Modelling the development and arrangement of the primary vascular structure in plants

Background 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 tissue

Adult conspecific density affects Janzen-Connell patterns by modulating the recruitment exclusion zones

Plant-soil negative feedback (NF) is a well-established phenomenon that, by preventing the dominance of a single species, allows species coexistence and promotes the maintenance of biodiversity. At community scale, localized NF may cause the formation of exclusion zones under adult conspecifics leading to Janzen-Connell (JC) distribution. In this study, we explore the connection between adult density, either conspecifics or heterospecifics, on the probability of occurrence of JC distributions. Using an individual-based modelling approach, we simulated the formation of exclusion zones due to the build-up of NF in proximity of conspecific adult plants and assessed the frequency of JC distribution in relation to conspecifics and heterospecifics density ranging from isolated trees to closed forest stands. We found that JC recruitment distribution is very common in the case of an isolated tree when NF was strong and capable to form an exclusion zone under the parent tree. At very low NF intensity, a prevalence of the decreasing pattern was observed because, under such conditions, the inhibitory effect due to the presence of the mother tree was unable to overcome the clustering effect of the seed dispersal kernel. However, if NF is strong the JC frequency suddenly decreases in stands with a continuous conspecific cover likely as a result of progressive expansion of the exclusion zone surrounding all trees in closed forest stands. Finally, our simulations showed that JC distribution should not be frequent in the case of rare species immersed in a matrix of heterospecific adults. Overall, the model shows that a plant suffering from strong NF in monospecific stands can rarely exhibit a recruitment pattern fitting the JC model. Such counterintuitive results would provide the means to reconcile the well-established NF framework with part the forest ecologists’ community that is still skeptical towards the JC model.SynthesisOur model highlights the complex interconnection between NF intensity, stand density, and recruitment patterns explaining where and why the JC distribution occurs. Moreover, predicting the occurrence of JC in relation to stand density we clarify the relevance of this ecological phenomenon for future integration in plant community frameworks

PhenoCaB : a new phenological model based on carbon balance in boreal conifers

Traditional phenological models use chilling and thermal forcing (temperature sum or degree-days) to predict budbreak. Because of the heightening impact of climate and other related biotic or abiotic stressors, a model with greater biological support is needed to better predict budbreak. Here, we present an original mechanistic model based on the physiological processes taking place before and during budbreak of conifers. As a general principle, we assume that phenology is driven by the carbon status of the plant, which is closely related to environmental variables and the annual cycle of dormancy-activity. The carbon balance of a branch was modelled from autumn to winter with cold acclimation and dormancy and from winter to spring when deacclimation and growth resumption occur. After being calibrated in a field experiment, the model was validated across a large area (> 34 000 km 2 ), covering multiple conifers stands in Québec (Canada) and across heated plots for the SPRUCE experiment in Minnesota (USA). The model accurately predicted the observed dates of budbreak in both Québec (±3.98 d) and Minnesota (±7.98 d). The site-independent calibration provides interesting insights on the physiological mechanisms underlying the dynamics of dormancy break and the resumption of vegetative growth in spring

Self-organization in the development of plant spatial patterns

The study of self-organization is a relatively new field that received great attention in the last decades related to the study of complex systems. In particular, self-organizing properties of some systems are particularly important in the development of spatial patterns, and their analysis could lead to interesting insights into their functioning. Self-organization is a process in which pattern at the global level of a system emerges solely from the interactions among the lower-level components of the system and the best tool to study such interactions is the use of mathematical models to simulate the emergent behaviour of the system. This thesis addresses two specific problems related to pattern formation in plants at different scales. The first topic is the emergence of vegetation patterns at landscape level. Different putative mechanisms have been proposed as drivers of vegetation pattern formation in different environments. The most studied mechanism is related to short range positive feedbacks and long range negative feedbacks between plants and the available water. Such explanation provides important insights on the dynamics of arid and semiarid environments where water is a limiting factor, but fails to explain the emergence of similar patterns in humid environments. For this reason we formulated a mathematical model to test the effects of the release of autotoxic compounds during litter decomposition, i.e. plant-soil negative feedback, on the emergence of vegetation patterns, in particular the formation of ring structures by clonal plants. Model simulations show that the formation of rings can be explained by autotoxicity and that resource scarcity is not a necessary condition. Moreover, we further developed the model to consider both water and toxic compounds influences on plant biomass growth in order to assess the relative importance of the two mechanisms. Numerical simulations show that water/biomass feedbacks lead to stable spatial patterns, while autotoxicity has a destabilizing effect on the system, leading to unstable patterns that continuously evolve in time. The second topic is the differentiation of primary vascular patterns at cellular/tissue level. Most of the attention has focused on the genetic regulation and the hormonal control of specific aspects of the development of vascular tissues. In this study, we formulated a model defining a set of logical and functional rules to simulate the differentiation of procambium, phloem and xylem and their emerging spatial patterns, starting from an homogeneous group of undifferentiated cells. Specific attention has been given to the factors responsible for the intra- and inter-specific variability of the arrangements observed in plants. Simulation results show that the model is capable of reproducing most vascular patterns observed in plants, from primitive and simple structures constituted of a single strand of vascular bundles (protostele), to more complex and evolved ones, with separated vascular bundles arranged in an ordered pattern within the plant section (e.g. eustele). Presented results demonstrate, as a proof of concept, that a common genetic-molecular machinery can be at the base of different spatial patterns of plant vascular tissues

VISmaF: Synthetic Tree for Immersive Virtual Visualization in Smart Farming. Part I: Scientific Background Review and Model Proposal

