1,721,003 research outputs found
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
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–
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
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
A Sight on Single-Cell Transcriptomics in Plants Through the Prism of Cell-Based Computational Modeling Approaches: Benefits and Challenges for Data Analysis
No full textSingle-cell technology is a relatively new and promising way to obtain high-resolution transcriptomic data mostly used for animals during the last decade. However, several scientific groups developed and applied the protocols for some plant tissues. Together with deeply-developed cell-resolution imaging techniques, this achievement opens up new horizons for studying the complex mechanisms of plant tissue architecture formation. While the opportunities for integrating data from transcriptomic to morphogenetic levels in a unified system still present several difficulties, plant tissues have some additional peculiarities. One of the plants’ features is that cell-to-cell communication topology through plasmodesmata forms during tissue growth and morphogenesis and results in mutual regulation of expression between neighboring cells affecting internal processes and cell domain development. Undoubtedly, we must take this fact into account when analyzing single-cell transcriptomic data. Cell-based computational modeling approaches successfully used in plant morphogenesis studies promise to be an efficient way to summarize such novel multiscale data. The inverse problem’s solutions for these models computed on the real tissue templates can shed light on the restoration of individual cells’ spatial localization in the initial plant organ—one of the most ambiguous and challenging stages in single-cell transcriptomic data analysis. This review summarizes new opportunities for advanced plant morphogenesis models, which become possible thanks to single-cell transcriptome data. Besides, we show the prospects of microscopy and cell-resolution imaging techniques to solve several spatial problems in single-cell transcriptomic data analysis and enhance the hybrid modeling framework opportunities
Feedbacks between vegetation pattern and resource loss enhance degradation potential in drylands
No full textConceptual frameworks of dryland degradation commonly include ecohydrological feedbacks between landscape spatial organization and resource loss, so that decreasing cover and size of vegetation patches result in higher water and soil losses, which lead to further vegetation loss. However, the impacts of these feedbacks on dryland dynamics in response to external stress have barely been tested. Using a spatially-explicit model, we mimicked feedbacks between vegetation pattern and landscape resource loss by establishing a negative dependence of plant establishment on bare-soil hydrological connectivity. We assessed the impact of various feedback strengths on the response of dryland ecosystems to changing human and climatic pressure. The connectivity-mediated feedbacks decrease the amount of pressure required to cause a critical shift to a degraded state and increase the pressure release needed to achieve the ecosystem recovery. The impact of these feedbacks is markedly non-linear, which is explained by the non-linear increase in bare-soil hydrological connectivity with decreasing vegetation cover. Modelling studies on dryland vegetation dynamics not accounting for the connectivity-mediated feedbacks studied here may underestimate the degradation potential of drylands in response to external stress. Our results also suggest that changes in vegetation pattern and associated hydrological connectivity may be more informative early-warning indicators of dryland degradation than changes in vegetation cover
Feedbacks between vegetation pattern and resource loss dramatically decrease ecosystem resilience and restoration potential in a simple dryland model
No full textConceptual frameworks of dryland degradation commonly include ecohydrological feedbacks between landscape spatial organization and resource loss, so that decreasing cover and size of vegetation patches result in higher water and soil losses, which lead to further vegetation loss. However, the impacts of these feedbacks on dryland dynamics in response to external stress have barely been tested. Using a spatially-explicit model, we represented feedbacks between vegetation pattern and landscape resource loss by establishing a negative dependence of plant establishment on the connectivity of runoff-source areas (e.g., bare soils). We assessed the impact of various feedback strengths on the response of dryland ecosystems to changing external conditions. In general, for a given external pressure, these connectivity-mediated feedbacks decrease vegetation cover at equilibrium, which indicates a decrease in ecosystem resistance. Along a gradient of gradual increase of environmental pressure (e.g., aridity), the connectivity-mediated feedbacks decrease the amount of pressure required to cause a critical shift to a degraded state (ecosystem resilience). If environmental conditions improve, these feedbacks increase the pressure release needed to achieve the ecosystem recovery (restoration potential). The impact of these feedbacks on dryland response to external stress is markedly non-linear, which relies on the non-linear negative relationship between bare-soil connectivity and vegetation cover. Modelling studies on dryland vegetation dynamics not accounting for the connectivity-mediated feedbacks studied here may overestimate the resistance, resilience and restoration potential of drylands in response to environmental and human pressures. Our results also suggest that changes in vegetation pattern and associated hydrological connectivity may be more informative early-warning indicators of dryland degradation than changes in vegetation cover
An Individual Based Model of Wound Closure in Plant Stems
Full text linkWound closure in plant stems (after either fire or mechanical damage) is a complex, multi-scale process that involves the formation of a callous tissue (callus lips) responsible for cell proliferation and overgrowth at the injury edges, resulting in coverage of the scarred tissue. Investigating such phenomena, it is difficult to discriminate between cell-specific growth responses, associated with physiological adaptations, and cell proliferation reactions emerging from specific cambium dynamics due to changes in mechanical constrains. In particular, the effects of cell–cell mechanical interactions on the wound closure process have never been investigated. To understand to what extent callus lip formation depends on the intra-tissue mechanical balance of forces, we built a simplified individual-based model (IBM) of cell division and differentiation in a generic woody tissue. Despite its simplified physiological assumptions, the model was capable to simulate callus hyperproliferation and wound healing as an emergent property of the mechanical interactions between individual cells. The model output suggests that the existence of a scar alone does constrain the growth trajectories of the remaining proliferating cells around the injury, thus resulting in the wound closure, ultimately engulfing the damaged tissue in the growing stem
Vegetation Pattern Formation Due to Interactions Between Water Availability and Toxicity in Plant-Soil Feedback
No full textDevelopment of a comprehensive theory of the formation of vegetation patterns is still in progress. A prevailing view is to treat water availability as the main causal factor for the emergence of vegetation patterns. While successful in capturing the occurrence of multiple vegetation patterns in arid and semiarid regions, this hypothesis fails to explain the presence of vegetation patterns in humid environments. We explore the rich structure of a toxicity-mediated model of the vegetation pattern formation.
This model consists of three PDEs accounting for a dynamic balance between biomass, water, and toxic compounds. Different (ecologically feasible) regions of the model???s parameter space give rise to stable spatial vegetation patterns in Turing and non-Turing regimes. Strong negative feedback gives rise to dynamic spatial patterns that continuously move in space while retaining their stable topology
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