Molecular model of shikimate kinase from Mycobacterium tuberculosis

Tuberculosis (TB) resurged in the late 1980s and now kills approximately 3 million people a year. The reemergence of tuberculosis as a public health threat has created a need to develop new anti-mycobacterial agents. The shikimate pathway is an attractive target for herbicides and anti-microbial agents development because it is essential in algae, higher plants, bacteria, and fungi, but absent from mammals. Homologs to enzymes in the shikimate pathway have been identified in the genome sequence of Mycobacterium tuberculosis. Among them, the shikimate kinase I encoding gene (aroK) was proposed to be present by sequence homology. Accordingly, to pave the way for structural and functional efforts towards anti-mycobacterial agents development, here we describe the molecular modeling of M. tuberculosis shikimate kinase that should provide a structural framework on which the design of specific inhibitors may be based. © 2002 Elsevier Science (USA). All rights reserved.

A nonlinear model for the long-term hydro-thermal generation scheduling problem over multiple areas with transmission constraints

This paper presents a nonlinear model with individual representation of plants for the centralized long-term hydrothermal scheduling problem over multiple areas. In addition to common aspects of long-term scheduling, this model takes transmission constraints into account. The ability to optimize hydropower exchange among multiple areas is important because it enables further minimization of complementary thermal generation costs. Also, by considering transmission constraints for long-term scheduling, a more precise coupling with shorter horizon schedules can be expected. This is an important characteristic from both operational and economic viewpoints. The proposed model is solved by a sequential quadratic programming approach in the form of a prototype system for different case studies. An analysis of the benefits provided by the model is also presented. ©2009 IEEE.

Comparison of three molecular typing methods to assess genetic diversity for Mycobacterium tuberculosis

This study describes the comparison of three methods for genotyping of Mycobacterium tuberculosis, namely MIRU-VNTR (mycobacterial interspersed repetitive units-variable number of tandem repeats), spoligotyping and, for the first time, MLST (Multilocus Sequence Typing). In order to evaluate the discriminatory power of these methods, a total of 44 M. tuberculosis isolates obtained from sputum specimens of patients from Brazil were genotyped. Among the three methods, MLST showed the lowest discriminatory power compared to the other two techniques. MIRU-VNTR showed better discriminatory power when compared to spoligotyping, however, the combination of both methods provides the greatest level of discrimination and therefore this combination is the most useful genotyping tool to be applied to M. tuberculosis isolates. © 2013 Elsevier B.V.

Dynamics of bone healing after osteotomy with piezosurgery or conventional drilling - histomorphometrical, immunohistochemical, and molecular analysis

Background: Piezosurgery is an osteotomy system used in medical and dental surgery. Many studies have proven clinical advantages of piezosurgery in terms of quality of cut, maneuverability, ease of use, and safety. However, few investigations have tested its superiority over the traditional osteotomy systems in terms of dynamics of bone healing. Therefore, the aim of this study was to evaluate the dynamics of bone healing after osteotomies with piezosurgery and to compare them with those associated to traditional bone drilling.Methods: One hundred and ten rats were divided into two groups with 55 animals each. The animals were anesthetized and the tibiae were surgically exposed to create defects 2 mm in diameter by using piezosurgery (Piezo group) and conventional drilling (Drill group). Animals were sacrificed at 3, 7, 14, 30 and 60 days post-surgery. Bone samples were collected and processed for histological, histomorphometrical, immunohistochemical, and molecular analysis. The histological analysis was performed at all time points (n = 8) whereas the histomorphometrical analysis was performed at 7, 14, 30 and 60 days post-surgery (n = 8). The immunolabeling was performed to detect Vascular Endothelial Growth Factor (VEGF), Caspase-3 (CAS-3), Osteoprotegerin (OPG), Receptor Activator of Nuclear Factor kappa-B Ligand (RANKL), and Osteocalcin (OC) at 3, 7, and 14 days (n = 3). For the molecular analysis, animals were sacrificed at 3, 7 and 14 days, total RNA was collected, and quantification of the expression of 21 genes related to BMP signaling, Wnt signaling, inflammation, osteogenenic and apoptotic pathways was performed by qRT-PCR (n = 5).Results: Histologically and histomorphometrically, bone healing was similar in both groups with the exception of a slightly higher amount of newly formed bone observed at 30 days after piezosurgery (p < 0.05). Immunohistochemical and qRT-PCR analyses didn't detect significant differences in expression of all the proteins and most of the genes tested.Conclusions: Based on the results of our study we conclude that in a rat tibial bone defect model the bone healing dynamics after piezosurgery are comparable to those observed with conventional drilling. © 2013 Esteves et al.; licensee BioMed Central Ltd.

