Fast Identification Method Research Articles

X-linked recessive Menkes disease: identification of partial gene deletions in affected males.

Menkes disease is an X-linked recessive lethal disorder of copper metabolism, caused by defects in the ATP7A gene. Partial gene deletions comprise about 15% of the mutations causing Menkes disease. We have previously demonstrated identification of partial ATP7A deletions in patients by Southern blot analysis. In the present study, we report the use of three fast and reliable polymerase chain reaction (PCR)-based methods for the identification of partial ATP7A deletions in Menkes disease patients. First we demonstrate the use of multiplex PCR, a fast method for identification and rough localization of partial gene deletions, in which two exons of ATP7A are coamplified. Second, we present PCR amplification of genomic DNA across the deletion junctions, a method enabling identification of the deletion breakpoints and hence the exact size of the deletion. Finally, application of reverse transcription PCR (RT-PCR) for identification and localization of gene deletions at the cDNA level is demonstrated. By studying the mutation at the cDNA level the predicted effect of the mutation on the amino acid sequence and consequently the protein structure and function can be inferred. We demonstrate characterization of partial gene deletions in five patients, and in three of these we were able to determine the breakpoint sequences.

A possible pitfall in the identification of Burkholderia mallei using molecular identification systems based on the sequence of the flagellin fliC gene.

Amotile Burkholderia mallei and motile Burkholderia pseudomallei display a high similarity with regard to phenotype and clinical syndromes, glanders and melioidosis. The aim of this study was to establish a fast and reliable molecular method for identification and differentiation. Despite amotility, the gene of the filament forming flagellin (fliC) could be completely sequenced in two B. mallei strains. Only one mutation was identified discriminating between B. mallei and B. pseudomallei. A polymerase chain reaction-restriction fragment length polymorphism assay was designed making use of the absence of an AvaII recognition site in B. mallei. All seven B. mallei, 12 out of 15 B. pseudomallei and 36 closely related apathogenic Burkholderia thailandensis strains were identified correctly. However, in three B. pseudomallei strains a point mutation at gene position 798 (G to C) disrupted the AvaII site. Therefore, molecular systems based on the fliC sequence can be used for a reliable proof of strains of the three species but not for the differentiation of B. mallei and B. pseudomallei isolates.

A possible pitfall in the identification of Burkholderia mallei using molecular identification systems based on the sequence of the flagellin fliC gene

Amotile Burkholderia mallei and motile Burkholderia pseudomallei display a high similarity with regard to phenotype and clinical syndromes, glanders and melioidosis. The aim of this study was to establish a fast and reliable molecular method for identification and differentiation. Despite amotility, the gene of the filament forming flagellin ( fliC) could be completely sequenced in two B. mallei strains. Only one mutation was identified discriminating between B. mallei and B. pseudomallei. A polymerase chain reaction-restriction fragment length polymorphism assay was designed making use of the absence of an AvaII recognition site in B. mallei. All seven B. mallei, 12 out of 15 B. pseudomallei and 36 closely related apathogenic Burkholderia thailandensis strains were identified correctly. However, in three B. pseudomallei strains a point mutation at gene position 798 (G to C) disrupted the AvaII site. Therefore, molecular systems based on the fliC sequence can be used for a reliable proof of strains of the three species but not for the differentiation of B. mallei and B. pseudomallei isolates.

Fast identification of polymer additives by pyrolysis-gas chromatography/mass spectrometry

Thermoanalytical methods are especially useful in the analysis of polymer additives. This paper describes a fast method for the qualitative identification of additives in polymers originating from electronic waste. The method is based upon a double-shot pyrolyzer coupled to a gas chromatograph with mass spectrometry detection. The pyrolysis products of two samples of recycled ABS were studied and compared to those of a virgin ABS sample as a function of the pyrolysis mode. The identification of the additives was achieved on the basis of their mass spectra (MS) and comparison with standard MS-libraries.

Evaluation of gastric acid secretion at endoscopy with a modified Congo red test

Background: Markedly decreased or absent gastric acid production is associated with a number of clinically significant conditions, and identification of patients with hypo/achlorhydria may be important. However, current methods of assessing impaired acid secretion are unreliable, time-consuming, and/or complex. The aim of this prospective study was to evaluate a modified endoscopic Congo red test for the diagnosis of hypo/achlorhydria by correlation with a standard gastric acid secretory test. Methods: One hundred six consecutive outpatients with or without dyspeptic symptoms referred for endoscopy were evaluated by using a modified endoscopic Congo red test and a standard test of gastric acid secretion. The modified endoscopic Congo red test suggested hypo/achlorhydria when there was no color shift or a shift of small extent (less than one third of fundic mucosa). Hypo/achlorhydria by the standard gastric acid secretory test was defined as a maximal acid output of less than 6.9 mmol/hour in men and 5.0 mmol/hour in women. Results: The accuracy of the modified endoscopic Congo red test for the diagnosis of hypo/achlorhydria was 0.98 (95% CI [0.93, 0.99]). The sensitivity was 1.0 (95% CI [0.92, 1.00]) and specificity 0.96 (95% CI [0.88, 0.99]). All patients tolerated the modified endoscopic Congo red test well. Conclusion: The modified endoscopic Congo red is an accurate, simple, fast, inexpensive, and well-tolerated chromoendoscopic method for identification of patients with hypo/achlorhydria during routine upper endoscopy. (Gastrointest Endosc 2002;56:254-9.)

