Automatic classification of enzyme family in protein annotation

Most of the tasks in genome annotation can be at least partially automated. Since this annotation is time-consuming, facilitating some parts of the process - thus freeing the specialist to carry out more valuable tasks - has been the motivation of many tools and annotation environments. In particular, annotation of protein function can benefit from knowledge about enzymatic processes. The use of sequence homology alone is not a good approach to derive this knowledge when there are only a few homologues of the sequence to be annotated. The alternative is to use motifs. This paper uses a symbolic machine learning approach to derive rules for the classification of enzymes according to the Enzyme Commission (EC). Our results show that, for the top class, the average global classification error is 3.13%. Our technique also produces a set of rules relating structural to functional information, which is important to understand the protein tridimensional structure and determine its biological function. © 2009 Springer Berlin Heidelberg.

Acid dye biodegradation using saccharomyces cerevisiae immobilized with polyethyleneimine-treated sugarcane bagasse

Chemical reagents used by the textile industry are very diverse in their composition, ranging from inorganic compounds to polymeric compounds. Strong color is the most notable characteristic of textile effluents, and a large number of processes have been employed for color removal. In recent years, attention has been directed toward various natural solid materials that are able to remove pollutants from contaminated water at low cost, such as sugarcane bagasse. Cell immobilization has emerged as an alternative that offers many advantages in the biodegradation process, including the reuse of immobilized cells and high mechanical strength, which enables metabolic processes to occur under adverse conditions of pH, sterility, and agitation. Support treatment also increases the number of charges on the surface, thereby facilitating cell immobilization processes through adsorption and ionic bonds. Polyethyleneimine (PEI) is a polycationic compound known to have a positive effect on enzyme activity and stability. The aim of the present study was to investigate a low-cost alternative for the biodegradation and bioremediation of textile dyes, analyzing Saccharomyces cerevisiae immobilization in activated bagasse for the promotion of Acid Black 48 dye biodegradation in an aqueous solution. A 1 % concentration of a S. cerevisiae suspension was evaluated to determine cell immobilization rates. Once immobilization was established, biodegradation assays with free and immobilized yeast in PEI-treated sugarcane bagasse were evaluated for 240 h using UV-vis spectrophotometry. The analysis revealed significant relative absorbance values, indicating the occurrence of biodegradation in both treatments. Therefore, S. cerevisiae immobilized in sugarcane bagasse is very attractive for use in biodegradation processes for the treatment of textile effluents. © 2012 Springer Science+Business Media Dordrecht.

Antioxidant enzyme activity and hydrogen peroxide content during the drying of Arabica coffee beans

The development of the germination process and drought stress during the drying of coffee can generate reactive oxygen species, which can be neutralized by way of antioxidant mechanisms. No studies related to antioxidant enzymes during the drying of coffee were found in the literature, and considering their importance, the enzymatic activities of superoxide dismutase (SOD), guaiacol peroxidase (GPOX) and glutathione reductase (GR), and also the hydrogen peroxide content were evaluated during the drying of two types of coffee bean, one processed as natural coffee and the other as pulped natural coffee. The results showed a reduction in the SOD, GPOX and GR enzymatic activities of the natural coffee as compared to the pulped natural coffee during the drying period. Moreover, the hydrogen peroxide content of the natural coffee was greater than that of the pulped natural coffee. These results suggest the development of oxidative stress during the coffee drying process, controlled more efficiently in pulped natural coffee by the early action of GPOX during the drying process. Nevertheless, differential responses by SOD isoenzymes and possibly the role of other peroxidases also appear to be involved in the responses observed. © 2013 Springer-Verlag Berlin Heidelberg.

Immunosensor based on immobilization of antigenic peptide NS5A-1 from HCV and silk fibroin in nanostructured films

The peptide NS5A-1 (PPLLESWKDPDYVPPWHG), derived from hepatitis C virus (HCV) NS5A protein, was immobilized into layer-by-layer (LbL) silk fibroin (SF) films. Deposition was monitored by UV-vis absorption measurements at each bilayer deposited. The interaction SF/peptide film induced secondary structure in NS5A-1 as indicated by fluorescence and circular dichroism (CD) measurements. Voltammetric sensor (SF/NS5A-1) properties were observed when the composite film was tested in the presence of anti-HCV. The peptide-silk fibroin interaction studied here showed new architectures for immunosensors based on antigenic peptides and SF as a suitable immobilization matrix. © 2013 American Chemical Society.

