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PubMed1978

Transmission of herpes-simplex virus type 1 in a nursery for the newborn. Identification of viral isolates by D.N.A. "fingerprinting".

The occurrence of herpes-simplex-virus type-1 infections in two newborn infants in a nursery within a one-month period suggested the possibility of transmission in the nursery. One infant may have been infected by his father, who had active herpes labialis at the time of the child's birth. The source of the second infant's infection was not apparent. Viruses isolated from the two infants were "fingerprinted" by cleaving the virus-specific D.N.A. with several restriction endonucleases and comparing the electrophoretic patterns. Isolates from the two infants were identical and differed from other isolates from epidemiologically unrelated cases. This observation confirmed the possibility of transmission of herpes-simplex virus type 1 in the nursery, but did not define the mode of transmission. Type-1 infections are serious in neonates: one of the infants died and an oesophageal stricture developed in the other. The "fingerprinting" technique provides a useful epidemiological technique for tracing the transmission of herpes virus infections.

Adult↗
PubMed2003

Protein identification: the origins of peptide mass fingerprinting.

Peptide mass fingerprinting (PMF) grew from a need for a faster, more efficient method to identify frequently observed proteins in electrophoresis gels. We describe the genesis of the idea in 1989, and show the first demonstration with fast atom bombardment mass spectrometry. Despite its promise, the method was seldom used until 1992, with the coming of significantly more sensitive commercial instrumentation based on MALDI-TOF-MS. We recount the evolution of the method and its dependence on a number of technical breakthroughs, both in mass spectrometry and in other areas. We show how it laid the foundation for high-throughput, high-sensitivity methods of protein analysis, now known as proteomics. We conclude with recommendations for further improvements, and speculation of the role of PMF in the future.

Amino Acid Sequence↗
PubMed1993

Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology.

DNA fingerprinting of Mycobacterium tuberculosis has been shown to be a powerful epidemiologic tool. We propose a standardized technique which exploits variability in both the number and genomic position of IS6110 to generate strain-specific patterns. General use of this technique will permit comparison of results between different laboratories. Such comparisons will facilitate investigations into the international transmission of tuberculosis and may identify specific strains with unique properties such as high infectivity, virulence, or drug resistance.

Base Sequence↗
PubMed1996

Rapid identification of Candida species by DNA fingerprinting with PCR.

DNA polymorphisms in different species and strains of the genus Candida were assessed by amplifying genomic DNA with single nonspecific primers. This PCR method employed an arbitrary primer (the 10-mer AP3), a primer derived from the intergenic spacer regions (T3B), and the microsatellite primers (GTG)5 and (AC)10. Distinctive and reproducible sets of amplification products were observed for 26 different Candida and 8 other fungal species. The numbers and sizes of the amplification products were characteristic for each species. All yeast species tested could be clearly distinguished by their amplification patterns. With all primers, PCR fingerprints also displayed intraspecies variability. However, PCR profiles obtained from different strains of the same species were far more similar than those derived from different Candida species. By comparing species-specific PCR fingerprints of clinical isolates with those of reference strains, clinical isolates could be identified to the species level even if they could not be identified by routine biochemical methods.

Base Sequence↗
PubMed2002

Identification of Trichophyton rubrum by PCR fingerprinting.

OBJECTIVE: To observe the unique DNA profile and the relationship between DNA profile and phenotype of Trichophyton rubrum,and establish an effective molecular method to identify T. rubrum. METHODS: Three primers, including (GACA)(4), (GTG)(5) and M13 core sequence (5'-GAGGGTG-GCGGTTCT-3'), were used to distinguish variations among 20 clinical isolates of T. rubrum and Trichophyton mentagrophytes. RESULTS: Different PCR-fingerprinting was seen between T. rubrum and T. mentagrophytes using three different primers. 2 stains of T. rubrum were identified among 6 supposed T. mentagrophytes. CONCLUSIONS: T. rubrum can be distinguished using PCR, and (GACA)(4) is the most suitable primer.

DNA Fingerprinting↗
PubMedDate not supplied

[Identification of a Mycoplasma strain using fingerprinting of restriction enzyme hydrolysates of chromosomal DNA].

The heterogeneity among Mycoplasma gallisepticum strains was characterized by comparing genomic DNA from different strains. Two criteria were used for the comparison. 1. Analysis of SmaI and BglI restriction patterns. A method using a dialysis sack for preparation of mycoplasma DNA suitable for pulsed-field gel electrophoresis is described. 2. Comparison of "fingerprinting" patterns obtained as a result of Southern transfer of HindIII-digested DNA followed by hybridization with cloned repetitive M. gallisepticum sequences. It was shown that both types of patterns analyzed are strain-specific; moreover, we were able to identify as a A5969 the strain of M. gallisepticum which was wrongly referred to as S6 in our previous works (Mol. Biol. 1991. V. 25. P. 1643-1649; FEBS Lett. 1991. V. 291. P. 71-74).

