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PubMed2000

Forensic identification by DNA fingerprinting and mitochondrial DNA typing.

Short tandem repeats (STRs), that represent an important source of highly polymorphic markers in human genome, and mitochondrial DNA (mtDNA) typing, that its sequences were conserved within the same maternal lineage, facilitated by use of the polymerase chain reaction (PCR) provide a powerful tool for forensic identification. We report the analysis of 9 STR loci and mtDNA typing of a muscle biopsied sample with 2 months postmortem by comparison with the genotype of the relative. The DNA profile showed common alleles with that of the relative but only 12 from 20 alleles (60%) were identifiable. Then, we performed mt DNA sequencing of the hypervariable region I (HV I) and obtained 100 per cent homology with that of the relative. In conclusion, personal identification can be performed precisely by the data of DNA profile and mtDNA typing compared to the genotype of the relative.

Base Sequence↗
PubMed2005

PCR primers based on different portions of insertion elements can assist genetic relatedness studies, strain fingerprinting and species identification in rhizobia.

Using the sequence of an insertion element originally found in Rhizobium sullae, the nitrogen-fixing bacterial symbiont of the legume Hedysarum coronarium, we devised three primer pairs (inbound, outbound and internal primers) for the following applications: (a) tracing genetic relatedness within rhizobia using a method independent of ribosomal inheritance, based on the presence and conservation of IS elements; (b) achieve sensitive and reproducible bacterial fingerprinting; (c) enable a fast and unambiguous detection of rhizobia at the species level. In terms of taxonomy, while in line with part of the 16S rRNA gene- and glutamine synthetase I-based clustering, the tools appeared nonetheless more coherent with the actual geographical ranges of origin of rhizobial species, strengthening the European-Mediterranean connections and discerning them from the asian and american taxa. The fingerprinting performance of the outward-pointing primers, designed upon the inverted repeats, was shown to be at least as sensitive as BOX PCR, and to be functional on a universal basis with all 13 bacterial species tested. The primers designed on the internal part of the transposase gene instead proved highly species-specific for R. sullae, enabling selective distinction from its most related species, and testing positive on every R. sullae strain examined, fulfilling the need of PCR-mediated species identification. A general use of other IS elements for a combined approach to rhizobial taxonomy and ecology is proposed.

Base Sequence↗
PubMed1993

Comparison of DNA fingerprinting and serotyping for identification of avian Pasteurella multocida isolates.

The DNA fingerprint profiles and serotypes of 63 avian Pasteurella multocida field isolates, 13 attenuated vaccine isolates (propagated from vaccines manufactured by five companies), and 16 somatic reference strains were compared. DNA fingerprinting established the relationship of isolates that could not be distinguished by serotyping. Of the 76 isolates, 28 DNA fingerprint profiles and 12 somatic types were recognized. One isolate was nonreactive with 16 reference somatic and 5 reference capsule-type antisera. Thirty-one field isolates and seven vaccine isolates were identified as capsule type A. Twenty-nine field isolates and six vaccine isolates were nonencapsulated. Three field isolates were capsule type F. Isolates of capsule types B, D, and E were not found. One field isolate, identified as somatic type 7, had a DNA fingerprint identical to that of the somatic reference type 6 profile. Twelve field isolates had profiles identical to the somatic reference type 3 strain profile; 11 of these were identified as somatic type 3, 4, and 1 was identified as somatic type 3. The DNA fingerprint profiles of 50 field isolates and 13 attenuated vaccine isolates did not match profiles of the 16 somatic type reference strains. Twenty-five DNA fingerprint profiles were recognized from 30 of these field isolates. The DNA fingerprint profiles of 20 field isolates and 13 attenuated vaccine isolates were identical. Three somatic types (3; 3,4; and 4,16) were identified from the field isolates, and two somatic types (3 and 3,4) were identified from the attenuated vaccine isolates. DNA fingerprinting is useful for accurate identification and epidemiologic study of P. multocida isolates.

Animals↗
PubMedDate not supplied

Evaluation of descriptors and mini-fingerprints for the identification of molecules with similar activity.

