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At least 163 records · Page 9Linked to original sources

PubMed2006

Proteomic inventory of myocardial proteins from patients with chronic Chagas' cardiomyopathy.

Chronic Chagas' disease cardiomyopathy (CCC) is an often fatal outcome of Trypanosoma cruzi infection, with a poorer prognosis than other cardiomyopathies. CCC is refractory to heart failure treatments, and is the major indication of heart transplantation in Latin America. A diffuse myocarditis, plus intense myocardial hypertrophy, damage and fibrosis, in the presence of very few T. cruzi forms, are the histopathological hallmarks of CCC. To gain a better understanding of the pathophysiology of CCC, we analyzed the protein profile in the affected CCC myocardium. Homogenates from left ventricular myocardial samples of end-stage CCC hearts explanted during heart transplantation were subjected to two-dimensional electrophoresis with Coomassie blue staining; protein identification was performed by MALDI-ToF mass spectrometry and peptide mass fingerprinting. The identification of selected proteins was confirmed by immunoblotting. We demonstrated that 246 proteins matched in gels from two CCC patients. They corresponded to 112 distinct proteins. Along with structural/contractile and metabolism proteins, we also identified proteins involved in apoptosis (caspase 8, caspase 2), immune system (T cell receptor ss chain, granzyme A, HLA class I) and stress processes (heat shock proteins, superoxide dismutases, and other oxidative stress proteins). Proteins involved in cell signaling and transcriptional factors were also identified. The identification of caspases and oxidative stress proteins suggests the occurrence of active apoptosis and significant oxidative stress in CCC myocardium. These results generated an inventory of myocardial proteins in CCC that should contribute to the generation of hypothesis-driven experiments designed on the basis of the classes of proteins identified here.

Adult↗

PubMed2004

Microbial characterization during the early habitation of the International Space Station.

An evaluation of the microbiota from air, water, and surface samples provided a baseline of microbial characterization onboard the International Space Station (ISS) to gain insight into bacterial and fungal contamination during the initial stages of construction and habitation. Using 16S genetic sequencing and rep-PCR, 63 bacterial strains were isolated for identification and fingerprinted for microbial tracking. Of the bacterial strains that were isolated and fingerprinted, 19 displayed similarity to each other. The use of these molecular tools allowed for the identification of bacteria not previously identified using automated biochemical analysis and provided a clear indication of the source of several ISS contaminants. Strains of Bradyrhizobium and Sphingomonas unable to be identified using sequencing were identified by comparison of rep-PCR DNA fingerprints. Distinct DNA fingerprints for several strains of Methylobacterium provided a clear indication of the source of an ISS water supply contaminant. Fungal and bacterial data acquired during monitoring do not suggest there is a current microbial hazard to the spacecraft, nor does any trend indicate a potential health risk. Previous spacecraft environmental analysis indicated that microbial contamination will increase with time and will require continued surveillance.

Bacteria↗

PubMed2004

Rapid identification of stress-related fingerprint from whole bacterial cells of Bifidobacterium lactis using matrix assisted laser desorption/ionization mass spectrometry.

Whole cells of Bifidobacterium lactis were analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). Characteristic and reproducible mass spectra were obtained in the mass range from 6 to 19 kDa. After several days of bacterial cell storage at 4 degrees C (D0, D2, and D6), only minor signal differences were observed. Under identical and reproducible conditions, fourteen relevant diagnostic ions were identified. Moreover, control- and stress-related fingerprints were rapidly obtained using MALDI-TOFMS by comparison of protein patterns obtained from non-stressed (control) versus stressed cells (addition of bile salts during growth). After quantitative validation of the MALDI-MS data by a statistical approach, two and eight signals were assigned as control- and stress-specific ions, respectively. This work provides the evidence that MALDI-TOFMS can be used for the identification of stress-related fingerprint of B. lactis bacterial cells and could have a high potential for the assessment of the physiological status of the cells.

