Gene Expression Complex Networks: Synthesis, Identification, and Analysis

Thanks to recent advances in molecular biology, allied to an ever increasing amount of experimental data, the functional state of thousands of genes can now be extracted simultaneously by using methods such as cDNA microarrays and RNA-Seq. Particularly important related investigations are the modeling and identification of gene regulatory networks from expression data sets. Such a knowledge is fundamental for many applications, such as disease treatment, therapeutic intervention strategies and drugs design, as well as for planning high-throughput new experiments. Methods have been developed for gene networks modeling and identification from expression profiles. However, an important open problem regards how to validate such approaches and its results. This work presents an objective approach for validation of gene network modeling and identification which comprises the following three main aspects: (1) Artificial Gene Networks (AGNs) model generation through theoretical models of complex networks, which is used to simulate temporal expression data; (2) a computational method for gene network identification from the simulated data, which is founded on a feature selection approach where a target gene is fixed and the expression profile is observed for all other genes in order to identify a relevant subset of predictors; and (3) validation of the identified AGN-based network through comparison with the original network. The proposed framework allows several types of AGNs to be generated and used in order to simulate temporal expression data. The results of the network identification method can then be compared to the original network in order to estimate its properties and accuracy. Some of the most important theoretical models of complex networks have been assessed: the uniformly-random Erdos-Renyi (ER), the small-world Watts-Strogatz (WS), the scale-free Barabasi-Albert (BA), and geographical networks (GG). The experimental results indicate that the inference method was sensitive to average degree k variation, decreasing its network recovery rate with the increase of k. The signal size was important for the inference method to get better accuracy in the network identification rate, presenting very good results with small expression profiles. However, the adopted inference method was not sensible to recognize distinct structures of interaction among genes, presenting a similar behavior when applied to different network topologies. In summary, the proposed framework, though simple, was adequate for the validation of the inferred networks by identifying some properties of the evaluated method, which can be extended to other inference methods.

Enzymatic Resolution of Racemic Sulcatol by Lipase from Candida Antarctica in a Large Scale

Large scale enzymatic resolution of racemic sulcatol 2 has been useful for stereoselective biocatalysis. This reaction was fast and selective, using vinyl acetate as donor of acyl group and lipase from Candida antarctica (CALB) as catalyst. The large scale reaction (5.0 g, 39 mmol) afforded high optical purities for S-(+)-sulcatol 2 and R-(+)-sulcatyl acetate 3, i.e., ee > 99 per cent and good yields (45 per cent) within a short time (40 min). Thermodynamic parameters for the chemoesterification of sulcatol 2 by vinyl acetate were evaluated. The enthalpy and Gibbs free energy values of this reaction were negative, indicating that this process is exothermic and spontaneous which is in agreement with the reaction obtained enzymatically.

Performance of different immobilized lipases in palm oil biodiesel synthesis

Performance of different immobilized lipases in palm oil biodiesel synthesis. Optimized conditions for palm oil and ethanol enzymatic biodiesel synthesis were determined with different immobilized lipases SiO(2)-PVA-immobilized lipase from Pseudomonas fluorescens and acrylic resin-immobilized lipase, Novozym (R) 435, from Candida antartica, in solvent-free medium. A full factorial design assessed the influence of temperature (42 - 58 degrees C) and ethanol: palm oil (6:1 - 18:1) molar ratio on the transesterification yield. Main effects were adjusted by multiple regression analysis to linear models and the maximum transesterification yield was obtained at 42 degrees C and 18:1 ethanol: palm oil molar ratio. Mathematical models featuring total yield for each immobilized lipase were suitable to describe the experimental results.

