Using World of Warcraft to Teach Research Methods in Online Doctoral Education: A Student-Instructor Duoethnography

The educational potential of games has captured the ongoing interest of scholars and educators who have sought to understand when, how, and under what conditions games support the teaching and learning process. General knowledge of how games support literacy, scientific thinking, or social learning has been theorized and researched, but some applications of game-based learning remain unexplored. One area where much remains to be learned is within online doctoral education and particularly in the poorly understood area of research methods education. In this study, three doctoral students and an instructor collaboratively fieldtested a set of instructional activities within World of Warcraft that were designed to promote understanding of qualitative research methods. A duoethnographic approach was used to promote dual-perspective dialogue about the merits and challenges of using online gaming environments as field sites where research methods can be practiced and developed. Results illuminate merits, challenges, and areas of development as researchers that surfaced while completing the research methods activities. Directions for further research are suggested

Challenges for Coring Deep Permafrost on Earth and Mars

This is the published version. Final publication is available from Mary Ann Liebert, Inc., publishers http://www.dx.doi.org/10.1089/ast.2007.0159.A scientific drilling expedition to the High Lake region of Nunavut, Canada, was recently completed with the goals of collecting samples and delineating gradients in salinity, gas composition, pH, pe, and microbial abundance in a 400 m thick permafrost zone and accessing the underlying pristine subpermafrost brine. With a triple-barrel wireline tool and the use of stringent quality assurance and quality control (QA/QC) protocols, 200 m of frozen, Archean, mafic volcanic rock was collected from the lower boundary that separates the permafrost layer and subpermafrost saline water. Hot water was used to remove cuttings and prevent the drill rods from freezing in place. No cryopegs were detected during penetration through the permafrost. Coring stopped at the 535 m depth, and the drill water was bailed from the hole while saline water replaced it. Within 24 hours, the borehole iced closed at 125 m depth due to vapor condensation from atmospheric moisture and, initially, warm water leaking through the casing, which blocked further access. Preliminary data suggest that the recovered cores contain viable anaerobic microorganisms that are not contaminants even though isotopic analyses of the saline borehole water suggests that it is a residue of the drilling brine used to remove the ice from the upper, older portion of the borehole. Any proposed coring mission to Mars that seeks to access subpermafrost brine will not only require borehole stability but also a means by which to generate substantial heating along the borehole string to prevent closure of the borehole from condensation of water vapor generated by drilling. Astrobiology 8, 623–638

Sequence of the hyperplastic genome of the naturally competent Thermus scotoductus SA-01

<p>Abstract</p> <p>Background</p> <p>Many strains of <it>Thermus </it>have been isolated from hot environments around the world. <it>Thermus scotoductus </it>SA-01 was isolated from fissure water collected 3.2 km below surface in a South African gold mine. The isolate is capable of dissimilatory iron reduction, growth with oxygen and nitrate as terminal electron acceptors and the ability to reduce a variety of metal ions, including gold, chromate and uranium, was demonstrated. The genomes from two different <it>Thermus thermophilus </it>strains have been completed. This paper represents the completed genome from a second <it>Thermus </it>species - <it>T. scotoductus</it>.</p> <p>Results</p> <p>The genome of <it>Thermus scotoductus </it>SA-01 consists of a chromosome of 2,346,803 bp and a small plasmid which, together are about 11% larger than the <it>Thermus thermophilus </it>genomes. The <it>T. thermophilus </it>megaplasmid genes are part of the <it>T. scotoductus </it>chromosome and extensive rearrangement, deletion of nonessential genes and acquisition of gene islands have occurred, leading to a loss of synteny between the chromosomes of <it>T. scotoductus and T. thermophilus</it>. At least nine large inserts of which seven were identified as alien, were found, the most remarkable being a denitrification cluster and two operons relating to the metabolism of phenolics which appear to have been acquired from <it>Meiothermus ruber</it>. The majority of acquired genes are from closely related species of the Deinococcus-Thermus group, and many of the remaining genes are from microorganisms with a thermophilic or hyperthermophilic lifestyle. The natural competence of <it>Thermus scotoductus </it>was confirmed experimentally as expected as most of the proteins of the natural transformation system of <it>Thermus thermophilus </it>are present. Analysis of the metabolic capabilities revealed an extensive energy metabolism with many aerobic and anaerobic respiratory options. An abundance of sensor histidine kinases, response regulators and transporters for a wide variety of compounds are indicative of an oligotrophic lifestyle.</p> <p>Conclusions</p> <p>The genome of <it>Thermus scotoductus </it>SA-01 shows remarkable plasticity with the loss, acquisition and rearrangement of large portions of its genome compared to <it>Thermus thermophilus</it>. Its ability to naturally take up foreign DNA has helped it adapt rapidly to a subsurface lifestyle in the presence of a dense and diverse population which acted as source of nutrients. The genome of <it>Thermus scotoductus </it>illustrates how rapid adaptation can be achieved by a highly dynamic and plastic genome.</p

