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.

Modelagem e simulação da desidratação osmótica em pedaços de abacaxi utilizando o método de elementos finitos

Water loss and sugar gain were modelling during the osmotic dehydration process of pieces of pineaplle. The transfer of solute to the fruit and the water to the solution was based on Fick's 2nd law. The three dimensional model was solved by the finite element method with the usage of the software COMSOL Multiphysics 3.2. The main and cross diffusion coefficients and the Biot number were determined on the simulation and the deviation between the experimental and the simulated data were 4,28% to sucrose and 1,66 to the water.

Partially folded intermediates during trypsinogen denaturation

The equilibrium unfolding of bovine trypsinogen was studied by circular dichroism, differential spectra and size exclusion HPLC. The change in free energy of denaturation was = 6.99 ± 1.40 kcal/mol for guanidine hydrochloride and = 6.37 ± 0.57 kcal/mol for urea. Satisfactory fits of equilibrium unfolding transitions required a three-state model involving an intermediate in addition to the native and unfolded forms. Size exclusion HPLC allowed the detection of an intermediate population of trypsinogen whose Stokes radii varied from 24.1 ± 0.4 Å to 26.0 ± 0.3 Å for 1.5 M and 2.5 M guanidine hydrochloride, respectively. During urea denaturation, the range of Stokes radii varied from 23.9 ± 0.3 Å to 25.7 ± 0.6 Å for 4.0 M and 6.0 M urea, respectively. Maximal intrinsic fluorescence was observed at about 3.8 M urea with 8-aniline-1-naphthalene sulfonate (ANS) binding. These experimental data indicate that the unfolding of bovine trypsinogen is not a simple transition and suggest that the equilibrium intermediate population comprises one intermediate that may be characterized as a molten globule. To obtain further insight by studying intermediates representing different stages of unfolding, we hope to gain a better understanding of the complex interrelations between protein conformation and energetics.

Cloning, sequence analysis, and expression of cDNA coding for the major house dust mite allergen, Der f 1, in Escherichia coli

Our objective was to clone, express and characterize adult Dermatophagoides farinae group 1 (Der f 1) allergens to further produce recombinant allergens for future clinical applications in order to eliminate side reactions from crude extracts of mites. Based on GenBank data, we designed primers and amplified the cDNA fragment coding for Der f 1 by nested-PCR. After purification and recovery, the cDNA fragment was cloned into the pMD19-T vector. The fragment was then sequenced, subcloned into the plasmid pET28a(+), expressed in Escherichia coli BL21 and identified by Western blotting. The cDNA coding for Der f 1 was cloned, sequenced and expressed successfully. Sequence analysis showed the presence of an open reading frame containing 966 bp that encodes a protein of 321 amino acids. Interestingly, homology analysis showed that the Der p 1 shared more than 87% identity in amino acid sequence with Eur m 1 but only 80% with Der f 1. Furthermore, phylogenetic analyses suggested that D. pteronyssinus was evolutionarily closer to Euroglyphus maynei than to D. farinae, even though D. pteronyssinus and D. farinae belong to the same Dermatophagoides genus. A total of three cysteine peptidase active sites were found in the predicted amino acid sequence, including 127-138 (QGGCGSCWAFSG), 267-277 (NYHAVNIVGYG) and 284-303 (YWIVRNSWDTTWGDSGYGYF). Moreover, secondary structure analysis revealed that Der f 1 contained an a helix (33.96%), an extended strand (17.13%), a ß turn (5.61%), and a random coil (43.30%). A simple three-dimensional model of this protein was constructed using a Swiss-model server. The cDNA coding for Der f 1 was cloned, sequenced and expressed successfully. Alignment and phylogenetic analysis suggests that D. pteronyssinus is evolutionarily more similar to E. maynei than to D. farinae.