Computer-Generated Imagery (CGI) has received increasing interest in both research and the entertainment industry. Recent advancements in computer graphics allowed researchers and companies to create large-scale virtual environments with growing resolution and complexity. Among the different applications, the generation of biological assets is a relevant task that implies challenges due to the extreme complexity associated with natural structures. An example is represented by trees, whose composition made by thousands of leaves, branches, branchlets, and stems with oriented directions is hard to be modeled. Realistic 3D models of trees can be exploited for a wide range of applications including decision-making support, visualization of ecosystem changes over time, and for simple visualization purposes. In this review, we give an overview of the most common approaches used to generate 3D tree models, discussing both methodologies and available commercial software. We focus on strategies for modeling and rendering of plants, highlighting their accordance or not with botanical knowledge and biological models. We also present a proof of concept to link biological models and 3D rendering engines through Ordinary Differential Equations

The physiological mechanisms behind the earlywood-to-latewood transition: A process-based modeling approach.

In extratropical ecosystems, the growth of trees is cyclic, producing tree rings composed of large-lumen and thin-walled cells (earlywood) alternating with narrow-lumen and thick-walled cells (latewood). So far, the physiology behind wood formation processes and the associated kinetics has rarely been considered to explain this pattern. We developed a process-based mechanistic model that simulates the development of conifer tracheids, explicitly considering the processes of cell enlargement and the deposition and lignification of cell walls. The model assumes that (1) wall deposition gradually slows down cell enlargement and (2) the deposition of cellulose and lignin is regulated by the availability of soluble sugars. The model reliably reproduces the anatomical traits and kinetics of the tracheids of four conifer species. At the beginning of the growing season, low sugar availability in the cambium results in slow wall deposition that allows for a longer enlargement time; thus, large cells with thin walls (i.e., earlywood) are produced. In late summer and early autumn, high sugar availability produces narrower cells having thick cell walls (i.e., latewood). This modeling framework provides a mechanistic link between plant ecophysiology and wood phenology and significantly contributes to understanding the role of sugar availability during xylogenesis

Integration of a System Dynamics Model and 3D Tree Rendering—VISmaF Part II: Model Development, Results and Potential Agronomic Applications

Biological–mathematical models of trees can be exploited for a wide range of agronomic applications including crop management, visualization of ecosystem changes over time, in-field phenotyping, crop load effects, testing of plant functions, biomechanics, and many others. Some models propose a 3D output of tree that, in addition to having functionality to visualize the result, offers an additional tool for the evaluation of some parameters of the model itself (interception and amount of light, temperature, obstacles, physical competition between multiple trees). The present study introduces a biological–mathematical model of tree growth with a 3D output of its structure in a realtime 3D rendering environment (Unity©). Thanks to the virtual environment created in Unity©, it was possible to obtain variable environmental parameters (amount of light, temperature) used as inputs to the mathematical simulation of growth. The model is based on ordinary differential equations (ODEs) that compute the growth of each single internode in length (primary growth) and width (secondary growth) and the accumulation of growth inhibitors regulating the seasonal cyclicity of the tree. Virtual experiments were conducted varying environmental conditions (amount of light and temperature), and the species-specific characteristics of the simulated tree (number of buds, branching angle). The results have been analyzed showing also how the model can be adapted for the creation of different tree species and discussing the potential agronomic applications of model

Revisiting the Crabtree/Warburg effect in a dynamic perspective: a fitness advantage against sugar-induced cell death

The mechanisms beyond the Warburg effect in proliferative mammalian cells, as well as for the similar Crabtree effect in the yeast Saccharomyces cerevisiae, are still a matter of debate: why do cells shift from the energy-efficient respiration to the energy-inefficient fermentation at high sugar concentration? This review reports on the strong similarities of these phenomena in both cell types, discusses the current ideas, and provides a novel interpretation of their common functional mechanism in a dynamic perspective. This is achieved by analyzing another phenomenon, the sugar-induced-cell-death (SICD) occurring in yeast at high sugar concentration, to highlight the link between ATP depletion and cell death. The integration between SICD and the dynamic functioning of the glycolytic process, suggests a fitness advantage of the Crabtree/Warburg effect in the long term, which consists in the maintenance of the cell energetic homeostasis, therefore strategic for cell survival

Self-DNA Exposure Induces Developmental Defects and Germline DNA Damage Response in <i>Caenorhabditis elegans</i>

All organisms, from bacteria to mammals, sense and respond to foreign nucleic acids to fight infections in order to survive and preserve genome integrity across generations. The innate immune system is an evolutionarily conserved defence strategy. Complex organisms have developed various cellular processes to respond to and recognise not only infections, i.e., pathogen-associated molecular patterns (PAMPs), but also to sense injury and tissue dysfunctions, i.e., damage-associated molecular patterns (DAMPs). Mis-localized self-DNA can be sensed as DAMP by specific DNA-sensing pathways, and self-DNA chronic exposure can be detrimental to the organisms. Here, we investigate the effects of dietary delivered self-DNA in the nematode Caenorhabditis elegans. The hermaphrodite worms were fed on Escherichia coli genomic libraries: a C. elegans library (self) and a legume (Medicago truncatula) library (non-self). We show that the self-library diet affects embryogenesis, larval development and gametogenesis. DNA damage and activation of p53/CEP-1-dependent apoptosis occur in gonadal germ cells. Studies of self-DNA exposure in this model organism were not pursued up to now. The genetic tractability of C. elegans will help to identify the basic molecular pathways involved in such mechanisms. The specificity of the adverse effects associated with a self-DNA enriched diet suggests applications in biological pest control approaches