Single-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.
Different mechanisms, including equilibrium and non-equilibrium processes, have been taken into account as possible theoretical explanations of species coexistence. Despite the ample evidence on the ...existence of negative plant-soil feedback in both agriculture and natural vegetation, the role of these processes in the organization and dynamics of plant communities has so far been neglected. In this study, simulations by an individual-based competition model show how the intensity of negative feedback on individual plant performance can produce faster successional dynamics and allow species coexistence in two- and multi-species systems. The results show that even low levels of negative plant-soil feedback can enable species coexistence and often produce cyclic population dynamics. Moreover, the model highlights how negative feedback can generate positive reciprocal interspecific interactions at the population level, despite the fact that only competitive interactions is present between individual plants. In fact, competitive effects occur on a short-term scale, but positive reciprocal species interactions emerge only if negative feedback affects all species and if longer periods of simulation, more than the species life span, are considered. An important outcome of the model is the evidence that the effects at population level are timescale-dependent, thus showing the limitation of short-term species removal experiments used in traditional competition studies.
The metabolic shift between respiration and fermentation at high glucose concentration is a widespread phenomenon in microbial world, and it is relevant for the biotechnological exploitation of ...microbial cell factories, affecting the achievement of high-cell-densities in bioreactors. Starting from a model already developed for the yeast
Saccharomyces cerevisiae
, based on the System Dynamics approach, a general process-based model for two prokaryotic species of biotechnological interest, such as
Escherichia coli
and
Bacillus subtilis
, is proposed. The model is based on the main assumption that glycolytic intermediates act as central catabolic hub regulating the shift between respiratory and fermentative pathways. Furthermore, the description of a mixed fermentation with secondary by-products, characteristic of bacterial metabolism, is explicitly considered. The model also represents the inhibitory effect on growth and metabolism of self-produced toxic compounds relevant in assessing the late phases of high-cell density culture. Model simulations reproduced data from experiments reported in the literature with different strains of non-recombinant and recombinant
E. coli
and
B. subtilis
cultured in both batch and fed-batch reactors. The proposed model, based on simple biological assumptions, is able to describe the main dynamics of two microbial species of relevant biotechnological interest. It demonstrates that a reductionist System Dynamics approach to formulate simplified macro-kinetic models can provide a robust representation of cell growth and accumulation in the medium of fermentation by-products.
Plant invasions can have relevant impacts on biogeochemical cycles, whose extent, in Mediterranean ecosystems, have not yet been systematically assessed comparing litter carbon (C) and nitrogen (N) ...dynamics between invasive plants and native communities. We carried out a 1-year litterbag experiment in 4 different plant communities (grassland, sand dune, riparian and mixed forests) on 8 invasives and 24 autochthonous plant species, used as control. Plant litter was characterized for mass loss, N release, proximate lignin and litter chemistry by
C CPMAS NMR. Native and invasive species showed significant differences in litter chemical traits, with invaders generally showing higher N concentration and lower lignin/N ratio. Mass loss data revealed no consistent differences between native and invasive species, although some woody and vine invaders showed exceptionally high decomposition rate. In contrast, N release rate from litter was faster for invasive plants compared to native species. N concentration, lignin content and relative abundance of methoxyl and N-alkyl C region from
C CPMAS NMR spectra were the parameters that better explained mass loss and N mineralization rates. Our findings demonstrate that during litter decomposition invasive species litter has no different decomposition rates but greater N release rate compared to natives. Accordingly, invasives are expected to affect N cycle in Mediterranean plant communities, possibly promoting a shift of plant assemblages.
We introduce a mathematical model to describe the tritrophic interaction between crop,pest and the pest natural enemy where the release of Volatile Organic Compounds (VOCs) by crop istaken into ...account. The VOCs may be considered as an indirect defence mechanism of the plant asthey attract the pest natural enemies toward the attacked plants. The model dynamics is studied throughqualitative analysis and numerical simulations. The factors that may enhance pest disappearance areidentified. In particular, we show that VOCs may have a beneficial effect on the environment sincetheir release may be able to stabilize the model dynamics. Specifically, for the parameter values thatwe have explored, this effect can arise only when both the phenomena of VOCs basic plant release andVOCs plant release due to pest attack are present.
The Turing pattern formation is modeled by reaction - diffusion (RD) type partial differential equations , and it plays a crucial role in ecological studies. Big data analytics and suitable ...frameworks to manage and predict structures and configurations are mandatory. The processing and resolution procedures of mathematical models relies upon numerical schemes, and concurrently upon the related automated algorithms. Starting from a RD model for vegetation patterns, we propose a semi-automatic algorithm based on a smart numerical criterion for observing ecological reliable results. Numerical experiments are carried out in the case of spot's formations.
In this paper a semi-physical model for the vegetation burning in wildland fire is proposed. The model is developed with the final aim to simulate large scale wildland fires which spread on ...heterogeneous landscape. In a modular modelling approach, it can be seen as the cell model for a forest fire propagation tool to perform fast simulations for operational scope and fight fires interventions. It is constituted by a simple system of ordinary differential equations taking into account the main physico-chemical processes involved in the fire spreading while keeping the computation cost for simulations very low. Finally, the model is implemented in the modelling, at the intermediate scale (1 hectare), of the fire spreading in a homogeneous environment.
There are many ecological evidences that regular vegetation patterns in semi-arid regions may be interpreted has early warning signals of catastrophic transitions to an irreversible homogeneous ...bare-soil state (desertification). In this framework, the paper analyses the occurrence of catastrophic shifts between different moving vegetation patterns. The study is conducted by numerical simulations of a system of partial differential equation which describes the dynamics of the biomass and water as a reaction-diffusion process. The model also includes the effect of self-toxicity produced by the biomass, which increases the capability of the system to self-organize in the space and time. The analysis reveals the existence of a variety of different periodic patterns moving in the space, like travelling waves and/ or pulse-like backfiring solutions. The precipitation rate is considered as system parameter and its effect on the vegetation patterns evolutions is analysed.
Wound 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.
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