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PubMed1993

Application of DNA fingerprinting to enforcement of hunting regulations in Ontario.

DNA fingerprinting has been used in investigations of 40 cases of infractions of hunting regulations involving white-tailed deer (Odocoileus virginianus) and moose (Alces alces) in Ontario. In most of these cases, individual-specific DNA fingerprints obtained with the Jeffrey's 33.15 multilocus probe were used to link the animal remains found at the illegal kill site to blood and tissue samples of the dead animal associated with a suspect. DNA fingerprints from 27 white-tailed deer and 19 moose were obtained in order to establish the level of band-sharing in DNA fingerprints among unrelated individuals in each species. We also determined the levels of band-sharing among animals from the same region and calculated the probability of two individuals sharing the same DNA fingerprint. Details are presented from cases in which the evidence was presented and accepted by Ontario courts.

Animals↗
PubMedDate not supplied

DNA fingerprinting of Riemerella anatipestifer.

Seventeen restriction endonucleases were evaluated for use in DNA fingerprinting of Riemerella anatipestifer. Digestion of chromosomal DNA with either HinfI or DdeI restriction endonuclease, followed by submarine electrophoresis in agarose and staining with ethidium bromide, resulted in DNA fingerprint profiles that could be easily resolved. HinfI produced readable fingerprint patterns in the 2.7-20-kb range and was used to distinguish DNA fingerprint profiles among 89 strains of R. anatipestifer representing isolates from various avian species in the United States, the United Kingdom, Australia, Canada, Germany, and Israel. A total of 52 distinct DNA fingerprint profiles were found.

Animals↗
PubMed1999

New applications of low-C0tDNA as a DNA fingerprint probe.

New applications of low-C0t DNA are reported as probes for genetic identification and genome characterization. These fast and intermediately reannealing fractions have sometimes either been discarded in genomic library construction to enhance the probability of finding single copy genes, or they are used as resources for identifying individual repetitive sequences. In addition, they are used as blockers to enhance hybridization signals. C0t-1 DNA serves as a probe for DNA fingerprinting of human yeast artificial chromosomes. We have isolated low-C0t DNA from bacteria, fungus, plant, mussel, chicken, rat and fish from the sheared genomic DNA of the respective species. Low-C0t DNA is labeled to generate DNA fingerprints and for in situ hybridization. Individual specific DNA fingerprint profiles are observed and species-specific DNA fragments can be identified in bacteria, fungus, plants (Ginseng and Amaranthus) and mussel. When low-C0t DNA probes from rat, chicken and fish were employed, only smear profiles and no distinct DNA banding patterns were evident. In these species, individual clones can be used as a probe for DNA fingerprinting containing repetitive sequences after subcloning. The advantage of this approach is to quickly develop a useful probe for DNA fingerprinting for genetic identification and analysis without sequencing knowledge a priori. This represents an innovative approach to the use of these repetitive components of the genome.

Animals↗
PubMed1999

Characterization of beta-lactam-resistant Bacteroides fragilis isolates by use of PCR fingerprinting.

PCR fingerprinting was used for characterization of 35 beta-lactam-resistant Bacteroides fragilis strains isolated in Sweden and Hungary. Ten B. fragilis strains showed unique PCR fingerprints by use of the M13 core primer. Their main product was a DNA fragment with a length of 2000-bp which was absent in the other 25 strains and the reference strain B. fragilis ATCC 25285. The 2000-bp fragment from four imipenem-resistant strains gave rise to positive reactions in a specific PCR for detection of ccrA. Printed by the T3B primer, five B. fragilis strains, including the imipenem-resistant strains showed unique PCR fingerprints. The investigated imipenem-resistant strains produced carbapenem-hydrolysing metallo-beta-lactamases. The study indicates that the unique PCR fingerprinting profiles shown in highly beta-lactam resistant B. fragilis strains are correlated to antimicrobial resistance. The PCR fingerprinting technique is a useful tool for differentiation of Bacteroides fragilis strains with high-level beta-lactam resistance.

Journal Article↗
PubMed1988

Fingerprinting cell lines: use of human hypervariable DNA probes to characterize mammalian cell cultures.

Hypervariable DNA sequences may be used as probes to derive DNA "finger-prints" for individuals. To assess the use of the human 33.15 and 33.6 probes (isolated by Jeffreys and coworkers) for characterizing cell lines of nonhuman origin, DNA from different stocks of Chinese hamster (CH) cells was screened. All CHO (ovary) sublines could be readily distinguished from CH-V79 sublines by their fingerprints, but where two stocks had been derived recently from the same line, their fingerprints were nearly identical. Similarly fingerprints of HPRT-deficient mutants derived from one cell stock were identical. A V79 x CHO fusion hybrid showed equal fingerprint band-sharing with each parent line, while early-passage diploid CH cells had a fingerprint closer to CHO than to V79. Thus these data introduce a simple means of typing cell lines to avoid cross-contamination, of checking cell hybrids, and of assessing the divergence of cell stocks from one another.

