Author Archives: Bora Zivkovic

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 http://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.

Survival Of The Fittest: Even Cancer Cells Follow The Laws Of Evolution:

Scientists from The Institute of Advanced Studies at Princeton and the University of California discovered that the underlying process in tumor formation is the same as for life itself–evolution. After analyzing a half million gene mutations, the researchers found that although different gene mutations control different cancer pathways, each pathway was controlled by only one set of gene mutations.

New Report Details Historic Mass Extinction Of Amphibians; Humans Worsen Spread Of Deadly Emerging Infectious Disease:

Amphibians, reigning survivors of past mass extinctions, are sending a clear, unequivocal signal that something is wrong, as their extinction rates rise to unprecedented levels, according to a paper published by the Proceedings of the National Academy of Sciences (PNAS). Humans are exacerbating two key natural threats – climate change and a deadly disease that is jumping from one species to another.

Anything But Modest: The Mouse Continues To Contribute To Humankind:

“Big things come in small packages,” the saying goes, and it couldn’t be more true when discussing the mouse. This little creature has become a crucial part of human history through its contributions in understanding human genetics and disease.

If A Street Tree Falls … What Does It Take To Make Sound Policy?:

There’s little debate that, when a tree falls near a city street, it makes a sound. But other questions are more difficult to answer: Who is affected by the falling tree and how? Who is liable for the damage? And who is responsible for deciding how to replace the tree?

Egg P Bodies Protect Maternal Gene Messages:

A cell decides what proteins to make based on the messages it receives from its genome. Sometimes messages are held back to be read later, and in most cell types these delayed messages are stored and eventually marked for destruction in P bodies (processing bodies).

Elephant Memories May Hold Key To Survival:

A recent study by the Wildlife Conservation Society and the Zoological Society of London (ZSL) suggests that old female elephants–and perhaps their memories of distant, life-sustaining sources of food and water–may be the key to survival during the worst of times.

Fry Me Kangaroo Brown, Sport:

Skippy could be on more menus following a report that expanding the kangaroo industry would significantly cut greenhouse gases.

‘Lost Tribe’ Of Clinician-scientists: Medical Doctors Who Do Research Could Be A Dying Breed:

The road from disease research to disease cure isn’t usually a smooth one. One role which bridges the laboratory and the clinic is that of the “clinician-scientist” – a doctor who understands disease both in the patient and in the Petri dish. Yet an editorial published in Disease Models & Mechanisms (DMM), contends that clinician-scientists in the UK and elsewhere are not prospering, but rather are “under threat in a hostile environment.”

Complex Decision? Don’t Sleep On It:

Neither snap judgements nor sleeping on a problem are any better than conscious thinking for making complex decisions, according to new research.

Are Pronghorns Smarter Than Classical European Royalty?:

Over the past two decades, John Byers has proven that female pronghorns are smarter than many humans when it comes to mate selection. Rather than going for the male with the biggest body or most impressive horns, female pronghorns expend a ton of energy searching for the most vigor and best stamina; traits that will give their offspring the greatest chance of success.

Bugs Put The Heat In Chili Peppers:

If you’re a fan of habañero salsa or like to order Thai food spiced to five stars, you owe a lot to bugs, both the crawling kind and ones you can see only with a microscope. New research shows they are the ones responsible for the heat in chili peppers.

Humans Implicated In Prehistoric Animal Extinctions With New Evidence:

Research led by UK and Australian scientists sheds new light on the role that our ancestors played in the extinction of Australia’s prehistoric animals. The new study provides the first evidence that Tasmania’s giant kangaroos and marsupial ‘rhinos’ and ‘leopards’ were still roaming the island when humans first arrived.

Olympic Games: Researchers Explore What Makes Better Athletes, The Physiology Of Performance, And More:

The world-record pace for the marathon continues to improve for both men and women. For men, the record pace for the marathon is now about as fast as the record pace for the 10,000-meter run just after World War II. Today, champion athletes are running more than four times farther at speeds of well under five minutes per mile.