A genomic catalog of Earth’s microbiomes

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes

Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations

Microorganisms in the terrestrial deep biosphere host up to 20% of the earth's biomass and are suggested to be sustained by the gases hydrogen and carbon dioxide. A metagenome analysis of three deep subsurface water types of contrasting age (from &lt;20 to several thousand years) and depth (171 to 448 m) revealed phylogenetically distinct microbial community subsets that either passed or were retained by a 0.22 mu m filter. Such cells of &lt;0.22 mu m would have been overlooked in previous studies relying on membrane capture. Metagenomes from the three water types were used for reconstruction of 69 distinct microbial genomes, each with &gt;86% coverage. The populations were dominated by Proteobacteria, Candidate divisions, unclassified archaea and unclassified bacteria. The estimated genome sizes of the &lt;0.22 mu m populations were generally smaller than their phylogenetically closest relatives, suggesting that small dimensions along with a reduced genome size may be adaptations to oligotrophy. Shallow 'modern marine' water showed community members with a predominantly heterotrophic lifestyle. In contrast, the deeper, 'old saline' water adhered more closely to the current paradigm of a hydrogen-driven deep biosphere. The data were finally used to create a combined metabolic model of the deep terrestrial biosphere microbial community.Supplementary information available for this article at http://www.nature.com/ismej/journal/v10/n5/suppinfo/ismej2015185s1.html</p

Methane bursts as a trigger for intermittent lake-forming climates on post-Noachian Mars

Lakes existed on Mars later than 3.6 billion years ago, according to sedimentary evidence for deltaic deposition. The observed fluviolacustrine deposits suggest that individual lake-forming climates persisted for at least several thousand years (assuming dilute flow). But the lake watersheds’ little-weathered soils indicate a largely dry climate history, with intermittent runoff events. Here we show that these observational constraints, although inconsistent with many previously proposed triggers for lake-forming climates, are consistent with a methane burst scenario. In this scenario, chaotic transitions in mean obliquity drive latitudinal shifts in temperature and ice loading that destabilize methane clathrate. Using numerical simulations, we find that outgassed methane can build up to atmospheric levels sufficient for lake-forming climates, if methane clathrate initially occupies more than 4% of the total volume in which it is thermodynamically stable. Such occupancy fractions are consistent with methane production by water–rock reactions due to hydrothermal circulation on early Mars. We further estimate that photochemical destruction of atmospheric methane curtails the duration of individual lake-forming climates to less than a million years, consistent with observations. We conclude that methane bursts represent a potential pathway for intermittent excursions to a warm, wet climate state on early Mars

ELECTROLYSIS AND EXTRACTION OF SOME LANTHANONS FROM AQUEOUS ELECTROLYTES WITH LITHIUM AMALGAM

Phase transfer of Pr by electrolysis at a lithium amalgam cathode was found to be linear with time for fixed electrolysis conditions. The rate of electrolysis of Pr decreased with increasing lithium citrate concentration. Extraction of Pm from Pm--Gd mixtures with saturated lithium amalgam was found to vary with virtually any change in electrolyte composition. The Pm extraction was first order with respect to Pm concentration, but the extraction rate decreased with increasing excess citrate concentration. The presence of Gd did not affect the extraction of Pm very much at Gd concentrations less than 0.1 M, but at higher concentrations of Gd the amount of Pm extracted was diminished. The results indicate that the exchange reactions are very fast and it may be possible to interpret rate data in terms of equilibria in the electrolyte phase. (auth

ELECTROLYSIS AND EXTRACTION OF SOME LANTHANONS FROM AQUEOUS ELECTROLYTES WITH LITHIUM AMALGAM

Phase transfer of Pr by electrolysis at a lithium amalgam cathode was found to be linear with time for fixed electrolysis conditions. The rate of electrolysis of Pr decreased with increasing lithium citrate concentration. Extraction of Pm from Pm--Gd mixtures with saturated lithium amalgam was found to vary with virtually any change in electrolyte composition. The Pm extraction was first order with respect to Pm concentration, but the extraction rate decreased with increasing excess citrate concentration. The presence of Gd did not affect the extraction of Pm very much at Gd concentrations less than 0.1 M, but at higher concentrations of Gd the amount of Pm extracted was diminished. The results indicate that the exchange reactions are very fast and it may be possible to interpret rate data in terms of equilibria in the electrolyte phase. (auth