Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data

Motivation: DNA assembly programs classically perform an all-against-all comparison of reads to identify overlaps, followed by a multiple sequence alignment and generation of a consensus sequence. If the aim is to assemble a particular segment, instead of a whole genome or transcriptome, a target-specific assembly is a more sensible approach. GenSeed is a Perl program that implements a seed-driven recursive assembly consisting of cycles comprising a similarity search, read selection and assembly. The iterative process results in a progressive extension of the original seed sequence. GenSeed was tested and validated on many applications, including the reconstruction of nuclear genes or segments, full-length transcripts, and extrachromosomal genomes. The robustness of the method was confirmed through the use of a variety of DNA and protein seeds, including short sequences derived from SAGE and proteome projects.

Intraspecific variation in 16S rRNA gene of Mycoplasma synoviae determined by DNA sequencing

Mycoplasma synoviae (MS) is an important avian pathogen may cause both respiratory disease and joint inflammation synovitis in poultry, causing economic losses to the Brazilian poultry industry. The genotypic variation in 16S rRNA gene is unknown. Partial sequences of 16S rRNA gene of 19 strains of M. synoviae were sequenced and analyzed in order to obtain molecular characterization and evaluation of the genetic variability of strains from distinct Brazilian areas of poultry production. Different polymorphic patterns were observed. The number of polymorphic alterations in the studied strains ranged from 0 to 6. The nucleotide variations, including deletion, insertion and substitutions, ranged from 3 to 5. The genotypic diversity observed in this study may be explained by spontaneous mutations that may occur when a lineage remains in the same flock for long periods. The culling and reposition in poultry flocks may be responsible for the entry of new strains in different areas. (C) 2008 Elsevier Ltd. All rights reserved.

Study of DNA damage with a new system for irradiation of samples in a nuclear reactor

In this paper, we report results of a quantitative analysis of the effects of neutrons on DNA, and, specifically, the production of simple and double breaks of plasmid DNA in aqueous solutions with different concentrations of free-radical scavengers. The radiation damage to DNA was evaluated by electrophoresis through agarose gels. The neutron and gamma doses were measured separately with thermoluminescent detectors. In this work, we have also demonstrated usefulness of a new system for positioning and removing samples in channel BH#3 of the IEA-R1 reactor at the Instituto de Pesquisas Energeticas e Nucleares (Brazil) without necessity of interrupting the reactor operation. (C) 2010 Elsevier Ltd. All rights reserved.

New mechanical samples positioning system for irradiations on a radial channel at nuclear research reactor in a full-power continuous operation

This paper describes a new mechanical samples positioning system that allows the safe placement and removal of biological samples for prolonged irradiation, in a nuclear reactor during full-power continuous operation. Also presented herein the materials of construction and operating principles. Additionally, this sample positioning system is compared with an existing pneumatic and automated transfer system, already available at the research reactors. The system consists of a mechanical arm with a claw, which can deliver the samples for irradiations without reactor shutdown. It was installed in the lEA-R1 research reactor at Instituto de Pesquisas Energeticas e Nucleares (IPEN), Sao Paulo, Brazil, and for the past 5 years, the system has successfully operated and allowed the conducting of important experiments. As a result of its introduction, the facility has been in a position to positively respond to the increased demand in studies of biology, medicine, physics, engineering, detector/dosimeter calibrations, etc. It is one example of the appropriated technologies that save energy and resources. (C) 2010 Elsevier Ltd. All rights reserved.

Purification, characterization and sequencing of the major beta-1,3-glucanase from the midgut of Tenebrio molitor larvae

