Isolation and genotype analysis of rubella virus from a case of Guillain-Barre syndrome

Rubella virus (RV) infection has sporadically been linked to Guillain-Barre syndrome (GBS), but the association with RV has been based only on clinical and/or serological backgrounds. In the present case it was possible to isolate RV (genotype 1a) from cerebrospinal fluid and peripheral blood mononuclear cells of an 18-year-old woman diagnosed with GBS after clinical manifestations of rubella. This report contributes to confirm RV as one of the triggering pathogens of this peripheral nervous system disease. (C) 2008 Elsevier B.V. All rights reserved.

Diversity and quantitative analysis of Archaea in aggressive periodontitis and periodontally healthy subjects

P>Aim To investigate the diversity, levels and proportions of Archaea in the subgingival biofilm of generalized aggressive periodontitis (GAgP; n=30) and periodontally healthy (PH; n=30) subjects. Materials and methods Diversity was determined by sequencing archaeal 16S rRNA gene libraries from 20 samples (10/group). The levels and proportions of Archaea were analysed by quantitative PCR (qPCR) in four and two samples/subject in GAgP and PH groups, respectively. Results Archaea were detected in 27/28 subjects and 68% of the sites of the GAgP group, and in 26/30 subjects and 58.3% sites of the PH group. Methanobrevibacter oralis was found in all 20 samples studied, Methanobacterium curvum/congolense in three GAgP and six PH samples, and Methanosarcina mazeii in four samples from each group. The levels and proportions of Archaea were higher in GAgP than in PH, whereas no differences were observed between the two probing depth category sites from the GAgP group. Conclusion Archaea were frequently found in subjects with periodontal health and GAgP, especially M. oralis. However, the higher levels and proportions (Archaea/total prokaryotes) of this domain observed in GAgP in comparison with PH subjects indicate a possible role of some of these microorganisms as an environmental modifier in GAgP.

Trypanosoma rangeli isolates of bats from Central Brazil: Genotyping and phylogenetic analysis enable description of a new lineage using spliced-leader gene sequences

Trypanosoma rangeli infects several mammalian orders but has never confidently been described in Chiroptera, which are commonly parasitized by many trypanosome species. Here, we described trypanosomes from bats captured in Central Brazil identified as T rangeli,.T. dionisii, T cruzimarinkellei and T cruzi. Two isolates, Tra643 from Platyrrhinus lineatus and Tra1719 from Artibeus plamirostris were identified as T rangeli by morphological, biological and molecular methods, and confirmed by phylogenetic analyses. Analysis using SSU rDNA sequences clustered these bat trypanosomes together with T rangeli from other hosts, and separated them from other trypanosomes from bats. Genotyping based on length and sequence polymorphism of PCR-amplified intergenic spliced-leader gene sequences assigned Tra1719 to the lineage A whereas Tra643 was shown to be a new genotype and was assigned to the new lineage E. To our knowledge, these two isolates are the earliest T rangeli from bats and the first isolates from Central Brazil molecularly characterized. Rhodnius stali captured for this study was found infected by T rangeli and T cruzi. (c) 2008 Elsevier B.V. All rights reserved.

Phylogeny of snake trypanosomes inferred by SSU rDNA sequences, their possible transmission by phlebotomines, and taxonomic appraisal by molecular, cross-infection and morphological analysis

