Estudo clássico e quântico da dissociação molecular induzida por laser

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

An intriguing model for 5S rDNA sequences dispersion in the genome of freshwater stingray Potamotrygon motoro (Chondrichthyes: Potamotrygonidae)

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

Severity of Brazilian sickle cell disease patients: severity scores and feasibility of the Bayesian network model use

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Effects of uremic solutes on reactive oxygen species in vitro model systems as a possibility of support the renal function management

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Geoffroy's side-necked turtle [Phrynops geoffroanus (Schweigger, 1812), Testudines: Chelidae] as a model for evolutionary ecotoxicology: relationship between environmental contamination, conditions and genetic variability

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Structural and functional insights into the conductive pili of Geobacter sulfurreducens revealed in molecular dynamics simulations

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

Diversidade cariotípica e molecular de Leptodactylus (Anura, Leptodactylidae) e obtenção de sondas cromossomo-específicas de anfíbio por citometria de fluxo

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

An introductory informatics theoretical framework, based on an integrable lattice model using quantized function algebras, for studying DNA-ionized gas interaction system

Usually we observe that Bio-physical systems or Bio-chemical systems are many a time based on nanoscale phenomenon in different host environments, which involve many particles can often not be solved explicitly. Instead a physicist, biologist or a chemist has to rely either on approximate or numerical methods. For a certain type of systems, called integrable in nature, there exist particular mathematical structures and symmetries which facilitate the exact and explicit description. Most integrable systems, we come across are low-dimensional, for instance, a one-dimensional chain of coupled atoms in DNA molecular system with a particular direction or exist as a vector in the environment. This theoretical research paper aims at bringing one of the pioneering ‘Reaction-Diffusion’ aspects of the DNA-plasma material system based on an integrable lattice model approach utilizing quantized functional algebras, to disseminate the new developments, initiate novel computational and design paradigms.

Estudos da interação de peptídeos antimicrobianos com modelo de membrana por simulações de dinâmica molecular

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

A macroscopic kinetic model for DNA polymerase elongation and high-fidelity nucleotide election

The enzymatically catalyzed template-directed extension of ssDNA/primer complex is an impor-tant reaction of extraordinary complexity. The DNA polymerase does not merely facilitate the insertion of dNMP, but it also performs rapid screening of substrates to ensure a high degree of fidelity. Several kinetic studies have determined rate constants and equilibrium constants for the elementary steps that make up the overall pathway. The information is used to develop a macro-scopic kinetic model, using an approach described by Ninio [Ninio J., 1987. Alternative to the steady-state method: derivation of reaction rates from first-passage times and pathway probabili-ties. Proc. Natl. Acad. Sci. U.S.A. 84, 663–667]. The principle idea of the Ninio approach is to track a single template/primer complex over time and to identify the expected behavior. The average time to insert a single nucleotide is a weighted sum of several terms, in-cluding the actual time to insert a nucleotide plus delays due to polymerase detachment from ei-ther the ternary (template-primer-polymerase) or quaternary (+nucleotide) complexes and time delays associated with the identification and ultimate rejection of an incorrect nucleotide from the binding site. The passage times of all events and their probability of occurrence are ex-pressed in terms of the rate constants of the elementary steps of the reaction pathway. The model accounts for variations in the average insertion time with different nucleotides as well as the in-fluence of G+C content of the sequence in the vicinity of the insertion site. Furthermore the model provides estimates of error frequencies. If nucleotide extension is recognized as a compe-tition between successful insertions and time delaying events, it can be described as a binomial process with a probability distribution. The distribution gives the probability to extend a primer/template complex with a certain number of base pairs and in general it maps annealed complexes into extension products.

