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PubMed1969

Epidemiological fingerprinting of Pseudomonas aeruginosa by the production of and sensitivity of pyocin and bacteriophage.

A new method has been devised to trace cross-infection by Pseudomonas aeruginosa. Unknown strains growing logarithmically in liquid media were treated with mitomycin C to induce the liberation of pyocin and phage. The lysates were then tested against 27 selected indicator strains, and the zones of clearing were differentiated as to killing by pyocin or lysis by phage. Twenty-four standard pyocin-phage lysates were then applied to each of the unknowns, and the sensitivity pattern was recorded. Thus, an "epidemiological fingerprint" consisting of 51 operational characteristics was established for each isolate. Organisms from the same source had identical or similar fingerprints, but organisms from different origins could easily be distinguished. Pyocin production, pyocin sensitivity, and phage production were found to be stable genetic characters; however, spontaneous mutations in phage sensitivity were frequently encountered. The epidemiological fingerprint has proven to be a sensitive tool in establishing the identity or dissimilarity of unknown strains. This method has been of great value in tracing the epidemiology of P. aeruginosa in the hospital environment. Each of the 157 P. aeruginosa strains tested has been typable by this method.

Bacteriocins↗
PubMed1981

Oligonucleotide fingerprinting of ribonucleic acids of infectious bronchitis virus strains.

A total of 11 distinct oligonucleotide fingerprints were obtained in studies of the ribonucleic acids of 13 isolates of infectious bronchitis virus. 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 infectious bronchitis virus.

Coronaviridae↗
PubMed1989

Hypervariable DNA fingerprinting in Escherichia coli: minisatellite probe from bacteriophage M13.

Extensive restriction-fragment-length polymorphism was revealed in Escherichia coli strains by using a region of the bacteriophage M13 genome as a DNA hybridization probe. This variation was observed across natural strains, in clinical samples, and to a lesser extent in laboratory strains. The sequence in M13 which revealed this fingerprint pattern was a region of the gene III coat protein, which contains two clusters of a 15-base-pair repeat. Oligonucleotides made to a consensus of these repeats also revealed the fingerprint profile. While this consensus sequence has significant homology to the lambda chi site sequence, an oligonucleotide made of the chi sequence did not reveal polymorphic fingerprint patterns in E. coli. The strain variation revealed by the M13 and M13-derived oligonucleotide probes will be useful for bacterial characterization and should find use in studies of bacterial evolution and population dynamics. The findings raise questions about what these repeated sequences are and why they are so variable.

Biological Evolution↗
PubMed1986

An outbreak of group B meningococcal disease: tracing the causative strain of Neisseria meningitidis by DNA fingerprinting.

Following an outbreak of meningococcal disease in three schoolchildren in a small community in northern Norway, DNA fingerprinting, serotyping with monoclonal antibodies, serogrouping, and sulfonamide sensitivity testing were applied for characterization and tracing of the causative agent. The three case isolates were genomically indistinguishable, sulfonamide-resistant, serogroup B, serotype 15 meningococci. Throat specimens were collected from 552 healthy contacts, including all children below age 17 and their parents. Among the 36 carrier isolates (carrier rate, 6.5%) 13 showed DNA fingerprints identical, or almost identical, to the index pattern. All of these 13 isolates were sulfonamide resistant, 12 were of serotype 15, and 8 were of polysaccharide serogroup B (5 were nongroupable). These closely related isolates were almost exclusively recovered from schoolchildren of 2 of 15 small villages, one of which included the homes of two of the patients. The remaining 23 carrier isolates were nonresistant, non-type 15 meningococci of widely differing DNA restriction patterns. Our results confirm that DNA fingerprinting has potential as an efficient tool in practical meningococcal epidemiology.

Adolescent↗
PubMed1988

Genome fingerprinting of Pseudomonas aeruginosa indicates colonization of cystic fibrosis siblings with closely related strains.

