Crystallographic structure and substrate-binding interactions of the molybdate-binding protein of the phytopathogen Xanthomonas axonopodis pv. citri

In Xanthomonas axonopodis pv. citri (Xac or X citri), the modA gene codes for a periplasmic protein (ModA) that is capable of binding molybdate and tungstate as part of the ABC-type transporter required for the uptake of micronutrients. In this study, we report the crystallographic structure of the Xac ModA protein with bound molybdate. The Xac ModA structure is similar to orthologs with known three-dimensional structures and consists of two nearly symmetrical domains separated by a hinge region where the oxyanion-binding site lies. Phylogenetic analysis of different ModA orthologs based on sequence alignments revealed three groups of molybdate-binding proteins: bacterial phytopathogens, enterobacteria and soil bacteria. Even though the ModA orthologs are segregated into different groups, the ligand-binding hydrogen bonds are mostly conserved, except for Archaeglobus fulgidus ModA. A detailed discussion of hydrophobic interactions in the active site is presented and two new residues, Ala(38) and Ser(151), are shown to be part of the ligand-binding pocket. (c) 2007 Elsevier B.V All rights reserved.

T3 rapidly modulates TSH beta mRNA stability and translational rate in the pituitary of hypothyroid rats

Whereas it is well known that T3 inhibits TSH beta gene transcription, its effects on TSH beta mRNA stability and translation have been poorly investigated. This study examined these possibilities, by evaluating the TSH beta transcripts poly(A) tail length, translational rate and binding to cytoskeleton, in pituitaries of thyroidectomized and sham-operated rats treated with T3 or saline, and killed 30 min thereafter. The hypothyroidism induced an increase of TSH beta transcript poly(A) tail, as well as of its content in ribosomes and attachment to cytoskeleton. The hypothyroid rats acutely treated with T3 exhibited a reduction of TSH beta mRNA poly(A) tail length and recruitment to ribosomes, indicating that this treatment decreased the stability and translation rate of TSH beta mRNA. Nevertheless, acute T3 administration to sham-operated rats provoked an increase of TSH beta transcripts binding to ribosomes. These data add new insight to an important role of T3 in rapidly regulating TSH gene expression at posttranscriptional level. (C) 2010 Elsevier Ireland Ltd. All rights reserved.

Enhancement of Th1 Lung Immunity Induced by Recombinant Mycobacterium bovis Bacillus Calmette-Guerin Attenuates Airway Allergic Disease

Mycobacterium bovis Bacillus Calmette-Guerin (BCG) has been shown to down-regulate experimental allergic asthma, a finding that reinforced the hygiene hypothesis. We have previously found that recombinant BCG (rBCG) strain that express the genetically detoxified Si subunit of pertussis toxin (rBCG-S1PT) exerts an adjuvant effect that enhances Th1 responses against BCG proteins. Here we investigated the effect of this rBCG-S1PT on the classical ovalbumin-induced mouse model of allergic lung disease. We found that rBCG-S1PT was more effective than wild-type BCG in preventing Th2-mediated allergic immune responses. The inhibition of allergic lung disease was not associated with increased concentration of suppressive cytokines or with an increased number of pulmonary regulatory T cells but was positively correlated with the increase in IFN-gamma-producing T cells and T-bet expression in the lung. In addition, an IL-12-dependent mechanism appeared to be important to the inhibition of lung allergic disease. The inhibition of allergic inflammation was found to be restricted to the lung because when allergen challenge was given by the intraperitoneal route, rBCG-S1PT administration failed to inhibit peritoneal allergic inflammation and type 2 cytokine production. Our work offers a nonclassical interpretation for the hygiene hypothesis indicating that attenuation of lung allergy by rBCG could be due to the enhancement of local lung Th1 immunity induced by rBCG-S1PT. Moreover, it highlights the possible use of rBCG strains as multipurpose immunomodulators by inducing specific immunity against microbial products while protecting against allergic asthma.

