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Convergence of Y Chromosome STR Haplotypes from Different SNP Haplogroups Compromises Accuracy of Haplogroup Prediction

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Journal of Genetics and Genomics 2015年第7期42卷 403-407页

作者： Chuan-Chao Wang Ling-Xiang Wang Rukesh Shrestha Shaoqing Wen manfei zhang Xinzhu Tong Li Jin Hui Li State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemprary Anthropology School of Life Sciences and Institutes of Biomedical SciencesFudan University CAS-MPG Partner Institute for Computational Biology Shangai Institutes for Biological Sciences of Chinese Academy of Sciences

The paternally inherited Y chromosome has been widely used in forensics for personal identification, in anthropology and population genetics to understand origin and migration of human populations, and also in medical and clinical studies （Wang and Li, 2013; Wang et al., 2014）. There are two kinds of extremely useful markers in Y chromosome, single nucle- otide polymorphism （SNP） and short tandem repeats （STRs）. With a very low mutation rate on the order of 3.0 x 10-8 mutations/nucleotide/generation （Xue et al., 2009）, SNP markers have been used in constructing a robust phylogeny tree linking all the Y chromosome lineages from world pop- ulations （Karafet et al., 2008）. Those lineages determined by the pattern of SNPs are called haplogroups. That is to say, we have to genotype an appropriate number of SNPs in order to assign a given Y chromosome to a haplogroup. Compared with SNPs, the mutation rates of STR markers are about four to five orders of magnitude higher （Gusmgo et al., 2005; Ballantyne et al., 2010）. Typing STR has advantages of saving time and cost compared with typing SNPs in phylogenetic assignment of a Y chromosome （Wang et al., 2010）. A set of STR values for an individual is called a haplotype. Because of the disparity in mutation rates between SNP and STR, one SNP haplogroup could actually comprise many STR haplotypes （Wang et al., 2010）. It is most interesting that STR variability is clustered more by haplogroups than by populations （Bosch et al., 1999; Behar et al., 2004）, which indicates that STR haplotypes could be used to infer the haplogroup information of a given Y chromosome. There has been increasing interest in this cost- effective strategy for predicting the haplogroup from a given STR haplotype when SNP data are unavailable. For instance, Vadim Urasin＇s YPredictor （http：//***/）, Whit Atheys＇ haplogroup predictor （http：//***/hapest5/）（Athey, 2005, 2006）, and haplogroup classifier of Arizona University （Schlecht et

关键词： STR Convergence of Y Chromosome STR Haplotypes from Different SNP Haplogroups Compromises Accuracy of Haplogroup Prediction SNP SNPs

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Genetic evidence for facial variation being a composite phenotype of cranial variation and facial soft tissue thickness

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Journal of Genetics and Genomics 2022年第10期49卷 934-942页

作者： Wei Qian manfei zhang Kaiwen Wan Yunxia Xie Siyuan Du Jiarui Li Xiongzheng Mu Jiange Qiu Xiangyang Xue Xiahai Zhuang Yingzhi Wu Fan Liu Sijia Wang State Key Laboratory of Genetic Engineering Human Phenome InstituteZhangjiang Fudan International Innovation CenterFudan UniversityShanghai 201203China School of Computer Science Fudan UniversityShanghai 200438China CAS Key Laboratory of Computational Biology Shanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai 200031China School of Data Science Fudan UniversityShanghai 200433China Academy of Medical Science Zhengzhou UniversityZhengzhouHenan 450052China Department of Plastic Surgery Huashan HospitalFudan UniversityShanghai 200040China CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of GenomicsUniversity of Chinese Academy of SciencesBeijing 100101China School of Future Technology University of Chinese Academy of SciencesBeijing 101408China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunmingYunnan 650223China

Facial and cranial variation represent a multidimensional set of highly correlated and heritable *** is known about the genetic basis explaining this *** develop a software package ALo SFL for simultaneous localization of facial and cranial landmarks from head computed tomography(CT)images,apply it in the analysis of head CT images of 777 Han Chinese women,and obtain a set of phenotypes representing variation in face,skull and facial soft tissue thickness(FSTT).Association analysis of 301 single nucleotide polymorphisms(SNPs)from 191 distinct genomic loci previously associated with facial variation reveals an unexpected larger number of loci showing significant associations(P<1e-3)with cranial phenotypes than expected under the null(O/E=3.39),suggesting facial and cranial phenotypes share a substantial proportion of genetic *** FSTT to a SNP-only model shows a large impact in explaining facial variance.A gene ontology analysis reveals that bone morphogenesis and osteoblast differentiation likely underlie our cranial-significant ***,this study simultaneously investigates the genetic effects on both facial and cranial variation of the same sample,supporting that facial variation is a composite phenotype of cranial variation and FSTT.

