Genetic Programming (GP) is an important approach to deal with complex problem analysis and modeling, and has been applied in a wide range of areas. The development of GP involves various aspects, including design of ...Genetic Programming (GP) is an important approach to deal with complex problem analysis and modeling, and has been applied in a wide range of areas. The development of GP involves various aspects, including design of genetic operators, evolutionary controls and implementations of heuristic strategy, evaluations and other mechanisms. When designing genetic operators, it is necessary to consider the possible limitations of encoding methods of individuals. And when selecting evolutionary control strategies, it is also necessary to balance search efficiency and diversity based on representation characteristics as well as the problem itself. More importantly, all of these matters, among others, have to be implemented through tedious coding work. Therefore, GP development is both complex and time-consuming. To overcome some of these difficulties that hinder the enhancement of GP development efficiency, we explore the feasibility of mutual assistance among GP variants, and then propose a rapid GP prototyping development method based on πGrammatical Evolution (πGE). It is demonstrated through regression analysis experiments that not only is this method beneficial for the GP developers to get rid of some tedious implementations, but also enables them to concentrate on the essence of the referred problem, such as individual representation, decoding means and evaluation. Additionally, it provides new insights into the roles of individual delineations in phenotypes and semantic research of individuals.展开更多
The inheritance of stripe disease resistance in a rice restorer line C224 was analyzed using the mixed effect model of major gene plus polygene for quantitative traits.In addition,the resistance was investigated in se...The inheritance of stripe disease resistance in a rice restorer line C224 was analyzed using the mixed effect model of major gene plus polygene for quantitative traits.In addition,the resistance was investigated in seven crosses of C224 with maintainer lines.The results showed that the stripe resistance of C224 was controlled by two major genes with additive-dominance-epistasis effects plus polygenes with additive-dominance effects （E-1 model）.These two genes had additive effects of-12.47% and-24.75%,respectively,showing negative dominance effects.There were significant epistasis and interaction effects between the two major genes.The heritability of the two major genes was 92.12%,while that of polygenes was 2.74%,indicating that the stripe resistance had dominant major gene effect.Of the seven crosses,five displayed high or medium resistance to the stripe disease.展开更多
Introduction In the past 10 years, more than 100 different genetically engineered mice have been developed with an abnormality in spermatogenesis. More than half of these male infertility animal models have been repor...Introduction In the past 10 years, more than 100 different genetically engineered mice have been developed with an abnormality in spermatogenesis. More than half of these male infertility animal models have been reported in the past three years alone. Spermatogenic defects in these models vary considerably, ranging from the inappropriate migration of primordial germ cells to the inability of mature spermatozoa to bind the zona pellucida. Many of展开更多
The research hotspot in post-genomic era is from sequence to function. Building genetic regulatory network (GRN) can help to understand the regulatory mechanism between genes and the function of organisms. Probabilist...The research hotspot in post-genomic era is from sequence to function. Building genetic regulatory network (GRN) can help to understand the regulatory mechanism between genes and the function of organisms. Probabilistic GRN has been paid more attention recently. This paper discusses the Hidden Markov Model (HMM) approach served as a tool to build GRN. Different genes with similar expression levels are considered as different states during training HMM. The probable regulatory genes of target genes can be found out through the resulting states transition matrix and the determinate regulatory functions can be predicted using nonlinear regression algorithm. The experiments on artificial and real-life datasets show the effectiveness of HMM in building GRN.展开更多
