Cell-PLoc 2.0 is a package of web-servers evolved from Cell-PLoc (Chou, K.C. & Shen, H.B., Nature Protocols, 2008, 2:153-162) by a top-down approach to improve the power for predicting subcellular localization of ...Cell-PLoc 2.0 is a package of web-servers evolved from Cell-PLoc (Chou, K.C. & Shen, H.B., Nature Protocols, 2008, 2:153-162) by a top-down approach to improve the power for predicting subcellular localization of proteins in various organisms. It contains six predictors: Euk-mPLoc 2.0, Hum-mPLoc 2.0, Plant-mPLoc, Gpos-mPLoc, Gneg-mPLoc, and Virus-mPLoc, specialized for eukaryotic, human, plant, Gram- positive bacterial, Gram-negative bacterial, and virus proteins, respectively. Compared with Cell-PLoc, the predictors in the Cell-PLoc 2.0 have the following advantageous features: (1) they all have the capacity to deal with the multiplex proteins that can simultaneiously exist, or move between, two or more subcellular location sites;(2) no accession number is needed for the input of a query protein even if using the “high- level” GO (gene ontology) prediction engine;(3) the functional domain information and sequential evolution information are fused into the “ab initio” sequence-based prediction engine to enhance its accuracy. In this protocol, a step- to-step guide is provided for how to use the web server predictors in the Cell-PLoc 2.0 package, which is freely accessible to the public at http://www.csbio.sjtu.edu.cn/bioinf/Cell-PLoc-2/.展开更多
Polymorphisms within gene coding regions represent the most important part of the overall genetic diversity of rice.We characterized the gene-coding sequence-haplotype(gcHap)diversity of 45963 rice genes in 3010 rice ...Polymorphisms within gene coding regions represent the most important part of the overall genetic diversity of rice.We characterized the gene-coding sequence-haplotype(gcHap)diversity of 45963 rice genes in 3010 rice accessions.With an average of 226±390 gcHaps per gene in rice populations,rice genes could be classified into three main categories:12865 conserved genes,10254 subspecific differentiating genes,and 22844 remaining genes.We found that 39218 rice genes carry>255179 major gcHaps of potential functional importance.Most(87.5%)of the detected gcHaps were specific to subspecies or populations.The inferred proto-ancestors of local landrace populations reconstructed from conserved predominant(ancient)gcHaps correlated strongly with wild rice accessions from the same geographic regions,supporting a multiorigin(domestication)model of Oryza sativa.Past breeding efforts generally increased the gcHap diversity of modern varieties and'caused significant frequency shifts in predominant gcHaps of 14266 genes due to independent selection in the two subspecies.Low frequencies of“favorable”gcHaps at most known genes related to rice yield in modern varieties suggest huge potential for rice improvement by mining and pyramiding of favorable gcHaps.The gcHap data were demonstrated to have greater power than SNPs for the detection of causal genes that affect complex traits.The rice gcHap diversity dataset generated in this study would facilitate rice basic research and improvement in the future.展开更多
The presence of oxygen functional groups is detrimental to the capacitive performance of porous carbon electrode in organic electrolyte. In this regards, hydrogen thermal reduction has been demonstrated effective appr...The presence of oxygen functional groups is detrimental to the capacitive performance of porous carbon electrode in organic electrolyte. In this regards, hydrogen thermal reduction has been demonstrated effective approach in removing the unstable surface oxygen while maintaining the high porosity of carbon matrix. However, the exact evolution mechanism of various oxygen species during this process, as well as the correlation with electrochemical properties, is still under development. Herein, biomass-based porous carbon is adopted as the model material to trace its structure evolution of oxygen removal under hydrogen thermal reduction process with the temperature range of 400–800 °C. The optimum microstructure with low oxygen content of 0.90% and proper pore size distribution was achieved at 700°C. XPS, TPRMS and Boehm titration results indicate that the oxygen elimination undergoes three distinctive