Development of a three-dimensional nonlinear viscoelastic constitutive model of solid propellant

A three dimensional nonlinear viscoelastic constitutive model for the solid propellant is developed. In their earlier work, the authors have developed an isotropic constitutive model and verified it for one dimensional case. In the present work, the validity of the model is extended to three-dimensional cases. Large deformation, dewetting and cyclic loading effects are treated as the main sources of nonlinear behavior of the solid propellant. Viscoelastic dewetting criteria is used and the softening of the solid propellant due to dewetting is treated by the modulus decrease. The nonlinearities during cyclic loading are accounted for by the functions of the octahedral shear strain measure. The constitutive equation is implemented into a finite element code for the analysis of propellant grains. A commercial finite element package ‘ABAQUS’ is used for the analysis and the model is introduced into the code through a user subroutine. The model is evaluated with different loading conditions and the predicted values are in good agreement with the measured ones. The resulting model applied to analyze a solid propellant grain for the thermal cycling load.

Phenotypic correlations and path analysis for plant architecture traits and grain production in three generations of cowpea

ABSTRACT The objective of this study was to analyze the phenotypic correlation and path analysis of traits related to plant architecture, earliness and grain yield in F2, BC1 and BC2 generations, from crosses between cowpea cultivars BRS Carijó and BR14 Mulato. Most phenotypic correlations of the examined traits were concordant in statistical significance, with approximate values ​​among the examined generations. For the trait seed weight, significant and positive phenotypic correlations were observed in the three generations only for the trait number of secondary branches. The values ​​of the direct effects were in agreement with the values ​​of the phenotypic correlations, which indicate true association by the phenotypic correlation among the traits of grain yield examined. Path analysis indicated that the selection of productive plants will result in early plants and an increased number of secondary branches. In F2, plants with shorter length of the main branch and shorter length of secondary branches can be obtained. The causal model explained 15 to 30% of the total variation in grain weight in relation to the traits examined. The analyses indicated the possibility of selecting plants with a higher and early grain yield, shorter length of primary branches and lower number of nodes, which are important variables for mechanical or semi-mechanical harvesting.

Gastric acid secretion response in the Cebus apella: a monkey model of chronic Chagas disease

The objective was to study the secretory pattern, both basal and stimulated either by histamine (0.1 mg/kg) or pentagastrin (64 ug/kg) in eighteen Cebus apella monkeys chronically infected with different T. cruzi strains (CA1, n=10; Colombian, n=4 and Tulahuen, n=4) and to describe the morphological findings in the gastrointestinal tract in twelve infected (6 sacrificed and 6 spontaneously dead) and four healthy monkeys. All infected monkeys and 35 healthy ones were evaluated by contrast X-ray examination. No differences were observed in basal acid output between control and infected groups. Animals infected with the Tulahuen and Colombian strains showed significant lower values of peak acid output in response to histamine or pentagastrin (p<0.01 and p<0.05 respectively; "t" test) in comparison to the controls. Barium contrast studies showed enlargement and dilatation of the colon in three infected animals. Histopathological lesions were seen in 75% of the autopsied animals either in colon alone (33%) or both, in colon and esophagus (42%). The normal secretion observed in the CA1 infected group could be due to a lower virulence of the strain, a lower esophagic tropism or the necessity of a longer post-infection time to cause lesions.

Transmission of Schistosoma mansoni under experimental conditions using the bovine - Biomphalaria glabrata - bovine model

Three calves experimentally infected with Schistosoma mansoni, and passing viable eggs in feces, as well as 5 normal calves (coming from a non-endemic area for schistosomiasis) kept as controls, were maintained in an enclosure (850 m² in area). In this enclosure, a tank with water received 500 laboratory reared Biomphalaria glabrata. All the control calves were infected for a period ranging from 79 to 202 days after the beginning of the experiment, and afterwards presented viable S. mansoni eggs in feces. The mean worm recovery was 555. The snail population increased throughout the experimental period, showing a high number of B. glabrata infected with S. mansoni (42% on average). According to the present study, bovine has been suggested as having potentially a role in the maintenance of the life cycle of S. mansoni

Preliminary study towards a novel experimental model to study localized cutaneous leishmaniasis caused bY Leishmania (Leishmania) mexicana

