Simulation of marked root hair curling in Rhizobium-legume symbiosis

The soil bacterium Rhizobium infects its leguminous host plants in temperate regions of the world mostly by way of the growing root hairs. Root hair curling is a prerequisite for root hair infection, although sidelong root hair infections occasionally have been observed. The processes underlying Rhizobium -induced root hair curling are unknown.
Computer simulation of root hair growth indicates that one-sided tip growth inhibition by Rhizobium can result in root hair curling when three conditions are simultaneously fulfilled: 1) rhizobial growth inhibition is strong enough to prevent removal out of the tip growth range: 2) root hair surface growth between the attached Rhizobium and the root hair top is inhibited; 3) rhizobial growth inhibition is limited to one side of the root hair.
The results predict that root hair curling by stimulation of tip growth is improbable. This study accentuates the need for information about the growth processes contributing to tip growth in leguminous root hairs.     

Ion-specific diffusion rates through transmembrane protein channels. A molecular dynamics study

The migration of different alkali metal cations through a transmembrane model channel is simulated by means of the molecular dynamics technique. The parameters of the model are chosen in close relation to the gramicidin A channel. Coulomb- and van der Waals-type potentials between the ions and flexible carbonyl groups of the pore-forming molecule are used to describe the ion channel interaction. The diffusion properties of the ions are obtained from three-dimensional trajectory calculations. The diffusion rates for the different ions Li+, Na+, K+ and Rb+ are affected not only by the mass of the particles but also very strongly by their size. The latter effect is more pronounced for rigid channels, i.e., for binding vibrational frequencies of the CO groups with v greater than 400 cm-1. In this range the selectivity sequence for the diffusion rates is the inverse of that expected from normal rate theory but agrees with that found in experiments for gramicidin A.     

Is male back space limiting? An investigation into the reproductive demography of the giant water bug,Abedus indentatus (Heteroptera: Belostomatidae)

Because male giant water bugs in the subfamily Belostomatinae provide parental care by brooding eggs on their back, an accurate assessment can be made of both the actual and potential reproductive capacity of males. Two operational sex-ratio (OSR) indices were developed and empirically measured for a population of giant water bug, Abedus indentatus,in California. One index was based on reproductive rates measured in the laboratory; the other index was based on reproductive resources observed in the field. Both OSR indices suggest that the operational sex ratio fluctuates between maleskewed ratios in the summer and femaleskewed ratios in the winter. This pattern appears to be the consequence of two factors. First, the adult sex ratio is significantly female biased. Second, although males can outreproduce females at high ambient temperatures, the reverse is true at low temperatures. Possible reasons for the female-skewed adult sex ratio are examined, including differential recruitment, differential mortality, and sampling bias.     

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.     

A note on sequence-dependence of DNA structure

A circular dichroism study was conducted on the solution structure of several different oligonucleotides, whose X-ray structures have been solved. It is suggested that in aqueous solution the oligonucleotides can form structures that maintain geometrical elements which are typical of B-DNA, A-DNA, and their intermediate forms. It is shown that 5'GGATGGGAG:5'CTCCCATCC, which forms an A-DNA helix in the crystal state (McCall et al. 1986), in aqueous solution maintains an A-DNA like structure at temperatures below 10 degrees C. At temperatures between 10 degrees C and 25 degrees C it shows a tendency to form an intermediate structure between A-DNA and B-DNA. Also, it is shown that TFE does not cause a transition from B-DNA to A-DNA helix in short DNA fragments, but instead disrupts the helix.     

On the mechanical characterization of compact bone structure using the homogenization theory

In a previous paper (Crolet et al., 1993, J. Biomechanics 26, 677–687), a modelling of the mechanical behavior of compact bone was presented, in which the homogenization theory was the basic tool of computation. In this simulation, approximations were used for the modelling of the lamellae and the osteons: the lamella and the osteon were divided into cylindrical sectors, each sector being approximated as a parallelepiped having a periodic structure (fibrous composite for the lamella, superimposition of plates for the osteon). The present study deals with a new model without these approximations. First, it can be proved that the homogenized elasticity tensor for a lamella, which has a non-periodic structure, is obtained at each geometrical point as a homogenized tensor of a periodic problem. Similarly, for the osteonal structure, the components of the homogenized tensor are determined at each point as the result of a periodic homogenization.

