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At least 1,243 records · Page 69Linked to original sources

PubMed2003

Gas-chromatographic lipid profiles in identification of currently known slowly growing environmental mycobacteria.

Cellular fatty acid analysis by GLC is widely used in the species identification of mycobacteria. Combining mycolic acid cleavage products with shorter cellular fatty acids increases the informative value of the analysis. A key has been created to aid in the identification of all currently known slowly growing environmental species. In this scheme, the species are classified into six categories, each characterized by a combination of fatty markers shared by those species. Within each category, individual species may be distinguished by the presence or absence of specific marker substances, such as methyl-branched fatty acids or secondary alcohols. This study also describes earlier unpublished GLC profiles of 14 rare, slowly growing, environmental mycobacteria, Mycobacterium asiaticum, Mycobacterium botniense, Mycobacterium branderi, Mycobacterium conspicuum, Mycobacterium cookii, Mycobacterium doricum, Mycobacterium heckeshornense, Mycobacterium heidelbergense, Mycobacterium hiberniae, Mycobacterium kubicae, Mycobacterium lentiflavum, Mycobacterium scrofulaceum, Mycobacterium triplex and Mycobacterium tusciae. Though no single identification technique alone, even sequencing of an entire single gene such as 16S rRNA, can identify all mycobacterial species accurately, GLC has proven to be both reliable and reproducible in the identification of slowly growing mycobacteria. In cases of earlier unknown species, it generates useful information that allows their further classification and may lead to the description of novel species.

Chromatography, Gas↗

PubMed2006

Rapid molecular identification of fungal pathogens in corneal samples from suspected keratomycosis cases.

An increase in the incidence of fungal infections has highlighted the need for rapid and precise detection and identification methods in clinical mycology. This report describes the data obtained on corneal samples from 24 patients with suspected keratomycosis using a conventional cultural approach in parallel with PCR amplification and sequencing of the internal transcribed spacers (ITSs) of the rDNA regions. Using the cultural approach, seven samples (58.3 % of the 12 samples positive for an infectious pathogen) tested positive for a fungal aetiology, with final identification taking a mean time of more than 5 days. In two cases, diagnosis required 10 days. Using the ITS-based molecular approach, a direct diagnosis was obtained in only five of the seven fungus-positive cases (71.4 %) starting from the clinical samples, but identification was still possible in all seven cases within 24 h (by using 16 h cultures for the two remaining cases). Despite the less-than-optimal sensitivity when working directly on clinical samples, the obtained data indicate that the molecular strategy used in this study is a useful complement to the conventional diagnostic approaches used for keratomycosis and, in particular, allows precise and fast fungal identification, in response to the clinical requirements. Similar studies on larger panels of patients and on different clinical samples are required for further investigation of the clinical potential of ITS-based approaches in the diagnosis of mycotic infections.

Base Sequence↗

PubMed2006

Fast and reliable PCR/sequencing/RFLP assay for identification of fungi in onychomycoses.

Fusarium spp. and other non-dermatophyte fungi are repeatedly isolated from abnormal nails. To investigate whether these fungi are the aetiological agents of infection or simply transient contaminants, a PCR/sequencing/RFLP assay was developed for direct and routine identification of the infecting fungi in onychomycosis. Fungal DNA was readily extracted using a commercial kit after dissolving nail fragments in a Na2S solution. Amplification of part of the 28S rDNA by PCR was performed with universal primers and the fungal species were identified by sequencing. The PCR/sequencing results were comparable with microbiological identification from the same nail sample. In addition to dermatophytes, Fusarium spp. and other less frequently isolated non-dermatophyte fungi were identified as single fungal agents in onychomycosis. Moreover, mixed infections were clearly demonstrated in 10% of cases by RFLP analysis of PCR products. Identification of infectious agents could be obtained in 2 days, whilst results from fungal cultures take 1-3 weeks. Rapid and reliable molecular identification of the infectious fungus expedites the choice of appropriate antifungal therapy, thereby improving the cure rate of onychomycosis.

DNA, Fungal↗

PubMed2004

The Arabidopsis root transcriptome by serial analysis of gene expression. Gene identification using the genome sequence.

