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Applying molecular genetic tools to tiger conservation

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Integrative Zoology 2010年第4期5卷 351-362页

作者： Shu-jin LUo Warren E.joHNSoN stephen j.o’brien School of Life Sciences Peking UniversityBeijingChina Laboratory of Genomic Diversity National Cancer InstituteFrederickMDUSA

The utility of molecular genetic approaches in conservation of endangered taxa is now commonly *** the past decade,conservation genetic analyses based on mitochondrial DNA sequencing and microsatellite genotyping have provided powerful tools to resolve taxonomy uncertainty of tiger subspecies,to define conservation units,to reconstruct phylogeography and demographic history,to examine the genetic ancestry of extinct subspecies,to assess population genetic status non-invasively,and to verify genetic background of captive tigers *** genetic status of tiger subspecies and populations and implications for developing strategies for the survival of this charismatic species both in situ and ex situ are discussed.

关键词： conservation genetics mitochondrial DNA microsatellite subspecies tiger

New Gene Variants Associated with the Risk of Chronic HBV Infection

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Virologica Sinica 2020年第4期35卷 378-387页

作者： Mengjie Fan jing Wang Sa Wang Tengyan Li Hong Pan Hankui Liu Huifang Xu Daria V.Zhernakova stephen j.o’brien Zhenru Feng Le Chang Erhei Dai jianhua Lu Hongli Xi Yanyan Yu jianguo Zhang Binbin Wang Zheng Zeng Department of Infectious Diseases Peking University First HospitalBeijing 100034China Department of Medical Genetics and Development Biology School of Medical BasicCapital Medical UniversityBeijing 100069China Center for Genetics National Research Institute for Family PlanningBeijing 100081China BGI-Shenzhen Shenzhen 518083China BGI Genomics BGI-ShenzhenShenzhen 518083China Laboratory of Genomic Diversity Center for Computer TechnologiesITMO UniversitySt.PetersburgRussia 197101 Guy Harvey oceanographic Center Halmos College of Natural Sciences and OceanographyNova Southeastern UniversityFt LauderdaleFL 33004USA Department of Laboratory Medicine Peking University First HospitalBeijing 100034China The Fifth Hospital of Shijiazhuang Shijiazhuang 050024China

Some patients with chronic hepatitis B virus(HBV)infection failed to clear HBV,even persistently continue to produce antibodies to *** we performed a two stage genome wide association study in a cohort of Chinese patients designed to discover single nucleotide variants that associate with HBV infection and clearance of *** first stage involved genome wide exome sequencing of 101 cases(HBsAg plus anti-HBs positive)compared with 102 control patients(antiHBs positive,HBsAg negative).over 80%of individual sequences displayed 209 sequence ***,uncertain bases[10%or low-quality base calls([50%)were filtered and compared to the human reference genome *** the second stage,579 chronic HBV infected cases and 439 HBV clearance controls were sequenced with selected genes from the first *** there were no significant associated gene variants in the first stage,two significant gene associations were discovered when the two stages were assessed in a combined *** association showed rs506121-“T”allele[within the dedicator of cytokinesis 8(DoCK8)gene]was higher in chronic HBV infection group than that in clearance group(P=0.002,oR=0.77,95%CI[0.65,0.91]).The second association involved rs2071676—A allele within the Carbonic anhydrase(CA9)gene that was significantly elevated in chronic HBV infection group compared to the clearance group(P=0.0003,oR=1.35,95%CI[1.15,1.58]).Upon replication these gene associations would suggest the influence of DoCK8 and CA9 as potential risk genetic factors in the persistence of HBV infection.

