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PubMed2026

CamK-DB: A k-mer MinHash fingerprint database for reference-free genotyping of Camellia accessions.

Tea (Camellia sinensis L.), a major global economic crop in Asia, poses challenges for genetic identification because its highly heterozygous, repetitive genome reduces the efficacy of conventional single-nucleotide polymorphism (SNP) and microsatellite markers, and interspecific hybridization further complicates the situation. To address these issues, CamK-DB was developed as a reference-free Camellia fingerprinting database built on MIKE MinHash sketches. We curated 418 candidate resequencing datasets, and built a database using standardized 5× genome-coverage fingerprints. Each accession is stored as a MIKE. jac fingerprint generated with k = 21 and recommended sketch/pre_cnt = 2000. CamK-DB provides a command-line interface for data management and a custom C++ query engine that computes top-10 matches using Jaccard similarity, complemented by a QT-based graphical interface for interactive analysis. This resource offers a robust and scalable framework for precise and routine germplasm identification, genomic phylogenetic inference, and strategic breeding program design. CamK-DB (database and code) is publicly available at https://github.com/sc-zhang/CamK-DB. CamK-DB binaries are provided for Windows 10/11 and Linux (x86_64, glibc ≥ 2.27).

Databases, Genetic↗

PubMed1987

DNA fingerprinting of Streptococcus zooepidemicus (Lancefield group C) as an aid to epidemiological study.

A collection of Streptococcus zooepidemicus strains from human and animal infections was examined for DNA banding patterns after nuclease digestion and agarose gel electrophoresis. The large variety of DNA fingerprints found revealed the complexity of the species but showed that isolates from clusters of outbreaks had identical prints. The results confirmed the specificity of bacteriocin and bacteriophage typing of S. zooepidemicus; the technique also gave useful profiles on untypable strains. Strains with common bacteriocin and biotyping patterns from sporadic infections could be differentiated by their DNA fingerprints. In several outbreaks and incidents, more than one strain of S. zooepidemicus were encountered, and the importance of carefully interpreting typing data is stressed. Chromosomal DNA fingerprinting is a very efficient technique for demonstrating differences between strains of S. zooepidemicus, and its use is recommended for future epidemiological studies of this infectious agent.

Animals↗

PubMed2005

Genome physical mapping from large-insert clones by fingerprint analysis with capillary electrophoresis: a robust physical map of Penicillium chrysogenum.

Physical mapping with large-insert clones is becoming an active area of genomics research, and capillary electrophoresis (CE) promises to revolutionize the physical mapping technology. Here, we demonstrate the utility of the CE technology for genome physical mapping with large-insert clones by constructing a robust, binary bacterial artificial chromosome (BIBAC)-based physical map of Penicillium chrysogenum. We fingerprinted 23.1x coverage BIBAC clones with five restriction enzymes and the SNaPshot kit containing four fluorescent-ddNTPs using the CE technology, and explored various strategies to construct quality physical maps. It was shown that the fingerprints labeled with one or two colors, resulting in 40-70 bands per clone, were assembled into much better quality maps than those labeled with three or four colors. The selection of fingerprinting enzymes was crucial to quality map construction. From the dataset labeled with ddTTP-dROX, we assembled a physical map for P.chrysogenum, with 2-3 contigs per chromosome and anchored the map to its chromosomes. This map represents the first physical map constructed using the CE technology, thus providing not only a platform for genomic studies of the penicillin-producing species, but also strategies for efficient use of the CE technology for genome physical mapping of plants, animals and microbes.

Chromosomes, Artificial, Bacterial↗

PubMed1989

DNA fingerprints from hypervariable mitochondrial genotypes.

Conventional surveys of restriction-fragment polymorphisms in mitochondrial DNA of menhaden fish (Brevoortia tyrannus/patronus complex) and chuckwalla lizards (Sauromalus obesus) revealed exceptionally high levels of genetic variation, attributable to differences in mtDNA size as well as in restriction sites. The observed probabilities that any two randomly drawn individuals differed detectably in mtDNA genotype were 0.998 and 0.983 in the two species, respectively. Thus, the variable gel profiles provided unique mtDNA "fingerprints" for most conspecific animals assayed. mtDNA fingerprints differ from nuclear DNA fingerprints in several empirical respects and should find special application in the genetic assessment of maternity.

Animals↗

PubMed2006

Long-term results of phototherapeutic keratectomy for corneal map-dot-fingerprint dystrophy (Cogan-Guerry).

