Phase transitions in systems with two species of molecular motors

Systems with two species of active molecular motors moving on (cytoskeletal) filaments into opposite directions are studied theoretically using driven lattice gas models. The motors can unbind from and rebind to the filaments. Two motors are more likely to bind on adjacent filament sites if they belong to the same species. These systems exhibit (i) Continuous phase transitions towards states with spontaneously broken symmetry, where one motor species is largely excluded from the filament, (ii) Hysteresis of the total current upon varying the relative concentrations of the two motor species, and (iii) Coexistence of traffic lanes with opposite directionality in multi-filament systems. These theoretical predictions should be experimentally accessible.Comment: 7 pages, 4 figures, epl style (.cls-file included), to appear in Europhys. Lett. (http://www.edpsciences.org/epl

Lack of increased availability of root-derived C may explain the low N2O emission from low N-urine patches

Urine deposition on grassland causes significant N2O losses, which in some cases may result from increased denitrification stimulated by labile compounds released from scorched plant roots. Two 12-day experiments were conducted in 13C-labelled grassland monoliths to investigate the link between N2O production and carbon mineralization following application of low rates of urine-N. Measurements of N2O and CO2 emissions from the monoliths as well as δ13C signal of evolved CO2 were done on day -4, -1, 0, 1, 2, 4, 5, 6 and 7 after application of urine corresponding to 3.1 and 5.5 g N m-2 in the first and second experiment, respectively. The δ13C signal was also determined for soil organic matter, dissolved organic C and CO2 evolved by microbial respiration. In addition, denitrifying enzyme activity (DEA) and nitrifying enzyme activity (NEA) were measured on day -1, 2 and 7 after the first urine application event. Urine did not affect DEA, whereas NEA was enhanced 2 days after urine application. In the first experiment, urine had no significant effect on the N2O flux, which was generally low (-8 to 14 μg N2O-N m-2 h-1). After the second application event, the N2O emission increased significantly to 87 μg N2O-N m-2 h-1 and the N2O emission factor for the added urine-N was 0.18 %. However, the associated 13C signal of soil respiration was unaffected by urine. Consequently, the increased N2O emission from the simulated low N-urine patches was not caused by enhanced denitrification stimulated by labile compounds released from scorched plant roots

Transport by molecular motors in the presence of static defects

The transport by molecular motors along cytoskeletal filaments is studied theoretically in the presence of static defects. The movements of single motors are described as biased random walks along the filament as well as binding to and unbinding from the filament. Three basic types of defects are distinguished, which differ from normal filament sites only in one of the motors' transition probabilities. Both stepping defects with a reduced probability for forward steps and unbinding defects with an increased probability for motor unbinding strongly reduce the velocities and the run lengths of the motors with increasing defect density. For transport by single motors, binding defects with a reduced probability for motor binding have a relatively small effect on the transport properties. For cargo transport by motors teams, binding defects also change the effective unbinding rate of the cargo particles and are expected to have a stronger effect.Comment: 20 pages, latex, 7 figures, 1 tabl

Stochastic simulations of cargo transport by processive molecular motors

We use stochastic computer simulations to study the transport of a spherical cargo particle along a microtubule-like track on a planar substrate by several kinesin-like processive motors. Our newly developed adhesive motor dynamics algorithm combines the numerical integration of a Langevin equation for the motion of a sphere with kinetic rules for the molecular motors. The Langevin part includes diffusive motion, the action of the pulling motors, and hydrodynamic interactions between sphere and wall. The kinetic rules for the motors include binding to and unbinding from the filament as well as active motor steps. We find that the simulated mean transport length increases exponentially with the number of bound motors, in good agreement with earlier results. The number of motors in binding range to the motor track fluctuates in time with a Poissonian distribution, both for springs and cables being used as models for the linker mechanics. Cooperativity in the sense of equal load sharing only occurs for high values for viscosity and attachment time.Comment: 40 pages, Revtex with 13 figures, to appear in Journal of Chemical Physic

Deterministic and stochastic descriptions of gene expression dynamics

A key goal of systems biology is the predictive mathematical description of gene regulatory circuits. Different approaches are used such as deterministic and stochastic models, models that describe cell growth and division explicitly or implicitly etc. Here we consider simple systems of unregulated (constitutive) gene expression and compare different mathematical descriptions systematically to obtain insight into the errors that are introduced by various common approximations such as describing cell growth and division by an effective protein degradation term. In particular, we show that the population average of protein content of a cell exhibits a subtle dependence on the dynamics of growth and division, the specific model for volume growth and the age structure of the population. Nevertheless, the error made by models with implicit cell growth and division is quite small. Furthermore, we compare various models that are partially stochastic to investigate the impact of different sources of (intrinsic) noise. This comparison indicates that different sources of noise (protein synthesis, partitioning in cell division) contribute comparable amounts of noise if protein synthesis is not or only weakly bursty. If protein synthesis is very bursty, the burstiness is the dominant noise source, independent of other details of the model. Finally, we discuss two sources of extrinsic noise: cell-to-cell variations in protein content due to cells being at different stages in the division cycles, which we show to be small (for the protein concentration and, surprisingly, also for the protein copy number per cell) and fluctuations in the growth rate, which can have a significant impact.Comment: 23 pages, 5 figures; Journal of Statistical physics (2012

