Cyprinidae is the largest fish family in the world and contains about 210 genera and 2010 species. Appropriate DNA markers must be selected for the phylogenetic analyses of Cyprinidae. In present study, the 1st intron...Cyprinidae is the largest fish family in the world and contains about 210 genera and 2010 species. Appropriate DNA markers must be selected for the phylogenetic analyses of Cyprinidae. In present study, the 1st intron of the S7 ribosomal protein (r-protein) gene is first used to examine the relationships among cyprinid fishes. The length of the 1st intron obtained by PCR amplification ranges from 655 to 859 bp in the 16 cyprinid species investigated, and is 602 bp in Myxocyprinus asiaticus. Out of the alignment of 925 nucleotide sites obtained, the parsimony informative sites are 499 and occupy 54% of the total sites. The results indicate that the 1st intron sequences of the S7 r-protein gene in cyprinids are rich in informative sites and vary remarkably in sequence divergence from 2.3% between close species to 66.6% between distant species. The bootstrap values of the interior nodes in the NJ (neighbor-joining) and MP (most-parsimony) trees based on the present S7 r-protein gene data are higher than展开更多
为了研究ifitm基因的功能,本研究从猪肾PK15细胞中克隆了猪的3个ifitm c DNA序列,分析了猪ifitm1、ifitm2和ifitm3基因的染色体定位及其与其他物种基因序列的同源关系,并对不同ifitm在不同组织的表达进行分析和检测。结果显示,猪ifitm...为了研究ifitm基因的功能,本研究从猪肾PK15细胞中克隆了猪的3个ifitm c DNA序列,分析了猪ifitm1、ifitm2和ifitm3基因的染色体定位及其与其他物种基因序列的同源关系,并对不同ifitm在不同组织的表达进行分析和检测。结果显示,猪ifitm和人、鼠ifitm具有相同的基因和蛋白结构,进化上与牛ifitm高度同源,ifitm1和ifitm3在脾、肾、心、肝等组织中大量表达,而ifitm2只在脾和肾中检测到表达,在其他组织中的表达量相对较小。猪ifitm基因的克隆、生物信息学及组织表达分析为进一步研究其在猪细胞中的功能奠定了基础。展开更多
The reliability of real-time embedded software directly determines the reliability of the whole real-time embedded sys- tem, and the effective software testing is an important way to ensure software quality and reliab...The reliability of real-time embedded software directly determines the reliability of the whole real-time embedded sys- tem, and the effective software testing is an important way to ensure software quality and reliability. Based on the analysis of the characteristics of real-time embedded software, the formal method is introduced into the real-time embedded software testing field and the real-time extended finite state machine （RT-EFSM） model is studied firstly. Then, the time zone division method of real-time embedded system is presented and the definition and description methods of time-constrained transition equivalence class （timeCTEC） are presented. Furthermore, the approaches of the testing sequence and test case generation are put forward. Finally, the proposed method is applied to a typical avionics real- time embedded software testing practice and the examples of the timeCTEC, testing sequences and test cases are given. With the analysis of the testing result, the application verification shows that the proposed method can effectively describe the real-time embedded software state transition characteristics and real-time requirements and play the advantages of the formal methods in accuracy, effectiveness and the automation supporting. Combined with the testing platform, the real-time, closed loop and automated simulation testing for real-time embedded software can be realized effectively.展开更多
To explore correlation between the tk gene structure of pseudorabies virus (PRV) and its virulence, to study the effect of the gene mutation on PRV biological properties, and to investigate mechinism of reduced virule...To explore correlation between the tk gene structure of pseudorabies virus (PRV) and its virulence, to study the effect of the gene mutation on PRV biological properties, and to investigate mechinism of reduced virulence, thymidine kinase (TK)-deficient mutant of pseudorabies virus strain Hubei (PRV HB) was isolated by selection for resistance to 5-bromodeoxyuridine. The tk genes of PRV HB and its TK mutant were cloned and sequenced. 1587 base pairs of the tk gene and flanking regions of wild-type (wt) virus were sequenced, which included an open reading frame (ORF) of 1098 bp encoding a protein of 366 amino acids. The ORF contained two 137-bp repeated sequences, which were connected by an adenosine. 1458 bp of the tk and flanking regions of TK- mutant were sequenced. Analysis of the tk gene sequence of TK mutant indicated that one of 137 bp repeated sequence and the connecting adenosine in the tk gene of the wt virus was deleted and a repeated sequence of 8 nucleotides (GCGCGCC) was inserted. All展开更多