PURPOSE: Patients with corneal map-dot-fingerprint dystrophy suffer typically from recurrent corneal erosion, disturbed vision, or both. The purpose of this study was to assess the morphologic and functional long-term results of minimal invasive subepithelial phototherapeutic keratectomy (PTK) for corneal map-dot-fingerprint dystrophy. METHODS: Of a total of 390 PTKs performed between October 1994 and January 2004, 15 PTKs on 15 eyes of 11 patients were included in this single-center study. All patients had symptoms of recurrent corneal erosion; in 12 eyes, reduced visual acuity was observed. The median duration of complaints was 18 months. Using 193-nm excimer laser (MEL 60/70; Carl Zeiss-Meditec), a manually guided spot profile was applied in 7 cases (pulse energy, 12 mJ; repetition rate, 2/s or 3/s; 189-425 pulses). In 8 cases, a scanning slit mode was chosen (intended ablation, 1 microm/scan; repetition rate, 20/s; 150-483 pulses). In each case, a broad deepithelialization of the Bowman layer was followed by application of defocused overlapping laser pulses. RESULTS: Complete epithelial closure was achieved after an average of 3.5 +/- 0.6 days (median, 3 days). The mean follow-up was 4.8 +/- 3.0 years, with a maximum of 9.3 years. Best corrected visual acuity increased from 0.7 +/- 0.26 preoperatively to 0.9 +/- 0.16 postoperatively. The keratometric central power remained constant (preoperatively, 43.0 +/- 1.6 D; postoperatively, 42.6 +/- 1.0 D). The average keratometric astigmatism remained constant (1.3 +/- 0.9 D, preoperatively; 1.0 +/- 0.5 D, postoperatively). In the early postoperative stage, subtle superficial corneal opacities ("haze") were observed in 6 eyes (40%), being completely reversible during the follow-up in 5 cases. No recurrence of corneal erosion was observed during the follow-up. Asymptomatic dystrophic signs in the midperiphery became visible in 2 eyes 3 and 5 years after PTK. CONCLUSION: For corneal map-dot-fingerprint dystrophy, PTK using an excimer laser with low pulse energy and low number of pulses can be considered an effective and minimal invasive treatment modality to achieve a fast and durable epithelial closure, to prevent recurrent corneal erosions, and to increase visual acuity in most patients.

Adult↗

PubMed1992

Evaluation of the PhP system for biochemical-fingerprint typing of strains of Salmonella of serotype Typhimurium.

The Phene Plate (PhP) system of biochemical fingerprinting of bacteria is a computerised typing system, based on quantitative measurements of the kinetics of several biochemical reactions of bacteria grown in liquid medium in microtitration plates. For each isolate tested, it yields a biochemical fingerprint comprising several kinds of quantitative data which are useful for establishing similarities among strains with a personal-computer program. In this study, a set of 16 specific substrates was chosen to differentiate strains of Salmonella of serotype Typhimurium. The system was evaluated for its typability, reproducibility and discriminatory power in tests with a collection of 100 epidemiologically unrelated Typhimurium strains and results were compared with those obtained by phage typing. At an identity level of 0.980, strains were assigned by this method to 51 biochemical phenotypes (BPTs), giving a diversity index of 0.963 and a resolution index of 0.210. In contrast, 24 phage types (PTs) were identified among these isolates (a diversity index of 0.901). The combined use of biochemical fingerprinting by the PhP system and phage typing discriminated 82 phenotypes (a diversity index of 0.994). Stability of markers in each of the methods was also evaluated after subculture of 20 strains for 21 consecutive days. Only nine biochemical reactions were found that were subject to small, but measurable, changes for at least one isolate. These changes slightly decreased the mean similarity coefficients among strains but the overall BPTs of the strains showed changes in four strains (20%). In contrast, eight strains (40%) showed changes in their PTs after this treatment. It is concluded that the PhP system is a highly discriminatory and reproducible method for typing Typhimurium strains. It is easy to perform, and may be used alone or in combination with phage typing in epidemiological studies of Typhimurium strains.

Bacterial Typing Techniques↗

PubMed1995

Attenuated typhoid vaccine Salmonella typhi Ty21a: fingerprinting and quality control.