Enzyme replacement therapy for Anderson-Fabry disease.

Anderson-Fabry disease is an X-linked defect of glycosphingolipid metabolism. Progressive renal insufficiency is a major source of morbidity, additional complications result from cardio- and cerebro-vascular involvement. Survival is reduced among affected males and symptomatic female carriers. To evaluate the effectiveness and safety of enzyme replacement therapy compared to other interventions, placebo or no interventions, for treating Anderson-Fabry disease. We searched 'Clinical Trials' on The Cochrane Library, MEDLINE, EMBASE, LILACS and the Cystic Fibrosis and Genetic Disorders Group's Inborn Errors of Metabolism Trials Register (date of the most recent search: 11 September 2012). The original search was performed in September 2008.Date of the most recent search of the Cystic Fibrosis and Genetic Disorders Group's Inborn Errors of Metabolism Trials Register: 11 September 2012. Randomized controlled trials of agalsidase alfa or beta in participants diagnosed with Anderson-Fabry disease. Two authors selected relevant trials, assessed methodological quality and extracted data. Six trials comparing either agalsidase alfa or beta in 223 participants fulfilled the selection criteria.Both trials comparing agalsidase alfa to placebo reported on globotriaosylceramide concentration in plasma and tissue; aggregate results were non-significant. One trial reported pain scores, there was a statistically significant improvement for participants receiving treatment at up to three months, mean difference -2.10 (95% confidence interval (CI) -3.79 to -0.41); at up to five months, mean difference -1.90 (95% CI -3.65 to -0.15); and at up to six months, mean difference -2.00 (95% CI -3.66 to -0.34). There was a significant difference in pain-related quality of life at over five months and up to six months, mean difference -2.10 (95% CI -3.92 to -0.28) but not at other time-points. Neither trial reported deaths.One of the three trials comparing agalsidase beta to placebo reported on globotriaosylceramide concentration in plasma and tissue and showed significant improvement: kidney, mean difference -1.70 (95% CI -2.09 to -1.31); heart, mean difference -0.90 (95% CI -1.18 to -0.62); and composite results (renal, cardiac, and cerebrovascular complications and death), mean difference -4.80 (95% CI -5.45 to -4.15). There was no significant difference between groups for death; no trials reported on pain.Only one trial compared agalsidase alfa to agalsidase beta. There was no significant difference between the groups for any adverse events, risk ratio 0.36 (95% CI 0.08 to 1.59), or any serious adverse events; risk ratio 0.30; 95% CI 0.03 to 2.57). Six small, poor quality randomised controlled trials provide no robust evidence for use of either agalsidase alfa and beta to treat Anderson-Fabry disease.

A metabolic pathway assembled by enzyme selection may support herbivory of leaf-cutter ants on plant starch

Mutualistic associations shape the evolution in different organism groups. The association between the leaf-cutter ant Atta sexdens and the basidiomycete fungus Leucoagaricus gongylophorus has enabled them to degrade starch from plant material generating glucose, which is a major food source for both mutualists. Starch degradation is promoted by enzymes contained in the fecal fluid that ants deposit on the fungus culture in cut leaves inside the nests. To understand the dynamics of starch degradation in ant nests, we purified and characterized starch degrading enzymes from the ant fecal fluid and from laboratory cultures of L. gongylophorus and found that the ants intestine positively selects fungal α-amylase and a maltase likely produced by the ants, as a negative selection is imposed to fungal maltase and ant α-amylases. Selected enzymes are more resistant to catabolic repression by glucose and proposed to structure a metabolic pathway in which the fungal α-amylase initiates starch catalysis to generate byproducts which are sequentially degraded by the maltase to produce glucose. The pathway is responsible for effective degradation of starch and proposed to represent a major evolutionary innovation enabling efficient starch assimilation from plant material by leaf-cutters. © 2013 Elsevier Ltd.

