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Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'

<p>Abstract</p> <p>Background</p> <p>Metagenomic sequence data are proving to be a vast resource for the discovery of biological components. Yet analysis of this data to identify functional RNAs lags behind efforts to characterize protein diversity. The genome of '<it>Candidatus </it>Pelagibacter ubique' HTCC 1062 is the closest match for approximately 20% of marine metagenomic sequence reads. It is also small, contains little non-coding DNA, and has strikingly low GC content.</p> <p>Results</p> <p>To aid the discovery of RNA motifs within the marine metagenome we exploited the genomic properties of '<it>Cand</it>. P. ubique' by targeting our search to long intergenic regions (IGRs) with relatively high GC content. Analysis of known RNAs (rRNA, tRNA, riboswitches etc.) shows that structured RNAs are significantly enriched in such IGRs. To identify additional candidate structured RNAs, we examined other IGRs with similar characteristics from '<it>Cand</it>. P. ubique' using comparative genomics approaches in conjunction with marine metagenomic data. Employing this strategy, we discovered four candidate structured RNAs including a new riboswitch class as well as three additional likely <it>cis</it>-regulatory elements that precede genes encoding ribosomal proteins S2 and S12, and the cytoplasmic protein component of the signal recognition particle. We also describe four additional potential RNA motifs with few or no examples occurring outside the metagenomic data.</p> <p>Conclusion</p> <p>This work begins the process of identifying functional RNA motifs present in the metagenomic data and illustrates how existing completed genomes may be used to aid in this task.</p

Emerging technologies for the integration and intensification of downstream bioprocesses

Downstream processing is currently the major bottleneck for bioproduct generation. In contrast to the advances in fermentation processes, the tools used for downstream processes have struggled to keep pace in the last 20 years. Purification bottlenecks are quite serious, as these processes can account for up to 80% of the total production cost. Coupled with the emergence of new classes of bioproducts, for example, virus-like particles or plasmidic DNA, this has created a great need for superior alternatives. In this review, improved downstream technologies, including aqueous two-phase systems, expanded bed adsorption chromatography, convective flow systems, and fibre-based adsorbent systems, have been discussed. These adaptive methods are more suited to the burgeoning downstream processing needs of the future, enabling the cost-efficient production of new classes biomaterials with a high degree of purity, and thereby hold the promise to become indispensable tools in the pharmaceutical and food industries.Fil: D’Souza, Roy N.. Universitat Bremen; AlemaniaFil: Azevedo, Ana M.. Universidad de Lisboa; PortugalFil: Aires Barros, M. Raquel. Universidad de Lisboa; PortugalFil: Krajnc, Nika Lendero. BIA Separations; EsloveniaFil: Kramberger, Petra. BIA Separations; EsloveniaFil: Carbajal, Maria Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto Multidisciplinario de Biología Celular. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Instituto Multidisciplinario de Biología Celular. Universidad Nacional de La Plata. Instituto Multidisciplinario de Biología Celular; ArgentinaFil: Grasselli, Mariano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto Multidisciplinario de Biología Celular. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Instituto Multidisciplinario de Biología Celular. Universidad Nacional de La Plata. Instituto Multidisciplinario de Biología Celular; ArgentinaFil: Meyer, Ronald. Universitat Bremen; AlemaniaFil: Fernandez Lahore, Marcelo. Universitat Bremen; Alemani

An Optical Precursor to the Recent X-ray Outburst of the Black Hole Binary GRO J1655-40

The All Sky Monitor on the Rossi X-ray Timing Explorer detected an X-ray (2-12 keV) outburst from the black hole binary GRO J1655-40 beginning near April 25, 1996. Optical photometry obtained April 20-24, 1996 shows a steady brightening of the source in B, V, R, and I beginning about six days before the start of the X-ray outburst. The onset of the optical brightening was earliest in I and latest in B. However, the rate of the optical brightening was fastest in B and slowest in I. The order of the increases in the different optical filters suggests that the event was an "outside-in" disturbance of the accretion disk. The substantial delay between the optical rise and the rise of the X-rays may provide indirect support for the advection-dominated accretion flow model of the inner regions of the accretion disk.Comment: 8 pages, 2 figures, Latex (uses the standard AAS style file aas2pp4.sty), accepted for publication in the ApJ Letter

