Abstract:
:To date, it has been problematic to accurately quantify multiple nucleic acid sequences, representing microbial targets, in multi-target mixtures using oligonucleotide microarrays, primarily due to nonspecific target binding (i.e., cross-hybridization). While some studies ignore the effects of nonspecific binding, other studies have developed approaches to minimize nonspecific binding, such as physical modeling to design highly specific probes, subtracting nonspecific signal using mismatch probes, and/or removing nonspecific duplexes by scanning through a range of wash stringencies. We have developed an alternative approach that, in contrast to previous approaches, uses nonspecific target binding as a source of information. Specifically, the new approach uses hybridization patterns (fingerprints) to quantify specific nucleic acid targets in complex target mixtures. We evaluated the approach by mixing together in vitro transcribed 28S rRNA targets at varying concentrations (up to 1.0 nM), and hybridizing the 24 mixtures to microarrays (n=3160 probes, in duplicate). Three independent Latin-square-designed experiments revealed accurate quantification of the targets. The regression between actual concentration of targets and those determined by the approach were highly positively correlated with high R(2) values (e.g., R(2)=0.90, n=6 targets; R(2)=0.84, n=8 targets; R(2)=0.82, n=10 targets).
journal_name
J Microbiol Methodsjournal_title
Journal of microbiological methodsauthors
Pozhitkov AE,Nies G,Kleinhenz B,Tautz D,Noble PAdoi
10.1016/j.mimet.2008.05.013subject
Has Abstractpub_date
2008-09-01 00:00:00pages
92-102issue
1eissn
0167-7012issn
1872-8359pii
S0167-7012(08)00175-9journal_volume
75pub_type
杂志文章abstract::A discontinuous lactate dehydrogenase coupled assay is described for the evaluation of the pyruvate carboxylase activity (Pc, EC 6.4.1.1) in a glutamate overproducing strain of Corynebacterium glutamicum. After an initial permeabilisation period of the cells, the method consisted of the fluorometric determination of t...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/s0167-7012(99)00104-9
更新日期:1999-12-01 00:00:00
abstract::The immunoglobulin degrading enzyme of Streptococcus pyogenes, IdeS, is an unusual cysteine protease produced by group A streptococci for which the only known substrate is immunoglobulin G (IgG). To date, IdeS has not been found to cleave any of the known synthetic substrates that other cysteine proteases hydrolyse, t...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2007.04.017
更新日期:2007-08-01 00:00:00
abstract::A method to detect and enumerate bacterial colonies grown on membrane filters (MF) was described. The colonies were stained with an ethanolic solution of 0.1% Amido black 10B. The procedure yielded the rapid detection of colonies as compared to a conventional plate counting method. ...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/s0167-7012(03)00170-2
更新日期:2003-11-01 00:00:00
abstract::Quantification of the biosurfactants produced by a variety of microorganisms is a time taking and difficult task due to the lack of rapid, efficient and accurate methods. This work presents a simple turbidometric method for quantification of crude biosurfactants based on their property to become insoluble at low pH va...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2008.09.010
更新日期:2009-01-01 00:00:00
abstract::To rapidly and simply determine whether or not bacterial colonies growing on agar were Vibrio parahaemolyticus, we developed an immunochromatographic assay (VP-ICA) using two different monoclonal antibodies (designated mAb-VP34 and mAb-VP109) against the delta subunit of V. parahaemolyticus-F0F1 ATP synthase. The epit...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2015.06.009
更新日期:2015-09-01 00:00:00
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...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2015.03.003
更新日期:2015-05-01 00:00:00
abstract::Streptococcus gordonii, a commensal bacterium of the human oral cavity, is a potential live vaccine vector. In this study, we have developed a system that delivers a vaccine antigen gene onto the chromosome of S. gordonii. The system consisted of a recipient strain, that is a thymidine auxotroph constructed by deletio...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2016.04.003
更新日期:2016-06-01 00:00:00
abstract::A 16S rRNA gene-based fingerprinting method was developed for the identification of Azotobacteraceae and tested onto 48 soil isolates and 28 reference strains belonging to the free-living nitrogen-fixing bacterial group and to the most common species found in soil samples. According to this method, the 16S rRNA gene w...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2004.01.006