Live attenuated vaccines, developed with molecular genetical techniques, require new approaches for their quality control. To develop novel quality control tests that enhanced and extended existing procedures, the attenuated vaccine strain Salmonella typhi Ty21a and its parent strain Ty2 were characterized by pulsed-field gel electrophoresis (PFGE) and direct nucleotide sequence analysis. Mutant and parent strains were distinguished using fingerprints generated by the resolution on PFGE of chromosomal DNA digested with each of the enzymes SfiI, SpeI or XbaI. These fingerprints were stable through multiple in vitro passages of the vaccine strain and were identical from one batch of vaccine to another. It was also possible to distinguish between the mutant and parent strains by direct nucleotide sequence analysis of the galE gene. This analysis identified two base changes in the gene from strain Ty21a: a single base deletion causing a frameshift that would result in a truncated gene product, accounting for the galE phenotype; and a transition that eliminated an AluI restriction site. The consequent change in the AluI fingerprint of the galE gene in strain Ty21a provided a rapid, PCR-based alternative to the use of differential media or biochemical assays for the identification of the vaccine strain.

Amino Acid Sequence↗

PubMed2002

Latent fingerprint detection with SYPRO Rose Plus Protein Blot Stain.

Lanthanide complexes are employed in photoluminescence detection of fingerprints because their long luminescence lifetimes allow use of time-resolved imaging techniques to suppress problematic background fluorescence. To date, however, these complexes have been unsuccessful when used in developing old fingerprints on porous substrates. SYPRO Rose Plus Protein Blot Stain remedies this shortcoming; it lends itself to smooth surfaces as well, thus having potential as a universal fingerprint reagent.

Coloring Agents↗

PubMed2005

Fingerprinting protocol for images based on additive homomorphic property.

Homomorphic property of public-key cryptosystems is applied for several cryptographic protocols, such as electronic cash, voting system, bidding protocols, etc. Several fingerprinting protocols also exploit the property to achieve an asymmetric system. However, their enciphering rate is extremely low and the implementation of watermarking technique is difficult. In this paper, we propose a new fingerprinting protocol applying additive homomorphic property of Okamoto-Uchiyama encryption scheme. Exploiting the property ingenuously, the enciphering rate of our fingerprinting scheme can be close to the corresponding cryptosystem. We study the problem of implementation of watermarking technique and propose a successful method to embed an encrypted information without knowing the plain value. The security can also be protected for both a buyer and a merchant in our scheme.

Algorithms↗

PubMed2006

Fingerprint recognition using model-based density map.

Utilizing more information other than minutiae is much helpful for large-scale fingerprint recognition applications. In this paper, we proposed a polynomial model to approximate the density map of fingerprints and used the model's parameters as a novel kind of feature for fingerprint representation. Thus, the density information can be utilized into the matching stage with a low additional storage cost. A decision-level fusion scheme is further used to combine the density map matching with conventional minutiae-based matching and experimental results showed a much better performance than using single minutiae-based matching.

Algorithms↗

PubMed1997

Studies of polymorphic DNA fingerprinting and lipid pattern of Mycobacterium tuberculosis patient isolates in Japan.

Strain differentiation by DNA restriction fragment length polymorphism (RFLP) has been used mainly for the epidemiological purpose of Mycobacterium tuberculosis infection. In this study, we tried to connect the molecular and phenotypic characteristics of M. tuberculosis patient isolates by comparing the DNA fingerprints obtained by RFLP using IS6110 and lipid patterns using two-dimensional thin-layer chromatography (2-D TLC) with silica gel, since M. tuberculosis has a lipid-rich cell envelope which contributes to the virulence and immunomodulatory properties. We found that 66 isolates of M. tuberculosis from tuberculosis patients showed that the occurrence of IS6110 varied from 1 to 24 copies. The IS6110 patterns were highly variable among isolates. Fifty different RFLP patterns were observed, and 12 RFLP patterns were shared by two or more strains. By computerized analysis of the RFLP patterns of M. tuberculosis patient isolates, we found that 95% of the isolates fell into seven clusters, from A to G, with at least two isolates in each (> 30% similarity). Among the cellular lipids, the phospholipid composition did not differ by strain, whereas the glycolipid pattern differed markedly. Especially, the relative concentration of cord factor and sulfolipid, both of which were known as virulent factors, varied by strain. The fingerprints of some strains showed an association between the DNA and glycolipid patterns, even though some of the same DNA fingerprint strains showed differences in lipid patterns. Among the patient isolates, M. tuberculosis strain 249 possessed a specific glycolipid with 2-O-methyl-L-rhamnose and L-rhamnose, which is rarely found in other strains. This glycolipid showed serological activity against the sera of tuberculosis patients, even if the reactivity was not as strong as trehalose dimycolate. It also showed the inhibition of phagosome-lysosome fusion in macrophages, suggesting involvement with virulence. These results suggest that RFLP analysis using IS6110 is useful for clustering the human isolates of M. tuberculosis, however, for further strain differentiation on virulence, a lipid analysis provides more information.

