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You searched for: Journal name Journal of microbiological methods Remove constraint Journal name: Journal of microbiological methods Publication year rev 7985-2015 Remove constraint Publication year rev: 7985-2015 Source 2015 v.112 Remove constraint Source: 2015 v.112
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1. Analysis of variations in band positions for normalization in across-gel denaturing gradient gel electrophoresis

Author:
Yuko Matsushita; Kohji Yamamura; Sho Morimoto; Zhihua Bao; Daisuke Kurose; Ikuo Sato; Shigenobu Yoshida; Seiya Tsushima
Source:
Journal of microbiological methods 2015 v.112 pp. 11-20
ISSN:
0167-7012
Subject:
DNA; Nematoda; denaturing gradient gel electrophoresis; fungi; gels; soil; statistical analysis
Abstract:
... Variation in band position between gels is a well-known problem in denaturing gradient gel electrophoresis (DGGE). However, few reports have evaluated the degree of variation in detail. In this study, we investigated the variation in band positions of DNA samples extracted from soil, normalized using reference positions within marker lanes for DGGE in three organismal (bacterial, fungal, and nemat ...
DOI:
10.1016/j.mimet.2015.02.011

2. Development and evaluation of a culture-independent method for source determination of fecal wastes in surface and storm waters using reverse transcriptase-PCR detection of FRNA coliphage genogroup gene sequences

Author:
Jack Paar; Mark M. Doolittle; Manju Varma; Shawn Siefring; Kevin Oshima; Richard A. Haugland
Source:
Journal of microbiological methods 2015 v.112 pp. 28-35
ISSN:
0167-7012
Subject:
RNA; coliphages; drainage systems; feces; genetic markers; humans; nucleotide sequences; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; stormwater; surface water; wastewater
Abstract:
... A method, incorporating recently improved reverse transcriptase-PCR primer/probe assays and including controls for detecting interferences in RNA recovery and analysis, was developed for the direct, culture-independent detection of genetic markers from FRNA coliphage genogroups I, II & IV in water samples. Results were obtained from an initial evaluation of the performance of this method in analys ...
DOI:
10.1016/j.mimet.2015.02.015

3. Development of a novel in vitro onychomycosis model for the evaluation of topical antifungal activity

Author:
Reindert Sleven; Ellen Lanckacker; Gaëlle Boulet; Peter Delputte; Louis Maes; Paul Cos
Source:
Journal of microbiological methods 2015 v.112 pp. 73-75
ISSN:
0167-7012
Subject:
antifungal agents; antifungal properties; cattle; drugs; hooves; models
Abstract:
... A novel in vitro onychomycosis model was developed to easily predict the topical activity potential of novel antifungal drugs. The model encompasses drug activity and diffusion through bovine hoof slices in a single experimental set-up. Results correspond well with the antifungal susceptibility assay and Franz cell diffusion test. ...
DOI:
10.1016/j.mimet.2015.03.009

4. Evaluation of a real-time PCR and a loop-mediated isothermal amplification for detection of Xanthomonas arboricola pv. pruni in plant tissue samples

Author:
Ana Palacio-Bielsa; Pablo López-Soriano; Andreas Bühlmann; Joop van Doorn; Khanh Pham; Miguel A. Cambra; Isabel M. Berruete; Joël F. Pothier; Brion Duffy; Antonio Olmos; María M. López
Source:
Journal of microbiological methods 2015 v.112 pp. 36-39
ISSN:
0167-7012
Subject:
Xanthomonas arboricola pv. pruni; almonds; leaves; loop-mediated isothermal amplification; plant tissues; quantitative polymerase chain reaction; risk
Abstract:
... Operational capacity of real-time PCR and loop-mediated isothermal amplification (LAMP) diagnostic assays for detection of Xanthomonas arboricola pv. pruni was established in a ring-test involving four laboratories. Symptomatic and healthy almond leaf samples with two methods of sample preparation were analyzed. Kappa coefficient, sensitivity, specificity, likelihood ratios and post-test probabili ...
DOI:
10.1016/j.mimet.2015.03.005

5. Evaluation of an immunochromatographic assay for detection of PBP2a on non-Staphylococcus aureus clinical isolates

Author:
Benoit Mantion; Laurent Cavalié; Marie-Françoise Prère
Source:
Journal of microbiological methods 2015 v.112 pp. 46-48
ISSN:
0167-7012
Subject:
immunoaffinity chromatography; methicillin; polymerase chain reaction
Abstract:
... We evaluated the immunochromatographic assay PBP2a Culture Colony Test (Alere™) on 50 samples of methicillin resistant and sensitive non-Staphylococcus aureus isolates belonging to ten species. Because it is rapid and reliable, this test should be advantageous as routine test in place of mecA/C PCR. ...
DOI:
10.1016/j.mimet.2015.02.014

