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PubMed2004

Impact of biological factors on binding media identification in art objects: identification of animal glue in the presence of Aspergillus niger.

The materials and especially organic materials used for creation of art objects can be utilized by various microorganisms for their growth and facilitate the microbial colonization of the object. An understanding of the chemical alterations in artefacts caused by the presence of microorganisms can be crucial for correct identification of the materials initially used for the artefact creation--nowadays an important step in restoration and/or art-historical investigation of the art object. The present article describes a model experiment in which we investigated the possible chemical alterations in animal glue films used as substrate for growth of the fungus Aspergillus niger. The sterilized animal glue solution was poured into Petri dishes, inoculated with Aspergillus niger, and subsequently incubated at 15 degrees C for 0, 7, 9, 14, and 28 days. After interruption of incubation, the content of the Petri dish was analyzed for amino acid composition by the GC-MS based method. It was found that the growth of Aspergillus niger on animal glue films did not cause significant changes in the amino acid composition of the film and had no impact on animal glue identification.

Adhesives↗
PubMed1996

Utility of Albicans ID plate for rapid identification of Candida albicans in clinical samples. Rapid identification of Candida albicans.

Albicans ID (bioMérieux, Marcy l'Etoile, France) is a ready-to-use medium that contains a chromogenic substrate that allows rapid detection and specific identification of Candida albicans. We have evaluated its clinical performance by culturing 846 clinical specimens from pregnant women and neonates. A 99.2% sensitivity and a 100% specificity were observed in the identification of C. albicans isolates from primary culture.

Bacteriological Techniques↗
PubMed2005

Implantation of radio frequency identification device (RFID) microchip in disaster victim identification (DVI).

The tsunami catastrophe of December 2004 left more than 200,000 dead. Disaster victim identification (DVI) teams were presented with the unprecedented challenge of identifying thousands of mostly markedly putrefied and partially skeletised bodies. To this end, an adequate body tagging method is essential. Conventional body bag tagging in terms of writing on body bags and placing of tags inside body bags proved unsatisfactory and problem prone due to consequences of cold storage, formalin (formaldehyde) embalming and body numbers inside storage facilities. The placement of radio frequency identification device (RFID) microchips inside victim bodies provided a practical solution to problems of body tagging and attribution in the DVI setting encountered by the Austrian DVI team in Thailand in early 2005.

Austria↗
PubMed2005

Accuracy of identification of grating contrast by human observers: Bayesian models of V1 contrast processing show correspondence between discrimination and identification performance.

This paper presents the results of a contrast identification study, where accuracy in identification is quantified as mutual information between stimulus contrast and observer's response. The stimulus was a set of 2-8 gratings, spanning the range of visible contrasts. Gratings from the set were presented individually for 500 ms, and the observer had to respond by giving the number label corresponding to the contrast of the grating presented. Mutual information increased with set size up to a maximum of around 2.35 bits, i.e., only 5 clearly identifiable contrasts. Set sizes greater than 5 showed a plateau or decline in performance. These data were well fit by Bayesian models of V1 contrast coding, with the parameters obtained by fitting the contrast discrimination results of Chirimuuta and Tolhurst [Chirimuuta, M., & Tolhurst, D. J. (2005). Does a Bayesian model of V1 contrast coding offer a neurophysiological account of human contrast discrimination? Vision Research].

Adult↗
PubMed1999

Identification of a ribonuclease H gene in both Mycoplasma genitalium and Mycoplasma pneumoniae by a new method for exhaustive identification of ORFs in the complete genome sequences.

Exhaustive identification of open reading frames in complete genome sequences is a difficult task. It is possible that important genes are missed. In our efforts to reanalyze the intergenic regions of Mycoplasma genitalium and Mycoplasma pneumoniae, we have newly identified a number of new open reading frames (ORFs) in both M. genitalium and M. pneumoniae. The most significant identification was that of a ribonuclease H enzyme in both species which until now has not been identified or assumed absent and interpreted as such. In this paper we discuss the biological importance of RNase H and its evolutionary implication. We also stress the usefulness of our method for identifying new ORFs by reanalyzing intergenic regions of existing ORFs in complete genome sequences.

Genome, Bacterial↗
PubMed2001

Identification of the human crooked neck gene by comparative gene identification.

