共查询到20条相似文献,搜索用时 15 毫秒
1.
Thierry?De Baere Anne?Van Keerberghen Peter?Van Hauwe Hans?De Beenhouwer An?Boel Gerda?Verschraegen Geert?Claeys Mario?Vaneechoutte
Background
Currently, most laboratories identify yeasts routinely on the basis of morphology and biochemical reactivity. This approach has quite often limited discriminatory power and may require long incubation periods. Due to the increase of fungal infections and due to specific antifungal resistence patterns for different species, accurate and rapid identification has become more important. Several molecular techniques have been described for fast and reliable identification of yeast isolates, but interlaboratory exchangeability of identification schemes of molecular techniques has hardly been studied. Here, we compared amplified ITS2 fragment length determination by an ABI Prism 310 (Applied Biosystems, Foster City, Ca.) capillary electrophoresis system with that obtained by a CEQ8000 (Beckman Coulter, Fullerton, Ca.) capillary electrophoresis system. 相似文献2.
Background
The rapid and accurate identification of species is a critical component of large-scale biodiversity monitoring programs. DNA arrays (micro and macro) and DNA barcodes are two molecular approaches that have recently garnered much attention. Here, we compare these two platforms for identification of an important group, the mammals. 相似文献3.
Jitka Trtkova Petr Pavlicek Lenka Ruskova Petr Hamal Dagmar Koukalova Vladislav Raclavsky 《BMC microbiology》2009,9(1):234-21
Background
Rapid, easy, economical and accurate species identification of yeasts isolated from clinical samples remains an important challenge for routine microbiological laboratories, because susceptibility to antifungal agents, probability to develop resistance and ability to cause disease vary in different species. To overcome the drawbacks of the currently available techniques we have recently proposed an innovative approach to yeast species identification based on RAPD genotyping and termed McRAPD (Melting curve of RAPD). Here we have evaluated its performance on a broader spectrum of clinically relevant yeast species and also examined the potential of automated and semi-automated interpretation of McRAPD data for yeast species identification. 相似文献4.
16S rRNA gene sequencing on a benchtop sequencer: accuracy for identification of clinically important bacteria
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G.S. Watts K. Youens‐Clark M.J. Slepian D.M. Wolk M.M. Oshiro G.S. Metzger D. Dhingra L.D. Cranmer B.L. Hurwitz 《Journal of applied microbiology》2017,123(6):1584-1596
Aims
Test the choice of 16S rRNA gene amplicon and data analysis method on the accuracy of identification of clinically important bacteria utilizing a benchtop sequencer.Methods and Results
Nine 16S rRNA amplicons were tested on an Ion Torrent PGM to identify 41 strains of clinical importance. The V1–V2 region identified 40 of 41 isolates to the species level. Three data analysis methods were tested, finding that the Ribosomal Database Project's SequenceMatch outperformed BLAST and the Ion Reporter Metagenomics analysis pipeline. Lastly, 16S rRNA gene sequencing mixtures of four species through a six log range of dilution showed species were identifiable even when present as 0·1% of the mixture.Conclusions
Sequencing the V1–V2 16S rRNA gene region, made possible by the increased read length Ion Torrent PGM sequencer's 400 base pair chemistry, may be a better choice over other commonly used regions for identifying clinically important bacteria. In addition, the SequenceMatch algorithm, freely available from the Ribosomal Database Project, is a good choice for matching filtered reads to organisms. Lastly, 16S rRNA gene sequencing's sensitivity to the presence of a bacterial species at 0·1% of a mixture suggests it has sufficient sensitivity for samples in which important bacteria may be rare.Significance and Impact of the Study
We have validated 16S rRNA gene sequencing on a benchtop sequencer including simple mixtures of organisms; however, our results highlight deficits for clinical application in place of current identification methods. 相似文献5.
Véronique Apaire-Marchais Marie Kempf Corinne Lefrançois Agnès Marot Patricia Licznar Jane Cottin Daniel Poulain Raymond Robert 《BMC microbiology》2008,8(1):157
Background
Candida species have become the fourth most-frequent cause of nosocomial bloodstream infections in immunocompromised patients. Therefore, rapid identification of pathogenic fungi to species level has been considered critical for treatment. Conventional diagnostic procedures such as blood culture or biochemical tests are lacking both sensitivity and species specificity, so development of rapid diagnostic is essential. 相似文献6.
