DEAR EDITOR,The COVID-19 pandemic caused by SARS-CoV-2 continues to pose a tremendous threat to human society. SARS-CoV-2is airborne and transmits primarily through social contact;however, whether cold chain-related t...DEAR EDITOR,The COVID-19 pandemic caused by SARS-CoV-2 continues to pose a tremendous threat to human society. SARS-CoV-2is airborne and transmits primarily through social contact;however, whether cold chain-related transmission has occurred remains highly debated(Han & Liu, 2022;Lewis,2021;Ma et al., 2021;Mallapaty et al., 2021;Pang et al.,2020;Wu et al., 2021). Here, we present a novel method and identify two transmission routes based on lineage-specific reductions in the SARS-CoV-2 evolutionary rate.展开更多
Splicing of pre-RNA is a key step in regulating eukaryotic gene expression.Most human genes undergo alternative splicing(AS),where the splice sites in a single gene can be selectively paired to produce multiple isofor...Splicing of pre-RNA is a key step in regulating eukaryotic gene expression.Most human genes undergo alternative splicing(AS),where the splice sites in a single gene can be selectively paired to produce multiple isoforms,greatly expanding the functional diversity(Pan et al.,2008;Wang et al.,2008).The regulation of AS plays a critical role in many cellular activities,such as cell differentiation.Therefore,the dysregulation of AS can lead to a variety of diseases,including cancers(Scotti and Swanson,2016).展开更多
The bacterial family Mycobacteriaceae includes pathogenic and nonpathogenic bacteria,and systematic research on their genome and phenome can give comprehensive perspectives for exploring their disease mechanism.In thi...The bacterial family Mycobacteriaceae includes pathogenic and nonpathogenic bacteria,and systematic research on their genome and phenome can give comprehensive perspectives for exploring their disease mechanism.In this study,the pheno-types of Mycobacteriaceae were inferred from available phenomic data,and 82 microbial phenotypic traits were recruited as data elements of the microbial phenome.This Mycobacteriaceae phenome contains five categories and 20 subcategories of polyphasic phenotypes,and three categories and eight subcategories of functional phenotypes,all of which are complemen-tary to the existing data standards of microbial phenotypes.The phenomic data of Mycobacteriaceae strains were compiled by literature mining,third-party database integration,and bioinformatics annotation.The phenotypes were searchable and comparable from the website of the Mycobacteriaceae Phenome Atlas(MPA,https://www.biosi no.org/mpa/).A topological data analysis of MPA revealed the co-evolution between Mycobacterium tuberculosis and virulence factors,and uncovered potential pathogenicity-associated phenotypes.Two hundred and sixty potential pathogen-enriched pathways were found by Fisher's exact test.The application of MPA may provide novel insights into the pathogenicity mechanism and antimicrobial targets of Mycobacteriaceae.展开更多
基金supported by the National Key Research and Development Project (2020YFC0847000,2021YFC0863300, 2020YFC0845900)the Strategic Priority Research Program of the Chinese Academy of Sciences (XDPB17)+1 种基金the National Natural Science Foundation of China (31100273, 91731304,31172073)Shandong Academician Workstation Program#170401 (to G.P.Z.)。
文摘DEAR EDITOR,The COVID-19 pandemic caused by SARS-CoV-2 continues to pose a tremendous threat to human society. SARS-CoV-2is airborne and transmits primarily through social contact;however, whether cold chain-related transmission has occurred remains highly debated(Han & Liu, 2022;Lewis,2021;Ma et al., 2021;Mallapaty et al., 2021;Pang et al.,2020;Wu et al., 2021). Here, we present a novel method and identify two transmission routes based on lineage-specific reductions in the SARS-CoV-2 evolutionary rate.
基金supported by the National Key Research and Development Program of China(2021YFF0703702 to G.Z.2021YFA1300503 and 2018YFA0107602 to Z.W.)+1 种基金the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB38040100 to Z.W.and XDB38030100 to G.Z.)the Starry Night Science Fund at Shanghai Institute for Advanced Study of Zhejiang University(SN-ZJU-SIAS-009 to Z.W.)。
文摘Splicing of pre-RNA is a key step in regulating eukaryotic gene expression.Most human genes undergo alternative splicing(AS),where the splice sites in a single gene can be selectively paired to produce multiple isoforms,greatly expanding the functional diversity(Pan et al.,2008;Wang et al.,2008).The regulation of AS plays a critical role in many cellular activities,such as cell differentiation.Therefore,the dysregulation of AS can lead to a variety of diseases,including cancers(Scotti and Swanson,2016).
基金supported by the National Key R&D Program of China(2021YFF0703702,2021YFC2301502,and 2018YFA0900704)the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB38030100)+1 种基金Shanghai Municipal Science and Technology Major Project(2017SHZDZX01)the Biological Resources Programme,Chinese Academy of Sciences(KFJ-BRP-017-79 and KFJ-BRP-009-001).
文摘The bacterial family Mycobacteriaceae includes pathogenic and nonpathogenic bacteria,and systematic research on their genome and phenome can give comprehensive perspectives for exploring their disease mechanism.In this study,the pheno-types of Mycobacteriaceae were inferred from available phenomic data,and 82 microbial phenotypic traits were recruited as data elements of the microbial phenome.This Mycobacteriaceae phenome contains five categories and 20 subcategories of polyphasic phenotypes,and three categories and eight subcategories of functional phenotypes,all of which are complemen-tary to the existing data standards of microbial phenotypes.The phenomic data of Mycobacteriaceae strains were compiled by literature mining,third-party database integration,and bioinformatics annotation.The phenotypes were searchable and comparable from the website of the Mycobacteriaceae Phenome Atlas(MPA,https://www.biosi no.org/mpa/).A topological data analysis of MPA revealed the co-evolution between Mycobacterium tuberculosis and virulence factors,and uncovered potential pathogenicity-associated phenotypes.Two hundred and sixty potential pathogen-enriched pathways were found by Fisher's exact test.The application of MPA may provide novel insights into the pathogenicity mechanism and antimicrobial targets of Mycobacteriaceae.
