Translational regulation is a critical step in the process of gene expression and governs the synthesis of proteins from mRNAs.Many studies have revealed translational regulation in plants in response to various envir...Translational regulation is a critical step in the process of gene expression and governs the synthesis of proteins from mRNAs.Many studies have revealed translational regulation in plants in response to various environmental stimuli.However,there have been no studies documenting the comprehensive landscape of translational regulation and allele-specific translational efficiency in multiple plant tissues,especially those of rice,a main staple crop that feeds nearly half of the world’s population.Here we used RNA sequencing and ribosome profiling data to analyze the transcriptome and translatome of an elite hybrid rice,Shanyou 63(SY63),and its parental varieties Zhenshan 97 and Minghui 63.The results revealed that gene expression patterns varied more among tissues than among varieties at the transcriptional and translational levels.We identified 3392 upstream open reading frames(uORFs),and the uORF-containing genes were enriched in transcription factors.Only 668 of 13492 long non-coding RNAs could be translated into peptides.Finally,we discovered numerous genes with allele-specific translational efficiency in SY63 and demonstrated that some cis-regulatory elements may contribute to allelic divergence in translational efficiency.Overall,these findings may improve our understanding of translational regulation in rice and provide information for molecular breeding research.展开更多
In recent years,exploring the relationship between community structure and node centrality in complex networks has gained significant attention from researchers,given its fundamental theoretical significance and pract...In recent years,exploring the relationship between community structure and node centrality in complex networks has gained significant attention from researchers,given its fundamental theoretical significance and practical implications.To address the impact of network communities on target nodes and effectively identify highly influential nodes with strong propagation capabilities,this paper proposes a novel influential spreaders identification algorithm based on density entropy and community structure(DECS).The proposed method initially integrates a community detection algorithm to obtain the community partition results of the networks.It then comprehensively considers the internal and external density entropies and degree centrality of the target node to evaluate its influence.Experimental validation is conducted on eight networks of varying sizes through susceptible–infected–recovered(SIR)propagation experiments and network static attack experiments.The experimental results demonstrate that the proposed method outperforms five other node centrality methods under the same comparative conditions,particularly in terms of information spreading capability,thereby enhancing the accurate identification of critical nodes in networks.展开更多
Objective:To investigate the dynamic regulation of self-assembled aggregations(SAA)in Coptidis Rhizoma decoction on the permeability of intestinal tissue and the mechanism underlying.Methods:The effects of SAA on berb...Objective:To investigate the dynamic regulation of self-assembled aggregations(SAA)in Coptidis Rhizoma decoction on the permeability of intestinal tissue and the mechanism underlying.Methods:The effects of SAA on berberine(Ber)absorption were respectively analyzed in an in situ intestinal perfusion model and in an Ussing Chamber jejunum model with or without Peyer’s patches(PPs).The expression levels of ZO-1,Occludin and Claudin-1 were detected by immunofluorescence to evaluate the tight junction(TJ)between intestinal epithelium cells.The expression levels of T-box-containing protein expressed in T cells,signal transducers and activators of tranion-6,retinoic acid receptor-related orphan receptor ct and forkhead box P3 in PPs were detected by the reverse transcription-polymerase chain reaction and the secretions of interferon-c(IFN-c),interleukin-4(IL-4),interleukin-17(IL-17)and transforming growth factor-b(TGF-b)in PPs were evaluated by immunohistochemistry,to reflect the differentiation of T lymphocyte in PPs to helper T(Th)cell 1,Th2,Th17 and regulatory T(Treg)cell.To confirm the correlation between SAA in Coptidis Rhizoma decoction,PPs-associated immunity and intestinal epithelium permeability,SAA were administrated on an Ussing Chamber jejunum model with immunosuppressed PPs and evaluated its influences on intestinal tissue permeability and TJ proteins expression.Results:SAA in Coptidis Rhizoma decoction could dose-dependently promote Ber absorption in jejunum segment,with the participation of PPs.The dose-dependent and dynamical regulations of SAA on permeability of intestinal tissue and TJ proteins expression level between intestinal epithelium cells occurred along with the dynamically changed T lymphocyte differentiation and immune effectors secretion in PPs.The administration of SAA on immunosuppressed PPs exhibited dose-dependent PPs activation,inducing dynamic promotion on intestinal tissue permeability and inhibition on TJ proteins expression.Conclusion:SAA can improve the Ber absorption in small intestine,through the PPs-associated immunity induced dynamic regulation on intestinal tissue permeability and TJ proteins expression.These findings might enlighten the research of traditional Chinese medicine decoction.展开更多
基金supported by the National Natural Science Foundation of China(31871269 and 32270712)the Hubei Provincial Natural Science Foundation of China(2019CFA014)a starting research grant for High-level Talents from Guangxi University.
