Category Archives: Science News

Could not resist….
Network Features of the Mammalian Circadian Clock:

The circadian clock is the biological clock found throughout the body that coordinates the timing of molecular and cellular processes on a 24-hour rhythm. It is composed of numerous transcription factors that feed back and control their own expression. To explore how the clock functions in the face of genetic perturbations, we disrupted its function by knocking down gene expression of known clock genes in a dose-dependent fashion. We measured the expression of clock genes following knockdown and constructed perturbation-based network models to describe, visualize, and mine the results. We reported several novel network features, such as signal propagation through interacting genetic modules and proportional responses whereby levels of expression are altered commensurately with changing levels of the gene. We also observed several examples where a gene is up-regulated following knockdown of its paralog, suggesting the clock network utilizes active compensatory mechanisms rather than simple redundancy to confer robustness and maintain function. We propose that the network features we observe act in concert as a genetic buffering system to maintain clock function in the face of genetic and environmental perturbation.

Amazonian Amphibian Diversity Is Primarily Derived from Late Miocene Andean Lineages:

The Neotropics, which includes South and Central America, contains half of remaining rainforests and the largest reservoir of amphibian diversity. Why there are so many species in certain areas and how such diversity arose before the Quaternary (i.e., more that 1.8 million years ago [MYA]) are largely unstudied. One hypothesis is that the Amazon Basin was the key source of diversity, and species dispersed from there to other areas. Here, we reconstruct a time-calibrated phylogeny and track, in space and time, the distribution of the endemic and species-rich clade of poison frogs (Dendrobatidae) during the Cenozoic (more than 65 MYA) across the continental Neotropics. Our results indicate a far more complex pattern of lineage dispersals and radiations during the past 10 MY. Rather than the Amazon Basin being the center of origin, our results show that the diversity stemmed from repeated dispersals from adjacent areas, especially from the Andes. We also found a recurrent pattern of colonization of Central America from the Chocó at 4-5 MY earlier than the formation of the Panamanian Land Bridge at 1.5 MYA. Thus, the major patterns of dispersals and radiations in the Neotropics were already set by ∼5-6 MYA (the Miocene-Pliocene boundary), but the ongoing process of Neotropical radiation is still happening now, especially in the Chocó-Central America region and Amazonian rainforest.

Transmission Dynamics and Prospects for the Elimination of Canine Rabies:

Canine rabies has been successfully eliminated from Western Europe and North America, but in the developing world, someone dies every ten minutes from this horrific disease, which is primarily spread by domestic dogs. A quantitative understanding of rabies transmission dynamics in domestic dog populations is crucial to determining whether global elimination can be achieved. The unique pathology of rabies allowed us to trace case-to-case transmission directly, during a rabies outbreak in northern Tanzania. From these unusual data, we generated a detailed analysis of rabies transmission biology and found evidence for surprisingly low levels of transmission. We also analysed outbreak data from around the world and found that the transmission of canine rabies has been inherently low throughout its global historic range, explaining the success of control efforts in developed countries. However, we show that when birth and death rates in domestic dog populations are high, such as in our study populations in Tanzania, it is more difficult to maintain population-level immunity in between vaccination campaigns. Nonetheless, we conclude that, although the level of vaccination coverage required is higher than would be predicted from naïve transmission models, global elimination of canine rabies can be achieved through appropriately designed, sustained domestic dog vaccination campaigns.

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How Moths Key Into Scent Of A Flower:

Moths need just the essence of a flower’s scent to identify it, according to new research from The University of Arizona in Tucson. Although a flower’s odor can be composed of hundreds of chemicals, a moth uses just a handful to recognize the flower.

Naked Mole Rats May Hold Clues To Successful Aging:

Naked mole rats resemble pink, wrinkly, saber-toothed sausages and would never win a beauty contest, even among other rodents. But these natives of East Africa are the champs for longevity among rodents, living nine times longer than similar-sized mice. Not only do they have an extraordinarily long lifespan, but they maintain good health for most of it and show remarkable resistance to cancer.

Climate Change Hurting Hares: White Snowshoe Hares Can’t Hide On Brown Earth:

University of Montana researcher Scott Mills and his students have noticed an exceptional number of white snowshoe hares on brown earth. He contends that climate change and the color mismatch are causing much more hare mortality.

How Hyenas ‘Inherit’ Their Social Status:

An international team of scientists from the Leibniz Institute for Zoo and Wildlife Research (IZW) in Berlin, Germany, and the University of Sheffield, UK, now answered the question how social status is inherited in one of the most social of all mammals, the spotted hyena.

Collared Coyote Leaves Record Of 150-Mile Trek:

A coyote collared with a global positioning system tracking device in upstate New York last spring was trapped this winter 150 miles away in eastern Pennsylvania, giving researchers a record — in unprecedented detail — of its movements over an eight-month period.

Climate Change Affecting Europe’s Birds Now, Say Researchers:

Climate change is already having a detectable impact on birds across Europe, says a Durham University and RSPB-led scientific team publishing their findings to create the world’s first indicator of the climate change impacts on wildlife at a continental scale.

Diversity Of Birds Buffer Against West Nile Virus:

North American scientists studying West Nile virus have shown that more diverse bird populations can help to buffer people against infection. Since the virus first spread to North America it has reached epidemic proportions and claimed over 1,100 human lives. “This is an important example of the links between biodiversity and human health”, commented Dr Stuart Butchart, BirdLife’s Global Research and Indicators Coordinator.

Archaeologists Find Earliest Known Domestic Horses:

An international team of archaeologists has uncovered the earliest known evidence of horses being domesticated by humans. The discovery suggests that horses were both ridden and milked. The findings could point to the very beginnings of horse domestication and the origins of the horse breeds we know today. Led by the Universities of Exeter and Bristol (UK), the research is published on Friday 6 March 2009 in journal Science.

Seven New Species Of Deep-sea Coral Discovered:

Scientists identified seven new species of bamboo coral discovered on a NOAA-funded mission in the deep waters of the Papahānaumokuākea Marine National Monument. Six of these species may represent entirely new genera, a remarkable feat given the broad classification a genus represents.*

Lake Michigan Fish Populations Threatened By Decline Of Tiny Creature:

The quick decline of a tiny shrimp-like species, known scientifically as Diporeia, is related to the aggressive population growth of non-native quagga mussels in the Great Lakes, say NOAA scientists. As invasive mussel numbers increase, food sources for Diporeia and many aquatic species have steadily and unilaterally declined.

Captive Bred Black Tiger Prawns Lack Lust, ‘Prawnography’ Shows:

A researcher has studied hours of prawn “sex tapes” to find out why prawns bred in captivity did not go on to breed well.

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First Fossil Brain: Shark Relative That Lived 300 Million Years Ago Yields Very Rare Specimen:

A 300-million-year-old brain of a relative of sharks and ratfish has been revealed by French and American scientists using synchrotron holotomography at the European Synchrotron Radiation Facility (ESRF). It is the first time that the soft tissue of such an old fossil brain has ever been found.

Evidence Appears To Show How And Where Brain’s Frontal Lobe Works:

A Brown University study of stroke victims has produced evidence that the frontal lobe of the human brain controls decision-making along a continuum from abstract to concrete, from front to back.

Physical Fitness Improves Spatial Memory, Increases Size Of Brain Structure:

When it comes to the hippocampus, a brain structure vital to certain types of memory, size matters. Numerous studies have shown that bigger is usually better. Now researchers have found that elderly adults who are more physically fit tend to have bigger hippocampi and better spatial memory than those who are less fit.

Sex Is In The Brain, Whether It Be Lack Of Sexual Interest Or Hypoactive Sexual Desire Disorder:

More than 40 percent of women ages 18-59 experience sexual dysfunction, with lack of sexual interest — hypoactive sexual desire disorder, or HSDD — being the most commonly reported complaint, according to medical researchers. While some question the validity of this diagnosis, a multidisciplinary team from the Stanford University School of Medicine is devoted to objective investigation of such problems.

Wave Of Brain Activity Linked To Anticipation Captured:

Neuroscientists at Georgetown University Medical Center have, for the first time, shown what brain activity looks like when someone anticipates an action or sensory input which soon follows.

New And Unexpected Mechanism Identified How The Brain Responds To Stress:

Chronic stress takes a physical and emotional toll on our bodies and scientists are working on piecing together a medical puzzle to understand how we respond to stress at the cellular level in the brain. Being able to quickly and successfully respond to stress is essential for survival.

How Microscopic Changes To Brain Cause Schizophrenic Behavior In Mice:

Disrupting the function of a key molecule in the brain leads to microscopic brain abnormalities and schizophrenia-like behavior in mice. These abnormalities are similar to those seen in the autopsied brains of people who diagnosed with schizophrenia in life, according to a team of scientists at the Scripps Research Institute.

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, 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.
First, one for our new Palaeontology Collection:
Bird-Like Anatomy, Posture, and Behavior Revealed by an Early Jurassic Theropod Dinosaur Resting Trace:

Fossil tracks made by non-avian theropod dinosaurs commonly reflect the habitual bipedal stance retained in living birds. Only rarely-captured behaviors, such as crouching, might create impressions made by the hands. Such tracks provide valuable information concerning the often poorly understood functional morphology of the early theropod forelimb. Here we describe a well-preserved theropod trackway in a Lower Jurassic (~198 million-year-old) lacustrine beach sandstone in the Whitmore Point Member of the Moenave Formation in southwestern Utah. The trackway consists of prints of typical morphology, intermittent tail drags and, unusually, traces made by the animal resting on the substrate in a posture very similar to modern birds. The resting trace includes symmetrical pes impressions and well-defined impressions made by both hands, the tail, and the ischial callosity. The manus impressions corroborate that early theropods, like later birds, held their palms facing medially, in contrast to manus prints previously attributed to theropods that have forward-pointing digits. Both the symmetrical resting posture and the medially-facing palms therefore evolved by the Early Jurassic, much earlier in the theropod lineage than previously recognized, and may characterize all theropods.

An Indicator of the Impact of Climatic Change on European Bird Populations:

Rapid climatic change poses a threat to global biodiversity. There is extensive evidence that recent climatic change has affected animal and plant populations, but no indicators exist that summarise impacts over many species and large areas. We use data on long-term population trends of European birds to develop such an indicator. We find a significant relationship between interspecific variation in population trend and the change in potential range extent between the late 20th and late 21st centuries, forecasted by climatic envelope models. Our indicator measures divergence in population trend between bird species predicted by climatic envelope models to be favourably affected by climatic change and those adversely affected. The indicator shows a rapid increase in the past twenty years, coinciding with a period of rapid warming.

Serial Position Learning in Honeybees:

Learning of stimulus sequences is considered as a characteristic feature of episodic memory since it contains not only a particular item but also the experience of preceding and following events. In sensorimotor tasks resembling navigational performance, the serial order of objects is intimately connected with spatial order. Mammals and birds develop episodic(-like) memory in serial spatio-temporal tasks, and the honeybee learns spatio-temporal order when navigating between the nest and a food source. Here I examine the structure of the bees’ memory for a combined spatio-temporal task. I ask whether discrimination and generalization are based solely on simple forms of stimulus-reward learning or whether they require sequential configurations. Animals were trained to fly either left or right in a continuous T-maze. The correct choice was signaled by the sequence of colors (blue, yellow) at four positions in the access arm. If only one of the possible 4 signals is shown (either blue or yellow), the rank order of position salience is 1, 2 and 3 (numbered from T-junction). No learning is found if the signal appears at position 4. If two signals are shown, differences at positions 1 and 2 are learned best, those at position 3 at a low level, and those at position 4 not at all. If three or more signals are shown these results are corroborated. This salience rank order again appeared in transfer tests, but additional configural phenomena emerged. Most of the results can be explained with a simple model based on the assumption that the four positions are equipped with different salience scores and that these add up independently. However, deviations from the model are interpreted by assuming stimulus configuration of sequential patterns. It is concluded that, under the conditions chosen, bees rely most strongly on memories developed during simple forms of associative reward learning, but memories of configural serial patterns contribute, too.

Genetic Structure of the Polymorphic Metrosideros (Myrtaceae) Complex in the Hawaiian Islands Using Nuclear Microsatellite Data:

Five species of Metrosideros (Myrtaceae) are recognized in the Hawaiian Islands, including the widespread M. polymorpha, and are characterized by a multitude of distinctive, yet overlapping, habit, ecological, and morphological forms. It remains unclear, despite several previous studies, whether the morphological variation within Hawaiian Metrosideros is due to hybridization, genetic polymorphism, phenotypic plasticity, or some combination of these processes. The Hawaiian Metrosideros complex has become a model system to study ecology and evolution; however this is the first study to use microsatellite data for addressing inter-island patterns of variation from across the Hawaiian Islands. Ten nuclear microsatellite loci were genotyped from 143 individuals of Metrosideros. We took advantage of the bi-parental inheritance and rapid mutation rate of these data to examine the validity of the current taxonomy and to investigate whether Metrosideros plants from the same island are more genetically similar than plants that are morphologically similar. The Bayesian algorithm of the program STRUCTURE was used to define genetic groups within Hawaiian Metrosideros and the closely related taxon M. collina from the Marquesas and Austral Islands. Several standard and nested AMOVAs were conducted to test whether the genetic diversity is structured geographically or taxonomically. The results suggest that Hawaiian Metrosideros have dynamic gene flow, with genetic and morphological diversity structured not simply by geography or taxonomy, but as a result of parallel evolution on islands following rampant island-island dispersal, in addition to ancient chloroplast capture. Results also suggest that the current taxonomy requires major revisions in order to reflect the genetic structure revealed in the microsatellite data.