The software OSTEON, which is the computational method associated with this model, allows one to obtain a better understanding of the effects of many bony parameters. The obtained results are in accordance with experimental data.     

Molecular dynamics study of interaction of dimyristoyl phosphotidyl choline with water

We present here results of molecular dynamics (MD) simulations on hydrated bilayers of 40 molecules of 1-2-dimyristoyl-sn-glycero-3-phosphatidyl choline (DMPC) in liquid crystalline (Lα) phase using two different models (i) with same (A) conformation for all DMPC molecules, (ii) with alternate rows having different (A and B reported in crystallographic studies on DMPC) conformations. The bilayers were hydrated using 776 and 1064 water molecules. Simulations have been carried out at 310K with AMBER 4.0 program, using united atom force field for 200 pico seconds (ps) after equilibration. During heating and equilibration constant pressure temperature (PT) conditions were maintained while in simulation of equillibrated bilayers constant volume temperature (VT) conditions were used. Subaveraged atomic coordinates were used to calculate geometric parameters of lipid molecules and lipid water interaction. Our results show larger flexibility of polar head group and glycerol region in Lα phase compared to gel or non-hydrated bilayers. Chain disorder was more towards end. Sn-2 chains were more disordered. Use of two types of starting conformations increased disorder. Trans fraction of chain torsional angle was higher in non-hydrated bilayer. However it was more disordered due to ‘swing’ movement of chains because of distortion in torsional angles α2 and 03 due to absence of water molecules. Trans fraction of the chains, order parameter and water penetration showed general agreement with the available experimental results. On the whole MD technique was found to be quite useful for depicting microscopic behaviour of liquid crystalline system and correlating the same with macroscopic changes observed experimentally.     

Free Air Temperature Increase (FATI): a new tool to study global warming effects on plants in the field

A new technique, called Free Air Temperature Increase (FATI), was developed to artificially induce increased canopy temperature in field conditions without the use of enclosures. This acronym was chosen in analogy with FACE (Free Air CO₂ Enrichment), a technique which produces elevated CO₂ concentrations [CO₂] in open field conditions. The FATI system simulates global warming in small ecosystems of limited height, using infrared heaters from which all radiation below 800 nm is removed by selective cut-off filters to avoid undesirable photomorpho-genetic effects. An electronic control circuit tracks the ambient canopy temperature in an unheated reference plot with thermocouples, and modulates the radiant energy from the lamps to produce a 2.5°C increment in the canopy temperature of an associated heated plot (continuously day and night). This pre-set target differential is relatively-constant over time due to the fast response of the lamps and the use of a proportional action controller (the standard deviation of this increment was <1°C in a 3 week field study with 1007 measurements). Furthermore, the increase in leaf temperature does not depend on the vertical position within the canopy or on the height of the stand. Possible applications and alternative designs are discussed.     

Modeling of nitrogen transformations and translocations

Different submodels within complex model packages on N regimes-for plant N-uptake, net N-mineralization, nitrate leaching and microbial N immobilization-are critically reviewed mainly with regard to their prediction ability on the basis of three comparative papers. Only for some of the processes adequate statistical evaluation of the models was possible. Compared to the other statistically evaluable process, nitrate leaching, modeling of plant N-uptake yields the better results. Most models for mineralization use arbitrary approaches rather than empirical ones. Although only approximate estimates of N mineralisation were at hand, the models generally behave expectedly poor. Only one model-DAISY-out of 16 involved in the comparison uses an explicit microbial biomass sub-model including microbial growth, decline and maintenance terms. So DAISY is the only model coupling C and N cycles. But what is true for an individual model describing the C and N transformation of a lab incubation experiment seems to be valid for most of the complex simulation work on the C and N regimes: this model was said to be overparameterized with respect to the available data.