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At least 685 records · Page 38Linked to original sources
PubMed1990

Detection of somatic mutations in tumours of diverse types by DNA fingerprinting with M13 phage DNA.

Hybridization of M13 phage DNA to Southern blots of human DNA produces an individual-specific DNA fingerprint. In this study, tumour and lymphocyte DNA from a series of patients with melanoma, Merkel-cell carcinoma, Burkitt's lymphoma and Wilms' tumour was probed with M13 DNA to detect somatic mutations in the DNA of the tumours. Somatic changes were observed in tumour DNA of 16 out of the 28 cases examined. This frequency compared favourably with the frequency with which tumour-specific changes have been found when using the Jeffreys DNA fingerprinting probe 33.15, and demonstrates that M13 DNA provides a useful additional probe for the study of somatic changes in tumours. The finding that multiple DNA fragments were lost or gained in DNA fingerprints from individual tumours indicates a marked degree of complexity in the genetic changes involved in the evolution of certain human cancers.

Bacteriophages↗
PubMed2006

An agent-based system to discover protein-protein interactions, identify protein complexes and proteins with multiple peptide mass fingerprints.

Proteins "work together" by actually binding to form multicomponent complexes that carry out specific functions. Proteomic analyses based on the mass spectrum are now key methods to determine the components in protein complexes. The protein-protein interaction or functional association may be known to exist among the extracted protein spots while analyzing the proteins on the 2D gel. In this study, we develop an agent-based system, namely AgentMultiProtIdent, which integrated two protein identification tools and a variety of databases storing relations among proteins and used to discover protein-protein interactions and protein functional associations, and identify protein complexes and proteins with multiple peptide mass fingerprints as input. The system takes Multiple Peptide Mass Fingerprints (PMFs) as a whole in the protein complex or protein identification. With the relations among proteins, it may greatly improve the accuracy of identification of protein complexes. Also, possible relationship of the multiple peptide mass fingerprints, such as ontology relation, can be discovered by our system, especially in the identification of protein complexes. The agent-based system is now available on the Web at http://dbms104.csie.ncu.edu.tw/ approximately protein/NEW2/.

Animals↗
PubMed2005

Fingerprint chromatogram analysis of extracts from the leaves of Tripterygium wilfordii Hook. F. by high performance liquid chromatography.

A simple and reliable high performance liquid chromatographic (HPLC) method has been developed and validated for the study of fingerprint chromatograms of extracts from the leaves of Tripterygium wilfordii Hook. F. (TWHF) and for controlling the quality of the herb. HPLC separation of the extracts was performed on a Lichrospher RP-18 column and detected by ultraviolet absorbance at 210 nm. The column temperature was maintained at 35 degrees C. A mobile phase composed of acetonitrile:H2O in the ratio of 39:61 (v/v) was found to be most suitable for this separation at a flow rate of 0.8 mL/min with isocratic elution. Under the chromatographic conditions described, the peak profile of the 10 components collected within 35 min made up the fingerprint of the extracts from leaves of TWHF with universal features. The fingerprint chromatograms had a good stability, precision, and reproducibility. The similarity of the extracts from leaves of TWHF collected in summer and winter was studied with triptolide as a reference peak. The method is suitable for differentiation of extracts from the leaves of TWHF, and can be used as a quality control method for this herb.

Chromatography, High Pressure Liquid↗
PubMed2006

Application of LC/MS and ICP/MS for establishing the fingerprint spectrum of the traditional Chinese medicinal preparation Gan-Lu-Yin.

We developed a method to analyze the fingerprint spectrum qualitatively and quantitatively for the traditional Chinese herbal medicinal preparation Gan-Lu-Yin with HPLC combined with photodiode array detection, and MS, and to identify the preparation's 14 main components including baicalin, baicalein, oroxylin A-7-O-glucuronide, wogonin-7-O-glucuronide, wogonin, and oroxylin A in Radix Scutellariae; naringin and neohesperidin in Aurantii fructus; liquiritigenin, liquiritin, and glycyrrhizic acid in Radix Glycyrrhizae. In LC/UV assay, a Cosmosil 5C18-MS-II column was used as the stationary phase, and a gradient of potassium dihydrogen phosphate, ACN, and water as the elute solution. The UV detection wavelengths were 250 and 280 nm. In LC/MS assay, a gradient of phosphoric acid, ACN, and water was used as the elute solution, and electrospray positive ion mode ((+)-ESI) as the analytic mode. In order to explore the distribution of trace metal elements effectively in Gan-Lu-Yin, a microwave digestion method was used for sample treatment, and an inductively coupled plasma MS assay was used to analyze fingerprint spectra of the inorganic metals in Gan-Lu-Yin. Combined with fingerprint spectra of organic compounds by LC/UV and LC/MS, it was expected to provide effective quality control in the production of Gan-Lu-Yin.