The epidemiology of Pseudomonas aeruginosa infection at a cystic fibrosis (CF) center was monitored over a 3-year period. A total of 835 isolates from 72 unrelated patients and 22 siblings with CF were analyzed by genome fingerprinting and serotyping, bacteriophage typing, and pyocin typing. For genome fingerprinting, bacterial chromosomes were digested with one of the restriction endonucleases SpeI, DraI, XbaI, SspI, and NheI, which cut only rarely, and subsequently separated by field inversion gel electrophoresis. The physical genome analysis allowed us to classify P. aeruginosa strains in terms of DNA relatedness. Related strains differed by fewer than six DraI bands in the fingerprint, whereas unrelated strains differed by more than 20 DraI bands. All unrelated CF patients were colonized with different strains. The absence of a nosocomial spread of organisms at the CF center was attributed to the strict hygiene measures observed at the hospital. CF siblings were harboring either identical or closely related strains; transmission within the family is thought to be the most likely cause.

Bacteriophage Typing↗
PubMed1990

Characterization of prototype and clinically defined strains of Streptococcus suis by genomic fingerprinting.

A collection of Streptococcus suis strains from animal and human infections was examined for DNA-banding patterns after restriction endonuclease digestion and agarose gel electrophoresis. The endonuclease HaeIII produced the most discriminating restriction profiles among 23 serotypes studied. DNA from serotypes 9, 11, 12, and 16 was resistant to HaeIII cleavage. DNA from serotypes 9 through 16 was cleaved with HindIII and showed substantial genomic differences. We also examined 106 epidemiologically unrelated strains isolated from cases of pig meningitis or pneumonia and 5 strains isolated from cases of human meningitis in order to compare genomic fingerprinting and serotyping as epidemiological tools. Heterogeneity was found among fingerprints of serologically identical isolates, indicating genetic diversity within some serotypes. DNA fingerprints of some serotype 2 strains from different sources appeared identical, suggesting a clonal relationship among strains of this serotype. The data suggest that this technique represents an important tool for examining the natural history of disease caused by S. suis.

Animals↗
PubMed1978

Extraction and fingerprint analysis of simian virus 40 large and small T-antigens.

A study of simian virus 40 (SV40) T-antigens isolated from productively infected CV1 cells using a variety of different extraction procedures showed that under some conditions the highest molecular weight form of T-Ag (large-T) isolated comigrated on sodium dodecyl sulfate-polyacrylamide gel electrophoresis with large-T from SV40-transformed H65-90B cells. Other faster-migrating forms of large-T are probably generated during the extraction procedure by a protease which is active at low pH, and such forms are probably experimental artifacts. After extraction under conditions which minimize proteolytic degradation of large-T, a further form of T-antigen was isolated; this has an apparent molecular weight in the range 15,000 to 20,000 and is referred to as small-t. Fingerprint analysis of [35S]methionine-labeled SV40 proteins showed that small-t has 10 to 12 methionine peptides whereas large-T has 15 to 18 methionine peptides. All but two of the methionine tryptic peptides present in small-t are also present in large-T. The fingerprint data also showed that T-antigens have no peptides in common with SV40 VP1. Experiments using reagents which inhibit posttranslational cleavage of encephalomyocarditis virus polyproteins showed that these reagents do not affect the synthesis of small-t and suggest that it is not made by proteolytic cleavage of large-T in vivo. An alternative model, which proposes that large-T and small-t are synthesized independently, is discussed in terms of the fingerprint data and the number of methionine tryptic peptides predicted from the primary sequence of SV40 DNA.

Antigens, Neoplasm↗
PubMed2003

Childhood constipation is not associated with characteristic fingerprint patterns.

BACKGROUND: It has been suggested that there is an association between simple arch fingerprint patterns and severe childhood constipation. If real, this association might be useful to predict which children have a poor prognosis. AIM: To see how many severely constipated children have simple arches, compared to non-constipated controls and their first degree relatives. METHODS: Fingerprints were classified by two blinded assessors in 30 children requiring surgery for refractory constipation, and 30 children with appendicitis, and the first degree relatives of both groups. Colonic transit times and clinical outcomes were also evaluated among constipated children. RESULTS: At least one simple arch was found in similar numbers of constipated children (13%) and their families (16%), and control children (7%) and their families (13%). Arch positivity was commoner among relatives of arch positive (6/6) than arch negative children (14/54), regardless of bowel history. Arch positivity did not identify children with prolonged transit times, nor those who required colectomy. CONCLUSIONS: Fingerprint patterns are not associated with severe childhood constipation, do not aid their management, and do not support a genetic aetiology for this problem.