Immobilization and stabilization of microbial lipases by multipoint covalent attachment on aldehyde-resin affinity: Application of the biocatalysts in biodiesel synthesis

Microbial lipase preparations from Thermomyces lanuginosus (TLL) and Pseudomonas fluorescens (PFL) were immobilized by multipoint covalent attachment on Toyopearl AF-amino-650M resin and the most active and thermal stable derivatives used to catalyze the transesterificanon reaction of babassu and palm oils with ethanol in solvent-free media For this different activating agents mainly glutaraldehyde glycidol and epichlorohydrin were used and immobilization parameters were estimated based on the hydrolysis of olive oil emulsion and butyl butyrate synthesis ILL immobilized on glyoxyl-resin allowed obtaining derivatives with the highest hydrolytic activity (HA(der)) and thermal stability between 27 and 31 times more stable than the soluble lipase Although PFL derivatives were found to be less active and thermally stables similar formation of butyl butyrate concentrations were found for both ILL and PFL derivatives The highest conversion into biodiesel was found in the transesterification of palm oil catalyzed by both ILL and PFL glyoxyl-derivatives (c) 2010 Elsevier B V All rights reserved

Enzymatic synthesis of monoglycerides by esterification reaction using Penicillium camembertii lipase immobilized on epoxy SiO(2)-PVA composite

Glycerol-fatty acid esterification has been conducted with lipase from Penicillium camembertii lipase immobilized on epoxy SiO(2)-PVA in solvent-free media, with the major product being 1-monoglyceride, a useful food emulsifier. For a given set of initial conditions, the influence of reaction was measured in terms of product formation and selectivity using different fatty acids as acyl donors. Results were found to be relatively dependent of the chain length of the fatty acids, showing high specificity for both myristic and palmytic acids attaining final mixture that fulfills the requirements established by the World Health Organization to be used as food emulsifiers. (C) 2010 Elsevier B.V. All rights reserved.

Screening of lipases for the synthesis of xylitol monoesters by chemoenzymatic esterification and the potential of microwave and ultrasound irradiations to enhance the reaction rate

Lipases from different sources, Pseudomonas fluorescens (AK lipase), Burkholderia cepacia (PS lipase), Penicillium camembertii (lipase G) and Porcine pancreas lipase (PPL), previously immobilized on epoxy SiO(2)-PVA, were screened for the synthesis of xylitol monoesters by esterification of the protected xylitol using oleic acid as acyl donor group. Among all immobilized derivatives, the highest esterification yield was achieved by P. camembertii lipase, showing to be attractive alternative to bulk chemical routes to satisfy increasing commercial demands. Further experiments were performed to determine the influence of fatty acids chain size on the reaction yield and the feasibility of using non-conventional heating systems (microwave and ultrasound irradiations) to enhance the reaction rate. (C) 2010 Elsevier B.V. All rights reserved.

Multipoint covalent immobilization of lipase on chitosan hybrid hydrogels: influence of the polyelectrolyte complex type and chemical modification on the catalytic properties of the biocatalysts

This work aimed at the production of stabilized derivatives of Thermomyces lanuginosus lipase (TLL) by multipoint covalent immobilization of the enzyme on chitosan-based matrices. The resulting biocatalysts were tested for synthesis of biodiesel by ethanolysis of palm oil. Different hydrogels were prepared: chitosan alone and in polyelectrolyte complexes (PEC) with kappa-carrageenan, gelatin, alginate, and polyvinyl alcohol (PVA). The obtained supports were chemically modified with 2,4,6-trinitrobenzene sulfonic acid (TNBS) to increase support hydrophobicity, followed by activation with different agents such as glycidol (GLY), epichlorohydrin (EPI), and glutaraldehyde (GLU). The chitosan-alginate hydrogel, chemically modified with TNBS, provided derivatives with higher apparent hydrolytic activity (HA(app)) and thermal stability, being up to 45-fold more stable than soluble lipase. The maximum load of immobilized enzyme was 17.5 mg g(-1) of gel for GLU, 7.76 mg g(-1) of gel for GLY, and 7.65 mg g(-1) of gel for EPI derivatives, the latter presenting the maximum apparent hydrolytic activity (364.8 IU g(-1) of gel). The three derivatives catalyzed conversion of palm oil to biodiesel, but chitosan-alginate-TNBS activated via GLY and EPI led to higher recovered activities of the enzyme. Thus, this is a more attractive option for both hydrolysis and transesterification of vegetable oils using immobilized TLL, although industrial application of this biocatalyst still demands further improvements in its half-life to make the enzymatic process economically attractive.

