United States Department of Energy

About: United States Department of Energy is a government organization based out in Washington D.C., District of Columbia, United States. It is known for research contribution in the topics: Coal & Catalysis. The organization has 13656 authors who have published 14177 publications receiving 556962 citations. The organization is also known as: DOE & Department of Energy.

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

Abstract: Microbiomes from every environment contain a myriad of uncultivated archaeal and bacterial viruses, but studying these viruses is hampered by the lack of a universal, scalable taxonomic framework. We present vConTACT v.2.0, a network-based application utilizing whole genome gene-sharing profiles for virus taxonomy that integrates distance-based hierarchical clustering and confidence scores for all taxonomic predictions. We report near-identical (96%) replication of existing genus-level viral taxonomy assignments from the International Committee on Taxonomy of Viruses for National Center for Biotechnology Information virus RefSeq. Application of vConTACT v.2.0 to 1,364 previously unclassified viruses deposited in virus RefSeq as reference genomes produced automatic, high-confidence genus assignments for 820 of the 1,364. We applied vConTACT v.2.0 to analyze 15,280 Global Ocean Virome genome fragments and were able to provide taxonomic assignments for 31% of these data, which shows that our algorithm is scalable to very large metagenomic datasets. Our taxonomy tool can be automated and applied to metagenomes from any environment for virus classification.

Genomic islands and the ecology and evolution of Prochlorococcus

Abstract: Prochlorococcus ecotypes are a useful system for exploring the origin and function of diversity among closely related microbes. The genetic variability between phenotypically distinct strains that differ by less that 1% in 16S ribosomal RNA sequences occurs mostly in genomic islands. Island genes appear to have been acquired in part by phage-mediated lateral gene transfer, and some are differentially expressed under light and nutrient stress. Furthermore, genome fragments directly recovered from ocean ecosystems indicate that these islands are variable among cooccurring Prochlorococcus cells. Genomic islands in this free-living photoautotroph share features with pathogenicity islands of parasitic bacteria, suggesting a general mechanism for niche differentiation in microbial species.

Adsorption of CO2 on Zeolites at Moderate Temperatures

Abstract: Pressure swing adsorption (PSA) and temperature swing adsorption (TSA) are potential techniques for removing carbon dioxide (CO2) from high-pressure fuel gas streams. Zeolites are suitable candidate sorbents for use in these processes; however, the systems would be even more energy efficient if the sorbents were operational at moderate or high temperatures, especially for the removal of CO2 from high-pressure gas streams, such as those from integrated gasification combined-cycle (IGCC) systems. Competitive gas adsorption tests with gas mixtures representing both coal combustion and coal gasification gas streams were conducted in an atmospheric flow reactor with five zeolites at 120 °C. Promising results of preferential adsorption of CO2 were observed with two of these zeolites. However, the CO2 adsorption capacity was significantly lower at 120 °C than at ambient temperature. Volumetric gas adsorption tests of CO2 and nitrogen (N2) on these two zeolites were conducted at 120 °C, up to a pressure of 300 ps...

Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris

Abstract: Thermostable enzymes and thermophilic cell factories may afford economic advantages in the production of many chemicals and biomass-based fuels. Here we describe and compare the genomes of two thermophilic fungi, Myceliophthora thermophila and Thielavia terrestris. To our knowledge, these genomes are the first described for thermophilic eukaryotes and the first complete telomere-to-telomere genomes for filamentous fungi. Genome analyses and experimental data suggest that both thermophiles are capable of hydrolyzing all major polysaccharides found in biomass. Examination of transcriptome data and secreted proteins suggests that the two fungi use shared approaches in the hydrolysis of cellulose and xylan but distinct mechanisms in pectin degradation. Characterization of the biomass-hydrolyzing activity of recombinant enzymes suggests that these organisms are highly efficient in biomass decomposition at both moderate and high temperatures. Furthermore, we present evidence suggesting that aside from representing a potential reservoir of thermostable enzymes, thermophilic fungi are amenable to manipulation using classical and molecular genetics.