Bifidobacterium↗

PubMed1992

DNA fingerprinting transforms the art of cell authentication.

The increasing diversity of new cell cultures is seriously stretching the capabilities of traditional methods of identification. DNA fingerprinting is set to play an important role in increasing confidence in the authenticity of cultures in research and industry.

Animals↗

PubMed1985

Plasmid fingerprinting. A tool for bacterial strain identification and surveillance of nosocomial and community-acquired infections.

Plasmid fingerprinting provides a rapid and dependable means of identifying bacterial isolates of the same strain. The stability, wide distribution, and diverse nature and size of extrachromosomal elements make it suitable for virtually all bacterial genera. There are many different procedures available for plasmid screening, and the one chosen depends primarily on the types of organisms to be analyzed. Some procedures are better suited to gram-positive organisms; others are better for visualizing the very large plasmids often seen in Pseudomonas and Rhizobium species. The key to the plasmid fingerprinting technique is agarose gel electrophoresis. In this step of the technique, it is important to differentiate open circular from closed circular forms of plasmids and to recognize the "smile effect." Plasmid fingerprinting can be utilized for epidemiologic studies of both nosocomial and community-acquired infections. The use of restriction endonuclease analysis can greatly enhance the ability of the investigator to differentiate strains that harbor only a single plasmid. Plasmid fingerprinting often provides the only differential characteristic for strains involved in epidemics.

Bacteria↗

PubMed2002

Evaluation of proteome reference maps for cross-species identification of proteins by peptide mass fingerprinting.

We tested whether proteome reference maps established for one species can be used for cross-species protein identification by comparing two-dimensional protein gel patterns and protein identification data of two closely related bacterial strains and four plant species. First, proteome profiles of two strains of the fully sequenced bacterium Sinorhizobium meliloti were compared as an example of close relatedness, high reproducibility and sequence availability. Secondly, the proteome profiles of three legumes (Medicago truncatula, Melilotus alba and Trifolium subterraneum), and the nonlegume rice (Oryza sativa) were analysed to test cross-species similarities. In general, we found stronger similarities in gel patterns of the arrayed proteins between the two bacterial strains and between the plant species than could be expected from the sequence similarities. However, protein identity could not be concluded from their gel position, not even when comparing strains of the same species. Surprisingly, in the bacterial strains peptide mass fingerprinting was more reliable for species-specific protein identification than N-terminal sequencing. While peptide masses were found to be unreliable for cross-species protein identification, we present useful criteria to determine confident matching against species-specific expressed sequence tag databases. In conclusion, we present evidence that cautions the use of proteome reference maps and peptide mass fingerprinting for cross-species protein identification.

Electrophoresis, Gel, Two-Dimensional↗

PubMed1995

DNA fingerprinting and forensic medicine.

In forensic medicine, DNA fingerprinting for identification is becoming a necessary procedure. A method to radiolabel M13 DNA probe by primer extension using a specific oligonucleotide primer was developed. The method specifically labeled the two 15 bp repeats in M13 DNA which hybridize to target DNA giving rise to DNA fingerprinting patterns. The M13 probe labeled by this method has proven useful for individual identification, paternity testing and monitoring reconstitution in bone marrow transplantation. The genetic locus D1S80 and D17S30 containing a variable number of tandem repeats (VNTR) have also been successfully amplified from human genomic DNA isolated from blood (50 ng from each sample) by the polymerase chain reaction (PCR) using oligonucleotide primers complementary to the flanking sequences as primers for amplification. DNA bands were detected by ethidium bromide staining after electrophoresis on agarose gels. Analysis of this VNTR locus was thus achieved without the need for Southern blot or radioactive material. The small size of the DNA fragments produced in the PCR amplification permited good resolution of individual alleles. The precise specification of the number of tandem repeats present in each allelic fragment was reproducible from one analysis to another.

Base Sequence↗

PubMed2006

[AFLP fingerprinting of Pinellia ternata and its application].

