The reconstruction of demographic history using ancient and modern genomic resources reveals extensive interactions and admixture between ancient nomadic pastoralists and the social organizations of the Chinese Centra...The reconstruction of demographic history using ancient and modern genomic resources reveals extensive interactions and admixture between ancient nomadic pastoralists and the social organizations of the Chinese Central Plain.However,the extent to which Y-chromosome genetic legacies from nomadic emperor-related ancestral lineages influence the Chinese paternal gene pool remains unclear.Here,we genotype 2717 ethnolinguistically diverse samples belonging to C2a lineages,perform whole-genome sequencing on 997 representative samples,and integrate these data with ancient genomic sequences.We reconstruct the evolutionary histories of Northern Zhou-,Qing emperor-,and pastoralist-related lineages to assess their genetic impact on modern Chinese populations.This reassembled fine-scale Ychromosome phylogeny identifies deep divergence and five Neolithic expansion events contributing differently to the formation of northern Chinese populations.Phylogeographic modeling indicates that the nomadic empires of the Northern Zhou and Qing dynasties genetically originated from the Mongolian Plateau.Phylogenetic topology and shared haplotype patterns show that three upstream ancestors of Northern Zhou(C2a1a1b1a2a1b-FGC28857),Donghu tribe(C2a1a1b1-F1756),and Qing(C2a1a3a2-F10283)emperor-related lineages expanded during the middle Neolithic,contributing significantly to genetic flow between ancient northeastern Asians and modern East Asians.Notably,this study reveals limited direct contributions of Emperor Wu of Northern Zhou’s lineages to modern East Asians.展开更多
Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the pathogen responsible for coronavirus disease 2019(COVID-19),continues to evolve,giving rise to more variants and global reinfections.Previous research ha...Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the pathogen responsible for coronavirus disease 2019(COVID-19),continues to evolve,giving rise to more variants and global reinfections.Previous research has demonstrated that barcode segments can effectively and cost-efficiently identify specific species within closely related populations.In this study,we designed and tested RNA barcode segments based on genetic evolutionary relationships to facilitate the efficient and accurate identification of SARS-CoV-2 from extensive virus samples,including human coronaviruses(HCoVs)and SARSr-CoV-2 lineages.Nucleotide sequences sourced from NCBI and GISAID were meticulously selected and curated to construct training sets,encompassing 1733 complete genome sequences of HCoVs and SARSr-CoV-2 lineages.Through genetic-level species testing,we validated the accuracy and reliability of the barcode segments for identifying SARS-CoV-2.Subsequently,75 main and subordinate species-specific barcode segments for SARS-CoV-2,located in ORF1ab,S,E,ORF7a,and N coding sequences,were intercepted and screened based on single-nucleotide polymorphism sites and weighted scores.Post-testing,these segments exhibited high recall rates(nearly 100%),specificity(almost 30%at the nucleotide level),and precision(100%)performance on identification.They were eventually visualized using one and two-dimensional combined barcodes and deposited in an online database(http://virusbarcodedatabase.top/).The successful integration of barcoding technology in SARS-CoV-2 identification provides valuable insights for future studies involving complete genome sequence polymorphism analysis.Moreover,this cost-effective and efficient identification approach also provides valuable reference for future research endeavors related to virus surveillance.展开更多
Objective To learn the rabies genome molecular characteristics and compare the difference of China rabies lineages. Methods The complete genomes of 12 strains from different China rabies lineages were amplified and se...Objective To learn the rabies genome molecular characteristics and compare the difference of China rabies lineages. Methods The complete genomes of 12 strains from different China rabies lineages were amplified and sequenced, and all the China street strain genomes （total 43）, Arctic and Arctic-like genomes were aligned using ClustalX2, the genome homologies were analyzed using MegAlign software, and the phylogenetic trees were constructed by MEGA 5. Results First Arctic-like rabies genome in China （CO, H1202D） was reported, and we supplemented the rabies genome data of China, ensuring at least one genome was available in each China lineage. The genome size of China V （11908nt） is obviously shorter than other lineages＇ （11923-11925nt） for the difference of N-P non-coding regions. Among different lineages, the genome homologies are almost under 90%. CQH1202D （China IV lineage） has close relationship with strains from South Korea and they share about 95% genome similarities. Conclusion The molecular characteristics of 6 different China rabies lineages were compared and analyzed from genome level, which benefits for continued comprehensive rabies surveillance, rabies prevention and control in China.展开更多
Avian infectious bronchitis(IB)is a highly contagious infectious disease caused by infectious bronchitis virus(IBV),which is prevalent in many countries worldwide and causes serious harm to the poultry industry.At pre...Avian infectious bronchitis(IB)is a highly contagious infectious disease caused by infectious bronchitis virus(IBV),which is prevalent in many countries worldwide and causes serious harm to the poultry industry.At present,many commercial IBV vaccines have been used for the prevention and control of IB;however,IB outbreaks occur frequently.In this study,two new strains of IBV,SX/2106 and SX/2204,were isolated from two flocks which were immunized with IBV H120 vaccine in central China.Phylogenetic and recombination analysis indicated that SX/2106,which was clustered into the GI-19 lineage,may be derived from recombination events of the GI-19 and GI-7 strains and the LDT3-A vaccine.Genetic analysis showed that SX/2204 belongs to the GVI-1 lineage,which may have originated from the recombination of the GI-13 and GVI-1 strains and the H120 vaccine.The virus cross-neutralization test showed that the antigenicity of SX/2106 and SX/2204 was different from H120.Animal experiments found that both SX/2106 and SX/2204 could replicate effectively in the lungs and kidneys of chickens and cause disease and death,and H120 immunization could not provide effective protection against the two IBV isolates.It is noteworthy that the pathogenicity of SX/2204 has significantly increased compared to the GVI-1 strains isolated previously,with a mortality rate up to 60%.Considering the continuous mutation and recombination of the IBV genome to produce new variant strains,it is important to continuously monitor epidemic strains and develop new vaccines for the prevention and control of IBV epidemics.展开更多