关键词： Facial variation Cranial variation Association analysis Single nucleotide polymorphism Facial soft tissue thickness Computed tomography

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Large-scale genome-wide scans do not support petaloid toenail as a Mendelian trait

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Journal of Genetics and Genomics 2016年第12期43卷 702-704页

作者： manfei zhang Sijie Wu Juan zhang Yajun Yang Jingze Tan Haijuan Guan Yu Liu Kun Tang Jean Krutmann Shuhua Xu Li Jin Yaqun Guan Hui Li Sijia Wang Ministry of Education Key Laboratory of Contemporary Anthropology Collaborative Innovation Center for Genetics and DevelopmentSchool of Life SciencesFudan UniversityShanghai 200438China Chinese Academy of Sciences Key Laboratory of Computational Biology CAS-MPG Partner Institute for Computational BiologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghai 200031China University of Chinese Academy of Sciences Beijing 100049China Fudan-Taizhou Institute of Health Sciences Taizhou 225300China IUF-Leibniz Research Institute for Environmental Medicine Dusseldorf 40225Germany School of Life Science and Technology Shanghai Tech UniversityShanghai 200031China Department of Biochemistry and Molecular Biology Preclinical Medicine CollegeXinjiang Medical UniversityUrumqi 830011China

Petaloid toenail, or accessory nail of the fifth toe, is a physical trait characterized by the presence of an additional tiny toenail on the small toe. Since it can occasionally cause disfigurement and tenderness while wearing tight shoes or walking, standard surgical matricectomy is often carried out to repair the petaloid toenail （Chi and Wang, 2004）. Chinese legends recorded petaloid toenails as a trait unique to Han Chinese （Gao, 2010）, but population- based studies are largely absent.

关键词： meta mode than

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A genome-wide association study of facial morphology identifies novel genetic loci in Han Chinese

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Journal of Genetics and Genomics 2021年第3期48卷 198-207页

作者： Yin Huang Dan Li Lu Qiao Yu Liu Qianqian Peng Sijie Wu manfei zhang Yajun Yang Jingze Tan Shuhua Xu Li Jin Sijia Wang Kun Tang Stefan Grunewald Chinese Academy of Sciences Key Laboratory of Computational Biology CAS-MPG Partner Institute for Computational BiologyShanghai Institute of Nutrition and HealthShanghai Institutes for Biological SciencesUniversity of Chinese Academy of SciencesCASShanghai 200031China DeepBlue Technology(Shanghai)Co. LtdShanghai 200336China State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology School of Life SciencesFudan UniversityShanghai 200433China Fudan-Taizhou Institute of Health Sciences Taizhou 225300China Collaborative Innovation Center of Genetics and Development Shanghai 200438China f Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunmingYunnan 650223China School of Life Science and Technology ShanghaiTech UniversityShanghai 201210China

The human face is a heritable surface with many complex sensory *** recent years,many genetic loci associated with facial features have been reported in different populations,yet there is a lack of studies on the Han Chinese ***,we report a genome-wide association study of 3D normal human faces of 2,659 Han Chinese with autosegment phenotypes of facial *** identify singlenucleotide polymorphisms(SNPs)encompassing four genomic regions showing significant associations with different facial regions,including SNPs in DENND1 B associated with the chin,SNPs among PISRT1 associated with eyes,SNPs between DCHS2 and SFRP2 associated with the nose,and SNPs in VPS13 B associated with the *** replicate 24 SNPs from previously reported genetic loci in different populations,whose candidate genes are DCHS2,SUPT3 H,HOXD1,SOX9,PAX3,and *** results provide a more comprehensive understanding of the genetic basis of variation in human facial morphology.

关键词： Genome-wide association study Facial morphology Automatic phenotyping Visualization

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Literature Review of Chinese Government Investment Research

Literature Review of Chinese Government Investment Research

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第二届（2010）金融风险与公司财务管理国际研讨会

作者： SUN Xiufeng zhang manfei School of Management Dalian University of Technology Dalian China 116024

＜正＞As government investment plays a significant role in promoting economic growth;Chinese scholars do more and more researches on government *** paper will review the literatures from the following four aspects: management mode,capital source,performance evaluation,behavior mechanism and effect,then point out the deficiencies of existing researches and the future research directions.

