Analysis of genotypic variation in genes associated with virulence in Aggregatibacter actinomycetemcomitans clinical isolates

Background and Objective: Although certain serotypes of Aggregatibacter actinomycetemcomitans are associated more with aggressive periodontitis than are other serotypes, the correlation between distinct lineages and virulence traits in this species is poorly understood. This study aimed to evaluate the polymorphism of genes encoding putative virulence factors of clinical isolates, and to correlate these findings with A. actinomycetemcomitans serotypes, genotypes and periodontal status of the hosts. Material and Methods: Twenty-six clinical isolates from diverse geographic populations with different periodontal conditions were evaluated. Genotyping was performed using pulse-field gel electrophoresis. Polymorphisms in the genes encoding leukotoxin, Aae, ApaH and determinants for serotype-specific O polysaccharide were investigated. Results: The isolates were classified into serotypes a-f, and exhibited three apaH genotypes, five aae alleles and 25 macrorestriction profiles. Two serotype b isolates (7.7%), obtained from Brazilian patients with aggressive periodontitis, were associated with the highly leukotoxic genotype; these isolates showed identical fingerprint patterns and aae and apaH genotypes. Serotype c, obtained from various periodontal conditions, was the most prevalent among Brazilian isolates, and isolates were distributed in two aae alleles, but formed a genetically distinct group based on apaH analysis. Cluster analysis showed a close relationship between fingerprinting genotypes and serotypes/apaH genotypes, but not with aae genotypes. Conclusion: Apart from the deletion in the ltx promoter region, no disease-associated markers were identified. Non-JP2-like strains recovered from individuals with periodontal disease exhibited considerable genetic variation regarding aae/apaH genotypes, serotypes and XhoI DNA fingerprints.

Investigation of a new GRASP-based clustering algorithm applied to biological data

A large amount of biological data has been produced in the last years. Important knowledge can be extracted from these data by the use of data analysis techniques. Clustering plays an important role in data analysis, by organizing similar objects from a dataset into meaningful groups. Several clustering algorithms have been proposed in the literature. However, each algorithm has its bias, being more adequate for particular datasets. This paper presents a mathematical formulation to support the creation of consistent clusters for biological data. Moreover. it shows a clustering algorithm to solve this formulation that uses GRASP (Greedy Randomized Adaptive Search Procedure). We compared the proposed algorithm with three known other algorithms. The proposed algorithm presented the best clustering results confirmed statistically. (C) 2009 Elsevier Ltd. All rights reserved.

Femtosecond laser ablation on dental hard tissues-Analysis of ablated profile near an interface using local effective intensity

This study evaluated the process of ablation produced by a Ti:Sapphire femtosecond laser under different average powers taking place at the enamel/dentin interface. Based on the geometry of ablated microcavities the effective intensity for ablation was obtained. This study shows the validity for the local effective intensity analysis and allows a quantification of the variation in the ablation geometry taking place at the interface of two naturally different materials. It shows that the variation of the diameter of the ablated region as a function of the cavity depth comes essentially from a mechanism of effective intensity attenuation, as a result of a series of complex effects. Additionally, our data are sufficient to predict that a discontinuity on the ablation profile will occur on the interface between two biological media: enamel-dentin, showing a suddenly jump on the ablated cavity dimensions.

Femtosecond light distribution at skin and liver of rats: analysis for use in optical diagnostics

In this study we investigated the light distribution under femtosecond laser illumination and its correlation with the collected diffuse scattering at the surface of ex-vivo rat skin and liver. The reduced scattering coefficients mu`s for liver and skin due to different scatterers have been determined with Mie-scattering theory for each wavelength (800, 630, and 490 nm). Absorption coefficients mu(a) were determined by diffusion approximation equation in correlation with measured diffused reflectance experimentally for each wavelength (800, 630, and 490 nm). The total attenuation coefficient for each wavelength and type of tissue were determined by linearly fitting the log based normalized intensity. Both tissues are strongly scattering thick tissues. Our results may be relevant when considering the use of femtosecond laser illumination as an optical diagnostic tool. [GRAPHICS] A typical sample of skin exposed to 630 nm laser light (C) 2010 by Astro Ltd. Published exclusively by WILEY-VCH Verlag GmbH & Co. KGaA

Synthesis, characterization, crystal structure, and biological studies of vanadium complexes with glycolic acid