The mitochondrial genome is a prominent research topic due to its indispensable role in organisms and its application in many research disciplines.However,few studies have investigated intraspecies mitogenomic variati...The mitochondrial genome is a prominent research topic due to its indispensable role in organisms and its application in many research disciplines.However,few studies have investigated intraspecies mitogenomic variation.In this study,69 mitogenomes of the Black-throated Tit(Aegithalos concinnus)were assembled and annotated from a large number of short reads generated using high-throughput sequencing technology.Comparative analyses revealed that mitogenomic characteristics such as length,gene and nucleotide composition,codon usage,and duplicated control regions were relatively conserved despite substantial intraspecies morphological changes.Yet,all the individuals from the subspecies A.c.iredalei had one more nucleotide in the 12S rRNA than the other studied subspecies.Phylogenetic analyses showed five distinct lineages based on the complete mitogenomes and the 13 combined protein-coding genes,whereas only four lineages were observed when using the duplicate control regions.Most interestingly,each lineage had both copies of the control regions of the comprising individuals,indicating that the paralogous control regions were more similar than the orthologous sequences from the distinct lineages.This suggested the control regions had undergone concerted evolution.The Black-throated Tit has complex evolutionary history and needs further investigating the taxonomic status of these lineages,as well as the underlying evolutionary processes.Our findings call for more research on intraspecies mitogenomic variation.展开更多
While Influenza B viruses currently circulating worldwide are of two distinct evolutionary hemagglutinin lineages, current trivalent inactivated influenza virus vaccines (TIV) contain only a single component. Single d...While Influenza B viruses currently circulating worldwide are of two distinct evolutionary hemagglutinin lineages, current trivalent inactivated influenza virus vaccines (TIV) contain only a single component. Single doses of TIV containing B antigen of B/Florida/4/2006 (Yamagata-like) or B/Brisbane/60/2008 (Victoria-like) were administered during 2008/2009 and 2009/2010 influenza seasons, respectively. The objective of this study was to evaluate the immunological response against different lineages of B antigens in school-aged children. A non-randomized sero-epidemiological study was conducted and the immunogenicity responses based on sero-protection rate and geometric mean titre ratio (GMTR) of hemagglutination inhibition (HI) antibodies were measured before and after immunization as well as post-influenza season. Our results suggested that school-aged children under the age of 9 years receiving TIV vaccination induced and retained higher level of sero-protection rate (66.7% and 69% for the 2008-09 and 2009-10 season, respectively) to the homologous lineage than the heterologous lineage post-vaccination (19.4% and 27.6% for the 2008-09 and 2009-10 season, respectively). The need for the quadrivalent TIV by including both lineages of influenza B viruses is recommended in this study, particularly for children under the age of 9 years.展开更多
Human embryonic development is orchestrated by a sophisticated network of cell-cell communication and molecular interactions.Intercellular crosstalk and specific signal stimuli play crucial roles in shaping distinct c...Human embryonic development is orchestrated by a sophisticated network of cell-cell communication and molecular interactions.Intercellular crosstalk and specific signal stimuli play crucial roles in shaping distinct cell lineages,essential for cell fate determination and lineage identity maintenance[1].Here,to address challenges posed by the scarcity and potential ethical concerns of human embryo resources.展开更多
All eukaryotic genomes have genes with introns in variable sizes.As far as spliceosomal introns are concerned,there are at least three basic parameters to stratify introns across diverse eukaryotic taxa:size,number,an...All eukaryotic genomes have genes with introns in variable sizes.As far as spliceosomal introns are concerned,there are at least three basic parameters to stratify introns across diverse eukaryotic taxa:size,number,and sequence context.The number parameter is highly variable in lower eukaryotes,especially among protozoan and fungal species,which ranges from less than4%to 78%of the genes.Over greater evolutionary time scales,the number parameter undoubtedly increases as observed in higher plants and higher vertebrates,reaching greater than 12.5 exons per gene in average among mammalian genomes.The size parameter is more complex,where multiple modes appear at work.Aside from intronless genes,there are three other types of intron-containing genes:half-sized,minimal,and size-expandable introns.The half-sized introns have only been found in a limited number of genomes among protozoan and fungal lineages and the other two types are prevalent in all animal and plant genomes.Among the size-expandable introns,the sizes of plant introns are expansion-limited in that the large introns exceeding 1000 bp are fewer in numbers and transposon-free as compared to the large introns among animals,where the larger introns are filled with transposable elements and appear expansion-flexible,reaching several kilobasepairs(kbp)and even thousands of kbp in size.Most of the intron parameters can be studied as signatures of the specific splicing machineries of different eukaryotic lineages and are highly relevant to the regulation of gene expression and functionality.In particular,the transcription-splicing-export coupling of eukaryotic intron dispensing leads to a working hypothesis that all intron parameters are evolved to be efficient and function-related in processing and routing the spliced transcripts.展开更多
