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PubMed1988

Simplified identification of aerobic spore-formers in the investigation of foods.

Bacillus spp. are among the main spoilage organisms in food due to their versatile metabolism and heat-resistant spores. Except for B. cereus, no specific identification method is available, although information about Bacillus spp. would be useful in monitoring good manufacturing practice. A simplified identification scheme for aerobic spore-formers for routine laboratory use was elaborated by reducing the number of tests to be performed; 20 Bacillus spp. common in foods were considered. Besides cell morphology six biochemical characters were selected that proved most efficient in identification. In addition, methods were developed and modified to determine these characters by only 3 tests. By applying the simplified identification scheme, 766 strains of bacilli isolated from various foods were tested and species identity of 714 strains (93%) could be determined. Most aerobic spore-formers from foods were B. subtilis, B. pumilus and B. licheniformis. The spectrum of mesophilic bacilli isolated from natural sources was broad and comprised some 20 different species. Only one-third of the thermophilic isolates proved to be identical with, or similar to, B. stearothermophilus, while the rest were identified as five other species. The simplified method merits main application in ecological studies of foods.

Bacillus↗

PubMed1994

A non-isotopic DNA hybridisation assay for the identification of Staphylococcus aureus isolated from foods.

A digoxygenin-labelled total genomic DNA probe was used to identify Staphylococcus aureus. Isolation and identification of organisms was possible in less than 4 days. Identification alone could be completed in less than 2 days, compared with over 5 days for identification of isolates by multipoint inoculation. The probe showed excellent discrimination of S. aureus from other staphylococci and from a wide range of bacteria commonly associated with milk and meat. The effectiveness of this probe was tested against cultural isolation of staphylococci in milk using Baird-Parker agar followed by identification using multipoint inoculation and API Staph. The probe gave comparable results to the conventional methods and, for large sample numbers, offered lower cost and greater ease of use.

Animals↗

PubMed1993

Nonlinear identification of the PCO2 control system in man.

Two approaches to identification of the PCO2 system in man are described. The first uses a nonlinear 'black box' NARMAX identification package, while the second method uses a structured two-compartment Belville model. The data were obtained from volunteers breathing either room air or a controlled gas mixture, controlled via a pseudorandom M-sequence. Measurements were made of respiratory gas flow and PCO2 content of inspired and expired gases. The identification results indicate that a low-order dynamic model with nonlinear polynomial expansion gave the best fit to the data. In contrast, the Belville model gave best results with a two-compartment linear model, mainly because of difficulties in the optimisation routines when the Belville model was not linear. Thus, modern systemic methods of excitation and identification appear to be appropriate for modelling this respiratory subsystem of humans.

Adult↗

PubMed1995

Individual identification by means of conventional bitewing film and subtraction radiography.

An analysis of simulated post- and antemortem (p.m. and a.m.) victim radiographs was performed. Existing pairs of bitewing radiographs randomly sampled from a large population of adolescents were used. Two categories of individuals were included based on dental therapy conditions (none or few simple fillings). Subtraction images were performed of pairs of bitewings originating from the same individual (identical images) and different individuals (non-identical images) within each group. Four observers were asked to match the bitewings and to assess the subtraction images with respect to identity based on the score system: 1 = 'eliminated', 2 = 'possible', 3 = 'likely', or 4 = 'certain'. Three observers each mismatched the film radiographs among two out of 12 individuals without fillings. True positive identification (identified by scores 2 + 3 + 4) of subtraction images were made in 10-12 individuals out of a possible 12. The range of false positive (FP) and false negative (FN) scorings was 3-15 and 0-2, respectively. All observers were capable of correctly matching bitewings originating in the 12 individuals with amalgam fillings. By use of subtraction radiography, 12-14 identical images out of a possible 15 were assessed correctly. The range of FP and FN scorings of subtraction images in this group was 1-4 and 1, respectively. Defining only score 4 as positive identification, the sensitivity of the subtraction technique decreased from approximately 0.90 to 0.70 in both categories of individuals, while specificity increased to almost 1.00 from 0.82 vs. 0.96 in the categories with and without dental restorations. Bitewing radiographs from single individuals within a group of individuals were sufficiently identical to allow for valid identification by a strict criterion. The subtraction technique may add to the subjective matching of radiographs as a screening test in victim identification.

Adolescent↗

PubMed1984

Use of and cost savings with morphologic criteria and the spot indole test as a routine means of identification of Escherichia coli.

