echovirus 18 Circulating in Mainland China from 2015 to 2016
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作者 Xiangpeng Chen Tianjiao Ji +3 位作者 Jiayun Guo Wei Wang Wenbo Xu Zhengde Xie 《中国病毒学:英文版》 CAS CSCD 2019年第1期50-58,共9页
Echovirus 18(E18), a serotype of Enterovirus B(EV-B) species, is an important pathogen in aseptic meningitis. E18 had rarely been detected in mainland China, but became the predominant pathogen associated with viral e... Echovirus 18(E18), a serotype of Enterovirus B(EV-B) species, is an important pathogen in aseptic meningitis. E18 had rarely been detected in mainland China, but became the predominant pathogen associated with viral encephalitis(VE) and meningitis in Hebei province for the first time in 2015. To investigate the molecular epidemiology and genetic characteristics of E18 in mainland China, sixteen E18 strains from patient throat swabs with hand, foot, and mouth disease(HFMD) in six provinces in China collected between 2015 and 2016, and four E18 strains isolated from 18 patient cerebrospinal fluid specimens with VE in Hebei Province in 2015 were obtained and sequenced. Combined with the sequences from the GenBank database, we performed an extensive genetic analysis. Phylogenetic analysis of VP1 gene sequences revealed that all E18 strains from mainland China after 2015 belonged to subgenotype C2. There were no obvious specific differences in phylogenetic and variation analyses of E18 genome sequences between HFMD and VE/meningitis strains. Potential multiple recombination may have occurred in the 50-untranslated region and in the P2 and P3 nonstructural protein-encoding regions of E18 strains from China. The current E18 strains were potential multiplerecombinant viruses. Overall, these findings supported that E18 caused HFMD, VE, and meningitis, although there were no significant associations between clinical features and viral genomic characteristics. 展开更多
关键词 GENETIC CHARACTERISTICS ECHOVIRUS 18 (E18) GENOME ENTEROVIRUS Recombination
DNMT3A/3B overexpression might be correlated with poor patient survival, hypermethylation and low expression of ESR1/PGR in endometrioid carcinoma: an analysis of The Cancer Genome Atlas
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作者 Dan He Xiao Wang +3 位作者 Yan Zhang Jian Zhao Rui Han Ying Dong 《中华医学杂志:英文版》 SCIE CAS CSCD 2019年第2期161-170,共10页
Background:DNA methylation is involved in numerous biologic events and associates with transcriptional gene silencing, playing an important role in the pathogenesis of endometrial cancer.ESR1/PGR frequently undergoes ... Background:DNA methylation is involved in numerous biologic events and associates with transcriptional gene silencing, playing an important role in the pathogenesis of endometrial cancer.ESR1/PGR frequently undergoes de novo methylation and loss expression in a wide variety of tumors, including breast, colon, lung, and brain tumors.However, the mechanisms underlying estrogen and progesterone receptors (ER/PR) loss in endometrial cancer have not been studied extensively.The aims of this study were to determine the expression of DNA (cytosine-5)-methyltransferase 3A/3B (DNMT3A/3B) in endometrial cancer to investigate whether the methylation catalyzed by DNMT3A/3B contributes to low ER/PR expression.Methods:The clinicopathologic information and RNA-Seq expression data of DNMT3A/3B of 544 endometrial cancers were derived from The Cancer Genome Atlas (TCGA) uterine cancer cohort in May 2018.RNA-Seq level of DNMT3A/3B was compared between these clinicopathologic factors with t-test or one-way analysis of variance.Results:DNMT3A/3B was overexpressed in endometrioid carcinoma (EEC) and was even higher in non-endometrioid carcinoma (NEEC) (DNMT3A, EEC vs.NEEC:37.6% vs.69.9%, t=-7.440, P<0.001;DNMT3B, EEC vs.NEEC:42.4% vs.72.8 %, t=-6.897, P<0.001).In EEC, DNMT3A overexpression was significantly correlated with the hypermethylation and low expression of the ESR1 and PGR (P<0.05).The same trend was observed in the DNMT3B overexpression subgroup.In the ESR1/PGR low-expression subgroups, as much as 83.1% of ESR1 and 59.5% of PGR were hypermethylated, which was significantly greater than the ESR1/PGR high-expression subgroups (31.3% and 11.9%, respectively).However, the above phenomena were absent in NEEC, while DNMT3A/3B overexpression, ESR1/PGR hypermethylation, and low ER/PR expression occurred much more often.In univariate analysis, DNMT3A/3B overexpressions were significantly correlated with worse prognosis.In multivariate analysis, only DNMT3A was an independent predictor of disease-free survival (P<0.05).Conclusions:DNM 展开更多
关键词 DNA (cytosine-5)-methyltransferase 3A/3B ESTROGENS RECEPTOR Progesterone RECEPTOR Endometrial carcinoma The Cancer Genome ATLAS
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