A Objective3 This study was to understand the genetic variation characters of the H9N2 subtype avian influenza virus isolate （A/Chicken/ Hebei/WD/98, abbreviated as WD98） by comparing with other reference strains. I...A Objective3 This study was to understand the genetic variation characters of the H9N2 subtype avian influenza virus isolate （A/Chicken/ Hebei/WD/98, abbreviated as WD98） by comparing with other reference strains. I-Method3 Eight complete genes were amplified by RT-PCR and sequenced. The homology and genetic evolution relationship were analyzed between these sequences and that of the seven reference strains. [Result] The whole genomic sequence of WD98 strain was 91.1% -95.8% homologous to that of seven reference strains tested. This isolate shared the highest homology （95.8%） to D/HK/Y280/97 and the lowest homology （91.1% ） to C/Pak/2/99. The HA cleavage site of the WD98 strain was R-S-S-R G, and the 226th amino acid at receptor-binding site was Gin. [ Condmion] WD98 strain belongs to mildly pathogenic avian in- fluenza virus and may not infect human. The genetic relationship is the closest between A/Chicken/Hebei/wD/98 and A/duck/HongKong/Y280/ 97, both of which belong to the sub-line of A/Chicken/Beijing/1/94 in Eurasian line. And A/Chicken/Hebei/WD/98 and A/Chicken/Beijing/1/94 are genetically distant within the same sub-line.展开更多
Full genomic sequence of a newly isolated persistent infection strain of classical swine fever virus was firstly determined. It was demonstrated by sequence analyses that nucleotides homologies of this strain compared...Full genomic sequence of a newly isolated persistent infection strain of classical swine fever virus was firstly determined. It was demonstrated by sequence analyses that nucleotides homologies of this strain compared with virulent Shimen and vaccine HCLV were 89.7%and 87.7%, and homologies of amino acids were 94.8%and 93.3%, respectively. The sequencing results primarily suggest a tighter relationship between this persistent infection strain and virulent Shimen strain than vaccine HCLV strain.展开更多
The aim of this study is to explore the genomic molecular organization and genogroup of human nomvirus from infected infants in Guangzhou of China. Primers were designed according to the genomic sequence of norovims i...The aim of this study is to explore the genomic molecular organization and genogroup of human nomvirus from infected infants in Guangzhou of China. Primers were designed according to the genomic sequence of norovims in the GenBank, and the nomvirus genome was amplified by RT-PCR. The PCR- products were cloned into T vector and sequenced, and the genomic nucleotide sequences were analyzed with the programs CLUSTAL W/X, DNASTAR and RAT （Recombination Analysis Tool）. The NVgz01 strain genome is 7558 bp in length and encodes three open reading frames （GenBank accession No. is DQ369797）. The genomic sequences of NVgz01 were compared with those of nomvirus in GenBank, which revealed that the homology with genogroup Ⅱ ranges between 76%-90%, and genogroup Ⅰ between 43%-44%. The ORF1 region shared 94% and 88% identity with Mc37 and Famiington strains, respectively; the capsid region （ORF2） shared 65% and 94% identity with Mc37 and Farmington strains, respectively. Phylogenetic trees were reconstructed by the neighbor-joining method. Comparative complete sequence analysis of the NVgz01 with reported human norovirus genomic sequences revealed that this isolate belongs to genogroup Ⅱ . The ORF1 and ORF2 regions shared different identity with Mc37 and Fannington strains, suggesting NVgz01 could be a recombinant virus.展开更多
To analyze the genomic molecular structure and genotype of human astrovirus isolated from infant in Guangzhou of China, the primers were designed based on the genomic sequence of astrovirus from the C, enBank and the ...To analyze the genomic molecular structure and genotype of human astrovirus isolated from infant in Guangzhou of China, the primers were designed based on the genomic sequence of astrovirus from the C, enBank and the target sequence were amplified by RT-PCR. Then the PCR-products were cloned to T vector and sequenced. The genomic nucleotide sequences were analyzed by the programs CLUSTAL W and DNASTAR. It was found that the full genomic length of HASTVgz01 strain was 6721 bp and the ORFs were 6558 bp. The 5＇ and 3＇UTR were 82 and 81 nucleotides. The genome included 3 open reading frames （ORFs） ： ORFla, ORFlb and ORF2. The 5＇-terminal ORFla started at nueleotide 83 and extended to nucleotide 2845. ORFlb （nt 2785 to nt 4332） overlaped ORFla by 61 nueleotides. The 3＇-terminal ORF2 began at nucleotide 4325 and terminated at nucleotide 6640. ORF2 had 2316 nucleotides. Compared with other astrovirus sequences in GenBank, the homology of the amino acid sequence of ORF2 of HASTVgz01 strain with that of serotype 4 was 93%. Homology with other serotypes ranged from 61% to 70%. The complete nucleotide sequence of astrovirus HASTVgz01 strain isolated from Guangzhou in China was 6721 bp in length, GenBank accession NO. DQ344027. Comparing the ORF2 of astrovirus HASTVgz01 with the known sequences of types 1-8 the highest homology was serotype 4 （93%）. Comparative sequence analysis of the HASTVgz01 ORF2 with the reported human astrovirus sequences revealed that the isolated astrovirus belongs to genotype （serotype） 4.展开更多
To isolate the novel genes related to human hepatocellular carcinoma (HCC), we sequenced P1-derived artificial chromosome PAC579 (D17S926 locus) mapped in the minimum LOH (loss of heterozygosity) deletion region of ch...To isolate the novel genes related to human hepatocellular carcinoma (HCC), we sequenced P1-derived artificial chromosome PAC579 (D17S926 locus) mapped in the minimum LOH (loss of heterozygosity) deletion region of chromosome 17p13.3 in HCC, Four novel genes mapped in this genomic sequence area were isolated and cloned by wet-lab experiments, and the exons of these genes were located. 0-60 kb of this genomic sequence including the genes of interest was scanned with five different computational exon prediction programs as well as four splice site recognition programs. After analyzing and comparing the computationally predicted results with the wet-lab experiment results, some potential exons were predicted in the genomic sequence by using these programs.展开更多
Coding sequences (CDS) are commonly used for transient gene expression, in yeast two-hybrid screening, to verify protein interactions and in prokaryotic gene expression studies. CDS are most commonly obtained using co...Coding sequences (CDS) are commonly used for transient gene expression, in yeast two-hybrid screening, to verify protein interactions and in prokaryotic gene expression studies. CDS are most commonly obtained using complementary DNA (cDNA) derived from messenger RNA (mRNA) extracted from plant tissues and generated by reverse transcription. However, some CDS are difficult to acquire through this process as they are expressed at extremely low levels or have specific spatial and/or temporal expression patterns in vivo. These challenges require the development of alternative CDS cloning technologies. In this study, we found that the genomic intron-containing gene coding sequences (gDNA) from Arabidopsis thaliana, Oryza sativa, Brassica napus, and Glycine max can be correctly transcribed and spliced into mRNA in Nicotiana benthamiana. In contrast, gDNAs from Triticum aestivum and Sorghum bicolor did not function correctly. In transient expression experiments, the target DNA sequence is driven by a constitutive promoter. Theoretically, a sufficient amount of mRNA can be extracted from the N. benthamiana leaves, making it conducive to the cloning of CDS target genes. Our data demonstrate that N. benthamiana can be used as an effective host for the cloning CDS of plant genes.展开更多