关键词： government investment infrastructure construction economic growth

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Journal of Integrative Agriculture 2024年第11期23卷 3788-3800页

作者： Chengdong Yang manfei Luo Xue zhang Linlin Ye Ge Yu Yi Lü Yi Chen Taixu Chen Xuejian Wang Wanzhen Feng Qinghe Chen School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication) Hainan University Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests of Ministry of Education School of Tropical Agriculture and Forestry Hainan University Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests

Litchi downy blight, caused by the plant pathogenic oomycete Peronophythora litchii, is one of the most devastating diseases on litchi and resulted in huge economic losses. Autophagy plays an essential role in the development and pathogenicity of the filamentous fungi. However, the function of autophagy in oomycetes remain elusive. Here, an autophagy-related protein Atg3 homolog PlAtg3 was identified and characterized in P. litchii. The absence of PlATG3 through the CRISPR/Cas9 gene replacement strategy compromised vegetative growth and sexual/asexual development. Cytological analyses revealed that the deletion of PlATG3 impaired autophagosome formation with monodansylcadaverine(MDC) staining and significantly disrupted zoospore release due to defects of sporangial cleavage with FM4-64 staining. Atg8 is considered to be an autophagy marker protein in various species. Western blot analysis indicated that PlAtg3 is involved in degradation of PlAtg8-PE. Interestingly, PlAtg3 was unable to interact with PlAtg8 in yeast two hybrid(Y2H) assays, possibly due to the absence of the Atg8 family interacting motif(AIM) in PlAtg3. Furthermore, pathogenicity assays revealed that the deletion of PlATG3 considerably reduced the virulence of P. litchii. Taken together, our data reveal that PlAtg3 plays an important role in radial growth, asexual/sexual development, sporangial cleavage and zoospore release, autophagosome formation, and pathogenicity in P. litchii. This study contributes to a better understanding of the pathogenicity mechanisms of P. litchii and provides insights for the development of more effective strategies to control oomycete diseases.

关键词： PlAtg3 sporangial cleavage autophagy pathogenicity Peronophythora litchii

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泾惠渠灌区地下水位埋深的动态特征及影响因素分析

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南水北调与水利科技 2018年第2期16卷 164-170,195页

作者：张曼菲周维博长安大学环境科学与工程学院西安710054 长安大学旱区地下水文与生态效应教育部重点实验室西安710054

地下水作为陕西泾惠渠灌区的重要水源,对其动态特征的研究在灌区水资源开发利用方面具有重要的指导意义。根据泾惠渠灌区1981-2010年的地下水位平均埋深资料,采用线性倾向估计法、累积距平法、Sen斜率估计法、Mann-Kendall趋势检验法对... 详细信息

地下水作为陕西泾惠渠灌区的重要水源,对其动态特征的研究在灌区水资源开发利用方面具有重要的指导意义。根据泾惠渠灌区1981-2010年的地下水位平均埋深资料,采用线性倾向估计法、累积距平法、Sen斜率估计法、Mann-Kendall趋势检验法对泾惠渠灌区地下水位埋深动态序列进行年际变化分析;采用滑动T检验法和双向回归突变分析法分析序列突变性;采用主成分分析法和灰色关联分析法确定影响灌区地下水埋深动态的主要因素。结果表明:灌区1981-2010年地下水位平均埋深基本呈增加趋势,突变点出现在1994年,1994年之前影响灌区地下水埋深动态的主要因素为蒸发量,1994年之后主要影响因素为蒸发量、地下水开采量和灌渠引水量。

关键词：泾惠渠灌区地下水位埋深趋势分析突变检验影响因素

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通量上边界渗透系数随埋深增加指数衰减的地下水流系统

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地质科技情报 2015年第4期34卷 189-193页

作者：张曼菲孙蓉琳梁杏中国地质大学环境学院武汉430074 中国地质大学生物地质与环境地质国家重点实验室武汉430074

地下水流系统理论是当代水文地质学的核心概念框架,研究不同控制因素对盆地地下水流系统发育模式的影响具有重要意义。近年来的研究表明利用通量上边界能够更好地揭示盆地不同要素对地下水流系统模式转化的影响。基于通量上边界,采用数... 详细信息

地下水流系统理论是当代水文地质学的核心概念框架,研究不同控制因素对盆地地下水流系统发育模式的影响具有重要意义。近年来的研究表明利用通量上边界能够更好地揭示盆地不同要素对地下水流系统模式转化的影响。基于通量上边界,采用数值模拟方法,研究稳定流条件下,渗透系数随埋深呈指数衰减的非均质含水层对盆地地下水流系统模式转化的影响。结果表明:随着渗透系数随埋深指数衰减程度的加大,盆地潜水面整体抬升,盆地上部地下水流速增大,水力梯度增大;同时,盆地地下水流系统由复杂的多级次水流系统到单一的局部水流系统,顺向局部水流系统占据的空间消减,而逆向局部水流系统占据的空间增大,流速近似为零的局部滞留区域向左下方移动。

