1,077 research outputs found
System Dynamics modeling of tumor growth: a possible tool for optimization of pharmacological treatment?
No full textProcess-based modeling has been widely used to simulate the behavior of all kinds of biological systems. Recent modeling studies on plants, proposed a new concept of autotoxicity as a main driver, along environmental gradients, of plant systems development (Mazzoleni et al., 2010). The release of autotoxic compounds was showed to be responsible for the generation of ring-like spatial patterns of individual plants, presenting an increase of dead biomass in their central growth zone (Cartenì et al., 2012). This has been recently associated to the levels of washing out of turnover products, showing that the occurrence of spatial patterns is dependent on the balance between positive and negative feedbacks by nutrients and toxic products respectively (Marasco et al., 2013).
In oncology, simulation modeling was used to understand and predict tumor growth and also to anticipate the effects of different therapies (Anderson and Quaranta, 2008). In this work we discuss the possible application of the autotoxicity hypothesis on modeling the growth of solid tumors. In particular, simulations are implemented showing the development and the spatial arrangement, in relation to different levels of vascularization, of 3 different layers: (i) proliferating, (ii) quiescent and (iii) necrotic cell
Modeling the dynamic development of vascular bundles in plants: radial patterns in stems and roots
No full textSpontaneous spatial pattern formation as a result of dynamic interactions is common in nature at all scales. In plant development and morphogenesis, several regular patterns have been widely studied such as the establishment of the main axes, organ shapes and venation.
The radial arrangement of plant vascular bundles and other tissues, i.e. the stele, varies between species and organs. The topic has been analyzed in morphological, physiological and genetic studies and discussed in terms of evolutionary perspectives. In the last decades, simulation models have proven to be useful tools for hypotheses testing on complex systems. Several studies have been carried out using computer simulation in plant development. Two main mechanisms have been proposed for the generation of venation in plants, the canalization hypothesis by Sachs et al. (1969) and the pre-pattern theory by local activation and long-range inhibition formulated by Meinhardt (1976, 1998). Both approaches have been applied to several developmental problems like axes establishment, phyllotaxis, SAM and RAM functioning and leaf venation. So far, no modeling effort has been done yet on the formation of primary structures observed in different plant taxa.
In this study we propose a new 2D cellular automaton model based on the spatial dynamics (reaction-diffusion) of hypothetical autocatalytic substrate-depleting morphogens, which promote the differentiation of procambium, phloem and xylem. The model defines a set of logical and functional rules to simulate activation of procambial and vascular cell differentiation in stem and root radial sections.
Simulation results show that our model is capable of qualitatively reproduce most stelar structures, simulating the dynamic development of different radial spatial patterns of vascular bundles
Hybrid Modelling in Agriculture
No full textA New Paradigm for Sustainable Development in Agriculture: Mathematics & AI Get Into the Fiel
Modelling the development and arrangement of the primary vascular structure in plants
No full textBackground and Aims The process of vascular development in plants results in the formation of a specific array of bundles that run throughout the plant in a characteristic spatial arrangement. Although much is known about the genes involved in the specification of procambium, phloem and xylem, the dynamic processes and interactions that define the development of the radial arrangement of such tissues remain elusive. Methods This study presents a spatially explicit reaction-diffusion model defining a set of logical and functional rules to simulate the differentiation of procambium, phloem and xylem and their spatial patterns, starting from a homogeneous group of undifferentiated cells. Key Results Simulation results showed that the model is capable of reproducing most vascular patterns observed in plants, from primitive and simple structures made up of a single strand of vascular bundles (protostele), to more complex and evolved structures, with separated vascular bundles arranged in an ordered pattern within the plant section (e.g. eustele). Conclusions The results presented demonstrate, as a proof of concept, that a common genetic-molecular machinery can be the basis of different spatial patterns of plant vascular development. Moreover, the model has the potential to become a useful tool to test different hypotheses of genetic and molecular interactions involved in the specification of vascular tissues
A novel systems dynamics model for simulation of yeast batch, fed-batch and continuous cultures.
No full textModelling of microbial cell cultures is essential for design, optimization and control of processes of biotechnological interest. Models can vary from the simple “black box” descriptions to more complex “cybernetic” approaches, but they usually lack flexibility in representing the microbial population dynamics including feedbacks from environment.
On the contrary, the innovative model recently proposed [1] and based on the principle of Systems Dynamics, highlights how the decline and arrest of cell proliferation depends on the accumulation of self-produced inhibitory compounds in the medium. The model (developed in SIMILE and MATLAB R2012b) focused on the yeast Saccharomyces cerevisiae, a microorganism of major biotechnological importance, and considers the main metabolic routes of glucose assimilation during aerobic growth in batch, continuous and fed-batch reactors.
