Category Archives: Science News

There are 31 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Climate Change, Habitat Loss, Protected Areas and the Climate Adaptation Potential of Species in Mediterranean Ecosystems Worldwide:

Mediterranean climate is found on five continents and supports five global biodiversity hotspots. Based on combined downscaled results from 23 atmosphere-ocean general circulation models (AOGCMs) for three emissions scenarios, we determined the projected spatial shifts in the mediterranean climate extent (MCE) over the next century. Although most AOGCMs project a moderate expansion in the global MCE, regional impacts are large and uneven. The median AOGCM simulation output for the three emissions scenarios project the MCE at the end of the 21st century in Chile will range from 129-153% of its current size, while in Australia, it will contract to only 77-49% of its current size losing an area equivalent to over twice the size of Portugal. Only 4% of the land area within the current MCE worldwide is in protected status (compared to a global average of 12% for all biome types), and, depending on the emissions scenario, only 50-60% of these protected areas are likely to be in the future MCE. To exacerbate the climate impact, nearly one third (29-31%) of the land where the MCE is projected to remain stable has already been converted to human use, limiting the size of the potential climate refuges and diminishing the adaptation potential of native biota. High conversion and low protection in projected stable areas make Australia the highest priority region for investment in climate-adaptation strategies to reduce the threat of climate change to the rich biodiversity of the mediterranean biome.

Autosomal Resequence Data Reveal Late Stone Age Signals of Population Expansion in Sub-Saharan African Foraging and Farming Populations:

A major unanswered question in the evolution of Homo sapiens is when anatomically modern human populations began to expand: was demographic growth associated with the invention of particular technologies or behavioral innovations by hunter-gatherers in the Late Pleistocene, or with the acquisition of farming in the Neolithic? We investigate the timing of human population expansion by performing a multilocus analysis of≥20 unlinked autosomal noncoding regions, each consisting of ~6 kilobases, resequenced in ~184 individuals from 7 human populations. We test the hypothesis that the autosomal polymorphism data fit a simple two-phase growth model, and when the hypothesis is not rejected, we fit parameters of this model to our data using approximate Bayesian computation. The data from the three surveyed non-African populations (French Basque, Chinese Han, and Melanesians) are inconsistent with the simple growth model, presumably because they reflect more complex demographic histories. In contrast, data from all four sub-Saharan African populations fit the two-phase growth model, and a range of onset times and growth rates is inferred for each population. Interestingly, both hunter-gatherers (San and Biaka) and food-producers (Mandenka and Yorubans) best fit models with population growth beginning in the Late Pleistocene. Moreover, our hunter-gatherer populations show a tendency towards slightly older and stronger growth (~41 thousand years ago, ~13-fold) than our food-producing populations (~31 thousand years ago, ~7-fold). These dates are concurrent with the appearance of the Late Stone Age in Africa, supporting the hypothesis that population growth played a significant role in the evolution of Late Pleistocene human cultures.

Reinforcement Learning or Active Inference?:

This paper questions the need for reinforcement learning or control theory when optimising behaviour. We show that it is fairly simple to teach an agent complicated and adaptive behaviours using a free-energy formulation of perception. In this formulation, agents adjust their internal states and sampling of the environment to minimize their free-energy. Such agents learn causal structure in the environment and sample it in an adaptive and self-supervised fashion. This results in behavioural policies that reproduce those optimised by reinforcement learning and dynamic programming. Critically, we do not need to invoke the notion of reward, value or utility. We illustrate these points by solving a benchmark problem in dynamic programming; namely the mountain-car problem, using active perception or inference under the free-energy principle. The ensuing proof-of-concept may be important because the free-energy formulation furnishes a unified account of both action and perception and may speak to a reappraisal of the role of dopamine in the brain.

Transcriptomic Profiling of Central Nervous System Regions in Three Species of Honey Bee during Dance Communication Behavior:

We conducted a large-scale transcriptomic profiling of selected regions of the central nervous system (CNS) across three species of honey bees, in foragers that were performing dance behavior to communicate to their nestmates the location, direction and profitability of an attractive floral resource. We used microarrays to measure gene expression in bees from Apis mellifera, dorsata and florea, species that share major traits unique to the genus and also show striking differences in biology and dance communication. The goals of this study were to determine the extent of regional specialization in gene expression and to explore the molecular basis of dance communication. This “snapshot” of the honey bee CNS during dance behavior provides strong evidence for both species-consistent and species-specific differences in gene expression. Gene expression profiles in the mushroom bodies consistently showed the biggest differences relative to the other CNS regions. There were strong similarities in gene expression between the central brain and the second thoracic ganglion across all three species; many of the genes were related to metabolism and energy production. We also obtained gene expression differences between CNS regions that varied by species: A. mellifera differed the most, while dorsata and florea tended to be more similar. Species differences in gene expression perhaps mirror known differences in nesting habit, ecology and dance behavior between mellifera, florea and dorsata. Species-specific differences in gene expression in selected CNS regions that relate to synaptic activity and motor control provide particularly attractive candidate genes to explain the differences in dance behavior exhibited by these three honey bee species. Similarities between central brain and thoracic ganglion provide a unique perspective on the potential coupling of these two motor-related regions during dance behavior and perhaps provide a snapshot of the energy intensive process of dance output generation. Mushroom body results reflect known roles for this region in the regulation of learning, memory and rhythmic behavior.

Chemosensory Cues to Conspecific Emotional Stress Activate Amygdala in Humans:

Alarm substances are airborne chemical signals, released by an individual into the environment, which communicate emotional stress between conspecifics. Here we tested whether humans, like other mammals, are able to detect emotional stress in others by chemosensory cues. Sweat samples collected from individuals undergoing an acute emotional stressor, with exercise as a control, were pooled and presented to a separate group of participants (blind to condition) during four experiments. In an fMRI experiment and its replication, we showed that scanned participants showed amygdala activation in response to samples obtained from donors undergoing an emotional, but not physical, stressor. An odor-discrimination experiment suggested the effect was primarily due to emotional, and not odor, differences between the two stimuli. A fourth experiment investigated behavioral effects, demonstrating that stress samples sharpened emotion-perception of ambiguous facial stimuli. Together, our findings suggest human chemosensory signaling of emotional stress, with neurobiological and behavioral effects.

Bio-Benchmarking of Electronic Nose Sensors:

Electronic noses, E-Noses, are instruments designed to reproduce the performance of animal noses or antennae but generally they cannot match the discriminating power of the biological original and have, therefore, been of limited utility. The manner in which odorant space is sampled is a critical factor in the performance of all noses but so far it has been described in detail only for the fly antenna. Here we describe how a set of metal oxide (MOx) E-Nose sensors, which is the most commonly used type, samples odorant space and compare it with what is known about fly odorant receptors (ORs). Compared with a fly’s odorant receptors, MOx sensors from an electronic nose are on average more narrowly tuned but much more highly correlated with each other. A set of insect ORs can therefore sample broader regions of odorant space independently and redundantly than an equivalent number of MOx sensors. The comparison also highlights some important questions about the molecular nature of fly ORs. The comparative approach generates practical learnings that may be taken up by solid-state physicists or engineers in designing new solid-state electronic nose sensors. It also potentially deepens our understanding of the performance of the biological system.

The Impact of National Institutes of Health Funding on U.S. Cardiovascular Disease Research:

Intense interest surrounds the recent expansion of US National Institutes of Health (NIH) budgets as part of economic stimulus legislation. However, the relationship between NIH funding and cardiovascular disease research is poorly understood, making the likely impact of this policy change unclear. The National Library of Medicine’s PubMed database was searched for articles published from 1996 to 2006, originating from U.S. institutions, and containing the phrases “cardiolog,” “cardiovascular,” or “cardiac,” in the first author’s department. Research methodology, journal of publication, journal impact factor, and receipt of NIH funding were recorded. Differences in means and trends were tested with t-tests and linear regression, respectively, with P≤0.05 for significance. Of 117,643 world cardiovascular articles, 36,684 (31.2%) originated from the U.S., of which 10,293 (28.1%) received NIH funding. The NIH funded 40.1% of U.S. basic science articles, 20.3% of overall clinical trials, 18.1% of randomized-controlled, and 12.2% of multicenter clinical trials. NIH-funded and total articles grew significantly (65 articles/year, P<0.001 and 218 articles/year, P<0.001, respectively). The proportion of articles receiving NIH funding was stable, but grew significantly for basic science and clinical trials (0.87%/year, P<0.001 and 0.67%/year, P = 0.029, respectively). NIH-funded articles had greater journal impact factors than non NIH-funded articles (5.76 vs. 3.71, P<0.001). NIH influence on U.S. cardiovascular research expanded in the past decade, during the period of NIH budget doubling. A substantial fraction of research is now directly funded and thus likely sensitive to budget fluctuations, particularly in basic science research. NIH funding predicts greater journal impact.

Lots of cool papers today in 4 out of 7 PLoS journals! As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks – you go and look for your own favourites:

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On Fridays I usually take a look at new papers in all seven PLoS journals. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Circadian Clock Genes Contribute to the Regulation of Hair Follicle Cycling:

The hair follicle renews itself by repeatedly cycling among growth, regression, and rest phases. One function of hair follicle cycling is to allow seasonal changes in hair growth. Understanding the regulation of hair follicle cycling is also of interest because abnormal regulation of hair cycle control genes is responsible for several types of human hair growth disorders and skin cancers. We report here that Clock and Bmal1 genes, which control circadian rhythms, are also important for the regulation of hair follicle cycling, a biological process of much longer duration than 24 hours. Detailed analysis of skin from mice mutated for central clock genes indicates a significant delay in the progression of the hair growth phase. We show that clock genes affect the expression of key cell cycle control genes and that keratinocytes in a critical compartment of the hair follicles in Bmal1 mutant mice are halted in the G1 phase of the cell cycle. These findings provide novel insight into circadian control mechanisms in modulating the progression of cyclic biological processes on different time scales.

Impact of Selection and Demography on the Diffusion of Lactase Persistence:

The lactase enzyme allows lactose digestion in fresh milk. Its activity strongly decreases after the weaning phase in most humans, but persists at a high frequency in Europe and some nomadic populations. Two hypotheses are usually proposed to explain the particular distribution of the lactase persistence phenotype. The gene-culture coevolution hypothesis supposes a nutritional advantage of lactose digestion in pastoral populations. The calcium assimilation hypothesis suggests that carriers of the lactase persistence allele(s) (LCT*P) are favoured in high-latitude regions, where sunshine is insufficient to allow accurate vitamin-D synthesis. In this work, we test the validity of these two hypotheses on a large worldwide dataset of lactase persistence frequencies by using several complementary approaches. We first analyse the distribution of lactase persistence in various continents in relation to geographic variation, pastoralism levels, and the genetic patterns observed for other independent polymorphisms. Then we use computer simulations and a large database of archaeological dates for the introduction of domestication to explore the evolution of these frequencies in Europe according to different demographic scenarios and selection intensities. Our results show that gene-culture coevolution is a likely hypothesis in Africa as high LCT*P frequencies are preferentially found in pastoral populations. In Europe, we show that population history played an important role in the diffusion of lactase persistence over the continent. Moreover, selection pressure on lactase persistence has been very high in the North-western part of the continent, by contrast to the South-eastern part where genetic drift alone can explain the observed frequencies. This selection pressure increasing with latitude is highly compatible with the calcium assimilation hypothesis while the gene-culture coevolution hypothesis cannot be ruled out if a positively selected lactase gene was carried at the front of the expansion wave during the Neolithic transition in Europe.

Bioluminescent Imaging of Trypanosoma brucei Shows Preferential Testis Dissemination Which May Hamper Drug Efficacy in Sleeping Sickness:

Human African trypanosomiasis or sleeping sickness, caused by two subspecies of Trypanosoma brucei, is endemic in Subsaharan Africa. There is no vaccine and the currently used drugs are toxic and can cause severe side effects and even death. At present, we do not know how and when parasites can leave the blood and penetrate into organs (especially the brain). Such knowledge will be very helpful to develop and validate new drugs that can clear the parasite from both the blood and the tissues. In this study, we developed a novel technique allowing us to track the parasites in a live animal by the use of light signals. By following the luminescent parasites in the mouse we showed that, interestingly, the organisms migrate very early in infection to the testes. Here, they may be protected from the immune system and from drugs. Indeed when treating the mice with a sub-optimal dose of medicine, the parasites in this location were not cleared and subsequently could cause a reinvasion into the blood of the host.

Does Genetic Diversity Predict Health in Humans?:

Genetic diversity, especially at genes important for immune functioning within the Major Histocompatibility Complex (MHC), has been associated with fitness-related traits, including disease resistance, in many species. Recently, genetic diversity has been associated with mate preferences in humans. Here we asked whether these preferences are adaptive in terms of obtaining healthier mates. We investigated whether genetic diversity (heterozygosity and standardized mean d2) at MHC and nonMHC microsatellite loci, predicted health in 153 individuals. Individuals with greater allelic diversity (d2) at nonMHC loci and at one MHC locus, linked to HLA-DRB1, reported fewer symptoms over a four-month period than individuals with lower d2. In contrast, there were no associations between MHC or nonMHC heterozygosity and health. NonMHC-d2 has previously been found to predict male preferences for female faces. Thus, the current findings suggest that nonMHC diversity may play a role in both natural and sexual selection acting on human populations.