Neurobiologists Discover Individuals Who ‘Hear’ Movement:

Individuals with synesthesia perceive the world in a different way from the rest of us. Because their senses are cross-activated, some synesthetes perceive numbers or letters as having colors or days of the week as possessing personalities, even as they function normally in the world.

Humans’ Response To Risk Can Be Unnecessarily Dangerous:

The traffic light ahead of you is turning yellow. Do you gun the engine and speed through the intersection, trusting that others will wait for their green, or do you slow down and wait your turn?

Perfectly Proportioned Legs Keep Water Striders Striding:

The amazing water strider — known for its ability to walk on water — came within just a hair of sinking into evolutionary oblivion. Scientists in France and the United Kingdom are reporting that the insect’s long, flexible legs have an optimal length that keeps it afloat.

Entomologists Use ‘Love Potion’ To Detect Hidden Cerambycid Beetles:

Cerambycid beetles, also known as long-horned beetles, can cause severe damage to standing trees, logs and lumber. How then might they be promptly detected and their numbers swiftly controlled?

Gene For Sexual Switching In Melons Provides Clues To Evolution Of Sex:

A newly discovered function for a hormone in melons suggests it plays a role in how sexual systems evolve in plants. The study, conducted by French and American scientists, appeared recently in the journal Science.

Nine To Twenty Individual Fire Ant Queens Started U.S. Fire Ant Population:

The current U.S. population of red imported fire ants–which infest millions of acres across the southern states–can be traced back to nine to 20 queens in Mobile, Ala.

For The Birds Or For Me? Why Do Conservationists Really Help Wildlife?:

Volunteers who take part in conservation efforts may do it more for themselves than the wildlife they are trying to protect, a University of Alberta case study shows.

Duck-billed Dinosaurs Outgrew Predators To Survive:

With long limbs and a soft body, the duck-billed hadrosaur had few defenses against predators such as tyrannosaurs. But new research on the bones of this plant-eating dinosaur suggests that it had at least one advantage: It grew to adulthood much faster than its predators, giving it superiority in size.

Massive Numbers Of Critically Endangered Western Lowland Gorillas Discovered In Republic Of Congo:

The world’s population of critically endangered western lowland gorillas recently received a huge boost when the Wildlife Conservation Society released a census showing massive numbers of these secretive great apes alive and well in the Republic of Congo.

Less REM Sleep Associated With Being Overweight Among Children And Teens:

Children and teens who get less sleep, especially those who spend less time in rapid eye movement (REM) sleep, may be more likely to be overweight, according to a new report.

Why The Slow-Paced World Could Make It Difficult To Catch A Ball:

BBSRC researchers at the University of Birmingham have uncovered new information about the way that we perceive fast moving, incoming objects – such as tennis or cricket balls.

Why Some Smokers Become Addicted With Their First Cigarette:

New research from The University of Western Ontario reveals how the brain processes the ‘rewarding’ and addictive properties of nicotine, providing a better understanding of why some people seemingly become hooked with their first smoke.

Acidification Of Sea Hampers Reproduction Of Marine Species:

By absorbing carbon dioxide from the atmosphere, and from the human use of fossil fuels, the world’s seas function as a giant buffer for the Earth’s life support system. The chemical balance of the sea has long been regarded as immovable.

Next Generation Tool For Visualizing Genomic Data Introduced:

Researchers are collecting vast amounts of diverse genomic data with ever-increasing speed, but effective ways to visualize these data in an integrated manner have lagged behind the ability to generate them.

Hot Peppers Really Do Bring The Heat:

Chili peppers can do more than just make you feel hot; the active chemical in peppers can directly induce thermogenesis, the process by which cells convert energy into heat, according to a new study.

Female Guppies Risk Death To Avoid Sexual Harassment:

Sexual harassment from male guppies is so bad that long-suffering females will risk their lives to escape it, according to new research from Dr Safi Darden and Dr Darren Croft from Bangor University.