Taura syndrome virus(TSV) is one of the important pathogenic agents of Penaeus vannami,which causes prawn infection with serious disease in China in recent years.245 samples collected from 26 farms of Zhangzhou,Xiamen...Taura syndrome virus(TSV) is one of the important pathogenic agents of Penaeus vannami,which causes prawn infection with serious disease in China in recent years.245 samples collected from 26 farms of Zhangzhou,Xiamen,Shenzhen,Yangjiang,Ningbo and Guangzhou.were detected for TSV with RT-PCR,the positive rates were 100%,33.3%,40.7%,50% and 40%,respectively.Southern blotting and nucleotide sequencing were performed to confirm the specificity of the amplified RT-PCR products.The homology of 231bp nucleotide sequences reached 98.3%-100% when analysed and compared with the GenBank using the BLAST program.Phylogenetic analyses clustered the TSV isolates into two groups: one contained USA and Chinese Taiwan isolates;the other contained Vietnam isolate(YN1) and 21 isolates of China's Mainland.The 21 China isolates clustered into one branch,while the YN1 distributed in another branch.5 strains from Guangzhou and 2 strains from Shenzhen constituted one subcluster of the China branch.展开更多
Genotyping platforms,as critical supports for genomics,genetics,and molecular breeding,have been well implemented at national institutions/universities in developed countries and multinational seed companies that poss...Genotyping platforms,as critical supports for genomics,genetics,and molecular breeding,have been well implemented at national institutions/universities in developed countries and multinational seed companies that possess high-throughput,automatic,large-scale,and shared facilities.In this study,we integrated an improved genotyping by target sequencing(GBTS)system with capture-in-solution(liquid chip)technology to develop a multiple single-nucleotide polymorphism(mSNP)approach in which mSNPs can be captured from a single amplicon.From one 40K maize mSNP panel,we developed three types of markers(40K mSNPs,251K SNPs,and 690K haplotypes),and generated multiple panels with various marker densities(1K–40K mSNPs)by sequencing at different depths.Comparative genetic diversity analysis was performed with genic versus intergenic markers and di-allelic SNPs versus non-typical SNPs.Compared with the one-amplicon-one-SNP system,mSNPs and within-mSNP haplotypes are more powerful for genetic diversity detection,linkage disequilibrium decay analysis,and genome-wide association studies.The technologies,protocols,and application scenarios developed for maize in this study will serve as a model for the development of mSNP arrays and highly efficient GBTS systems in animals,plants,and microorganisms.展开更多
During the last decade,the generation and accumulation of petabase-scale high-throughput sequencing data have resulted in great challenges,including access to human data,as well as transfer,storage,and sharing of enor...During the last decade,the generation and accumulation of petabase-scale high-throughput sequencing data have resulted in great challenges,including access to human data,as well as transfer,storage,and sharing of enormous amounts of data.To promote data-driven biological research,the Korean government announced that all biological data generated from government-funded research projects should be deposited at the Korea BioData Station(K-BDS),which consists of multiple databases for individual data types.Here,we introduce the Korean Nucleotide Archive(KoNA),a repository of nucleotide sequence data.As of July 2022,the Korean Read Archive in KoNA has collected over 477 TB of raw next-generation sequencing data from national genome projects.To ensure data quality and prepare for international alignment,a standard operating procedure was adopted,which is similar to that of the International Nucleotide Sequence Database Collaboration.The standard operating procedure includes quality control processes for submitted data and metadata using an automated pipeline,followed by manual examination.To ensure fast and stable data transfer,a high-speed transmission system called GBox is used in KoNA.Furthermore,the data uploaded to or downloaded from KoNA through GBox can be readily processed using a cloud computing service called Bio-Express.This seamless coupling of KoNA,GBox,and Bio-Express enhances the data experience,including submission,access,and analysis of raw nucleotide sequences.KoNA not only satisfies the unmet needs for a national sequence repository in Korea but also provides datasets to researchers globally and contributes to advances in genomics.The KoNA is available at https://www.kobic.re.kr/kona/.展开更多
