Rates of gene rearrangement and nucleotide substitution are correlated in the mitochondrial genomes of insects

A number of studies indicated that lineages of animals with high rates of mitochondrial (mt) gene rearrangement might have high rates of mt nucleotide substitution. We chose the hemipteroid assemblage and the Insecta to test the idea that rates of mt gene rearrangement and mt nucleotide substitution are correlated. For this purpose, we sequenced the mt genome of a lepidopsocid from the Psocoptera, the only order of hemipteroid insects for which an entire mtDNA sequence is not available. The mt genome of this lepidopsocid is circular, 16,924 bp long, and contains 37 genes and a putative control region; seven tRNA genes and a protein-coding gene in this genome have changed positions relative to the ancestral arrangement of mt genes of insects. We then compared the relative rates of nucleotide substitution among species from each of the four orders of hemipteroid insects and among the 20 insects whose mt genomes have been sequenced entirely. All comparisons among the hernipteroid insects showed that species with higher rates of gene rearrangement also had significantly higher rates of nucleotide substitution statistically than did species with lower rates of gene rearrangement. In comparisons among the 20 insects, where the mt genomes of the two species differed by more than five breakpoints, the more rearranged species always had a significantly higher rate of nucleotide substitution than the less rearranged species. However, in comparisons where the mt genomes of two species differed by five or less breakpoints, the more rearranged species did not always have a significantly higher rate of nucleotide substitution than the less rearranged species. We tested the statistical significance of the correlation between the rates of mt gene rearrangement and mt nucleotide substitution with nine pairs of insects that were phylogenetically independent from one 2 another. We found that the correlation was positive and statistically significant (R-2 = 0.73, P = 0.01; R-s = 0.67, P < 0.05). We propose that increased rates of nucleotide substitution may lead to increased rates of gene rearrangement in the mt genomes of insects.

An approach to verifying and debugging simulation models governed by ordinary differential equations: Part 1. Methodology for residual generation

For dynamic simulations to be credible, verification of the computer code must be an integral part of the modelling process. This two-part paper describes a novel approach to verification through program testing and debugging. In Part 1, a methodology is presented for detecting and isolating coding errors using back-to-back testing. Residuals are generated by comparing the output of two independent implementations, in response to identical inputs. The key feature of the methodology is that a specially modified observer is created using one of the implementations, so as to impose an error-dependent structure on these residuals. Each error can be associated with a fixed and known subspace, permitting errors to be isolated to specific equations in the code. It is shown that the geometric properties extend to multiple errors in either one of the two implementations. Copyright (C) 2003 John Wiley Sons, Ltd.

Balancing the number and size of sites: An economic approach to the optimal design of cluster samples

The design of randomized controlled trials entails decisions that have economic as well as statistical implications. In particular, the choice of an individual or cluster randomization design may affect the cost of achieving the desired level of power, other things being equal. Furthermore, if cluster randomization is chosen, the researcher must decide how to balance the number of clusters, or sites, and the size of each site. This article investigates these interrelated statistical and economic issues. Its principal purpose is to elucidate the statistical and economic trade-offs to assist researchers to employ randomized controlled trials that have desired economic, as well as statistical, properties. (C) 2003 Elsevier Inc. All rights reserved.

Synthesis of optically complex core-shell colloidal suspensions: Pathways to multiplexed biological screening

The ability to generate enormous random libraries of DNA probes via split-and-mix synthesis on solid supports is an important biotechnological application of colloids that has not been fully utilized to date. To discriminate between colloid-based DNA probes each colloidal particle must be 'encoded' so it is distinguishable from all other particles. To this end, we have used novel particle synthesis strategies to produce large numbers of optically encoded particle suitable for DNA library synthesis. Multifluorescent particles with unique and reproducible optical signatures (i.e., fluorescence and light-scattering attributes) suitable for high-throughput flow cytometry have been produced. In the spectroscopic study presented here, we investigated the optical characteristics of multi-fluorescent particles that were synthesized by coating silica 'core' particles with up to six different fluorescent dye shells alternated with non-fluorescent silica 'spacer' shells. It was observed that the diameter of the particles increased by up to 20% as a result of the addition of twelve concentric shells and that there was a significant reduction in fluorescence emission intensities from inner shells as an increasing number of shells were deposited.