There is not an experimental model of localized cutaneous leishmaniasis (LCL) caused by Leishmania (Leishmania) mexicana. The aim of the present study was to characterize the clinical and histological features of Peromyscus yucatanicus experimentally infected with L. (L.) mexicana. A total of 54 P. yucatanicus (groups of 18) were inoculated with 1x10(6) promastigotes of L. (L.) mexicana in the base of the tail. They were euthanized at three and six months post experimental infection. The control group was inoculated with RPMI-1640. The predominant clinical sign observed was a single ulcerated lesion in 27.77% (5/18) and in 11.11% (2/18) P. yucatanicus at three and six months respectively. The histological pattern described as chronic granulomatous inflammation with or without necrosis was found in 7/7 (100%) biopsies of euthanized P. yucatanicus at three (n = 5) and six (n = 2) months, respectively. These results resembled clinical and histological features caused by L. (L.) mexicana in humans, and support the possibility to employ P. yucatanicus as a novel experimental model to study LCL caused by this parasite.

Leaf herbivory on three tree species in a monodominant and two other Terra firme forests on Maracá Island, Brazil

The aim of this study was to test the hypothesis that the monodominant non-pioneer Peltogyne gracilipes, typically does not suffer density-dependent herbivory (Janzen-Connell model). Two components of intraspecific variation in leaf herbivory were measured: 1) the variation between individuals in the population at the same time and 2) the temporal variation in rates of damage to each individual. The study was carried out on Maracá Island, Roraima, Brazil in three plots (50 m χ 50 m) in each of three forest types: Peltogyne-rich forest (PRF), Peltogyne-poor forest (PPF), and forest without Peltogyne (FWP). Two other non-pioneer species (Ecclinusa guianensis and Pradosia surinamensis) were chosen for comparison because they were fairly abundant and their seedlings could be readily identified. The values of leaf area removed by herbivores of trees and seedlings of the three study species were in the range reported for other tropical tree species (2-16%, standing damage). There were no differences within species between forests. However, there was a significant difference among species but this was not correlated with seedling density. Peltogyne seedlings showed no evidence of density-dependent herbivory as predicted by the Janzen-Connell model despite the fact that adult trees were observed to suffer a mass defoliation in April 1992. This result suggests that Peltogyne may be dominant partly due to escape from herbivory in the early stages of its life although it may suffer occasional mass defoliation as an adult.

Forest structure of artificial islands in the Tucuruí dam reservoir in northern Brazil: a test core-area model

Construction of hydroelectric dams in tropical regions has been contributing significantly to forest fragmentation. Alterations at edges of forest fragments impact plant communities that suffer increases in tree damage and dead, and decreases in seedling recruitment. This study aimed to test the core-area model in a fragmented landscape caused by construction of a hydroelectric power plant in the Brazilian Amazon. We studied variations in forest structure between the margin and interiors of 17 islands of 8-100 hectares in the Tucuruí dam reservoir, in two plots (30 and >100m from the margin) per island. Mean tree density, basal area, seedling density and forest cover did not significantly differ between marginal and interior island plots. Also, no significant differences were found in liana density, dead tree or damage for margin and interior plots. The peculiar topographic conditions associated with the matrix habitat and shapes of the island seem to extend edge effects to the islands' centers independently of the island size, giving the interior similar physical microclimatic conditions as at the edges. We propose a protocol for assessing the ecological impacts of edge effects in fragments of natural habitat surrounded by induced (artificial) edges. The protocol involves three steps: (1) identification of focal taxa of particular conservation or management interest, (2) measurement of an "edge function" that describes the response of these taxa to induced edges, and (3) use of a "Core-Area Model" to extrapolate edge function parameters to existing or novel situations.

Synanthropic trends in urban andextraurban taxocenoses of Sarcophaginae (Diptera) in three central european cities

An attempt has been made to characterize the synanthropic trends in Sarcophaginae of three Central European cities, viz. Brno, Bratislava and Budapest. The polar ordination of both sarcophagine taxa and of their taxocenoses revealed clear-cut trends towards culturophily and synanthropy in the male preconnubial aggregations of Sarchophaginae evidencing that this group of high Diptera represent an excellent model for the study of this phenomenon.