Large-scale identification of genes expressed in roots of the model plant Arabidopsis was performed by serial analysis of gene expression (SAGE), on a total of 144,083 sequenced tags, representing at least 15,964 different mRNAs. For tag to gene assignment, we developed a computational approach based on 26,620 genes annotated from the complete sequence of the genome. The procedure selected warrants the identification of the genes corresponding to the majority of the tags found experimentally, with a high level of reliability, and provides a reference database for SAGE studies in Arabidopsis. This new resource allowed us to characterize the expression of more than 3,000 genes, for which there is no expressed sequence tag (EST) or cDNA in the databases. Moreover, 85% of the tags were specific for one gene. To illustrate this advantage of SAGE for functional genomics, we show that our data allow an unambiguous analysis of most of the individual genes belonging to 12 different ion transporter multigene families. These results indicate that, compared with EST-based tag to gene assignment, the use of the annotated genome sequence greatly improves gene identification in SAGE studies. However, more than 6,000 different tags remained with no gene match, suggesting that a significant proportion of transcripts present in the roots originate from yet unknown or wrongly annotated genes. The root transcriptome characterized in this study markedly differs from those obtained in other organs, and provides a unique resource for investigating the functional specificities of the root system. As an example of the use of SAGE for transcript profiling in Arabidopsis, we report here the identification of 270 genes differentially expressed between roots of plants grown either with NO3- or NH4NO3 as N source.

Arabidopsis↗

PubMed2003

NARMAX representation and identification of ankle dynamics.

Representation and identification of a parallel pathway description of ankle dynamics as a model of the nonlinear autoregressive, moving average exogenous (NARMAX) class is considered. A nonlinear difference equation describing this ankle model is derived theoretically and shown to be of the NARMAX form. Identification methods for NARMAX models are applied to ankle dynamics and its properties investigated via continuous-time simulations of experimental conditions. Simulation results show that 1) the outputs of the NARMAX model match closely those generated using continuous-time methods and 2) NARMAX identification methods applied to ankle dynamics provide accurate discrete-time parameter estimates. Application of NARMAX identification to experimental human ankle data models with high cross-validation variance accounted for.

Ankle↗

PubMed2002

Estimation of kinetic parameters without input functions: analysis of three methods for multichannel blind identification.

Compartment modeling of dynamic medical image data implies that the concentration of the tracer over time in a particular region of the organ of interest is well modeled as a convolution of the tissue response with the tracer concentration in the blood stream. The tissue response is different for different tissues while the blood input is assumed to be the same for different tissues. The kinetic parameters characterizing the tissue responses can be estimated by multichannel blind identification methods. These algorithms use the simultaneous measurements of concentration in separate regions of the organ; if the regions have different responses, the measurement of the blood input function may not be required. Three blind identification algorithms are analyzed here to assess their utility in medical imaging: eigenvector-based algorithm for multichannel blind deconvolution; cross relations; and iterative quadratic maximum-likelihood (IQML). Comparisons of accuracy with conventional (not blind) identification techniques where the blood input is known are made as well. Tissue responses corresponding to a physiological two-compartment model are primarily considered. The statistical accuracies of estimation for the three methods are evaluated and compared for multiple parameter sets. The results show that IQML gives more accurate estimates than the other two blind identification methods.

Algorithms↗

PubMed2006

Discriminative analysis of lip motion features for speaker identification and speech-reading.

There have been several studies that jointly use audio, lip intensity, and lip geometry information for speaker identification and speech-reading applications. This paper proposes using explicit lip motion information, instead of or in addition to lip intensity and/or geometry information, for speaker identification and speech-reading within a unified feature selection and discrimination analysis framework, and addresses two important issues: 1) Is using explicit lip motion information useful, and, 2) if so, what are the best lip motion features for these two applications? The best lip motion features for speaker identification are considered to be those that result in the highest discrimination of individual speakers in a population, whereas for speech-reading, the best features are those providing the highest phoneme/word/phrase recognition rate. Several lip motion feature candidates have been considered including dense motion features within a bounding box about the lip, lip contour motion features, and combination of these with lip shape features. Furthermore, a novel two-stage, spatial, and temporal discrimination analysis is introduced to select the best lip motion features for speaker identification and speech-reading applications. Experimental results using an hidden-Markov-model-based recognition system indicate that using explicit lip motion information provides additional performance gains in both applications, and lip motion features prove more valuable in the case of speech-reading application.

