Along with the develoipment of high-throughput sequencing technologies,both sample size and SNP number are increasing rapidly in genome-wide association studies(GWAS),and the associated computation is more challenging...Along with the develoipment of high-throughput sequencing technologies,both sample size and SNP number are increasing rapidly in genome-wide association studies(GWAS),and the associated computation is more challenging than ever.Here,we present a memory-efficient,visualization-enhanced,and parallel-accelerated R package called“r MVP”to address the need for improved GWAS computation.r MVP can 1)effectively process large GWAS data,2)rapidly evaluate population structure,3)efficiently estimate variance components by Efficient Mixed-Model Association e Xpedited(EMMAX),Factored Spectrally Transformed Linear Mixed Models(Fa ST-LMM),and Haseman-Elston(HE)regression algorithms,4)implement parallel-accelerated association tests of markers using general linear model(GLM),mixed linear model(MLM),and fixed and random model circulating probability unification(Farm CPU)methods,5)compute fast with a globally efficient design in the GWAS processes,and 6)generate various visualizations of GWASrelated information.Accelerated by block matrix multiplication strategy and multiple threads,the association test methods embedded in r MVP are significantly faster than PLINK,GEMMA,and Farm CPU_pkg.r MVP is freely available at https://github.com/xiaolei-lab/r MVP.展开更多
Objective Large numbers of archeological relics from the Neolithic period are widely distributed in all tributaries of the Yellow River. The early humans tended to reside along the river valleys, and developed small b...Objective Large numbers of archeological relics from the Neolithic period are widely distributed in all tributaries of the Yellow River. The early humans tended to reside along the river valleys, and developed small but characteristically decentralized ancient valley culture. It is universally acknowledged that the agriculture exchange between China and western countries and the moderate展开更多
Seed development in angiosperms requires a 2：1 maternal-to-paternal genome ratio （2m：lp） in the endo- sperm. When the ratio is disrupted, the seed development is impaired. Rice interploidy crosses result in endosp...Seed development in angiosperms requires a 2：1 maternal-to-paternal genome ratio （2m：lp） in the endo- sperm. When the ratio is disrupted, the seed development is impaired. Rice interploidy crosses result in endosperm failures, but the underlying molecular mechanisms remain unclear. Here, we report that the defective endosperm in rice interploidy crosses was associated with nonadditive expression of small RNAs and protein-coding genes. Interestingly, 24-nt small interfering RNAs were enriched in the 5＇ and 3＇ flanking sequences of nonadditively expressed genes in the interploidy crosses and were negatively associated with the expression of imprinted genes. Furthermore, some PRC2 family genes and DNA methylaUon-related genes including OsMETlb and OsCMT3a were upregulated in the 2x4 cross （polli- nating a diploid ＂mother＂ with a tetraploid ＂father＂） but repressed in the reciprocal cross. These different epigenetic effects could lead to precocious or delayed cellularization during endosperm development. Notably, many endosperm-preferred genes, including starch metabolic and storage protein genes during grain filling, were found to be associated with DNA methylation or H3K27me3, which are repressed in both 2×4 and 4 ×2 crosses. WUSCHEL homeobox2 （WOX2）-Iike （WOX2L）, an endosperm-preferred gene, was expressed specifically in the rice endosperm, in contrast to WOX2 expression in the Arabidopsis embryo. Disruption of WOX2L in transgenic rice by CRISPR/Cas9-mediated gene editing blocked starch and protein accumulation, resulting in seed abortion. In addition to gene repression, disrupting epigenetic process in the interploidy crosses also induced expression of stress-responsive genes. Thus, maintaining the 2m：lp genome ratio in the endosperm is essential for normal grain development in rice and other cereal crops.展开更多