Chromatography, Liquid↗
PubMed2003

Proteome analysis of hairy root from Panax ginseng C.A. Meyer using peptide fingerprinting, internal sequencing and expressed sequence tag data.

As an initial step to the comprehensive proteomic analysis of Panax ginseng C. A. Meyer, protein mixtures extracted from the cultured hairy root of Panax ginseng were separated by two-dimensional polyacrylamide gel electrophoresis (2-DE). The protein spots were analyzed and identified by peptide finger printing and internal amino acid sequencing by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) and electrospray ionization quadrupole-time of flight mass spectrometry (ESI Q-TOF MS), respectively. More than 300 protein spots were detected on silver stained two-dimensional (2-D) gels using pH 3-10, 4-7, and 4.5-5.5 gradients. Major protein spots (159) were analyzed by peptide fingerprinting or de novo sequencing and the functions of 91 of these proteins were identified. Protein identification was achieved using the expressed sequence tag (EST) database from Panax ginseng and the protein database of plants like Arabidopsis thaliana and Oryza sativa. However, peptide mass fingerprinting by MALDI-TOF MS alone was insufficient for protein identification because of the lack of a genome database for Panax ginseng. Only 17 of the 159 protein spots were verified by peptide mass fingerprinting using MALDI-TOF MS whereas 87 out of 102 protein spots, which included 13 of the 17 proteins identified by MALDI-TOF MS, were identified by internal amino acid sequencing using tandem mass spectrometry analysis by ESI Q-TOF MS. When the internal amino acid sequences were used as identification markers, the identification rate exceeded 85.3%, suggesting that a combination of internal sequencing and EST data analysis was an efficient identification method for proteome analysis of plants having incomplete genome data like ginseng. The 2-D patterns of the main root and leaves of Panax ginseng differed from that of the cultured hairy root, suggesting that some proteins are exclusively expressed by different tissues for specific cellular functions. Proteome analysis will undoubtedly be helpful for understanding the physiology of Panax ginseng.

Databases, Protein↗
PubMed2004

Assessment of protein spot components applying correspondence analysis for peptide mass fingerprint data.

Proteins separated by two-dimensional gel electrophoresis (2-DE) may be distributed over several spots. Otherwise, one spot may contain more than one component. The same protein occurring in several spots supposedly represents differently modified protein species that might be of biological relevance. Identification of spots with peptide mass fingerprinting and database searching leads only to the detection of the major spot components. If a spot also contains additional minor protein components, quantitation of spots with protein staining techniques or antibody detection becomes misleading. In order to find spots containing minor components we applied correspondence analysis, a multivariate data exploration method, to peptide mass fingerprint data. Correspondence analysis using peak lists revealed groups of spots containing the same protein with their characteristic mass-to-charge ratio (m/z) values. In order to detect different protein spot components an interactive threshold setting and removal of m/z values with subsequent recalculation of the correspondence analysis using our software tool CorrAn are performed. The usefulness of this methodical approach was shown by a data set of peptide mass fingerprints of 284 spots of Helicobacter pylori 26695 separated by 2-DE.

Bacterial Proteins↗
PubMed2007

Prediction-based fingerprints of protein-protein interactions.

