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.

On the stabilization of conducting pernigraniline salt by the synthesis and oxidation of polyaniline in hydrophobic ionic liquids

The electrochemical polymerization of aniline in a hydrophobic room-temperature ionic liquid and the spectroelectrochemical characterization of the formed film are presented. The polymerization occurs without the presence of acid in 1-butyl-2,3-dimethylimidazolium bis(trifluoromethanesulfonyl)imide (BMMITFSI), leading to a very stable electroactive material where no degradation was observed even at high applied potentials. Both in situ UV-Vis and Raman spectroscopic studies provided evidence for the stabilization of pernigraniline salt at high oxidation potentials and that this polyaniline state is the conducting form, as was corroborated by in situ resistance measurements. These data are indicative that low conductivity is not an intrinsic property of pernigraniline salt and this point must be reconsidered.

On the template synthesis of nanostructured inorganic/organic hybrid films

Prussian Blue has been introduced as a mediator to achieve stable, sensitive, reproducible, and interference-free biosensors. However, Na(+), Li(+), H(+), and all group II cations are capable to block the activity of Prussian Blue and, because Na(+) can be found in most human fluids, Prussian Blue analogs have already been developed to overcome this problem. These analogs, such as copper hexacyanoferrate, have also been introduced in a conducting polypyrrole matrix to create hybrid materials (copper hexacyanoferrate/polypyrrole, CuHCNFe/Ppy) with improved mechanical and electrochemical characteristics. Nowadays, the challenges in amperometric enzymatic biosensors consist of improving the enzyme immobilization and in making the chemical signal transduction more efficient. The incorporation of nanostructured materials in biosensors can optimize both steps and a nanostructured hybrid CuHCNFe/Ppy mediator has been developed using a template of colloidal polystyrene particles. The nanostructured material has achieved sensitivities 7.6 times higher than the bulk film during H(2)O(2) detection and it has also presented better results in other analytical parameters such as time response and detection limit. Besides, the nanostructured mediator was successfully applied at glucose biosensing in electrolytes containing Prussian Blue blocking cations. (C) 2008 The Electrochemical Society.

Preparation and characterization of Mo/W bimetallic carbides by using different synthesis methods

Molybdenum and tungsten bimetallic oxides were synthetized according to the following methods: Pechini, coprecipitation and solid state reaction (SSR). After the characterization, those solids were carbureted at programmed temperature. The carburation process was monitored by checking the consumption of carburant hydrocarbon and CO produced. The monitoring process permits to avoid or to diminish the formation of pirolytic carbon.

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.

Evaluation of the catalytic properties of Burkholderia cepacia lipase immobilized on non-commercial matrices to be used in biodiesel synthesis from different feedstocks

The objective of this work was to produce an immobilized form of lipase from Burkholderia cepacia (lipase PS) with advantageous catalytic properties and stability to be used in the ethanolysis of different feedstocks, mainly babassu oil and tallow beef. For this purpose lipase PS was immobilized on two different non-commercial matrices, such as inorganic matrix (niobium oxide, Nb(2)O(5)) and a hybrid matrix (polysiloxane-polyvinyl alcohol, SiO(2)-PVA) by covalent binding. The properties of free and immobilized enzymes were searched and compared. The best performance regarding all the analyzed parameters (biochemical properties, kinetic constants and thermal stability) were obtained when the lipase was immobilized on SiO(2)-PVA. The superiority of this immobilized system was also confirmed in the transe-sterification of both feedstocks, attained higher yields and productivities. (C) 2010 Elsevier Ltd. All rights reserved.

Synthesis of Nb(2)O(5)center dot nH(2)O nanoparticles by water-in-oil microemulsion

Hydrous niobium oxide (Nb(2)O(5)center dot nH(2)O) nanoparticles had been Successfully prepared by water-in-oil microemulsion. They were characterized by X-ray diffraction (XRD), thermal analysis (TG/DTG), Fourier transform infrared spectroscopy (FTIR), BET surface area measurement, transmission electron microscopy (TEM), scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDS). The results showed that the nanoparticle was exactly Nb(2)O(5)center dot nH(2)O with spherical shape. Their BET surface area was 60 m(2) g(-1). XRD results showed that Nb(2)O(5)center dot nH(2)O nanoparticles with crystallite size in nanometer scale were formed. The crystallinity and crystallity size increased with increasing annealing temperature. TT-phase of Nb(2)O(5) was obtained when the sample is annealed at 550 degrees C. (C) 2009 Elsevier B.V. All rights reserved.

