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PubMed1995

[Analysis of human DNA fingerprints by using fluorescein labelled probe JH12.6].

A method of analysis of human DNA fingerprints has been established by using fluorescein (Fl-11-dUTP) labelled probe JH12.6. The clear and high distinctive patterns of human DNA fingerprints were obtained with this method. The DNA fingerprints of 78 unrelated individuals living in Yunnan province of China were detected, and their probability of chance association between random individuals was calculated as 7.4 x 10(-11), and their mean allelic frequency as 0.09. Comparing of DNA fingerprints with labelling probe JH12.6 by using between radioactive 32P and fluorescein showed that the method by using fluorescein labelled probe JH12.6 was simple, fast, safe and economical. It can totally replace the method by using radioactive 32P labelled probe JH12.6, and it can be broadly applied in forensic medicine and other fields.

DNA Fingerprinting↗
PubMed1996

[Transmission of sensitive and resistant strains of Mycobacterium tuberculosis in The Netherlands, 1993-1995, studied by means of DNA fingerprinting].

OBJECTIVE: Determination of the contribution of recent transmission of both sensitive and drug-resistant Mycobacterium tuberculosis strains to the number of tuberculosis cases in the Netherlands. DESIGN: Descriptive study. SETTING: National Institute for Public Health and Environment, Bilthoven, the Netherlands. METHODS: Since 1993 all isolates of M. tuberculosis in the Netherlands are sent to the national reference laboratory for surveillance purposes. The strains with IS6110 DNA fingerprint, isolated from January 1993 to July 1995, were analysed for clustering of DNA patterns (clustering of identical DNA patterns was assumed to represent recent transmission of tuberculosis). A transmission index was calculated from the ratio of the number recently infected tuberculosis patients and the number of source patients. RESULTS: Among 2,217 M. tuberculosis isolates, 1,313 unique DNA fingerprints were observed, while 264 DNA patterns occurred more than once. 904 (41%) DNA fingerprints were part of a cluster of identical fingerprints. The mean cluster size was 3.42. The 232 resistant strains showed significantly less clustering (33% versus 42%, p < 0.02) and a smaller transmission index (0.27 versus 0.42, p < 0.02) compared with sensitive strains. CONCLUSION: Recent transmission contributes to the magnitude of the tuberculosis problem in the Netherlands. The epidemiological situation would, however, lead to gradual elimination of the disease were it not for introduction of tuberculosis from other countries. Transmission of resistant strains is relatively limited. Micro-epidemics caused by resistant M. tuberculosis strains were not observed.

DNA Fingerprinting↗
PubMed1976

Familial fingerprint body myopathy.

Muscle biopsy specimens from two half brothers with a congenital benign muscle disorder and from their mother, clinically unaffected, were studied by histochemistry and electron microscopy. In the children's biopsy specimens, the ultrastructural examination showed numerous fingerprint bodies located at the periphery of the muscle fibers. The histochemical pattern was different in these two specimens. In the mother's biopsy specimen, while fingerprint bodies were not found, the muscle fibers showed slight but definite changes. Even if the fingerprint bodies by themselves are not specific for a particular muscle disease, their occurrence in two half brothers is a valid argument in favor of the individalization of the fingerprint body myopathy, which has been previously described.

Adult↗
PubMed2001

Improvements in pentosan polysulfate sodium quality assurance using fingerprint electropherograms.