Big Genomes Facilitate the Comparative Identification of Regulatory Elements:

The identification of regulatory sequences in animal genomes remains a significant challenge. Comparative genomic methods that use patterns of evolutionary conservation to identify non-coding sequences with regulatory function have yielded many new vertebrate enhancers. However, these methods have not contributed significantly to the identification of regulatory sequences in sequenced invertebrate taxa. We demonstrate here that this differential success, which is often attributed to fundamental differences in the nature of vertebrate and invertebrate regulatory sequences, is instead primarily a product of the relatively small size of sequenced invertebrate genomes. We sequenced and compared loci involved in early embryonic patterning from four species of true fruit flies (family Tephritidae) that have genomes four to six times larger than those of Drosophila melanogaster. Unlike in Drosophila, where virtually all non-coding DNA is highly conserved, blocks of conserved non-coding sequence in tephritids are flanked by large stretches of poorly conserved sequence, similar to what is observed in vertebrate genomes. We tested the activities of nine conserved non-coding sequences flanking the even-skipped gene of the teprhitid Ceratis capitata in transgenic D. melanogaster embryos, six of which drove patterns that recapitulate those of known D. melanogaster enhancers. In contrast, none of the three non-conserved tephritid non-coding sequences that we tested drove expression in D. melanogaster embryos. Based on the landscape of non-coding conservation in tephritids, and our initial success in using conservation in tephritids to identify D. melanogaster regulatory sequences, we suggest that comparison of tephritid genomes may provide a systematic means to annotate the non-coding portion of the D. melanogaster genome. We also propose that large genomes be given more consideration in the selection of species for comparative genomics projects, to provide increased power to detect functional non-coding DNAs and to provide a less biased view of the evolution and function of animal genomes.

Lip-Reading Aids Word Recognition Most in Moderate Noise: A Bayesian Explanation Using High-Dimensional Feature Space:

Watching a speaker’s facial movements can dramatically enhance our ability to comprehend words, especially in noisy environments. From a general doctrine of combining information from different sensory modalities (the principle of inverse effectiveness), one would expect that the visual signals would be most effective at the highest levels of auditory noise. In contrast, we find, in accord with a recent paper, that visual information improves performance more at intermediate levels of auditory noise than at the highest levels, and we show that a novel visual stimulus containing only temporal information does the same. We present a Bayesian model of optimal cue integration that can explain these conflicts. In this model, words are regarded as points in a multidimensional space and word recognition is a probabilistic inference process. When the dimensionality of the feature space is low, the Bayesian model predicts inverse effectiveness; when the dimensionality is high, the enhancement is maximal at intermediate auditory noise levels. When the auditory and visual stimuli differ slightly in high noise, the model makes a counterintuitive prediction: as sound quality increases, the proportion of reported words corresponding to the visual stimulus should first increase and then decrease. We confirm this prediction in a behavioral experiment. We conclude that auditory-visual speech perception obeys the same notion of optimality previously observed only for simple multisensory stimuli.

And one from yesterday:
A Genome Wide Survey of SNP Variation Reveals the Genetic Structure of Sheep Breeds:

The genetic structure of sheep reflects their domestication and subsequent formation into discrete breeds. Understanding genetic structure is essential for achieving genetic improvement through genome-wide association studies, genomic selection and the dissection of quantitative traits. After identifying the first genome-wide set of SNP for sheep, we report on levels of genetic variability both within and between a diverse sample of ovine populations. Then, using cluster analysis and the partitioning of genetic variation, we demonstrate sheep are characterised by weak phylogeographic structure, overlapping genetic similarity and generally low differentiation which is consistent with their short evolutionary history. The degree of population substructure was, however, sufficient to cluster individuals based on geographic origin and known breed history. Specifically, African and Asian populations clustered separately from breeds of European origin sampled from Australia, New Zealand, Europe and North America. Furthermore, we demonstrate the presence of stratification within some, but not all, ovine breeds. The results emphasize that careful documentation of genetic structure will be an essential prerequisite when mapping the genetic basis of complex traits. Furthermore, the identification of a subset of SNP able to assign individuals into broad groupings demonstrates even a small panel of markers may be suitable for applications such as traceability.

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Underlying Sleep Problem Linked To Attention-deficit/hyperactivity Disorder In Children:

A study in the March 1 issue of the journal SLEEP suggests the presence of an intrinsic sleep problem specific to attention-deficit/hyperactivity disorder (ADHD) and supports the idea that children with ADHD may be chronically sleep deprived and have abnormal REM sleep.

Butterfly Found To Be New Species, Because Of Its Mustache:

After nearly a century in the Natural History Museum collections, a new butterfly species has been discovered because of its mustache.

Coffee Cultivation Good For Diversity In Agrarian Settlements But Not In Forests:

Coffee shrubs, both in themselves and because they are most often cultivated in the shade of large trees, can have a positive impact on plant and animal diversity in those parts of the landscape that are deforested and dominated by agriculture. What constitutes a dilemma for consumers wishing to shop ecologically is that when coffee is grown in a forest, which is also common, the impact on diversity is negative.

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What Is A Virus? Research Suggests A Broader Definition May Be Needed:

The strange interaction of a parasitic wasp, the caterpillar in which it lays its eggs and a virus that helps it overcome the caterpillar’s immune defenses has some scientists rethinking the definition of a virus. In an essay in the journal Science, Donald Stoltz, a professor of microbiology and immunology at Dalhousie University, in Halifax, Nova Scotia, and James Whitfield, a professor of entomology at the University of Illinois, report that a new study also appearing in Science shows how the diverse ways in which viruses operate within and among the organisms they encounter may not be fully appreciated. The study, from a team of researchers led by the Université François Rabelais, in Tours, France, found that the genes that encode a virus that helps wasps successfully parasitize caterpillars are actually integrated into the wasps’ own chromosomes. These genes, which they show to be related to those from another known group of viruses, are an indivisible part of the wasp’s genetic heritage; they are passed down from one generation to another of parasitoid wasps.
While it is not unusual for virus DNA to become embedded in the chromosomes of their hosts, in this case the wasp is not the only “host” of the virus. The viral genes do replicate (copy themselves) inside the wasp (the permanent host), but they actually target – and act upon – the immune system of the caterpillar (a more transient host).

Birds’ Movements Reveal Climate Change In Action:

The northward and inland movement of North American birds, confirmed by thousands of citizen-observations, has provided new and powerful evidence that climate change is having a serious impact on natural systems, according to a new report by Audubon (BirdLife in the USA). The findings signal the need for dramatic policy changes to combat pervasive ecological disruption.

More…..

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There are 19 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, 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:
Leptin Affects Life History Decisions in a Passerine Bird: A Field Experiment:

Organisms face trade-offs regarding their life-history strategies, such as decisions of single or multiple broods within a year. In passerines displaying facultative multiple breeding, the probability of laying a second clutch is influenced by several life-history factors. However, information about the mechanistic background of these trade-offs is largely lacking. Leptin is a protein hormone produced by white fat cells, and acts as a signal between peripheral energy depots and the central nervous system. In addition, leptin affects cells at all levels of the reproductive axis and plays a critical role in regulating the allocation of metabolic energy to reproduction. As such, it is possible that leptin levels influence the decision of whether or not to invest time and energy into a second clutch. Accordingly, we expect a treatment with exogenous leptin to result in an increased number of second broods. At a later stage during the first brood, female great tits were treated either with long-term leptin-filled cholesterol pellets (the experimental birds) or with pellets containing only cholesterol (the control birds). We found that leptin-treated females were significantly more likely to have a second brood and that the earlier females were more likely to lay a second clutch than the late females. As both timing of first brood and treatment with leptin were important in the decision of having multiple broods, the trade-offs involved in the breeding strategy most likely depend on multiple factors. Presumably leptin has evolved as a signal of energy supply status to regulate the release of reproductive hormones so that reproduction is coordinated with periods of sufficient nutrients. This study investigated the role of leptin as a mediator between energy resources and reproductive output, providing a fundamentally new insight into how trade-offs work on a functional basis.

Universal Artifacts Affect the Branching of Phylogenetic Trees, Not Universal Scaling Laws:

The superficial resemblance of phylogenetic trees to other branching structures allows searching for macroevolutionary patterns. However, such trees are just statistical inferences of particular historical events. Recent meta-analyses report finding regularities in the branching pattern of phylogenetic trees. But is this supported by evidence, or are such regularities just methodological artifacts? If so, is there any signal in a phylogeny? In order to evaluate the impact of polytomies and imbalance on tree shape, the distribution of all binary and polytomic trees of up to 7 taxa was assessed in tree-shape space. The relationship between the proportion of outgroups and the amount of imbalance introduced with them was assessed applying four different tree-building methods to 100 combinations from a set of 10 ingroup and 9 outgroup species, and performing covariance analyses. The relevance of this analysis was explored taking 61 published phylogenies, based on nucleic acid sequences and involving various taxa, taxonomic levels, and tree-building methods. All methods of phylogenetic inference are quite sensitive to the artifacts introduced by outgroups. However, published phylogenies appear to be subject to a rather effective, albeit rather intuitive control against such artifacts. The data and methods used to build phylogenetic trees are varied, so any meta-analysis is subject to pitfalls due to their uneven intrinsic merits, which translate into artifacts in tree shape. The binary branching pattern is an imposition of methods, and seldom reflects true relationships in intraspecific analyses, yielding artifactual polytomies in short trees. Above the species level, the departure of real trees from simplistic random models is caused at least by two natural factors -uneven speciation and extinction rates; and artifacts such as choice of taxa included in the analysis, and imbalance introduced by outgroups and basal paraphyletic taxa. This artifactual imbalance accounts for tree shape convergence of large trees. There is no evidence for any universal scaling in the tree of life. Instead, there is a need for improved methods of tree analysis that can be used to discriminate the noise due to outgroups from the phylogenetic signal within the taxon of interest, and to evaluate realistic models of evolution, correcting the retrospective perspective and explicitly recognizing extinction as a driving force. Artifacts are pervasive, and can only be overcome through understanding the structure and biological meaning of phylogenetic trees.

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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, 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:
Rich Pickings Near Large Communal Roosts Favor ‘Gang’ Foraging by Juvenile Common Ravens, Corvus corax:

Ravens (Corvus corax) feed primarily on rich but ephemeral carcasses of large animals, which are usually defended by territorial pairs of adults. Non-breeding juveniles forage socially and aggregate in communal winter roosts, and these appear to function as ‘information centers’ regarding the location of the rare food bonanzas: individuals search independently of one another and pool their effort by recruiting each other at roosts. However, at a large raven roost in Newborough on Anglesey, North Wales, some juveniles have been observed recently to forage in ‘gangs’ and to roost separately from other birds. Here we adapt a general model of juvenile common raven foraging behavior where, in addition to the typical co-operative foraging strategy, such gang foraging behavior could be evolutionarily stable near winter raven roosts. We refocus the model on the conditions under which this newly documented, yet theoretically anticipated, gang-based foraging has been observed. In the process, we show formally how the trade off between search efficiency and social opportunity can account for the existence of the alternative social foraging tactics that have been observed in this species. This work serves to highlight a number of fruitful avenues for future research, both from a theoretical and empirical perspective.

Does My Step Look Big In This? A Visual Illusion Leads To Safer Stepping Behaviour:

Tripping is a common factor in falls and a typical safety strategy to avoid tripping on steps or stairs is to increase foot clearance over the step edge. In the present study we asked whether the perceived height of a step could be increased using a visual illusion and whether this would lead to the adoption of a safer stepping strategy, in terms of greater foot clearance over the step edge. The study also addressed the controversial question of whether motor actions are dissociated from visual perception. 21 young, healthy subjects perceived the step to be higher in a configuration of the horizontal-vertical illusion compared to a reverse configuration (p = 0.01). During a simple stepping task, maximum toe elevation changed by an amount corresponding to the size of the visual illusion (p<0.001). Linear regression analyses showed highly significant associations between perceived step height and maximum toe elevation for all conditions. The perceived height of a step can be manipulated using a simple visual illusion, leading to the adoption of a safer stepping strategy in terms of greater foot clearance over a step edge. In addition, the strong link found between perception of a visual illusion and visuomotor action provides additional support to the view that the original, controversial proposal by Goodale and Milner (1992) of two separate and distinct visual streams for perception and visuomotor action should be re-evaluated.

