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At least 1,243 records · Page 69Linked to original sources
PubMed2006

Capillary zone electrophoresis method for fingerprint of allantoic fluid in normal and infected SPF embryonated chicken eggs.

A capillary zone electrophoresis method was developed for fingerprint determination of allantoic fluid in specific pathogen free (SPF) embryonated chicken eggs. The effects of some crucial parameters, such as buffer type, pH, wavelength and running voltage on the separation were studied systematically. The components of the allantoic fluid were well separated using a fused-silica uncoated capillary with an effective length of 50 cm and an internal diameter of 50 microm. One hundred millimolars sodium tetraborate buffer containing 20 mM sodium dihydrogen phosphate with a final pH 9.8 was used as a running buffer. Comparative fingerprints of allantoic fluid in normal and infected with infectious bronchitis virus (IBV) SPF embryonated chicken eggs were also evaluated. The results showed that there were significant differences between composition of normal allantoic fluid and allantoic fluid infected with IBV, which led to different migration behavior. This method was shown to be stable and reproducible with a relative standard deviation of less than 5% for both migration time and peak current.

Allantois↗
PubMed2005

A ribosomal RNA gene intergenic spacer based PCR and DGGE fingerprinting method for the analysis of specific rhizobial communities in soil.

A direct molecular method for assessing the diversity of specific populations of rhizobia in soil, based on nested PCR amplification of 16S-23S ribosomal RNA gene (rDNA) intergenic spacer (IGS) sequences, was developed. Initial generic amplification of bacterial rDNA IGS sequences from soil DNA was followed by specific amplification of (1) sequences affiliated with Rhizobium leguminosarum "sensu lato" and (2) R. tropici. Using analysis of the amplified sequences in clone libraries obtained on the basis of soil DNA, this two-sided method was shown to be very specific for rhizobial subpopulations in soil. It was then further validated as a direct fingerprinting tool of the target rhizobia based on denaturing gradient gel electrophoresis (DGGE). The PCR-DGGE approach was applied to soils from fields in Brazil cultivated with common bean (Phaseolus vulgaris) under conventional or no-tillage practices. The community fingerprints obtained allowed the direct analysis of the respective rhizobial community structures in soil samples from the two contrasting agricultural practices. Data obtained with both primer sets revealed clustering of the community structures of the target rhizobial types along treatment. Moreover, the DGGE profiles obtained with the R. tropici primer set indicated that the abundance and diversity of these organisms were favoured under NT practices. These results suggest that the R. leguminosarum-as well as R. tropici-targeted IGS-based nested PCR and DGGE are useful tools for monitoring the effect of agricultural practices on these and related rhizobial subpopulations in soils.

Agriculture↗
PubMed2005

The development of a matrix-assisted laser desorption/ionization mass spectrometry-based method for the protein fingerprinting and identification of Aeromonas species using whole cells.

This report describes the development of a method to detect the waterborne pathogen Aeromonas using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The genus Aeromonas is one of several medically significant genera that have gained prominence due to their evolving taxonomy and controversial role in human diseases. In this study, MALDI-MS was applied to the characterization of seventeen species of Aeromonas. These seventeen species were represented by thirty-two strains, which included type, reference and clinical isolates. Intact cells from each strain were used to generate a reproducible library of protein mass spectral fingerprints or m/z signatures. Under the test conditions used, peak lists of the mass ions observed in each species revealed that three mass ions were conserved among all the seventeen species tested. These common mass ions having an average m/z of 6301, 12,160 or 12,254, and 13,450, can be potentially used as genus-specific biomarkers to identify Aeromonas in unknown samples. A dendrogram generated using the m/z signatures of all the strains tested indicated that the mass spectral data contained sufficient information to distinguish between genera, species, and strains. There are several advantages of using MALDI-MS based protein mass spectral fingerprinting of whole cells for the identification of microorganisms as well as for their differentiation at the sub-species level: (1) the capability to detect proteins, (2) high throughput, and (3) relatively simple sample preparation techniques. The accuracy and speed with which data can be obtained makes MALDI-MS a powerful tool especially suited for environmental monitoring and detection of biological hazards.