6. Identifying Haemophilus haemolyticus and Haemophilus influenzae by SYBR Green real-time PCR

Author:
Roger Latham; Bowen Zhang; Stephen Tristram
Source:
Journal of microbiological methods 2015 v.112 pp. 67-69
ISSN:
0167-7012
Subject:
Haemophilus haemolyticus; Haemophilus influenzae; algorithms; copper; quantitative polymerase chain reaction; zinc
Abstract:
... SYBR Green real time PCR assays for protein D (hpd), fuculose kinase (fucK) and [Cu, Zn]-superoxide dismutase (sodC) were designed for use in an algorithm for the identification of Haemophilus influenzae and H. haemolyticus. When tested on 127 H. influenzae and 60 H. haemolyticus all isolates were identified correctly. ...
DOI:
10.1016/j.mimet.2015.03.001

7. Impact of metagenomic DNA extraction procedures on the identifiable endophytic bacterial diversity in Sorghum bicolor (L. Moench)

Author:
Mapula Kgomotso Annah Maropola; Jean-Baptiste Ramond; Marla Trindade
Source:
Journal of microbiological methods 2015 v.112 pp. 104-117
ISSN:
0167-7012
Subject:
Agrobacterium; DNA; Erwinia; Herbaspirillum; Microbacterium; Pseudomonas; Sorghum bicolor; Sphingobacterium; Stenotrophomonas; analytical kits; bacterial communities; cetyltrimethylammonium bromide; community structure; endophytes; genes; growth promotion; metagenomics; microbiome; plant growth; plant tissues; polymerase chain reaction; restriction fragment length polymorphism; ribosomal RNA; sequence analysis
Abstract:
... Culture-independent studies rely on the quantity and quality of the extracted environmental metagenomic DNA (mDNA). To fully access the plant tissue microbiome, the extracted plant mDNA should allow optimal PCR applications and the genetic content must be representative of the total microbial diversity. In this study, we evaluated the endophytic bacterial diversity retrieved using different mDNA e ...
DOI:
10.1016/j.mimet.2015.03.012

8. Numerical solution of a microbial growth model applied to dynamic environments

Author:
Si Zhu; Guibing Chen
Source:
Journal of microbiological methods 2015 v.112 pp. 76-82
ISSN:
0167-7012
Subject:
computer software; differential equation; foods; growth curves; growth models; microbial growth; microorganisms; temperature
Abstract:
... The Baranyi and Roberts model is one of the most frequently used microbial growth models. It has been successfully applied to numerous studies of various microorganisms in different food products. Under dynamic conditions, the model is implicitly formulated as a set of two coupled differential equations which could be numerically solved using the Runge–Kutta method. In this study, a simplified num ...
DOI:
10.1016/j.mimet.2015.03.003

9. Optimisation of DNA extraction and validation of PCR assays to detect Mycobacterium avium subsp. paratuberculosis

Author:
Verlaine J. Timms; Hazel M. Mitchell; Brett A. Neilan
Source:
Journal of microbiological methods 2015 v.112 pp. 99-103
ISSN:
0167-7012
Subject:
DNA; Mycobacterium avium subsp. paratuberculosis; analytical kits; blood; boiling; cows; feces; genes; herds; polymerase chain reaction; ribosomal RNA; sonication
Abstract:
... The aim of this study was to investigate DNA extraction methods and PCR assays suitable for the detection of Mycobacterium paratuberculosis in bovine tissue. The majority of methods currently used to detect M. paratuberculosis have been developed using bovine samples, such as faeces, blood or tissue and, in many cases, have been based on detection from pooled samples from a herd. However most stud ...
DOI:
10.1016/j.mimet.2015.03.016

10. Phytochip: Development of a DNA-microarray for rapid and accurate identification of Pseudo-nitzschia spp and other harmful algal species

Author:
Charlotte Noyer; Anne Abot; Lidwine Trouilh; Véronique Anton Leberre; Catherine Dreanno
Source:
Journal of microbiological methods 2015 v.112 pp. 55-66
ISSN:
0167-7012
Subject:
Alexandrium; Bacillariophyceae; DNA libraries; DNA microarrays; Karenia; algal blooms; cost effectiveness; cultured cells; data collection; light microscopy; microorganisms; molecular biology; molecular cloning; monitoring; oligonucleotide probes; operon; phytoplankton; poisonous algae; polymerase chain reaction; public health; ribosomal DNA; ribosomal RNA; seawater; toxicity; water quality
Abstract:
... Detection of harmful algal blooms has become a challenging concern because of the direct impacts on public health and economy. The identification of toxic dinoflagellates and diatoms in monitoring programs requires an extensive taxonomic expertise and is time consuming. Advances in molecular biology have allowed the development of new approaches, more rapid, accurate and cost-effective for detecti ...
DOI:
10.1016/j.mimet.2015.03.002

