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At least 307 records · Page 17Linked to original sources

PubMed2006

Use of fluorescence spectroscopy to differentiate yeast and bacterial cells.

This study focuses on the characterization of bacterial and yeast species through their autofluorescence spectra. Lactic acid bacteria (Lactobacillus sp.), and yeast (Saccharomyces sp.) were cultured under controlled conditions and studied for variations in their autofluorescence, particularly in the area representative of tryptophan residues of proteins. The emission and excitation spectra clearly reveal that bacterial and yeast species can be differentiated by their intrinsic fluorescence with UV excitation. The possibility of differentiation between different strains of Saccharomyces yeast was also studied, with clear differences observed for selected strains. The study shows that fluorescence can be successfully used to differentiate between yeast and bacteria and between different yeast species, through the identification of spectroscopic fingerprints, without the need for fluorescent staining.

Fluorescence↗

PubMed2006

Number and accuracy of T-DNA insertions in transgenic banana (Musa spp.) plants characterized by an improved anchored PCR technique.

Nineteen transgenic banana plants, produced via Agrobacterium-mediated transformation, were analyzed for the integration of T-DNA border regions using an improved anchored PCR technique. The method described is a relatively fast, three-step procedure (restriction digestion of genomic DNA, ligation of 'vectorette'-type adaptors, and a single round of suppression PCR) for the amplification of specific T-DNA border-containing genomic fragments. Most transgenic plants carried a low number of inserts and the method was suitable for a detailed characterization of the integration events, including T-DNA border integrity as well as the insertion of non-T-DNA vector sequences, which occurred in 26% of the plants. Furthermore, the particular band pattern generated by four enzyme/primer combinations for each individual plant served as a fingerprint, allowing the identification of plants representing identical transformation events. Genomic Southern hybridization and nucleotide sequence analysis of amplification products confirmed the data obtained by anchored PCR. Sequencing of seven right or left border junction regions revealed different T-DNA processing events for each plant, indicating a relatively low frequency of precisely nicked T-DNA integration among the plants studied.

Base Sequence↗

PubMed1991

Analysis of benzophenones by gas chromatography/Fourier transform-infrared spectrometry.

A gas chromatograph/Fourier transform-infrared spectrometric analysis of benzophenones, as hydrolyzed products of benzodiazepine, was evaluated and the vapor phase spectra obtained were compared with those measured in the condensed phase. Each infrared spectrum obtained in the vapor phase showed a much greater difference in comparison to differences found in those in the condensed phase, especially in the fingerprint region. The identification of 14 benzophenones by their infrared spectra in the vapor phase was possible. The detection limits for these benzophenones were between 50-100 ng with high signal-to-noise ratios. The vapor phase spectra of the benzophenones were unique and the analytical method allowed the differentiation of closely related classes of drugs, such as benzophenones.

Benzodiazepines↗

PubMed2006

Proteomic expression analysis of cardiomyocytes subjected to proteasome inhibition.

We hypothesized that impaired proteasomal function affects gene expression in cardiomyocytes. To identify those genes, a proteomics-based analysis of neonatal rat cardiac myocytes treated with the proteasome inhibitor MG132 in comparison to vehicle treated control cells was performed. MG132 treatment induced reproducible changes in the protein expression profile, which was analyzed by two-dimensional difference gel electrophoresis followed by tryptic peptide mass fingerprinting for spot identification by MALDI-TOF mass spectrometry. The identified protein alterations could be grouped into three major categories: (1) induction of small heat shock proteins (HSPs) with chaperonic function, such as HSP27, alphaB-crystallin, and cardiovascular HSP, (2) altered expression of actin associated proteins, such as cofilin-1 and transgelin, and (3) induction of antioxidant proteins, such as peroxiredoxin-1, superoxide dismutase-1, and hemeoxygenase-1. Northern blotting revealed that expression was regulated at the mRNA level. Given that proteasomal activity is decreased in cardiovascular diseases, alterations in proteasome-dependent control of mRNA expression could provide a novel mechanism by which disease progression is modulated.