Coevolution of Interacting Fertilization Proteins:

When a sperm meets an egg, it must display the correct recognition proteins to achieve fertilization. Given the importance of fertilization one would think these proteins are perfected and do not change over time; however, recent studies show that they do change and quite rapidly. Thus, the sperm and egg must change together in harmony, through a process called coevolution, so the species can successfully reproduce. We followed the sperm-egg coevolutionary process at the level of genes: one that makes the protective egg coat and a sperm gene which opens that coat for fertilization. By examining their DNA sequences in two abalone species, we revealed two coevolutionary signatures. In one case, we discovered an association of variants between the egg and sperm genes, the origin of which could be strong preference for compatible variants. In the second case, we demonstrated that both genes changed at correlated rates over millions of years of evolution. Whenever one gene had accelerated in one species, the other showed a parallel acceleration in that same species. These unique signatures help us to understand coevolution by revealing its strength within natural populations and by showing that it has acted consistently over long time periods.

Saccadic Compression of Rectangle and Kanizsa Figures: Now You See It, Now You Don’t:

Observers misperceive the location of points within a scene as compressed towards the goal of a saccade. However, recent studies suggest that saccadic compression does not occur for discrete elements such as dots when they are perceived as unified objects like a rectangle. We investigated the magnitude of horizontal vs. vertical compression for Kanizsa figure (a collection of discrete elements unified into single perceptual objects by illusory contours) and control rectangle figures. Participants were presented with Kanizsa and control figures and had to decide whether the horizontal or vertical length of stimulus was longer using the two-alternative force choice method. Our findings show that large but not small Kanizsa figures are perceived as compressed, that such compression is large in the horizontal dimension and small or nil in the vertical dimension. In contrast to recent findings, we found no saccadic compression for control rectangles. Our data suggest that compression of Kanizsa figure has been overestimated in previous research due to methodological artifacts, and highlight the importance of studying perceptual phenomena by multiple methods.

The Roles and Interactions of Symbiont, Host and Environment in Defining Coral Fitness:

Reef-building corals live in symbiosis with a diverse range of dinoflagellate algae (genus Symbiodinium) that differentially influence the fitness of the coral holobiont. The comparative role of symbiont type in holobiont fitness in relation to host genotype or the environment, however, is largely unknown. We addressed this knowledge gap by manipulating host-symbiont combinations and comparing growth, survival and thermal tolerance among the resultant holobionts in different environments. Offspring of the coral, Acropora millepora, from two thermally contrasting locations, were experimentally infected with one of six Symbiodinium types, which spanned three phylogenetic clades (A, C and D), and then outplanted to the two parental field locations (central and southern inshore Great Barrier Reef, Australia). Growth and survival of juvenile corals were monitored for 31-35 weeks, after which their thermo-tolerance was experimentally assessed. Our results showed that: (1) Symbiodinium type was the most important predictor of holobiont fitness, as measured by growth, survival, and thermo-tolerance; (2) growth and survival, but not heat-tolerance, were also affected by local environmental conditions; and (3) host population had little to no effect on holobiont fitness. Furthermore, coral-algal associations were established with symbiont types belonging to clades A, C and D, but three out of four symbiont types belonging to clade C failed to establish a symbiosis. Associations with clade A had the lowest fitness and were unstable in the field. Lastly, Symbiodinium types C1 and D were found to be relatively thermo-tolerant, with type D conferring the highest tolerance in A. millepora. These results highlight the complex interactions that occur between the coral host, the algal symbiont, and the environment to shape the fitness of the coral holobiont. An improved understanding of the factors affecting coral holobiont fitness will assist in predicting the responses of corals to global climate change.

There are 9 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Numbers in the Blind’s ‘Eye’:

Although lacking visual experience with numerosities, recent evidence shows that the blind perform similarly to sighted persons on numerical comparison or parity judgement tasks. In particular, on tasks presented in the auditory modality, the blind surprisingly show the same effect that appears in sighted persons, demonstrating that numbers are represented through a spatial code, i.e. the Spatial-Numerical Association of Response Codes (SNARC) effect. But, if this is the case, how is this numerical spatial representation processed in the brain of the blind? Here we report that, although blind and sighted people have similarly organized numerical representations, the attentional shifts generated by numbers have different electrophysiological correlates (sensorial N100 in the sighted and cognitive P300 in the blind). These results highlight possible differences in the use of spatial representations acquired through modalities other than vision in the blind population.

Adaptive Radiation in Mediterranean Cistus (Cistaceae):

Adaptive radiation in Mediterranean plants is poorly understood. The white-flowered Cistus lineage consists of 12 species primarily distributed in Mediterranean habitats and is herein subject to analysis. We conducted a “total evidence” analysis combining nuclear (ncpGS, ITS) and plastid (trnL-trnF, trnK-matK, trnS-trnG, rbcL) DNA sequences and using MP and BI to test the hypothesis of radiation as suggested by previous phylogenetic results. One of the five well-supported lineages of the Cistus-Halimium complex, the white-flowered Cistus lineage, comprises the higher number of species (12) and is monophyletic. Molecular dating estimates a Mid Pleistocene (1.04±0.25 Ma) diversification of the white-flowered lineage into two groups (C. clusii and C. salviifolius lineages), which display asymmetric characteristics: number of species (2 vs. 10), leaf morphologies (linear vs. linear to ovate), floral characteristics (small, three-sepalled vs. small to large, three- or five-sepalled flowers) and ecological attributes (low-land vs. low-land to mountain environments). A positive phenotype-environment correlation has been detected by historical reconstructions of morphological traits (leaf shape, leaf labdanum content and leaf pubescence). Ecological evidence indicates that modifications of leaf shape and size, coupled with differences in labdanum secretion and pubescence density, appear to be related to success of new species in different Mediterranean habitats. The observation that radiation in the Cistus salviifolius lineage has been accompanied by the emergence of divergent leaf traits (such as shape, pubescence and labdanum secretion) in different environments suggets that radiation in the group has been adaptive. Here we argued that the diverse ecological conditions of Mediterranean habitats played a key role in directing the evolution of alternative leaf strategies in this plant group. Key innovation of morphological characteristics is supported by our dated phylogeny, in which a Mediterranean climate establishment (2.8 Ma) predated the adaptive radiation of the white-flowered Cistus.

Our system was down fpr the past 17.5 hours so I could not post this last night, so here it is now. There are 22 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Relativity Theory and Time Perception: Single or Multiple Clocks?:

Current theories of interval timing assume that humans and other animals time as if using a single, absolute stopwatch that can be stopped or reset on command. Here we evaluate the alternative view that psychological time is represented by multiple clocks, and that these clocks create separate temporal contexts by which duration is judged in a relative manner. Two predictions of the multiple-clock hypothesis were tested. First, that the multiple clocks can be manipulated (stopped and/or reset) independently. Second, that an event of a given physical duration would be perceived as having different durations in different temporal contexts, i.e., would be judged differently by each clock. Rats were trained to time three durations (e.g., 10, 30, and 90 s). When timing was interrupted by an unexpected gap in the signal, rats reset the clock used to time the “short” duration, stopped the “medium” duration clock, and continued to run the “long” duration clock. When the duration of the gap was manipulated, the rats reset these clocks in a hierarchical order, first the “short”, then the “medium”, and finally the “long” clock. Quantitative modeling assuming re-allocation of cognitive resources in proportion to the relative duration of the gap to the multiple, simultaneously timed event durations was used to account for the results. These results indicate that the three event durations were effectively timed by separate clocks operated independently, and that the same gap duration was judged relative to these three temporal contexts. Results suggest that the brain processes the duration of an event in a manner similar to Einstein’s special relativity theory: A given time interval is registered differently by independent clocks dependent upon the context.

Mobile Phone Based Clinical Microscopy for Global Health Applications:

Light microscopy provides a simple, cost-effective, and vital method for the diagnosis and screening of hematologic and infectious diseases. In many regions of the world, however, the required equipment is either unavailable or insufficiently portable, and operators may not possess adequate training to make full use of the images obtained. Counterintuitively, these same regions are often well served by mobile phone networks, suggesting the possibility of leveraging portable, camera-enabled mobile phones for diagnostic imaging and telemedicine. Toward this end we have built a mobile phone-mounted light microscope and demonstrated its potential for clinical use by imaging P. falciparum-infected and sickle red blood cells in brightfield and M. tuberculosis-infected sputum samples in fluorescence with LED excitation. In all cases resolution exceeded that necessary to detect blood cell and microorganism morphology, and with the tuberculosis samples we took further advantage of the digitized images to demonstrate automated bacillus counting via image analysis software. We expect such a telemedicine system for global healthcare via mobile phone – offering inexpensive brightfield and fluorescence microscopy integrated with automated image analysis – to provide an important tool for disease diagnosis and screening, particularly in the developing world and rural areas where laboratory facilities are scarce but mobile phone infrastructure is extensive.

Climatic Changes Lead to Declining Winter Chill for Fruit and Nut Trees in California during 1950-2099:

Winter chill is one of the defining characteristics of a location’s suitability for the production of many tree crops. We mapped and investigated observed historic and projected future changes in winter chill in California, quantified with two different chilling models (Chilling Hours, Dynamic Model). Based on hourly and daily temperature records, winter chill was modeled for two past temperature scenarios (1950 and 2000), and 18 future scenarios (average conditions during 2041-2060 and 2080-2099 under each of the B1, A1B and A2 IPCC greenhouse gas emissions scenarios, for the CSIRO-MK3, HadCM3 and MIROC climate models). For each scenario, 100 replications of the yearly temperature record were produced, using a stochastic weather generator. We then introduced and mapped a novel climatic statistic, “safe winter chill”, the 10% quantile of the resulting chilling distributions. This metric can be interpreted as the amount of chilling that growers can safely expect under each scenario. Winter chill declined substantially for all emissions scenarios, with the area of safe winter chill for many tree species or cultivars decreasing 50-75% by mid-21st century, and 90-100% by late century. Both chilling models consistently projected climatic conditions by the middle to end of the 21st century that will no longer support some of the main tree crops currently grown in California, with the Chilling Hours Model projecting greater changes than the Dynamic Model. The tree crop industry in California will likely need to develop agricultural adaptation measures (e.g. low-chill varieties and dormancy-breaking chemicals) to cope with these projected changes. For some crops, production might no longer be possible.

Archaeogenetic Evidence of Ancient Nubian Barley Evolution from Six to Two-Row Indicates Local Adaptation:

Archaeobotanical samples of barley (Hordeum vulgare L.) found at Qasr Ibrim display a two-row phenotype that is unique to the region of archaeological sites upriver of the first cataract of the Nile, characterised by the development of distinctive lateral bracts. The phenotype occurs throughout all strata at Qasr Ibrim, which range in age from 3000 to a few hundred years. We extracted ancient DNA from barley samples from the entire range of occupancy of the site, and studied the Vrs1 gene responsible for row number in extant barley. Surprisingly, we found a discord between the genotype and phenotype in all samples; all the barley had a genotype consistent with the six-row condition. These results indicate a six-row ancestry for the Qasr Ibrim barley, followed by a reassertion of the two-row condition. Modelling demonstrates that this sequence of evolutionary events requires a strong selection pressure. The two-row phenotype at Qasr Ibrim is caused by a different mechanism to that in extant barley. The strength of selection required for this mechanism to prevail indicates that the barley became locally adapted in the region in response to a local selection pressure. The consistency of the genotype/phenotype discord over time supports a scenario of adoption of this barley type by successive cultures, rather than the importation of new barley varieties associated with individual cultures.

Beyond Marine Reserves: Exploring the Approach of Selecting Areas where Fishing Is Permitted, Rather than Prohibited:

Marine populations have been declining at a worrying rate, due in large part to fishing pressures. The challenge is to secure a future for marine life while minimizing impacts on fishers and fishing communities. Rather than selecting areas where fishing is banned – as is usually the case with spatial management – we assess the concept of designating areas where fishing is permitted. We use spatial catch statistics for thirteen commercial fisheries on Canada’s west coast to determine the minimum area that would be needed to maintain a pre-ascribed target percentage of current catches. We found that small reductions in fisheries yields, if strategically allocated, could result in large unfished areas that are representative of biophysical regions and habitat types, and have the potential to achieve remarkable conservation gains. Our approach of selecting fishing areas instead of reserves could help redirect debate about the relative values that society places on conservation and extraction, in a framework that could gain much by losing little. Our ideas are intended to promote discussions about the current status quo in fisheries management, rather than providing a definitive solution.

Understanding Oceanic Migrations with Intrinsic Biogeochemical Markers:

Migratory marine vertebrates move annually across remote oceanic water masses crossing international borders. Many anthropogenic threats such as overfishing, bycatch, pollution or global warming put millions of marine migrants at risk especially during their long-distance movements. Therefore, precise knowledge about these migratory movements to understand where and when these animals are more exposed to human impacts is vital for addressing marine conservation issues. Because electronic tracking devices suffer from several constraints, mainly logistical and financial, there is emerging interest in finding appropriate intrinsic markers, such as the chemical composition of inert tissues, to study long-distance migrations and identify wintering sites. Here, using tracked pelagic seabirds and some of their own feathers which were known to be grown at different places and times within the annual cycle, we proved the value of biogeochemical analyses of inert tissue as tracers of marine movements and habitat use. Analyses of feathers grown in summer showed that both stable isotope signatures and element concentrations can signal the origin of breeding birds feeding in distinct water masses. However, only stable isotopes signalled water masses used during winter because elements mainly accumulated during the long breeding period are incorporated into feathers grown in both summer and winter. Our findings shed new light on the simple and effective assignment of marine organisms to distinct oceanic areas, providing new opportunities to study unknown migration patterns of secretive species, including in relation to human-induced mortality on specific populations in the marine environment.