stages(intermolecular dehydration, hydrogenation and decomposition reactions). The optimum microstructure with low oxygen content of 0.90% and proper pore size distribution was achieved at 700 °C. Benefiting from the stable electrochemical interface and the optimized porous structure, the as-obtained HAC-700 exhibit significantly suppressed self-discharge and leak current, with improved cycling stability, which is attributable to the stabilization of electrochemical interface between carbon surface and electrolyte. The result provides insights for rational design of surface chemistry for high-performance carbon electrode towards advanced energy storage.展开更多
Rural decline is a global issue accompanied by the regional imbalanced development and dysfunction in rural areas.Coordinated interaction among production,living,and ecological functions is essential for the sustainab...Rural decline is a global issue accompanied by the regional imbalanced development and dysfunction in rural areas.Coordinated interaction among production,living,and ecological functions is essential for the sustainability of rural regional systems.Based on the framework of“element-structure-function”,an indicator system was constructed to explore the evolution characteristics and driving factors of rural regional functions in the farming-pastoral ecotone of northern China(FPENC)using the models of entropy-based TOPSIS(Technique for Order of Preference by Similarity to Ideal Solution),revised vertical and horizontal comparison,and GeoDetector.The results indicated a gradual synergy of rural production,living,and ecological functions during the period 2000–2020.Improvements were observed in production and living functions,and higher ecological function was found in Hebei,Inner Mongolia,Liaoning,and Shaanxi.However,conflicts between ecological function and production and living functions were evident in Shanxi,Gansu,and Ningxia.The spatial structure played a dominant role in determining rural production,living,and ecological functions,with ratios of 38%,56%,and 84%,respectively.Land and industry emerged as the main driving factors influencing the evolution of rural regional functions.Notably,combined interactions of rural permanent population and primary industry output(0.73),grassland area and tertiary industry output(0.58),and forest area and tertiary industry output(0.72)were responsible for the changes observed in rural production,living,and ecological functions,respectively.The findings suggest that achieving coordinated development of rural regional functions can be accomplished by establishing differentiated rural sustainable development strategies that consider the coupling of population,land,and industry in FPENC.展开更多
文摘Cell-PLoc 2.0 is a package of web-servers evolved from Cell-PLoc (Chou, K.C. & Shen, H.B., Nature Protocols, 2008, 2:153-162) by a top-down approach to improve the power for predicting subcellular localization of proteins in various organisms. It contains six predictors: Euk-mPLoc 2.0, Hum-mPLoc 2.0, Plant-mPLoc, Gpos-mPLoc, Gneg-mPLoc, and Virus-mPLoc, specialized for eukaryotic, human, plant, Gram- positive bacterial, Gram-negative bacterial, and virus proteins, respectively. Compared with Cell-PLoc, the predictors in the Cell-PLoc 2.0 have the following advantageous features: (1) they all have the capacity to deal with the multiplex proteins that can simultaneiously exist, or move between, two or more subcellular location sites;(2) no accession number is needed for the input of a query protein even if using the “high- level” GO (gene ontology) prediction engine;(3) the functional domain information and sequential evolution information are fused into the “ab initio” sequence-based prediction engine to enhance its accuracy. In this protocol, a step- to-step guide is provided for how to use the web server predictors in the Cell-PLoc 2.0 package, which is freely accessible to the public at http://www.csbio.sjtu.edu.cn/bioinf/Cell-PLoc-2/.
基金funded by the National Key Research and Development Program of China(2016YFD0100301)the National Natural Science Foundation of China(31771762)+1 种基金the Agricultural Science,and Technology Innovation Program and the Cooperation and Innovation Mission(CAAS-ZD>CT202001)the Talent Introduction Program(RC311901)of Anhui Agricultural University.