Child↗
PubMed1981

Prevalence of map-dot-fingerprint changes in the cornea.

Map-dot-fingerprint basement-membrane abnormalities of the cornea are common in the general population, affecting as many as 76% of persons over age 50 and 42% of persons of all ages. The prevalence of this condition in the general population is not significantly different from that found in families of patients with recurrent corneal erosions and map-dot-fingerprint corneal changes. Despite this extremely high prevalence of basement-membrane changes the incidence of recurrent erosive symptoms in total groups of patients with basement-membrane changes is quite rare, suggesting that these 2 entities are possibly not related. Although previous observers have suggested an autosomal dominant mode of inheritance of these basement-membrane changes, our data raise the possibility that map-dot-fingerprint basement-membrane changes represent an age-dependent, degenerative condition of the cornea. We were unable, however, to prove either hypothesis.

Adolescent↗
PubMed2004

Evaluation of AFLPs for germplasm fingerprinting and assessment of genetic diversity in cultivars of tomato (Lycopersicon esculentum L.).

Cultivated tomato (L. esculentum L.) germplasm exhibits limited genetic variation compared with wild Lycopersicon species. Amplified fragment length polymorphism (AFLP) markers were used to evaluate genetic variation among 74 cultivars, primarily from California, and to fingerprint germplasm to determine if cultivar-specific patterns could be obtained. All 74 cultivars were genotyped using 26 AFLP primer combinations; of the 1092 bands scored, 102 AFLP bands (9.3%) were polymorphic. Pair-wise genetic similarity coefficients (Jaccard and Nei-Li) were calculated. Jaccard coefficients varied from 0.16 to 0.98 among cultivar pairs, and 72% of pair-wise comparisons exceeded 0.5. UPGMA (unweighted pair-group method with arithmetic averaging) clustering and principle component analysis revealed four main clusters, I-IV; most modern hybrid cultivars grouped in II, whereas most vintage cultivars grouped in I. Clusters III and IV contained three and two cultivars, respectively. Some groups of cultivars closely related by pedigree exhibited high bootstrap values, but lower values (<50%) were obtained for cluster II and its four subgroups. Unique fingerprints for all 74 cultivars were obtained by a minimum of seven AFLP primer pairs, despite inclusion of some closely related cultivars. This study demonstrated that AFLP markers are effective for obtaining unique fingerprints of, and assessing genetic diversity among, tomato cultivars.

Base Sequence↗
PubMed2000

Searching for molecules with similar biological activity: analysis by fingerprint profiling.

We have recently developed a mini-fingerprint (MFP) representation for small molecules that performs well in database searches for compounds with similar biological activity. The MFP consists of only 54 bit positions that account for numerical ranges of three two-dimensional (2D) descriptors or the presence or absence of defined structural fragments. Here we present an analysis method, termed fingerprint profiling, to systematically compare bit patterns of compounds belonging to different biological activity classes. Some but not all bit positions were variably occupied in seven different activity classes and responsible for the detection of structure-activity differences. The analysis has made it possible to rank bit positions and encoded molecular descriptors according to their importance for our similarity search calculations. Fingerprint profiling can be applied to any keyed bit string representation and should be helpful, for example, to analyze descriptor distributions in large compound databases.

Computer-Aided Design↗
PubMed2003

Fingerprint matching using recurrent autoassociative memory.

An efficient method for fingerprint searching using recurrent autoassociative memory is proposed. This algorithm uses recurrent autoassociative memory, which uses a connectivity matrix to find if the pattern being searched is already stored in the database. The advantage of this memory is that a big database is to be searched only if there is a matching pattern. Fingerprint comparison is usually based on minutiae matching, and its efficiency depends on the extraction of minutiae. This process may reduce the speed, when large amount of data is involved. So, in the proposed method, a simple approach has been adopted, wherein first determines the closely matched fingerprint images, and then determines the minutiae of only those images for finding the more appropriate one. The gray level value of pixels along with its neighboring ones are considered for the extraction of minutiae, which is more easier than using ridge information. This approach is best suitable when database size is large.

