The organized three-dimensional chromosome architecture in the cell nucleus provides scaffolding for precise regulation of gene expression.When the cell changes its identity in the cell-fate decision-making process,ex...The organized three-dimensional chromosome architecture in the cell nucleus provides scaffolding for precise regulation of gene expression.When the cell changes its identity in the cell-fate decision-making process,extensive rearrangements of chromo-some structures occur accompanied by large-scale adaptations of gene expression,underscoring the importance of chromosome dynamics in shaping genome function.Over the last two decades,rapid development of experimental methods has provided unprecedented data to characterize the hierarchical structures and dynamic properties of chromosomes.In parallel,these enormous data offer valuable opportunities for developing quantitative computational models.Here,we review a variety of large-scale polymer models developed to investigate the structures and dynamics of chromosomes.Different from the underlying modeling strategies,these approaches can be classified into data-driven(‘top-down’)and physics-based(‘bottom-up’)categories.We discuss their contributions to offering valuable insights into the relationships among the structures,dynamics,and functions of chromosomes and propose the perspective of developing data integration approaches from different experimental technologies and multidisciplinary theoretical/simulation methods combined with different modeling strategies.展开更多
With the decline in fish resources worldwide,the ecological dominance and economic importance of crustaceans have obviously increased.Among crustacean species,mantis shrimps are increasingly dominant in many coastal w...With the decline in fish resources worldwide,the ecological dominance and economic importance of crustaceans have obviously increased.Among crustacean species,mantis shrimps are increasingly dominant in many coastal waters of the world.In China,Oratosquilla oratoria is the most widely distributed and productive species of mantis shrimp,and its relative resource density is the highest in the Bohai Sea.In this study,we analysed the long-term and monthly population characteristics of O.oratoria in the Bohai Sea,including its relative resource density,body size and spatial distribution.The results showed that the relative resource density of O.oratoria in the Bohai Sea increased from 3.59 kg/h in 1982 to 14.48 kg/h in 2018,and the percentage of this species that serves as a fishery resource increased from 4.22%in 1982 to 35.27%in 2018,based on the mean relative resource density in May and August.The relative resource density of O.oratoria in the fishing moratorium season from May to August was significantly higher than that in the other months of fishing season,and the relative resource density decreased rapidly after the fishing moratorium ended.The relative resource density of O.oratoria was the highest in summer(August),followed by in autumn(October)and spring(May),and it was the lowest in winter(January).The relative resource density of O.oratoria in the western Bohai Sea was higher than that in the eastern Bohai Sea.The mean body weight of O.oratoria in the Bohai Sea decreased from 21.95 g in 1982 to 14.34 g in 2018,based on the mean body weight in May and August.The body size of O.oratoria in the fishing moratorium season was significantly higher than that in the fishing season,and the body size decreased rapidly after the fishing moratorium ended.Overall,in the context of declining resources of most fishery species,the relative resource density of O.oratoria increased due to its hardiness and adaptability,and its body size decreased under intensive fishing over the past 30 years.The fishing moratorium system h展开更多
为揭示南宁市土地利用的时空变化规律,运用地理信息系统(Geographic information system,GIS)技术和土地利用动态度、利用程度和转移矩阵等方法,深入分析1990—2020年南宁市土地利用的时空演变特征。结果表明,1990—2020年南宁市各土地...为揭示南宁市土地利用的时空变化规律,运用地理信息系统(Geographic information system,GIS)技术和土地利用动态度、利用程度和转移矩阵等方法,深入分析1990—2020年南宁市土地利用的时空演变特征。结果表明,1990—2020年南宁市各土地利用类型的变化明显、土地利用变化的总体速度加快,建设用地和未利用地增加且表现为增速,耕地、林地、草地和水域减少且表现为减速;南宁市的土地利用程度处于中等水平,随着人为活动对土地的不断干扰和影响,土地利用程度水平呈逐渐升高的趋势;30年间南宁市共有1051.61 km2的土地利用类型发生转移,其中建设用地和未利用地表现为净转入特征,耕地、林地、草地、水域表现为净转出特征。展开更多
Molecular dynamics simulations were applied to normal conformational Glutathione (GSH) and GSH over zwitterionic and hydrophobic surfaces respectively. Conformational analysis of GSH during the simulation time on RMSD...Molecular dynamics simulations were applied to normal conformational Glutathione (GSH) and GSH over zwitterionic and hydrophobic surfaces respectively. Conformational analysis of GSH during the simulation time on RMSD, conformational flexibility and dihedral distribution were performed. The re- sults showed that zwitterionic structure maintains the normal conformations of GSH to a better extent, which should be a first good proof of the hypothesis of "maintain of normal structure".展开更多
Molecular dynamics simulations are applied to the initial stage of polyalanine13 conformational transi- tion from α-helix to random coil in aqueous environment and the interaction of polyalanine13 with zwitterionic a...Molecular dynamics simulations are applied to the initial stage of polyalanine13 conformational transi- tion from α-helix to random coil in aqueous environment and the interaction of polyalanine13 with zwitterionic and hydrophobic surfaces respectively in the same condition. The analysis of secondary structure, hydrogen bonds, RMSD, dihedral distribution, and the degree of adsorption are performed. The results show that zwitterionic structure maintains the natural behavior of polyalanine13 in water to a better extent, which should be an indirect proof of the hypothesis of "maintain of normal structure."展开更多
基金supported by the National Natural Science Foundation of China(grant no.32201020)the general program(grant no.2023A04J0083)+1 种基金the Guangzhou–HKUST(GZ)joint funding program(grant no.2023A03J0060)of Guangzhou Municipal Science and Technology Projectfunded by the Municipal Key Laboratory Construction Program of Guangzhou Municipal Science and Technology Project(grant no.2023A03J0003).
