Scale-free network topology and multifractality in weighted planar stochastic lattice

We propose a weighted planar stochastic lattice (WPSL) formed by the random sequential partition of a plane into contiguous and non-overlapping blocks and find that it evolves following several non-trivial conservation laws, namely $\sum_i^N x_i^{n-1} y_i^{4/n-1}$ is independent of time $\forall \ n$, where $x_i$ and $y_i$ are the length and width of the $i$th block. Its dual on the other hand, obtained by replacing each block with a node at its center and common border between blocks with an edge joining the two vertices, emerges as a network with a power-law degree distribution $P(k)\sim k^{-\gamma}$ where $\gamma=5.66$ revealing scale-free coordination number disorder since $P(k)$ also describes the fraction of blocks having $k$ neighbours. To quantify the size disorder, we show that if the $i$th block is populated with $p_i\sim x_i^3$ then its distribution in the WPSL exhibits multifractality.Comment: 7 pages, 8 figures, To appear in New Journal of Physics (NJP

Glass transition in self organizing cellular patterns

We have considered the dynamical evolution of cellular patterns controlled by a stochastic Glauber process determined by the deviations of local cell topology from that of a crystalline structure. Above a critical temperature evolution is towards a common equilibrium state from any initial configuration, but beneath this temperature there is a dynamical phase transition, with a start from a quasi-random state leading to non-equilibrium glassy freezing whereas an ordered start rests almost unchanged. A temporal persistence function decays exponentially in the high temperature equilibrating state but has a characteristic slow non-equilibrium aging-like behaviour in the low temperature glassy phase.Comment: Added references, text minor change

Perfil fermentativo da silagem de Brachiaria brizantha cv. Piatã com diferentes aditivos

A possibilidade de uso das gramíneas na forma de silagem, principalmente do gênero das Brachiariasp., deveriam ser mais estudadas no Brasil, que possui grandes áreas de pastagens implantadas com estas espécies. Contudo, são escassos os trabalhos na literatura com uso de aditivos para estas gramíneas. Nesse contexto, objetivou-se avaliar o perfil fermentativo da silagem de Brachiaria brizantha cv. Piatã tratada com diferentes aditivos. A forrageira foi colhida e ensilada em silos experimentais de PVC. O delineamento experimental utilizado foi inteiramente casualizado, fornecendo 4 repetições por tratamento, sendo os cinco tratamentos os diferentes aditivos: T1 ? controle; T2 ? inoculante microbiano SiloMax Centurium (Matsuda); T3 ? inoculante ênzimo-microbianoSil All C4 (Alltech do Brasil); T4 ? fubá de milho (10% na matéria natural) e T5 ? glicerina bruta (10% na matéria natural), totalizando 20 silos experimentais. Foram observados menores valores de pH de 4,22 e 4,29 e, maiores valores de acidez titulável de 53,00 e 52,81 mL de NaOH 0,1N para silagens contendo fubá de milho e glicerina bruta, respectivamente. Recomenda-se ainclusão de 10% de fubá de milho e glicerina bruta na matéria natural na ensilagem de Piatã, pois promove melhor perfil fermentativo

Exponential Distribution of Locomotion Activity in Cell Cultures

In vitro velocities of several cell types have been measured using computer controlled video microscopy, which allowed to record the cells' trajectories over several days. On the basis of our large data sets we show that the locomotion activity displays a universal exponential distribution. Thus, motion resulting from complex cellular processes can be well described by an unexpected, but very simple distribution function. A simple phenomenological model based on the interaction of various cellular processes and finite ATP production rate is proposed to explain these experimental results.Comment: 4 pages, 3 figure

Efeito de temperaturas altas no sistema fotossintetico e na produção de tubérculos em genótipos de batata (Solanum tuberosum).

O presente trabalho teve como objetivo conhecer o efeito das altas temperaturas no sistema fotossintético e na produtividade em batata.ENPOS UFPEL

Complex networks theory for analyzing metabolic networks

One of the main tasks of post-genomic informatics is to systematically investigate all molecules and their interactions within a living cell so as to understand how these molecules and the interactions between them relate to the function of the organism, while networks are appropriate abstract description of all kinds of interactions. In the past few years, great achievement has been made in developing theory of complex networks for revealing the organizing principles that govern the formation and evolution of various complex biological, technological and social networks. This paper reviews the accomplishments in constructing genome-based metabolic networks and describes how the theory of complex networks is applied to analyze metabolic networks.Comment: 13 pages, 2 figure