Aeromonas↗
PubMed2004

High-throughput peptide mass fingerprinting of soybean seed proteins: automated workflow and utility of UniGene expressed sequence tag databases for protein identification.

Identification of anonymous proteins from two-dimensional (2-D) gels by peptide mass fingerprinting is one area of proteomics that can greatly benefit from a simple, automated workflow to minimize sample contamination and facilitate high-throughput sample processing. In this investigation we outline a workflow employing robotic automation at each step subsequent to 2-D gel electrophoresis. As proof-of-concept, 96 protein spots from a 2-D gel were analyzed using this approach. Whole protein (1 mg) from mature, dry soybean (Glycine max [L.] Merr.) cv. Jefferson seed was resolved by high resolution 2-D gel electrophoresis. Approximately 150 proteins were observed after staining with Coomassie Blue. The rather low number of detected proteins was due to the fact that the dynamic range of protein expression was greater than 100-fold. The most abundant proteins were seed storage proteins which in total represented over 60% of soybean seed protein. Using peptide mass fingerprinting 44 protein spots were identified. Identification of soybean proteins was greatly aided by the use of annotated, contiguous Expressed Sequence Tag (EST) databases which are available for public access (UniGene, ftp.ncbi.nih.gov/repository/UniGene/). Searches were orders of magnitude faster when compared to searches of unannotated EST databases and resulted in a higher frequency of valid, high-scoring matches. Some abundant, non seed storage proteins identified in this investigation include an isoelectric series of sucrose binding proteins, alcohol dehydrogenase and seed maturation proteins. This survey of anonymous seed proteins will serve as the basis for future comparative analysis of seed-filling in soybean as well as comparisons with other soybean varieties.

Databases, Genetic↗
PubMed2005

Research on processing medicinal herbs with multi-steps infrared macro-fingerprint method.

How to apply rapid and effective method to research medicinal herbs, the representative of complicated mixture system, is the current study focus for analysts. The functions of non-processed and processed medicinal herbs are greatly different, so controlling the processing procedure is highly important for guarantee of the curative effect. Almost, the conventional criteria of processing are based on personal sensory experience. There is no scientific and impersonal benchmark. In this article, we take Rehmannia for example, conducting a systematic study on the process of braising Rehmannia with yellow wine by using the multi-steps infrared (IR) macro-fingerprint method. The method combines three steps: conventional Fourier transform infrared spectroscopy (FT-IR), second derivative spectroscopy, and two-dimensional infrared (2D-IR) correlation spectroscopy. Based on the changes in different types of IR spectra during the process, we can infer the optimal end-point of processing Rehmannia and the main transformations during the process. The result provides a scientific explanation to the traditional sensory experience based recipe: the end-point product is "dark as night and sweet as malt sugar". In conclusion, the multi-steps IR macro-fingerprint method, which is rapid and reasonable, can play an important role in controlling the processing of medicinal herbs.

Carbohydrate Conformation↗
PubMed2005

Peptide mass fingerprinting.

Peptide mass fingerprinting by MALDI-MS and sequencing by tandem mass spectrometry have evolved into the major methods for identification of proteins following separation by two-dimensional gel electrophoresis, SDS-PAGE or liquid chromatography. One main technological goal of proteome analyses beside high sensitivity and automation was the comprehensive analysis of proteins. Therefore, the protein species level with the essential information on co- and post-translational modifications must be achieved. The power of peptide mass fingerprinting for protein identification was described here, as exemplified by the identification of protein species with high molecular masses (spectrin alpha and beta), low molecular masses (elongation factor EF-TU fragments), splice variants (alpha A crystallin), aggregates with disulfide bridges (alkylhydroperoxide reductase), and phosphorylated proteins (heat shock protein 27). Helpful tools for these analyses were the use of the minimal protein identifier concept and the software program MS-Screener to remove mass peaks assignable to contaminants and neighbor spots.

