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Insect Science 2018年第6期25卷 928-945页

作者： Ruchir Mishra Joanna C.Chiu Gang Hua Nilesh R.Tawari Michael J.Adang Ashfaq A.Sial Department of Entomology College of Agricultural and Environmental SciencesUniversity of GeorgiaAthensGeorgiaUSA. Department of Entomology and Nematology College of Agricultural and Environmental SciencesUniversity of CaliforniaDavisCall-fomiaUSA. Department of Biochemistry and Molecular Biology University of GeorgiaAthensGeorgiaUSA . Computational and Systems Biology Genome Institute of SingaporeSingapore.

Global climate change and acquired resistance to insecticides are threats to world food *** suzukii,a devastating invasive pest in many parts of the world,causes substantial economic losses to fruit production industries,forcing farmers to apply broad-spectrum insecticides frequently,This could lead to the development of insecticide *** determined the Lethal Concentration 50 (median lethal concen- tration,LC50)values of zeta-cypermethrin,spinosad,and malathion insecticides against *** colonies established from Clarke and Pierce county Georgia,United States. The LC50 values were 3 fold higher in the Pierce county population for all insecticide *** then used RNA sequencing to analyze the responses of Pierce and Clarke population flies surviving a LC50 treatment of the 3 *** identified a high num- ber of differentially expressed genes that are likely involved in detoxification and reduced cuticular penetration,especially in the Pierce population,with extensive overlap in differ- entially expressed genes between the 3 insecticide ***,we predicted fewer nonsynonymous single nucleotide variants having deleterious effects on protein function among detoxification,insecticide target,and cuticular protein encoding genes in Pierce *** a combination of increased gene expression and fewer deleterious single nu- cleotide variants highlights molecular mechanisms underlying the higher LC50 values for Pierce population flies.

关键词： differentially expressed genes Drosophila suzukii high throughput sequenc- ing insecticide response insertions and deletions single nucleotide variants

The genome-wide landscape of small insertion and deletion mutations in Monopterus albus

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Journal of Genetics and Genomics 2019年第2期46卷 75-86页

作者： Feng Chen Fengling Lai Majing Luo Yu-San Han Hanhua Cheng Rongjia Zhou Hubei Key Laboratory of Cell Homeostasis College of Life Sciences Wuhan University Institute of Fisheries Science College of Life Science "National Taiwan University"

Insertion and deletion(indel) mutations, which can trigger single nucleotide substitutions on the flanking regions of genes, may generate abundant materials for disease defense, reproduction, species survival and evolution. However, genetic and evolutionary mechanisms of indels remain elusive. We establish a comparative genome-transcriptome-alignment approach for a large-scale identification of indels in Monopterus population. Over 2000 indels in 1738 indel genes, including 1-21 bp deletions and 1-15 bp insertions, were detected. Each indel gene had ～1.1 deletions/insertions, and 2-4 alleles in population. Frequencies of deletions were prominently higher than those of insertions on both genome and population levels. Most of the indels led to in frame mutations with multiples of three and majorly occurred in non-domain regions, indicating functional constraint or tolerance of the indels. All indel genes showed higher expression levels than non-indel genes during sex reversal. Slide window analysis of global expression levels in gonads showed a significant positive correlation with indel density in the genome. Moreover, indel genes were evolutionarily conserved and evolved slowly compared to nonindel genes. Notably, population genetic structure of indels revealed divergent evolution of Monopterus population, as bottleneck effect of biogeographic isolation by Taiwan Strait, China.

关键词： Sex determination Insertions deletions Evolution Reproduction

Immunogenetic factors driving formation of ultralong VH CDR3 in Bos taurus antibodies

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Cellular & Molecular Immunology 2019年第1期16卷 53-64页