Malus sieversii, a wild progenitor of domesticated apple, is distributed in western Xinjiang of China, eastern part of Kazakhstan and Kyrgyzstan in Central Asia. To well understand the genetic structure and the his- t...Malus sieversii, a wild progenitor of domesticated apple, is distributed in western Xinjiang of China, eastern part of Kazakhstan and Kyrgyzstan in Central Asia. To well understand the genetic structure and the his- torical demography of this important germplasm resource, we sampled 15 populations with 110 individuals of Malus sieversii from the Yili Valley and the western mountains of the Junggar Basin, Xinjiang, and sequenced two nrDNA fragments for these 110 individuals. Meanwhile, we modeled and compared species distributions under the current and the Last Glacial Maximum climatic conditions. The results showed that populations of M. sieversfi from Xinjiang had low levels of genetic diversity and genetic differentiation. During the LGM period, populations of M. sieversfi had lost their northern distributions in the western mountains of the Junggar Basin. M. sieversfi has ex- perienced a demographic expansion from the south of the Yili Valley to the north of the western mountains of the Junggar Basin during the warm interglacial epochs. Due to the high sensibility of M. sieversii to disturbance, we proposed more attention should be paid to the M. sieversfi populations in the western mountains of the Junggar Basin.展开更多
Objective:To summarize the precise association between pulmonary tuberculosis(PTB) and P2x7 A1513 C gene polymorphism.Methods:PubMed and Google Scholar web-databases were searched for the studies reporting the associa...Objective:To summarize the precise association between pulmonary tuberculosis(PTB) and P2x7 A1513 C gene polymorphism.Methods:PubMed and Google Scholar web-databases were searched for the studies reporting the association of P2x7 A1513 C polymorphism and PTB risk.A meta-analysis was performed for the selected case-control studies and pooled odds ratios(ORs) and 95%confidence intervals(95%CIs) were calculated for all the genetic models.Results:Eleven studies comprising 2 678 controls and 2 113 PTB cases were included in this meta-analysis.We observed overall no significant risk in all the five genetic models.When stratified population by the ethnicity,Caucasian population failed to show any risk of PTB in all the genetics models.In Asian ethnicity,variant allele(C vs.A:P=0.001;QR=1.375,95%CI=1.159-1.632) and heterozygous genotype(AC vs.AA:P=0.001;OR=1.570,95%CI=1.269-1.944) demonstrated significant increased risk of PTB.Likewise,recessive genetic model(CC+AC vs.AA:P=0.001;OR=1.540,95%CI= 1.255-1.890) also demonstrated increased risk of PTB in Asians.Conclusions:Our meta-analysis did not suggest the association of P2x7 A1513 C polymorphism with PTB risk in overall or separately in Caucasian population.However,it plays a significant risk factor for predisposing PTB in Asians.Future larger sample and expression studies are needed to validate this association.展开更多
Background: Liver weight is a complex trait, controlled by polygenic factors and differs within populations. Dissecting the genetic architecture underlying these variations will facilitate the search for key role cand...Background: Liver weight is a complex trait, controlled by polygenic factors and differs within populations. Dissecting the genetic architecture underlying these variations will facilitate the search for key role candidate genes involved directly in the hepatomegaly process and indirectly involved in related diseases etiology.Methods: Liver weight of 506 mice generated from 39 different Collaborative Cross(CC) lines with both sexes at age 20 weeks old was determined using an electronic balance. Genomic DNA of the CC lines was genotyped with high-density single nucleotide polymorphic markers.Results: Statistical analysis revealed a significant(P < 0.05) variation of liver weight between the CC lines, with broad sense heritability(H^2) of 0.32 and genetic coefficient of variation(CV_G) of 0.28. Subsequently, quantitative trait locus(QTL) mapping was performed, and results showed a significant QTL only for females on chromosome 8 at genomic interval 88.61-93.38 Mb(4.77 Mb). Three suggestive QTL were mapped at chromosomes 4, 12 and 13. The four QTL were designated as LWL1-LWL4 referring to liver weight loci 1-4 on chromosomes 8, 4, 12 and 13,respectively.Conclusion: To our knowledge, this report presents, for the first time, the utilization of the CC for mapping QTL associated with baseline liver weight in mice. Our findings demonstrate that liver weight is a complex trait controlled by multiple genetic factors that differ significantly between sexes.展开更多
The paper offers an overview of quantum and macro gravity, two of the three pillars of the Grand Unified Theory (GUT), the other thermodynamics, developed in a series of papers since the solution of the gravitational ...The paper offers an overview of quantum and macro gravity, two of the three pillars of the Grand Unified Theory (GUT), the other thermodynamics, developed in a series of papers since the solution of the gravitational n-body problem in 1997 (J. Nonlinear Analysis, A-Series: Theory, Methods and Applications, Vol. 30, No. 8, 1997, pp. 5021 - 5032) and consolidated in the paper, The Grand Unified Theory (J. Nonlinear Analysis, A-Series: Theory: Method and Applications, Vol. 69, No. 3, 2008, pp. 823 - 831). GUT is further advanced by the paper, The Mathematics of GUT (J. Nonlinear Analysis, A-Series: Theory: Method and Applications, Vol. 71, 2009, pp. e420 - e431) and the discovery of more natural laws in the course of analyzing and explaining the disastrous final flight of the Columbia Space Shuttle in 2004 (J. Nonlinear Studies, Vol. 14, No. 3, 2007, pp. 241 - 260). Qualitative modeling was the key to the development of GUT and its theoretical and practical applications. The relevant natural laws of GUT that provide the foundations of the Unified Theory of Evolution are stated. GUT provides the basis for the development of the electromagnetic engine and the Unified Theory of Evolution, its theoretical application, for the development of appropriate technology for electromagnetic treatment of genetic diseases such as cancer, systemic lupos erythematosus, diabetes, muscular dystrophy and mental disorder, the central focus of this paper.展开更多