Background Pork quality can directly affect customer purchase tendency and meat quality traits have become valu-able in modern pork production.However,genetic improvement has been slow due to high phenotyping costs.In...Background Pork quality can directly affect customer purchase tendency and meat quality traits have become valu-able in modern pork production.However,genetic improvement has been slow due to high phenotyping costs.In this study,whole genome sequence(WGS)data was used to evaluate the prediction accuracy of genomic best linear unbiased prediction(GBLUP)for meat quality in large-scale crossbred commercial pigs.Results We produced WGS data(18,695,907 SNPs and 2,106,902 INDELs exceed quality control)from 1,469 sequenced Duroc×(Landrace×Yorkshire)pigs and developed a reference panel for meat quality including meat color score,marbling score,L*(lightness),a*(redness),and b*(yellowness)of genomic prediction.The prediction accuracy was defined as the Pearson correlation coefficient between adjusted phenotypes and genomic estimated breeding values in the validation population.Using different marker density panels derived from WGS data,accuracy differed substantially among meat quality traits,varied from 0.08 to 0.47.Results showed that MultiBLUP outperform GBLUP and yielded accuracy increases ranging from 17.39%to 75%.We optimized the marker density and found medium-and high-density marker panels are beneficial for the estimation of heritability for meat quality.Moreover,we conducted genotype imputation from 50K chip to WGS level in the same population and found average concord-ance rate to exceed 95%and r^(2)=0.81.Conclusions Overall,estimation of heritability for meat quality traits can benefit from the use of WGS data.This study showed the superiority of using WGS data to genetically improve pork quality in genomic prediction.展开更多
The journey to implement cancer genomic medicine(CGM)in oncology practice began in the 1980s,which is considered the dawn of genetic and genomic cancer research.At the time,a variety of activating oncogenic alteration...The journey to implement cancer genomic medicine(CGM)in oncology practice began in the 1980s,which is considered the dawn of genetic and genomic cancer research.At the time,a variety of activating oncogenic alterations and their functional significance were unveiled in cancer cells,which led to the development of molecular targeted therapies in the 2000s and beyond.Although CGM is still a relatively new discipline and it is difficult to predict to what extent CGM will benefit the diverse pool of cancer patients,the National Cancer Center(NCC)of Japan has already contributed considerably to CGM advancement for the conquest of cancer.Looking back at these past achievements of the NCC,we predict that the future of CGM will involve the following:1)A biobank of paired cancerous and non-cancerous tissues and cells from various cancer types and stages will be developed.The quantity and quality of these samples will be compatible with omics analyses.All biobank samples will be linked to longitudinal clinical information.2)New technologies,such as whole-genome sequencing and artificial intelligence,will be introduced and new bioresources for functional and pharmacologic analyses(e.g.,a patient-derived xenograft library)will be systematically deployed.3)Fast and bidirectional translational research(bench-to-bedside and bedside-to-bench)performed by basic researchers and clinical investigators,preferably working alongside each other at the same institution,will be implemented;4)Close collaborations between academia,industry,regulatory bodies,and funding agencies will be established.5)There will be an investment in the other branch of CGM,personalized preventive medicine,based on the individual's genetic predisposition to cancer.展开更多
Long-PCR amplification, clone and primer-walking sequencing methods were employed in determine the complete sequence of mitochondrial genome of tokay (Gekko gecko). The genome is 16 435 bp in size, contains 13 protein...Long-PCR amplification, clone and primer-walking sequencing methods were employed in determine the complete sequence of mitochondrial genome of tokay (Gekko gecko). The genome is 16 435 bp in size, contains 13 protein-coding, 2 ribosomal and 22 transfer RNA genes. The mt genome of Gekko is similar to most of the vertebrates in gene components, order, orientation, tRNA structures, low percentage of guanine and high percentage of thymine, and skews of base GC and AT. Base A was preferred at third codon positions for protein genes is similar to amphibians and fishes rather than amnion vertebrates. The standard stop codes (TAA) present only in three protein genes, less than those of most vertebrates. Transfer RNA genes range in length from 63 to 76 nt, their planar structure present characteristic clover leaf, except for tRNA-Cys and tRNA-Ser (AGY) because of lacking the D arm.展开更多
A new avirulent,heat-resistance HB92 strain of newcastle Disease Virus(NDV)was acquired from Australia V4 strain.Its complete nucleotides sequence was first determined.The entire genome of NDV HB92 consists of 15186 n...A new avirulent,heat-resistance HB92 strain of newcastle Disease Virus(NDV)was acquired from Australia V4 strain.Its complete nucleotides sequence was first determined.The entire genome of NDV HB92 consists of 15186 nucleotides(GenBank accession no.AY225110).It was demonstrated by sequence analysis that nucleotides homology of HB92 strain with virulent strain ZJ1 were 83.9%,and the homology compared with avirulent vaccine strain La Sota and B1 were 94.0%and 93.5%,respectively.These results might be contributive to the study of the molecular mechanism of evolution of the NDV strain HB92 and to develop the engineered recombinant vaccine.展开更多
