A SequenceSpace analysis of Lys49 phospholipases A2: Clues towards identification of residues involved in a novel mechanism of membrane damage and in myotoxicity

'SequenceSpace' analysis is a novel approach which has been used to identify unique amino acids within a subfamily of phospholipases A2 (PLA2) in which the highly conserved active site residue Asp49 is substituted by Lys (Lys49-PLA2s). Although Lys49-PLA2s do not bind the catalytic co-factor Ca2+ and possess extremely low catalytic activity, they demonstrate a Ca2+-independent membrane damaging activity through a poorly understood mechanism, which does not involve lipid hydrolysis. Additionally, Lys49-PLA2s possess combined myotoxic, oedema forming and cardiotoxic pharmacological activities, however the structural basis of these varied functions is largely unknown. Using the 'SequenceSpace' analysis we have identified nine residues highly unique to the Lys49-PLA2 sub-family, which are grouped in three amino acid clusters in the active site, hydrophobic substrate binding channel and homodimer interface regions. These three highly specific residue clusters may have relevance for the Ca2+-independent membrane damaging activity. Of a further 15 less stringently conserved residues, nine are located in two additional clusters which are well isolated from the active site region. The less strictly conserved clusters have been used in predictive sequence searches to correlate amino acid patterns in other venom PLA2s with their pharmacological activities, and motifs for presynaptic and combined toxicities are proposed.

Decrease of the DNA damage levels after sperm preparation by layering method

The aim of this prospective study was to determine the DNA fragmentation levels before and after sperm preparation by layering method. A total of 78 patients submitted to assisted reproduction technology (ART) for infertility treatment were evaluated. Ejaculated spermatozoa were obtained by masturbation on the day of ART procedure. The evaluation of DNA fragmentation was performed in the fresh semen and after preparation by a layering method, respectively. After washing with PBS, the sperm pellets were smears and then processed for the terminal deoxyribonucleotidyl transferase (TdT)-mediated dUTP nick-end labelling (TUNEL) assay that was performed using a Cell Death Detection Kit with tetramethylrhodamine-labelled dUTP. For quantitative evaluation, 200 spermatozoa in randomly selected areas on microscope slides were evaluated and the percentage of TUNEL positive spermatozoa was determined. If ≥20% of selected sperm were TUNEL positive, the exam was considered abnormal. The mean percentage of DNA sperm fragmentation before sperm preparation was 17±8.3% and after 7.8±6.5% (p<0.0001). The exam was considered normal in 49 patients before preparation and in 73 patients after (p<0.0001). The sperm preparation with a layering method for the ART procedure is effective to select sperm with a significant decrease of the DNA damage.

Tethered DNA scaffolds on optical sensor platforms for detection of hipO gene from Campylobacter jejuni

DNA biosensors have gained increased attention over traditional diagnostic methods due to their fast and responsive operation and cost-effective design. The specificity of DNA biosensors relies on single-stranded oligonucleotide probes immobilized to a transduction platform. Here, we report the development of biosensors to detect the hippuricase gene (hipO) from Campylobacter jejuni using direct covalent coupling of thiol- and biotin-labeled single-stranded DNA (ssDNA) on both surface plasmon resonance (SPR) and diffraction optics technology (DOT, dotLab) transduction platforms. This is the first known report of the dotLab to detect targeted DNA. Application of 6-mercapto-1-hexanol as a spacer thiol for SPR gold surface created a self-assembled monolayer that removed unbound ssDNA and minimized non-specific detection. The detection limit of SPR sensors was shown to be 2.5 nM DNA while dotLab sensors demonstrated a slightly decreased detection limit of 5.0 nM (0.005 μM). It was possible to reuse the SPR sensor due to the negligible changes in sensor sensitivity (∼9.7 × 10 -7 ΔRU) and minimal damage to immobilized probes following use, whereas dotLab sensors could not be reused. Results indicated feasibility of optical biosensors for rapid and sensitive detection of the hipO gene of Campylobacter jejuni using specific ssDNA as a probe. © 2011 Elsevier B.V.