Blood examination by microhaematocrit and haemoculture of 459 snakes belonging to 37 species revealed 24% trypanosome prevalence in species of Viperidae (Crotalus durissus and Bothrops jararaca) and Colubridae (Pseudoboa nigra). Trypanosome cultures from C. durissus and P. nigra were behaviourally and morphologically indistinguishable. In addition, the growth and morphological features of a trypanosome from the sand fly Viannaniyia tuberculata were similar to those of snake isolates. Cross-infection experiments revealed a lack of host restriction, as snakes of 3 species were infected with the trypanosome from C. durissus. Phylogeny based on ribosomal sequences revealed that snake trypanosomes clustered together with the sand fly trypanosome, forming a new phylogenetic lineage within Trypanosoma closest to a clade of lizard trypanosomes transmitted by sand flies dagger. The clade of trypanosomes from snakes and lizards suggests an association between the evolutionary histories of these trypanosomes and their squamate hosts. Moreover, data strongly indicated that these trypanosomes are transmitted by sand flies. The flaws of the current taxonomy of snake trypanosomes are discussed, and the need for molecular parameters to be adopted is emphasized. To our knowledge, this is the first molecular phylogenetic study of snake trypanosomes.

A bivariate regression model for matched paired survival data: local influence and residual analysis

The use of bivariate distributions plays a fundamental role in survival and reliability studies. In this paper, we consider a location scale model for bivariate survival times based on the proposal of a copula to model the dependence of bivariate survival data. For the proposed model, we consider inferential procedures based on maximum likelihood. Gains in efficiency from bivariate models are also examined in the censored data setting. For different parameter settings, sample sizes and censoring percentages, various simulation studies are performed and compared to the performance of the bivariate regression model for matched paired survival data. Sensitivity analysis methods such as local and total influence are presented and derived under three perturbation schemes. The martingale marginal and the deviance marginal residual measures are used to check the adequacy of the model. Furthermore, we propose a new measure which we call modified deviance component residual. The methodology in the paper is illustrated on a lifetime data set for kidney patients.

Characterization and spectroscopic analysis of phenol-ethanol hydrogen bonded clusters

Different hydrogen bonded clusters involving phenol and ethanol are studied theoretically using MP2/aug-cc-pVDZ. Nine different 1: 1 clusters are obtained and analyzed according to their stability and spectroscopic properties. Different isomeric forms of ethanol are considered. Attention is also devoted to the spectral shift of the characteristic pi -> pi* transition of phenol. Using TDHF, CIS, CIS(D) and TDB3LYP in aug-cc-pVDZ basis set, all results agree that a red shift is obtained when phenol is the hydrogen donor and a blue shift is obtained in the opposite case. These results are used to rationalize the red shift observed for phenol in liquid ethanol. (C) 2010 Elsevier B.V. All rights reserved.

Self-adjoint extensions and spectral analysis in the Calogero problem

In this paper, we present a mathematically rigorous quantum-mechanical treatment of a one-dimensional motion of a particle in the Calogero potential alpha x(-2). Although the problem is quite old and well studied, we believe that our consideration based on a uniform approach to constructing a correct quantum-mechanical description for systems with singular potentials and/or boundaries, proposed in our previous works, adds some new points to its solution. To demonstrate that a consideration of the Calogero problem requires mathematical accuracy, we discuss some `paradoxes` inherent in the `naive` quantum-mechanical treatment. Using a self-adjoint extension method, we construct and study all possible self-adjoint operators (self-adjoint Hamiltonians) associated with a formal differential expression for the Calogero Hamiltonian. In particular, we discuss a spontaneous scale-symmetry breaking associated with self-adjoint extensions. A complete spectral analysis of all self-adjoint Hamiltonians is presented.

Self-adjoint extensions and spectral analysis in the generalized Kratzer problem

We present a mathematically rigorous quantum-mechanical treatment of a one-dimensional non-relativistic motion of a particle in the potential field V(x) = g(1)x(-1) + g(2)x(-2), x is an element of R(+) = [0, infinity). For g(2) > 0 and g(1) < 0, the potential is known as the Kratzer potential V(K)(x) and is usually used to describe molecular energy and structure, interactions between different molecules and interactions between non-bonded atoms. We construct all self-adjoint Schrodinger operators with the potential V(x) and represent rigorous solutions of the corresponding spectral problems. Solving the first part of the problem, we use a method of specifying self-adjoint extensions by (asymptotic) self-adjoint boundary conditions. Solving spectral problems, we follow Krein`s method of guiding functionals. This work is a continuation of our previous works devoted to the Coulomb, Calogero and Aharonov-Bohm potentials.