Hordeum californicum （2n = 2x = 14, HH） is resistant to several wheat diseases and tolerant to lower nitrogen. In this study, a molecular karyotype of H. californicum chromosomes in the Triticum aestivum L. cv. Chin...Hordeum californicum （2n = 2x = 14, HH） is resistant to several wheat diseases and tolerant to lower nitrogen. In this study, a molecular karyotype of H. californicum chromosomes in the Triticum aestivum L. cv. Chinese Spring （CS）-H. californicum amphidiploid （2n = 6x = 56, AABBDDHH） was established. By genomic in situ hybridization （GISH） and multicolor fluorescent in situ hybridization （FISH） using repetitive DNA clones （pTa71, pTa794 and pSc119.2） as probes, the H. californicum chromosomes could be differentiated from each other and from the wheat chromosomes unequivocally. Based on molecular karyotype and marker analyses, 12 wheat--alien chromosome lines, including four disomic addition lines （DAH1, DAH3, DAH5 and DAH6）, five telosomic addition lines （MtH7L, MtHIS, MtH1L, DtH6S and DtH6L）, one multiple addition line involving H. californicum chromosome H2, one disomic substitution line （DSH4） and one translocation line （TH7S/1BL）, were identified from the progenies derived from the crosses of CS-H. californicum amphidiploid with common wheat varieties. A total of 482 EST （expressed sequence tag） or SSR （simple sequence repeat） markers specific for individual H. californicum chromosomes were identified, and 47, 50, 45, 49, 21, 51 and 40 markers were assigned to chromosomes H1, H2, H3, H4, H5, H6 and H7, respectively. According to the chromosome allocation of these markers, chromosomes H2, H3, H4, H5, and H7 of H. californicum have relationship with wheat homoeologous groups 5, 2, 6, 3, and 1, and hence could be designated as 5Hc, 2He, 6Hc, 3Hc and 1Hc, respectively. The chromosomes H1 and H6 were designated as 7Hc and 4Hc, respectively, by referring to SSR markers located on rye chromosomes.展开更多
Inner ear hair cells are important for maintaining hearing.Irreversible damage to hair cells is an important cause of sensorineural deafness.Electromagnetic radiation,especially high-power microwave,is an important th...Inner ear hair cells are important for maintaining hearing.Irreversible damage to hair cells is an important cause of sensorineural deafness.Electromagnetic radiation,especially high-power microwave,is an important threat to human health in modern society and war.However,it is not clear whether high-power microwave has an effect on cochlea hair cells.This study aimed to assess the effects of high-power microwave on cochlear hair cells in guinea pigs,and investigate the potential protection of these cells against high-power microwave-induced damage by recombinant adenovirus A20.Based on experimental results,a 65 W/cm^(2) irradiation density applied to guinea pigs in this study to establish a high-power microwave inner ear injury model.In addition,pAdEeay-1/A20 was injected via a round window into experimental guinea pig cochlea,whereas artificial perilymph was injected into the control group.Auditory function was assessed by testing the auditory brainstem response threshold,and damage to cochlear hair cells was investigated by cell counting and scanning electron microscopy observations of the basilar membrane.Inner ear injury was observed 6 hours after 65 W/cm^( 2 ) of irradiation and the auditory brainstem response threshold was significantly higher in the irradiation group(P<0.05)compared with other groups.Propidium iodide staining and scanning electron microscopy results indicated that significant morphological changes occurred after radiation,especially to inner hair cells,which exhibited remarkable damage and the presence of several unknown spherical substances.Auditory brainstem response threshold was decreased in the pAdEeay-1/A20 group compared with the artificial perilymph group;moreover,damage to hair cells was milder in the pAdEeay-1/A20 group compared with the control group(P<0.01).Thus,high-power microwave can cause damage to cochlear hair cells,as well as hearing loss with prolonged exposure and/or high dosage.In this regard,65 W/cm^( 2 ) of irradiation for 6 hours is a reliable target dose for obser展开更多
目的检验中文版儿童自我报告结局测量信息系统(child self-reported Chinese version of pediatric PROMIS,C-C-Ped-PROMIS)八大简表在哮喘儿童与青少年人群中的可行性及信效度。方法便利抽样法选取上海市2所医院的8~17周岁儿童和青少...目的检验中文版儿童自我报告结局测量信息系统(child self-reported Chinese version of pediatric PROMIS,C-C-Ped-PROMIS)八大简表在哮喘儿童与青少年人群中的可行性及信效度。方法便利抽样法选取上海市2所医院的8~17周岁儿童和青少年哮喘患者为研究对象,采用一般资料调查表、C-C-Ped-PROMIS及哮喘控制问卷对其进行调查,采用问卷有效回收率及回答有效性来分析其可行性,并检验其信效度。结果儿童身体功能-移动性、身体功能-上肢功能、疲劳、疼痛影响、焦虑、愤怒、抑郁症状、同伴关系各简表条目总分相关系数介于0.520~0.843之间,均具有单维度因子结构,Cronbach’sα系数介于0.813~0.916之间,Guttma折半系数介于0.754~0.902之间。结论儿童自我报告结局测量信息系统简表具有良好的可行性和信效度,可用于中国哮喘儿童与青少年生理、心理及社会等各方面健康结局的测评。展开更多
