Predição de promotores de Bacillus subtilis usando técnicas de aprendizado de máquina

One of the most important goals of bioinformatics is the ability to identify genes in uncharacterized DNA sequences on world wide database. Gene expression on prokaryotes initiates when the RNA-polymerase enzyme interacts with DNA regions called promoters. In these regions are located the main regulatory elements of the transcription process. Despite the improvement of in vitro techniques for molecular biology analysis, characterizing and identifying a great number of promoters on a genome is a complex task. Nevertheless, the main drawback is the absence of a large set of promoters to identify conserved patterns among the species. Hence, a in silico method to predict them on any species is a challenge. Improved promoter prediction methods can be one step towards developing more reliable ab initio gene prediction methods. In this work, we present an empirical comparison of Machine Learning (ML) techniques such as Na¨ýve Bayes, Decision Trees, Support Vector Machines and Neural Networks, Voted Perceptron, PART, k-NN and and ensemble approaches (Bagging and Boosting) to the task of predicting Bacillus subtilis. In order to do so, we first built two data set of promoter and nonpromoter sequences for B. subtilis and a hybrid one. In order to evaluate of ML methods a cross-validation procedure is applied. Good results were obtained with methods of ML like SVM and Naïve Bayes using B. subtilis. However, we have not reached good results on hybrid database

Cyclodextrin glycosyltransferase from Bacillus licheniformis: Optimization of production and its properties

Cyclodextrin glycosyltransferase (EC 2.4.1.19) is an enzyme that produces cyclodextrins from starch via an intramolecular transglycosylation reaction. An alkalophilic Bacillus strain, isolated from cassava peels, was identified as Bacillus licheniformis. CGTase production by this strain was better when potato starch was used as carbon source, followed by cassava starch and amylopectin. Glucose and amylose, on the other hand, acted as synthesis repressors. When the cultivation was supplemented with sodium ions and had the pH adjusted between 6.0 and 9.0, the microorganism maintained the growth and enzyme production capacity. This data is interesting because it contradicts the concept that alkalophilic microorganisms do not grow in this pH range. After ultrafiltration-centrifugation, one protein of 85.2 kDa with CGTase activity was isolated. This protein was identified in plates with starch and phenolphthalein. Determination of the optimum temperature showed higher activities at 25 degrees C and 55 degrees C, indicating the possible presence of more than one CGTase in the culture filtrate. Km and Vmax values were 1.77 mg/mL and 0.0263 U/mg protein, respectively, using potato starch as substrate.

Effect of vaccination and the immunomodulators bacillus of Calmette-Guerin, Avridine and Propionibacterium acnes on rabies in mice

Responses: of vaccination and treatment to immunomodulators against rabies in mice were evaluated through macrophage inhibition factor (MIF), intra-pad inoculation (IPI) and serum neutralization (SN) tests and by the detection of gamma-interferon (IFN-gamma). Onco-BCG, Avridine and Propionibacterium acnes were administered to groups of mice. Higher survival rates were found in animals treated with P. acnes. Lower levels of IFN-gamma were observed in the groups of infected and vaccinated mice. The IPI was not effective on detecting the response of delayed-type hypersensitivity. Vaccine induced in the infected animals a more intense response to MIF reaction. (C) 1998 Elsevier B.V. Ltd. All rights reserved.

Effect of the bacillus of Calmette-Guerin, Propionibacterium acnes and avridine as immunomodulators in antirabies vaccination of mice using the Fuenzalida-Palacios mouse brain vaccine

Using the laboratory mice, Fuenzalida-Palacios mouse brain human rabies vaccine was administered in groups of animals previously inoculated with rabies virus and then submitted to treatments with the immunomodulators onco-BCG, avridine and Plopionibacterium acnes. Humoral and cellular immune responses were evaluated through the macrophage inhibition factor (MIF), intra-pad inoculation (IPI) and serum neutralization (SN) tests and by the detection of gamma-interferon (IFN-gamma). The IPI test was not effective in detecting the response of delayed-type hypersensitivity, contrary to MIF, which showed the immune cellular response. Higher levels of IFN-gamma were observed in the groups of mice vaccinated and treated with avridine and P. acnes. Although immunomodulating activities have been detected, the use of adjuvants with the Fuenzalida-Palacios type vaccine in mice did not reveal any encouraging results. (C) 1999 Elsevier B.V. Ltd. All rights reserved.