Dental implants have restored masticatory function to over 100000000 individuals,yet almost 1000000 implants fail each year due to peri-implantitis,a disease triggered by peri-implant microbial dysbiosis.Our ability t...Dental implants have restored masticatory function to over 100000000 individuals,yet almost 1000000 implants fail each year due to peri-implantitis,a disease triggered by peri-implant microbial dysbiosis.Our ability to prevent and treat peri-implantitis is hampered by a paucity of knowledge of how these biomes are acquired and the factors that engender normobiosis.Therefore,we combined a 3-month interventional study of 15 systemically and periodontally healthy adults with whole genome sequencing,finescale enumeration and graph theoretics to interrogate colonization dynamics in the pristine peri-implant sulcus.We discovered that colonization trajectories of implants differ substantially from adjoining teeth in acquisition of new members and development of functional synergies.Source-tracking algorithms revealed that this niche is initially seeded by bacteria trapped within the coverscrew chamber during implant placement.These pioneer species stably colonize the microbiome and exert a sustained influence on the ecosystem by serving as anchors of influential hubs and by providing functions that enable cell replication and biofilm maturation.Unlike the periodontal microbiome,recruitment of new members to the peri-implant community occurs on nepotistic principles.Maturation is accompanied by a progressive increase in anaerobiosis,however,the predominant functionalities are oxygen-dependent over the 12-weeks.The peri-implant community is easily perturbed following crown placement,but demonstrates remarkable resilience;returning to pre-perturbation states within three weeks.This study highlights important differences in the development of the periodontal and peri-implant ecosystems,and signposts the importance of placing implants in periodontally healthy individuals or following the successful resolution of periodontal disease.展开更多
Objective Pseudomonas aeruginosa(P.aeruginosa)is a prevalent pathogenic bacterium involved in meningitis;however,the virulence factors contributing to this disease remain poorly understood.Methods The virulence of the...Objective Pseudomonas aeruginosa(P.aeruginosa)is a prevalent pathogenic bacterium involved in meningitis;however,the virulence factors contributing to this disease remain poorly understood.Methods The virulence of the P.aeruginosa A584,isolated from meningitis samples,was evaluated by constructing in vitro blood-brain barrier and in vivo systemic infection models.qPCR,whole-genome sequencing,and drug efflux assays of A584 were performed to analyze the virulence factors.Results Genomic sequencing showed that A584 formed a phylogenetic cluster with the reference strains NY7610,DDRC3,Pa58,and Pa124.Its genome includes abundant virulence factors,such as hemolysin,the Type IV secretion system,and pyoverdine.A584 is a multidrug-resistant strain,and its wide-spectrum resistance is associated with enhanced drug efflux.Moreover,this strain caused significantly more severe damage to the blood-brain barrier than the standard strain,PAO1.qPCR assays further revealed the downregulation of the blood-brain barrier-associated proteins Claudin-5 and Occludin by A584.During systemic infection,A584 exhibited a higher capacity of brain colonization than PAO1(37.1×10^(6) CFU/g brain versus 2.5×10^(6) CFU/g brain),leading to higher levels of the proinflammatory factors IL-1βand TNF-α.Conclusion This study sheds light on the virulence factors of P.aeruginosa involved in meningitis.展开更多
The potherb mustard Xuecai(XC)cultivar is a cruciferous vegetable that is popular either fresh or pickled.Due to the deep notches in the edges of leaves in mustard XC,this plant can be said to have multipinnately lobe...The potherb mustard Xuecai(XC)cultivar is a cruciferous vegetable that is popular either fresh or pickled.Due to the deep notches in the edges of leaves in mustard XC,this plant can be said to have multipinnately lobed leaves.The net photosynthesis of lobed leaves is significantly greater than that of simple leaves.However,the molecular mechanism of leaf shape variation has not been determined.Here,we used HiFi and Hi-C data to assemble the XC genome.The genome was 961.72 Mb in size,with a contig N50 value of 6.565 Mb.The XC genome was compared with four previously sequenced mustard genomes,and the genomic collinearity regions,SNPs,and indels were identified.Five BjRCO genes were found on chromosome(Chr.)A10 in potherb mustard XC when the BjRCO gene locus was compared against other sequenced B.juncea genomes.Segmental duplication was found to contribute to the BjRCO gene copy number.The transcript expression of BjRCO genes was greater in multipinnately lobed leaves than in sawtooth-like leaves.Together,these findings indicate that both the greater copy number and the expression level of BjRCO genes regulate leaf shape from simple to complex in B.juncea.Gene editing of the BjRCO gene from XC changed the leaf shape from multipinnately lobed to simple.The high-quality XC genome sequence not only provides new insight into B.juncea leaf-type genomics but also helps in deciphering leaf shape variation.Our study provides insights into the variation and evolution of important traits in Brassica plants through a comparative analysis of the sequenced genomes.展开更多
Ectromelia virus(ECTV),a member of the Orthopoxvirus genus,serves as both a causative agent of mousepox and a pivotal surrogate model for studying highly pathogenic orthopoxviruses.Although genomic data on ECTV remain...Ectromelia virus(ECTV),a member of the Orthopoxvirus genus,serves as both a causative agent of mousepox and a pivotal surrogate model for studying highly pathogenic orthopoxviruses.Although genomic data on ECTV remains limited,we report the isolation and characterization of a novel strain,ECTV-C-Tan-GD01,obtained from rodents in Guangdong Province,China.Nanopore sequencing yielded a complete genome(199 annotated genes,including one gene truncated at the C-terminus)with inverted terminal repeats(ITRs)harboring a conserved hairpin structure.Notably,a frameshift-inducing“G”deletion in the EV159 gene resulted in the truncation of a semaphorin-like protein.In vitro assays demonstrated cell-associated viral replication kinetics,with maximum titers achieved earlier in Vero/HeLa cells(72 h)than in BHK-21/CEF cells(84 h).Murine challenge experiments revealed extreme virulence(LD50<1 plaque-forming unit(PFU)via intranasal/footpad routes)and hepatosplenic tropism.Furthermore,ECTV-C-Tan-GD01 exhibited utility in evaluating orthopoxvirus countermeasures:a single dose of vaccinia virus Tiantan(VTT)or non-replicating vaccinia virus Tiantan(NTV)conferred cross-protection,while tecovirimat(ST-246),cidofovir(CDV),and brincidofovir(initially CMX001)significantly reduced viral loads and pathology.This study establishes ECTV-C-Tan-GD01 as a dual-purpose resource for probing orthopoxvirus evolution and advancing therapeutic development.展开更多
The inappropriate use of cephalosporins lead to the occurrence and global spread of bacteria resistant to these antimicrobials.In this study,we isolated four Escherichia albertii strains from broilers in eastern China...The inappropriate use of cephalosporins lead to the occurrence and global spread of bacteria resistant to these antimicrobials.In this study,we isolated four Escherichia albertii strains from broilers in eastern China.The antimicrobial susceptibility and genomic characterization of these E.albertii isolates were determined.Our results revealed that these four E.albertii isolates exhibited resistance to tetracyclines,chloramphenicol,β-lactams,aminoglycosides,polymyxin B,sulfonamides,quinolones,and other antimicrobials.Among them,EA04 isolate was multidrug resistant and harbored extended-spectrumβ-lactamases(ESBL)genes blaCTX-Mand blaTEM.Whole genome sequencing and core-genome multilocus sequence typing(cgMLST)based on all ST4638 E.albertii for EA04 inferred highly probable epidemiological links between selected human isolates.Additionally,the ESBL genes blaTEM-141and blaCTX-M-55were coexistent in an approximately 75 kb Inc FII plasmid pEA04.2 in EA04.Comparative analysis indicated that genes blaTEM-141and blaCTX-M-55were located in IS15-blaCTX-M-55-wbu C-blaTEM-141-IS26 region,which similar structures were identified in various bacteria.Furthermore,the plasmid pEA04.2 could be transferable to E.coli EC600 and lead to the resistance to third-generation cephalosporins.These results suggested that chicken potentially serve as a reservoir for multidrug resistant E.albertii,which increases the risk of horizontal transfer of antimicrobial resistance between humans,animals and environment.展开更多