OBJECTIVE: To obtain more information on DNA fingerprintings and to confirm the genetic relationships of ten wide populations of Pinellia tornata. METHOD: Collect wide-type or cultivated P. tornata from ten major production areas nation-wide as material. Twelve combinations of EcoR I and Mse I primers were used to asses divergence among ten populations. The data were analyzed using unweighted pair-group method, based on arithmetic averages (UPGMA) bootstrap analysis. Cluster analyses were performed by using NTSYSpc software version 2.1. The alkaloid was extracted from P. ternate with chlorolform and determined in UV absorption spectroscop. RESULT: 1,673 bands were applied with 12 combinations. These results of cluster were congruent with differences in total alkloids. CONCLUSION: The results of the study showed a potential application of AFLP fingerprinting for identification of P. ternata.

Alkaloids↗

PubMed2005

Role of forensic doctors in Thailand's tsunami: experiences from Chulalongkorn Medical School.

Personal identification was the major task of forensic doctors in Thailand's Tsunami. Identification can be done by visual identification, circumstantial evidence and physical evidence. Among the physical evidences dental data is the most effective method of identification, followed by fingerprint and DNA. A disaster Identification team should be set up to handle the problems and plan for the future.

Autopsy↗

PubMed2006

Molecular analysis of microbial communities identified in different developmental stages of Ixodes scapularis ticks from Westchester and Dutchess Counties, New York.

Ixodes scapularis ticks play an important role in the transmission of a wide variety of pathogens between various mammalian species, including humans. Pathogens transmitted by ticks include Borrelia, Anaplasma and Babesia. Although ticks may harbour both pathogenic and non-pathogenic microflora, little is known about how the diversity of the microflora within ticks may influence the transmission of pathogens. To begin addressing this question, we examined the composition of bacterial communities present in Ixodes scapularis collected from Westchester and Dutchess Counties, New York State, at different developmental and nutritional stages. Genetic fingerprints of bacterial populations were generated by temporal temperature gradient gel electrophoresis (TTGE) separation of individual polymerase chain reaction (PCR)-amplified 16S rRNA gene fragments, followed by DNA sequence analysis for bacterial identification. The fingerprints of the TTGE bands were grouped into five clusters. The most abundant DNA sequence found in all the samples was Rickettsia, followed by Pseudomonas and Borrelia. Ralstonia, Anaplasma, Enterobacterias, Moraxella, Rhodococcus and uncultured proteobacterium were present as well. We also determined the prevalence of Anaplasma phagocytophilum and Borrelia burgdorferi by PCR and DNA sequence analysis. Statistical analyses indicated significant variations in the bacterial communities depending on tick developmental stage and degree of engorgement. We suggest that these two elements affect microbial diversity within the tick and may in turn influence pathogen transmission to humans and animals after tick bite.

Animals↗

PubMed1992

[Comparison of fingerprints using a personal computer and graphic software sold on market].

We compared the fingerprint images using a personal computer and a graphic software sold on market. The fingerprints of thumb of left hand recorded by pressing and rolling on paper were input in computer using image scanner. These two fingerprint images were overlapped by moving and rotation on the computer screen, and were fitted well. This result showed that the fingerprints recorded by any way from one person were fitted. Latent and accused's fingerprints were also input in computer using image scanner. These images were analyzed by the same procedure. These two fingerprints were part by unfitting. It was decided these two fingerprints were not derived from one person. We also considered the possibility that the latent fingerprint was the reversed one. Then, the image was reversed of its color on the screen of computer (black to white and white to black) and compared by the same procedure. In this experiment, two fingerprint images were not fitted in a part. This showed that the reversed fingerprint was also able to be analyzed by this procedure. For the comparison of fingerprints, this report showed the ability of the personal computer and software which can be obtained easily from market. Following the improvement of the hardware and software used in this examination in near future, the computerized identification of fingerprints like this study will become more accurate and convenient.