关键词：通量上边界渗透系数指数衰减盆地地下水系统

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不同原因张口呼吸对儿童颌面部发育的影响

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临床耳鼻咽喉头颈外科杂志 2023年第8期37卷 626-631页

作者：张曼菲金莹玉张红佳王青森陈继跃张铭韩泽利解放军总医院第四医学中心口腔科北京100142 解放军总医院第四医学中心耳鼻咽喉头颈外科解放军总医院第六医学中心耳鼻咽喉头颈外科医学部

目的探究不同原因张口呼吸对儿童颌面部发育的影响。方法选择151例患儿作为研究对象。依据不同病因将其分为49例腺样体肥大组(A组)、52例扁桃体肥大组(B组)、50例腺样体伴扁桃体肥大组(C组)。选择同期的健康儿童作为本次试验的对照组,... 详细信息

目的探究不同原因张口呼吸对儿童颌面部发育的影响。方法选择151例患儿作为研究对象。依据不同病因将其分为49例腺样体肥大组(A组)、52例扁桃体肥大组(B组)、50例腺样体伴扁桃体肥大组(C组)。选择同期的健康儿童作为本次试验的对照组,共45例。分析A组、B组、C组与对照组的反射鼻咽腔测量参数、面部发育指标及头影参数,研究A组、B组、C组安氏Ⅱ类、安氏Ⅲ类的发生率。结果A组、B组、C组的反射鼻咽腔测量参数与对照组比较,差异有统计学意义(P<0.05),头影参数发生改变且各组间不同(P<0.05)。A组和C组的安氏Ⅱ类发生率较高,B组和C组的安氏Ⅲ类发生率较高(P<0.05)。结论腺样体肥大会导致下颌骨后缩,扁桃体肥大会造成下颌前伸,腺样体肥大及扁桃体肥大均容易导致下颌骨出现顺时针旋转的状态。为避免患儿发育不协调,临床应尽早对患儿的颌面部情况进行纠正。

关键词：腺样体肥大扁桃体肥大儿童面部发育

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182颗恒牙邻面牙釉质厚度的测量研究

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中华口腔医学杂志 2020年第7期55卷 488-493页

作者：边媛媛雷建锋侯静怡张曼菲厉松首都医科大学口腔医学院正畸科 100050 首都医科大学中心实验室 100069

目的通过显微CT测量182颗恒牙邻面牙釉质厚度,以期为正畸临床邻面去釉提供参考。方法2016年5月至2018年2月于首都医科大学口腔医学院口腔颌面外科门诊收集筛选182颗离体恒牙[来源于正畸减数和重度牙周炎患者,牙齿提供者均为北京市居民,... 详细信息

目的通过显微CT测量182颗恒牙邻面牙釉质厚度,以期为正畸临床邻面去釉提供参考。方法2016年5月至2018年2月于首都医科大学口腔医学院口腔颌面外科门诊收集筛选182颗离体恒牙[来源于正畸减数和重度牙周炎患者,牙齿提供者均为北京市居民,汉族,年龄(39.5±10.6)岁,90%的牙齿来源于50岁以下的患者],并根据牙位进行分类,用流体树脂于牙齿近远中邻面接触区做标记后进行小动物计算机体层显像扫描,对影像资料进行三维重建及测量,分析各牙位牙齿近中和远中邻面牙釉质厚度、近中和远中邻面接触区至面距离、近中和远中邻面接触区至釉质牙骨质界距离、牙冠近远中向宽度。结果邻面牙釉质厚度从前牙区[(0.63±0.16)mm]到磨牙区[(1.46±0.25)mm]逐渐增厚。上颌左侧第二磨牙远中邻面至右侧第二磨牙远中邻面的牙釉质厚度均值之和为31.60 mm,下颌左侧第二磨牙远中邻面至右侧第二磨牙远中邻面的牙釉质厚度均值之和为29.68 mm。前牙区邻面接触区垂直向位置靠近牙冠切1/3,磨牙区邻面接触区更接近牙冠中1/3。近中和远中邻面牙釉质厚度与牙冠近远中向宽度均呈正相关关系(P均<0.05)。结论本组离体牙结果显示,切牙区近远中邻面牙釉质厚度较小,磨牙区较大;临床应在前牙区靠近切端、在后牙区靠近龈方进行邻面去釉。

关键词：牙釉质牙列,恒显微CT 邻面去釉

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