Lactiplantibacillus plantarum MWFLp-182 was originally isolated from the feces of long-living elderly individuals in Hezhou city,Guangxi,China.L.plantarum MWFLp-182 showed favorable gastric and intestinal tolerance co...Lactiplantibacillus plantarum MWFLp-182 was originally isolated from the feces of long-living elderly individuals in Hezhou city,Guangxi,China.L.plantarum MWFLp-182 showed favorable gastric and intestinal tolerance compared with Lactiplantibacillus rhamnosus GG(LGG).L.plantarum MWFLp-182 was further examined for its antioxidant and anti-inflammatory activity in ABAP-treated HT-29 cells.Importantly,it enhanced the expression of anti-inflammatory factor(interleukin-10(IL-10)),antioxidant cytokines(superoxide dismutase(SOD),glutathione peroxidase(GPx),nuclear factor erythroid 2-related factor(Nrf2),and hemeoxygenase 1(HO-1)),B-cell lymphoma-2(Bcl-2),and tight junction(Zonula occludens protein 1(ZO-1),Claudin-1,and Occludin)proteins and genes,and reduced reactive oxygen species(ROS).The complete genome of L.plantarum MWFLp-182 contained a single circular chromosome that was 3257196 bp long,with a G+C content of 44.49%,and a single circular plasmid that was 53560 bp long.The genes tpx,trx A,trx B,npr,nrd H,dps,rec A,gpx,gsh A and ars C in this strain were related to antioxidant function;the key genes involved in antioxidant function were further investigated.In this study,we identified a probiotic candidate with antioxidant properties.展开更多
Background Breed identification is useful in a variety of biological contexts.Breed identification usually involves two stages,i.e.,detection of breed-informative SNPs and breed assignment.For both stages,there are se...Background Breed identification is useful in a variety of biological contexts.Breed identification usually involves two stages,i.e.,detection of breed-informative SNPs and breed assignment.For both stages,there are several methods proposed.However,what is the optimal combination of these methods remain unclear.In this study,using the whole genome sequence data available for 13 cattle breeds from Run 8 of the 1,000 Bull Genomes Project,we compared the combinations of three methods(Delta,FST,and In)for breed-informative SNP detection and five machine learning methods(KNN,SVM,RF,NB,and ANN)for breed assignment with respect to different reference population sizes and difference numbers of most breed-informative SNPs.In addition,we evaluated the accuracy of breed identification using SNP chip data of different densities.Results We found that all combinations performed quite well with identification accuracies over 95%in all scenarios.However,there was no combination which performed the best and robust across all scenarios.We proposed to inte-grate the three breed-informative detection methods,named DFI,and integrate the three machine learning methods,KNN,SVM,and RF,named KSR.We found that the combination of these two integrated methods outperformed the other combinations with accuracies over 99%in most cases and was very robust in all scenarios.The accuracies from using SNP chip data were only slightly lower than that from using sequence data in most cases.Conclusions The current study showed that the combination of DFI and KSR was the optimal strategy.Using sequence data resulted in higher accuracies than using chip data in most cases.However,the differences were gener-ally small.In view of the cost of genotyping,using chip data is also a good option for breed identification.展开更多
Citrus leaf blotch virus （CLBV） is a member of the genus Citrivirus, in the family Betaflexiviridae. It has been reported CLBV could infect kiwi, citrus and sweet cherry in China. Of 289 citrus samples from six regi...Citrus leaf blotch virus （CLBV） is a member of the genus Citrivirus, in the family Betaflexiviridae. It has been reported CLBV could infect kiwi, citrus and sweet cherry in China. Of 289 citrus samples from six regions of China, 15 were detected to be infected with CLBV in this study. The complete genome of four isolates of CLBV was obtained from Reikou in Sichuan （CLBV-LH）, Yura Wase in Zhejiang （CLBV-YL）, Bingtangcheng in Hunan （CLBV-BT）, Fengjie 72-1 in Chongqing （CLBV- F J）, respectively. While they all represented 8 747 nucleotides in monopartite size, excluding the poly（A） tail, each of the isolates coded three open reading frames （ORFs）. Identity of the four isolates ranged from 98.9 to 99.8% to each other and from 96.8 to 98.1% to the citrus references in GenBank by multiple alignment of genomes. A phylogenetic tree based on the genome sequences of available CLBV isolates indicated that the four isolates were clustered together, suggesting that CLBV isolates from citrus in China did not have obvious variation. This is the first report of the complete nucleotide sequences of CLBV isolates infecting citrus in China.展开更多
Pathogenic Escherichia coli cause chicken colibacillosis, which is economically devastating to the poultry in- dustry worldwide （Bagheri et al., 2014）. Owing to in- creasing antibiotic resistance, phage therapy reag...Pathogenic Escherichia coli cause chicken colibacillosis, which is economically devastating to the poultry in- dustry worldwide （Bagheri et al., 2014）. Owing to in- creasing antibiotic resistance, phage therapy reagents have been developed to treat bacterial infections （Xu et al., 2015）.展开更多
基金supported by subproject of National Program on Key Basic Research Project (973 Program )(2005CB523001)
文摘A Objective3 This study was to understand the genetic variation characters of the H9N2 subtype avian influenza virus isolate （A/Chicken/ Hebei/WD/98, abbreviated as WD98） by comparing with other reference strains. I-Method3 Eight complete genes were amplified by RT-PCR and sequenced. The homology and genetic evolution relationship were analyzed between these sequences and that of the seven reference strains. [Result] The whole genomic sequence of WD98 strain was 91.1% -95.8% homologous to that of seven reference strains tested. This isolate shared the highest homology （95.8%） to D/HK/Y280/97 and the lowest homology （91.1% ） to C/Pak/2/99. The HA cleavage site of the WD98 strain was R-S-S-R G, and the 226th amino acid at receptor-binding site was Gin. [ Condmion] WD98 strain belongs to mildly pathogenic avian in- fluenza virus and may not infect human. The genetic relationship is the closest between A/Chicken/Hebei/wD/98 and A/duck/HongKong/Y280/ 97, both of which belong to the sub-line of A/Chicken/Beijing/1/94 in Eurasian line. And A/Chicken/Hebei/WD/98 and A/Chicken/Beijing/1/94 are genetically distant within the same sub-line.