Predicting distributions of known and unknown reptile species in Madagascar

Despite the importance of tropical biodiversity(1), informative species distributional data are seldom available for biogeographical study or setting conservation priorities(2,3). Modelling ecological niche distributions of species offers a potential soluion(4-7); however, the utility of old locality data from museums, and of more recent remotely sensed satellite data, remains poorly explored, especially for rapidly changing tropical landscapes. Using 29 modern data sets of environmental land coverage and 621 chameleon occurrence localities from Madagascar ( historical and recent), here we demonstrate a significant ability of our niche models in predicting species distribution. At 11 recently inventoried sites, highest predictive success (85.1%) was obtained for models based only on modern occurrence data (74.7% and 82.8% predictive success, respectively, for pre-1978 and all data combined). Notably, these models also identified three intersecting areas of over-prediction that recently yielded seven chameleon species new to science. We conclude that ecological niche modelling using recent locality records and readily available environmental coverage data provides informative biogeographical data for poorly known tropical landscapes, and offers innovative potential for the discovery of unknown distributional areas and unknown species.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62843/1/nature02205.pd

Influence of Race on the Female Athlete Triad

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An AMR Study of the Common Envelope Phase of Binary Evolution

The hydrodynamic evolution of the common envelope phase of a low mass binary composed of a 1.05 Msun red giant and a 0.6 Msun companion has been followed for five orbits of the system using a high resolution method in three spatial dimensions. During the rapid inspiral phase, the interaction of the companion with the red giant's extended atmosphere causes about 25% of the common envelope to be ejected from the system, with mass continuing to be lost at the end of the simulation at a rate ~ 2 Msun/yr. In the process the resulting loss of angular momentum and energy reduces the orbital separation by a factor of seven. After this inspiral phase the eccentricity of the orbit rapidly decreases with time. The gravitational drag dominates hydrodynamic drag at all times in the evolution, and the commonly-used Bondi-Hoyle-Lyttleton prescription for estimating the accretion rate onto the companion significantly overestimates the true rate. On scales comparable to the orbital separation, the gas flow in the orbital plane in the vicinity of the two cores is subsonic with the gas nearly corotating with the red giant core and circulating about the red giant companion. On larger scales, 90% of the outflow is contained within 30 degrees of the orbital plane, and the spiral shocks in this material leave an imprint on the density and velocity structure. Of the energy released by the inspiral of the cores, only about 25% goes toward ejection of the envelope.Comment: 18 pages, 11 figures, submitted to ApJ; accepted versio

The Global Emerging Infection Surveillance and Response System (GEIS), a U.S. government tool for improved global biosurveillance: a review of 2009

The Armed Forces Health Surveillance Center, Global Emerging Infections Surveillance and Response System (AFHSC-GEIS) has the mission of performing surveillance for emerging infectious diseases that could affect the United States (U.S.) military. This mission is accomplished by orchestrating a global portfolio of surveillance projects, capacity-building efforts, outbreak investigations and training exercises. In 2009, this portfolio involved 39 funded partners, impacting 92 countries. This article discusses the current biosurveillance landscape, programmatic details of organization and implementation, and key contributions to force health protection and global public health in 2009

A10 – Human Factors Considerations of UAS Procedures and Control Stations: Tasks PC-1 through PC-3 Pilot and Crew (PC) Subtask, Recommended Requirements and Operational Procedures

The Alliance for System Safety of UAS through Research Excellence (ASSURE) conducted research focused on minimum pilot procedures and operational practices used by unmanned aircraft systems (UAS) operators today for the purpose of developing recommendations. This research recommends four pilot and 46 operational minimum procedures to operate a civil single-engine, fixed-wing, single-pilot-configured UAS flying in beyond visual line-of-sight (BVLOS) conditions. These recommendations are anticipated to support potential future aircrew procedure requirements for UAS larger than 55 lbs. operating in the National Airspace System (NAS). These procedures were validated using representative Control Stations in simulated environments