Algorithms↗

PubMed2004

Identification of complex systems based on neural and Takagi-Sugeno fuzzy model.

The paper describes a neuro-fuzzy identification approach, which uses numerical data as a starting point. The proposed method generates a Takagi-Sugeno fuzzy model, characterized with transparency, high accuracy and a small number of rules. The process of self-organizing of the identification model consists of three phases: clustering of the input-output space using a self-organized neural network; determination of the parameters of the consequent part of a rule from over-determined batch least-squares formulation of the problem, using singular value decomposition algorithm; and on-line adaptation of these parameters using recursive least-squares method. The verification of the proposed identification approach is provided using four different problems: two benchmark identification problems, speed estimation for a dc motor drive, and estimation of the temperature in a tunnel furnace for clay baking.

Journal Article↗

PubMed2001

Absolute identification with simple and complex stimuli.

It is well known that people can perfectly identify only a handful of distinct unidimensional stimuli, such as line lengths, but can identify thousands of complex stimuli, such as letters and words. This result is consistent with capacity limits in identifying unidimensional stimuli but not complex stimuli. The experiments reported here tested this theoretical dissociation using Luce's (1963) Similarity Choice Model to measure the psychological distance between stimuli in line-length-identification and letter-identification tasks. The psychological distance between line-length stimuli decreased with the number of to-be-identified stimuli; this result is concordant with capacity limits in unidimensional absolute identification. Surprisingly, the opposite result held in letter identification. Psychological distance between letters increased with an increased number of to-be-identified stimuli. This result indicates an opposite type of processing deficit: People process letters more efficiently with more choices.

Cognition↗

PubMed2004

Odour identification as a marker for postoperative cognitive dysfunction: a pilot study.

The onset of postoperative cognitive dysfunction is delayed in some elderly surgical patients and the condition may persist. Increasing age is a risk factor for both postoperative cognitive dysfunction and dementia. Major surgery may unmask an underlying dementia; we report findings of a pilot study designed to inform this hypothesis. Impaired odour identification ability is a characteristic of the preclinical phase of some neuro-degenerative diseases. This pilot study was designed to establish whether odour identification deficit is a marker for postoperative cognitive dysfunction, particularly in elderly patients genetically predisposed to develop late-onset Alzheimer's disease. We found no association between odour identification ability and postoperative cognitive dysfunction in 53 patients aged 62-86, undergoing major non-cardiac surgery under general anaesthesia. Our pilot study showed that a high number of patients genetically predisposed to develop Alzheimer's disease is required to test the utility of odour identification as a marker for postoperative cognitive dysfunction.

Aged↗

PubMed1985

The scope and limitations of four methods for the rapid identification of Enterobacteriaceae in foods.

Four methods for the identification of Enterobacteriaceae in cooked frozen meat have been appraised. Although these methods could be modified to improve efficiency they could be clearly classified into two categories: (i) those that allow identification to genus level and which often cannot discriminate between two genera without the help of additional reactions; (ii) those that allow identification to species level and which only occasionally require additional reactions to differentiate one species from another. A different evaluation criterion was followed for each of these categories. In the first, as methods lead to final identification by means of data furnished by the manufacturer or via a number code which does not indicate probability, reactions were compared with those obtained by classical methods. In the second group, every number code admits three possibilities and indicates a probable biotype for each, thus reducing the risk of faulty interpretation on the part of the operator while also compensating for deficiencies of certain reactions. Evaluation was therefore based on the percentage of correctly identified cases per species. Efficiencies of the main biochemical reactions are also discussed.

Bacteriological Techniques↗

PubMed1986

A probability matrix for the identification of species of Vibrio and related genera.