碱基编辑技术起源于CRISPR/Cas系统,是目前最新的基因定点修饰技术。根据碱基编辑器的功能特点,可将碱基编辑器分为胞嘧啶碱基编辑器(cytosine base editor,CBE)、腺嘌呤碱基编辑器(adenine base editor,ABE)、糖基化酶碱基编辑器(glyco...碱基编辑技术起源于CRISPR/Cas系统,是目前最新的基因定点修饰技术。根据碱基编辑器的功能特点,可将碱基编辑器分为胞嘧啶碱基编辑器(cytosine base editor,CBE)、腺嘌呤碱基编辑器(adenine base editor,ABE)、糖基化酶碱基编辑器(glycosylase base editor,GBE)、腺嘌呤碱基颠换编辑器(adenine transversion base editor,AYBE)、双碱基编辑器(dual base editor,DBE)和引导编辑器(prime editor,PE)。自碱基编辑系统诞生以来,已经广泛运用于动植物的研究中,并且已经证明了它在动植物遗传改良和疾病治疗中具有巨大应用价值。猪作为一种重要的农业经济动物和优良的动物疾病模型,对其进行遗传改良则变得十分重要。碱基编辑技术因其操作便利、高效、副产物少以及性价比高等特点,被迅速应用于动植物的遗传改良,并为人类的基因治疗提供技术支持。本文着重介绍了碱基编辑技术的开发、优化、应用特点、存在的问题以及对未来的展望,并总结了其在猪中的应用。以期为相关科研工作者了解碱基编辑技术提供参考。展开更多
Anuran metamorphosis involves systematic transformations of individual organs in a thyroid hormone (TH)-dependent manner. Morphological and cellular studies have shown that the removal of larval or- gans/tissues such ...Anuran metamorphosis involves systematic transformations of individual organs in a thyroid hormone (TH)-dependent manner. Morphological and cellular studies have shown that the removal of larval or- gans/tissues such the tail and the tadpole intestinal epithelium is through programmed cell death or apop- tosis. Recent molecular investigations suggest that TH regulates metamorphosis by regulating target gene expression through thyroid hormone receptors (TRs), which are DNA-binding transcription factors. Cloning and characterization of TH response genes show that diverse groups of early response genes are induced by TH. The products of these TH response genes are believed to directly or indirectly affect the expression and/or functions of cell death genes, which are conserved at both sequence and function levels in different animal species. A major challenge for future research lies at determining the signaling pathways leading to the activation of apoptotic processes and whether different death genes are involved in the regulation of apoptosis in different tissues/organs to effect tissue-specific transformations.展开更多
文摘Genetic Programming (GP) is an important approach to deal with complex problem analysis and modeling, and has been applied in a wide range of areas. The development of GP involves various aspects, including design of genetic operators, evolutionary controls and implementations of heuristic strategy, evaluations and other mechanisms. When designing genetic operators, it is necessary to consider the possible limitations of encoding methods of individuals. And when selecting evolutionary control strategies, it is also necessary to balance search efficiency and diversity based on representation characteristics as well as the problem itself. More importantly, all of these matters, among others, have to be implemented through tedious coding work. Therefore, GP development is both complex and time-consuming. To overcome some of these difficulties that hinder the enhancement of GP development efficiency, we explore the feasibility of mutual assistance among GP variants, and then propose a rapid GP prototyping development method based on πGrammatical Evolution (πGE). It is demonstrated through regression analysis experiments that not only is this method beneficial for the GP developers to get rid of some tedious implementations, but also enables them to concentrate on the essence of the referred problem, such as individual representation, decoding means and evaluation. Additionally, it provides new insights into the roles of individual delineations in phenotypes and semantic research of individuals.
基金supported by the Guiding Plans for Natural Sciences Foundation of Liaoning Province,China(Grant No.20092207)the Special Foundation for Young Scientists of Liaoning Rice Research Institute,Shenyang,China(Grant No.DZS-2008-1)
文摘The inheritance of stripe disease resistance in a rice restorer line C224 was analyzed using the mixed effect model of major gene plus polygene for quantitative traits.In addition,the resistance was investigated in seven crosses of C224 with maintainer lines.The results showed that the stripe resistance of C224 was controlled by two major genes with additive-dominance-epistasis effects plus polygenes with additive-dominance effects （E-1 model）.These two genes had additive effects of-12.47% and-24.75%,respectively,showing negative dominance effects.There were significant epistasis and interaction effects between the two major genes.The heritability of the two major genes was 92.12%,while that of polygenes was 2.74%,indicating that the stripe resistance had dominant major gene effect.Of the seven crosses,five displayed high or medium resistance to the stripe disease.