Combinations of 65 preferred 1D/2D molecular descriptors and 143 single structural keys were evaluated for their performance in compound classification focused on biological activity. The analysis was based on principal component analysis of descriptor combinations and facilitated by use of a genetic algorithm and different scoring functions. In these calculations, several descriptor combinations with greater than 95% prediction accuracy were identified. A set of 40 preferred structural keys was incorporated into a small binary fingerprint designed to search databases for compounds with biological activity similar to query molecules. The performance of mini-fingerprints was tested by systematic similarity search calculations in a database consisting of compounds belonging to seven biological activity classes, which had not been used to select effective descriptors. In these blind test calculations, mini-fingerprints correctly identified approximately 54% of compounds sharing similar biological activity and with 1% false positives. Thus, although the design of mini-fingerprints is conceptually simple, they perform well in activity-oriented similarity searching.

Computing Methodologies↗
PubMed2005

Evaluation of novel sample identification approach based on chromatographic fingerprint set correlation homogeneity analysis.

Instead of usual rationale for chromatographic fingerprint based sample identification which relies upon visual inspection or principal component analysis of raw or aligned chromatograms novel nonparametric statistical measure of fingerprint set homogeneity is proposed. Randomization test is applied for significance analysis of fingerprint set homogeneity while average maximum crosscorrelation is used as a merit function. Chromatogram sets generated by random selection from standard and unknown sample chromatogram collections are compared with respect to merit function values with set of chromatograms that represents standard and/or unknown sample. In that instance fingerprint homogeneity significance is represented by the fraction of random chromatogram sets that have higher merit values than the standard and/or unknown sample sets. A set of peptide maps corresponding to different haemoglobin variants has been selected for evaluation of proposed test. This approach is compared to chromatogram alignment based on correlation optimized warping coupled with principal component or cluster analysis. Proposed method is simple i.e. straightforward sample identification procedure which reliability has been evaluated here. Impact of this approach on peptide mapping validation and system suitability analysis is discussed.

Chromatography, Liquid↗
PubMed1994

Pulsed-field fingerprinting of listeriae: identification of genomic divisions for Listeria monocytogenes and their correlation with serovar.

Clamped homogeneous electric field (CHEF) electrophoresis was optimized for genomic analyses of Listeria monocytogenes. Various human, animal, food, and environmental isolates, as well as strains representing other Listeria species, were separately digested with rarely cutting endonucleases. Of 176 L. monocytogenes strains analyzed, the enzymes AscI and ApaI established 63 and 72 unique restriction endonuclease digestion profiles (REDP), respectively. The 22 non-L. monocytogenes strains exhibited 18 AscI and 19 ApaI unique REDP. Statistical analyses of REDP information using the Dice coincidence index and principal component analysis revealed two distinct genomic divisions of L. monocytogenes that also correlated with the flagellar (H) antigen type: division I contained serovar 1/2a, 1/2c, 3a, and 3c stains and division II contained serovar 1/2b, 3b, 4b, 4d, and 4e strains. Division I isolates digested with ApaI were further grouped into cluster IA (serovar 1/2c and 3c) and cluster IB (serovar 1/2a and 3a) strains. Likewise, division II isolates digested with ApaI were further grouped into cluster IIA (serovar 1/2b and 3b) and cluster IIB (serovar 4b, 4d, and 4e) strains. These data indicate that genotypic data generated by CHEF can be directly related to phenotypic data generated by serotyping for establishing the overall relatedness of isolates. Moreover, these data further substantiate that CHEF analysis is a reproducible and highly discriminating method for characterizing L. monocytogenes strains at the molecular level.

Animals↗
PubMed2000

Identification by RNA fingerprinting of genes differentially expressed during the development of the basidiomycete Lentinula edodes.

