Molecular Modeling Approaches for Determining Gene Function: application to a Putative Poly-A Binding Protein from Leishmania amazonensis (LaPABP)

The great expansion in the number of genome sequencing projects has revealed the importance of computational methods to speed up the characterization of unknown genes. These studies have been improved by the use of three dimensional information from the predicted proteins generated by molecular modeling techniques. In this work, we disclose the structure-function relationship of a gene product from Leishmania amazonensis by applying molecular modeling and bioinformatics techniques. The analyzed sequence encodes a 159 aminoacids polypeptide (estimated 18 kDa) and was denoted LaPABP for its high homology with poly-A binding proteins from trypanosomatids. The domain structure, clustering analysis and a three dimensional model of LaPABP, basically obtained by homology modeling on the structure of the human poly-A binding protein, are described. Based on the analysis of the electrostatic potential mapped on the model's surface and conservation of intramolecular contacts responsible for folding stabilization we hypothesize that this protein may have less avidity to RNA than it's L. major counterpart but still account for a significant functional activity in the parasite. The model obtained will help in the design of mutagenesis experiments aimed to elucidate the mechanism of gene expression in trypanosomatids and serve as a starting point for its exploration as a potential source of targets for a rational chemotherapy.

Models for the estimation of thermodynamic properties of layered double hydroxides: application to the study of their anion exchange characteristics

Several models for the estimation of thermodynamic properties of layered double hydroxides (LDHs) are presented. The predicted thermodynamic quantities calculated by the proposed models agree with experimental thermodynamic data. A thermodynamic study of the anion exchange process on LDHs is also made using the described models. Tables for the prediction of monovalent anion exchange selectivities on LDHs are provided. Reasonable agreement is found between the predicted and the experimental monovalent anion exchange selectivities.

The Shadow Moiré method using the phase shifting technique and digital image processing: computational implementation and application to the 3D-reconstruction of a buckled plate

The Shadow Moiré fringe patterns are level lines of equal depth generated by interference between a master grid and its shadow projected on the surface. In simplistic approach, the minimum error is about the order of the master grid pitch, that is, always larger than 0,1 mm, resulting in an experimental technique of low precision. The use of a phase shift increases the accuracy of the Shadow Moiré technique. The current work uses the phase shifting method to determine the surfaces three-dimensional shape using isothamic fringe patterns and digital image processing. The current study presents the method and applies it to images obtained by simulation for error evaluation, as well as to a buckled plate, obtaining excellent results. The method hands itself particularly useful to decrease the errors in the interpretation of the Moiré fringes that can adversely affect the calculations of displacements in pieces containing many concave and convex regions in relatively small areas.

Mathematical modeling of electro-rotation spectra of small particles in liquid solutions: Application to human erythrocyte aggregates

Electro-rotation can be used to determine the dielectric properties of cells, as well as to observe dynamic changes in both dielectric and morphological properties. Suspended biological cells and particles respond to alternating-field polarization by moving, deforming or rotating. While in linearly polarized alternating fields the particles are oriented along their axis of highest polarizability, in circularly polarized fields the axis of lowest polarizability aligns perpendicular to the plane of field rotation. Ellipsoidal models for cells are frequently applied, which include, beside sphere-shaped cells, also the limiting cases of rods and disks. Human erythrocyte cells, due to their particular shape, hardly resemble an ellipsoid. The additional effect of rouleaux formation with different numbers of aggregations suggests a model of circular cylinders of variable length. In the present study, the induced dipole moment of short cylinders was calculated and applied to rouleaux of human erythrocytes, which move freely in a suspending conductive medium under the effect of a rotating external field. Electro-rotation torque spectra are calculated for such aggregations of different length. Both the maximum rotation speeds and the peak frequencies of the torque are found to depend clearly on the size of the rouleaux. While the rotation speed grows with rouleaux length, the field frequency nup is lowest for the largest cell aggregations where the torque shows a maximum.

Random amplified polymorphic DNA analysis of DNA extracted from Trichuris trichiura (Linnaeus, 1771) eggs and its prospective application to paleoparasitological studies

Random amplified polymorphic DNA analysis was applied to DNAs extracted from Trichuris trichiura eggs recovered from human fecal samples. Four out of 6 primers tested displayed 18 distinct and well defined polymorphic patterns, ranging from 650 to 3200 base pairs. These results, upon retrieval and DNA sequencing of some of these bands from agarose gels, might help in establishing T. trichiura specific genetic markers, not available yet, and an important step to design primers to be used in molecular diagnosis approaches.