基金Supported by National Basic Research Developmental Project ( G19990 1190 0 ) . Gen Bank NO.:AF40 7339
文摘Full genomic sequence of a newly isolated persistent infection strain of classical swine fever virus was firstly determined. It was demonstrated by sequence analyses that nucleotides homologies of this strain compared with virulent Shimen and vaccine HCLV were 89.7%and 87.7%, and homologies of amino acids were 94.8%and 93.3%, respectively. The sequencing results primarily suggest a tighter relationship between this persistent infection strain and virulent Shimen strain than vaccine HCLV strain.
文摘The aim of this study is to explore the genomic molecular organization and genogroup of human nomvirus from infected infants in Guangzhou of China. Primers were designed according to the genomic sequence of norovims in the GenBank, and the nomvirus genome was amplified by RT-PCR. The PCR- products were cloned into T vector and sequenced, and the genomic nucleotide sequences were analyzed with the programs CLUSTAL W/X, DNASTAR and RAT （Recombination Analysis Tool）. The NVgz01 strain genome is 7558 bp in length and encodes three open reading frames （GenBank accession No. is DQ369797）. The genomic sequences of NVgz01 were compared with those of nomvirus in GenBank, which revealed that the homology with genogroup Ⅱ ranges between 76%-90%, and genogroup Ⅰ between 43%-44%. The ORF1 region shared 94% and 88% identity with Mc37 and Famiington strains, respectively; the capsid region （ORF2） shared 65% and 94% identity with Mc37 and Farmington strains, respectively. Phylogenetic trees were reconstructed by the neighbor-joining method. Comparative complete sequence analysis of the NVgz01 with reported human norovirus genomic sequences revealed that this isolate belongs to genogroup Ⅱ . The ORF1 and ORF2 regions shared different identity with Mc37 and Fannington strains, suggesting NVgz01 could be a recombinant virus.
文摘To analyze the genomic molecular structure and genotype of human astrovirus isolated from infant in Guangzhou of China, the primers were designed based on the genomic sequence of astrovirus from the C, enBank and the target sequence were amplified by RT-PCR. Then the PCR-products were cloned to T vector and sequenced. The genomic nucleotide sequences were analyzed by the programs CLUSTAL W and DNASTAR. It was found that the full genomic length of HASTVgz01 strain was 6721 bp and the ORFs were 6558 bp. The 5＇ and 3＇UTR were 82 and 81 nucleotides. The genome included 3 open reading frames （ORFs） ： ORFla, ORFlb and ORF2. The 5＇-terminal ORFla started at nueleotide 83 and extended to nucleotide 2845. ORFlb （nt 2785 to nt 4332） overlaped ORFla by 61 nueleotides. The 3＇-terminal ORF2 began at nucleotide 4325 and terminated at nucleotide 6640. ORF2 had 2316 nucleotides. Compared with other astrovirus sequences in GenBank, the homology of the amino acid sequence of ORF2 of HASTVgz01 strain with that of serotype 4 was 93%. Homology with other serotypes ranged from 61% to 70%. The complete nucleotide sequence of astrovirus HASTVgz01 strain isolated from Guangzhou in China was 6721 bp in length, GenBank accession NO. DQ344027. Comparing the ORF2 of astrovirus HASTVgz01 with the known sequences of types 1-8 the highest homology was serotype 4 （93%）. Comparative sequence analysis of the HASTVgz01 ORF2 with the reported human astrovirus sequences revealed that the isolated astrovirus belongs to genotype （serotype） 4.
基金The authors would like to thank Shanghai Genecore Company for finishing all the sequencing work.Thanks are due to Dr. Sun Fenyong, Dr. Ren Gongyi and Dr. Han Liwei for their excellent experimental work. Thanks also go to Prof. Gu Xiaocheng, Luo Jingchu
文摘To isolate the novel genes related to human hepatocellular carcinoma (HCC), we sequenced P1-derived artificial chromosome PAC579 (D17S926 locus) mapped in the minimum LOH (loss of heterozygosity) deletion region of chromosome 17p13.3 in HCC, Four novel genes mapped in this genomic sequence area were isolated and cloned by wet-lab experiments, and the exons of these genes were located. 0-60 kb of this genomic sequence including the genes of interest was scanned with five different computational exon prediction programs as well as four splice site recognition programs. After analyzing and comparing the computationally predicted results with the wet-lab experiment results, some potential exons were predicted in the genomic sequence by using these programs.
