Convergence of molecular dynamics simulations of membrane proteins

The central question in evaluating almost any result from a molecular dynamics simulation is whether the calculation has converged. Unfortunately, assessing the ergodicity of a single trajectory is very difficult to do. In this work, we assess the sampling of molecular dynamics simulations of the membrane protein rhodopsin by comparing the results from 26 independent trajectories, each run for 100 ns. By examining principal components and cluster populations, we show that rhodopsin's fluctuations are not well described by 100 ns of dynamics, and that the sampling is not fully converged even for individual loops. The results serve as a reminder of the caution required when interpreting molecular dynamics simulations of macromolecules.     

Cooperative hunting behavior,prey selectivity and prey handling by pack ice killer whales (Orcinus orca), type B,in Antarctic Peninsula waters

Currently, there are three recognized ecotypes (or species) of killer whales (Orcinus orca) in Antarctic waters, including type B, a putative prey specialist on seals, which we refer to as “pack ice killer whale” (PI killer whale). During January 2009, we spent a total of 75.4 h observing three different groups of PI killer whales hunting off the western Antarctic Peninsula. Observed prey taken included 16 seals and 1 Antarctic minke whale (Balaenoptera bonaerensis). Weddell seals (Leptonychotes weddellii) were taken almost exclusively (14/15 identified seal kills), despite the fact that they represented only 15% of 365 seals identified on ice floes; the whales entirely avoided taking crabeater seals (Lobodon carcinophaga; 82% relative abundance) and leopard seals (Hydrurga leptonyx; 3%). Of the seals killed, the whales took 12/14 (86%) off ice floes using a cooperative wave‐washing behavior; they produced 120 waves during 22 separate attacks and successfully took 12/16 (75%) of the Weddell seals attacked. The mean number of waves produced per successful attack was 4.1 (range 1–10) and the mean attack duration was 30.4 min (range 15–62). Seal remains that we examined from one of the kills provided evidence of meticulous postmortem prey processing perhaps best termed “butchering.”     

Antarctic killer whales make rapid,round-trip movements to subtropical waters: evidence for physiological maintenance migrations?

Killer whales (Orcinus orca) are important predators in high latitudes, where their ecological impact is mediated through their movements. We used satellite telemetry to provide the first evidence of migration for killer whales, characterized by fast (more than 12 km h(-1), 6.5 knots) and direct movements away from Antarctic waters by six of 12 type B killer whales tagged when foraging near the Antarctic Peninsula, including all tags transmitting for more than three weeks. Tags on five of these whales revealed consistent movements to subtropical waters (30-37° S) off Uruguay and Brazil, in surface water temperatures ranging from -1.9°C to 24.2°C; one 109 day track documented a non-stop round trip of almost 9400 km (5075 nmi) in just 42 days. Although whales travelled slower in the warmest waters, there was no obvious interruption in swim speed or direction to indicate calving or prolonged feeding. Furthermore, these movements were aseasonal, initiating over 80 days between February and April; one whale returned to within 40 km of the tagging site at the onset of the austral winter in June. We suggest that these movements may represent periodic maintenance migrations, with warmer waters allowing skin regeneration without the high cost of heat loss: a physiological constraint that may also affect other whales.     

Tree Community Change across 700 km of Lowland Amazonian Forest from the Andean Foothills to Brazil

We describe patterns of tree community change along a 700-km transect through terra firme forests of western Amazonia, running from the base of the Andes in Ecuador to the Peru–Brazil border. Our primary question is whether floristic variation at large scales arises from many gradual changes or a few abrupt ones. Data from 54 1-ha tree plots along the transect support the latter model, showing two sharp discontinuities in community structure at the genus level. One is located near the Ecuador–Peru border, where the suite of species that dominates large areas of Ecuadorean forest declines abruptly in importance to the east. This discontinuity is underlain by a subterranean paleoarch and congruent with a change in soil texture. A second discontinuity is associated with the shift from clay to white sand soils near Iquitos. We hypothesize that the first discontinuity is part of an edaphic boundary that runs along the Andean piedmont and causes a transition from tree communities preferring richer, younger soils near the base of the Andes to those preferring poorer, older soils farther east. Because the floristic changes observed at this discontinuity are conserved for large distances to the east and west of it, the discontinuity is potentially key for understanding floristic variation in western Amazonia. The significant floristic turnover at the Ecuador–Peru border suggests that the only large protected area in the region—Ecuador's Yasuní National Park—is not adequate protection for the very diverse tree communities that cover vast areas of northern Peru.     