更新日期:2004-05-01 00:00:00
abstract::Cryptosporidium parvum is an enteric coccidian parasite that is recognised as a frequent cause of water-borne disease in humans. We report for the first time on use of the in vitro HCT-8 cell culture-quantitative PCR (qPCR) assay and the in vivo SCID-mouse bioassay for evaluating critical factors that reduce or elimin...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2010.01.017
更新日期:2010-03-01 00:00:00
abstract::Site-directed mutagenesis is one of the most widely used techniques in life sciences. Here we describe an improved and simplified method for introducing mutations at desired sites. It consists of an inverse PCR using a plasmid template and two partially complementary primers. The synthesis step is followed by annealin...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2014.08.003
更新日期:2014-11-01 00:00:00
abstract::An oligonucleotide-microarray method was developed for the detection of Kitasatospora species in soil samples. The 16S-23S rDNA internal transcribed spacer (ITS) sequence of these antibiotics-producing actinomycetes was applied to design short oligonucleotide probes. Two different 26-mers were synthesized, specific to...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2005.07.012
更新日期:2006-05-01 00:00:00
abstract::A strain-specific assay was developed for the detection of viable Lactobacillus on cattle feed. The DNA sequences of the 16S rRNA gene and four different 16S/23S rRNA intergenic spacer regions (ISR) from Lactobacillus sp. HOFG1 were determined. Based on these sequences, a strain-specific primer was designed for the am...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2004.12.002
更新日期:2005-05-01 00:00:00
abstract::Neuraminidase was produced by 32.1% and 28.5% of Porphyromonas from dogs with and without periodontitis, respectively; and by 31.8% of bacteria from humans. The presence of neuraminidase in Porphyromonas spp. suggests that this enzyme can be involved with the pathogenesis of the periodontal disease, and the use of thi...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2013.06.017
更新日期:2013-09-01 00:00:00
abstract:OBJECTIVES:Galactomannan (GM) and Aspergillus DNA detection are useful tools for the diagnosis of invasive pulmonary aspergillosis (IPA), primarily in blood and bronchoscopy samples. This study aimed to evaluate the utility of both markers for detection of Aspergillus in sputum from patients with allergic bronchopulmon...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2017.06.016
更新日期:2017-09-01 00:00:00
abstract::Contaminated eukaryotic cell cultures are frequently responsible for unreliable results. Regulatory entities request that cell cultures must be mycoplasma-free. Mycoplasma contamination remains a significant problem for cell cultures and may have an impact on biological analysis since they affect many cell parameters....
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2015.08.010
更新日期:2015-11-01 00:00:00
abstract::Expressed sequence tags (ESTs) from fungal-infected plant tissues are composed of a mixture of plant and fungal sequences. Using freely available software and tools, a novel procedure is described for distinguishing plant and fungal DNA sequences. Although the GenBank non-redundant (NR) database is larger and therefor...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/s0167-7012(03)00067-8
更新日期:2003-09-01 00:00:00
abstract::Specific molecular determination and classification of ammonia-oxidizing bacteria have relied on the use of conventional markers such as 16S rDNA. However, this gene does not satisfactorily provide a wide vision of all phylogenetic lineages. Despite the initial expectations, the use of functional genes as for example ...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2003.11.019
更新日期:2004-04-01 00:00:00
abstract::Haemophilus parasuis infection is of considerable economic importance in the swine industry due to high morbidity and mortality in naive swine populations. Accurate detection and identification of the causative agent are difficult, yet necessary, for disease control. In this study, a simple and rapid method of cross-p...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2017.11.005
更新日期:2018-01-01 00:00:00
abstract::In order to reduce the risk of transmission of infectious diseases through transplantation of tissue allografts, one should examine tissues for the presence of microorganisms. However, there are no detailed tissue banking guidelines describing the culture method or incubation time to be used. Therefore, we compared tw...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2007.05.014
