Cassava bacterial blight (CBB), incited by Xanthomonas axonopodis pv. manihotis ( Xam ), is the most important bacterial disease of cassava, a staple food source for millions of people in developing countries. Here we present a widely applicable strategy for elucidating the virulence components of a pathogen population. We report Illumina-based draft genomes for 65 Xam strains and deduce the phylogenetic relatedness of Xam across the areas where cassava is grown. Using an extensive database of effector proteins from animal and plant pathogens, we identify the effector repertoire for each sequenced strain and use a comparative sequence analysis to deduce the least polymorphic of the conserved effectors. These highly conserved effectors have been maintained over 11 countries, three continents, and 70 y of evolution and as such represent ideal targets for developing resistance strategies.
The immersed boundary method is a mathematical formulation and numerical method for solving fluidstructure interaction problems. For many biological problems, such as models that include the cell membrane, the immersed structure is a two-dimensional infinitely thin elastic shell immersed in an incompressible viscous fluid. When the shell is modeled as a hyperelastic material, forces can be computed by taking the variational derivative of an energy density functional. A new method for computing a continuous force function on the entire surface of the shell is presented here. The new method is compared to a previous formulation where the surface and energy functional are discretized before forces are computed. For the case of Stokes flow, a method for computing quadrature weights is provided to ensure the integral of the elastic spread force density remains zero throughout a dynamic simulation. Tests on the method are conducted and show that it yields more accurate force computations than previous formulations as well as more accurate geometric information such as mean curvature. The method is then applied to a model of a red blood cell in capillary flow and a 3D model of cellular blebbing.Studies on surface representations have generally been conducted separately from those on force computations. In [15,16], the authors focus on representing thin surfaces continuously with spherical harmonic or radial basis function (RBF) interpolants. In both cases, force computations are treated through simple explicit expressions for surface tension [15] or fiber elasticity [16]. The authors do not consider finding forces through variational derivatives.Boundary integral methods (BIMs) have been progressing concurrently with the IB method and have been used by others to model fluid-structure interactions in zero Reynolds number flow [17][18][19][20]. In BI methods, the "hydrodynamic traction jump" across the membrane [17], which is equivalent to the Lagrangian elastic force density per unit current area [20], must be computed independently prior to integration. [21] and [22] both demonstrate the use of a spectrally convergent spherical harmonic representation for surfaces that allows for the calculation of force in BIMs. However, the computations in [21] and [22] both follow the traditional formulation of BI methods in computing the traction jump from a system of equations involving the Cauchy stress tensor, which itself comes from a series of tensor expansions. Additionally, BI methods require numerical schemes to resolve integrals that are singular at the immersed surfaces.The aim of this work is to provide a "bridge" between the fields of surface representation and energybased force functions within the IB method. Our goal is to use the continuous surface representations from [15] to formulate a continuous function that represents the force density on the membrane as a function of its curvilinear coordinates. In this manner, we avoid the discretization error from surface representation. The advantages of the approach presen...
We present a new method for the geometric reconstruction of elastic surfaces simulated by the immersed boundary method with the goal of simulating the motion and interactions of cells in whole blood. Our method uses parameterfree radial basis functions for high-order meshless parametric reconstruction of point clouds and the elastic force computations required by the immersed boundary method. This numerical framework allows us to consider the effect of endothelial geometry and red blood cell motion on the motion of platelets. We find red blood cells to be crucial for understanding the motion of platelets, to the point that the geometry of the vessel wall has a negligible effect in the presence of RBCs. We describe certain interactions that force the platelets to remain near the endothelium for extended periods, including a novel platelet motion that can be seen only in 3-dimensional simulations that we term "unicycling. " We also observe red blood cell-mediated interactions between platelets and the endothelium for which the platelet has reduced speed. We suggest that these behaviors serve as mechanisms that allow platelets to better maintain vascular integrity.
We present new algorithms for the parallelization of Eulerian–Lagrangian interaction operations in the immersed boundary method. Our algorithms rely on two well-studied parallel primitives: key-value sort and segmented reduce. The use of these parallel primitives allows us to implement our algorithms on both graphics processing units (GPUs) and on other shared-memory architectures. We present strong and weak scaling tests on problems involving scattered points and elastic structures. Our tests show that our algorithms exhibit near-ideal scaling on both multicore CPUs and GPUs.
We present new algorithms for the parallelization of Eulerian-Lagrangian interaction operations in the immersed boundary method. Our algorithms rely on two well-studied parallel primitives: key-value sort and segmented reduce. The use of these parallel primitives allows us to implement our algorithms on both graphics processing units (GPUs) and on other shared memory architectures. We present strong and weak scaling tests on problems involving scattered points and elastic structures. Our tests show that our algorithms exhibit near-ideal scaling on both multicore CPUs and GPUs.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.