A mixed model QTL analysis for sugarcane multiple-harvest-location trial data

Sugarcane-breeding programs take at least 12 years to develop new commercial cultivars. Molecular markers offer a possibility to study the genetic architecture of quantitative traits in sugarcane, and they may be used in marker-assisted selection to speed up artificial selection. Although the performance of sugarcane progenies in breeding programs are commonly evaluated across a range of locations and harvest years, many of the QTL detection methods ignore two- and three-way interactions between QTL, harvest, and location. In this work, a strategy for QTL detection in multi-harvest-location trial data, based on interval mapping and mixed models, is proposed and applied to map QTL effects on a segregating progeny from a biparental cross of pre-commercial Brazilian cultivars, evaluated at two locations and three consecutive harvest years for cane yield (tonnes per hectare), sugar yield (tonnes per hectare), fiber percent, and sucrose content. In the mixed model, we have included appropriate (co)variance structures for modeling heterogeneity and correlation of genetic effects and non-genetic residual effects. Forty-six QTLs were found: 13 QTLs for cane yield, 14 for sugar yield, 11 for fiber percent, and 8 for sucrose content. In addition, QTL by harvest, QTL by location, and QTL by harvest by location interaction effects were significant for all evaluated traits (30 QTLs showed some interaction, and 16 none). Our results contribute to a better understanding of the genetic architecture of complex traits related to biomass production and sucrose content in sugarcane.

Molecular and Electronic Structure of the Peptide Subunit of Geobacter sulfurreducens Conductive Phi from First Principles

The respiration of metal oxides by the bacterium Geobacter sulfurreducens requires the assembly of a small peptide (the GS pilin) into conductive filaments termed pili. We gained insights into the contribution of the GS pilin to the pilus conductivity by developing a homology model and performing molecular dynamics simulations of the pilin peptide in vacuo and in solution. The results were consistent with a predominantly helical peptide containing the conserved a-helix region required for pilin assembly but carrying a short carboxy-terminal random-coiled segment rather than the large globular head of other bacterial pilins. The electronic structure of the pain was also explored from first principles and revealed a biphasic charge distribution along the pilin and a low electronic HOMO-LUMO gap, even in a wet environment. The low electronic band gap was the result of strong electrostatic fields generated by the alignment of the peptide bond dipoles in the pilin's alpha-helix and by charges from ions in solution and amino acids in the protein. The electronic structure also revealed some level of orbital delocalization in regions of the pilin containing aromatic amino acids and in spatial regions of high resonance where the HOMO and LUMO states are, which could provide an optimal environment for the hopping of electrons under thermal fluctuations. Hence, the structural and electronic features of the pilin revealed in these studies support the notion of a pilin peptide environment optimized for electron conduction.

Effects of selective bile duct ligation on liver parenchyma in young animals: histologic and molecular evaluations

Background/Purpose: The mechanisms of increased collagen production and liver parenchyma fibrosis are poorly understood. These phenomena are observed mainly in children with biliary obstruction (BO), and in a great number of patients, the evolution to biliary cirrhosis and hepatic failure leads to the need for liver transplantation before adolescence. However, pediatric liver transplantation presents with biliary complications in 20% to 30% of cases in the postoperative period. Intra-or extrahepatic stenosis of bile ducts is frequent and may lead to secondary biliary cirrhosis and the need for retransplantation. It is unknown whether biliary stenosis involving isolated segments or lobes may affect the adjacent nonobstructed lobes by paracrine or endocrine means, leading to fibrosis in this parenchyma. Therefore, the present study aimed to create an experimental model of selective biliary duct ligation in young animals with a subsequent evaluation of the histologic and molecular alterations in liver parenchyma of the obstructed and nonobstructed lobes. Methods: After a pilot study to standardize the surgical procedures, weaning rats underwent ligation of the bile ducts of the median, left lateral, and caudate liver lobes. The bile duct of the right lateral lobe was kept intact. To avoid intrahepatic biliary duct collaterals neoformation, the parenchymal connection between the right lateral and median lobes was clamped. The animals were divided into groups according to the time of death: 1, 2, 3, 4, and 8 weeks after surgical procedure. After death, the median and left lateral lobes (with BO) and the right lateral lobe (without BO [NBO]) were harvested separately. A group of 8 healthy nonoperated on animals served as controls. Liver tissues were subjected to histologic evaluation and quantification of the ductular proliferation and of the portal fibrosis. The expressions of smooth muscle alpha-actin (alpha-SMA), desmin, and transforming growth factor beta 1 genes were studied by molecular analyses (semiquantitative reverse transcriptase-polymerase chain reaction and real-time polymerase chain reaction, a quantitative method). Results: Histologic analyses revealed the occurrence of ductular proliferation and collagen formation in the portal spaces of both BO and NBO lobes. These phenomena were observed later in NBO than BO. Bile duct density significantly increased 1 week after duct ligation; it decreased after 2 and 3 weeks and then increased again after 4 and 8 weeks in both BO and NBO lobes. The portal space collagen area increased after 2 weeks in both BO and NBO lobes. After 3 weeks, collagen deposition in BO was even higher, and in NBO, the collagen area started decreasing after 2 weeks. Molecular analyses revealed increased expression of the alpha-SMA gene in both BO and NBO lobes. The semiquantitative and quantitative methods showed concordant results. Conclusions: The ligation of a duct responsible for biliary drainage of the liver lobe promoted alterations in the parenchyma and in the adjacent nonobstructed parenchyma by paracrine and/or endocrine means. This was supported by histologic findings and increased expression of alpha-SMA, a protein related to hepatic fibrogenesis. (C) 2012 Elsevier Inc. All rights reserved.