The major beta-1,3-glucanase from Tenebrio molitor (TLam) was purified to homogeneity (yield, 6%; enrichment, 113 fold; specific activity, 4.4 U/mg). TLam has a molecular weight of 50 kDa and a pH optimum of 6. It is an encloglucanase that hydrolyzes beta-1,3-glucans as laminarin and yeast beta-1,3-1,6-glucan, but is inactive toward other polysaccharides (as unbranched beta-1,3-glucans or mixed beta-1,3-1,4-glucan from cereals) or disaccharides. The enzyme is not inhibited by high substrate concentrations and has low processivity (0.6). TLam has two ionizable groups involved in catalysis, and His, Tyr and Arg residues plus a divalent ion at the active site. A Cys residue important for TLam activity is exposed after laminarin binding. The cDNA coding for this enzyme was cloned and sequenced. It belongs to glycoside hydrolase family 16, and is related to other insect glucanases and glucan-binding proteins. Sequence analysis and homology modeling allowed the identification of some residues (E174, E179, H204, Y304, R127 and R181) at the active site of the enzyme, which may be important for TLam activity. TLam efficiently lyses fungal cells, suggesting a role in making available walls and cell contents to digestion and in protecting the midgut from pathogen infections. (C) 2009 Elsevier Ltd. All rights reserved.

Sequencing of Spodoptera frugiperda midgut trehalases and demonstration of secretion of soluble trehalase by midgut columnar cells

Both soluble (SfTre1) and membrane-bound (SfTre2) trehalases occur along the midgut of Spodoptera frugiperda larvae. Released SfTre2 was purified as a 67 kDa protein. Its K(m) (1.6 mM) and thermal stability (half life 10 min at 62 degrees C) are different from the previously isolated soluble trehalase (K(m) = 0.47 mM; 100% stable at 62 degrees C). Two cDNAs coding for S. frugiperda trehalases have been cloned using primers based on consensus sequences of trehalases and having as templates a cDNA library prepared from total polyA-containing RNA extracted from midguts. One cDNA codes for a trehalase that has a predicted transmembrane sequence and was defined as SfTre2. The other, after being cloned and expressed, results in a recombinant trehalase with a K(m) value and thermal stability like those of native soluble trehalase. This enzyme was defined as SfTre1 and, after it was used to generate antibodies, it was immunolocalized at the secretory vesicles and at the glycocalyx of columnar cells. Escherichia coli trehalase 3D structure and sequence alignment with SfTre1 support a proposal regarding the residue modulating the pKa value of the proton donor.

Fast batch injection analysis of H(2)O(2) using an array of Pt-modified gold microelectrodes obtained from split electronic chips

A fast and robust analytical method for amperometric determination of hydrogen peroxide (H(2)O(2)) based on batch injection analysis (BIA) on an array of gold microelectrodes modified with platinum is proposed. The gold microelectrode array (n = 14) was obtained from electronic chips developed for surface mounted device technology (SMD), whose size offers advantages to adapt them in batch cells. The effect of the dispensing rate, volume injected, distance between the platinum microelectrodes and the pipette tip, as well as the volume of solution in the cell on the analytical response were evaluated. The method allows the H(2)O(2) amperometric determination in the concentration range from 0.8 mu mol L(-1) to 100 mu mol L(-1). The analytical frequency can attain 300 determinations per hour and the detection limit was estimated in 0.34 mu mol L(-1) (3 sigma). The anodic current peaks obtained after a series of 23 successive injections of 50 mu L of 25 mu mol L(-1) H(2)O(2) showed an RSD < 0.9%. To ensure the good selectivity to detect H(2)O(2), its determination was performed in a differential mode, with selective destruction of the H(2)O(2) with catalase in 10 mmol L(-1) phosphate buffer solution. Practical application of the analytical procedure involved H(2)O(2) determination in rainwater of Sao Paulo City. A comparison of the results obtained by the proposed ampermetric method with another one which combines flow injection analysis (FIA) with spectrophotometric detection showed good agreement. (C) 2011 Elsevier B.V. All rights reserved.

Time Evolution of the Activation Energy in a Batch Chemical Oscillator

The batch-operated bromate/phosphate/acetone/dual catalyst system was studied at four temperatures between 5 and 35 degrees C. The dynamics was simultaneously followed by potential measurements with platinum and bromide selective electrodes, and spectroscopically at two different wavelengths. By simultaneously recording these four time series it was possible to characterize the dynamics of the sequential oscillations that evolve in time. The existence of three sequential oscillatory patterns at each temperature allowed estimating the activation energies in each case. Along with the activation energy of the induction period, it was possible to trace the time evolution of the overall activation energy at four different stages as the reaction proceeds. The study was carried out for two different sets of initial concentrations and it was observed that the overall activation energy increases as reactants turn into products. This finding was propounded as a result of the decrease in the driving force, or the system`s affinity, of the catalytic oxidative bromination of acetone with acidic bromate, as the closed system evolves toward the thermodynamic equilibrium.

