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
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
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
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
Most extant angiosperms belong to Mesangiospermae(eudicots,monocots,magnoliids,Chloranthales,and Ceratophyllales).Resolving the evolutionary relationships among these five lineages is essential for understanding the e...Most extant angiosperms belong to Mesangiospermae(eudicots,monocots,magnoliids,Chloranthales,and Ceratophyllales).Resolving the evolutionary relationships among these five lineages is essential for understanding the early diversification of angiosperms.However,the rapid early diversification of angiosperms within a short geological period complicates the untangling of phylogenetic relationships among these Mesangiospermae lineages.Here,we used 177 publicly available angiosperm genomes to reconstruct the phylogeny of Mesangiospermae using multiple orthology inference approaches,character coding schemes,and data filtering criteria.We further investigated the potential causes of phylogenetic discordance and inferred phylogenetic networks to explore reticulation events among the five Mesangiospermae lineages.Coalescent simulation analyses suggested that a combination of incomplete lineage sorting and hybridization could explain the extensive discordance among nuclear genes in the Mesangiospermae backbone.Cytonuclear discordance was also observed among the five Mesangiospermae lineages,likely resulting from ancient hybridization.Furthermore,systematic errors in species network inference cannot be excluded.Our findings indicate that deep phylogenetic discordances among the five Mesangiospermae lineages are shaped by multiple factors,particularly pervasive ancient hybridization.展开更多
What are the origins,historical development,and lineages of the reincarnation system of Living Buddhas in Tibetan Buddhism?What kind of academic framework is"Han-Tibetan Buddhist Studies"?In an interview wit...What are the origins,historical development,and lineages of the reincarnation system of Living Buddhas in Tibetan Buddhism?What kind of academic framework is"Han-Tibetan Buddhist Studies"?In an interview with this journal,Professor Shen Weirong ofTsinghua University discusses these issues on the basis of his research.展开更多
Lin Shuran and her husband Fang Chuxiang are exceptional artists who are often mentioned together when talking about contemporary Lingnan art.Compared to her husband’s fame in the field of flower-andbird painting,Lin...Lin Shuran and her husband Fang Chuxiang are exceptional artists who are often mentioned together when talking about contemporary Lingnan art.Compared to her husband’s fame in the field of flower-andbird painting,Lin shows unique artistic sensitivity as a female inheritor of the Lingnan School and quietly preserves the cultural lineage of Lingnan painting.展开更多
Germinal matrix hemorrhage in preterm neonates often leads to white matter injury,contributing to long-term neurodevelopmental impairments.As resident brain immune cells,microglia play a complex role in injury respons...Germinal matrix hemorrhage in preterm neonates often leads to white matter injury,contributing to long-term neurodevelopmental impairments.As resident brain immune cells,microglia play a complex role in injury response,including inflammation and repair.Although colony-stimulating factor 1 receptor inhibitors such as PLX5622 enable the selective depletion of microglia,their therapeutic potential in neonatal germinal matrix hemorrhage remains underexplored.Here,we used a collagenase-induced germinal matrix hemorrhage model in postnatal day 5 mice,and intraperitoneally administered PLX562272 hours post-germinal matrix hemorrhage to achieve targeted,temporary microglial depletion during the peak injury response.We then assessed the effects of this delayed intervention on oligodendrocyte lineage cell maturation,white matter integrity,and neurobehavioral outcomes.Additionally,RNA sequencing data from a germinal matrix hemorrhage rat model were analyzed using weighted gene co-expression network analysis to identify the critical phases for interventions.RNA sequencing data revealed a critical period in which key synaptic functions declined while immune responses intensified post-germinal matrix hemorrhage,thus pinpointing the critical response phases for potential interventions.Delayed PLX5622 treatment effectively depleted activated microglia,protecting against white matter injury and enhancing oligodendrocyte lineage cell maturation and myelination in subcortical white matter regions.Moreover,magnetic resonance imaging analysis revealed reduced brain lesion volumes in treated mice.Behaviorally,PLX5622-treated mice exhibited significant improvements in motor coordination and reduced hyperactivity compared with vehicle-treated germinal matrix hemorrhage model mice.These findings suggest that,when timed to avoid interference with initial oligodendrocyte lineage cell proliferation,targeted microglial depletion with PLX5622 significantly mitigates white matter damage and improves neurobehavioral outcomes in neonatal germinal matrix hemorrhage.The present study highlights the therapeutic potential of selectively modulating microglial reactivity to support neurodevelopment in preterm infants with brain injury.展开更多