Computer Graphics↗

PubMed1997

Investigation of a methicillin-resistant Staphylococcus aureus (MRSA) outbreak in an Irish hospital: triplex PCR and DNA amplification fingerprinting.

Methicillin-resistant Staphylococcus aureus (MRSA) is becoming a problematic nosocomial pathogen. A continuing increase in numbers of isolates is reported from Irish hospitals each year. Preventing cross-infection and the further spread of endemic strains requires effective control measures. This necessitates the development of sensitive methods for both detection and genetic identification of MRSA isolates. In this study, 48 MRSA strains isolated in the Cork University Hospital were analysed between January and July 1995 using a one-tube triplex-polymerase chain reaction (PCR), wherein three genes, the methicillin-resistance gene (mecA), femA and the extracellular thermonuclease gene, nuc, were simultaneously amplified. Methicillin-sensitive S. aureus (MSSA) and coagulase-negative staphylococci (CNS) were also tested and the assay was found to be MRSA specific. The genetic relationship among this collection of MRSA isolates was also investigated. A single primer, RW3A, derived from a well-characterized, repetitive sequence found in Mycoplasma pneumoniae produced discriminating DNA fragment arrays with all the study organisms. The patterns were reproducible, even after several passages of the isolates. Quantitative analysis of the patterns divided the collection into two main groups, DAF group I representing 48% of the collection and DAF group II a further 19%. The remaining strains showed unrelated patterns. To fully outline the distribution of MRSA in this area a larger study will be necessary. This paper outlines the applicability of both the identification and fingerprinting techniques to local strains.

Cross Infection↗

PubMed2004

HPLC-DAD-MS identification of bioactive secondary metabolites from Ferula communis roots.

A simple HPLC method was developed to distinguish between 'poisonous' and 'non-poisonous' chemotypes of Ferula communis. The method was performed on a C8 reverse phase analytical column using a binary eluent (aqueous TFA 0.01%-TFA 0.01% in acetonitrile) under gradient condition. The two chemotypes showed different fingerprints. The identification of five coumarins and eleven daucane derivatives by HPLC-diode array detection (HPLC-DAD) and HPLC-MS is described. A coumarin, not yet described, was detected.

Chromatography, High Pressure Liquid↗

PubMed1989

Application of different chromosomal DNA restriction digest fingerprints to specific and subspecific identification of Campylobacter isolates.

Eleven strains comprising representatives of different subspecies, biotypes, and serotypes of Campylobacter jejuni and reference strains of C. coli, C. fetus subsp. fetus, C. hyointestinalis, and C. sputorum subsp. sputorum were studied to assess the utility of different DNA profiles for measuring fine differences between allied bacteria. Strains were compared by analyses of HaeIII and XhoI digest patterns of chromosomal DNA and Southern blot hybridization patterns of XhoI digests obtained with an Escherichia coli 16S + 23S rRNA gene probe. Visual comparisons and numerical analyses of the HaeIII and XhoI digest patterns both revealed clear differences between the five Campylobacter species and between representatives of C. jejuni subspecies and biotypes. Only strains with the same Penner serotype gave identical total digest polymorphisms. The advantages of XhoI total digests and Southern blot hybridization patterns were that they were less complex than the HaeIII patterns and easier to compare visually. However, numerical analysis of XhoI data resulted in reduced discrimination. We conclude that DNA fingerprinting using either HaeIII or XhoI fragment polymorphisms has considerable potential as a generally applicable method for identification of Campylobacter isolates, especially at the infrasubspecific level.

Blotting, Southern↗

PubMed2006

Orthogonal projection (OP) technique applied to pattern recognition of fingerprints of the herbal medicine houttuynia cordata Thunb. and its final injection products.