Sleep Restriction Increases the Risk of Developing Cardiovascular Diseases by Augmenting Proinflammatory Responses through IL-17 and CRP:

Sleep restriction, leading to deprivation of sleep, is common in modern 24-h societies and is associated with the development of health problems including cardiovascular diseases. Our objective was to investigate the immunological effects of prolonged sleep restriction and subsequent recovery sleep, by simulating a working week and following recovery weekend in a laboratory environment. After 2 baseline nights of 8 hours time in bed (TIB), 13 healthy young men had only 4 hours TIB per night for 5 nights, followed by 2 recovery nights with 8 hours TIB. 6 control subjects had 8 hours TIB per night throughout the experiment. Heart rate, blood pressure, salivary cortisol and serum C-reactive protein (CRP) were measured after the baseline (BL), sleep restriction (SR) and recovery (REC) period. Peripheral blood mononuclear cells (PBMC) were collected at these time points, counted and stimulated with PHA. Cell proliferation was analyzed by thymidine incorporation and cytokine production by ELISA and RT-PCR. CRP was increased after SR (145% of BL; p<0.05), and continued to increase after REC (231% of BL; p<0.05). Heart rate was increased after REC (108% of BL; p<0.05). The amount of circulating NK-cells decreased (65% of BL; p<0.005) and the amount of B-cells increased (121% of BL; p<0.005) after SR, but these cell numbers recovered almost completely during REC. Proliferation of stimulated PBMC increased after SR (233% of BL; p<0.05), accompanied by increased production of IL-1β (137% of BL; p<0.05), IL-6 (163% of BL; p<0.05) and IL-17 (138% of BL; p<0.05) at mRNA level. After REC, IL-17 was still increased at the protein level (119% of BL; p<0.05). 5 nights of sleep restriction increased lymphocyte activation and the production of proinflammatory cytokines including IL-1β IL-6 and IL-17; they remained elevated after 2 nights of recovery sleep, accompanied by increased heart rate and serum CRP, 2 important risk factors for cardiovascular diseases. Therefore, long-term sleep restriction may lead to persistent changes in the immune system and the increased production of IL-17 together with CRP may increase the risk of developing cardiovascular diseases.

Estimating the Worldwide Extent of Illegal Fishing:

Illegal and unreported fishing contributes to overexploitation of fish stocks and is a hindrance to the recovery of fish populations and ecosystems. This study is the first to undertake a world-wide analysis of illegal and unreported fishing. Reviewing the situation in 54 countries and on the high seas, we estimate that lower and upper estimates of the total value of current illegal and unreported fishing losses worldwide are between $10 bn and $23.5 bn annually, representing between 11 and 26 million tonnes. Our data are of sufficient resolution to detect regional differences in the level and trend of illegal fishing over the last 20 years, and we can report a significant correlation between governance and the level of illegal fishing. Developing countries are most at risk from illegal fishing, with total estimated catches in West Africa being 40% higher than reported catches. Such levels of exploitation severely hamper the sustainable management of marine ecosystems. Although there have been some successes in reducing the level of illegal fishing in some areas, these developments are relatively recent and follow growing international focus on the problem. This paper provides the baseline against which successful action to curb illegal fishing can be judged.

How Many Loci Does it Take to DNA Barcode a Crocus?:

DNA barcoding promises to revolutionize the way taxonomists work, facilitating species identification by using small, standardized portions of the genome as substitutes for morphology. The concept has gained considerable momentum in many animal groups, but the higher plant world has been largely recalcitrant to the effort. In plants, efforts are concentrated on various regions of the plastid genome, but no agreement exists as to what kinds of regions are ideal, though most researchers agree that more than one region is necessary. One reason for this discrepancy is differences in the tests that are used to evaluate the performance of the proposed regions. Most tests have been made in a floristic setting, where the genetic distance and therefore the level of variation of the regions between taxa is large, or in a limited set of congeneric species. Here we present the first in-depth coverage of a large taxonomic group, all 86 known species (except two doubtful ones) of crocus. Even six average-sized barcode regions do not identify all crocus species. This is currently an unrealistic burden in a barcode context. Whereas most proposed regions work well in a floristic context, the majority will – as is the case in crocus – undoubtedly be less efficient in a taxonomic setting. However, a reasonable but less than perfect level of identification may be reached – even in a taxonomic context. The time is ripe for selecting barcode regions in plants, and for prudent examination of their utility. Thus, there is no reason for the plant community to hold back the barcoding effort by continued search for the Holy Grail. We must acknowledge that an emerging system will be far from perfect, fraught with problems and work best in a floristic setting.

Evidence for Directional Selection at a Novel Major Histocompatibility Class I Marker in Wild Common Frogs (Rana temporaria) Exposed to a Viral Pathogen (Ranavirus):

Whilst the Major Histocompatibility Complex (MHC) is well characterized in the anuran Xenopus, this region has not previously been studied in another popular model species, the common frog (Rana temporaria). Nor, to date, have there been any studies of MHC in wild amphibian host-pathogen systems. We characterise an MHC class I locus in the common frog, and present primers to amplify both the whole region, and specifically the antigen binding region. As no more than two expressed haplotypes were found in over 400 clones from 66 individuals, it is likely that there is a single class I locus in this species. This finding is consistent with the single class I locus in Xenopus, but contrasts with the multiple loci identified in axolotls, providing evidence that the diversification of MHC class I into multiple loci likely occurred after the Caudata/Anura divergence (approximately 350 million years ago) but before the Ranidae/Pipidae divergence (approximately 230 mya). We use this locus to compare wild populations of common frogs that have been infected with a viral pathogen (Ranavirus) with those that have no history of infection. We demonstrate that certain MHC supertypes are associated with infection status (even after accounting for shared ancestry), and that the diseased populations have more similar supertype frequencies (lower FST) than the uninfected. These patterns were not seen in a suite of putatively neutral microsatellite loci. We interpret this pattern at the MHC locus to indicate that the disease has imposed selection for particular haplotypes, and hence that common frogs may be adapting to the presence of Ranavirus, which currently kills tens of thousands of amphibians in the UK each year.

Does Sleep Play a Role in Memory Consolidation? A Comparative Test:

Sleep is a pervasive characteristic of mammalian species, yet its purpose remains obscure. It is often proposed that ‘sleep is for the brain’, a view that is supported by experimental studies showing that sleep improves cognitive processes such as memory consolidation. Some comparative studies have also reported that mammalian sleep durations are higher among more encephalized species. However, no study has assessed the relationship between sleep and the brain structures that are implicated in specific cognitive processes across species. The hippocampus, neocortex and amygdala are important for memory consolidation and learning and are also in a highly actived state during sleep. We therefore investigated the evolutionary relationship between mammalian sleep and the size of these brain structures using phylogenetic comparative methods. We found that evolutionary increases in the size of the amygdala are associated with corresponding increases in NREM sleep durations. These results are consistent with the hypothesis that NREM sleep is functionally linked with specializations of the amygdala, including perhaps memory processing.

Decision-Making in Research Tasks with Sequential Testing:

In a recent controversial essay, published by JPA Ioannidis in PLoS Medicine, it has been argued that in some research fields, most of the published findings are false. Based on theoretical reasoning it can be shown that small effect sizes, error-prone tests, low priors of the tested hypotheses and biases in the evaluation and publication of research findings increase the fraction of false positives. These findings raise concerns about the reliability of research. However, they are based on a very simple scenario of scientific research, where single tests are used to evaluate independent hypotheses. In this study, we present computer simulations and experimental approaches for analyzing more realistic scenarios. In these scenarios, research tasks are solved sequentially, i.e. subsequent tests can be chosen depending on previous results. We investigate simple sequential testing and scenarios where only a selected subset of results can be published and used for future rounds of test choice. Results from computer simulations indicate that for the tasks analyzed in this study, the fraction of false among the positive findings declines over several rounds of testing if the most informative tests are performed. Our experiments show that human subjects frequently perform the most informative tests, leading to a decline of false positives as expected from the simulations. For the research tasks studied here, findings tend to become more reliable over time. We also find that the performance in those experimental settings where not all performed tests could be published turned out to be surprisingly inefficient. Our results may help optimize existing procedures used in the practice of scientific research and provide guidance for the development of novel forms of scholarly communication.

Biogeography of Photosynthetic Light-Harvesting Genes in Marine Phytoplankton:

Photosynthetic light-harvesting proteins are the mechanism by which energy enters the marine ecosystem. The dominant prokaryotic photoautotrophs are the cyanobacterial genera Prochlorococcus and Synechococcus that are defined by two distinct light-harvesting systems, chlorophyll-bound protein complexes or phycobilin-bound protein complexes, respectively. Here, we use the Global Ocean Sampling (GOS) Project as a unique and powerful tool to analyze the environmental diversity of photosynthetic light-harvesting genes in relation to available metadata including geographical location and physical and chemical environmental parameters. All light-harvesting gene fragments and their metadata were obtained from the GOS database, aligned using ClustalX and classified phylogenetically. Each sequence has a name indicative of its geographic location; subsequent biogeographical analysis was performed by correlating light-harvesting gene budgets for each GOS station with surface chlorophyll concentration. Using the GOS data, we have mapped the biogeography of light-harvesting genes in marine cyanobacteria on ocean-basin scales and show that an environmental gradient exists in which chlorophyll concentration is correlated to diversity of light-harvesting systems. Three functionally distinct types of light-harvesting genes are defined: (1) the phycobilisome (PBS) genes of Synechococcus; (2) the pcb genes of Prochlorococcus; and (3) the iron-stress-induced (isiA) genes present in some marine Synechococcus. At low chlorophyll concentrations, where nutrients are limited, the Pcb-type light-harvesting system shows greater genetic diversity; whereas at high chlorophyll concentrations, where nutrients are abundant, the PBS-type light-harvesting system shows higher genetic diversity. We interpret this as an environmental selection of specific photosynthetic strategy. Importantly, the unique light-harvesting system isiA is found in the iron-limited, high-nutrient low-chlorophyll region of the equatorial Pacific. This observation demonstrates the ecological importance of isiA genes in enabling marine Synechococcus to acclimate to iron limitation and suggests that the presence of this gene can be a natural biomarker for iron limitation in oceanic environments.

A Rice Gene of De Novo Origin Negatively Regulates Pathogen-Induced Defense Response:

How defense genes originated with the evolution of their specific pathogen-responsive traits remains an important problem. It is generally known that a form of duplication can generate new genes, suggesting that a new gene usually evolves from an ancestral gene. However, we show that a new defense gene in plants may evolve by de novo origination, resulting in sophisticated disease-resistant functions in rice. Analyses of gene evolution showed that this new gene, OsDR10, had homologs only in the closest relative, Leersia genus, but not other subfamilies of the grass family; therefore, it is a rice tribe-specific gene that may have originated de novo in the tribe. We further show that this gene may evolve a highly conservative rice-specific function that contributes to the regulation difference between rice and other plant species in response to pathogen infections. Biologic analyses including gene silencing, pathologic analysis, and mutant characterization by transformation showed that the OsDR10-suppressed plants enhanced resistance to a broad spectrum of Xanthomonas oryzae pv. oryzae strains, which cause bacterial blight disease. This enhanced disease resistance was accompanied by increased accumulation of endogenous salicylic acid (SA) and suppressed accumulation of endogenous jasmonic acid (JA) as well as modified expression of a subset of defense-responsive genes functioning both upstream and downstream of SA and JA. These data and analyses provide fresh insights into the new biologic and evolutionary processes of a de novo gene recruited rapidly.

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Monday night – the day when four of the PLoS journals publish new articles – here is a sample. 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, 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:
Wings, Horns, and Butterfly Eyespots: How Do Complex Traits Evolve?:

Throughout their evolutionary history, organisms have evolved numerous complex morphological, physiological, and behavioral adaptations to increase their chances of survival and reproduction. Insects have evolved wings and flight, which allowed them to better disperse [2], beetles have grown horns to fight over females [3], and moths and butterflies have decorated their wings with bright circles of colored scales to scare off predators [4]. The way that most of these and other adaptations first evolved, however, is still largely unknown. In the last two decades we have learned that novel traits appear to be built using old genes wired in novel ways [5], but it is still a mystery whether these novel traits evolve when genes are rewired de novo, one at a time, into new developmental networks, or whether clusters of pre-wired genes are co-opted into the development of the new trait. The speed of evolution of novel complex traits is likely to depend greatly on which of these two mechanisms underlies their origin. It is important, thus, to understand how novel complex traits evolve.

An Unbiased Scientific Record Should Be Everyone’s Agenda:

A large and growing literature details the many ways by which research and the subsequent published record can be inappropriately influenced, including publication bias [1], outcome reporting bias [2], financial [3] and non-financial [4] competing interests, sponsors’ control of study data and publication [5], and restrictions on access to data and materials [6]. But it can be difficult for an editor, reading a submitted manuscript, to disentangle these many influences and to understand whether the work ultimately represents valid science. Any journal has stories to tell of attempts to unduly influence the publication process–such as the author who repeatedly appeals a manuscript’s rejection, claiming the reviewers are incompetent and demanding evaluation by a specific list of preferred experts, or the biotech company that refuses to publicly deposit the microarray data underlying their findings. Sometimes distortion of the scientific record may be limited in scope, relating to just one paper. But when a single company funds virtually an entire research agenda on a particular topic, there is the potential for wider and far more damaging distortion. In a detailed analysis of documentation released as part of a class-action lawsuit relating to the drug gabapentin (Neurontin), Kay Dickersin has described “…a remarkable assemblage of evidence of reporting biases that amount to outright deception of the biomedical community, and suppression of scientific truth concerning the effectiveness of Neurontin for migraine, bipolar disorders, and pain…” ([7], summarized in [8]). Here we propose five ways in which authors and editors can mitigate the effects of biased agendas on the published scientific record.

