Movement rules determine nomadic species' responses to resource supplementation and degradation.

In environments that vary unpredictably, many animals are nomadic, moving in an irregular pattern that differs from year to year. Exploring the mechanisms of nomadic movement is needed to understand how animals survive in highly variable environments, and to predict behavioural and population responses to environmental change. We developed a network model to identify plausible mechanisms of nomadic animal movement by comparing the performance of multiple movement rules along a continuum from nomadism to residency. Using simulations and analytical results, we explored how different types of habitat modifications (that augment or decrease resource availability) might affect the abundance and movement rates of animals following each of these rules. Movement rules for which departure from patches depended on resource availability and/or competition performed almost equally well and better than residency or uninformed movement under most conditions, even though animals using each rule moved at substantially different rates. Habitat modifications that stabilized resources, either by resource supplementation or degradation, eroded the benefits of informed nomadic movements, particularly for movements based on resource availability alone. These results suggest that simple movement rules can explain nomadic animal movements and determine species' responses to environmental change. In particular, landscape stabilization and supplementation might be useful strategies for promoting populations of resident animals, but would be less beneficial for managing highly mobile species, many of which are threatened by habitat disruption and changes in climate.

Bench-scale evaluation of aerosol delivery for biostimulation and bioaugmentation in the vadose zone.

Aerosol delivery was evaluated for distributing biostimulation and bioaugmentation amendments in vadose zones. This technique involves transporting amendments as micron-scale aerosol droplets in injected gas. Microcosm experiments were designed to characterize reductive dechlorination of trichloroethene (TCE) under unsaturated conditions when delivering components as aerosols. Delivering amendments and/or microbes as aqueous aerosols resulted in complete dechlorination of TCE, similar to controls operated under saturated conditions. Reductive dechlorination was achieved with manual injection of a bioaugmentation culture suspended in soybean oil into microcosms. However, aerosol delivery of the culture in soybean oil induced little reductive dechlorination activity. Overall, the results indicate that delivery as aqueous aerosols may be a viable option for delivery of amendments to enhance vadose zone bioremediation at the field-scale.

Efficient exploration of chemical space by fragment-based screening.

Screening methods seek to sample a vast chemical space in order to identify starting points for further chemical optimisation. Fragment based drug discovery exploits the superior sampling of chemical space that can be achieved when the molecular weight is restricted. Here we show that commercially available fragment space is still relatively poorly sampled and argue for highly sensitive screening methods to allow the detection of smaller fragments. We analyse the properties of our fragment library versus the properties of X-ray hits derived from the library. We particularly consider properties related to the degree of planarity of the fragments.

Protein-ligand docking against non-native protein conformers.

In the validation of protein-ligand docking protocols, performance is mostly measured against native protein conformers, i.e. each ligand is docked into the protein conformation from the structure that contained that ligand. In real-life applications, however, ligands are docked against non-native conformations of the protein, i.e. the apo structure or a structure of a different protein-ligand complex. Here, we have constructed an extensive test set for assessing docking performance against non-native protein conformations. This new test set is built on the Astex Diverse Set (which we recently constructed for assessing native docking performance) and contains 1112 non-native structures for 65 drug targets. Using the protein-ligand docking program GOLD, the Astex Diverse Set and the new Astex Non-native Set, we established that, whereas docking performance (top-ranked solution within 2 A rmsd of the experimental binding mode) is approximately 80% for native docking, this drops to 61% for non-native docking. A similar drop-off is observed for sampling performance (any solution within 2 A): 91% for native docking vs 72% for non-native docking. No significant differences were observed between docking performance against apo and nonapo structures. We found that, whereas small variations in protein conformation are generally tolerated by our rigid docking protocol, larger protein movements result in a catastrophic drop-off in performance. Some docking performance and nearly all sampling performance can be recovered by considering dockings produced against a small number of non-native structures simultaneously. Docking against non-native structures of complexes containing ligands that are similar to the docked ligand also significantly improves both docking performance and sampling performance.

Rarity value and species extinction: the anthropogenic Allee effect.

Standard economic theory predicts that exploitation alone is unlikely to result in species extinction because of the escalating costs of finding the last individuals of a declining species. We argue that the human predisposition to place exaggerated value on rarity fuels disproportionate exploitation of rare species, rendering them even rarer and thus more desirable, ultimately leading them into an extinction vortex. Here we present a simple mathematical model and various empirical examples to show how the value attributed to rarity in some human activities could precipitate the extinction of rare species-a concept that we term the anthropogenic Allee effect. The alarming finding that human perception of rarity can precipitate species extinction has serious implications for the conservation of species that are rare or that may become so, be they charismatic and emblematic or simply likely to become fashionable for certain activities.