关键词： Whole exome sequencing HBV infection DoCK8 CA9 Variation

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应用微卫星分型方法进行大熊猫父亲鉴定

遗传 2003年第5期25卷 504-510页

作者：张志和沈富军孙姗 Victor A.David 张安居 stephen j.o'brien 成都大熊猫繁育研究基地成都610081 美国国立癌症研究所基因组多样性实验室马里兰217021201

选用18对大熊猫特异的微卫星引物对成都动物园、成都大熊猫繁育研究基地的大熊猫幼子及其母亲和可疑父亲DNA作了PCR扩增。扩增产物在ABI373测序仪上做基因扫描。应用Genotyper672软件处理分型数据,经Cervus2.0软件对亲子关系进行分析。... 详细信息

选用18对大熊猫特异的微卫星引物对成都动物园、成都大熊猫繁育研究基地的大熊猫幼子及其母亲和可疑父亲DNA作了PCR扩增。扩增产物在ABI373测序仪上做基因扫描。应用Genotyper672软件处理分型数据,经Cervus2.0软件对亲子关系进行分析。结果表明,在母子关系确实的情况下,18个基因座联合的父亲鉴定排除概率E为0.999921,置信度为95%。而在母子关系不清的条件下,E=0.994109,但置信度低于80%。由于圈养大熊猫的母子关系都是确实的。因此,基因型分析的结果能有效确认出这些大熊猫之间的父子关系。但要准确鉴定出野生大熊猫的亲缘关系,我们还需更多的微卫星标记。

关键词：微卫星基因分型大熊猫亲子鉴定

鼻咽癌高发区非癌人群HLA-A＊02分子多态性及分布

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中国输血杂志 2013年第4期26卷 320-323页

作者：汤敏中李军蔡永林郑裕明廖建 stephen j.o'brien 曾毅北京工业大学生命科学与生物工程学院北京100124 梧州市红十字会医院鼻咽癌病因学及分子机理重点实验室苍梧县鼻咽癌防治所流行病学室 National Cancer Institute at the National Institutes of Health USA 中国疾病预防控制中心传染病预防控制国家重点实验室

目的了解中国南方鼻咽癌高发区非癌人群HLA-A*02等位基因多态性及其分布特点。方法采用PCR-SSoP方法对来源于广西鼻咽癌高发区的342例非癌对照标本作HLA-A基因分型;等位基因频率统计采用直接计数法,并应用卡方检验将其与已报道的中国南... 详细信息

目的了解中国南方鼻咽癌高发区非癌人群HLA-A*02等位基因多态性及其分布特点。方法采用PCR-SSoP方法对来源于广西鼻咽癌高发区的342例非癌对照标本作HLA-A基因分型;等位基因频率统计采用直接计数法,并应用卡方检验将其与已报道的中国南方及北方汉族群体HLA-A*02等位基因频率作比较。结果所检测的广西鼻咽癌高发区非癌人群的HLA-A*02等位基因分布频率为33.77%(231/684),共检测出5种HLA-A*02等位基因亚型,检出比例依次为:A*02∶03占48.92%(113/231)、A*02∶07占33.77%(78/231)、A*02∶01占9.52%(22/231)、A*02∶06占7.36%(17/231)和A*02∶11占0.05%(1/231);对比分析显示A*02∶01、A*02∶03、A*02∶06及A*02∶07在不同地区汉族人群中呈现出明显的分布差异(P<0.05)。结论中国南方鼻咽癌高发区非癌人群HLA-A*02等位基因中以A*02∶03最为常见、A*02∶07次之,其HLA-A*02等位基因亚型与中国其地域的汉族人群相比存在明显的差异分布特征,提示该等位基因亚型是人群分析中较好的多态性标志。

关键词： HLA 分子多态性 A*02等位基因鼻咽癌高发区非癌人群中国南方汉族

Apples to oranges:environmentally derived,dynamic regulation of serotonin neuron subpopulations in adulthood?

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Neural Regeneration Research 2025年第9期20卷 2596-2597页

作者： Christopher j.o’Connell Matthew j.Robson Department of Genetics College of MedicineHarvard UniversityBostonMAUSA james L.Winkle College of Pharmacy Division of Pharmaceutical SciencesUniversity of CincinnatiCincinnatiOHUSA Neuroscience Graduate Program College of MedicineUniversity of CincinnatiCincinnatiOHUSA

Traumatic brain injury(TBI)is a public health problem with an undue economic burden that impacts nearly every age,ethnic,and gender group across the globe(Capizzi et al.,2020).TBIs are often sustained during a dynamic range of exposures to energetic environmental forces and as such outcomes are typically heterogeneous regarding severity and pathology(Capizzi et al.,2020).