MIDAS (Migraine Disability Assessment): a valuable tool for work-site identification of migraine in workers in Brazil.

MIDAS was developed as a fast and efficient method for identification of migraine in need of medical evaluation and treatment. It was necessary to translate MIDAS, originally written in English, so as to apply it in Brazil and make it usable by individuals from a variety of social-economic-cultural backgrounds. To translate and to apply MIDAS in Brazil. Assessment of a sample of workers regularly employed by an oil refinery. Refinaria Presidente Bernardes, Cubatão, São Paulo, Brazil. 404 workers of the company who correctly answered a questionnaire for the identification and evaluation of headache. When the individual considered it to be pertinent to his own needs, there was the option to answer MIDAS as well. MIDAS, originally written in English, was translated into Brazilian Portuguese by a neurologist and by a translator specializing in medical texts. The final version of the translation was obtained when, for ten patients to whom it was applied, the text seemed clear and the results were consistent over three sessions. Prevalence and types of primary headaches, evaluation of MIDAS as a tool for identification of more severe cases. From the total of 419 questionnaires given to the employees, 404 were returned correctly completed. From these, 160 persons were identified as presenting headaches, 44 of whom considered it worthwhile answering MIDAS. Nine of these individuals who answered MIDAS were identified as severe cases of migraine due to disability caused by the condition. An interview on a later date confirmed these results. Three were cases of chronic daily headache (transformed migraine) and six were cases of migraine. MIDAS translated to Brazilian Portuguese was a useful tool for identifying severe cases of migraine and of transformed migraine in a working environment. The workers did not consider MIDAS to be difficult to answer. Their high level of voluntary participation demonstrates that this medical condition was of real interest among the workers, whether they were sufferers or not.

Fast identification of Echinacea purpurea dried roots using near-infrared spectroscopy.

Near-infrared (NIR) reflectance spectroscopy was used to develop a fast identification method for Echinacea purpurea dried milled roots. Method development was carried out using a PLS (partial least-squares) algorithm and pretreatment options. The aim of this qualitative analysis was to confirm the identity of E. purpurea and to detect the presence of fraud, i.e., samples adulterated or substituted by Echinacea angustifolia, Echinacea pallida, or Parthenium integrifolium. Specificity was demonstrated by testing a validation set against the method. A total of 10% of the E. purpurea batches (true samples) and 0% of the false samples from that validation set were misidentified by the method. The misidentification was due to the difference in particle size distribution of one E. purpurea batch compared to that of the other samples. Adulterated E. purpurea samples can be detected at a minimum of 10% of adulteration. This study demonstrates that NIR spectroscopy is a good tool for the fast identification of E. purpurea roots if the samples are milled using the same procedure as for the calibration samples. The method is robust with respect to the origin of the samples and can be used routinely by the pharmaceutical industry or herbal suppliers to avoid mislabeling errors or adulteration.

Weed seeds identification by machine vision

The implementation of new methods for reliable and fast identification and classification of seeds is of major technical and economical importance in the agricultural industry. As in ocular inspection, the automatic classification of seeds should be based on knowledge of seed size, shape, color and texture. In this work, we assess the discriminating power of these characteristics for the unique identification of seeds of 57 weed species. Using the performance of a naı̈ve Bayes classifier as selection criterion, we identified a nearly optimal set of 12 (six morphological+four color+two textural) seed characteristics to be used as classification parameters. We found that, as expected, size and shape characteristics have larger discriminating power than color and textural ones. However, all these features are required to reach an identification performance acceptable for practical applications. In spite of its simplicity, the naı̈ve Bayes classifier reveals itself surprisingly good for the identification of seed species. This might be due to the careful selection of the feature set, leading to nearly independent parameters as assumed by this method. We also found that, using the same feature set, a more sophisticated classifier based on an artificial neural network committee performs only slightly better than this simple Bayesian approach.