DNA damage induced by the anthracycline cosmomycin D in DNA repair-deficient cells

Anthracyclines have been widely used as antitumor agents, playing a crucial role in the successful treatment of many types of cancer, despite some side effects related to cardiotoxicity. New anthracyclines have been designed and tested, but the first ones discovered, doxorubicin and daunorubicin, continue to be the drugs of choice. Despite their extensive use in chemotherapy, little is known about the DNA repair mechanisms involved in the removal of lesions caused by anthracyclines. The anthracycline cosmomycin D is the main product isolated from Streptomyces olindensis, characterized by a peculiar pattern of glycosylation with two trisaccharide rings attached to the A ring of the tetrahydrotetracene. We assessed the induction of apoptosis (Sub-G(1)) by cosmomycin D in nucleotide excision repair-deficient fibroblasts (XP-A and XP-C) as well as the levels of DNA damage (alkaline comet assay). Treatment of XP-A and XP-C cells with cosmomycin D resulted in apoptosis in a time-dependent manner, with highest apoptosis levels observed 96 h after treatment. The effects of cosmomycin D were equivalent to those obtained with doxorubicin. The broad caspase inhibitor Z-VAD-FMK strongly inhibited apoptosis in these cells, and DNA damage induced by cosmomycin D was confirmed by alkaline comet assay. Cosmomycin D induced time-dependent apoptosis in nucleotide excision repair-deficient fibroblasts. Despite similar apoptosis levels, cosmomycin D caused considerably lower levels of DNA damage compared to doxorubicin. This may be related to differences in structure between cosmomycin D and doxorubicin.

Eugenol modifies the excitability of rat sciatic nerve and superior cervical ganglion neurons

Eugenol is a phenylpropene obtained from the essential oils of plants such as clove and basil which has ample use in dentistry. Eugenol possesses analgesic effects that may be related to the inhibition of voltage-dependent Na(+) channels and/or to the activation of TRPV1 receptors or both. In the present study, electrophysiological parameters were taken from the compound action potentials of the isolated rat sciatic nerve and from neurons of the superior cervical ganglion (SCG) impaled with sharp microelectrodes under current-clamp conditions. In the isolated rat sciatic nerve, eugenol inhibited the compound action potential in a concentration-dependent manner. Action potentials recorded from SCG neurons were inhibited by eugenol with an IC(50) of 0.31 mM. At high concentrations (2 mM), during brief applications. eugenol caused significant action potential blockade while it did not interfere with the resting membrane potential or the membrane input resistance. Surprisingly, however, at low eugenol concentrations (0.6 mM), during long time applications, a reversible reduction (by about 50%) in the input membrane resistance was observed, suggesting the possible involvement of a secondary delayed effect of eugenol to reduce neuronal excitability. (C) 2010 Elsevier Ireland Ltd. All rights reserved.

Interactions of mast cell degranulating peptides with model membranes: A comparative biophysical study

In the last decade, there has been renewed interest in biologically active peptides in fields like allergy, autoimmume diseases and antibiotic therapy. Mast cell degranulating peptides mimic G-protein receptors, showing different activity levels even among homologous peptides. Another important feature is their ability to interact directly with membrane phospholipids, in a fast and concentration-dependent way. The mechanism of action of peptide HR1 on model membranes was investigated comparatively to other mast cell degranulating peptides (Mastoparan, Eumenitin and Anoplin) to evidence the features that modulate their selectivity. Using vesicle leakage, single-channel recordings and zeta-potential measurements, we demonstrated that HR1 preferentially binds to anionic bilayers, accumulates, folds, and at very low concentrations, is able to insert and create membrane spanning ion-selective pores. We discuss the ion selectivity character of the pores based on the neutralization or screening of the peptides charges by the bilayer head group charges or dipoles. (C) 2009 Elsevier Inc. All rights reserved.

A review on the combination of binary classifiers in multiclass problems

Several real problems involve the classification of data into categories or classes. Given a data set containing data whose classes are known, Machine Learning algorithms can be employed for the induction of a classifier able to predict the class of new data from the same domain, performing the desired discrimination. Some learning techniques are originally conceived for the solution of problems with only two classes, also named binary classification problems. However, many problems require the discrimination of examples into more than two categories or classes. This paper presents a survey on the main strategies for the generalization of binary classifiers to problems with more than two classes, known as multiclass classification problems. The focus is on strategies that decompose the original multiclass problem into multiple binary subtasks, whose outputs are combined to obtain the final prediction.