As a supplementary of [Xu L. Front. Electr. Electron. Eng. China, 2010, 5（3）： 281-328], this paper outlines current status of efforts made on Bayesian Ying- Yang （BYY） harmony learning, plus gene analysis appli- ...As a supplementary of [Xu L. Front. Electr. Electron. Eng. China, 2010, 5（3）： 281-328], this paper outlines current status of efforts made on Bayesian Ying- Yang （BYY） harmony learning, plus gene analysis appli- cations. At the beginning, a bird＇s-eye view is provided via Gaussian mixture in comparison with typical learn- ing algorithms and model selection criteria. Particularly, semi-supervised learning is covered simply via choosing a scalar parameter. Then, essential topics and demand- ing issues about BYY system design and BYY harmony learning are systematically outlined, with a modern per- spective on Yin-Yang viewpoint discussed, another Yang factorization addressed, and coordinations across and within Ying-Yang summarized. The BYY system acts as a unified framework to accommodate unsupervised, su- pervised, and semi-supervised learning all in one formu- lation, while the best harmony learning provides novelty and strength to automatic model selection. Also, mathe- matical formulation of harmony functional has been ad- dressed as a unified scheme for measuring the proximity to be considered in a BYY system, and used as the best choice among others. Moreover, efforts are made on a number of learning tasks, including a mode-switching factor analysis proposed as a semi-blind learning frame- work for several types of independent factor analysis, a hidden Markov model （HMM） gated temporal fac- tor analysis suggested for modeling piecewise stationary temporal dependence, and a two-level hierarchical Gaus- sian mixture extended to cover semi-supervised learning, as well as a manifold learning modified to facilitate au- tomatic model selection. Finally, studies are applied to the problems of gene analysis, such as genome-wide asso- ciation, exome sequencing analysis, and gene transcrip- tional regulation.展开更多
[目的]建立目标基因测序技术，对后纵韧带骨化（ossification of the posterior longitud inalligament，OPLL）患者的11个已知致病基因进行突变筛查，探讨OPLL与致病基因突变的关系。[方法]提取6例OPLL患者外周血全基因组DNA，利用Gen...[目的]建立目标基因测序技术，对后纵韧带骨化（ossification of the posterior longitud inalligament，OPLL）患者的11个已知致病基因进行突变筛查，探讨OPLL与致病基因突变的关系。[方法]提取6例OPLL患者外周血全基因组DNA，利用GenCap目标基因捕获技术（北京迈基诺公司），设计骨形态发生蛋白-2（bone morphogenetic pro—tein2，BMP2）、骨形态发生蛋白-4（bone morphogenetic protein4，BMP4）、骨形态发生蛋白-9（bone morphogenetic protein 9，BMP9）、Ⅺ型胶原蛋白以（collagen type XI alpha 2，COLllA2）、Ⅵ型胶原蛋白理1（collagen type VIM pha1，COL6A1）、核苷酸焦磷酸酶（ectonucleotide pyrophosphatase／phosphodiesterase 1，ENPPl）、成纤维细胞生长因子2（fibroblast growth factor 2，FGF2）、成纤维细胞生长因子受体1（fibroblast growth factor receptor 1，FGFRl）、成纤维细胞生长因子受体2（fibroblast growth factor receptor2，FGFR2）、转化生长因子一β3（transforming growth factor beta3，TGFB3）和转化生长因子一8受体2（transforming growth factor beta receptorII，TGFBR2）基因外显子区域特异性捕获探针，与基因组DNA文库进行杂交，将目标基因组区域的DNA片段进行富集后，再利用illumina hiseq2000第二代测序仪进行测序，通过数据分析，确定突变位点，对选定的突变位点用Sanger测序法进行验证。[结果]设计合成的目标基因特异性捕获探针可有效地捕捉并富集基因组DNA的目标靶片段。目标区域平均测序深度为426．85～976．15，99．30％-100％目标区域覆盖度。在1例患者中发现COL6A1基因的1个错义突变，此位点检测结果与Sanger测序结果完全一致。[结论]目标基因测序技术成功发现了OPLL患者的致病基因突变。该方法快速而有效，对深入研究OPLL的分子病因学有重要意义。展开更多
基金This work was supported by the Chinese Academy of Sciences (Grant No. KSCX2-SW-101B)the National Natural Science Foundation of China (Grant No. 39830050).