Synthesis, characterization, crystal structure, and biological studies of two complexes with glycolic acid are described. The solid complexes were formulated as K2[VO(C2H2O3)(C2H3O3)2] H2O (1) and K2[{VO2(C2H2O3)}2] (2) and characterized by X-ray studies, Fourier transform infrared spectroscopy (FTIR), Electron paramagnetic resonance (EPR), and magnetic susceptibility. Conversion of 1 to 2 was studied in aqueous solution by UV-Vis spectroscopy and in the solid state by diffuse reflectance spectroscopy. Complex 2 contains dinuclear [{VO2(C2H2O3)}2]2- anions in which glycolate(2-) is a five-membered chelating ring formed by carboxylate and -hydroxy groups. The geometry around the vanadium in 2 was interpreted as intermediate between a trigonal bipyramid and a square pyramid. Vanadium(IV) is pentacoordinate in 1 as a distorted square pyramid. Complex 1 contains a vanadyl group (V=O) surrounded by two oxygens from deprotonated carboxylate and hydroxy groups forming a five-membered ring. Two oxygens from different glycolates(1-) are bonded to the (V=O) also. Biological analysis for potential cytotoxic effects of 1 was performed using Human Cervix Adenocarcinoma (HeLa) cells, a human cervix adenocarcinoma-derived cell line. After incubation for 48 h, 1 causes 90 and 95% of HeLa cells death at 20 and 200 mol L-1, respectively.

The Crystal Complex of Phosphofructokinase-2 of Escherichia coli with Fructose-6-phosphate KINETIC AND STRUCTURAL ANALYSIS OF THE ALLOSTERIC ATP INHIBITION

Substrate inhibition by ATP is a regulatory feature of the phosphofructokinases isoenzymes from Escherichia coli (Pfk-1 and Pfk-2). Under gluconeogenic conditions, the loss of this regulation in Pfk-2 causes substrate cycling of fructose-6-phosphate (fructose-6-P) and futile consumption of ATP delaying growth. In the present work, we have broached the mechanism of ATP-induced inhibition of Pfk-2 from both structural and kinetic perspectives. The crystal structure of Pfk-2 in complex with fructose-6-P is reported to a resolution of 2 angstrom. The comparison of this structure with the previously reported inhibited form of the enzyme suggests a negative interplay between fructose-6-P binding and allosteric binding of MgATP. Initial velocity experiments show a linear increase of the apparent K(0.5) for fructose-6-P and a decrease in the apparent k(cat) as a function of MgATP concentration. These effects occur simultaneously with the induction of a sigmoidal kinetic behavior (n(H) of approximately 2). Differences and resemblances in the patterns of fructose-6-P binding and the mechanism of inhibition are discussed for Pfk-1 and Pfk-2, as an example of evolutionary convergence, because these enzymes do not share a common ancestor.

Comparative electrochemical study of 5832-9 stainless steel at different media of biological interest

The electrochemical behavior of ISO 5832-9 stainless steel at 37 degrees C in 0.9% NaCl, Ringer Lactate and minimum essential medium (MEM) has been studied, using linear voltammetry, and surface analysis by SEM and EDS. Mechanical and toxicity tests were made. ISO 5832-9 is passivated at corrosion potential (E) and it does not present pitting corrosion on the media studied from to 50 in V above the transpassivation potential (Ei). SEM and EDS analysis have shown that the sample previously immersed in MEM presents a diffirent behavior at 50 in V above El: the manganese oxide inclusions are absent in the surface. E. values and passivation current density values j(pass) changed according to the following. E(corr, RL) < E(corr,NaCl) < E(corr, MEM) and J (MEM) << j(RL) congruent to j(NaCl) The stainless steel was characterized as non toxic in the cytotoxicity assay

Immobilization of Catalysts of Biological Interest on Porous Oxidized Silicon Surfaces

The present paper deals with the immobilization of redox mediators and proteins onto protected porous silicon surfaces to obtain their direct electrochemical reactions and to retain their bioactivities. This paper shows that MP-11 and viologens are able to establish chemical bonds with 3-aminopropyltriethoxylsilane-modified porous silicon surface. The functionalization of the surfaces have been fully characterized by energy dispersive X-ray analysis (EDX) and X-ray photoelectron spectroscopy (XPS) to examine the immobilization of these mediators onto the solid surface. Amperometric and open circuit potential measurements have shown the direct electron transfer between glucose oxidase and the electrode in the presence of the viologen mediator covalently linked to the 3-aminopropyltriethoxylsilane (APTES)-modified porous silicon surfaces.