Sewage sludge application to agricultural land as soil physical conditioner

Water resource quality is a concern of today's society and, as a consequence, low pollutant wastewaters and sludges are being increasingly treated, resulting in continuous production of sewage sludge. Sewage sludge (SS) can be used as soil physical conditioner of agricultural or degraded lands, due to its organic C component. The objective of this research was to evaluate the long-term SS effects on soil physical quality of properties such as bulk density, porosity, permeability and water retention of degraded soils treated with annual SS applications. The SS rates were calculated according to the crop N demand. The field experiment consisted of three treatments: mineral fertilization, 10 and 20 Mg ha-1 of SS (once and twice the SS quantity to meet the maize N demand, respectively), in annual applications to the surface layer of a eutroferric Red Latosol. SS reduced bulk density, increased macroporosity and decreased microporosity after the third application, but did not significantly alter the soil permeability and physical quality as measured by the S index in the surface layer.

Behavioral avoidance tests to evaluate effects of cattle slurry and dairy sludge application to soil¹

The application of organic wastes to agricultural soils is not risk-free and can affect soil invertebrates. Ecotoxicological tests based on the behavioral avoidance of earthworms and springtails were performed to evaluate effects of different fertilization strategies on soil quality and habitat function for soil organisms. These tests were performed in soils treated with: i) slurry and chemical fertilizers, according to the conventional fertilization management of the region, ii) conventional fertilization + sludge and iii) unfertilized reference soil. Both fertilization strategies contributed to soil acidity mitigation and caused no increase in soil heavy metal content. Avoidance test results showed no negative effects of these strategies on soil organisms, compared with the reference soil. However, results of the two fertilization managements differed: Springtails did not avoid soils fertilized with dairy sludge in any of the tested combinations. Earthworms avoided soils treated with sludge as of May 2004 (DS1), when compared with conventional fertilization. Possibly, the behavioral avoidance of earthworms is more sensitive to soil properties (other than texture, organic matter and heavy metal content) than springtails

Investigation of the occurrence of pesticide residues in rural wells and surface water following application to tobacco

In this work the exposure of wells and surface water to pesticides, commonly used for tobacco cropping, was assessed. Water consumption wells and surface water flows were sampled at different times. After a preconcentration step with solid phase extraction (SPE), the selected pesticides were determined by gas chromatography with electron capture detection (GC-ECD) or high performance liquid chromatography with diode array detection (HPLC-DAD). No pesticides were detected in the well water samples and surface water flow in the winter season. However, in the spring and summer higher concentrations of chlorpyrifos and imidacloprid were found in the water source samples. Atrazine, simazine and clomazone were also found. The occurrence of pesticides in collected water samples was related with the application to tobacco.

Determination of phenobarbital in human plasma by a specific liquid chromatography method: application to a bioequivalence study

A liquid chromatography method was developed and validated for the determination of phenobarbital in human plasma using phenytoin as internal standard. The drugs were extracted from plasma by liquid-liquid extraction and separated isocratically on a C12 analytical column, maintained at 35 ºC, with water:acetonitrile:methanol (58.8:15.2:26, v/v/v) as mobile phase, run at a flow rate of 1.2 mL/min with detection at 205 nm. The method was linear in the range of 0.1-4 μg/mL (r²=0.9999) and demonstrated acceptable results for the precision, accuracy and stability studies. The method was successfully applied for the bioequivalence study of two tablet formulations (test and reference) of phenobarbital 100 mg after single oral dose administration to healthy human volunteers.

Simultaneous determination of moxifloxacin and H2 receptor antagonist in pharmaceutical dosage formulations by RP-HPLC: application to in vitro drug interactions

Simultaneous determination of moxifloxacin (MOX) and H2-antagonists was first time developed in bulk and formulations. Purospher STAR C18 (250 x 4.6 mm, 5 μm) column was used. The mobile phase (methanol: water: ACN, 60:45:5 v/v/v, pH 2.7) was delivered at a flow rate of 1.0 mL min-1, eluent was monitored at 236, 270 and 310 nm for cimetidine, famotidine and ranitidine, respectively. The proposed method is specific, accurate (98-103%), precise (intra-day and inter-day variation 0.098-1.970%) and linear (r>0.998). The LOD and LOQ were 0.006-0.018 and 0.019-0.005 μg mL-1, respectively. The statistical parameters were applied to verify the results. The method is applicable to routine analysis of formulations and interaction of MOX with H2-antagonist.