The use of primary isolation plate colonial morphologic criteria (CMC) of a flat, nonmucoid, lactose-fermenting, gram-negative rod on MacConkey agar and the spot indole (SI) test from the sheep blood agar plate was evaluated as a means for identification of Escherichia coli in comparison to kit (Micro-ID, API-20E) and conventional biochemical testing. In this preliminary phase of comparison of accuracy, 427 isolates of E. coli (69.8%) from a total of 612 isolates of lactose-fermenting gram-negative rods were evaluated. Of these E. coli isolates, 357 (83.6%) fit the CMC and were SI positive; 3 (less than 1% error rate) were not E. coli. In the second phase of the evaluation, using CMC and SI alone as a means for identification of E. coli, 472 (57.6%) E. coli isolates from a total of 820 Enterobacteriaceae isolates were assessed. Of these E. coli isolates, 326 could be identified using only CMC and SI (69.1% of the E. coli isolates and 39.8% of all Enterobacteriaceae isolates); 146 (30.9%) required additional biochemical testing because of atypical colonial morphology, because of the investigator's inability to differentiate colony types on both media or lack of isolated colonies on either of the two required media, or because as isolates from sterile body sites they were processed directly to Micro-ID kits. A minimum of 40% savings on Enterobacteriaceae identification schemes without compromising accuracy was calculated. As of November 1983, a direct (labor and materials) cost savings of approximately +200.80 per 100 Enterobacteriaceae identifications was projected.

Agar↗

PubMed1985

Identification of gram-negative bacilli using the Autobac IDX.

The Autobac IDX is a new system for the rapid identification of clinically significant members of the Enterobacteriaceae and Aeromonas, Acinetobacter, Alcaligenes, Flavobacterium, Moraxella, and Pseudomonas species. The use of 18 differentially inhibitory compounds such as dyes and antibiotics along with a computerized algorithm based on a multivariate analysis provides the basis for the identification of 30 different groups of gram-negative bacilli. Required preliminary tests include observations on the presence or absence of swarming on a sheep blood agar plate and noting the following: growth, lactose fermentation, and bile precipitation from a MacConkey plate. Spot indole and spot oxidase tests must be performed as well. Identification by the Autobac IDX System takes 3-6 hr after completion of the preliminary tests. From a total of 403 isolates tested, the Autobac system agreed with the MicroID AND N/F systems on 382 identifications (94.8%). Four isolates, two Acinetobacter anitratus, one Serratia marcescens and one Moraxella osloensis could not be identified by IDX. Additional testing was required on 35 (8.7%) of the isolates.

Bacteria↗

PubMed1993

Species identification and determination of high-level aminoglycoside resistance among enterococci. Comparison study of sterile body fluid isolates, 1985-1991.

Enterococcus spp. have become the third most common cause of nosocomial infections. High-level aminoglycoside resistance (HLR), an important clinical concern, has been associated with some species of the enterococci. We evaluated the Vitek and API 20S systems for species identification and the Vitek for the detection of HLR. Enterococci from nosocomial infections (208 strains) at the University of Iowa Hospital (1985-1991) were tested by Vitek, API 20S, and reference methods. The error rate for species identification was 6.7% for the API 20S and 5.8% for the Vitek Gram-positive identification (GPI) cards. Both systems tended to incorrectly identify other enterococcal species as Enterococcus faecium. HLR was found in Enterococcus faecalis and E. faecium isolates only. The highest rates of HLR to streptomycin alone (17.9%) and with gentamicin (13.5%) was observed among E. faecalis strains, and to gentamicin alone (7.3%) was found among E. faecium isolates. No apparent differences in HLR rates were found from year-to-year over the 7-year enterococcus sample interval. Susceptibility errors for Vitek were among the streptomycin tests only. Our results demonstrated acceptable performance by the Vitek cards for enterococcal species identification and the detection of HLR. API 20S also provided an acceptable ability to speciate the enterococci within its data base, however, both systems must be improved by adding other clinical important Enterococcus species.

Aminoglycosides↗

PubMed1992

A species-specific DNA probe for Providencia stuartii identification.