Joint Experimental and Theoretical Analysis of Order Disorder Effects in Cubic BaZrO(3) Assembled Nanoparticles under Decaoctahedral Shape

Periodic first-principles calculations based on density functional theory at the B3LYP level has been carried out to investigate the photoluminescence (PL) emission of BaZrO(3) assembled nanoparticles at room temperature. The defect created in the nanocrystals and their resultant electronic features lead to a diversification of electronic recombination within the BaZrO(3) band gap. Its optical phenomena are discussed in the light of photoluminescence emission at the green-yellow region around 570 nm. The theoretical model for displaced atoms and/or angular changes leads to the breaking of the local symmetry, which is based on the refined structure provided by Rietveld methodology. For each situation a band structure, charge mapping, and density of states were built and analyzed. X-ray diffraction (XRD) patterns, UV-vis measurements, and field emission scanning electron microscopy (FE-SEM) images are essential for a full evaluation of the crystal structure and morphology.

Structural and thermodynamic analysis of thrombin:suramin interaction in solution and crystal phases

Suramin is a hexasulfonated naphthylurea which has been recently characterized as a non-competitive inhibitor of human alpha-thrombin activity over fibrinogen, although its binding site and mode of interaction with the enzyme remain elusive. Here, we determined two X-ray structure of the thrombin: suramin complex, refined at 2.4 angstrom resolution. While a single thrombin: suramin complex was found in the asymmetric unit cell of the crystal, some of the crystallographic contacts with symmetrically related molecules are mediated by both the enzyme and the ligand. Molecular dynamics simulations with the 1:1 complex demonstrate a large rearrangement of suramin in the complex, but with the protein scaffold and the more extensive protein-ligand regions keep unchanged. Small-angle X-ray scattering measurements at high micromolar concentration demonstrate a suramin-induced dimerization of the enzyme. These data indicating a dissimilar binding mode in the monomeric and oligomeric states, with a monomeric, 1:1 complex to be more likely to exist at the thrombin physiological, nanomolar concentration range. Collectively, close understanding on the structural basis for interaction is given which might establish a basis for design of suramin analogues targeting thrombin. Crown Copyright (C) 2009 Published by Elsevier B.V. All rights reserved.

Synthesis and Structural Analysis of New Palladium(II) Thiosaccharinates with Triphenylphosphane or Diphosphanes

A series of palladium(II) thiosaccharinates with triphenylphosphane (PPh(3)), bis(diphenylphosphanyl)methane (dppm), and bis(diphenylphosphanyl)ethane (dppe) have been prepared and characterized. From mixtures of thiosaccharin, Htsac, and palladium(II) acetylacetonate, Pd(acac)(2), the palladium(II) thiosaccharinate, Pd(tsac)(2) (tsac: thiosaccharinate anion) (1) was prepared. The reaction of I with PPh(3), dppm, and dppe leads to the mononuclear species Pd(tsac)(2)(PPh(3))(2)center dot MeCN (2), [Pd(tsac)(2)(dppm)] (3), Pd(tsac)(2)(dppm)(2) (4), and [Pd(tsac)(2)(dppe)]center dot MeCN (5). Compounds 2, 4, and 5 have been prepared also by the reaction of Pd(acac)(2) with the corresponding phosphane and Htsac. All the new complexes have been characterized by chemical analysis, UV/Vis, IR, and Raman spectroscopy. Some of them have been also characterized by NMR spectroscopy. The crystalline structures of complexes 3, and 5 have been studied by X-ray diffraction techniques. Complex 3 crystallizes in the monoclinic space group P2(1)/n with a = 16.3537(2), b = 13.3981(3), c = 35.2277(7) angstrom, beta = 91.284(1)degrees, and Z = 8 molecules per unit cell, and complex 5 in P2(1)/n with a = 10.6445(8), b = 26.412(3), c = 15.781(2) angstrom, beta = 107.996(7)degrees, and Z = 4. In compounds 3 and 5, the palladium ions are in a distorted square planar environment. They are closely related, having two sulfur atoms of two thiosaccharinate anions, and two phosphorus atoms of one molecule of dppm or dppe, respectively, bonded to the Pd(II) atom. The molecular structure of complex 3 is the first reported for a mononuclear Pd(II)-dppm-thionate system.

