An Auxin Transport-Based Model of Root Branching in Arabidopsis thaliana

Root architecture is a crucial part of plant adaptation to soil heterogeneity and is mainly controlled by root branching. The process of root system development can be divided into two successive steps: lateral root initiation and lateral root development/emergence which are controlled by different fluxes of the plant hormone auxin. While shoot architecture appears to be highly regular, following rules such as the phyllotactic spiral, root architecture appears more chaotic. We used stochastic modeling to extract hidden rules regulating root branching in Arabidopsis thaliana. These rules were used to build an integrative mechanistic model of root ramification based on auxin. This model was experimentally tested using plants with modified rhythm of lateral root initiation or mutants perturbed in auxin transport. Our analysis revealed that lateral root initiation and lateral root development/emergence are interacting with each other to create a global balance between the respective ratio of initiation and emergence. A mechanistic model based on auxin fluxes successfully predicted this property and the phenotype alteration of auxin transport mutants or plants with modified rythms of lateral root initiation. This suggests that root branching is controlled by mechanisms of lateral inhibition due to a competition between initiation and development/emergence for auxin

Morphological Plant Modeling: Unleashing Geometric and Topological Potential within the Plant Sciences

The geometries and topologies of leaves, flowers, roots, shoots, and their arrangements have fascinated plant biologists and mathematicians alike. As such, plant morphology is inherently mathematical in that it describes plant form and architecture with geometrical and topological techniques. Gaining an understanding of how to modify plant morphology, through molecular biology and breeding, aided by a mathematical perspective, is critical to improving agriculture, and the monitoring of ecosystems is vital to modeling a future with fewer natural resources. In this white paper, we begin with an overview in quantifying the form of plants and mathematical models of patterning in plants. We then explore the fundamental challenges that remain unanswered concerning plant morphology, from the barriers preventing the prediction of phenotype from genotype to modeling the movement of leaves in air streams. We end with a discussion concerning the education of plant morphology synthesizing biological and mathematical approaches and ways to facilitate research advances through outreach, cross-disciplinary training, and open science. Unleashing the potential of geometric and topological approaches in the plant sciences promises to transform our understanding of both plants and mathematics

A multi-scale model of the interplay between cell signalling and hormone transport in specifying the root meristem of Arabidopsis thaliana

The growth of the root of Arabidopsis thaliana is sustained by the meristem, a region of cell proliferation and differentiation which is located in the root apex and generates cells which move shootwards, expanding rapidly to cause root growth. The balance between cell division and differentiation is maintained via a signalling network, primarily coordinated by the hormones auxin, cytokinin and gibberellin. Since these hormones interact at different levels of spatial organisation, we develop a multi-scale computational model which enables us to study the interplay between these signalling networks and cell cell communication during the specification of the root meristem. We investigate the responses of our model to hormonal perturbations, validating the results of our simulations against experimental data. Our simulations suggest that one or more additional components are needed to explain the observed expression patterns of a regulator of cytokinin signalling, ARR1, in roots not producing gibberellin. By searching for novel network components, we identify two mutant lines that affect significantly both root length and meristem size, one of which also differentially expresses a central component of the interaction network (SHY2). More generally, our study demonstrates how a multi-scale investigation can provide valuable insight into the spatio-temporal dynamics of signalling networks in biological tissues

PlantGL: a Python-based geometric library for 3D plant modelling at different scales

In this paper, we present PlantGL, an open-source graphic toolkit for the creation, simulation and analysis of 3D virtual plants. This C++ geometric library is embedded in the Python language which makes it a powerful user-interactive platform for plant modeling in various biological application domains. PlantGL makes it possible to build and manipulate geometric models of plants or plant parts, ranging from tissues and organs to plant populations. Based on a scene graph augmented with primitives dedicated to plant representation, several methods are provided to create plant architectures from either field measurements or procedural algorithms. Because they are particularly useful in plant design and analysis, special attention has been paid to the definition and use of branching system envelopes. Several examples from different modelling applications illustrate how PlantGL can be used to construct, analyse or manipulate geometric models at different scales ranging from tissues to plant communities

Evidence of mild respiratory disease in men with congenital absence of the vas deferens.

Cystic fibrosis (CF) is a severe disorder, whose main characteristics are, in addition to congenital absence of the vas deferens (CAVD), progressive lung disease, pancreatic insufficiency and elevated sweat chloride levels; CAVD without any other manifest clinical evidence is commonly suggested to be a form of CF with primarily genital expression. We undertook this study to test the hypothesis that men with a CAVD phenotype could be more CF-like than it is usually assumed. Each subject from a population of 42 patients suffering from CAVD was screened for a panel of 16 mutations plus the intron 8 5-thymidine allele of the CF gene (5T), and underwent a thorough clinical evaluation which included a detailed anamnesis, anthropometric data, chest and paranasal sinuses X-rays, pulmonary function tests, sputum cultures, stool chymotrypsin determination, sweat test and, in a limited number of patients, Nasal Potential Difference (NPD) measurement. The genotype analysis detected one compound heterozygote, 23 heterozygotes and 15 individuals carrying the 5T allele; sweat chloride was positive in six, borderline in 11 and negative in 25 subjects; NPD was abnormal in 2/12 patients. Medical history and clinical examination were consistent with respiratory disease in 20 cases; there was radiological evidence of pulmonary hyperinflation in 37/39 and of sinus disease in 20/42 patients; Staphylococcus aureus was cultivated in the sputum of 9/36, Haemophilus influentiae in 3/36 subjects and three patients showed functional evidence of airway obstruction. These findings were equally distributed among sweat positive, borderline and negative patients. These results raise questions about the supposed benignancy of the CAVD condition. A close follow-up of men with CAVD could ascertain potential complications