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[PMID]: 29458464 [Au] Autor: Melo LA; Ventura JA; Costa H; Kitajima EW; Ferreira J; Bedendo IP [Ad] Endereço: 1​Departamento de Fitopatologia e Nematologia, ESALQ, Universidade de São Paulo, Caixa Postal 09, 13418-900 Piracicaba, SP, Brazil. [Ti] Título: Delineation of a novel subgroup 16SrXIII-J phytoplasma, a 'Candidatus Phytoplasma hispanicum'-related strain, based on computer-simulated RFLP and phylogenetic analysis. [So] Source: Int J Syst Evol Microbiol;68(3):962-966, 2018 Mar. [Is] ISSN: 1466-5034 [Cp] País de publicação: England [La] Idioma: eng [Ab] Resumo: Symptoms of fruit phyllody and slow growth, which are suggestive of phytoplasma infection, were observed in strawberry plants cultivated in commercial fields. In order to provide evidence of association of phytoplasma with affected plants, assays for detecting and identifying were performed through computer-simulated restriction fragment length polymorphism (RFLP) and phylogenetic analysis. Total DNA was extracted from symptomatic and asymptomatic samples and used as template in nested PCR primed by the primers P1/Tint followed by R16F2n/16R2. Amplified DNA fragments of 1.2 kb from the 16S rRNA gene revealed the presence of phytoplasma in all symptomatic samples. Molecular detection was confirmed by electron transmission microscopy, which evidenced pleomorphic bodies in the phloem vessels. Nucleotide sequence representative of the strawberry phytoplasma shared 97.2 to 99 % similarity with phytoplasmas currently classified as members of the distinct subgroups within the 16SrXIII group. Similarity coefficient (F) values ranged from 0.70 to 0.92, indicating that strawberry phytoplasma delineates a new strain in addition to 'Candidatus Phytoplasma hispanicum'-related strains. The evolutionary tree displayed that this strain emerges as a new branch in relation to those previously described. The novel strain, designated SFP (strawberry fruit phyllody) phytoplasma represents the new 16SrXIII-J subgroup and its sequence, denominated SFP-Br02, was deposited in the GenBank database (EU719108). These findings contribute for the knowledge of the genetic diversity existing among members of the group 16SrXIII and establishes strawberry as an additional host of representatives of this group in Brazil. [Mh] Termos MeSH primário: Fragaria/microbiologia Filogenia Phytoplasma/classificação Doenças das Plantas/microbiologia Polimorfismo de Fragmento de Restrição [Mh] Termos MeSH secundário: Técnicas de Tipagem Bacteriana Brasil Primers do DNA DNA Bacteriano/genética Reação em Cadeia da Polimerase RNA Ribossômico 16S/genética Análise de Sequência de DNA [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (DNA Primers); 0 (DNA, Bacterial); 0 (RNA, Ribosomal, 16S) [Em] Mês de entrada: 1803 [Cu] Atualização por classe: 180308 [Lr] Data última revisão: 180308 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 180221 [St] Status: MEDLINE [do] DOI: 10.1099/ijsem.0.002547

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[PMID]: 29205973 [Au] Autor: Xia X; Ding M [Ad] Endereço: School of Forensic Medicine, China Medical University, Shenyang 110000, China. [Ti] Título: [Application of COâ…  Gene Mini-barcoding in Species Identification of Hair]. [So] Source: Fa Yi Xue Za Zhi;32(6):441-443, 2016 Dec. [Is] ISSN: 1004-5619 [Cp] País de publicação: China [La] Idioma: chi [Ab] Resumo: OBJECTIVES: To identify the species of mammalian hair using COâ…  gene mini-barcoding technology. METHODS: A pair of universal primers for mammalian COâ…  gene mini-barcoding were designed. The hair DNA samples of experimental animals from 11 species in 5 orders, mammalia was amplified by PCR technology with universal primers, and the PCR products were sequenced by bi-directional DNA and after the sequences splicing the results were deposited into the BOLD database to perform the homology comparison. RESULTS: The DNA of hair from all experiment animal species could be totally amplified by the mini-barcoding universal primers designed in this study. The length of amplified fragment was 147 bp. The result of homology comparison in the database showed that the closest matching species were consistent with the experiment animal species. In addition