ALBERT

Description: Motivation: Ultra-high-throughput sequencing produces duplicate and near-duplicate reads, which can consume computational resources in downstream applications. A tool that collapses such reads should reduce storage and assembly complications and costs. Results: We developed Fulcrum to collapse identical and near-identical Illumina and 454 reads (such as those from PCR clones) into single error-corrected sequences; it can process paired-end as well as single-end reads. Fulcrum is customizable and can be deployed on a single machine, a local network or a commercially available MapReduce cluster, and it has been optimized to maximize ease-of-use, cross-platform compatibility and future scalability. Sequence datasets have been collapsed by up to 71%, and the reduced number and improved quality of the resulting sequences allow assemblers to produce longer contigs while using less memory. Availability and implementation: Source code and a tutorial are available at http://pringlelab.stanford.edu/protocols.html under a BSD-like license. Fulcrum was written and tested in Python 2.6, and the single-machine and local-network modes depend on a modified version of the Parallel Python library (provided). Contact: erik.m.lehnert@gmail.com Supplementary information: Supplementary information is available at Bioinformatics online.

Description: In this Letter, we analyse the distributions of stellar ages in giant molecular clouds (GMCs) in spiral arms, interarm spurs and at large galactic radii, where the spiral arms are relatively weak. We use the results of numerical simulations of galaxies, which follow the evolution of GMCs and include star particles where star formation events occur. We find that GMCs in spiral arms tend to have predominantly young (〈10 Myr) stars. By contrast, clouds which are the remainders of spiral arm giant molecular asssociations that have been sheared into interarm GMCs contain fewer young (〈10 Myr) stars and more ~20 Myr stars. We also show that clouds which form in the absence of spiral arms, due to local gravitational and thermal instabilities, contain preferentially young stars. We propose that the age distributions of stars in GMCs will be a useful diagnostic to test different cloud evolution scenarios, the origin of spiral arms and the success of numerical models of galactic star formation. We discuss the implications of our results in the context of Galactic and extragalactic molecular clouds.

Description: In a single well-mixed population, equally abundant neutral alleles are equally likely to persist. However, in spatially complex populations structured by an asymmetric dispersal mechanism, such as a coastal population where larvae are predominantly moved downstream by currents, the eventual frequency of neutral haplotypes will depend on their initial spatial location. In our study of the progression of two spatially separate, genetically distinct introductions of the European green crab (Carcinus maenas) along the coast of eastern North America, we captured this process in action. We documented the shift of the genetic cline in this species over 8 y, and here we detail how the upstream haplotypes are beginning to dominate the system. This quantification of an evolving genetic boundary in a coastal system demonstrates that novel genetic alleles or haplotypes that arise or are introduced into upstream retention zones (regions whose export of larvae is not balanced by import from elsewhere) will increase in frequency in the entire system. This phenomenon should be widespread when there is asymmetrical dispersal, in the oceans or on land, suggesting that the upstream edge of a species’ range can influence genetic diversity throughout its distribution. Efforts to protect the upstream edge of an asymmetrically dispersing species’ range are vital to conserving genetic diversity in the species.

Description: We investigate cloud–cloud collisions and giant molecular cloud evolution in hydrodynamic simulations of isolated galaxies. The simulations include heating and cooling of the interstellar medium (ISM), self-gravity and stellar feedback. Over time-scales 〈5 Myr most clouds undergo no change, and mergers and splits are found to be typically two-body processes, but evolution over longer time-scales is more complex and involves a greater fraction of intercloud material. We find that mergers or collisions occur every 8–10 Myr (1/15th of an orbit) in a simulation with spiral arms, and once every 28 Myr (1/5th of an orbit) with no imposed spiral arms. Both figures are higher than expected from analytic estimates, as clouds are not uniformly distributed in the galaxy. Thus, clouds can be expected to undergo between zero and a few collisions over their lifetime. We present specific examples of cloud–cloud interactions in our results, including synthetic CO maps. We would expect cloud–cloud interactions to be observable, but find they appear to have little or no impact on the ISM. Due to a combination of the clouds’ typical geometries, and moderate velocity dispersions, cloud–cloud interactions often better resemble a smaller cloud nudging a larger cloud. Our findings are consistent with the view that spiral arms make little difference to overall star formation rates in galaxies, and we see no evidence that collisions likely produce massive clusters. However, to confirm the outcome of such massive cloud collisions we ideally need higher resolution simulations.