Local Stressors Reduce Coral Resilience to Bleaching:

Coral bleaching, during which corals lose their symbiotic dinoflagellates, typically corresponds with periods of intense heat stress, and appears to be increasing in frequency and geographic extent as the climate warms. A fundamental question in coral reef ecology is whether chronic local stress reduces coral resistance and resilience from episodic stress such as bleaching, or alternatively promotes acclimatization, potentially increasing resistance and resilience. Here we show that following a major bleaching event, Montastraea faveolata coral growth rates at sites with higher local anthropogenic stressors remained suppressed for at least 8 years, while coral growth rates at sites with lower stress recovered in 2-3 years. Instead of promoting acclimatization, our data indicate that background stress reduces coral fitness and resilience to episodic events. We also suggest that reducing chronic stress through local coral reef management efforts may increase coral resilience to global climate change.

Hypocretin-2 Saporin Lesions of the Ventrolateral Periaquaductal Gray (vlPAG) Increase REM Sleep in Hypocretin Knockout Mice:

Ten years ago the sleep disorder narcolepsy was linked to the neuropeptide hypocretin (HCRT), also known as orexin. This disorder is characterized by excessive day time sleepiness, inappropriate triggering of rapid-eye movement (REM) sleep and cataplexy, which is a sudden loss of muscle tone during waking. It is still not known how HCRT regulates REM sleep or muscle tone since HCRT neurons are localized only in the lateral hypothalamus while REM sleep and muscle atonia are generated from the brainstem. To identify a potential neuronal circuit, the neurotoxin hypocretin-2-saporin (HCRT2-SAP) was used to lesion neurons in the ventral lateral periaquaductal gray (vlPAG). The first experiment utilized hypocretin knock-out (HCRT-ko) mice with the expectation that deletion of both HCRT and its target neurons would exacerbate narcoleptic symptoms. Indeed, HCRT-ko mice (n = 8) given the neurotoxin HCRT2-SAP (16.5 ng/23nl/sec each side) in the vlPAG had levels of REM sleep and sleep fragmentation that were considerably higher compared to HCRT-ko given saline (+39%; n = 7) or wildtype mice (+177%; n = 9). However, cataplexy attacks did not increase, nor were levels of wake or non-REM sleep changed. Experiment 2 determined the effects in mice where HCRT was present but the downstream target neurons in the vlPAG were deleted by the neurotoxin. This experiment utilized an FVB-transgenic strain of mice where eGFP identifies GABA neurons. We verified this and also determined that eGFP neurons were immunopositive for the HCRT-2 receptor. vlPAG lesions in these mice increased REM sleep (+79% versus saline controls) and it was significantly correlated (r = 0.89) with loss of eGFP neurons. These results identify the vlPAG as one site that loses its inhibitory control over REM sleep, but does not cause cataplexy, as a result of hypocretin deficiency.

Susceptibility to Infection and Immune Response in Insular and Continental Populations of Egyptian Vulture: Implications for Conservation:

A generalized decline in populations of Old World avian scavengers is occurring on a global scale. The main cause of the observed crisis in continental populations of these birds should be looked for in the interaction between two factors – changes in livestock management, including the increased use of pharmaceutical products, and disease. Insular vertebrates seem to be especially susceptible to diseases induced by the arrival of exotic pathogens, a process often favored by human activities, and sedentary and highly dense insular scavengers populations may be thus especially exposed to infection by such pathogens. Here, we compare pathogen prevalence and immune response in insular and continental populations of the globally endangered Egyptian vulture under similar livestock management scenarios, but with different ecological and evolutionary perspectives. Adult, immature, and fledgling vultures from the Canary Islands and the Iberian Peninsula were sampled to determine a) the prevalence of seven pathogen taxa and b) their immunocompetence, as measured by monitoring techniques (white blood cells counts and immunoglobulins). In the Canarian population, pathogen prevalence was higher and, in addition, an association among pathogens was apparent, contrary to the situation detected in continental populations. Despite that, insular fledglings showed lower leukocyte profiles than continental birds and Canarian fledglings infected by Chlamydophila psittaci showed poorer cellular immune response. A combination of environmental and ecological factors may contribute to explain the high susceptibility to infection found in insular vultures. The scenario described here may be similar in other insular systems where populations of carrion-eaters are in strong decline and are seriously threatened. Higher susceptibility to infection may be a further factor contributing decisively to the extinction of island scavengers in the present context of global change and increasing numbers of emerging infectious diseases.

Quality of Pharmaceutical Advertisements in Medical Journals: A Systematic Review:

Journal advertising is one of the main sources of medicines information to doctors. Despite the availability of regulations and controls of drug promotion worldwide, information on medicines provided in journal advertising has been criticized in several studies for being of poor quality. However, no attempt has been made to systematically summarise this body of research. We designed this systematic review to assess all studies that have examined the quality of pharmaceutical advertisements for prescription products in medical and pharmacy journals. Studies were identified via searching electronic databases, web library, search engine and reviewing citations (1950 – February 2006). Only articles published in English and examined the quality of information included in pharmaceutical advertisements for prescription products in medical or pharmacy journals were included. For each eligible article, a researcher independently extracted the data on the study methodology and outcomes. The data were then reviewed by a second researcher. Any disagreements were resolved by consensus. The data were analysed descriptively. The final analysis included 24 articles. The studies reviewed advertisements from 26 countries. The number of journals surveyed in each study ranged from four to 24 journals. Several outcome measures were examined including references and claims provided in advertisements, availability of product information, adherence to codes or guidelines and presentation of risk results. The majority of studies employed a convenience-sampling method. Brand name, generic name and indications were usually provided. Journal articles were commonly cited to support pharmaceutical claims. Less than 67% of the claims were supported by a systematic review, a meta-analysis or a randomised control trial. Studies that assessed misleading claims had at least one advertisement with a misleading claim. Two studies found that less than 28% of claims were unambiguous clinical claims. Most advertisements with quantitative information provided risk results as relative risk reduction. Studies were conducted in 26 countries only and then the generalizability of the results is limited. Evidence from this review indicates that low quality of journal advertising is a global issue. As information provided in journal advertising has the potential to change doctors’ prescribing behaviour, ongoing efforts to increase education about drug promotion are crucial. The results from our review suggest the need for a global pro-active and effective regulatory system to ensure that information provided in medical journal advertising is supporting the quality use of medicines.

Still getting all my Legos together after the trip, here are some of the highlight from various PLoS journals from last Friday and today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

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There are 23 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

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There are 20 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

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There are 12 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Reef Endemism, Host Specificity and Temporal Stability in Populations of Symbiotic Dinoflagellates from Two Ecologically Dominant Caribbean Corals:

The dinoflagellate genus Symbiodinium forms symbioses with numerous protistan and invertebrate metazoan hosts. However, few data on symbiont genetic structure are available, hindering predictions of how these populations and their host associations will fair in the face of global climate change. Here, Symbiodinium population structure from two of the Caribbean’s ecologically dominant scleractinian corals, Montastraea faveolata and M. annularis, was examined. Tagged colonies on Florida Keys and Bahamian (i.e., Exuma Cays) reefs were sampled from 2003-2005 and their Symbiodinium diversity assessed via internal transcribed spacer 2 (ITS2) rDNA and three Symbiodinium Clade B-specific microsatellite loci. Generally, the majority of host individuals at a site harbored an identical Symbiodinium ITS2 “type” B1 microsatellite genotype. Notably, symbiont genotypes were largely reef endemic, suggesting a near absence of dispersal between populations. Relative to the Bahamas, sympatric M. faveolata and M. annularis in the Florida Keys harbored unique Symbiodinium populations, implying regional host specificity in these relationships. Furthermore, within-colony Symbiodinium population structure remained stable through time and environmental perturbation, including a prolonged bleaching event in 2005. Taken together, the population-level endemism, specificity and stability exhibited by Symbiodinium raises concerns about the long-term adaptive capacity and persistence of these symbioses in an uncertain future of climate change.

Eyes Wide Shut: Amygdala Mediates Eyes-Closed Effect on Emotional Experience with Music:

The perceived emotional value of stimuli and, as a consequence the subjective emotional experience with them, can be affected by context-dependent styles of processing. Therefore, the investigation of the neural correlates of emotional experience requires accounting for such a variable, a matter of an experimental challenge. Closing the eyes affects the style of attending to auditory stimuli by modifying the perceptual relationship with the environment without changing the stimulus itself. In the current study, we used fMRI to characterize the neural mediators of such modification on the experience of emotionality in music. We assumed that closed eyes position will reveal interplay between different levels of neural processing of emotions. More specifically, we focused on the amygdala as a central node of the limbic system and on its co-activation with the Locus Ceruleus (LC) and Ventral Prefrontal Cortex (VPFC); regions involved in processing of, respectively, ‘low’, visceral-, and ‘high’, cognitive-related, values of emotional stimuli. Fifteen healthy subjects listened to negative and neutral music excerpts with eyes closed or open. As expected, behavioral results showed that closing the eyes while listening to emotional music resulted in enhanced rating of emotionality, specifically of negative music. In correspondence, fMRI results showed greater activation in the amygdala when subjects listened to the emotional music with eyes closed relative to eyes open. More so, by using voxel-based correlation and a dynamic causal model analyses we demonstrated that increased amygdala activation to negative music with eyes closed led to increased activations in the LC and VPFC. This finding supports a system-based model of perceived emotionality in which the amygdala has a central role in mediating the effect of context-based processing style by recruiting neural operations involved in both visceral (i.e. ‘low’) and cognitive (i.e. ‘high’) related processes of emotions.

Contrasting Role of Octopamine in Appetitive and Aversive Learning in the Crab Chasmagnathus:

Biogenic amines are implicated in reinforcing associative learning. Octopamine (OA) is considered the invertebrate counterpart of noradrenaline and several studies in insects converge on the idea that OA mediates the reward in appetitive conditioning. However, it is possible to assume that OA could have a different role in an aversive conditioning. Here we pharmacologically studied the participation of OA in two learning processes in the crab Chasmagnathus granulatus, one appetitive and one aversive. It is shown that the aversive memory is impaired by an OA injection applied immediately or 30 minutes after the last training trial. By contrast, the appetitive memory is blocked by OA antagonists epinastine and mianserine, but enhanced by OA when injected together with the supply of a minimum amount of reinforcement. Finally, double-learning experiments in which crabs are given the aversive and the appetitive learning either successively or simultaneously allow us to study the interaction between both types of learning and analyze the presumed action of OA. We found that the appetitive training offered immediately, but not one hour, after an aversive training has an amnesic effect on the aversive memory, mimicking the effect and the kinetic of an OA injection. Our results demonstrate that the role of OA is divergent in two memory processes of opposite signs: on the one hand it would mediate the reinforcement in appetitive learning, and on the other hand it has a deleterious effect over aversive memory consolidation.

There are 10 new articles published Friday night and 8 new articles published tonight in PLoS ONE. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

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There are 19 new articles published last night and 22 new articles published today in PLoS ONE. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Energy Stores Are Not Altered by Long-Term Partial Sleep Deprivation in Drosophila melanogaster:

Recent human studies reveal a widespread association between short sleep and obesity. Two hypotheses, which are not mutually exclusive, might explain this association. First, genetic factors that reduce endogenous sleep times might also impact energy stores, an assertion that we confirmed in a previous study. Second, metabolism may be altered by chronic partial sleep deprivation. Here we address the second assertion by measuring the impact of long-term partial sleep deprivation on energy stores using Drosophila as a model. We subjected flies to long-term partial sleep deprivation via two different methods: a mechanical stimulus and a light stimulus. We then measured whole-body triglycerides and glycogen, two important sources of energy for the fly, and compared them to un-stimulated controls. We also measured changes in energy stores in response to a random circadian clock shift. Sex and line-dependent alterations in glycogen and/or triglyceride levels occurred in response to the circadian clock shift and in flies subjected to a single night of sleep deprivation using light. Thus, consistent with previous studies, our findings suggest that acute sleep loss and changes to the circadian clock can alter metabolism. Significant changes in energy stores were also observed when flies were subjected to chronic sleep loss via the mechanical stimulus, although not the light stimulus. Interestingly, mechanical stimulation resulted in the same change in energy stores even when it was not associated with sleep deprivation, suggesting that the changes are caused by stress rather than sleep loss. These findings emphasize the importance of taking stress into account when evaluating the relationship between sleep loss and metabolism.

Explaining Lengths and Shapes of Yeast by Scaling Arguments:

Lengths and shapes are approached in different ways in different fields: they serve as a read-out for classifying genes or proteins in cell biology whereas they result from scaling arguments in condensed matter physics. Here, we propose a combined approach with examples illustrated for the fission yeast Schizosaccharomyces pombe.

Certainty in Categorical Judgment of Size:

The certainty of judgment (or self-confidence) has been traditionally studied in relation with the accuracy. However, from an observer’s viewpoint, certainty may be more closely related to the consistency of judgment than to its accuracy: consistent judgments are objectively certain in the sense that any external observer can rely on these judgments to happen. The regions of certain vs. uncertain judgment were determined in a categorical rating experiment. The participants rated the size of visual objects on a 5-point scale. There was no feedback so that there were no constraints of accuracy. Individual data was examined, and the ratings were characterized by their frequency distributions (or categories). The main result was that the individual categories always presented a core of certainty where judgment was totally consistent, and large peripheries where judgment was inconsistent. In addition, the geometry of cores and boundaries exhibited several phenomena compatible with the literature on visual categorical judgment. The ubiquitous presence of cores in absence of accuracy constraints provided insights about objective certainty that may complement the literature on subjective certainty (self-confidence) and the accuracy of judgment.