Algorithms↗
PubMed2002

Randomly Amplified DNA Fingerprinting: A Culmination of DNA Marker Technologies Based on Arbitrarily-Primed PCR Amplification.

Arbitrarily-primed DNA markers can be very useful for genetic fingerprinting and for facilitating positional cloning of genes. This class of technologies is particularly important for less studied species, for which genome sequence information is generally not known. The technologies include Randomly Amplified Polymorphic DNA (RAPD), DNA Amplification Fingerprinting (DAF), and Amplified Fragment Length Polymorphism (AFLP). We have modified the DAF protocol to produce a robust PCR-based DNA marker technology called Randomly Amplified DNA Fingerprinting (RAF). While the protocol most closely resembles DAF, it is much more robust and sensitive because amplicons are labelled with either radioactive 33P or fluorescence in a 30-cycle PCR, and then separated and detected on large polyacrylamide sequencing gels. Highly reproducible RAF markers were readily amplified from either purified DNA or alkali-treated intact leaf tissue. RAF markers typically display dominant inheritance. However, a small but significant portion of the RAF markers exhibit codominant inheritance and represent microsatellite loci. RAF compares favorably with AFLP for efficiency and reliability on many plant genomes, including the very large and complex genomes of sugarcane and wheat. While the two technologies detect about the same number of markers per large polyacrylamide gel, advantages of RAF over AFLP include: (i) no requirement for enzymatic template preparation, (ii) one instead of two PCRs, and (iii) overall cost. RAF and AFLP were shown to differ in the selective basis of amplification of markers from genomes and could therefore be used in complementary fashion for some genetic studies.

Journal Article↗
PubMed2004

Somatic mutations in stilbene estrogen-induced Syrian hamster kidney tumors identified by DNA fingerprinting.

Kidney tumors from stilbene estrogen (diethylstilbestrol)-treated Syrian hamsters were screened for somatic genetic alterations by Random Amplified Polymorphic DNA-polymerase chain-reaction (RAPD-PCR) fingerprinting. Fingerprints from tumor tissue were generated by single arbitrary primers and compared with fingerprints for normal tissue from the same animal, as well as normal and tumor tissues from different animals. Sixty one of the arbitrary primers amplified 365 loci that contain approximately 476 kbp of the hamster genome. Among these amplified DNA fragments, 44 loci exhibited either qualitative or quantitative differences between the tumor tissues and normal kidney tissues. RAPD-PCR loci showing decreased and increased intensities in tumor tissue DNA relative to control DNA indicate that loci have undergone allelic losses and gains, respectively, in the stilbene estrogen-induced tumor cell genome. The presence or absence of the amplified DNA fragments indicate homozygous insertions or deletions in the kidney tumor DNA compared to the age-matched normal kidney tissue DNA. Seven of 44 mutated loci also were present in the kidney tissues adjacent to tumors (free of macroscopic tumors). The presence of mutated loci in uninvolved (non-tumor) surrounding tissue adjacent to tumors from stilbene estrogen-treated hamsters suggests that these mutations occurred in the early stages of carcinogenesis. The cloning and sequencing of RAPD amplified loci revealed that one mutated locus had significant sequence similarity with the hamster Cyp1A1 gene. The results show the ability of RAPD-PCR to detect and isolate, in a single step, DNA sequences representing genetic alterations in stilbene estrogen-induced cancer cells, including losses of heterozygosity, and homozygous deletion and insertion mutations. RAPD-PCR provides an alternative molecular approach for studying cancer cytogenetics in stilbene estrogen-induced tumors in humans and experimental models. Although the exact functional importance of mutated loci is unknown, this study indicates that these altered loci may participate during tumor progression in the kidney.

Journal Article↗
PubMed1999

Evidence for genetic transmission of thyroid peroxidase autoantibody epitopic "fingerprints".