Complex samples from polymer production, plant extracts or biotechnology mixtures can be characterized by fingerprints. Currently, the standard approach for sample characterization employs near-infrared (NIR) spectroscopy fingerprinting. Up to now, however, fingerprints obtained by chromatography or electrophoresis could only be visually evaluated. This type of inspection is very labor-intensive and difficult to validate. In order to transfer the use of fingerprints from spectroscopy to electrophoresis, spectra-like properties must be obtained through a complete alignment of the electropherograms. This has been achieved by interpolation and wavelet filtering of the baseline signal in the present work. The resulting data have been classified by several algorithms. The methods under survey include self-organizing maps (SOMs), artificial neural networks (ANNs), soft independent modeling of class analogy (SIMCA) and k-nearest neighbors (KNNs). In order to test the performance of this combined approach in practice, it was applied to the quality assurance of pentosan polysulfate (PPS). A recently developed capillary electrophoresis (CE) method using indirect UV detection was employed in these studies [1]. All algorithms were well capable of classifying the examined PPS test batches. Even minor variations in the PPS composition, not perceptible by visual inspection, could be automatically detected. The whole method has been validated by classifying various (n = 400) unknown PPS quality assurance samples, which have been correctly identified without exception.

Algorithms↗
PubMed2000

Adsorption of Sodium Dodecyl Sulfate to Colloidal Titanium Dioxide: An Electrophoretic Fingerprinting Investigation.

The adsorption of sodium dodecyl sulfate to colloidal titanium dioxide was investigated using the electrophoretic fingerprinting approach. An electrophoretic fingerprint is a contour diagram of the observed electrophoretic mobility as a function of the bulk solution pH and plambda, the log of the bulk solution conductivity. Surfactant adsorption was observed to be strong under acidic conditions, as illustrated in the dramatic changes in the electrophoretic fingerprints. Electrokinetic data were compared with adsorption isotherm data obtained by a depletion method and good qualitative agreement was found. The observed pH changes associated with surfactant adsorption suggested ligand exchange as a possible mechanism of adsorption. Electrophoretic fingerprinting was shown to be a powerful means of examining surfactant adsorption to colloidal particles. Copyright 2000 Academic Press.

Journal Article↗
PubMed1993

DNA amplification fingerprinting of the Azolla-Anabaena symbiosis.

The Azolla-Anabaena symbiosis has been used for centuries as a nitrogen biofertilizer in rice paddies. Genetic improvement of the symbiosis has been limited by the difficulty in identifying Azolla-Anabaena accessions and Anabaena azollae strains. The recently developed technique of DNA amplification fingerprinting (DAF) was applied to this problem. DAF uses single, short, oligonucleotide primers of arbitrary sequence to direct amplification of a characteristic set of DNA products by a thermostable DNA polymerase in a thermocycling reaction. The products are separated in polyacrylamide gels and detected by silver staining. DAF could easily distinguish and positively identify accessions of Azolla-Anabaena with DNA extracted from the intact symbiosis. The contribution of prokaryotic Anabaena sequences to the fingerprint of the intact symbiosis, however, ranged from 0 to 77%, depending on the primer sequence. Therefore, DNA extracted from the intact symbiosis would not be suitable for Azolla taxonomy studies. The fingerprints of Anabaena strains isolated by sucrose gradient centrifugation from different species of Azolla could be easily distinguished, and DAF patterns were used to confirm the maternal pattern of transmission of Anabaena in a sexual hybrid. Template DNA extracted from roots was used to produce fingerprints for Azolla without interference from the microsymbiont. Comparison of the patterns from the parents and a hybrid gave strong evidence confirming sexual hybridization.

Anabaena↗
PubMed2003

Elemental fingerprint analysis of barley (Hordeum vulgare) using inductively coupled plasma mass spectrometry, isotope-ratio mass spectrometry, and multivariate statistics.