to the matching degree of （98.99%）, all homology matching degree of the other experiment animals were 100%, and the intraspecific genetic distance of was 1%. The interspecific genetic distance was ten times more than the intraspecific genetic distance which could be used for species identification. CONCLUSIONS: The COâ…  gene mini-barcode technology is established and can provide fast and accurate species identification for hair of mammals. [Mh] Termos MeSH primário: Pelo Animal Código de Barras de DNA Taxonômico Cabelo [Mh] Termos MeSH secundário: Animais Primers do DNA Reação em Cadeia da Polimerase Especificidade da Espécie [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (DNA Primers) [Em] Mês de entrada: 1802 [Cu] Atualização por classe: 180308 [Lr] Data última revisão: 180308 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 171206 [St] Status: MEDLINE [do] DOI: 10.3969/j.issn.1004-5619.2016.06.012

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[PMID]: 28453672 [Au] Autor: Tian S; Das R [Ad] Endereço: Department of Biochemistry. [Ti] Título: Primerize-2D: automated primer design for RNA multidimensional chemical mapping. [So] Source: Bioinformatics;33(9):1405-1406, 2017 May 01. [Is] ISSN: 1367-4811 [Cp] País de publicação: England [La] Idioma: eng [Ab] Resumo: Summary: Rapid RNA synthesis of comprehensive single mutant libraries and targeted multiple mutant libraries is enabling new multidimensional chemical approaches to solve RNA structures. PCR assembly of DNA templates and in vitro transcription allow synthesis and purification of hundreds of RNA mutants in a cost-effective manner, with sharing of primers across constructs allowing significant reductions in expense. However, these protocols require organization of primer locations across numerous 96 well plates and guidance for pipetting, non-trivial tasks for which informatics and visualization tools can prevent costly errors. We report here an online tool to accelerate synthesis of large libraries of desired mutants through design and efficient organization of primers. The underlying program and graphical interface have been experimentally tested in our laboratory for RNA domains with lengths up to 300 nucleotides and libraries encompassing up to 960 variants. In addition to the freely available Primerize-2D server, the primer design code is available as a stand-alone Python package for broader applications. Availability and Implementation: http://primerize2d.stanford.edu. Contact: rhiju@stanford.edu. Supplementary information: Supplementary data are available at Bioinformatics online. [Mh] Termos MeSH primário: Primers do DNA Mutação RNA/química Análise de Sequência de RNA/métodos Software [Mh] Termos MeSH secundário: Conformação de Ácido Nucleico Reação em Cadeia da Polimerase/métodos RNA/genética [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (DNA Primers); 63231-63-0 (RNA) [Em] Mês de entrada: 1801 [Cu] Atualização por classe: 180308 [Lr] Data última revisão: 180308 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 170429 [St] Status: MEDLINE [do] DOI: 10.1093/bioinformatics/btw814

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[PMID]: 29111407 [Au] Autor: Chahorm K; Prakitchaiwattana C [Ad] Endereço: Department of Food Technology, Faculty of Science, Chulalongkorn University, Patumwan, Bangkok 10330, Thailand. [Ti] Título: Application of Reverse Transcriptase-PCR-DGGE as a rapid method for routine determination of Vibrio spp. in foods. [So] Source: Int J Food Microbiol;264:46-52, 2018 Jan 02. [Is] ISSN: 1879-3460 [Cp] País de publicação: Netherlands [La] Idioma: eng [Ab] Resumo: The aim of this research was to evaluate the feasibility of PCR-DGGE and Reverse Transcriptase-PCR-DGGE techniques for rapid detection of Vibrio species in foods. Primers GC567F and 680R were initially evaluated for amplifying DNA and cDNA of ten references Vibrio species by PCR method. The GC-clamp PCR amplicons were separated according to their sequences by the DGGE using 10% (w/v) polyacrylamide gel containing 45-70% urea and formamide denaturants. Two pair of Vibrio species, which could not be differentiated on the gel, was Vibrio fluvialis - Vibrio furnissii and Vibrio parahaemolyticus - Vibrio harveyi. To determine the detection