Adult-born oligodendrocytes are continuously produced in the brains of rodents.The functional role of these cells has been linked to the motor-related activities of healthy animals and is vital for acquiring new motor...Adult-born oligodendrocytes are continuously produced in the brains of rodents.The functional role of these cells has been linked to the motor-related activities of healthy animals and is vital for acquiring new motor skills.However,the relationship between these cells and the control of motor-related activities has not been investigated in pathological conditions.Therefore,the aim of this study is to investigate the role of oligodendrocytes in depression-related motor deficits and the effects of training.Psychomotor retardation is a key symptom of depression.Consistent with the impairments observed in rodent motor performance,the proliferation and activation of adult-born oligodendrocytes are altered in a corticosterone-induced stress paradigm.Therapeutic rotarod training can alleviate these symptoms by reversing the aforementioned changes.Notably,these alterations are particularly pronounced in layer I of the motor cortex.Thus,this study provides evidence of the potential functional involvement of adult-born oligodendrocytes in the motor impairments observed in the depressed animals.Additionally,it offers preliminary results for further investigation into layer I of the motor cortex in relation to these pathological conditions.展开更多
The Saccostrea mordax Gould,1850 is a typical intertidal species,whose genetic differentiation is influenced by various factors,including geological and climatic changes.To explore the genetic structure and historical...The Saccostrea mordax Gould,1850 is a typical intertidal species,whose genetic differentiation is influenced by various factors,including geological and climatic changes.To explore the genetic structure and historical population characteristics of Saccostrea mordax,we sequenced the mitochondrial cytochrome c oxidase subunit I(COI)gene from 58 specimens sampled from four locations in the western Pacific.Additionally,103 individuals from the Persian Gulf and western Pacific(from databases)were included for phylogenetic analysis.The Bayesian Inference tree showed that all specimens were divided into two clades,i.e.,the Persian Gulf population and the western Pacific population.Spatial molecular variance analysis indicated significant genetic differentiation between the two populations,and isolation by distance analysis revealed a positive correlation between genetic differentiation and geographic distance.Neutrality tests and Bayesian Skyline Plot suggested that both populations underwent expansions during the late Pleistocene.This study revealed the population history of Saccostrea mordax and described a new lineage,Saccostrea mordax lineage D,providing a foundation for understanding oyster biodiversity formation and genetic resource conservation.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
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 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(32370228 and W2511024)(B.Z.)the Natural Science Foundation of Jiangsu Province(BK20250004)(B.Z.)+3 种基金the Collaborative Innovation Center for Modern Crop Production co-sponsored by the Province and Ministry(B.Z.)the Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD)(B.Z.)the Postdoctoral Fellowship Program of the China Postdoctoral Science Foundation(CPSF)(GZC20240730)(X.M.)the Jiangsu Funding Program for Excellent Postdoctoral Talent(2024ZB023)(X.M.).
文摘Most extant angiosperms belong to Mesangiospermae(eudicots,monocots,magnoliids,Chloranthales,and Ceratophyllales).Resolving the evolutionary relationships among these five lineages is essential for understanding the early diversification of angiosperms.However,the rapid early diversification of angiosperms within a short geological period complicates the untangling of phylogenetic relationships among these Mesangiospermae lineages.Here,we used 177 publicly available angiosperm genomes to reconstruct the phylogeny of Mesangiospermae using multiple orthology inference approaches,character coding schemes,and data filtering criteria.We further investigated the potential causes of phylogenetic discordance and inferred phylogenetic networks to explore reticulation events among the five Mesangiospermae lineages.Coalescent simulation analyses suggested that a combination of incomplete lineage sorting and hybridization could explain the extensive discordance among nuclear genes in the Mesangiospermae backbone.Cytonuclear discordance was also observed among the five Mesangiospermae lineages,likely resulting from ancient hybridization.Furthermore,systematic errors in species network inference cannot be excluded.Our findings indicate that deep phylogenetic discordances among the five Mesangiospermae lineages are shaped by multiple factors,particularly pervasive ancient hybridization.
文摘What are the origins,historical development,and lineages of the reincarnation system of Living Buddhas in Tibetan Buddhism?What kind of academic framework is"Han-Tibetan Buddhist Studies"?In an interview with this journal,Professor Shen Weirong ofTsinghua University discusses these issues on the basis of his research.
文摘Lin Shuran and her husband Fang Chuxiang are exceptional artists who are often mentioned together when talking about contemporary Lingnan art.Compared to her husband’s fame in the field of flower-andbird painting,Lin shows unique artistic sensitivity as a female inheritor of the Lingnan School and quietly preserves the cultural lineage of Lingnan painting.
基金supported by the National Key Research and Development Program of China,No.2022YFC2704801(to CZhu)the National Natural Science Foundation of China,Nos.U21A20347(to CZhu),82203969(to YX),82371472(to XZ)+3 种基金Health Commission of Henan Province,Nos.SBGJ202303039(to XZ),SBGJ202301009(to CZhu),YQRC2024018(to XZ),YQRC2024019(to YX)Henan Science and Technology Department,Nos.242102311054(to XZ),241111521300(to CZhu),GZS2023003(to XW)Swedish Research Council,Nos.2022-01019(to CZhu),2021-01950(to XW)Swedish Governmental Grants to Scientists Working in Healthcare,Nos.ALFGBG-1005209(to CZhu),ALFBG-1005257(to XW),ALFGBG-965197(to CZhu).