Correlation Between Molecular Conformation, Packing, and Dynamics in Oligofluorenes: A Theoretical/Experimental Study

Fluorene-based systems have shown great potential as components in organic electronics and optoelectronics (organic photovoltaics, OPVs, organic light emitting diodes, OLEDs, and organic transistors, OTFTs). These systems have drawn attention primarily because they exhibit strong blue emission associated with relatively good thermal stability. It is well-known that the electronic properties of polymers are directly related to the molecular conformations and chain packing of polymers. Here, we used three oligofluorenes (trimer, pentamer, and heptamer) as model systems to theoretically investigate the conformational properties of fluorene molecules, starting with the identification of preferred conformations. The hybrid exchange correlation functional, OPBE, and ZINDO/S-CI showed that each oligomer exhibits a tendency to adopt a specific chain arrangement, which could be distinguished by comparing their UV/vis electronic absorption and C-13 NMR spectra. This feature was used to identify the preferred conformation of the oligomer chains in chloroform-cast films by comparing experimental and theoretical UV/vis and C-13 NMR spectra. Moreover, the oligomer chain packing and dynamics in the films were studied by DSC and several solid state NMR techniques, which indicated that the phase behavior of the films may be influenced by the tendency that each oligomeric chain has to adopt a given conformation.

New insights on reaction pathway selectivity promoted by crown ether phase-transfer catalysis: Model ab initio calculations of nucleophilic fluorination

Crown ethers have the ability of solubilizing inorganic salts in apolar solvents and to promote chemical reactions by phase-transfer catalysis. However, details on how crown ethers catalyze ionic S(N)2 reactions and control selectivity are not well understood. In this work, we have used high level theoretical calculations to shed light on the details of phase-transfer catalysis mechanism of KF reaction with alkyl halides promoted by 18-crown-6. A complete analysis of the of the model reaction between KF(18-crown-6) and ethyl bromide reveals that the calculations can accurately predict the product ratio and the overall kinetics. Our results point out the importance of the K* ion and of the crown ether ring in determining product selectivity. While the K* ion favors the S(N)2 over the E2 anti pathway, the crown ether ring favors the S(N)2 over E2 syn route. The combination effects lead to a predicted 94% for the S(N)2 pathway in excellent agreement with the experimental value of 92%. A detailed analysis of the overall mechanism of the reaction under phase-transfer conditions also reveals that the KBr product generated in the nucleophilic fluorination acts as an inhibitor of the 18-crown-6 catalyst and it is responsible for the observed slow reaction rate. (C) 2012 Elsevier B.V. All rights reserved.