Numeric reconstruction of cytoskeleton with finite element method and topology optimization method

The importance of mechanical aspects related to cell activity and its environment is becoming more evident due to their influence in stem cell differentiation and in the development of diseases such as atherosclerosis. The mechanical tension homeostasis is related to normal tissue behavior and its lack may be related to the formation of cancer, which shows a higher mechanical tension. Due to the complexity of cellular activity, the application of simplified models may elucidate which factors are really essential and which have a marginal effect. The development of a systematic method to reconstruct the elements involved in the perception of mechanical aspects by the cell may accelerate substantially the validation of these models. This work proposes the development of a routine capable of reconstructing the topology of focal adhesions and the actomyosin portion of the cytoskeleton from the displacement field generated by the cell on a flexible substrate. Another way to think of this problem is to develop an algorithm to reconstruct the forces applied by the cell from the measurements of the substrate displacement, which would be characterized as an inverse problem. For these kind of problems, the Topology Optimization Method (TOM) is suitable to find a solution. TOM is consisted of an iterative application of an optimization method and an analysis method to obtain an optimal distribution of material in a fixed domain. One way to experimentally obtain the substrate displacement is through Traction Force Microscopy (TFM), which also provides the forces applied by the cell. Along with systematically generating the distributions of focal adhesion and actin-myosin for the validation of simplified models, the algorithm also represents a complementary and more phenomenological approach to TFM. As a first approximation, actin fibers and flexible substrate are represented through two-dimensional linear Finite Element Method. Actin contraction is modeled as an initial stress of the FEM elements. Focal adhesions connecting actin and substrate are represented by springs. The algorithm was applied to data obtained from experiments regarding cytoskeletal prestress and micropatterning, comparing the numerical results to the experimental ones

Pair approximation for a model of vertical and horizontal transmission of parasites.

We apply Stochastic Dynamics method for a differential equations model, proposed by Marc Lipsitch and collaborators (Proc. R. Soc. Lond. B 260, 321, 1995), for which the transmission dynamics of parasites occurs from a parent to its offspring (vertical transmission), and by contact with infected host (horizontal transmission). Herpes, Hepatitis and AIDS are examples of diseases for which both horizontal and vertical transmission occur simultaneously during the virus spreading. Understanding the role of each type of transmission in the infection prevalence on a susceptible host population may provide some information about the factors that contribute for the eradication and/or control of those diseases. We present a pair mean-field approximation obtained from the master equation of the model. The pair approximation is formed by the differential equations of the susceptible and infected population densities and the differential equations of pairs that contribute to the former ones. In terms of the model parameters, we obtain the conditions that lead to the disease eradication, and set up the phase diagram based on the local stability analysis of fixed points. We also perform Monte Carlo simulations of the model on complete graphs and Erdös-Rényi graphs in order to investigate the influence of population size and neighborhood on the previous mean-field results; by this way, we also expect to evaluate the contribution of vertical and horizontal transmission on the elimination of parasite. Pair Approximation for a Model of Vertical and Horizontal Transmission of Parasites.

Quantification of cellular action fibers alignment from confocal microscopic images.

The cellular rheology has recently undergone a rapid development with particular attention to the cytoskeleton mechanical properties and its main components - actin filaments, intermediate filaments, microtubules and crosslinked proteins. However it is not clear what are the cellular structural changes that directly affect the cell mechanical properties. Thus, in this work, we aimed to quantify the structural rearrangement of these fibers that may emerge in changes in the cell mechanics. We created an image analysis platform to study smooth muscle cells from different arteries: aorta, mammary, renal, carotid and coronary and processed respectively 31, 29, 31, 30 and 35 cell image obtained by confocal microscopy. The platform was developed in Matlab (MathWorks) and it uses the Sobel operator to determine the actin fiber image orientation of the cell, labeled with phalloidin. The Sobel operator is used as a filter capable of calculating the pixel brightness gradient, point to point, in the image. The operator uses vertical and horizontal convolution kernels to calculate the magnitude and the angle of the pixel intensity gradient. The image analysis followed the sequence: (1) opens a given cells image set to be processed; (2) sets a fix threshold to eliminate noise, based on Otsu's method; (3) detect the fiber edges in the image using the Sobel operator; and (4) quantify the actin fiber orientation. Our first result is the probability distribution II(Δθ) to find a given fiber angle deviation (Δθ) from the main cell fiber orientation θ0. The II(Δθ) follows an exponential decay II(Δθ) = Aexp(-αΔθ) regarding to its θ0. We defined and determined a misalignment index α of the fibers of each artery kind: coronary αCo = (1.72 ‘+ or =’ 0.36)rad POT -1; renal αRe = (1.43 + or - 0.64)rad POT -1; aorta αAo = (1.42 + or - 0.43)rad POT -1; mammary αMa = (1.12 + or - 0.50)rad POT -1; and carotid αCa = (1.01 + or - 0.39)rad POT -1. The α of coronary and carotid are statistically different (p < 0.05) among all analyzed cells. We discussed our results correlating the misalignment index data with the experimental cell mechanical properties obtained by using Optical Magnetic Twisting Cytometry with the same group of cells.