It is a crucial issue to determine the origins of herbal medicinal materials and identify the quality grades and fakes of their final products collected from different pharmaceutical corporations. Pattern recognition technique may assist the manufacturers to achieve this purpose and effectively control the quality of their products. In this work, a widely used method in chemometrics, orthogonal projection (OP) technique, was applied to discrimination analysis and identification of fingerprints of the herbal medicine houttuynia cordata Thunb. (HCT) and its final injection products. The advantages of the OP technique are clearly shown after comparing with the conventional methods such as principal component analysis (PCA), Mahalanobis distance (MD), and similarity comparison method (SCM). Three different sources of medicinal material HCT and its final injection products from six different manufacturers were studied under 'sixfold', 'threefold' and 'threefold-bis' cross-validation procedures. The good performance of the proposed method in determination and identification of unknown samples shows it could be a powerful tool for quality control in herbal medicine production and other related research fields.

Chemistry Techniques, Analytical↗

PubMed2006

Automatic and efficient decomposition of two-dimensional structures of small molecules for fragment-based high-throughput docking.

The computer program DAIM (Decomposition and Identification of Molecules) has been developed to automatically break up compounds in small-molecule libraries for fragment-based docking as well as database analysis. Here, DAIM is evaluated on 130 ligands derived from known crystal structures of ligand-protein complexes. The decomposition and a new fingerprint-based identification technique are used to select anchor fragments for docking. The docking results show that the DAIM selection is superior to size-based or random selection of fragments. To evaluate the usefulness for analyzing the fragment composition of a large library, DAIM is applied to a collection of about 1.85 million commercially available compounds. Interestingly, it is found that the set of most frequent cyclic and acyclic fragments originating from the decomposition of the 1.85 million molecules shows a large overlap with the most frequent fragments in a library of 5120 known drugs. DAIM has been successfully used in the in silico screening for inhibitors of beta-secretase and EphB4 kinase by fragment-based high-throughput docking. Possible future applications for de novo ligand design are briefly discussed.

Amyloid Precursor Protein Secretases↗

PubMed2001

[Application of fingerprint analysis and computer pattern interpretation in identification and quality evaluation of traditional Chinese medicines].

The fingerprint analysis technique used in the quality control of TCM through identifying charactreristics and evaluating stability is set up with the rapid development of instrument analyses and computer pattern interpretation. There are many kinds of methods for establishment of fingerpirnt of TCM mainly including chromatography, spectroscopic method, x-ray diffraction and molecular biological technique. The methods of computer pattern interpretation in fingerprint of TCM includes fuzzy information analysis, artificial neural networks and gray relational grade cluster.

China↗

PubMed1997

PCR detection, identification to species level, and fingerprinting of Campylobacter jejuni and Campylobacter coli direct from diarrheic samples.

Three sets of primers were designed for PCR detection and differentiation of Campylobacter jejuni and Campylobacter coli. The first PCR assay was designed to coidentify C. jejuni and C. coli based on their 16S rRNA gene sequences. The second PCR assay, based on the hippuricase gene sequence, identified all tested reference strains of C. jejuni and also strains of that species which lack detectable hippuricase activity. The third PCR assay, based on the sequence of a cloned (putative) aspartokinase gene and the downstream open reading frame, identified all tested reference strains of C. coli. The assays will find immediate application in the rapid identification to species level of isolates. The assays combine with a protocol for purification of total DNA from fecal samples to allow reproducible PCR identification of campylobacters directly from stools. Of 20 clinical samples from which campylobacters had been cultured, we detected C. jejuni in 17, C. coli in 2, and coinfection of C. jejuni and Campylobacter hyointestinalis in 1. These results were concordant with culture and phenotypic identification to species level. Strain typing by PCR-restriction fragment length polymorphism of the flagellin (flaA) gene detected identical flaA types in fecal DNA and the corresponding campylobacter isolate. Twenty-five Campylobacter-negative stool samples gave no reaction with the PCR assays. These PCR assays can rapidly define the occurrence, species incidence, and flaA genotypes of enteropathogenic campylobacters.

Amidohydrolases↗