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.     

Evidence that Northern Pioneering Pines with Tuberculate Mycorrhizae are Unaffected by Varying Soil Nitrogen Levels

Tuberculate mycorrhizae on Pinus contorta (lodgepole pine) have previously been shown to reduce acetylene, but an outstanding question has been to what degree these structures could meet the nitrogen requirements of the tree. We compared the growth, tissue nitrogen contents, and stable nitrogen isotope ratios of P. contorta growing in gravel pits to the same species growing on adjacent intact soil. Trees growing in severely nitrogen deficient gravel pits had virtually identical growth rates and tissue nitrogen contents to those growing on intact soil that had nitrogen levels typical for the area. δ¹⁵N values for trees in the gravel pits were substantially lower than δ¹⁵N values for trees on intact soil, and isotope ratios in vegetation were lower than the isotope ratios of the soil. The form of soil nitrogen in the gravel pits was almost exclusively nitrate, while ammonium predominated in the intact soil. Discrimination against ¹⁵N during plant uptake of soil nitrate in the highly N-deficient soil should be weak or nonexistent. Therefore, the low δ¹⁵N in the gravel pit trees suggests that trees growing in gravel pits were using another nitrogen source in addition to the soil. Precipitation-borne nitrogen in the study area is extremely low. In conjunction with our other work, these findings strongly suggests that P. contorta and its microbial symbionts or associates fix nitrogen in sufficient amounts to sustain vigorous tree growth on the most nitrogen-deficient soils.