An unfitted radial basis function generated finite difference method applied to thoracic diaphragm simulations

The thoracic diaphragm is the muscle that drives the respiratory cycle of a human being. Using a system of partial differential equations (PDEs) that models linear elasticity we compute displacements and stresses in a two-dimensional cross section of the diaphragm in its contracted state. The boundary data consists of a mix of displacement and traction conditions. If these are imposed as they are, and the conditions are not compatible, this leads to reduced smoothness of the solution. Therefore, the boundary data is first smoothed using the least-squares radial basis function generated finite difference (RBF-FD) framework. Then the boundary conditions are reformulated as a Robin boundary condition with smooth coefficients. The same framework is also used to approximate the boundary curve of the diaphragm cross section based on data obtained from a slice of a computed tomography (CT) scan. To solve the PDE we employ the unfitted least-squares RBF-FD method. This makes it easier to handle the geometry of the diaphragm, which is thin and non-convex. We show numerically that our solution converges with high-order towards a finite element solution evaluated on a fine grid. Through this simplified numerical model we also gain an insight into the challenges associated with the diaphragm geometry and the boundary conditions before approaching a more complex three-dimensional model

Rapid Identification of Malaria Vaccine Candidates Based on α-Helical Coiled Coil Protein Motif

To identify malaria antigens for vaccine development, we selected α-helical coiled coil domains of proteins predicted to be present in the parasite erythrocytic stage. The corresponding synthetic peptides are expected to mimic structurally “native” epitopes. Indeed the 95 chemically synthesized peptides were all specifically recognized by human immune sera, though at various prevalence. Peptide specific antibodies were obtained both by affinity-purification from malaria immune sera and by immunization of mice. These antibodies did not show significant cross reactions, i.e., they were specific for the original peptide, reacted with native parasite proteins in infected erythrocytes and several were active in inhibiting in vitro parasite growth. Circular dichroism studies indicated that the selected peptides assumed partial or high α-helical content. Thus, we demonstrate that the bioinformatics/chemical synthesis approach described here can lead to the rapid identification of molecules which target biologically active antibodies, thus identifying suitable vaccine candidates. This strategy can be, in principle, extended to vaccine discovery in a wide range of other pathogens

An unfitted radial basis function generated finite difference method applied to thoracic diaphragm simulations

The thoracic diaphragm is the muscle that drives the respiratory cycle of a human being. Using a system of partial differential equations (PDEs) that models linear elasticity we compute displacements and stresses in a two-dimensional cross section of the diaphragm in its contracted state. The boundary data consists of a mix of displacement and traction conditions. If these are imposed as they are, and the conditions are not compatible, this leads to reduced smoothness of the solution. Therefore, the boundary data is first smoothed using the least-squares radial basis function generated finite difference (RBF-FD) framework. Then the boundary conditions are reformulated as a Robin boundary condition with smooth coefficients. The same framework is also used to approximate the boundary curve of the diaphragm cross section based on data obtained from a slice of a computed tomography (CT) scan. To solve the PDE we employ the unfitted least-squares RBF-FD method. This makes it easier to handle the geometry of the diaphragm, which is thin and non-convex. We show numerically that our solution converges with high-order towards a finite element solution evaluated on a fine grid. Through this simplified numerical model we also gain an insight into the challenges associated with the diaphragm geometry and the boundary conditions before approaching a more complex three-dimensional model.

An unfitted radial basis function generated finite difference method applied to thoracic diaphragm simulations

The thoracic diaphragm is the muscle that drives the respiratory cycle of a human being. Using a system of partial differential equations (PDEs) that models linear elasticity we compute displacements and stresses in a two-dimensional cross section of the diaphragm in its contracted state. The boundary data consists of a mix of displacement and traction conditions. If these are imposed as they are, and the conditions are not compatible, this leads to reduced smoothness of the solution. Therefore, the boundary data is first smoothed using the least-squares radial basis function generated finite difference (RBF-FD) framework. Then the boundary conditions are reformulated as a Robin boundary condition with smooth coefficients. The same framework is also used to approximate the boundary curve of the diaphragm cross section based on data obtained from a slice of a computed tomography (CT) scan. To solve the PDE we employ the unfitted least-squares RBF-FD method. This makes it easier to handle the geometry of the diaphragm, which is thin and non-convex. We show numerically that our solution converges with high-order towards a finite element solution evaluated on a fine grid. Through this simplified numerical model we also gain an insight into the challenges associated with the diaphragm geometry and the boundary conditions before approaching a more complex three-dimensional model.