Inductively coupled plasma mass spectrometry (ICP-MS) and isotope-ratio mass spectrometry (IR-MS) have been used to examine the multi-elemental composition and (15)N/(14)N and (13)C/(12)C isotope ratios of three spring barley (Hordeum vulgare) genotypes (Orthega, Barke, and Bartok) grown in three typical Danish agricultural soils (North Jutland, West Jutland, and East Zealand) differing in soil fertility. The aim of the study was to examine whether it was possible to generate a unique elemental fingerprint of individual barley genotypes irrespective of the elemental imprint plants had received from soils differing in fertility and agricultural practice. Multivariate statistics were used to analyze the elemental fingerprints of the barley genotypes at different times during a full growing season from early tillering to full maturity of the barley grains. Initially, 36 elements were analyzed in the plant samples but this number was subsequently reduced to 15 elements: B, Ba, C, Ca, Cu, Fe, K, Mg, Mn, N, Na, P, S, Sr, and Zn. These elements exceeded the limit of detection ( LOD) for all genotypes, soil types, and plant growth stages and for these elements the accuracy was better than 90% compared with apple leaf certified reference material (CRM). Principal component analysis (PCA) separated multi-elemental data in accordance with soil type when plants of similar physiological age were compared, whereas this separation disappeared if plants of all ages were compared simultaneously. Isotope ratios (delta(15)N) of plants also proved to be a highly accurate property for classification of samples according to soil type. In contrast, the differences in delta(13)C were too small to enable such classification. The differences in delta(15)N among soils were so pronounced that separation of samples according to the physiological age of plants became redundant. However, delta(15)N and the multi-elemental analysis revealed no differences between the three barley genotypes, indicating that the influence of soil chemistry and possibly also climate and agricultural practice was too large to allow an unique elemental fingerprint for the genotypes. This finding was substantiated by analyzing the multi-elemental composition of grain from two additional genotypes (Otira and Barthos) grown at the north and east locations, respectively. PCA showed not only that the elemental fingerprints of these two genotypes were similar to those of the others, but also that the soil in which the plant had been growing could be accurately predicted on the basis of the PCA scores from the genotypes Orthega, Barke, and Bartok. Similar conclusions could be drawn using delta(15)N data.

Agriculture↗
PubMed2005

Prediction of plasma protein binding of drugs using Kier-Hall valence connectivity indices and 4D-fingerprint molecular similarity analyses.

A 115 compound dataset for HSA binding is divided into the training set and the test set based on molecular similarity and cluster analyses. Both Kier-Hall valence connectivity indices and 4D-fingerprint similarity measures were applied to this dataset. Four different predictive schemes (SM, SA, SR, SC) were applied to the test set based on the similarity measures of each compound to the compounds in the training set. The first algorithmic scheme (SM) predicts the binding affinity of a test compound using only the most similar training set compound's binding affinity. This scheme has relatively poor predictivity based both on Kier-Hall valence connectivity indices similarity measures and 4D-fingerprints similarity analyses. The other three algorithmic schemes (SM SR, SC), which assign a weighting coefficient to each of the top-ten most similar training set compounds, have reasonable predictivity of a test set. The algorithmic scheme which categorizes the most similar compounds into different weighted clusters predicts the test set best. The 4D-fingerprints provide 36 different individual IPE/IPE type molecular similarity measures. This study supports that some types of similarity measures are highly similar to one another for this dataset. Both the Kier-Hall valence connectivity indices similarity measures and the 4D-fingerprints have nearly same predictivity for this particular dataset.

Algorithms↗
PubMed1993

A new approach to input device key design using fingerprints.

A new approach to designing input device keys is proposed, and a TV remote controller is used as an example to demonstrate the new approach for studying the relationship between fingerprints and key geometry. One hundred subjects' fingerprints of thumbs and index fingers of both hands were collected, and a computer program was used for converting the fingerprint to a bitmap form. Subsequently, the data were analysed to provide some guidelines for determining the key size and key shape for the input device. Finally, the fingerprints were used to study the pattern of finger press and the justification for keycap curvature for finger placement. The results showed that the new approach can be useful in guiding designers of input device keys. A further benefit of this study is in providing a more systematic approach with considerable general potential for studying input device keys.

Journal Article↗
PubMed1986

Prediction of the occurrence of the ADP-binding beta alpha beta-fold in proteins, using an amino acid sequence fingerprint.

