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At least 433 records · Page 24Linked to original sources
PubMed2005

Fingerprint quality control of Tianjihuang by high-performance liquid chromatography-photodiode array detection.

A novel, simple and accurate fingerprint method was developed using high-performance liquid chromatography-photodiode array detection (HPLC-DAD) for the quality control of Hypericum japonicum thunb (Tianjihuang), a Chinese herbal medicine used for the treatment of several bacterial diseases, infectious hepatitis, gastrointestinal disorder, internal hemorrhage and tumors. For the first time, the feasibility and advantages of employing chromatographic fingerprint were investigated and demonstrated for the evaluation of Tianjihuang by systematically comparing chromatograms with a professional analytical software recommended by State Food and Drug Administration (SFDA). Our results revealed that the chromatographic fingerprint combining similarity evaluation could efficiently identify and distinguish raw herbs of Tianjihuang from different sources. The effects resulted from collecting locations, harvesting time and storage time on herbal chromatographic fingerprints were also examined.

Chromatography, High Pressure Liquid↗
PubMed2006

High-performance thin-layer chromatographic fingerprints of isoflavonoids for distinguishing between Radix Puerariae Lobate and Radix Puerariae Thomsonii.

The roots of Pueraria lobata (Wild.) Ohwi and Pueraria thomsonii Benth have been officially recorded in all editions of Chinese Pharmacopoeia under the same monograph 'Gegen' (Radix Puerariae, RP). However, in its 2005 edition, the two species were separated into both individual monographs, namely 'Gegen' (Radix Puerariae Lobatae, RPL) and 'Fenge' (Radix Puerariae Thomsonii, RPT), respectively, due to their obvious content discrepancy of puerarin, the major active constituent. In present paper, the fingerprint of high-performance thin-layer chromatography (HPTLC) combining digital scanning profiling was developed to identify and distinguish the both species in detail. The unique properties of the HPTLC fingerprints were validated by analyzing ten batches of Pueraria lobata and P. thomsonii samples, respectively. The common pattern of the HPTLC images of the roots of Pueraria spp. and the respective different ratios of the chemical distribution can directly discern the two species. The corresponding digital scanning profiles provided an easy way for quantifiable comparison among the samples. Obvious difference in ingredient content and HPTLC patterns of the two species questioned their bio-equivalence and explained that recording both species separately in the current edition of Chinese Pharmacopoeia (2005 edition) is reasonable due to not only the content of major constituent, puerarin, but also the peak-to-peak distribution in the fingerprint and integration value of the total components. Furthermore, the HPTLC fingerprint is also suitable for rapid and simple authentication and comparison of the subtle difference among samples with identical plant resource but different geographic locations.

Chromatography, Thin Layer↗
PubMed2006

Fingerprinting quality control of Qianghuo by high-performance liquid chromatography-photodiode array detection.

A novel, simple and accurate fingerprint method was developed using high-performance liquid chromatography-photodiode array detection (HPLC-DAD) for the quality control of Qianghuo, a Tibetan folk and Chinese herbal medicine used as a diaphoretic, an antifebrile and an anodyne. For the first time, the feasibility and advantages of employing chromatographic fingerprint were investigated and demonstrated for the evaluation of Qianghuo by systematically comparing chromatograms of aqueous extracts with the professional analytical software recommended by State Food and Drug Administration (SFDA). Our results revealed that the chromatographic fingerprint combing similarity evaluation could efficiently identify and distinguish raw herbs of Qianghuo from different sources and different species. The effects on Notopterygium forbesii Boiss (Apiaceae) chromatographic fingerprints resulted from collecting locations, harvesting time were also examined.

Apiaceae↗
PubMed2000

Analysis of different de-esterification mechanisms for pectin by enzymatic fingerprinting using endopectin lyase and endopolygalacturonase II from A. niger.

A series of pectins with different distribution patterns of methyl ester groups was produced by treatment with either plant (p-PME) or fungal pectin methyl esterases (f-PME) and compared with those obtained by base catalysed de-esterification. The products generated by digestion of these pectins with either endopectin lyase (PL) or endopolygalacturonase II (PG II) from Aspergillus niger were analysed using matrix assisted laser desorption ionisation mass spectrometry (MALDIMS) and high-performance anion-exchange chromatography with pulsed amperometric or UV detection (HPAEC-PAD/UV). Time course analysis using MALDIMS was used to identify the most preferred substrate for each enzyme. For PL, this was shown to be fully methyl esterified HG whereas for PG II, long regions of HG without any methyl esterification, as produced by p-PME was the optimal substrate. The blockwise de-esterification caused by p-PME treatment gave a decrease of partly methylated oligomers in PL fingerprints, which did not effect the relative composition of partly methylated oligomers. PG II fingerprints showed a constant increase of monomers and oligomers without any methyl ester groups with decreasing degree of esterification (DE), but almost no change in the concentration of partly methylated compounds. PL fingerprints of f-PME and chemically treated pectins showed decreasing amounts of partly methyl esterified oligomers with decreasing DE, together with a relative shift towards longer oligomers. PG II fingerprints were characterised by an increase of partly methylated and not methylated oligomers with decreasing DE. But differences were also seen between these two forms of homogenous de-esterification. Introduction of a certain pattern of methyl ester distribution caused by selective removal of certain methyl ester groups by f-PME is the most reasonable explanation for the detected differences.