Blotting, Southern↗
PubMed2001

16S rDNA-based identification of bacteria from conjunctival swabs by PCR and DGGE fingerprinting.

PURPOSE: Establishment of a new molecular biology technique for the identification of multiple bacteria from the ocular environment, which can be applied supplementarily to cultivation in cases of severe bacterial infections. METHODS: From 60 human conjunctivae (29 with purulent and 31 with nonpurulent conjunctivitis), swabs were taken and DNA was extracted. Fragments of 200 bp, spanning the V3 region of the eubacterial 16S rDNA, were amplified by polymerase chain reaction (PCR) and separated by denaturing gradient gel electrophoresis (DGGE). For phylogenetic identification, DGGE bands were excised and directly sequenced, or 16S rDNA clone libraries were constructed and clones were screened by DGGE. Sequences were compared with sequences of known bacteria listed in the EMBL database. Furthermore, the results were compared with results obtained from conventional cultivation. RESULTS: 16S rDNA could be amplified from 25 of 29 investigated swabs taken from purulent conjunctivitis eyes and from 2 of 31 investigated swabs taken from nonpurulent conjunctivitis eyes. Sixteen samples showed monomicrobial and 11 samples showed polymicrobial infections. The following genera (n is number of samples) were detected: Staphylococcus (n = 8), Corynebacterium (n = 7), Propionibacterium (n = 7), Streptococcus (n = 6), Bacillus (n = 2), Acinetobacter (n = 3), Pseudomonas (n = 3), Proteus (n = 1), and Brevundimonas (n = 1). Four sequences could not be identified to the genus level. They had highest sequence similarities both to sequences of Pantoea and Enterobacter (n = 1), Kingella and Neisseria (n = 1), Serratia and Aranicola (n = 1), and Leuconostoc and Weissella (n = 2), respectively. Culture was only positive for coagulase-negative staphylococci (n = 9), Corynebacteria (n = 3), Staphylococcus aureus (n = 1), Streptococcus sp. (n = 1), Proteus sp. (n = 1), Klebsiella oxytoca (n = 1), and Pseudomonas aeruginosa (n = 1). In total, 45% of the 60 analyzed conjunctival swabs were PCR positive, whereas only 22% were culture positive. No sample positive by culture gave negative results by PCR. CONCLUSIONS: 16S rDNA sequence analyses and DGGE fingerprinting are appropriate methods for the detection and identification of monomicrobial as well as polymicrobial ocular infections of bacteria that might not be detected by conventional cultivation.

Bacteria↗
PubMed1992

[Physical examination of the victim of alleged rape].

The medical examination of presumed victims of sexual assault can be important evidence in criminal cases, hence, its documentation has to be conducted very carefully. A thorough physical examination must always include a search for the marks of brute force or strangulation. The correct preservation of body fluids and swabs is essential, especially since new DNA "finger-printing" techniques ("genetic fingerprinting") may accomplish identification of the offender.

DNA Fingerprinting↗
PubMed1992

Multilocus DNA fingerprint analysis of cell banks: stability studies and culture identification in human B-lymphoblastoid and mammalian cell lines.

The technique of multilocus DNA fingerprinting has great potential for the authentication of animal cell cultures and in identification of cross-contamination. The Alec Jeffreys probes 33.6 and 33.15 were used as multilocus probes to demonstrate the consistent DNA fingerprint profiles in human peripheral blood and its derivative Epstein-Barr virus (EBV) transformed B-lymphoblastoid cultures maintained by repeated subculture for six months. However, fingerprint analysis of EBV transformed cultures generated from small numbers of cells showed that the majority (seven of eight cultures) had anomalous profiles. Some of these altered profiles shared common features not seen in the peripheral blood pattern. Analysis of seven murine hybridoma clones from a single fusion experiment revealed only two clones which could not be distinguished using probe 33.15. Further studies of master and distribution cell banks for eleven cell lines demonstrated consistent fingerprint profiles in all cases except one (U937). However, this cell line showed only minor differences in the master and distribution bank profiles. These data indicate that, while changes in fingerprint profile may be identified in exceptional instances, the multilocus fingerprinting method using probes 33.6 and 33.15 is a powerful and reliable tool in the quality control of animal cell cultures.

Animals↗
PubMed2003

Identification of Candida spp. by randomly amplified polymorphic DNA analysis and differentiation between Candida albicans and Candida dubliniensis by direct PCR methods.