文摘Coding sequences (CDS) are commonly used for transient gene expression, in yeast two-hybrid screening, to verify protein interactions and in prokaryotic gene expression studies. CDS are most commonly obtained using complementary DNA (cDNA) derived from messenger RNA (mRNA) extracted from plant tissues and generated by reverse transcription. However, some CDS are difficult to acquire through this process as they are expressed at extremely low levels or have specific spatial and/or temporal expression patterns in vivo. These challenges require the development of alternative CDS cloning technologies. In this study, we found that the genomic intron-containing gene coding sequences (gDNA) from Arabidopsis thaliana, Oryza sativa, Brassica napus, and Glycine max can be correctly transcribed and spliced into mRNA in Nicotiana benthamiana. In contrast, gDNAs from Triticum aestivum and Sorghum bicolor did not function correctly. In transient expression experiments, the target DNA sequence is driven by a constitutive promoter. Theoretically, a sufficient amount of mRNA can be extracted from the N. benthamiana leaves, making it conducive to the cloning of CDS target genes. Our data demonstrate that N. benthamiana can be used as an effective host for the cloning CDS of plant genes.
基金supported by a Technical Innovation of Crossbred in Swine and Breed High Fertility Lines Project(2022B0202090002)a Local Innovative and Research Teams Project of Guangdong Province(2019BT02N630)+1 种基金a Natural Science Foundation of Guangdong Province project(2018B030313011)Innovative Teams of Modern Agriculture and Industry Technology System of Guangdong Province(2022KJ26).
文摘Background Pork quality can directly affect customer purchase tendency and meat quality traits have become valu-able in modern pork production.However,genetic improvement has been slow due to high phenotyping costs.In this study,whole genome sequence(WGS)data was used to evaluate the prediction accuracy of genomic best linear unbiased prediction(GBLUP)for meat quality in large-scale crossbred commercial pigs.Results We produced WGS data(18,695,907 SNPs and 2,106,902 INDELs exceed quality control)from 1,469 sequenced Duroc×(Landrace×Yorkshire)pigs and developed a reference panel for meat quality including meat color score,marbling score,L*(lightness),a*(redness),and b*(yellowness)of genomic prediction.The prediction accuracy was defined as the Pearson correlation coefficient between adjusted phenotypes and genomic estimated breeding values in the validation population.Using different marker density panels derived from WGS data,accuracy differed substantially among meat quality traits,varied from 0.08 to 0.47.Results showed that MultiBLUP outperform GBLUP and yielded accuracy increases ranging from 17.39%to 75%.We optimized the marker density and found medium-and high-density marker panels are beneficial for the estimation of heritability for meat quality.Moreover,we conducted genotype imputation from 50K chip to WGS level in the same population and found average concord-ance rate to exceed 95%and r^(2)=0.81.Conclusions Overall,estimation of heritability for meat quality traits can benefit from the use of WGS data.This study showed the superiority of using WGS data to genetically improve pork quality in genomic prediction.
文摘The journey to implement cancer genomic medicine(CGM)in oncology practice began in the 1980s,which is considered the dawn of genetic and genomic cancer research.At the time,a variety of activating oncogenic alterations and their functional significance were unveiled in cancer cells,which led to the development of molecular targeted therapies in the 2000s and beyond.Although CGM is still a relatively new discipline and it is difficult to predict to what extent CGM will benefit the diverse pool of cancer patients,the National Cancer Center(NCC)of Japan has already contributed considerably to CGM advancement for the conquest of cancer.Looking back at these past achievements of the NCC,we predict that the future of CGM will involve the following:1)A biobank of paired cancerous and non-cancerous tissues and cells from various cancer types and stages will be developed.The quantity and quality of these samples will be compatible with omics analyses.All biobank samples will be linked to longitudinal clinical information.2)New technologies,such as whole-genome sequencing and artificial intelligence,will be introduced and new bioresources for functional and pharmacologic analyses(e.g.,a patient-derived xenograft library)will be systematically deployed.3)Fast and bidirectional translational research(bench-to-bedside and bedside-to-bench)performed by basic researchers and clinical investigators,preferably working alongside each other at the same institution,will be implemented;4)Close collaborations between academia,industry,regulatory bodies,and funding agencies will be established.5)There will be an investment in the other branch of CGM,personalized preventive medicine,based on the individual's genetic predisposition to cancer.
文摘Long-PCR amplification, clone and primer-walking sequencing methods were employed in determine the complete sequence of mitochondrial genome of tokay (Gekko gecko). The genome is 16 435 bp in size, contains 13 protein-coding, 2 ribosomal and 22 transfer RNA genes. The mt genome of Gekko is similar to most of the vertebrates in gene components, order, orientation, tRNA structures, low percentage of guanine and high percentage of thymine, and skews of base GC and AT. Base A was preferred at third codon positions for protein genes is similar to amphibians and fishes rather than amnion vertebrates. The standard stop codes (TAA) present only in three protein genes, less than those of most vertebrates. Transfer RNA genes range in length from 63 to 76 nt, their planar structure present characteristic clover leaf, except for tRNA-Cys and tRNA-Ser (AGY) because of lacking the D arm.
基金Supported by Hubei Natural Science Foundation(2002AB144)
文摘A new avirulent,heat-resistance HB92 strain of newcastle Disease Virus(NDV)was acquired from Australia V4 strain.Its complete nucleotides sequence was first determined.The entire genome of NDV HB92 consists of 15186 nucleotides(GenBank accession no.AY225110).It was demonstrated by sequence analysis that nucleotides homology of HB92 strain with virulent strain ZJ1 were 83.9%,and the homology compared with avirulent vaccine strain La Sota and B1 were 94.0%and 93.5%,respectively.These results might be contributive to the study of the molecular mechanism of evolution of the NDV strain HB92 and to develop the engineered recombinant vaccine.
基金supported by National Institutes of Health R03DE027492 to Shareef Dabdoubsupported by National Institutes of Health,project number 7R01DE027857-06supported by National Institutes of Health R56DE033913 awarded to Purnima Kumar.
