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Molecular epidemiology of coxsackievirus A16 circulating in children in Beijing, China from 2010 to 2019

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World Journal of Pediatrics 2021年第5期17卷 508-516页

作者： Ya-Fang Hu Li-Ping Jia Fang-Yuan Yu Li-Ying Liu Qin-Wei Song Hui-Jin Dong Jie Deng Yuan Qian Lin-Qing Zhao Li Deng Hui Huang Ru-Nan Zhu Laboratory of Virology.Beijing Key Laboratory of Etiology of Viral Diseases in Children Capital Institute of Pediatrics2 Yabao RoadChaoyang DistrictBeijing 100020China Department of Clinical Laboratory Shanghai Children's HospitalShanghai Jiaotong UniversityLuding Road 355Putuo DistrictShanghai 200040China Department of Clinical Laboratory Children's Hospital of Capital Institute of Pediatrics2 Yabao RoadBeijing 100020China Department of Infectious Diseases Children's Hospital of Capital Institute of Pediatrics2 Yabao RoadBeijing 100020China

Background Coxsackievirus A16(CVA16)is one of the major etiological agents of hand,foot and mouth discase(HFMD).This study aimed to investigate the molecular epidemiology and evolutionary characteristics of *** Throat swabs were collected from children with HFMD and suspected HFMD during ***(EVs)were detected and typed by real-ime reverse transcription-polymerase chain reaction(RT-PCR)and *** genotype,evolutionary rate,the most recent common ancestor,population dynamics and selection pressure of CVA16 were analyzed based on viral protein gene(VPI)by bioinformatics *** A total of 4709 throat swabs were *** were detected in 3180 samples and 814 were CVA16 *** than 81%of CVA 16-positive children were under 5 years *** prevalence of CVA 16 showed obvious periodic fluctuations with a high level during 2010--2012 followed by an apparent decline during ***,the activities of CVA16 increased gradually during *** the Beijing CVA16 strains belonged to sub-genotype BI,and B Ib was the dominant *** B Ic strain was detected in Bejing for the first time in *** estimated mean evolutionary rate of VPI gene was 4.49x 103 substitution/site/*** gradually fixed at site-23 of VP1 since *** sites were detected under episodic positive selection,one of which(site-223)located in neutralizing linear epitope *** The dominant strains of CVA 16 belonged to clade B lb and evolved in a fast evolutionary rate during 2010-2019 in *** provide more favorable data for HFMD prevention and control,it is necessary to keep attention on molecular epidemiological and evolutionary characteristics of CVA16.

关键词： Coxsackievirus A16 genetic evolution Molecular epidemiology Phylogenetic analysis

Evidence for the paternal mitochondrial DNA in the crucian carp-like fish lineage with hybrid origin

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Science China(Life Sciences) 2020年第1期63卷 102-115页

作者： Shi Wang Ni Jiao Lu Zhao Meiwen Zhang Pei Zhou Xuexue Huang Fangzhou Hu Conghui Yang Yuqin Shu Wuhui Li Chun Zhang Min Tao Bo Chen Ming Ma Shaojun Liu State Key Laboratory of Developmental Biology of Freshwater Fish Hunan Normal UniversityChangsha 410081China College of Life Sciences Hunan Normal UniversityChangsha 410081China College of Chemistry and Chemical Engineering Hunan Normal UniversityChangsha 410081China Key Laboratory of Tropical and Subtropical Fisheries Resource Application and Cultivation Ministry of AgriculturePearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhou 510380China

In terms of taxonomic status,common carp(Cyprinus carpio,Cyprininae)and crucian carp(Carassius auratus,Cyprininae)are different species;however,in this study,a newborn homodiploid crucian carp-like fish(2n=100)(2nNCRC)lineage(F1–F3)was established from the interspecific hybridization of female common carp(2n=100)×male blunt snout bream(Megalobrama amblycephala,Cultrinae,2n=48).The phenotypes and genotypes of 2 n NCRC differed from those of its parents but were closely related to those of the existing diploid crucian *** further sequenced the whole mitochondrial(mt)genomes of the 2n NCRC lineage from F1 to *** paternal mt DNA fragments were stably embedded in the mt-genomes of F1–F3 generations of 2n NCRC to form chimeric DNA *** with this chimeric process,numerous base sites of F1–F3 generations of 2 n NCRC underwent *** of these mutation sites were consistent with the existing diploid crucian ***,the mt DNA organization and nucleotide composition of 2n NCRC were more similar to those of the existing diploid crucian carp than those of the *** inheritable chimeric DNA fragments and mutant loci in the mt-genomes of different generations of 2nNCRC provided important evidence of the mt DNA change process in the newborn lineage derived from hybridization of different *** findings demonstrated for the first time that the paternal mt DNA were transmitted into the mt-genomes of homodiploid lineage,which provided new insights into the existence of paternal mt DNA in the mt DNA inheritance.