Antibodies, Bacterial↗

PubMed2006

Trichophyton species: use of volatile fingerprints for rapid identification and discrimination.

BACKGROUND: Fungal infection of the skin is a common clinical problem, and laboratory confirmation of the diagnosis is important to ensure appropriate treatment. The identification of the species of fungus is also important, because different fungal species have different modes of transmission, and this may be of importance both in preventing re-infection and in avoidance of infection of others. OBJECTIVES: This study examined the potential of using volatile production patterns for the detection and discrimination between four Trichophyton species (T. mentagrophytes, T. rubrum, T. verrucosum and T. violaceum) in vitro on solid media and in broth culture. METHODS: Two different sensor array systems (conducting polymer and metal oxide sensors) were examined for comparing the qualitative volatile fingerprints produced in the headspace by these species over periods of 24-120 h. The relative sensitivity of detection of two of the species (T. mentagrophytes, T. rubrum) was determined for log 1 to log 7 inoculum levels over the same time period. RESULTS: The conducting polymer-based system was unable to differentiate between species based on volatile fingerprints over the experimental period. However, metal oxide-based sensor arrays were found to be able to differentiate between the four species within 96 h of growth using principal component analysis which accounted for approximately 94% of the data in principal components 1 and 2 based on the qualitative volatile production patterns. This differentiation was confirmed by cluster analysis of the data using Euclidean distance and Ward's linkage. Studies of the sensitivity of detection showed that for T. mentagrophytes and T. rubrum it was possible to differentiate between log 3, log 5 and log 7 inoculum levels within 96 h. CONCLUSIONS: This is the first detailed study of the use of qualitative volatile fingerprints for identification and discrimination of dermatophytes. This approach could have potential for rapid identification of patient samples, reducing significantly the time to treatment.

Biosensing Techniques↗

PubMed1975

Fingerprinting studies of the maturation of ribosomal RNA in mammalian cells.

32P-labelled ribosomal RNA of L 5178 Y cells (a mouse cell line) was digested with T1 ribonuclease and fingerprinted by electrophoresis at pH 3.5 on cellulose acetate and homochromatography on DEAE-cellulose thin-layer plate. From this, it can be concluded that 18-S and 28-S RNA have different and characteristic fingerprints and that the number, the size and the frequency of the large T1 oligonucleotides demonstrate that the guanylic residues are randomly interspaced along the molecule. Using a double-labelling technique with 32P-labelled 45-S RNA and 14C-labelled 18-S RNA or 28-S RNA, long T1 oligonucleotides of the 45-S RNA can be divided into three classes: (a) those which are lost during the transition, (b) those which are present in the 18-S RNA and (c) those which are present in the 28-S RNA. These results provide direct evidence for the existence of one common precursor for the two mature ribosomal RNAs. The comparison of the fingerprints of T1-ribonuclease-digested 47-S, 45-S and 41-S RNA shows that the 47-S and 41-S RNA have a characteristic ribosomal pattern. Finally the size, the number and the mobility of the oligonucleotides present in the different RNA precursors but absent from the mature RNA demonstrate that the non-conversed RNA pieces do not have a monotonous and repetitive sequence.

Cell Line↗

PubMed2006

Development of a GC-MS method for the simultaneous analysis of latent fingerprint components.

Latent fingerprint residue is a complex mixture of organic and inorganic compounds. A full understanding of the composition of this mixture and how it changes after deposition is lacking. Three solvent systems were compared for the simultaneous extraction and derivatization with ethyl chloroformate of selected amino and fatty acids from a nonporous substrate (Mylar for subsequent analysis by gas chromatography-mass spectrometry. A solvent system comprised of sodium hydroxide, ethanol, and pyridine was found to be the most effective. This method was applied to the analysis of latent fingerprint residue deposited on Mylar and preliminary data are presented. Twelve amino acids (e.g., serine, glycine, and aspartic acid) and 10 fatty acids (e.g., tetradecanoic, hexadecanoic, and octadecanoic acids) were identified. The potential application of this method to further the understanding of latent fingerprint chemistry has been demonstrated.

Amino Acids↗

PubMed1995

Molecular analysis of Helicobacter pylori populations in antral biopsies from individual patients using randomly amplified polymorphic DNA (RAPD) fingerprinting.

