Identification of protein coding regions using the modified Gabor-wavelet transform

An important topic in genomic sequence analysis is the identification of protein coding regions. In this context, several coding DNA model-independent methods based on the occurrence of specific patterns of nucleotides at coding regions have been proposed. Nonetheless, these methods have not been completely suitable due to their dependence on an empirically predefined window length required for a local analysis of a DNA region. We introduce a method based on a modified Gabor-wavelet transform (MGWT) for the identification of protein coding regions. This novel transform is tuned to analyze periodic signal components and presents the advantage of being independent of the window length. We compared the performance of the MGWT with other methods by using eukaryote data sets. The results show that MGWT outperforms all assessed model-independent methods with respect to identification accuracy. These results indicate that the source of at least part of the identification errors produced by the previous methods is the fixed working scale. The new method not only avoids this source of errors but also makes a tool available for detailed exploration of the nucleotide occurrence.

The beta modified Weibull distribution

A five-parameter distribution so-called the beta modified Weibull distribution is defined and studied. The new distribution contains, as special submodels, several important distributions discussed in the literature, such as the generalized modified Weibull, beta Weibull, exponentiated Weibull, beta exponential, modified Weibull and Weibull distributions, among others. The new distribution can be used effectively in the analysis of survival data since it accommodates monotone, unimodal and bathtub-shaped hazard functions. We derive the moments and examine the order statistics and their moments. We propose the method of maximum likelihood for estimating the model parameters and obtain the observed information matrix. A real data set is used to illustrate the importance and flexibility of the new distribution.

A generalized modified Weibull distribution for lifetime modeling

A four parameter generalization of the Weibull distribution capable of modeling a bathtub-shaped hazard rate function is defined and studied. The beauty and importance of this distribution lies in its ability to model monotone as well as non-monotone failure rates, which are quite common in lifetime problems and reliability. The new distribution has a number of well-known lifetime special sub-models, such as the Weibull, extreme value, exponentiated Weibull, generalized Rayleigh and modified Weibull distributions, among others. We derive two infinite sum representations for its moments. The density of the order statistics is obtained. The method of maximum likelihood is used for estimating the model parameters. Also, the observed information matrix is obtained. Two applications are presented to illustrate the proposed distribution. (C) 2008 Elsevier B.V. All rights reserved.

Log-modified Weibull regression models with censored data: Sensitivity and residual analysis

This paper proposes a regression model considering the modified Weibull distribution. This distribution can be used to model bathtub-shaped failure rate functions. Assuming censored data, we consider maximum likelihood and Jackknife estimators for the parameters of the model. We derive the appropriate matrices for assessing local influence on the parameter estimates under different perturbation schemes and we also present some ways to perform global influence. Besides, for different parameter settings, sample sizes and censoring percentages, various simulations are performed and the empirical distribution of the modified deviance residual is displayed and compared with the standard normal distribution. These studies suggest that the residual analysis usually performed in normal linear regression models can be straightforwardly extended for a martingale-type residual in log-modified Weibull regression models with censored data. Finally, we analyze a real data set under log-modified Weibull regression models. A diagnostic analysis and a model checking based on the modified deviance residual are performed to select appropriate models. (c) 2008 Elsevier B.V. All rights reserved.

General results for the beta-modified Weibull distribution

We study in detail the so-called beta-modified Weibull distribution, motivated by the wide use of the Weibull distribution in practice, and also for the fact that the generalization provides a continuous crossover towards cases with different shapes. The new distribution is important since it contains as special sub-models some widely-known distributions, such as the generalized modified Weibull, beta Weibull, exponentiated Weibull, beta exponential, modified Weibull and Weibull distributions, among several others. It also provides more flexibility to analyse complex real data. Various mathematical properties of this distribution are derived, including its moments and moment generating function. We examine the asymptotic distributions of the extreme values. Explicit expressions are also derived for the chf, mean deviations, Bonferroni and Lorenz curves, reliability and entropies. The estimation of parameters is approached by two methods: moments and maximum likelihood. We compare by simulation the performances of the estimates from these methods. We obtain the expected information matrix. Two applications are presented to illustrate the proposed distribution.

Genetic potential of a maize population from Southern Brazil for the modified convergent-divergent selection scheme

Maize (Zea mays L.) is a very important cereal to world-wide economy which is also true for Brazil, particularly in the South region. Grain yield and plant height have been chosen as important criteria by breeders and farmers from Santa Catarina State (SC), Brazil. The objective of this work was to estimate genetic-statistic parameters associated with genetic gain for grain yield and plant height, in the first cycle of convergent-divergent half-sib selection in a maize population (MPA1) cultivated by farmers within the municipality of Anchieta (SC). Three experiments were carried out in different small farms at Anchieta using low external agronomic inputs; each experiment represented independent samples of half-sib families, which were evaluated in randomized complete blocks with three replications per location. Significant differences among half-sib families were observed for both variables in all experiments. The expected responses to truncated selection of the 25% better families in each experiment were 5.1, 5.8 and 5.2% for reducing plant height and 3.9, 5.7 and 5.0% for increasing grain yield, respectively. The magnitudes of genetic-statistic parameters estimated evidenced that the composite population MPA1 exhibits enough genetic variability to be used in cyclical process of recurrent selection. There were evidences that the genetic structure of the base population MPA1, as indicated by its genetic variability, may lead to expressive changes in the traits under selection, even under low selection pressure.

