New and Exciting in PLoS ONE

There are 57 new articles in PLoS ONE this week. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. Here are my own picks for the week - you go and look for your own favourites:

How Do Humans Control Physiological Strain during Strenuous Endurance Exercise?:

Distance running performance is a viable model of human locomotion. To evaluate the physiologic strain during competitions ranging from 5-100 km, we evaluated heart rate (HR) records of competitive runners (n = 211). We found evidence that: 1) physiologic strain (% of maximum HR (%HRmax)) increased in proportional manner relative to distance completed, and was regulated by variations in running pace; 2) the %HRmax achieved decreased with relative distance; 3) slower runners had similar %HRmax response within a racing distance compared to faster runners, and despite differences in pace, the profile of %HRmax during a race was very similar in runners of differing ability; and 4) in cases where there was a discontinuity in the running performance, there was evidence that physiologic effort was maintained for some time even after the pace had decreased. The overall results suggest that athletes are actively regulating their relative physiologic strain during competition, although there is evidence of poor regulation in the case of competitive failures.

Oil and Gas Projects in the Western Amazon: Threats to Wilderness, Biodiversity, and Indigenous Peoples:

The western Amazon is the most biologically rich part of the Amazon basin and is home to a great diversity of indigenous ethnic groups, including some of the world's last uncontacted peoples living in voluntary isolation. Unlike the eastern Brazilian Amazon, it is still a largely intact ecosystem. Underlying this landscape are large reserves of oil and gas, many yet untapped. The growing global demand is leading to unprecedented exploration and development in the region. We synthesized information from government sources to quantify the status of oil development in the western Amazon. National governments delimit specific geographic areas or "blocks" that are zoned for hydrocarbon activities, which they may lease to state and multinational energy companies for exploration and production. About 180 oil and gas blocks now cover ~688,000 km2 of the western Amazon. These blocks overlap the most species-rich part of the Amazon. We also found that many of the blocks overlap indigenous territories, both titled lands and areas utilized by peoples in voluntary isolation. In Ecuador and Peru, oil and gas blocks now cover more than two-thirds of the Amazon. In Bolivia and western Brazil, major exploration activities are set to increase rapidly. Without improved policies, the increasing scope and magnitude of planned extraction means that environmental and social impacts are likely to intensify. We review the most pressing oil- and gas-related conservation policy issues confronting the region. These include the need for regional Strategic Environmental Impact Assessments and the adoption of roadless extraction techniques. We also consider the conflicts where the blocks overlap indigenous peoples' territories.

Claims of Potential Expansion throughout the U.S. by Invasive Python Species Are Contradicted by Ecological Niche Models:

Recent reports from the United States Geological Survey (USGS) suggested that invasive Burmese pythons in the Everglades may quickly spread into many parts of the U.S. due to putative climatic suitability. Additionally, projected trends of global warming were predicted to significantly increase suitable habitat and promote range expansion by these snakes. However, the ecological limitations of the Burmese python are not known and the possible effects of global warming on the potential expansion of the species are also unclear. Here we show that a predicted continental expansion is unlikely based on the ecology of the organism and the climate of the U.S. Our ecological niche models, which include variables representing climatic extremes as well as averages, indicate that the only suitable habitat in the U.S. for Burmese pythons presently occurs in southern Florida and in extreme southern Texas. Models based on the current distribution of the snake predict suitable habitat in essentially the only region in which the snakes are found in the U.S. Future climate models based on global warming forecasts actually indicate a significant contraction in suitable habitat for Burmese pythons in the U.S. as well as in their native range. The Burmese python is strongly limited to the small area of suitable environmental conditions in the United States it currently inhabits due to the ecological niche preferences of the snake. The ability of the Burmese python to expand further into the U.S. is severely limited by ecological constraints. Global warming is predicted to significantly reduce the area of suitable habitat worldwide, underscoring the potential negative effects of climate change for many species.

Ocean Surface Winds Drive Dynamics of Transoceanic Aerial Movements:

Global wind patterns influence dispersal and migration processes of aerial organisms, propagules and particles, which ultimately could determine the dynamics of colonizations, invasions or spread of pathogens. However, studying how wind-mediated movements actually happen has been hampered so far by the lack of high resolution global wind data as well as the impossibility to track aerial movements. Using concurrent data on winds and actual pathways of a tracked seabird, here we show that oceanic winds define spatiotemporal pathways and barriers for large-scale aerial movements. We obtained wind data from NASA SeaWinds scatterometer to calculate wind cost (impedance) models reflecting the resistance to the aerial movement near the ocean surface. We also tracked the movements of a model organism, the Cory's shearwater (Calonectris diomedea), a pelagic bird known to perform long distance migrations. Cost models revealed that distant areas can be connected through "wind highways" that do not match the shortest great circle routes. Bird routes closely followed the low-cost "wind-highways" linking breeding and wintering areas. In addition, we found that a potential barrier, the near surface westerlies in the Atlantic sector of the Intertropical Convergence Zone (ITCZ), temporally hindered meridional trans-equatorial movements. Once the westerlies vanished, birds crossed the ITCZ to their winter quarters. This study provides a novel approach to investigate wind-mediated movements in oceanic environments and shows that large-scale migration and dispersal processes over the oceans can be largely driven by spatiotemporal wind patterns.