Chemoenzymatic synthesis: a strategy to obtain xylitol monoesters

BACKGROUND: Fatty acid sugar esters are used as non-ionic surfactants in cosmetics, foodstuffs and pharmaceuticals. In particular, monoesters of xylitol have attracted industrial interest due to their outstanding biological activities. In this work, xylitol monoesters were obtained by chemoenzymatic synthesis, in which, first, xylitol was made soluble in organic solvent by chemo-protecting reaction, followed by enzymatic esterification reaction using different acyl donors. A commercial immobilized Candida antartica lipase was used as catalyst, and reactions with pure xylitol were carried out to generate data for comparison. RESULTS: t-BuOH was found to be the most suitable solvent to carry out esterification reactions with both pure and protected xylitol. The highest yields were obtained for reactions carried out with pure xylitol, but in this case by-products, such as di- and tri-esters isomers were formed, which required a multi-step purification process. For the systems with protected xylitol, conversions of 86%, 58% and 24% were achieved using oleic, lauric and butyric acids, respectively. The structures of the monoesters were confirmed by (13)C- and (1)H-NMR and microanalysis. CONCLUSION: The chemoenzymatic synthesis of xylitol monoesters avoided laborious downstream processing when compared with reactions performed with pure xylitol. Monoesters production from protected xylitol was shown to be a practical, economical, and clean route for this process, allowing a simple separation, because there are no other products formed besides xylitol monoesters and residual xylitol. (C) 2009 Society of Chemical Industry

On the finite element modeling of fatigue crack growth in pressurized cylindrical shells

A methodology for the computational modeling of the fatigue crack growth in pressurized shell structures, based on the finite element method and concepts of Linear Elastic Fracture Mechanics, is presented. This methodology is based on that developed by Potyondy [Potyondy D, Wawrzynek PA, Ingraffea, AR. Discrete crack growth analysis methodology for through crack in pressurized fuselage structures. Int J Numer Methods Eng 1995;38:1633-1644], which consists of using four stress intensity factors, computed from the modified crack integral method, to predict the fatigue propagation life as well as the crack trajectory, which is computed as part of the numerical simulation. Some issues not presented in the study of Potyondy are investigated herein such as the influence of the crack increment size and the number of nodes per element (4 or 9 nodes) on the simulation results by means of a fatigue crack propagation simulation of a Boeing 737 airplane fuselage. The results of this simulation are compared with experimental results and those obtained by Potyondy [1]. (C) 2008 Elsevier Ltd. All rights reserved.

Energy and exergy analysis of ethanol production process from banana fruit

An alternative for ethanol production, is the use of vegetable waste, such as excess of banana production, that are evaluated in 2,400,000 t/year, which includes: residual banana fruit and lignocellulosic material. This paper analyzes the energetic and exergetic behavior to carry the process developed at laboratory scale to a plant processing of banana for the ethanol production, involving: growing and transport of the vegetable material, hydrolysis of banana fruit, sugar fermentation, ethanol distillation and utility plant. Finally, energy and exergy indicators are obtained. The results show a positive energy balance when banana fruit is used for ethanol production, but some process modification must be done looking for improving the exergetic efficiency in ethanol production.

Knowledge transfer in product development processes: A case study in small and medium enterprises (SMEs) of the metal-mechanic sector from Sao Paulo, Brazil

This paper reports a research that evaluated the product development methodologies used in Brazilian small and medium-sized metal-mechanic enterprises (SMEs), in a specific region of Sao Paulo. The tool used for collecting the data was a questionnaire, which was developed and applied through interviews conducted by the researchers in 32 companies. The main focus of this paper can be condensed in the synthesis-question ""Is only the company responsible for the development?"" which was analyzed thoroughly. The results obtained from this analysis were evaluated directly (through the respective percentages of answers) and statistically (through the search of an index which demonstrates if two questions are related). The results point to a degree of maturity in SMEs, which allows product development to be conducted in cooperation networks. (C) 2007 Elsevier Ltd. All rights reserved.