文摘Polymorphisms within gene coding regions represent the most important part of the overall genetic diversity of rice.We characterized the gene-coding sequence-haplotype(gcHap)diversity of 45963 rice genes in 3010 rice accessions.With an average of 226±390 gcHaps per gene in rice populations,rice genes could be classified into three main categories:12865 conserved genes,10254 subspecific differentiating genes,and 22844 remaining genes.We found that 39218 rice genes carry>255179 major gcHaps of potential functional importance.Most(87.5%)of the detected gcHaps were specific to subspecies or populations.The inferred proto-ancestors of local landrace populations reconstructed from conserved predominant(ancient)gcHaps correlated strongly with wild rice accessions from the same geographic regions,supporting a multiorigin(domestication)model of Oryza sativa.Past breeding efforts generally increased the gcHap diversity of modern varieties and'caused significant frequency shifts in predominant gcHaps of 14266 genes due to independent selection in the two subspecies.Low frequencies of“favorable”gcHaps at most known genes related to rice yield in modern varieties suggest huge potential for rice improvement by mining and pyramiding of favorable gcHaps.The gcHap data were demonstrated to have greater power than SNPs for the detection of causal genes that affect complex traits.The rice gcHap diversity dataset generated in this study would facilitate rice basic research and improvement in the future.
基金National Science Foundation for Excellent Young Scholars of China (21922815)Key Research and Development (R&D) Projects of Shanxi Province (201903D121007)+3 种基金Natural Science Foundations of Shanxi Province (201801D221156)DNL Cooperation Fund of CAS (DNL180308)Science and Technology Service Network Initiative of CAS (KFJ-STS-ZDTP-068)Youth Innovation Promotion Association of CAS。
文摘The presence of oxygen functional groups is detrimental to the capacitive performance of porous carbon electrode in organic electrolyte. In this regards, hydrogen thermal reduction has been demonstrated effective approach in removing the unstable surface oxygen while maintaining the high porosity of carbon matrix. However, the exact evolution mechanism of various oxygen species during this process, as well as the correlation with electrochemical properties, is still under development. Herein, biomass-based porous carbon is adopted as the model material to trace its structure evolution of oxygen removal under hydrogen thermal reduction process with the temperature range of 400–800 °C. The optimum microstructure with low oxygen content of 0.90% and proper pore size distribution was achieved at 700°C. XPS, TPRMS and Boehm titration results indicate that the oxygen elimination undergoes three distinctive stages(intermolecular dehydration, hydrogenation and decomposition reactions). The optimum microstructure with low oxygen content of 0.90% and proper pore size distribution was achieved at 700 °C. Benefiting from the stable electrochemical interface and the optimized porous structure, the as-obtained HAC-700 exhibit significantly suppressed self-discharge and leak current, with improved cycling stability, which is attributable to the stabilization of electrochemical interface between carbon surface and electrolyte. The result provides insights for rational design of surface chemistry for high-performance carbon electrode towards advanced energy storage.
基金National Natural Science Foundation of China,No.42271275Key Program of National Natural Science Foundation of China,No.41931293。
文摘Rural decline is a global issue accompanied by the regional imbalanced development and dysfunction in rural areas.Coordinated interaction among production,living,and ecological functions is essential for the sustainability of rural regional systems.Based on the framework of“element-structure-function”,an indicator system was constructed to explore the evolution characteristics and driving factors of rural regional functions in the farming-pastoral ecotone of northern China(FPENC)using the models of entropy-based TOPSIS(Technique for Order of Preference by Similarity to Ideal Solution),revised vertical and horizontal comparison,and GeoDetector.The results indicated a gradual synergy of rural production,living,and ecological functions during the period 2000–2020.Improvements were observed in production and living functions,and higher ecological function was found in Hebei,Inner Mongolia,Liaoning,and Shaanxi.However,conflicts between ecological function and production and living functions were evident in Shanxi,Gansu,and Ningxia.The spatial structure played a dominant role in determining rural production,living,and ecological functions,with ratios of 38%,56%,and 84%,respectively.Land and industry emerged as the main driving factors influencing the evolution of rural regional functions.Notably,combined interactions of rural permanent population and primary industry output(0.73),grassland area and tertiary industry output(0.58),and forest area and tertiary industry output(0.72)were responsible for the changes observed in rural production,living,and ecological functions,respectively.The findings suggest that achieving coordinated development of rural regional functions can be accomplished by establishing differentiated rural sustainable development strategies that consider the coupling of population,land,and industry in FPENC.
