High-speed rail(HSR) has formed a networked operational scale in China. Any internal or external disturbance may deviate trains’ operation from the planned schedules, resulting in primary delays or even cascading del...High-speed rail(HSR) has formed a networked operational scale in China. Any internal or external disturbance may deviate trains’ operation from the planned schedules, resulting in primary delays or even cascading delays on a network scale. Studying the delay propagation mechanism could help to improve the timetable resilience in the planning stage and realize cooperative rescheduling for dispatchers. To quickly and effectively predict the spatial-temporal range of cascading delays, this paper proposes a max-plus algebra based delay propagation model considering trains’ operation strategy and the systems’ constraints. A double-layer network based breadth-first search algorithm based on the constraint network and the timetable network is further proposed to solve the delay propagation process for different kinds of emergencies. The proposed model could deal with the delay propagation problem when emergencies occur in sections or stations and is suitable for static emergencies and dynamic emergencies. Case studies show that the proposed algorithm can significantly improve the computational efficiency of the large-scale HSR network. Moreover, the real operational data of China HSR is adopted to verify the proposed model, and the results show that the cascading delays can be timely and accurately inferred, and the delay propagation characteristics under three kinds of emergencies are unfolded.展开更多
A rat model of spinal cord injury was established using the weight drop method. A cavity formed 14 days following spinal cord injury, and compact scar tissue formed by 56 days. Enzyme-linked immunosorbent assay and po...A rat model of spinal cord injury was established using the weight drop method. A cavity formed 14 days following spinal cord injury, and compact scar tissue formed by 56 days. Enzyme-linked immunosorbent assay and polymerase chain reaction enzyme-linked immunosorbent assay results demonstrated that glial fibrillary acidic protein and telomerase expression increased gradually after injury, peaked at 28 days, and then gradually decreased. Spearman rank correlation showed a positive correlation between glial fibrillary acidic protein expression and telomerase expression in the glial scar. These results suggest that telomerase promotes glial scar formation.展开更多
Diatoms comprise a diverse and ecologically important group of eukaryotic phytoplankton that signifi- cantly contributes to marine primary production and global carbon cycling. Phaeodactylum tricornutum is commonly us...Diatoms comprise a diverse and ecologically important group of eukaryotic phytoplankton that signifi- cantly contributes to marine primary production and global carbon cycling. Phaeodactylum tricornutum is commonly used as a model organism for studying diatom biology. Although its genome was sequenced in 2008, a high-quality genome annotation is still not available for this diatom. Here we report the develop- ment of an integrated proteogenomic pipeline and its application for improved annotation of P. tricornutum genome using mass spectrometry （MS）-based proteomics data. Our proteogenomic analysis unambigu- ously identified approximately 8300 genes and revealed 606 novel proteins, 506 revised genes, 94 splice variants, 58 single amino acid variants, and a holistic view of post-translational modifications in P. tricor- nutum. We experimentally confirmed a subset of novel events and obtained MS evidence for more than 200 micropeptides in P. tricornutum. These findings expand the genomic landscape of P. tricornutum and provide a rich resource for the study of diatom biology. The proteogenomic pipeline we developed in this study is applicable to any sequenced eukaryote and thus represents a significant contribution to the toolset for eukaryotic proteogenomic analysis. The pipeline and its source code are freely available at https：//sourceforge.net/projects/gapeproteogeno mic.展开更多
Protein lysine methylation is a prevalent post-translational modification(PTM)and plays critical roles in all domains of life.However,its extent and function in photosynthetic organisms are still largely unknown.Cyano...Protein lysine methylation is a prevalent post-translational modification(PTM)and plays critical roles in all domains of life.However,its extent and function in photosynthetic organisms are still largely unknown.Cyanobacteria are a large group of prokaryotes that carry out oxygenic photosynthesis and are applied extensively in studies of photosynthetic mechanisms and environmental adaptation.Here we integrated propionylation of monomethylated proteins,enrichment of the modified peptides,and mass spectrometry(MS)analysis to identify monomethylated proteins in Synechocystis sp.PCC 6803(Synechocystis).Overall,we identified 376 monomethylation sites in270 proteins,with numerous monomethylated proteins participating in photosynthesis and carbon metabolism.We subsequently demonstrated that Cpc M,a previously identified asparagine methyltransferase in Synechocystis,could catalyze lysine monomethylation of the potential aspartate aminotransferase Sll0480 both in vivo and in vitro and regulate the enzyme activity of Sll0480.The loss of Cpc M led to decreases in the maximum quantum yield in primary photosystemⅡ(PSⅡ)and the efficiency of energy transfer during the photosynthetic reaction in Synechocystis.We report the first lysine monomethylome in a photosynthetic organism and present a critical database for functional analyses of monomethylation in cyanobacteria.The large number of monomethylated proteins and the identification of Cpc M as the lysine methyltransferase in cyanobacteria suggest that reversible methylation may influence the metabolic process and photosynthesis in both cyanobacteria and plants.展开更多
基金supported by the National Natural Science Foundation of China (U1834211, 61925302, 62103033)the Open Research Fund of the State Key Laboratory for Management and Control of Complex Systems (20210104)。
文摘High-speed rail(HSR) has formed a networked operational scale in China. Any internal or external disturbance may deviate trains’ operation from the planned schedules, resulting in primary delays or even cascading delays on a network scale. Studying the delay propagation mechanism could help to improve the timetable resilience in the planning stage and realize cooperative rescheduling for dispatchers. To quickly and effectively predict the spatial-temporal range of cascading delays, this paper proposes a max-plus algebra based delay propagation model considering trains’ operation strategy and the systems’ constraints. A double-layer network based breadth-first search algorithm based on the constraint network and the timetable network is further proposed to solve the delay propagation process for different kinds of emergencies. The proposed model could deal with the delay propagation problem when emergencies occur in sections or stations and is suitable for static emergencies and dynamic emergencies. Case studies show that the proposed algorithm can significantly improve the computational efficiency of the large-scale HSR network. Moreover, the real operational data of China HSR is adopted to verify the proposed model, and the results show that the cascading delays can be timely and accurately inferred, and the delay propagation characteristics under three kinds of emergencies are unfolded.