limit, in the community of 10 reference strains containing the same viable population, distinct DNA bands of 3 species; Vibrio cholerae, Vibrio mimicus and Vibrio alginolyticus were consistently observed by PCR-DGGE technique. In fact, 5 species; Vibrio cholerae, Vibrio mimicus, Vibrio alginolyticus, Vibrio parahaemolyticus and Vibrio fluvialis consistently observed by Reverse Transcriptase-PCR-DGGE. In the community containing different viable population increasing from 10 to 10 CFU/mL, PCR-DGGE analysis only detected the two most prevalent species, while RT-PCR-DGGE detected the five most prevalent species. Therefore, Reverse Transcriptase-PCR-DGGE was also selected for detection of various Vibrio cell conditions, including viable cell (VC), injured cells from frozen cultures (IVC) and injured cells from frozen cultures with pre-enrichment (PIVC). It was found that cDNA band of all cell conditions gave the same migratory patterns, except that multiple cDNA bands of Plesiomonas shigelloides under IVC and PIVC conditions were found. When Reverse Transcriptase-PCR-DGGE was used for detecting Vibrio parahaemolyticus in the pathogen-spiked food samples, Vibrio parahaemolyticus could be detected in the spiked samples containing at least 10 CFU/g of this pathogen. The results obtained also corresponded to standard method (USFDA, 2004). In comparison with the detection of the Vibrio profiles in fourteen food samples using standard method, Reverse Transcriptase-PCR-DGGE resulted in 100%, 75% and 50% similarity in 3, 1 and 6 food samples, respectively. [Mh] Termos MeSH primário: Eletroforese em Gel de Gradiente Desnaturante/métodos Reação em Cadeia da Polimerase Via Transcriptase Reversa/métodos Vibrio alginolyticus/genética Vibrio cholerae/genética Vibrio mimicus/genética Vibrio parahaemolyticus/genética [Mh] Termos MeSH secundário: Primers do DNA/genética Microbiologia de Alimentos/métodos Técnicas de Amplificação de Ácido Nucleico/métodos Reação em Cadeia da Polimerase/métodos DNA Polimerase Dirigida por RNA Vibrio alginolyticus/classificação Vibrio alginolyticus/isolamento & purificação Vibrio cholerae/classificação Vibrio cholerae/isolamento & purificação Vibrio mimicus/classificação Vibrio mimicus/isolamento & purificação Vibrio parahaemolyticus/classificação Vibrio parahaemolyticus/isolamento & purificação [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (DNA Primers); EC 2.7.7.49 (RNA-Directed DNA Polymerase) [Em] Mês de entrada: 1802 [Cu] Atualização por classe: 180226 [Lr] Data última revisão: 180226 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 171108 [St] Status: MEDLINE

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[PMID]: 28457784 [Au] Autor: Vandenbussche F; Lefebvre DJ; De Leeuw I; Van Borm S; De Clercq K [Ad] Endereço: Molecular Platform, OD Viral Diseases, CODA-CERVA, Groeselenberg 99, 1180 Brussels, Belgium. [Ti] Título: Laboratory validation of two real-time RT-PCR methods with 5'-tailed primers for an enhanced detection of foot-and-mouth disease virus. [So] Source: J Virol Methods;246:90-94, 2017 Aug. [Is] ISSN: 1879-0984 [Cp] País de publicação: Netherlands [La] Idioma: eng [Ab] Resumo: The 3D and 5UTR real-time RT-PCR assays (RT-qPCR) from Callahan et al. (2002) and Reid et al. (2002) are commonly used reference methods for the detection of foot-and-mouth disease virus (FMDV). For an optimal detection of FMDV in clinical samples, it is advised to use both assays simultaneously (King et al., 2006). Recently, Vandenbussche et al. (2016) showed that the addition of 5'-tails to the FMDV-specific primers enhances the detection of FMDV in both the 3D and the 5UTR RT-qPCR assay. To validate the 3D and 5UTR RT-qPCR assays with 5'-tailed primers for diagnostic purposes, both assays were run in parallel in a triplex one-step RT-qPCR protocol with beta-actin as an internal control and synthetic RNA as an external control. We obtained low limits of detection and high linearity's, high repeatability and reproducibility, near 100% analytical specificity and >99% diagnostic accuracy for both assays. It was concluded that the 3D and 5UTR RT-qPCR assays with 5'-tailed primers are particularly suited for the detection of FMDV as well as to exclude the presence of FMDV. [Mh] Termos MeSH primário: Regiões 5´ não Traduzidas Primers do DNA Vírus da Febre Aftosa/isolamento & purificação Febre Aftosa/diagnóstico Reação em Cadeia da Polimerase Via Transcriptase Reversa/métodos [Mh] Termos MeSH secundário: Animais Febre Aftosa/virologia Vírus da Febre Aftosa/genética RNA Viral/sangue RNA Viral/genética Reprodutibilidade dos Testes Sensibilidade e Especificidade Ovinos/virologia Suínos/virologia [Pt] Tipo de publicação: JOURNAL ARTICLE; VALIDATION STUDIES [Nm] Nome de substância: 0 (5' Untranslated Regions); 0 (DNA Primers); 0 (RNA, Viral) [Em] Mês de entrada: 1802 [Cu] Atualização por classe: 180226 [Lr] Data última revisão: 180226 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 170502 [St] Status: MEDLINE

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[PMID]: 28456667 [Au] Autor: Chantratita W; Song KS; Nimse SB; Pongthanapisith V; Thongbaiphet N; Wongtabtim G; Pasomsub E; Angkanavin K; Sonawane MD; Warkad SD; Kim T [Ad] Endereço: Virology Laboratory, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand. Electronic address: wasun.cha@mahidol.ac.th. [Ti] Título: 6 HCV Genotyping 9G test for HCV 1a, 1b, 2, 3, 4 and 6 (6a, 6f, 6i and 6n) with high accuracy. [So] Source: J Virol Methods;246:95-99, 2017 Aug. [Is] ISSN: 1879-0984 [Cp] País de publicação: Netherlands [La] Idioma: eng [Ab] Resumo: According to EASL guidelines and WHO recommendations, the accurate detection of HCV genotypes such as HCV 1a, HCV1b, HCV 2, HCV 3, HCV 4, and HCV 6 (6a, 6f, 6i, 6n) is crucial for the efficient treatment of hepatitis C. HCV Genotyping 9G test allows simultaneous genotyping of HCV 1a, 1b, 2, 3, 4, and 6 (6a, 6f, 6i, and 6n) in clinical samples in 30min. The performance of the test was evaluated by comparison with sequence analysis. Serum samples (n=152) from HCV-infected patients (n=110) and healthy individuals (n=42) were processed under blinded codes. The k coefficient (kappa) values indicated high agreement between the HCV Genotyping 9G test and sequencing. The sensitivity and specificity of the test were 99.1% and 99.7%, respectively. The results indicate that HCV Genotyping 9G test is rapid, reliable, sensitive, and accurate for screening and genotyping of HCV in the clinical specimens. [Mh] Termos MeSH primário: Técnicas de Genotipagem/métodos Hepacivirus/genética [Mh] Termos MeSH secundário: Primers do DNA Genótipo Hepacivirus/classificação Seres Humanos Cirrose Hepática/virologia Reação em Cadeia da Polimerase/métodos Sensibilidade e Especificidade Análise de Sequência de DNA Proteínas não Estruturais Virais/genética [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (DNA Primers); 0 (Viral Nonstructural Proteins) [Em] Mês de entrada: 1802 [Cu] Atualização por classe: 180226 [Lr] Data última revisão: 180226 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 170501 [St] Status: MEDLINE

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[PMID]: 29232417 [Au] Autor: Natonek-Wisniewska M; Krzyscin P [Ad] Endereço: Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Balice, Poland. [Ti] Título: Evaluation of the suitability of mitochondrial DNA for species identification of microtraces and forensic traces. [So] Source: Acta Biochim Pol;64(4):705-708, 2017. [Is] ISSN: 1734-154X [Cp] País de publicação: Poland [La] Idioma: eng [Ab] Resumo: The objective of the study was to demonstrate how mitochondrial DNA (mtDNA) can be used to determine the species origin of animal microtraces. The study included pieces of cat and dog hair without the root, a fragment of cooked chicken bone (0.1g), three goose down samples (0.028 g), a pork swab, a pork scratching (5×5×5 mm), and pork lard (0.22 g). DNA was isolated from all of these samples using the method appropriate for the particular source material. The extracts had DNA concentration exceeding 5.4 ng/µl with A purity range of 1.14-1.88. Next, the samples were subjected to PCR and real-time PCR with species-specific primers and primers complementary to mitochondrial DNA (mtDNA). Control reactions based on the amplification of eukaryotic-specific fragment (18S rRNA) were additionally performed. PCR and real-time PCR products for detection of species-specific mtDNA were obtained for all templates, whereas during the detection of eukaryote DNA no product was