文摘Introduction In the past 10 years, more than 100 different genetically engineered mice have been developed with an abnormality in spermatogenesis. More than half of these male infertility animal models have been reported in the past three years alone. Spermatogenic defects in these models vary considerably, ranging from the inappropriate migration of primordial germ cells to the inability of mature spermatozoa to bind the zona pellucida. Many of
文摘The research hotspot in post-genomic era is from sequence to function. Building genetic regulatory network (GRN) can help to understand the regulatory mechanism between genes and the function of organisms. Probabilistic GRN has been paid more attention recently. This paper discusses the Hidden Markov Model (HMM) approach served as a tool to build GRN. Different genes with similar expression levels are considered as different states during training HMM. The probable regulatory genes of target genes can be found out through the resulting states transition matrix and the determinate regulatory functions can be predicted using nonlinear regression algorithm. The experiments on artificial and real-life datasets show the effectiveness of HMM in building GRN.
基金supported by the National Basic Research Special Program of China (2012FY111500)the Innovation Research Group Program of Chinese Academy of Sciences and State Administration of Foreign Experts Affairs of China (KZCX2-YW-T09)+1 种基金the State International Science and Technology Cooperation Program of China (2010DFA92720)the Program of the Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences
文摘Malus sieversii, a wild progenitor of domesticated apple, is distributed in western Xinjiang of China, eastern part of Kazakhstan and Kyrgyzstan in Central Asia. To well understand the genetic structure and the his- torical demography of this important germplasm resource, we sampled 15 populations with 110 individuals of Malus sieversii from the Yili Valley and the western mountains of the Junggar Basin, Xinjiang, and sequenced two nrDNA fragments for these 110 individuals. Meanwhile, we modeled and compared species distributions under the current and the Last Glacial Maximum climatic conditions. The results showed that populations of M. sieversfi from Xinjiang had low levels of genetic diversity and genetic differentiation. During the LGM period, populations of M. sieversfi had lost their northern distributions in the western mountains of the Junggar Basin. M. sieversfi has ex- perienced a demographic expansion from the south of the Yili Valley to the north of the western mountains of the Junggar Basin during the warm interglacial epochs. Due to the high sensibility of M. sieversii to disturbance, we proposed more attention should be paid to the M. sieversfi populations in the western mountains of the Junggar Basin.
文摘Objective:To summarize the precise association between pulmonary tuberculosis(PTB) and P2x7 A1513 C gene polymorphism.Methods:PubMed and Google Scholar web-databases were searched for the studies reporting the association of P2x7 A1513 C polymorphism and PTB risk.A meta-analysis was performed for the selected case-control studies and pooled odds ratios(ORs) and 95%confidence intervals(95%CIs) were calculated for all the genetic models.Results:Eleven studies comprising 2 678 controls and 2 113 PTB cases were included in this meta-analysis.We observed overall no significant risk in all the five genetic models.When stratified population by the ethnicity,Caucasian population failed to show any risk of PTB in all the genetics models.In Asian ethnicity,variant allele(C vs.A:P=0.001;QR=1.375,95%CI=1.159-1.632) and heterozygous genotype(AC vs.AA:P=0.001;OR=1.570,95%CI=1.269-1.944) demonstrated significant increased risk of PTB.Likewise,recessive genetic model(CC+AC vs.AA:P=0.001;OR=1.540,95%CI= 1.255-1.890) also demonstrated increased risk of PTB in Asians.Conclusions:Our meta-analysis did not suggest the association of P2x7 A1513 C polymorphism with PTB risk in overall or separately in Caucasian population.However,it plays a significant risk factor for predisposing PTB in Asians.Future larger sample and expression studies are needed to validate this association.