Main feature of the model is represented by the metabolic shift between respiration and fermentation occurring in S. cerevisiae (a Crabtree positive yeast) at high sugar concentration, as a function of the levels of glycolysis process.
The same modelling approach has been extended to Crabtree negative yeasts (Kluyveromyces sp.), to shed light on the Crabtree (glucose) effect, a “metabolic paradox” which still remains to be fully explained [2].
References
[1]
S. Mazzoleni, C. Landi, F. Cartenì, E. de Alteriis, F. Giannino, L. Paciello, P. Parascandola
A novel process-based model of microbial growth: self-inhibition in Saccharomyces cerevisiae aerobic fed-batch cultures Microb Cell Fact, 14 (2015), p. 109
[2]
T. Pfeiffer, A. Morley An evolutionary perspective on the Crabtree effect. Front Mol Biosci, 1 (2014), pp. 1–
Modelling the spatial arrangement of vascular bundles in plants
No full textThe spatial arrangement of vascular bundles varies between plant species and organs. A novel reaction-diffusion 2D model is presented defining a set of logical and functional rules able to simulate the differentiation of procambium, phloem and xylem. The model shows that a common mechanism, lying behind the formation of vascular tissues, is able to qualitatively reproduce most stelar structures observed
Water limitation and negative plant-soil feedback explain vegetation patterns along rainfall gradient
No full textThe formation of vegetation patterns has been widely studied and discussed over the years and it has been related to two different mechanisms: depletion of water in the center of vegetation patches and production of toxicity by the decomposition of plant residues in soil. In this work we present a spatially explicit model that combines these two processes showing that negative plant-soil feedbacks can explain the development of different vegetation patterns also when water is not a limiting factor. This also demonstrates that the toxicity effects may change the stability properties of the vegetation patterns
Large-signal device simulation in time- and frequency-domain: a comparison
No full textThe aim of this paper is to compare the most common time- and frequency-domain numerical techniques for the determination of the steady-state solution in the physics-based simulation of a semiconductor device driven by a time-periodic generator. The shooting and harmonic balance (HB) techniques are applied to the solution of the discretized drift-diffusion device model coupled to the external circuit embedding the semiconductor device, thus providing a fully nonlinear mixed mode simulation. The comparison highlights the strong and weak points of the two approaches, basically showing that the time-domain solution is more robust with respect to the initial condition, while the HB solution provides a more rapid convergence once the initial datum is close enough to the solution itsel
Self-DNA in Caenorhabditis elegans Affects the Production of Specific Metabolites: Evidence from LC-MS and Chemometric Studies
No full textThe worm Caenorhabditis elegans, with its short lifecycle and well-known genetic and metabolic pathways, stands as an exemplary model organism for biological research. Its simplicity and genetic tractability make it an ideal system for investigating the effects of different conditions on its metabolism. The chemical analysis of this nematode was performed to identify specific metabolites produced by the worms when fed with either self- or nonself-DNA. A standard diet with OP50 feeding was used as a control. Different development stages were sampled, and their chemical composition was assessed by liquid chromatography–mass spectrometry combined with chemometrics, including both principal component analysis and orthogonal partial least squares discriminant analysis tools. The obtained data demonstrated that self-DNA-treated larvae, when arrested in their cycle, showed significant decreases in dynorphin, an appetite regulator of the nematode, and in N-formyl glycine, a known longevity promoter in C. elegans. Moreover, a substantial decrease was also recorded in the self-DNA-fed adults for the FMRF amide neuropeptide, an embryogenesis regulator, and for a dopamine derivative modulating nematode locomotion. In conclusion, this study allowed for the identification of key metabolites affected by the self-DNA diet, providing interesting hints on the main molecular pathways involved in its biological inhibitory effects
Self-dna inhibitory effects: Underlying mechanisms and ecological implications
No full textDNA is usually known as the molecule that carries the instructions necessary for cell functioning and genetic inheritance. A recent discovery reported a new functional role for extracellular DNA. After fragmentation, either by natural or artificial decomposition, small DNA molecules (between ~50 and ~2000 bp) exert a species specific inhibitory effect on individuals of the same species. Evidence shows that such effect occurs for a wide range of organisms, suggesting a general biological process. In this paper we explore the possible molecular mechanisms behind those findings and discuss the ecological implications, specifically those related to plant species coexistenc
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