Comparison of different schemes to treat long-range electrostatic interactions in molecular dynamics simulations of a protein crystal

Eight molecular dynamics simulations of a ubiquitin crystal unit cell were performed to investigate the effect of different schemes to treat the long-range electrostatic interactions as well as the need to include counter ions. A crystal system was chosen as the test system, because the higher charge density compared with a protein in solution makes it more sensitive to the way of treating the electrostatic interactions. Three different schemes of treating the long-range interactions were compared: straight cutoff, reaction-field approximation, and a lattice-sum method (P3M). For each of these schemes, two simulations were performed, one with and one without the counter ions. Two additional simulations with a reaction-field force and different initial placements of the counter ions were performed to examine the effect of the initial positions of the ions. The inclusion of long-range electrostatic interactions using either a reaction-field or a lattice-sum method proved to be necessary for the simulation of crystals. These two schemes did not differ much in their ability to reproduce the crystallographic structure. The inclusion of counter ions, on the other hand, seems not necessary for obtaining a stable simulation. The initial positions of the ions have a visible but small effect on the simulation.     

Adipose-derived adult stromal cells heal critical-size mouse calvarial defects

In adults and children over two years of age, large cranial defects do not reossify successfully, posing a substantial biomedical burden. The osteogenic potential of bone marrow stromal (BMS) cells has been documented. This study investigates the in vivo osteogenic capability of adipose-derived adult stromal (ADAS) cells, BMS cells, calvarial-derived osteoblasts and dura mater cells to heal critical-size mouse calvarial defects. Implanted, apatite-coated, PLGA scaffolds seeded with ADAS or BMS cells produced significant intramembranous bone formation by 2 weeks and areas of complete bony bridging by 12 weeks as shown by X-ray analysis, histology and live micromolecular imaging. The contribution of implanted cells to new bone formation was 84-99% by chromosomal detection. These data show that ADAS cells heal critical-size skeletal defects without genetic manipulation or the addition of exogenous growth factors.     

Identification by genome scanning approach (GSA) of a microsatellite tightly associated with the apple scab resistance gene Vm.

For all known major apple scab resistance genes except Vr, molecular markers have been published. However, the precise position of some of these genes, in the apple genome, remains to be identified. Knowledge about the relative position of apple scab resistance genes is necessary to preliminarily evaluate the probability of success of their pyramidization. Pyramidization of different resistance genes into the same genotype is a reliable way to create cultivars with durable apple scab resistance. Applying the genome scanning approach (GSA), we identified the linkage group of the scab resistance gene Vm, derived from Malus micromalus, and we found a new molecular marker tightly associated with the gene. The simple sequence repeat Hi07h02, previously mapped on linkage group 17, cosegregates with the Vm gene (no recombinants in the 95 plants tested). The already published sequence-characterized amplified region Vm marker OPB12(687) was found to be linked at about 5 cM from the resistance gene and, therefore, this marker also maps on linkage group 17 of apple. This is the first report of the discovery of a major apple scab resistance gene on linkage group 17. The advantages of using GSA for the identification of molecular markers for qualitative traits are discussed.     

Species-specific detection of Lobaria pulmonaria (lichenized ascomycete) diaspores in litter samples trapped in snow cover

The foliose lichen Lobaria pulmonaria has suffered a substantial decline in central and northern Europe during the twentieth century and is now considered to be critically endangered in many European lowland regions. Based on demographic studies, it has been proposed that under the present environmental conditions and forest management regimes, dispersal of diaspores and subsequent establishment of new thalli are insufficient to maintain the remnant small lowland populations. Chances of long-term survival may therefore be reduced. The data and analytical power of these demographic studies are limited. Since lichen diaspores show very few species-specific morphological characteristics, and are therefore almost indistinguishable, the accurate assessment of diaspore flux would be a fundamental first step in better understanding the life cycle of L. pulmonaria. Here we present a new molecular approach to investigate the dispersal of L. pulmonaria diaspores in its natural environment by specifically identifying small amounts of DNA in snow litter samples at varying distances from known sources. We used a species-specific polymerase chain reaction (PCR) primer pair to amplify the ribosomal internal transcribed spacer region (ITS rDNA) and a sensitive automated PCR product detection system using fluorescent labelled primers. We detected considerable amounts of naturally dispersed diaspores, deposited as far as 50 m away from the closest potential source. Diaspores were only found in the direction of the prevailing wind. Diaspore deposition varied from 1.2 diaspores per m(2) per day at 50 m distance from the source to 15 diaspores per m(2) per day at 1 m distance. The method described in this paper opens up perspectives for studies of population dynamics and dispersal ecology mainly in lichenized ascomycetes but also in other organisms with small, wind-dispersed diaspores.     

TDP-1, a toxic component causing tibial dyschondroplasia in broiler chickens, and trichothecenes from Fusarium roseum 'Graminearum'.

Fusarium roseum 'Graminearum' was isolated from overwintered oats in Alaska and was tested for its ability to cause tibial dyschondroplasia (TDP) in broiler chickens. The water-soluble fraction was tested and found to cause TDP. In addition, diacetoxyscirpenol and 7-hydroxydiacetoxyscirpenol were identified in the acetonitrile fraction of the extracts and caused mild mouth lesions in chickens. Six major water-soluble components were purified by thin-layer chromatography and tested for toxicity to chick embryos. One of the six components, called TDP-1, was found to be lethal to chick embryos. There was a 100% incidence of TDP in chickens fed a diet containing 75 ppm (wt/wt) of pure TDP-1, thus establishing the cause and effect relationship between TDP and TDP-1. Analyses by thin-layer chromatography and mass spectrometry revealed that TDP-1 is polar and ninhydrin positive, exhibits fluorescence with UV irradiation, and is a nitrogen-containing component with an empirical formula of C15H20N2O4.     

Effect of transepithelial concentration gradients on the passive fluxes of sodium across toad bladder

Summary Bidirectional sodium fluxes across toad bladder were measured after eliminating active transport with ouabain. Mucosal sodium concentration,C _m , was progressively reduced (from 114 to 3mm) while serosal sodium remained constant. Potential difference was maintained at zero by current passage. The ratio,Q, of the bulk permeability coefficient for sodium,P, to the tracer sodium permeability coefficientP ^*, was found to remain constant asC _m decreased. Equations were derived on this basis for bidirectional fluxes and forP andP ^* as functions ofC _m , which corresponded closely to the observed data. The explanation for the observed value ofQ and its constancy under these conditions is uncertain.     

Concentrationo-dependence of nonelectrolyte permeability of toad bladder

Summary A theoretical formulation was derived for the dependence of bulk solute permeability,P, defined as net flux :- concentration gradient, c, across any membrane in which solute concentration is controlling for net flux, . According to this formulation, is stimulated by increments in trans concentration,c ₂, in the rangec ₂/c ₁=0.0–0.1. Net flux of urea across toad bladder down concentration gradients was shown to be stimulated threefold by small increments in trans urea concentration. The theory also predicts that, in the absence of concentration gradients, tracer permeability,P ^*, defined as tracer flux :- tracer concentration, will be independent ofc provided thatP=P ^*, but will diminish with increasingc ifP/P ^*<1.P/P ^* was not significantly different from unity for urea, and bothP andP ^* were independent ofc in the absence of concentration gradients. However,P/P ^* was significantly less than unity (0.90 and 0.85) for thiourea and mannitol, respectively. In conformity with theory,P ^* (and alsoP) of these two solutes, measured asc was increased by 3–4 orders of magnitude, diminished progressively. These effects are more consistent with this formulation than with transport via a saturable carrier.