文摘Germinal matrix hemorrhage in preterm neonates often leads to white matter injury,contributing to long-term neurodevelopmental impairments.As resident brain immune cells,microglia play a complex role in injury response,including inflammation and repair.Although colony-stimulating factor 1 receptor inhibitors such as PLX5622 enable the selective depletion of microglia,their therapeutic potential in neonatal germinal matrix hemorrhage remains underexplored.Here,we used a collagenase-induced germinal matrix hemorrhage model in postnatal day 5 mice,and intraperitoneally administered PLX562272 hours post-germinal matrix hemorrhage to achieve targeted,temporary microglial depletion during the peak injury response.We then assessed the effects of this delayed intervention on oligodendrocyte lineage cell maturation,white matter integrity,and neurobehavioral outcomes.Additionally,RNA sequencing data from a germinal matrix hemorrhage rat model were analyzed using weighted gene co-expression network analysis to identify the critical phases for interventions.RNA sequencing data revealed a critical period in which key synaptic functions declined while immune responses intensified post-germinal matrix hemorrhage,thus pinpointing the critical response phases for potential interventions.Delayed PLX5622 treatment effectively depleted activated microglia,protecting against white matter injury and enhancing oligodendrocyte lineage cell maturation and myelination in subcortical white matter regions.Moreover,magnetic resonance imaging analysis revealed reduced brain lesion volumes in treated mice.Behaviorally,PLX5622-treated mice exhibited significant improvements in motor coordination and reduced hyperactivity compared with vehicle-treated germinal matrix hemorrhage model mice.These findings suggest that,when timed to avoid interference with initial oligodendrocyte lineage cell proliferation,targeted microglial depletion with PLX5622 significantly mitigates white matter damage and improves neurobehavioral outcomes in neonatal germinal matrix hemorrhage.The present study highlights the therapeutic potential of selectively modulating microglial reactivity to support neurodevelopment in preterm infants with brain injury.
基金supported by Hong Kong Health and Medical Research Fund,No.02133206(to KFS).
文摘Adult-born oligodendrocytes are continuously produced in the brains of rodents.The functional role of these cells has been linked to the motor-related activities of healthy animals and is vital for acquiring new motor skills.However,the relationship between these cells and the control of motor-related activities has not been investigated in pathological conditions.Therefore,the aim of this study is to investigate the role of oligodendrocytes in depression-related motor deficits and the effects of training.Psychomotor retardation is a key symptom of depression.Consistent with the impairments observed in rodent motor performance,the proliferation and activation of adult-born oligodendrocytes are altered in a corticosterone-induced stress paradigm.Therapeutic rotarod training can alleviate these symptoms by reversing the aforementioned changes.Notably,these alterations are particularly pronounced in layer I of the motor cortex.Thus,this study provides evidence of the potential functional involvement of adult-born oligodendrocytes in the motor impairments observed in the depressed animals.Additionally,it offers preliminary results for further investigation into layer I of the motor cortex in relation to these pathological conditions.
基金Supported by the Key R&D Program of Shandong Province(No.2023CXGC010411)the National Key R&D Program of China(Nos.2023YFD2400800,2022YFD2401301,2022FY100304)+2 种基金the National Natural Science Foundation of China(Nos.42076092,41906083,41776179)the Strategic Priority Research Program of the Chinese Academy of Sciences(No.XDB42000000)the Earmarked Fund for Modern Agro-industry Technology Research System(No.CARS-47)。
文摘The Saccostrea mordax Gould,1850 is a typical intertidal species,whose genetic differentiation is influenced by various factors,including geological and climatic changes.To explore the genetic structure and historical population characteristics of Saccostrea mordax,we sequenced the mitochondrial cytochrome c oxidase subunit I(COI)gene from 58 specimens sampled from four locations in the western Pacific.Additionally,103 individuals from the Persian Gulf and western Pacific(from databases)were included for phylogenetic analysis.The Bayesian Inference tree showed that all specimens were divided into two clades,i.e.,the Persian Gulf population and the western Pacific population.Spatial molecular variance analysis indicated significant genetic differentiation between the two populations,and isolation by distance analysis revealed a positive correlation between genetic differentiation and geographic distance.Neutrality tests and Bayesian Skyline Plot suggested that both populations underwent expansions during the late Pleistocene.This study revealed the population history of Saccostrea mordax and described a new lineage,Saccostrea mordax lineage D,providing a foundation for understanding oyster biodiversity formation and genetic resource conservation.
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.