A fast method for identification of symmetrical components for power system protection

This paper presents a novel dynamic technique for identifying and measuring the symmetrical components of three-phase voltage or current waveforms in electrical power systems. The proposed technique is based on stochastic estimation theory. The problem is formulated as an estimation problem and presented in state space form. The algorithm is then used to estimate the active and reactive components of the positive, negative and zero components of unsymmetrical waveforms. The method is tested using practical study cases. Different factors affecting the identification process such as data window size, sampling frequency and number of samples are studied. Effects of bad data on the solution accuracy are also studied. The speed of convergence is examined by changing the estimator initial conditions. The results obtained show that the proposed technique can estimate and track the symmetrical components of non-stationary three-phase unbalance voltage or current waveforms in noisy environments. Fast accurate solutions are guaranteed regardless of the initial conditions. It is also shown that bad measurements have no effect on the final accuracy of the estimation.

Identification of barley and rye varieties using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry with neural networks.

Cereal varieties are normally identified using time-consuming methods such as visual examination of either the intact grain or one-dimensional electrophoretic patterns of the grain storage proteins. A fast method for identification of wheat (Triticum aestivum L.) varieties has previously been developed, which combines analysis of alcohol-soluble wheat proteins (gliadins) using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry with neural networks. Here we have applied the same method for the identification of both barley (Hordeum vulgare L.) and rye (Secale cereale L.) varieties. For barley, 95% of the mass spectra were correctly classified. This is an encouraging result, since in earlier experiments only a grouping into subsets of varieties was possible. However, the method was not useful in the classification of rye, due to the strong similarity between mass spectra of different varieties.

Forensic entomology in Germany

Forensic entomology (FE) is increasingly gaining international recognition. In Germany, however, the development of FE has been stagnating, mainly because of the lack of cooperation between police, forensic medicine and entomology. In 1997 a co-operative research project ‘Forensic Entomology’ was started in Frankfurt/Main at the Center of Legal Medicine and the Research Institute Senckenberg. The aim of this project is to establish FE in Germany as a firmly integrated component of the securing of evidence from human cadavers in cases of suspected homicide. For this purpose we developed a forensic insect collecting kit, and policemen are educated for greater acceptance and better application of FE. The scientific programme focusses on the investigation of the insect succession on cadavers in urban and rural habitats. This also includes new indicator groups (e.g. parasitic wasps) for a more precise calculation of the late post mortem interval. Recently a DNA-based reliable and fast identification method especially for the immature stages of necrophagous insects became part of the project. Preliminary results are reported and two case studies presented.

Estimation of unsaturated hydrocarbon pollutants in air based on selective gas chromatography with ozone.

Regular monitoring of toxic organic pollutants in air is a very important issue in environmental pollution control. Among these, unsaturated hydrocarbon pollutants (UHP) such as ethylene and beta-propylene and another 18 olefins are of prime importance. A very fast method for the individual identification of UHPs in air is proposed. This method is based on gas-chromatographic separation with selective detection of unsaturated organic compounds (UOC) and on the chemical reaction of UOC with ozone in the gas phase. In view of the mathematical model derived for this ozonation process, a comparison of FID-chromatogram and ozonogram can be carried out for identification of the contaminants. This identification can be performed without preliminary separation in the presence of the main components. The method provides a high sensitivity (< 0.005 to 0.72 mass %) and selectivity.

A Fast Identification Method for Fruit Surface DefectBased on Fractal Characters

A Fast Identification Method for Fruit Surface DefectBased on Fractal Characters

Quantification of amphetamine plasma concentrations by gas chromatography coupled to mass spectrometry

We developed a fast and sensitive method for identification and quantification of plasma concentrations of amphetamine using gas chromatography with mass spectrometry detection (GC–MS). Amphetamine-d 8 served as internal standard. The method involves a single extraction procedure and an easy treatment of the samples that allowed no losses during the evaporation process. Derivatisation of amphetamine with N-methyl-bis(trifluoroacetamide), a potent acylating agent, provides many advantages to the method compared with common derivatisation reactions usually used for amphetamines. The limits of detection and quantification following this method were 0.43 and 1.42 ng/ml, respectively. The assay has been successfully employed in the quantification of amphetamine in plasma samples from healthy volunteers at four different doses.

Carrier detection and presymptomatic identification of Wilson disease in Chinese by non-isotopic linkage analysis with four short tandem repeat polymorphisms.

Wilson disease (WD) is an autosomal recessive disorder of copper metabolism. To establish an efficient, accurate and fast diagnostic method for carrier detection and presymptomatic identification of WD in Chinese population, we studied haplotypes of short tandem repeat (STR) polymorphisms flanking the WD gene in 40 Chinese WD families. The results suggested that this genetic diagnosis system based on the four STR polymorphisms is of high value for the detection of potential carriers and WD homozygotes in families with at least one previously affected child. It is an efficient, accurate and fast diagnostic method that can be well suited for routine use in clinical laboratories.