Background:Cell replacement therapy has been envisioned as a promising treatment for neurodegenerative diseases.Due to the ethical concerns of ESCs-derived neural progenitor cells(NPCs)and tumorigenic potential of iPS...Background:Cell replacement therapy has been envisioned as a promising treatment for neurodegenerative diseases.Due to the ethical concerns of ESCs-derived neural progenitor cells(NPCs)and tumorigenic potential of iPSCs,reprogramming of somatic cells directly into multipotent NPCs has emerged as a preferred approach for cell transplantation.Methods:Mouse astrocytes were reprogrammed into NPCs by the overexpression of transcription factors(TFs)Foxg1,Sox2,and Brn2.The generation of subtypes of neurons was directed by the force expression of cell-type specific TFs Lhx8 or Foxa2/Lmx1a.Results:Astrocyte-derived induced NPCs(AiNPCs)share high similarities,including the expression of NPC-specific genes,DNA methylation patterns,the ability to proliferate and differentiate,with the wild type NPCs.The AiNPCs are committed to the forebrain identity and predominantly differentiated into glutamatergic and GABAergic neuronal subtypes.Interestingly,additional overexpression of TFs Lhx8 and Foxa2/Lmx1a in AiNPCs promoted cholinergic and dopaminergic neuronal differentiation,respectively.Conclusions:Our studies suggest that astrocytes can be converted into AiNPCs and lineage-committed AiNPCs can acquire differentiation potential of other lineages through forced expression of specific TFs.Understanding the impact of the TF sets on the reprogramming and differentiation into specific lineages of neurons will provide valuable strategies for astrocyte-based cell therapy in neurodegenerative diseases.展开更多
The genotyping methods of Mycobacterium tuberculosis would dramatically improve our understanding of the molecular epidemiology of tuberculosis. 3,929 isolates, from a National Survey of Drug-Resistant Tuberculosis in...The genotyping methods of Mycobacterium tuberculosis would dramatically improve our understanding of the molecular epidemiology of tuberculosis. 3,929 isolates, from a National Survey of Drug-Resistant Tuberculosis in 2007 in China, were successfully genotyped by large sequence polymorphisms and 15 loci variable number tandem repeats. We found that 2,905(2,905/3,929, 73.9%) cases belonged to Lineage 2, dominated in the east and central regions, 975 cases(975/3,929, 24.8%) were Lineage 4, highly prevailed in the west regions, and 36 and 13 cases were Lineage 3 and Lineage 1, respectively. We also explored the associations between lineages(Lineage 2 vs. Lineage 4) and clinical characteristics by logistic regression. For Lineage 2, the risk factors were Han-ethnicity population and fever. However, for Lineage 4, they were occupation(farmer), and degree of education(non-literate). Fully understanding of the distribution of Mycobacterium tuberculosis lineage and its risk factors would play a critical role in tuberculosis prevention, control, and treatment.展开更多
Mesenchymal stem cells(MSCs)have emerged as a highly promising strategy in regenerative medicine due to their self-renewal,pluripotency and immunomodulatory properties.MSCs are nonhematopoietic,multipotent stem cells ...Mesenchymal stem cells(MSCs)have emerged as a highly promising strategy in regenerative medicine due to their self-renewal,pluripotency and immunomodulatory properties.MSCs are nonhematopoietic,multipotent stem cells that can differentiate into various mesodermal lineages and modulate the immune system.The therapeutic potential of MSCs from different tissues has been widely explored in preclinical models and clinical trials for human diseases,ranging from autoimmune diseases and inflammatory disorders to neurodegenerative diseases and orthopedic injuries.The therapeutic effects of MSCs can be mediated through the release of bioactive molecules,including growth factors,cytokines,and extracellular vesicles,which play crucial roles in modulating the local cellular environment,promoting tissue repair,angiogenesis,and cell survival,and exerting anti-inflammatory effects.MSCs can also interact with various immune cells,such as T cells,B cells,dendritic cells,and macrophages,modulating the immune response through both direct cell‒cell interactions and the release of immunoregulatory molecules.This review delves into the molecular mechanisms,signaling pathways,and regulatory factors that underpin the therapeutic effects of MSCs.This review also highlights the clinical applications and challenges associated with the use of MSC-based drugs to promote the safety and efficacy of MSC-based therapies.Overall,this comprehensive review provides valuable insights into the current state of MSC research and its potential for transforming the field of regenerative medicine as well as immune-mediated inflammatory diseases.展开更多
Human parainfluenza viruses(HPIV)are common viral pathogens in acute respiratory infection(ARI).We aimed to describe the epidemiological and molecular characteristics of HPIV from ARI patients.This cross-sectional stu...Human parainfluenza viruses(HPIV)are common viral pathogens in acute respiratory infection(ARI).We aimed to describe the epidemiological and molecular characteristics of HPIV from ARI patients.This cross-sectional study was conducted using respiratory samples from 9,696 ARI patients between 2016 and 2020 in southern China.All samples were analyzed by quantitative real-time polymerase chain reaction to determine the presence of HPIV and other common respiratory viruses.Descriptive statistics were performed to determine the temporal and population distribution of HPIV.The fulllength hemagglutinin-neuraminidase(HN)gene of HPIV3-positive samples was sequenced for phylogenetic analysis.A total of 577(6.0%)patients tested positive for HPIV,with HPIV3 being the predominant serotype,accounting for 46.8%of cases.Notably,66.0%of these HPIV-positive cases were children aged 0-2 years.The prevalence of HPIV infections showed a decreased trend and altered peak during 2016-2020.Cough,fever,sputum production,and rhinorrhea were common respiratory symptoms in HPIV-positive patients.The majority of cases had pneumonia(63.4%).Human rhinovirus(HRV)and human coronavirus(HCoV)were the most common coinfection viruses in HPIV-positive cases,with proportions of 20.1%and 14.4%,respectively.Phylogenetic analysis revealed that the predominant lineage of HPIV3 was C3f(86.0%),followed by lineage C3a(8.0%),C3d(4.0%),and C3b(2.0%).These findings help to better understand the epidemiology of HPIV,and improve public health strategies to prevent and control HPIV infections in southern China.展开更多