A sensitive and robust lc-ms/ms method with monolithic column and electrospray ionization for the quantitation of efavirenz in human plasma: application to a bioequivalence study

An LC-MS/MS method has been developed for the determination of efavirenz (EFZ) in human plasma using hydrochlorothiazide as internal standard (I.S.). An ESI negative mode with multiple reaction-monitoring was used monitoring the transitions m/z 313.88→69.24 (EFZ) and 296.02→204.76 (I.S.). Samples were extracted using liquid-liquid extraction. The total run time was 2.0 min. The separation was achieved with HPLC-RP using a monolithic column. The assay was linear in the concentration range of 100 - 5000 ng mL-1. The mean recovery was 83%. Intra- and inter-day precision were < 9.5% and < 8.9%, respectively and accuracy was in the range ± 8.33%. The method was successfully applied to a bioequivalence study.

Laboratory projects using inquiry-based learning: an application to a practical inorganic course

This paper reports how laboratory projects (LP) coupled to inquiry-based learning (IBL) were implemented in a practical inorganic chemistry course. Several coordination compounds have been successfully synthesised by students according to the proposed topics by the LP-IBL junction, and the chemistry of a number of metals has been studied. Qualitative data were collected from written reports, oral presentations, lab-notebook reviews and personal discussions with the students through an experimental course with undergraduate second-year students at the Universidad Nacional de Colombia during the last 5 years. Positive skills production was observed by combining LP and IBL. Conceptual, practical, interpretational, constructional (questions, explanations, hypotheses), communicational, environmental and application abilities were revealed by the students throughout the experimental course.

Development and validation of a stability-indicating HPLC method for the determination of buclizine hydrochloride in tablets and oral suspension and its application to dissolution studies

A method using liquid chromatography has been developed and validated for determination of buclizine in pharmaceutical formulations and in release studies. Isocratic chromatography was performed on a C18 column with methanol:water (80:20 v/v, pH 2.6) as mobile phase, at a flow rate of 1.0 mL/min, and UV detection at 230 nm. The method was linear, accurate, precise, sensible and robust. The dissolution test was optimized and validated in terms of dissolution medium, apparatus agitation and rotation speed. The presented analytical and dissolution procedures can be conveniently adopted in the quality and stability control of buclizine in tablets and oral suspension.

Determination of levodopa in human plasma by high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS): application to a bioequivalence study

A sensitive, accurate and simple method using HPLC-MS/MS was developed and validated for levodopa quantitation in human plasma. Analysis was achieved on a pursuit® C18 analytical column (5 µm; 150 x 4.6 mm i.d.) using a mobile phase (methanol and water , 90:10, v/v) containing formic acid 0.5% v/v, after extracting the samples using a simple protein plasma precipitation with perchloric acid. The developed method was validated in accordance with ANVISA guidelines and was successfully applied to a bioequivalence study in 60 healthy volunteers demonstrating the feasibility and reliability of the proposed method.

A pH optode based on thymol blue: application to determination of CO2 using flow injection analysis system

An optode based on thymol blue (TB), an acid-based indicator, has been constructed and evaluated as a detector in FIA system for CO2 determination. The dye was chemically immobilised on the surface of a bifurcated glass optical fibre bundle, using silanisation in organic media. In FIA system, hydrogen carbonate or carbonate samples are injected in a buffer carrier solution, and then are mixed with phosphoric acid solution to generate CO2, which diffuses through a PTFE membrane, in order to be collected in an acceptor carrier fluid, pumped towards to detection cell, in which the optode was adapted. The proposed system presents two linear response ranges, from 1.0 x 10-3 to 1.0 x 10-2 mol l-1, and from 2.0 x 10-2 to 0.10 mol l-1. The sampling frequency was 11 sample h-1, with good repeatability (R.S.D < 4 %, n = 10). In flow conditions the optode lifetime was 170 h. The system was applied in the analysis of commercial mineral water and the results obtained in the hydrogen carbonate determination did not differ significantly from those obtained by potentiometry, at a confidence level of 95 %.