Decaying Raphia farinifera Palm Trees Provide a Source of Sodium for Wild Chimpanzees in the Budongo Forest, Uganda:

For some years, chimpanzees have been observed eating the pith of decaying palm trees of Raphia farinifera in the Budongo Forest, Uganda. The reasons for doing this have until now been unknown. An analysis of the pith for mineral content showed high levels of sodium to be present in the samples. By contrast, lower levels were found in bark of other tree species, and also in leaf and fruit samples eaten by chimpanzees. The differences between the Raphia samples and the non-Raphia samples were highly significant (p<0.001). It is concluded that Raphia provides a rich and possibly essential source of sodium for the Budongo chimpanzees. Comparison of a chewed sample (wadge) of Raphia pith with a sample from the tree showed a clear reduction in sodium content in the chewed sample. Black and white colobus monkeys in Budongo Forest also feed on the pith of Raphia. At present, the survival of Raphia palms in Budongo Forest is threatened by the use of this tree by local tobacco farmers.

Contemporary Parallel Diversification, Antipredator Adaptations and Phenotypic Integration in an Aquatic Isopod:

It is increasingly being recognized that predation can be a strong diversifying agent promoting ecological divergence. Adaptations against different predatory regimes can emerge over short periods of time and include many different traits. We studied antipredator adaptations in two ecotypes of an isopod (Asellus aquaticus) that have, diverged in parallel in two Swedish lakes over the last two decades. We quantified differences in escape speed, morphology and behavior for isopods from different ecotypes present in these lakes. Isopods from the source habitat (reed) coexist with mainly invertebrate predators. They are more stream-profiled and have higher escape speeds than isopods in the newly colonized stonewort habitat, which has higher density of fish predators. Stonewort isopods also show more cautious behaviors and had higher levels of phenotypic integration between coloration and morphological traits than the reed isopods. Colonization of a novel habitat with a different predation regime has thus strengthened the correlations between pigmentation and morphology and weakened escape performance. The strong signature of parallelism for these phenotypic traits indicates that divergence is likely to be adaptive and is likely to have been driven by differences in predatory regimes. Furthermore, our results indicate that physical performance, behavior and morphology can change rapidly and in concert as new habitats are colonized.

There have been 19 new articles Monday night and 11 new articles Tuesday night in PLoS ONE. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

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Just trying to catch up with the publicartions in various PLoS Journals this past week. Here are some interesting titles.
As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

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Just because I am galivanting in Lindau does not mean I could not take a look at the brand new papers published in PLoS ONE, PLoS Biology, PLoS Medicine and PLoS Neglected Tropical Diseases last night. A few titles caught my eye – take a look. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Characteristics of Medical Research News Reported on Front Pages of Newspapers:

The placement of medical research news on a newspaper’s front page is intended to gain the public’s attention, so it is important to understand the source of the news in terms of research maturity and evidence level. We searched LexisNexis to identify medical research reported on front pages of major newspapers published from January 1, 2000 to December 31, 2002. We used MEDLINE and Google Scholar to find journal articles corresponding to the research, and determined their evidence level. Of 734 front-page medical research stories identified, 417 (57%) referred to mature research published in peer-reviewed journals. The remaining 317 stories referred to preliminary findings presented at scientific or press meetings; 144 (45%) of those stories mentioned studies that later matured (i.e. were published in journals within 3 years after news coverage). The evidence-level distribution of the 515 journal articles quoted in news stories reporting on mature research (3% level I, 21% level II, 42% level III, 4% level IV, and 31% level V) differed from that of the 170 reports of preliminary research that later matured (1%, 19%, 35%, 12%, and 33%, respectively; chi-square test, P = .0009). No news stories indicated evidence level. Fewer than 1 in 5 news stories reporting preliminary findings acknowledged the preliminary nature of their content. Only 57% of front-page stories reporting on medical research are based on mature research, which tends to have a higher evidence level than research with preliminary findings. Medical research news should be clearly referenced and state the evidence level and limitations to inform the public of the maturity and quality of the source.

Racial Differences in the Human Endogenous Circadian Period:

The length of the endogenous period of the human circadian clock (tau) is slightly greater than 24 hours. There are individual differences in tau, which influence the phase angle of entrainment to the light/dark (LD) cycle, and in doing so contribute to morningness-eveningness. We have recently reported that tau measured in subjects living on an ultradian LD cycle averaged 24.2 hours, and is similar to tau measured using different experimental methods. Here we report racial differences in tau. Subjects lived on an ultradian LD cycle (1.5 hours sleep, 2.5 hours wake) for 3 days. Circadian phase assessments were conducted before and after the ultradian days to determine the change in circadian phase, which was attributed to tau. African American subjects had a significantly shorter tau than subjects of other races. We also tested for racial differences in our previous circadian phase advancing and phase delaying studies. In the phase advancing study, subjects underwent 4 days of a gradually advancing sleep schedule combined with a bright light pulse upon awakening each morning. In the phase delaying study, subjects underwent 4 days of a gradually delaying sleep schedule combined with evening light pulses before bedtime. African American subjects had larger phase advances and smaller phase delays, relative to Caucasian subjects. The racial differences in tau and circadian phase shifting have important implications for understanding normal phase differences between individuals, for developing solutions to the problems of jet lag and shift work, and for the diagnosis and treatment of circadian rhythm based sleep disorders such as advanced and delayed sleep phase disorder.

Seasonal Hunger: A Neglected Problem with Proven Solutions:

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Most of the world’s acute hunger and undernutrition occurs not in conflicts and natural disasters but in the annual “hunger season,” the time of year when the previous year’s harvest stocks have dwindled, food prices are high, and jobs are scarce.
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We know what works in fighting seasonal hunger and undernutrition: there are identifiable policy and program successes in contexts around the world, but they often operate on a small scale and in isolation.
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Community-based interventions to treat acute undernutrition and promote growth of preschool children are examples of successful interventions that should be scaled up.
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Global scale-up of a basic “minimum essential” intervention package against seasonal hunger would cost around 0.1% of global GDP and save millions of lives, while protecting millions more from severe illness.
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Focusing on seasonal hunger would be an effective way to leverage resources for the attainment of the hunger-related Millennium Development Goal.

Bad Taste Protects Fruit Flies from Eating a Toxic Amino Acid in Plants:

Besides enhancing the pleasure of eating, our sense of taste can steer us away from poisonous foods. Many plants, for example, produce bitter-tasting toxins, such as caffeine and quinine, to deter predation by herbivores from cows to insects. But it remains a mystery how animals developed their capacity to detect–and so avoid–the tens of thousands of plant toxins, which include alkaloids, phenolics, and nonprotein amino acids. The best-known toxic nonprotein amino acid is L-canavanine, which accumulates in the seeds of alfalfa (Medicago sativa) and many other leguminosae. L-canavanine is so similar to the amino acid L-arginine that it gets incorporated into proteins, rendering them dysfunctional. A few insects have developed strategies for counteracting this toxin, including larvae of the beetle Caryedes brasiliensis, which depend entirely on seeds of the legume Dioclea megacarpa and catabolize L-canavanine into harmless compounds. However, the vast majority of insects are susceptible to L-canavanine, and little is known about their ability to detect it in plants.

Clean Water Should Be Recognized as a Human Right:

At the March 2009 United Nations (UN) meetings coinciding with the World Water Forum, Canada, Russia, and the United States refused to support a declaration that would recognize water as a basic human right. The special resolution proposed by Germany and Spain, and endorsed by the President of the UN General Assembly, was instead rejected in favor of further examination of issues of access to safe drinking water and sanitation [1].
Opposition to this declaration runs counter to considerable evidence that access to clean water, which is essential for health, is under threat. According to the World Health Organization, 1.2 billion people worldwide do not have access to clean drinking water, and a further 2.6 billion lack adequate sanitation services. These numbers are expected to rise. The UN has estimated that 2.8 billion people in 48 countries will be living in conditions of water stress or scarcity by 2025 [2].

Parks and Tourism:

Why should it matter how many people visit national parks? In a word: politics. Protected areas are not only physical places, reservoirs of biodiversity, and sources of ecosystem services, such as breathable air and drinkable water. They are also human political constructs, and they are under ever-increasing pressures from growing human populations and resource demands. Visitors may bring them the political capital to survive.
Biologists have pointed out for decades that protected areas are not playgrounds, but life-support systems for the planet’s population of humans, as well as its other species. Economists estimate that ecosystem services worldwide contribute twice as much to the human economy each year as all forms of human industry combined–many trillions of dollars [1],[2]. At regional scale, ecosystem services from National Wildlife Refuges in the contiguous 48 states of the Unites States have been valued at US$27 billion annually [3]. The human economic value of conserving biodiversity is many orders of magnitude higher than the funds invested in it [2],[4]-[9]. The cost of buying all of the world’s biodiversity hotspots outright has been estimated at around US$100 billion–less than five-years’ expenditure on soft drinks in the US [10]. But the actual funds allocated worldwide each year, a few billion dollars in total, are <5% of minimum requirements for effective conservation [11]. This compares with the trillions of dollars spent in 2009 to prop up financial systems in the US, European Union, and China [12].

There are 15 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
A Principal Component Analysis of 39 Scientific Impact Measures:

The impact of scientific publications has traditionally been expressed in terms of citation counts. However, scientific activity has moved online over the past decade. To better capture scientific impact in the digital era, a variety of new impact measures has been proposed on the basis of social network analysis and usage log data. Here we investigate how these new measures relate to each other, and how accurately and completely they express scientific impact. We performed a principal component analysis of the rankings produced by 39 existing and proposed measures of scholarly impact that were calculated on the basis of both citation and usage log data. Our results indicate that the notion of scientific impact is a multi-dimensional construct that can not be adequately measured by any single indicator, although some measures are more suitable than others. The commonly used citation Impact Factor is not positioned at the core of this construct, but at its periphery, and should thus be used with caution.

Cool Sex? Hibernation and Reproduction Overlap in the Echidna:

During hibernation there is a slowing of all metabolic processes, and thus it is normally considered to be incompatible with reproduction. In Tasmania the egg-laying mammal, the echidna (Tachyglossus aculeatus) hibernates for several months before mating in mid-winter, and in previous studies we observed males with females that were still hibernating. We monitored the reproductive activity of radio-tracked echidnas by swabbing the reproductive tract for sperm while external temperature loggers provided information on the timing of hibernation. Additional information was provided by camera traps and ultrasound imaging. More than a third of the females found in mating groups were torpid, and the majority of these had mated. Some females re-entered deep torpor for extended periods after mating. Ultrasound examination showed a developing egg in the uterus of a female that had repeatedly re-entered torpor. The presence of fresh sperm in cloacal swabs taken from this female on three occasions after her presumed date of fertilization indicated she mated several times after being fertilized. The mating of males with torpid females is the result of extreme competition between promiscuous males, while re-entry into hibernation by pregnant females could improve the possibility of mating with a better quality male.

More than 9,000,000 Unique Genes in Human Gut Bacterial Community: Estimating Gene Numbers Inside a Human Body:

Estimating the number of genes in human genome has been long an important problem in computational biology. With the new conception of considering human as a super-organism, it is also interesting to estimate the number of genes in this human super-organism. We presented our estimation of gene numbers in the human gut bacterial community, the largest microbial community inside the human super-organism. We got 552,700 unique genes from 202 complete human gut bacteria genomes. Then, a novel gene counting model was built to check the total number of genes by combining culture-independent sequence data and those complete genomes. 16S rRNAs were used to construct a three-level tree and different counting methods were introduced for the three levels: strain-to-species, species-to-genus, and genus-and-up. The model estimates that the total number of genes is about 9,000,000 after those with identity percentage of 97% or up were merged. By combining completed genomes currently available and culture-independent sequencing data, we built a model to estimate the number of genes in human gut bacterial community. The total number of genes is estimated to be about 9 million. Although this number is huge, we believe it is underestimated. This is an initial step to tackle this gene counting problem for the human super-organism. It will still be an open problem in the near future.

Let’s take a look at all seven PLoS journals today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

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There are 14 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

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There are 20 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
A Fish Eye Out of Water: Ten Visual Opsins in the Four-Eyed Fish, Anableps anableps:

The “four-eyed” fish Anableps anableps has numerous morphological adaptations that enable above and below-water vision. Here, as the first step in our efforts to identify molecular adaptations for aerial and aquatic vision in this species, we describe the A. anableps visual opsin repertoire. We used PCR, cloning, and sequencing to survey cDNA using unique primers designed to amplify eight sequences from five visual opsin gene subfamilies, SWS1, SWS2, RH1, RH2, and LWS. We also used Southern blotting to count opsin loci in genomic DNA digested with EcoR1 and BamH1. Phylogenetic analyses confirmed the identity of all opsin sequences and allowed us to map gene duplication and divergence events onto a tree of teleost fish. Each of the gene-specific primer sets produced an amplicon from cDNA, indicating that A. anableps possessed and expressed at least eight opsin genes. A second PCR-based survey of genomic and cDNA uncovered two additional LWS genes. Thus, A. anableps has at least ten visual opsins and all but one were expressed in the eyes of the single adult surveyed. Among these ten visual opsins, two have key site haplotypes not found in other fish. Of particular interest is the A. anableps-specific opsin in the LWS subfamily, S180γ, with a SHYAA five key site haplotype. Although A. anableps has a visual opsin gene repertoire similar to that found in other fishes in the suborder Cyprinodontoidei, the LWS opsin subfamily has two loci not found in close relatives, including one with a key site haplotype not found in any other fish species. A. anableps opsin sequence data will be used to design in situ probes allowing us to test the hypothesis that opsin gene expression differs in the distinct ventral and dorsal retinas found in this species.