Animals↗
PubMed1988

Genomic mapping by fingerprinting random clones: a mathematical analysis.

Results from physical mapping projects have recently been reported for the genomes of Escherichia coli, Saccharomyces cerevisiae, and Caenorhabditis elegans, and similar projects are currently being planned for other organisms. In such projects, the physical map is assembled by first "fingerprinting" a large number of clones chosen at random from a recombinant library and then inferring overlaps between clones with sufficiently similar fingerprints. Although the basic approach is the same, there are many possible choices for the fingerprint used to characterize the clones and the rules for declaring overlap. In this paper, we derive simple formulas showing how the progress of a physical mapping project is affected by the nature of the fingerprinting scheme. Using these formulas, we discuss the analytic considerations involved in selecting an appropriate fingerprinting scheme for a particular project.

Animals↗
PubMed2003

Fingerprint profiling of acid hydrolyzates of polysaccharides extracted from the fruiting bodies and spores of Lingzhi by high-performance thin-layer chromatography.

Modern extraction and planar chromatographic instrumentation were employed for the fingerprint profiling of carbohydrates from an important and popular medicinal mushroom commonly known as Lingzhi. For the first time, the feasibility of employing the high-performance thin-layer chromatography (HPTLC) peak profiles (fingerprints) of carbohydrates for the screening of various Lingzhi species/products was demonstrated. An analytical procedure was developed such that upon acid hydrolysis of the polysaccharides extracted from various Lingzhi samples, fingerprint profiles that reveal the relative amounts of the degradation products, such as mono- and oligosaccharides, can be obtained using HPTLC plates (Si 50000) for separation and 4-aminobenzoic acid as the post-chromatographic derivatization reagent for detection. Also, using automated multiple development (AMD), the acid hydrolyzates from Lingzhi, consisting of simple and more complex sugars, can be separated simultaneously with high degree of automation. An important finding was that unique fingerprint patterns were observed in the monosaccharide profiles between two highly valued Lingzhi species, Ganoderma applanatum and Ganoderma lucidum, under total or partial acid hydrolysis conditions. Additionally, the HPTLC fingerprint profiles of carbohydrates were obtained from the extracts of the spores and fruiting bodies of Lingzhi and compared.

Acids↗
PubMed2004

Comparison of high-speed counter-current chromatography and high-performance liquid chromatography on fingerprinting of Chinese traditional medicine.

Active constituents of Chinese traditional medicine (CTM) are influenced by soils, climates, and growth stages. Therefore, fingerprint is important in quality control of CTM. Our studies showed for the first time that high-speed counter-current chromatography (HSCCC) could be applied in the development of fingerprint of CTM. Twelve components were separated from extracts of three crude samples of Salvia miltiorrhiza Bunge, which were collected from different growth locations. All 12 components of each sample were isolated within 13 h coming with good correspondence by using HSCCC. Relative standard deviation (R.S.D.) values of the retention time in HSCCC separation was less than 3% satisfied the precision requirements of national standards in the fingerprint development. As a new approach, HSCCC was compared to the conventional approach-HPLC in our experiments. The fingerprint developed by HPLC comprised 11 peaks that collected within 45 min. R.S.D. values of retention times of the corresponding peaks in HPLC analysis were very small (maximum 0.66% and average 0.10%). In conclusion, HSCCC was a feasible method to be used in the development of fingerprint of CTM.

Chromatography, High Pressure Liquid↗
PubMed2006

Pretreatments of chromatographic fingerprints for quality control of herbal medicines.

Pretreatments of chromatographic fingerprints are important for quality control of herbal medicines and they include data correction and data transformation. The data correction can reduce the variations of experimental procedures, and data transformation can put different weights on the different parts of the fingerprints. In this paper, a new target peak alignment (TPA) procedure has been proposed to correct the retention time shifts, multiplicative scattering correction (MSC) has been introduced for response correction. Then the similarity of the fingerprints with mean and median fingerprints is used to evaluate the quality of herbal medicines (HMs). Furthermore, different data transformation methods with kernel principal component analysis (PCA) have been applied to the data and their effects were discussed. The proposed approaches have been demonstrated by the essential oils data set of a herbal medicine, named Houttuynia cordata (HC), containing samples from different geographic origins. The experimental results indicate that the proposed approaches may be helpful in the quality control of herbal medicines by fingerprints.

Chromatography, Gas↗
PubMed2004

A novel approach to identify the presence of fingerprints on wet surfaces.

