Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “FINGERPRINTS”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 451 records · Page 25Linked to original sources
PubMed1989

Genetic analysis of Streptococcus pneumoniae serotypes with the use of DNA fingerprinting.

Molecular genetic similarities among a Streptococcus pneumoniae library were examined by comparing DNA restriction endonuclease banding patterns (fingerprints) after nuclease digestion and agarose gel electrophoresis. Densitometric scanning graphs of DNA fingerprints on photonegative film were compared for similarity, i.e., the percentage of shared bands. Comparison of serotypes 1, 3, 12, 14, and 25 revealed 54% +/- 9% similarity. Fingerprints within serogroups IX and XVIII did not differ from non-cross-reactive types. Intraserotypic comparison of strains of type 25 (n = 5) revealed 89% +/- 4% similarity. Five strains of type 3 were 75% +/- 19% similar; however, two of these strains had 96% similarity and three strains had 98% +/- 2% similarity, perhaps suggesting subtypes with serotype 3. Substantial DNA fingerprint differences were found among serotypes and significantly greater similarity among strains of a given type. Thus, DNA analyses used on other gram-positive bacteria are applicable to pneumococci.

DNA, Bacterial↗
PubMed1996

Progress with the PRINTS protein fingerprint database.

PRINTS is a compendium of protein motif 'fingerprints' derived from the OWL composite sequence database. Fingerprints are groups of motifs within sequence alignments whose conserved nature allows them to be used as signatures of family membership. To date, 400 fingerprints have been constructed and stored in Prints, the size of which has doubled in the last year. The current version, 9.0, encodes approximately 2000 motifs, covering a range of globular and membrane proteins, modular polypeptides, and so on. Fingerprints inherently offer improved diagnostic reliability over single motif methods by virtue of the mutual context provided by motif neighbours. PRINTS thus provides a useful adjunct to the widely used PROSITE dictionary of patterns. The database is now accessible via the Database Browser on the UCL Bioinformatics server at http://www.biochem.ucl.ac.uk/bsm/dbbrowser .

Amino Acid Sequence↗
PubMed1997

Novel developments with the PRINTS protein fingerprint database.

The PRINTS database of protein family 'fingerprints' is a diagnostic resource that complements the PROSITE dictionary of sites and patterns. Unlike regular expressions, fingerprints exploit groups of conserved motifs within sequence alignments to build characteristic signatures of family membership. Thus fingerprints inherently offer improved diagnostic reliability by virtue of the mutual context provided by motif neighbours. To date, 600 fingerprints have been constructed and stored in PRINTS, representing a 50% increase in the size of the database in the last year. The current version, 13.0, encodes approximately 3000 motifs, covering a range of globular and membrane proteins, modular polypeptides, and so on. The database is accessible via UCL's Bioinformatics World Wide Web (WWW) server at http://www.biochem.ucl.ac.uk/bsm/dbbrowser / . We describe here progress with the database, its Web interface, and a recent exciting development: the integration of a novel colour alignment editor (http://www.biochem.ucl.ac.uk/bsm/dbbrowser++ +/CINEMA ), which allows visualisation and interactive manipulation of PRINTS alignments over the Internet.

Amino Acid Sequence↗
PubMed1989

DNA fingerprinting of spontaneously hypertensive and Wistar-Kyoto rats: implications for hypertension research.

Probes to hypervariable minisatellite regions of DNA identify multiple loci scattered over the autosomal chromosomes and produce a complex Southern blot pattern of fragments termed a DNA 'fingerprint'. As concern has been raised that different stocks of spontaneously hypertensive rats (SHR) and Wistar-Kyoto rats (WKY) may not be biologically identical, we have compared the DNA of SHR and WKY from several sources using two such probes which identify different sets of minisatellite sequences. While the DNA fingerprints of SHR from the various sources were identical, variability was observed in those of WKY, indicating genetic heterogeneity between different WKY stocks. In animals from one of the commercial suppliers even inter-rat variability in DNA fingerprints was seen, suggesting genetic heterogeneity within that single colony. These observations indicate that experimental results obtained using WKY from different sources may not be directly comparable and could provide an explanation for some of the conflicting data that exist on the comparative characteristics of SHR and WKY. In separate studies, direct comparisons both of the DNA fingerprints of SHR and WKY and of SHR and stroke-prone spontaneously hypertensive rats (SHRSP) showed multiple differences between the strains. The polymorphisms seen could provide useful linkage markers in locating the chromosomal sites of the genetic loci responsible for raised blood pressure in the SHR and the propensity to strokes in the SHRSP.