Computational Method to Determine Reflected Ultrasonic Signals From Arbitrary-Geometry Targets

A computational method based on the impulse response and on the discrete representation computational concept is proposed for the determination of the echo responses from arbitrary-geometry targets. It is supposed that each point of the transducer aperture can be considered as a source radiating hemispherical waves to the reflector. The local interaction with each of the hemispherical waves at the reflector surface can be modeled as a plane wave impinging on a planar surface, using the respective reflection coefficient. The method is valid for all field regions and can be performed for any excitation waveform radiated from an arbitrary acoustic aperture. The effects of target geometry, position, and material on both the amplitude and the shape of the echo response are studied. The model is compared with experimental results obtained using broadband transducers together with plane and cylindrical concave rectangular reflectors (aluminum, brass, and acrylic), as well as a circular cavity placed on a plane surface, in a water medium. The method can predict the measured echoes accurately. This paper shows an improved approach of the method, considering the reflection coefficient for all incident hemispherical waves arriving at each point of the target surface.

Swarm Intelligence applied in synthesis of hunting strategies in a three-dimensional environment

Systems of distributed artificial intelligence can be powerful tools in a wide variety of practical applications. Its most surprising characteristic, the emergent behavior, is also the most answerable for the difficulty in. projecting these systems. This work proposes a tool capable to beget individual strategies for the elements of a multi-agent system and thereof providing to the group means on obtaining wanted results, working in a coordinated and cooperative manner as well. As an application example, a problem was taken as a basis where a predators` group must catch a prey in a three-dimensional continuous ambient. A synthesis of system strategies was implemented of which internal mechanism involves the integration between simulators by Particle Swarm Optimization algorithm (PSO), a Swarm Intelligence technique. The system had been tested in several simulation settings and it was capable to synthesize automatically successful hunting strategies, substantiating that the developed tool can provide, as long as it works with well-elaborated patterns, satisfactory solutions for problems of complex nature, of difficult resolution starting from analytical approaches. (c) 2007 Elsevier Ltd. All rights reserved.

Synthesis, characterization, and bactericidal properties of composites based on crosslinked resins containing silver

Two different commercial crosslinked resins (Amberlite GT73 and Amberlite IRC748) were employed for anchoring silver. The -SH and -N(CH2COOH)2 groups, respectively, present on these resins were used for Ag+ chelation from an aqueous solution. The Ag+ ions were reduced with three different reductants: hydrazine, hydroxylamine, and formaldehyde (under an alkaline pH). The produced composites were characterized with thermogravimetry/differential thermogravimetry and scanning electron microscopy combined with a backscattered scanning electron detector. Energy-dispersive X-ray spectroscopy coupled to scanning electron microscopy allowed the observation of submicrometer particles of silver, and chemical microanalysis of emitted X-rays revealed the presence of metal on the internal and external surfaces of the composite microspheres. The amount of incorporated silver was determined by titration. The antibacterial activity of the silver/resin composites was determined toward 10(3)-10(7) cells/mL dilutions of the auxotrophic AB1157 Escherichia coli strain; the networks containing anchored submicrometer silver particles were completely bactericidal within a few minutes because of the combined action of silver and functional groups of the resins. (c) 2007 Wiley Periodicals, Inc.

Catalytic conversion of wastes from the bioethanol production into carbon nanomaterials

This work addressed the production of carbon nanomaterials (CNMs) by catalytic conversion of wastes from the bioethanol industry, in the form of either sugarcane bagasse or corn-derived distillers dried grains with solubles (DDGS). Both bagasse and DDGS were pyrolysed at temperatures in the range of 600-1000 degrees C. The pyrolyzate gases were then used as CNM growth agents by chemical vapor deposition on stainless steel meshes, serving as both catalysts and substrates. CNM synthesis temperatures of 750-1000 degrees C were explored, and it was determined that their growth was most pronounced at 1000 degrees C. The nanomaterials produced from pyrolysis of bagasse were in the form of long, straight, multi-wall nanotubes with smooth walls and axially uniform diameters. Typical lengths were circa 50 mu m and diameters were in the range of 20-80 nm. The nanomaterials produced from pyrolysis of DDGS were in the form of long, entangled, rope-like structures with rugged walls, and axially non-uniform diameters. Typical diameters were in the range of 100-300 nm and their lengths were in the tens of microns. This process also produces a bio-syngas byproduct that is enriched in hydrogen. (C) 2011 Elsevier B.V. All rights reserved.