In the present study, randomly amplified polymorphic DNA (RAPD) fingerprinting has been used to analyse multiple single colony isolates of Helicobacter pylori from antral biopsies in an attempt to ascertain whether or not multiple strains are present in individual patients using single biopsy samples. The RAPD fingerprints derived from single colonies obtained from the same biopsy specimen were in all cases indistinguishable. The previously noted heterogeneity between H. pylori strains from different individuals was confirmed. RAPD fingerprinting, combined with a simple method of template preparation, was shown to be an excellent method for H. pylori strain differentiation. The results of this study indicate that the H. pylori population is homogeneous in individual patients at a single gastric site.

Bacterial Typing Techniques↗

PubMed1990

No excess of homozygosity at loci used for DNA fingerprinting.

Variable number of tandem repeat (VNTR) loci are extremely valuable for the forensic technique known as DNA fingerprinting because of their hypervariability. Nevertheless, the use of these loci in forensics has been controversial. One criticism of DNA fingerprinting is that the VNTR loci used for the "fingerprints" violate the assumption of Hardy-Weinberg equilibrium (H-W), making it difficult to calculate the probability of observing a genotype in the population. If one can assume H-W, the probability of observing the pair of alleles constituting an individual's genotype can be calculated by taking the product of the alleles' frequencies in the population and multiplying by two if the alleles are different. The evidence cited against assuming H-W is homozygote excess, which is presumed to be caused by an undetected mixture of two or more populations with limited interpopulational mating and distinct allele frequencies. For most VNTR loci, measurement error makes it impossible to test these claims by standard methods. The Lifecodes database of three VNTR loci used for forensics was used to show that the claimed excess of homozygotes is not necessarily real because many heterozygotes with similar allele sizes are misclassified as homozygotes. A simple test of H-W that takes such misclassifications into account was developed to test for an overall excess or dearth of heterozygotes in the sample (the complement of homozygote dearth or excess). The application of this test to the Lifecodes database revealed that there was no consistent evidence of violation of H-W for the Caucasian, black, or Hispanic populations.

DNA↗

PubMed1998

Fingerprinting of cyanobacteria based on PCR with primers derived from short and long tandemly repeated repetitive sequences.

The presence of repeated DNA (short tandemly repeated repetitive [STRR] and long tandemly repeated repetitive [LTRR]) sequences in the genome of cyanobacteria was used to generate a fingerprint method for symbiotic and free-living isolates. Primers corresponding to the STRR and LTRR sequences were used in the PCR, resulting in a method which generate specific fingerprints for individual isolates. The method was useful both with purified DNA and with intact cyanobacterial filaments or cells as templates for the PCR. Twenty-three Nostoc isolates from a total of 35 were symbiotic isolates from the angiosperm Gunnera species, including isolates from the same Gunnera species as well as from different species. The results show a genetic similarity among isolates from different Gunnera species as well as a genetic heterogeneity among isolates from the same Gunnera species. Isolates which have been postulated to be closely related or identical revealed similar results by the PCR method, indicating that the technique is useful for clustering of even closely related strains. The method was applied to nonheterocystus cyanobacteria from which a fingerprint pattern was obtained.

Journal Article↗

PubMed1999

Polynucleotide probes that target a hypervariable region of 16S rRNA genes to identify bacterial isolates corresponding to bands of community fingerprints.

Temperature gradient gel electrophoresis (TGGE) is well suited for fingerprinting bacterial communities by separating PCR-amplified fragments of 16S rRNA genes (16S ribosomal DNA [rDNA]). A strategy was developed and was generally applicable for linking 16S rDNA from community fingerprints to pure culture isolates from the same habitat. For this, digoxigenin-labeled polynucleotide probes were generated by PCR, using bands excised from TGGE community fingerprints as a template, and applied in hybridizations with dot blotted 16S rDNA amplified from bacterial isolates. Within 16S rDNA, the hypervariable V6 region, corresponding to positions 984 to 1047 (Escherichia coli 16S rDNA sequence), which is a subset of the region used for TGGE (positions 968 to 1401), best met the criteria of high phylogenetic variability, required for sufficient probe specificity, and closely flanking conserved priming sites for amplification. Removal of flanking conserved bases was necessary to enable the differentiation of closely related species. This was achieved by 5' exonuclease digestion, terminated by phosphorothioate bonds which were synthesized into the primers. The remaining complementary strand was removed by single-strand-specific digestion. Standard hybridization with truncated probes allowed differentiation of bacteria which differed by only two bases within the probe target site and 1.2% within the complete 16S rDNA. However, a truncated probe, derived from an excised TGGE band of a rhizosphere community, hybridized with three phylogenetically related isolates with identical V6 sequences. Only one of the isolates comigrated with the excised band in TGGE, which was shown to be due to identical sequences, demonstrating the utility of a combined TGGE and V6 probe approach.

Actinobacillus↗