Animals↗
PubMed1983

Ontogeny of yellow fever 17D vaccine: RNA oligonucleotide fingerprint and monoclonal antibody analyses of vaccines produced world-wide.

Yellow fever 17D vaccines are currently manufactured with approval of the World Health Organization (WHO) in 11 countries. These vaccines have proven highly efficacious and safe. Nevertheless, they have not been fully characterized genetically, a problem for future standardization and modernization of vaccine manufacture now being proposed by WHO. Vaccines in use are derived from two distinct substrains (17D-204 and 17DD) which represent independently maintained passage series from original 17D. In this study, all 17D vaccines produced world-wide were characterized by RNA oligonucleotide fingerprinting. Forty-two large oligonucleotides were compared, and differences from an arbitrarily selected reference strain (produced by Connaught Laboratories in the U.S.A.) were determined. With one exception (vaccine produced in South Africa), fingerprints of vaccines derived from substrain 17D-204 were identical. The South African primary seed differed in position of one oligonucleotide, reflecting a charge shift due to a single base change. This difference occurred within one egg passage; a further change in the South African vaccine occurred within one or two passages from primary seed. No antigenic differences between 17D-204-derived vaccines (including South Africa) were demonstrated by neutralization tests using monoclonal antibody. Vaccines derived from the 17DD substrain consistently differed from 17D-204 vaccines in the absence of one oligonucleotide (No. 37). This change probably occurred during 40 additional egg passages in development of the 17DD vaccines. A clear antigenic difference was shown between 17D-204 and 17DD substrain vaccines using monoclonal antibody. 17DD vaccines showed minor genotypic differences, suggesting a higher degree of genetic instability than 17D-204 vaccines. No oligonucleotide fingerprint differences were found between avian leukosis virus (ALV)-free and ALV-contaminated vaccines. No definite genomic correlate of neurovirulence was defined by fingerprinting strains with a history of encephalitic complications in man or of failure to pass monkey neurovirulence tests. Parent Asibi virus showed several oligonucleotide differences and was serologically distinct from 17D vaccine.

Antibodies, Monoclonal↗
PubMed1984

Oligonucleotide fingerprint analysis of strains of Getah virus isolated in Japan and Malaysia.

Eighteen strains of Getah virus isolated from mosquitoes, swine and horses in Japan (1956 to 1981), and one strain isolated in Malaysia (1955), were analysed by RNase T1-resistant oligonucleotide fingerprinting. All fingerprints showed a poly(A) tract. The fingerprint pattern of the Malaysian strain was quite different from those of the Japanese strains. Although most of the recent Japanese isolates shared many large oligonucleotide spots in common, the patterns were not identical even among the strains obtained in one locality in the same year. These results suggest that the Getah virus genome undergoes mutation rather frequently. However, there is a tendency for the isolates of the same year to show greater similarity. The fingerprint patterns of certain host-dependent temperature-sensitive (ts) mutants differed from that of the parental strain. Also, there were some differences in large oligonucleotide spots between strain JaNAr12380M isolated in suckling mouse brain (SMB) and strain JaNAr12380A isolated in C6/36 cells, despite the fact that both strains were derived from the same wild mosquito homogenate. In addition, many host-dependent ts mutants were present in strain JaNAr12380A, whereas no such mutants were observed in strain JaNAr12380M. It is concluded that there is considerable variation in the strains of Getah virus infecting mosquitoes in the wild, and also that the variants or mutants present in mosquitoes might be subject to selection during viral multiplication in the mammalian host.

