Computer Science Applications


Publications
35

Increased Biosynthetic Gene Dosage in a Genome-Reduced Defensive Bacterial Symbiont

Citation
Lopera et al. (2017). mSystems 2 (6)
Names
“Didemniditutus” “Didemniditutus mandelae”
Abstract
Secondary metabolites, which are small-molecule organic compounds produced by living organisms, provide or inspire drugs for many different diseases. These natural products have evolved over millions of years to provide a survival benefit to the producing organism and often display potent biological activity with important therapeutic applications. For instance, defensive compounds in the environment may be cytotoxic to eukaryotic cells, a property exploitable for cancer treatment. Here, we desc

Genome-Enabled Insights into the Ecophysiology of the Comammox Bacterium “ Candidatus Nitrospira nitrosa”

Citation
Camejo et al. (2017). mSystems 2 (5)
Names
Ca. Nitrospira nitrosa
Abstract
Nitrospira -like bacteria are among the most diverse and widespread nitrifiers in natural ecosystems and the dominant nitrite oxidizers in wastewater treatment plants (WWTPs). The recent discovery of comammox-like Nitrospira strains, capable of complete oxidation of ammonia to nitrate, raises new questions about specific traits responsible for the functional versatility and adaptation of this genus to a variety of environments. The availability of

Metatranscriptomics Supports the Mechanism for Biocathode Electroautotrophy by “ Candidatus Tenderia electrophaga”

Citation
Eddie et al. (2017). mSystems 2 (2)
Names
Tenderia electrophaga Ts
Abstract
Bacteria that directly use electrodes as metabolic electron donors (biocathodes) have been proposed for applications ranging from microbial electrosynthesis to advanced bioelectronics for cellular communication with machines. However, just as we understand very little about oxidation of analogous natural insoluble electron donors, such as iron oxide, the organisms and extracellular electron transfer (EET) pathways underlying the electrode-cell direct electron transfer processes are

Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids

Citation
Jungbluth et al. (2017). Scientific Data 4 (1)
Names
“Geothermarchaeota” “Hydrothermota” Hydrothermus pacificus Ts Hydrothermarchaeum profundi Ts “Hydrothermarchaeota”
Abstract
AbstractThe global deep subsurface biosphere is one of the largest reservoirs for microbial life on our planet. This study takes advantage of new sampling technologies and couples them with improvements to DNA sequencing and associated informatics tools to reconstruct the genomes of uncultivated Bacteria and Archaea from fluids collected deep within the Juan de Fuca Ridge subseafloor. Here, we generated two metagenomes from borehole observatories located 311 meters apart and, using binning tools

Proteome Remodeling in Response to Sulfur Limitation in “ Candidatus Pelagibacter ubique”

Citation
Smith et al. (2016). mSystems 1 (4)
Names
Ca. Pelagibacter ubique
Abstract
“ Ca . Pelagibacter ubique” is a key driver of marine biogeochemistry cycles and a model for understanding how minimal genomes evolved in free-living anucleate organisms. This study explores the unusual sulfur acquisition strategy that has evolved in these cells, which lack assimilatory sulfate reduction and instead rely on reduced sulfur compounds found in oxic marine environments to meet their cellular quotas. Our findings demonstrate that the sulfur acquis