In forensic science, one of the major problems is trying to reveal the presence of fingerprints on wet surfaces. Not often are fingerprints left in protect environments, so we have to detect their presence on the most different surfaces, after they underwent to the action of atmospheric agents or have been found, for example, on objects floating in the water. Small Particle Reagents (SPR) is a technique performed to detect latent fingerprints left on wet or moist surfaces based upon the reaction between the fatty-acid residuals present in the traces and hydrophobic tails of the specific reagents. Those tails are linked to a hydrophilic head reacting with a titanium dioxide salt giving a white precipitate plainly detectable. In this report, we want to show that exalting fingerprints left on plastic, glass and metal wet surfaces is possible with the SPR technique independently on the time fingerprints were in contact with water, as we performed in our experimental procedure. Results in details.

Dermatoglyphics↗
PubMed2006

Chemical fingerprint analysis of rhizomes of Gymnadenia conopsea by HPLC-DAD-MSn.

A high-performance liquid chromatography-diode array detection-tandem mass spectrometry (HPLC-DAD-MS(n)) method has been firstly developed for chemical fingerprint analysis of rhizomes of Gymnadenia conopsea R. Br. and rapid identification of major compounds in the fingerprints. Comparing the UV and MS spectra with those of reference compounds, seven main peaks in the fingerprints were identified as adenosine (1), 4-hydroxybenzyl alcohol (2), 4-hydroxybenzyl aldehyde (3), dactylorhin B (4), loroglossin (5), dactylorhin A (6) and militarine (7). Compounds 4-7 were succinate derivative esters and firstly discovered from this species. The Computer Aided Similarity Evaluation System (CASES) for chromatographic fingerprint of traditional Chinese medicine was employed to evaluate the similarities of 10 samples of the rhizomes of G. conopsea collected from Sichuan, Qinghai and Hebei provinces, Tibet autonomous region of China, and Nepal. These samples from different sources had similar chemical fingerprints. This method is specific and may serve for quality identification and comprehensive evaluation of this traditional Tibetan remedy.

Chromatography, High Pressure Liquid↗
PubMed2003

On learning to estimate the block directional image of a fingerprint using a hierarchical neural network.

This paper presents a hierarchical neural network architecture for computing fingerprints block directional images. Two separately trained neural networks are connected in series. First, the fingerprint image is divided into 16x16 blocks, each block is submitted to the first network which is a back propagation neural network. It has four counters in its output layer one for each direction to count the main directional codes in each fingerprint block. The output of this network is considered the feature vector for the fingerprint block, which is then submitted to the second network. The second network is a self-organized feature maps neural network uses an unsupervised learning strategy to group the fingerprint blocks into distinct directional classes. In this scheme, there is more than one sub-class for each directional class, an agglomerative hierarchical cluster algorithm for merging two clusters is used to merge two classes if their corresponding distances are below a specified threshold. Results obtained with a real world data set indicate the effectiveness of the proposed architecture.

Algorithms↗
PubMed2003

Fingerprint analysis of Flos Carthami by capillary electrophoresis.

Capillary electrophoresis (CE) was employed in fingerprint analysis of Flos Carthami. A standardized procedure was used to develop the CE fingerprint. An electrophoretic profile of genuine Flos Carthami from Fengqiu, He'nan, China, was first established as the characteristic fingerprint. This profile was then used to identify and assess the consistency of the herb. A study with a limited number of samples from nine sources showed a fair consistency in their CE fingerprints with that of the genuine sample. Flos Carthami was well distinguished from Stigma Croci, a possible substitute in traditional Chinese medicine, and Flos Hemerocallis, a commercial adulterant, by comparing the fingerprints of each herb.

Asteraceae↗
PubMedDate not supplied

Design and evaluation of a molecular fingerprint involving the transformation of property descriptor values into a binary classification scheme.

A new fingerprint design concept is introduced that transforms molecular property descriptors into two-state descriptors and thus permits binary encoding. This transformation is based on the calculation of statistical medians of descriptor distributions in large compound collections and alleviates the need for value range encoding of these descriptors. For binary encoded property descriptors, bit positions that are set off capture as much information as bit positions that are set on, different from conventional fingerprint representations. Accordingly, a variant of the Tanimoto coefficient has been defined for comparison of these fingerprints. Following our design idea, a prototypic fingerprint termed MP-MFP was implemented by combining 61 binary encoded property descriptors with 110 structural fragment-type descriptors. The performance of this fingerprint was evaluated in systematic similarity search calculations in a database containing 549 molecules belonging to 38 different activity classes and 5000 background molecules. In these calculations, MP-MFP correctly recognized approximately 34% of all similarity relationships, with only 0.04% false positives, and performed better than previous designs and MACCS keys. The results suggest that combinations of simplified two-state property descriptors have predictive value in the analysis of molecular similarity.

Computing Methodologies↗
PubMedDate not supplied

Similarity search profiling reveals effects of fingerprint scaling in virtual screening.