11. Comparison of modified Chicago sky blue stain and potassium hydroxide mount for the diagnosis of dermatomycoses and onychomycoses

Author:
Zhong Liu; Ping Sheng; Yan-Ping Yang; Wen Li; Wen-Ming Huang; Jie-Di Wang; Yi-Ming Fan
Source:
Journal of microbiological methods 2015 v.112 pp. 21-23
ISSN:
0167-7012
Subject:
dermatomycoses; disease diagnosis; microbial culture; potassium hydroxide; screening
Abstract:
... The diagnostic value of modified Chicago sky blue (CSB) stain and potassium hydroxide (KOH) mount for superficial mycoses was compared using fungal culture as gold standard. The sensitivity and screening time of the CSB stain were superior to the KOH mount. The CBS stain is simple, quick and reliable for diagnosing superficial mycoses. ...
DOI:
10.1016/j.mimet.2015.02.013

12. Detecting volatile compounds from Kraft lignin degradation in the headspace of microbial cultures by selected ion flow tube mass spectrometry (SIFT-MS)

Author:
Andrew Gibson; Lada Malek; Robert F.H. Dekker; Brian Ross
Source:
Journal of microbiological methods 2015 v.112 pp. 40-45
ISSN:
0167-7012
Subject:
Absidia; Flammulina velutipes; Ischnoderma; Laetiporus sulphureus; Pholiota; aluminum foil; carbon; formaldehyde; formic acid; fungi; headspace analysis; ions; lignin; mass spectrometry; methanol; oxidation; volatile compounds
Abstract:
... Selected Ion Flow Tube Mass Spectrometry (SIFT-MS) was used to quantify methanol and other volatile compounds in the headspace of one bacterial and 12 fungal lignin-degrading microbial cultures. Cultures were grown in 250mL Erlenmeyer flasks capped with aluminum foil containing 40mL of nutrient media using Kraft lignin (0.3% w/v) as the sole carbon source. Analysis was done using SIFT-MS with H3O⁺ ...
DOI:
10.1016/j.mimet.2015.03.008

13. Development and evaluation of a latex agglutination test for the rapid serodiagnosis of tularemia

Author:
Waldemar Rastawicki; Natalia Rokosz-Chudziak; Anna Chróst; Rafał Gierczyński
Source:
Journal of microbiological methods 2015 v.112 pp. 1-2
ISSN:
0167-7012
Subject:
Francisella tularensis; antibodies; blood serum; cost effectiveness; latex; latex agglutination test; mixing; rapid methods; serodiagnosis; tularemia
Abstract:
... A latex agglutination test (LAT) was developed for a rapid detection of antibodies against Francisella tularensis. The assay is performed by mixing serum with antigen-coated latex beads and read within 5min. Developed LAT has been proved to be a specific, sensitive, fast, easy-to-perform and cost-efficient tool for the routine diagnosis of tularemia. ...
DOI:
10.1016/j.mimet.2015.02.012

14. Different antimicrobial susceptibility testing methods to detect ertapenem resistance in enterobacteriaceae: VITEK2, MicroScan, Etest, disk diffusion, and broth microdilution

Author:
Miae Lee; Hae-Sun Chung
Source:
Journal of microbiological methods 2015 v.112 pp. 87-91
ISSN:
0167-7012
Subject:
Enterobacteriaceae; antibiotic resistance; automation; beta-lactamase; disk diffusion antimicrobial test; ertapenem; hospitals; microbiology; minimum inhibitory concentration; phenotype; screening
Abstract:
... We investigated different antimicrobial susceptibility testing methods to detect ertapenem resistance in Enterobacteriaceae. A total of 72 Enterobacteriaceae isolates were collected from a clinical microbiology laboratory of a tertiary university hospital, all of which were detected ertapenem resistance by the VITEK2 system. Bacterial identification and antimicrobial susceptibility were determined ...
DOI:
10.1016/j.mimet.2015.03.014

15. Effects of bacterial inactivation methods on downstream proteomic analysis

Author:
Andy Lin; Eric D. Merkley; Brian H. Clowers; Janine R. Hutchison; Helen W. Kreuzer
Source:
Journal of microbiological methods 2015 v.112 pp. 3-10
ISSN:
0167-7012
Subject:
DNA; Escherichia coli; Yersinia pestis; algorithms; autoclaves; autoclaving; data quality; databases; ethanol; irradiation; liquid chromatography; protein content; proteins; proteomics; tandem mass spectrometry
Abstract:
... Inactivation of pathogenic microbial samples is often necessary for the protection of researchers and to comply with local and federal regulations. By its nature, biological inactivation causes changes to microbial samples, potentially affecting observed experimental results. While inactivation-induced damage to materials such as DNA has been evaluated, the effect of various inactivation strategie ...
DOI:
10.1016/j.mimet.2015.01.015

