Genomic variations,such as single-nucleotide polymorphisms(SNPs),underlie differences in our susceptibility to diseases and manifest the way our body responds to treatments.Currently,fluorescence imaging is the mainst...Genomic variations,such as single-nucleotide polymorphisms(SNPs),underlie differences in our susceptibility to diseases and manifest the way our body responds to treatments.Currently,fluorescence imaging is the mainstream approach for genetic analysis.With the rapid advances in fluorescence-based next-generation sequencing(NGS)technologies,a haplotype map of the human genome is under construction.However,the optical diffraction limit(200–300 nm)of fluorophores restricts the resolution to be of about 1000 bp.展开更多
[Objective] The aim of this study is to understand the genetic characteristics of a grain shape mutant and its possible role in genetic improvement of grain yield in rice. [Method] On the basis of the collection of T-...[Objective] The aim of this study is to understand the genetic characteristics of a grain shape mutant and its possible role in genetic improvement of grain yield in rice. [Method] On the basis of the collection of T-DNA tag lines, the progeny of homozygous plants carrying T-DNA insertion were screened for mutants with mutated phenotypes. The genetic analysis of the mutant and test for the linkage between the mutated phenotype and the T-DNA insertion were carried out to determine its genetic characteristics. [Result] In the present study, a grain shape mutant induced by T-DNA insertion in rice was identified, which showed small grain. Genetic analysis of the mutant showed that the two types of phenotype, normal and small grain in the segregating populations derived from the T-DNA heterozygotes, fit the ratio of 3∶1. Test for Basta resistance showed that all the mutants were resistant while the normal plants segregated for resistant and susceptible by the ratio of 2∶1. The results indicated that the mutant phenotype cosegregated with Bar gene. The small grain mutant caused by T-DNA insertion was confirmed by PCR amplification aiming at T-DNA. [Conclusion] The grain shape mutant is useful for isolation of the tagged gene and genetic improvement in rice.展开更多
DNA-mediated synthesis of nanopartides is a powerful method to access exclusive shapes and surface properties. Previous studies employed seeds containing low-energy facets, such as a simple cubic palladium seed, in th...DNA-mediated synthesis of nanopartides is a powerful method to access exclusive shapes and surface properties. Previous studies employed seeds containing low-energy facets, such as a simple cubic palladium seed, in the synthesis of Pd-Au bimetallic nanoparticles; however, few studies have investigated whether DNA molecules are influential when a seed containing high-energy facets is used. Seeds enclosed by high-energy facets act as facile nucleation sites in nanopartide growth and could suppress the effect of DNA. We report the DNA-encoded control of the morphological evolution of bimetallic Pd@Au core-shell nanoparticles from a concave palladium nanocube seed containing high-indexed facets. Based on detailed spectroscopic and microscopic studies of time-dependent growth of bimetallic nanoparticles, we found that the DNA molecules containing 10 repeating units of thymine, guanine, cytosine, or adenine （referred to as T10, G10, C10, and A10, respectively） show a unique interaction with the surface of the seed and the precursor. The most important factor is the binding affinity of the nucleobase to the Pd surface; A10 shows the highest binding affinity and can stabilize the high energy surfaces of the seed. Initially, the growth of bases with lower binding affiru＇ties （T10, G10, and C10） is completely dictated by the seed＇s surface energy, but later growth can be influenced by different DNA sequences, providing four Pd@Au bimetallic nanopartides with unique morphologies. The effect of these DNA molecules with medium or low binding affinities can only be observed when more Au is deposited. We propose a scheme for DNA-controlled growth. These results provide insights into the factors governing the DNA-mediated growth of core-shell structures using seeds with high-energy sites, and the insights can be readily applied to other bimetallic systems.展开更多
逆转录病毒的活动和多种疾病的发生密切相关,其可通过整合自身基因组到宿主基因组中进行大量有害扩增.与此同时,宿主细胞可根据逆转录病毒的整合位置来启动相关通路抑制其活动.因此整合位点的选择是决定逆转录病毒和宿主命运的关键步骤...逆转录病毒的活动和多种疾病的发生密切相关,其可通过整合自身基因组到宿主基因组中进行大量有害扩增.与此同时,宿主细胞可根据逆转录病毒的整合位置来启动相关通路抑制其活动.因此整合位点的选择是决定逆转录病毒和宿主命运的关键步骤.尽管国际上已有报道称逆转录病毒在宿主基因组上整合并不随机,并发现了跨逆转录病毒种属的不同DNA基序偏好性,但是这些不足以解释一些基序偏好较弱的逆转录病毒如何获得整合特异性.DNA结构特征,如DNA形状被提出可以影响DNA结合蛋白与DNA结合的亲和力,但DNA形状对不同逆转录病毒整合的影响机制尚不清楚.本研究通过构建QRIS(quantify the retrovirus integration specificity)机器学习框架,定量评估了DNA形状对逆转录病毒整合位点的影响.通过系统地研究跨越四个种属的六种逆转录病毒,本研究发现,DNA形状可以独立地或与DNA基序协同调控逆转录病毒的整合.基于此,可将六种逆转录病毒分为三类:“强兼性偏好型”“弱兼性偏好型”和“强形状偏好型”逆转录病毒.此外本研究发现,即使没有特定偏好的DNA基序,“强形状偏好型”逆转录病毒也可以通过DNA形状获得整合特异性.本文基于机器学习对于大规模逆转录病毒插入位点特性的研究,揭示了DNA结构特征在逆转录病毒致病位点选择中的重要作用.该发现在临床方面为治疗逆转录病毒的策略提供了新靶点和新思路,在应用方面有助于更精确地设计慢病毒载体用于基因编辑和基因治疗.此外,本文建立的机器学习框架也为其他种类病毒的整合特异性研究提供了新方法和新视角.展开更多
文摘Genomic variations,such as single-nucleotide polymorphisms(SNPs),underlie differences in our susceptibility to diseases and manifest the way our body responds to treatments.Currently,fluorescence imaging is the mainstream approach for genetic analysis.With the rapid advances in fluorescence-based next-generation sequencing(NGS)technologies,a haplotype map of the human genome is under construction.However,the optical diffraction limit(200–300 nm)of fluorophores restricts the resolution to be of about 1000 bp.