Characterization of the temperature, load and damage effects using piezoelectric transducer patches based on fuzzy clustering

Structural Health Monitoring (SHM) denotes a system with the ability to detect and interpret adverse changes in a structure. One of the critical challenges for practical implementation of SHM system is the ability to detect damage under changing environmental conditions. This paper aims to characterize the temperature, load and damage effects in the sensor measurements obtained with piezoelectric transducer (PZT) patches. Data sets are collected on thin aluminum specimens under different environmental conditions and artificially induced damage states. The fuzzy clustering algorithm is used to organize the sensor measurements into a set of clusters, which can attribute the variation in sensor data due to temperature, load or any induced damage.

A malware detection system inspired on the human immune system

Malicious programs (malware) can cause severe damage on computer systems and data. The mechanism that the human immune system uses to detect and protect from organisms that threaten the human body is efficient and can be adapted to detect malware attacks. In this paper we propose a system to perform malware distributed collection, analysis and detection, this last inspired by the human immune system. After collecting malware samples from Internet, they are dynamically analyzed so as to provide execution traces at the operating system level and network flows that are used to create a behavioral model and to generate a detection signature. Those signatures serve as input to a malware detector, acting as the antibodies in the antigen detection process. This allows us to understand the malware attack and aids in the infection removal procedures. © 2012 Springer-Verlag.

Crystallographic portrayal of different conformational states of a Lys49 phospholipase A2 homologue: Insights into structural determinants for myotoxicity and dimeric configuration

Catalytically inactive phospholipase A2 (PLA2) homologues play key roles in the pathogenesis induced by snake envenomation, causing extensive tissue damage via a mechanism still unknown. Although, the amino acid residues directly involved in catalysis are conserved, the substitution of Asp49 by Arg/Lys/Gln or Ser prevents the binding of the essential calcium ion and hence these proteins are incapable of hydrolyzing phospholipids. In this work, the crystal structure of a Lys49-PLA2 homologue from Bothrops brazili (MTX-II) was solved in two conformational states: (a) native, with Lys49 singly coordinated by the backbone oxygen atom of Val31 and (b) complexed with tetraethylene glycol (TTEG). Interestingly, the TTEG molecule was observed in two different coordination cages depending on the orientation of the nominal calcium-binding loop and of the residue Lys49. These structural observations indicate a direct role for the residue Lys49 in the functioning of a catalytically inactive PLA2 homologue suggesting a contribution of the active site-like region in the expression of pharmacological effects such as myotoxicity and edema formation. Despite the several crystal structures of Lys49-PLA2 homologues already determined, their biological assembly remains controversial with two possible conformations. The extended dimer with the hydrophobic channel exposed to the solvent and the compact dimer in which the active site-like region is occluded by the dimeric interface. In the MTX-II crystal packing analysis was found only the extended dimer as a possible stable quaternary arrangement. © 2012 Elsevier B.V.

NF-kB overexpression and decreased immunoexpression of AR in the muscular layer is related to structural damages and apoptosis in cimetidine-treated rat vas deferens

Background: Cimetidine, histamine H2 receptors antagonist, has caused adverse effects on the male hormones and reproductive tract due to its antiandrogenic effect. In the testes, peritubular myoid cells and muscle vascular cells death has been associated to seminiferous tubules and testicular microvascularization damages, respectively. Either androgen or histamine H2 receptors have been detected in the mucosa and smooth muscular layer of vas deferens. Thus, the effect of cimetidine on this androgen and histamine-dependent muscular duct was morphologically evaluated.Methods: The animals from cimetidine group (CMTG; n=5) received intraperitoneal injections of 100 mg/kg b.w. of cimetidine for 50 days; the control group (CG) received saline solution. The distal portions of vas deferens were fixed in formaldehyde and embedded in paraffin. Massońs trichrome-stained sections were subjected to morphological and the following morphometrical analyzes: epithelial perimeter and area of the smooth muscular layer. TUNEL (Terminal deoxynucleotidyl-transferase mediated dUTP Nick End Labeling) method, NF-kB (nuclear factor kappa B) and AR (androgen receptors) immunohistochemical detection were also carried out. The birefringent collagen of the muscular layer was quantified in picrosirius red-stained sections under polarized light. The muscular layer was also evaluated under Transmission Electron Microscopy (TEM).Results: In CMTG, the mucosa of vas deferens was intensely folded; the epithelial cells showed numerous pyknotic nuclei and the epithelial perimeter and the area of the muscular layer decreased significantly. Numerous TUNEL-labeled nuclei were found either in the epithelial cells, mainly basal cells, or in the smooth muscle cells which also showed typical features of apoptosis under TEM. While an enhanced NF-kB immunoexpression was found in the cytoplasm of muscle cells, a weak AR immunolabeling was detected in these cells. In CMTG, no significant difference was observed in the birefringent collagen content of the muscular layer in comparison to CG.Conclusions: Cimetidine induces significant damages in the epithelium; a possible antiandrogenic effect on the basal cells turnover should be considered. The cimetidine-induced muscle cells apoptosis confirms the susceptibility of these cells to this drug. The parallelism between enhanced cytoplasmic NF-kB immunolabeling in the damaged muscular tissue and muscle cell apoptosis suggests that this drug may avoid the translocation of NF-kB to the nucleus and interfere in the control of NF-kB-mediated smooth muscle cell apoptosis. The decreased immunoexpression of ARs verified in the damaged muscular tissue reinforces this possibility. © 2013 Koshimizu et al.; licensee BioMed Central Ltd.