关键词： sustained orange dynamic

Apples to oranges:environmentally derived,dynamic regulation of serotonin neuron subpopulations in adulthood?

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Neural Regeneration Research 2025年第09期 2596-2597页

作者： Christopher j.o'Connell Matthew j.Robson Department of Genetics College of Medicine Harvard University james L. Winkle College of Pharmacy Division of Pharmaceutical SciencesUniversity of Cincinnati Neuroscience Graduate Program College of MedicineUniversity of Cincinnati

Traumatic brain injury(TBI) is a public health problem with an undue economic burden that impacts nearly every age,ethnic,and gender group across the globe(Capizzi et al.,2020).TBIs are often sustained during a dynamic range of exposures to energetic environmental forces and as such outcomes are typically heterogeneous regarding severity and pathology(Capizzi et al.,2020).

关键词：

中国及其他分布区域野生虎的系统地理学和遗传起源研究进展

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Zoological Research 2006年第4期27卷 441-448页

作者：罗述金 jae-heup Kim Warren E.johnson Dale G.Miquelle 黄世强潘文石 james L.D.Smith stephen j.o'brien Laboratory of Genomic Diversity National Cancer InstituteFrederickMaryland 21702United States of America Department of Fisheries Wildlifeand Conservation BiologyUniversity of MinnesotaSt. PaulMinnesota 55108United States of America Wildlife Conservation Society Russian Far East ProgramBronxNew YorkUnited States of America 北京动物园北京大学生命科学学院

世界野生虎(Pantheratigris)传统上被划分为8个亚种,其中3个亚种已于20世纪灭绝,而剩余种群的生存仍然受到偷猎、栖息地丧失和片断化的威胁。作为唯一栖息着4个现存虎亚种的国家,中国在世界虎的保护事业中负有重要责任,然而其野生和圈... 详细信息

世界野生虎(Pantheratigris)传统上被划分为8个亚种,其中3个亚种已于20世纪灭绝,而剩余种群的生存仍然受到偷猎、栖息地丧失和片断化的威胁。作为唯一栖息着4个现存虎亚种的国家,中国在世界虎的保护事业中负有重要责任,然而其野生和圈养虎的分类地位却仍然不确定。最近一项研究(Luoetal,2004)从所有现存野生虎分布地区(包括中国)采集了134份“基准样品”(即原产野外或有确定地域起源的个体生物样品),对虎的系统地理学、种群结构以及遗传起源进行了全面分析。所用的分子标记包括四千碱基对的线粒体DNA、30个核基因组微卫星位点,以及MHC-DRB基因。研究结果表明,虽然虎的整体遗传多态性较低,但是种群分化程度很高,它们被划分为6个,而不是5个现存亚种(1)西伯利亚虎(***);(2)苏门答腊虎(***);(3)孟加拉虎(***);(4)华南虎(***);(5)印支虎(***);(6)新定义的亚种马来虎,暂命名为***。由于所研究样本量有限,目前暂定的华南虎亚种还需进一步确定。现有华南虎圈养种群包括遗传关系相距较远的两支一支与印支虎(***)无异;而另一支则与其他种群均相距甚远,可能代表了真正的华南虎(***)。利用分子生物学方法对中国动物园中圈养虎的遗传起源调查亟待进行,以确认该圈养种群整体的遗传独特性或者非独特性。换言之,这将是确认华南虎是否仍然存在的关键。

关键词：虎系统地理学中国亚种分化遗传起源

4号染色体短臂微卫星多态性与鼻咽癌相关性的研究

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4号染色体短臂微卫星多态性与鼻咽癌相关性的研究

A REDUCED oRDER SCHWARZ METHoD FoR NoNLINEAR MULTISCALE ELLIPTIC EQUATIoNS BASED oN TWo-LAYER NEURAL NETWoRKS

第六次全国医学遗传学学术会议

作者：郭秀婵 stephen j.o’brien Cheryl Winkler Kevin Scott Holli Hutcheson Victor David Bailey Kessing 刘彦郑裕明廖建 Guy de The 和曾毅中国疾病预防控制中心病毒病所肿瘤室美国国家癌症研究所基因组多样性研究室广西梧州市肿瘤防治研究所广西苍梧县鼻咽癌防治所法国巴士德研究所