Eletrônica molecular via método híbrido DFT/FGNE em anéis fenilas acoplados a eletrodos metálicos de nanotubos de carbono: a regra de conformação e quiralidade molecular

Nesta tese, investigamos detalhadamente as propriedades de transporte eletrônico, conformacional e de simetria de estruturas de Nanotubos de Carbono de Parede Simples zigzag (9,0), NCPS zz9, acopladas a anéis fenilas (2, 3, 4 e 5) sob influência de campo elétrico externo (voltagem) via método híbrido da Teoria do Funcional Densidade (DFT) do tipo B3LYP 6-311G(d,p) combinado com Função de Green de Não Equilíbrio (FGNE) e Teoria de Grupo. Verificamos uma boa relação entre: 1- o índice quiral () por Teoria de Grupo e a lei do cos2 (, ângulo diedral) por geometria sob a influência de campo elétrico externo, pois  só depende das posições atômicas (), das conformações, e também está fortemente correlacionada a corrente que passa através do sistema; 2- a condutância normalizada (G/Go) é proporcional a cos2 na região do gap (EHOMO-ELUMO), isto é, nas regiões onde ocorre a ressonância e a resistência diferencial negativa (RDN); 3- o gráfico Fowler-Northeim (FN) exibe mínimo de voltagem (Vmin) que ocorre sempre que a cauda de um pico de transmissão ressonante entra na janela de voltagem, isto é, quando nessas estruturas ocorre uma RDN, pois o número de RDN na curva I-V está associado ao número de Vmin no gráfico FN e pode ser explicado pelo modelo de transporte molecular coerente; 4- a altura da barreira (EF - EHOMO e ELUMO - EF) como função do comprimento molecular; 5- Vmin como função da altura da barreira (EF - EHOMO) e do comprimento molecular. Assim, 1 implica que a conformação molecular desempenha um papel preponderante na determinação das propriedades de transporte da junção; 2 sugere que a lei do cos2 tem uma aplicabilidade mais geral independentemente da natureza dos eletrodos; 3 serve como um instrumento espectroscópico e também para identificar a molécula na junção; 4 e 5 a medida que o comprimento molecular atinge um certo valor (1,3nm) o Vmin permanece praticamente inalterado. Os resultados mostraram que as propriedades estruturais sofrem alterações significativas com o aumento da voltagem que estão em boa concordância com os valores encontrados na literatura. O comportamento das curvas IxV e G/GoxV perdem sua dependência linear para dar origem a um comportamento não linear com aparecimento de RDN. Tal ponto revela a modificação estrutural sofrida pelo sistema. A curva IxV confirmou as afirmações que foram feitas através da análise estrutural para o sistema considerado e mostrou como se dá o fluxo de carga nos sistemas analisados.

Efeitos do exercício voluntario na recuperação de hemissecção da medula espinhal: mudanças na rede perineuronal e acetilação de histonas

A prática regular de exercícios físicos previne e combate várias doenças ao longo do tempo, destacando-se como excelente ferramenta terapêutica para o tratamento de lesões no sistema nervoso central (SNC). Após uma transecção (completa ou incompleta/hemissecção) da medula espinhal, células gliais reativas secretam substâncias inibitórias à regeneração axonal como, por exemplo, as moléculas de proteoglicanas de sulfato de condroitina (PGSCs) que exercem papel importante na formação de uma barreira físico-química, chamada cicatriz glial, que impede o crescimento dos axônios danificados pela lesão. Pesquisas que envolvem modelo experimental de lesão da medula espinhal e reabilitação por exercício físico têm obtido promissores resultados. No entanto, os mecanismos fisiológicos e moleculares pelos quais promovem esses resultados positivos ainda são pouco conhecidos. O objetivo do presente trabalho foi analisar a recuperação da função motora da pata posterior após protocolo de exercício físico voluntario em modelo experimental de hemissecção da medula espinhal e investigar dois mecanismos moleculares envolvidos na recuperação funcional: a degradação de PGSCs nas redes perineuronais e acetilação de histonas. Para isso, vinte e quatro (24) ratos da linhagem Wistar (Rattus novergicus) foram utilizados e separados em 3 grupos (controle, treinados e não treinados). Com exceção do grupo controle, todos os animais foram habituados a rodas de corridas e em seguidas foram submetidos a uma cirurgia experimental de hemissecção da medula espinhal, na altura da 8a vertebra torácica. Nossos resultados demonstraram que o exercício voluntário em rodas de corrida após lesão experimental da medula espinhal promoveu recuperação da função motora da pata posterior afetada, porém não observamos diferenças qualitativas na acetilação de histonas e degradação de PGSCs entre os grupos.