Because Candida species have innately highly variable antifungal susceptibilities, the availability of a fast and reliable species identification test is very important so that suitable and effective therapeutic measures may be taken. Using three oligonucleotide primers, we established a randomly amplified polymorphic DNA (RAPD) analysis method that enabled direct identification of the most common opportunistic pathogenic Candida species. RAPD analysis revealed a characteristic molecular fingerprint for each Candida species. Differences between the profiles for Candida albicans and C. dubliniensis were evident. RAPD analysis is a relatively easy, reproducible, and reliable technique that can be useful in providing genetic fingerprints for the identification of strains. In addition, a collection of different C. albicans strains was identified by a specific PCR based on multiple secreted aspartic proteinase (SAP) genes and the dipeptidyl aminopeptidase (DAP2) gene. Our findings demonstrate that PCR based upon the SAP and DAP2 sequences is a simple, rapid, clear, and direct technique for the identification and differentiation of C. albicans and C. dubliniensis.

Candida↗
PubMed2004

[Identification on Chinese materia medica liquoric root by X-ray diffraction Fourier fingerprint pattern method].

OBJECTIVE: To develop a new identification and analysis method of Chinese medicinal materia Liquoric Root. METHODS: Powder X-ray diffraction Fourier fingerprint pattern. RESULTS: Experiments and analysis were carried out on ten samples. The standard X-ray diffraction Fourier fingerprint pattern and characteristic diffraction peaks of Liquoric Root were obtained. CONCLUSION: This method can be used for identification of Chinese medicinal materia Liquoric Root.

Drugs, Chinese Herbal↗
PubMed2001

Strategy for protein isoform identification from expressed sequence tags and its application to peptide mass fingerprinting.

Expressed Sequence Tags (ESTs) are an invaluable resource for protein identification and characterisation in proteomics. They allow proteins to be identified in the absence of genome sequence data. When EST sequences are used for protein identification, they are usually first processed into contigs to reduce redundancy and generate longer sequences from the overlapping ESTs. However, the process of generating contigs may accidentally group biologically meaningful isoforms together. Here we report means of discovering isoforms in EST sequences and how to use this information in the framework of protein identification and characterisation with peptide mass fingerprinting. We illustrate our strategies with examples from the dbEST database as well as protein isoforms from two-dimensional polyacrylamide gels.

Amino Acid Sequence↗
PubMed2002

Comparative bioinformatic analysis of complete proteomes and protein parameters for cross-species identification in proteomics.

Peptide mass fingerprinting (PMF) remains the most amenable technique for protein identification in proteomics, using mass spectrometry as the primary analytical technique coupled with bioinformatics. This relies on the presence of the amino acid sequence of the protein in the current databanks. Despite this, it is desirable to be able to use the technique for organisms whose genomes are not yet fully sequenced and apply cross-species protein identification. In this study, we have re-examined the feasibility of such approaches by considering the extent of protein similarity between genome sequences using a data set of 29 complete bacterial and two eukaryotic genomes. A range of protein and peptide features are considered, including protein isoelectric focussing point, protein mass, and amino acid conservation. The effectiveness of PMF approaches has then been tested with a series of computer simulations with varying peptide number and mass accuracy for several cross-species tests. The results show that PMF alone is unsuitable in general for divergent species jumps, or when protein similarity is less than 70% identity. Despite this, there exists a considerable enrichment above random of tryptic peptide conservation and PMF promises to remain useful when combined with other data than just peptide masses for cross-species protein identification.

Algorithms↗
PubMed2000

Identification of differentially expressed genes by mutually subtracted RNA fingerprinting.

A mutually subtracted RNA fingerprinting (SuRF) method has been developed that allows efficient identification of differentially expressed sequence tags between two samples. Mutual subtractions of two RNA samples are achieved by first synthesizing cDNAs using oligo(dT) coupled with magnetic beads which are then reciprocally hybridized to starting RNA samples to remove common mRNAs between them. The second step involves differential fingerprinting of the subtracted RNA samples by polymerase chain reaction with specially designed degenerate primers. SuRF was applied to identify alteration in gene expression pertinent to osteogenic sarcoma which was achieved by employing the method between FOB (an immortalized fetal osteoblast) and MG63 (an osteosarcoma) cell lines. An estimated 10% of the total expressed genes in these two cell types were screened by the method. This analysis identified 96 differentially expressed sequences, none of which was identified repeatedly. A subset of these sequences was subsequently confirmed to have differential expression between the two cell types. Removal of common mRNAs prior to differential display should diminish redundant identification of abundant genes and increase the chance of identifying rare differentially expressed genes.