16. Establishment of a counter-selectable markerless mutagenesis system in Veillonella atypica

Author:
Peng Zhou; Xiaoli Li; Fengxia Qi
Source:
Journal of microbiological methods 2015 v.112 pp. 70-72
ISSN:
0167-7012
Subject:
Veillonella atypica; genes; mutagenesis; sigma factors
Abstract:
... Using an alternative sigma factor ecf3 as target, we successfully established the first markerless mutagenesis system in the Veillonella genus. This system will be a valuable tool for mutagenesis of multiple genes for gene function analysis as well as for gene regulation studies in Veillonella. ...
DOI:
10.1016/j.mimet.2015.03.010
PubMed:
25771833
PubMed Central:
PMC4388892

17. Establishment of the straightforward electro-transformation system for Phytophthora infestans and its comparison with the improved PEG/CaCl2 transformation

Author:
Lei Dong; Xiangyuan Zhu; Haichen Cui; Makoto Ojika; Ruigang Wang; Huirong Liu
Source:
Journal of microbiological methods 2015 v.112 pp. 83-86
ISSN:
0167-7012
Subject:
DNA; Phytophthora infestans; electroporation; genetic transformation; genetic vectors; green fluorescent protein; pathogens; potatoes; protoplasts; zoospores
Abstract:
... Phytophthora infestans is the most devastating pathogen of potato. For the biology study of P. infestans at the molecular level, one of the difficulties is the technique for the genetic transformation. In this study, the straightforward electro-transformation system was established for P. infestans with a green fluorescent protein expression vector and compared with the improved PEG/CaCl2 mediated ...
DOI:
10.1016/j.mimet.2015.03.013

18. Evaluation of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry for species identification of Nonfermenting Gram-Negative Bacilli

Author:
Marisa Almuzara; Claudia Barberis; Germán Traglia; Angela Famiglietti; Maria Soledad Ramirez; Carlos Vay
Source:
Journal of microbiological methods 2015 v.112 pp. 24-27
ISSN:
0167-7012
Subject:
Gram-negative bacteria; matrix-assisted laser desorption-ionization mass spectrometry; phenotype; species identification
Abstract:
... Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) to identify 396 Nonfermenting Gram-Negative Bacilli clinical isolates was evaluated in comparison with conventional phenotypic tests and/or molecular methods.MALDI-TOF MS identified to species level 256 isolates and to genus or complex level 112 isolates. It identified 29 genera including uncommon species. ...
DOI:
10.1016/j.mimet.2015.03.004

19. Monitoring Campylobacter in the poultry production chain — From culture to genes and beyond

Author:
Mathilde H. Josefsen; Arun K. Bhunia; Eva Olsson Engvall; Mette S.R. Fachmann; Jeffrey Hoorfar
Source:
Journal of microbiological methods 2015 v.112 pp. 118-125
ISSN:
0167-7012
Subject:
Campylobacter; automation; bacteria; biosensors; chromatography; genes; meat; microarray technology; monitoring; poultry production; quantitative polymerase chain reaction; screening; sequence analysis; slaughterhouses
Abstract:
... Improved monitoring tools are important for the control of Campylobacter bacteria in poultry production. Standardized reference culture methods issued by national and international standardization organizations are time-consuming, cumbersome and not amenable to automation for screening of large numbers of samples. The ultimate goal for rapid monitoring of Campylobacter is to prevent contaminated m ...
DOI:
10.1016/j.mimet.2015.03.007
CHORUS:
10.1016/j.mimet.2015.03.007

20. Rapid real-time PCR methods to distinguish Salmonella Enteritidis wildtype field isolates from vaccine strains Salmovac SE/Gallivac SE and AviPro SALMONELLA VAC E

Author:
Sven Maurischat; Istvan Szabo; Beatrice Baumann; Burkhard Malorny
Source:
Journal of microbiological methods 2015 v.112 pp. 92-98
ISSN:
0167-7012
Subject:
Salmonella Enteritidis; decision making; genome; herds; humans; live vaccines; melting; poultry; quantitative polymerase chain reaction; salmonellosis; sequence analysis; serotypes; single nucleotide polymorphism
Abstract:
... Salmonella enterica serovar Enteritidis is a major non-typhoid Salmonella serovar causing human salmonellosis mainly associated with the consumption of poultry and products thereof. To reduce infections in poultry, S. Enteritidis live vaccine strains AviPro SALMONELLA VAC E and Salmovac SE/Gallivac SE have been licensed and used in several countries worldwide. To definitively diagnose a S. Enterit ...
DOI:
10.1016/j.mimet.2015.03.015