Social Research on Neglected Diseases of Poverty: Continuing and Emerging Themes:

Neglected tropical diseases (NTDs) exist and persist for social and economic reasons that enable the vectors and pathogens to take advantage of changes in the behavioral and physical environment. Persistent poverty at household, community, and national levels, and inequalities within and between sectors, contribute to the perpetuation and re-emergence of NTDs. Changes in production and habitat affect the physical environment, so that agricultural development, mining and forestry, rapid industrialization, and urbanization all result in changes in human uses of the environment, exposure to vectors, and vulnerability to infection. Concurrently, political instability and lack of resources limit the capacity of governments to manage environments, control disease transmission, and ensure an effective health system. Social, cultural, economic, and political factors interact and influence government capacity and individual willingness to reduce the risks of infection and transmission, and to recognize and treat disease. Understanding the dynamic interaction of diverse factors in varying contexts is a complex task, yet critical for successful health promotion, disease prevention, and disease control. Many of the research techniques and tools needed for this purpose are available in the applied social sciences. In this article we use this term broadly, and so include behavioral, population and economic social sciences, social and cultural epidemiology, and the multiple disciplines of public health, health services, and health policy and planning. These latter fields, informed by foundational social science theory and methods, include health promotion, health communication, and heath education.

Reduction of Dopamine Level Enhances the Attractiveness of Male Drosophila to Other Males:

Dopamine is an important neuromodulator in animals and its roles in mammalian sexual behavior are extensively studied. Drosophila as a useful model system is widely used in many fields of biological studies. It has been reported that dopamine reduction can affect female receptivity in Drosophila and leave male-female courtship behavior unaffected. Here, we used genetic and pharmacological approaches to decrease the dopamine level in dopaminergic cells in Drosophila, and investigated the consequence of this manipulation on male homosexual courtship behavior. We find that reduction of dopamine level can induce Drosophila male-male courtship behavior, and that this behavior is mainly due to the increased male attractiveness or decreased aversiveness towards other males, but not to their enhanced propensity to court other males. Chemical signal input probably plays a crucial role in the male-male courtship induced by the courtees with reduction of dopamine. Our finding provides insight into the relationship between the dopamine reduction and male-male courtship behavior, and hints dopamine level is important for controlling Drosophila courtship behavior.

Brain Correlates of Non-Symbolic Numerosity Estimation in Low and High Mathematical Ability Children:

Previous studies have implicated several brain areas as subserving numerical approximation. Most studies have examined brain correlates of adult numerical approximation and have not considered individual differences in mathematical ability. The present study examined non-symbolic numerical approximation in two groups of 10-year-olds: Children with low and high mathematical ability. The aims of this study were to investigate the brain mechanisms associated with approximate numerosity in children and to assess whether individual differences in mathematical ability are associated with differential brain correlates during the approximation task. The results suggest that, similarly to adults, multiple and distributed brain areas are involved in approximation in children. Despite equal behavioral performance, there were differences in the brain activation patterns between low and high mathematical ability groups during the approximation task. This suggests that individual differences in mathematical ability are reflected in differential brain response during approximation.

Localisation and Function of the Endocannabinoid System in the Human Ovary:

Although anandamide (AEA) had been measured in human follicular fluid and is suggested to play a role in ovarian follicle and oocyte maturity, its exact source and role in the human ovary remains unclear. Immunohistochemical examination of normal human ovaries indicated that the endocannabinoid system was present and widely expressed in the ovarian medulla and cortex with more intense cannabinoid receptor 2 (CB2) than CB1 immunoreactivity in the granulosa cells of primordial, primary, secondary, tertiary follicles, corpus luteum and corpus albicans. The enzymes, fatty acid amide hydrolase (FAAH) and N-acyclphosphatidylethanolamine-phospholi ​pase D (NAPE-PLD), were only found in growing secondary and tertiary follicles and corpora lutea and albicantes. The follicular fluid (FF) AEA concentrations of 260 FF samples, taken from 37 infertile women undergoing controlled ovarian hyperstimulation for in vitro fertilisation and intracytoplasmic sperm injection with embryo transfer, were correlated with ovarian follicle size (P = 0.03). Significantly higher FF AEA concentrations were also observed in mature follicles (1.43±0.04 nM; mean±SEM) compared to immature follicles (1.26±0.06 nM), P = 0.0142 and from follicles containing morphologically assessed mature oocytes (1.56±0.11 nM) compared to that containing immature oocytes (0.99±0.09 nM), P = 0.0011. ROC analysis indicated that a FF AEA level of 1.09 nM could discriminate between mature and immature oocytes with 72.2% sensitivity and 77.14% specificity, whilst plasma AEA levels and FF AEA levels on oocyte retrieval day were not significantly different (P = 0.23). These data suggest that AEA is produced in the ovary, is under hormonal control and plays a role in folliculogenesis, preovulatory follicle maturation, oocyte maturity and ovulation.

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There are 19 new articles in PLoS ONE published on 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, 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:
Kestrel-Prey Dynamic in a Mediterranean Region: The Effect of Generalist Predation and Climatic Factors:

Most hypotheses on population limitation of small mammals and their predators come from studies carried out in northern latitudes, mainly in boreal ecosystems. In such regions, many predators specialize on voles and predator-prey systems are simpler compared to southern ecosystems where predator communities are made up mostly of generalists and predator-prey systems are more complex. Determining food limitation in generalist predators is difficult due to their capacity to switch to alternative prey when the basic prey becomes scarce. We monitored the population density of a generalist raptor, the Eurasian kestrel Falco tinnunculus over 15 years in a mountainous Mediterranean area. In addition, we have recorded over 11 years the inter-annual variation in the abundance of two main prey species of kestrels, the common vole Microtus arvalis and the eyed lizard Lacerta lepida and a third species scarcely represented in kestrel diet, the great white-toothed shrew Crocidura russula. We estimated the per capita growth rate (PCGR) to analyse population dynamics of kestrel and predator species. Multimodel inference determined that the PCGR of kestrels was better explained by a model containing the population density of only one prey species (the common vole) than a model using a combination of the densities of the three prey species. The PCGR of voles was explained by kestrel abundance in combination with annual rainfall and mean annual temperature. In the case of shrews, growth rate was also affected by kestrel abundance and temperature. Finally, we did not find any correlation between kestrel and lizard abundances.

Mass Stranding of Marine Birds Caused by a Surfactant-Producing Red Tide:

In November-December 2007 a widespread seabird mortality event occurred in Monterey Bay, California, USA, coincident with a massive red tide caused by the dinoflagellate Akashiwo sanguinea. Affected birds had a slimy yellow-green material on their feathers, which were saturated with water, and they were severely hypothermic. We determined that foam containing surfactant-like proteins, derived from organic matter of the red tide, coated their feathers and neutralized natural water repellency and insulation. No evidence of exposure to petroleum or other oils or biotoxins were found. This is the first documented case of its kind, but previous similar events may have gone undetected. The frequency and amplitude of red tides have increased in Monterey Bay since 2004, suggesting that impacts on wintering marine birds may continue or increase.

Is Altruistic Behavior Associated with Major Depression Onset?:

Previous cross-sectional study showed altruistic behaviors were harmful on major depression (MD). It is needed to investigate the impact of altruistic behaviors by its contents on the development of MD prospectively. The National Survey of Midlife Development in the United States (MIDUS) in 1995-1996 and the MIDUS Psychological Experience Follow-Up study in 1998 were analyzed (weighted N = 563). Financial support of 10 or more dollars per month had a significant impact on the development of MD in comparison to no financial support (OR: 2.64, 95% CI: 1.05-6.62). Unpaid assistance and providing emotional support were not significantly associated with the development of MD in later life. Those who provide financial contribution to individuals other than family members can be at risk of developing MD.

Probing Evolutionary Repeatability: Neutral and Double Changes and the Predictability of Evolutionary Adaptation:

The question of how organisms adapt is among the most fundamental in evolutionary biology. Two recent studies investigated the evolution of Escherichia coli in response to challenge with the antibiotic cefotaxime. Studying five mutations in the β-lactamase gene that together confer significant antibiotic resistance, the authors showed a complex fitness landscape that greatly constrained the identity and order of intermediates leading from the initial wildtype genotype to the final resistant genotype. Out of 18 billion possible orders of single mutations leading from non-resistant to fully-resistant form, they found that only 27 (1.5×10−7%) pathways were characterized by consistently increasing resistance, thus only a tiny fraction of possible paths are accessible by positive selection. I further explore these data in several ways. Allowing neutral changes (those that do not affect resistance) increases the number of accessible pathways considerably, from 27 to 629. Allowing multiple simultaneous mutations also greatly increases the number of accessible pathways. Allowing a single case of double mutation to occur along a pathway increases the number of pathways from 27 to 259, and allowing arbitrarily many pairs of simultaneous changes increases the number of possible pathways by more than 100 fold, to 4800. I introduce the metric ‘repeatability,’ the probability that two random trials will proceed via the exact same pathway. In general, I find that while the total number of accessible pathways is dramatically affected by allowing neutral or double mutations, the overall evolutionary repeatability is generally much less affected. These results probe the conceivable pathways available to evolution. Even when many of the assumptions of the analysis of Weinreich et al. (2006) are relaxed, I find that evolution to more highly cefotaxime resistant β-lactamase proteins is still highly repeatable.

Phylogenomics: Gene Duplication, Unrecognized Paralogy and Outgroup Choice:

Comparative genomics has revealed the ubiquity of gene and genome duplication and subsequent gene loss. In the case of gene duplication and subsequent loss, gene trees can differ from species trees, thus frequent gene duplication poses a challenge for reconstruction of species relationships. Here I address the case of multi-gene sets of putative orthologs that include some unrecognized paralogs due to ancestral gene duplication, and ask how outgroups should best be chosen to reduce the degree of non-species tree (NST) signal. Consideration of expected internal branch lengths supports several conclusions: (i) when a single outgroup is used, the degree of NST signal arising from gene duplication is either independent of outgroup choice, or is minimized by use of a maximally closely related post-duplication (MCRPD) outgroup; (ii) when two outgroups are used, NST signal is minimized by using one MCRPD outgroup, while the position of the second outgroup is of lesser importance; and (iii) when two outgroups are used, the ability to detect gene trees that are inconsistent with known aspects of the species tree is maximized by use of one MCRPD, and is either independent of the position of the second outgroup, or is maximized for a more distantly related second outgroup. Overall, these results generalize the utility of closely-related outgroups for phylogenetic analysis.

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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, 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:
Lipid Profile and Serum Characteristics of the Blind Subterranean Mole Rat, Spalax:

Spalax (blind subterranean mole rat), is a mammal adapted to live in fluctuating oxygen levels, and can survive severe hypoxia and hypercapnia. The adaptive evolution of Spalax to underground life resulted in structural and molecular-genetic differences comparing to above-ground mammals. These differences include higher myocardial maximal oxygen consumption, increased lung diffusion capacity, increased blood vessels density, and unique expression patterns of cancer and angiogenesis related genes such as heparanase, vascular endothelial growth factor, and P53. Here we elucidate the main characteristics of Spalax lipid profile, as well as its main antioxidant and serum parameters. Compared to human, Spalax possesses lower total-cholesterol, low density lipoproteins (LDL) and triglycerides levels, and higher levels of high density lipoproteins (HDL). Apolipoprotein A-I and apolipoprotein B-100 were significantly lower in Spalax compared to human. Paraoxonase (PON) 1 arylesterase activity, was higher in Spalax compared to both human and mouse serum levels. Analysis of serum chemistry of Spalax revealed special features in this mammal. Spalax possesses a unique lipid profile with high HDL and low LDL lipoproteins. The antioxidant serum content in the mole rat is higher than that of human and mouse. Serum C reactive protein (CRP) levels are significantly lower in Spalax compared to that of human or mouse, reflecting low levels of inflammation. These differences between Spalax, human and mouse are due to several factors including the intensive activity life-style that Spalax pursue underground, dietary components, and evolutionary genetic adaptations. Unfolding the genetic basis of these differences will probably result in unique treatments for a variety of human diseases such as dyslipedemias, inflammation and cancer.

Quantitative Trait Evolution and Environmental Change:

Given the recent changes in climate, there is an urgent need to understand the evolutionary ability of populations to respond to these changes. We performed individual-based simulations with different shapes of the fitness curve, different heritabilities, different levels of density compensation, and different autocorrelation of environmental noise imposed on an environmental trend to study the ability of a population to adapt to changing conditions. The main finding is that when there is a positive autocorrelation of environmental noise, the outcome of the evolutionary process is much more unpredictable compared to when the noise has no autocorrelation. In addition, we found that strong selection resulted in a higher load, and more extinctions, and that this was most pronounced when heritability was low. The level of density-compensation was important in determining the variance in load when there was strong selection, and when genetic variance was lower when the level of density-compensation was low. The strong effect of the details of the environmental fluctuations makes predictions concerning the evolutionary future of populations very hard to make. In addition, to be able to make good predictions we need information on heritability, fitness functions and levels of density compensation. The results strongly suggest that patterns of environmental noise must be incorporated in future models of environmental change, such as global warming.

