Simulation methods with extended stability for stiff biochemical Kinetics

Background  

With increasing computer power, simulating the dynamics of complex systems in chemistry and biology is becoming increasingly routine. The modelling of individual reactions in (bio)chemical systems involves a large number of random events that can be simulated by the stochastic simulation algorithm (SSA). The key quantity is the step size, or waiting time, τ, whose value inversely depends on the size of the propensities of the different channel reactions and which needs to be re-evaluated after every firing event. Such a discrete event simulation may be extremely expensive, in particular for stiff systems where τ can be very short due to the fast kinetics of some of the channel reactions. Several alternative methods have been put forward to increase the integration step size. The so-called τ-leap approach takes a larger step size by allowing all the reactions to fire, from a Poisson or Binomial distribution, within that step. Although the expected value for the different species in the reactive system is maintained with respect to more precise methods, the variance at steady state can suffer from large errors as τ grows.     

Antennal sensory organs in the millipede Eurypauropus ornatus: Fine structure of the flagella and globulus

On the antennal tip of Eurypauropus ornatus are 3 threadlike sensilla—the flagella, and a single spheroid sensillum—the globulus. Each of the 3 flagella is innervated by 2 groups of sensory cells. One group contains 4 cells, the other, 5. All cells of the “four group” and 3 of the “five group” are comprised of single cilia and unbranched dendrites which extend along the lumen of the flagellum. Two cells of the “five group” have double cilia and pairs of unbranched dendrites. One pair also enters the flagellum and the other pair terminates beneath the flagellar base to form a concentric array of lamellae. No pores are present in the cuticular wall. Eight sensory cells innervate the globulus. They are arranged in 3 groups, one triplet and 2 pairs, in addition to a single cell. The single cell contains a pair of cilia whose unbranched dendrites differentiate into tubular bodies that are inserted into the base of the globulus. Each of the other 7 sensory cells has a single cilium. Their unbranched dendrites penetrate into the globulus in 3 groups as described for the sensory cells. The dendrites in each group terminate in an individual pore channel at the globulus tip and completely fuse with the electron-dense material that plugs the pore channel. Based on structural similarities to sensilla having known functions, it is probable that the flagella and the globulus are chemoreceptors, the former responding to odors, the latter sensitive to substances in aqueous solution.     

The cell cycle modulated glycoprotein GP115 is one of the major yeast proteins containing glycosylphosphatidylinositol

The cell cycle modulated protein gp115 (115 kDa, isoelectric point about 4.8-5) of Saccharomyces cerevisiae undergoes various post-translational modifications. It is N-glycosylated during its maturation along the secretory pathway where an intermediary precursor of 100 kDa (p100), dynamically related to the mature gp115 protein, is detected at the level of endoplasmic reticulum. Moreover, we have shown by the use of metabolic labeling with [35S]methionine, [3H]palmitic acid and myo-[3H]inositol combined with high resolution two-dimensional gel electrophoresis and immunoprecipitation with a specific antiserum, that gp115 is one of the major palmitate- and inositol-containing proteins in yeast. These results, and the susceptibility of gp115 to phosphatidylinositol-specific phospholipase C treatment strongly indicate that gp115 contains the glycosylphosphatidylinositol (GPI) structure as membrane anchor domain. The two-dimensional analysis of the palmitate- and inositol-labeled proteins has also allowed the characterization of other polypeptides which possibly contain a GPI structure.