A Thirty Million Year-Old Inherited Heteroplasmy:

Due to essentially maternal inheritance and a bottleneck effect during early oogenesis, newly arising mitochondrial DNA (mtDNA) mutations segregate rapidly in metazoan female germlines. Consequently, heteroplasmy (i.e. the mixture of mtDNA genotypes within an organism) is generally resolved to homoplasmy within a few generations. Here, we report an exceptional transpecific heteroplasmy (predicting an alanine/valine alloacceptor tRNA change) that has been stably inherited in oniscid crustaceans for at least thirty million years. Our results suggest that this heteroplasmy is stably transmitted across generations because it occurs within mitochondria and therefore escapes the mtDNA bottleneck that usually erases heteroplasmy. Consistently, at least two oniscid species possess an atypical trimeric mitochondrial genome, which provides an adequate substrate for the emergence of a constitutive intra-mitochondrial heteroplasmy. Persistence of a mitochondrial polymorphism on such a deep evolutionary timescale suggests that balancing selection may be shaping mitochondrial sequence evolution in oniscid crustaceans.

Sleep Modulates the Neural Substrates of Both Spatial and Contextual Memory Consolidation:

It is known that sleep reshapes the neural representations that subtend the memories acquired while navigating in a virtual environment. However, navigation is not process-pure, as manifold learning components contribute to performance, notably the spatial and contextual memory constituents. In this context, it remains unclear whether post-training sleep globally promotes consolidation of all of the memory components embedded in virtual navigation, or rather favors the development of specific representations. Here, we investigated the effect of post-training sleep on the neural substrates of the consolidation of spatial and contextual memories acquired while navigating in a complex 3D, naturalistic virtual town. Using fMRI, we mapped regional cerebral activity during various tasks designed to tap either the spatial or the contextual memory component, or both, 72 h after encoding with or without sleep deprivation during the first post-training night. Behavioral performance was not dependent upon post-training sleep deprivation, neither in a natural setting that engages both spatial and contextual memory processes nor when looking more specifically at each of these memory representations. At the neuronal level however, analyses that focused on contextual memory revealed distinct correlations between performance and neuronal activity in frontal areas associated with recollection processes after post-training sleep, and in the parahippocampal gyrus associated with familiarity processes in sleep-deprived participants. Likewise, efficient spatial memory was associated with posterior cortical activity after sleep whereas it correlated with parahippocampal/medial temporal activity after sleep deprivation. Finally, variations in place-finding efficiency in a natural setting encompassing spatial and contextual elements were associated with caudate activity after post-training sleep, suggesting the automation of navigation. These data indicate that post-training sleep modulates the neural substrates of the consolidation of both the spatial and contextual memories acquired during virtual navigation.

A Semantic Web Management Model for Integrative Biomedical Informatics:

Data, data everywhere. The diversity and magnitude of the data generated in the Life Sciences defies automated articulation among complementary efforts. The additional need in this field for managing property and access permissions compounds the difficulty very significantly. This is particularly the case when the integration involves multiple domains and disciplines, even more so when it includes clinical and high throughput molecular data. The emergence of Semantic Web technologies brings the promise of meaningful interoperation between data and analysis resources. In this report we identify a core model for biomedical Knowledge Engineering applications and demonstrate how this new technology can be used to weave a management model where multiple intertwined data structures can be hosted and managed by multiple authorities in a distributed management infrastructure. Specifically, the demonstration is performed by linking data sources associated with the Lung Cancer SPORE awarded to The University of Texas MDAnderson Cancer Center at Houston and the Southwestern Medical Center at Dallas. A software prototype, available with open source at www.s3db.org, was developed and its proposed design has been made publicly available as an open source instrument for shared, distributed data management. The Semantic Web technologies have the potential to addresses the need for distributed and evolvable representations that are critical for systems Biology and translational biomedical research. As this technology is incorporated into application development we can expect that both general purpose productivity software and domain specific software installed on our personal computers will become increasingly integrated with the relevant remote resources. In this scenario, the acquisition of a new dataset should automatically trigger the delegation of its analysis.

Controlling Population Evolution in the Laboratory to Evaluate Methods of Historical Inference:

Natural populations of known detailed past demographic history are extremely valuable to evaluate methods of historical inference, yet are extremely rare. As an alternative approach, we have generated multiple replicate microsatellite data sets from laboratory-cultured populations of a gonochoric free-living nematode, Caenorhabditis remanei, that were constrained to pre-defined demographic histories featuring different levels of migration among populations or bottleneck events of different magnitudes. These data sets were then used to evaluate the performances of two recently developed population genetics methods, BAYESASS+, that estimates recent migration rates among populations, and BOTTLENECK, that detects the occurrence of recent bottlenecks. Migration rates inferred by BAYESASS+ were generally over-estimates, although these were often included within the confidence interval. Analyses of data sets simulated in-silico, using a model mimicking the laboratory experiments, produced less biased estimates of the migration rates, and showed increased efficiency of the program when the number of loci and sampled genotypes per population was higher. In the replicates for which the pre-bottleneck laboratory-cultured populations did not significantly depart from a mutation/drift equilibrium, an important assumption of the program BOTTLENECK, only a portion of the bottleneck events were detected. This result was confirmed by in-silico simulations mirroring the laboratory bottleneck experiments. More generally, our study demonstrates the feasibility, and highlights some of the limits, of the approach that consists in generating molecular genetic data sets by controlling the evolution of laboratory-reared nematode populations, for the purpose of validating methods inferring population history.