Animals↗

PubMedDate not supplied

Pharmacology of the human red cell voltage-dependent cation channel; Part I. Activation by clotrimazole and analogues.

The activation and pharmacological modulation of the nonselective voltage-dependent cation (NSVDC) channel from human erythrocytes were studied. Basic channel activation was achieved by suspending red cells in a low Cl(-) Ringer (2 mM), where a positive membrane potential (V(m) = E(Cl)) immediately developed. Voltage- and time-dependent activation of the NSVDC channel occurred, reaching a cation conductance (g+) of 1.5-2.0 microS cm(-2). In the presence of the classical Gárdos channel blocker clotrimazole (0-50 microM), activation occurred faster, and g+ saturated dose-dependently (EC50 = 14 microM) at a value of about 4 microS cm(-2). The clotrimazole analogues TRAM-34, econazole, and miconazole also stimulated the channel, whereas the chemically more distant Gárdos channel inhibitors nitrendipine and cetiedil had no effects. Although the potency for modulation of the NSVDC channel is much lower than the IC50 value for Gárdos channel inhibition, clotrimazole (and its analogues) constitutes the first chemical class of positive modulators of the NSVDC channel. This may be an important pharmacological "fingerprint" in the identification of the cloned equivalent of the erythrocyte channel.

Azepines↗

PubMed2006

New ligand-based approach for the discovery of antitrypanosomal compounds.

The antitrypanosomal activity of 10 already synthesized compounds was in silico predicted as well as in vitro and in vivo explored against Trypanosoma cruzi. For the computational study, an approach based on non-stochastic linear fingerprints to the identification of potential antichagasic compounds is introduced. Molecular structures of 66 organic compounds, 28 with antitrypanosomal activity and 38 having other clinical uses, were parameterized by means of the TOMOCOMD-CARDD software. A linear classification function was derived allowing the discrimination between active and inactive compounds with a confidence of 95%. As predicted, seven compounds showed antitrypanosomal activity (%AE>70) against epimastigotic forms of T. cruzi at a concentration of 100mug/mL. After an unspecific cytotoxic assay, three compounds were evaluated against amastigote forms of the parasite. An in vivo test was carried out for one of the studied compounds.

Animals↗

PubMed2004

Identification of a new autoantibody in patients with chronic hepatitis.

To comprehensively study autoantibodies in patients with chronic hepatitis (CH), especially those with hepatitis C virus (HCV) infection, proteins extracted from HepG2 cells were separated by two-dimensional electrophoresis. Spots reacting with sera from 15 patients with CH-C were detected by Western blotting. Proteins extracted from the spots were subjected to mass spectroscopy for identification by mass fingerprinting. Antigenicity of the proteins identified was confirmed by Western blotting and enzyme-linked immunoabsorbent assay. The localization of the autoantigens so detected was investigated by immunohistochemistry. Among 20 protein spots detected, four were identified as actin, heat shock protein (HSP) 70, HSP60, and a novel protein (hepalaminin). Hepalaminin consists of two domains of laminin beta-2 and a specific domain. Autoantibodies against the specific domain were detected in 60.8% of patients with CH-C, 37.7% of those with CH-B, 42.3% of those with autoimmune CH, 28.6% of nonalcoholic steatohepatitis, 10.0% of asymptomatic HCV carriers, but in no healthy volunteers. Antihepalaminin positivity in CH-C and CH-B was related to histologic grading. Immunohistochemical staining demonstrated that hepalaminin is present in the cytoplasm of hepatocytes and cholangiocytes but not of fibroblasts or the vascular epithelium. Hepalaminin is a novel protein expressed in hepatocytes and cholangiocytes. Autoimmunity to this protein may exacerbate inflammation in chronic viral hepatitis.

Amino Acid Sequence↗

PubMed2006

Analysis of the secondary structure of expansion segment 39 in ribosomes from fungi, plants and mammals.