Drosophila melanogaster serves as a useful model organism for functional genomic studies, and its genome project was recently completed. We previously described a comparative-gene-identification approach to assist human ortholog gene identification that involves applying an entire proteome as an alignment template. Analysis of the available 14100 Drosophila protein sequences revealed that 37% of them (5228 sequences) might lead to discoveries of novel human genes. Upon further database interrogations, we found several putative full-length human gene transcripts, including the human crooked neck (crn) gene. Based on sequence gap-closure experiments using reverse transcriptase-polymerase chain reaction as well as bioinformatic analysis, we found that the assembled human cDNA contig of crooked neck gene was at least 3903 base pairs in length with alternative splicing variations which encoded mainly for a 687-amino-acid residue protein. The human crooked neck gene was located on chromosome 20 with at least 15 exons. The unique features of the 16 copies of the tetratrico peptide repeat (TPR) motif were conserved in the yeast, fly and human crooked neck orthologous proteins, which were important for spliceosome assembly in cells.

Amino Acid Sequence↗
PubMed2007

Multianalyte chemical identification and quantitation using a single radio frequency identification sensor.

We demonstrate an approach for multianalyte chemical identification and quantitation using a single conventional radio frequency identification (RFID) tag that has been adapted for chemical sensing. Unlike other approaches of using RFID sensors, where a special tag should be designed at a much higher cost, we utilize a conventional RFID tag and coat it with a chemically sensitive film. As an example, we demonstrate detection of several vapors of industrial, health, law enforcement, and security interest (ethanol, methanol, acetonitrile, water vapors) with a single 13.56-MHz RFID tag coated with a solid polymer electrolyte sensing film. By measuring simultaneously several parameters of the complex impedance from such an RFID sensor and applying multivariate statistical analysis methods, we were able to identify and quantify several vapors of interest. With a careful selection of the sensing film and measurement conditions, we achieved parts-per-billion vapor detection limits in air. These RFID sensors are very attractive as ubiquitous multianalyte distributed sensor networks.

Acetonitriles↗
PubMed2004

Multiple independent identification decisions: a method of calibrating eyewitness identifications.

Two experiments (N = 147 and N = 90) explored the use of multiple independent lineups to identify a target seen live. In Experiment 1, simultaneous face, body, and sequential voice lineups were used. In Experiment 2, sequential face, body, voice, and clothing lineups were used. Both studies demonstrated that multiple identifications (by the same witness) from independent lineups of different features are highly diagnostic of suspect guilt (G. L. Wells & R. C. L. Lindsay, 1980). The number of suspect and foil selections from multiple independent lineups provides a powerful method of calibrating the accuracy of eyewitness identification. Implications for use of current methods are discussed.

Decision Making↗
PubMed1996

Identification of the spinocerebellar ataxia type 2 gene using a direct identification of repeat expansion and cloning technique, DIRECT.

Spinocerebellar ataxia type 2 (SCA2) is an autosomal dominant, neurodegenerative disorder that affects the cerebellum and other areas of the central nervous system. We have devised a novel strategy, the direct identification of repeat expansion and cloning technique (DIRECT), which allows selective detection of expanded CAG repeats and cloning of the genes involved. By applying DIRECT, we identified an expanded CAG repeat of the gene for SCA2. CAG repeats of normal alleles range in size from 15 to 24 repeat units, while those of SCA2 chromosomes are expanded to 35 to 59 repeat units. The SCA2 cDNA is predicted to code for 1,313 amino acids-with the CAG repeats coding for a polyglutamine tract. DIRECT is a robust strategy for identification of pathologically expanded trinucleotide repeats and will dramatically accelerate the search for causative genes of neuropsychiatric diseases caused by trinucleotide repeat expansions.

Amino Acid Sequence↗
PubMed2003

Identification of a novel human constitutive androstane receptor (CAR) agonist and its use in the identification of CAR target genes.

The orphan nuclear constitutive androstane receptor (CAR) is proposed to play a central role in the response to xenochemical stress. Identification of CAR target genes in humans has been limited by the lack of a selective CAR agonist. We report the identification of 6-(4-chlorophenyl)imidazo[2,1-b][1,3]thiazole-5-carbaldehyde O-(3,4-dichlorobenzyl)oxime (CITCO) as a novel human CAR agonist with the following characteristics: (a) potent activity in an in vitro fluorescence-based CAR activation assay; (b) selectivity for CAR over other nuclear receptors, including the xenobiotic pregnane X receptor (PXR); (c) the ability to induce human CAR nuclear translocation; and (d) the ability to induce the prototypical CAR target gene CYP2B6 in primary human hepatocytes. Using primary cultures of human hepatocytes, the effects of CITCO on gene expression were compared with those of the PXR ligand rifampicin. The relative expression of a number of genes encoding proteins involved in various aspects of steroid and xenobiotic metabolism was analyzed. Notably, CAR and PXR activators differentially regulated the expression of several genes, demonstrating that these two nuclear receptors subserve overlapping but distinct biological functions in human hepatocytes.