Electrocombustion of humic acid and removal of algae from aqueous solutions

This paper reports experiments involving the electrochemical combustion of humic acid (HA) and removal of algae from pond water. An electrochemical flow reactor with a boron-doped diamond film anode was used and constant current experiments were conducted in batch recirculation mode. The mass transfer characteristics of the electrochemical device were determined by voltammetric experiments in the potential region of water stability, followed by a controlled current experiment in the potential region of oxygen evolution. The average mass transfer coefficient was 5.2 x 10(-5) m s(-1). The pond water was then processed to remove HA and algae in the conditions in which the reaction combustion occurred under mass transfer control. To this end, the mass transfer coefficient was used to estimate the initial limiting current density applied in the electrolytic experiments. As expected, all the parameters analyzed here-solution absorbance at 270 nm, total phenol concentration and total organic carbon concentration-decayed according to first-order kinetics. Since the diamond film anode successfully incinerated organic matter, the electrochemical system proved to be predictable and programmable.

TiO(2)-PHOTOCATALYZED DEGRADATION OF PHENOL IN SALINE MEDIA IN AN ANNULAR REACTOR: HYDRODYNAMICS, LUMPED KINETICS, INTERMEDIATES, AND ACUTE TOXICITY

The photocatalytic degradation of phenol in aqueous suspensions of TiO(2) under different salt concentrations in an annular reactor has been investigated. In all cases, complete removal of phenol and mineralization degrees above 90% were achieved. The reactor operational parameters were optimized and its hydrodynamics characterized in order to couple mass balance equations with kinetic ones. The photodegradation of the organics followed a Langmuir-Hinshelwood-Hougen- Watson lumped kinetics. From GC/MS analyses, several intermediates formed during oxidation have been identified. The main ones were catechol, hydroquinone, and 3-phenyl-2-propenal, in this order. The formation of negligible concentrations of 4-chlorophenol was observed only in high salinity medium. Acute toxicity was determined by using Artemia sp. as the test organism, which indicated that intermediate products were all less toxic than phenol and a significant abatement of the overall toxicity was accomplished, regardless of the salt concentration.

In situ differentiation of labile/inert metal species in Brazilian tropical rivers by means of a time-controlled batch-procedure based on TEPHA resin

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

Quali/quantitative characterization of biogas produced in batch digesters supplied with six distinct substrates

Com a finalidade de se analisar quali/quantitativamente o biogás produzido por 6 tipos de substratos, efetuou-se a presente pesquisa no DER/FCAV/UNESP- SP, Brasil. Os substratos utilizados na digestão anaeróbia foram caracterizados como: 1- Esterco de aves de postura (EAP); 2- Esterco de aves de postura triturado (EAPT); 3- Esterco de aves de corte com cama de maravalha (EACM); 4- Esterco de aves de corte com cama de maravalha triturado (EACMT); 5- Esterco de aves de corte com cama de casca de amendoim (EACA), e 6- Esterco de aves de corte com cama de casca de amendoim triturado (EACAT). Dos resultados obtidos, concluiu-se que, em relação à produção acumulada de biogás, o substrato EAPT foi superior aos demais, enquanto EACM apresentou produção acumulada inferior. em geral, os substratos triturados apresentaram maior quantidade de biogás acumulado em relação aos não triturados, exceto o EACAT, com 20,9 m³ inferior ao EACA. O período de produção máxima de biogás teve início entre 45 e 60 dias, começando a decair a partir dos 120 dias. Aos 57 dias após o enchimento dos biodigestores, o gás produzido possuía teores de CH4 superiores a 53%, e a partir dos 99 dias, todos produziram biogás com teores de CH4 superiores a 70%. Os substratos EAP e EAPT apresentaram maiores concentrações de metano no biogás.

