Genome-Wide Identification of Small RNAs in the Opportunistic Pathogen Enterococcus faecalis V583

Small RNA molecules (sRNAs) are key mediators of virulence and stress inducible gene expressions in some pathogens. In this work we identify sRNAs in the Gram positive opportunistic pathogen Enterococcus faecalis. We characterized 11 sRNAs by tiling microarray analysis, 5′ and 3′ RACE-PCR, and Northern blot analysis. Six sRNAs were specifically expressed at exponential phase, two sRNAs were observed at stationary phase, and three were detected during both phases. Searches of putative functions revealed that three of them (EFA0080_EFA0081 and EFB0062_EFB0063 on pTF1 and pTF2 plasmids, respectively, and EF0408_EF04092 located on the chromosome) are similar to antisense RNA involved in plasmid addiction modules. Moreover, EF1097_EF1098 shares strong homologies with tmRNA (bi-functional RNA acting as both a tRNA and an mRNA) and EF2205_EF2206 appears homologous to 4.5S RNA member of the Signal Recognition Particle (SRP) ribonucleoprotein complex. In addition, proteomic analysis of the ΔEF3314_EF3315 sRNA mutant suggests that it may be involved in the turnover of some abundant proteins. The expression patterns of these transcripts were evaluated by tiling array hybridizations performed with samples from cells grown under eleven different conditions some of which may be encountered during infection. Finally, distribution of these sRNAs among genome sequences of 54 E. faecalis strains was assessed. This is the first experimental genome-wide identification of sRNAs in E. faecalis and provides impetus to the understanding of gene regulation in this important human pathogen

Spatial theory and human behavior

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/45971/1/10110_2005_Article_BF01952731.pd

A 1,000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics

An integrated barley transcript map (consensus map) comprising 1,032 expressed sequence tag (EST)-based markers (total 1,055 loci: 607 RFLP, 190 SSR, and 258 SNP), and 200 anchor markers from previously published data, has been generated by mapping in three doubled haploid (DH) populations. Between 107 and 179 EST-based markers were allocated to the seven individual barley linkage groups. The map covers 1118.3 cM with individual linkage groups ranging from 130 cM (chromosome 4H) to 199 cM (chromosome 3H), yielding an average marker interval distance of 0.9 cM. 475 EST-based markers showed a syntenic organisation to known colinear linkage groups of the rice genome, providing an extended insight into the status of barley/rice genome colinearity as well as ancient genome duplications predating the divergence of rice and barley. The presented barley transcript map is a valuable resource for targeted marker saturation and identiWcation of candidate genes at agronomically important loci. It provides new anchor points for detailed studies in comparative grass genomics and will support future attempts towards the integration of genetic and physical mapping information

Uncertainty, spatial proximity, and the stability of oligopoly pricing

One of the most pervasive characteristics of mature oligopolistic industries is their reluctance to engage in price competition, and their channeling of competitive efforts into rivalry using advertising and other marketing costs as well as product differentiation. This leads to questions concerning the nature of the economic and social matrix within which such firms operate, and these questions in turn motivate the theorist to construct frameworks that yield such results. Spatial proximity has generally been accepted as an intensifier of price competition, but in many local oligopolistic markets it seems to act as an inhibitor of price competition. In this paper I attempt to study the role of uncertainty in explaining the 'rivalrous consonance of interests' which tends to keep prices above the competitive level in spatially concentrated markets. By using Weibull density functions to approximate subjective expectations of firms, I seek to cast light upon some of the factors that play a role in explaining this apparent paradox.

Understanding the Influences of Thermal and Mixture Inhomogeneities on the Auto-Ignition Process in a Controlled Auto-Ignition (CAI) Engine Using LES

This work applies Large Eddy Simulation (LES) to the combustion process within a CAI engine. The chemical reaction is treated with a pre-tabulation approach based on homogeneous reactor simulations. At this juncture, a five-dimensional chemistry database is employed where the thermochemical properties are a function of the unburnt gas temperature, the air-fuel ratio, the exhaust gas ratio, the pressure, and the reaction progress variable. Statistical quantities are gathered for 20 simulated cycles and the averaged pressure curves get compared to measurements. The simulation data are then used to provide further insight into the auto-ignition process. It will be shown how thermochemical states are distributed within the cylinder and how the ignition quality depends on them. A statistical analysis is conducted to identify manifolds in the multi-dimensional scalar space along which the conditions leading to ignition evolve. Furthermore the strong influence in between consecutive cycles caused by the exhaust gas is investigated to identify the mechanism of cycle-to-cycle variations