Description: Coral reefs provide habitats for a disproportionate number of marine species relative to the small area of the oceans that they occupy. The mutualism between the cnidarian animal hosts and their intracellular dinoflagellate symbionts provides the nutritional foundation for coral growth and formation of reef structures, because algal photosynthesis can provide 〉90% of the total energy of the host. Disruption of this symbiosis ("coral bleaching") is occurring on a large scale due primarily to anthropogenic factors and poses a major threat to the future of coral reefs. Despite the importance of this symbiosis, the cellular mechanisms involved in its establishment, maintenance, and breakdown remain largely unknown. We report our continued development of genomic tools to study these mechanisms in Aiptasia , a small sea anemone with great promise as a model system for studies of cnidarian–dinoflagellate symbiosis. Specifically, we have generated de novo assemblies of the transcriptomes of both a clonal line of symbiotic anemones and their endogenous dinoflagellate symbionts. We then compared transcript abundances in animals with and without dinoflagellates. This analysis identified 〉900 differentially expressed genes and allowed us to generate testable hypotheses about the cellular functions affected by symbiosis establishment. The differentially regulated transcripts include 〉60 encoding proteins that may play roles in transporting various nutrients between the symbiotic partners; many more encoding proteins functioning in several metabolic pathways, providing clues regarding how the transported nutrients may be used by the partners; and several encoding proteins that may be involved in host recognition and tolerance of the dinoflagellate.

Description: This paper explores how the stochastic accretion of planetesimals on to white dwarfs would be manifested in observations of their atmospheric pollution. Archival observations of pollution levels for unbiased samples of DA and non-DA white dwarfs are used to derive the distribution of inferred accretion rates, confirming that rates become systematically lower as sinking time (assumed here to be dominated by gravitational settling) is decreased, with no discernable dependence on cooling age. The accretion rates expected from planetesimals that are all the same mass (i.e., a mono-mass distribution) are explored both analytically and using a Monte Carlo model, quantifying how measured accretion rates inevitably depend on sinking time, since different sinking times probe different times since the last accretion event. However, that dependence is so dramatic that a mono-mass distribution can be excluded within the context of this model. Consideration of accretion from a broad distribution of planetesimal masses uncovers an important conceptual difference: accretion is continuous (rather than stochastic) for planetesimals below a certain mass, and the accretion of such planetesimals determines the rate typically inferred from observations; smaller planetesimals dominate the rates for shorter sinking times. A reasonable fit to the observationally inferred accretion rate distributions is found with model parameters consistent with a collisionally evolved mass distribution up to Pluto-mass, and an underlying accretion rate distribution consistent with that expected from descendants of debris discs of main-sequence A stars. With these parameters, while both DA and non-DA white dwarfs accrete from the same broad planetesimal distribution, this model predicts that the pollution seen in DAs is dominated by the continuous accretion of 〈35 km objects, and that in non-DAs by 〉35 km objects (though the dominant size varies between stars by around an order of magnitude from this reference value). Furthermore, observations that characterize the dependence of inferred accretion rates on sinking time and cooling age (including a consideration of the effect of thermohaline convection on models used to derive those rates), and the decadal variability of DA accretion signatures, will improve constraints on the mass distribution of accreted material and the lifetime of the disc through which it is accreted.

Description: The area around the town of Northwich in Cheshire, U. K., has a long history of catastrophic ground subsidence caused by a combination of natural dissolution and collapsing abandoned mine workings within the underlying Triassic halite bedrock geology. In the village of Marston, the Trent and Mersey Canal crosses several abandoned salt mine workings and previously subsiding areas, the canal being breached by a catastrophic subsidence event in 1953. This canal section is the focus of a long-term monitoring study by conventional geotechnical topographic and microgravity surveys. Results of 20 years of topographic time-lapse surveys indicate specific areas of local subsidence that could not be predicted by available site and mine abandonment plan and shaft data. Subsidence has subsequently necessitated four phases of temporary canal bank remediation. Ten years of microgravity time-lapse data have recorded major deepening negative anomalies in specific sections that correlate with topographic data. Gravity 2D modeling using available site data found upwardly propagating voids, and associated collapse material produced a good match with observed microgravity data. Intrusive investigations have confirmed a void at the major anomaly. The advantages of undertaking such long-term studies for near-surface geophysicists, geotechnical engineers, and researchers working in other application areas are discussed.