The CATH classification revisited-architectures reviewed and new ways to characterize structural divergence in superfamilies

The latest version of CATH (class, architecture, topology, homology) (version 3.2), released in July 2008 (http://www.cathdb.info), contains 1 14215 domains, 2178 Homologous superfamilies and 1110 fold groups. We have assigned 20 330 new domains, 87 new homologous superfamilies and 26 new folds since CATH release version 3.1. A total of 28 064 new domains have been assigned since our NAR 2007 database publication (CATH version 3.0). The CATH website has been completely redesigned and includes more comprehensive documentation. We have revisited the CATH architecture level as part of the development of a `Protein Chart` and present information on the population of each architecture. The CATHEDRAL structure comparison algorithm has been improved and used to characterize structural diversity in CATH superfamilies and structural overlaps between superfamilies. Although the majority of superfamilies in CATH are not structurally diverse and do not overlap significantly with other superfamilies, similar to 4% of superfamilies are very diverse and these are the superfamilies that are most highly populated in both the PDB and in the genomes. Information on the degree of structural diversity in each superfamily and structural overlaps between superfamilies can now be downloaded from the CATH website.

XRCC1 haploinsufficiency in mice has little effect on aging, but adversely modifies exposure-dependent susceptibility

Oxidative DNA damage plays a role in disease development and the aging process. A prominent participant in orchestrating the repair of oxidative DNA damage, particularly single-strand breaks, is the scaffold protein XRCC1. A series of chronological and biological aging parameters in XRCC1 heterozygous (HZ) mice were examined. HZ and wild-type (WT) C57BL/6 mice exhibit a similar median lifespan of similar to 26 months and a nearly identical maximal life expectancy of similar to 37 months. However, a number of HZ animals (7 of 92) showed a propensity for abdominal organ rupture, which may stem from developmental abnormalities given the prominent role of XRCC1 in endoderm and mesoderm formation. For other end-points evaluated-weight, fat composition, blood chemistries, condition of major organs, tissues and relevant cell types, behavior, brain volume and function, and chromosome and telomere integrity-HZ mice exhibited by-and-large a normal phenotype. Treatment of animals with the alkylating agent azoxymethane resulted in both liver toxicity and an increased incidence of precancerous lesions in the colon of HZ mice. Our study indicates that XRCC1 haploinsufficiency in mammals has little effect on chronological longevity and many key biological markers of aging in the absence of environmental challenges, but may adversely affect normal animal development or increase disease susceptibility to a relevant genotoxic exposure.

Human endogenous RNAs: Implications for the immunomodulation of Toll-like receptor 3

Toll-like receptors (TLRs), a family of mammalian receptors, are able to recognize nucleic acids. TLR3 recognizes double-stranded (ds)RNA, a product of the replication of certain viruses. Polyinosinic-polycytidylic acid, referred to as poly(I:C), an analog of viral dsRNA, interacts with TLR3 thereby eliciting immunoinflammatory responses characteristic of viral infection or down-regulating the expression of chemokine receptor CXCR4. It is known that dsRNA also directly activates interferon (IFN)-induced enzymes, such as the RNA-dependent protein kinase (PKR). In the present study, the mRNA expression of TLR3, CXCR4, IFN gamma and PKR was investigated in a culture of peripheral blood mononuclear cells (PBMCs) stimulated with poly(I:C) and endogenous RNA from human PBMCs. No cytotoxic effect on the cells or on the proliferation of CD3(+), CD4(+) and CD8(+) cells was observed. TLR3 expression in the PBMCs in the presence of poly(I:C) was up-regulated 9.5-fold, and TLR3 expression in the PBMCs treated with endogenous RNA was down-regulated 1.8-fold (p=0.002). The same trend was observed for IFN gamma where in the presence of poly(I:C) an 8.7-fold increase was noted and in the presence of endogenous RNA a 3.1-fold decrease was observed. In the culture activated with poly(1:C), mRNA expression of CXCR4 increased 8.0-fold and expression of PKR increased 33.0-fold. Expression of these genes decreased in the culture treated with endogenous RNA when compared to the culture without stimulus. Thus, high expression of mRNA for TLR3, IFN gamma, CXCR4 and PKR was observed in the presence of poly(I:C) and low expression was observed in the cells cultured with endogenous RNA. In conclusion, TLR3 may play major physiological roles that are not in the context of viral infection. It is possible that RNA released from cells could contain enough double-stranded structures to regulate cell activation. The involvement of endogenous RNA in endogenous gene expression and its implications in the regulation thereof, are still being studied, and will have significant implications in the future.