Cells, Cultured↗
PubMed2002

A mass spectrometry-based proteomic approach for identification of serine/threonine-phosphorylated proteins by enrichment with phospho-specific antibodies: identification of a novel protein, Frigg, as a protein kinase A substrate.

Although proteins phosphorylated on tyrosine residues can be enriched by immunoprecipitation with anti-phosphotyrosine antibodies, it has been difficult to identify proteins that are phosphorylated on serine/threonine residues because of lack of immunoprecipitating antibodies. In this report, we describe several antibodies that recognize phosphoserine/phosphothreonine-containing proteins by Western blotting. Importantly, these antibodies can be used to enrich for proteins phosphorylated on serine/threonine residues by immunoprecipitation, as well. Using these antibodies, we have immunoprecipitated proteins from untreated cells or those treated with calyculin A, a serine/threonine phosphatase inhibitor. Mass spectrometry-based analysis of bands from one-dimensional gels that were specifically observed in calyculin A-treated samples resulted in identification of several known serine/threonine-phosphorylated proteins including drebrin 1, alpha-actinin 4, and filamin-1. We also identified a protein, poly(A)-binding protein 2, which was previously not known to be phosphorylated, in addition to a novel protein without any obvious domains that we designate as Frigg. Frigg is widely expressed and was demonstrated to be a protein kinase A substrate in vitro. We identified several in vivo phosphorylation sites by tandem mass spectrometry using Frigg protein immunoprecipitated from cells. Our method should be applicable as a generic strategy for enrichment and identification of serine/threonine-phosphorylated substrates in signal transduction pathways.

Amino Acid Sequence↗
PubMed1995

A comparative study of the BBL crystal enteric/nonfermenter identification system and the biomerieux API20E and API20NE identification systems after overnight incubation.

The BBL Crystal Enteric/Nonfermenter (Crystal, Becton Dickinson Microbiology Systems) is a new multi-test identification system for Gram negative rods requiring no oil overlay or addition of reagents. One hundred and three selected Gram negative rod isolates from routine clinical specimens were tested in parallel using the appropriate API20E or API20NE (BioMerieux) reading after overnight incubation. The isolates included in the study, and the number tested, were as follows: Acinetobacter sp, 8; Aeromonas hydrophila, 1; Citrobacter diversus, 1; Citrobacter freundii, 1; Escherichia coli, 13; Enterobacter aerogenes, 10; Enterobacter agglomerans, 2; Enterobacter cloacae, 6; Klebsiella oxytoca, 6; Klebsiella pneumoniae, 12; Morganella morganii, 2; Proteus mirabilis, 6; Pseudomonas aeruginosa, 21; Salmonella sp, 2; Salmonella typhi, 1; Serratia marcescens, 1; Shigella sonnei, 2; Shigella sp, 2; Vibrio metschnikovii, 1; Xanthomonas maltophilia, 3; and, Yersinia enterocolitica, 2. The API20E and API20NE systems combined identified 74.8% (77/103) and the Crystal 97.1% (100/103) of isolates. Twenty six isolates required repeat and/or additional tests for correct identification with the API systems compared to 3 with the Crystal. Crystal is more convenient than API for routine clinical use because it requires fewer repeat and/or extra tests, and is easier and less time consuming to use.

Bacterial Typing Techniques↗
PubMedDate not supplied

Comparison of the QuadFERM+ 2-hr identification system with conventional carbohydrate degradation tests for confirmatory identification of Neisseria gonorrhoeae.

The QuadFERM+ (Analytab Products, Plainview, NY) rapid identification system was evaluated for its ability to identify correctly Neisseria gonorhoeae isolates from specimens obtained at a sexually transmitted disease clinic. One hundred eighty-five isolates (115 N. gonorrhoeae, 45 Neisseria meningitidis, 16 Neisseria species, and nine Branhamella catarrhalis; fresh isolates, frozen stock cultures, and cultures referred from local health agencies) were tested with the QuadFERM+ system and conventional biochemical tests. The two discrepant results were obtained with QuadFERM+, for a lactose-positive isolate of Neisseria sicca and a maltose-positive N. meningitidis. Both were negative by conventional sugar degradation tests. The N. sicca was negative when repeated in the QuadFERM+, and the N. meningitidis reverted from maltose-positive to maltose-negative after 3 hr. Twelve beta-lactamase positive organisms (six N. gonorrhoeae plus six B. catarrhalis) and 173 beta-lactamase-negative organisms showed 100% agreement between the acidometric QuadFERM+ beta-lactamase test and the conventional starch-iodine method. Thus the QuadFERM+ is a rapid and acceptable alternative for the identification of N. gonorrhoeae in a sexually transmitted disease clinic.