Alternative Splicing↗
PubMed1990

Discrepancy in the diagnoses of hydatidiform mole by macroscopic and microscopic findings and the deoxyribonucleic acid fingerprint method.

Ten cases of hydatidiform mole were analyzed by the deoxyribonucleic acid fingerprint method. Deoxyribonucleic acid samples were prepared from hydatidiform mole tissue of hydatidiform mole and maternal and paternal blood. A case of partial hydatidiform mole diagnosed by histologic findings was revealed to be complete hydatidiform mole by deoxyribonucleic acid fingerprinting.

Chorionic Gonadotropin↗
PubMed1989

Zygosity determination of multiple pregnancy by deoxyribonucleic acid fingerprints.

We used a new method of deoxyribonucleic acid analysis to determine zygosity in multiple pregnancies. This method uses a minisatellite core probe, requires only a small amount of deoxyribonucleic acid, and detects the restriction fragment length polymorphisms that are a result of allelic differences in the number of tandem repeats that contain the core sequence. Southern blot hybridization showed an individual-specific deoxyribonucleic acid fingerprint and each polymorphic band in the sibling could be identified within one (but not both) of the parents. Identical deoxyribonucleic acid fingerprints among the siblings of multiple pregnancy indicate they must be monozygotic. This method is sufficiently reliable and rapid so the determination of zygosity in multiple pregnancy can be made the same day the fetal deoxyribonucleic acid is made available.

DNA↗
PubMed2003

Functional fingerprints of folds: evidence for correlated structure-function evolution.

Using structural similarity clustering of protein domains: protein domain universe graph (PDUG), and a hierarchical functional annotation: gene ontology (GO) as two evolutionary lenses, we find that each structural cluster (domain fold) exhibits a distribution of functions that is unique to it. These functional distributions are functional fingerprints that are specific to characteristic structural clusters and vary from cluster to cluster. Furthermore, as structural similarity threshold for domain clustering in the PDUG is relaxed we observe an influx of earlier-diverged domains into clusters. These domains join clusters without destroying the functional fingerprint. These results can be understood in light of a divergent evolution scenario that posits correlated divergence of structural and functional traits in protein domains from one or few progenitors.

Adenosine Triphosphate↗
PubMed2003

Development of oil hydrocarbon fingerprinting and identification techniques.

Oil, refined product, and pyrogenic hydrocarbons are the most frequently discovered contaminants in the environment. To effectively determine the fate of spilled oil in the environment and to successfully identify source(s) of spilled oil and petroleum products is, therefore, extremely important in many oil-related environmental studies and liability cases. This article briefly reviews the recent development of chemical analysis methodologies which are most frequently used in oil spill characterization and identification studies and environmental forensic investigations. The fingerprinting and data interpretation techniques discussed include oil spill identification protocol, tiered analytical approach, generic features and chemical composition of oils, effects of weathering on hydrocarbon fingerprinting, recognition of distribution patterns of petroleum hydrocarbons, oil type screening and differentiation, analysis of "source-specific marker" compounds, determination of diagnostic ratios of specific oil constituents, stable isotopic analysis, application of various statistical and numerical analysis tools, and application of other analytical techniques. The issue of how biogenic and pyrogenic hydrocarbons are distinguished from petrogenic hydrocarbons is also addressed.

Accidents↗
PubMed2003

Factors affecting the robustness of metabolite fingerprinting using 1H NMR spectra.