alpha-Hydroxynitrile lyase protein from Xylella fastidiosa: Cloning, expression, and characterization

Xylella fastidiosa is a xylem-restricted plant pathogen that causes a range of diseases in several and important crops. Through comparative genomic sequence analysis many genes were identified and, among them, several potentially involved in plant-pathogen interaction. The experimental determination of the primary sequence of some markedly expressed proteins for X fastidiosa and the comparison with the nucleic acids sequence of genome identified one of them as being SCJ21.16 (XFa0032) gene product. The comparative analysis of this protein against SWISSPROT database, in special, resulted in similarity with a-hydroxynitrile lyase enzyme (HNL) from Arabidopsis thaliana, causing interest for being one of the most abundant proteins both in the whole cell extract as well as in the extracellular protein fraction. It is known that HNL enzyme are involved in a process termed ""cyanogenesis"", which catalyzes the dissociation of alpha-hydroxinitrile into carbonyle and HCN when plant tissue is damaged. Although the complete genome sequences of X.fastidiosa are available and the cyanogenesis process is well known, the biological role of this protein in this organism is not yet functionally characterized. In this study we presented the cloning, expression, characterization of recombinant HNL from X fastidiosa, and its probable function in the cellular metabolism. The successful cloning and heterologous expression in Escherichia coli resulted in a satisfactory amount of the recombinant HNL expressed in a soluble, and active form giving convenient access to pure enzyme for biochemical and structural studies. Finally, our results confirmed that the product of the gene XFa0032 can be positively assigned as FAD-independent HNLs. (C) 2009 Elsevier Ltd. All rights reserved.

Efeitos biológicos dos campos eletromagnéticos de ultra alta freqüência

Vários estudos têm sugerido que seres vivos podem ser suscetíveis aos campos eletromagnéticos (CEMs). Os supostos efeitos dos Campos Eletromagnéticos de Ultra Alta Freqüência (CEMUAFs) em sistemas biológicos são pouco conhecidos. Os relatos de um possível efeito biológico dependente da alteração de estados de oxidação entre pares de radicais sugerem um mecanismo de transdução orgânica para os campos. Outros trabalhos obtiveram alterações na sinalização celular e defesas antioxidantes após a exposição CEMUAFs e, tais alterações, poderiam ser um agente causador de doenças como, por exemplo, a leucemia infantil, esta já correlacionada com a exposição aos CEMs. Desta forma o objetivo deste estudo foi investigar se o CEMUAF (834 MHz) poderia interferir com o balanço oxidativo de planárias e ratos, assim como, estudar a participação de enzimas responsáveis pela hidrólise de nucleotídeos, enzimas estas reconhecidas por serem influenciadas pela ação de radicais livres. As planárias foram expostas por 1, 3 e 6 dias (8 h/dia). Após a exposição foi feito um homogenato de todo o corpo de cada animal. Foi encontrado um aumento na atividade da superóxido desmutase (SOD) e um decréscimo na atividade da catalase (CAT) e na defesa antioxidante não-enzimática (TRAP) após 6 dias de exposição. Adicionalmente, houve um aumento na freqüência de micronúcleos (MN) após 3 e 6 dias de exposição. Não houve alteração nos parâmetros de dano oxidativo a lipídios (TBARS) e proteínas (Carbonil) em nenhum dos tempos de exposição. Estes resultados sugerem um aumento nos níveis de radicais livres e de danos aos ácidos nucléicos. Estudos posteriores deverão determinar se estes efeitos apresentam ou não associações do tipo causa e efeito. Foram utilizados três modelos com ratos. No primeiro modelo, animais com idades de 30, 80 e 210 dias foram expostos por 6 dias (7:30 h/dia). Não foram encontradas mudanças nos parâmetros de TRAP, TBARS e Carbonil em nenhuma das idades expostas ao CEMUAF. Estes resultados sugerem que os tempos de exposição utilizados não foram suficientes para causar alguma mudança perceptível nos parâmetros de estresse oxidativo. No segundo modelo, utilizou-se o sangue e fígado dos neonatos expostos ao CEMUAF ainda no útero de suas mães durante todo o seu desenvolvimento embrionário (8:30 h/dia). Não foram encontradas mudanças em nenhum parâmetro oxidativo. Foi encontrado um aumento na freqüência de MN nas hemácias, sugerindo um efeito genotóxico da irradiação do celular afetando o tecido hematopoiético dos fetos. No terceiro modelo, utilizou-se o sangue de ratos adultos (180 dias) expostos por 12 dias (8:30 h/dia). Os níveis da hidrólise de ATP e ADP estavam aumentados no grupo irradiado. Nenhum efeito foi observado nas atividades da SOD e da CAT, sugerindo nenhuma participação de radicais livres nestes resultados. Ainda são necessários muitíssimos estudos para determinar quais os mecanismos transdutores dos CEMUAFs em sistemas biológicos e de que forma esta interação ocorre, porém estes resultados sugerem: (a) um papel para os radicais livres sobre, pelo menos, alguns dos efeitos atribuídos aos CEMUAFs e (b) que os organismos em fase de formação podem ser mais sensíveis aos campos. Por fim, sugerimos que sistemas biológicos podem sofrer a ação da irradiação com uma quantidade de energia muito menor do que a esperada para promover algum efeito no metabolismo.