A DNA probe is described that can be used for identification of Providencia stuartii by means of filter hybridization assays. The probe, which is a fragment of the P. stuartii phoN gene coding for an acid phosphatase, appeared to be able to recognize only P. stuartii strains in slot-blot hybridization experiments performed with total DNA extracted from 545 strains of 64 different Gram-negative bacterial species, including all the major representatives of the family Enterobacteriaceae. Owing to the problems that may be often encountered for correct identification of P. stuartii at the species level when using commercial identification systems, this probe may result useful for fast and reliable identification of P. stuartii strains for taxonomical, epidemiological and diagnostic studies.

Acid Phosphatase↗

PubMed1995

Identification of enteroviruses by indirect immunofluorescence using monoclonal antibodies.

BACKGROUND: Serum neutralization (Nt) is used most often to type enterovirus isolates, but it is labor-intensive, expensive, and supplies of reference antisera for Nt are limited. Alternative methods of enterovirus typing are needed. OBJECTIVES: To investigate the use of indirect immunofluorescence (IFA) with commercially available monoclonal antibodies (MAbs) as an alternative to Nt for the identification of enteroviruses. STUDY DESIGN: Two MAb blends (one for coxsackie B viruses and one for echoviruses 4, 6, 9, 11, 30, and 34) and a coxsackie A9 MAb were used to screen 465 clinical isolates over a period of two years. Virus isolates which tested positive with one of the blends were typed with the individual MAbs of the respective blend. Individual MAbs for polioviruses 1, 2, and 3 acquired late in the study were used to screen 45 viral isolates. RESULTS: The antibodies identified 251/465 (54%) of the total number of isolates tested. IFA results for 451 of 465 viral isolates were in agreement with conventional identification methods. The sensitivity of the IFA screen using the MAb blends and coxsackie A9 MAb was 93% and the specificity was 99%. Thirteen discrepant isolates were negative by IFA, with twelve positive by Nt for echovirus 30 and one isolate positive by Nt for coxsackie A9. The remaining discrepant isolate was positive by IFA for both coxsackie A9 and coxsackie B5, but positive by Nt for coxsackie A9 only. CONCLUSIONS: IFA is highly specific for the identification of enteroviruses, but may not be sensitive enough to identify all strains within an enterovirus type. Procedures which utilize an IFA screen and confirm final results by Nt decrease turnaround time and reduce the number of cell culture tubes required for the identification of each enterovirus isolate.

Journal Article↗

PubMed2006

Trypanosome identification in wild tsetse populations in Tanzania using generic primers to amplify the ribosomal RNA ITS-1 region.

Tsetse flies transmit many species of trypanosomes in Africa, some of which are human and livestock pathogens of major medical and socio-economic impact. Identification of trypanosomes is essential to assess the disease risk posed by particular tsetse populations. We have developed a single generic PCR test to replace the multiple species-specific PCR tests used previously to identify the trypanosome species carried by individual tsetse flies. In the generic PCR test, inter-species size variation in the PCR product of the internal transcribed spacer (ITS-1) region of the ribosomal RNA repeat region enables species identification. The test was applied to identify trypanosomes in midgut samples stored on FTA cards from wild-caught flies in two regions of Tanzania. Identifications were verified by sequencing the amplified ITS-1 region and/or species-specific PCR tests. The method facilitated the identification of large numbers of field samples quickly and accurately. Whereas species-specific tests are incapable of recognising previously unknown species, the generic test enabled a new species to be identified by the unique size of the amplified product. Thus, even without access to any isolate of this new species, we could collect data on its distribution, prevalence and co-occurrence with other trypanosomes. The combined molecular and ecological profiles should facilitate the isolation and full biological characterization of this species in the future.

Animals↗

PubMed2006

Category-specific visual identification of filtered objects in Alzheimer's disease.

The category-specific deficit in object identification as function of spatial frequency (SF) content and priming effect was investigated. Twenty-two patients with Alzheimer Disease (AD) and 24 control subjects performed an object identification task. The objects belonged to living and nonliving categories. In the study phase an episodic trace of objects was created. In the identification phase, each object was revealed in a sequence of frames wherein the object was represented by an increasingly less and less filtered image up to complete version. A recall phase followed immediately after the identification phase. While the priming was preserved in mild-AD but not in moderate-AD, no difference was observed in the recall task. Moreover, although patients showed a decline in performance for both categories compared to controls, this decline was more rapid for living things especially in patients with more severe disease. Present results indicate a semantic memory deficit along with a disruption of perceptual representation. Data were discussed referring to perceptual/functional, domain-specific knowledge, and prefrontal cortex (PFC) theories.