文摘Cyprinidae is the largest fish family in the world and contains about 210 genera and 2010 species. Appropriate DNA markers must be selected for the phylogenetic analyses of Cyprinidae. In present study, the 1st intron of the S7 ribosomal protein (r-protein) gene is first used to examine the relationships among cyprinid fishes. The length of the 1st intron obtained by PCR amplification ranges from 655 to 859 bp in the 16 cyprinid species investigated, and is 602 bp in Myxocyprinus asiaticus. Out of the alignment of 925 nucleotide sites obtained, the parsimony informative sites are 499 and occupy 54% of the total sites. The results indicate that the 1st intron sequences of the S7 r-protein gene in cyprinids are rich in informative sites and vary remarkably in sequence divergence from 2.3% between close species to 66.6% between distant species. The bootstrap values of the interior nodes in the NJ (neighbor-joining) and MP (most-parsimony) trees based on the present S7 r-protein gene data are higher than
文摘为了研究ifitm基因的功能,本研究从猪肾PK15细胞中克隆了猪的3个ifitm c DNA序列,分析了猪ifitm1、ifitm2和ifitm3基因的染色体定位及其与其他物种基因序列的同源关系,并对不同ifitm在不同组织的表达进行分析和检测。结果显示,猪ifitm和人、鼠ifitm具有相同的基因和蛋白结构,进化上与牛ifitm高度同源,ifitm1和ifitm3在脾、肾、心、肝等组织中大量表达,而ifitm2只在脾和肾中检测到表达,在其他组织中的表达量相对较小。猪ifitm基因的克隆、生物信息学及组织表达分析为进一步研究其在猪细胞中的功能奠定了基础。
基金supported by the Aviation Science Foundation of China
文摘The reliability of real-time embedded software directly determines the reliability of the whole real-time embedded sys- tem, and the effective software testing is an important way to ensure software quality and reliability. Based on the analysis of the characteristics of real-time embedded software, the formal method is introduced into the real-time embedded software testing field and the real-time extended finite state machine （RT-EFSM） model is studied firstly. Then, the time zone division method of real-time embedded system is presented and the definition and description methods of time-constrained transition equivalence class （timeCTEC） are presented. Furthermore, the approaches of the testing sequence and test case generation are put forward. Finally, the proposed method is applied to a typical avionics real- time embedded software testing practice and the examples of the timeCTEC, testing sequences and test cases are given. With the analysis of the testing result, the application verification shows that the proposed method can effectively describe the real-time embedded software state transition characteristics and real-time requirements and play the advantages of the formal methods in accuracy, effectiveness and the automation supporting. Combined with the testing platform, the real-time, closed loop and automated simulation testing for real-time embedded software can be realized effectively.