Generation of aldehyde-derived protein modifications in ethanol-exposed heart

Background: Although excessive ethanol consumption is known to lead to a variety of adverse effects in the heart, the molecular mechanisms of such effects have remained poorly defined. We hypothesized that posttranslational covalent binding of reactive molecular species to proteins occurs in the heart in response to acute ethanol exposure. Methods: The generation of protein adducts with several aldehydic species was examined by using monospecific antibodies against adducts with malondialdehyde (MDA), acetaldehyde (AA), MDA-AA hybrids, and hydroxyethyl radicals. Specimens of heart tissue were obtained from rats after intraperitoneal injections with alcohol (75 mmol/kg body weight) with or without pretreatment with cyanamide (0.05 mmol/kg body weight), an aldehyde dehydrogenase inhibitor. Results: The amounts of MDA and unreduced AA adducts were found to be significantly increased in the heart of the rats treated with ethanol, cyanamide, or both, whereas no other adducts were detected in statistically significant quantities. Immunohistochemical studies for characterization of adduct distribution revealed sarcolemmal adducts of both MDA and AA in the rats treated with ethanol and cyanamide in addition to intracellular adducts, which were also present in the group treated with ethanol alone. Conclusions: These findings support the role of enhanced lipid peroxidation and the generation of protein-aldehyde condensates in vivo as a result of excessive ethanol intake. These findings may have implications in the molecular mechanisms of cardiac dysfunction in alcoholics.

Efeito da restrição hídrica sobre o crescimento de clones de eucalipto

O estabelecimento e o crescimento inicial de espécies florestais no campo são fortemente afetados pela disponibilidade de água no solo e pela época de plantio, por isso, o presente trabalho estuda o impacto do déficit hídrico no crescimento de mudas de dois clones do híbrido Eucalyptus grandis x Eucalyptus urophylla, ambos submetidos a 4 níveis de déficit hídrico, em duas épocas de plantio. O estudo foi realizado na área experimental do Núcleo de Estudos e Difusão de Tecnologia em Florestas, Recursos Hídricos e Agricultura Sustentável (NEDTEC), do Centro de Ciências Agrárias da Universidade Federal do Espírito Santo (CCA-UFES), localizado no município de Jerônimo Monteiro. O trabalho foi realizado em duas épocas distintas, sendo a primeira no período de 09 de fevereiro a 09 de junho de 2009 e a segunda no período de 11 de julho a 07 de novembro de 2009, visando à realização das observações em diferentes condições de regime de radiação, déficit de pressão do vapor do ar, temperatura, umidade relativa do ar e velocidade do vento. O delineamento experimental utilizado foi o inteiramente ao acaso em parcelas subdivididas 2 x 4, alocando-se os 4 níveis de déficits hídricos na parcela principal e as 2 épocas nas subparcelas, com três repetições. Os manejos hídricos aplicados foram: Déficit 0 (D0) sem déficit, Déficit 1(D1) corte da irrigação aos 30 dias de experimentação, permanecendo até o final do experimento, Déficit 2 (D2) corte da irrigação aos 30 dias de experimentação, suspensão da irrigação por 60 dias e posterior retomada da irrigação por mais 30 dias; Déficit 3 (D3) corte da irrigação aos 60 dias de experimentação, prolongando até o final do experimento. Os dados experimentais foram submetidos à análise de variância, e quando significativas, as médias foram comparadas pelo teste de média Tukey a 5% de probabilidade, para cada clone estudado. Com este trabalho, foi possível avaliar o impacto de diferentes déficits hídricos, no crescimento inicial das plantas, em duas épocas do ano e avaliar o incremento no desenvolvimento das plantas durante a aplicação dos tratamentos, com retiradas de amostras médias de cada tratamento a cada 30 dias. As variáveis medidas nos dois experimentos foram altura total da planta, diâmetro ao nível do coleto, número de folhas, área foliar, matéria seca de folhas, matéria seca de haste e ramos, matéria seca de raízes e matéria seca total. Foram avaliadas as variáveis climáticas durante todo o período experimental, nas duas épocas, a fim de determinar a condição do clima em cada época. Para os dois clones estudados, em geral, os déficits hídricos promoveram a redução das variáveis morfológicas estudadas e a época experimental foi o fator que mais influenciou a redução do crescimento das plantas. Sendo que a Época 1 foi a que proporcionou resultados superiores, e a Época 2 foi a que prejudicou mais o desenvolvimento das plantas, reduzindo significativamente todas as variáveis morfológicas em todos os déficits hídricos, inclusive o D0.