Enzyme effects on extruded diets for dogs with soybean meal as a substitute for poultry by-product meal

The effects of exogenous enzymes supplementation on kibble diets for dogs formulated with soybean meal (SBM) as a substitute for poultry by-product meal (PM) was investigated on nutrient digestibility, fermentation products formation, post-prandial urea response and selected faecal bacteria counts. Two kibble diets with similar compositions were used in two trials: PM-based diet (28.9% of PM; soybean hulls as a fibre source) and SBM-based diet (29.9% of SBM). In experiment 1, the SBM diet was divided into three diets: SBM-0, without enzyme addition; SBM-1, covered after extrusion with 7500U protease/kg and 45U cellulase/kg; and SBM-2, covered with 15000U protease/kg and 90U cellulase/kg. In experiment 2, the SBM diet was divided into three diets: SBM-0; SBM-1, covered with 140U protease/kg; 8U cellulase/kg, 800U pectinase/kg, 60U phytase/kg, 40U betaglucanase/kg and 20U xylanase/kg; and SMB-2, covered with 700U protease/kg, 40U cellulase/kg, 4000U pectinase/kg, 300U phytase/kg, 200U betaglucanase/kg and 100U xylanase/kg. Each experiment followed a block design with six dogs per diet. Data were submitted to analysis of variance and means compared by orthogonal and polynomial contrasts (p<0.05). In both experiments, nutrients and energy digestibility did not differ between diets (p>0.05). SBM consumption resulted in increased faecal moisture and production (p<0.05), without effect on faecal score. Higher concentration of propionate, acetate and lactate, and lower ammonia and pH were found in the faeces of dogs fed SBM (p<0.05). Higher post-prandial urea was verified in dogs fed SBM (p<0.05). In experiment 2, the addition of enzymes increased faecal concentration of propionate, acetate and total short-chain fatty acid (p<0.05) and tended to reduce post-prandial urea concentration (p=0.06). Although with similar digestibility, SBM shows a worse utilization of absorbed amino acids than the PM. Soybean oligosaccharides can beneficially change gut fermentation product formation. Enzymes can increase the gut fermentation activity and improve the SBM proteic value. © 2013 Blackwell Verlag GmbH.

Enzyme use in kibble diets formulated with wheat bran for dogs: Effects on processing and digestibility

Recently, there is an interest in technologies that favour the use of coproducts for animal nutrition. The effect of adding two enzyme mixtures in diets for dogs formulated with wheat bran (WB) was evaluated. Two foods with similar compositions were formulated: negative control (NC; without WB) and test diet (25% of WB). The test diet was divided into four treatments: without enzyme (positive control), enzyme mixture 1 (ENZ1; added before extrusion β-glucanase, xylanase, cellulase, glucoamylase, phytase); enzyme mixture 2 (ENZ2; added before extrusion the ENZ1 more α-amylase); enzyme mixture 2 added after the extrusion (ENZ2ex). ENZ1 and ENZ2 were used to evaluate the enzyme effect on extruder pre-conditioner (processing additive) and ENZ2ex to evaluate the effect of enzyme supplementation for the animal. Digestibility was measured through total collection of faeces and urine. The experiment followed a randomized block design with five treatments (diets) and six dogs per diet, totalling 30 dogs (7.0 ± 1.2 years old and 11.0 ± 2.2 kg of body weight). Data were submitted to analysis of variance and means compared by Tukey's test and orthogonal contrasts (p < 0.05). Reducing sugars showed an important reduction after extrusion, suggesting the formation of carbohydrate complexes. The apparent total tract digestibility (ATTD) of dry matter, organic matter, crude protein, acid-hydrolysed fat and energy was higher in NC than in diets with WB (p < 0.001), without effects of enzyme additions. WB diets resulted in higher faecal production and concentration of short-chain fatty acids (SCFA) and reduced pH and ammonia concentration (p < 0.01), with no effect of enzyme addition. The enzyme addition did not result in improved digestibility of a diet high in non-starch polysaccharides; however, only ATTD was measured and nutrient fermentation in the large intestine may have interfered with the results obtained. WB modified fermentation product formation in the colon of dogs. © 2013 Blackwell Verlag GmbH.

Electrochemical Properties of Oxo-Manganese Complex Biomimicking Enzyme Active Sites and Its Electrocatalytic Application for Dopamine Determination

This work describes the characterization of the [Mn2 IV,IVO2(terpy)2(H2O)2]4+ complex in aqueous solution by UV-vis spectrophotometry, cyclic voltammetry, and linear sweep voltammetry with a rotating disk electrode. The pH effect, potential scan rate, effect of perfluorosulfonate polymer, and anion of supporting electrode on the electrochemical behavior of the modified electrode for better performance were investigated. The potential peak of the modified electrode was linearly dependent upon the ratio [ionic charge]/[ionic radius]. The modified electrode exerted an electrocatalytic effect on dopamine oxidation in aqueous solution with a decrease in the overpotential compared with the unmodified glassy carbon electrode. This way, the modified electrode showed an enzymatic biomimicking behavior. Tafel plot analyses were used to elucidate the kinetics and mechanism of dopamine oxidation. © 2013 Springer Science+Business Media New York.