Structural modeling and mutational analysis of yeast eukaryotic translation initiation factor 5A reveal new critical residues and reinforce its involvement in protein synthesis

Eukaryotic translation initiation factor 5A (eIF5A) is a protein that is highly conserved and essential for cell viability. This factor is the only protein known to contain the unique and essential amino acid residue hypusine. This work focused on the structural and functional characterization of Saccharomyces cerevisiae eIF5A. The tertiary structure of yeast eIF5A was modeled based on the structure of its Leishmania mexicana homologue and this model was used to predict the structural localization of new site-directed and randomly generated mutations. Most of the 40 new mutants exhibited phenotypes that resulted from eIF-5A protein-folding defects. Our data provided evidence that the C-terminal alpha-helix present in yeast eIF5A is an essential structural element, whereas the eIF5A N-terminal 10 amino acid extension not present in archaeal eIF5A homologs, is not. Moreover, the mutants containing substitutions at or in the vicinity of the hypusine modification site displayed nonviable or temperature-sensitive phenotypes and were defective in hypusine modification. Interestingly, two of the temperature-sensitive strains produced stable mutant eIF5A proteins - eIF5A(K56A) and eIF5A(Q22H,L93F)- and showed defects in protein synthesis at the restrictive temperature. Our data revealed important structural features of eIF5A that are required for its vital role in cell viability and underscored an essential function of eIF5A in the translation step of gene expression.

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.

Camptosemin, a tetrameric lectin of Camptosema ellipticum: structural and functional analysis

Lectins have been classified into a structurally diverse group of proteins that bind carbohydrates and glycoconjugates with high specificity. They are extremely useful molecules in the characterization of saccharides, as drug delivery mediators, and even as cellular surface makers. In this study, we present camptosemin, a new lectin from Camptosema ellipticum. It was characterized as an N-acetyl-d-galactosamine-binding homo-tetrameric lectin, with a molecular weight around 26 kDa/monomers. The monomers were stable over a wide range of pH values and exhibited pH-dependent oligomerization. Camptosemin promoted adhesion of breast cancer cells and hemagglutination, and both activities were inhibited by its binding of sugar. The stability and unfolding/folding behavior of this lectin was characterized using fluorescence and far-UV circular dichroism spectroscopies. The results indicate that chemical unfolding of camptosemin proceeds as a two-state monomer-tetramer process. In addition, small-angle X-ray scattering shows that camptosemin behaves as a soluble and stable homo-tetramer molecule in solution.

Sequence and Structural Analysis of the 5 ` Noncoding Region of Hepatitis C Virus in Patients With Chronic Infection

Hepatitis C virus (HCV), exhibits considerable genetic diversity, but presents a relatively well conserved 5 ` noncoding region (5 ` NCR) among all genotypes. In this study, the structural features and translational efficiency of the HCV 5 ` NCR sequences were analyzed using the programs RNAfold, RNAshapes and RNApdist and with a bicistronic dual luciferase expression system, respectively. RNA structure prediction software indicated that base substitutions will alter potentially the 5 ` NCR structure. The heterogeneous sequence observed on 5 ` NCR led to important changes in their translation efficiency in different cell culture lines. Interactions of the viral RNA with cellular transacting factors may vary according to the cell type and viral genome polymorphisms that may result in the translational efficiency observed. J. Med. Virol. 81: 1212-1219, 2009. (C) 2009 Wiley-Liss, Inc.