作者： Thaddeus C Deiss Melissa Vadnais Feng Wang Patricia L Chen Ali Torkamani Waithaka Mwangi Marie-Paule Lefranc Michael F Criscitiello Vaughn V Smider Comparative Immunogenetics Laboratory Department of Veterinary PathobiologyCollege of Veterinary Medicine and Biomedical SciencesTexas A&M UniversityCollege StationTX 77843USA Department of Molecular Medicine The Scripps Research InstituteLa JollaCA 92037USA California Institute for Biomedical Research La JollaCA 92037USA Department of Integrative Structural and Computational Biology The Scripps Research InstituteLa JollaCA 92037USA Department of Diagnostic Medicine and Pathobiology College of Veterinary MedicineKansas State UniversityManhattanKS 66506USA IMGT the International ImMunoGeneTics information systemLaboratoire d’ImmunoGénétique MoléculaireInstitut de Génétique HumaineCNRSUniversity of MontpellierMontpellier 34396France Department of Microbial Pathogenesis and Immunology College of MedicineTexas A&M UniversityBryanTX 77807USA Fabrus Inc.La JollaCA 92037USA

The antibody repertoire of Bos taurus is characterized by a subset of variable heavy(VH)chain regions with ultralong third complementarity determining regions(CDR3)which,compared to other species,can provide a potent response to challenging antigens like HIV *** unusual CDR3 can range to over seventy highly diverse amino acids in length and form uniqueβ-ribbon‘stalk’and disulfide bonded‘knob’structures,far from the typical antigen binding *** genetic components and processes for forming these unusual cattle antibody VH CDR3 are not well *** we analyze sequences of Bos taurus antibody VH domains and find that the subset with ultralong CDR3 exclusively uses a single variable gene,IGHV1-7(VHBUL)rearranged to the longest diversity gene,*** eight nucleotide duplication at the 3′end of IGHV1-7 encodes a longer V-region producing an extended Fβ-strand that contributes to the stalk in a rearranged CDR3.A low amino acid variability was observed in CDR1 and CDR2,suggesting that antigen binding for this subset most likely only depends on the *** a novel,potentially AID mediated,deletional diversification mechanism of the *** VH ultralong CDR3 knob was discovered,in which interior codons of the IGHD8-2 region are removed while maintaining integral structural components of the knob and descending strand of the stalk in *** deletions serve to further diversify cysteine positions,and thus disulfide bonded ***,both germline and somatic genetic factors and processes appear to be involved in diversification of this structurally unusual cattle VH ultralong CDR3 repertoire.

关键词： bovine complementarity determining region 3 repertoire diversification deletions immunoglobulin heavy chain

Prevalence of hepatocarcinoma-related hepatitis B virus mutants in patients in grey zone of treatment

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World Journal of Gastroenterology 2019年第38期25卷 5883-5896页

作者： Ana Isabel Gil-García Antonio Madejón Irene Francisco-Recuero Ana López-López Emiliana Villafranca Miriam Romero Araceli García Antonio Olveira Rocío Mena Juan Ramón Larrubia Javier García-Samaniego Hepatology Unit Hospital Universitario La PazMadrid 28046Spain Centro de Investigación Biomédica en Red Instituto de Salud Carlos IIIMadrid 28029Spain Instituto de Investigación del Hospital Universitario la Paz Madrid 28046Spain Biochemistry Department Faculty of MedicineUniversidad Autónoma de MadridMadrid 28029Spain Instituto de Genética Médica y Molecular Hospital Universitario La PazMadrid 28046Spain Translational Hepatology Unit Hospital General Universitario de GuadalajaraGuadalajara 19002Castilla-La ManchaSpain

BACKGROUND Antiviral treatment of patients with chronic hepatitis B(CHB)in the grey zone of treatment comands risk management in order to optimize the health *** this sense,the identification of HBV mutants related with an increased risk of hepatocellular carcinoma(HCC)could be useful to identify subpopulations with potential indication of antiviral *** To analyze the prevalence/persistence of hepatitis B virus(HBV)preS and basal core promoter(BCP)/precore/core variants associated to HCC development in CHB patients in the grey *** Work was designed as a longitudinal retrospective study,including 106 plasma samples from 31 patients with CHB in the grey zone of treatment:Hepatitis B e antigen negative,HBV-DNA levels between 12-20000 IU/mL,normal or discordant transaminase levels during follow up and mild/moderate necroinflammatory activity in liver biopsy or Fibroscan(up to 9.5 kPa).Serum HBVDNA was tested using the Abbott Real Time HBV Assay and the BCP/precore/core and the hepatitis B surface antigen(HBsAg)coding regions were analyzed in positive samples by PCR/bulk-sequencing to identify the HCCrelated HBV *** High-risk HCC related mutants were detected in 24(77%)patients:19(61%)in the BCP/precore/core,and 7(23%)in the HBsAg coding region(2 preS1 and 5 preS2 deletions).The prevalence of preS deletions was genotype-dependent:3/5(60%)patients with preS2 deletions and 1/2 with preS1 deletions were infected with the HBV-E *** HBV-E was the most prevalent in sub-Saharan patients,a correlation between preS deletions and ethnicity was also found:6/8(75%)sub-Saharan vs 1/19(5%)Caucasian patients had preS deletions(P=0.00016).Remarkably,this correlation was maintained in those patients infected with HBV-A,a minor genotype in sub-Saharan patients:2/2 patients infected with HBV-A from West Africa vs 0/6 of Caucasian origin had preS *** HCC related variants were the major strains and persisted over time(up to 48 mo).Pa