obtained for dog and cat hair only. The poor quality of the obtained DNA did not prevent the analysis. The results showed that mitochondrial DNA is suitable for identification of small or highly processed samples, in which genomic DNA often cannot be analyzed. [Mh] Termos MeSH primário: DNA Mitocondrial/genética Genética Forense/métodos Reação em Cadeia da Polimerase em Tempo Real/métodos [Mh] Termos MeSH secundário: Animais Gatos Primers do DNA DNA Mitocondrial/isolamento & purificação Cães Análise de Alimentos/métodos Cabelo/fisiologia Carne Vermelha Reprodutibilidade dos Testes Especificidade da Espécie [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (DNA Primers); 0 (DNA, Mitochondrial) [Em] Mês de entrada: 1802 [Cu] Atualização por classe: 180223 [Lr] Data última revisão: 180223 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 171213 [St] Status: MEDLINE [do] DOI: 10.18388/abp.2017_2304

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[PMID]: 28741076 [Au] Autor: Tzelepis G; Bejai S; Sattar MN; Schwelm A; Ilbäck J; Fogelqvist J; Dixelius C [Ad] Endereço: Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, P.O. Box 7080, 75007, Uppsala, Sweden. Georgios.Tzelepis@slu.se. [Ti] Título: Detection of Verticillium species in Swedish soils using real-time PCR. [So] Source: Arch Microbiol;199(10):1383-1389, 2017 Dec. [Is] ISSN: 1432-072X [Cp] País de publicação: Germany [La] Idioma: eng [Ab] Resumo: Verticillium species are soilborne plant pathogens, responsible for big yield losses worldwide. Here, we report improved procedures to generate DNA from Verticillium species imbedded in farm soils. Using new genomic sequence information, primers for V. dahliae, V. albo-atrum, V. tricorpus, and V. longisporum were designed. In a survey of 429 samples from intensively farmed soil of two Swedish regions, only V. dahliae and V. longisporum were identified. A bias towards V. longisporum (40%) was seen in the south, whereas V. dahliae was more frequent in the western region (19%). Analyses of soil and leaf samples from 20 sugar beet fields, where foliar wilting had been observed, revealed V. dahliae DNA in all leaf and soil samples and V. longisporum in 18 soil samples, illustrating host choice and longevity of the V. longisporum microsclerotia. This study demonstrates the applicability of new molecular diagnostic tools that are important for growers of variable crops. [Mh] Termos MeSH primário: Brassicaceae/microbiologia DNA Fúngico/genética Verticillium/genética Verticillium/isolamento & purificação [Mh] Termos MeSH secundário: Primers do DNA/genética Doenças das Plantas/microbiologia Reação em Cadeia da Polimerase em Tempo Real Solo/química Microbiologia do Solo Suécia Verticillium/classificação [Pt] Tipo de publicação: JOURNAL ARTICLE [Nm] Nome de substância: 0 (DNA Primers); 0 (DNA, Fungal); 0 (Soil) [Em] Mês de entrada: 1802 [Cu] Atualização por classe: 180221 [Lr] Data última revisão: 180221 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 170726 [St] Status: MEDLINE [do] DOI: 10.1007/s00203-017-1412-z

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[PMID]: 28466090 [Au] Autor: Ogawa A; Celikkol-Aydin S; Gaylarde C; Baptista-Neto JA; Beech I [Ad] Endereço: Department Microbiology and Plant Biology, University of Oklahoma, Norman, USA. [Ti] Título: Microbiomes of Biofilms on Decorative Siliceous Stone: Drawbacks and Advantages of Next Generation Sequencing. [So] Source: Curr Microbiol;74(7):848-853, 2017 Jul. [Is] ISSN: 1432-0991 [Cp] País de publicação: United States [La] Idioma: eng [Ab] Resumo: Next Generation Sequencing (NGS), using the Illumina metabarcoding system, showed differences between biofilm communities on three degraded siliceous stone church façades in central Rio de Janeiro. Two church biofilms (on granite and augen gneiss) were dominated by Actinobacteria; the third (granite), surrounded by trees and further from intense vehicular traffic, by Gammaproteobacteria. Yeast-like forms of Basidiomycetes and Ascomycetes were major fungi on all facades, but 22.8% of Operational Taxonomic Units could not be assigned to any fungal taxon after DNA amplification with ITS primers and analysis with the UNITE database, indicating the need for more fungal NGS studies. The pipeline used in