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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, 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:
Estimating Mass Properties of Dinosaurs Using Laser Imaging and 3D Computer Modelling:

Body mass reconstructions of extinct vertebrates are most robust when complete to near-complete skeletons allow the reconstruction of either physical or digital models. Digital models are most efficient in terms of time and cost, and provide the facility to infinitely modify model properties non-destructively, such that sensitivity analyses can be conducted to quantify the effect of the many unknown parameters involved in reconstructions of extinct animals. In this study we use laser scanning (LiDAR) and computer modelling methods to create a range of 3D mass models of five specimens of non-avian dinosaur; two near-complete specimens of Tyrannosaurus rex, the most complete specimens of Acrocanthosaurus atokensis and Strutiomimum sedens, and a near-complete skeleton of a sub-adult Edmontosaurus annectens. LiDAR scanning allows a full mounted skeleton to be imaged resulting in a detailed 3D model in which each bone retains its spatial position and articulation. This provides a high resolution skeletal framework around which the body cavity and internal organs such as lungs and air sacs can be reconstructed. This has allowed calculation of body segment masses, centres of mass and moments or inertia for each animal. However, any soft tissue reconstruction of an extinct taxon inevitably represents a best estimate model with an unknown level of accuracy. We have therefore conducted an extensive sensitivity analysis in which the volumes of body segments and respiratory organs were varied in an attempt to constrain the likely maximum plausible range of mass parameters for each animal. Our results provide wide ranges in actual mass and inertial values, emphasizing the high level of uncertainty inevitable in such reconstructions. However, our sensitivity analysis consistently places the centre of mass well below and in front of hip joint in each animal, regardless of the chosen combination of body and respiratory structure volumes. These results emphasize that future biomechanical assessments of extinct taxa should be preceded by a detailed investigation of the plausible range of mass properties, in which sensitivity analyses are used to identify a suite of possible values to be tested as inputs in analytical models.

Avian Incubation Inhibits Growth and Diversification of Bacterial Assemblages on Eggs:

Microbial infection is a critical source of mortality for early life stages of oviparous vertebrates, but parental defenses against infection are less well known. Avian incubation has been hypothesized to reduce the risk of trans-shell infection by limiting microbial growth of pathogenic bacteria on eggshells, while enhancing growth of commensal or beneficial bacteria that inhibit or competitively exclude pathogens. We tested this hypothesis by comparing bacterial assemblages on naturally incubated and experimentally unincubated eggs at laying and late incubation using a universal 16S rRNA microarray containing probes for over 8000 bacterial taxa. Before treatment, bacterial assemblages on individual eggs from both treatment groups were dissimilar to one another, as measured by clustering in non-metric dimensional scaling (NMDS) ordination space. After treatment, assemblages of unincubated eggs were similar to one another, but those of incubated eggs were not. Furthermore, assemblages of unincubated eggs were characterized by high abundance of six indicator species while incubated eggs had no indicator species. Bacterial taxon richness remained static on incubated eggs, but increased significantly on unincubated eggs, especially in several families of Gram-negative bacteria. The relative abundance of individual bacterial taxa did not change on incubated eggs, but that of 82 bacterial taxa, including some known to infect the interior of eggs, increased on unincubated eggs. Thus, incubation inhibits all of the relatively few bacteria that grow on eggshells, and does not appear to promote growth of any bacteria.

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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, 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:
Respiratory Evolution Facilitated the Origin of Pterosaur Flight and Aerial Gigantism:

Pterosaurs, enigmatic extinct Mesozoic reptiles, were the first vertebrates to achieve true flapping flight. Various lines of evidence provide strong support for highly efficient wing design, control, and flight capabilities. However, little is known of the pulmonary system that powered flight in pterosaurs. We investigated the structure and function of the pterosaurian breathing apparatus through a broad scale comparative study of respiratory structure and function in living and extinct archosaurs, using computer-assisted tomographic (CT) scanning of pterosaur and bird skeletal remains, cineradiographic (X-ray film) studies of the skeletal breathing pump in extant birds and alligators, and study of skeletal structure in historic fossil specimens. In this report we present various lines of skeletal evidence that indicate that pterosaurs had a highly effective flow-through respiratory system, capable of sustaining powered flight, predating the appearance of an analogous breathing system in birds by approximately seventy million years. Convergent evolution of gigantism in several Cretaceous pterosaur lineages was made possible through body density reduction by expansion of the pulmonary air sac system throughout the trunk and the distal limb girdle skeleton, highlighting the importance of respiratory adaptations in pterosaur evolution, and the dramatic effect of the release of physical constraints on morphological diversification and evolutionary radiation.

The Maintenance of Traditions in Marmosets: Individual Habit, Not Social Conformity? A Field Experiment:

Social conformity is a cornerstone of human culture because it accelerates and maintains the spread of behaviour within a group. Few empirical studies have investigated the role of social conformity in the maintenance of traditions despite an increasing body of literature on the formation of behavioural patterns in non-human animals. The current report presents a field experiment with free-ranging marmosets (Callithrix jacchus) which investigated whether social conformity is necessary for the maintenance of behavioural patterns within groups or whether individual effects such as habit formation would suffice. Using a two-action apparatus, we established alternative behavioural patterns in six family groups composed of 36 individuals. These groups experienced only one technique during a training phase and were thereafter tested with two techniques available. The monkeys reliably maintained the trained method over a period of three weeks, despite discovering the alternative technique. Three additional groups were given the same number of sessions, but those 21 individuals could freely choose the method to obtain a reward. In these control groups, an overall bias towards one of the two methods was observed, but animals with a different preference did not adjust towards the group norm. Thirteen of the fifteen animals that discovered both techniques remained with the action with which they were initially successful, independent of the group preference and the type of action (Binomial test: exp. proportion: 0.5, p<0.01). The results indicate that the maintenance of behavioural patterns within groups 1) could be explained by the first rewarded manipulation and subsequent habit formation and 2) do not require social conformity as a mechanism. After an initial spread of a behaviour throughout a group, this mechanism may lead to a superficial appearance of conformity without the involvement of such a socially and cognitively complex mechanism. This is the first time that such an experiment has been conducted with free-ranging primates.

Estimating Genetic Ancestry Proportions from Faces:

Ethnicity can be a means by which people identify themselves and others. This type of identification mediates many kinds of social interactions and may reflect adaptations to a long history of group living in humans. Recent admixture in the US between groups from different continents, and the historically strong emphasis on phenotypic differences between members of these groups, presents an opportunity to examine the degree of concordance between estimates of group membership based on genetic markers and on visually-based estimates of facial features. We first measured the degree of Native American, European, African and East Asian genetic admixture in a sample of 14 self-identified Hispanic individuals, chosen to cover a broad range of Native American and European genetic admixture proportions. We showed frontal and side-view photographs of the 14 individuals to 241 subjects living in New Mexico, and asked them to estimate the degree of NA admixture for each individual. We assess the overall concordance for each observer based on an aggregated measure of the difference between the observer and the genetic estimates. We find that observers reach a significantly higher degree of concordance than expected by chance, and that the degree of concordance as well as the direction of the discrepancy in estimates differs based on the ethnicity of the observer, but not on the observers’ age or sex. This study highlights the potentially high degree of discordance between physical appearance and genetic measures of ethnicity, as well as how perceptions of ethnic affiliation are context-specific. We compare our findings to those of previous studies and discuss their implications.

Short Lag Times for Invasive Tropical Plants: Evidence from Experimental Plantings in Hawai’i:

The lag time of an invasion is the delay between arrival of an introduced species and its successful spread in a new area. To date, most estimates of lag times for plants have been indirect or anecdotal, and these estimates suggest that plant invasions are often characterized by lag times of 50 years or more. No general estimates are available of lag times for tropical plant invasions. Historical plantings and documentation were used to directly estimate lag times for tropical plant invasions in Hawai’i. Historical planting records for the Lyon Arboretum dating back to 1920 were examined to identify plants that have since become invasive pests in the Hawaiian Islands. Annual reports describing escape from plantings were then used to determine the lag times between initial plantings and earliest recorded spread of the successful invaders. Among 23 species that eventually became invasive pests, the average lag time between introduction and first evidence of spread was 14 years for woody plants and 5 years for herbaceous plants. These direct estimates of lag times are as much as an order of magnitude shorter than previous, indirect estimates, which were mainly based on temperate plants. Tropical invaders may have much shorter lag times than temperate species. A lack of direct and deliberate observations may have also inflated many previous lag time estimates. Although there have been documented cases of long lag times due to delayed arrival of a mutualist or environmental changes over time, this study suggests that most successful invasions are likely to begin shortly after arrival of the plant in a suitable habitat, at least in tropical environments. Short lag times suggest that controlled field trials may be a practical element of risk assessment for plant introductions.

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High-tech Tests Allow Anthropologists To Track Ancient Hominids Across The Landscape:

Dazzling new scientific techniques are allowing archaeologists to track the movements and menus of extinct hominids through the seasons and years as they ate their way across the African landscape, helping to illuminate the evolution of human diets.

Neural Mapping Paints Haphazard Picture Of Odor Receptors:

Despite the striking aromatic differences between coffee, peppermint, and pine, a new mapping of the nose’s neural circuitry suggests a haphazard patchwork where the receptors for such disparate scents are as likely as not to be neighbors.

Mass Media Often Failing In Its Coverage Of Global Warming, Says Climate Researcher:

“Business managers of media organizations, you are screwing up your responsibility by firing science and environment reporters who are frankly the only ones competent to do this,” said climate researcher and policy analyst Stephen Schneider, in assessing the current state of media coverage of global warming and related issues.

This was a busy week for me (hence light posting) so I was amiss somewhat with pointing out cool new PLoS articles. So, let’s see what’s new in PLoS Genetics, PLoS Medicine, PLoS Computational Biology, PLoS Biology, PLoS Pathogens, PLoS Neglected Tropical Diseases and PLoS ONE this week. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. Here are my own picks for the week – you go and look for your own favourites:
A Basal Sauropodomorph (Dinosauria: Saurischia) from the Ischigualasto Formation (Triassic, Carnian) and the Early Evolution of Sauropodomorpha:

The earliest dinosaurs are from the early Late Triassic (Carnian) of South America. By the Carnian the main clades Saurischia and Ornithischia were already established, and the presence of the most primitive known sauropodomorph Saturnalia suggests also that Saurischia had already diverged into Theropoda and Sauropodomorpha. Knowledge of Carnian sauropodomorphs has been restricted to this single species. We describe a new small sauropodomorph dinosaur from the Ischigualsto Formation (Carnian) in northwest Argentina, Panphagia protos gen. et sp. nov., on the basis of a partial skeleton. The genus and species are characterized by an anteroposteriorly elongated fossa on the base of the anteroventral process of the nasal; wide lateral flange on the quadrate with a large foramen; deep groove on the lateral surface of the lower jaw surrounded by prominent dorsal and ventral ridges; bifurcated posteroventral process of the dentary; long retroarticular process transversally wider than the articular area for the quadrate; oval scars on the lateral surface of the posterior border of the centra of cervical vertebrae; distinct prominences on the neural arc of the anterior cervical vertebra; distal end of the scapular blade nearly three times wider than the neck; scapular blade with an expanded posterodistal corner; and medial lamina of brevis fossa twice as wide as the iliac spine. We regard Panphagia as the most basal sauropodomorph, which shares the following apomorphies with Saturnalia and more derived sauropodomorphs: basally constricted crowns; lanceolate crowns; teeth of the anterior quarter of the dentary higher than the others; and short posterolateral flange of distal tibia. The presence of Panphagia at the base of the early Carnian Ischigualasto Formation suggests an earlier origin of Sauropodomorpha during the Middle Triassic.

Sensory Integration Regulating Male Courtship Behavior in Drosophila:

The courtship behavior of Drosophila melanogaster serves as an excellent model system to study how complex innate behaviors are controlled by the nervous system. To understand how the underlying neural network controls this behavior, it is not sufficient to unravel its architecture, but also crucial to decipher its logic. By systematic analysis of how variations in sensory inputs alter the courtship behavior of a naïve male in the single-choice courtship paradigm, we derive a model describing the logic of the network that integrates the various sensory stimuli and elicits this complex innate behavior. This approach and the model derived from it distinguish (i) between initiation and maintenance of courtship, (ii) between courtship in daylight and in the dark, where the male uses a scanning strategy to retrieve the decamping female, and (iii) between courtship towards receptive virgin females and mature males. The last distinction demonstrates that sexual orientation of the courting male, in the absence of discriminatory visual cues, depends on the integration of gustatory and behavioral feedback inputs, but not on olfactory signals from the courted animal. The model will complement studies on the connectivity and intrinsic properties of the neurons forming the circuitry that regulates male courtship behavior.

Invasive Snails and an Emerging Infectious Disease: Results from the First National Survey on Angiostrongylus cantonensis in China:

Eosinophilic meningitis is caused by the rat lungworm (Angiostrongylus cantonensis). This parasite is endemic in Southeast Asia, Australia, the Caribbean, and on Pacific Islands. Moreover, the disease is emerging in mainland China, which might be related to the spread of two invasive snail species (Achatina fulica and Pomacea canaliculata). Thus far, the biggest angiostrongyliasis outbreak in China occurred in 2006 in Beijing, involving 160 patients. However, detailed information about the national distribution of A. cantonensis and its intermediate hosts is still lacking, and the importance of the two invasive snail species for disease transmission is not well understood. Therefore, a national survey on the distribution of A. cantonensis and its intermediate hosts in China was carried out in 2006/2007. It was found that A. fulica and P. canaliculata were implicated in most angiostrongyliasis outbreaks, and that the distribution of A. cantonensis closely matched that of these snails. The two invasive snail species facilitated the expansion of the parasite, thus probably leading to the emergence of angiostrongyliasis, a previously rare disease, in mainland China.

