Metastable behavior in Markov processes with internal states

A perturbation framework is developed to analyze metastable behavior in stochastic processes with random internal and external states. The process is assumed to be under weak noise conditions, and the case where the deterministic limit is bistable is considered. A general analytical approximation is derived for the stationary probability density and the mean switching time between metastable states, which includes the pre exponential factor. The results are illustrated with a model of gene expression that displays bistable switching. In this model, the external state represents the number of protein molecules produced by a hypothetical gene. Once produced, a protein is eventually degraded. The internal state represents the activated or unactivated state of the gene; in the activated state the gene produces protein more rapidly than the unactivated state. The gene is activated by a dimer of the protein it produces so that the activation rate depends on the current protein level. This is a well studied model, and several model reductions and diffusion approximation methods are available to analyze its behavior. However, it is unclear if these methods accurately approximate long-time metastable behavior (i.e., mean switching time between metastable states of the bistable system). Diffusion approximations are generally known to fail in this regard.     

para-hydroxybenzoate as an intermediate in the anaerobic transformation of phenol to benzoate

Anaerobic phenol transformation was studied using a consortium which transformed phenol to benzoate without complete mineralization of benzoate. Products of monofluorophenol transformation indicated para-carboxylation. Phenol and benzoate were detected during para-hydroxybenzoate (p-OHB) degradation. p-OHB was detected in phenol-transforming cultures containing 6-hydroxynicotinic acid (6-OHNA), a structural analogue of p-OHB, or at elevated initial concentrations of phenol (greater than or equal to 5 mM), or benzoate (greater than or equal to 10 mM).     

Isolation and characterization of the gene encoding yeast debranching enzyme.

Using a genetic screen aimed at identifying cellular factors involved in Ty1 transposition, we have identified a mutation in a host gene that reduces Ty1 transposition frequency. The mutant, dbr1, is also defective in the process of intron turnover. In dbr1 cells, excised introns derived from a variety of pre-mRNAs are remarkably stable and accumulate to levels exceeding that of the corresponding mRNA. The stable excised introns accumulate in the form of a lariat that is missing the linear sequences 3' of the branchpoint. The DBR1 gene has been isolated by complementation of the transposition phenotype. DBR1 is shown to encode debranching enzyme, an RNA processing activity that hydrolyzes the 2'-5' phosphodiester linkage at the branchpoint of excised intron lariats. In Saccharomyces cerevisiae, debranching enzyme plays a requisite role in the rapid turnover of excised introns, yet its function is not essential for viability.     

Pharynx, esophagus, and associated structures in the booklouse, Liposcelis divinatorius

Abstract. Ultrastructural features of the pharynx, esophagus, and associated intrinsic visceral muscular and nervous structures of the booklouse, Liposcelis divinatorius , were studied to determine whether the anatomical arrangements of these structures differed from the general pattern found in insects. The results are compared with previous light microscope studies of this tiny insect. Variations from the usual arrangement reported for intrinsic visceral muscles associated with the pharynx in insects are described. Intrinsic visceral muscles include a narrow band of circularly disposed fibers and both extra-circular and intra-circular longitudinally disposed fibers. This represents a departure from the slightly developed inner longitudinal and more prominent outer circular fibers seen in most insects. The outer surface of some circular muscle cells has apparently unique pouches packed with mitochondria, which contain many cristae. Numerous bacteroids appear in the esophageal epithelial cells and in the sub-esophageal ganglion. Nerve processes associated with the foregut contain neurotubules, synaptic vesicles, and electron-dense granules.