Evolutionary origins of human apoptosis and genome-stability gene networks

Apoptosis is essential for complex multicellular organisms and its failure is associated with genome instability and cancer. Interactions between apoptosis and genome-maintenance mechanisms have been extensively documented and include transactivation-independent and -dependent functions, in which the tumor-suppressor protein p53 works as a ‘molecular node’ in the DNA-damage response. Although apoptosis and genome stability have been identified as ancient pathways in eukaryote phylogeny, the biological evolution underlying the emergence of an integrated system remains largely unknown. Here, using computational methods, we reconstruct the evolutionary scenario that linked apoptosis with genome stability pathways in a functional human gene/protein association network. We found that the entanglement of DNA repair, chromosome stability and apoptosis gene networks appears with the caspase gene family and the antiapoptotic gene BCL2. Also, several critical nodes that entangle apoptosis and genome stability are cancer genes (e.g. ATM, BRCA1, BRCA2, MLH1, MSH2, MSH6 and TP53), although their orthologs have arisen in different points of evolution. Our results demonstrate how genome stability and apoptosis were co-opted during evolution recruiting genes that merge both systems. We also provide several examples to exploit this evolutionary platform, where we have judiciously extended information on gene essentiality inferred from model organisms to human

The Origin of Phenotypic Heterogeneity in a Clonal Cell Population In Vitro

BACKGROUND: The spontaneous emergence of phenotypic heterogeneity in clonal populations of mammalian cells in vitro is a rule rather than an exception. We consider two simple, mutually non-exclusive models that explain the generation of diverse cell types in a homogeneous population. In the first model, the phenotypic switch is the consequence of extrinsic factors. Initially identical cells may become different because they encounter different local environments that induce adaptive responses. According to the second model, the phenotypic switch is intrinsic to the cells that may occur even in homogeneous environments. PRINCIPAL FINDINGS: We have investigated the “extrinsic” and the “intrinsic” mechanisms using computer simulations and experimentation. First, we simulated in silico the emergence of two cell types in a clonal cell population using a multiagent model. Both mechanisms produced stable phenotypic heterogeneity, but the distribution of the cell types was different. The “intrinsic” model predicted an even distribution of the rare phenotype cells, while in the “extrinsic” model these cells formed small clusters. The key predictions of the two models were confronted with the results obtained experimentally using a myogenic cell line. CONCLUSIONS: The observations emphasize the importance of the “ecological” context and suggest that, consistently with the “extrinsic” model, local stochastic interactions between phenotypically identical cells play a key role in the initiation of phenotypic switch. Nevertheless, the “intrinsic” model also shows some other aspects of reality: The phenotypic switch is not triggered exclusively by the local environmental variations, but also depends to some extent on the phenotypic intrinsic robustness of the cells

Growth Based Morphogenesis of Vertebrate Limb Bud

Many genes and their regulatory relationships are involved in developmental phenomena. However, by chemical information alone, we cannot fully understand changing organ morphologies through tissue growth because deformation and growth of the organ are essentially mechanical processes. Here, we develop a mathematical model to describe the change of organ morphologies through cell proliferation. Our basic idea is that the proper specification of localized volume source (e.g., cell proliferation) is able to guide organ morphogenesis, and that the specification is given by chemical gradients. We call this idea “growth-based morphogenesis.” We find that this morphogenetic mechanism works if the tissue is elastic for small deformation and plastic for large deformation. To illustrate our concept, we study the development of vertebrate limb buds, in which a limb bud protrudes from a flat lateral plate and extends distally in a self-organized manner. We show how the proportion of limb bud shape depends on different parameters and also show the conditions needed for normal morphogenesis, which can explain abnormal morphology of some mutants. We believe that the ideas shown in the present paper are useful for the morphogenesis of other organs

A Multi-cell, Multi-scale Model of Vertebrate Segmentation and Somite Formation

Somitogenesis, the formation of the body's primary segmental structure common to all vertebrate development, requires coordination between biological mechanisms at several scales. Explaining how these mechanisms interact across scales and how events are coordinated in space and time is necessary for a complete understanding of somitogenesis and its evolutionary flexibility. So far, mechanisms of somitogenesis have been studied independently. To test the consistency, integrability and combined explanatory power of current prevailing hypotheses, we built an integrated clock-and-wavefront model including submodels of the intracellular segmentation clock, intercellular segmentation-clock coupling via Delta/Notch signaling, an FGF8 determination front, delayed differentiation, clock-wavefront readout, and differential-cell-cell-adhesion-driven cell sorting. We identify inconsistencies between existing submodels and gaps in the current understanding of somitogenesis mechanisms, and propose novel submodels and extensions of existing submodels where necessary. For reasonable initial conditions, 2D simulations of our model robustly generate spatially and temporally regular somites, realistic dynamic morphologies and spontaneous emergence of anterior-traveling stripes of Lfng. We show that these traveling stripes are pseudo-waves rather than true propagating waves. Our model is flexible enough to generate interspecies-like variation in somite size in response to changes in the PSM growth rate and segmentation-clock period, and in the number and width of Lfng stripes in response to changes in the PSM growth rate, segmentation-clock period and PSM length