文摘To explore correlation between the tk gene structure of pseudorabies virus (PRV) and its virulence, to study the effect of the gene mutation on PRV biological properties, and to investigate mechinism of reduced virulence, thymidine kinase (TK)-deficient mutant of pseudorabies virus strain Hubei (PRV HB) was isolated by selection for resistance to 5-bromodeoxyuridine. The tk genes of PRV HB and its TK mutant were cloned and sequenced. 1587 base pairs of the tk gene and flanking regions of wild-type (wt) virus were sequenced, which included an open reading frame (ORF) of 1098 bp encoding a protein of 366 amino acids. The ORF contained two 137-bp repeated sequences, which were connected by an adenosine. 1458 bp of the tk and flanking regions of TK- mutant were sequenced. Analysis of the tk gene sequence of TK mutant indicated that one of 137 bp repeated sequence and the connecting adenosine in the tk gene of the wt virus was deleted and a repeated sequence of 8 nucleotides (GCGCGCC) was inserted. All
文摘As a supplementary of [Xu L. Front. Electr. Electron. Eng. China, 2010, 5（3）： 281-328], this paper outlines current status of efforts made on Bayesian Ying- Yang （BYY） harmony learning, plus gene analysis appli- cations. At the beginning, a bird＇s-eye view is provided via Gaussian mixture in comparison with typical learn- ing algorithms and model selection criteria. Particularly, semi-supervised learning is covered simply via choosing a scalar parameter. Then, essential topics and demand- ing issues about BYY system design and BYY harmony learning are systematically outlined, with a modern per- spective on Yin-Yang viewpoint discussed, another Yang factorization addressed, and coordinations across and within Ying-Yang summarized. The BYY system acts as a unified framework to accommodate unsupervised, su- pervised, and semi-supervised learning all in one formu- lation, while the best harmony learning provides novelty and strength to automatic model selection. Also, mathe- matical formulation of harmony functional has been ad- dressed as a unified scheme for measuring the proximity to be considered in a BYY system, and used as the best choice among others. Moreover, efforts are made on a number of learning tasks, including a mode-switching factor analysis proposed as a semi-blind learning frame- work for several types of independent factor analysis, a hidden Markov model （HMM） gated temporal fac- tor analysis suggested for modeling piecewise stationary temporal dependence, and a two-level hierarchical Gaus- sian mixture extended to cover semi-supervised learning, as well as a manifold learning modified to facilitate au- tomatic model selection. Finally, studies are applied to the problems of gene analysis, such as genome-wide asso- ciation, exome sequencing analysis, and gene transcrip- tional regulation.
文摘[目的]建立目标基因测序技术，对后纵韧带骨化（ossification of the posterior longitud inalligament，OPLL）患者的11个已知致病基因进行突变筛查，探讨OPLL与致病基因突变的关系。[方法]提取6例OPLL患者外周血全基因组DNA，利用GenCap目标基因捕获技术（北京迈基诺公司），设计骨形态发生蛋白-2（bone morphogenetic pro—tein2，BMP2）、骨形态发生蛋白-4（bone morphogenetic protein4，BMP4）、骨形态发生蛋白-9（bone morphogenetic protein 9，BMP9）、Ⅺ型胶原蛋白以（collagen type XI alpha 2，COLllA2）、Ⅵ型胶原蛋白理1（collagen type VIM pha1，COL6A1）、核苷酸焦磷酸酶（ectonucleotide pyrophosphatase／phosphodiesterase 1，ENPPl）、成纤维细胞生长因子2（fibroblast growth factor 2，FGF2）、成纤维细胞生长因子受体1（fibroblast growth factor receptor 1，FGFRl）、成纤维细胞生长因子受体2（fibroblast growth factor receptor2，FGFR2）、转化生长因子一β3（transforming growth factor beta3，TGFB3）和转化生长因子一8受体2（transforming growth factor beta receptorII，TGFBR2）基因外显子区域特异性捕获探针，与基因组DNA文库进行杂交，将目标基因组区域的DNA片段进行富集后，再利用illumina hiseq2000第二代测序仪进行测序，通过数据分析，确定突变位点，对选定的突变位点用Sanger测序法进行验证。[结果]设计合成的目标基因特异性捕获探针可有效地捕捉并富集基因组DNA的目标靶片段。目标区域平均测序深度为426．85～976．15，99．30％-100％目标区域覆盖度。在1例患者中发现COL6A1基因的1个错义突变，此位点检测结果与Sanger测序结果完全一致。[结论]目标基因测序技术成功发现了OPLL患者的致病基因突变。该方法快速而有效，对深入研究OPLL的分子病因学有重要意义。