Structure of neprilysin in complex with the active metabolite of sacubitril

Sacubitril is an ethyl ester prodrug of LBQ657, the active neprilysin (NEP) inhibitor, and is a component of LCZ696 (sacubitril/valsartan). We report herein the three-dimensional structure of LBQ657 in complex with human NEP at 2Å resolution. The X-ray structure unravels the binding mode of the compound spanning the S1, S1’ and S2’ sub-pockets of the active site, consistent with a competitive inhibition mode. An induced fit conformational change upon binding of the P1’-biphenyl moiety of the inhibitor suggests an explanation for its selectivity against structurally homologous zinc metallopeptidases

Purification and crystallization of dengue and West Nile virus NS2B–NS3 complexes

Crystals of dengue serotype 2 and West Nile virus NS2B–NS3 protease complexes have been obtained and the crystals of both diffract to useful resolution. Sample homogeneity was essential for obtaining X-ray-quality crystals of the dengue protease. Controlled proteolysis produced a crystallizable fragment of the apo West Nile virus NS2B–NS3 and crystals were also obtained in the presence of a peptidic inhibitor

Structural determinants of MALT1 protease activity

The formation of the Carma1-BCL10-MALT1 complex is pivotal for T-cell receptor mediated activation of the transcription-factor NF-κB. Recently it was shown that in this complex MALT1 not only acts as a scaffolding protein but also possesses proteolytic activity mediated by its caspase-like domain. Here we show that, as described for caspases which play an essential role in apoptosis, proteolytic activity of MALT1 can be reconstituted by induced proximity. However, unlike caspases which cleave specifically C-terminal to an aspartate, MALT1 has an absolute specificity for arginine. We further determined the structure of the MALT1 domains responsible for proteolytic activity in the absence of ligand and in complex with a covalently bound substrate like inhibitor. The structures explain the specificity for cleavage after arginine, and show that the protease domain undergoes large conformational changes upon substrate binding that also affect the structure of the C-terminal Ig-like domain. This C-terminal Ig-like domain is required for MALT1 activity and likely important for the interaction of MALT1 with its binding partners

Interleukin 17A as an effective target for anti-inflammatory and antiparasitic treatment of toxoplasmic uveitis

Background. Toxoplasmosis is the most common cause of posterior uveitis in immunocompetent subjects. The requirement of limiting both parasite multiplication and tissue destruction suggests that the balance between T-helper (Th) 17 and T-regulatory cells is an important factor in toxoplasmosis-induced retinal damage. [br/] Methods. In a prospective clinical study of acute ocular toxoplasmosis, we assessed the cytokine pattern in aqueous humors of 10 affected patients. To determine the immunological mechanisms, we evaluated intraocular inflammation, parasite load, and immunological responses using messenger RNA and protein levels in a mouse model. Anti-interleukin 17A (IL-17A) monoclonal antibodies (mAbs) were administered with the parasite to evaluate the role of IL-17A. [br/] Results. Severe ocular inflammation and cytokine patterns comparable to human cases were observed, including IL-17A production. Neutralizing IL-17A decreased intraocular inflammation and parasite load in mice. Detailed studies revealed up-regulation of T-regulatory and Th1 pathways. When interferon gamma (IFN-gamma) was neutralized concomitantly, the parasite multiplication rate was partially restored. [br/] Conclusions. Local IL-17A production by resident cells plays a central role in the pathology of ocular toxoplasmosis. The balance between Th17 and Th1 responses (especially IFN-gamma) is crucial for the outcome of infection. This data reveals new in vivo therapeutic approaches by repressing inflammatory pathways using intravitreal injection of IL-17A mAb