Toxoplasma gondii: cloning, sequencing, expression, and antigenic characterization of ROP2, GRA5 and GRA7

Toxoplasma gondii is an intracellular obligate protozoan, which infects humans and warm-blooded animals. The aim of the present study was to clone the rop2, gra5 and gra7 genes from T. gondii RH strain and to produce recombinant proteins. The rop2, gra5 and gra7 gene fragments produced by polymerase chain reaction were cloned into the pET102/D-TOPO(R) vector which contains thioredoxin and polyhistidine tags at the C-and N-ends, respectively, and is expressed in Escherichia coli BL21(DE-3). The expression fusion proteins were found almost entirely in the insoluble form in the cell lysate. These recombinant proteins were purified with an Ni-NTA column. Concentrations of the recombinant antigens produced in the E. coli BL21-star ranged from 300 to 500 mu g/mL growth media, which was used to immunize rabbits. We observed an identity ranging from 96 to 97% when nucleotide sequences were compared to GenBank database sequences. Immunocharacterization of proteins was made by indirect immunofluorescence assay. These proteins will be used for serodiagnosis and vaccination.

Desenvolvimento e teste de um protótipo de reator de plasma com gaiola catódica rotatória para nitretação em lote de pequenas peças

The technique of ion nitriding, despite being fully consolidated in the industry, has great limitations when applied to the treatment of small parts. This is because effects that occur due to non-uniformity of the electric field, generate localized heating in parts, damaging the uniformity of nitrided layer. In addition, because the samples are treated static parts thereof are untreated. To expand the use of plasma nitriding, this work presents the development, assembly and testing of a prototype plasma reactor with rotatory cathodic cage [patent pending], able to meet these needs, giving the material a uniform treatment and opening doors to industrial scale production. The samples tested with hexagonal nuts are 6.0 mm in diameter, made of stainless steel AISI 304 nitrided at a pressure of 1 mbar in an atmosphere of 20% H2 + 80% N2 for 1 h. After treatment, testing visual inspection, optical microscopy and microhardness were carried out to check the effectiveness of the process for uniformity and hardness of the parts. All samples exhibited uniform color, and matte brownish, unlike the untreated samples, silver color and gloss. The hardness of the surface (top and sides) was 65% and even higher than the original hardness. The nitrided layer showed great uniformity in microstructure and thickness. It is concluded, therefore, that the unit was effective constructed for the purposes for which it was designed

Avaliação de catalisadores a base de carbeto e nitreto de molibdênio na obtenção de lactitol via hidrogenação da lactose

Seeking a greater appreciation of cheese whey was developed to process the hydrogenation of lactose for the production of lactitol, a polyol with high added value, using the catalyst Ni / activated carbon (15% and 20% nickel), the nitride Mo2N, the bimetallic carbide Ni-Mo/ activated carbon and carbide Mo2C. After synthesis, the prepared catalysts were analyzed by MEV, XRD, laser granulometry and B.E.T. The reactor used in catalytic hydrogenation of lactose was the type of bed mud with a pressure (68 atm), temperature (120 oC) and stirring speed (500 rpm) remained constant during the experiments. The system operated in batch mode for the solid and liquid and semi-continuous to gas. Besides the nature of the catalyst, we studied the influence of pH of reaction medium for Mo2C carbide as well as evaluating the character of the protein inhibitor and chloride ions on the activity of catalysts Ni (20%)/Activated Carbon and bimetallic carbide Ni-Mo/Activated Carbon. The decrease in protein levels was performed by coagulation with chitosan and adsorption of chloride ions was performed by ion exchange resins. In the process of protein adsorption and chloride ions, the maximum percentage extracted was about 74% and 79% respectively. The micrographs of the powders of Mo2C and Mo2N presented in the form of homogeneous clusters, whereas for the catalysts supported on activated carbon, microporous structure proved impregnated with small particles indicating the presence of metal. The results showed high conversion of lactose to lactitol 90% for the catalyst Ni (20%)/Activated Carbon at pH 6 and 46% for the carbide Mo2C pH 8 (after addition of NH4OH) using the commercial lactose. Monitoring the evolution of the constituents present in the reaction medium was made by liquid chromatography. A kinetic model of heterogeneous Langmuir Hinshelwood type was developed which showed that the estimated constants based catalysts promoted carbide and nitride with a certain speed the adsorption, desorption and production of lactitol