Study of surface free energy on a lattice-gas model applied to Liquid bridge

The pulmonary crackling and the formation of liquid bridges are problems that for centuries have been attracting the attention of scientists. In order to study these phenomena, it was developed a canonical cubic lattice-gas­ like model to explain the rupture of liquid bridges in lung airways [A. Alencar et al., 2006, PRE]. Here, we further develop this model and add entropy analysis to study thermodynamic properties, such as free energy and force. The simulations were performed using the Monte Carlo method with Metropolis algorithm. The exchange between gas and liquid particles were performed randomly according to the Kawasaki dynamics and weighted by the Boltzmann factor. Each particle, which can be solid (s), liquid (l) or gas (g), has 26 neighbors: 6 + 12 + 8, with distances 1, √2 and √3, respectively. The energy of a lattice's site m is calculated by the following expression: Em = ∑k=126 Ji(m)j(k) in witch (i, j) = g, l or s. Specifically, it was studied the surface free energy of the liquid bridge, trapped between two planes, when its height is changed. For that, was considered two methods. First, just the internal energy was calculated. Then was considered the entropy. It was fond no difference in the surface free energy between this two methods. We calculate the liquid bridge force between the two planes using the numerical surface free energy. This force is strong for small height, and decreases as the distance between the two planes, height, is increased. The liquid-gas system was also characterized studying the variation of internal energy and heat capacity with the temperature. For that, was performed simulation with the same proportion of liquid and gas particle, but different lattice size. The scale of the liquid-gas system was also studied, for low temperature, using different values to the interaction Jij.

Mechanical alterations in airway smooth muscle after interaction with indoor pollutant - A mathematical model

The viscoelasticity of mammalian lung is determined by the mechanical properties and structural regulation of the airway smooth muscle (ASM). The exposure to polluted air may deteriorate these properties with harmful consequences to individual health. Formaldehyde (FA) is an important indoor pollutant found among volatile organic compounds. This pollutant permeates through the smooth muscle tissue forming covalent bonds between proteins in the extracellular matrix and intracellular protein structure changing mechanical properties of ASM and inducing asthma symptoms, such as airway hyperresponsiveness, even at low concentrations. In the experimental scenario, the mechanical effect of FA is the stiffening of the tissue, but the mechanism behind this effect is not fully w1derstood. Thus, the aim of this study is to reproduce the mechanical behavior of the ASM, such as contraction and stretching, under FA action or not. For this, it was created a two-dimensional viscoelastic network model based on Voronoi tessellation solved using Runge-Kutta method of fourth order. The equilibrium configuration was reached when the forces in different parts of the network were equal. This model simulates the mechanical behavior of ASM through of a network of dashpots and springs. This dashpot-spring mechanical coupling mimics the composition of the actomyosin machinery of ASM through the contraction of springs to a minimum length. We hypothesized that formation of covalent bonds, due to the FA action, can be represented in the model by a simple change in the elastic constant of the springs, while the action of methacholinc (MCh) reduce the equilibrium length of the spring. A sigmoid curve of tension as a function of MCh doses was obtained, showing increased tension when the muscle strip was exposed to FA. Our simulations suggest that FA, at a concentration of 0.1 ppm, can affect the elastic properties of the smooth muscle fibers by a factor of 120%. We also analyze the dynamic mechanical properties, observing the viscous and elastic behavior of the network. Finally, the proposed model, although simple, ir1corporates the phenomenology of both MCh and FA and reproduces experirnental results observed with ir1 vitro exposure of smooth muscle to .FA. Thus, this new mechanical approach incorporates several well know features of the contractile system of the cells ir1 a tissue level model. The model can also be used in different biological scales.