Aedes↗
PubMed2025

Mapping transcriptional responses to cellular perturbation dictionaries with RNA fingerprinting.

Single-cell perturbation dictionaries provide systematic measurements of how cells respond to genetic and chemical perturbations, and create the opportunity to assign causal interpretations to observational data. Here, we introduce RNA fingerprinting, a statistical framework that maps transcriptional responses from new experiments onto reference perturbation dictionaries. RNA fingerprinting learns denoised perturbation "fingerprints" from single-cell data, then probabilistically assigns query cells to one or more candidate perturbations while accounting for uncertainty. We benchmark our method across ground-truth datasets, demonstrating accurate assignments at single-cell resolution, scalability to genome-wide screens, and the ability to resolve combinatorial perturbations. We demonstrate its broad utility across diverse biological settings: identifying context-specific regulators of p53 under ribosomal stress, characterizing drug mechanisms of action and dose-dependent off-target effects, and uncovering cytokine-driven B cell heterogeneity during secondary influenza infection in vivo. Together, these results establish RNA fingerprinting as a versatile framework for interpreting single-cell datasets by linking cellular states to the underlying perturbations which generated them.

Journal Article↗
PubMed2006

Performance evaluation of fingerprint verification systems.

This paper is concerned with the performance evaluation of fingerprint verification systems. After an initial classification of biometric testing initiatives, we explore both the theoretical and practical issues related to performance evaluation by presenting the outcome of the recent Fingerprint Verification Competition (FVC2004). FVC2004 was organized by the authors of this work for the purpose of assessing the state-of-the-art in this challenging pattern recognition application and making available a new common benchmark for an unambiguous comparison of fingerprint-based biometric systems. FVC2004 is an independent, strongly supervised evaluation performed at the evaluators' site on evaluators' hardware. This allowed the test to be completely controlled and the computation times of different algorithms to be fairly compared. The experience and feedback received from previous, similar competitions (FVC2000 and FVC2002) allowed us to improve the organization and methodology of FVC2004 and to capture the attention of a significantly higher number of academic and commercial organizations (67 algorithms were submitted for FVC2004). A new, "Light" competition category was included to estimate the loss of matching performance caused by imposing computational constraints. This paper discusses data collection and testing protocols, and includes a detailed analysis of the results. We introduce a simple but effective method for comparing algorithms at the score level, allowing us to isolate difficult cases (images) and to study error correlations and algorithm "fusion." The huge amount of information obtained, including a structured classification of the submitted algorithms on the basis of their features, makes it possible to better understand how current fingerprint recognition systems work and to delineate useful research directions for the future.

Algorithms↗
PubMed2004

Fingerprint classification using a feedback-based line detector.

We present a fingerprint classification algorithm in this paper. This algorithm classifies a fingerprint image into one of the five classes: Arch, Left loop, Right loop, Whorl, and Tented arch. We use a new low-dimensional feature vector obtained from the output of a novel oriented line detector presented here. Our line detector is a co-operative dynamical system that gives oriented lines and preserves multiple orientations at points where differently oriented lines meet. Our feature extraction process is based on characterizing the distribution of orientations around the fingerprint. We discuss three different classifiers: support vector machines, nearest-neighbor classifier, and neural network classifier. We present results obtained on a National Institute of Standards and Technology (NIST) fingerprint database and compare with other published results on NIST databases. All our classifiers perform equally well, and this suggests that our novel line detection and feature extraction process indeed captures all the crucial information needed for classification in this problem.

Journal Article↗
PubMed1989

DNA fingerprints of poultry.

Human minisatellite probes cross-hybridize to DNA of several species of poultry (chicken, duck, turkey and goose), and detect high levels of polymorphism. The resulting DNA fingerprints are individual specific, and allow the discrimination even between closely related birds. The pattern of poultry DNA fingerprints is different from that of humans and other animals, having a higher average proportion of large DNA fragments. Pedigree analysis revealed a low number of allelic pairs of variable DNA fragments, indicating that most of the alleles are unresolved in the DNA fingerprint or too small to be detected. The total number of detectable loci in broilers, using probe 33.6, was estimated as 62, of which 13 loci are on average scoreable and available for use. Poultry DNA fingerprints can be used for individual identification, linkage studies and as an aid in breeding programmes.