1H NMR spectroscopy is one of the techniques whose potential is currently being explored in the emerging field of metabolomics. It is a non-targeted method, producing signals for all proton-containing chemical species. For crude plant materials the spectra are always complex, with many signals overlapping. Hence a most suitable approach for analysing them is 'metabolite fingerprinting', which is aimed at highlighting compositional similarities and exploring the overall natural variability in a population of samples. The most commonly used method for this is principal component analysis (PCA), as it allows the whole spectral trace to be analysed and the vast quantity of information to be simplified. In this paper we investigate whether there are factors which may affect the NMR spectra in a way that subsequently decreases the robustness of the metabolite fingerprinting by PCA. Imperfections in the signal registration (i.e. inconsistency of the peak position) are generally detrimental to analysing whole traces by multivariate methods. The sources of such problems are illustrated through specially designed repeatability studies using potato and tomato samples, and the analysis of a tea dataset containing many samples. Careful sample preparation can help to limit peak shifts; for instance here by attempting to control the pH of the extracts. In addition, some compounds are susceptible to interactions affecting their chemical shifts and mathematical alignment of peaks may be necessary. Lastly factors such as resolution can also affect analyses and must be carefully adjusted. Our choice of examples aims to raise awareness of potential problems. We do not question the validity of the NMR approach, but point out those areas where special care may need to be taken.

Databases, Factual↗
PubMed2003

The role of chemical fingerprinting: application to Ephedra.

Ephedra sinica, known as Ma Huang, is one of the oldest medicinal herbs in Traditional Chinese Medicine (TCM). Preparations, namely teas, of E. sinica have been used for over 5000 years as a stimulant and as an antiasthmatic. In the West, extracts of E. sinica, E. intermedia or E. equisetina are most commonly used in dietary supplements as a stimulant and to promote weight loss. More than 50 species of Ephedra are native to both hemispheres, but the detection of ephedrine alkaloids has been limited to species in Eurasia. Currently, methods exist to quantitate the ephedrine alkaloids in extracts of plant material or dietary supplements, but the methods are not able to verify the extract is of an Ephedra species. Reverse phase high performance liquid chromatography with photodiode array detection was applied for the chemical fingerprinting of the Ephedra species. Two regions of comparison were determined in the chromatograms at 320 nm. The series of peaks between 52 and 64 min confirms an Ephedra species is being analyzed. The aforementioned peaks also could distinguish between Ephedra species from Eurasia, North America and South America. Peaks at ca. 57 and 59 min were isolated and determined to be two new compounds, 4-(2-eicosyloxycarbonyl-vinyl)-benzoic acid and 4-(2-docosyloxycarbonyl-vinyl)-benzoic acid respectively. Authentication of ground plant material as Ephedra can be achieved by this chemical fingerprinting method.

Alkaloids↗
PubMed2003

Investigating plant-plant interference by metabolic fingerprinting.

New analytical developments in post-genomic technologies are being introduced to the field of plant ecology. FT-IR fingerprinting coupled with chemometrics via cluster analysis is proposed as a tool for correlating global metabolic changes with abiotic or biotic perturbation and/or interactions. The current study concentrates on detecting chemical responses by inter-species competition between a monocotyledon Brachypodium distachyion and a dicotyledon Arabidopsis thaliana. Growth analysis of 42 days old plants showed differences in both species under competition. Clear changes in the FT-IR metabolic fingerprints of B. distachyion in competition with A. thaliana were observed, whilst there were no apparent chemical differences in the A. thaliana plant tissues. This study demonstrates the power of this approach in detecting changes in the global metabolic profiles of plants in response to biotic interactions, and we believe FT-IR is appropriate for rapid screening (10 s per sample) prior to targeted metabolite analyses.

Arabidopsis↗
PubMed2003

Fingerprinting suspended sediment sources in a large urban river system.