Based on the study of two Early Pleistocene human skulls found in Yunxian County,Hubei Province,China,Ji et al.(2024)suggested that Homo orientalis was the common ancestor of the sapiens lineage and the longi lineage,...Based on the study of two Early Pleistocene human skulls found in Yunxian County,Hubei Province,China,Ji et al.(2024)suggested that Homo orientalis was the common ancestor of the sapiens lineage and the longi lineage,and proposed that both the two lineages originated from East Asia.We further proposed that Genus Homo should be divided into two subgenera:Subgenus Homo and Subgenus Parahomo.All members of the sapiens lineage would be assigned to Subgenus Homo,and all members of the longi lineage would be grouped into Subgenus Parahomo.Homo(Parahomo)heidelbergensis and Homo(Parahomo)neanderthalensis also were the members of the longi lineage,an evolutionary branch spreaded from East Asia to Africa and Europe more than 600,000 years ago.This paper mainly makes an introduction to the speciation,classification and phylogeny of the longi lineage.The longi lineage and the sapiens lineage are″sister group″relationship,but the longi lineage is an extinct lineage,having nothing to do with our modern people.展开更多
Decades of research asserted that the oligodendroglial lineage comprises two cell types:oligodendrocyte precursor cells and oligodendrocytes.However,recent studies employing single-cell RNA sequencing techniques have ...Decades of research asserted that the oligodendroglial lineage comprises two cell types:oligodendrocyte precursor cells and oligodendrocytes.However,recent studies employing single-cell RNA sequencing techniques have uncovered novel cell states,prompting a revision of the existing terminology.Going forward,the oligodendroglial lineage should be delineated into five distinct cell states:oligodendrocyte precursor cells,committed oligodendrocyte precursor cells,newly formed oligodendrocytes,myelin-forming oligodendrocytes,and mature oligodendrocytes.This new classification system enables a deeper understanding of the oligodendroglia in both physiological and pathological contexts.Adopting this uniform terminology will facilitate comparison and integration of data across studies.This,including the consolidation of findings from various demyelinating models,is essential to better understand the pathogenesis of demyelinating diseases.Additionally,comparing injury models across species with varying regenerative capacities can provide insights that may lead to new therapeutic strategies to overcome remyelination failure.Thus,by standardizing terminology and synthesizing data from diverse studies across different animal models,we can enhance our understanding of myelin pathology in central nervous system disorders such as multiple sclerosis,Alzheimer's disease,and amyotrophic lateral sclerosis,all of which involve oligodendroglial and myelin dysfunction.展开更多
The crosstalk between megakaryocytic lineage cells and the skeletal system has just begun to be explored but remains largely elusive.Using conditional gene knockout mouse models,we demonstrated that loss of Beclin 1(B...The crosstalk between megakaryocytic lineage cells and the skeletal system has just begun to be explored but remains largely elusive.Using conditional gene knockout mouse models,we demonstrated that loss of Beclin 1(Becn1),a major regulator of mammalian autophagy,exclusively in the megakaryocytic lineage disrupted autophagy in platelets but did not compromise megakaryopoiesis or the formation and function of platelets.Unexpectedly,conditional Becn1 deletion in male mice led to a remarkable increase in bone mass with improved bone quality,in association with a decrease in sex hormone binding globulin(SHBG)and an increase in free testosterone(FT).In vivo Becn1 overexpression in megakaryocytic lineage-specific cells reduced bone mass and quality,along with an increase in SHBG and a decrease in FT.Transplantation of wild-type bone marrow cells into megakaryocytic lineage Becn1-deficient male mice restored bone mass and normalized SHBG and FT.Furthermore,bilateral orchiectomy of Becn1^(f/f);Pf4-iCre mice,which are crippled with the production of testosterone,resulted in a reduction in bone mass and quality,whereas in vivo overexpression of SHBG,specifically in the liver of Becn1^(f/f);Pf4-iCre mice,decreased FT and reduced bone mass and quality.In addition,metformin treatment,which induces SHBG expression,reduced FT and normalized bone mass in Becn1^(f/f);Pf4-iCre mice.We thus concluded that Becn1 of the megakaryocytic lineage is dispensable locally for platelet hemostasis but limits bone mass by increasing SHBG,which in turn reduces the FT of male mice.Our findings highlight a mechanism by which Becn1 from megakaryocytic lineage cells distally balances bone growth.展开更多
基金the financial support received from the National Natural Science Foundation of China(82202078)the National Social Science Foundation of China(23&ZD203)+4 种基金support for G.H.includes National Natural Science Foundation of China(82402203)the Open Project of the Key Laboratory of Forensic Genetics of the Ministry of Public Security(2022FGKFKT05)the Center for Archaeological Science of Sichuan University(23SASA01)the 1‧3‧5 Project for Disciplines of Excellence at West China Hospital,Sichuan University(ZYJC20002)the Sichuan Science and Technology Program(2024NSFSC1518).