Alleles↗
PubMed2006

Detection of visible and latent fingerprints using micro-X-ray fluorescence elemental imaging.

Using micro-X-ray fluorescence (MXRF), a novel means of detecting fingerprints was examined in which the prints were imaged based on their elemental composition. MXRF is a nondestructive technique. Although this method requires a priori knowledge about the approximate location of a print, it offers a new and complementary means for detecting fingerprints that are also left pristine for further analysis (including potential DNA extraction) or archiving purposes. Sebaceous fingerprints and those made after perspiring were detected based on elements such as potassium and chlorine present in the print residue. Unique prints were also detected including those containing lotion, saliva, banana, or sunscreen. This proof-of-concept study demonstrates the potential for visualizing fingerprints by MXRF on surfaces that can be problematic using current methods.

Chlorine↗
PubMed2006

Amino acid alanine reactivity with the fingerprint reagent ninhydrin. A detailed ab initio computational study.

Ninhydrin is one of the most widely used reagents for chemical development of fingerprints on porous surfaces. The detection is based on the reaction of ninhydrin with a monoacidic component of the fingerprint to form an intensively colored compound named Ruhemann's Purple. A computational study of the mechanisms and reaction energetics of the formation of Ruhemann's Purple from ninhydrin and alanine is presented. Such a study is significant from a forensic science point of view because of the strong interest in the forensic chemistry and law enforcement communities in developing alternatives to the current generation of ninhydrin like chemicals for the detection and development of latent fingerprints. Information about the mechanism of reaction between ninhydrin and amino acids can ultimately help to design compounds with stronger chromo-fluorogenic properties in aid of detecting fingerprints at crime scenes. The three most accepted mechanisms of formation have been considered using ab initio quantum mechanical calculations. At relatively high temperature ( approximately 100 degrees C) all three mechanisms are energetically feasible. However since it is recommended that forensic analyses be performed at room temperature, a revised mechanism is proposed for the formation of Ruhemann's Purple under this condition.

Alanine↗
PubMed2007

Infrared spectroscopic imaging for noninvasive detection of latent fingerprints.

The capability of Fourier transform infrared (FTIR) spectroscopic imaging to provide detailed images of unprocessed latent fingerprints while also preserving important trace evidence is demonstrated. Unprocessed fingerprints were developed on various porous and nonporous substrates. Data-processing methods used to extract the latent fingerprint ridge pattern from the background material included basic infrared spectroscopic band intensities, addition and subtraction of band intensity measurements, principal components analysis (PCA) and calculation of second derivative band intensities, as well as combinations of these various techniques. Additionally, trace evidence within the fingerprints was recovered and identified.

Dermatoglyphics↗
PubMed2005

Establishment of GC-MS fingerprint of fresh Houttuynia cordata.

Fresh Houttuynia cordata THUNB. is a Chinese materia medica generally used in Chinese medicine therapy. It possesses the actions of clearing heat, eliminating toxins, reducing swelling, discharging pus and relieving stagnation. However, dry H. cordata has traditionally been used in clinical application instead of the fresh counterpart. In this paper, the chemical profiles of H. cordata were established using fingerprinting techniques. A modified GC-MS method was developed in the comparison of fingerprints among fresh and dry herbs of H. cordata. It was shown that the varieties, as well as relative levels of chemical components, in the fresh herb were more abundant than in the dry counterpart. Fingerprinting profiles were found to be consistent for fresh herbs acquired from various production areas, but the relative abundance of peaks were varied. Besides, the chemical components among different medicinal portions of fresh herbs were found to be inconsistent. The developed fingerprint can be successfully applied to distinguish between fresh and dry herbs, as well as determining differentiation among different medicinal portions.