基金funded by the National Natural Science Foundation of China, No. 81060106
文摘A rat model of spinal cord injury was established using the weight drop method. A cavity formed 14 days following spinal cord injury, and compact scar tissue formed by 56 days. Enzyme-linked immunosorbent assay and polymerase chain reaction enzyme-linked immunosorbent assay results demonstrated that glial fibrillary acidic protein and telomerase expression increased gradually after injury, peaked at 28 days, and then gradually decreased. Spearman rank correlation showed a positive correlation between glial fibrillary acidic protein expression and telomerase expression in the glial scar. These results suggest that telomerase promotes glial scar formation.
基金This work was supported by the National Key Research and Development Program （2016YFA0501304）, the National Natural Science Foundation of China （grant no. 31570829）, and the Strategic Priority Research Program of the Chinese Academy of Sciences （grant no. XDB14030202）.
文摘Diatoms comprise a diverse and ecologically important group of eukaryotic phytoplankton that signifi- cantly contributes to marine primary production and global carbon cycling. Phaeodactylum tricornutum is commonly used as a model organism for studying diatom biology. Although its genome was sequenced in 2008, a high-quality genome annotation is still not available for this diatom. Here we report the develop- ment of an integrated proteogenomic pipeline and its application for improved annotation of P. tricornutum genome using mass spectrometry （MS）-based proteomics data. Our proteogenomic analysis unambigu- ously identified approximately 8300 genes and revealed 606 novel proteins, 506 revised genes, 94 splice variants, 58 single amino acid variants, and a holistic view of post-translational modifications in P. tricor- nutum. We experimentally confirmed a subset of novel events and obtained MS evidence for more than 200 micropeptides in P. tricornutum. These findings expand the genomic landscape of P. tricornutum and provide a rich resource for the study of diatom biology. The proteogenomic pipeline we developed in this study is applicable to any sequenced eukaryote and thus represents a significant contribution to the toolset for eukaryotic proteogenomic analysis. The pipeline and its source code are freely available at https：//sourceforge.net/projects/gapeproteogeno mic.
基金the National Natural Science Foundation of China(Grant No.31570829)the Chinese Academy of Sciences Grant QYZDY-SSW-SMC004+1 种基金the CAS Key Technology Talent Program(to MKY)the Open Fund of Key Laboratory of Experimental Marine Biology,Chinese Academy of Sciences(Grant No.KF2017NO3)。
文摘Protein lysine methylation is a prevalent post-translational modification(PTM)and plays critical roles in all domains of life.However,its extent and function in photosynthetic organisms are still largely unknown.Cyanobacteria are a large group of prokaryotes that carry out oxygenic photosynthesis and are applied extensively in studies of photosynthetic mechanisms and environmental adaptation.Here we integrated propionylation of monomethylated proteins,enrichment of the modified peptides,and mass spectrometry(MS)analysis to identify monomethylated proteins in Synechocystis sp.PCC 6803(Synechocystis).Overall,we identified 376 monomethylation sites in270 proteins,with numerous monomethylated proteins participating in photosynthesis and carbon metabolism.We subsequently demonstrated that Cpc M,a previously identified asparagine methyltransferase in Synechocystis,could catalyze lysine monomethylation of the potential aspartate aminotransferase Sll0480 both in vivo and in vitro and regulate the enzyme activity of Sll0480.The loss of Cpc M led to decreases in the maximum quantum yield in primary photosystemⅡ(PSⅡ)and the efficiency of energy transfer during the photosynthetic reaction in Synechocystis.We report the first lysine monomethylome in a photosynthetic organism and present a critical database for functional analyses of monomethylation in cyanobacteria.The large number of monomethylated proteins and the identification of Cpc M as the lysine methyltransferase in cyanobacteria suggest that reversible methylation may influence the metabolic process and photosynthesis in both cyanobacteria and plants.