An amino acid sequence "fingerprint" has been derived that can be used to test if a particular sequence will fold into a beta alpha beta-unit with ADP-binding properties. It was deduced from a careful analysis of the known three-dimensional structures of ADP-binding beta alpha beta-folds. This fingerprint is in fact a set of 11 rules describing the type of amino acid that should occur at a specific position in a peptide fragment. The total length of this fingerprint varies between 29 and 31 residues. By checking against all possible sequences in a database, it appeared that every peptide, which exactly follows this fingerprint, does indeed fold into an ADP-binding beta alpha beta-unit.

Amino Acid Sequence↗
PubMed1990

Rubredoxin reductase of Pseudomonas oleovorans. Structural relationship to other flavoprotein oxidoreductases based on one NAD and two FAD fingerprints.

The oxidation of alkanes to alkanols by Pseudomonas oleovorans involves a three-component enzyme system: alkane hydroxylase, rubredoxin and rubredoxin reductase. Alkane hydroxylase and rubredoxin are encoded by the alkBFGHJKL operon, while previous studies indicated that rubredoxin reductase is most likely encoded on the second alk cluster: the alkST operon. In this study we show that alkT encodes the 41 x 10(3) Mr rubredoxin reductase, on the basis of a comparison of the expected amino acid composition of AlkT and the previously established amino acid composition of the purified rubredoxin reductase. The alkT sequence revealed significant similarities between AlkT and several NAD(P)H and FAD-containing reductases and dehydrogenases. All of these enzymes contain two ADP binding sites, which can be recognized by a common beta alpha beta-fold or fingerprint, derived from known structures of cofactor binding enzymes. By means of this amino acid fingerprint we were able to determine that one ADP binding site in rubredoxin reductase (AlkT) is located at the N terminus and is involved in FAD binding, while the second site is located in the middle of the sequence and is involved in the binding of NAD or NADP. In addition, we derived from the sequences of FAD binding reductases a second amino acid fingerprint for FAD binding, and we used this fingerprint to identify a third amino acid sequence in AlkT near the carboxy terminus for binding of the flavin moiety of FAD. On the basis of the known architecture and relative spatial orientations of the NAD and FAD binding sites in related dehydrogenases, a model for part of the tertiary structure of AlkT was developed.

Amino Acid Sequence↗
PubMed1989

Protein fingerprinting: a novel virus identification system.

Viral proteins separated by one-dimensional SDS-PAGE produce protein binding patterns (fingerprints) which are unique for different viruses. We have applied this concept successfully for the development of a practical and objective virus identification system which is applicable to most viruses. The method is simple, specific, and, unlike the currently available methods, free from all virus-specific reagents. Interference by host protein bands in SDS-PAGE preparations of virus-infected cell lysates was eliminated consistently by treating virus infected cell cultures with optimum concentration of NaCl for selective inhibition of host protein synthesis. The method utilizes the comparison of protein fingerprints of 'unknown' viruses with protein fingerprints of reference viruses stored in a computer data base, using pattern recognition software. All 113 'unknown' virus strains were correctly identified to the genus level by the protein fingerprint method, when compared with the conventional virus identification methods.

Animals↗
PubMedDate not supplied

Exclusion of a man charged with murder by DNA fingerprinting.

DNA fingerprinting was used to demonstrate that two murder-rapes committed in 1983 and 1986, respectively, were connected. The probability of chance association of the fingerprint was calculated as 5.8 x 10(-8). The man who had been charged with the murder was excluded because his DNA fingerprint did not match sperm DNA fingerprints obtained from swabs and clothing attributed to the two victims.

Autoradiography↗
PubMed1995

Development of latent fingerprints using preferential DC sputter deposition.

It was shown that a DC metal sputtering process with thermalised atoms, preferentially deposits metal onto fingerprint ridges. This method can be successfully used for the development of latent fingerprints. Four target metals were tested--copper, zinc, platinum, and gold--with platinum showing superior results for latent fingerprint development on clear polythene substrates. A comparison of platinum sputtering and cyanoacrylate fuming followed by rhodamine-6G staining, was conducted for 1-year-old fingerprint deposits. Platinum sputtering showed significantly higher sensitivity, and produced better overall results.