analysis of the V4 region of rRNA bacterial gene sequences influenced the taxa detected, with two major classes and many genera identified only by the pipeline using the Greengenes, and not the Silva, database. Principal Components Analysis separated façade biofilms into the appropriate three groups and indicated greater dissimilarity of the tree-surrounded church biofilm from the others, confirmed by Jaccard Similarity coefficients, suggesting that local environment influences community composition more than stone type. NGS allows rapid and detailed analysis of microbiomes, but results must be carefully assessed and must not be used as the sole indication of community composition. [Mh] Termos MeSH primário: Bactérias/isolamento & purificação Fungos/isolamento & purificação Sedimentos Geológicos/microbiologia Sequenciamento de Nucleotídeos em Larga Escala/métodos Microbiota [Mh] Termos MeSH secundário: Bactérias/classificação Bactérias/genética Fenômenos Fisiológicos Bacterianos Biofilmes Primers do DNA Fungos/classificação Fungos/genética Fungos/fisiologia Compostos de Silício/análise [Pt] Tipo de publicação: EVALUATION STUDIES; JOURNAL ARTICLE [Nm] Nome de substância: 0 (DNA Primers); 0 (Silicon Compounds) [Em] Mês de entrada: 1802 [Cu] Atualização por classe: 180212 [Lr] Data última revisão: 180212 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 170504 [St] Status: MEDLINE [do] DOI: 10.1007/s00284-017-1257-3

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[PMID]: 29304124 [Au] Autor: Krehenwinkel H; Fong M; Kennedy S; Huang EG; Noriyuki S; Cayetano L; Gillespie R [Ad] Endereço: Department of Environmental Sciences, Policy and Management, University of California, Mulford Hall, Berkeley, California, United States of America. [Ti] Título: The effect of DNA degradation bias in passive sampling devices on metabarcoding studies of arthropod communities and their associated microbiota. [So] Source: PLoS One;13(1):e0189188, 2018. [Is] ISSN: 1932-6203 [Cp] País de publicação: United States [La] Idioma: eng [Ab] Resumo: PCR amplification bias is a well-known problem in metagenomic analysis of arthropod communities. In contrast, variation of DNA degradation rates is a largely neglected source of bias. Differential degradation of DNA molecules could cause underrepresentation of taxa in a community sequencing sample. Arthropods are often collected by passive sampling devices, like malaise traps. Specimens in such a trap are exposed to varying periods of suboptimal storage and possibly different rates of DNA degradation. Degradation bias could thus be a significant issue, skewing diversity estimates. Here, we estimate the effect of differential DNA degradation on the recovery of community diversity of Hawaiian arthropods and their associated microbiota. We use a simple DNA size selection protocol to test for degradation bias in mock communities, as well as passively collected samples from actual Malaise traps. We compare the effect of DNA degradation to that of varying PCR conditions, including primer choice, annealing temperature and cycle number. Our results show that DNA degradation does indeed bias community analyses. However, the effect of this bias is of minor importance compared to that induced by changes in PCR conditions. Analyses of the macro and microbiome from passively collected arthropod samples are thus well worth pursuing. [Mh] Termos MeSH primário: Artrópodes/genética Artrópodes/microbiologia Código de Barras de DNA Taxonômico/métodos DNA/análise DNA/genética Microbiota/genética [Mh] Termos MeSH secundário: Animais Artrópodes/classificação Biodiversidade Código de Barras de DNA Taxonômico/estatística & dados numéricos Primers do DNA Ecossistema Hawaii Metagenoma Metagenômica/métodos Metagenômica/estatística & dados numéricos Reação em Cadeia da Polimerase/métodos Viés de Seleção [Pt] Tipo de publicação: JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T [Nm] Nome de substância: 0 (DNA Primers); 9007-49-2 (DNA) [Em] Mês de entrada: 1801 [Cu] Atualização por classe: 180210 [Lr] Data última revisão: 180210 [Sb] Subgrupo de revista: IM [Da] Data de entrada para processamento: 180106 [St] Status: MEDLINE [do] DOI: 10.1371/journal.pone.0189188

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