The structure of expansion segment 39, ES39, in eukaryotic 23 S-like ribosomal RNA was analysed using a combination of chemical and enzymic reagents. Ribosomes were isolated from yeast, wheat, mouse, rat and rabbit, five organisms representing three different eukaryotic kingdoms. The isolated ribosomes were treated with structure-sensitive chemical and enzymic reagents and the modification patterns analysed by primer extension and gel electrophoresis on an ABI 377 automated DNA sequencer. The expansion segment was relatively accessible to modification by both enzymic and chemical probes, suggesting that ES39 was exposed on the surface of the ribosomes. The collected modification data were used in secondary structure modelling of the expansion segment. Despite considerable variation in both sequence and length between organisms from different kingdoms, the structure analysis of the expansion segment gave rise to structural fingerprints that allowed identification of homologous structures in ES39 from fungi, plants and mammals. The homologous structures formed an initial helix and an invariant hairpin connected to the initial helix via a long single-stranded loop. The remaining part of the ES39 sequences accounted for most of the length variation seen between the analysed species. This part could form additional, albeit less similar, hairpins. A comparison of ES39 sequences from other fungi, plants and mammals showed that identical structures could be formed in these organisms.

Animals↗

PubMedDate not supplied

[Ear print as an identification method].

In recent years, the analysis of earprints has been developed in the field of legal and forensic medicine, with the aim of acquiring an identification tool similar to fingerprints. In the present paper, we review the current status of earprint identification from both a medical and a legal perspective. The objective is to introduce an area of knowledge which, is spite of its closeness, is not familiar to otolaryngologists, and to present the up to date scientific evidence. First, identification in general, and earprint analysis in particular, are situated in a historical context. Second, an approximation is made to the complexity of earprint analysis, introducing conceptual problems of the method, and possible solutions. Next, a discussion on the legal peculiarities of the validity of the method is undertaken from the forensic point of view, and finally, current development is pointed.

Ear, External↗

PubMed1999

A one-step fluorescent detection method for lipid fingerprints; Eu(TTA)3.2TOPO.

This paper describes the development of a one-step fluorescent lipid reagent that involves europium chelates whose generic formula can be represented as europium(organic ligand)3.2(synergic reagent). An optimized formulation is presented and a comparison with physical developer was conducted which showed the new technique to be very good when fresh fingerprints were recovered but inferior to physical developer on aged prints (over a week). In addition, the compatibility of the technique with sequential methods such as ninhydrin and DFO is reported. The experimentation, results and chemical formulation of this study were presented to delegates of the International Symposium on Fingerprint Detection and Identification held in Israel in June 1995. Prior to that a patent application had been made.

Dermatoglyphics↗

PubMed2004

Integrated sample preparation and MALDI mass spectrometry on a microfluidic compact disk.

High-throughput microfluidic processing of protein digests integrated with matrix-assisted laser desorption/ionization (MALDI) mass spectrometry on a compact disk (CD) is described. Centrifugal force moves liquid through multiple microstructures, each containing a 10-nL reversed-phase chromatography column. The CD enables parallel preparation of 96 samples with volumes ranging from one to several microliters. The peptides in the digests are concentrated, desalted, and subsequently eluted from the columns directly into MALDI target areas (200 x 400 microm) on the CD using a solvent containing the MALDI matrix. After crystallization, the CD is inserted into the MALDI instrument for peptide mass fingerprinting and database identification at a routine sensitivity down to the 200-amol level. Detection of proteolytic peptides down to the 50-amol level is demonstrated. The success rate of the CD technology in protein identification is about twice that of the C(18) ZipTips and standard MALDI steel targets. The CDs are operated using robotics to transfer samples and reagents from microcontainers to the processing inlets on the disposable CD and spinning to control the movement of liquid through the microstructures.