Copper↗
PubMed1990

DNA alterations in prostatic adenocarcinoma and benign prostatic hyperplasia: detection by DNA fingerprint analyses.

DNA fingerprinting can be utilized to examine a large number of autosomal loci throughout the human genome. Alterations in banding patterns observed on DNA fingerprint analyses reflect DNA alterations ranging from single base changes to complex chromosomal rearrangements. In this report, we describe the application of this technique to prostatic adenocarcinoma (CAP) and benign prostatic hyperplasia (BPH). The majority of CAP cases (12 of 14) displayed alterations in at least 1 of the approximately 30 resolvable bands obtained by fingerprint analyses when compared with DNA obtained from peripheral white blood cells. Unexpectedly, 5 of the 12 cases of BPH examined revealed at least 1 identifiable band alteration in the prostatic tissue. These findings demonstrate the usefulness of fingerprint analyses in the examination of cancer-associated genetic alterations. They also suggest the presence of observable genetic alterations in BPH.

Adenocarcinoma↗
PubMed2005

Constructing plasma protein binding model based on a combination of cluster analysis and 4D-fingerprint molecular similarity analyses.

Based on 2D-connectivity molecular similarity and cluster analyses, a dataset for HSA binding is divided into the training set and the test set. 4D-fingerprint similarity measures were applied to this dataset. Four different predictive schemes (SM, SA, SR, and SC) were applied to the test set based on the similarity measures of each compound to the compounds in the training set. The first algorithmic scheme (SM), which only takes the most similar compound in the training set into consideration, predicts the binding affinity of a test compound. This scheme has relatively poor predictivity based on 4D-fingerprint similarity analyses. The other three algorithmic schemes (SM, SR, and SC), which assign a weighting coefficient to each of the top-ten most similar training set compounds, have reasonable predictivity of a test set. The algorithmic scheme which categorizes the most similar compounds into different weighted clusters predicts the test set best. The 4D-fingerprints provide 36 different individual IPE/IPE type molecular similarity measures. Further investigation shows that the NP/HA, HS/HA, and HA/HA IPE/IPE type measures predict the test set well. Moreover, these three IPE/IPE type similarity measures are very similar to one another for the particular training and test sets investigated. The 4D-fingerprints have relatively high predictivity for this particular dataset.

Algorithms↗
PubMed2004

Fingerprinting of Salvia miltiorrhiza Bunge by non-aqueous capillary electrophoresis compared with high-speed counter-current chromatography.

The component of the traditional Chinese medicine (TCM) can be influenced by soil, climate, and growth stage, and fingerprint is an important means in its quality control. Our previous studies showed that high-speed counter-current chromatography (HSCCC) was helpful in the development of fingerprint of TCM. Since the HSCCC method is new, it is necessary to compare it with conventional ones, such as high-performance liquid chromatography (HPLC), thin-layer chromatography (TLC) and high-performance capillary electrophoresis (HPCE). Comparison with HPLC was conducted in our previous study. In this study, HSCCC was compared with non-aqueous capillary electrophoresis (NACE). With NACE, seven stable components were separated within 55 min, respectively, from three crude samples of Salvia miltiorrhiza Bunge from different growth locations. In HSCCC separation, 12 components were separated, respectively, with good correspondence and precision within 13 h. Both NACE and HSCCC were effective in showing whole concentration distribution of all kinds of constituents. Principles of these two methods were very different, which led to different elution sequences and relative contents of peaks. HSCCC showed better performance in analysis of tanshinones, which made its fingerprint containing more chemical information than that of NACE. It was further proven that HSCCC could be a feasible and cost-effective method in the development of the fingerprint of TCM.

Countercurrent Distribution↗
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↗