With the rapid development of high-throughput sequencing technologies and the accumulation of large-scale multi-omics data,deep learning(DL)has emerged as a powerful tool to solve complex biological problems,with part...With the rapid development of high-throughput sequencing technologies and the accumulation of large-scale multi-omics data,deep learning(DL)has emerged as a powerful tool to solve complex biological problems,with particular promise in plant genomics.This review systematically examines the progress of DL applications in DNA,RNA,and protein sequence analysis,covering key tasks such as gene regulatory element identification,gene function annotation,and protein structure prediction,and highlighting how these DL applications illuminate research of plants,including horticultural plants.We evaluate the advantages of different neural network architectures and their applications in different biology studies,as well as the development of large language models(LLMs)in genomic modelling,such as the plantspecific models PDLLMs and AgroNT.We also briefly introduce the general workflow of the basic DL model for plant genomics study.While DL has significantly improved prediction accuracy in plant genomics,its broader application remains constrained by several challenges,including the limited availability of well-annotated data,computational capacity,innovative model architectures adapted to plant genomes,and model interpretability.Future advances will require interdisciplinary collaborations to develop DL applications for intelligent plant genomic research frameworks with broader applicability.展开更多
BACKGROUND:The mechanisms underlying hypothermic liver injury necessitate investigation for the development of effective diagnostic and therapeutic approaches.We aim to establish a model of hypothermic liver injury to...BACKGROUND:The mechanisms underlying hypothermic liver injury necessitate investigation for the development of effective diagnostic and therapeutic approaches.We aim to establish a model of hypothermic liver injury to explore the hepatic alterations,thereby facilitating the prevention and treatment of the liver injury associated with hypothermia.METHODS:The mice were placed in a−20℃ environment,to establish a hypothermic injury model.The liver function,metabolites,and proteins expression were measured by thromboelastography,histopathology,metabolomics and western blotting,respectively.Furthermore,apoptosis and pathway changes in the liver cells conducted with target metabolites were examined and verified.RESULTS:According to the prolonged righting reflex recovery time and death occurrence,the mice with the anal temperature(AT)dropping to 20℃ or 15℃ were used to establish a model of hypothermia.The model mice showed changes in alanine aminotransferase(ALT),aspartate transaminase(AST),and coagulation indicators.HE staining results indicated that liver tissue in the AT 20℃ mice had large hemorrhagic patches,while the AT 15℃ mice displayed significant congestion,along with extensive infiltration of inflammatory cells around the central vein.Metabolomic and Kyoto Encyclopedia of Genes and Genomes(KEGG)analyses of target metabolites revealed a significant increase in 3-hydroxybutyric acid and changes in the cyclic adenosine monophosphate(cAMP)signaling pathway in the liver tissue of hypothermic mice.The hypothermic mice showed decreases in levels of cAMP,protein kinase A C-α(PKA C-α),and phosphorylated BCL-2/BCL-XL-associated death promoter(p-Bad)and an increase in BCL-2/BCLXL-associated death promoter(Bad)level in the liver.These protein changes and apoptosis were intensified by 3-hydroxybutyric acid in liver cells.CONCLUSION:Hypothermia may induce apoptosis in the liver cell which may be related to the changes of the cAMP-PKA pathway proteins expression.These findings provide a basis for the treatment of hypothermic injury.展开更多
基金supported by the National Natural Science Foundation of China(Grant Nos.U23A20210,31722048,and 32102382)Central Public-interest Scientific Institution Basal Research Fund,The Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Horticultural Crops,Ministry of Agriculture and Rural Affairs,China.
文摘With the rapid development of high-throughput sequencing technologies and the accumulation of large-scale multi-omics data,deep learning(DL)has emerged as a powerful tool to solve complex biological problems,with particular promise in plant genomics.This review systematically examines the progress of DL applications in DNA,RNA,and protein sequence analysis,covering key tasks such as gene regulatory element identification,gene function annotation,and protein structure prediction,and highlighting how these DL applications illuminate research of plants,including horticultural plants.We evaluate the advantages of different neural network architectures and their applications in different biology studies,as well as the development of large language models(LLMs)in genomic modelling,such as the plantspecific models PDLLMs and AgroNT.We also briefly introduce the general workflow of the basic DL model for plant genomics study.While DL has significantly improved prediction accuracy in plant genomics,its broader application remains constrained by several challenges,including the limited availability of well-annotated data,computational capacity,innovative model architectures adapted to plant genomes,and model interpretability.Future advances will require interdisciplinary collaborations to develop DL applications for intelligent plant genomic research frameworks with broader applicability.
基金supported by a grant from the Liaoning Provincial Science&Technology Committee(2023-BS-032,2021JH2/10300024).
文摘BACKGROUND:The mechanisms underlying hypothermic liver injury necessitate investigation for the development of effective diagnostic and therapeutic approaches.We aim to establish a model of hypothermic liver injury to explore the hepatic alterations,thereby facilitating the prevention and treatment of the liver injury associated with hypothermia.METHODS:The mice were placed in a−20℃ environment,to establish a hypothermic injury model.The liver function,metabolites,and proteins expression were measured by thromboelastography,histopathology,metabolomics and western blotting,respectively.Furthermore,apoptosis and pathway changes in the liver cells conducted with target metabolites were examined and verified.RESULTS:According to the prolonged righting reflex recovery time and death occurrence,the mice with the anal temperature(AT)dropping to 20℃ or 15℃ were used to establish a model of hypothermia.The model mice showed changes in alanine aminotransferase(ALT),aspartate transaminase(AST),and coagulation indicators.HE staining results indicated that liver tissue in the AT 20℃ mice had large hemorrhagic patches,while the AT 15℃ mice displayed significant congestion,along with extensive infiltration of inflammatory cells around the central vein.Metabolomic and Kyoto Encyclopedia of Genes and Genomes(KEGG)analyses of target metabolites revealed a significant increase in 3-hydroxybutyric acid and changes in the cyclic adenosine monophosphate(cAMP)signaling pathway in the liver tissue of hypothermic mice.The hypothermic mice showed decreases in levels of cAMP,protein kinase A C-α(PKA C-α),and phosphorylated BCL-2/BCL-XL-associated death promoter(p-Bad)and an increase in BCL-2/BCLXL-associated death promoter(Bad)level in the liver.These protein changes and apoptosis were intensified by 3-hydroxybutyric acid in liver cells.CONCLUSION:Hypothermia may induce apoptosis in the liver cell which may be related to the changes of the cAMP-PKA pathway proteins expression.These findings provide a basis for the treatment of hypothermic injury.