Topological multi-contour decomposition for image analysis and image retrieval

Successful classification, information retrieval and image analysis tools are intimately related with the quality of the features employed in the process. Pixel intensities, color, texture and shape are, generally, the basis from which most of the features are Computed and used in such fields. This papers presents a novel shape-based feature extraction approach where an image is decomposed into multiple contours, and further characterized by Fourier descriptors. Unlike traditional approaches we make use of topological knowledge to generate well-defined closed contours, which are efficient signatures for image retrieval. The method has been evaluated in the CBIR context and image analysis. The results have shown that the multi-contour decomposition, as opposed to a single shape information, introduced a significant improvement in the discrimination power. (c) 2008 Elsevier B.V. All rights reserved,

Soliton solutions for quasilinear Schrodinger equations with critical growth

In this paper we establish the existence of standing wave solutions for quasilinear Schrodinger equations involving critical growth. By using a change of variables, the quasilinear equations are reduced to semilinear one. whose associated functionals are well defined in the usual Sobolev space and satisfy the geometric conditions of the mountain pass theorem. Using this fact, we obtain a Cerami sequence converging weakly to a solution v. In the proof that v is nontrivial, the main tool is the concentration-compactness principle due to P.L. Lions together with some classical arguments used by H. Brezis and L. Nirenberg (1983) in [9]. (C) 2009 Elsevier Inc. All rights reserved.

Resampling Strategies for Deforming MLS Surfaces

Moving-least-squares (MLS) surfaces undergoing large deformations need periodic regeneration of the point set (point-set resampling) so as to keep the point-set density quasi-uniform. Previous work by the authors dealt with algebraic MLS surfaces, and proposed a resampling strategy based on defining the new points at the intersections of the MLS surface with a suitable set of rays. That strategy has very low memory requirements and is easy to parallelize. In this article new resampling strategies with reduced CPU-time cost are explored. The basic idea is to choose as set of rays the lines of a regular, Cartesian grid, and to fully exploit this grid: as data structure for search queries, as spatial structure for traversing the surface in a continuation-like algorithm, and also as approximation grid for an interpolated version of the MLS surface. It is shown that in this way a very simple and compact resampling technique is obtained, which cuts the resampling cost by half with affordable memory requirements.

Front tracking with moving-least-squares surfaces

The representation of interfaces by means of the algebraic moving-least-squares (AMLS) technique is addressed. This technique, in which the interface is represented by an unconnected set of points, is interesting for evolving fluid interfaces since there is]to surface connectivity. The position of the surface points can thus be updated without concerns about the quality of any surface triangulation. We introduce a novel AMLS technique especially designed for evolving-interfaces applications that we denote RAMLS (for Robust AMLS). The main advantages with respect to previous AMLS techniques are: increased robustness, computational efficiency, and being free of user-tuned parameters. Further, we propose a new front-tracking method based on the Lagrangian advection of the unconnected point set that defines the RAMLS surface. We assume that a background Eulerian grid is defined with some grid spacing h. The advection of the point set makes the surface evolve in time. The point cloud can be regenerated at any time (in particular, we regenerate it each time step) by intersecting the gridlines with the evolved surface, which guarantees that the density of points on the surface is always well balanced. The intersection algorithm is essentially a ray-tracing algorithm, well-studied in computer graphics, in which a line (ray) is traced so as to detect all intersections with a surface. Also, the tracing of each gridline is independent and can thus be performed in parallel. Several tests are reported assessing first the accuracy of the proposed RAMLS technique, and then of the front-tracking method based on it. Comparison with previous Eulerian, Lagrangian and hybrid techniques encourage further development of the proposed method for fluid mechanics applications. (C) 2008 Elsevier Inc. All rights reserved.