As part of an ongoing project to understand the molecular mechanisms of fruit body development in Lentinula edodes (Shiitake mushroom), RNA fingerprinting by arbitrarily primed PCR (RAP-PCR) was used to identify differentially expressed genes in RNA populations from four stages of L. edodes development vegetative mycelium, primordium, young fruit body and mature fruit body. From 30 RNA fingerprints, we cloned and sequenced 33 RAP fragments after their differential expression patterns had been verified by reverse Northern dot-blot hybridization. Thirteen RAP fragments show high sequence similarity to known gene products which are involved in (1) transport across the plasma membrane (drug efflux pump and sugar transporter); (2) cell cycle control (cyclin B); (3) signal transduction and transcriptional regulation (mitogen-activated protein kinase, Cdc39/Not1, PriA, Jun-D); (4) intracellular molecule trafficking (ubiquitin, plasma membrane proton ATPase, and alpha-adaptin); (5) mitochondrial biogenesis (mitochondrial processing peptidase beta-subunit, mitochondrial glycerol-3-phosphate dehydrogenase); and (6) intermediary metabolism (fructose 1,6 bisphosphatase). The transcript levels for plasma membrane proton ATPase and alpha-adaptin remained constant, whereas the other eleven genes were differentially expressed during L. edodes. development. The expression profiles of the genes suggest that transport across the plasma membrane is important in the mycelial stage. Specific signal transduction and transcriptional controls may play important roles during the initiation of primordia and the formation of young fruiting bodies. When the mushroom matures, expression of genes involved in metabolic pathways becomes prominent. The isolation of these genes indicates their involvement in homobasidiomycete development and suggests new directions for molecular studies on mechanisms of mushroom development.

Amino Acid Sequence↗
PubMed2006

Molecular and electronic structure in NaCl electrolytes of varying concentration: identification of spectral fingerprints.

Near edge x-ray absorption spectra at the Na K edge in aqueous NaCl electrolytes are presented as a function of concentration. The spectra are modeled by electronic structure calculations. We find and identify the orbital origin of two spectral fingerprints with sensitivity to the Na+-H2O distance and the Na+-Cl- distance in the electrolyte. Interionic interaction is found to be crucial for the description of the electrolytes at high concentrations.

Journal Article↗
PubMed2006

[Metabolite fingerprint and biomarkers identification of rat urine after dosed with ginsenoside Rg3 based on ultra high performance liquid chromatography/time-of-flight mass spectrometry (UPLC/TOF-MS)].

Porous particles of 1.7 microm was employed for ultra high performance liquid chromatography (UPLC), resulting in higher peak capacity, greater resolution and increased sensitivity in comparison with high performance liquid chromatography (HPLC). Time-of-flight mass spectrometer (TOF-MS) with a lockmass interface was used for the structure identification through exact mass and MS/MS experiment. The hyphenation of these two technologies made it a suitable platform for analysis of complex samples and identification of unknown compounds. Ginsenoside Rg3 has been considered as the major active component of Panax ginseng. Effect of the administration of a single dose of the Ginsenoside Rg3 to male Sprague Dawley rats on the urinary metabolite profiles of a range of endogenous metabolites had been investigated using UPLC/TOF-MS. Urine samples were collected from both dosed and control animals. Analysis of these samples revealed marked changes in the pattern of endogenous metabolites due to the effect of Ginsenoside Rg3. Significant disturbances in the urinary metabolite were observed in the first day after dose. Endogenous metabolites with significant up-regulation identified by accurate mass and MS/MS were xanthurenic acid, and kynurenic acid.

Animals↗
PubMed1997

Transmission of Mycobacterium tuberculosis by a fiberoptic bronchoscope. Identification by DNA fingerprinting.

CONTEXT: An ongoing restriction fragment length polymorphism (RFLP) study of Mycobacterium tuberculosis isolates from tuberculosis (TB) cases revealed an identical 10-banded IS6110 RFLP pattern unique to 2 patients diagnosed as having TB 6 months apart. Their only identifiable link was care at the same hospital. OBJECTIVE: To determine if nosocomial transmission had occurred. DESIGN: Traditional and molecular epidemiologic investigation. MEASUREMENTS: We reviewed medical charts and bronchoscopic records, examined hospital locations visited by both patients, evaluated hospital ventilation systems, and observed cleaning and disinfection of bronchoscopes. RESULTS: A patient with cough, hoarseness, and fever underwent bronchoscopy and was diagnosed as having TB. A second patient with a mediastinal mass underwent bronchoscopy 2 days later and was diagnosed as having small cell carcinoma. Following 6 months of chemotherapy and radiation therapy, the second patient developed fever and an infiltrate of the right upper lobe of the lung. Bronchoscopic washings revealed acid-fast bacilli and were culture positive for M tuberculosis. Both patients had undergone bronchoscopy with the same instrument in the same operating room with no intervening bronchoscopies. Bronchoscope cleaning and disinfection procedures were inconsistent with national guidelines. CONCLUSIONS: A contaminated bronchoscope was the most likely source of M tuberculosis transmission between these 2 patients. The RFLP analysis of M tuberculosis isolates was responsible for detecting this nosocomial source of transmission and led to the implementation of public health measures to prevent further spread of infection and disease. This study emphasizes the need for continued vigilance in endoscope cleaning techniques.

