DNA shuffling技术是一项全新的体外人工进化模式,它通过基因在分子水平上的重组,再定向筛选具有预期性状的突变体,获得同时具有多个亲本基因的特征的突变基因。该文介绍DNA shuffling技术的基本原理,并列举了由该技术发展而来的新技术...DNA shuffling技术是一项全新的体外人工进化模式,它通过基因在分子水平上的重组,再定向筛选具有预期性状的突变体,获得同时具有多个亲本基因的特征的突变基因。该文介绍DNA shuffling技术的基本原理,并列举了由该技术发展而来的新技术及其在基因工程疫苗领域的应用,展望了DNAshuffling技术的发展方向。展开更多
A new image encryption approach is proposed.First,a sort transformation based on nonlinear chaoticalgorithm is used to shuffle the positions of image pixels.Then the states of hyper-chaos are used to change the greyva...A new image encryption approach is proposed.First,a sort transformation based on nonlinear chaoticalgorithm is used to shuffle the positions of image pixels.Then the states of hyper-chaos are used to change the greyvalues of the shuffled image according to the changed chaotic values of the same position between the above nonlinearchaotic sequence and the sorted chaotic sequence.The experimental results demonstrate that the image encryptionscheme based on a shuffling map shows advantages of large key space and high-level security.Compared with someencryption algorithms,the suggested encryption scheme is more secure.展开更多
A Pseudomonas sp. strain IOCa11 exhibiting broad substrate profile for polycyclic aromatic hydrocarbons (PAHs) degradation was isolated by enrichment techniques from oil-contaminated soil. We applied genome shuffling ...A Pseudomonas sp. strain IOCa11 exhibiting broad substrate profile for polycyclic aromatic hydrocarbons (PAHs) degradation was isolated by enrichment techniques from oil-contaminated soil. We applied genome shuffling of Pseudomonas sp. strain IOCa11 to achieve improved degradation of PAHs. The initial mutant population was generated by nitrosoguanidine treatment and population exhibiting improved phenotype was subjected to multiple round of protoplast fusion in order to allow recombination between genomes. Mutant, designated as SF-IOC11-16A, obtained after recursive protoplast fusion showed substantial improvement in ability to degrade PAHs in liquid media. It could degrade 98% DBT in 72 hours in comparison to 74% by the wild parent strain. Similar improvement in degradation of the naphthalene (NAP), phenanthrene (PHE), and benzo (α) pyrene (BAP) was also observed in shuffled strain. The shuffled strain was also able to grow at higher concentration of PAHs and degrade them efficiently. The results indicate that genome shuffling can successfully be used to improve the PAHs degradation capability of bacteria.展开更多
An ancient hexaploidization event in the most but not all Asteraceae plants,may have been responsible for shaping the genomes of many horticultural,ornamental,and medicinal plants that promoting the prosperity of the ...An ancient hexaploidization event in the most but not all Asteraceae plants,may have been responsible for shaping the genomes of many horticultural,ornamental,and medicinal plants that promoting the prosperity of the largest angiosperm family on the earth.However,the duplication process of this hexaploidy,as well as the genomic and phenotypic diversity of extant Asteraceae plants caused by paleogenome reorganization,are still poorly understood.We analyzed 11 genomes from 10 genera in Asteraceae,and redated the Asteraceae common hexaploidization(ACH)event∼70.7–78.6 million years ago(Mya)and the Asteroideae specific tetraploidization(AST)event∼41.6–46.2 Mya.Moreover,we identified the genomic homologies generated from the ACH,AST and speciation events,and constructed a multiple genome alignment framework for Asteraceae.Subsequently,we revealed biased fractionations between the paleopolyploidization produced subgenomes,suggesting the ACH and AST both are allopolyplodization events.Interestingly,the paleochromosome reshuffling traces provided clear evidence for the two-step duplications of ACH event in Asteraceae.Furthermore,we reconstructed ancestral Asteraceae karyotype(AAK)that has 9 paleochromosomes,and revealed a highly flexible reshuffling of Asteraceae paleogenome.Of specific significance,we explored the genetic diversity of Heat Shock Transcription Factors(Hsfs)associated with recursive whole-genome polyploidizations,gene duplications,and paleogenome reshuffling,and revealed that the expansion of Hsfs gene families enable heat shock plasticity during the genome evolution of Asteraceae.Our study provides insights on polyploidy and paleogenome remodeling for the successful establishment of Asteraceae,and is helpful for further communication and exploration of the diversification of plant families and phenotypes.展开更多