Extracellular β-fructofuranosidase from Fusarium graminearum: Stability of the spray-dried enzyme in the presence of different carbohydrates

Microbial enzymes have been used for various biotechnological applications; however, enzyme stabilization remains a challenge for industries and needs to be considered. This study describes the effects of spray-drying conditions on the activity and stability of β-fructofuranosidase from Fusarium graminearum. The extracellular enzyme β-fructofuranosidase was spray dried in the presence of stabilizers, including starch (Capsul) (SC), microcrystalline cellulose (MC), trehalose (TR), lactose (LC) and β-cyclodextrin (CD). In the presence of TR (2% w/v), the enzymatic activity was fully retained. After 1 year of storage, 74% of the enzymatic activity was maintained with the CD stabilizer (10% w/v). The residual activity was maintained as high as 80% for 1 h at 70°C when MC, SC and CD (5% w/v) stabilizers were used. Spray drying with carbohydrates was effective in stabilizing the F. graminearum β-fructofuranosidase, improved enzymatic properties compared to the soluble enzyme and demonstrated a potential use in future biotechnology applications. © 2013 Informa UK Ltd. All rights reserved.

Continuous production of xylooligosaccharides in a packed bed reactor with immobilized-stabilized biocatalysts of xylanase from Aspergillus versicolor

The production of xylooligosaccharides (XOS) using a packed-bed enzymatic reactor was studied at lab-scale. For this, a xylanase from Aspergillus versicolor was immobilized on different supports. The optimal derivative was xylanase immobilized on glyoxyl-agarose supports. This derivative preserved 85% of its catalytic activity; it was around 700-fold more stable than the soluble enzyme after incubation at 60. °C and was able to be reused for at least 10 1. h-cycles retaining full catalytic activity. About 18% of oligosaccharides with prebiotic interest (X2-X6) were produced by the glyoxyl derivative in batch hydrolysis. The production of xylobiose was 2.5-fold higher using the immobilized preparation than with soluble enzyme and small concentrations of xylose (<0.1%) were observed only at the end of the reaction. The derivative was employed on a packed bed reactor, and the continuous operation with no recirculation reached 56% and 70% of the end of reaction with flow rates of 60. mL/h and 12. mL/h, respectively. In continuous operation with recirculation at a flow rate of 60. mL/h, the reaction was completed after four hours. © 2013 Elsevier B.V.

Effect of a thermoascus aurantiacus thermostable enzyme cocktail on wheat bread quality

Thermophilic fungus Thermoascus aurantiacus (CBMAI 756) on solid-state fermentation using corncob as a nutrient source produces an enzyme pool with the potential to be used in bread making. In this paper, the use of this enzyme cocktail as a wheat bread improver was reported. Both products released by flour arabinoxylan degradation and bread quality were investigated. The main product released through enzyme activity after prolonged incubation was xylose indicating the presence of xylanase; however, a small amount of xylobiose and arabinose also confirmed the presence of xylosidase and α-L- arabinofuranosidase, respectively. Enzyme mixture in vitro mainly attacked water-unextractable arabinoxylan contributing to beneficial effect in bread making. The use of an optimal enzyme concentration (35 U xylanase/100 g of flour) increased specific volume (22%), reduced crumb firmness (25%), and reduced amylopectin retrogradation (17%) during bread storage. In conclusion, the enzyme cocktail produced by T. aurantiacus CBMAI 756 can improve wheat bread quality. © 2013 Elsevier Ltd.

Imobilização de invertase comercial e de Saccharomyces cerevisiae em sabugo de milho e bagaço de cana-de-açúcar

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Filmes nanoestruturados para a detecção de glicose e sacarose em bebidas comerciais

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Sínteses e caracterização de microesferas de poli (álcool vinilico) e sua utilização como suportes para imobilização de lipase produzida por Rhizomucor miehei e seu estudo catalítico na reação de transesterificação do óleo de soja para a produção de biodiesel via rota etílica

Pós-graduação em Microbiologia - IBILCE