The role of asymmetries in rock-paper-scissors biodiversity models.

The maintenance of biodiversity is a long standing puzzle in ecology. It is a classical result that if the interactions of the species in an ecosystem are chosen in a random way, then complex ecosystems can't sustain themselves, meaning that the structure of the interactions between the species must be a central component on the preservation of biodiversity and on the stability of ecosystems. The rock-paper-scissors model is one of the paradigmatic models that study how biodiversity is maintained. In this model 3 species dominate each other in a cyclic way (mimicking a trophic cycle), that is, rock dominates scissors, that dominates paper, that dominates rock. In the original version of this model, this dominance obeys a 'Z IND 3' symmetry, in the sense that the strength of dominance is always the same. In this work, we break this symmetry, studying the effects of the addition of an asymmetry parameter. In the usual model, in a two dimensional lattice, the species distribute themselves according to spiral patterns, that can be explained by the complex Landau-Guinzburg equation. With the addition of asymmetry, new spatial patterns appear during the transient and the system either ends in a state with spirals, similar to the ones of the original model, or in a state where unstable spatial patterns dominate or in a state where only one species survives (and biodiversity is lost).

Low energy elastic and electronically inelastic electron scattering from biomolecules.

Reactions initiated by collisions with low-energy secondary electrons has been found to be the prominent mechanism toward the radiation damage on living tissues through DNA strand breaks. Now it is widely accepted that during the interaction with these secondary species the selective breaking of chemical bonds is triggered by dissociative electron attachment (DEA), that is, the capture of the incident electron and the formation of temporary negative ion states [1,2,3]. One of the approaches largely used toward a deeper understanding of the radiation damage to DNA is through modeling of DEA with its basic constituents (nucleotide bases, sugar and other subunits). We have tried to simplify this approach and attempt to make it comprehensible at a more fundamental level by looking at even simple molecules. Studies involving organic systems such as carboxylic acids, alcohols and simple ¯ve-membered heterocyclic compounds are taken as starting points for these understanding. In the present study we investigate the role played by elastic scattering and electronic excitation of molecules on electron-driven chemical processes. Special attention is focused on the analysis of the in°uence of polarization and multichannel coupling e®ects on the magnitude of elastic and electronically inelastic cross-sections. Our aim is also to investigate the existence of resonances in the elastic and electronically inelastic channels as well as to characterize them with respect to its type (shape, core-excited or Feshbach), symmetry and position. The relevance of these issues is evaluated within the context of possible applications for the modeling of discharge environments and implications in the understanding of mutagenic rupture of DNA chains. The scattering calculations were carried out with the Schwinger multichannel method (SMC) [4] and its implementation with pseudopotentials (SMCPP) [5] at di®erent levels of approximation for impact energies ranging from 0.5 eV to 30 eV. References [1] B. Boudai®a, P. Cloutier, D. Hunting, M. A. Huels and L. Sanche, Science 287, 1658 (2000). [2] X. Pan, P. Cloutier, D. Hunting and L. Sanche, Phys. Rev. Lett. 90, 208102 (2003). [3] F. Martin, P. D. Burrow, Z. Cai, P. Cloutier, D. Hunting and L. Sanche, Phys. Rev. Lett. 93, 068101 (2004). [4] K. Takatsuka and V. McKoy, Phys. Rev. A 24, 2437 (1981); ibid. Phys. Rev. A 30, 1734 (1984). [5] M. H. F. Bettega, L. G. Ferreira and M. A. P. Lima, Phys. Rev. A 47, 1111 (1993).

CANTAR PARA QUÊ? A música gospel no processo de midiatização: o caso do programa Esquenta!