Autoimmune thyroid disease is characterized by the tendency to cluster in families and by IgG class autoantibodies to antigens such as thyroid peroxidase (TPO). The epitopes recognized by polyclonal serum autoantibodies can be quantitatively fingerprinted using four recombinant human TPO autoantibodies (expressed as Fab) that define A and B domain epitopes in an immunodominant region. To determine whether these fingerprints are genetically transmitted, we analyzed fingerprints of 63 members of 7 multiplex Old Order Amish families and 17 individuals from 4 Hashimoto thyroiditis families. Inhibition of serum autoantibody binding to [125I]TPO by the recombinant Fab was used to assess recognition of the TPO immunodominant region (4 Fab combined) and recognition of domain A or B (individual Fab). Complex segregation analysis was performed using a unified model (POINTER). For the 4 Fab combined inhibition phenotype, the no transmission model was rejected (chi2(4) = 20.67; P < 0.0032), and the most parsimonious model includes a major gene effect. More importantly, evidence for genetic transmission was obtained for the phenotype defined by the ratio of inhibition by subdomain Fab B1:B2. Thus, for this ratio (reflecting recognition of the B domain), the no transmission model was rejected chi2(4) = 63.59; P < 0.000008). Moreover, the polygenic hypothesis could be rejected, but not the major locus hypothesis, suggesting that major genes might be involved in familial transmission of this trait. In conclusion, our findings suggest that autoantibody recognition of the TPO immunodominant region and the TPO B domain is genetically transmitted. These data may open the way to the identification by candidate analysis or positional cloning of at least one gene responsible for the development of Hashimoto's thyroiditis.

Autoantibodies↗
PubMed2005

Establishment of HPLC-DAD-MS fingerprint of fresh Houttuynia cordata.

A HPLC-DAD-MS fingerprint method of fresh Houttuynia cordata THUNB. was developed basing on the consistent chromatographic features among 11 batches of authentic samples. Major chemical components including phenolic compounds, flavones and alkaloids were simultaneously analyzed. Eleven common peaks in the fingerprint were chosen and identified by comparing their UV and ESI-MS data with the authentic compounds. The unique properties of this HPLC-DAD-MS fingerprint were successfully applied to analyze and differentiate samples from different geographical origins, processing methods and various medicinal parts of H. cordata. The results showed that these variations will give rise to differences in identities and/or abundance of chemical compounds, indicating that a comprehensive quality evaluation of those major ingredients in H. cordata is critical to assess and represent its overall quality.

China↗
PubMed2006

Chemical fingerprinting of Shexiang Baoxin Pill and simultaneous determination of its major constituents by HPLC with evaporative light scattering detection and electrospray mass spectrometric detection.

High-performance Liquid Chromatography (HPLC) with evaporative light scattered detection (ELSD) and electrospray ionization mass spectrometric detection (ESI-MS) was employed to establish chemical fingerprint of Shexiang Baoxin Pill (SBP) and to simultaneously determinate its seven major constituents, including cholic acid, deoxycholic acid, ursodeoxycholic acid, chenodeoxycholic acid, cinobufagin, recibufogenin, and ginsenoside Rb1. The analysis was performed on a C18 column with water-acetonitrile gradient elution, and the investigated constituents were authenticated by comparing their retention times and mass spectra with those of reference compounds. The proposed method was applied to analyze nine SBP samples and produced data with acceptable linearity, precision, stability and accuracy. Both the chemical fingerprints and quantification data were used to evaluate the quality of various SBP products. The proposed method allows obtaining chemical fingerprint and quantification of multi-components in one run, and therefore can be readily utilized as a comprehensive quality control approach for traditional Chinese medicine.

Chromatography, High Pressure Liquid↗
PubMed2006

Differentiation of rhizoma et radix polygoni cuspidati from closely related herbs by HPLC fingerprinting.

An HPLC-DAD fingerprinting profile of Rhizoma Et Radix Polygoni Cuspidati was established basing on the consistent chromatographic features of 24 authentic herb samples. The major types of chemical constituents, stilbenes and anthraquinones, were analyzed and included in the fingerprint. Eight common peaks of Polygonum Cuspidatum were identified by using HPLC-MS. The developed fingerprint was applied to differentiate Rhizoma Et Radix Polygoni Cuspidati from Radix Polygoni Multiflori and Radix Et Rhizoma Rhei. Although the three herbs belong to the family of Polygonaceae, the results indicated that these could be differentiated by using the established method.

Chromatography, High Pressure Liquid↗