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You searched for: Journal name Journal of microbiological methods Remove constraint Journal name: Journal of microbiological methods Publication year rev 7987-2013 Remove constraint Publication year rev: 7987-2013 Source 2013 v.92 no.3 Remove constraint Source: 2013 v.92 no.3
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1. Comparison of two molecular assays with conventional blood culture for diagnosis of sepsis

Author:
Eva Leitner; Harald H. Kessler; Walter Spindelboeck; Martin Hoenigl; Csilla Putz-Bankuti; Vanessa Stadlbauer-Köllner; Robert Krause; Andrea J. Grisold; Gebhard Feierl; Rudolf E. Stauber
Source:
Journal of microbiological methods 2013 v.92 no.3 pp. 253-255
ISSN:
0167-7012
Subject:
blood; diagnostic techniques; disease diagnosis; molecular biology; sepsis (infection)
Abstract:
... In this small study, the LightCycler® SeptiFast, and the SepsiTest™ were compared with blood culture. The SeptiFast showed a higher sensitivity (42.9%) and specificity (88.2%) when compared to blood culture than the SepsiTest™ (28.6 and 85.3%). The SeptiFast provides more species specific results, although the identification panel is smaller. ...
DOI:
10.1016/j.mimet.2012.12.012

2. Detecting laboratory DNA contamination using polyester-rayon wipes: A method validation study

Author:
E. Marielle Remillard; Laura K. Taylor; Julie Layshock; Sheila Van Cuyk; Kristin M. Omberg
Source:
Journal of microbiological methods 2013 v.92 no.3 pp. 358-365
ISSN:
0167-7012
Subject:
DNA; Escherichia coli; detection limit; polymerase chain reaction
Abstract:
... Due to the high sensitivity of many PCR assays, extraneous target DNA in a laboratory setting can lead to false positive results. To assess the presence of extraneous DNA, many laboratories use gauze wipes to sample laboratory surfaces. The accuracy, precision, limits of detection, linearity, and robustness of a wipe test method and each associated wipe processing step were evaluated using E. coli ...
DOI:
10.1016/j.mimet.2013.01.003

3. Development of variable number of tandem repeats typing schemes for Ralstonia solanacearum, the agent of bacterial wilt, banana Moko disease and potato brown rot

Author:
Carine Aya N'Guessan; Sylvain Brisse; Anne-Claire Le Roux-Nio; Stéphane Poussier; Daouda Koné; Emmanuel Wicker
Source:
Journal of microbiological methods 2013 v.92 no.3 pp. 366-374
ISSN:
0167-7012
Subject:
plant pathogenic bacteria; bacterial wilt; loci; ecotypes; monitoring; phylogeny; minisatellite repeats; soil; disease outbreaks; capillary electrophoresis; phylotype; genotyping; Ralstonia solanacearum; potatoes; screening; bananas
Abstract:
... Ralstonia solanacearum is an important soil borne bacterial plant pathogen causing bacterial wilt on many important crops. To better monitor epidemics, efficient tools that can identify and discriminate populations are needed. In this study, we assessed variable number of tandem repeats (VNTR) genotyping as a new tool for epidemiological surveillance of R. solanacearum phylotypes, and more specifi ...
DOI:
10.1016/j.mimet.2013.01.012

4. Direct identification of bacteria causing urinary tract infections by combining matrix-assisted laser desorption ionization-time of flight mass spectrometry with UF-1000i urine flow cytometry

Author:
X.-H. Wang; G. Zhang; Y.-Y. Fan; X. Yang; W.-J. Sui; X.-X. Lu
Source:
Journal of microbiological methods 2013 v.92 no.3 pp. 231-235
ISSN:
0167-7012
Subject:
antibiotics; bacteria; bacterial infections; computer software; flow cytometry; genes; matrix-assisted laser desorption-ionization mass spectrometry; pathogens; patients; ribosomal RNA; therapeutics; urinary tract diseases; urine
Abstract:
... Rapid identification of bacterial pathogens from clinical specimens is essential to establish an adequate empirical antibiotic therapy to treat urinary tract infections (UTIs). We used matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) combined with UF-1000i urine flow cytometry of urine specimens to quickly and accurately identify bacteria causing UTIs. We ...
DOI:
10.1016/j.mimet.2012.12.016

5. Efficient multiplex simple sequence repeat genotyping of the oomycete plant pathogen Phytophthora infestans

Author:
Ying Li; David E.L. Cooke; Evert Jacobsen; Theo van der Lee
Source:
Journal of microbiological methods 2013 v.92 no.3 pp. 316-322
ISSN:
0167-7012
Subject:
DNA; Phytophthora infestans; alleles; capillary electrophoresis; cost effectiveness; data collection; databases; fluorescence; genotype; genotyping; loci; microsatellite repeats; plant pathogens; ploidy; polymerase chain reaction; screening; Great Britain; Netherlands
Abstract:
... Genotyping is fundamental to population analysis. To accommodate fast, accurate and cost-effective genotyping, a one-step multiplex PCR method employing twelve simple sequence repeat (SSR) markers was developed for high-throughput screening of Phytophthora infestans populations worldwide. The SSR markers reported for this species were evaluated and the twelve most informative and easily scored wer ...
DOI:
10.1016/j.mimet.2012.11.021