Florescimento em cana-de-açúcar

O florescimento da cana-de-açúcar é um processo fisiológico complexo formado por vários estádios de desenvolvimento, e cada estádio tem a sua própria necessidade ambiental e fisiológica. Os fatores externos relacionados com o florescimento são: fotoperíodo, temperatura, umidade e radiação solar, além da fertilidade do solo. Por outro lado, os fatores internos envolvem fitocromo, hormônios, florígeno, ácidos nucleicos, dentre outros. A intensidade do processo de florescimento e as consequências na qualidade da cana-de-açúcar variam com a variedade e com o clima. A redução do volume de caldo é o principal fator no qual o florescimento interfere, resultante do aumento do teor de fibras. Como as demais Poaceae, a cana-de-açúcar floresce, frutifica e morre, garantindo a perpetuação da espécie. Dessa forma, o homem procura interferir na natureza tentando evitar o florescimento da cana-de-açúcar, seja por meio de melhoramento genético ou por meio de reguladores vegetais. em áreas comerciais de produção de cana-de-açúcar, onde há condições ideais para o florescimento da cultura, é recomendado o uso de variedade com potencial menos florífero. E, quando não é possível esse manejo varietal, o uso de inibidores do florescimento é a melhor alternativa para evitar mais perdas no conteúdo de sacarose.

Desenvolvimento de sistemas farmacêuticos emulsionados para veiculação gênica

Broadly speaking, the concept of gene therapy involves the transfer of a genetic material into a cell, tissue, or organ in order to cure a disease or at least improve the clinical status of a patient. Making it simple, gene therapy consists in the insertion of functional genes into cells containing defective genes by substituting, complementing or inhibiting them. The achievement of a foreigner DNA expression into a population of cells requires its transfer to the target. Therefore, it is a key issue to create systems able to transfer and protect the DNA until it reaches the target, the vectors. The disadvantages related to the use of viral vectors have encouraged efforts to develop emulsions as non-viral vectors. In fact, they are easily produced, present controllable stability and enable transfection. The aim of this work was to develop an emulsion for gene therapy and evaluate its ability to compact nucleic acids by the development of a complex with the plasmid pIRES2-EGFP. The first step was to determine the Hydrophilic Lipophilic Balance (HLB) of the Captex® 355 (oily internal phase of the emulsion) through long and short term stability assays. Based on the results, emulsions composed of Captex® 355, Tween 20® and Span 60® with 10.7 HLB were produced by three different methods: phase inversion, spontaneous emulsification and sonication. The results showed that the lowest diameter and best stability of the emulsions were achieved by the sonication method. The cationic emulsions were made by adding DOTAP to the basic emulsion. Its association with pIRES2-EGFP was evaluated by electrophoresis. Several rates of emulsion and DNA were evaluated and the results showed that 100% of the complex was formed when the rate DOTAP/DNA(nmol/µg) was 130. In conclusion, the overall results show the ability of the proposed emulsion to compact pIRES2-EGFP, which is a requirement to a successful transfection. Therefore, such formulation may be considered a promising candidate for gene therapy

