Life in Hot Carbon Monoxide: The Complete Genome Sequence of Carboxydothermus hydrogenoformans Z-2901

We report here the sequencing and analysis of the genome of the thermophilic bacterium Carboxydothermus hydrogenoformans Z-2901. This species is a model for studies of hydrogenogens, which are diverse bacteria and archaea that grow anaerobically utilizing carbon monoxide (CO) as their sole carbon source and water as an electron acceptor, producing carbon dioxide and hydrogen as waste products. Organisms that make use of CO do so through carbon monoxide dehydrogenase complexes. Remarkably, analysis of the genome of C. hydrogenoformans reveals the presence of at least five highly differentiated anaerobic carbon monoxide dehydrogenase complexes, which may in part explain how this species is able to grow so much more rapidly on CO than many other species. Analysis of the genome also has provided many general insights into the metabolism of this organism which should make it easier to use it as a source of biologically produced hydrogen gas. One surprising finding is the presence of many genes previously found only in sporulating species in the Firmicutes Phylum. Although this species is also a Firmicutes, it was not known to sporulate previously. Here we show that it does sporulate and because it is missing many of the genes involved in sporulation in other species, this organism may serve as a “minimal” model for sporulation studies. In addition, using phylogenetic profile analysis, we have identified many uncharacterized gene families found in all known sporulating Firmicutes, but not in any non-sporulating bacteria, including a sigma factor not known to be involved in sporulation previously

Phylogenomics of the Reproductive Parasite Wolbachia pipientis wMel: A Streamlined Genome Overrun by Mobile Genetic Elements

The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are found in a variety of invertebrate species, are of great interest due to their diverse interactions with different hosts, which range from many forms of reproductive parasitism to mutualistic symbioses. Analysis of the wMel genome, in particular phylogenomic comparisons with other intracellular bacteria, has revealed many insights into the biology and evolution of wMel and Wolbachia in general. For example, the wMel genome is unique among sequenced obligate intracellular species in both being highly streamlined and containing very high levels of repetitive DNA and mobile DNA elements. This observation, coupled with multiple evolutionary reconstructions, suggests that natural selection is somewhat inefficient in wMel, most likely owing to the occurrence of repeated population bottlenecks. Genome analysis predicts many metabolic differences with the closely related Rickettsia species, including the presence of intact glycolysis and purine synthesis, which may compensate for an inability to obtain ATP directly from its host, as Rickettsia can. Other discoveries include the apparent inability of wMel to synthesize lipopolysaccharide and the presence of the most genes encoding proteins with ankyrin repeat domains of any prokaryotic genome yet sequenced. Despite the ability of wMel to infect the germline of its host, we find no evidence for either recent lateral gene transfer between wMel and D. melanogaster or older transfers between Wolbachia and any host. Evolutionary analysis further supports the hypothesis that mitochondria share a common ancestor with the α-Proteobacteria, but shows little support for the grouping of mitochondria with species in the order Rickettsiales. With the availability of the complete genomes of both species and excellent genetic tools for the host, the wMel–D. melanogaster symbiosis is now an ideal system for studying the biology and evolution of Wolbachia infections

Efficient supersonic air vehicle design using the Service-Oriented Computing Environment (SORCER)

The Air Force Research Lab’s Multidisciplinary Science and Technology Center is investigating conceptual design processes and computing frameworks that could significantly impact the design of the next generation efficient supersonic air vehicle (ESAV). The ESAV conceptual design process must accommodate appropriate fidelity multidisciplinary engineering analyses (MDAs) to assess the impact of new air vehicle technologies. These analyses may be coupled and computationally expensive, posing a challenge due to the large number of air vehicle configurations analyzed during conceptual design. In light of these observations, a design process using the Service-Oriented Computing Environment (SORCER) software is implemented to combine propulsion, structures, aerodynamics, aeroelasticity, and performance in an integrated MDA. The SORCER software provides the automation and tight integration to grid computing resources necessary to achieve the volume of appropriate fidelity analyses required. Two design studies are performed using a gradient-based optimization method to produce long and short range ESAV wing designs. The studies demonstrate the capability of the ESAV MDA, the optimization algorithm, and the computational scalability and reliability of the SORCER software

Efficient supersonic air vehicle design using the Service-Oriented Computing Environment (SORCER)

The Air Force Research Lab’s Multidisciplinary Science and Technology Center is investigating conceptual design processes and computing frameworks that could significantly impact the design of the next generation efficient supersonic air vehicle (ESAV). The ESAV conceptual design process must accommodate appropriate fidelity multidisciplinary engineering analyses (MDAs) to assess the impact of new air vehicle technologies. These analyses may be coupled and computationally expensive, posing a challenge due to the large number of air vehicle configurations analyzed during conceptual design. In light of these observations, a design process using the Service-Oriented Computing Environment (SORCER) software is implemented to combine propulsion, structures, aerodynamics, aeroelasticity, and performance in an integrated MDA. The SORCER software provides the automation and tight integration to grid computing resources necessary to achieve the volume of appropriate fidelity analyses required. Two design studies are performed using a gradient-based optimization method to produce long and short range ESAV wing designs. The studies demonstrate the capability of the ESAV MDA, the optimization algorithm, and the computational scalability and reliability of the SORCER software

Efficient supersonic air vehicle design using the Service-Oriented Computing Environment (SORCER)

The Air Force Research Lab’s Multidisciplinary Science and Technology Center is investigating conceptual design processes and computing frameworks that could significantly impact the design of the next generation efficient supersonic air vehicle (ESAV). The ESAV conceptual design process must accommodate appropriate fidelity multidisciplinary engineering analyses (MDAs) to assess the impact of new air vehicle technologies. These analyses may be coupled and computationally expensive, posing a challenge due to the large number of air vehicle configurations analyzed during conceptual design. In light of these observations, a design process using the Service-Oriented Computing Environment (SORCER) software is implemented to combine propulsion, structures, aerodynamics, aeroelasticity, and performance in an integrated MDA. The SORCER software provides the automation and tight integration to grid computing resources necessary to achieve the volume of appropriate fidelity analyses required. Two design studies are performed using a gradient-based optimization method to produce long and short range ESAV wing designs. The studies demonstrate the capability of the ESAV MDA, the optimization algorithm, and the computational scalability and reliability of the SORCER software