基金Israeli Centers of Research ExcellenceWellcome Trust,Grant/Award Number:085906/Z/08/Z,075491/Z/04,090532/Z/09/Z+1 种基金Edmond J.Safra Center for Bioinformatics at Tel-Aviv UniversityTel-Aviv University
文摘Background: Liver weight is a complex trait, controlled by polygenic factors and differs within populations. Dissecting the genetic architecture underlying these variations will facilitate the search for key role candidate genes involved directly in the hepatomegaly process and indirectly involved in related diseases etiology.Methods: Liver weight of 506 mice generated from 39 different Collaborative Cross(CC) lines with both sexes at age 20 weeks old was determined using an electronic balance. Genomic DNA of the CC lines was genotyped with high-density single nucleotide polymorphic markers.Results: Statistical analysis revealed a significant(P < 0.05) variation of liver weight between the CC lines, with broad sense heritability(H^2) of 0.32 and genetic coefficient of variation(CV_G) of 0.28. Subsequently, quantitative trait locus(QTL) mapping was performed, and results showed a significant QTL only for females on chromosome 8 at genomic interval 88.61-93.38 Mb(4.77 Mb). Three suggestive QTL were mapped at chromosomes 4, 12 and 13. The four QTL were designated as LWL1-LWL4 referring to liver weight loci 1-4 on chromosomes 8, 4, 12 and 13,respectively.Conclusion: To our knowledge, this report presents, for the first time, the utilization of the CC for mapping QTL associated with baseline liver weight in mice. Our findings demonstrate that liver weight is a complex trait controlled by multiple genetic factors that differ significantly between sexes.
文摘The paper offers an overview of quantum and macro gravity, two of the three pillars of the Grand Unified Theory (GUT), the other thermodynamics, developed in a series of papers since the solution of the gravitational n-body problem in 1997 (J. Nonlinear Analysis, A-Series: Theory, Methods and Applications, Vol. 30, No. 8, 1997, pp. 5021 - 5032) and consolidated in the paper, The Grand Unified Theory (J. Nonlinear Analysis, A-Series: Theory: Method and Applications, Vol. 69, No. 3, 2008, pp. 823 - 831). GUT is further advanced by the paper, The Mathematics of GUT (J. Nonlinear Analysis, A-Series: Theory: Method and Applications, Vol. 71, 2009, pp. e420 - e431) and the discovery of more natural laws in the course of analyzing and explaining the disastrous final flight of the Columbia Space Shuttle in 2004 (J. Nonlinear Studies, Vol. 14, No. 3, 2007, pp. 241 - 260). Qualitative modeling was the key to the development of GUT and its theoretical and practical applications. The relevant natural laws of GUT that provide the foundations of the Unified Theory of Evolution are stated. GUT provides the basis for the development of the electromagnetic engine and the Unified Theory of Evolution, its theoretical application, for the development of appropriate technology for electromagnetic treatment of genetic diseases such as cancer, systemic lupos erythematosus, diabetes, muscular dystrophy and mental disorder, the central focus of this paper.
文摘碱基编辑技术起源于CRISPR/Cas系统,是目前最新的基因定点修饰技术。根据碱基编辑器的功能特点,可将碱基编辑器分为胞嘧啶碱基编辑器(cytosine base editor,CBE)、腺嘌呤碱基编辑器(adenine base editor,ABE)、糖基化酶碱基编辑器(glycosylase base editor,GBE)、腺嘌呤碱基颠换编辑器(adenine transversion base editor,AYBE)、双碱基编辑器(dual base editor,DBE)和引导编辑器(prime editor,PE)。自碱基编辑系统诞生以来,已经广泛运用于动植物的研究中,并且已经证明了它在动植物遗传改良和疾病治疗中具有巨大应用价值。猪作为一种重要的农业经济动物和优良的动物疾病模型,对其进行遗传改良则变得十分重要。碱基编辑技术因其操作便利、高效、副产物少以及性价比高等特点,被迅速应用于动植物的遗传改良,并为人类的基因治疗提供技术支持。本文着重介绍了碱基编辑技术的开发、优化、应用特点、存在的问题以及对未来的展望,并总结了其在猪中的应用。以期为相关科研工作者了解碱基编辑技术提供参考。
文摘Anuran metamorphosis involves systematic transformations of individual organs in a thyroid hormone (TH)-dependent manner. Morphological and cellular studies have shown that the removal of larval or- gans/tissues such the tail and the tadpole intestinal epithelium is through programmed cell death or apop- tosis. Recent molecular investigations suggest that TH regulates metamorphosis by regulating target gene expression through thyroid hormone receptors (TRs), which are DNA-binding transcription factors. Cloning and characterization of TH response genes show that diverse groups of early response genes are induced by TH. The products of these TH response genes are believed to directly or indirectly affect the expression and/or functions of cell death genes, which are conserved at both sequence and function levels in different animal species. A major challenge for future research lies at determining the signaling pathways leading to the activation of apoptotic processes and whether different death genes are involved in the regulation of apoptosis in different tissues/organs to effect tissue-specific transformations.