Proteome analysis of human dorsolateral prefrontal cortex using shotgun mass spectrometry

The prefrontal cortex executes important functions such as differentiation of conflicting thoughts, correct social behavior and personality expression, and is directly implicated in different neurodegenerative diseases. We performed a shotgun proteome analysis that included IEF fractionation, RP-LC, and MALDI-TOF/TOF mass spectrometric analysis of tryptic digests from a pool of seven human dorsolateral prefrontal cortex protein extracts. In this report, we present a catalog of 387 proteins expressed in these samples, identified by two or more peptides and high confidence search scores. These proteins are involved in different biological processes such as cell growth and/or maintenance, metabolism/energy pathways, cell communication/signal trarisduction, protein metabolism, transport, regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism, and immune response. This analysis contributes to the knowledge of the human brain proteome by adding sample diversity and protein expression data from an alternative technical approach. It will also aid comparative studies of different brain areas and medical conditions, with future applications in basic and clinical research.

Simultaneous analysis of five antidepressant drugs using direct injection of biofluids in a capillary restricted-access media-liquid chromatography-tandem mass spectrometry system

Direct analysis, with minimal sample pretreatment, of antidepressant drugs, fluoxetine, imipramine, desipramine, amitriptyline, and nortriptyline in biofluids was developed with a total run time of 8 min. The setup consists of two HPLC pumps, injection valve, capillary RAM-ADS-C18 pre-column and a capillary analytical C 18 column connected by means of a six-port valve in backflush mode. Detection was performed with ESI-MS/MS and only 1 mu m of sample was injected. Validation was adequately carried out using FLU-d(5) as internal standard. Calibration curves were constructed under a linear range of 1-250 ng mL(-1) in plasma, being the limit of quantification (LOQ), determined as 1 ng mL(-1), for all the analytes. With the described approach it was possible to reach a quantified mass sensitivity of 0.3 pg for each analyte (equivalent to 1.1-1.3 fmol), translating to a lower sample consumption (in the order of 103 less sample than using conventional methods). (C) 2008 Elsevier B.V. All rights reserved.

Fluoxetine and norfluoxetine analysis by direct injection of human plasma in a column switching liquid chromatographic system

A column switching LC method is presented for the analysis of fluoxetine (FLU) and norfluoxetine (NFLU) by direct injection of human plasma using a lab-made restricted access media (RAM) column. A RAM-BSA-octadecyl silica (C-18) column (40 min x 4.6 mm, 10 mu m) is evaluated in both backflush and foreflush elution modes and coupled with a C-18 lab-made (50 mm x 4.6 mm, 3 pm) analytical column in order to perform online sample preparation. Direct injection of 100 mu L, of plasma samples is possible with the developed approach. In addition, reduction of sample handling is obtained when compared with traditional liquid-liquid extraction (LLE) and SPE. The total analysis time is around 20 min. A LOQ of 15 ng/mL is achieved in a concentration range of 15-500 ng/mL, allowing the therapeutic drug monitoring of clinical samples. The precision values achieved are lower than 15% for all the evaluated points with adequate recovery and accuracy. Furthermore, no matrix interferences are found in the analysis and the proposed method shows to be an adequate alternative for analysis of FLU in plasma.

Polydimethylsiloxane/polypyrrole stir bar sorptive extraction and liquid chromatography (SBSE/LC-UV) analysis of antidepressants in plasma samples

A new polymeric coating consisting of a dual-phase, polydimethylsiloxane (PDMS) and polypyrrole (PPY) was developed for the stir bar sorptive extraction (SBSE) of antidepressants (mirtazapine, citalopram, paroxetine, duloxetine, fluoxetine and sertraline) from plasma samples, followed by liquid chromatography analysis (SBSE/LC-UV). The extractions were based on both adsorption (PPY) and sorption (PDMS) mechanisms. SBSE variables, such as extraction time, temperature, pH of the matrix, and desorption time were optimized, in order to achieve suitable analytical sensitivity in a short time period. The PDMS/PPY coated stir bar showed high extraction efficiency (sensitivity and selectivity) toward the target analytes. The quantification limits (LOQ) of the SBSE/LC-UV method ranged from 20 ng mL(-1) to 50 ng mL(-1), and the linear range was from LOQ to 500 ng mL(-1), with a determination coefficient higher than 0.99. The inter-day precision of the SBSE/LC-UV method presented a variation coefficient lower than 15%. The efficiency of the SBSE/LC-UV method was proved by analysis of plasma samples from elderly depressed patients. (C) 2008 Elsevier B.V. All rights reserved.