基金supported by the National Natural Science Foundation of China(Grant Nos.31730089,31672391,31702087,and 31701144)the National Key R&D Program of China(Grant No.2016YFD0101900)+2 种基金the Fundamental Research Funds for the Central Universities,China(Grant Nos.2662020DKPY007 and 2662019PY011)the National Science Foundation,USA(Grant No.DBI 1661348)the National Swine System Industry Technology System,China(Grant No.CARS-35)。
文摘Along with the develoipment of high-throughput sequencing technologies,both sample size and SNP number are increasing rapidly in genome-wide association studies(GWAS),and the associated computation is more challenging than ever.Here,we present a memory-efficient,visualization-enhanced,and parallel-accelerated R package called“r MVP”to address the need for improved GWAS computation.r MVP can 1)effectively process large GWAS data,2)rapidly evaluate population structure,3)efficiently estimate variance components by Efficient Mixed-Model Association e Xpedited(EMMAX),Factored Spectrally Transformed Linear Mixed Models(Fa ST-LMM),and Haseman-Elston(HE)regression algorithms,4)implement parallel-accelerated association tests of markers using general linear model(GLM),mixed linear model(MLM),and fixed and random model circulating probability unification(Farm CPU)methods,5)compute fast with a globally efficient design in the GWAS processes,and 6)generate various visualizations of GWASrelated information.Accelerated by block matrix multiplication strategy and multiple threads,the association test methods embedded in r MVP are significantly faster than PLINK,GEMMA,and Farm CPU_pkg.r MVP is freely available at https://github.com/xiaolei-lab/r MVP.
基金financially supported by the National Science Foundation of China (grant No. 41571177)
文摘Objective Large numbers of archeological relics from the Neolithic period are widely distributed in all tributaries of the Yellow River. The early humans tended to reside along the river valleys, and developed small but characteristically decentralized ancient valley culture. It is universally acknowledged that the agriculture exchange between China and western countries and the moderate
基金Funding for the research was provided by the National Natural Science Foundation of China （no. 31290213）, Research and Education innovation Consortium of Jiangsu Province （2013-2015）, Fundamental Research Funds for Central Universities （KYRC201204 and KYZ201202-1）, and Jiangsu Collaborative innovation Center for Modern Crop Production （2015-2017）.
文摘Seed development in angiosperms requires a 2：1 maternal-to-paternal genome ratio （2m：lp） in the endo- sperm. When the ratio is disrupted, the seed development is impaired. Rice interploidy crosses result in endosperm failures, but the underlying molecular mechanisms remain unclear. Here, we report that the defective endosperm in rice interploidy crosses was associated with nonadditive expression of small RNAs and protein-coding genes. Interestingly, 24-nt small interfering RNAs were enriched in the 5＇ and 3＇ flanking sequences of nonadditively expressed genes in the interploidy crosses and were negatively associated with the expression of imprinted genes. Furthermore, some PRC2 family genes and DNA methylaUon-related genes including OsMETlb and OsCMT3a were upregulated in the 2x4 cross （polli- nating a diploid ＂mother＂ with a tetraploid ＂father＂） but repressed in the reciprocal cross. These different epigenetic effects could lead to precocious or delayed cellularization during endosperm development. Notably, many endosperm-preferred genes, including starch metabolic and storage protein genes during grain filling, were found to be associated with DNA methylation or H3K27me3, which are repressed in both 2×4 and 4 ×2 crosses. WUSCHEL homeobox2 （WOX2）-Iike （WOX2L）, an endosperm-preferred gene, was expressed specifically in the rice endosperm, in contrast to WOX2 expression in the Arabidopsis embryo. Disruption of WOX2L in transgenic rice by CRISPR/Cas9-mediated gene editing blocked starch and protein accumulation, resulting in seed abortion. In addition to gene repression, disrupting epigenetic process in the interploidy crosses also induced expression of stress-responsive genes. Thus, maintaining the 2m：lp genome ratio in the endosperm is essential for normal grain development in rice and other cereal crops.