Melanopsin Bistability: A Fly’s Eye Technology in the Human Retina:

In addition to rods and cones, the human retina contains light-sensitive ganglion cells that express melanopsin, a photopigment with signal transduction mechanisms similar to that of invertebrate rhabdomeric photopigments (IRP). Like fly rhodopsins, melanopsin acts as a dual-state photosensitive flip-flop in which light drives both phototransduction responses and chromophore photoregeneration that bestows independence from the retinoid cycle required by rods and cones to regenerate photoresponsiveness following bleaching by light. To explore the hypothesis that melanopsin in humans expresses the properties of a bistable photopigment in vivo we used the pupillary light reflex (PLR) as a tool but with methods designed to study invertebrate photoreceptors. We show that the pupil only attains a fully stabilized state of constriction after several minutes of light exposure, a feature that is consistent with typical IRP photoequilibrium spectra. We further demonstrate that previous exposure to long wavelength light increases, while short wavelength light decreases the amplitude of pupil constriction, a fundamental property of IRP difference spectra. Modelling these responses to invertebrate photopigment templates yields two putative spectra for the underlying R and M photopigment states with peaks at 481 nm and 587 nm respectively. Furthermore, this bistable mechanism may confer a novel form of “photic memory” since information of prior light conditions is retained and shapes subsequent responses to light. These results suggest that the human retina exploits fly-like photoreceptive mechanisms that are potentially important for the modulation of non-visual responses to light and highlights the ubiquitous nature of photoswitchable photosensors across living organisms.

Stimulus Familiarity Affects Perceptual Restoration in the European Starling (Sturnus vulgaris):

Humans can easily restore a speech signal that is temporally masked by an interfering sound (e.g., a cough masking parts of a word in a conversation), and listeners have the illusion that the speech continues through the interfering sound. This perceptual restoration for human speech is affected by prior experience. Here we provide evidence for perceptual restoration in complex vocalizations of a songbird that are acquired by vocal learning in a similar way as humans learn their language. European starlings were trained in a same/different paradigm to report salient differences between successive sounds. The birds’ response latency for discriminating between a stimulus pair is an indicator for the salience of the difference, and these latencies can be used to evaluate perceptual distances using multi-dimensional scaling. For familiar motifs the birds showed a large perceptual distance if discriminating between song motifs that were muted for brief time periods and complete motifs. If the muted periods were filled with noise, the perceptual distance was reduced. For unfamiliar motifs no such difference was observed. The results suggest that starlings are able to perceptually restore partly masked sounds and, similarly to humans, rely on prior experience. They may be a suitable model to study the mechanism underlying experience-dependent perceptual restoration.

Induction of Empathy by the Smell of Anxiety:

The communication of stress/anxiety between conspecifics through chemosensory signals has been documented in many vertebrates and invertebrates. Here, we investigate how chemosensory anxiety signals conveyed by the sweat of humans (N = 49) awaiting an academic examination are processed by the human brain, as compared to chemosensory control signals obtained from the same sweat donors in a sport condition. The chemosensory stimuli were pooled according to the donation condition and administered to 28 participants (14 males) synchronously to breathing via an olfactometer. The stimuli were perceived with a low intensity and accordingly only about half of the odor presentations were detected by the participants. The fMRI results (event-related design) show that chemosensory anxiety signals activate brain areas involved in the processing of social emotional stimuli (fusiform gyrus), and in the regulation of empathic feelings (insula, precuneus, cingulate cortex). In addition, neuronal activity within attentional (thalamus, dorsomedial prefrontal cortex) and emotional (cerebellum, vermis) control systems were observed. The chemosensory perception of human anxiety seems to automatically recruit empathy-related resources. Even though the participants could not attentively differentiate the chemosensory stimuli, emotional contagion seems to be effectively mediated by the olfactory system.

Large-Scale Assessment of the Effect of Popularity on the Reliability of Research:

Based on theoretical reasoning it has been suggested that the reliability of findings published in the scientific literature decreases with the popularity of a research field. Here we provide empirical support for this prediction. We evaluate published statements on protein interactions with data from high-throughput experiments. We find evidence for two distinctive effects. First, with increasing popularity of the interaction partners, individual statements in the literature become more erroneous. Second, the overall evidence on an interaction becomes increasingly distorted by multiple independent testing. We therefore argue that for increasing the reliability of research it is essential to assess the negative effects of popularity and develop approaches to diminish these effects.

No Need to Discriminate? Reproductive Diploid Males in a Parasitoid with Complementary Sex Determination:

Diploid males in hymenopterans are generally either inviable or sterile, thus imposing a severe genetic load on populations. In species with the widespread single locus complementary sex determination (sl-CSD), sex depends on the genotype at one single locus with multiple alleles. Haploid (hemizygous) individuals are always males. Diploid individuals develop into females when heterozygous and into males when homozygous at the sex determining locus. Our comparison of the mating and reproductive success of haploid and diploid males revealed that diploid males of the braconid parasitoid Cotesia glomerata sire viable and fertile diploid daughters. Females mated to diploid males, however, produced fewer daughters than females mated to haploid males. Nevertheless, females did not discriminate against diploid males as mating partners. Diploid males initiated courtship display sooner than haploid males and were larger in body size. Although in most species so far examined diploid males were recognized as genetic dead ends, we present a second example of a species with sl-CSD and commonly occurring functionally reproductive diploid males. Our study suggests that functionally reproductive diploid males might not be as rare as hitherto assumed. We argue that the frequent occurrence of inbreeding in combination with imperfect behavioural adaptations towards its avoidance promote the evolution of diploid male fertility.

Gender Differences in the Motivational Processing of Babies Are Determined by Their Facial Attractiveness:

This study sought to determine how esthetic appearance of babies may affect their motivational processing by the adults. Healthy men and women were administered two laboratory-based tasks: a) key pressing to change the viewing time of normal-looking babies and of those with abnormal facial features (e.g., cleft palate, strabismus, skin disorders, Down’s syndrome and fetal alcohol syndrome) and b) attractiveness ratings of these images. Exposure to the babies’ images produced two different response patterns: for normal babies, there was a similar effort by the two groups to extend the visual processing with lower attractiveness ratings by men; for abnormal babies, women exerted greater effort to shorten the viewing time despite attractiveness ratings comparable to the men. These results indicate that gender differences in the motivational processing of babies include excessive (relative to the esthetic valuation) motivation to extend the viewing time of normal babies by men vs. shortening the exposure to the abnormal babies by women. Such gender-specific incentive sensitization phenomenon may reflect an evolutionary-derived need for diversion of limited resources to the nurturance of healthy offspring.

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Friday – the day to take a look at all seven PLoS journals and make my own personal picks. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Taking the Lag out of Jet Lag through Model-Based Schedule Design:

Traveling across several times zones can cause an individual to experience “jet lag,” which includes trouble sleeping at night and trouble remaining awake during the day. A major cause of these effects is the desynchronization between the body’s internal circadian clock and local environmental cues. A well-known intervention to resynchronize an individual’s clock with the environment is appropriately timed light exposure. Used as an intervention, properly timed light stimuli can reset an individual’s internal circadian clock to align with local time, resulting in more efficient sleep, a decrease in fatigue, and an increase in cognitive performance. The contrary is also true: poorly timed light exposure can prolong the resynchronization process. In this paper, we present a computational method for automatically determining the proper placement of these interventional light stimuli. We used this method to simulate shifting sleep-wake schedules (as seen in jet lag situations) and design interventions. Essential to our approach is the use of mathematical models that simulate the body’s internal circadian clock and its effect on human performance. Our results include quicker design of multiple schedule alternatives and predictions of substantial performance improvements relative to no intervention. Therefore, our methods allow us to use these models not only to assess schedules but also to interactively design schedules that will result in improved performance.

Allometry of the Duration of Flight Feather Molt in Birds:

The pace of life varies with body size and is generally slower among larger organisms. Larger size creates opportunities but also establishes constraints on time-dependent processes. Flying birds depend on large wing feathers that deteriorate over time and must be replaced through molting. The lengths of flight feathers increase as the 1/3 power of body mass, as one expects for a length-to-volume ratio. However, feather growth rate increases as only the 1/6 power of body mass, possibly because a two-dimensional feather is produced by a one-dimensional growing region. The longer time required to grow a longer feather constrains the way in which birds molt, because partially grown feathers reduce flight efficiency. Small birds quickly replace their flight feathers, often growing several feathers at a time in each wing. Larger species either prolong molt over two or more years, adopt complex patterns of multiple feather replacement to minimize gaps in the flight surface, or, among species that do not rely on flight for feeding, simultaneously molt all their flight feathers. We speculate that the extinct 70-kg raptor, Argentavis magnificens, must have undergone such a simultaneous molt, living off fat reserves for the duration.

Will the Public’s Health Fall Victim to the Home Foreclosure Epidemic?:

While policy makers worldwide have scrambled to counter its economic effects, the potential health implications of home foreclosure have received little empirical attention. Home foreclosure can be viewed as a stressful life event of prolonged duration, with multiple phases of variable intensity. Although no studies to date have reported the specific health effects of home foreclosure, we posit that foreclosure may be associated with a range of psychological and health behavior outcomes that, in turn, might increase chronic disease risk. Susceptibility to home foreclosure might involve both compositional and contextual dimensions. Delinquency management policies designed to prevent foreclosures from occurring are arguably best suited to protect the health of those at greatest risk.

Cardiac Arrest during Gamete Release in Chum Salmon Regulated by the Parasympathetic Nerve System:

Cardiac arrest caused by startling stimuli, such as visual and vibration stimuli, has been reported in some animals and could be considered as an extraordinary case of bradycardia and defined as reversible missed heart beats. Variability of the heart rate is established as a balance between an autonomic system, namely cholinergic vagus inhibition, and excitatory adrenergic stimulation of neural and hormonal action in teleost. However, the cardiac arrest and its regulating nervous mechanism remain poorly understood. We show, by using electrocardiogram (ECG) data loggers, that cardiac arrest occurs in chum salmon (Oncorhynchus keta) at the moment of gamete release for 7.39±1.61 s in females and for 5.20±0.97 s in males. The increase in heart rate during spawning behavior relative to the background rate during the resting period suggests that cardiac arrest is a characteristic physiological phenomenon of the extraordinarily high heart rate during spawning behavior. The ECG morphological analysis showed a peaked and tall T-wave adjacent to the cardiac arrest, indicating an increase in potassium permeability in cardiac muscle cells, which would function to retard the cardiac action potential. Pharmacological studies showed that the cardiac arrest was abolished by injection of atropine, a muscarinic receptor antagonist, revealing that the cardiac arrest is a reflex response of the parasympathetic nerve system, although injection of sotalol, a β-adrenergic antagonist, did not affect the cardiac arrest. We conclude that cardiac arrest during gamete release in spawning release in spawning chum salmon is a physiological reflex response controlled by the parasympathetic nervous system. This cardiac arrest represents a response to the gaping behavior that occurs at the moment of gamete release.

Shared Visual Attention and Memory Systems in the Drosophila Brain:

Selective attention and memory seem to be related in human experience. This appears to be the case as well in simple model organisms such as the fly Drosophila melanogaster. Mutations affecting olfactory and visual memory formation in Drosophila, such as in dunce and rutabaga, also affect short-term visual processes relevant to selective attention. In particular, increased optomotor responsiveness appears to be predictive of visual attention defects in these mutants. To further explore the possible overlap between memory and visual attention systems in the fly brain, we screened a panel of 36 olfactory long term memory (LTM) mutants for visual attention-like defects using an optomotor maze paradigm. Three of these mutants yielded high dunce-like optomotor responsiveness. We characterized these three strains by examining their visual distraction in the maze, their visual learning capabilities, and their brain activity responses to visual novelty. We found that one of these mutants, D0067, was almost completely identical to dunce1 for all measures, while another, D0264, was more like wild type. Exploiting the fact that the LTM mutants are also Gal4 enhancer traps, we explored the sufficiency for the cells subserved by these elements to rescue dunce attention defects and found overlap at the level of the mushroom bodies. Finally, we demonstrate that control of synaptic function in these Gal4 expressing cells specifically modulates a 20-30 Hz local field potential associated with attention-like effects in the fly brain. Our study uncovers genetic and neuroanatomical systems in the fly brain affecting both visual attention and odor memory phenotypes. A common component to these systems appears to be the mushroom bodies, brain structures which have been traditionally associated with odor learning but which we propose might be also involved in generating oscillatory brain activity required for attention-like processes in the fly brain.

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There are 16 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Looking for Landmarks: The Role of Expert Review and Bibliometric Analysis in Evaluating Scientific Publication Outputs:

Objective: To compare expert assessment with bibliometric indicators as tools to assess the quality and importance of scientific research papers. Shortly after their publication in 2005, the quality and importance of a cohort of nearly 700 Wellcome Trust (WT) associated research papers were assessed by expert reviewers; each paper was reviewed by two WT expert reviewers. After 3 years, we compared this initial assessment with other measures of paper impact. Shortly after publication, 62 (9%) of the 687 research papers were determined to describe at least a ‘major addition to knowledge’ -6 were thought to be ‘landmark’ papers. At an aggregate level, after 3 years, there was a strong positive association between expert assessment and impact as measured by number of citations and F1000 rating. However, there were some important exceptions indicating that bibliometric measures may not be sufficient in isolation as measures of research quality and importance, and especially not for assessing single papers or small groups of research publications. When attempting to assess the quality and importance of research papers, we found that sole reliance on bibliometric indicators would have led us to miss papers containing important results as judged by expert review. In particular, some papers that were highly rated by experts were not highly cited during the first three years after publication. Tools that link expert peer reviews of research paper quality and importance to more quantitative indicators, such as citation analysis would be valuable additions to the field of research assessment and evaluation.