Estimates of genetic parameters for total milk yield over multiple ages in Brazilian Murrah buffaloes using different models

The objective of this study was to estimate variance components and genetic parameters for accumulated 305-day milk yield (MY305) over multiple ages, from 24 to 120 months of age, applying random regression (RRM), repeatability (REP) and multi-trait (MT) models. A total of 4472 lactation records from 1882 buffaloes of the Murrah breed were utilized. The contemporary group (herd-year-calving season) and number of milkings (two levels) were considered as fixed effects in all models. For REP and RRM, additive genetic, permanent environmental and residual effects were included as random effects. MT considered the same random effects as did REP and RRM with the exception of permanent environmental effect. Residual variances were modeled by a step function with 1, 4, and 6 classes. The heritabilities estimated with RRM increased with age, ranging from 0.19 to 0.34, and were slightly higher than that obtained with the REP model. For the MT model, heritability estimates ranged from 0.20 (37 months of age) to 0.32 (94 months of age). The genetic correlation estimates for MY305 obtained by RRM (L23.res4) and MT models were very similar, and varied from 0.77 to 0.99 and from 0.77 to 0.99, respectively. The rank correlation between breeding values for MY305 at different ages predicted by REP, MT, and RRM were high. It seems that a linear and quadratic Legendre polynomial to model the additive genetic and animal permanent environmental effects, respectively, may be sufficient to explain more parsimoniously the changes in MY305 genetic variation with age.

A NS-2 simulation model for DNP3 protocol over IEEE 802.15.4 wireless protocol toward low cost simulation of Smart Grid applications

Faced with an imminent restructuring of the electric power system, over the past few years many countries have invested in a new paradigm known as Smart Grid. This paradigm targets optimization and automation of electric power network, using advanced information and communication technologies. Among the main communication protocols for Smart Grids we have the DNP3 protocol, which provides secure data transmission with moderate rates. The IEEE 802.15.4 is another communication protocol also widely used in Smart Grid, especially in the so-called Home Area Network (HAN). Thus, many applications of Smart Grid depends on the interaction of these two protocols. This paper proposes modeling, in the traditional network simulator NS-2, the integration of DNP3 protocol and the IEEE 802.15.4 wireless standard for low cost simulations of Smart Grid applications.

Function inferences from a molecular structural model of bacterial ParE toxin

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

Outbreak control and clinical, pathological, and epidemiological aspects and molecular characterization of a bovine herpesvirus type 5 on a feedlot farm in S(a)over-tildeo Paulo State

This paper describes the control, epidemiological, pathological, and molecular aspects of an outbreak of meningoencephalitis in calves due to bovine herpesvirus 5 at a feedlot with 540 animals in Sa (a) over tildeo Paulo State, Brazil. The introduction of new animals and contact between the resident animals and the introduced ones were most likely responsible for virus transmission. Bovine herpesvirus 1 vaccine was used, resulting in the efficacy of the outbreak control, although two bovine herpesvirus 1 positive animals, vaccinated and revaccinated, presented meningoencephalitis, thereby characterizing vaccinal failure.

Molecular model for hydrated biological tissues

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

A simple relativistic model of p(p)over-bar-]K+K-

We compare a model calculation with some available experimental data (LEAP 92) on KK̄ production. We believe the simplicity of the model makes it a useful tool for studying charm and beauty baryon production, for which also experimental data will soon be profuse.

MOLECULAR DYNAMICS STUDIES OF SIMPLE MODEL FLUIDS AND WATER CONFINED IN CARBON NANOTUBE

Molecular Dynamics (MD) simulation is one of the most important computational techniques with broad applications in physics, chemistry, chemical engineering, materials design and biological science. Traditional computational chemistry refers to quantum calculations based on solving Schrodinger equations. Later developed Density Functional Theory (DFT) based on solving Kohn-Sham equations became the more popular ab initio calculation technique which could deal with ~1000 atoms by explicitly considering electron interactions. In contrast, MD simulation based on solving classical mechanics equations of motion is a totally different technique in the field of computational chemistry. Electron interactions were implicitly included in the empirical atom-based potential functions and the system size to be investigated can be extended to ~106 atoms. The thermodynamic properties of model fluids are mainly determined by macroscopic quantities, like temperature, pressure, density. The quantum effects on thermodynamic properties like melting point, surface tension are not dominant. In this work, we mainly investigated the melting point, surface tension (liquid-vapor and liquid-solid) of model fluids including Lennard-Jones model, Stockmayer model and a couple of water models (TIP4P/Ew, TIP5P/Ew) by means of MD simulation. In addition, some new structures of water confined in carbon nanotube were discovered and transport behaviors of water and ions through nano-channels were also revealed.

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.