6. Efficient sequential repetitive gene deletions in Neurospora crassa employing a self-excising β-recombinase/six cassette

Author:
Edyta Szewczyk; Takao Kasuga; Zhiliang Fan
Source:
Journal of microbiological methods 2013 v.92 no.3 pp. 236-243
ISSN:
0167-7012
Subject:
Neurospora crassa; gene deletion; recycling; regulator genes; transcription factors
Abstract:
... Despite its long-standing history as a model organism, Neurospora crassa has limited tools for repetitive gene deletions utilizing recyclable self-excising marker systems. Here we describe, for the first time, the functionality of a bacterial recombination system employing β-recombinase acting on six recognition sequences (β-rec/six) in N. crassa, which allowed repetitive site-specific gene deleti ...
DOI:
10.1016/j.mimet.2012.12.004
CHORUS:
10.1016/j.mimet.2012.12.004

7. High-throughput analysis of the impact of antibiotics on the human intestinal microbiota composition

Author:
S.E. Ladirat; H.A. Schols; A. Nauta; M.H.C. Schoterman; B.J.F. Keijser; R.C. Montijn; H. Gruppen; F.H.J. Schuren
Source:
Journal of microbiological methods 2013 v.92 no.3 pp. 387-397
ISSN:
0167-7012
Subject:
Bacteroides; Bifidobacterium; Clostridium; Enterobacteriaceae; Lactobacillus; adults; antibiotics; bacteria; dose response; fermentation; humans; inoculum; intestinal microorganisms; microarray technology; phylogeny; screening
Abstract:
... Antibiotic treatments can lead to a disruption of the human microbiota. In this in-vitro study, the impact of antibiotics on adult intestinal microbiota was monitored in a new high-throughput approach: a fermentation screening-platform was coupled with a phylogenetic microarray analysis (Intestinal-chip). Fecal inoculum from healthy adults was exposed in a fermentation screening-platform to seven ...
DOI:
10.1016/j.mimet.2012.12.011

8. Quantitative PCR confirms culture as the gold standard for detection of lower airway infection by nontypeable Haemophilus influenzae in Australian Indigenous children with bronchiectasis

Author:
Kim M. Hare; Robyn L. Marsh; Michael J. Binks; Keith Grimwood; Susan J. Pizzutto; Amanda J. Leach; Anne B. Chang; Heidi C. Smith-Vaughan
Source:
Journal of microbiological methods 2013 v.92 no.3 pp. 270-272
ISSN:
0167-7012
Subject:
Haemophilus influenzae; children; quantitative polymerase chain reaction
Abstract:
... Correlation was observed between quantitative PCR and semi-quantitative culture for definition of Haemophilus influenzae infection in bronchoalveolar lavage specimens from 81 children with bronchiectasis. However, qPCR data correlated less well with airway neutrophilia, and supports continued use of culture as the gold standard for defining H. influenzae lower airway infection. ...
DOI:
10.1016/j.mimet.2012.12.013

9. Recovery and detection of botulinum neurotoxins from a nonporous surface

Author:
Matthew Lautenschlager; Susan E. Maslanka; Paris A. Paul; Suzanne R. Kalb; John R. Barr; Brian H. Raphael
Source:
Journal of microbiological methods 2013 v.92 no.3 pp. 278-280
ISSN:
0167-7012
Subject:
botulinum toxin; decontamination; enzyme-linked immunosorbent assay; mass spectrometry; stainless steel
Abstract:
... We describe the adaptation of a sample recovery method for botulinum neurotoxins from stainless steel. Botulinum toxin was recovered from surfaces left to dry for up to 16h and detected by either ELISA or EndoPep mass spectrometry methods. In addition, we demonstrate that this method can be used to evaluate the efficacy of surface decontamination procedures. ...
DOI:
10.1016/j.mimet.2012.12.019

10. Semi-circular microgrooves to observe active movements of individual Navicula pavillardii cells

Author:
Kazuo Umemura; Takahiro Haneda; Masashi Tanabe; Akira Suzuki; Yoshikazu Kumashiro; Kazuyoshi Itoga; Teruo Okano; Shigeki Mayama
Source:
Journal of microbiological methods 2013 v.92 no.3 pp. 349-354
ISSN:
0167-7012
Subject:
Navicula; cell movement; models
Abstract:
... We performed a trajectory analysis of movements of Navicula pavillardii diatom cells that were confined to semi-circular microgrooves with several different curvature radii. Using the semi-circular micropattern, we succeeded in observing change of velocity of the same cell before and after the stimulation by N,N-dimethyl-p-toluidine (DMT). Because the looped grooves had longer contour length than ...
DOI:
10.1016/j.mimet.2013.01.006

