Generation of initial molecular dynamics configurations in arbitrary geometries and in parallel

A computational pre-processing tool for generating initial configurations of molecules for molecular dynamics simulations in geometries described by a mesh of unstructured arbitrary polyhedra is described. The mesh is divided into separate zones and each can be filled with a single crystal lattice of atoms. Each zone is filled by creating an expanding cube of crystal unit cells, initiated from an anchor point for the lattice. Each unit cell places the appropriate atoms for the user-specified crystal structure and orientation. The cube expands until the entire zone is filled with the lattice; zones with concave and disconnected volumes may be filled. When the mesh is spatially decomposed into portions for distributed parallel processing, each portion may be filled independently, meaning that the entire molecular system never needs to fit onto a single processor, allowing very large systems to be created. The computational time required to fill a zone with molecules scales linearly with the number of cells in the zone for a fixed number of molecules, and better than linearly with the number of molecules for a fixed number of mesh cells. Our tool, molConfig, has been implemented in the open source C++ code OpenFOAM.     

Factor VIII-hydrolyzing IgG in acquired and congenital hemophilia

Anti-factor VIII (FVIII) inhibitory IgG may arise as alloantibodies to therapeutic FVIII in patients with congenital hemophilia A, or as autoantibodies to endogenous FVIII in individuals with acquired hemophilia. We have described FVIII-hydrolyzing IgG both in hemophilia A patients with anti-FVIII IgG and in acquired hemophilia patients. Here, we compared the properties of proteolytic auto- and allo-antibodies. Rates of FVIII hydrolysis differed significantly between the two groups of antibodies. Proline-phenylalanine-arginine-methylcoumarinamide was a surrogate substrate for FVIII-hydrolyzing autoantibodies. Our data suggest that populations of proteolytic anti-FVIII IgG in acquired hemophilia patients are different from that of inhibitor-positive hemophilia A patients.     

Simulated and measured nitrogen conditions in a manured and fertilised soil

The governing factors for soil nitrogen dynamics were identified with a simulation model. In addition, the model was used to interpret measurements from a plot fertilisation experiment in southwest Sweden.Simulated moisture and temperature conditions were the driving variables for the simulation of soil nitrogen dynamics and leaching during a 6-year period. The results of the simulation were compared with monthly observations on two plots with grain crops, one with liquid manure and commercial fertilisers applied and one with commercial fertilisers only.Simulated temporal variations of the nitrate and ammonium storages generally agreed with observations. The dominant role of the crops as a determinant of soil nitrogen conditions was demonstrated. A higher leaching loss from the plot with application of commerical fertilisers only occurred both in simulations and measurements compared to the plot with application of both commercial fertilisers and manure. The main reason was the higher N-application in the former treatment.The effect of water flows in macropores was interpreted as a delay of simulated leaching compared to observed leaching on some occasions in summer and early autumn. No direct effect of the macropores on the yearly rates of leaching could be seen.     

The NOD2-RICK complex signals from the plasma membrane

NOD2 plays an important role in the innate immunity of the intestinal tract. By sensing the muramyl dipeptide (MDP), a bacterial wall component, NOD2 triggers the NF-kappaB signaling pathway and promotes the release of proinflammatory cytokines such as interleukin-8. Mutations in Nod2 (1007FS, R702W, G908R) impinge on NOD2 functions and are associated with the pathogenesis of Crohn disease, a chronic inflammatory bowel disease. Although NOD2 is usually described as a cytosolic receptor for MDP, the protein is also localized at the plasma membrane, and the 1007FS mutation delocalizes NOD2 to the cytoplasm (Barnich, N., Aguirre, J. E., Reinecker, H. C., Xavier, R., and Podolsky, D. K. (2005) J. Cell Biol. 170, 21-26; McDonald, C., Chen, F. F., Ollendorff, V., Ogura, Y., Marchetto, S., Lecine, P., Borg, J. P., and Nunez, G. (2005) J. Biol. Chem. 280, 40301-40309). In this study, we demonstrate that membrane-bound versions of NOD2 and Crohn disease-associated mutants R702W and G908R are capable of responding to MDP and activating the NF-kappaB pathway from this location. In contrast, the 1007FS mutant remains unable to respond to MDP from the plasma membrane. We also show that NOD2 promotes the membrane recruitment of RICK, a serine-threonine kinase involved in NF-kappaB activation downstream of NOD2. Furthermore, the artificial attachment of RICK at the plasma membrane provokes a constitutive and strong activation of the NF-kappaB pathway and secretion of interleukin-8 showing that optimal RICK activity depends upon its subcellular localization. Finally, we show that endogenous RICK localizes at the plasma membrane in the THP1 cell line. Thus, our data suggest that NOD2 is responsible for the membrane recruitment of RICK to induce a regulated NF-kappaB signaling and production of proinflammatory cytokines.     