Detection of post-F1 fish hybrids in broodstock using molecular markers: Approaches for genetic management in aquaculture

Herein, we have developed molecular markers for nuclear genes to use in multiplex-PCR and PCR-RFLP, with the goal of characterising hybrid lines derived from crosses between pintado Pseudoplatystoma corruscans and cachara P. reticulatum. These markers, together with others described previously, were used to perform molecular identification analyses as genetic subsidies for Brazilian aquaculture. These analyses were performed due to the problems of high mortality in the offspring reported by the aquaculturist. From a total of 16 broodstock samples, 13 were genetically identified as hybrids; surprisingly, nine of these hybrids were found to be post-F1 lineages. These data show that the fertility of these animals can seriously affect the cultivated stocks, thus causing financial damage in this aquaculture system. The establishment of PCR-RFLP and multiplex-PCR as molecular techniques allows for both the correct management of these animals and the routine monitoring of production and trade of fish hybrids in aquaculture. Consequently, such tools will enable a sustainable development in the aquaculture industry. © 2012 Blackwell Publishing Ltd.

Assessment of the damage caused by flood rains and landslides in association with hurricane Michelle, october 2001: implications for economic, social and environmental development

Preface This study was prepared for the Government of Jamaica following the significant physical damage and economic losses that the country sustained as a result of flood rains associated with the development of Hurricane Michelle. The Planning Institute of Jamaica (PIOJ) submitted a request for assistance in undertaking a social, environmental and economic impact assessment to the Economic Commission for Latin America and the Caribbean (ECLAC) on 14 November 2001. ECLAC responded with haste and modified its work plan to accommodate the request. A request for training in the use of the ECLAC Methodology to be delivered to personnel in Jamaica was deferred until the first quarter of 2002, as it was impossible to mount such an initiative at such short notice. This appraisal considers the consequences of the three instances of heavy rainfall that brought on the severe flooding and loss of property and livelihoods. The study was prepared by three members of the ECLAC Natural Disaster Damage Assessment Team over a period of one week in order to comply with the request that it be presented to the Prime Minister on 3 December 2001. The team has endeavoured to complete a workload that would take two weeks with a team of 15 members working assiduously with data already prepared in preliminary form by the national emergency stakeholders. There is need for training in disaster assessment as evidenced by the data collected by the Jamaican officials engaged in the exercise. Their efforts in the future will be more focused and productive after they have received training in the use of the ECLAC Methodology. This study undertakes a sectoral analysis leading to an overall assessment of the damage. It appraises the macroeconomic and social effects and proposes some guidelines for action including mitigating actions subsequent to the devastation caused by the weather system. The team is grateful for the efforts of the Office of Disaster Preparedness and Emergency Management (ODPEM), the associated government ministries and agencies, the Statistical Institute of Jamaica (STATIN), the Planning Institute of Jamaica and the Inter American Development Bank (IDB) for assistance rendered to the team. Indeed, it is the recommendation of the team that STATIN is poised to play a pivotal role in any disaster damage assessment and should be taken on board in that regard. The direct and indirect damages have been assessed in accordance with the methodology developed by ECLAC (1). The results presented are based on the mission's estimates. The study incorporates the information made available to the team and evidence collected in interviews and visits to affected locations. It is estimated that the magnitude of the losses exceeds the country's capacity to address reparations and mitigation without serious dislocation of its development trajectory. The government may wish to approach the international community for assistance in this regard. This appraisal is therefore designed to provide the government and the international community with guidelines for setting national and regional priorities in rehabilitation and reconstruction or resettlement programmes. A purely economic conception of the problem would be limited. A more integrated approach would have a human face and consider the alleviation of human suffering in the affected areas while attending to the economic and fiscal fallout of the disaster. Questions of improved physical planning, watershed management, early warning, emergency response and structural preparedness for evacuation and sheltering the vulnerable population are seen as important considerations for the post disaster phase. Special attention and priority should be placed on including sustainability and increased governance criteria in making social and productive investments, and on allocating resources to the reinforcing and retrofitting of vulnerable infrastructure, basic lifelines and services as part of the reconstruction and rehabilitation strategy. The Jamaican society and government face the opportunity of undertaking action with the benefit of revised paradigms, embarking on institutional, legal and structural reforms to reduce economic, social and environmental vulnerability. The history of flood devastation in the very areas of Portland and St. Mary shows a recurrence of flooding. Accounts of flooding from the earliest recorded accounts pertaining to 1837 are available. Recurrences in 1937, 1940, 1943 and 2001 indicate an ever-present probability of recurrence of similar events. The Government may wish to consider the probable consequences of a part of its population living in flood plains and address its position vis-à­¶is land use and the probability of yet another recurrence of flood rains. (1) ECLAC/IDNDR, Manual for estimating the Socio-Economic Effects of Natural Disasters, May,1999.