Journal Article↗

PubMed2005

Site-specific H/D exchange of p-methoxyphenol studied by resonant two-photon ionization and mass-analyzed threshold ionization spectroscopy.

The origin of the S(1) <-- S(0) transition (E(1)) and the adiabatic ionization energy (IE) of cis-p-methoxyphenol-d(1)-OD are determined to be 33 660 and 62 302 cm(-1), whereas those of cis-p-methoxyphenol-d(1)-OCH(2)D are 33 669 and 62 323 cm(-1), respectively. Similarly, the E(1) and IE of trans-p-methoxyphenol-d(1)-OD are determined to be 33 563 and 62 191 cm(-1) and those of trans-p-methoxyphenol-d(1)-OCH(2)D are 33 575 and 62 216 cm(-1), respectively. Comparing these data with those of p-methoxyphenol suggests that the H/D exchange on the OH substituent gives rise to a red shift in both the E(1) and IE, whereas that on the OCH(3) group yields a blue shift. The mass-analyzed threshold ionization spectra of the selected isomers can be used as the fingerprints for molecular identification. Analysis of these cation spectra shows that the substituent-sensitive in-plane C-OH and C-OCH(3) bending (mode 9b) and breathing (mode 1) vibrations are active for all of these isomeric cations.

Journal Article↗

PubMedDate not supplied

Positive identification of an immigration test-case using human DNA fingerprints.

The human genome contains a set of minisatellites, each of which consists of tandem repeats of a DNA segment containing the 'core' sequence, a putative recombination signal in human DNA. Multiallelic variation in the number of tandem repeats occurs at many of these minisatellite loci. Hybridization probes consisting of tandem repeats of the core sequence detect many hypervariable minisatellites simultaneously in human DNA, to produce a DNA fingerprint that is completely individual-specific and shows somatic and germline stability. These DNA fingerprints are derived from a large number of highly informative dispersed autosomal loci and are suitable for linkage analysis in man, and for individual identification in, for example, forensic science and paternity testing. They can also be used to resolve immigration disputes arising from lack of proof of family relationships. To illustrate the potential for positive or inclusive identification, we now describe the DNA fingerprint analysis of an immigration case, the resolution of which would have been very difficult and laborious using currently available single-locus genetic markers.

DNA, Satellite↗

PubMed2001

Estimating the probability of identity among genotypes in natural populations: cautions and guidelines.

Individual identification using DNA fingerprinting methods is emerging as a critical tool in conservation genetics and molecular ecology. Statistical methods that estimate the probability of sampling identical genotypes using theoretical equations generally assume random associations between alleles within and among loci. These calculations are probably inaccurate for many animal and plant populations due to population substructure. We evaluated the accuracy of a probability of identity (P(ID)) estimation by comparing the observed and expected P(ID), using large nuclear DNA microsatellite data sets from three endangered species: the grey wolf (Canis lupus), the brown bear (Ursus arctos), and the Australian northern hairy-nosed wombat (Lasiorinyus krefftii). The theoretical estimates of P(ID) were consistently lower than the observed P(ID), and can differ by as much as three orders of magnitude. To help researchers and managers avoid potential problems associated with this bias, we introduce an equation for P(ID) between sibs. This equation provides an estimator that can be used as a conservative upper bound for the probability of observing identical multilocus genotypes between two individuals sampled from a population. We suggest computing the actual observed P(ID) when possible and give general guidelines for the number of codominant and dominant marker loci required to achieve a reasonably low P(ID) (e.g. 0.01-0.0001).

Animals↗

PubMed2005

Difference in mass analysis using labeled lysines (DIMAL-K): a new, efficient proteomic quantification method applied to the analysis of astrocytic secretomes.