文摘[Objective] The aim of this study is to understand the genetic characteristics of a grain shape mutant and its possible role in genetic improvement of grain yield in rice. [Method] On the basis of the collection of T-DNA tag lines, the progeny of homozygous plants carrying T-DNA insertion were screened for mutants with mutated phenotypes. The genetic analysis of the mutant and test for the linkage between the mutated phenotype and the T-DNA insertion were carried out to determine its genetic characteristics. [Result] In the present study, a grain shape mutant induced by T-DNA insertion in rice was identified, which showed small grain. Genetic analysis of the mutant showed that the two types of phenotype, normal and small grain in the segregating populations derived from the T-DNA heterozygotes, fit the ratio of 3∶1. Test for Basta resistance showed that all the mutants were resistant while the normal plants segregated for resistant and susceptible by the ratio of 2∶1. The results indicated that the mutant phenotype cosegregated with Bar gene. The small grain mutant caused by T-DNA insertion was confirmed by PCR amplification aiming at T-DNA. [Conclusion] The grain shape mutant is useful for isolation of the tagged gene and genetic improvement in rice.
文摘DNA-mediated synthesis of nanopartides is a powerful method to access exclusive shapes and surface properties. Previous studies employed seeds containing low-energy facets, such as a simple cubic palladium seed, in the synthesis of Pd-Au bimetallic nanoparticles; however, few studies have investigated whether DNA molecules are influential when a seed containing high-energy facets is used. Seeds enclosed by high-energy facets act as facile nucleation sites in nanopartide growth and could suppress the effect of DNA. We report the DNA-encoded control of the morphological evolution of bimetallic Pd@Au core-shell nanoparticles from a concave palladium nanocube seed containing high-indexed facets. Based on detailed spectroscopic and microscopic studies of time-dependent growth of bimetallic nanoparticles, we found that the DNA molecules containing 10 repeating units of thymine, guanine, cytosine, or adenine （referred to as T10, G10, C10, and A10, respectively） show a unique interaction with the surface of the seed and the precursor. The most important factor is the binding affinity of the nucleobase to the Pd surface; A10 shows the highest binding affinity and can stabilize the high energy surfaces of the seed. Initially, the growth of bases with lower binding affiru＇ties （T10, G10, and C10） is completely dictated by the seed＇s surface energy, but later growth can be influenced by different DNA sequences, providing four Pd@Au bimetallic nanopartides with unique morphologies. The effect of these DNA molecules with medium or low binding affinities can only be observed when more Au is deposited. We propose a scheme for DNA-controlled growth. These results provide insights into the factors governing the DNA-mediated growth of core-shell structures using seeds with high-energy sites, and the insights can be readily applied to other bimetallic systems.
文摘逆转录病毒的活动和多种疾病的发生密切相关,其可通过整合自身基因组到宿主基因组中进行大量有害扩增.与此同时,宿主细胞可根据逆转录病毒的整合位置来启动相关通路抑制其活动.因此整合位点的选择是决定逆转录病毒和宿主命运的关键步骤.尽管国际上已有报道称逆转录病毒在宿主基因组上整合并不随机,并发现了跨逆转录病毒种属的不同DNA基序偏好性,但是这些不足以解释一些基序偏好较弱的逆转录病毒如何获得整合特异性.DNA结构特征,如DNA形状被提出可以影响DNA结合蛋白与DNA结合的亲和力,但DNA形状对不同逆转录病毒整合的影响机制尚不清楚.本研究通过构建QRIS(quantify the retrovirus integration specificity)机器学习框架,定量评估了DNA形状对逆转录病毒整合位点的影响.通过系统地研究跨越四个种属的六种逆转录病毒,本研究发现,DNA形状可以独立地或与DNA基序协同调控逆转录病毒的整合.基于此,可将六种逆转录病毒分为三类:“强兼性偏好型”“弱兼性偏好型”和“强形状偏好型”逆转录病毒.此外本研究发现,即使没有特定偏好的DNA基序,“强形状偏好型”逆转录病毒也可以通过DNA形状获得整合特异性.本文基于机器学习对于大规模逆转录病毒插入位点特性的研究,揭示了DNA结构特征在逆转录病毒致病位点选择中的重要作用.该发现在临床方面为治疗逆转录病毒的策略提供了新靶点和新思路,在应用方面有助于更精确地设计慢病毒载体用于基因编辑和基因治疗.此外,本文建立的机器学习框架也为其他种类病毒的整合特异性研究提供了新方法和新视角.