更新日期:2007-08-01 00:00:00
abstract::Representational Difference Analysis (RDA) is an established technique used for isolation of specific genetic differences between or within bacterial species. This method was used to investigate the genetic basis of serovar-specificity and the relationship between serovar and virulence in Haemophilus parasuis. An RDA ...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2006.09.011
更新日期:2007-02-01 00:00:00
abstract::Leishmaniasis, caused by protozoa belonging to the genus Leishmania, is an important public health problem found in >90 countries and with still limited options for treatment. Development of new anti-leishmanial drugs is an urgent need and the identification of new active compounds is a limiting factor that can be acc...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2019.105732
更新日期:2019-11-01 00:00:00
abstract::Plant-associated bacteria produce quorum sensing (QS) signals for community (biofilm) formation and functioning in the rhizosphere. The QS-positive biofilm-forming rhizobacteria that excel benefits to the plants are now gaining increased importance for agricultural use due to their high competitiveness. However, there...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2018.11.018
更新日期:2019-01-01 00:00:00
abstract::DNA probes specific for rRNA of selected target species were utilised for the detection of beer spoilage bacteria of the genera Pectinatus and Megasphaera using a hybridisation protection assay (HPA). All the probes were modified during synthesis by addition of an amino linker arm at the 5' end or were internally modi...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2013.10.014
更新日期:2014-01-01 00:00:00
abstract::A multiplex-PCR (mPCR) assay was designed with species-specific primers which generate amplicons of 226bp, 434bp and 106bp for differentiating the species C. striatum, C. amycolatum, and C. xerosis, respectively. mPCR results were 100% in agreement with identifications achieved by 16S rRNA and rpoB gene sequencing and...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2017.09.002
更新日期:2017-11-01 00:00:00
abstract::Several outbreaks of foodborne yersiniosis have been documented and this disease continues to be source of infections transmitted through foods. The selective agars most commonly used to isolate Yersinia enterocolitica in clinical, food and environmental samples, cefsulodin-irgasan-novobiocin (CIN) and MacConkey (MAC)...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2007.11.019
更新日期:2008-02-01 00:00:00
abstract::Quantitative PCR is becoming the method of choice for the detection of pathogenic microorganisms and other targets in the environment. A major obstacle when amplifying DNA is the presence of inhibiting substances like humic acids that decrease the efficiency of PCR. We combined the polymeric adsorbent Supelite™ DAX-8 ...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2010.12.027
更新日期:2011-04-01 00:00:00
abstract::Bacterial fruit blotch (BFB) of cucurbits, caused by Acidovorax citrulli, is a major threat to commercial watermelon and melon production worldwide. At present, there are at least two genetically distinct sub-populations (group I and II) of A. citrulli that differ in host preference among cucurbit species and copper s...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2019.02.003
更新日期:2019-03-01 00:00:00
abstract::MALDI-TOF mass spectrometry (MALDI-TOF MS) is increasingly used as a reliable technique for species identification of bacterial pathogens. In this study we investigated the question of whether MALDI-TOF MS can be used for accurate sub-differentiation of strains and isolates of two important nosocomial pathogens Entero...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2014.02.015
更新日期:2014-05-01 00:00:00
abstract::A sensitive, selective, and rapid protocol for detecting Ralstonia solanacearum from soil and plant tissues was developed based on the integration of the rapid self-replicating ability of bacteriophages with quantitative PCR (q-PCR). Six bacteriophages were isolated and selected for their ability to specifically infec...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2008.11.008
更新日期:2009-03-01 00:00:00
abstract::We developed and evaluated RNA aptamers to analyze their potential for use in detecting Salmonella Enteritidis. The selected aptamer was observed to specifically bind to Salmonella Enteritidis without any cross-reactivity to other Salmonella serovars. Thus, this study suggests that aptamers specific to Salmonella Ente...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2012.01.014
更新日期:2012-04-01 00:00:00