Adsorption and detection of DNA dendrimers at carbon electrodes

Dendritic nucleic acids are highly branched and ordered molecular structures, possessing numerous single-stranded oligonucleotide arms, which hold great promise for enhancing the sensitivity of DNA biosensors. This article evaluates the interfacial behavior and redox activity of nucleic acid dendrimers at carbon paste electrodes, in comparison to DNA. Factors influencing the adsorption behavior, including the adsorption potential and time, solution conditions, or dendrimer concentration, are explored. The strong adsorption at the anodically pretreated carbon surface is exploited for an effective preconcentration step prior to the chronopotentiometric measurement of the surface species. Coupled with the numerous guanine oxidation sites, such stripping protocol offers remarkably low detection limits (e.g., 3 pM or 2.4 femtomole of the I-layer dendrimer following a 15 min accumulation). The new observations bear important implications upon future biosensing applications of nucleic dendrimers.

Clinical and microbiological studies of children and adolescents receiving orthodontic treatment

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Coagglutination for viral DNA preparation of canine parvovirus for molecular diagnosis

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements

We report a method for studying global DNA methylation based on using bisulfite treatment of DNA and simultaneous PCR of multiple DNA repetitive elements, such as Alu elements and long interspersed nucleotide elements (LINE). The PCR product, which represents a pool of approximately 15000 genomic loci, could be used for direct sequencing, selective restriction digestion or pyrosequencing, in order to quantitate DNA methylation. By restriction digestion or pyrosequencing, the assay was reproducible with a standard deviation of only 2% between assays. Using this method we found that almost two-thirds of the CpG methylation sites in Alu elements are mutated, but of the remaining methylation target sites, 87% were methylated. Due to the heavy methylation of repetitive elements, this assay was especially useful in detecting decreases in DNA methylation, and this assay was validated by examining cell lines treated with the methylation inhibitor 5-aza-2'deoxycytidine (DAC), where we found a 1-16% decrease in Alu element and 18-60% LINE methylation within 3 days of treatment. This method can be used as a surrogate marker of genome-wide methylation changes. In addition, it is less labor intensive and requires less DNA than previous methods of assessing global DNA methylation.

Enzimas termoestáveis: fontes, produção e aplicação industrial

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Study of the nucleolar cycle and ribosomal RNA distribution during meiosis in triatomines (Triatominae, Heteroptera)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Aggregation behavior of aqueous dioctadecyldimethylammonium bromide/monoolein mixtures: A multitechnique investigation on the composition and temperature

A recently described non-viral gene delivery system [dioctadecyldimethylammonium bromide (DODAB)/monoolein (MO)] has been studied in detail to improve knowledge on the interactions between lamellar (DODAB) and non-lamellar-forming (MO) lipids, as a means to enhance their final cell transfection efficiency. Indeed, the morphology, fluidity, and size of these cationic surfactant/neutral lipid mixtures play an important role in the ability of these systems to complex nucleic acids. The different techniques used in this work, namely dynamic light scattering (DLS), fluorescence spectroscopy, differential scanning calorimetry (DSC), cryogenic transmission electron microscopy (cryo-TEM), light microscopy (LM), and surface pressure-area isotherms, allowed fully characterization of the phase behavior and aggregate morphology of DODAB/MO mixtures at different molar ratios. Overall, the results indicate that the final morphology of DODAB/MO aggregates depends on the balance between the tendency of DODAB to form zero-curvature bilayer structures and the propensity of MO to form non-bilayer structures with negative curvature. These results also show that in the MO-rich region, an increase in temperature has a similar effect on aggregate morphology as an increase in MO concentration. (C) 2012 Elsevier B.V. All rights reserved.

Molecular physicochemical parameters predicting antioxidant activity of Brazilian natural products

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)