Polymerase chain reaction-based assay for specific detection of Rhizoctonia solani AG-3 isolates

Rhizoctonia solani AG-3 causes considerable yield loss in potato fields in eastern Canada and U.S.A. The accurate identification of AG-3 isolates is strategic prior to planting potatoes. To obtain a fast and reliable identification method, RAPD experiments were carried out to obtain specific genetic markers of AG-3 isolates. DNA from various isolates of R. solani was submitted to RAPD amplification using random 10 mers primers. One of the forty primers used yielded a 2.6 kbp fragment present in all isolates of AG-3. The specificity of this fragment was assessed by Southern blot analysis. It was partly sequenced and DNA primers were designed for PCR amplification experiments. A PCR-based restriction mapping method, using one restriction endonuclease, Xho I, was developed for specific detection of AG-3 isolates. Analysis of data showed that AG-3 isolates were distinct to other AGs R. solani. The detection method described here is very specific and reliable; it can be applied on plant tissue and soil infected with R. solani AG-3.

Identification of mycobacteria by thin layer chromatographic analysis of mycolic acids and conventional biochemical method: four years of experience.

Mycolic acids analysis by thin-layer chromatography (TLC) has been employed by several laboratories worldwide as a method for fast identification of mycobacteria. This method was introduced in Brazil by our laboratory in 1992 as a routine identification technique. Up to the present, 861 strains isolated were identified by mycolic acids TLC and by standard biochemical tests; 61% out of these strains came as clinical samples, 4% isolated from frogs and 35% as environmental samples. Mycobacterium tuberculosis strains identified by classical methods were confirmed by their mycolic acids contents (I, III and IV). The method allowed earlier differentiation of M. avium complex-MAC (mycolic acids I, IV and VI) from M. simiae (acids I, II and IV), both with similar biochemical properties. The method also permitted to distinguish M. fortuitum (acids I and V) from M. chelonae (acids I and II), and to detect mixed mycobacterial infections cases as M. tuberculosis with MAC and M. fortuitum with MAC. Concluding, four years experience shows that mycolic acids TLC is an easy, reliable, fast and inexpensive method, an important tool to put together conventional mycobacteria identification methods.

Identification of clinically important species of Enterococcus within 1 day with randomly amplified polymorphic DNA (RAPD).

The use of randomly amplified polymorphic DNA (RAPD) for rapid, reliable, and easily interpreted identification of enterococci was evaluated. Nineteen type strains of Enterococcus, 12 reference strains, and 114 clinical isolates of Enterococcus were analyzed. Discrimination was obtained between most type strains, the exceptions being Ent. casseliflavus and Ent. flavescens, which had relatively similar RAPD-profiles. Ent. faecalis and Ent. faecium were readily separated, and Ent. gallinarum and Ent. durans could also be identified. Extracts to be used in the polymerase chain reaction (PCR) were prepared directly from agar plate colonies, which made it possible to complete the identification procedure in one day. RAPD was proved to be a fast and reliable method for identification of most Enterococcus spp. of clinical significance.

Worst-load-increase direction method for fast identification of voltage-weakness indicators

The paper addresses the two problems of classifying the voltage vulnerability of a power-system operating point and ranking the nodes on the basis of their voltage weakness. A static approach is considered, which is based on load-flow equations and allows simultaneous computation of the global and local indices with very little computational effort. The system and node weaknesses are computed introducing the concept of most critical load-increase direction, defined as the direction in which a load increase corresponds to the maximum request of additional reactive-power generation. Node ranking requires the solution of a linear system only and allows identification of the weakest nodes and, in some case, of the weakest areas. The method has been compared to others available in the literature, with satisfactory results in the balance between accuracy and computational burden.

Hb Köln [&lt;FONT FACE=Symbol&gt;a&lt;/font&gt;2&lt;FONT FACE=Symbol&gt;b&lt;/font&gt;298(FG5) val-met] identified by DNA analysis in a Brazilian family

Hb Köln was identified by DNA analysis in a Brazilian patient. A four-year old Brazilian female, with jaundice since birth, presented an abnormal band, between A2 and S, in hemoglobin electrophoresis on a cellulose acetate membrane, and a band with electrophoretic migration similar to Hb C on agar gel. Thermic instability and isopropanol precipitation tests were positive. Heinz bodies were observed in the patient’s peripheral blood. Sequencing of the three exons of the &lt;FONT FACE="Symbol"&gt;b&lt;/font&gt; globin gene detected a transition from G to A in the first position of codon 98. This alteration does not create or abolish any known restriction site. In this case, confirmation of the mutation was accomplished by allele-specific oligonucleotide hybridization, which is a simple and fast identification method when the clinical data and hematological and electrophoretic patterns are suggestive of Hb Köln.