OBJECTIVE:To explore the mechanism of Xianglian Huazhuo formula(香连化浊方,XLHZ)blocking the development of chronic atrophic gastritis(CAG)to gastric cancer(GC)through bioinformatics analysis and in vitro.METHODS:Path...OBJECTIVE:To explore the mechanism of Xianglian Huazhuo formula(香连化浊方,XLHZ)blocking the development of chronic atrophic gastritis(CAG)to gastric cancer(GC)through bioinformatics analysis and in vitro.METHODS:Pathological morphology of gastric mucosa of rats were observed.High-throughput sequencing was used to analyze the miRNA expression profile of gastric mucosa.The miRanda,miRDB and miRWalk databases were used to predict the differential target genes.Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analysis were performed for differential target genes.Real-time quantitative reverse transcription polymerase chain reaction(qRTPCR)was used to verify the differentially expressed miRNAs and target genes.Western blot,EdU,wound healing and flow cytometry were used to observe the effect of XLHZ on epithelial-mesenchymal transition(EMT)markers,proliferation,migration,apoptosis and cell cycle of CAG cells in vitro.RESULTS:A total of five differentially expressed miRNAs and four differential target genes were screened in this study.GO analysis showed that the target genes were enriched in regulation of neuron development,regulation of transcription factor activity and regulation of RNA polymerase.KEGG pathways database differences in gene enrichment of target genes in the Wnt signaling pathway,Phospholipase D signaling pathway and mitogen-activated protein kinase signaling pathway.qRTPCR confirmed that miRNAs and its target genes were consistent with the screening results.In vitro,our study revealed that XLHZ could increase the expression of Ecadherin,decrease the expression of transforming growth factorβ1,vimentin andβ-catenin,inhibite the proliferation and migration of CAG cells,cause cell cycle arrest at G0/G1 and G2/M phase,induce the apoptosis of CAG cells,and prevent the progression of CAG to GC.CONCLUSION:This study provided a new idea for the mechanism of blocking the progression of CAG to GC by XLHZ,which may be related to the expression of miR-20a-3p,miR-320-3p,miR-34b-5p,展开更多
文摘Taura syndrome virus(TSV) is one of the important pathogenic agents of Penaeus vannami,which causes prawn infection with serious disease in China in recent years.245 samples collected from 26 farms of Zhangzhou,Xiamen,Shenzhen,Yangjiang,Ningbo and Guangzhou.were detected for TSV with RT-PCR,the positive rates were 100%,33.3%,40.7%,50% and 40%,respectively.Southern blotting and nucleotide sequencing were performed to confirm the specificity of the amplified RT-PCR products.The homology of 231bp nucleotide sequences reached 98.3%-100% when analysed and compared with the GenBank using the BLAST program.Phylogenetic analyses clustered the TSV isolates into two groups: one contained USA and Chinese Taiwan isolates;the other contained Vietnam isolate(YN1) and 21 isolates of China's Mainland.The 21 China isolates clustered into one branch,while the YN1 distributed in another branch.5 strains from Guangzhou and 2 strains from Shenzhen constituted one subcluster of the China branch.
基金This research is supported by the National Key Research and Development Program of China(2016YFD0101803 and 2017YFD0101201)the Central Public-interest Scientific Institution Basal Research Fund(Y2020PT20)+4 种基金the Agricultural Science and Technology Innovation Program(ASTIP)of the Chinese Academy of Agricultural Sciences(CAAS)(CAAS-XTCX2016009)the Key Research Area and Development Program of Guangdong Province(2018B020202008)the Shijiazhuang Science and Technology Incubation Program(191540089A)the Hebei Innovation Capability Enhancement Project(19962911D)Research activities at CIMMYT were supported by the Bill and Melinda Gates Foundation and the CGIAR Research Program MAIZE.
文摘Genotyping platforms,as critical supports for genomics,genetics,and molecular breeding,have been well implemented at national institutions/universities in developed countries and multinational seed companies that possess high-throughput,automatic,large-scale,and shared facilities.In this study,we integrated an improved genotyping by target sequencing(GBTS)system with capture-in-solution(liquid chip)technology to develop a multiple single-nucleotide polymorphism(mSNP)approach in which mSNPs can be captured from a single amplicon.From one 40K maize mSNP panel,we developed three types of markers(40K mSNPs,251K SNPs,and 690K haplotypes),and generated multiple panels with various marker densities(1K–40K mSNPs)by sequencing at different depths.Comparative genetic diversity analysis was performed with genic versus intergenic markers and di-allelic SNPs versus non-typical SNPs.Compared with the one-amplicon-one-SNP system,mSNPs and within-mSNP haplotypes are more powerful for genetic diversity detection,linkage disequilibrium decay analysis,and genome-wide association studies.The technologies,protocols,and application scenarios developed for maize in this study will serve as a model for the development of mSNP arrays and highly efficient GBTS systems in animals,plants,and microorganisms.
基金supported by the Next-generation Genome-InfraNET for the advancement of genome research and service(Grant No.2019M3C9A5069653)the Construction of biological data station(Grant No.2020M3A9I6A01036057)grants from the National Research Foundation of Korea.