Efeito da restrição hídrica sobre o crescimento de clones de eucalipto

O estabelecimento e o crescimento inicial de espécies florestais no campo são fortemente afetados pela disponibilidade de água no solo e pela época de plantio, por isso, o presente trabalho estuda o impacto do déficit hídrico no crescimento de mudas de dois clones do híbrido Eucalyptus grandis x Eucalyptus urophylla, ambos submetidos a 4 níveis de déficit hídrico, em duas épocas de plantio. O estudo foi realizado na área experimental do Núcleo de Estudos e Difusão de Tecnologia em Florestas, Recursos Hídricos e Agricultura Sustentável (NEDTEC), do Centro de Ciências Agrárias da Universidade Federal do Espírito Santo (CCA-UFES), localizado no município de Jerônimo Monteiro. O trabalho foi realizado em duas épocas distintas, sendo a primeira no período de 09 de fevereiro a 09 de junho de 2009 e a segunda no período de 11 de julho a 07 de novembro de 2009, visando à realização das observações em diferentes condições de regime de radiação, déficit de pressão do vapor do ar, temperatura, umidade relativa do ar e velocidade do vento. O delineamento experimental utilizado foi o inteiramente ao acaso em parcelas subdivididas 2 x 4, alocando-se os 4 níveis de déficits hídricos na parcela principal e as 2 épocas nas subparcelas, com três repetições. Os manejos hídricos aplicados foram: Déficit 0 (D0) sem déficit, Déficit 1(D1) corte da irrigação aos 30 dias de experimentação, permanecendo até o final do experimento, Déficit 2 (D2) corte da irrigação aos 30 dias de experimentação, suspensão da irrigação por 60 dias e posterior retomada da irrigação por mais 30 dias; Déficit 3 (D3) corte da irrigação aos 60 dias de experimentação, prolongando até o final do experimento. Os dados experimentais foram submetidos à análise de variância, e quando significativas, as médias foram comparadas pelo teste de média Tukey a 5% de probabilidade, para cada clone estudado. Com este trabalho, foi possível avaliar o impacto de diferentes déficits hídricos, no crescimento inicial das plantas, em duas épocas do ano e avaliar o incremento no desenvolvimento das plantas durante a aplicação dos tratamentos, com retiradas de amostras médias de cada tratamento a cada 30 dias. As variáveis medidas nos dois experimentos foram altura total da planta, diâmetro ao nível do coleto, número de folhas, área foliar, matéria seca de folhas, matéria seca de haste e ramos, matéria seca de raízes e matéria seca total. Foram avaliadas as variáveis climáticas durante todo o período experimental, nas duas épocas, a fim de determinar a condição do clima em cada época. Para os dois clones estudados, em geral, os déficits hídricos promoveram a redução das variáveis morfológicas estudadas e a época experimental foi o fator que mais influenciou a redução do crescimento das plantas. Sendo que a Época 1 foi a que proporcionou resultados superiores, e a Época 2 foi a que prejudicou mais o desenvolvimento das plantas, reduzindo significativamente todas as variáveis morfológicas em todos os déficits hídricos, inclusive o D0.