Scalable model-based configuration management of security services in complex enterprise networks

Security administrators face the challenge of designing, deploying and maintaining a variety of configuration files related to security systems, especially in large-scale networks. These files have heterogeneous syntaxes and follow differing semantic concepts. Nevertheless, they are interdependent due to security services having to cooperate and their configuration to be consistent with each other, so that global security policies are completely and correctly enforced. To tackle this problem, our approach supports a comfortable definition of an abstract high-level security policy and provides an automated derivation of the desired configuration files. It is an extension of policy-based management and policy hierarchies, combining model-based management (MBM) with system modularization. MBM employs an object-oriented model of the managed system to obtain the details needed for automated policy refinement. The modularization into abstract subsystems (ASs) segment the system-and the model-into units which more closely encapsulate related system components and provide focused abstract views. As a result, scalability is achieved and even comprehensive IT systems can be modelled in a unified manner. The associated tool MoBaSeC (Model-Based-Service-Configuration) supports interactive graphical modelling, automated model analysis and policy refinement with the derivation of configuration files. We describe the MBM and AS approaches, outline the tool functions and exemplify their applications and results obtained. Copyright (C) 2010 John Wiley & Sons, Ltd.

Formal validation of automated policy refinement in the management of network security systems

Policy hierarchies and automated policy refinement are powerful approaches to simplify administration of security services in complex network environments. A crucial issue for the practical use of these approaches is to ensure the validity of the policy hierarchy, i.e. since the policy sets for the lower levels are automatically derived from the abstract policies (defined by the modeller), we must be sure that the derived policies uphold the high-level ones. This paper builds upon previous work on Model-based Management, particularly on the Diagram of Abstract Subsystems approach, and goes further to propose a formal validation approach for the policy hierarchies yielded by the automated policy refinement process. We establish general validation conditions for a multi-layered policy model, i.e. necessary and sufficient conditions that a policy hierarchy must satisfy so that the lower-level policy sets are valid refinements of the higher-level policies according to the criteria of consistency and completeness. Relying upon the validation conditions and upon axioms about the model representativeness, two theorems are proved to ensure compliance between the resulting system behaviour and the abstract policies that are modelled.

Study of metals transfer from environment using teeth as biomonitor

We investigated chronic incorporation of metals in individuals from poor families, living in a small, restrict and allegedly contaminated area in Sao Paulo city, the surroundings of the Guarapiranga dam, responsible for water supply to 25% of the city population. A total of 59 teeth from individuals 7 to 60 years old were collected. The average concentrations of Pb, Cd, Fe, Zn, Mn, Ni and Cr were determined with an Atomic Absorption Spectrophotometer. The concentrations of all metals as function of the individuals` age exhibited a remarkable similarity: peaks between 7 and 10 years and sharply decreasing at higher ages, which could be attributed to alimentary habits and persistence to metals exposure all along the individuals` life span. From all the measured metals, lead and cadmium were a matter of much more concern since their measured values are close to the upper limits of the world wide averages. (C) 2009 Elsevier Ltd. All rights reserved.

Study of environmental burden of lead in children using teeth as bioindicator

The south region of Sao Paulo city hosts the Guarapiranga dam, responsible for water supply to 25% of the city population. Their surroundings have been subject to intense and irregular occupation by people from very low socioeconomics classes. Measurements undertaken on sediment and particulate materials in the dam revealed concentrations of lead. copper, zinc and cadmium above internationally accepted limits. Epidemiological and toxicological studies undertaken by the World Health Organization in individuals exhibiting lead concentrations in blood, near or below the maximum recommended (10 mu g dl(-1)), surprisingly revealed that toxic effects are more intense in individuals belonging to low socioeconomics classes. Motivated by these facts, we aimed at the investigation of chronic incorporation of lead. as well as the use of our BIOKINETICS code, which is based on an accepted ICRP biokinetics model for lead, in order to extrapolate the results from teeth to other organs. The focus of our data taking was children from poor families, living in a small, restrict and allegedly contaminated area in Sao Paulo city. Thus, a total of 74 human teeth were collected. The average concentration of lead in teeth of children 5 to 10 years old was determined by means of a high-resolution inductively coupled plasma mass spectrometer (ICP-MS). For standardization of the measurements, an animal bone certified material (H-Animal Bone), from the International Atomic Energy Agency, was analyzed. The amount of lead in children living in the surroundings of the dam, was approximately 40% higher than those from the control region, and the average lead concentration was equal to 1.3 mu g g(-1) approximately. Grouping the results in terms of gender, tooth type and condition, it was concluded that a carious molar of boys is a much more efficient contamination pathway for lead, resulting in concentrations 70% higher than in the control region. We also inferred the average concentrations of lead in other organs of these children, by making use of our BIOKINETIC code. (C) 2008 Elsevier Ltd. All rights reserved.