Blueberry-Enriched Diet Protects Rat Heart from Ischemic Damage:

Objectives: to assess the cardioprotective properties of a blueberry enriched diet (BD). Reactive oxygen species (ROS) play a major role in ischemia-related myocardial injury. The attempts to use synthetic antioxidants to block the detrimental effects of ROS have produced mixed or negative results precipitating the interest in natural products. Blueberries are readily available product with the highest antioxidant capacity among fruits and vegetables. Following 3-mo of BD or a regular control diet (CD), the threshold for mitochondrial permeability transition (tMPT) was measured in isolated cardiomyocytes obtained from young male Fischer-344 rats. Compared to CD, BD resulted in a 24% increase (p<0.001) of ROS indexed tMPT. The remaining animals were subjected to a permanent ligation of the left descending coronary artery. 24 hrs later resulting myocardial infarction (MI) in rats on BD was 22% less than in CD rats (p<0.01). Significantly less TUNEL(+) cardiomyocytes (2% vs 9%) and 40% less inflammation cells were observed in the myocardial area at risk of BD compared to CD rats (p<0.01). In the subgroup of rats, after coronary ligation the original diet was either continued or switched to the opposite one, and cardiac remodeling and MI expansion were followed by serial echocardiography for 10 weeks. Measurements suggested that continuation of BD or its withdrawal after MI attenuated or accelerated rates of post MI cardiac remodeling and MI expansion. A blueberry-enriched diet protected the myocardium from induced ischemic damage and demonstrated the potential to attenuate the development of post MI chronic heart failure.

Influence of Environment and Mitochondrial Heritage on the Ecological Characteristics of Fish in a Hybrid Zone:

Ecological characteristics (growth, morphology, reproduction) arise from the interaction between environmental factors and genetics. Genetic analysis of individuals’ life history traits might be used to improve our understanding of mechanisms that form and maintain a hybrid zone. A fish hybrid zone was used to characterize the process of natural selection. Data were collected during two reproductive periods (2001 and 2002) and 1117 individuals (nase, Chondrostama nasus nasus, sofie C. toxostoma toxostoma and hybrids) were sampled. Reproductive dates of the two parental species overlapped at sympatric sites. The nase had an earlier reproductive period than the sofie; males had longer reproductive periods for both species. Hybridisation between female nase and male sofie was the most likely. Hybrids had a reproductive period similar to the inherited parental mitochondrial type. Growth and reproductive information from different environments has been synthesised following a bayesian approach of the von Bertalanffy model. Hybrid life history traits appear to link with maternal heritage. Hybrid size from the age of two and size at first maturity appeared to be closer to the size of the maternal origin species (nase or sofie). Median growth rates for hybrids were similar and intermediate between those of the parental species. We observed variable life history traits for hybrids and pure forms in the different parts of the hybrid zone. Geometrical analysis of the hybrid fish shape gave evidence of two main morphologies with a link to maternal heritage. Selective mating seemed to be the underlying process which, with mitochondrial heritage, could explain the evolution of the studied hybrid zone. More generally, we showed the importance of studies on hybrid zones and specifically the study of individuals’ ecological characteristics, to improve our understanding of speciation.

Tree Species Traits Influence Soil Physical, Chemical, and Biological Properties in High Elevation Forests:

Previous studies have shown that plants often have species-specific effects on soil properties. In high elevation forests in the Southern Rocky Mountains, North America, areas that are dominated by a single tree species are often adjacent to areas dominated by another tree species. Here, we assessed soil properties beneath adjacent stands of trembling aspen, lodgepole pine, and Engelmann spruce, which are dominant tree species in this region and are distributed widely in North America. We hypothesized that soil properties would differ among stands dominated by different tree species and expected that aspen stands would have higher soil temperatures due to their open structure, which, combined with higher quality litter, would result in increased soil respiration rates, nitrogen availability, and microbial biomass, and differences in soil faunal community composition. We assessed soil physical, chemical, and biological properties at four sites where stands of aspen, pine, and spruce occurred in close proximity to one-another in the San Juan Mountains, Colorado. Leaf litter quality differed among the tree species, with the highest nitrogen (N) concentration and lowest lignin:N in aspen litter. Nitrogen concentration was similar in pine and spruce litter, but lignin:N was highest in pine litter. Soil temperature and moisture were highest in aspen stands, which, in combination with higher litter quality, probably contributed to faster soil respiration rates from stands of aspen. Soil carbon and N content, ammonium concentration, and microbial biomass did not differ among tree species, but nitrate concentration was highest in aspen soil and lowest in spruce soil. In addition, soil fungal, bacterial, and nematode community composition and rotifer, collembolan, and mesostigmatid mite abundance differed among the tree species, while the total abundance of nematodes, tardigrades, oribatid mites, and prostigmatid mites did not. Although some soil characteristics were unaffected by tree species identity, our results clearly demonstrate that these dominant tree species are associated with soils that differ in several physical, chemical, and biotic properties. Ongoing environmental changes in this region, e.g. changes in fire regime, frequency of insect outbreaks, changes in precipitation patterns and snowpack, and land-use change, may alter the relative abundance of these tree species over coming decades, which in turn will likely alter the soils.

There are 20 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
General Intelligence in Another Primate: Individual Differences across Cognitive Task Performance in a New World Monkey (Saguinus oedipus):

Individual differences in human cognitive abilities show consistently positive correlations across diverse domains, providing the basis for the trait of “general intelligence” (g). At present, little is known about the evolution of g, in part because most comparative studies focus on rodents or on differences across higher-level taxa. What is needed, therefore, are experiments targeting nonhuman primates, focusing on individual differences within a single species, using a broad battery of tasks. To this end, we administered a large battery of tasks, representing a broad range of cognitive domains, to a population of captive cotton-top tamarin monkeys (Saguinus oedipus). Using a Bayesian latent variable model, we show that the pattern of correlations among tasks is consistent with the existence of a general factor accounting for a small but significant proportion of the variance in each task (the lower bounds of 95% Bayesian credibility intervals for correlations between g and task performance all exceed 0.12). Individual differences in cognitive abilities within at least one other primate species can be characterized by a general intelligence factor, supporting the hypothesis that important aspects of human cognitive function most likely evolved from ancient neural substrates.

The Time-Course of Visual Categorizations: You Spot the Animal Faster than the Bird:

Since the pioneering study by Rosch and colleagues in the 70s, it is commonly agreed that basic level perceptual categories (dog, chair…) are accessed faster than superordinate ones (animal, furniture…). Nevertheless, the speed at which objects presented in natural images can be processed in a rapid go/no-go visual superordinate categorization task has challenged this “basic level advantage”. Using the same task, we compared human processing speed when categorizing natural scenes as containing either an animal (superordinate level), or a specific animal (bird or dog, basic level). Human subjects require an additional 40-65 ms to decide whether an animal is a bird or a dog and most errors are induced by non-target animals. Indeed, processing time is tightly linked with the type of non-targets objects. Without any exemplar of the same superordinate category to ignore, the basic level category is accessed as fast as the superordinate category, whereas the presence of animal non-targets induces both an increase in reaction time and a decrease in accuracy. These results support the parallel distributed processing theory (PDP) and might reconciliate controversial studies recently published. The visual system can quickly access a coarse/abstract visual representation that allows fast decision for superordinate categorization of objects but additional time-consuming visual analysis would be necessary for a decision at the basic level based on more detailed representations.

Feeding and Stocking Up: Radio-Labelled Food Reveals Exchange Patterns in Ants:

Food sharing is vital for a large number of species, either solitary or social, and is of particular importance within highly integrated societies, such as in colonial organisms and in social insects. Nevertheless, the mechanisms that govern the distribution of food inside a complex organizational system remain unknown.
Using scintigraphy, a method developed for medical imaging, we were able to describe the dynamics of food-flow inside an ant colony. We monitored the sharing process of a radio-labelled sucrose solution inside a nest of Formica fusca. Our results show that, from the very first load that enters the nest, food present within the colony acts as negative feedback to entering food. After one hour of the experiments, 70% of the final harvest has already entered the nest. The total foraged quantity is almost four times smaller than the expected storage capacity. A finer study of the spatial distribution of food shows that although all ants have been fed rapidly (within 30 minutes), a small area representing on average 8% of the radioactive surface holds more than 25% of the stored food. Even in rather homogeneous nests, we observed a strong concentration of food in few workers. Examining the position of these workers inside the nest, we found heavily loaded ants in the centre of the aggregate. The position of the centre of this high-intensity radioactive surface remained stable for the three consecutive hours of the experiments.
We demonstrate that the colony simultaneously managed to rapidly feed all workers (200 ants fed within 30 minutes) and build up food stocks to prevent food shortage, something that occurs rather often in changing environments. Though we expected the colony to forage to its maximum capacity, the flow of food entering the colony is finely tuned to the colony’s needs. Indeed the food-flow decreases proportionally to the food that has already been harvested, liberating the work-force for other tasks.

The Role of Demography and Markets in Determining Deforestation Rates Near Ranomafana National Park, Madagascar:

The highland forests of Madagascar are home to some of the world’s most unique and diverse flora and fauna and to some of its poorest people. This juxtaposition of poverty and biodiversity is continually reinforced by rapid population growth, which results in increasing pressure on the remaining forest habitat in the highland region, and the biodiversity therein. Here we derive a mathematical expression for the subsistence of households to assess the role of markets and household demography on deforestation near Ranomafana National Park. In villages closest to urban rice markets, households were likely to clear less land than our model predicted, presumably because they were purchasing food at market. This effect was offset by the large number of migrant households who cleared significantly more land between 1989-2003 than did residents throughout the region. Deforestation by migrant households typically occurred after a mean time lag of 9 years. Analyses suggest that while local conservation efforts in Madagascar have been successful at reducing the footprint of individual households, large-scale conservation must rely on policies that can reduce the establishment of new households in remaining forested areas.

Encouraging Expressions Affect the Brain and Alter Visual Attention:

Very often, encouraging or discouraging expressions are used in competitive contexts, such as sports practice, aiming at provoking an emotional reaction on the listener and, consequently, an effect on subsequent cognition and/or performance. However, the actual efficiency of these expressions has not been tested scientifically. To fill this gap, we studied the effects of encouraging, discouraging, and neutral expressions on event-related brain electrical activity during a visual selective attention task in which targets were determined by location, shape, and color. Although the expressions preceded the attentional task, both encouraging and discouraging messages elicited a similar long-lasting brain emotional response present during the visuospatial task. In addition, encouraging expressions were able to alter the customary working pattern of the visual attention system for shape selection in the attended location, increasing the P1 and the SP modulations while simultaneously fading away the SN. This was interpreted as an enhancement of the attentional processes for shape in the attended location after an encouraging expression. It can be stated, therefore, that encouraging expressions, as those used in sport practice, as well as in many other contexts and situations, do seem to be efficient in exerting emotional reactions and measurable effects on cognition.

Contact Profiles in Eight European Countries and Implications for Modelling the Spread of Airborne Infectious Diseases:

For understanding the spread of infectious diseases it is crucial to have knowledge of the patterns of contacts in a population during which the infection can be transmitted. Besides contact rates and mixing between age groups, the way individuals distribute their contacts across different locations may play an important role in determining how infections spread through a population. Representative surveys were performed in eight countries to assess the number of social contacts (talking to another person at close distance either with or without physical contact), using a diary approach in which participants recorded individual contacts. The overall sample size was 7290 respondents. We analyzed the reported numbers of contacts per respondent in six different settings (household, work, school, leisure, transportation and others) to define different contact profiles. The identification of the profiles and classification of respondents according to these profiles was conducted using a two-step cluster analysis algorithm as implemented in SPSS. We identified seven distinct contact profiles: respondents having (1) mixed: contacts predominantly at school, during transportation and leisure time, (2) contacts during leisure time, (3) contacts mainly in the household (large family), (4) contacts at work, (5) contacts solely at school, (6) contacts in other places and finally (7) respondents having a low number of contacts in any setting. Similar contact profiles can be found in all eight European countries which participated in the study. The distributions of respondents across the profiles were similar in all countries. The profiles are dominated by work, school and household contacts. But also contacts during leisure activities play an important role in the daily lives of a large fraction of individuals. A surprisingly large number of individuals has only few contacts in all locations. There was a distinct age-dependence in the distribution of the population across contact profiles. In contrast with earlier studies that focussed on the contribution of different age groups to the spread of an infectious disease, our results open up the opportunity to analyze how an infection spreads between locations and how locations as work or school are interconnected via household contacts. Mathematical models that take these local contact patterns into account can be used to assess the effect of intervention measures like school closure and cancelling of leisure activities on the spread of influenza.

Cocaine Modulates Locomotion Behavior in C. elegans:

Cocaine, a potent addictive substance, is an inhibitor of monoamine transporters, including DAT (dopamine transporter), SERT (serotonin transporter) and NET (norepinephrine transporter). Cocaine administration induces complex behavioral alterations in mammals, but the underlying mechanisms are not well understood. Here, we tested the effect of cocaine on C. elegans behavior. We show for the first time that acute cocaine treatment evokes changes in C. elegans locomotor activity. Interestingly, the neurotransmitter serotonin, rather than dopamine, is required for cocaine response in C. elegans. The C. elegans SERT MOD-5 is essential for the effect of cocaine, consistent with the role of cocaine in targeting monoamine transporters. We further show that the behavioral response to cocaine is primarily mediated by the ionotropic serotonin receptor MOD-1. Thus, cocaine modulates locomotion behavior in C. elegans primarily by impinging on its serotoninergic system.

Sport Hunting, Predator Control and Conservation of Large Carnivores:

Sport hunting has provided important economic incentives for conserving large predators since the early 1970’s, but wildlife managers also face substantial pressure to reduce depredation. Sport hunting is an inherently risky strategy for controlling predators as carnivore populations are difficult to monitor and some species show a propensity for infanticide that is exacerbated by removing adult males. Simulation models predict population declines from even moderate levels of hunting in infanticidal species, and harvest data suggest that African countries and U.S. states with the highest intensity of sport hunting have shown the steepest population declines in African lions and cougars over the past 25 yrs. Similar effects in African leopards may have been masked by mesopredator release owing to declines in sympatric lion populations, whereas there is no evidence of overhunting in non-infanticidal populations of American black bears. Effective conservation of these animals will require new harvest strategies and improved monitoring to counter demands for predator control by livestock producers and local communities.