鼻咽癌(NPC)是一种多因素复杂疾病。其发病过程涉及EB病毒慢性感染、环境致癌因素及宿主基因之间的相互作用。在这一过程中,那些宿主基因在EB病毒感染及鼻咽癌的发生发展中起了关键作用仍不清楚。本研究的目的是发现与鼻咽癌发生发展中... 详细信息

鼻咽癌(NPC)是一种多因素复杂疾病。其发病过程涉及EB病毒慢性感染、环境致癌因素及宿主基因之间的相互作用。在这一过程中,那些宿主基因在EB病毒感染及鼻咽癌的发生发展中起了关键作用仍不清楚。本研究的目的是发现与鼻咽癌发生发展中两个关键步骤相关的遗传变异, 即EB病毒持续性感染鼻咽部上皮细胞和鼻咽癌的形成。我们在广西梧州市及苍梧县鼻咽癌高发区收集汉族鼻咽癌患者350例、EB病毒壳抗原IgA抗体阳性者(IgA／VCA+)288例和EB病毒壳抗原IgA 抗体阴性者(IgA／VCA-)346例。对先前鼻咽癌家系研究显示的鼻咽癌易感区4号染色体短臂 (4p15．1-q12)进行了微卫星精细扫描,在18 Mb的范围内选择34个微卫星标记,包括319个等位基因,对其进行基因分型。比较分析NPC组和IgA／VCA+组等位基因频率结果显示,9个等位基因与鼻咽癌呈相关,其中5个为易感等位基因(oR=1．51-5．36,p=0．01-0．03),4个为限制性等位基因(oR 值为0．3-0．71,p值为0．02-0．045)。比较分析IgA／VCA+组和IgA／VCA-组及比较所有IgA／VCA+者(包括NPC患者)和IgA／VCA-者等位基因频率的结果显示,12个等位基因与EB病毒壳抗原IgA抗体持续存在相关,其中3个在两组比较中均呈显著相关。等位基因D4S3241-136(p=0．004,oR=1．9, 95％CI=1．2-3．0)和D4S3347-213(p=0．001,oR=1．6,95％CI=1．2-2．1)可增加EB病毒IgA／VCA抗体形成的危险,为易感基因;而等位基因D4S174-202(p=0．001,oR=0．5,95％CI=0．3-0．7)可限制IgA／VCA 抗体的形成。但上述结果经多因素比较校正后,均失去相关性。我们的研究结果不能确定该区域与非家族性鼻咽癌的形成相关,另一个家系研究的结果也未得出相关的结果,但本研究却提供了进一步发现鼻咽癌相关基因的研究模式。有关4号染色体短臂与EB病毒慢性持续感染及鼻咽癌的形成仍值得进一步深入研究。

关键词：鼻咽癌 4号染色体相关研究微卫星

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journal of Computational Mathematics 2024年第2期42卷 570-596页

作者： Shi Chen Zhiyan Ding Qin Li stephen j.Wright Mathematics Department University of Wisconsin-MadisonMadisonWI 53706USA Department of Mathematics University of California-BerkeleyBerkeley CA 94720USA Mathematics Department and Discovery Institute University of Wisconsin-Madison MadisonWI 53706USA Computer Sciences Department University of WisconsinMadisonWI 53706USA

Neural networks are powerful tools for approximating high dimensional data that have been used in many contexts,including solution of partial differential equations(PDEs).We describe a solver for multiscale fully nonlinear elliptic equations that makes use of domain decomposition,an accelerated Schwarz framework,and two-layer neural networks to approximate the boundary-to-boundarymap for the subdomains,which is the key step in the Schwarz ***,the boundary-to-boundary map requires solution of boundary-value elliptic problems on each *** leveraging the compressibility of multiscale problems,our approach trains the neural network offline to serve as a surrogate for the usual implementation of the boundary-to-boundary *** method is applied to a multiscale semilinear elliptic equation and a multiscale p-Laplace *** both cases we demonstrate significant improvement in efficiency as well as good accuracy and generalization performance.

关键词： Nonlinear homogenization Multiscale elliptic problem Neural networks Do-main decomposition