文摘Translational regulation is a critical step in the process of gene expression and governs the synthesis of proteins from mRNAs.Many studies have revealed translational regulation in plants in response to various environmental stimuli.However,there have been no studies documenting the comprehensive landscape of translational regulation and allele-specific translational efficiency in multiple plant tissues,especially those of rice,a main staple crop that feeds nearly half of the world’s population.Here we used RNA sequencing and ribosome profiling data to analyze the transcriptome and translatome of an elite hybrid rice,Shanyou 63(SY63),and its parental varieties Zhenshan 97 and Minghui 63.The results revealed that gene expression patterns varied more among tissues than among varieties at the transcriptional and translational levels.We identified 3392 upstream open reading frames(uORFs),and the uORF-containing genes were enriched in transcription factors.Only 668 of 13492 long non-coding RNAs could be translated into peptides.Finally,we discovered numerous genes with allele-specific translational efficiency in SY63 and demonstrated that some cis-regulatory elements may contribute to allelic divergence in translational efficiency.Overall,these findings may improve our understanding of translational regulation in rice and provide information for molecular breeding research.
基金Project supported by the National Natural Science Foundation of China(Grant No.61803264)。
文摘In recent years,exploring the relationship between community structure and node centrality in complex networks has gained significant attention from researchers,given its fundamental theoretical significance and practical implications.To address the impact of network communities on target nodes and effectively identify highly influential nodes with strong propagation capabilities,this paper proposes a novel influential spreaders identification algorithm based on density entropy and community structure(DECS).The proposed method initially integrates a community detection algorithm to obtain the community partition results of the networks.It then comprehensively considers the internal and external density entropies and degree centrality of the target node to evaluate its influence.Experimental validation is conducted on eight networks of varying sizes through susceptible–infected–recovered(SIR)propagation experiments and network static attack experiments.The experimental results demonstrate that the proposed method outperforms five other node centrality methods under the same comparative conditions,particularly in terms of information spreading capability,thereby enhancing the accurate identification of critical nodes in networks.
基金supported by the National Natural Science Foundation of China(grant numbers 81874348,81303239)the Natural Science Foundation of Anhui Province(grant numbers 1908085J29)+3 种基金the Key Research and Development Plan of Anhui Province(grant number 201904b11020023)the Open Project of State Key Laboratory of Natural Medicines(grant number SKLNMKF202007)the Provincial Foundation for Excellent Young Talents of Colleges and Universities of Anhui Province(grant number gxyqZD2018052)the Anhui Provincial Department of Education(grant number KJ2018A0282)。
文摘Objective:To investigate the dynamic regulation of self-assembled aggregations(SAA)in Coptidis Rhizoma decoction on the permeability of intestinal tissue and the mechanism underlying.Methods:The effects of SAA on berberine(Ber)absorption were respectively analyzed in an in situ intestinal perfusion model and in an Ussing Chamber jejunum model with or without Peyer’s patches(PPs).The expression levels of ZO-1,Occludin and Claudin-1 were detected by immunofluorescence to evaluate the tight junction(TJ)between intestinal epithelium cells.The expression levels of T-box-containing protein expressed in T cells,signal transducers and activators of tranion-6,retinoic acid receptor-related orphan receptor ct and forkhead box P3 in PPs were detected by the reverse transcription-polymerase chain reaction and the secretions of interferon-c(IFN-c),interleukin-4(IL-4),interleukin-17(IL-17)and transforming growth factor-b(TGF-b)in PPs were evaluated by immunohistochemistry,to reflect the differentiation of T lymphocyte in PPs to helper T(Th)cell 1,Th2,Th17 and regulatory T(Treg)cell.To confirm the correlation between SAA in Coptidis Rhizoma decoction,PPs-associated immunity and intestinal epithelium permeability,SAA were administrated on an Ussing Chamber jejunum model with immunosuppressed PPs and evaluated its influences on intestinal tissue permeability and TJ proteins expression.Results:SAA in Coptidis Rhizoma decoction could dose-dependently promote Ber absorption in jejunum segment,with the participation of PPs.The dose-dependent and dynamical regulations of SAA on permeability of intestinal tissue and TJ proteins expression level between intestinal epithelium cells occurred along with the dynamically changed T lymphocyte differentiation and immune effectors secretion in PPs.The administration of SAA on immunosuppressed PPs exhibited dose-dependent PPs activation,inducing dynamic promotion on intestinal tissue permeability and inhibition on TJ proteins expression.Conclusion:SAA can improve the Ber absorption in small intestine,through the PPs-associated immunity induced dynamic regulation on intestinal tissue permeability and TJ proteins expression.These findings might enlighten the research of traditional Chinese medicine decoction.