文摘The reconstruction of demographic history using ancient and modern genomic resources reveals extensive interactions and admixture between ancient nomadic pastoralists and the social organizations of the Chinese Central Plain.However,the extent to which Y-chromosome genetic legacies from nomadic emperor-related ancestral lineages influence the Chinese paternal gene pool remains unclear.Here,we genotype 2717 ethnolinguistically diverse samples belonging to C2a lineages,perform whole-genome sequencing on 997 representative samples,and integrate these data with ancient genomic sequences.We reconstruct the evolutionary histories of Northern Zhou-,Qing emperor-,and pastoralist-related lineages to assess their genetic impact on modern Chinese populations.This reassembled fine-scale Ychromosome phylogeny identifies deep divergence and five Neolithic expansion events contributing differently to the formation of northern Chinese populations.Phylogeographic modeling indicates that the nomadic empires of the Northern Zhou and Qing dynasties genetically originated from the Mongolian Plateau.Phylogenetic topology and shared haplotype patterns show that three upstream ancestors of Northern Zhou(C2a1a1b1a2a1b-FGC28857),Donghu tribe(C2a1a1b1-F1756),and Qing(C2a1a3a2-F10283)emperor-related lineages expanded during the middle Neolithic,contributing significantly to genetic flow between ancient northeastern Asians and modern East Asians.Notably,this study reveals limited direct contributions of Emperor Wu of Northern Zhou’s lineages to modern East Asians.
基金supported by grants from Key Research&Development Project of Nanhua Biomedical Co.,Ltd.(No.H202191490139)National Natural Science Foundation of China(No.31872866)+1 种基金China Postdoctoral Science Foundation(Nos.2021M701160 and 2022M721101)Funds of Hunan university(521119400156).
文摘Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the pathogen responsible for coronavirus disease 2019(COVID-19),continues to evolve,giving rise to more variants and global reinfections.Previous research has demonstrated that barcode segments can effectively and cost-efficiently identify specific species within closely related populations.In this study,we designed and tested RNA barcode segments based on genetic evolutionary relationships to facilitate the efficient and accurate identification of SARS-CoV-2 from extensive virus samples,including human coronaviruses(HCoVs)and SARSr-CoV-2 lineages.Nucleotide sequences sourced from NCBI and GISAID were meticulously selected and curated to construct training sets,encompassing 1733 complete genome sequences of HCoVs and SARSr-CoV-2 lineages.Through genetic-level species testing,we validated the accuracy and reliability of the barcode segments for identifying SARS-CoV-2.Subsequently,75 main and subordinate species-specific barcode segments for SARS-CoV-2,located in ORF1ab,S,E,ORF7a,and N coding sequences,were intercepted and screened based on single-nucleotide polymorphism sites and weighted scores.Post-testing,these segments exhibited high recall rates(nearly 100%),specificity(almost 30%at the nucleotide level),and precision(100%)performance on identification.They were eventually visualized using one and two-dimensional combined barcodes and deposited in an online database(http://virusbarcodedatabase.top/).The successful integration of barcoding technology in SARS-CoV-2 identification provides valuable insights for future studies involving complete genome sequence polymorphism analysis.Moreover,this cost-effective and efficient identification approach also provides valuable reference for future research endeavors related to virus surveillance.
基金supported by the National Science and Technology Major Project of the Ministry of Science and Technology of China(No.2012ZX10004215)
文摘Objective To learn the rabies genome molecular characteristics and compare the difference of China rabies lineages. Methods The complete genomes of 12 strains from different China rabies lineages were amplified and sequenced, and all the China street strain genomes （total 43）, Arctic and Arctic-like genomes were aligned using ClustalX2, the genome homologies were analyzed using MegAlign software, and the phylogenetic trees were constructed by MEGA 5. Results First Arctic-like rabies genome in China （CO, H1202D） was reported, and we supplemented the rabies genome data of China, ensuring at least one genome was available in each China lineage. The genome size of China V （11908nt） is obviously shorter than other lineages＇ （11923-11925nt） for the difference of N-P non-coding regions. Among different lineages, the genome homologies are almost under 90%. CQH1202D （China IV lineage） has close relationship with strains from South Korea and they share about 95% genome similarities. Conclusion The molecular characteristics of 6 different China rabies lineages were compared and analyzed from genome level, which benefits for continued comprehensive rabies surveillance, rabies prevention and control in China.
基金supported by the National Natural Science Foundation of China(32202788)the Special Research Fund of Shanxi Agricultural University for High-level Talents,China(2021XG004)+3 种基金the Fund for Shanxi“1331 Project”,China(20211331-13)the Shanxi Province Excellent Doctoral Work Award-Scientific Research Project,China(SXBYKY2021063,SXBYKY2021005,and SXBYKY 2022014)the earmarked fund for Modern Agro-industry Technology Research System of Shanxi Province,China(2023CYJSTX15-13)the Fundamental Research Program of Shanxi Province,China(202103021224156)。
文摘Avian infectious bronchitis(IB)is a highly contagious infectious disease caused by infectious bronchitis virus(IBV),which is prevalent in many countries worldwide and causes serious harm to the poultry industry.At present,many commercial IBV vaccines have been used for the prevention and control of IB;however,IB outbreaks occur frequently.In this study,two new strains of IBV,SX/2106 and SX/2204,were isolated from two flocks which were immunized with IBV H120 vaccine in central China.Phylogenetic and recombination analysis indicated that SX/2106,which was clustered into the GI-19 lineage,may be derived from recombination events of the GI-19 and GI-7 strains and the LDT3-A vaccine.Genetic analysis showed that SX/2204 belongs to the GVI-1 lineage,which may have originated from the recombination of the GI-13 and GVI-1 strains and the H120 vaccine.The virus cross-neutralization test showed that the antigenicity of SX/2106 and SX/2204 was different from H120.Animal experiments found that both SX/2106 and SX/2204 could replicate effectively in the lungs and kidneys of chickens and cause disease and death,and H120 immunization could not provide effective protection against the two IBV isolates.It is noteworthy that the pathogenicity of SX/2204 has significantly increased compared to the GVI-1 strains isolated previously,with a mortality rate up to 60%.Considering the continuous mutation and recombination of the IBV genome to produce new variant strains,it is important to continuously monitor epidemic strains and develop new vaccines for the prevention and control of IBV epidemics.