The recognition of protein interaction sites is an important intermediate step toward identification of functionally relevant residues and understanding protein function, facilitating experimental efforts in that regard. Toward that goal, the authors propose a novel representation for the recognition of protein-protein interaction sites that integrates enhanced relative solvent accessibility (RSA) predictions with high resolution structural data. An observation that RSA predictions are biased toward the level of surface exposure consistent with protein complexes led the authors to investigate the difference between the predicted and actual (i.e., observed in an unbound structure) RSA of an amino acid residue as a fingerprint of interaction sites. The authors demonstrate that RSA prediction-based fingerprints of protein interactions significantly improve the discrimination between interacting and noninteracting sites, compared with evolutionary conservation, physicochemical characteristics, structure-derived and other features considered before. On the basis of these observations, the authors developed a new method for the prediction of protein-protein interaction sites, using machine learning approaches to combine the most informative features into the final predictor. For training and validation, the authors used several large sets of protein complexes and derived from them nonredundant representative chains, with interaction sites mapped from multiple complexes. Alternative machine learning techniques are used, including Support Vector Machines and Neural Networks, so as to evaluate the relative effects of the choice of a representation and a specific learning algorithm. The effects of induced fit and uncertainty of the negative (noninteracting) class assignment are also evaluated. Several representative methods from the literature are reimplemented to enable direct comparison of the results. Using rigorous validation protocols, the authors estimated that the new method yields the overall classification accuracy of about 74% and Matthews correlation coefficients of 0.42, as opposed to up to 70% classification accuracy and up to 0.3 Matthews correlation coefficient for methods that do not utilize RSA prediction-based fingerprints. The new method is available at http://sppider.cchmc.org.

Artificial Intelligence↗
PubMed2001

Quantitative analysis and molecular species fingerprinting of triacylglyceride molecular species directly from lipid extracts of biological samples by electrospray ionization tandem mass spectrometry.

Herein we describe a rapid, simple, and reliable method for the quantitative analysis and molecular species fingerprinting of triacylglycerides (TAG) directly from chloroform extracts of biological samples. Previous attempts at direct TAG quantitation by positive-ion electrospray ionization mass spectrometry (ESI/MS) were confounded by the presence of overlapping peaks from choline glycerophospholipids requiring chromatographic separation of lipid extracts prior to ESI/MS analyses. By exploiting the rapid loss of phosphocholine from choline glycerophospholipids, in conjunction with neutral-loss scanning for individual fatty acids, overlapping peaks in the ESI mass spectrum were deconvoluted generating a detailed molecular species fingerprint of individual TAG molecular species directly from chloroform extracts of biological samples. This method readily detects as little as 0.1 pmol of each TAG molecular species from chloroform extracts and is linear over a 1000-fold dynamic range. The sensitivity of individual TAG molecular species to ESI/MS/MS analyses correlated with the unsaturation index and inversely correlated with total aliphatic chain length of TAG. An algorithm was developed which identifies sensitivity factors, thereby allowing the rapid quantitation and molecular species fingerprinting of TAG molecular species directly from chloroform extracts of biological samples.

Animals↗
PubMed1995

Identification and strain differentiation of 'Bacteroides fragilis group' species and Prevotella bivia by PCR fingerprinting.

Using single consensus primers of genomic nucleotide sequences, PCR-generated fingerprints were used for identification and differentiation of the Bacteroides fragilis group (B. fragilis, B. thetaiotaomicron, B. ovatus, B. distasonis, B. vulgatus) and Prevotella bivia (B. bivius) by comparing the DNA profiles with those of reference strains from the American Type Culture Collection and German Culture Collection. When primed by a single primer phage M13 core sequence, intra-species specific differences and species-specific bands were detected. Using primers derived from the evolutionarily conserved tRNA gene sequence, species-specific patterns were produced. A computer program, GelManager, was used to analyze the profiles and generate dendrograms. The correlation coefficients determined from the DNA fingerprint profiles of the clinical isolates (using the M13 core primer) fell within a narrow range, reflecting a high level of homology within the species. Based on the dendrograms, strains of one species were clearly differentiated from strains of other species. For comparison, SDS-PAGE analysis of whole cell extracts was also performed to obtain protein band patterns of various strains. Because of the simplicity of the PCR fingerprinting method and the ease of performance of computerized evaluation of data, this technique is a useful method for both species and strain differentiation, as well as for characterization of Bacteroides species and Prevotella bivia.

Journal Article↗
PubMed1997

RAPD fingerprinting for the distinction of Prevotella intermedia sensu stricto from Prevotella nigrescens.