Evaluation of the rabbit as a model for Chagas disease - II: histopathologic studies of the heart, digestive tract and skeletal muscle

In order to investigate the value of the rabbit as an experimental model for Chagas' disease, seventy one animals were inoculated with different Trypanosoma cruzi strains and routes. The rabbits were submitted to necropsy in acute (earlier than three months of infection), recent chronic (three to six months) and late chronic (later than six months) phases. Myocarditis, generally focal and endomysial, occurred in 94.1%, 66.7% and 70.8% of the infected rabbits respectively in the acute, recent chronic and late chronic phases. The myocardial inflammatory exudate was composed by mononuclear cells, and also polymorphonuclear cells in the acute phase. In most cases of the late chronic phase, the myocarditis was similar to that described in the indeterminate form of human chagasic patients. Initial fibrosis occurred in the three phases but was more severe and frequent in the early chronic. Advanced fibrosis occurred only in the late chronic phase. Tissue parasites occurred only in the acute phase. The digestive tract and skeletal muscles showed mild and occasional lesions. Our data indicate that experimentally infected chagasic rabbits repeat some lesions similar to that of humans chagasic patients, specially that of the indeterminate form. So, it may be a useful, however not an ideal, model.

Chromoblastomycosis murine model and in vitro test to evaluate the sensitivity of Fonsecaea pedrosoi to ketoconazole, itraconazole and saperconazole

An experimental model of murine chromoblastomycosis and in vitro tests with Fonsecaea pedrosoi were used to test the sensitivity of this fungus to three different antimycotics. The experimental model was standardized in BALB/c mice inoculated intraperitoneally with a 10(6) CFU/ml suspension of a F. pedrosoi isolate. Clinical infection was evident after 5 days of inoculation. Three groups of 27 mice each were used in the experiment. One group was treated with ketoconazole (KTZ), another with itraconazole (ITZ) and the other with saperconazole (SPZ). Antimycotic therapy was continued for 21 days. The control group consisted of 40 mice which were inoculated, but not treated. Infection was documented by macroscopic and microscopic examination of affected tissue in addition to culture of tissue macerates. Minimal inhibitory concentrations (MIC) and minimal fungicidal concentrations (MFC) for the F. pedrosoi strain used were done. The in vitro results showed that SPZ was the most active with MIC 0.01 mg/ml and MFC 0.1 mg/ml, followed by ITZ. SPZ was also the most effective in vivo since 63% of the treated animals (p=0.01) showed a curative effect after the observation period. We concluded that SPZ had the best in vitro and in vivo activity against F. pedrosoi.

Reinfection in American Cutaneous Leishmaniasis: Evaluation of Clinical Outcomes in the Hamster Model

There is no clear understanding of the outcome of reinfection in New World cutaneous leishmaniasis, and its role in the relationship to the development of protection or secondary disease. For this reason, reinfection experiments with homologous (Leishmania panamensis-L. panamensis) and heterologous (L. major-L. panamensis) species of leishmaniae were conducted in the hamster model. The different protocols for primary infections prior to the challenge with L. panamensis were as follows: (a) L. major, single promastigote injection, (b) L. major, three booster infections, (c) L. panamensis, followed by antimonial treatment to achieve subclinical infection, (d) L. panamensis, with active lesions, (e) sham infected, naive controls. Although all reinfected hamsters developed lesions upon challenge, animals with active primary lesions due to L. panamensis, and receiving booster infections of L. major had the most benign secondary lesions (58-91% and 69-76% smaller than controls, respectively, P<0.05). Subclinically infected animals had intermediate lesions (40-64% smaller than controls, P<0.05), while hamsters which received a single dose of L. major had no significant improvement over controls. Our results suggested that L. major could elicit a cross protective response to L. panamensis, and that the presence and number of amastigotes persisting after a primary infection may influence the clinical outcome of reinfections.