Task duplication has been widely adopted to mitigate the impact of stragglers that run much longer than normal tasks. However,task duplication on data pipelining case would generate excessive traffic over the datacent...Task duplication has been widely adopted to mitigate the impact of stragglers that run much longer than normal tasks. However,task duplication on data pipelining case would generate excessive traffic over the datacenter networks. In this paper, we study minimizing the traffic cost for data pipelining task replications and design a controller that chooses the data generated by the first finished task and discards data generated later by other replications belonging to the same task. Each task replication communicates with the controller when it finishes a data processing, which causes additional network overhead. Hence, we try to reduce the network overhead and make a trade-off between the delay of data block and the network overhead. Finally, extensive simulation results demonstrate that our proposal can minimize network traffic cost under data pipelining case.展开更多
Let <i><span>n</span></i><span> respondents rank order </span><i><span>d</span></i><span> items, and suppose that <img src="Edit_c36450fa-1b61-...Let <i><span>n</span></i><span> respondents rank order </span><i><span>d</span></i><span> items, and suppose that <img src="Edit_c36450fa-1b61-4116-be40-5bede8274d30.bmp" alt="" /></span><span><span>. Our main task is to uncover and display the structure of the observed rank data by an exploratory riffle shuffling procedure which sequentially decomposes the n voters into a finite number of coherent groups plus a noisy group: where the noisy group represents the outlier voters and each coherent group is composed of a finite number of coherent clusters. We consider exploratory riffle shuffling of a set of items to be equivalent to optimal two blocks seriation of the items with crossing of some scores between the two blocks. A riffle shuffled coherent cluster of voters within its coherent group is essentially characterized by the following facts: 1) Voters have identical first TCA factor score, where TCA designates taxicab correspondence analysis, an L</span><sub><span>1</span></sub><span> variant of corresponden</span><span>ce analysis;2) Any preference is easily interpreted as riffle shuffling of its items;3) The nature of different riffle shuffling of items can be seen in the structure of the contingency table of the first-order marginals constructed from the Borda scorings of the voters;4) The first TCA factor scores of the items of a coherent cluster are interpreted as Borda scale of the items. We also introduce a crossing index, which measures the extent of crossing of scores of voters between the two blocks seriation of the items. The novel approach is explained on the benchmarking SUSHI data set, where we show that this data set has a very si</span><span>mple structure, which can also be communicated in a tabular form.</span></span>展开更多
DNA shuffling是蛋白质定向进化的一种常用策略,其优点是可以快速积累多突变效果,但同时由于突变数较多,其中真正发挥作用的突变及其结构基础往往不清楚。β-葡萄糖苷酶是纤维素高效降解的限速酶,良好的热稳定性是影响其实际催化效率的...DNA shuffling是蛋白质定向进化的一种常用策略,其优点是可以快速积累多突变效果,但同时由于突变数较多,其中真正发挥作用的突变及其结构基础往往不清楚。β-葡萄糖苷酶是纤维素高效降解的限速酶,良好的热稳定性是影响其实际催化效率的关键因素。该研究以DNA shuffling策略产生的热稳定性β-葡萄糖苷酶突变体Bgl3-6511(含60个突变,T_(50)值比野生型提高4.6℃)为研究对象,通过序列比对、定点突变和热稳定性测定,对其中的有益突变进行鉴定。结果显示,6个单点突变Y50F、R52H、R56K、V65I、T67A和P143A分别将该酶的T_(50)值提高2.9、4.2、1.5、2.8、3.2、1.2℃。同时,鉴定到5个有害突变将该酶的T_(50)值降低1.0~3.4℃。将获得单点有益突变进行组合,获得T_(50)值提高13.4℃的M6(Y50F/R52H/R56K/V65I/T67A/P143A),说明DNA shuffling策略积累的有害突变确实损害了性能优化。结构分析和分子动力学模拟显示,有益突变主要是通过增强分子内氢键、π-π键和稳定二级结构发挥作用。该研究对Bgl3-6511中的单点有益突变进行鉴定,对其结构基础进行了分析,并获得了热稳定性更加优良的突变酶,相关信息可为其他酶的分子改造提供有益借鉴。展开更多
基金Supported by Research Fond for the Doctoral of Higher Education of China,the Hunan Natural Science Foundation under Grant No.05JJ30121the Scientific Research Fund of Hunan Provincial Education Department under Grant No.08B011Educational Research Fund of Hunan Provincial Education Department under Grant No.09C013
文摘A new image encryption approach is proposed.First,a sort transformation based on nonlinear chaoticalgorithm is used to shuffle the positions of image pixels.Then the states of hyper-chaos are used to change the greyvalues of the shuffled image according to the changed chaotic values of the same position between the above nonlinearchaotic sequence and the sorted chaotic sequence.The experimental results demonstrate that the image encryptionscheme based on a shuffling map shows advantages of large key space and high-level security.Compared with someencryption algorithms,the suggested encryption scheme is more secure.