Particle size and concentration of poly(epsilon-caprolactone) and adipate modified starch blend on mineralization in soils with differing textures

The objective of this study was to evaluate the effect of particle size and concentration of poly(F.-caprolactone) and adipate modified starch blend on mineralization in soils with differing textures, comparing it with polyethylene under the same experimental conditions. Two soil types were used: a Kandiudalfic Eutrudox with a clayey texture and an Arenic Hapludult with a sandy texture. The two different plastic specimens were incorporated in the form of plastic films with three increasing particle sizes and six doses, from 0 to 2.5 mg C g(-1) soil. Each plastic dose was incorporated into 200 g of soil placed in a hermetically closed jar at 28 degrees C, and incubated for a 120-day period to determine CO(2) evolution. Once again it was confirmed that polyethylene is almost non-biodegradable, in contrast to PCL/S, which can be defined as a biodegradable material. Soil texture affected the mineralization kinetics of the plastic specimens, with higher values for the clayey soil. No changes in soil microbial biomass-C or -N were observed by adding polyethylene and PCL/S to the soil. Also, no significant differences were observed on seed emergence and development of rice seedlings (Oryza sativa L.) in plastic modified soil. (C) 2009 Elsevier Ltd. All rights reserved.

Cytotoxicity and Endothelial Cell Adhesion of Lyophilized and Irradiated Bovine Pericardium Modified With Silk Fibroin and Chitosan

Grafts of biological tissues have been used since the 1960s as an alternative to the mechanical heart prostheses. Nowadays, the most consolidated treatment to bovine pericardial (BP) bioprostheses is the crosslinking with glutaraldehyde (GA), although GA may induce calcification in vivo. In previous work, our group demonstrated that electron beam irradiation applied to lyophilized BP in the absence of oxygen promoted crosslinks among collagen fibers of BP tissue. In this work, the incorporation of silk fibroin (SF) and chitosan (CHIT) in the BP not treated with GA was studied. The samples were irradiated and then analyzed for their cytotoxicity and the ability of adhesion and growth of endothelial cells. Initially, all samples showed cytotoxicity. However, after a few washing cycles, the cytotoxicity due to acetic acid and ethanol residues was removed from the biomaterial making it suitable for the biofunctional test. The samples modified with SF/CHIT and electron beam irradiated favored the adhesion and growth of endothelial cells throughout the tissue.

Biochemical and biophysical characterization of lysozyme modified by PEGylation

PEGylation is a strategy that has been used to improve the biochemical properties of proteins and their physical and thermal stabilities. In this study, hen egg-white lysozyme (EC 3.2.1.17; LZ) was modified with methoxypolyethylene glycol-p-nitrophenyl carbonate (mPEG-pNP, MW 5000). This PEGylation of LZ produced conjugates that retained full enzyme activity with glycol chitosan, independent of degree of enzyme modification; its biological activity with the substrate Micrococcus lysodeikticus was altered according to its degree of modification. The conjugate obtained with a low degree of mPEG-pNP/NH(2) modification was studied by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF), demonstrating a spectral peak at m/z 19,988 Da with 77% of its original enzymatic activity. Spectroscopic studies of Fourier transform infrared (FIR) and circular dichroism (CD) did not show any relevant differences in protein structure between the native and conjugate LZ. Studies of the effects of pH and temperature on PEGylated LZ indicated that the conjugate was active over a broad pH range, stable at 50 degrees C, and demonstrated resistance to proteolytic degradation. (C) 2010 Elsevier B.V. All rights reserved.

Batch purification of high-purity lysozyme from egg white and characterization of the enzyme modified by PEGylation

PEGylation is one of the most promising and extensively studied strategies for improving the pharmacological properties of proteins as well as their physical and thermal stability. Purified lysozyme obtained from hen egg white by batch mode was modified by PEGylation with methoxypolyethyleneglycol succinimidyl succinato (mPEG-SS, MW 5000). The conjugates produced retained full enzyme activity with the substrate glycol chitosan, independent of degree of enzyme modification, although lysozyme activity with the substrate Micrococcus lysodeikticus was altered according to the degree of modification. The conjugate with a low degree of modification by mPEG-SS retained 67% of its enzyme activity with the M. lysodeikticus substrate. The mPEG-SS was also shown to be a highly reactive polymer. The effects of pH and temperature on PEGylated lysozymes indicated that the conjugate was active over a wide pH range and was stable up to 50 degrees C. This conjugate also showed resistance to proteolytic degradation, remained stable in human serum, and displayed greater antimicrobial activity than native lysozyme against Gram-negative bacteria.