关键词： hybridization homodiploid common carp blunt snout bream crucian carp mitochondrial genome genetic evolution

Accelerated evolution of H7N9 Subtype Influenza Virus under Vaccination Pressure

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Virologica Sinica 2021年第5期36卷 1124-1132页

作者： Yifan Wu Jingkai Hu Xuanjiang Jin Xiao Li Jinfeng Wang Mengmeng Zhang Jianglin Chen Shumin Xie Wenbao Qi Ming Liao Weixin Jia National Avian Influenza Para-Reference Laboratory(Guangzhou) College of Veterinary MedicineSouth China Agricultural UniversityGuangzhou 510642China Key Laboratory of Zoonosis Key Laboratory of Animal Vaccine DevelopmentMinistry of Agriculture and Rural AffairsGuangzhou 510642China Guangdong Laboratory for Lingnan Modern Agriculture Guangzhou 510642China National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control Guangzhou 510642China Key Laboratory of Zoonoses Prevention and Control of Guangdong Province Guangzhou 510642China

No avian H7 N9 outbreaks have occurred since the introduction of H7 N9 inactivated vaccine in the fall of ***,H7 N9 is still prevalent in *** surveil the prevalence,genetic characteristics,and antigenic changes of H7 N9,over7000 oropharyngeal and cloaca swab specimens were collected from live poultry markets and farms in 15 provinces of China from 2017 to 2019.A total of 85 influenza virus subtype H7 N9 strains were isolated and 20 representative strains were selected for genetic analysis and antigenicity *** indicated the decreased prevalence of low-pathogenic H7 N9 strains while highly-pathogenic H7 N9 strains became dominated since the introduction of *** analysis showed that strains from 2019 formed an independent small branch and were genetically distant to strains isolated in 2013–*** of key amino acid sites showed that the virus strains may adapt to the host environment evolutionally through *** analysis predicted additional potential glycosylation sites for HA and NA genes in the 2019 *** analysis of HA gene in strains isolated from 2018 to 2019 showed that there were an increased nucleotide substitution rate and an increased mutation rate in the first and second nucleotides of coding codons within the open reading *** hemagglutination inhibition(HI)assay showed that H7-Re1 and H7-Re2 exhibited a lower HI titer for isolates from 2019,while H7-Re3 and r LN79 showed a high HI *** protective effect of the vaccine decreased after15 months of ***,under vaccination pressure,the evolution of influenza virus subtype H7 N9 has accelerated.

关键词： H7N9 genetic evolution Epidemiological investigation Hemagglutination inhibition assay Vaccination pressure

Tuning Synaptic Connections Instead of Weights by genetic Algorithm in Spiking Policy Network

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Machine Intelligence Research 2024年第5期21卷 906-918页

作者： Duzhen Zhang Tielin Zhang Shuncheng Jia Qingyu Wang Bo Xu School of Artificial Intelligence University of Chinese Academy of SciencesBeijing100049China Institute of Automation Chinese Academy of Sciences(CAS)Beijing100190China Center for Excellence in Brain Science and Intelligence Technology Chinese Academy of Sciences(CAS)Shanghai200031China

Learning from interaction is the primary way that biological agents acquire knowledge about their environment and *** deep reinforcement learning(DRL)explores a computational approach to learning from interaction and has made significant progress in solving various ***,despite its power,DRL still falls short of biological agents in terms of energy *** the underlying mechanisms are not fully understood,we believe that the integration of spiking communication between neurons and biologically-plausible synaptic plasticity plays a prominent role in achieving greater energy *** this biological intuition,we optimized a spiking policy network(SPN)using a genetic algorithm as an energy-efficient alternative to *** SPN mimics the sensorimotor neuron pathway of insects and communicates through event-based *** by biological research showing that the brain forms memories by creating new synaptic connections and rewiring these connections based on new experiences,we tuned the synaptic connections instead of weights in the SPN to solve given *** results on several robotic control tasks demonstrate that our method can achieve the same level of performance as mainstream DRL methods while exhibiting significantly higher energy efficiency.