11. The Vibrio harveyi bioassay used routinely to detect AI-2 quorum sensing inhibition is confounded by inconsistent normalization across marine matrices

Author:
Walter M. Blair; Gregory J. Doucette
Source:
Journal of microbiological methods 2013 v.92 no.3 pp. 250-252
ISSN:
0167-7012
Subject:
Vibrio harveyi; bioassays; quorum sensing; screening
Abstract:
... The Vibrio harveyi autoinducer-2 (AI-2) bioassay is used routinely to screen for inhibition of the AI-2 quorum sensing system. The present study utilizes three well-described bacterial strains to demonstrate that inconsistent normalization across matrices undermines the assay's use in screening marine samples for AI-2 inhibition. ...
DOI:
10.1016/j.mimet.2012.12.023

12. A combination approach for rapid and high yielding purification of bacterial minicells

Author:
Mehul Jivrajani; Neeta Shrivastava; Manish Nivsarkar
Source:
Journal of microbiological methods 2013 v.92 no.3 pp. 340-343
ISSN:
0167-7012
Subject:
ceftriaxone; cost effectiveness; filtration; fluorescence microscopy; particle size
Abstract:
... A method for bacterial minicell purification was developed by combining antibiotic (ceftriaxone) lysis and filtration. This method is fast, cost effective and facilitates high yield of purified minicells, with no parent strain contamination as confirmed by fluorescent microscopy, average particle size and polydispersity index. ...
DOI:
10.1016/j.mimet.2012.12.002

13. A novel single-step multiplex polymerase chain reaction assay for the detection of diarrheagenic Escherichia coli

Author:
Miyuki Fujioka; Yoshimitsu Otomo; Chowdhury Rafiqul Ahsan
Source:
Journal of microbiological methods 2013 v.92 no.3 pp. 289-292
ISSN:
0167-7012
Subject:
Shiga toxin-producing Escherichia coli; antigens; diarrhea; enteroinvasive Escherichia coli; enteropathogenic Escherichia coli; enterotoxigenic Escherichia coli; feces; genes; humans; polymerase chain reaction; rapid methods
Abstract:
... Escherichia coli that causes diarrhea in humans is referred to as diarrheagenic E. coli (DEC), and has been categorized into the following 5 groups: shigatoxin-producing E. coli (STEC), enteropathogenic E. coli (EPEC), enteroinvasive E. coli (EIEC), enteroaggregative E. coli (EAggEC), and enterotoxigenic E. coli (ETEC). In this study, we developed a novel one-step multiplex polymerase chain reacti ...
DOI:
10.1016/j.mimet.2012.12.010

14. A rapid and repeatable method to deposit bioaerosols on material surfaces

Author:
M. Worth Calfee; Sang Don Lee; Shawn P. Ryan
Source:
Journal of microbiological methods 2013 v.92 no.3 pp. 375-380
ISSN:
0167-7012
Subject:
bioaerosols; concrete; decontamination; spore dispersal; spores; stainless steel; surface area; surface roughness; wood
Abstract:
... A simple method for repeatably inoculating surfaces with a precise quantity of aerosolized spores was developed. Laboratory studies were conducted to evaluate the variability of the method within and between experiments, the spatial distribution of spore deposition, the applicability of the method to complex surface types, and the relationship between material surface roughness and spore recoverie ...
DOI:
10.1016/j.mimet.2013.01.015

15. Agrobacterium tumefaciens-mediated transformation of the soybean pathogen Phomopsis longicolla

Author:
Shuxian Li; John B. Ridenour; Hun Kim; Robert L. Hirsch; John C. Rupe; Burton H. Bluhm
Source:
Journal of microbiological methods 2013 v.92 no.3 pp. 244-245
ISSN:
0167-7012
Subject:
Agrobacterium; Diaporthe longicolla; conidia; genomics; insertional mutagenesis; pathogens; soybeans
Abstract:
... To facilitate functional genomics in the soybean pathogen Phomopsis longicolla, we developed a robust Agrobacterium tumefaciens-mediated transformation system that yielded 150–250 transformants per 1×10⁶ conidia of P. longicolla. This first report of P. longicolla transformation provides a useful tool for insertional mutagenesis in an increasingly important pathogen of soybean. ...
DOI:
10.1016/j.mimet.2012.12.015