文摘The organized three-dimensional chromosome architecture in the cell nucleus provides scaffolding for precise regulation of gene expression.When the cell changes its identity in the cell-fate decision-making process,extensive rearrangements of chromo-some structures occur accompanied by large-scale adaptations of gene expression,underscoring the importance of chromosome dynamics in shaping genome function.Over the last two decades,rapid development of experimental methods has provided unprecedented data to characterize the hierarchical structures and dynamic properties of chromosomes.In parallel,these enormous data offer valuable opportunities for developing quantitative computational models.Here,we review a variety of large-scale polymer models developed to investigate the structures and dynamics of chromosomes.Different from the underlying modeling strategies,these approaches can be classified into data-driven(‘top-down’)and physics-based(‘bottom-up’)categories.We discuss their contributions to offering valuable insights into the relationships among the structures,dynamics,and functions of chromosomes and propose the perspective of developing data integration approaches from different experimental technologies and multidisciplinary theoretical/simulation methods combined with different modeling strategies.
基金The National Key Research and Development Program of China under contract No.2018YFD0900902the Central Public-Interest Scientific Institution Basal Research Fund,Yellow Sea Fisheries Research Institute,Chinese Academy of Fishery Sciences,under contract Nos 2022YJ01 and 2021TD01the Special Funds for Taishan Scholar Project of Shandong Province.
文摘With the decline in fish resources worldwide,the ecological dominance and economic importance of crustaceans have obviously increased.Among crustacean species,mantis shrimps are increasingly dominant in many coastal waters of the world.In China,Oratosquilla oratoria is the most widely distributed and productive species of mantis shrimp,and its relative resource density is the highest in the Bohai Sea.In this study,we analysed the long-term and monthly population characteristics of O.oratoria in the Bohai Sea,including its relative resource density,body size and spatial distribution.The results showed that the relative resource density of O.oratoria in the Bohai Sea increased from 3.59 kg/h in 1982 to 14.48 kg/h in 2018,and the percentage of this species that serves as a fishery resource increased from 4.22%in 1982 to 35.27%in 2018,based on the mean relative resource density in May and August.The relative resource density of O.oratoria in the fishing moratorium season from May to August was significantly higher than that in the other months of fishing season,and the relative resource density decreased rapidly after the fishing moratorium ended.The relative resource density of O.oratoria was the highest in summer(August),followed by in autumn(October)and spring(May),and it was the lowest in winter(January).The relative resource density of O.oratoria in the western Bohai Sea was higher than that in the eastern Bohai Sea.The mean body weight of O.oratoria in the Bohai Sea decreased from 21.95 g in 1982 to 14.34 g in 2018,based on the mean body weight in May and August.The body size of O.oratoria in the fishing moratorium season was significantly higher than that in the fishing season,and the body size decreased rapidly after the fishing moratorium ended.Overall,in the context of declining resources of most fishery species,the relative resource density of O.oratoria increased due to its hardiness and adaptability,and its body size decreased under intensive fishing over the past 30 years.The fishing moratorium system h
文摘为揭示南宁市土地利用的时空变化规律,运用地理信息系统(Geographic information system,GIS)技术和土地利用动态度、利用程度和转移矩阵等方法,深入分析1990—2020年南宁市土地利用的时空演变特征。结果表明,1990—2020年南宁市各土地利用类型的变化明显、土地利用变化的总体速度加快,建设用地和未利用地增加且表现为增速,耕地、林地、草地和水域减少且表现为减速;南宁市的土地利用程度处于中等水平,随着人为活动对土地的不断干扰和影响,土地利用程度水平呈逐渐升高的趋势;30年间南宁市共有1051.61 km2的土地利用类型发生转移,其中建设用地和未利用地表现为净转入特征,耕地、林地、草地、水域表现为净转出特征。
基金Supported by the Specialized Research Fund for the Doctoral Program of Higher Education (Grant No. 20050319010)the Special Program for Key Basic Research of the Ministry of Science and Technology, China (Grant No. 2005CCa00400)the "Program for Six Most Needed Sorts of Human Resource", Jiangsu Province, China
文摘Molecular dynamics simulations were applied to normal conformational Glutathione (GSH) and GSH over zwitterionic and hydrophobic surfaces respectively. Conformational analysis of GSH during the simulation time on RMSD, conformational flexibility and dihedral distribution were performed. The re- sults showed that zwitterionic structure maintains the normal conformations of GSH to a better extent, which should be a first good proof of the hypothesis of "maintain of normal structure".
基金Supported by the National High Technology Research and Development Program of China (Grant No. 2006AA032Z445)the Special program for Key Basic Research of the Ministry of Science and Technology of China (Grant No. 2005CCA00400)+2 种基金the Specialized Research Fund for the Doctoral Program of Higher Education (Grant No. 20050319010)the Research Foundation of Development and Reform Commission of Jiangsu Province of China (Grant No. 2005103SB9b542)the Research Foundation of Education Bureau of Jiangsu Province of China (Grant Nos. JHjd03-008 and JHB05-21)
文摘Molecular dynamics simulations are applied to the initial stage of polyalanine13 conformational transi- tion from α-helix to random coil in aqueous environment and the interaction of polyalanine13 with zwitterionic and hydrophobic surfaces respectively in the same condition. The analysis of secondary structure, hydrogen bonds, RMSD, dihedral distribution, and the degree of adsorption are performed. The results show that zwitterionic structure maintains the natural behavior of polyalanine13 in water to a better extent, which should be an indirect proof of the hypothesis of "maintain of normal structure."