Metodologias para reconhecimento de padrões em sistemas SHM utilizando a técnica da Impedância Eletromecânica (E/M)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Genotoxicidade humana e fármacos antidepressivos: avaliação da duloxetina em culturas de linfócitos

Fármacos antidepressivos são largamente utilizados no tratamento sintomático do transtorno depressivo. Inúmeras pesquisas atuais sobre a depressão vêm contribuindo para o avanço da terapia farmacológica e para o surgimento de novos fármacos antidepressivos. Diretrizes atuais para testes de genotoxicidade de novos medicamentos sugerem a importante utilidade de ensaios que detectem danos ao DNA, ou seja, testes para avaliar a indução de quebras no DNA. Entretanto, o número escasso de dados sobre a genotoxicidade de fármacos faz com que seja reduzido o número de fármacos que realmente podem ser usados em segurança. Portanto, é de extrema importância estudos sobre a avaliação genotoxicológica de fármacos, principalmente, drogas utilizadas por um longo período de tempo como é o caso dos antidepressivos. A duloxetina é um antidepressivo novo, pertencente à classe dos inibidores seletivos da recaptação de serotonina e noradrenalina (ISRSN), utilizada no tratamento sintomático da depressão. Apesar da existência de trabalhos demonstrando que alguns fármacos antidepressivos são genotóxicos, não existe até hoje nenhum estudo sobre a possível genotoxicidade da duloxetina em células de origem humana. Assim, o presente estudo tem como objetivo explorar o possível potencial genotóxico in vitro da duloxetina em culturas primárias de linfócitos humanos através das técnicas de detecção de aberrações cromossômicas e micronúcleos. Culturas primárias de linfócitos sanguíneos de voluntários sadios foram expostas a diferentes concentrações de duloxetina (10-150 ng/ml) e ciclofosfamida (6 μg/ml) como controle positivo. Aberrações cromossômicas estruturais, índice mitótico, índice de divisão nuclear, índice de binucleação, número de células com um, dois, três e quatro micronúcleos e o número de células com pontes nucleoplasmáticas foram avaliadas. Todos os índices das culturas incubadas com duloxetina foram significativamente menores que aqueles dos grupos controles, indicando um certo grau de citotoxicidade da droga. Entretanto, só as concentrações de 100 e 150 ng/ml provocaram o aumento significativo da presença de aberrações cromossômicas e micronúcleos. Considerando que essas concentrações ficam perto do limite superior da faixa terapêutica da droga usada em humanos, nossos resultados alertam já sobre a necessidade de aprofundar no conhecimento da genotoxicidade humana da duloxetina.