Aspergillus niger↗
PubMed2001

Fingerprints classification using artificial neural networks: a combined structural and statistical approach.

This paper describes a fingerprint classification algorithm using Artificial Neural Networks (ANN). Fingerprints are classified into six categories: arches, tented arches, left loops, right loops, whorls and twin loops. The algorithm extracts a string of symbols using the block directional image of a fingerprint, which represents the set of structural features for this image. The moment representing the statistical feature of the pattern is computed for this string and its Euclidean Distance Measures (EDM) are computed by using this moment. Our discrimination system uses a multilayer artificial neural network composed of six subnetworks one for each class. The classifier was tested on 1,500 images of good quality in the Egyptian Fingerprints database; images with poor quality were rejected. In the six-class problem the network achieved 95% classification accuracy. In the five-class problem when we place whorls and twin loops together in the same category the classification accuracy was around 99%. In the four-class problem when we place arches and tented arches in the same class the classification accuracy was 99%.

Algorithms↗
PubMed1986

Restriction enzyme fingerprinting of enterobacterial plasmids: a simple strategy with wide application.

Restriction enzyme fingerprints were generated from purified plasmid DNA from 324 clinical isolates that belonged to 7 enterobacterial genera and 88 single plasmids in Escherichia coli K 12 according to the following strategy. Purified plasmid DNA was digested with PstI. The number of fragments detected in a 0.8 agarose gel was used to determine which 2 of 6 restriction enzymes including PstI was most likely to provide a fingerprint comprising sufficient fragments to ensure specificity but sufficiently few to allow easy visual assessment and minimize coincidental matching. When PstI produced greater than 20 fragments, EcoRI and HindIII were used; when PstI generated less than 6 fragments Bsp 1286 and AvaII were used and SmaI was employed when between 6 and 20 fragments were obtained from PstI digests. Using a minimum of 12 fragments from a combination of 2 enzymes as the criterion for characterizing a strain/plasmid, satisfactory 2-enzyme fingerprints were obtained from 87% of the strains and plasmids studied using PstI and no more than two additional enzymes per strain. Of the remaining 54 strains, 51 harboured only small plasmids (less than 10 kb) and 3 produced satisfactory fingerprints when digested with a fourth enzyme.

Chromosome Mapping↗
PubMed1987

Protein fingerprinting for the determination of relatedness in Acinetobacter calcoaceticus subspecies anitratus isolated from patients in a surgical intensive care unit.

The use of protein fingerprinting for the establishment of relatedness among isolates of Acinetobacter calcoaceticus subspecies anitratus, isolated from patients in a surgical intensive care unit was examined. Polyacrylamide gel electrophoresis was used to analyze the cellular proteins from whole cell lysates of 14 intensive care unit A calcoaceticus subspecies anitratus isolates and 11 control strains. Antimicrobial susceptibilities and plasmid profiles were also determined for all isolates. All intensive care unit A calcoaceticus subspecies anitratus isolates exhibited identical cellular protein fingerprints, no detectable plasmids, and minimum inhibitory concentrations within +/- 1 log2 dilution of the mode value for each of the antimicrobial agents tested. The other clinical isolates demonstrated a range of antimicrobial susceptibilities, various numbers and sizes of plasmids, and distinctly different protein fingerprints. These data indicate that protein fingerprinting may be useful as an epidemiologic tool in A calcoaceticus subspecies anitratus outbreaks and this method deserves further study.

Acinetobacter↗
PubMed1988

A comparison of DNA and immunoblot fingerprinting of the SII biotype of coagulase negative staphylococci.

Thirty-eight isolates of the SII biotype of coagulase negative staphylococci were examined by phase typing, antibiograms, DNA and immunoblot fingerprinting. Multiple isolates were available from 5 patients with clinically proven infections and from 12 further patients who were epidemiologically distinct. Only 3 of the isolates were phage typable and antibiograms produced only 9 types. All isolates were typable by both DNA and immunoblot fingerprinting and reproducibility was excellent provided the conditions were standardized. Discrimination was better with immunoblot fingerprinting (17 types) than DNA fingerprinting (11 types). Both techniques were successful in assessing the significance of multiple isolates from a single patient.