基金financially supported by the National Natural Science Foundation of China(Grant No.32060310)a grant from the Department of Education of Guangxi.
文摘The mitochondrial genome is a prominent research topic due to its indispensable role in organisms and its application in many research disciplines.However,few studies have investigated intraspecies mitogenomic variation.In this study,69 mitogenomes of the Black-throated Tit(Aegithalos concinnus)were assembled and annotated from a large number of short reads generated using high-throughput sequencing technology.Comparative analyses revealed that mitogenomic characteristics such as length,gene and nucleotide composition,codon usage,and duplicated control regions were relatively conserved despite substantial intraspecies morphological changes.Yet,all the individuals from the subspecies A.c.iredalei had one more nucleotide in the 12S rRNA than the other studied subspecies.Phylogenetic analyses showed five distinct lineages based on the complete mitogenomes and the 13 combined protein-coding genes,whereas only four lineages were observed when using the duplicate control regions.Most interestingly,each lineage had both copies of the control regions of the comprising individuals,indicating that the paralogous control regions were more similar than the orthologous sequences from the distinct lineages.This suggested the control regions had undergone concerted evolution.The Black-throated Tit has complex evolutionary history and needs further investigating the taxonomic status of these lineages,as well as the underlying evolutionary processes.Our findings call for more research on intraspecies mitogenomic variation.
文摘While Influenza B viruses currently circulating worldwide are of two distinct evolutionary hemagglutinin lineages, current trivalent inactivated influenza virus vaccines (TIV) contain only a single component. Single doses of TIV containing B antigen of B/Florida/4/2006 (Yamagata-like) or B/Brisbane/60/2008 (Victoria-like) were administered during 2008/2009 and 2009/2010 influenza seasons, respectively. The objective of this study was to evaluate the immunological response against different lineages of B antigens in school-aged children. A non-randomized sero-epidemiological study was conducted and the immunogenicity responses based on sero-protection rate and geometric mean titre ratio (GMTR) of hemagglutination inhibition (HI) antibodies were measured before and after immunization as well as post-influenza season. Our results suggested that school-aged children under the age of 9 years receiving TIV vaccination induced and retained higher level of sero-protection rate (66.7% and 69% for the 2008-09 and 2009-10 season, respectively) to the homologous lineage than the heterologous lineage post-vaccination (19.4% and 27.6% for the 2008-09 and 2009-10 season, respectively). The need for the quadrivalent TIV by including both lineages of influenza B viruses is recommended in this study, particularly for children under the age of 9 years.
基金supported by the National Key R&D Program of China(2024YFA1107000,2021YFA11020000,and 2022YFC2702200)the National Natural Science Foundation of China(32488101,32470843,32370842,32400662,and 32270850)+5 种基金the Chenguang and Shuguang Program of Shanghai Education Development Foundation and Shanghai Municipal Education Commission(24CGA22 and 22SG20)the fellowship from the China Postdoctoral Science Foundation(2023M742657 and GZB20240549)the Shanghai Post-doctoral Excellence Program(2023594)the Science and Technology Commission of Shanghai Municipality(21JC1405500)the Fundamental Research Funds for the Central Universities(22120240319 and 22120240255)the Peak Disciplines(Type IV)of Institutions of Higher Learning in Shanghai.
文摘Human embryonic development is orchestrated by a sophisticated network of cell-cell communication and molecular interactions.Intercellular crosstalk and specific signal stimuli play crucial roles in shaping distinct cell lineages,essential for cell fate determination and lineage identity maintenance[1].Here,to address challenges posed by the scarcity and potential ethical concerns of human embryo resources.
基金supported by the National Natural Science Foundation of China(31101063,31271386)National Basic Research Program of China(2010CB126604,2011CB944100,2011CB944101)
文摘All eukaryotic genomes have genes with introns in variable sizes.As far as spliceosomal introns are concerned,there are at least three basic parameters to stratify introns across diverse eukaryotic taxa:size,number,and sequence context.The number parameter is highly variable in lower eukaryotes,especially among protozoan and fungal species,which ranges from less than4%to 78%of the genes.Over greater evolutionary time scales,the number parameter undoubtedly increases as observed in higher plants and higher vertebrates,reaching greater than 12.5 exons per gene in average among mammalian genomes.The size parameter is more complex,where multiple modes appear at work.Aside from intronless genes,there are three other types of intron-containing genes:half-sized,minimal,and size-expandable introns.The half-sized introns have only been found in a limited number of genomes among protozoan and fungal lineages and the other two types are prevalent in all animal and plant genomes.Among the size-expandable introns,the sizes of plant introns are expansion-limited in that the large introns exceeding 1000 bp are fewer in numbers and transposon-free as compared to the large introns among animals,where the larger introns are filled with transposable elements and appear expansion-flexible,reaching several kilobasepairs(kbp)and even thousands of kbp in size.Most of the intron parameters can be studied as signatures of the specific splicing machineries of different eukaryotic lineages and are highly relevant to the regulation of gene expression and functionality.In particular,the transcription-splicing-export coupling of eukaryotic intron dispensing leads to a working hypothesis that all intron parameters are evolved to be efficient and function-related in processing and routing the spliced transcripts.