Adult↗
PubMed2003

MALDI/MS peptide mass fingerprinting for proteome analysis: identification of hydrophobic proteins attached to eucaryote keratinocyte cytoplasmic membrane using different matrices in concert.

BACKGROUND: MALDI-TOF-MS has become an important analytical tool in the identification of proteins and evaluation of their role in biological processes. A typical protocol consists of sample purification, separation of proteins by 2D-PAGE, enzymatic digestion and identification of proteins by peptide mass fingerprint. Unfortunately, this approach is not appropriate for the identification of membrane or low or high pI proteins. An alternative technique uses 1D-PAGE, which results in a mixture of proteins in each gel band. The direct analysis of the proteolytic digestion of this mixture is often problematic because of poor peptide detection and consequent poor sequence coverage in databases. Sequence coverage can be improved through the combination of several matrices. RESULTS: The aim of this study was to trust the MALDI analysis of complex biological samples, in order to identify proteins that interact with the membrane network of keratinocytes. Peptides obtained from protein trypsin digestions may have either hydrophobic or hydrophilic sections, in which case, the direct analysis of such a mixture by MALDI does not allow desorbing of all peptides. In this work, MALDI/MS experiments were thus performed using four different matrices in concert. The data were analysed with three algorithms in order to test each of them. We observed that the use of at least two matrices in concert leads to a twofold increase of the coverage of each protein. Considering data obtained in this study, we recommend the use of HCCA in concert with the SA matrix in order to obtain a good coverage of hydrophilic proteins, and DHB in concert with the SA matrix to obtain a good coverage of hydrophobic proteins. CONCLUSION: In this work, experiments were performed directly on complex biological samples, in order to see systematic comparison between different matrices for real-life samples and to show a correlation that will be applicable to similar studies. When 1D gel is needed, each band may contain a great number of proteins, each present in small amounts. To improve the proteins coverage, we have performed experiments with some matrices in concert. These experiments enabled reliable identification of proteins, without the use of Nanospray MS/MS experiments.

Journal Article↗
PubMed2007

Pores and ridges: high-resolution fingerprint matching using level 3 features.

Fingerprint friction ridge details are generally described in a hierarchical order at three different levels, namely, Level 1 (pattern), Level 2 (minutia points), and Level 3 (pores and ridge contours). Although latent print examiners frequently take advantage of Level 3 features to assist in identification, Automated Fingerprint Identification Systems (AFIS) currently rely only on Level 1 and Level 2 features. In fact, the Federal Bureau of Investigation's (FBI) standard of fingerprint resolution for AFIS is 500 pixels per inch (ppi), which is inadequate for capturing Level 3 features, such as pores. With the advances in fingerprint sensing technology, many sensors are now equipped with dual resolution (500 ppi/1,000 ppi) scanning capability. However, increasing the scan resolution alone does not necessarily provide any performance improvement in fingerprint matching, unless an extended feature set is utilized. As a result, a systematic study to determine how much performance gain one can achieve by introducing Level 3 features in AFIS is highly desired. We propose a hierarchical matching system that utilizes features at all the three levels extracted from 1,000 ppi fingerprint scans. Level 3 features, including pores and ridge contours, are automatically extracted using Gabor filters and wavelet transform and are locally matched using the Iterative Closest Point (ICP) algorithm. Our experiments show that Level 3 features carry significant discriminatory information. There is a relative reduction of 20 percent in the equal error rate (EER) of the matching system when Level 3 features are employed in combination with Level 1 and 2 features. This significant performance gain is consistently observed across various quality fingerprint images.

