酶功能的识别对理解生命活动的机制、推进生命科学的发展有重要作用。然而现有的酶EC编号预测方法,并未充分利用蛋白质序列信息,在识别精度上仍有所不足。针对上述问题,本研究提出一种基于层级特征和全局特征的EC编号预测网络(EC number...酶功能的识别对理解生命活动的机制、推进生命科学的发展有重要作用。然而现有的酶EC编号预测方法,并未充分利用蛋白质序列信息,在识别精度上仍有所不足。针对上述问题,本研究提出一种基于层级特征和全局特征的EC编号预测网络(EC number prediction network using hierarchical features and global features,ECPN-HFGF)。该方法首先通过残差网络提取蛋白质序列通用特征,并通过层级特征提取模块和全局特征提取模块进一步提取蛋白质序列的层级特征和全局特征,之后结合两种特征信息的预测结果,采用多任务学习框架,实现酶EC编号的精确预测。计算实验结果表明,ECPN-HFGF方法在蛋白质序列EC编号预测任务上性能最佳,宏观F1值和微观F1值分别达到95.5%和99.0%。ECPN-HFGF方法能有效结合蛋白质序列的层级特征和全局特征,快速准确预测蛋白质序列EC编号,比当前常用方法预测精确度更高,能够为酶学研究和酶工程应用的发展提供一种高效的思路和方法。展开更多
Multi-generational planting of Eucalyptus species degrades soil quality but the introduction of legumes can improve soil fertility and microbial diversity.However,the effects of introducing non-legume native tree spec...Multi-generational planting of Eucalyptus species degrades soil quality but the introduction of legumes can improve soil fertility and microbial diversity.However,the effects of introducing non-legume native tree species on soil nutrients and bacterial community structure remain poorly understood.This study investigated the impacts of the conversion of third generation monoculture Eucalyptus plantations to mixed systems including Eucalyptus urograndis with Cinnamomum camphora(EC)and E.urograndis with Castanopsis hystrix(EH),on soil chemical and biochemical properties and bacterial community structure,diversity and functions.First generation E.urophylla plantations were the control.Results show that planting the third generation Eucalyptus led to a significant decrease in p H,organic matter,nutrient content,enzyme activities(invertin,acid phosphataes,and urease),and bacterialα-diversity compare to the controls.However,the mixed planting showed significant improvement in soil chemical and biochemical attributes and bacterialα-diversity,although the E.urograndis and C.hystrix planting had no improvement.Chloroflexi(oligotrophic bacteria)were significantly enriched in third generation Eucalyptus and Eucalyptus+C.hystrix,while proteobacteria increased significantly in the E.urograndis with C.camphora plantings.The relative abundance of multiple metabolic pathways increased significantly in the third generation Eucalyptus plantations whereas membrane transportrelated genes were enriched in soils of the mixed systems.The changes in bacterial community structures in the two mixed systems were driven by diversity,organic matter and acid phosphatase,while bacterial functions were affected by invertase,NO_(3)^(-)-N,diversity and urease.These results suggest that the transformation of successive monoculture Eucalyptus plantations into mixed plantations reduces the depletion of soil nutrients and enhances the ecological function of soil microorganisms.展开更多
文摘酶功能的识别对理解生命活动的机制、推进生命科学的发展有重要作用。然而现有的酶EC编号预测方法,并未充分利用蛋白质序列信息,在识别精度上仍有所不足。针对上述问题,本研究提出一种基于层级特征和全局特征的EC编号预测网络(EC number prediction network using hierarchical features and global features,ECPN-HFGF)。该方法首先通过残差网络提取蛋白质序列通用特征,并通过层级特征提取模块和全局特征提取模块进一步提取蛋白质序列的层级特征和全局特征,之后结合两种特征信息的预测结果,采用多任务学习框架,实现酶EC编号的精确预测。计算实验结果表明,ECPN-HFGF方法在蛋白质序列EC编号预测任务上性能最佳,宏观F1值和微观F1值分别达到95.5%和99.0%。ECPN-HFGF方法能有效结合蛋白质序列的层级特征和全局特征,快速准确预测蛋白质序列EC编号,比当前常用方法预测精确度更高,能够为酶学研究和酶工程应用的发展提供一种高效的思路和方法。
基金fully funded by the Natural Science Foundation of Guangdong Province(Grant No.2020A1515011404)Guangxi Major Science and Technology Project(Grant No.AA17204087-9)+2 种基金Guangdong Forestry SciTech Innovation Platform Project(Grant No.2020-KYXM-09)China National Key R&D Program during the 13th Five-year Plan Period(Grant No.2016YFD0600504)the Operation Project for Guangdong Zhanjiang Eucalyptus Forest Ecosystem National Positioning Observation and Research Station(Grant No.2019132141)。
文摘Multi-generational planting of Eucalyptus species degrades soil quality but the introduction of legumes can improve soil fertility and microbial diversity.However,the effects of introducing non-legume native tree species on soil nutrients and bacterial community structure remain poorly understood.This study investigated the impacts of the conversion of third generation monoculture Eucalyptus plantations to mixed systems including Eucalyptus urograndis with Cinnamomum camphora(EC)and E.urograndis with Castanopsis hystrix(EH),on soil chemical and biochemical properties and bacterial community structure,diversity and functions.First generation E.urophylla plantations were the control.Results show that planting the third generation Eucalyptus led to a significant decrease in p H,organic matter,nutrient content,enzyme activities(invertin,acid phosphataes,and urease),and bacterialα-diversity compare to the controls.However,the mixed planting showed significant improvement in soil chemical and biochemical attributes and bacterialα-diversity,although the E.urograndis and C.hystrix planting had no improvement.Chloroflexi(oligotrophic bacteria)were significantly enriched in third generation Eucalyptus and Eucalyptus+C.hystrix,while proteobacteria increased significantly in the E.urograndis with C.camphora plantings.The relative abundance of multiple metabolic pathways increased significantly in the third generation Eucalyptus plantations whereas membrane transportrelated genes were enriched in soils of the mixed systems.The changes in bacterial community structures in the two mixed systems were driven by diversity,organic matter and acid phosphatase,while bacterial functions were affected by invertase,NO_(3)^(-)-N,diversity and urease.These results suggest that the transformation of successive monoculture Eucalyptus plantations into mixed plantations reduces the depletion of soil nutrients and enhances the ecological function of soil microorganisms.