基金supported by the Technology Support Program of Jiangsu Province (No. BE2012306)the Program of Introducing Talents of Discipline to Universities (No. B08025)+1 种基金the Project No.7 from Science and High-Tech Based Major Program of Agriculture Committee of Shanghai Municipal Administration (No.20127)the Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD)
文摘Hordeum californicum （2n = 2x = 14, HH） is resistant to several wheat diseases and tolerant to lower nitrogen. In this study, a molecular karyotype of H. californicum chromosomes in the Triticum aestivum L. cv. Chinese Spring （CS）-H. californicum amphidiploid （2n = 6x = 56, AABBDDHH） was established. By genomic in situ hybridization （GISH） and multicolor fluorescent in situ hybridization （FISH） using repetitive DNA clones （pTa71, pTa794 and pSc119.2） as probes, the H. californicum chromosomes could be differentiated from each other and from the wheat chromosomes unequivocally. Based on molecular karyotype and marker analyses, 12 wheat--alien chromosome lines, including four disomic addition lines （DAH1, DAH3, DAH5 and DAH6）, five telosomic addition lines （MtH7L, MtHIS, MtH1L, DtH6S and DtH6L）, one multiple addition line involving H. californicum chromosome H2, one disomic substitution line （DSH4） and one translocation line （TH7S/1BL）, were identified from the progenies derived from the crosses of CS-H. californicum amphidiploid with common wheat varieties. A total of 482 EST （expressed sequence tag） or SSR （simple sequence repeat） markers specific for individual H. californicum chromosomes were identified, and 47, 50, 45, 49, 21, 51 and 40 markers were assigned to chromosomes H1, H2, H3, H4, H5, H6 and H7, respectively. According to the chromosome allocation of these markers, chromosomes H2, H3, H4, H5, and H7 of H. californicum have relationship with wheat homoeologous groups 5, 2, 6, 3, and 1, and hence could be designated as 5Hc, 2He, 6Hc, 3Hc and 1Hc, respectively. The chromosomes H1 and H6 were designated as 7Hc and 4Hc, respectively, by referring to SSR markers located on rye chromosomes.
基金supported by grants from the National Natural Science Foundation of China(No.81873702,81470694,to WY)Chongqing Natural Science Foundation of China(No.cstc2017jcyjAX0407,to WY)Southwest Hospital Foundation of China(No.SWH2016JCZD-02,to WY).
文摘Inner ear hair cells are important for maintaining hearing.Irreversible damage to hair cells is an important cause of sensorineural deafness.Electromagnetic radiation,especially high-power microwave,is an important threat to human health in modern society and war.However,it is not clear whether high-power microwave has an effect on cochlea hair cells.This study aimed to assess the effects of high-power microwave on cochlear hair cells in guinea pigs,and investigate the potential protection of these cells against high-power microwave-induced damage by recombinant adenovirus A20.Based on experimental results,a 65 W/cm^(2) irradiation density applied to guinea pigs in this study to establish a high-power microwave inner ear injury model.In addition,pAdEeay-1/A20 was injected via a round window into experimental guinea pig cochlea,whereas artificial perilymph was injected into the control group.Auditory function was assessed by testing the auditory brainstem response threshold,and damage to cochlear hair cells was investigated by cell counting and scanning electron microscopy observations of the basilar membrane.Inner ear injury was observed 6 hours after 65 W/cm^( 2 ) of irradiation and the auditory brainstem response threshold was significantly higher in the irradiation group(P<0.05)compared with other groups.Propidium iodide staining and scanning electron microscopy results indicated that significant morphological changes occurred after radiation,especially to inner hair cells,which exhibited remarkable damage and the presence of several unknown spherical substances.Auditory brainstem response threshold was decreased in the pAdEeay-1/A20 group compared with the artificial perilymph group;moreover,damage to hair cells was milder in the pAdEeay-1/A20 group compared with the control group(P<0.01).Thus,high-power microwave can cause damage to cochlear hair cells,as well as hearing loss with prolonged exposure and/or high dosage.In this regard,65 W/cm^( 2 ) of irradiation for 6 hours is a reliable target dose for obser
文摘目的检验中文版儿童自我报告结局测量信息系统(child self-reported Chinese version of pediatric PROMIS,C-C-Ped-PROMIS)八大简表在哮喘儿童与青少年人群中的可行性及信效度。方法便利抽样法选取上海市2所医院的8~17周岁儿童和青少年哮喘患者为研究对象,采用一般资料调查表、C-C-Ped-PROMIS及哮喘控制问卷对其进行调查,采用问卷有效回收率及回答有效性来分析其可行性,并检验其信效度。结果儿童身体功能-移动性、身体功能-上肢功能、疲劳、疼痛影响、焦虑、愤怒、抑郁症状、同伴关系各简表条目总分相关系数介于0.520~0.843之间,均具有单维度因子结构,Cronbach’sα系数介于0.813~0.916之间,Guttma折半系数介于0.754~0.902之间。结论儿童自我报告结局测量信息系统简表具有良好的可行性和信效度,可用于中国哮喘儿童与青少年生理、心理及社会等各方面健康结局的测评。