Fingerprint scaling is a method to increase the performance of similarity search calculations. It is based on the detection of bit patterns in keyed fingerprints that are signatures of specific compound classes. Application of scaling factors to consensus bits that are mostly set on emphasizes signature bit patterns during similarity searching and has been shown to improve search results for different fingerprints. Similarity search profiling has recently been introduced as a method to analyze similarity search calculations. Profiles separately monitor correctly identified hits and other detected database compounds as a function of similarity threshold values and make it possible to estimate whether virtual screening calculations can be successful or to evaluate why they fail. This similarity search profile technique has been applied here to study fingerprint scaling in detail and better understand effects that are responsible for its performance. In particular, we have focused on the qualitative and quantitative analysis of similarity search profiles under scaling conditions. Therefore, we have carried out systematic similarity search calculations for 23 biological activity classes under scaling conditions over a wide range of scaling factors in a compound database containing approximately 1.3 million molecules and monitored these calculations in similarity search profiles. Analysis of these profiles confirmed increases in hit rates as a consequence of scaling and revealed that scaling influences similarity search calculations in different ways. Based on scaled similarity search profiles, compound sets could be divided into different categories. In a number of cases, increases in search performance under scaling conditions were due to a more significant relative increase in correctly identified hits than detected false-positives. This was also consistent with the finding that preferred similarity threshold values increased due to fingerprint scaling, which was well illustrated by similarity search profiling.

Journal Article↗
PubMed2004

Enzyme activity fingerprinting with substrate cocktails.

In the postgenomic era, emphasis is shifting from protein identification to protein functional analysis. Enzyme function can be characterized by measuring activity across series of substrates, which generates an activity profile or fingerprint. Activity fingerprinting is particularly useful to differentiate closely related enzymes. Previously reported fingerprinting methods use series of parallel measurements, which are complex and difficult to reproduce. Here we report a new method for fingerprinting enzyme activities based on using mixtures of substrates, or substrate cocktails, in a single reaction that is then analyzed by HPLC. The fingerprints produced are highly reproducible and allow functional differentiation and classification of closely related enzymes, as demonstrated for a series of lipases and esterases. The method is practical, general, and flexible in terms of reaction conditions and can be adapted to any reaction type.

Enzymes↗
PubMed1996

XFINGER: a tool for searching and visualising protein fingerprints and patterns.

A tool for searching pattern and fingerprint databases is described. Fingerprints are groups of motifs excised from conserved regions of sequence alignments and used for iterative database scanning. The constituent motifs are thus encoded as small alignments in which sequence information is maximised with each database pass; they therefore differ from regular-expression patterns, in which alignments are reduced to single consensus sequences. Different database formats have evolved to store these disparate types of information, namely the PROSITE dictionary of patterns and the PRINTS fingerprint database, but programs have not been available with the flexibility to search them both. We have developed a facility to do this: the system allows query sequences to be scanned against either PROSITE, the full PRINTS database, or against individual fingerprints. The results of fingerprint searches are displayed simultaneously in both text and graphical windows to render them more tangible to the user. Where structural coordinates are available, identified motifs may be visualised in a 3D context. The program runs on Silicon Graphics machines using GL graphics libraries and on machines with X servers supporting the PEX extension: its use is illustrated here by depicting the location of low-density lipoprotein-binding (LDL) motifs and leucine-rich repeats in a mosaic G-protein-coupled receptor (GPCR).

Amino Acid Sequence↗
PubMed2003

A pilot study to investigate effects of inulin on Caco-2 cells through in vitro metabolic fingerprinting.

Metabolic fingerprints are novel measurement tools to evaluate the biochemical status of a living organism by using 1H NMR and multivariate data analysis (MVDA). In this way, a quick evaluation of changes in health or diseased state can be made, reflected in alterations of metabolic patterns. Normally, metabolic fingerprinting is based on in vivo studies. These studies often represent a labor-intensive and expensive manner of investigation. In vitro studies are not hampered by these disadvantages, thus constituting an interesting alternative. In this research, results are presented of a pilot experiment in which metabolic fingerprinting was combined with an in vitro model. For this purpose, differentiated Caco-2 cells were exposed to inulin and its fermentative metabolites, both dissolved in culture medium. Cells were incubated for 0 or 48 h. Cell fractions were analyzed by NMR, then subsequently with MVDA. Differences in treatment provided detectable variations in the time of metabolic patterns of cell contents. Results indicated that glucose metabolism linked to glutamate was of major importance in the effects of inulin and its metabolites on Caco-2 cells under the conditions of our study. Metabolic fingerprinting in combination with an in vitro model appears to be a feasible technique with which to visualize metabolic patterns of cell contents and provides an efficient place for the generation of hypotheses about the metabolic pathways involved. In vitro metabolic fingerprinting may be of great benefit in the future for a better understanding of the relationship between nutrition and health.

Alanine↗