Polymer Matrix-Based Piezoelectric Composite for Structural Health Monitoring

Structural health monitoring (SHM) refers to the procedure of assessing the structure conditions continuously so it is an alternative to conventional nondestructive evaluation (NDE) techniques [1]. With the growing developments in sensor technology acoustic emission (AE) technology has been attracting attention in SHM applications. AE are characterized by waves produced by the sudden internal stress redistribution caused by the changes in the internal structure, such as fatigue, crack growth, corrosion, etc. Piezoelectric materials such as Lead Zirconate Titanate (PZT) ceramic have been widely used as sensor due to its high electromechanical coupling factor and piezoelectric d coefficients. Because of the poor mechanical characteristic and the lack in the formability of the ceramic, polymer matrix-based piezoelectric composites have been studied in the last decade in order to obtain better properties in comparison with a single phase material. In this study a composite film made of polyurethane (PU) and PZT ceramic particles partially recovered with polyaniline (PAni) was characterized and used as sensor for AE detection. Preliminary results indicate that the presence of a semiconductor polymer (PAni) recovering the ceramic particles, make the poling process easier and less time consuming. Also, it is possible to observe that there is a great potential to use such type of composite as sensor for structure health monitoring.

Estudo de sensores PZT aplicados à detecção de danos em tubulações

Pós-graduação em Engenharia Elétrica - FEIS

Nonlinear formulation based on FEM, Mazars damage criterion and Fick's law applied to failure assessment of reinforced concrete structures subjected to chloride ingress and reinforcements corrosion

Structural durability is an important design criterion, which must be assessed for every type of structure. In this regard, especial attention must be addressed to the durability of reinforced concrete (RC) structures. When RC structures are located in aggressive environments, its durability is strongly reduced by physical/chemical/mechanical processes that trigger the corrosion of reinforcements. Among these processes, the diffusion of chlorides is recognized as one of major responsible of corrosion phenomenon start. To accurate modelling the corrosion of reinforcements and to assess the durability of RC structures, a mechanical model that accounts realistically for both concrete and steel mechanical behaviour must be considered. In this context, this study presents a numerical nonlinear formulation based on the finite element method applied to structural analysis of RC structures subjected to chloride penetration and reinforcements corrosion. The physical nonlinearity of concrete is described by Mazars damage model whereas for reinforcements elastoplastic criteria are adopted. The steel loss along time due to corrosion is modelled using an empirical approach presented in literature and the chloride concentration growth along structural cover is represented by Fick's law. The proposed model is applied to analysis of bended structures. The results obtained by the proposed numerical approach are compared to responses available in literature in order to illustrate the evolution of structural resistant load after corrosion start. (C) 2014 Elsevier Ltd. All rights reserved.

2 '-Deoxyguanosine, 2 '-deoxycytidine, and 2 '-deoxyadenosine adducts resulting from the reaction of tetrahydrofuran with DNA bases

A recent study showed that tetrahydrofuran (THF), a widely used solvent, is carcinogenic in experimental animals. Despite its carcinogenic activity, there is a paucity of information regarding cellular toxicity, biomolecular damage, and genotoxicity induced by THF. We describe here the structural characterization of adducts produced by the reaction of oxidized THF with 2'-deoxyguanosine (dGuo-THF 1 and dGuo-THF 2), 2'-deoxyadenosine (dAdo-THF), and 2'-deoxycytidine (dCyd-THF). Adducts were isolated from in vitro reactions by reverse-phase HPLC and fully characterized on the basis of spectroscopic measurements. The stable derivatives obtained by the reduction of adducts with NaBH4 ( the case of dGuo-THF 1, dCyd-THF, and dAdo-THF) and the stable adduct dGuo-THF 2 were used as standards for optimization of chromatographic separations for adduct detection in DNA through HPLC/ESI/MSMS. Using this methodology, we successfully detected the four adducts in calf thymus DNA reacted with oxidized THF. The present study also provides evidence that rat liver microsomal monooxigenases oxidize THF to the reactive electrophilic compounds that are able to damage the DNA molecule, as indicated by a significant increase in adduct dGuo-THF 1 level when NADPH was added to the THF/ microsomes/dGuo incubation mixtures. Our data point to DNA-THF adducts as possible contributing factors to the toxicological effects of THF exposure.