基金This work was supported in part by research grants from the National Basic Research Program of China(973 ProgramGrant No.2014CB965001 to JZ)Innovative Research Groups of the National Natural Science Foundation of China(#81221001 to JZ)+2 种基金Joint Research Fund for Overseas Chinese,Hong Kong and Macao Young Scientists of the National Natural Science Foundation of China(#81329002 to JZ)the National Institutes of Health:2R56NS041858-15A1(JZ),1R01NS097195-01(JZ),and R03 NS094071-01(YH)the State of Nebraska,DHHS-LB606 Stem Cell 2009-10 to JZ.
文摘Background:Cell replacement therapy has been envisioned as a promising treatment for neurodegenerative diseases.Due to the ethical concerns of ESCs-derived neural progenitor cells(NPCs)and tumorigenic potential of iPSCs,reprogramming of somatic cells directly into multipotent NPCs has emerged as a preferred approach for cell transplantation.Methods:Mouse astrocytes were reprogrammed into NPCs by the overexpression of transcription factors(TFs)Foxg1,Sox2,and Brn2.The generation of subtypes of neurons was directed by the force expression of cell-type specific TFs Lhx8 or Foxa2/Lmx1a.Results:Astrocyte-derived induced NPCs(AiNPCs)share high similarities,including the expression of NPC-specific genes,DNA methylation patterns,the ability to proliferate and differentiate,with the wild type NPCs.The AiNPCs are committed to the forebrain identity and predominantly differentiated into glutamatergic and GABAergic neuronal subtypes.Interestingly,additional overexpression of TFs Lhx8 and Foxa2/Lmx1a in AiNPCs promoted cholinergic and dopaminergic neuronal differentiation,respectively.Conclusions:Our studies suggest that astrocytes can be converted into AiNPCs and lineage-committed AiNPCs can acquire differentiation potential of other lineages through forced expression of specific TFs.Understanding the impact of the TF sets on the reprogramming and differentiation into specific lineages of neurons will provide valuable strategies for astrocyte-based cell therapy in neurodegenerative diseases.
基金supported by the National Natural Science Foundation of China(81273144)Beijing Natural Science Foundation Program and Scientific Research Key Program of Beijing Municipal Commission of Education(KZ201510025024)+1 种基金the Fundamental Research Funds for the Central Universities(2017JBM071)the China Postdoctoral Science Foundation(2017M620595)
文摘The genotyping methods of Mycobacterium tuberculosis would dramatically improve our understanding of the molecular epidemiology of tuberculosis. 3,929 isolates, from a National Survey of Drug-Resistant Tuberculosis in 2007 in China, were successfully genotyped by large sequence polymorphisms and 15 loci variable number tandem repeats. We found that 2,905(2,905/3,929, 73.9%) cases belonged to Lineage 2, dominated in the east and central regions, 975 cases(975/3,929, 24.8%) were Lineage 4, highly prevailed in the west regions, and 36 and 13 cases were Lineage 3 and Lineage 1, respectively. We also explored the associations between lineages(Lineage 2 vs. Lineage 4) and clinical characteristics by logistic regression. For Lineage 2, the risk factors were Han-ethnicity population and fever. However, for Lineage 4, they were occupation(farmer), and degree of education(non-literate). Fully understanding of the distribution of Mycobacterium tuberculosis lineage and its risk factors would play a critical role in tuberculosis prevention, control, and treatment.
基金supported,in part,by the Shenzhen Fundamental Research Program(JCYJ20220818100617036)the Shenzhen Medical Research Funds(B2402033)+3 种基金the National Natural Science Foundation of China(82261160395,82430078,82230081,82250710175,and 82004395)the Guangdong Provincial Science and Technology Innovation Council Grant(2017B030301018)the Shenzhen Key Laboratory of Cell Microenvironment Grant(ZDSYS20140509142721429)the Guangdong Provincial Bureau of Traditional Chinese Medicine Project(20212203)。
文摘Mesenchymal stem cells(MSCs)have emerged as a highly promising strategy in regenerative medicine due to their self-renewal,pluripotency and immunomodulatory properties.MSCs are nonhematopoietic,multipotent stem cells that can differentiate into various mesodermal lineages and modulate the immune system.The therapeutic potential of MSCs from different tissues has been widely explored in preclinical models and clinical trials for human diseases,ranging from autoimmune diseases and inflammatory disorders to neurodegenerative diseases and orthopedic injuries.The therapeutic effects of MSCs can be mediated through the release of bioactive molecules,including growth factors,cytokines,and extracellular vesicles,which play crucial roles in modulating the local cellular environment,promoting tissue repair,angiogenesis,and cell survival,and exerting anti-inflammatory effects.MSCs can also interact with various immune cells,such as T cells,B cells,dendritic cells,and macrophages,modulating the immune response through both direct cell‒cell interactions and the release of immunoregulatory molecules.This review delves into the molecular mechanisms,signaling pathways,and regulatory factors that underpin the therapeutic effects of MSCs.This review also highlights the clinical applications and challenges associated with the use of MSC-based drugs to promote the safety and efficacy of MSC-based therapies.Overall,this comprehensive review provides valuable insights into the current state of MSC research and its potential for transforming the field of regenerative medicine as well as immune-mediated inflammatory diseases.
基金supported by grants from the National Mega Project on Major Infectious Disease Prevention of China(2017ZX10103011)Guangdong Marine Economy Development Special Project of China(NO.GDNRC[2022]35)+1 种基金the National Natural Science Foundation of China(82171675,82101775,82071352,82341094)Guangdong Basic and Applied Basic Research Foundation of China(2022A1515011156).
