ALBERT

Description: Biotic gas generation from the degradation of organic carbon in marine sediments supplies and maintains gas hydrates throughout the world’s oceans. In nascent, ultraslow-spreading ocean basins, methane generation can also be abiotic, occurring during the high-temperature (〉200 °C) serpentinization of ultramafic rocks. Here, we report on the evolution of a growing Arctic gas- and gas hydrate–charged sediment drift on oceanic crust in eastern Fram Strait, a tectonically controlled, deep-water gateway between the subpolar North Atlantic and Arctic Oceans. Ultraslow-spreading ridges between northwest Svalbard and northeast Greenland permit the sustained interaction of a mid-ocean ridge transform fault and developing sediment drift, on both young (〈10 Ma) and old (〉10 Ma) oceanic crust, since the late Miocene. Geophysical data image the gas-charged drift and crustal structure and constrain the timing of a major 30 km lateral displacement of the drift across the Molloy transform fault. We describe the buildup of a 2 m.y., long-lived gas hydrate– and free gas–charged drift system on young oceanic crust that may be fed and maintained by a dominantly abiotic methane source. Ultraslow-spreading, sedimented ridge flanks represent a previously unrecognized carbon reservoir for abiotic methane that could supply and maintain deep-water methane hydrate systems throughout the Arctic.

Description: This is a personal history of my structural studies of icosahedral viruses that evolved from crystallographic studies, to hybrid methods with electron cryo-microscopy and image reconstruction (cryoEM) and then developed further by incorporating a variety of physical methods to augment the high resolution crystallographic studies. It is not meant to be comprehensive, even for my own work, but hopefully provides some perspective on the growth of our understanding of these remarkable biologic assemblies. The goal is to provide a historical perspective for those new to the field and to emphasize the limitations of any one method, even those that provide atomic resolution information about viruses.

Description: Redox-sensitive detrital grains such as pyrite and uraninite in sedimentary successions provide one of the most conspicuous geological clues to a different composition of the Archean and early Paleoproterozoic atmosphere. Today, these minerals are rapidly chemically weathered within short transport distances. Prior to the rise of oxygen, low O 2 concentrations allowed their survival in siliciclastic deposits with grain erosion tied only to physical transport processes. After the rise of oxygen, redox-sensitive detrital grains effectively vanish from the sedimentary record. To get a better understanding of the timing of this transition, we examined sandstones recorded in a scientific drill core from the South African 2.415 Ga Koegas Subgroup, a mixed siliciclastic and iron formation–bearing unit deposited on the western deltaic margin of the Kaapvaal craton in early Paleoproterozoic time. We observed detrital pyrite and uraninite grains throughout all investigated sandstone beds in the section, indicating the rise of oxygen is younger than 2.415 Ga. To better understand how observations of detrital pyrite and uraninite in sedimentary rocks can quantitatively constrain Earth surface redox conditions, we constructed a model of grain erosion from chemical weathering and physical abrasion to place an upper limit on ancient environmental O 2 concentrations. Even conservative model calculations for deltaic depositional systems with sufficient transport distances (approximately hundreds of kilometers) show that redox-sensitive detrital grains are remarkably sensitive to environmental O 2 concentrations, and they constrain the Archean and early Paleoproterozoic atmosphere to have 〈3.2 x 10 –5 atm of molecular O 2 . These levels are lower than previously hypothesized for redox-sensitive detrital grains, but they are consistent with estimates made from other redox proxy data, including the anomalous fractionation of sulfur isotopes. The binary loss of detrital pyrite and uraninite from the sedimentary record coincident with the rise of oxygen indicates that atmospheric O 2 concentrations rose substantially at this time and were never again sufficiently low (〈0.01 atm) to enable survival and preservation of these grains in short transport systems.

Description: : The Galaxy platform has developed into a fully featured collaborative workbench, with goals of inherently capturing provenance to enable reproducible data analysis, and of making it straightforward to run one’s own server. However, many Galaxy platform tools rely on the presence of reference data, such as alignment indexes, to function efficiently. Until now, the building of this cache of data for Galaxy has been an error-prone manual process lacking reproducibility and provenance. The Galaxy Data Manager framework is an enhancement that changes the management of Galaxy’s built-in data cache from a manual procedure to an automated graphical user interface (GUI) driven process, which contains the same openness, reproducibility and provenance that is afforded to Galaxy’s analysis tools. Data Manager tools allow the Galaxy administrator to download, create and install additional datasets for any type of reference data in real time. Availability and implementation: The Galaxy Data Manager framework is implemented in Python and has been integrated as part of the core Galaxy platform. Individual Data Manager tools can be defined locally or installed from a ToolShed, allowing the Galaxy community to define additional Data Manager tools as needed, with full versioning and dependency support. Contact: dan@bx.psu.edu . or anton@bx.psu.edu Supplementary information: Supplementary data is available at Bioinformatics online.

Description: Motivation: Cancer researchers seeking immunotherapy targets in cancer cells need tools to locate highly expressed proteins unique to cancer cells. Missense mutation and frameshift location reporter (MMuFLR), a Galaxy-based workflow, analyzes next-generation sequencing paired read RNA-seq output to reliably identify small frameshift mutations and missense mutations in highly expressed protein-coding genes. MMuFLR ignores known SNPs, low quality reads and poly-A/T sequences. For each frameshift and missense mutation identified, MMuFLR provides the location and sequence of the amino acid substitutions in the novel protein candidates for direct input into epitope evaluation tools. Availability: http://toolshed.g2.bx.psu.edu/ Contact: rath0096@umn.edu or johns198@umn.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: The DNA structure in phage capsids is determined by DNA–DNA interactions and bending energy. The effects of repulsive interactions on DNA interaxial distance were previously investigated, but not the effect of DNA bending on its structure in viral capsids. By varying packaged DNA length and through addition of spermine ions, we transform the interaction energy from net repulsive to net attractive. This allowed us to isolate the effect of bending on the resulting DNA structure. We used single particle cryo-electron microscopy reconstruction analysis to determine the interstrand spacing of double-stranded DNA encapsidated in phage capsids. The data reveal that stress and packing defects, both resulting from DNA bending in the capsid, are able to induce a long-range phase transition in the encapsidated DNA genome from a hexagonal to a cholesteric packing structure. This structural observation suggests significant changes in genome fluidity as a result of a phase transition affecting the rates of viral DNA ejection and packaging.

Description: We developed an algorithm named ViReMa (Viral-Recombination-Mapper) to provide a versatile platform for rapid, sensitive and nucleotide-resolution detection of recombination junctions in viral genomes using next-generation sequencing data. Rather than mapping read segments of pre-defined lengths and positions, ViReMa dynamically generates moving read segments. ViReMa initially attempts to align the 5' end of a read to the reference genome(s) with the Bowtie seed-based alignment. A new read segment is then made by either extracting any unaligned nucleotides at the 3' end of the read or by trimming the first nucleotide from the read. This continues iteratively until all portions of the read are either mapped or trimmed. With multiple reference genomes, it is possible to detect virus-to-host or inter-virus recombination. ViReMa is also capable of detecting insertion and substitution events and multiple recombination junctions within a single read. By mapping the distribution of recombination events in the genome of flock house virus, we demonstrate that this information can be used to discover de novo functional motifs located in conserved regions of the viral genome.