An Ancient Gene Network Is Co-opted for Teeth on Old and New Jaws:

During evolution, teeth originated deep in the pharynx of ancient and extinct jawless fishes. Later, with the evolution of bony fish, teeth appeared in the mouth, as in most current vertebrates, although some living fishes retain teeth in the posterior pharynx. We integrate comparative morphology, paleontology, and molecular biology to infer the genetic control of the first dentition. We identify Hox genes as important components of an ancient dental gene-regulatory circuit and pinpoint subsequent modifications to this gene network that accompanied the evolution of toothed oral jaws. Furthermore, we highlight a set of genes conserved in the construction of all teeth, regardless of location and lineage. This core dental gene network is evolutionarily essential: nature appears never to have made a dentition without it.

Malaria Control with Transgenic Mosquitoes:

Malaria has been eliminated from a large part of the world. By the mid-twentieth century both North America and Europe were free of the disease, although both had suffered greatly during the prior century [1,2]. While a variety of means were used to achieve this eradication, the most important are thought to be reducing the number of breeding sites for malaria vectors and improving residential areas to separate humans from mosquitoes. Other parts of the world have not been so fortunate. In sub-Saharan Africa, it is now estimated that there are more than 360 million clinical cases and one million deaths due to malaria each year [3,4]. Furthermore, despite ambitious goals such as those of the Roll Back Malaria Initiative to halve malaria deaths by 2010, mortality from the disease has actually risen halfway through the program [5]. Clearly the tools we have to control malaria, or the ways in which we are using them, are not working. The failure of existing methods for malaria control has sparked interest in several new approaches. These include better and cheaper antimalarial drugs [6], renewed efforts to find a vaccine [7], and the development of genetically modified mosquitoes (GMMs) designed either to reduce population sizes or to replace existing populations with vectors unable to transmit the disease. In this review we describe some of the efforts currently underway to create GMMs and assess some of the obstacles they face.

Can Monkeys Choose Optimally When Faced with Noisy Stimuli and Unequal Rewards?:

Decisions are commonly based on multiple sources of information. In a forced choice task, for example, sensory information about the identity of a stimulus may be combined with prior information about the amount of reward associated with each choice. We employed a well-characterized motion discrimination task to examine how animals combine such sources of information and whether they weigh these components so as to harvest rewards optimally. Two monkeys discriminated the direction of motion in a family of noisy random dot stimuli. The animals were informed before each trial whether reward outcomes were equal or unequal for the two alternatives, and if unequal, which alternative promised the larger reward. Predictably, choices were biased toward the larger reward in the unequal reward conditions. We develop a decision-making model that describes the animals’ sensitivities to the visual stimulus and permits us to calculate the choice bias that yields optimal reward harvesting. We find that the monkeys’ performance is close to optimal; remarkably, the animals garner 98%+ of their maximum possible rewards. This study adds to the growing evidence that animal foraging behavior can approach optimality and provides a rigorous theoretical basis for understanding the computations underlying optimality in this and related tasks.

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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, 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:
Individual Recognition in Domestic Cattle (Bos taurus): Evidence from 2D-Images of Heads from Different Breeds:

In order to maintain cohesion of groups, social animals need to process social information efficiently. Visual individual recognition, which is distinguished from mere visual discrimination, has been studied in only few mammalian species. In addition, most previous studies used either a small number of subjects or a few various views as test stimuli. Dairy cattle, as a domestic species allow the testing of a good sample size and provide a large variety of test stimuli due to the morphological diversity of breeds. Hence cattle are a suitable model for studying individual visual recognition. This study demonstrates that cattle display visual individual recognition and shows the effect of both familiarity and coat diversity in discrimination. We tested whether 8 Prim’Holstein heifers could recognize 2D-images of heads of one cow (face, profiles, ¾ views) from those of other cows. Experiments were based on a simultaneous discrimination paradigm through instrumental conditioning using food rewards. In Experiment 1, all images represented familiar cows (belonging to the same social group) from the Prim’Holstein breed. In Experiments 2, 3 and 4, images were from unfamiliar (unknown) individuals either from the same breed or other breeds. All heifers displayed individual recognition of familiar and unfamiliar individuals from their own breed. Subjects reached criterion sooner when recognizing a familiar individual than when recognizing an unfamiliar one (Exp 1: 3.1±0.7 vs. Exp 2: 5.2±1.2 sessions; Z = 1.99, N = 8, P = 0.046). In addition almost all subjects recognized unknown individuals from different breeds, however with greater difficulty. Our results demonstrated that cattle have efficient individual recognition based on categorization capacities. Social familiarity improved their performance. The recognition of individuals with very different coat characteristics from the subjects was the most difficult task. These results call for studies exploring the mechanisms involved in face recognition allowing interspecies comparisons, including humans.

Compactness Determines the Success of Cube and Octahedron Self-Assembly:

Nature utilizes self-assembly to fabricate structures on length scales ranging from the atomic to the macro scale. Self-assembly has emerged as a paradigm in engineering that enables the highly parallel fabrication of complex, and often three-dimensional, structures from basic building blocks. Although there have been several demonstrations of this self-assembly fabrication process, rules that govern a priori design, yield and defect tolerance remain unknown. In this paper, we have designed the first model experimental system for systematically analyzing the influence of geometry on the self-assembly of 200 and 500 µm cubes and octahedra from tethered, multi-component, two-dimensional (2D) nets. We examined the self-assembly of all eleven 2D nets that can fold into cubes and octahedra, and we observed striking correlations between the compactness of the nets and the success of the assembly. Two measures of compactness were used for the nets: the number of vertex or topological connections and the radius of gyration. The success of the self-assembly process was determined by measuring the yield and classifying the defects. Our observation of increased self-assembly success with decreased radius of gyration and increased topological connectivity resembles theoretical models that describe the role of compactness in protein folding. Because of the differences in size and scale between our system and the protein folding system, we postulate that this hypothesis may be more universal to self-assembling systems in general. Apart from being intellectually intriguing, the findings could enable the assembly of more complicated polyhedral structures (e.g. dodecahedra) by allowing a priori selection of a net that might self-assemble with high yields.

Phytoliths Analysis for the Discrimination of Foxtail Millet (Setaria italica) and Common Millet (Panicum miliaceum):

Foxtail millet (Setaria italica) and Common millet (Panicum miliaceum) are the oldest domesticated dry farming crops in Eurasia. Identifying these two millets in the archaeobotanical remains are still problematic, especially because the millet grains preserve only when charred. Phytoliths analysis provides a viable method for identifying this important crop. However, to date, the identification of millet phytoliths has been questionable, because very little study has been done on their morphometry and taxonomy. Particularly, no clear diagnostic feature has been used to distinguish between Foxtail millet and Common millet. Here we examined the anatomy and silicon structure patterns in the glumes, lemmas, and paleas from the inflorescence bracts in 27 modern plants of Foxtail millet, Common millet, and closely related grasses, using light microscopy with phase-contrast and microscopic interferometer. Our research shows that five key diagnostic characteristics in phytolith morphology can be used to distinguish Foxtail millet from Common millet based on the presence of cross-shaped type, regularly arranged papillae, Ω-undulated type, endings structures of epidermal long cell, and surface ridgy line sculpture in the former species. We have established identification criteria that, when used together, give the only reliable way of distinguishing between Foxtail millet and Common millet species based on their phytoliths characteristics, thus making a methodological contribution to phytolith research. Our findings also have important implications in the fields of plant taxonomy, agricultural archaeology, and the culture history of ancient civilizations.

Ancient Horizontal Gene Transfer from Bacteria Enhances Biosynthetic Capabilities of Fungi:

Polyketides are natural products with a wide range of biological functions and pharmaceutical applications. Discovery and utilization of polyketides can be facilitated by understanding the evolutionary processes that gave rise to the biosynthetic machinery and the natural product potential of extant organisms. Gene duplication and subfunctionalization, as well as horizontal gene transfer are proposed mechanisms in the evolution of biosynthetic gene clusters. To explain the amount of homology in some polyketide synthases in unrelated organisms such as bacteria and fungi, interkingdom horizontal gene transfer has been evoked as the most likely evolutionary scenario. However, the origin of the genes and the direction of the transfer remained elusive. We used comparative phylogenetics to infer the ancestor of a group of polyketide synthase genes involved in antibiotic and mycotoxin production. We aligned keto synthase domain sequences of all available fungal 6-methylsalicylic acid (6-MSA)-type PKSs and their closest bacterial relatives. To assess the role of symbiotic fungi in the evolution of this gene we generated 24 6-MSA synthase sequence tags from lichen-forming fungi. Our results support an ancient horizontal gene transfer event from an actinobacterial source into ascomycete fungi, followed by gene duplication. Given that actinobacteria are unrivaled producers of biologically active compounds, such as antibiotics, it appears particularly promising to study biosynthetic genes of actinobacterial origin in fungi. The large number of 6-MSA-type PKS sequences found in lichen-forming fungi leads us hypothesize that the evolution of typical lichen compounds, such as orsellinic acid derivatives, was facilitated by the gain of this bacterial polyketide synthase.

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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, 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:
Genetic Determinants of Financial Risk Taking:

Individuals vary in their willingness to take financial risks. Here we show that variants of two genes that regulate dopamine and serotonin neurotransmission and have been previously linked to emotional behavior, anxiety and addiction (5-HTTLPR and DRD4) are significant determinants of risk taking in investment decisions. We find that the 5-HTTLPR s/s allele carriers take 28% less risk than those carrying the s/l or l/l alleles of the gene. DRD4 7-repeat allele carriers take 25% more risk than individuals without the 7-repeat allele. These findings contribute to the emerging literature on the genetic determinants of economic behavior.

Empathy Is Moderated by Genetic Background in Mice:

Empathy, as originally defined, refers to an emotional experience that is shared among individuals. When discomfort or alarm is detected in another, a variety of behavioral responses can follow, including greater levels of nurturing, consolation or increased vigilance towards a threat. Moreover, changes in systemic physiology often accompany the recognition of distressed states in others. Employing a mouse model of cue-conditioned fear, we asked whether exposure to conspecific distress influences how a mouse subsequently responds to environmental cues that predict this distress. We found that mice are responsive to environmental cues that predict social distress, that their heart rate changes when distress vocalizations are emitted from conspecifics, and that genetic background substantially influences the magnitude of these responses. Specifically, during a series of pre-exposure sessions, repeated experiences of object mice that were exposed to a tone-shock (CS-UCS) contingency resulted in heart rate deceleration in subjects from the gregarious C57BL/6J (B6) strain, but not in subjects from the less social BALB/cJ (BALB) strain. Following the pre-exposure sessions, subjects were individually presented with the CS-only for 5 consecutive trials followed by 5 consecutive pairings of the CS with the UCS. Pre-exposure to object distress increased the freezing responses of B6 mice, but not BALB mice, on both the CS-only and the CS-UCS trials. These physiological and behavioral responses of B6 mice to social distress parallel features of human empathy. Our paradigm thus has construct and face validity with contemporary views of empathy, and provides unequivocal evidence for a genetic contribution to the expression of empathic behavior.

Adverse Drug Reactions in Hospital In-Patients: A Prospective Analysis of 3695 Patient-Episodes:

Adverse drug reactions (ADRs) are a major cause of hospital admissions, but recent data on the incidence and clinical characteristics of ADRs which occur following hospital admission, are lacking. Patients admitted to twelve wards over a six-month period in 2005 were assessed for ADRs throughout their admission. Suspected ADRs were recorded and analysed for causality, severity and avoidability and whether they increased the length of stay. Multivariable analysis was undertaken to identify the risk factors for ADRs. The 5% significance level was used when assessing factors for inclusion in multivariable models. Out of the 3695 patient episodes assessed for ADRs, 545 (14.7%, 95% CI 13.6-15.9%) experienced one or more ADRs. Half of ADRs were definitely or possibly avoidable. The patients experiencing ADRs were more likely to be older, female, taking a larger number of medicines, and had a longer length of stay than those without ADRs. However, the only significant predictor of ADRs, from the multivariable analysis of a representative sample of patients, was the number of medicines taken by the patient with each additional medication multiplying the hazard of an ADR episode by 1.14 (95% CI 1.09, 1.20). ADRs directly increased length of stay in 147 (26.8%) patients. The drugs most frequently associated with ADRs were diuretics, opioid analgesics, and anticoagulants. In conclusion, approximately one in seven hospital in-patients experience an ADR, which is a significant cause of morbidity, increasing the length of stay of patients by an average of 0.25 days/patient admission episode. The overall burden of ADRs on hospitals is high, and effective intervention strategies are urgently needed to reduce this burden.