A collection of 70 oral strains including reference strains and clinical isolates identified as Prevotella intermedia sensu lato was constituted to cover a large clinical and geographical diversity. Electrophoresis of the enzyme malate dehydrogenase allowed the identification of the 70 study strains as Prevotella intermedia sensu stricto (n= 36), Prevotella nigrescens (n= 31) and three unclassified strains. By using four primers, DNA fingerprints were generated from 20 strains as random amplified polymorphic DNA (RAPD). Matching co-migrating amplicon positions by pairwise comparison allowed the clustering of the fingerprints as two groups coincident with the P. intermedia/P. nigrescens assignment by enzyme electrophoresis of malate dehydrogenase. Our data suggest that isolates identified asP. intermedia sensu lato by conventional criteria can be speciated asP. intermedia sensu stricto or P. nigrescens by RAPD fingerprinting.

Journal Article↗
PubMed1981

Oligonucleotide fingerprinting of the RNA of different strains of infectious bronchitis virus.

11 distinct oligonucleotide fingerprints were obtained in studies of the RNA of 13 isolates of IBV. Different serotypes had distinct fingerprints, but so did varieties within a serotype; allowing a greater degree of strain differentiation than was previously possible. Some conclusions can be drawn from the fingerprints concerning theories of origin and spread of IBV.

Coronaviridae↗
PubMed1991

Leukoplakia of the cornea presenting as fingerprint epithelial lines: a case report.

Opacities in association with fingerprint patterns of the epithelium were seen in the upper half of the right cornea of a 52-year-old patient complaining of decreased vision. Removal of the corneal epithelium from the involved area resulted in visual improvement and normalization of corneal appearance. Histological examination of the removed epithelium failed to reveal the typical intraepithelial formation of basement membrane invaginations even in the areas corresponding to the fingerprint patterns. Moderate to severe degree of atypia were seen in the epithelial cells. No abnormalities were observed in 3 conjunctival specimens excised at the time of epithelial removal. The diagnosis of corneal dysplasia (leukoplakia) was made. Our report is the first description of epithelial fingerprint patterns of the cornea associated with leukoplakia.

Basement Membrane↗
PubMed1989

Demonstration of spontaneous XX/XY chimerism by DNA fingerprinting.

The M13 bacteriophage probe, which makes possible the establishment of DNA fingerprints, was used to study a phenotypically normal woman with a 46XY karyotype and her twin brother. Identical fingerprints and positive hybridization with a series of Y-specific probes were obtained on blood samples from the siblings. DNA from a skin biopsy of the woman yielded a clearly different pattern and displayed no Y-specific hybridization, indicating that she is a spontaneous chimera. This study illustrates the use of DNA fingerprinting as a powerful and simple aid to the diagnosis of natural chimerism.

Adult↗
PubMed1989

Probe walking: development of novel probes for DNA fingerprinting.

The tandem repeat of a 28-base-pair (bp) sequence downstream of the human c-Ha-ras-1 oncogene was studied as a probe for DNA fingerprinting. Multiple hypervariable patterns were observed by Southern hybridization at low stringency. The patterns were specific to individuals, indicating the availability of the 28-bp repeat as a probe for DNA fingerprinting. Moreover, we cloned the tandem repeat of a 33-bp sequence, which cross-hybridized with the 28-bp repeat. This 33-bp repeat detected another set of hypervariable restriction fragments by Southern hybridization at the same stringency. These results suggests that 'probe walking' can be employed to develop novel probes that provide different DNA fingerprints.

Blotting, Southern↗
PubMed1983

Restriction endonuclease DNA fingerprinting of respiratory, foetal and perinatal foal isolates of equine herpesvirus type 1.

DNA was prepared from 43 equine herpesvirus type 1 (EHV 1) isolates, 11 of which were from horses with respiratory disease, 22 from aborted equine foetuses, and 10 from foals that died perinatally. The restriction endonuclease DNA fingerprints of 10 of the 11 respiratory isolates, known with certainty to have been recovered from horses with respiratory disease, were entirely different from all but 3 of the 32 foetal or perinatal foal isolates. The exceptional respiratory isolate, EHV 1 Army 183, had a foetal (F) strain fingerprint but this virus cannot be said with certainty to have been isolated from the respiratory tract. The 3 exceptional foetal isolates, had respiratory (R) strain fingerprints, and were recovered from single sporadic abortions. There are no exceptions to the view that only R strains have been isolated from naturally occurring respiratory disease. Also it is clear that major epizootics of abortion (abortion storms) and of perinatal foal mortality are caused by F strains. The data together with an analysis of the epidemiological patterns, particularly in Australia, strongly support the view that F and R strains be regarded as separate species, EHV 1 and 4 respectively.