Algorithms↗
PubMed2003

Fourier transform ion cyclotron resonance mass spectrometry with NanoLC/microelectrospray ionization and matrix-assisted laser desorption/ionization: analytical performance in peptide mass fingerprint analysis.

Protein identifications by peptide mass fingerprint analyses with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) were performed using microelectrospray ionization coupled to nano liquid chromatography (NanoLC), as well as using matrix-assisted laser desorption/ionization (MALDI). Tryptic digests of bovine serum albumin (BSA), diluted down to femtomole quantities, have been desalted by fast NanoLC under isocratic elution conditions as the high resolving power of FT-ICR MS enables peptides to be separated during the mass analysis stage of the experiment. The high mass accuracy achieved with FT-ICR MS (a few ppm with external calibration) facilitated unambiguous protein identification from protein database searches, even when only a few tryptic peptides of a protein were detected. Statistical confidence in the database search results was further improved by internal calibration due to increased mass accuracy. Matrix-assisted laser desorption/ionization and micro electrospray ionization (ESI) FT-ICR showed good mass accuracies in the low femtomole range, yet a better sensitivity was observed with MALDI. However, in higher femtomole ranges slightly lower mass accuracies were observed with MALDI FT-ICR than with microESI FT-ICR due to scan-to-scan variations of the ion population in the ICR cell. Database search results and protein sequence coverage results from NanoLC FT-ICR MS and MALDI FT-ICR MS, as well as the effect of mass accuracy on protein identification for the peptide mass fingerprint analysis are evaluated.

Animals↗
PubMed1997

Single strand conformation polymorphism analysis of PCR-tDNA fingerprinting to address the identification of Bacillus species.

The suitability of tDNA-PCR fingerprinting to identify species of the genus Bacillus was tested on 75 strains. Strains belonging to the same species or the same phylogenetic cluster were correctly grouped. Among B. stearothermophilus strains, different pattern types were found. This could be due to the unclear taxonomic situation of these strains, rather than to a failure of the tDNA-PCR. Single strand conformation polymorphism (SSCP) of the PCR products allowed species discrimination within the 'B. subtilis group', but not within the 'B. cereus group'. The tDNA-PCR, alone or coupled with SSCP analysis, is useful to address Bacillus species identification, particularly for those species which are not phylogenetically tightly clustered.

Bacillus cereus↗
PubMed2002

Stable isotope labelling in vivo as an aid to protein identification in peptide mass fingerprinting.

Peptide mass fingerprinting (PMF) is a powerful technique for identification of proteins derived from in-gel digests by virtue of their matrix-assisted laser desorption/ionization-time of flight mass spectra. However, there are circumstances where the under-representation of peptides in the mass spectrum and the complexity of the source proteome mean that PMF is inadequate as an identification tool. In this paper, we show that identification is substantially enhanced by inclusion of composition data for a single amino acid. Labelling in vivo with a stable isotope labelled amino acid (in this paper, decadeuterated leucine) identifies the number of such amino acids in each digest fragment, and show a considerable gain in the ability of PMF to identify the parent protein. The method is tolerant to the extent of labelling, and as such, may be applicable to a range of single cell systems.

Deuterium↗
PubMed2005

Fingerprint evidence in England and Wales--the revised standard.

Evidence of personal identity, often based solely on the comparison of a single finger impression, or fragment of an impression, has been accepted by courts of law at all levels in England and Wales since 1901, when the fingerprint system of identification was first adopted by police forces. Fingerprint identification is used by police forces world-wide, not only for the identification of latent fingermarks left at crime scenes, but also as the basis for ensuring accuracy in the criminal record system. For more than a century fingerprint evidence has been shown without doubt to be the best form of personal identification yet devised and millions of comparisons and subsequent identifications have been effected world-wide without any flaw in the system having been detected. From 1953-2001 it was the usual practice in England and Wales for the police to proffer fingerprint evidence showing 16 common matching characteristics, or features in agreement, between the two impressions being compared. In 1996 the Association of Chief Police Officers (ACPO) commissioned a review of the existing methods of presenting fingerprint evidence before the courts and on 11 June 2001 a new standard of fingerprint evidence was adopted by the police forces of England and Wales. This paper describes how the new standard was developed and implemented and why it was considered necessary to move away from the existing 16-point standard.

Criminal Law↗