16. Analysis of artifacts suggests DGGE should not be used for quantitative diversity analysis

Author:
Julia W. Neilson; Fiona L. Jordan; Raina M. Maier
Source:
Journal of microbiological methods 2013 v.92 no.3 pp. 256-263
ISSN:
0167-7012
Subject:
Firmicutes; alpha-Proteobacteria; bacterial communities; beta-Proteobacteria; community structure; denaturing gradient gel electrophoresis; genes; quantitative analysis; quantitative polymerase chain reaction; ribosomal DNA; ribosomal RNA; species diversity
Abstract:
... PCR-denaturing gradient gel electrophoresis (PCR-DGGE) is widely used in microbial ecology for the analysis of comparative community structure. However, artifacts generated during PCR-DGGE of mixed template communities impede the application of this technique to quantitative analysis of community diversity. The objective of the current study was to employ an artificial bacterial community to docum ...
DOI:
10.1016/j.mimet.2012.12.021
PubMed:
23313091
PubMed Central:
PMC3957434

17. Application of IgY to sandwich enzyme-linked immunosorbent assays, lateral flow devices, and immunopillar chips for detecting staphylococcal enterotoxins in milk and dairy products

Author:
Wanchun Jin; Keiko Yamada; Mai Ikami; Noritada Kaji; Manabu Tokeshi; Yusuke Atsumi; Makoto Mizutani; Atsushi Murai; Akira Okamoto; Takao Namikawa; Yoshinobu Baba; Michio Ohta
Source:
Journal of microbiological methods 2013 v.92 no.3 pp. 323-331
ISSN:
0167-7012
Subject:
Staphylococcus aureus; agglutination; antibodies; chickens; detection limit; dose response; enterotoxins; enzyme-linked immunosorbent assay; ice cream; immunoglobulin G; immunoglobulin Y; latex; milk; rabbits; risk; screening; staphylococcal intoxication; yogurt
Abstract:
... Staphylococcal enterotoxins (SEs), produced by Staphylococcus aureus, are a major cause of staphylococcal food poisoning. Traditionally, sandwich enzyme-linked immunosorbent assay (ELISA) and reverse passive latex agglutination with rabbit antibody IgG have been used to detect SEs. However, most of these kits require a long processing time and there is a risk of false-positive results since IgG re ...
DOI:
10.1016/j.mimet.2013.01.001

18. Application of peptide nucleic acid (PNA)-PCR clamping technique to investigate the community structures of rhizobacteria associated with plant roots

Author:
Masao Sakai; Makoto Ikenaga
Source:
Journal of microbiological methods 2013 v.92 no.3 pp. 281-288
ISSN:
0167-7012
Subject:
DNA; community structure; cucumbers; genes; mitochondria; plastids; polymerase chain reaction; restriction fragment length polymorphism; rhizosphere bacteria; ribosomal RNA; roots; spinach
Abstract:
... The contamination of plant organelle (mitochondria and plastid) genes in the DNA extraction step becomes a major drawback in investigating the community structures of bacteria associated with plant samples. This is because organelle small subunit ribosomal RNA (SSU rRNA) genes are easily amplified by polymerase chain reaction (PCR) with a set of universal primers for bacteria. To suppress the PCR ...
DOI:
10.1016/j.mimet.2012.09.036

19. Construction of a marker system for the evaluation of competitiveness for legume nodulation in Rhizobium strains

Author:
Carmen Sánchez-Cañizares; Jose Palacios
Source:
Journal of microbiological methods 2013 v.92 no.3 pp. 246-249
ISSN:
0167-7012
Subject:
Rhizobium leguminosarum; genetic markers; nodulation; peas
Abstract:
... A marker system has been set up for the analysis of competitiveness of Rhizobium leguminosarum strains for legume nodulation. The strains generated incorporate gusA and celB marker genes at identical positions and allow efficient scoring of single and double infections. Based on this system, we have found that strain UPM791 outcompetes 3841 for nodulation in pea. This technique will be useful to d ...
DOI:
10.1016/j.mimet.2012.12.022

20. Development of culture medium using extruded bean as a nitrogen source for yeast growth

Author:
Karla A. Batista; Luiz Artur M. Bataus; Ivan T.N. Campos; Kátia F. Fernandes
Source:
Journal of microbiological methods 2013 v.92 no.3 pp. 310-315
ISSN:
0167-7012
Subject:
beans; protein synthesis; Komagataella pastoris; nitrogen; recombinant proteins; yeasts; yeast extract; peptones; Saccharomyces cerevisiae; culture media
Abstract:
... In this study extruded bean was used as a nitrogen source substitute in culture medium formulation. A 3-factor simplex-lattice mixture design was used to establish better growth conditions. Completely substituted medium resulted in 43% of increase in the growth of Saccharomyces cerevisiae. Mixtures containing 1% extruded bean and 1% yeast extract, or 1% extruded bean and 1% peptone presented growt ...
DOI:
10.1016/j.mimet.2013.01.002