文摘Dental implants have restored masticatory function to over 100000000 individuals,yet almost 1000000 implants fail each year due to peri-implantitis,a disease triggered by peri-implant microbial dysbiosis.Our ability to prevent and treat peri-implantitis is hampered by a paucity of knowledge of how these biomes are acquired and the factors that engender normobiosis.Therefore,we combined a 3-month interventional study of 15 systemically and periodontally healthy adults with whole genome sequencing,finescale enumeration and graph theoretics to interrogate colonization dynamics in the pristine peri-implant sulcus.We discovered that colonization trajectories of implants differ substantially from adjoining teeth in acquisition of new members and development of functional synergies.Source-tracking algorithms revealed that this niche is initially seeded by bacteria trapped within the coverscrew chamber during implant placement.These pioneer species stably colonize the microbiome and exert a sustained influence on the ecosystem by serving as anchors of influential hubs and by providing functions that enable cell replication and biofilm maturation.Unlike the periodontal microbiome,recruitment of new members to the peri-implant community occurs on nepotistic principles.Maturation is accompanied by a progressive increase in anaerobiosis,however,the predominant functionalities are oxygen-dependent over the 12-weeks.The peri-implant community is easily perturbed following crown placement,but demonstrates remarkable resilience;returning to pre-perturbation states within three weeks.This study highlights important differences in the development of the periodontal and peri-implant ecosystems,and signposts the importance of placing implants in periodontally healthy individuals or following the successful resolution of periodontal disease.
基金supported by National Natural Science Foundation of China,China(32170102)Natural Science Foundation of Tianjin(21JCYBJC01420)the Fundamental Research Funds for the Central Universities(63233050)。
文摘Objective Pseudomonas aeruginosa(P.aeruginosa)is a prevalent pathogenic bacterium involved in meningitis;however,the virulence factors contributing to this disease remain poorly understood.Methods The virulence of the P.aeruginosa A584,isolated from meningitis samples,was evaluated by constructing in vitro blood-brain barrier and in vivo systemic infection models.qPCR,whole-genome sequencing,and drug efflux assays of A584 were performed to analyze the virulence factors.Results Genomic sequencing showed that A584 formed a phylogenetic cluster with the reference strains NY7610,DDRC3,Pa58,and Pa124.Its genome includes abundant virulence factors,such as hemolysin,the Type IV secretion system,and pyoverdine.A584 is a multidrug-resistant strain,and its wide-spectrum resistance is associated with enhanced drug efflux.Moreover,this strain caused significantly more severe damage to the blood-brain barrier than the standard strain,PAO1.qPCR assays further revealed the downregulation of the blood-brain barrier-associated proteins Claudin-5 and Occludin by A584.During systemic infection,A584 exhibited a higher capacity of brain colonization than PAO1(37.1×10^(6) CFU/g brain versus 2.5×10^(6) CFU/g brain),leading to higher levels of the proinflammatory factors IL-1βand TNF-α.Conclusion This study sheds light on the virulence factors of P.aeruginosa involved in meningitis.
基金supported by grants from the National Natural Science Foundation of China(32002056)the Science and Technology Research Key Project of Henan Province,China(242102111138)。
文摘The potherb mustard Xuecai(XC)cultivar is a cruciferous vegetable that is popular either fresh or pickled.Due to the deep notches in the edges of leaves in mustard XC,this plant can be said to have multipinnately lobed leaves.The net photosynthesis of lobed leaves is significantly greater than that of simple leaves.However,the molecular mechanism of leaf shape variation has not been determined.Here,we used HiFi and Hi-C data to assemble the XC genome.The genome was 961.72 Mb in size,with a contig N50 value of 6.565 Mb.The XC genome was compared with four previously sequenced mustard genomes,and the genomic collinearity regions,SNPs,and indels were identified.Five BjRCO genes were found on chromosome(Chr.)A10 in potherb mustard XC when the BjRCO gene locus was compared against other sequenced B.juncea genomes.Segmental duplication was found to contribute to the BjRCO gene copy number.The transcript expression of BjRCO genes was greater in multipinnately lobed leaves than in sawtooth-like leaves.Together,these findings indicate that both the greater copy number and the expression level of BjRCO genes regulate leaf shape from simple to complex in B.juncea.Gene editing of the BjRCO gene from XC changed the leaf shape from multipinnately lobed to simple.The high-quality XC genome sequence not only provides new insight into B.juncea leaf-type genomics but also helps in deciphering leaf shape variation.Our study provides insights into the variation and evolution of important traits in Brassica plants through a comparative analysis of the sequenced genomes.
基金supported by the Natural Science Foundation of Beijing(7254390)the Youth Science Foundation of Chinese Center for Disease Control and Prevention(2024A103)to W.C.C,the National Key ResearchDevelopment Program of China(2022YFC2304100,2023YFD1800405).
文摘Ectromelia virus(ECTV),a member of the Orthopoxvirus genus,serves as both a causative agent of mousepox and a pivotal surrogate model for studying highly pathogenic orthopoxviruses.Although genomic data on ECTV remains limited,we report the isolation and characterization of a novel strain,ECTV-C-Tan-GD01,obtained from rodents in Guangdong Province,China.Nanopore sequencing yielded a complete genome(199 annotated genes,including one gene truncated at the C-terminus)with inverted terminal repeats(ITRs)harboring a conserved hairpin structure.Notably,a frameshift-inducing“G”deletion in the EV159 gene resulted in the truncation of a semaphorin-like protein.In vitro assays demonstrated cell-associated viral replication kinetics,with maximum titers achieved earlier in Vero/HeLa cells(72 h)than in BHK-21/CEF cells(84 h).Murine challenge experiments revealed extreme virulence(LD50<1 plaque-forming unit(PFU)via intranasal/footpad routes)and hepatosplenic tropism.Furthermore,ECTV-C-Tan-GD01 exhibited utility in evaluating orthopoxvirus countermeasures:a single dose of vaccinia virus Tiantan(VTT)or non-replicating vaccinia virus Tiantan(NTV)conferred cross-protection,while tecovirimat(ST-246),cidofovir(CDV),and brincidofovir(initially CMX001)significantly reduced viral loads and pathology.This study establishes ECTV-C-Tan-GD01 as a dual-purpose resource for probing orthopoxvirus evolution and advancing therapeutic development.