Electrospun silk-elastin-like fiber mats for tissue engineering applications

Protein-based polymers are present in a wide variety of organisms fulfilling structural and mechanical roles. Advances in protein engineering and recombinant DNA technology allow the design and production of recombinant protein-based polymers (rPBPs) with an absolute control of its composition. Although the application of recombinant proteins as biomaterials is still an emerging technology, the possibilities are limitless and far superior to natural or synthetic materials, as the complexity of the structural design can be fully customized. In this work, we report the electrospinning of two new genetically engineered silk-elastin-like proteins (SELPs) consisting of alternate silk- and elastin-like blocks. Electrospinning was performed with formic acid and aqueous solutions at different concentrations without addition of further agents. The size and morphology of the electrospun structures was characterized by scanning electron microscopy showing to be dependent of concentration and solvent used. Treatment with air saturated with methanol was employed to stabilize the structure and promote water insolubility through a time-dependent conversion of random coils into β-sheets (FTIR). The resultant methanol-treated electrospun mats were characterized for swelling degree (570-720%), water vapour transmission rate (1083 g/m2/day) and mechanical properties (modulus of elasticity of ~126 MPa). Furthermore, the methanol-treated SELP fiber mats showed no cytotoxicity and were able to support adhesion and proliferation of normal human skin fibroblasts. Adhesion was characterized by a filopodia-mediated mechanism. These results demonstrate that SELP fiber mats can provide promising solutions for the development of novel biomaterials suitable for tissue engineering applications.

A practical framework for the generation and selection of strategic plans of action, The relevance of timeframe considerations and a systems thinking approach

The paper proposes a methodology especially focused on the generation of strategic plans of action, emphasizing the relevance of having a structured timeframe classification for the actions. The methodology explicitly recognizes the relevance of long-term goals as strategic drivers, which must insure that the complex system is capable to effectively respond to changes in the environment. In addition, the methodology employs engineering systems techniques in order to understand the inner working of the system and to build up alternative plans of action. Due to these different aspects, the proposed approach features higher flexibility compared to traditional methods. The validity and effectiveness of the methodology has been demonstrated by analyzing an airline company composed by 5 subsystems with the aim of defining a plan of action for the next 5 years, which can either: improve efficiency, redefine mission or increase revenues.

Zinc supplementation, production and quality of coffee beans

Besides its importance in the coffee tree nutrition, there is almost no information relating zinc nutrition and bean quality. This work evaluated the effect of zinc on the coffee yield and bean quality. The experiment was conducted with Coffea arabica L. in "Zona da Mata" region, Minas Gerais, Brazil. Twelve plots were established at random with 4 competitive plants each. Treatments included plants supplemented with zinc (eight plots) and control without zinc supplementation (four plots). Plants were subjected to two treatments: zinc supplementation and control. Yield, number of defective beans, beans attacked by berry borers, bean size, cup quality, beans zinc concentration, potassium leaching, electrical conductivity, color index, total tritable acidity, pH, chlorogenic acids contents and ferric-reducing antioxidant activity of beans were evaluated. Zinc positively affected quality of coffee beans, which presented lower percentage of medium and small beans, lower berry borer incidence, lower potassium leaching and electrical conductivity, higher contents of zinc and chlorogenic acids and higher antioxidant activity in comparison with control beans.

Survival analysis: a tool in the study of post-harvest diseases in peaches

Survival analysis is applied when the time until the occurrence of an event is of interest. Such data are routinely collected in plant diseases, although applications of the method are uncommon. The objective of this study was to use two studies on post-harvest diseases of peaches, considering two harvests together and the existence of random effect shared by fruits of a same tree, in order to describe the main techniques in survival analysis. The nonparametric Kaplan-Meier method, the log-rank test and the semi-parametric Cox's proportional hazards model were used to estimate the effect of cultivars and the number of days after full bloom on the survival to the brown rot symptom and the instantaneous risk of expressing it in two consecutive harvests. The joint analysis with baseline effect, varying between harvests, and the confirmation of the tree effect as a grouping factor with random effect were appropriate to interpret the phenomenon (disease) evaluated and can be important tools to replace or complement the conventional analysis, respecting the nature of the variable and the phenomenon.