Synthesis of PID controllers for a class of time delay systems

In this paper we use the Hermite-Biehler theorem to establish results on the design of proportional plus integral plus derivative (PID) controllers for a class of time delay systems. Using the property of interlacing at high frequencies of the class of systems considered and linear programming we obtain the set of all stabilizing PID controllers. As far as we know, previous results on the synthesis of PID controllers rely on the solution of transcendental equations. This paper also extends previous results on the synthesis of proportional controllers for a class of delay systems Of retarded type to a larger class of delay systems. (C) 2009 Elsevier Ltd. All rights reserved.

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.

Synthesis, characterization and evaluation of phosphorylated resins in the removal of Pb(2+) from aqueous solutions

Phosphinic-derivative poly(styrene-co-divinylbenzene)-based on PS-DVB copolymers with different porosity degrees have been prepared by aromatic electrophilic substitution reaction using PCl(3)/AlCl(3) followed by base-promoted hydrolysis. The phosphorylation reaction was analyzed by infra-red spectroscopy (FTIR), scanning electron microscopy (SEM), and thermogravimetry (TG/DTG). In addition, the phosphorous content of the phosphorylated copolymers was determined by spectrophotometry using the method based on sodium molybdate reactant so that the extension of that modification could be assessed. The performance of the phosphorylated resins in the extraction of Pb(2+) from aqueous solutions in a batch system was also evaluated. The Pb(2+) content was determined by atomic absorption spectrometry (AAS). These materials presented excellent extraction capacity under the contact time of 30 min and pH 6.

Recombinant rabies virus glycoprotein synthesis in bioreactor by transfected Drosophila melanogaster S2 cells carrying a constitutive or an inducible promoter

S2 cell populations (S2AcRVGP2K and S2MtRVGP-Hy) were selected after transfection of gene expression vectors carrying the cDNA encoding the rabies virus glycoprotein (RVGP) gene under the control of the constitutive (actin) or inductive (metallothionein) promoters. These cell populations were cultivated in a 1 L bioreactor mimicking a large scale bioprocess. Cell cultures were carried out at 90 rpm and monitored/controlled for temperature (28 degrees C) and dissolved oxygen (10 or 50% air saturation). Cell growth attained similar to 1.5-3 x 10(7) cells/mL after 3-4 clays of cultivation. The constitutive synthesis of RVGP in S2AcRVGP2K cells led to values of 0.76 mu g/10(7) cells at day 4 of culture. The RVGP synthesis in S2MtRVGP-Hy cell fraction increased upon CuSO(4) induction attaining specific productivities of 1.5-2 mu g/10(7) cells at clays 4-5. RVGP values in supernatant as a result of cell lysis were always very low (<0.2 mu g/mL) indicating good integrity of cells in culture. Overall the RVGP productivity was of 1.5-3 mg/L. Our data showed an important influence of dissolved oxygen on RVGP synthesis allowing a higher and sustained productivity by S2MtRVGP-Hy cells when cultivated with a DO of 10% air saturation. The RVGP productivity in bioreactors shown here mirrors those previously observed for T-flasks and shaker bottles and allow the preparation of the large RVGP quantities required for studies of structure and function. (C) 2010 Elsevier B.V. All rights reserved.

Optimal synthesis of anaerobic digester networks

The objective of this paper is to develop a mathematical model for the synthesis of anaerobic digester networks based on the optimization of a superstructure that relies on a non-linear programming formulation. The proposed model contains the kinetic and hydraulic equations developed by Pontes and Pinto [Chemical Engineering journal 122 (2006) 65-80] for two types of digesters, namely UASB (Upflow Anaerobic Sludge Blanket) and EGSB (Expanded Granular Sludge Bed) reactors. The objective function minimizes the overall sum of the reactor volumes. The optimization results show that a recycle stream is only effective in case of a reactor with short-circuit, such as the UASB reactor. Sensitivity analysis was performed in the one and two-digester network superstructures, for the following parameters: UASB reactor short-circuit fraction and the EGSB reactor maximum organic load, and the corresponding results vary considerably in terms of digester volumes. Scenarios for three and four-digester network superstructures were optimized and compared with the results from fewer digesters. (C) 2009 Elsevier B.V. All rights reserved.