Carol Iversen Lee Lancashire Michael Waddington Stephen Forsythe Graham Ball 《BMC microbiology》2006,6(1):28-8
Background
Enterobacter sakazakii is an emergent pathogen associated with ingestion of infant formula and accurate identification is important in both industrial and clinical settings. Bacterial species can be difficult to accurately characterise from complex biochemical datasets and computer algorithms can potentially simplify the process. 相似文献7.
Identification of human pathogens isolated from blood using microarray hybridisation and signal pattern recognition 总被引:2,自引:0,他引:2
Herbert Wiesinger-Mayr Klemens Vierlinger Rudolf Pichler Albert Kriegner Alexander M Hirschl Elisabeth Presterl Levente Bodrossy Christa Noehammer 《BMC microbiology》2007,7(1):78
Background
Pathogen identification in clinical routine is based on the cultivation of microbes with subsequent morphological and physiological characterisation lasting at least 24 hours. However, early and accurate identification is a crucial requisite for fast and optimally targeted antimicrobial treatment. Molecular biology based techniques allow fast identification, however discrimination of very closely related species remains still difficult. 相似文献8.
Background
An important goal of comparative genomics is the identification of functional elements through conservation analysis. Phylo-HMM was recently introduced to detect conserved elements based on multiple genome alignments, but the method has not been rigorously evaluated. 相似文献9.
Ting Gao Hui Yao Jingyuan Song Yingjie Zhu Chang Liu Shilin Chen 《BMC evolutionary biology》2010,10(1):324
Background
Five DNA regions, namely, rbcL, matK, ITS, ITS2, and psbA-trnH, have been recommended as primary DNA barcodes for plants. Studies evaluating these regions for species identification in the large plant taxon, which includes a large number of closely related species, have rarely been reported. 相似文献10.
Geert?Claeys Thierry?De Baere Georges?Wauters Patricia?Vandecandelaere Gerda?Verschraegen An?Muylaert Mario?Vaneechoutte
Background
Enterobacter aerogenes and Klebsiella pneumoniae are common isolates in clinical microbiology and important as producers of extended spectrum β-lactamases (ESBL). The discrimination between both species, which is routinely based on biochemical characteristics, is generally accepted to be straightforward. Here we report that genotypically unrelated strains of E. aerogenes can be misidentified as K. pneumoniae by routine laboratories using standard biochemical identification and using identification automates. 相似文献11.
Mingming Xin Yu Wang Yingyin Yao Na Song Zhaorong Hu Dandan Qin Chaojie Xie Huiru Peng Zhongfu Ni Qixin Sun 《BMC plant biology》2011,11(1):61
Background
Biotic and abiotic stresses, such as powdery mildew infection and high temperature, are important limiting factors for yield and grain quality in wheat production. Emerging evidences suggest that long non-protein coding RNAs (npcRNAs) are developmentally regulated and play roles in development and stress responses of plants. However, identification of long npcRNAs is limited to a few plant species, such as Arabidopsis, rice and maize, no systematic identification of long npcRNAs and their responses to abiotic and biotic stresses is reported in wheat. 相似文献12.
Background
One of the important goals in the post-genomic era is to determine the regulatory elements within the non-coding DNA of a given organism's genome. The identification of functional cis-regulatory modules has proven difficult since the component factor binding sites are small and the rules governing their arrangement are poorly understood. However, the genomes of suitably diverged species help to predict regulatory elements based on the generally accepted assumption that conserved blocks of genomic sequence are likely to be functional. To judge the efficacy of strategies that prefilter by sequence conservation it is important to know to what extent the converse assumption holds, namely that functional elements common to both species will fall within these conserved blocks. The recently completed sequence of a second Drosophila species provides an opportunity to test this assumption for one of the experimentally best studied regulatory networks in multicellular organisms, the body patterning of the fly embryo. 相似文献13.
Storage protein profiles in Spanish and runner market type peanuts and potential markers 总被引:1,自引:0,他引:1
Background
Proteomic analysis has proven to be the most powerful method for describing plant species and lines, and for identification of proteins in complex mixtures. The strength of this method resides in high resolving power of two-dimensional electrophoresis (2-DE), coupled with highly sensitive mass spectrometry (MS), and sequence homology search. By using this method, we might find polymorphic markers to differentiate peanut subspecies. 相似文献14.