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There are 15 new articles published Friday night and 15 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, 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:
Impact of Climate Change on the Relict Tropical Fish Fauna of Central Sahara: Threat for the Survival of Adrar Mountains Fishes, Mauritania:

Four central Sahara mountainous massifs provide habitats for relict populations of fish. In the Adrar of Mauritania all available data on the presence and distribution of fish come from pre-1960 surveys where five fish species were reported: Barbus pobeguini, Barbus macrops, Barbus mirei, Sarotherodon galilaeus, and Clarias anguillaris. Since 1970, drought has had a severe impact in the Adrar where rainfall decreased by 35%. To investigate whether the relict populations of fish have survived the continuing drought, a study was carried out from 2004 to 2008. An inventory of perennial bodies of water was drawn up using a literature review and analysis of topographical and hydrological maps. Field surveys were carried out in order to locate the bodies of water described in the literature, identify the presence of fish, determine which species were present and estimate their abundance. The thirteen sites where the presence of fish was observed in the 1950s -Ksar Torchane, Ilij, Molomhar, Agueni, Tachot, Hamdoun, Terjit, Toungad, El Berbera, Timagazine, Dâyet el Mbârek, Dâyet et-Tefla, Nkedeï- were located and surveyed. The Ksar Torchane spring -type locality and the only known locality of B. mirei- has dried up at the height of the drought in 1984, and any fish populations have since become extinct there. The Timagazine, Dâyet el Mbârek and Dâyet et-Tefla pools have become ephemeral. The Hamdoun guelta appears to be highly endangered. The fish populations at the other sites remain unchanged. Four perennial pools which are home to populations of B. pobeguini are newly recorded. The tropical relict fish populations of the Adrar mountains of Mauritania appear to be highly endangered. Of thirteen previously recorded populations, four have become extinct since the beginning of the drought period. New fish population extinctions may occur should low levels of annual rainfall be repeated.

Social Distance Evaluation in Human Parietal Cortex:

Across cultures, social relationships are often thought of, described, and acted out in terms of physical space (e.g. “close friends” “high lord”). Does this cognitive mapping of social concepts arise from shared brain resources for processing social and physical relationships? Using fMRI, we found that the tasks of evaluating social compatibility and of evaluating physical distances engage a common brain substrate in the parietal cortex. The present study shows the possibility of an analytic brain mechanism to process and represent complex networks of social relationships. Given parietal cortex’s known role in constructing egocentric maps of physical space, our present findings may help to explain the linguistic, psychological and behavioural links between social and physical space.

Metabolic and Behavioral Compensations in Response to Caloric Restriction: Implications for the Maintenance of Weight Loss:

Metabolic and behavioral adaptations to caloric restriction (CR) in free-living conditions have not yet been objectively measured. Forty-eight (36.8±1.0 y), overweight (BMI 27.8±0.7 kg/m2) participants were randomized to four groups for 6-months; Control: energy intake at 100% of energy requirements; CR: 25% calorie restriction; CR+EX: 12.5% CR plus 12.5% increase in energy expenditure by structured exercise; LCD: low calorie diet (890 kcal/d) until 15% weight reduction followed by weight maintenance. Body composition (DXA) and total daily energy expenditure (TDEE) over 14-days by doubly labeled water (DLW) and activity related energy activity (AREE) were measured after 3 (M3) and 6 (M6) months of intervention. Weight changes at M6 were −1.0±1.1% (Control), −10.4±0.9% (CR), −10.0±0.8% (CR+EX) and −13.9±0.8% (LCD). At M3, absolute TDEE was significantly reduced in CR (−454±76 kcal/d) and LCD (−633±66 kcal/d) but not in CR+EX or controls. At M6 the reduction in TDEE remained lower than baseline in CR (−316±118 kcal/d) and LCD (−389±124 kcal/d) but reached significance only when CR and LCD were combined (−351±83 kcal/d). In response to caloric restriction (CR/LCD combined), TDEE adjusted for body composition, was significantly lower by −431±51 and −240±83 kcal/d at M3 and M6, respectively, indicating a metabolic adaptation. Likewise, physical activity (TDEE adjusted for sleeping metabolic rate) was significantly reduced from baseline at both time points. For control and CR+EX, adjusted TDEE (body composition or sleeping metabolic rate) was not changed at either M3 or M6. For the first time we show that in free-living conditions, CR results in a metabolic adaptation and a behavioral adaptation with decreased physical activity levels. These data also suggest potential mechanisms by which CR causes large inter-individual variability in the rates of weight loss and how exercise may influence weight loss and weight loss maintenance.

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So, let’s see what’s new in PLoS Genetics, PLoS Computational Biology and PLoS Pathogens this week. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. Here are my own picks for the week – you go and look for your own favourites:
Social Contact Networks and Disease Eradicability under Voluntary Vaccination:

Interest in infectious disease models that incorporate the effects of human behavior has been growing in recent years. However, most of these models predict that it should never be possible to eradicate a disease under voluntary vaccination, due to nonvaccinating “free riders” that emerge when vaccine coverage is high. This prediction contradicts the fact that smallpox was eradicated under a voluntary vaccination policy in many jurisdictions, and that other diseases such as polio are likewise near eradication. These previous models assumed that populations mix homogeneously. However, for some diseases, such as HIV and smallpox, individuals are more likely to get the disease from certain social contacts. Here we show that using a network model that captures this social structure can reconcile the previous theories to the empirical fact that diseases can be eradicated under voluntary vaccination. When infection is transmitted only through close contacts in the network, then an outbreak can be quickly contained using only voluntary vaccination. However, when infection can potentially be transmitted to almost everyone in the network (such as for measles), a disease outbreak can never be contained using voluntary vaccination. This latter observation may have some relevance to the Measles-Mumps-Rubella autism “vaccine scare.”

Genome-Wide Association Studies in an Isolated Founder Population from the Pacific Island of Kosrae:

Isolated populations have contributed to the discovery of loci with simple Mendelian segregation and large effects on disease risk or trait variation. We hypothesized that the use of isolated populations might also facilitate the discovery of common alleles contributing to complex traits with relatively larger effects. However, the use of association analyses to map common loci influencing trait variation in large, inbred cohorts introduces analytic challenges, as extensive relatedness between subjects violates the assumptions of independence upon which traditional association test statistics are based. We developed an analytic strategy to perform genome-wide association studies in an inbred family containing over 2,800 individuals from the island of Kosrae, Federated States of Micronesia. No alleles with large effect were observed with strong statistical support in any of the 15 traits examined, suggesting that the contribution of individual common variants to complex trait variation in Kosraens is typically not much greater than that observed in other populations. We show that the effects of many loci previously identified in Caucasian populations are indistinguishable in Caucasians and Kosraens, despite very different population genetics and environmental influences.

A Gene-Based Linkage Map for Bicyclus anynana Butterflies Allows for a Comprehensive Analysis of Synteny with the Lepidopteran Reference Genome:

Lepidopterans (butterflies and moths) are a rich and diverse order of insects, which, despite their economic impact and unusual biological properties, are relatively underrepresented in terms of genomic resources. The genome of the silkworm Bombyx mori has been fully sequenced, but comparative lepidopteran genomics has been hampered by the scarcity of information for other species. This is especially striking for butterflies, even though they have diverse and derived phenotypes (such as color vision and wing color patterns) and are considered prime models for the evolutionary and developmental analysis of ecologically relevant, complex traits. We focus on Bicyclus anynana butterflies, a laboratory system for studying the diversification of novelties and serially repeated traits. With a panel of 12 small families and a biphasic mapping approach, we first assigned 508 expressed genes to segregation groups and then ordered 297 of them within individual linkage groups. We also coarsely mapped seven color pattern loci. This is the richest gene-based map available for any butterfly species and allowed for a broad-coverage analysis of synteny with the lepidopteran reference genome. Based on 462 pairs of mapped orthologous markers in Bi. anynana and Bo. mori, we observed strong conservation of gene assignment to chromosomes, but also evidence for numerous large- and small-scale chromosomal rearrangements. With gene collections growing for a variety of target organisms, the ability to place those genes in their proper genomic context is paramount. Methods to map expressed genes and to compare maps with relevant model systems are crucial to extend genomic-level analysis outside classical model species. Maps with gene-based markers are useful for comparative genomics and to resolve mapped genomic regions to a tractable number of candidate genes, especially if there is synteny with related model species. This is discussed in relation to the identification of the loci contributing to color pattern evolution in butterflies.

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, 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:
Web Queries as a Source for Syndromic Surveillance:

In the field of syndromic surveillance, various sources are exploited for outbreak detection, monitoring and prediction. This paper describes a study on queries submitted to a medical web site, with influenza as a case study. The hypothesis of the work was that queries on influenza and influenza-like illness would provide a basis for the estimation of the timing of the peak and the intensity of the yearly influenza outbreaks that would be as good as the existing laboratory and sentinel surveillance. We calculated the occurrence of various queries related to influenza from search logs submitted to a Swedish medical web site for two influenza seasons. These figures were subsequently used to generate two models, one to estimate the number of laboratory verified influenza cases and one to estimate the proportion of patients with influenza-like illness reported by selected General Practitioners in Sweden. We applied an approach designed for highly correlated data, partial least squares regression. In our work, we found that certain web queries on influenza follow the same pattern as that obtained by the two other surveillance systems for influenza epidemics, and that they have equal power for the estimation of the influenza burden in society. Web queries give a unique access to ill individuals who are not (yet) seeking care. This paper shows the potential of web queries as an accurate, cheap and labour extensive source for syndromic surveillance.

The Fetal Hypothalamus Has the Potential to Generate Cells with a Gonadotropin Releasing Hormone (GnRH) Phenotype:

Neurospheres (NS) are colonies of neural stem and precursor cells capable of differentiating into the central nervous system (CNS) cell lineages upon appropriate culture conditions: neurons, and glial cells. NS were originally derived from the embryonic and adult mouse striatum subventricular zone. More recently, experimental evidence substantiated the isolation of NS from almost any region of the CNS, including the hypothalamus. Here we report a protocol that enables to generate large quantities of NS from both fetal and adult rat hypothalami. We found that either FGF-2 or EGF were capable of inducing NS formation from fetal hypothalamic cultures, but that only FGF-2 is effective in the adult cultures. The hypothalamic-derived NS are capable of differentiating into neurons and glial cells and most notably, as demonstrated by immunocytochemical detection with a specific anti-GnRH antibody, the fetal cultures contain cells that exhibit a GnRH phenotype upon differentiation. This in vitro model should be useful to study the molecular mechanisms involved in GnRH neuronal differentiation.

The Cost of Simplifying Air Travel When Modeling Disease Spread:

Air travel plays a key role in the spread of many pathogens. Modeling the long distance spread of infectious disease in these cases requires an air travel model. Highly detailed air transportation models can be over determined and computationally problematic. We compared the predictions of a simplified air transport model with those of a model of all routes and assessed the impact of differences on models of infectious disease. Using U.S. ticket data from 2007, we compared a simplified “pipe” model, in which individuals flow in and out of the air transport system based on the number of arrivals and departures from a given airport, to a fully saturated model where all routes are modeled individually. We also compared the pipe model to a “gravity” model where the probability of travel is scaled by physical distance; the gravity model did not differ significantly from the pipe model. The pipe model roughly approximated actual air travel, but tended to overestimate the number of trips between small airports and underestimate travel between major east and west coast airports. For most routes, the maximum number of false (or missed) introductions of disease is small (<1 per day) but for a few routes this rate is greatly underestimated by the pipe model. If our interest is in large scale regional and national effects of disease, the simplified pipe model may be adequate. If we are interested in specific effects of interventions on particular air routes or the time for the disease to reach a particular location, a more complex point-to-point model will be more accurate. For many problems a hybrid model that independently models some frequently traveled routes may be the best choice. Regardless of the model used, the effect of simplifications and sensitivity to errors in parameter estimation should be analyzed.

Antiproliferative Effect of Ascorbic Acid Is Associated with the Inhibition of Genes Necessary to Cell Cycle Progression:

Ascorbic acid (AA), or Vitamin C, is most well known as a nutritional supplement with antioxidant properties. Recently, we demonstrated that high concentrations of AA act on PMP22 gene expression and partially correct the Charcot-Marie-Tooth disease phenotype in a mouse model. This is due to the capacity of AA, but not other antioxidants, to down-modulate cAMP intracellular concentration by a competitive inhibition of the adenylate cyclase enzymatic activity. Because of the critical role of cAMP in intracellular signalling, we decided to explore the possibility that ascorbic acid could modulate the expression of other genes. Using human pangenomic microarrays, we found that AA inhibited the expression of two categories of genes necessary for cell cycle progression, tRNA synthetases and translation initiation factor subunits. In in vitro assays, we demonstrated that AA induced the S-phase arrest of proliferative normal and tumor cells. Highest concentrations of AA leaded to necrotic cell death. However, quiescent cells were not susceptible to AA toxicity, suggesting the blockage of protein synthesis was mainly detrimental in metabolically-active cells. Using animal models, we found that high concentrations of AA inhibited tumor progression in nude mice grafted with HT29 cells (derived from human colon carcinoma). Consistently, expression of tRNA synthetases and ieF2 appeared to be specifically decreased in tumors upon AA treatment. AA has an antiproliferative activity, at elevated concentration that could be obtained using IV injection. This activity has been observed in vitro as well in vivo and likely results from the inhibition of expression of genes involved in protein synthesis. Implications for a clinical use in anticancer therapies will be discussed.