The above-ground coarse wood productivity of 104 Neotropical forest plots

The net primary production of tropical forests and its partitioning between long‐lived carbon pools (wood) and shorter‐lived pools (leaves, fine roots) are of considerable importance in the global carbon cycle. However, these terms have only been studied at a handful of field sites, and with no consistent calculation methodology. Here we calculate above‐ground coarse wood carbon productivity for 104 forest plots in lowland New World humid tropical forests, using a consistent calculation methodology that incorporates corrections for spatial variations in tree‐size distributions and wood density, and for census interval length. Mean wood density is found to be lower in more productive forests. We estimate that above‐ground coarse wood productivity varies by more than a factor of three (between 1.5 and 5.5 Mg C ha^?1 a^?1) across the Neotropical plots, with a mean value of 3.1 Mg C ha^?1 a^?1. There appear to be no obvious relationships between wood productivity and rainfall, dry season length or sunshine, but there is some hint of increased productivity at lower temperatures. There is, however, also strong evidence for a positive relationship between wood productivity and soil fertility. Fertile soils tend to become more common towards the Andes and at slightly higher than average elevations, so the apparent temperature/productivity relationship is probably not a direct one. Coarse wood productivity accounts for only a fraction of overall tropical forest net primary productivity, but the available data indicate that it is approximately proportional to total above‐ground productivity. We speculate that the large variation in wood productivity is unlikely to directly imply an equivalent variation in gross primary production. Instead a shifting balance in carbon allocation between respiration, wood carbon and fine root production seems the more likely explanation.     

Neurological Soft Signs in Individuals with Pathological Gambling

Increased neurological soft signs (NSSs) have been found in a number of neuropsychiatric syndromes, including chemical addiction. The present study examined NSSs related to perceptual-motor and visuospatial processing in a behavioral addiction viz., pathological gambling (PG). As compared to mentally healthy individuals, pathological gamblers displayed significantly poorer ability to copy two- and three-dimensional figures, to recognize objects against a background noise, and to orient in space on a road-map test. Results indicated that PG is associated with subtle cerebral cortical abnormalities. Further prospective clinical research is needed to address the NSSs'' origin and chronology (e.g., predate or follow the development of PG) as well as their response to therapeutic interventions and/or their ability to predict such a response.     

Quantifying Ecological Literacy in an Adult Western Community: The Development and Application of a New Assessment Tool and Community Standard

Knowledge and understanding about how the Earth functions and supports life create the foundation for ecological literacy. Industrialisation, urbanisation and population growth have resulted in changed relationships between many human communities and the natural world. A potential consequence is a compromised capability to make well-informed decisions about how to live sustainably. To gain a measure of ecological literacy within the South Australian community, we collaborated with senior scientists and educators to develop and apply an instrument with the capacity to determine indicative levels of ecological knowledge and understanding. A formal, variable credit, multiple-choice assessment instrument was distributed online to groups and individuals within diverse community sectors and industries. Quantitative analyses of scores indicated that levels of ecological knowledge and understanding within a self-selected sample of over one thousand individuals ranged from very low to extremely high, with the majority of respondents achieving moderate to high scores. This instrument has a demonstrated capacity to determine indicative levels of ecological literacy within and between individuals and groups. It is able to capture mastery of ecological knowledge and understanding achieved through both formal and informal pathways. Using the results, we have been able to establish a range of standards and an aspirational target score for the South Australian community. The value of this work is in its potential to deliver insights into relationships between humans and the rest of the natural world, and into characteristics of eco-literate individuals and communities, that might not otherwise emerge.     

NOTICES

Schmitt, M. B., Baur, S. &; Von Malitz, F. 1980. Observations on the Steppe Buzzard in the Transvaal: Ostrich 51:151-159.

During a three year study 247 Steppe Buzzards Buteo buteo vulpinus were captured in the Transvaal, South Africa. Density, mensural data and moult are discussed and compared with findings from the Cape Province. Linear density is 7,3 times lower in the Transvaal as compared with the Cape. Identification criteria for second-year birds are given. Second-year birds moult primaries descendently and symmetrically, secondary moult is mainly ascendent and symmetrical, tail moult irregular but symmetrical. Adult birds moult irregularly. Recorded food items are listed.