DNA, Complementary↗
PubMed1993

Rapid identification of proteins by peptide-mass fingerprinting.

BACKGROUND: Developments in 'soft' ionisation techniques have revolutionized mass-spectro-metric approaches for the analysis of protein structure. For more than a decade, such techniques have been used, in conjuction with digestion b specific proteases, to produce accurate peptide molecular weight 'fingerprints' of proteins. These fingerprints have commonly been used to screen known proteins, in order to detect errors of translation, to characterize post-translational modifications and to assign diulphide bonds. However, the extent to which peptide-mass information can be used alone to identify unknown sample proteins, independent of other analytical methods such as protein sequence analysis, has remained largely unexplored. RESULTS: We report here on the development of the molecular weight search (MOWSE) peptide-mass database at the SERC Daresbury Laboratory. Practical experience has shown that sample proteins can be uniquely identified from a few as three or four experimentally determined peptide masses when these are screened against a fragment database that is derived from over 50 000 proteins. Experimental errors of a few Daltons are tolerated by the scoring algorithms, thus permitting the use of inexpensive time-of-flight mass spectrometers. As with other types of physical data, such as amino-acid composition or linear sequence, peptide masses provide a set of determinants that are sufficiently discriminating to identify or match unknown sample proteins. CONCLUSION: Peptide-mass fingerprints can prove as discriminating as linear peptide sequences, but can be obtained in a fraction of the time using less protein. In many cases, this allows for a rapid identification of a sample protein before committing it to protein sequence analysis. Fragment masses also provide information, at the protein level, that is complementary to the information provided by large-scale DNA sequencing or mapping projects.

Journal Article↗
PubMed2000

Identification of pediococci by ribotyping.

Pediococci are among the most prevalent microbial contaminants in breweries and they can cause ropiness and the accumulation of high levels of diacetyl in beer. The accurate identification of pediococci is important, because different species do not possess equal spoilage potential. In this study, 18 Pediococcus strains, mainly of brewery origin, were first identified using phenotypical characterization (API 50 CHL and SDS-PAGE profiling), and then ribotyped using a RiboPrinterR System. Six Pediococcus type strains and three other Pediococcus strains were used as references. Ribotyping showed higher discriminative capacity than phenotypical identification methods. Strains could be identified to species level and in many cases, differentiated even at strain level using this genetic fingerprinting method. The identifications performed by ribotyping were confirmed by 16S rDNA sequencing of selected strains. Automated ribotyping was found to be a rapid and reliable method for identifying pediococci, but requires the construction of a comprehensive fingerprint library.

Bacterial Typing Techniques↗
PubMed2006

Identification of the unidentified deceased: turnaround times, methods, and demographics in Fulton County, Georgia.

CONTEXT: Multiple methods may be employed in an attempt to identify deceased individuals who are unidentified when reported to the medical examiner or coroner. The success and turnaround times of various methods differ. OBJECTIVE: To determine the number of deaths initially involving unidentified individuals, their demographics, the methods used and turnaround times for cases in which identification was successful and the portion of cases that remain unidentified for significant periods of time. DESIGN, SETTING, AND PARTICIPANTS: Retrospective case review of all decedents who were initially unidentified when death was reported to the Fulton County Medical Examiner in Atlanta, Georgia, during a 1-year period between May 2003 and May 2004. MAIN OUTCOME MEASURES: Rate per 1000 deaths which involved an unidentified decedent, tabulation of methods used to make identifications, and rate of cases remaining unidentified. RESULTS: Of 2279 deaths reported to the office, 100 were originally unidentified, resulting in a rate of 44 unidentified decedents per 1000 deaths reported. Those who remained unidentified involved 6 cases, resulting in a "cold case" rate of 2.6 per 1000 deaths. Seventy-eight percent were identified within 2 days, and the most common successful methods were visual identification (52%) and fingerprints (31%). Dental (10%), x-ray (4%), and other methods (6%) were least commonly used. Of the 94 persons identified, all identifications occurred within 29 days. DNA procedures were not needed in most cases, and in the few cases where such tests were needed, results were either unavailable or failed to show a match with known samples. CONCLUSIONS: The majority of unidentified deceased individuals were identified within 2 days, with visual verification or fingerprints accounting for about 83% of methods successfully employed. The medical examiner noted a rate of 44 unidentified deceased persons per 1000 death reports, with an ultimate "cold case" (long-term unidentified) rate of about 2.6 cases per 1000 death reports. These data may be useful in developing office policy and procedure regarding the procedural and temporal aspects of investigations centered on achieving identification and making dispositions of unidentified deceased bodies.

Adolescent↗