Abortion, Veterinary↗
PubMed2001

Molecular fingerprinting of bacterial populations in groundwater and bottled mineral water.

Monitoring the hygienic quality of drinking waters by determining the concentration of fecal indicators with traditional plate count techniques suffers from important drawbacks. In this work, the potential of PCR-DGGE (polymerase chain reaction - denaturing gradient gel electrophoresis) analysis of 16S rDNA genes to fingerprint the bacterial populations of mineral water and groundwater was investigated. A rapid and simple pretreatment to concentrate and release bacterial DNA prior to PCR was explored. This pretreatment was successful for commercially bottled mineral water. For groundwater, an additional resuscitation step was required to obtain a PCR signal. It was clear that the groundwater under scrutiny contained a more diverse bacterial community than the mineral water. A comparison was made between four kinds of mineral waters and one sample of groundwater using the developed procedures. For each kind of water, bacterial populations cultured on R2A plates were also subjected to PCR-DGGE. Comparison of the fingerprints of the plated samples and the original samples suggested the presence of viable but nonculturable bacteria in the waters. The obtained cluster dendrogram indicated that each kind of water was characterized by a specific molecular fingerprint. The sensitivity of the whole of the procedure was between 10(4) and 10(5) cfu ml(-1) as determined using a pure culture of Escherichia coli. The described PCR-DGGE method can constitute the basis of a new and interesting strategy to monitor in a relatively rapid way (less than 24 h) the bacterial quality of waters such as mineral water, groundwater and certain types of reclaimed water.

Beverages↗
PubMed1996

Rearrangements at a DNA-fingerprint locus in the rice blast fungus.

Populations of the rice blast fungus, Magnaporthe grisea, can be sorted into clonal lineages based on restriction fragment length polymorphisms (RFLPs) detected with the repetitive DNA sequence MGR586. Mechanisms that produce DNA-fingerprint variation among lineages, are not known. In the process of analyzing the meiotic segregation of MGR586 RFLPs we identified a novel polymorphism, called MGR586-P2, in one member of a sister-spore pair from a complete tetrad. Molecular cloning revealed that P2 was generated by a nearby insertion of a novel, long-terminal-repeat (LTR)-containing retrotransposon. Genetic analysis showed that P2 and its progenitor polymorphism (P1) are alleles of a single polymorphic locus termed MGR586-PL (PL). Surprisingly, we found that a strain harboring PL recurrently produced clonal descendants harboring P1, P2 and possibly a third allele designated P3. PL is not located near a telomeric region. Our results show that some DNA-fingerprint loci may be hypervariable and undergo recurrent rearrangements. These findings have implications for interpreting DNA-fingerprint profiles from M. grisea populations.

Ascomycota↗
PubMed1990

Differential diagnosis between complete mole and hydropic abortus by deoxyribonucleic acid fingerprints.

We used a new method of deoxyribonucleic acid fingerprint analysis to obtain the differential diagnosis between complete mole and hydropic abortus. This method with a deoxyribonucleic acid minisatellite probe requires only a small amount of tissue sample and peripheral blood, and presents individual specific restriction fragment length polymorphisms (deoxyribonucleic acid "fingerprints") by simultaneous detection of many hypervariable regions (minisatellite regions) widely dispersed in the human genome. Southern blot hybridization showed that in cases of complete mole, all polymorphic fragments were exclusively inherited from the father. Some of the polymorphic bands of paternal deoxyribonucleic acid were not observed in molar deoxyribonucleic acid. However, in the hydropic abortus, the polymorphic fragments could be traced back to its parent. These results indicate that deoxyribonucleic acid fingerprints could distinguish the abnormal fertilization of complete mole (androgenesis) from the normal fertilization of hydropic abortus by identifying the difference in genetic variations between complete mole and hydropic abortus at the deoxyribonucleic acid level.

Blotting, Southern↗