Stochastic Chemical Reactions in Micro-domains

Traditional chemical kinetics may be inappropriate to describe chemical reactions in micro-domains involving only a small number of substrate and reactant molecules. Starting with the stochastic dynamics of the molecules, we derive a master-diffusion equation for the joint probability density of a mobile reactant and the number of bound substrate in a confined domain. We use the equation to calculate the fluctuations in the number of bound substrate molecules as a function of initial reactant distribution. A second model is presented based on a Markov description of the binding and unbinding and on the mean first passage time of a molecule to a small portion of the boundary. These models can be used for the description of noise due to gating of ionic channels by random binding and unbinding of ligands in biological sensor cells, such as olfactory cilia, photo-receptors, hair cells in the cochlea.Comment: 33 pages, Journal Chemical Physic

Resting Behaviour of Broilers in Three Different Rearing Systems

The highest number of broilers is reared in the intensive fattening system on the floor with litter. Besides the intensive systems some sustainable rearing ways are also brought forward (ecological, biologic-dynamic, organic, etc.). The aim of this study was to establish the possible differences in resting behaviour of broilers in three rearing systems: intensive on the floor, free range, and organic system. The results showed great varieties between intensive and less intensive systems. In the intensive system on the floor animals rested statistically highly significantly more than in other two systems. However no differences in the behaviour of broilers in the stall were noticed, ifcompared to broilers in free range and those in the organic system. Comparison of the outdoor area showed that broilers rested statistically significantly more in the organic system. The reasons for different resting behaviour could be in leg weakness, body weight, group size, health problems, age, housing system, etc. Our research did not confirm our hypothesis that the older broilers rest more

Realistic boundary conditions for stochastic simulations of reaction-diffusion processes

Many cellular and subcellular biological processes can be described in terms of diffusing and chemically reacting species (e.g. enzymes). Such reaction-diffusion processes can be mathematically modelled using either deterministic partial-differential equations or stochastic simulation algorithms. The latter provide a more detailed and precise picture, and several stochastic simulation algorithms have been proposed in recent years. Such models typically give the same description of the reaction-diffusion processes far from the boundary of the simulated domain, but the behaviour close to a reactive boundary (e.g. a membrane with receptors) is unfortunately model-dependent. In this paper, we study four different approaches to stochastic modelling of reaction-diffusion problems and show the correct choice of the boundary condition for each model. The reactive boundary is treated as partially reflective, which means that some molecules hitting the boundary are adsorbed (e.g. bound to the receptor) and some molecules are reflected. The probability that the molecule is adsorbed rather than reflected depends on the reactivity of the boundary (e.g. on the rate constant of the adsorbing chemical reaction and on the number of available receptors), and on the stochastic model used. This dependence is derived for each model.Comment: 24 pages, submitted to Physical Biolog

EVALUATION OF GROWTH AND CARCASS TRAITS BETWEEN 42 AND 58 DAYS OF AGE IN CHICKENS DIVERGENTLY SELECTED FOR BODY WEIGHT

The effect of divergent selection for high (H) or low (L) body weight at eight weeks of age for 25 generations on growth and carcass traits between 42 and 58 days of age was studied. The chicks were reared in individual cages under standard management conditions. Selection for low 8-week body weight has resulted in higher relative body weight increase for the period from 42 to 58 days of age compared to chickens from the high line. Body weight increased by about 72 % in the low line and by about 56 and 44 %, respectively in the males and females in the high line. In both lines of chickens dressing out percentage and the percentage of abdominal, subcutaneous and total fat increased with body weight, whereas percentage of m. pectoralis superficialis and m. pectoralis profundus remained roughly constant. Percentage of skin decreased with increasing of body weight. In both lines females had a higher percentage of total fat than males. There was evidence that total fat content increased independently of animal body weight with a certain age. Fixed age comparisons of feed conversion ratios showed no differences in feed conversion between the two divergently selected lines of chicks

Biophysics of high density nanometer regions extracted from super-resolution single particle trajectories: application to voltage-gated calcium channels and phospholipids.

The cellular membrane is very heterogenous and enriched with high-density regions forming microdomains, as revealed by single particle tracking experiments. However the organization of these regions remain unexplained. We determine here the biophysical properties of these regions, when described as a basin of attraction. We develop two methods to recover the dynamics and local potential wells (field of force and boundary). The first method is based on the local density of points distribution of trajectories, which differs inside and outside the wells. The second method focuses on recovering the drift field that is convergent inside wells and uses the transient field to determine the boundary. Finally, we apply these two methods to the distribution of trajectories recorded from voltage gated calcium channels and phospholipid anchored GFP in the cell membrane of hippocampal neurons and obtain the size and energy of high-density regions with a nanometer precision