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There are 18 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Variable Food Begging Calls Are Harbingers of Vocal Learning:

Vocal learning has evolved in only a few groups of mammals and birds. The developmental and evolutionary origins of vocal learning remain unclear. The imitation of a memorized sound is a clear example of vocal learning, but is that when vocal learning starts? Here we use an ontogenetic approach to examine how vocal learning emerges in a songbird, the chipping sparrow. The first vocalizations of songbirds, food begging calls, were thought to be innate, and vocal learning emerges later during subsong, a behavior reminiscent of infant babbling. Here we report that the food begging calls of male sparrows show several characteristics associated with learned song: male begging calls are highly variable between individuals and are altered by deafening; the production of food begging calls induces c-fos expression in a forebrain motor nucleus, RA, that is involved with the production of learned song. Electrolytic lesions of RA significantly reduce the variability of male calls. The male begging calls are subsequently incorporated into subsong, which in turn transitions into recognizable attempts at vocal imitation. Females do not sing and their begging calls are not affected by deafening or RA lesion. Our results suggest that, in chipping sparrows, intact hearing can influence the quality of male begging calls, auditory-sensitive vocal variability during food begging calls is the first step in a modification of vocal output that eventually culminates with vocal imitation.

Infectious Prions in Pre-Clinical Deer and Transmission of Chronic Wasting Disease Solely by Environmental Exposure:

Key to understanding the epidemiology and pathogenesis of prion diseases, including chronic wasting disease (CWD) of cervids, is determining the mode of transmission from one individual to another. We have previously reported that saliva and blood from CWD-infected deer contain sufficient infectious prions to transmit disease upon passage into naïve deer. Here we again use bioassays in deer to show that blood and saliva of pre-symptomatic deer contain infectious prions capable of infecting naïve deer and that naïve deer exposed only to environmental fomites from the suites of CWD-infected deer acquired CWD infection after a period of 15 months post initial exposure. These results help to further explain the basis for the facile transmission of CWD, highlight the complexities associated with CWD transmission among cervids in their natural environment, emphasize the potential utility of blood-based testing to detect pre-clinical CWD infection, and could augur similar transmission dynamics in other prion infections.

Hmm, I usually do this on Fridays, but I was busy. So here is a Saturday sampler of papers from all seven PLoS journals published last week. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click.

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There are 15 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
The Timing of the Shrew: Continuous Melatonin Treatment Maintains Youthful Rhythmic Activity in Aging Crocidura russula:

Laboratory conditions nullify the extrinsic factors that determine the wild expected lifespan and release the intrinsic or potential lifespan. Thus, wild animals reared in a laboratory often show an increased lifespan, and consequently an increased senescence phase. Senescence is associated with a broad suite of physiological changes, including a decreased responsiveness of the circadian system. The time-keeping hormone melatonin, an important chemical player in this system, is suspected to have an anti-aging role. The Greater White-toothed shrew Crocidura russula is an ideal study model to address questions related to aging and associated changes in biological functions: its lifespan is short and is substantially increased in captivity; daily and seasonal rhythms, while very marked the first year of life, are dramatically altered during the senescence process which starts during the second year. Here we report on an investigation of the effects of melatonin administration on locomotor activity of aging shrews.1) The diel fluctuations of melatonin levels in young, adult and aging shrews were quantified in the pineal gland and plasma. In both, a marked diel rhythm (low diurnal concentration; high nocturnal concentration) was present in young animals but then decreased in adults, and, as a result of a loss in the nocturnal production, was absent in old animals. 2) Daily locomotor activity rhythm was monitored in pre-senescent animals that had received either a subcutaneous melatonin implant, an empty implant or no implant at all. In non-implanted and sham-implanted shrews, the rhythm was well marked in adults. A marked degradation in both period and amplitude, however, started after the age of 14-16 months. This pattern was considerably delayed in melatonin-implanted shrews who maintained the daily rhythm for significantly longer. This is the first long term study (>500 days observation of the same individuals) that investigates the effects of continuous melatonin delivery. As such, it sheds new light on the putative anti-aging role of melatonin by demonstrating that continuous melatonin administration delays the onset of senescence. In addition, the shrew appears to be a promising mammalian model for elucidating the precise relationships between melatonin and aging.

Toward the Restoration of Hand Use to a Paralyzed Monkey: Brain-Controlled Functional Electrical Stimulation of Forearm Muscles:

Loss of hand use is considered by many spinal cord injury survivors to be the most devastating consequence of their injury. Functional electrical stimulation (FES) of forearm and hand muscles has been used to provide basic, voluntary hand grasp to hundreds of human patients. Current approaches typically grade pre-programmed patterns of muscle activation using simple control signals, such as those derived from residual movement or muscle activity. However, the use of such fixed stimulation patterns limits hand function to the few tasks programmed into the controller. In contrast, we are developing a system that uses neural signals recorded from a multi-electrode array implanted in the motor cortex; this system has the potential to provide independent control of multiple muscles over a broad range of functional tasks. Two monkeys were able to use this cortically controlled FES system to control the contraction of four forearm muscles despite temporary limb paralysis. The amount of wrist force the monkeys were able to produce in a one-dimensional force tracking task was significantly increased. Furthermore, the monkeys were able to control the magnitude and time course of the force with sufficient accuracy to track visually displayed force targets at speeds reduced by only one-third to one-half of normal. Although these results were achieved by controlling only four muscles, there is no fundamental reason why the same methods could not be scaled up to control a larger number of muscles. We believe these results provide an important proof of concept that brain-controlled FES prostheses could ultimately be of great benefit to paralyzed patients with injuries in the mid-cervical spinal cord.

Scale-Free Music of the Brain:

There is growing interest in the relation between the brain and music. The appealing similarity between brainwaves and the rhythms of music has motivated many scientists to seek a connection between them. A variety of transferring rules has been utilized to convert the brainwaves into music; and most of them are mainly based on spectra feature of EEG. In this study, audibly recognizable scale-free music was deduced from individual Electroencephalogram (EEG) waveforms. The translation rules include the direct mapping from the period of an EEG waveform to the duration of a note, the logarithmic mapping of the change of average power of EEG to music intensity according to the Fechner’s law, and a scale-free based mapping from the amplitude of EEG to music pitch according to the power law. To show the actual effect, we applied the deduced sonification rules to EEG segments recorded during rapid-eye movement sleep (REM) and slow-wave sleep (SWS). The resulting music is vivid and different between the two mental states; the melody during REM sleep sounds fast and lively, whereas that in SWS sleep is slow and tranquil. 60 volunteers evaluated 25 music pieces, 10 from REM, 10 from SWS and 5 from white noise (WN), 74.3% experienced a happy emotion from REM and felt boring and drowsy when listening to SWS, and the average accuracy for all the music pieces identification is 86.8%(κ = 0.800, P<0.001). We also applied the method to the EEG data from eyes closed, eyes open and epileptic EEG, and the results showed these mental states can be identified by listeners. The sonification rules may identify the mental states of the brain, which provide a real-time strategy for monitoring brain activities and are potentially useful to neurofeedback therapy.

Adaptive Response to DNA-Damaging Agents in Natural Saccharomyces cerevisiae Populations from “Evolution Canyon”, Mt. Carmel, Israel:

Natural populations of most organisms, especially unicellular microorganisms, are constantly exposed to harsh environmental factors which affect their growth. UV radiation is one of the most important physical parameters which influences yeast growth in nature. Here we used 46 natural strains of Saccharomyces cerevisiae isolated from several natural populations at the “Evolution Canyon” microsite (Nahal Oren, Mt. Carmel, Israel). The opposing slopes of this canyon share the same geology, soil, and macroclimate, but they differ in microclimatic conditions. The interslope differences in solar radiation (200%-800% more on the “African” slope) caused the development of two distinct biomes. The south-facing slope is sunnier and has xeric, savannoid “African” environment while the north-facing slope is represented by temperate, “European” forested environment. Here we studied the phenotypic response of the S. cerevisiae strains to UVA and UVC radiations and to methyl methanesulfonate (MMS) in order to evaluate the interslope effect on the strains’ ability to withstand DNA-damaging agents. We exposed our strains to the different DNA-damaging agents and measured survival by counting colony forming units. The strains from the “African” slope were more resilient to both UVA and MMS than the strains from the “European” slope. In contrast, we found that there was almost no difference between strains (with similar ploidy) from the opposite slopes, in their sensitivity to UVC radiation. These results suggest that the “African” strains are more adapted to higher solar radiation than the “European” strains. We also found that the tetraploids strains were more tolerant to all DNA-damaging agents than their neighboring diploid strains, which suggest that high ploidy level might be a mechanism of adaptation to high solar radiation. Our results and the results of parallel studies with several other organisms, suggest that natural selection appears to select, at a microscale, for adaptive complexes that can tolerate the higher UV radiation on the “African” slope.

There are 16 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
A Standard System to Study Vertebrate Embryos:

Staged embryonic series are important as reference for different kinds of biological studies. I summarise problems that occur when using ‘staging tables’ of ‘model organisms’. Investigations of developmental processes in a broad scope of taxa are becoming commonplace. Beginning in the 1990s, methods were developed to quantify and analyse developmental events in a phylogenetic framework. The algorithms associated with these methods are still under development, mainly due to difficulties of using non-independent characters. Nevertheless, the principle of comparing clearly defined newly occurring morphological features in development (events) in quantifying analyses was a key innovation for comparative embryonic research. Up to date no standard was set for how to define such events in a comparative approach. As a case study I compared the external development of 23 land vertebrate species with a focus on turtles, mainly based on reference staging tables. I excluded all the characters that are only identical for a particular species or general features that were only analysed in a few species. Based on these comparisons I defined 104 developmental characters that are common either for all vertebrates (61 characters), gnathostomes (26), tetrapods (3), amniotes (7), or only for sauropsids (7). Characters concern the neural tube, somite, ear, eye, limb, maxillary and mandibular process, pharyngeal arch, eyelid or carapace development. I present an illustrated guide listing all the defined events. This guide can be used for describing developmental series of any vertebrate species or for documenting specimen variability of a particular species. The guide incorporates drawings and photographs as well as consideration of species identifying developmental features such as colouration. The simple character-code of the guide is extendable to further characters pertaining to external and internal morphological, physiological, genetic or molecular development, and also for other vertebrate groups not examined here, such as Chondrichthyes or Actinopterygii. An online database to type in developmental events for different stages and species could be a basis for further studies in comparative embryology. By documenting developmental events with the standard code, sequence heterochrony studies (i.e. Parsimov) and studies on variability can use this broad comparative data set.

The Effect of the Crosstalk between Photoperiod and Temperature on the Heading-Date in Rice:

Photoperiod and temperature are two important environmental factors that influence the heading-date of rice. Although the influence of the photoperiod on heading has been extensively reported in rice, the molecular mechanism for the temperature control of heading remains unknown. This study reports an early heading mutant derived from tissue culture lines of rice and investigates the heading-date of wild type and mutant in different photoperiod and temperature treatments. The linkage analysis showed that the mutant phenotype cosegregated with the Hd1 locus. Sequencing analysis found that the mutant contained two insertions and several single-base substitutions that caused a dramatic reduction in Hd1mRNA levels compared with wild type. The expression patterns of Hd1 and Hd3a were also analyzed in different photoperiod and temperature conditions, revealing that Hd1 mRNA levels displayed similar expression patterns for different photoperiod and temperature treatments, with high expression levels at night and reduced levels in the daytime. In addition, Hd1 displayed a slightly higher expression level under long-day and low temperature conditions. Hd3a mRNA was present at a very low level under low temperature conditions regardless of the day-length. This result suggests that suppression of Hd3a expression is a principle cause of late heading under low temperature and long-day conditions.

The Role of Dopamine in Drosophila Larval Classical Olfactory Conditioning:

Learning and memory is not an attribute of higher animals. Even Drosophila larvae are able to form and recall an association of a given odor with an aversive or appetitive gustatory reinforcer. As the Drosophila larva has turned into a particularly simple model for studying odor processing, a detailed neuronal and functional map of the olfactory pathway is available up to the third order neurons in the mushroom bodies. At this point, a convergence of olfactory processing and gustatory reinforcement is suggested to underlie associative memory formation. The dopaminergic system was shown to be involved in mammalian and insect olfactory conditioning. To analyze the anatomy and function of the larval dopaminergic system, we first characterize dopaminergic neurons immunohistochemically up to the single cell level and subsequent test for the effects of distortions in the dopamine system upon aversive (odor-salt) as well as appetitive (odor-sugar) associative learning. Single cell analysis suggests that dopaminergic neurons do not directly connect gustatory input in the larval suboesophageal ganglion to olfactory information in the mushroom bodies. However, a number of dopaminergic neurons innervate different regions of the brain, including protocerebra, mushroom bodies and suboesophageal ganglion. We found that dopamine receptors are highly enriched in the mushroom bodies and that aversive and appetitive olfactory learning is strongly impaired in dopamine receptor mutants. Genetically interfering with dopaminergic signaling supports this finding, although our data do not exclude on naïve odor and sugar preferences of the larvae. Our data suggest that dopaminergic neurons provide input to different brain regions including protocerebra, suboesophageal ganglion and mushroom bodies by more than one route. We therefore propose that different types of dopaminergic neurons might be involved in different types of signaling necessary for aversive and appetitive olfactory memory formation respectively, or for the retrieval of these memory traces. Future studies of the dopaminergic system need to take into account such cellular dissociations in function in order to be meaningful.