Moisture sorption isotherm characteristics of freeze-dried D-limonene emulsions in modified chitosan and maltodextrin

This article reports on modified chitosan as an alternative substance for protecting loss of volatile compounds during freeze drying. Moisture sorption isotherms of freeze-dried D-limonene emulsions in modified chitosan were determined at 15, 25, and 35 degrees C. The data were adjusted to the GAB model. Maltodextrin was used in a parallel experiment. Flavor released from microcapsules was measured. The monolayer humidity, the sorption heat, the diffusivity coefficients, and the surface area of freeze-dried D-limonene emulsions were determined.

EVALUATION OF THE INFLUENCE OF THE PROTEINIC QUALITY OF THE GENETICALLY MODIFIED AND ORGANIC SOY BEANS IN THE GROWTH OF TWO GENERATIONS OF RATS WISTAR

Feijo, T.S., Cardozo, SX, Daleprane, J.B., Sabaa Srur, A.U.O. & Boaventura, G.T. [Evaluation of the influence of the proteinic quality of the genetically modified and organic soy beans in the growth of two generations of rats Wistar.] Avaliacao da influencia da qualidade proteica da soja geneticamente modificada e organica no crescimento de duas geracoes de ratos Wistar. Revista Brasileira de Medicina Veterinaria, 31(3):139-144, 2009. Programa de Pos-Graduacao em Patologia, Hospital Universitario Antonio Pedro. Centro de Ciencias Medicas, Universidade Federal Fluminense. Rua Marques do Parana, 303, Niteroi, RJ 24030-210, Brasil. E-mail: sergian@ufnj.br Sixty four Wistar rats, male of two consecutive generations determined as F(0) and F(1) were used to study the cumulative effect of two variety soy beans, cultivated with organic seasoning and genetically modified, The animals of each generation were divided into three groups of eight rats each fed on diets consisted of organic soy, soy genetically modified and casein respectively. All the animals received water and the diet ad libitum for period of 28 days. Where the diet consumption and the animals weight were evaluated. After statistic analysis of the results no expressive differences were observed on diet consumption, weight variation, protein efficient ratio and food efficiency ratio on same group of animals in the different generations. On the other hand, significant difference was found on final proteinic retention on animal descendants of the same groups; however of different generations. With this, the supplementation of organic soy with L-cistin provided better avail of this protein in relation to the protein of the soy genetically modified. However, this supplementation did not reveal efficiency in keeping the proteinic employment from one generation to another one, since soy varieties presented better performance on F(0) generation when compared with F(1).

Antitumor effects of snake venom chemically modified Lys49 phospholipase A(2)-like BthTX-I and a synthetic peptide derived from its C-terminal region

The present work evaluates both in vitro and in vivo antitumor activity of BPB-modified BthTX-I and its cationic synthetic peptide derived from the 115-129 C-terminal region. BPB-BthTX-1 presented cytotoxicity of 10-40% on different tumor cell lines, which were also susceptible to the lytic action of the synthetic peptide. Injection of the modified protein or the peptide in mice, 5 days after transplantation of S 180 tumor cells, reduced 30 and 36% of the tumor size on day 14th and 76 and 79% on day 60th, respectively, when compared to the untreated control group. Thus, these antitumor properties might be of interest in the development of therapeutic strategies against cancer. (C) 2009 The International Association for Biologicals. Published by Elsevier Ltd. All rights reserved.

Hydrothermal Stability of Modified Silica Membranes for Gas Separation

A new class of hybrid molecular sieve silica (MSS) membranes is developed and tested against standard and organic templated membranes. The hybrid membrane is synthesized by the standard sol-gel process, integrating a template (methyltriethoxysilane - MTES) and a C6 surfactant (triethylhexylammonium bromide) into the silica film matrix. After hydro treatment under a relative humidity of 96% for 50h, the hybrid membrane shows no changes in its gas separation capabilities or energy of mobility. The structural characteristics and integrity of the hybrid membrane are retained due to a high concentration of organophilic functional groups and alkoxides observed using 29 Si NMR. In contrast, the structural integrity of the membranes prepared with non-templated films deteriorated during the hydro treatment due to a large percentage of silanol groups (Si-OH) which react with water. The hybrid membranes underwent a decrease in the H2/CO2 selectivity of only 1% whereas for the non-templated membrane a 21% decrease was observed. The transport mechanism of the hybrid membranes is activated as permeation increased with temperature. The activation energy for the permeation of H2 is positive while negative for CO2. The H2 permeation obtained was 3x 10 -8 mol.m -2 .s -1 .Pa -1 and permselectivities for H2/CO2 and H2/N2 varied between 1-7 and 31-34, respectively.