关键词： Hepatitis B virus Hepatocellular carcinoma PreS deletions Hepatitis B virus treatment Grey zone

Glutathione S-transferase M1 polymorphism and esophagealcancer risk:An updated meta-analysis based on 37 studies

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World Journal of Gastroenterology 2016年第5期22卷 1911-1918页

作者： Quan-Jun Lu Ya-Cong Bo Yan Zhao Er-Jiang Zhao Wolde Bekalo Sapa Ming-Jie Yao Dan-Dan Duan Yi-Wei Zhu Wei-Quan Lu Ling Yuan Department of Nutrition and Food Hygiene College of Public HealthZhengzhou UniversityZhengzhou 450001Henan ProvinceChina Department of Epidemiology and Biostatistics College of Public HealthZhengzhou UniversityZhengzhou 450001Henan ProvinceChina Affiliated Tumor Hospital of Zhengzhou University Henan Tumor HospitalZhengzhou 450003Henan ProvinceChina School of Basic Medical Sciences Peking UniversityBeijing 100191China Department of Radiotherapy Affiliated Tumor Hospital of Zhengzhou UniversityHenan Tumor HospitalZhengzhou 450003Henan ProvinceChina

AIM: To evaluate the relationship between glutathione S-transferase M1(GSTM1) polymorphism and susceptibility to esophageal cancer(EC).METHODS: A comprehensive search of the United States National Library of Medicine Pub Med database and the Elsevier, Springer, and China National Knowledge Infrastructure databases for all relevant studies was conducted using combinations of the following terms: "glutathione S-transferase M1", "GSTM1", "polymorphism", and "EC"(until November 1, 2014). The statistical analysis was performed using the SAS software(v.9.1.3; SAS Institute, Cary, NC, United States) and the Review Manager software(v.5.0; Oxford, England); crude odds ratios(ORs) with 95% confidence intervals(CIs) were used to assess the association between the GSTM1 null genotype and the risk of ***: A total of 37 studies involving 2236 EC cases and 3243 controls were included in this metaanalysis. We observed that the GSTM1 null genotype was a significant risk factor for EC in most populations(OR = 1.33, 95%CI: 1.12-1.57, P_(heterogeneity) < 0.000001, and I2 = 77.0%), particularly in the Asian population(OR = 1.53, 95%CI: 1.26-1.86, P_(heterogeneity)< 0.000001, and I2 = 77.0%), but not in the Caucasian population(OR = 1.02, 95%CI: 0.87-1.19, P_(heterogeneity) = 0.97, and I2 = 0%).CONCLUSION: The GSTM1 null polymorphism may be associated with an increased risk for EC in Asian but not Caucasian populations.

关键词： Meta-analysis glutathione S-transferaseM1 Polymorphism Esophageal cancer deletions

Diagnosis of Laron syndrome using monoplex-polymerase chain reaction technology with a whole-genome amplification template: A case report

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World Journal of Clinical Cases 2019年第23期7卷 4029-4035页

作者： Adina Neumann Miguel Angel Alcantara-Ortigoza Ariadna Gonzalez-del Angel Felipe Camargo-Diaz Esther Lopez-Bayghen Laboratorio de Investigacion y Diagnostico Molecular Instituto de Infertilidad y Genetica Mexico SCINGENESMexico City 05320Mexico Instituto Nacional de Pediatria Torre de InvestigacionMexico City 04530Mexico Laboratorio de Biologia Molecular Departamento de Genetica HumanaInstituto Nacional de PediatriaMexico City 04530Mexico Departamento de Toxicologia Centro de Investigacion y de Estudios Avanzados del Instituto Politecnico Nacional(CINVESTAV-IPN)Mexico City 07360Mexico