Purification and characterization of two xylanases from alkalophilic and thermophilic Bacillus licheniformis 77-2

The alkalophilic bacteria Bacillus licheniformis 77-2 produces significant quantities of thermostable cellulase-free xylanases. The crude xylanase was purified to apparent homogeneity by gel filtration (G-75) and ionic exchange chromatography (carboxymethyl sephadex, Q sepharose, and Mono Q), resulting in the isolation of two xylanases. The molecular masses of the enzymes were estimated to be 17 kDa (X-I) and 40 kDa (X-II), as determined by SDS-PAGE. The K(m) and V(max) values were 1.8 mg/mL and 7.05 U/mg protein (X-I), and 1.05 mg/mL and 9.1 U/mg protein (X-II). The xylanases demonstrated optimum activity at pH 7.0 and 8.0-10.0 for xylanase X-I and X-II, respectively, and, retained more than 75% of hydrolytic activity up to pH 11.0. The purified enzymes were most active at 70 and 75 degrees C for X-I and X-II, respectively, and, retained more than 90% of hydrolytic activity after 1 h of heating at 50 degrees C and 60 degrees C for X-I and X-II, respectively. The predominant products of xylan hydrolysates indicated that these enzymes were endoxylanases.

Optimization of cyclodextrin glucanotransferase production from Bacillus clausii E16 in submerged fermentation using response surface methodology

Cyclodextrin glucanotransferase production from Bacillus clausii E16, a new bacteria isolated from Brazilian soil samples was optimized in shake-flask cultures. A 2 4 full-factorial central composite design was performed to optimize the culture conditions, using a response surface methodology the combined effect among the soluble starch concentration, the peptone concentration, the yeast extract concentration, and the initial pH value of the culture medium was investigated. The optimum concentrations of the components, determined by a 2(4) full-factorial central composite design, were 13.4 g/L soluble starch, 4.9 g/L peptone, 5.9 g/L yeast extract, and initial pH 10.1. Under these optimized conditions, the maximum cyclodextrin glucanotransferase activity was 5.9 U/mL after a 48-h fermentation. This yield was 68% higher than that obtained when the microorganism was cultivated in basal culture medium.

Cyclodextrin glycosyltransferase production by new Bacillus sp. strains isolated from brazilian soil

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

Bacillus lehensis-an alkali-tolerant bacterium isolated from cassava starch wastewater: optimization of parameters for cyclodextrin glycosyltransferase production

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Effects of the electrolytic treatment on Bacillus subtilis

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Screening of bacterial strains for pectinolytic activity: characterization of the polygalacturonase produced by Bacillus sp

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

Properties of a biosurfactant produced by Bacillus pumilus using vinasse and waste frying oil as alternative carbon sources

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Correlation of temperature induced conformation change with optimum catalytic activity in the recombinant G/11 xylanase A from Bacillus subtilis strain 168 (1A1)

The 1.7 angstrom resolution crystal structure of recombinant family G/11 beta-1,4-xylanase (rXynA) from Bacillus subtilis 1A1 shows a jellyroll fold in which two curved P-sheets form the active-site and substrate-binding cleft. The onset of thermal denaturation of rXynA occurs at 328 K, in excellent agreement with the optimum catalytic temperature. Molecular dynamics simulations at temperatures of 298-328 K demonstrate that below the optimum temperature the thumb loop and palm domain adopt a closed conformation. However, at 328 K these two domains separate facilitating substrate access to the active-site pocket, thereby accounting for the optimum catalytic temperature of the rXynA. (c) 2005 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Characterization of a cellulase-free xylanase producing Bacillus sp for biobleaching of kraft pulp

Application of the xylanase in the pulp bleaching process has been shown to be effective in decreasing the amount of chlorinating agents in the process and improving the brightness of the pulp. The use of thermostable cellulase-free xylanase might enhance both the technical and economic feasibility of the process. In this work an alkalophylic strain of Bacillus sp 77-2, was isolated which showed a high production of xylanase and free cellulases. The xylanase of Bacillus sp displayed an optimum pH of 6.0 (with 70% activity at pH 9.0), all optimum temperature of 60 degrees C, pH stability in the range 5-10 and thermal stability of 50 degrees C. These characteristics are important to the kraft pulp bleaching because they are similar to those found in the industrial paper environment.