Tessellations and Pattern Formation in Plant Growth and Development

The shoot apical meristem (SAM) is a dome-shaped collection of cells at the apex of growing plants from which all above-ground tissue ultimately derives. In Arabidopsis thaliana (thale cress), a small flowering weed of the Brassicaceae family (related to mustard and cabbage), the SAM typically contains some three to five hundred cells that range from five to ten microns in diameter. These cells are organized into several distinct zones that maintain their topological and functional relationships throughout the life of the plant. As the plant grows, organs (primordia) form on its surface flanks in a phyllotactic pattern that develop into new shoots, leaves, and flowers. Cross-sections through the meristem reveal a pattern of polygonal tessellation that is suggestive of Voronoi diagrams derived from the centroids of cellular nuclei. In this chapter we explore some of the properties of these patterns within the meristem and explore the applicability of simple, standard mathematical models of their geometry.Comment: Originally presented at: "The World is a Jigsaw: Tessellations in the Sciences," Lorentz Center, Leiden, The Netherlands, March 200

Nanopore sequencing of PCR products enables multicopy gene family reconstruction

International audienceThe importance of gene amplifications in evolution is more and more recognized. Yet, tools to study multi-copy gene families are still scarce, and many such families are overlooked using common sequencing methods. Haplotype reconstruction is even harder for polymorphic multi-copy gene families. Here, we show that all variants (or haplotypes) of a multi-copy gene family present in a single genome, can be obtained using Oxford Nanopore Technologies sequencing of PCR products, followed by steps of mapping, SNP calling and haplotyping. As a proof of concept, we acquired the sequences of highly similar variants of the cidA and cidB genes present in the genome of the Wolbachia wPip, a bacterium infecting Culex pipiens mosquitoes. Our method relies on a wide database of cid genes, previously acquired by cloning and Sanger sequencing. We addressed problems commonly faced when using mapping approaches for multi-copy gene families with highly similar variants. In addition, we confirmed that PCR amplification causes frequent chimeras which have to be carefully considered when working on families of recombinant genes. We tested the robustness of the method using a combination of bioinformatics (read simulations) and molecular biology approaches (sequence acquisitions through cloning and Sanger sequencing, specific PCRs and digital droplet PCR). When different haplotypes present within a single genome cannot be reconstructed from short reads sequencing, this pipeline confers a high throughput acquisition, gives reliable results as well as insights of the relative copy numbers of the different variants

Tessellations and Pattern Formation in Plant Growth and Development

The shoot apical meristem (SAM) is a dome-shaped collection of cells at the apex of growing plants from which all above-ground tissue ultimately derives. In Arabidopsis thaliana (thale cress), a small flowering weed of the Brassicaceae family (related to mustard and cabbage), the SAM typically contains some three to five hundred cells that range from five to ten microns in diameter. These cells are organized into several distinct zones that maintain their topological and functional relationships throughout the life of the plant. As the plant grows, organs (primordia) form on its surface flanks in a phyllotactic pattern that develop into new shoots, leaves, and flowers. Cross-sections through the meristem reveal a pattern of polygonal tessellation that is suggestive of Voronoi diagrams derived from the centroids of cellular nuclei. In this chapter we explore some of the properties of these patterns within the meristem and explore the applicability of simple, standard mathematical models of their geometry

Metabolic recovery in professional road cyclists: A 31P-MRS Study

Purpose: Aerobic training of professional road cyclists is linked to tremendous aerobic capacities that have never been clearly related to what occur in skeletal muscles submitted to a specific exercise. The aim of the present study was to examine specifically metabolic recovery after an incremental cycling exercise performed until exhaustion in professional road cyclists as compared with moderately trained subjects and so using 31P- MRS. Methods: Subjects performed a progressive cycling exercise on a cycloergometer until exhaustion, then they were positioned back in the magnet (delay lower than 45 s) for recovery scanning. 31P spectra of thigh muscles were time averaged in 2-s blocks at rest and for 15 min throughout the recovery period. Results: For a significantly more intense exercise (477 ± 28 vs 334 ± 24 W in controls; P < 0.001), professional road cyclists displayed similar end-of-exercise extrapolated pH values (6.43 ± 0.16 vs 6.34 ± 0.05 in controls) and a significantly higher PCr concentration (20.1 ± 0.8 vs 13.3 ± 0.5 mM in controls, P < 0.001). The pH recovery kinetics provided the evidence of metabolic adaptations related to a specific training in professional cyclists with a significantly faster rate (P < 0.01) of pH return toward basal values (32.8 ± 18.9 vs 10.8 ± 6.7 mM·min-1). On the contrary, no significant difference was measured for the PCr recovery kinetics. At rest, PDE concentration was significantly higher in professional cyclists (2.50 ± 0.80 vs 1.76 ± 0.42 mM), likely indicating a difference regarding fiber-type composition. Discussion: The present data demonstrated for the first time that the tremendous aerobic capacity in professional cyclists is linked to faster pH recovery kinetics after a specific cycling exercise. Copyrigh

Liberation Deliverable 5.2: Report on Economic Models Calibrated to Case-Study Landscapes

Deliverable 5.2 Liberation: LInking farmland Biodiversity to Ecosystem seRvices for effective eco-functional intensification. 7th Framework Programme Theme KBBE.2012.1.2-02 Managing semi-natural habitats and on-farm biodiversity to optimise ecological service

Effects of a prior high-intensity knee-extension exercise on muscle recruitment and energy cost: a combined local and global investigation in humans.

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