关键词： Spiking neural networks genetic evolution bio-inspired learning agent&cognitive architectures robotic control

Analysis of the diversity and function of the alleles of the rice blast resistance genes Piz-t, Pita and Pik in 24 rice cultivars

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Journal of Integrative Agriculture 2016年第7期15卷 1423-1431页

作者： WANG Yan ZHAO Jia-ming ZHANG Li-xia WANG Ping WANG Shi-wei WANG Hui WANG Xiao-xi LIU Zhi-heng ZHENG Wen-jing Plant Protection College Shenyang Agricultural University Agricultural Crops Molecular Improving Laboratory Liaoning Academy of Agricultural Sciences Department of Plant Pathology China Agricultural University

Understanding the sequence diversity of rice blast resistance genes is important for breeding new resistant rice cultivars against the rice blast fungusMagnaporthe oryzae. In this study, we selected 24 rice cultivars with different genetic back-grounds to study the alelic diversity of rice blast resistance genesPiz-t, Pitaand Pik. For Piz-t, a total of 17 alelic types were found within the 24 cultivars. Blast inoculations showed that most of the mutations can affect the function of the resistance gene. For Pita, except for the difference at the 918th amino acid, a majority of the 21 mutations were detected among the cultivars. Inoculations with blast isolates carryingAvr-Pita revealed that cultivars with mutations in other sites except for the 918th amino acid did not affect the function of thePita gene. ForPik, a total of six alelic types were found within the 24 cultivars, but ifve of them lost the function of the resistance gene. In addition, we found thatPiz-t, Pita and Pik were expressed constitutively in the 24 rice cultivars and the expression level was not related to resistance. Our results have provided the sequence diversity information of the resistance genesPiz-t, Pita and Pik among the popular rice cultivars grown in the northeast region of China. Keywords：resistance gene, avirulence gene, aleles, function, genetic evolution zae（M. oryzae）, is one of the most destructive diseases in rice production worldwide. Over the years, comprehensive studies on rice blast resistance have been conducted （Silue et al. 1992）. The resistance in newly cultivated rice cultivars to M. oryzae can be lost quickly due to the high level of instability in the genome of the fungus （Bonmanet al. 1992）. Previous studies show that cultivars with durable and broad-spectrum resistance againstM. oryzae carry multiple major resistance （R） and minor resistance genes （Liuet al. 2014）. An effective way to control rice blast disease is, therefore, to breed rice cultivars with multiple R

关键词： resistance gene avirulence gene aleles function genetic evolution

Relatively rapid evolution rates of SARS-CoV-2 spike gene at the primary stage of massive vaccination

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Biosafety and Health 2022年第4期4卷 228-233页

作者： Jing Yang Min Han Liang Wang Likui Wang Tianrui Xu Linhuan Wu Juncai Ma Gary Wong Wenjun Liu George F.Gao Yuhai Bi CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of MicrobiologyCenter for Influenza Research and Early-warning(CASCIRE)CAS-TWAS Center of Excellence for Emerging Infectious Diseases(CEEID)Chinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Department of Anatomy and Cell Biology McGill UniversityMontreal H3A0G4Canada Microbial Resource and Big Data Center Chinese National Microbiology Data Center(NMDC)Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Institut Pasteur of Shanghai Chinese Academy of SciencesShanghai 200031China

A series of stringent non-pharmacological and pharmacological interventions were implemented to contain the pandemic but the pandemic ***,vaccination breakthrough infection and reinfection in convalescent coronavirus disease 2019(COVID-19)cases have been ***,severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)variants emerged with mutations in spike(S)gene,the target of most current ***,the mutations exhibit a trend of immune escape from the *** the scientific question that if the vaccination drives genetic or antigenic drifts of SARS-CoV-2 remains *** performed correlation analyses to uncover the impacts of wide vaccination on epidemiological characteristics of *** addition,we investigated the evolutionary dynamics and genetic diversity of SARS-CoV-2 under immune pressure by utilizing the Bayesian phylodynamic inferences and the lineage entropy calculation *** found that vaccination coverage was negatively related to the infections,severe cases,and deaths of COVID-19 *** the increasing vaccination coverage,the lineage diversity of SARS-CoV-2 dampened,but the rapid mutation rates of the S gene were identified,and the vaccination could be one of the explanations for driving mutations in S ***,new epidemics resurged in several countries with high vaccination coverage,questioning their current pandemic control ***,integrated vaccination and non-pharmacological interventions are critical to control the ***,novel vaccine preparation should enhance its capabilities to curb both disease severity and infection possibility.

