Uncovering the Identity and Metabolism of Bacterial CoA-RNA

Coenzyme A is an indispensable molecule in all known life with roles in metabolism, gene regulation, and macromolecule synthesis. As CoA is derived from RNA itself, it’s incorporation into RNA by in vitro methods has proven useful in research probing the origin of life based on the RNA World theory. The discovery in contemporary bacteria of RNA modified with CoA, however, provided an unexpected twist to previously well-characterized bacterial systems. The identity of sequences associated with CoA-RNA has been elusive since their discovery in 2009 based on the difficulties in isolation while maintaining RNA quality. The aim of this study is to develop a specific CoA-RNA capture protocol to uncover the sequence identities for the further understanding of CoA-RNA function. While the free thiol of CoA can be used to purify the CoA-RNA from total bacterial RNA, the success of process depends on the specific release from the purification matrix. This work details the characterization of recombinant Nudix CoA pyrophosphohydrolases from various organisms for their use in CoA hydrolysis and CoA-RNA metabolism, as well as for the development and successful implementation of a specific CoA-RNA capture protocol. The use of this protocol for the construction of high quality NGS libraries is vital to the elucidation of CoA-RNA function via bioinformatic analysis, for its potential ranges from a simple stabilization adduct to contemporary examples of RNA World era coenzyme-conjugated ribozymes

Survival and Cardioprotective Benefits of Long-Term Blueberry Enriched Diet in Dilated Cardiomyopathy Following Myocardial Infarction in Rats

Despite remarkable progress in treatment of chronic heart failure (CHF) over the last two decades, mortality, personal suffering and cost remain staggering, and effective interventions are still a challenge. Previously we reported that a blueberry-enriched diet (BD) attenuated necroapoptosis and inflammation in periinfarct area in a rat model of myocardial infarction (MI).To test the hypothesis that BD will attenuate the course of CHF, including mortality and cardiac remodeling during the first year after induction of MI in rats.Two weeks after coronary artery ligation, rats were divided into two groups of similar average MI size, measured by echocardiography, and then 12-mo dietary regimens were initiated as follows: ad libitum regular diet (control, CD, n = 27) and isocaloric food with 2% blueberry supplement (BD, n = 27) also available ad libitum. These dietary groups were compared to each other and to sham group (SH). Mortality over the 12 mo was reduced by 22% in BD compared with CD (p<0.01). In the course of developing CHF, BD had no effect on the body weight, heart rate or blood pressure. Bi-monthly Echo revealed significant attenuation of the LV chamber remodeling, LV posterior wall thinning, and MI expansion in BD compared with CD. In fact, BD arrested the MI expansion.This is the first experimental evidence that a blueberry-enriched diet has positive effects on the course of CHF and thus warrants consideration for clinical evaluation

Groundwater in the Inner Bluegrass Karst Region, Kentucky

The hydrogeology of about 12% of the 5600 km2 Inner Bluegrass Karst Region of central Kentucky was investigated by water tracing and other techniques. Using fluorescent dyes adsorbed on fabric and charcoal detectors, 96 traces (average length 2.7 km, maximum length 15 km) resulted in the identification of 38 groundwater basins (with areas up to 15 km2). Within the basins, subsurface flow is in a dendritic conduit system at depths up to 30 m below the surface, while in the interbasin areas which separate them flow is generally less than 5 m deep. Each groundwater basin discharges at a spring whose median discharge is approximately 20 l/s·km2 of basin area. The largest spring (Royal Spring) in the study area has a median discharge greater than 300 l/s (Meinzer second magnitude). The Ordovician Lexington Limestone which underlies the region is thin bedded with shale partings and argillaceous units. Within groundwater basins, sinkhole drains and other conduits have breached the interbedded shales and descend nearly vertically to a level determined by equilibrium flow in the larger conduits. The general location and flow directions in groundwater basins is probably determined by a potentiometric gradient prior to conduit development, and some basins are localized by a favorably oriented regional joint set or other structural element. Otherwise, lithologic and structural factors have little influence in the occurrence and flow of subsurface water in the region

Can Honey Bees Assist in Area Reduction and Landmine Detection?

