Simulation studies of permeation through two-dimensional ideal polymer networks

We study the diffusion process through an ideal polymer network, using numerical methods. Polymers are modeled by random walks on the bonds of a two-dimensional square lattice. Molecules occupy the lattice cells and may jump to the nearest-neighbor cells, with probability determined by the occupation of the bond separating the two cells. Subjected to a concentration gradient across the system, a constant average current flows in the steady state. Its behavior appears to be a non-trivial function of polymer length, mass density and temperature, for which we offer qualitative explanations.Comment: 8 pages, 4 figure

Gas permeation through a polymer network

We study the diffusion of gas molecules through a two-dimensional network of polymers with the help of Monte Carlo simulations. The polymers are modeled as non-interacting random walks on the bonds of a two-dimensional square lattice, while the gas particles occupy the lattice cells. When a particle attempts to jump to a nearest-neighbor empty cell, it has to overcome an energy barrier which is determined by the number of polymer segments on the bond separating the two cells. We investigate the gas current $J$ as a function of the mean segment density $\rho$, the polymer length $\ell$ and the probability $q^{m}$ for hopping across $m$ segments. Whereas $J$ decreases monotonically with $\rho$ for fixed $\ell$, its behavior for fixed $\rho$ and increasing $\ell$ depends strongly on $q$. For small, non-zero $q$, $J$ appears to increase slowly with $\ell$. In contrast, for $q=0$, it is dominated by the underlying percolation problem and can be non-monotonic. We provide heuristic arguments to put these interesting phenomena into context.Comment: Dedicated to Lothar Schaefer on the occasion of his 60th birthday. 11 pages, 3 figure

A non-canonical RNA silencing pathway promotes mRNA degradation in basal fungi

The increasing knowledge on the functional relevance of endogenous small RNAs (esRNAs) as riboregulators has stimulated the identification and characterization of these molecules in numerous eukaryotes. In the basal fungus Mucor circinelloides, an emerging opportunistic human pathogen, esRNAs that regulate the expression of many protein coding genes have been described. These esRNAs share common machinery for their biogenesis consisting of an RNase III endonuclease Dicer, a single Argonaute protein and two RNA-dependent RNA polymerases. We show in this study that, besides participating in this canonical dicer-dependent RNA interference (RNAi) pathway, the rdrp genes are involved in a novel dicer-independent degradation process of endogenous mRNAs. The analysis of esRNAs accumulated in wild type and silencing mutants demonstrates that this new rdrp-dependent dicer-independent regulatory pathway, which does not produce sRNA molecules of discrete sizes, controls the expression of target genes promoting the specific degradation of mRNAs by a previously unknown RNase. This pathway mainly regulates conserved genes involved in metabolism and cellular processes and signaling, such as those required for heme biosynthesis, and controls responses to specific environmental signals. Searching the Mucor genome for candidate RNases to participate in this pathway, and functional analysis of the corresponding knockout mutants, identified a new protein, R3B2. This RNase III-like protein presents unique domain architecture, it is specifically found in basal fungi and, besides its relevant role in the rdrp-dependent dicer-independent pathway, it is also involved in the canonical dicer-dependent RNAi pathway, highlighting its crucial role in the biogenesis and function of regulatory esRNAs. The involvement of RdRPs in RNA degradation could represent the first evolutionary step towards the development of an RNAi mechanism and constitutes a genetic link between mRNA degradation and post-transcriptional gene silencing

Controls on the global distribution of contourite drifts: Insights from an eddy-resolving ocean model

Contourite drifts are anomalously high sediment accumulations that form due to reworking by bottom currents. Due to the lack of a comprehensive contourite database, the link between vigorous bottom water activity and drift occurrence has yet to be demonstrated on a global scale. Using an eddy-resolving ocean model and a new georeferenced database of 267 contourites, we show that the global distribution of modern contourite drifts strongly depends on the configuration of the world’s most powerful bottom currents, many of which are associated with global meridional overturning circulation. Bathymetric obstacles frequently modify flow direction and intensity, imposing additional finer-scale control on drift occurrence. Mean bottom current speed over contourite-covered areas is only slightly higher (2.2cm/s) than the rest of the global ocean (1.1cm/s), falling below proposed thresholds deemed necessary to re-suspend and redistribute sediments (10–15cm/s). However, currents fluctuate more frequently and intensely over areas with drifts, highlighting the role of intermittent, high-energy bottom current events in sediment erosion, transport, and subsequent drift accumulation. We identify eddies as a major driver of these bottom current fluctuations, and we find that simulated bottom eddy kinetic energy is over three times higher in contourite-covered areas in comparison to the rest o.f the ocean. Our work supports previous hypotheses which suggest that contourite deposition predominantly occurs due to repeated acute events as opposed to continuous reworking under average-intensity background flow conditions. This suggests that the contourite record should be interpreted in terms of a bottom current’s susceptibility to experiencing periodic, high-speed current events. Our results also highlight the potential role of upper ocean dynamics in contourite sedimentation through its direct influence on deep eddy circulation

Verotoxin-Producing <i>Escherichia coli</i> in Sheep Grazing an Irrigated Pasture or Arid Rangeland Forages

Worldwide, verotoxin-producing Escherichia coli (VTEC) have been recognized as the cause of many sporadic cases or major outbreaks of human illnesses involving consumption of contaminated meat, especially beef. Although sheep products have not been linked to reported human illnesses, their role as a food safety risk factor should not be ignored. The objective of this study was to assess VTEC prevalence in two groups of ewes (20 each) grazing an irrigated pasture or arid range in a western United States environment (Nevada) over 1 year (summer of 1999 to summer of 2000). A random sample ( n = 504) of potential VTEC isolates were tested for verotoxicity and were screened for the presence (polymerase chain reaction [PCR]) and expression (VTEC-reversed passive latex agglutination assay) of the toxin genes (i.e., VT1 and VT2). Forty-one VTEC isolates (16 having only the VT1 gene and 25 having both VT1 And VT2 genes) were detected in both groups of ewes. Except for seven isolates, the genotype and phenotype data matched. All the isolates (nonmotile [H–]) were non-O157:H7 VTEC (i.e., O91:H– [ n = 25], O128:H– [ n = 9], and untypeable ones [ n = 7]). More infected ewes (nine versus three) and different VTEC strains were found in the irrigated pasture than in the arid range. Because our ewes were shedding two VTEC serotypes known to cause human illnesses, it is beneficial to identify VTEC-positive sheep before slaughter as an initial control point before entering the food chain. </jats:p