Towards Zero Training for Brain-Computer Interfacing:

Electroencephalogram (EEG) signals are highly subject-specific and vary considerably even between recording sessions of the same user within the same experimental paradigm. This challenges a stable operation of Brain-Computer Interface (BCI) systems. The classical approach is to train users by neurofeedback to produce fixed stereotypical patterns of brain activity. In the machine learning approach, a widely adapted method for dealing with those variances is to record a so called calibration measurement on the beginning of each session in order to optimize spatial filters and classifiers specifically for each subject and each day. This adaptation of the system to the individual brain signature of each user relieves from the need of extensive user training. In this paper we suggest a new method that overcomes the requirement of these time-consuming calibration recordings for long-term BCI users. The method takes advantage of knowledge collected in previous sessions: By a novel technique, prototypical spatial filters are determined which have better generalization properties compared to single-session filters. In particular, they can be used in follow-up sessions without the need to recalibrate the system. This way the calibration periods can be dramatically shortened or even completely omitted for these 'experienced' BCI users. The feasibility of our novel approach is demonstrated with a series of online BCI experiments. Although performed without any calibration measurement at all, no loss of classification performance was observed.

Relaxation of Selective Constraints Causes Independent Selenoprotein Extinction in Insect Genomes:

Selenoproteins are a diverse family of proteins notable for the presence of the 21st amino acid, selenocysteine. Until very recently, all metazoan genomes investigated encoded selenoproteins, and these proteins had therefore been believed to be essential for animal life. Challenging this assumption, recent comparative analyses of insect genomes have revealed that some insect genomes appear to have lost selenoprotein genes. In this paper we investigate in detail the fate of selenoproteins, and that of selenoprotein factors, in all available arthropod genomes. We use a variety of in silico comparative genomics approaches to look for known selenoprotein genes and factors involved in selenoprotein biosynthesis. We have found that five insect species have completely lost the ability to encode selenoproteins and that selenoprotein loss in these species, although so far confined to the Endopterygota infraclass, cannot be attributed to a single evolutionary event, but rather to multiple, independent events. Loss of selenoproteins and selenoprotein factors is usually coupled to the deletion of the entire no-longer functional genomic region, rather than to sequence degradation and consequent pseudogenisation. Such dynamics of gene extinction are consistent with the high rate of genome rearrangements observed in Drosophila. We have also found that, while many selenoprotein factors are concomitantly lost with the selenoproteins, others are present and conserved in all investigated genomes, irrespective of whether they code for selenoproteins or not, suggesting that they are involved in additional, non-selenoprotein related functions. Selenoproteins have been independently lost in several insect species, possibly as a consequence of the relaxation in insects of the selective constraints acting across metazoans to maintain selenoproteins. The dispensability of selenoproteins in insects may be related to the fundamental differences in antioxidant defense between these animals and other metazoans.

Prion Infected Meat-and-Bone Meal Is Still Infectious after Biodiesel Production:

The epidemic of bovine spongiform encephalopathy (BSE) has led to a world-wide drop in the market for beef by-products, such as Meat-and-Bone Meal (MBM), a fat-containing but mainly proteinaceaous product traditionally used as an animal feed supplement. While normal rendering is insufficient, the production of biodiesel from MBM has been suggested to destroy infectivity from transmissible spongiform encephalopathies (TSEs). In addition to producing fuel, this method simultaneously generates a nutritious solid residue. In our study we produced biodiesel from MBM under defined conditions using a modified form of alkaline methanolysis. We evaluated the presence of prion in the three resulting phases of the biodiesel reaction (Biodiesel, Glycerol and Solid Residue) in vitro and in vivo. Analysis of the reaction products from 263K scrapie infected MBM led to no detectable immunoreactivity by Western Blot. Importantly, and in contrast to the biochemical results the solid MBM residue from the reaction retained infectivity when tested in an animal bioassay. Histochemical analysis of hamster brains inoculated with the solid residue showed typical spongiform degeneration and vacuolation. Re-inoculation of these brains into a new cohort of hamsters led to onset of clinical scrapie symptoms within 75 days, suggesting that the specific infectivity of the prion protein was not changed during the biodiesel process. The biodiesel reaction cannot be considered a viable prion decontamination method for MBM, although we observed increased survival time of hamsters and reduced infectivity greater than 6 log orders in the solid MBM residue. Furthermore, results from our study compare for the first time prion detection by Western Blot versus an infectivity bioassay for analysis of biodiesel reaction products. We could show that biochemical analysis alone is insufficient for detection of prion infectivity after a biodiesel process.