Aged↗

PubMed2004

Tools for target identification and validation.

Reliable technologies for addressing target identification and validation are the foundation of successful drug development. Microarrays have been well utilized in genomics/proteomics approaches for gene/protein expression profiling and tissue/cell-scale target validation. Besides being used as an essential step in analyzing high-throughput experiments such as those involving microarrays, bioinformatics can also contribute to the processes of target identification and validation by providing functional information about target candidates and positioning information to biological networks. Antisense technologies (including RNA interference technology, which is recently very 'hot') enable sequence-based gene knockdown at the RNA level. Zinc finger proteins are a DNA transcription-targeting version of knockdown. Chemical genomics and proteomics are emerging tools for generating phenotype changes, thus leading to target and hit identifications. NMR-based screening, as well as activity-based protein profiling, are trying to meet the requirement of high-throughput target identification.

Animals↗

PubMed2005

Determination of the limits of identification and quantitation of selected organochlorine and organophosphorous pesticide residues in surface water by full-scan gas chromatography/mass spectrometry.

In this work, we report a reliable method for quantitation and determination of the limits of identification of 14 organochlorine and organophosphorous pesticide (OPP) residues in surface water. The method features the simultaneous identification and quantitation of targeted pesticides and the possibility of identification of any other eluting compounds. The method is based on liquid-liquid extraction (LLE) with a mixture of petroleum ether and dichloromethane (70:30, v/v) followed by gas chromatographic separation and a full-scan mass spectrometric detection (GC-MS). The method presents a new validation parameter, limit of identification (LOI) which is defined for our purpose as the lowest analyte concentration that yields a library searchable mass spectrum. The method is linear over the range 0.048-1.20microgL(-1) for nine pesticides and 0.024-0.60microgL(-1) for the other five pesticides. Correlation coefficients vary between 0.988 and 0.998. Limits of detection (LODs) vary between 0.005 and 0.05microgL(-1) for 4,4'-DDT and LOIs vary between 0.012 and 0.048microgL(-1).

Alkanes↗

PubMed2005

Hyphenated chromatographic techniques for the rapid screening and identification of antioxidants in methanolic extracts of pharmaceutically used plants.

Phytochemical analysis is an important scientific research area, which normally relies on a number of rather laborious and time-consuming techniques for compound identification. Isolation of the ingredients of plant extracts in adequate quantities for spectral and biological analysis was the basis of this research. In this paper the possibility of on-line rapid screening of antioxidant components in methanolic plant extracts and their subsequent identification is reported. Based exclusively on hyphenated chromatographic techniques the methanolic extracts of Tilia europea, Urtica dioica, Lonicera periclymenum and Hypericum perforatum are initially screened for their antioxidant components via an on-line DPPH and ABTS radical scavenging technique. Structural elucidation of the active analytes is achieved by means of LC-MS and LC-UV-SPE-NMR. After the determination of the appropriate LC gradient, a minimal number of chromatographic runs with these hyphenated techniques are adequate for the acquisition of the necessary data, leading to the identification of the targeted compounds. Based on their UV, NMR and MS spectra, the antioxidant compounds identified in the extracts under study were found to be either flavonoid glycosides or mono- and dicaffeoylquinic acids. Although the aim of the study was to show the great potential of the LC-UV-NMR-DPPH/ABTS approach for the rapid screening and identification of plant constituents, the results produced in the course of this study also have some merit by themselves. Some of the compounds detected are reported for the first time in the specific plant extracts.

Antioxidants↗

PubMed2006

Identification and quantitation of cis-ketoconazole impurity by capillary zone electrophoresis-mass spectrometry.

trans-Ketoconazole was identified and quantified as impurity of cis-ketoconazole, an antifungal compound, by capillary zone electrophoresis-electrospray-mass spectrometry (CZE-ESI-MS). The chirality of this impurity was demonstrated separating their enantiomers by adding heptakis-(2,3,6-tri-O-methyl)-beta-cyclodextrin to the separation buffer in capillary electrophoresis (CE) with UV detection. However, MS detection was hyphenated to the CE instrument for its identification. As both compounds are diastereomers, they have the same m/z values and are needed to be separated prior to the MS identification. A 0.4M ammonium formate separation buffer at pH 3.0 enabled the separation of the impurity from cis-ketoconazole. Under these conditions, the optimization of ESI-MS parameters (composition and flow of the sheath-liquid, drying temperature, drying gas flow, and capillary potential) was carried out to obtain the best MS sensitivity. CZE-ESI-MS optimized conditions enabled the identification of trans-ketoconazole as impurity of cis-ketoconazole. In addition, the quantitation of this impurity was achieved in different samples: cis-ketoconazole standard and three different pharmaceutical formulations (two tablets and one syrup) containing this standard. In all cases, percentages higher than 2.0 were determined for the impurity. According to ICH guidelines, these values required the identification and quantitation of any impurity in drug substances and products.