Esta pesquisa tem por objetivo analisar sob quais aspectos se dá a interação entre mídia e religião, bem como as tensões ou continuidades que a aproximação do ‘sagrado’ com o ‘profano’ na sociedade midiatizada evoca. Para tal, elegemos como objeto de estudo a participação dos artistas evangélicos no Programa Esquenta!, exibido nas tardes de domingo, pela Rede Globo. Tomamos como referencial teórico os conceitos de cultura gospel, de midiatização, especialmente o conceito de bios midiático, e a discussão sobre secularização proposta por Habermas. A metodologia empregada prevê duas etapas. A primeira consiste numa uma análise de conteúdo de cinco edições do programa que contaram com a participação de artistas evangélicos, exibidas nos anos de 2013 e 2014. Nesse momento, o objetivo foi perceber o lugar que a música gospel ocupa dentro da proposta do programa. A segunda etapa consiste na realização de dois grupos de discussão, um formado por evangélicos e o outro por não-evangélicos, para compreender como os conteúdos religiosos deslocados de seu contexto original são ressignificados pela audiência. Resulta desta pesquisa a observação de que a participação dos artistas gospel no Esquenta! oferece novos modos de olhar que ampliam o conceito de cultura gospel, bem como legitima a mídia como lugar de experiência religiosa. Além disso, ilustra a perspectiva habermasiana ao refletir a dupla afetação entre universo religioso e vida secular, que emerge do entrecruzamento entre mídia e religião.

Influência dos fatores abióticos na composição química dos óleos essenciais.

Os óleos essenciais constituem um dos mais importantes grupos de matérias primas para as indústrias de alimentos, farmacêutica, perfumaria e afins. São constituídos por uma mistura complexa de diversas classes de substâncias, dentre elas os fenilpropanóides, mono e sesquiterpenos, pertencentes ao metabolismo secundários das plantas. O metabolismo secundário por sua vez pode ser influenciado, dentre outros, por fatores genéticos, climáticos (temperatura, intensidade de luz, efeito sazonal, etc.) e edáficos. Observa-se que, grande parte das espécies popularmente utilizadas, encontra-se próxima ao estado silvestre, mantendo forte interação com o ambiente. Informações sobre o efeito de condições ambientais no metabolismo secundário de plantas provêm principalmente de esforços da pesquisa para maximizar a produção de constituintes ativos de espécies medicinais e aromáticas. Como aplicação prática, avanços no sentido de compreender a influência dos fatores ambientais na regulação de biossíntese de metabólitos secundários, podem contribuir para um aumento na produção de compostos de interesse nestas espécies. Neste artigo será abordada a ação de alguns fatores abióticos no rendimento e composição de óleos essenciais, com base nos dados da literatura, sem a pretensão de esgotar este extenso tema.

Influência do horário de corte no rendimento de óleo essencial de alfavaquinha e alecrim.

O objetivo do presente trabalho foi avaliar o efeito do horário de coleta no rendimento de óleo essencial de alfavaquinha (Ocimum selloi) e alecrim (Rosmarinus officinalis L.). O experimento foi realizado na EMBRAPA Meio Ambiente, localizada no município de Jaguariúna-SP. As plantas foram colhidas no campo experimental da EMBRAPA em cinco diferentes horários (8h30min, 10h30min, 12h30min, 14h30min e 16h30min). Os óleos essenciais das folhas foram extraídos por hidrodestilação em aparelho tipo Clevenger modificado. O delineamento experimental utilizado foi o inteiramente casualizado, com quatro repetições, tendo como tratamento os horários de coleta. Os resultados obtidos demonstram que o melhor horário para coleta de Ocimum selloi, visando a extração de óleo essencial é no período da manhã, antes das 10h e 30 minutos, e para Rosmarinus officinalis. L. o melhor horário é a partir das 16h e 30 minutos. Para as duas plantas estudadas o menor percentual de óleo essencial foi obtido ás 12h e 30 minutos, não sendo assim recomendado coleta neste horário para extração de óleo essencial.

Óleos essenciais e extratos vegetais no controle de fitopatógenos de grãos de soja.