Ecological Niche Models and Coalescent Analysis of Gene Flow Support Recent Allopatric Isolation of Parasitoid Wasp Populations in the Mediterranean:

The integration of multiple complementary approaches is a powerful way to understand the processes of diversification and speciation. The parasitoid wasp Aphidius transcaspicus Telenga (Hymenoptera: Braconidae) is a parasitoid of Hyalopterus aphids across a wide geographic range. This species shows a remarkable degree of genetic structure among western, central, and eastern Mediterranean population clusters. In this paper we attempt to better characterize this genetic structure. We use a Bayesian coalescent analysis of gene flow under the Isolation with Migration model using mitochondrial and microsatellite markers together with climate-based ecological niche models to better understand the genetic structure of A. transcaspicus in the Mediterranean. The coalescent analysis revealed low levels of migration among western and eastern Mediterranean populations (Nm<1) that were not statistically distinguishable from zero. Niche models showed that localities within population clusters each occupy areas of continuously high environmental suitability, but are separated from each other by large regions of completely unsuitable habitat that could limit dispersal. Overall, environmental characteristics were similar among the population clusters, though significant differences did emerge. These results support contemporary allopatric isolation of Mediterranean populations of A. transcaspicus, which together with previous analyses indicating partial behaviorally mediated reproductive isolation, suggest that the early stages of cryptic speciation may be in progress.

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There are 17 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
PER3 Polymorphism Predicts Cumulative Sleep Homeostatic but Not Neurobehavioral Changes to Chronic Partial Sleep Deprivation:

The variable number tandem repeat (VNTR) polymorphism 5-repeat allele of the circadian gene PERIOD3 (PER35/5) has been associated with cognitive decline at a specific circadian phase in response to a night of total sleep deprivation (TSD), relative to the 4-repeat allele (PER34/4). PER35/5 has also been related to higher sleep homeostasis, which is thought to underlie this cognitive vulnerability. To date, no study has used a candidate gene approach to investigate the response to chronic partial sleep deprivation (PSD), a condition distinct from TSD and one commonly experienced by millions of people on a daily and persistent basis. We evaluated whether the PER3 VNTR polymorphism contributed to cumulative neurobehavioral deficits and sleep homeostatic responses during PSD. PER35/5 (n = 14), PER34/5 (n = 63) and PER34/4 (n = 52) healthy adults (aged 22-45 y) demonstrated large, but equivalent cumulative decreases in cognitive performance and physiological alertness, and cumulative increases in sleepiness across 5 nights of sleep restricted to 4 h per night. Such effects were accompanied by increasing daily inter-subject variability in all groups. The PER3 genotypes did not differ significantly at baseline in habitual sleep, physiological sleep structure, circadian phase, physiological sleepiness, cognitive performance, or subjective sleepiness, although during PSD, PER35/5 subjects had slightly but reliably elevated sleep homeostatic pressure as measured physiologically by EEG slow-wave energy in non-rapid eye movement sleep compared with PER34/4 subjects. PER3 genotypic and allelic frequencies did not differ significantly between Caucasians and African Americans. The PER3 VNTR polymorphism was not associated with individual differences in neurobehavioral responses to PSD, although it was related to one marker of sleep homoeostatic response during PSD. The comparability of PER3 genotypes at baseline and their equivalent inter-individual vulnerability to sleep restriction indicate that PER3 does not contribute to the neurobehavioral effects of chronic sleep loss.

Maternal Obesity Induced by Diet in Rats Permanently Influences Central Processes Regulating Food Intake in Offspring:

Hypothalamic systems which regulate appetite may be permanently modified during early development. We have previously reported hyperphagia and increased adiposity in the adult offspring of rodents fed an obesogenic diet prior to and throughout pregnancy and lactation. We now report that offspring of obese (OffOb) rats display an amplified and prolonged neonatal leptin surge, which is accompanied by elevated leptin mRNA expression in their abdominal white adipose tissue. At postnatal Day 30, before the onset of hyperphagia in these animals, serum leptin is normal, but leptin-induced appetite suppression and phosphorylation of STAT3 in the arcuate nucleus (ARC) are attenuated; the level of AgRP-immunoreactivity in the hypothalamic paraventricular nucleus (PVH), which derives from neurones in the ARC and is developmentally dependent on leptin, is also diminished. We hypothesise that prolonged release of abnormally high levels of leptin by neonatal OffOb rats leads to leptin resistance and permanently affects hypothalamic functions involving the ARC and PVH. Such effects may underlie the developmental programming of hyperphagia and obesity in these rats.

Exercise-Training in Young Drosophila melanogaster Reduces Age-Related Decline in Mobility and Cardiac Performance:

Declining mobility is a major concern, as well as a major source of health care costs, among the elderly population. Lack of mobility is a primary cause of entry into managed care facilities, and a contributing factor to the frequency of damaging falls. Exercise-based therapies have shown great promise in sustaining mobility in elderly patients, as well as in rodent models. However, the genetic basis of the changing physiological responses to exercise during aging is not well understood. Here, we describe the first exercise-training paradigm in an invertebrate genetic model system. Flies are exercised by a mechanized platform, known as the Power Tower, that rapidly, repeatedly, induces their innate instinct for negative geotaxis. When young flies are subjected to a carefully controlled, ramped paradigm of exercise-training, they display significant reduction in age-related decline in mobility and cardiac performance. Fly lines with improved mitochondrial efficiency display some of the phenotypes observed in wild-type exercised flies. The exercise response in flies is influenced by the amount of protein and lipid, but not carbohydrate, in the diet. The development of an exercise-training model in Drosophila melanogaster opens the way to direct testing of single-gene based genetic therapies for improved mobility in aged animals, as well as unbiased genetic screens for loci involved in the changing response to exercise during aging.

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Today, we unveil a brand new PLoS ONE Collection – the Prokaryotic Genome Collection. The Collection was edited by Niyaz Ahmed, who wrote an introductory Overview.
In other news, there are 17 new articles published last night and another 17 new articles published tonight in PLoS ONE. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

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There are 13 new articles in PLoS ONE today, as well as 12 articles published Friday night. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
The Multifaceted Origin of Taurine Cattle Reflected by the Mitochondrial Genome:

A Neolithic domestication of taurine cattle in the Fertile Crescent from local aurochsen (Bos primigenius) is generally accepted, but a genetic contribution from European aurochsen has been proposed. Here we performed a survey of a large number of taurine cattle mitochondrial DNA (mtDNA) control regions from numerous European breeds confirming the overall clustering within haplogroups (T1, T2 and T3) of Near Eastern ancestry, but also identifying eight mtDNAs (1.3%) that did not fit in haplogroup T. Sequencing of the entire mitochondrial genome showed that four mtDNAs formed a novel branch (haplogroup R) which, after the deep bifurcation that gave rise to the taurine and zebuine lineages, constitutes the earliest known split in the mtDNA phylogeny of B. primigenius. The remaining four mtDNAs were members of the recently discovered haplogroup Q. Phylogeographic data indicate that R mtDNAs were derived from female European aurochsen, possibly in the Italian Peninsula, and sporadically included in domestic herds. In contrast, the available data suggest that Q mtDNAs and T subclades were involved in the same Neolithic event of domestication in the Near East. Thus, the existence of novel (and rare) taurine haplogroups highlights a multifaceted genetic legacy from distinct B. primigenius populations. Taking into account that the maternally transmitted mtDNA tends to underestimate the extent of gene flow from European aurochsen, the detection of the R mtDNAs in autochthonous breeds, some of which are endangered, identifies an unexpected reservoir of genetic variation that should be carefully preserved.

A Genome Scan for Positive Selection in Thoroughbred Horses:

Thoroughbred horses have been selected for exceptional racing performance resulting in system-wide structural and functional adaptations contributing to elite athletic phenotypes. Because selection has been recent and intense in a closed population that stems from a small number of founder animals Thoroughbreds represent a unique population within which to identify genomic contributions to exercise-related traits. Employing a population genetics-based hitchhiking mapping approach we performed a genome scan using 394 autosomal and X chromosome microsatellite loci and identified positively selected loci in the extreme tail-ends of the empirical distributions for (1) deviations from expected heterozygosity (Ewens-Watterson test) in Thoroughbred (n = 112) and (2) global differentiation among four geographically diverse horse populations (FST). We found positively selected genomic regions in Thoroughbred enriched for phosphoinositide-mediated signalling (3.2-fold enrichment; P<0.01), insulin receptor signalling (5.0-fold enrichment; P<0.01) and lipid transport (2.2-fold enrichment; P<0.05) genes. We found a significant overrepresentation of sarcoglycan complex (11.1-fold enrichment; P<0.05) and focal adhesion pathway (1.9-fold enrichment; P<0.01) genes highlighting the role for muscle strength and integrity in the Thoroughbred athletic phenotype. We report for the first time candidate athletic-performance genes within regions targeted by selection in Thoroughbred horses that are principally responsible for fatty acid oxidation, increased insulin sensitivity and muscle strength: ACSS1 (acyl-CoA synthetase short-chain family member 1), ACTA1 (actin, alpha 1, skeletal muscle), ACTN2 (actinin, alpha 2), ADHFE1 (alcohol dehydrogenase, iron containing, 1), MTFR1 (mitochondrial fission regulator 1), PDK4 (pyruvate dehydrogenase kinase, isozyme 4) and TNC (tenascin C). Understanding the genetic basis for exercise adaptation will be crucial for the identification of genes within the complex molecular networks underlying obesity and its consequential pathologies, such as type 2 diabetes. Therefore, we propose Thoroughbred as a novel in vivo large animal model for understanding molecular protection against metabolic disease.

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There are 18 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
Mathematical Logic in the Human Brain: Syntax:

Theory predicts a close structural relation of formal languages with natural languages. Both share the aspect of an underlying grammar which either generates (hierarchically) structured expressions or allows us to decide whether a sentence is syntactically correct or not. The advantage of rule-based communication is commonly believed to be its efficiency and effectiveness. A particularly important class of formal languages are those underlying the mathematical syntax. Here we provide brain-imaging evidence that the syntactic processing of abstract mathematical formulae, written in a first order language, is, indeed efficient and effective as a rule-based generation and decision process. However, it is remarkable, that the neural network involved, consisting of intraparietal and prefrontal regions, only involves Broca’s area in a surprisingly selective way. This seems to imply that despite structural analogies of common and current formal languages, at the neural level, mathematics and natural language are processed differently, in principal.

Phylogeny and Biogeography of Hawkmoths (Lepidoptera: Sphingidae): Evidence from Five Nuclear Genes:

The 1400 species of hawkmoths (Lepidoptera: Sphingidae) comprise one of most conspicuous and well-studied groups of insects, and provide model systems for diverse biological disciplines. However, a robust phylogenetic framework for the family is currently lacking. Morphology is unable to confidently determine relationships among most groups. As a major step toward understanding relationships of this model group, we have undertaken the first large-scale molecular phylogenetic analysis of hawkmoths representing all subfamilies, tribes and subtribes. The data set consisted of 131 sphingid species and 6793 bp of sequence from five protein-coding nuclear genes. Maximum likelihood and parsimony analyses provided strong support for more than two-thirds of all nodes, including strong signal for or against nearly all of the fifteen current subfamily, tribal and sub-tribal groupings. Monophyly was strongly supported for some of these, including Macroglossinae, Sphinginae, Acherontiini, Ambulycini, Philampelini, Choerocampina, and Hemarina. Other groupings proved para- or polyphyletic, and will need significant redefinition; these include Smerinthinae, Smerinthini, Sphingini, Sphingulini, Dilophonotini, Dilophonotina, Macroglossini, and Macroglossina. The basal divergence, strongly supported, is between Macroglossinae and Smerinthinae+Sphinginae. All genes contribute significantly to the signal from the combined data set, and there is little conflict between genes. Ancestral state reconstruction reveals multiple separate origins of New World and Old World radiations. Our study provides the first comprehensive phylogeny of one of the most conspicuous and well-studied insects. The molecular phylogeny challenges current concepts of Sphingidae based on morphology, and provides a foundation for a new classification. While there are multiple independent origins of New World and Old World radiations, we conclude that broad-scale geographic distribution in hawkmoths is more phylogenetically conserved than previously postulated.

Migration of Whooper Swans and Outbreaks of Highly Pathogenic Avian Influenza H5N1 Virus in Eastern Asia:

Evaluating the potential involvement of wild avifauna in the emergence of highly pathogenic avian influenza H5N1 (hereafter H5N1) requires detailed analyses of temporal and spatial relationships between wild bird movements and disease emergence. The death of wild swans (Cygnus spp.) has been the first indicator of the presence of H5N1 in various Asian and European countries; however their role in the geographic spread of the disease remains poorly understood. We marked 10 whooper swans (Cygnus cygnus) with GPS transmitters in northeastern Mongolia during autumn 2006 and tracked their migratory movements in relation to H5N1 outbreaks. The prevalence of H5N1 outbreaks among poultry in eastern Asia during 2003-2007 peaked during winter, concurrent with whooper swan movements into regions of high poultry density. However outbreaks involving poultry were detected year round, indicating disease perpetuation independent of migratory waterbird presence. In contrast, H5N1 outbreaks involving whooper swans, as well as other migratory waterbirds that succumbed to the disease in eastern Asia, tended to occur during seasons (late spring and summer) and in habitats (areas of natural vegetation) where their potential for contact with poultry is very low to nonexistent. Given what is known about the susceptibility of swans to H5N1, and on the basis of the chronology and rates of whooper swan migration movements, we conclude that although there is broad spatial overlap between whooper swan distributions and H5N1 outbreak locations in eastern Asia, the likelihood of direct transmission between these groups is extremely low. Thus, our data support the hypothesis that swans are best viewed as sentinel species, and moreover, that in eastern Asia, it is most likely that their infections occurred through contact with asymptomatic migratory hosts (e.g., wild ducks) at or near their breeding grounds.

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