Bacterial Typing Techniques↗
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↗
PubMedDate not supplied

Small molecule shape-fingerprints.

The optimal overlap between two molecular structures is a useful measure of shape similarity. However, it usually requires significant computation. This work describes the design of shape-fingerprints: binary bit strings that encode molecular shape. Standard measures of similarity between two shape-fingerprints are shown to be an excellent surrogate for similarity based on volume overlap but several orders of magnitude faster to compute. Consequently, shape-fingerprints can be used for clustering of large data sets, evaluating the diversity of compound libraries, as descriptors in SAR and as a prescreen for exact shape comparison against large virtual databases. Our results show that a small set of shapes can be used to build these fingerprints and that this set can be applied universally.

Journal Article↗
PubMedDate not supplied

Novel 2D fingerprints for ligand-based virtual screening.

This paper describes the development of a set of new 2D fingerprints for the purposes of virtual screening in a pharmaceutical environment. The new fingerprints are based on established ones: the changes in their design included the introduction of overlapping pharmacophore feature types, feature counts for pharmacophore and structural fingerprints, as well as changes in the resolution in property description for property fingerprints. The effects of each of these changes on virtual screening performance were monitored using two types of training sets, emulating different stages in the drug discovery process. The results demonstrate that these changes all lead to an improvement in virtual screening performance.

Chemistry↗
PubMedDate not supplied

The PRINTS database of protein fingerprints: a novel information resource for computational molecular biology.

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. Fingerprints inherently offer improved diagnostic reliability over single motif methods by virtue of the mutual context provided by motif neighbors. To date, 650 fingerprints have been constructed and stored in PRINTS, the size of which has doubled in the last 2 years. The current version, 14.0, encodes 3500 motifs, covering a range of globular and membrane proteins, modular polypeptides, and so on. The database is now accessible via the UCL Bioinformatics Server on http:@ www.biochem.ucl.ac.uk/bsm/dbbrowser/. We describe here progress with the database, its compilation and interrogation software, and its Web interface.

Amino Acid Sequence↗
PubMed2004

Novel cyclooxygenase-1 inhibitors discovered using affinity fingerprints.

We used protein affinity fingerprints to discover structurally novel inhibitors of cyclooxygenase-1 (COX-1) by screening a selected number of compounds, thus providing an alternative to extensive screening. From the affinity fingerprints of 19 known COX-1 inhibitors, a computational model for COX-1 inhibition was constructed and used to select candidate inhibitors from our compound library to be tested in the COX-1 assay. Subsequent refinement of the model by including affinity fingerprints of inactive compounds identified three molecules that were more potent than ibuprofen, a commonly used COX-1 inhibitor. These compounds are structurally distinct from those used to build the model and were discovered by testing only 62 library compounds. The discovery of these leads demonstrates the efficiency with which affinity fingerprints can identify novel bioactive chemotypes from known drugs.

Anti-Inflammatory Agents, Non-Steroidal↗
PubMed2004

Electrospray ionization mass spectrometry fingerprinting of propolis.

Crude ethanolic extracts of propolis, a natural resin, have been directly analysed using electrospray ionization mass (ESI-MS) and tandem mass spectrometry (ESI-MS/MS) in the negative ion mode. European, North American and African samples have been analyzed, but emphasis has been given to Brazilian propolis which displays diverse and region-dependent chemical composition. ESI-MS provides characteristic fingerprint mass spectra, with propolis samples being divided into well-defined groups directly related to their geographical origins. Chemometric multivariate analysis statistically demonstrates the reliability of the ESI-MS fingerprinting method for propolis. On-line ESI-MS/MS tandem mass spectrometry of characteristic [M - H](-) ion markers provides an additional dimension of fingerprinting selectivity, while structurally characterizing the ESI-MS marker components of propolis. By comparison with standards, eight such markers have been identified: para-coumaric acid, 3-methoxy-4-hydroxycinnamaldehyde, 2,2-dimethyl-6-carboxyethenyl-2H-1-benzopyran, 3-prenyl-4-hydroxycinnamic acid, chrysin, pinocembrin, 3,5-diprenyl-4-hydroxycinnamic acid and dicaffeoylquinic acid. The negative mode ESI-MS fingerprinting method is capable of discerning distinct composition patterns to typify, to screen the sample origin and to reveal characteristic details of the more polar and acidic chemical components of propolis samples from different regions of the world.

Journal Article↗
PubMed2005

Electrospray ionization mass spectrometry fingerprinting of beer.