Antifungal Agents↗

PubMed2006

Separation and identification of isomeric acidic degradation products of organophosphorus chemical warfare agents by capillary electrophoresis-ion trap mass spectrometry.

Capillary electrophoresis (CE) coupled to ion trap mass spectrometry (MS) was evaluated for the separation and identification of chemical warfare agent degradation products (alkylphosphonic acids and alkyl alkylphosphonic acids). Different analytical parameters were optimized in negative ionization mode such as electrolyte composition (15 mM CH(3)COONH(4), pH 8.8), sheath liquid composition (MeOH/H(2)O/NH(3), 75:25:2, v/v/v), nebulization and ion trapping conditions. A standard mixture of five alkylphosphonic (di)acids and five alkyl alkylphosphonic (mono)acids containing isomeric compounds was used in order to evaluate CE selectivity and MS identification capability. The obtained electropherograms revealed that CE selectivity was very limited in the case of alkyl alkylphosphonic acid positional isomers, whereas isomeric isopropylphosphonic and propylphosphonic acids were baseline-separated. CE-MS-MS experiments provided an unambiguous identification of each isomeric co-migrating alkyl alkylphosphonic acids thanks to the presence of specific fragment ions. On the other hand, CE separation was mandatory for the identification of isomeric alkylphosphonic acids, which led to the same fragment ion and could not be differentiated by MS-MS. The developed method was applied to the analysis of soil extracts spiked with the analytes (before or after extraction treatment) and appeared to be very promising since resolution and sensitivity were similar to those observed in deionized water. Especially, analytes were detected and identified in soil extract spiked at 5 microg mL(-1) with each compound before extraction treatment.

Chemical Warfare Agents↗

PubMed2006

Comparison of the reliability of the identification with diode array detector and mass spectrometry.

The reliability of compound identification by low resolution mass spectrometry (MS) was quantitatively compared with that for diode array detection (DAD). The quantity of the information obtained with one parent ion and two characteristic daughter ions at low resolution MS-MS was compared with that obtained by UV-vis spectra with large wavelength range from DAD. It was shown that if the UV-vis spectra are reproducible, i.e. with low RSD values for selected wavelengths and relative absorption, the reliability of the identification with DAD is comparable with the one for low resolution MS-MS. Because the sensitivity of the DAD is one or two orders of magnitude lower than that of mass spectrometry, on-column focusing was applied and reliable identification was achieved at 1 ppb concentration. The surprisingly high reliability of identification obtained with contemporary DADs should increase the analysts' confidence in this method of detection/confirmation.

Animals↗

PubMed2005

Tentative identification of hemoglobin variants in the Bio-Rad VARIANT II Hb A1C method.

OBJECTIVE: To evaluate if peak characteristics, the retention time, and percentage of total hemoglobin of an unknown peak on the Bio-Rad VARIANT II Hb A1c method may be used to establish a tentative identification of hemoglobin variants. METHOD: The peak characteristics, retention time, and percentage of total hemoglobin obtained on abnormal peaks found on the Bio-Rad VARIANT II Hb A1c method were tabulated and evaluated against the identification of the hemoglobin variant established by the Bio-Rad beta thalassemia HPLC method and hemoglobin electrophoresis at both acid and alkaline pH. RESULTS: Some hemoglobin variants show specific peak characteristics, retention times, and percentage of total hemoglobin on the Bio-Rad VARIANT II Hb A1c method that allows for tentative identification of the hemoglobin variant. The retention times and percentage of hemoglobin variant for the common hemoglobin variants E, D, S, and C obtained on the Bio-Rad VARIANT II Hb A1c method are tabulated below. CONCLUSION: Peak characteristics, retention times, and percentage of hemoglobin variant may be used to establish the presence of a hemoglobin variant and to provide a tentative identification of some hemoglobin variants on the Bio-Rad VARIANT II Hb A1c method.

Chromatography, High Pressure Liquid↗