Honey bees have recently received considerable attention from the popular press as an innovative method to detect a variety of explosives, landmines and UXO. Many of these reports are inaccurate and may encourage individuals and demining groups to “sell” a service that they poorly understand or lack the experience to properly apply. As the developers of this technology, we offer the following summary about the current status of this alternative for landmine detection, including its strengths and limitations

Response of Lactobacillus plantarum WCFS1 to the Gram-Negative Pathogen-Associated Quorum Sensing Molecule N-3-Oxododecanoyl Homoserine Lactone

The bacterial quorum sensing phenomenon has been well studied since its discovery and has traditionally been considered to include signaling pathways recognized exclusively within either Gram-positive or Gram-negative bacteria. These groups of bacteria synthesize structurally distinct signaling molecules to mediate quorum sensing, where Gram-positive bacteria traditionally utilize small autoinducing peptides (AIPs) and Gram-negatives use small molecules such as acyl-homoserine lactones (AHLs). The structural differences between the types of signaling molecules have historically implied a lack of cross-talk among Gram-positive and Gram-negative quorum sensing systems. Recent investigations, however, have demonstrated the ability for AIPs and AHLs to be produced by non-canonical organisms, implying quorum sensing systems may be more universally recognized than previously hypothesized. With that in mind, our interests were piqued by the organisms Lactobacillus plantarum, a Gram-positive commensal probiotic known to participate in AIP-mediated quorum sensing, and Pseudomonas aeruginosa, a characterized Gram-negative pathogen whose virulence is in part controlled by AHL-mediated quorum sensing. Both health-related organisms are known to inhabit the human gut in various instances, both are characterized to elicit distinct effects on host immunity, and some studies hint at the putative ability of L. plantarum to degrade AHLs produced by P. aeruginosa. We therefore wanted to determine if L. plantarum cultures would respond to the addition of N-(3-oxododecanoyl)-L-homoserine lactone (3OC12) from P. aeruginosa by analyzing changes on both the transcriptome and proteome over time. Based on the observed upregulation of various two-component systems, response regulators, and native quorum sensing related genes, the resulting data provide evidence of an AHL recognition and response by L. plantarum

The Microarcsecond Sky and Cosmic Turbulence

Radio waves are imprinted with propagation effects from ionized media through which they pass. Owing to electron density fluctuations, compact sources (pulsars, masers, and compact extragalactic sources) can display a wide variety of scattering effects. These scattering effects, particularly interstellar scintillation, can be exploited to provide *superresolution*, with achievable angular resolutions (<~ 1 microarcsecond) far in excess of what can be obtained by very long baseline interferometry on terrestrial baselines. Scattering effects also provide a powerful sub-AU probe of the microphysics of the interstellar medium, potentially to spatial scales smaller than 100 km, as well as a tracer of the Galactic distribution of energy input into the interstellar medium through a variety of integrated measures. Coupled with future gamma-ray observations, SKA observations also may provide a means of detecting fainter compact gamma-ray sources. Though it is not yet clear that propagation effects due to the intergalactic medium are significant, the SKA will either detect or place stringent constraints on intergalactic scattering.Comment: 20 pages, 8 figures in 8 PostScript files, to appear in "Science with the Square Kilometer Array," eds. C. Carilli and S. Rawlings, New Astronomy Reviews (Elsevier: Amsterdam

Event detection using roles and relationships of entities

A method, system, and computer program product for event detection using roles and relationships of entities are provided in the illustrative embodiments. A training event and a set of entities participating in the training event are identified in a training data. For a first entity in the set of entities, a first role occupied by the entity in the event is determined. A behavior attribute is assigned to the first role. A relationship of the first role with a second role corresponding to a second entity in the set of entities is determined. An event rule is constructed to detect an event corresponding to the training event in new data and comprising a plurality of roles, behavior attributes, and the relationship. The plurality of roles includes the first role and the second role, and the plurality of behavior attributes includes the behavior attribute assigned to the first role.Board of Regents, University of Texas Syste

VAST: An ASKAP Survey for Variables and Slow Transients

The Australian Square Kilometre Array Pathfinder (ASKAP) will give us an unprecedented opportunity to investigate the transient sky at radio wavelengths. In this paper we present VAST, an ASKAP survey for Variables and Slow Transients. VAST will exploit the wide-field survey capabilities of ASKAP to enable the discovery and investigation of variable and transient phenomena from the local to the cosmological, including flare stars, intermittent pulsars, X-ray binaries, magnetars, extreme scattering events, interstellar scintillation, radio supernovae and orphan afterglows of gamma ray bursts. In addition, it will allow us to probe unexplored regions of parameter space where new classes of transient sources may be detected. In this paper we review the known radio transient and variable populations and the current results from blind radio surveys. We outline a comprehensive program based on a multi-tiered survey strategy to characterise the radio transient sky through detection and monitoring of transient and variable sources on the ASKAP imaging timescales of five seconds and greater. We also present an analysis of the expected source populations that we will be able to detect with VAST.Comment: 29 pages, 8 figures. Submitted for publication in Pub. Astron. Soc. Australi