After just simple degassing, dilution, pH adjustment and direct flow injection, characteristic fingerprint spectra of beer samples have been obtained by fast (few seconds) electrospray ionization mass spectrometry (ESI-MS) analysis in both the negative and positive ion modes. A total of 29 samples belonging to the two main beer types (lagers and ales) and several beer subtypes from USA, Europe and Brazil could be clearly divided into three groups both by simple visual inspection of their ESI(+)-MS and ESI(-)-MS fingerprints as well as by chemometric treatment of the MS data. Diagnostic ions with contrasting relative abundances in both the positive and negative ion modes allow classification of beers into three major types: P = pale (light) colored (pilsener, pale ale), D = dark colored (bock, stout, porter, mild ale) and M = malt beer. For M beers, samples of a dark and artificially sweetened caramel beer produced in Brazil and known as Malzbiers were used. ESI-MS/MS on these diagnostic beer cations and anions, most of which are characterized as arising from ionization of simple sugars, oligosaccharides, and iso-alpha-acids, yield characteristic tandem mass spectra adding a second and optional MS dimension for improved selectivity for beer characterization by fingerprinting. Direct ESI-MS or ESI-MS/MS analysis can therefore provide fast and reliable fingerprinting characterization of beers, distinguishing between types with different chemical compositions. Other unusual polar components, impurities or additives, as well as fermentation defects or degradation products, could eventually be detected, making the technique promising for beer quality control.

Beer↗
PubMed1990

Physical mapping of human chromosomes by repetitive sequence fingerprinting.

We have developed an approach for identifying overlapping cosmid clones by exploiting the high density of repetitive sequences in complex genomes. Individual clones are fingerprinted, using a combination of restriction enzyme digestions followed by hybridization with selected classes of repetitive sequences. This "repeat fingerprinting" technique allows small regions of clone overlap (10-20%) to be unambiguously assigned. We demonstrate the utility of this approach, using the fingerprinting of 3145 cosmid clones (1.25 x coverage), containing one or more (GT)n repeats, from human chromosome 16. A statistical analysis was used to link these clones into 460 contiguous sequences (contigs), averaging 106 kilobases (kb) in length and representing approximately 54% (48.7 Mb) of the euchromatic arms of this chromosome. These values are consistent with theoretical calculations and indicate that 150- to 200-kb contigs can be generated with 1.5 x coverage. This strategy requires the fingerprinting of approximately one-fourth as many cosmids as random strategies requiring 50% minimum overlap for overlap detection. By "nucleating" at specific regions in the human genome, and exploiting the high density of interspersed sequences, this approach allows (i) the rapid generation of large (greater than 100-kb) contigs in the early stages of contig mapping and (ii) the production of a contig map with useful landmarks for rapid integration of the genetic and physical maps.

Chromosome Mapping↗
PubMed1997

FPC: a system for building contigs from restriction fingerprinted clones.

MOTIVATION: To meet the demands of large-scale sequencing, thousands of clones must be fingerprinted and assembled into contigs. To determine the order of clones, a typical experiment is to digest the clones with one or more restriction enzymes and measure the resulting fragments. The probability of two clones overlapping is based on the similarity of their fragments. A contig contains two or more overlapping clones and a minimal tiling path of clones is selected to be sequenced. Interactive software with algorithmic support is necessary to assemble the clones into contigs quickly. RESULTS: FPC (fingerprinted contigs) is an interactive program for building contigs from restriction fingerprinted clones. FPC uses an algorithm to cluster clones into contigs based on their probability of coincidence score. For each contig, it builds a consensus band (CB) map which is similar to a restriction map; but it does not try to resolve all the errors. The CB map is used to assign coordinates to the clones based on their alignment to the map and to provide a detailed visualization of the clone overlap. FPC has editing facilities for the user to refine the coordinates and to remove poorly fingerprinted clones. Functions are available for updating an FPC database with new clones. Contigs can easily be merged, split or deleted. Markers can be added to clones and are displayed with the appropriate contig. Sequence-ready clones can be selected and their sequencing status displayed. As such, FPC is an integrated program for the assembly of sequence-ready clones for large-scale sequencing projects.

Algorithms↗
PubMed1988

DNA fingerprints of Streptococcus pyogenes are M type specific.

DNA from group A streptococci of various M and T types was cleaved with endonucleases to produce a DNA fingerprint. Comparison of DNA fingerprints proved to be a very useful tool for studying the epidemiology of isolates from various outbreaks of streptococcal disease. Patterns of DNA fragments from HindIII digests of samples of total DNA were conserved among strains of the same M serotype yet were easily distinguished from those of different M serotypes. Different M types were associated with specific restriction enzyme profiles. DNA fingerprints of strains of the same M type were stable enough to establish a clonal relationship between strains obtained from an isolated outbreak of disease or strains endogenous to people geographically isolated by continent. Strains of the same serotype from different continents had very similar, but distinguishable, restriction profiles. Those strains unable to be typed with standard typing sera were also amenable to comparison because they yielded unique fingerprints.

Africa↗