A matrix for the probabilistic identification of species of Vibrio and related genera has been constructed using the data from 1091 strains collected throughout the world and classified. Thirty-eight phenons are included in the matrix, 31 of these represent previously identified species or biovars and seven represent phenons which could not be identified and may represent new species. The identification matrix incorporates 81 characters although a subset of 30 tests can be used to distinguish the 38 phenons from each other. The additional 51 tests were included to assist the identification of some strains for which the initial 30 tests were inadequate. No significant cluster overlap was found at the 5% level and the identification score for the Hypothetical Median Organism of each cluster exceeded 0.9999 in all cases.

Probability↗

PubMed1990

The identification, typing and fingerprinting of Salmonella: laboratory aspects and epidemiological applications.

Since the 1930s, traditional methods of strain identification based on serotyping and phage typing have been the foundation of salmonella epidemiology. Although the incidence of diseases such as typhoid and paratyphoid has decreased in recent years, food-poisoning caused by non-typhoidal salmonella strains has now reached epidemic proportions in many countries, despite improvements in sanitation and hygiene. Precise strain identification is an essential prerequisite for epidemiological investigations aimed at combating the spread of these strains and eradicating the sources of infection. Modern methods of genotypic typing, particularly those based on physical characterization of the plasmid content of the organism have already proved invaluable for the identification and differentiation of strains in many outbreaks. These plasmid typing methods are now increasingly used with serotyping and phage typing for many epidemiological investigations. Other methods of genotypic typing, particularly those based on recognition of small differences in chromosome structure, are not yet practical for the examination of large numbers of strains. Nevertheless, improvements in small-scale methods for chromosomal DNA extraction coupled with the increasing use of non-isotopic labels for identification of restriction fragment length polymorphisms may provide a new dimension to Salmonella epidemiology.

Animals↗

PubMed2004

Utilization of AFLP markers for PCR-based identification of Aspergillus carbonarius and indication of its presence in green coffee samples.

AIMS: The objective of this work was to test whether ochratoxin A (OTA) production of Aspergillus niger and A. carbonarius is linked to a certain genotype and to identify marker sequences with diagnostic value aiding identification of A. carbonarius, a fungus of major concern regarding OTA production in food and food raw materials. METHODS AND RESULTS: Aspergillus niger and A. carbonarius were isolated mainly from Brazilian coffee sources. The ability of isolates to produce OTA was tested by thin layer chromatography (TLC). Strains were genetically characterized by AFLP fingerprinting and compared with each other and with reference strains. Cluster analysis of fingerprints showed clear separation of A. niger from A. carbonarius strains. To obtain marker sequences, AFLP fragments were isolated from silver stained polyacrylamide gels, cloned and sequenced. Sequences obtained were used to develop species- specific PCR primers for the identification of A. carbonarius in pure culture and in artificially and naturally infected samples of green coffee. CONCLUSIONS: No clear correlation between genetic similarity of the strains studied and their potential to produce OTA was found. The PCR assays designed are a useful and specific tool for identification and highly sensitive detection of A. carbonarius. SIGNIFICANCE AND IMPACT OF THE STUDY: The developed PCR assays allow specific and sensitive detection and identification of A. carbonarius, a fungus considered to be one of the major causative agents for OTA in coffee and grape-derived products. Assays may provide powerful tools to improve quality control and consumer safety in the food processing industry.

Aspergillus↗

PubMed2005

Combined application of methods to taxonomic identification of Saccharomyces strains in fermenting botrytized grape must.

AIMS: Although numerous physiological and molecular methods have been proposed for yeast taxonomy, the unambiguous separation of Saccharomyces sensu stricto species in natural samples is still an incompletely resolved issue. In this study the power of various methods was compared in the identification of strains isolated from fermenting botrytized grape musts. METHODS AND RESULTS: Conventional taxonomic and physiological tests and molecular methods developed for rapid identification were used. CONCLUSIONS: None of the methods tested was sufficiently powerful. However, the combination of electrophoretic karyotyping and the PCR-RFLP of MET2 with growth tests at 10 and 37 degrees C provided results sufficient for species identification of Saccharomyces wine strains which were not interspecific hybrids or recombinants. SIGNIFICANCE AND IMPACT OF THE STUDY: The proposed combination of molecular and physiological methods allows specific taxonomic identification and separation of Saccharomyces wine strains without extensive genetic and molecular analysis. The proposed combined approach can also identify hybrids and recombinants.