A utilização de sementes sadias é um importante método para diminuir a ocorrência de doenças desde o inicio de seu cultivo. Uma das alternativas ao uso de agrotóxicos é a utilização de óleos essenciais e extratos de plantas que possuam propriedades tóxicas aos fitopatógenos. O objetivo deste trabalho foi avaliar o efeito de óleos essenciais e extratos hidroalcoólicos de plantas medicinais na sanidade e germinação de sementes de soja. Os óleos essenciais e os extratos hidroalcoólicos foram diluídos em água destilada, na concentração de 2 mg/mL para os extratos e 20% para os óleos essenciais. Em seguida, as sementes foram pulverizadas com os tratamentos e secas a sombra durante 4 horas em temperatura ambiente (25ºC). Os tratamentos utilizados foram: T1=testemunha (água destilada); T2 = óleo essencial de gengibre; T3 = óleo essencial de limão Taiti; T4 = extrato de pariparoba e T5 = extrato de penicilina. Os testes de germinação e sanidade foram realizados segundo as Regras para Análises de Sementes (RAS). Os resultados obtidos no teste de germinação demonstraram que o percentual de germinação inicial das sementes não tratadas (4%) encontrava-se muito abaixo dos níveis recomendados pelas RAS (80%), não tendo como avaliar a interferência dos tratamentos na germinação. Em função deste resultado, foi realizado o teste de sanidade visando o tratamento de grãos. O óleo essencial de gengibre apresentou uma redução da incidência de 75% de Cladosporium sp; Rhizopus sp.; Fusarium spp. quando comparado à testemunha. Pode-se concluir que o óleo essencial de gengibre na concentração de 20% apresenta atividade positiva no controle de Cladosporium sp, Rhizopus sp e Fusarium spp em grãos de soja.

Efeito de diferentes concentrações do óleo de nim no crescimento micelial de fungos entomopatogênicos e Trichoderma harzianum.

A associação de extratos de origem vegetal com fungos entomopatogênicos pode aumentar a eficiência do controle biológico de pragas e doenças de plantas e ainda reduzir custos e impactos ambientais. No presente trabalho foi avaliado o efeito do óleo de nim, incorporado ao meio BDA (Batata-dextrose-ágar) nas concentrações de 0, 1, 10, 100, 1.000, 10.000 e 100.000 μ/L, sobre o crescimento micelial de Metarhizium anisopliae, Beauveria bassiana, Trichoderma harzianum e Lecanicillium lecanii. O óleo de nim foi adicionado ao meio antes e após a esterilização em autoclave por 20 min. e 1 atm. Na parte central das placas de Petri contendo os meios foi transferido um disco de micélio dos agentes de biocontrole e mantidas em sala de incubação a 27 ± 2°C. O crescimento da colônia foi avaliado diariamente por seis dias, considerando dois sentidos do diâmetro. Cada placa correspondeu a uma repetição sendo cinco placas por tratamento. O óleo de nim adicionado antes e após autoclavagem em todas as concentrações testadas, estimularam o crescimento micelial de todos os agentes de biocontrole. Esta associação é de grande valia para o controle biológico, pode aumentar a eficiência destes fungos e reduzir impactos ambientais.

Bioprospection of Petit Verdot grape pomace as a source of anti-inflammatory compounds.

The aim of this study was to evaluate the anti-inflammatory activity of Petit Verdot Extract and hexane, chloroform and ethyl acetate fractions obtained from grape pomace, in addition to identifying active compounds. The PVE and EAF reduced significantly paw edema and neutrophil migration when compared with control groups. The PVE reduced levels of TNF-α and IL1-β in the peritoneal fluid, whereas the EAF did not reduce cytokines significantly. Two hydroxybenzoic acids, two proanthocyanidins, three flavan-3-ol monomers and three anthocyanins were identified in the PVE and EAF by LC-MS/MS. The stilbene transresveratrol was identified only in the EAF. The phenolic compounds were quantified using HPLC-DAD analysis, except for the stilbenes, which were not sensible for the detection by the method. Since PVE and EAF showed significantly anti-inflammatory effects and high concentration of phenolic compounds, we concluded that Petit Verdot pomace could be an interesting source of anti-inflammatory bioactives.

Genetic associations between scrotal circumference and body weight measured at different ages in Canchim cattle.

2015

Águas superficiais na bacia do Ribeirão Água Parada no município de Bauru-SP: potencial de utilização para o abastecimento público

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)