Desiccation↗
PubMed2005

Multi-component HPLC fingerprinting of Radix Salviae Miltiorrhizae and its LC-MS-MS identification.

The multi-component fingerprinting method of Radix Salviae Miltiorrhizae (Root of Salvia miltiorrhiza BGE.), an important and popular medicinal herb in traditional Chinese medicine, was studied using reverse-phase HPLC and LC-MS-MS. Extract containing both the water-soluble phenolic compounds and nonpolar diterpenoid compounds known to be the herb's main bioactive components was prepared by a two-step extractive procedure. An HPLC fingerprinting method which can simultaneously separate these two types of compounds was established with gradient elution mode and photodiode array detection at 280 nm. Eighteen peaks in this HPLC fingerprint were structurally identified by employing LC-MS-MS techniques. The electrospray ionization (ESI) MS-MS spectra of most salvianolic acids displayed a characteristic behavior of loss of danshensu and caffeic acid moieties, while those of tanshinones showed a particular behavior of loss of H2O which is quite different from the fragmentation pattern in electron ionization mass spectrometry (EI-MS). The HPLC fingerprints of 7 batches of crude drugs showed similar separation pattern and provided much chemical information of the pharmacologically-active compounds in the crude drugs, which is useful for the authentication and quality evaluation of this medicinal herb.

Chromatography, High Pressure Liquid↗
PubMed2005

Improved fingerprint identification with supervised filtering enhancement.

An important step in the fingerprint identification system is the reliable extraction of distinct features from fingerprint images. Identification performance is directly related to the enhancement of fingerprint images during or after the enrollment phase. Among the various enhancement algorithms, artificial-intelligence-based feature-extraction techniques are attractive owing to their adaptive learning properties. We present a new supervised filtering technique that is based on a dynamic neural-network approach to develop a robust fingerprint enhancement algorithm. For pattern matching, a joint transform correlation (JTC) algorithm has been incorporated that offers high processing speed for real-time applications. Because the fringe-adjusted JTC algorithm has been found to yield a significantly better correlation output compared with alternate JTCs, we used this algorithm for the identification process. Test results are presented to verify the effectiveness of the proposed algorithm.

Algorithms↗
PubMed2006

Detection and mapping of latent fingerprints by laser-induced breakdown spectroscopy.

Detection of latent fingerprints on a Si wafer by laser-induced breakdown spectroscopy (LIBS) is demonstrated using approximately 120 fs pulses at 400 nm with energies of 84 +/- 7 microJ. The presence of a fingerprint ridge is found by observing the Na emission lines from the transferred skin oil. The presence of the thin layer of transferred oil was also found to be sufficient to suppress the LIBS signal from the Si substrate, giving an alternative method of mapping the latent fingerprint using the Si emission. A two-dimensional image of a latent fingerprint can be successfully collected using these techniques.

Dermatoglyphics↗
PubMed2005

Comparing bacterial DNA microarray fingerprints.

Epidemiologic and forensic investigations often require assays to detect subtle genetic differences between closely related microorganisms. Typically, gel electrophoresis is used to compare randomly amplified DNA fragments between microbial samples, where the patterns of DNA fragment sizes are viewed as genotype 'fingerprints'. The limited genomic sample captured on a gel, however, is not always sufficient to discriminate closely related strains. This paper examines the application of microarray technology to DNA fingerprinting as a high-resolution alternative to gel-based methods. The so-called universal microarray, which uses short oligonucleotide probes that do not target specific genes or species, is intended to be applicable to all microorganisms because it does not require prior knowledge of genomic sequence. In principle, closely related strains can be distinguished if enough independent oligonucleotide probes are used on the microarray, i.e., if the genome is sufficiently sampled. In practice, we confront noisy data, imperfectly matched hybridizations, and a high-dimensional inference problem. We describe the statistical problems of microarray fingerprinting, outline similarities with and differences from more conventional microarray applications, and illustrate a statistical measurement error model to fingerprint 10 closely related strains from three Bacillus species, and 3 strains from non-Bacillus species.

Journal Article↗