Effect of alcohol on perceived exertion in relation to heart rate and blood lactate

The purpose of the study was to determine whether the perception of exertion is affected by alcohol during physical performance and whether altered self-rating of exertion is the result of an altered perception per se or of an altered physical capacity to perform work. Ten healthy men participated. Each subject was his own control and received an alcohol dose corresponding to 1 g.kg-1 body mass in 40% solution in the experimental session. The exercise test was performed on a cycle ergometer with an initial intensity of 50 W which was increased stepwise by 50 W at 4-min intervals up to near-maximal. The rating of perceived exertion (RPE) did not differ between alcohol and control sessions. Alcohol induced a significant increase in heart rate during exercise at 50 W (delta x = 8 beats.min-1) and at 100 W (delta x = 10 beats.min-1), while the change at higher intensities was insignificant. The systolic blood pressure and the blood lactate concentration were not significantly changed by alcohol. It is concluded that a moderate dose of alcohol does not alter RPE during physical exercise either per se or secondarily to an altered physical capacity to perform work.     

Morphological and histochemical evidence of mitoribosomes in Manduca sexta.

The mitochondria found in the neurons of the frontal ganglion of Manduca sexta contained numerous mitoribosomes. The mitochondria of the glial and perineural cells did not contain mitoribosomes. The mitoribosomes were digested in RNase whereas phospholipase C digested the cellular membranes but had no effect on the mitoribosomes.     

Analyzing gastrocnemius EMG-activity and sway data from quiet and perturbed standing.

In an experiment, we combined force plate measurements and surface EMG in studying quiet and perturbed standing, involving MS (Multiple sclerosis) and controls. The aim of this paper is to report the results thus obtained on the relation between filtered gastrocnemius (GA) EMG and the anterior-posterior center-of-pressure (A/P COP) coordinate. The main finding is the good correspondence between A/P COP and the filtered GA EMG in the low frequency range. The EMG envelope was calculated using a zero-lag filter. Combining this with time shifts around 250-350 ms produced a high correlation (85.5+/-8.4%) between the GA-EMG envelope and the A/P COP. This EMG-COP relation was closest when using a low cut-off frequency value around 1 Hz in calculating the EMG envelope. Based on this filtering procedure we estimated the average EMG-COP time shift to be 283+/-43 ms between the GA-EMG envelope and A/P COP (which "lags" behind EMG envelope). This shift is consistent with the 1 Hz cut-off and phase shift produced by a corresponding critically damped second-order filter, and is about twice the corresponding twitch time. These results suggest that GA is to a large extent responsible for the phasic control of the anterior-posterior balance during quiet standing. A small difference (p<0.03) was found between mean time shift thus obtained for controls (n=4) and MS (n=6) while sway area showed a major difference (p<0.01). The paper also compares three alternative filters for numerical calculation of the EMG-envelope.     

Evaluating the annual nature of juvenile rings in Bolivian tropical rainforest trees

Knowledge on juvenile tree growth is crucial to understand how trees reach the canopy in tropical forests. However, long-term data on juvenile tree growth are usually unavailable. Annual tree rings provide growth information for the entire life of trees and their analysis has become more popular in tropical forest regions over the past decades. Nonetheless, tree ring studies mainly deal with adult rings as the annual character of juvenile rings has been questioned. We evaluated whether juvenile tree rings can be used for three Bolivian rainforest species. First, we characterized the rings of juvenile and adult trees anatomically. We then evaluated the annual nature of tree rings by a combination of three indirect methods: evaluation of synchronous growth patterns in the tree- ring series, ¹⁴C bomb peak dating and correlations with rainfall. Our results indicate that rings of juvenile and adult trees are defined by similar ring-boundary elements. We built juvenile tree-ring chronologies and verified the ring age of several samples using ¹⁴C bomb peak dating. We found that ring width was correlated with rainfall in all species, but in different ways. In all, the chronology, rainfall correlations and ¹⁴C dating suggest that rings in our study species are formed annually.