Background
Correct identification and cryptic biodiversity revelation for marine organisms are pressing since the marine life is important in maintaining the balance of ecological system and is facing the problem of biodiversity crisis or food safety. DNA barcoding has been proved successful to provide resolution beyond the boundaries of morphological information. Nassarius, the common mudsnail, plays an important role in marine environment and has problem in food safety, but the classification of it is quite confused because of the complex morphological diversity.Methodology/Principal Findings
Here we report a comprehensive barcoding analysis of 22 Nassarius species. We integrated the mitochondrial and nuclear sequences and the morphological characters to determine 13 Nassarius species studied and reveal four cryptic species and one pair synonyms. Distance, monophyly, and character–based barcoding methods were employed.Conclusions/Significance
Such successful identification and unexpected cryptic discovery is significant for Nassarius in food safety and species conversation and remind us to pay more attention to the hidden cryptic biodiversity ignored in marine life. Distance, monophyly, and character–based barcoding methods are all very helpful in identification but the character-based method shows some advantages. 相似文献15.
Almir S Zanca Renato Vicentini Fausto A Ortiz-Morea Luiz EV Del Bem Marcio J da Silva Michel Vincentz Fabio TS Nogueira 《BMC plant biology》2010,10(1):260
Background
MicroRNAs (miRNAs) are small regulatory RNAs, some of which are conserved in diverse plant genomes. Therefore, computational identification and further experimental validation of miRNAs from non-model organisms is both feasible and instrumental for addressing miRNA-based gene regulation and evolution. Sugarcane (Saccharum spp.) is an important biofuel crop with publicly available expressed sequence tag and genomic survey sequence databases, but little is known about miRNAs and their targets in this highly polyploid species. 相似文献16.
Background
Symbiotic N2 fixation in legumes is constrained by many factors, including the paucity of suitable soil rhizobia To maximise growth of legume species therefore often requires the application of effective rhizobia as inoculants. But where native strains out-compete introduced rhizobia for nodule formation, it is important that the competitiveness of selected strains is tested in the field and glasshouse prior to their recommendation as commercial inoculants. However the methodology for strain identification inside nodules has often proved difficult and thus limited this field of research. In this study, the suitability of the antibiotic resistance technique (both intrinsic low-resistance fingerprinting and high-resistance marking) and the serological indirect ELISA method were assessed for their ability to detect selected Cyclopia rhizobia under glasshouse and field conditions. The four rhizobial strains that were used, namely PPRICI3, UCT40a, UCT44b and UCT61a, were isolated from wild Cyclopia species growing in the Western Cape fynbos of South Africa. 相似文献17.
Ralph Feltens Renate Görner Stefan Kalkhof Helke Gröger-Arndt Martin von Bergen 《BMC evolutionary biology》2010,10(1):95
Background
The use of molecular biology-based methods for species identification and establishing phylogenetic relationships has supplanted traditional methods relying on morphological characteristics. While PCR-based methods are now the commonly accepted gold standards for these types of analysis, relatively high costs, time-consuming assay development or the need for a priori information about species-specific sequences constitute major limitations. In the present study, we explored the possibility to differentiate between 13 different species from the genus Drosophila via a molecular proteomic approach. 相似文献18.
Genomic taxonomy of vibrios 总被引:1,自引:0,他引:1
Cristiane C Thompson Carolina P Ana Vicente Rangel C Souza Ana Tereza R Vasconcelos Tammi Vesth Nelson Alves Jr David W Ussery Tetsuya Iida Fabiano L Thompson 《BMC evolutionary biology》2009,9(1):258-16
Background
Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i. e. data that can be used to distinguish different taxonomic levels, such as species and genera) from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA), supertrees, Average Amino Acid Identity (AAI), genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios. 相似文献19.
Bjorn Kloosterman AM Anithakumari Pierre-Yves Chibon Marian Oortwijn Gerard C van der Linden Richard GF Visser Christian WB Bachem 《BMC plant biology》2012,12(1):17
Background
With the completion of genome sequences belonging to some of the major crop plants, new challenges arise to utilize this data for crop improvement and increased food security. The field of genetical genomics has the potential to identify genes displaying heritable differential expression associated to important phenotypic traits. Here we describe the identification of expression QTLs (eQTLs) in two different potato tissues of a segregating potato population and query the potato genome sequence to differentiate between cis- and trans-acting eQTLs in relation to gene subfunctionalization. 相似文献20.
Xuan Wang Yong-Feng Fu Rui-Ying Wang Li Li Ya-Hui Cao Yan-Qiong Chen Hua-Zhen Zhao Qiang-Qiang Zhang Ji-Qin Wu Xin-Hua Weng Xun-Jia Cheng Li-Ping Zhu 《PloS one》2014,9(5)