Here we describe an original strategy for unbiased quantification of protein expression called difference in mass analysis using labeled lysine (K) (DIMAL-K). DIMAL-K is based on the differential predigestion labeling of lysine residues in complex protein mixtures. The method is relevant for proteomic analysis by two-dimensional electrophoresis and MALDI-TOF mass spectrometry. Protein labeling on lysine residues uses two closely related chemical reagents, S-methyl thioacetimidate and S-methyl thiopropionimidate. Using protein standards, we demonstrated that 1) the chemical labeling was quantitative, specific, and rapid; 2) the differentially labeled proteins co-migrated on two-dimensional gels; and 3) the identification by mass fingerprinting and the relative quantification of the proteins were possible from a single MALDI-TOF mass spectrum. The power of the method was tested by comparing and quantifying the secretion of proteins in normal and proinflammatory astrocytic secretomes (20 microg). We showed that DIMAL-K was more sensitive and accurate than densitometric image analysis and allowed the detection and quantification of novel proteins.

Animals↗

PubMed1997

The possibilities and limitations of nucleic acid amplification technology in diagnostic microbiology.

Nucleic acid amplification technology is examined from the critical viewpoint of a clinical microbiologist working in a routine diagnostic bacteriology laboratory. Widely recognised limitations of amplification technology include those of false-positive and false-negative results, the difficulty of obtaining quantitative results, the problem of using this technology for susceptibility testing, and the difficulty of detecting routinely the wide range of possible pathogens contained in a clinical sample. On the positive side, amplification technology brings welcome new possibilities for rapid detection of specific pathogens in a sample, including viruses, slowly growing bacteria, fastidious or uncultivable bacteria, fungi and protozoa. Other possible applications include screening normally sterile clinical samples for non-specific bacterial contamination and the use of amplification-based DNA fingerprinting methods for identification and typing of microorganisms. Nevertheless, it is predicted that-in contrast to research and reference facilities-routine bacteriology laboratories will continue to rely on culture as the preferred 'amplification method' for most diagnostic applications.

Bacteria↗

PubMed2005

Edge currents in superconductors with a broken time-reversal symmetry.

We analyze edge currents and edge bands at the surface of a time-reversal symmetry breaking dx2-y2 + id(xy) superconductor. We show that the currents have large Friedel oscillations with two interfering frequencies: square root of 2kF from subgap states, and 2kF from the continuum. The results are based independently on a self-consistent slave-boson mean-field theory for the t-J model on a triangular lattice, and on a T-matrix scattering theory calculation. The shape of the edge-state band, as well as the particular frequency square root of 2kF of the Friedel oscillations, are attributes unique for the dx2-y2 + id(xy) case, and may be used as a fingerprint for its identification. Extensions to different time-reversal symmetry breaking superconductors can be achieved within the same approach.

Journal Article↗

PubMed2002

Identification and characterization of Leuconostoc fallax strains isolated from an industrial sauerkraut fermentation.

Lactic acid bacterial strains were isolated from brines sampled after 7 days of an industrial sauerkraut fermentation, and six strains were selected on the basis of susceptibility to bacteriophages. Bacterial growth in cabbage juice was monitored, and the fermentation end products were identified, quantified, and compared to those of Leuconostoc mesenteroides. Identification by biochemical fingerprinting, endonuclease digestion of the 16S-23S intergenic transcribed spacer region, and sequencing of variable regions V1 and V2 of the 16S rRNA gene indicated that the six selected sauerkraut isolates were Leuconostoc fallax strains. Random amplification of polymorphic DNA fingerprints indicated that the strains were distinct from one another. The growth and fermentation patterns of the L. fallax isolates were highly similar to those of L. mesenteroides. The final pH of cabbage juice fermentation was 3.6, and the main fermentation end products were lactic acid, acetic acid, and mannitol for both species. However, none of the L. fallax strains exhibited the malolactic reaction, which is characteristic of most L. mesenteroides strains. These results indicated that in addition to L. mesenteroides, a variety of L. fallax strains may be present in the heterofermentative stage of sauerkraut fermentation. The microbial ecology of sauerkraut fermentation appears to be more complex than previously indicated, and the prevalence and roles of L. fallax require further investigation.

Brassica↗