关键词： SARS-CoV-2 Vaccine genetic evolution genetic drift Antigenic drift Lineage divergence Epidemiological characteristics

genetic Advances in Genome and Phenotypic Characters of Domestic Dog

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Animal Husbandry and Feed Science 2020年第2期12卷 15-22页

作者： Li Jing Wan Jiusheng Chen Chao Deng Weidong Yue Rui Xiong Heli Li Liguang Kunming Police Dog Base of the Ministry of Public Security Kunming 650201China Key Laboratory of Police Dog Technology of the Ministry of Public Security Kunming 650201China School of Animal Science and Technology of Yunnan Agricultural University Kunming 650201China

Dogs represent such a rich potential resource to further understand diseases and genetic *** the genomes of three species of canine,human,and rat in terms of genome analysis,it is found that dogs are highly conservative with humans and *** special population structure of dogs makes it a good model for studying the diversity of morphology and behavior,the genetic basis of mammalian evolution,and *** article gives a brief review of recent advances in domestic dog origin and evolution,genomic structure,genetic variation in dog pheno-typic characteristics,and gene *** research results are expected to provide a better theoretical basis for canine genetic breeding re-search and provide new ideas and methods for the prevention,diagnosis and treatment of human diseases.

关键词： Domestic dog genetic evolution Genome Linkage disequilibrium Phenotypic trait genes

genetic Diversity and evolutionary Tendency Detected by Isozyme, RFLP and RAPD Markers in the Wild and Cultivated Soybean in China

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Agricultural Sciences in China 2000年第1期 48-55页

作者： Xu Donghe Soybean Research Institute Nanjing Agricultural University National Center of Soybean Improvement Ministry of Agriculture Nanjing 210095 China genetic Institute China Academy of Sciences Faculty of Agriculture Hokkaido University Sapporo 060 Japan

A large numbers of samples of wild soybean accessions and cultivated soybean landraces from various areas in China were analyzed by isozyrme, cytoplasmic DNA RFLP and nuclear DNA RAPD markers in order to reveal their genetic diversity. Greater comprehensive genetic diversity was detected in wild soybean than in cultivated soybean. The genetic plentifulness and the genetic dispersion of wild soybean were 180 (95. 2％) and 0. 2891 while those of cultivated soybean were 154(81.5％) and 0. 2091,respectively. On the most loci, especially on isozyme loci Idh1, Aph, Idh2,and Dia, cytoplasmic DNA RFLP loci cp Ⅰ , cp Ⅲ, mt Ⅳ a and mt Ⅳ b, and nuclear RAPD loci OPAP4-8, OPAP5-1, OPAP9-8 and OPAP20-8, the wild soybeans djffered remarkably from the cultivated ones in allele frequency. These markers could be used in further study on the evolution and origin of the cultivated soybean.

关键词： Wild soybean (Glycine soja Sieb. et Zucc. ) Cultivated soybean 〔Glycine max (L.)Merr.〕 genetic diversity genetic evolution

genetic Characteristics of <i>Citrus Tristeza Virus</i>Isolates from Cultivated Citrus in China Based on Coat Protein Gene

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Journal of Biosciences and Medicines 2021年第10期9卷 190-200页

作者： Yiqun Chen Xiaoshang You Bo Chen Long Yi College of Life Sciences Gannan Normal University Ganzhou China Bureau of Agriculture and Rural Affairs of Nanxiong Nanxiong China

Citrus tristeza virus (CTV) is an important citrus pathogen causing considerable economic loss to citrus production. Knowledge on genetic evolutionary of the CTV population in China remains limited. In this study, 1439 samples were collected from nine citrus-producing areas of China. The coat protein (CP) genes of CTV were amplified by RT-PCR, and sequenced to analyze the genetic evolution. Analysis of the base composition showed an AU preference pattern, with the GC content was lower than AU content. Nine CTV populations were clustered into one clade in neighbor-joining (NJ) tree, indicative of a close phylogenetic relationship among the populations in China. Analysis of molecular variation (AMOVA) revealed that 77.72% genetic variations of CTV populations were observed among populations, with an FST value of 0.223. The values of dN/dS and neutrality test of CP gene were ranged from 0.016 to 0.082 and -1.377 to 1.456, respectively, the results suggesting that all of nine CTV populations were relatively constantly maintained under purifying selection. Our study demonstrated the genetic characteristics and molecular evolution relationship of CTV populations in China, and provided a theoretical basis for scientific control of CTV.

关键词： Citrus Tristeza Virus Cultivated Citrus Coat Protein Gene genetic evolution