文摘Human parainfluenza viruses(HPIV)are common viral pathogens in acute respiratory infection(ARI).We aimed to describe the epidemiological and molecular characteristics of HPIV from ARI patients.This cross-sectional study was conducted using respiratory samples from 9,696 ARI patients between 2016 and 2020 in southern China.All samples were analyzed by quantitative real-time polymerase chain reaction to determine the presence of HPIV and other common respiratory viruses.Descriptive statistics were performed to determine the temporal and population distribution of HPIV.The fulllength hemagglutinin-neuraminidase(HN)gene of HPIV3-positive samples was sequenced for phylogenetic analysis.A total of 577(6.0%)patients tested positive for HPIV,with HPIV3 being the predominant serotype,accounting for 46.8%of cases.Notably,66.0%of these HPIV-positive cases were children aged 0-2 years.The prevalence of HPIV infections showed a decreased trend and altered peak during 2016-2020.Cough,fever,sputum production,and rhinorrhea were common respiratory symptoms in HPIV-positive patients.The majority of cases had pneumonia(63.4%).Human rhinovirus(HRV)and human coronavirus(HCoV)were the most common coinfection viruses in HPIV-positive cases,with proportions of 20.1%and 14.4%,respectively.Phylogenetic analysis revealed that the predominant lineage of HPIV3 was C3f(86.0%),followed by lineage C3a(8.0%),C3d(4.0%),and C3b(2.0%).These findings help to better understand the epidemiology of HPIV,and improve public health strategies to prevent and control HPIV infections in southern China.
文摘Based on the study of two Early Pleistocene human skulls found in Yunxian County,Hubei Province,China,Ji et al.(2024)suggested that Homo orientalis was the common ancestor of the sapiens lineage and the longi lineage,and proposed that both the two lineages originated from East Asia.We further proposed that Genus Homo should be divided into two subgenera:Subgenus Homo and Subgenus Parahomo.All members of the sapiens lineage would be assigned to Subgenus Homo,and all members of the longi lineage would be grouped into Subgenus Parahomo.Homo(Parahomo)heidelbergensis and Homo(Parahomo)neanderthalensis also were the members of the longi lineage,an evolutionary branch spreaded from East Asia to Africa and Europe more than 600,000 years ago.This paper mainly makes an introduction to the speciation,classification and phylogeny of the longi lineage.The longi lineage and the sapiens lineage are″sister group″relationship,but the longi lineage is an extinct lineage,having nothing to do with our modern people.
基金supported by KU Leuven Internal Funding(C3/21/012)the Research Foundation Flanders(FWO G092222N)(to LM)。
文摘Decades of research asserted that the oligodendroglial lineage comprises two cell types:oligodendrocyte precursor cells and oligodendrocytes.However,recent studies employing single-cell RNA sequencing techniques have uncovered novel cell states,prompting a revision of the existing terminology.Going forward,the oligodendroglial lineage should be delineated into five distinct cell states:oligodendrocyte precursor cells,committed oligodendrocyte precursor cells,newly formed oligodendrocytes,myelin-forming oligodendrocytes,and mature oligodendrocytes.This new classification system enables a deeper understanding of the oligodendroglia in both physiological and pathological contexts.Adopting this uniform terminology will facilitate comparison and integration of data across studies.This,including the consolidation of findings from various demyelinating models,is essential to better understand the pathogenesis of demyelinating diseases.Additionally,comparing injury models across species with varying regenerative capacities can provide insights that may lead to new therapeutic strategies to overcome remyelination failure.Thus,by standardizing terminology and synthesizing data from diverse studies across different animal models,we can enhance our understanding of myelin pathology in central nervous system disorders such as multiple sclerosis,Alzheimer's disease,and amyotrophic lateral sclerosis,all of which involve oligodendroglial and myelin dysfunction.
基金supported in part by grants from the National Natural Science Foundation of China(No.81673093,No.82170227,No.91649113,No.82470165,No.82000121,No.31771640)the Jiangsu Science and Technology Department(No.SBK20200191)+1 种基金the State Key Laboratory of Radiation Medicine and Protection of Soochow University(No.GZC00201)a project funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions.
文摘The crosstalk between megakaryocytic lineage cells and the skeletal system has just begun to be explored but remains largely elusive.Using conditional gene knockout mouse models,we demonstrated that loss of Beclin 1(Becn1),a major regulator of mammalian autophagy,exclusively in the megakaryocytic lineage disrupted autophagy in platelets but did not compromise megakaryopoiesis or the formation and function of platelets.Unexpectedly,conditional Becn1 deletion in male mice led to a remarkable increase in bone mass with improved bone quality,in association with a decrease in sex hormone binding globulin(SHBG)and an increase in free testosterone(FT).In vivo Becn1 overexpression in megakaryocytic lineage-specific cells reduced bone mass and quality,along with an increase in SHBG and a decrease in FT.Transplantation of wild-type bone marrow cells into megakaryocytic lineage Becn1-deficient male mice restored bone mass and normalized SHBG and FT.Furthermore,bilateral orchiectomy of Becn1^(f/f);Pf4-iCre mice,which are crippled with the production of testosterone,resulted in a reduction in bone mass and quality,whereas in vivo overexpression of SHBG,specifically in the liver of Becn1^(f/f);Pf4-iCre mice,decreased FT and reduced bone mass and quality.In addition,metformin treatment,which induces SHBG expression,reduced FT and normalized bone mass in Becn1^(f/f);Pf4-iCre mice.We thus concluded that Becn1 of the megakaryocytic lineage is dispensable locally for platelet hemostasis but limits bone mass by increasing SHBG,which in turn reduces the FT of male mice.Our findings highlight a mechanism by which Becn1 from megakaryocytic lineage cells distally balances bone growth.