Magnetotactic bacteria Magnetic navigation on the microscale

Magnetotactic bacteria are aquatic microorganisms with the ability to swim along the field lines of a magnetic field, which in their natural environment is provided by the magnetic field of the Earth. They do so with the help of specialized magnetic organelles called magnetosomes, vesicles containing magnetic crystals. Magnetosomes are aligned along cytoskeletal filaments to give linear structures that can function as intracellular compass needles. The predominant viewpoint is that the cells passively align with an external magnetic field, just like a macroscopic compass needle, but swim actively along the field lines, propelled by their flagella. In this minireview, we give an introduction to this intriguing bacterial behavior and discuss recent advances in understanding it, with a focus on the swimming directionality, which is not only affected by magnetic fields, but also by gradients of the oxygen concentration

Molecular Spiders with Memory

Synthetic bio-molecular spiders with "legs" made of single-stranded segments of DNA can move on a surface which is also covered by single-stranded segments of DNA complementary to the leg DNA. In experimental realizations, when a leg detaches from a segment of the surface for the first time it alters that segment, and legs subsequently bound to these altered segments more weakly. Inspired by these experiments we investigate spiders moving along a one-dimensional substrate, whose legs leave newly visited sites at a slower rate than revisited sites. For a random walk (one-leg spider) the slowdown does not effect the long time behavior. For a bipedal spider, however, the slowdown generates an effective bias towards unvisited sites, and the spider behaves similarly to the excited walk. Surprisingly, the slowing down of the spider at new sites increases the diffusion coefficient and accelerates the growth of the number of visited sites.Comment: 10 pages, 3 figure

Traffic of Molecular Motors

Molecular motors perform active movements along cytoskeletal filaments and drive the traffic of organelles and other cargo particles in cells. In contrast to the macroscopic traffic of cars, however, the traffic of molecular motors is characterized by a finite walking distance (or run length) after which a motor unbinds from the filament along which it moves. Unbound motors perform Brownian motion in the surrounding aqueous solution until they rebind to a filament. We use variants of driven lattice gas models to describe the interplay of their active movements, the unbound diffusion, and the binding/unbinding dynamics. If the motor concentration is large, motor-motor interactions become important and lead to a variety of cooperative traffic phenomena such as traffic jams on the filaments, boundary-induced phase transitions, and spontaneous symmetry breaking in systems with two species of motors. If the filament is surrounded by a large reservoir of motors, the jam length, i.e., the extension of the traffic jams is of the order of the walking distance. Much longer jams can be found in confined geometries such as tube-like compartments.Comment: 10 pages, latex, uses Springer styles (included), to appear in the Proceedings of "Traffic and Granular Flow 2005

Administration of Vitamin D Metabolites Affects RNA Expression of Xenobiotic Metabolising Enzymes and Function of ABC Transporters in Rats

From studies on different species and in cell culture systems, it has been suggested that vitamin D metabolites might affect themetabolism and elimination of xenobiotics. Although most studies performed on rodents and cell cultures report an upregulationof respective enzymes and transporters, data from the literature are inconsistent. Especially results obtained with sheep differ fromthese observations. As vitamin D metabolites are widely used as feed additives or therapeutics in livestock animals, we aimed toassess whether these differences indicate species-specific responses or occurred due to the very high dosages used in the rodentstudies. -erefore, we applied treatment protocols to rats that had been used previously in sheep or cattle. Forty-eight female ratswere divided into three treatment and corresponding placebo groups: (1) a single intraperitoneal injection of 1,25-(OH)2D3 orplacebo 12 h before sacrifice; (2) daily supplementation with 25-OHD3 by oral gavage or placebo for 10 days; and (3) a singleintramuscular injection of vitamin D3 10 days before sacrifice. In contrast to a previous study using sheep, treatment of rats with1,25-dihydroxyvitamin D3 did not result in an upregulation of cytochrome P450 3A isoenzymes (CYP3A), but a decrease wasfound in hepatic and intestinal expressions. In addition, a downregulation of P-glycoprotein (P-gp) and breast cancer resistanceprotein was found in the brain. Taken together, the stimulating effects of vitamin D metabolites on the expression of genesinvolved in the metabolism and elimination of xenobiotics reported previously for rodents and sheep could not be reproduced. Incontrast, we even observed a negative impact on the expression of CYP3A enzymes and their most important regulator, thepregnane X receptor. Most interestingly, we could demonstrate an effect of treatment with 25-hydroxyvitamin D3 and vitamin D3on the functional activity of ileal P-glycoprotein (P-gp) using the Ussing chamber technique.Fil: Klumpp, Karoline. University of Veterinary Medicine Hannover. Institute of Physiology and Cell Biology; AlemaniaFil: Lange, Frauke. University of Veterinary Medicine Hannover. Institute of Physiology and Cell Biology; AlemaniaFil: Muscher-Banse, Alexandra S.. University of Veterinary Medicine Hannover. Institute of Physiology and Cell Biology; AlemaniaFil: Schnepel, Nadine. University of Veterinary Medicine Hannover. Institute of Physiology and Cell Biology; AlemaniaFil: Hansen, Kathrin. University of Veterinary Medicine Hannover. Institute of Physiology and Cell Biology; AlemaniaFil: Lifschitz, Adrian Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Centro de Investigación Veterinaria de Tandil. Universidad Nacional del Centro de la Provincia de Buenos Aires. Centro de Investigación Veterinaria de Tandil. Provincia de Buenos Aires. Gobernación. Comision de Investigaciones Científicas. Centro de Investigación Veterinaria de Tandil; ArgentinaFil: Maté, María Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Centro de Investigación Veterinaria de Tandil. Universidad Nacional del Centro de la Provincia de Buenos Aires. Centro de Investigación Veterinaria de Tandil. Provincia de Buenos Aires. Gobernación. Comision de Investigaciones Científicas. Centro de Investigación Veterinaria de Tandil; ArgentinaFil: Wilkens, Mirja. University of Veterinary Medicine Hannover. Institute of Physiology and Cell Biology; Alemani