文摘A Pseudomonas sp. strain IOCa11 exhibiting broad substrate profile for polycyclic aromatic hydrocarbons (PAHs) degradation was isolated by enrichment techniques from oil-contaminated soil. We applied genome shuffling of Pseudomonas sp. strain IOCa11 to achieve improved degradation of PAHs. The initial mutant population was generated by nitrosoguanidine treatment and population exhibiting improved phenotype was subjected to multiple round of protoplast fusion in order to allow recombination between genomes. Mutant, designated as SF-IOC11-16A, obtained after recursive protoplast fusion showed substantial improvement in ability to degrade PAHs in liquid media. It could degrade 98% DBT in 72 hours in comparison to 74% by the wild parent strain. Similar improvement in degradation of the naphthalene (NAP), phenanthrene (PHE), and benzo (α) pyrene (BAP) was also observed in shuffled strain. The shuffled strain was also able to grow at higher concentration of PAHs and degrade them efficiently. The results indicate that genome shuffling can successfully be used to improve the PAHs degradation capability of bacteria.
基金This work was funded by the National Natural Science Foundation of China(32170236 and 31501333 to J.P.W.)the Hebei Natural Science Foundation(C2020209064 to J.P.W.)the Fundamental Research for the Hebei Province Universities(JQN2020018 to T.L.).
文摘An ancient hexaploidization event in the most but not all Asteraceae plants,may have been responsible for shaping the genomes of many horticultural,ornamental,and medicinal plants that promoting the prosperity of the largest angiosperm family on the earth.However,the duplication process of this hexaploidy,as well as the genomic and phenotypic diversity of extant Asteraceae plants caused by paleogenome reorganization,are still poorly understood.We analyzed 11 genomes from 10 genera in Asteraceae,and redated the Asteraceae common hexaploidization(ACH)event∼70.7–78.6 million years ago(Mya)and the Asteroideae specific tetraploidization(AST)event∼41.6–46.2 Mya.Moreover,we identified the genomic homologies generated from the ACH,AST and speciation events,and constructed a multiple genome alignment framework for Asteraceae.Subsequently,we revealed biased fractionations between the paleopolyploidization produced subgenomes,suggesting the ACH and AST both are allopolyplodization events.Interestingly,the paleochromosome reshuffling traces provided clear evidence for the two-step duplications of ACH event in Asteraceae.Furthermore,we reconstructed ancestral Asteraceae karyotype(AAK)that has 9 paleochromosomes,and revealed a highly flexible reshuffling of Asteraceae paleogenome.Of specific significance,we explored the genetic diversity of Heat Shock Transcription Factors(Hsfs)associated with recursive whole-genome polyploidizations,gene duplications,and paleogenome reshuffling,and revealed that the expansion of Hsfs gene families enable heat shock plasticity during the genome evolution of Asteraceae.Our study provides insights on polyploidy and paleogenome remodeling for the successful establishment of Asteraceae,and is helpful for further communication and exploration of the diversification of plant families and phenotypes.
文摘Task duplication has been widely adopted to mitigate the impact of stragglers that run much longer than normal tasks. However,task duplication on data pipelining case would generate excessive traffic over the datacenter networks. In this paper, we study minimizing the traffic cost for data pipelining task replications and design a controller that chooses the data generated by the first finished task and discards data generated later by other replications belonging to the same task. Each task replication communicates with the controller when it finishes a data processing, which causes additional network overhead. Hence, we try to reduce the network overhead and make a trade-off between the delay of data block and the network overhead. Finally, extensive simulation results demonstrate that our proposal can minimize network traffic cost under data pipelining case.
文摘Let <i><span>n</span></i><span> respondents rank order </span><i><span>d</span></i><span> items, and suppose that <img src="Edit_c36450fa-1b61-4116-be40-5bede8274d30.bmp" alt="" /></span><span><span>. Our main task is to uncover and display the structure of the observed rank data by an exploratory riffle shuffling procedure which sequentially decomposes the n voters into a finite number of coherent groups plus a noisy group: where the noisy group represents the outlier voters and each coherent group is composed of a finite number of coherent clusters. We consider exploratory riffle shuffling of a set of items to be equivalent to optimal two blocks seriation of the items with crossing of some scores between the two blocks. A riffle shuffled coherent cluster of voters within its coherent group is essentially characterized by the following facts: 1) Voters have identical first TCA factor score, where TCA designates taxicab correspondence analysis, an L</span><sub><span>1</span></sub><span> variant of corresponden</span><span>ce analysis;2) Any preference is easily interpreted as riffle shuffling of its items;3) The nature of different riffle shuffling of items can be seen in the structure of the contingency table of the first-order marginals constructed from the Borda scorings of the voters;4) The first TCA factor scores of the items of a coherent cluster are interpreted as Borda scale of the items. We also introduce a crossing index, which measures the extent of crossing of scores of voters between the two blocks seriation of the items. The novel approach is explained on the benchmarking SUSHI data set, where we show that this data set has a very si</span><span>mple structure, which can also be communicated in a tabular form.</span></span>