基金supported by the National Key Research and Development Program of China(2021YFD1800402)the National Natural Science Foundation of China(32172856,31972654 and 32302881)+1 种基金the Natural Science Foundation of Shanghai,China(22ZR1476100 and 23ZR1476600)the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences(SHVRI-ASTIP-2014-8)。
文摘The inappropriate use of cephalosporins lead to the occurrence and global spread of bacteria resistant to these antimicrobials.In this study,we isolated four Escherichia albertii strains from broilers in eastern China.The antimicrobial susceptibility and genomic characterization of these E.albertii isolates were determined.Our results revealed that these four E.albertii isolates exhibited resistance to tetracyclines,chloramphenicol,β-lactams,aminoglycosides,polymyxin B,sulfonamides,quinolones,and other antimicrobials.Among them,EA04 isolate was multidrug resistant and harbored extended-spectrumβ-lactamases(ESBL)genes blaCTX-Mand blaTEM.Whole genome sequencing and core-genome multilocus sequence typing(cgMLST)based on all ST4638 E.albertii for EA04 inferred highly probable epidemiological links between selected human isolates.Additionally,the ESBL genes blaTEM-141and blaCTX-M-55were coexistent in an approximately 75 kb Inc FII plasmid pEA04.2 in EA04.Comparative analysis indicated that genes blaTEM-141and blaCTX-M-55were located in IS15-blaCTX-M-55-wbu C-blaTEM-141-IS26 region,which similar structures were identified in various bacteria.Furthermore,the plasmid pEA04.2 could be transferable to E.coli EC600 and lead to the resistance to third-generation cephalosporins.These results suggested that chicken potentially serve as a reservoir for multidrug resistant E.albertii,which increases the risk of horizontal transfer of antimicrobial resistance between humans,animals and environment.
基金supported by the Natural Science Foundation of Guangxi,China(2020GXNSFBA297083)the National Natural Science Foundation of China(32072193)。
文摘Lactiplantibacillus plantarum MWFLp-182 was originally isolated from the feces of long-living elderly individuals in Hezhou city,Guangxi,China.L.plantarum MWFLp-182 showed favorable gastric and intestinal tolerance compared with Lactiplantibacillus rhamnosus GG(LGG).L.plantarum MWFLp-182 was further examined for its antioxidant and anti-inflammatory activity in ABAP-treated HT-29 cells.Importantly,it enhanced the expression of anti-inflammatory factor(interleukin-10(IL-10)),antioxidant cytokines(superoxide dismutase(SOD),glutathione peroxidase(GPx),nuclear factor erythroid 2-related factor(Nrf2),and hemeoxygenase 1(HO-1)),B-cell lymphoma-2(Bcl-2),and tight junction(Zonula occludens protein 1(ZO-1),Claudin-1,and Occludin)proteins and genes,and reduced reactive oxygen species(ROS).The complete genome of L.plantarum MWFLp-182 contained a single circular chromosome that was 3257196 bp long,with a G+C content of 44.49%,and a single circular plasmid that was 53560 bp long.The genes tpx,trx A,trx B,npr,nrd H,dps,rec A,gpx,gsh A and ars C in this strain were related to antioxidant function;the key genes involved in antioxidant function were further investigated.In this study,we identified a probiotic candidate with antioxidant properties.
基金funded by National Key Research and Development Program of China(2021YFD1200404)the Yangzhou University Interdisciplinary Research Foundation for Animal Science Discipline of Targeted Support(yzuxk202016)the Project of Genetic Improvement for Agricultural Species(Dairy Cattle)of Shandong Province(2019LZGC011).
文摘Background Breed identification is useful in a variety of biological contexts.Breed identification usually involves two stages,i.e.,detection of breed-informative SNPs and breed assignment.For both stages,there are several methods proposed.However,what is the optimal combination of these methods remain unclear.In this study,using the whole genome sequence data available for 13 cattle breeds from Run 8 of the 1,000 Bull Genomes Project,we compared the combinations of three methods(Delta,FST,and In)for breed-informative SNP detection and five machine learning methods(KNN,SVM,RF,NB,and ANN)for breed assignment with respect to different reference population sizes and difference numbers of most breed-informative SNPs.In addition,we evaluated the accuracy of breed identification using SNP chip data of different densities.Results We found that all combinations performed quite well with identification accuracies over 95%in all scenarios.However,there was no combination which performed the best and robust across all scenarios.We proposed to inte-grate the three breed-informative detection methods,named DFI,and integrate the three machine learning methods,KNN,SVM,and RF,named KSR.We found that the combination of these two integrated methods outperformed the other combinations with accuracies over 99%in most cases and was very robust in all scenarios.The accuracies from using SNP chip data were only slightly lower than that from using sequence data in most cases.Conclusions The current study showed that the combination of DFI and KSR was the optimal strategy.Using sequence data resulted in higher accuracies than using chip data in most cases.However,the differences were gener-ally small.In view of the cost of genotyping,using chip data is also a good option for breed identification.
基金supported by the National Natural Science Foundation of China (31501611)the Chongqing Research Program of Basic Research and Frontier Technology, China (cstc2017jcyjB X0016)+2 种基金the Chongqing Science and Technology Commission Project, China (cstc2016shmsztzx80003)the Fundamental Research Funds for the Central Universities, China (XDJK2016B21, SWU116012)the Special Fund for Agro-scientific Research in the Public Interest, China (201203076-01)
文摘Citrus leaf blotch virus （CLBV） is a member of the genus Citrivirus, in the family Betaflexiviridae. It has been reported CLBV could infect kiwi, citrus and sweet cherry in China. Of 289 citrus samples from six regions of China, 15 were detected to be infected with CLBV in this study. The complete genome of four isolates of CLBV was obtained from Reikou in Sichuan （CLBV-LH）, Yura Wase in Zhejiang （CLBV-YL）, Bingtangcheng in Hunan （CLBV-BT）, Fengjie 72-1 in Chongqing （CLBV- F J）, respectively. While they all represented 8 747 nucleotides in monopartite size, excluding the poly（A） tail, each of the isolates coded three open reading frames （ORFs）. Identity of the four isolates ranged from 98.9 to 99.8% to each other and from 96.8 to 98.1% to the citrus references in GenBank by multiple alignment of genomes. A phylogenetic tree based on the genome sequences of available CLBV isolates indicated that the four isolates were clustered together, suggesting that CLBV isolates from citrus in China did not have obvious variation. This is the first report of the complete nucleotide sequences of CLBV isolates infecting citrus in China.
基金supported by grants from the Nature Science Foundation of Shandong Province of China (grant nos.ZR2013CQ024 and ZR2015CM020)
文摘Pathogenic Escherichia coli cause chicken colibacillosis, which is economically devastating to the poultry in- dustry worldwide （Bagheri et al., 2014）. Owing to in- creasing antibiotic resistance, phage therapy reagents have been developed to treat bacterial infections （Xu et al., 2015）.