文摘During the last decade,the generation and accumulation of petabase-scale high-throughput sequencing data have resulted in great challenges,including access to human data,as well as transfer,storage,and sharing of enormous amounts of data.To promote data-driven biological research,the Korean government announced that all biological data generated from government-funded research projects should be deposited at the Korea BioData Station(K-BDS),which consists of multiple databases for individual data types.Here,we introduce the Korean Nucleotide Archive(KoNA),a repository of nucleotide sequence data.As of July 2022,the Korean Read Archive in KoNA has collected over 477 TB of raw next-generation sequencing data from national genome projects.To ensure data quality and prepare for international alignment,a standard operating procedure was adopted,which is similar to that of the International Nucleotide Sequence Database Collaboration.The standard operating procedure includes quality control processes for submitted data and metadata using an automated pipeline,followed by manual examination.To ensure fast and stable data transfer,a high-speed transmission system called GBox is used in KoNA.Furthermore,the data uploaded to or downloaded from KoNA through GBox can be readily processed using a cloud computing service called Bio-Express.This seamless coupling of KoNA,GBox,and Bio-Express enhances the data experience,including submission,access,and analysis of raw nucleotide sequences.KoNA not only satisfies the unmet needs for a national sequence repository in Korea but also provides datasets to researchers globally and contributes to advances in genomics.The KoNA is available at https://www.kobic.re.kr/kona/.
基金Construction Project of National Clinical Research Base of Traditional Chinese Medicine(Science Letter[2018]No.131,State Office of Traditional Chinese Medicine)Natural Science Foundation of Hebei Province:Study on the Mechanism of Action of Traditional Chinese Medicine on Disease and Syndrome(No.H2023423001)+6 种基金Key Research Project of the Ministry of Science and Technology(No.2018YFC1704100)Key Research Project of the Ministry of Science and Technology:Li Diangui Famous Old Chinese Medicine of Traditional Chinese Medicine Academic View Characteristic,Diagnosis and Treatment Methods and Experience of Prevention and Control of Major Diseases(No.2018YFC1704102)Provincial Science and Technology Program of Hebei Province:Prevention and Treatment of Gastric Cancer by Blocking the"Inflammation-Cancer Transformation"Based on the Theory of Turbidimetric Toxicity(No.21377724D)Provincial Science and Technology Program of Hebei Province:to Study the Clinical Efficacy and Mechanism of Huazhuo Jiedu Formula in the Treatment of Chronic Atrophic Gastritis based on Epidermal Growth Factor Receptor/Mitogen Activated Protein Kinase/Extracellular Signal-Regulated Kinase Signaling Pathway(No.21377740D)Scientific Research Project of Hebei Administration of Traditional Chinese Medicine:Clinical Study of Huazhuo Jiedu Formula Blocking the Pathological Evolution of Chronic Atrophic Gastritis(No.2022026)Scientific Research Project of Hebei Administration of Traditional Chinese Medicine:Study on the Medication Rules of Spleen and Stomach Diseases of Famous Yanzhao Medical Doctors Based on Data Mining(No.2022032)Scientific Research Project of Hebei Administration of Traditional Chinese Medicine:to Explore the Mechanism of Xianglian Huazhuo Formula in the Treatment of Chronic Atrophic Gastritis based on Transcriptomics(No.2023022)。
文摘OBJECTIVE:To explore the mechanism of Xianglian Huazhuo formula(香连化浊方,XLHZ)blocking the development of chronic atrophic gastritis(CAG)to gastric cancer(GC)through bioinformatics analysis and in vitro.METHODS:Pathological morphology of gastric mucosa of rats were observed.High-throughput sequencing was used to analyze the miRNA expression profile of gastric mucosa.The miRanda,miRDB and miRWalk databases were used to predict the differential target genes.Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analysis were performed for differential target genes.Real-time quantitative reverse transcription polymerase chain reaction(qRTPCR)was used to verify the differentially expressed miRNAs and target genes.Western blot,EdU,wound healing and flow cytometry were used to observe the effect of XLHZ on epithelial-mesenchymal transition(EMT)markers,proliferation,migration,apoptosis and cell cycle of CAG cells in vitro.RESULTS:A total of five differentially expressed miRNAs and four differential target genes were screened in this study.GO analysis showed that the target genes were enriched in regulation of neuron development,regulation of transcription factor activity and regulation of RNA polymerase.KEGG pathways database differences in gene enrichment of target genes in the Wnt signaling pathway,Phospholipase D signaling pathway and mitogen-activated protein kinase signaling pathway.qRTPCR confirmed that miRNAs and its target genes were consistent with the screening results.In vitro,our study revealed that XLHZ could increase the expression of Ecadherin,decrease the expression of transforming growth factorβ1,vimentin andβ-catenin,inhibite the proliferation and migration of CAG cells,cause cell cycle arrest at G0/G1 and G2/M phase,induce the apoptosis of CAG cells,and prevent the progression of CAG to GC.CONCLUSION:This study provided a new idea for the mechanism of blocking the progression of CAG to GC by XLHZ,which may be related to the expression of miR-20a-3p,miR-320-3p,miR-34b-5p,