Very few studies have attempted to quantify the sources of suspended sediment transported in urban river systems. In this study, statistically verified composite fingerprints and a multivariate mixing model have been used to identify the main sources of the suspended sediment transported by the River Aire and its main tributary, the River Calder. Because of the polluted nature of the Aire/Calder catchment and its effect on fingerprint property concentrations, source tracing was undertaken separately for the upper and lower reaches. The mean contributions from individual source types (i.e. surface materials from woodland, uncultivated and cultivated areas, channel bank material, road dust and solids from sewage treatment works) varied between the upper and lower reaches of the rivers, reflecting the change in land use from primarily pasture and moorland in the upper reaches to mainly urban areas (with some cultivated land) in the lower reaches. The suspended sediment in the upper reaches of the River Aire originates largely from channel bank sources (43-84%) and from uncultivated topsoil (16-57%). In the lower reaches of the Aire/Calder system, local sources of cultivated topsoil contribute 20-45% of the suspended sediment load and there is a significant contribution from urban sources, such as road dust (19-22%) and solids from sewage treatment works (14-18%). In the upper reaches, the proportion of sediment derived from each of the two main geological areas corresponds broadly to the proportion of the catchment occupied by each geological area. The relative contribution from the Rivers Aire and Calder to the suspended sediment load transported below the confluence demonstrates that most of the sediment is derived from the River Calder.

Journal Article↗
PubMed2006

Glycomic profiling of cells and tissues by mass spectrometry: fingerprinting and sequencing methodologies.

Over the past decade, rapid, high-sensitivity mass spectrometric strat-egies have been developed and optimized for screening for the types of N- and O-glycans present in a diverse range of biological material, including secretions, cell lines, tissues, and organs. These glycomic strategies are based on matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass fingerprinting of permethylated derivatives, combined with electrospray (ES) or MALDI tandem mass spectrometry (MS/MS) sequencing and gas chromatography (GC)-MS linkage analysis, complemented by chemical and enzymatic degradations. Protocols for these methods are described in the first part of this chapter. Glycomic experiments yield large volumes of MS data, and interpretation of the resulting spectra remains a time-consuming bottleneck in the process. In the second part of this chapter, we describe the use and operation of a mass spectral viewer program capable of displaying and automatically labeling spectra arising from MALDI fingerprinting of N-glycans.

Amino Acid Sequence↗
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↗
PubMed2000

Chemical fingerprinting for the evaluation of unintended secondary metabolic changes in transgenic food crops.

A common element in designed guidelines for assessment of the food safety of transgenic crops is centred on a comparative analytical analysis with conventionally bred crop plants, assuming that these products have a long history of safe use (i.e. OECD-principle of substantial equivalence). In this study we examine the utility of an off-line combination of 400 MHz proton (1H)-NMR spectroscopy and liquid chromatography (LC) for the multi-component comparison of low-molecular weight compounds (i.e. chemical fingerprinting) in complex plant matrices. The developed NMR-methodology can contribute to the demonstration of substantial equivalence by its ability to compare possible compositional alterations in a novel food crop with respect to related non-transgenic reference lines. In this respect a hierarchical approach is proposed by comparing the chemical fingerprints of the transgenic crop plant to those of: (1) isogenic parental or closely related lines bred at identical and multiple sites; (2) extended ranges of commercial varieties of that plant; and (3) downstream processing effects. This is of importance to assess the likelihood that some of the statistical differences in a transgenic crop plant may be false positives due to chance alone or arose from natural genetic and/or physiologic variations.

Animals↗
PubMed1999

AFLP genotyping and fingerprinting.

Amplified fragment length polymorphisms (AFLPs) are polymerase chain reaction (PCR)-based markers for the rapid screening of genetic diversity. AFLP methods rapidly generate hundreds of highly replicable markers from DNA of any organism; thus, they allow high-resolution genotyping of fingerprinting quality. The time and cost efficiency, replicability and resolution of AFLPs are superior or equal to those of other markers [allozymes, random amplified polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP), microsatellites], except that AFLP methods primarily generate dominant rather than co-dominant markers. Because of their high replicability and ease of use, AFLP markers have emerged as a major new type of genetic marker with broad application in systematics, pathotyping, population genetics, DNA fingerprinting and quantitative trait loci (QTL) mapping.

Journal Article↗