Bacteriological Techniques↗
PubMed2006

Identification of biochemically atypical Staphylococcus aureus clinical isolates with three automated identification systems.

Between January and April 2002, a total of 271 strains of Staphylococcus aureus were isolated from clinical specimens at Toho University Omori Hospital, Japan, including 201 (74.2 %) which were identified as meticillin-resistant S. aureus (MRSA). However, 34 (12.5 %) were biochemically atypical, because they did not produce acid on mannitol salt agar or did not agglutinate in Staphaurex testing but were categorized as MRSA by PCR analysis and by antibiotic susceptibility. Three automatic identification systems, AutoScan-4 (Dade Behring), BD Phoenix (Becton Dickinson) and Vitek 2 (bioMérieux), were evaluated by testing these atypical S. aureus isolates. The AutoScan-4 and Phoenix systems identified all 34 isolates as S. aureus. Without additional tests such as Staphaurex, observation of colony pigment and haemolysins on sheep blood agar, Vitek 2 identified only 16 isolates (47.1 %) as S. aureus with good or better confidence levels and misidentified one of the remaining isolates as Staphylococcus chromogenes. This study shows that it is possible to identify these physiologically atypical S. aureus isolates correctly by using the Phoenix and AutoScan-4 fully automatic identification systems.

Anti-Bacterial Agents↗
PubMed2006

Identification and differentiation of Legionella pneumophila and Legionella spp. with real-time PCR targeting the 16S rRNA gene and species identification by mip sequencing.

Fluorescent resonance energy transfer probes targeting the 16S rRNA gene were constructed for a sensitive and specific real-time PCR for identification and differentiation of Legionella pneumophila from other Legionella spp. For identification of non-L. pneumophila spp. by direct amplicon sequencing, two conventional PCR assays targeting the mip gene were established.

Bacterial Proteins↗
PubMed1983

Clinical comparison of the AutoMicrobic system gram-positive identification card, API Staph-Ident, and conventional methods in the identification of coagulase-negative Staphylococcus spp.

In an effort to rapidly identify coagulase-negative staphylococci (CNS), a clinical comparison was conducted with the AutoMicrobic system Gram-Positive Identification Card (GPI) (Vitek Systems, Inc.), the API Staph-Ident (Analytab Products), and the conventional methods of W. E. Kloos and K. H. Schleifer (W. E. Kloos and K. H. Schleifer, J. Clin. Microbiol. 1:82-88, 1975). CNS isolates tested included 157 from blood and 33 from urine in pure culture at greater than 10(5) CFU/ml. S. epidermidis accounted for 79.6 and 60.6% of the isolates from blood and urine, respectively. S. saprophyticus was the next most frequent urine isolate (27.4%). Other CNS species were isolated from blood and urine specimens with frequencies of less than 5%. Overall, the GPI correctly identified 158 (83.2%) of the 190 CNS, whereas the Staph-Ident identified 124 (65.3%) without further testing. This resulted in the GPI and Staph-Ident correctly identifying 95.9 and 74.5% of the S. epidermidis and 100 and 33% of the S. saprophyticus, respectively. The GPI misidentified 8 (47%) of the S. hominis and S. warneri isolates as S. saprophyticus, indicating the need for novobiocin testing. These data suggest that the GPI is a more definitive method for the rapid identification of S. epidermidis than the Staph-Ident and that both systems require additional testing to identify S. saprophyticus.

Bacteriological Techniques↗
PubMed1984

Direct identification and susceptibility testing of gram-negative bacilli from BACTEC bottles by use of the MS-2 system with updated bacterial identification software.

The Abbott MS-2 system (Abbott Laboratories, Diagnostic Division, Irving, Tex.), equipped with updated bacterial identification software (version 03.02), was used to perform both direct identification and susceptibility tests on gram-negative bacilli from positive BACTEC blood culture bottles. Ninety-eight of 101 Enterobacteriaceae strains, one strain of Acinetobacter calcoaceticus, and two strains of Pseudomonas aeruginosa were correctly identified by following a direct inoculation procedure. One Enterobacter sakazakii isolate was misidentified as Enterobacter cloacae. Ninety-seven percent of 936 direct susceptibility results were identical to the results obtained by using the standard MS-2 susceptibility procedure. Only five tests yielded a sensitive-direct and a resistant-standard MS-2 susceptibility result.

Bacteria↗