A flexible side information generation framework for distributed video coding

One of the most efficient approaches to generate the side information (SI) in distributed video codecs is through motion compensated frame interpolation where the current frame is estimated based on past and future reference frames. However, this approach leads to significant spatial and temporal variations in the correlation noise between the source at the encoder and the SI at the decoder. In such scenario, it would be useful to design an architecture where the SI can be more robustly generated at the block level, avoiding the creation of SI frame regions with lower correlation, largely responsible for some coding efficiency losses. In this paper, a flexible framework to generate SI at the block level in two modes is presented: while the first mode corresponds to a motion compensated interpolation (MCI) technique, the second mode corresponds to a motion compensated quality enhancement (MCQE) technique where a low quality Intra block sent by the encoder is used to generate the SI by doing motion estimation with the help of the reference frames. The novel MCQE mode can be overall advantageous from the rate-distortion point of view, even if some rate has to be invested in the low quality Intra coding blocks, for blocks where the MCI produces SI with lower correlation. The overall solution is evaluated in terms of RD performance with improvements up to 2 dB, especially for high motion video sequences and long Group of Pictures (GOP) sizes.

Microscopic analysis of "prato", "mussarela" and "mineiro" cheese sold in street markets of the City of S. Paulo, Southeastern Brazil

INTRODUCTION: Cheese should be produced from ingredients of good quality and processed under hygienic conditions. Further, cheese should be transported, stored and sold in an appropriate manner in order to avoid, among other things, the incorporation of extraneous materials (filth) of biological origin or otherwise, in contravention of the relevant food legislation. The aim of the study was to evaluate the hygienic conditions of "prato", "mussarela", and "mineiro" cheeses sold at the street food markets in the city of S. Paulo, Brazil. MATERIALS AND METHOD: Forty-seven samples of each of the three types of cheese were collected during the period from March, 1993 to February, 1994. The Latin square was used as a statistical model for sampling and random selection of the street markets from which to collect the cheese samples. The samples were analysed for the presence of extraneous matters outside for which purpose the samples were washed and filtered and inside, for which the methodology of enzymathic digestion of the sample with pancreatine, followed by filtering,was used. RESULTS AND CONCLUSION: Of the 141 samples analysed, 75.9% exhibited at least one sort of extraneous matters. For the "prato" and "mussarela" cheeses, the high number of contaminated samples was due mainly to extraneous matters present inside the cheese, whereas in the "mineiro" cheese, besides the internal filth, 100% of the samples had external filth.

Base molecular da hemocromatose hereditária não-clássica em Portugal

A Hemocromatose Hereditária (HH) é uma doença autossómica recessiva caracterizada pela absorção excessiva de ferro a nível intestinal e sua acumulação em órgãos vitais, podendo originar cardiomiopatia, cirrose e carcinoma hepatocelular. O correspondente diagnóstico molecular é obtido pela associação com genótipos específicos no gene HFE (homozigotia para p.Cys282Tyr ou heterozigotia composta p.Cys282Tyr/p.His63Asp). Contudo, nos países do sul da Europa, cerca de um terço dos doentes com diagnóstico clínico de HH não apresenta os referidos genótipos. Para identificar a base molecular da HH não-clássica em Portugal usaram-se metodologias de pesquisa geral de variantes genéticas (SSCP e dHPLC), Next-Generation Sequencing (NGS) e sequenciação de Sanger, cobrindo seis genes relacionados com o metabolismo do ferro em 303 doentes. Identificaram-se 69 variantes diferentes e de vários tipos, por ex. missense, nonsense, de splicing, que perturbam a transcrição do gene ou a regulação da tradução do mRNA. Seguidamente, realizaram-se estudos in silico e in vitro para esclarecer o significado etiológico de algumas das novas variantes. Concluiu-se que a base molecular desta patologia é bastante heterogénea e que a NGS é uma ferramenta adequada para efetuar a análise simultânea dos vários genes num grande número de amostras. Contudo, o estabelecimento da relevância clínica de algumas variantes requer a realização de estudos funcionais.