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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, 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 and Trophic Response of the Antarctic Bottom Fauna:

As Earth warms, temperate and subpolar marine species will increasingly shift their geographic ranges poleward. The endemic shelf fauna of Antarctica is especially vulnerable to climate-mediated biological invasions because cold temperatures currently exclude the durophagous (shell-breaking) predators that structure shallow-benthic communities elsewhere. We used the Eocene fossil record from Seymour Island, Antarctic Peninsula, to project specifically how global warming will reorganize the nearshore benthos of Antarctica. A long-term cooling trend, which began with a sharp temperature drop ~41 Ma (million years ago), eliminated durophagous predators–teleosts (modern bony fish), decapod crustaceans (crabs and lobsters) and almost all neoselachian elasmobranchs (modern sharks and rays)–from Antarctic nearshore waters after the Eocene. Even prior to those extinctions, durophagous predators became less active as coastal sea temperatures declined from 41 Ma to the end of the Eocene, ~33.5 Ma. In response, dense populations of suspension-feeding ophiuroids and crinoids abruptly appeared. Dense aggregations of brachiopods transcended the cooling event with no apparent change in predation pressure, nor were there changes in the frequency of shell-drilling predation on venerid bivalves. Rapid warming in the Southern Ocean is now removing the physiological barriers to shell-breaking predators, and crabs are returning to the Antarctic Peninsula. Over the coming decades to centuries, we predict a rapid reversal of the Eocene trends. Increasing predation will reduce or eliminate extant dense populations of suspension-feeding echinoderms from nearshore habitats along the Peninsula while brachiopods will continue to form large populations, and the intensity of shell-drilling predation on infaunal bivalves will not change appreciably. In time the ecological effects of global warming could spread to other portions of the Antarctic coast. The differential responses of faunal components will reduce the endemic character of Antarctic subtidal communities, homogenizing them with nearshore communities at lower latitudes.

Risks for Central Nervous System Diseases among Mobile Phone Subscribers: A Danish Retrospective Cohort Study:

The aim of this study was to investigate a possible link between cellular telephone use and risks for various diseases of the central nervous system (CNS). We conducted a large nationwide cohort study of 420 095 persons whose first cellular telephone subscription was between 1982 and 1995, who were followed through 2003 for hospital contacts for a diagnosis of a CNS disorder. Standardized hospitalization ratios (SHRs) were derived by dividing the number of hospital contacts in the cohort by the number expected in the Danish population. The SHRs were increased by 10-20% for migraine and vertigo. No associations were seen for amyotrophic lateral sclerosis, multiple sclerosis or epilepsy in women. SHRs decreased by 30-40% were observed for dementia (Alzheimer disease, vascular and other dementia), Parkinson disease and epilepsy among men. In analyses restricted to subscribers of 10 years or more, the SHRs remained similarly increased for migraine and vertigo and similarly decreased for Alzheimer disease and other dementia and epilepsy (in men); the other SHRs were close to unity. In conclusion, the excesses of migraine and vertigo observed in this first study on cellular telephones and CNS disease deserve further attention. An interplay of a healthy cohort effect and reversed causation bias due to prodromal symptoms impedes detection of a possible association with dementia and Parkinson disease. Identification of the factors that result in a healthy cohort might be of interest for elucidation of the etiology of these diseases.

A Ligand Channel through the G Protein Coupled Receptor Opsin:

The G protein coupled receptor rhodopsin contains a pocket within its seven-transmembrane helix (TM) structure, which bears the inactivating 11-cis-retinal bound by a protonated Schiff-base to Lys296 in TM7. Light-induced 11-cis-/all-trans-isomerization leads to the Schiff-base deprotonated active Meta II intermediate. With Meta II decay, the Schiff-base bond is hydrolyzed, all-trans-retinal is released from the pocket, and the apoprotein opsin reloaded with new 11-cis-retinal. The crystal structure of opsin in its active Ops* conformation provides the basis for computational modeling of retinal release and uptake. The ligand-free 7TM bundle of opsin opens into the hydrophobic membrane layer through openings A (between TM1 and 7), and B (between TM5 and 6), respectively. Using skeleton search and molecular docking, we find a continuous channel through the protein that connects these two openings and comprises in its central part the retinal binding pocket. The channel traverses the receptor over a distance of ca. 70 Å and is between 11.6 and 3.2 Å wide. Both openings are lined with aromatic residues, while the central part is highly polar. Four constrictions within the channel are so narrow that they must stretch to allow passage of the retinal β-ionone-ring. Constrictions are at openings A and B, respectively, and at Trp265 and Lys296 within the retinal pocket. The lysine enforces a 90° elbow-like kink in the channel which limits retinal passage. With a favorable Lys side chain conformation, 11-cis-retinal can take the turn, whereas passage of the all-trans isomer would require more global conformational changes. We discuss possible scenarios for the uptake of 11-cis- and release of all-trans-retinal. If the uptake gate of 11-cis-retinal is assigned to opening B, all-trans is likely to leave through the same gate. The unidirectional passage proposed previously requires uptake of 11-cis-retinal through A and release of photolyzed all-trans-retinal through B.

Phylogenetic Resolution and Quantifying the Phylogenetic Diversity and Dispersion of Communities:

Conservation biologists and community ecologists have increasingly begun to quantify the phylogenetic diversity and phylogenetic dispersion in species assemblages. In some instances, the phylogenetic trees used for such analyses are fully bifurcating, but in many cases the phylogenies being used contain unresolved nodes (i.e. polytomies). The lack of phylogenetic resolution in such studies, while certainly not preferred, is likely to continue particularly for those analyzing diverse communities and datasets with hundreds to thousands of taxa. Thus it is imperative that we quantify potential biases and losses of statistical power in studies that use phylogenetic trees that are not completely resolved. The present study is designed to meet both of these goals by quantifying the phylogenetic diversity and dispersion of simulated communities using resolved and gradually ‘unresolved’ phylogenies. The results show that: (i) measures of community phylogenetic diversity and dispersion are generally more sensitive to loss of resolution basally in the phylogeny and less sensitive to loss of resolution terminally; and (ii) the loss of phylogenetic resolution generally causes false negative results rather than false positives.

Probing Evolutionary Patterns in Neotropical Birds through DNA Barcodes:

The Neotropical avifauna is more diverse than that of any other biogeographic region, but our understanding of patterns of regional divergence is limited. Critical examination of this issue is currently constrained by the limited genetic information available. This study begins to address this gap by assembling a library of mitochondrial COI sequences, or DNA barcodes, for Argentinian birds and comparing their patterns of genetic diversity to those of North American birds. Five hundred Argentinian species were examined, making this the first major examination of DNA barcodes for South American birds. Our results indicate that most southern Neotropical bird species show deep sequence divergence from their nearest-neighbour, corroborating that the high diversity of this fauna is not based on an elevated incidence of young species radiations. Although species ages appear similar in temperate North and South American avifaunas, patterns of regional divergence are more complex in the Neotropics, suggesting that the high diversity of the Neotropical avifauna has been fueled by greater opportunities for regional divergence. Deep genetic splits were observed in at least 21 species, though distribution patterns of these lineages were variable. The lack of shared polymorphisms in species, even in species with less than 0.5M years of reproductive isolation, further suggests that selective sweeps could regularly excise ancestral mitochondrial polymorphisms. These findings confirm the efficacy of species delimitation in birds via DNA barcodes, even when tested on a global scale. Further, they demonstrate how large libraries of a standardized gene region provide insight into evolutionary processes.

Ticks Associated with Macquarie Island Penguins Carry Arboviruses from Four Genera:

Macquarie Island, a small subantarctic island, is home to rockhopper, royal and king penguins, which are often infested with the globally distributed seabird tick, Ixodes uriae. A flavivirus, an orbivirus, a phlebovirus, and a nairovirus were isolated from these ticks and partial sequences obtained. The flavivirus was nearly identical to Gadgets Gully virus, isolated some 30 year previously, illustrating the remarkable genetic stability of this virus. The nearest relative to the orbivirus (for which we propose the name Sandy Bay virus) was the Scottish Broadhaven virus, and provided only the second available sequences from the Great Island orbivirus serogroup. The phlebovirus (for which we propose the name Catch-me-cave virus) and the previously isolated Precarious Point virus were distinct but related, with both showing homology with the Finnish Uukuniemi virus. These penguin viruses provided the second and third available sequences for the Uukuniemi group of phleboviruses. The nairovirus (for which we propose the name Finch Creek virus) was shown to be related to the North American Tillamook virus, the Asian Hazara virus and Nairobi sheep disease virus. Macquarie Island penguins thus harbour arboviruses from at least four of the seven arbovirus-containing genera, with related viruses often found in the northern hemisphere.

Evolution of Genome Size and Complexity in Pinus:

Genome evolution in the gymnosperm lineage of seed plants has given rise to many of the most complex and largest plant genomes, however the elements involved are poorly understood. Gymny is a previously undescribed retrotransposon family in Pinus that is related to Athila elements in Arabidopsis. Gymny elements are dispersed throughout the modern Pinus genome and occupy a physical space at least the size of the Arabidopsis thaliana genome. In contrast to previously described retroelements in Pinus, the Gymny family was amplified or introduced after the divergence of pine and spruce (Picea). If retrotransposon expansions are responsible for genome size differences within the Pinaceae, as they are in angiosperms, then they have yet to be identified. In contrast, molecular divergence of Gymny retrotransposons together with other families of retrotransposons can account for the large genome complexity of pines along with protein-coding genic DNA, as revealed by massively parallel DNA sequence analysis of Cot fractionated genomic DNA. Most of the enormous genome complexity of pines can be explained by divergence of retrotransposons, however the elements responsible for genome size variation are yet to be identified. Genomic resources for Pinus including those reported here should assist in further defining whether and how the roles of retrotransposons differ in the evolution of angiosperm and gymnosperm genomes.

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There is some interesting stuff published in PLoS Medicine and PLoS Biology today:
What Should Be Done To Tackle Ghostwriting in the Medical Literature?:

Background to the debate: Ghostwriting occurs when someone makes substantial contributions to a manuscript without attribution or disclosure. It is considered bad publication practice in the medical sciences, and some argue it is scientific misconduct. At its extreme, medical ghostwriting involves pharmaceutical companies hiring professional writers to produce papers promoting their products but hiding those contributions and instead naming academic physicians or scientists as the authors. To improve transparency, many editors’ associations and journals allow professional medical writers to contribute to the writing of papers without being listed as authors provided their role is acknowledged. This debate examines how best to tackle ghostwriting in the medical literature from the perspectives of a researcher, an editor, and the professional medical writer.

Mutation Patterns in the Human Genome: More Variable Than Expected:

The development, survival, and reproduction of an organism depend on the genetic information that is carried in its genome, yet the transmission of genetic information is not perfectly accurate: new mutations occur at each generation. These mutations are the primary cause of the genetic diversity on which natural selection can operate, and hence are the sine qua non of evolution. A better knowledge of mutation processes is crucial for investigating the causes of genetic diseases or cancer and for understanding evolutionary processes. This knowledge is also important for different practical reasons. First, comparative sequence analysis is widely used to find functional elements within genomes. The basic principle of this approach is that functional elements are affected by natural selection, and hence can be recognized because they evolve either slower or faster than expected given the local mutation rate. Hence, to be able to annotate genomic sequences, it is necessary to have a good knowledge of the underlying pattern of mutation. Moreover, this knowledge is also essential for ensuring the accuracy of the methods that analyze sequence divergence to determine the phylogeny of species or the demographical history of populations. Finally, the study of mutational processes also provides valuable information about genome function in processes such as replication, repair, transcription, and recombination. During the last few years, several important factors affecting mutation rates have been uncovered. However, a paper in this issue of PLoS Biology [1] reveals an unexpected additional layer of complexity in the determinants of mutation rates.

Cryptic Variation in the Human Mutation Rate:

Understanding the process of mutation is important, not only mechanistically, but also because it has implications for the analysis of sequence evolution and population genetic inference. The mutation rate is known to differ between sites within the human genome. The most dramatic example of this is when a C is followed by G; both the C and G nucleotides have a rate of mutation that is between 10- and 20-fold higher than the rate at other sites. In addition, is it known that the mutation rate may be influenced by the nucleotides flanking the site. Here we show that there is also very substantial variation in the mutation rate that is not associated with the flanking nucleotides, or the CpG effect. Although this variation does not depend upon the adjacent nucleotides, there are nonrandom patterns of nucleotides surrounding sites that appear to be hypermutable, suggesting there are complex context effects that influence the mutation rate.

Gene Regulatory Network Interactions in Sea Urchin Endomesoderm Induction:

In recent years, “gene regulatory networks” (GRNs) have provided integrated views of gene interactions that control biological processes. One of the earliest networks to be activated in the developing zygotes is the one controlling endomesoderm development. In the sea urchin, this network includes several subnetworks that function in adjacent tiers of cells that form the endoderm and mesoderm of the developing embryo. Although classic embryological manipulations have shown that the precursors of the embryonic skeleton induce endomesoderm fate in adjacent cells, the GRNs regulating this interaction are not understood. To investigate these networks, we ectopically activated a GRN that operates in skeletogenic precursors and characterized the responding GRN in neighboring cells, which adopt an endomesoderm fate. By testing the responsiveness of every core factor in the responding GRN, which allowed us to identify a subset that executes the response to the induction, we demonstrated that the signaling molecule, ActivinB, is an essential component of this induction and that its function is physiologically relevant: it is required during normal embryonic development to activate the same GRN that responds to signals from skeletogenic precursors. Furthermore, the network response to ActivinB signaling reveals greater complexity in an additional uncharacterized inductive signal emitted by skeletogenic precursors. Our results thus highlight how interacting GRNs can be used to understand a fundamental signaling process.