Chromosomes, Fungal↗

PubMed2006

Comparison of 16S rRNA sequencing with conventional and commercial phenotypic techniques for identification of enterococci from the marine environment.

AIMS: To compare accuracy of genus and species level identification of presumptive enterococci isolates from the marine environment using conventional biochemical testing, four commercial identification systems and 16S rRNA sequence analysis. METHODS AND RESULTS: Ninety-seven environmental bacterial isolates identified as presumptive enterococci on mEI media were tested using conventional and Enterococcus genus screen biochemical tests, four commercial testing systems and 16S rRNA sequencing. Conventional and Enterococcus genus screen biochemical testing, 16S rRNA sequencing and two commercial test systems achieved an accuracy of > or = 94% for Enterococcus genus confirmation. Conventional biochemical testing and 16S rRNA sequencing achieved an accuracy of > or = 90% for species level identification. CONCLUSIONS: For confirmation of Enterococcus genus from mEI media, conventional or genus screen biochemical testing, 16S rRNA sequencing and the four commercial systems were correct 79-100% of the time. For speciation to an accuracy of 90% or better, either conventional biochemical testing or 16S rRNA sequencing is required. SIGNIFICANCE AND IMPACT OF THE STUDY: Accurate identification of presumptive environmental Enterococcus isolates to genus and species level is an integral part of laboratory quality assurance and further characterization of Enterococcus species from pollution incidents. This investigation determines the ability of six different methods to correctly identify environmental isolates.

Bacteriological Techniques↗

PubMed2006

Differential identification of Bacillus anthracis from environmental Bacillus species using microarray analysis.

AIMS: To determine whether microarray analysis could be employed for the differential identification of a range of environmental Bacillus sp. from four strains of Bacillus anthracis. METHODS AND RESULTS: Oligonucleotide probes were designed that were specific to virulence factor genes of B. anthracis (pag, lef and cap), the variable number tandem repeat region of the B. anthracis vrrA gene and to the 16S-23S rRNA intergenic transcribed spacer region (ITS) and pleiotropic regulator (plcR) regions of the Bacillus cereus subgroup species. Generic probes were also designed to hybridize with conserved regions of the 16S rRNA genes of Bacillus (as a positive control), Neisseria sp., Pseudomonas sp., Streptococcus sp., Mycobacterium sp. and to all members of the Enterobacteriaceae to allow simultaneous detection of these bacteria. Identification of B. anthracis was found to rely entirely on hybridization of DNA specific to regions of the pag, lef and cap genes. Cross-reaction was observed between B. anthracis and other Bacillus species with all the other Bacillus probes tested. Results obtained using microarray hybridizations were confirmed using conventional microbiological techniques and found to have very high comparability. CONCLUSIONS: Microarray-based assays are an effective method for the identification of B. anthracis from mixed-culture environmental samples without problems of false-positivity that have been observed with conventional PCR assays. SIGNIFICANCE AND IMPACT OF THE STUDY: Identification of environmental Bacillus sp. by conventional PCR is prone to potential for reporting false-positives. This study provides a method for the exclusion of such isolates.

Bacillus↗

PubMed2005

UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi.

Identification of ectomycorrhizal (ECM) fungi is often achieved through comparisons of ribosomal DNA internal transcribed spacer (ITS) sequences with accessioned sequences deposited in public databases. A major problem encountered is that annotation of the sequences in these databases is not always complete or trustworthy. In order to overcome this deficiency, we report on UNITE, an open-access database. UNITE comprises well annotated fungal ITS sequences from well defined herbarium specimens that include full herbarium reference identification data, collector/source and ecological data. At present UNITE contains 758 ITS sequences from 455 species and 67 genera of ECM fungi. UNITE can be searched by taxon name, via sequence similarity using blastn, and via phylogenetic sequence identification using galaxie. Following implementation, galaxie performs a phylogenetic analysis of the query sequence after alignment either to pre-existing generic alignments, or to matches retrieved from a blast search on the UNITE data. It should be noted that the current version of UNITE is dedicated to the reliable identification of ECM fungi. The UNITE database is accessible through the URL http://unite.zbi.ee

DNA, Ribosomal Spacer↗