BACKGROUND Laron syndrome(LS)is an autosomal recessive hereditary condition affecting only 1/1000000 *** cause is associated with mutations in the growth hormone(GH)receptor(GHR),leading to GH *** patients typically present with severe growth retardation,obesity,and abnormal sexual ***,LS diagnosis is performed ***,we assessed the efficiency of Pre-implantation Genetic Testing(PGT)coupled with monoplex-polymerase chain reaction(PCR)technology for detecting this monogenic disease in embryos from a couple confirmed as LS heterozygous carriers CASE SUMMARY The couple LS-carriers were confirmed by the presence of a first child born with *** couple underwent a standard in vitro fertilization(IVF)*** was collected from trophectoderm cells from day 5 *** genome amplification(WGA)was performed using a Sureplex DNA Amplification System and analyzed by PCR,targeting the deletion of the exons 5 and 6 in the GHR gene as well as PGT by Next-generation Sequencing(Illumina).Eleven embryos were collected and analyzed.27.3%were the wild type for GHR,45.5%were heterozygotes,and 18.2%homozygous *** embryo yielded no *** 2-embryos transfers were performed;2 normal homozygous and four heterozygous carriers were selected for *** first two transfers were unsuccessful,whereas the final transfer with two heterozygous embryos resulted in clinical *** genomic composition of the fetus was verified,applying the same techniques using amniocytes,extracted after 21 wk of the ongoing *** fetus was confirmed as GHR deletion in exon 5-6,carrier.A non-affected baby was *** Here,we present a case demonstrating that using WGA as a template in addition to PCR targeting specific gene regions,exons 5 and 6 on the GHR gene,could identify LS carrier *** provides evidence that WGA and PCR serve as an excellent tool to detect this specific monogenic disease in IVF e

关键词： Growth hormone insensitivity Growth hormone receptor mutations Intragenic deletions Molecular diagnosis Embryo diagnosis Laron syndrome Case report

SARS-CoV Genome Polymorphism: A Bioinformatics Study

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Genomics, Proteomics & Bioinformatics 2005年第1期3卷 18-35页

作者： Gordana M. Pavlovi-La■eti Nenad S. Miti Andrija M. Tomovi Mirjana D. Pavlovi Milo V.Beljanski Faculty of Mathematics University of Belgrade 11001 Belgrade Serbia and Montenegro Faculty of Mathematics University of Belgrade 11001 Belgrade Serbia and MontenegroFriedrich MiescherInstitute for Biomedical Research CH-4058 Basel Switzerland Institute of General and Physical Chemistry11001 Belgrade Serbia and Montenegro.Institute of General and Physical Chemistry11001 Belgrade Serbia and Montenegro.

A dataset of 103 SARS-CoV isolates （101 human patients and 2 palm civets） was investigated on different aspects of genome polymorphism and isolate classification. The number and the distribution of single nucleotide variations （SNVs） and insertions and deletions, with respect to a “profile”, were determined and discussed （“profile” being a sequence containing the most represented letter per position）. Distribution of substitution categories per codon positions, as well as synonymous and non-synonymous substitutions in coding regions of annotated isolates, was determined, along with amino acid （a.a.） property changes. Similar analysis was performed for the spike （S） protein in all the isolates （55 of them being predicted for the first time）. The ratio Ka/Ks confirmed that the S gene was subjected to the Darwinian selection during virus transmission from animals to humans. Isolates from the dataset were classified according to genome polymorphism and genotypes. Genome polymorphism yields to two groups, one with a small number of SNVs and another with a large number of SNVs, with up to four subgroups with respect to insertions and deletions. We identified three basic nine-locus genotypes： TTTT/TTCGG, CGCC/TTCAT, and TGCC/TTCGT, with four subgenotypes. Both classifications proposed are in accordance with the new insights into possible epidemiological spread, both in space and time.

关键词： SARS Coronavirus single nucleotide polymorphism insertions deletions spike protein phylogenesis