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New and Exciting in PLoS this week

First piece of news, there is a new PLoS app for iPad. Even if you don’t have this new gadget, you can download it and test-run it and post a review here – we appreciate all the feedback.

Second piece of news is that the PLoS physical office in San Francisco is moving to a new location – it was busting at its seams even back in 2007 when I went there, it is just too small to contain all the new employees that needed to be hired in order to keep up with the growth of the operation, especially PLoS ONE.

Third piece of news is that Brian Mossop just got hired as community manager for PLoS Hubs. Congratulations to my newest colleague!

Finally, my picks of the papers…. I was out of town, in Philadelphia, so did not have the opportunity to do this on Monday and Tuesday, thus today’s post covers picks from three days. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

Quantifying the Performance of Individual Players in a Team Activity:

Teamwork is a fundamental aspect of many human activities, from business to art and from sports to science. Recent research suggest that team work is of crucial importance to cutting-edge scientific research, but little is known about how teamwork leads to greater creativity. Indeed, for many team activities, it is not even clear how to assign credit to individual team members. Remarkably, at least in the context of sports, there is usually a broad consensus on who are the top performers and on what qualifies as an outstanding performance. In order to determine how individual features can be quantified, and as a test bed for other team-based human activities, we analyze the performance of players in the European Cup 2008 soccer tournament. We develop a network approach that provides a powerful quantification of the contributions of individual players and of overall team performance. We hypothesize that generalizations of our approach could be useful in other contexts where quantification of the contributions of individual team members is important.

Testing Evolutionary and Dispersion Scenarios for the Settlement of the New World:

Discussion surrounding the settlement of the New World has recently gained momentum with advances in molecular biology, archaeology and bioanthropology. Recent evidence from these diverse fields is found to support different colonization scenarios. The currently available genetic evidence suggests a “single migration” model, in which both early and later Native American groups derive from one expansion event into the continent. In contrast, the pronounced anatomical differences between early and late Native American populations have led others to propose more complex scenarios, involving separate colonization events of the New World and a distinct origin for these groups. Using large samples of Early American crania, we: 1) calculated the rate of morphological differentiation between Early and Late American samples under three different time divergence assumptions, and compared our findings to the predicted morphological differentiation under neutral conditions in each case; and 2) further tested three dispersal scenarios for the colonization of the New World by comparing the morphological distances among early and late Amerindians, East Asians, Australo-Melanesians and early modern humans from Asia to geographical distances associated with each dispersion model. Results indicate that the assumption of a last shared common ancestor outside the continent better explains the observed morphological differences between early and late American groups. This result is corroborated by our finding that a model comprising two Asian waves of migration coming through Bering into the Americas fits the cranial anatomical evidence best, especially when the effects of diversifying selection to climate are taken into account. We conclude that the morphological diversity documented through time in the New World is best accounted for by a model postulating two waves of human expansion into the continent originating in East Asia and entering through Beringia.

Born Knowing: Tentacled Snakes Innately Predict Future Prey Behavior:

Aquatic tentacled snakes (Erpeton tentaculatus) can take advantage of their prey’s escape response by startling fish with their body before striking. The feint usually startles fish toward the snake’s approaching jaws. But when fish are oriented at a right angle to the jaws, the C-start escape response translates fish parallel to the snake’s head. To exploit this latter response, snakes must predict the future location of the fish. Adult snakes can make this prediction. Is it learned, or are tentacled snakes born able to predict future fish behavior? Laboratory-born, naïve snakes were investigated as they struck at fish. Trials were recorded at 250 or 500 frames per second. To prevent learning, snakes were placed in a water container with a clear transparency sheet or glass bottom. The chamber was placed over a channel in a separate aquarium with fish below. Thus snakes could see and strike at fish, without contact. The snake’s body feint elicited C-starts in the fish below the transparency sheet, allowing strike accuracy to be quantified in relationship to the C-starts. When fish were oriented at a right angle to the jaws, naïve snakes biased their strikes to the future location of the escaping fish’s head, such that the snake’s jaws and the fish’s translating head usually converged. Several different types of predictive strikes were observed. The results show that some predators have adapted their nervous systems to directly compensate for the future behavior of prey in a sensory realm that usually requires learning. Instead of behavior selected during their lifetime, newborn tentacled snakes exhibit behavior that has been selected on a different scale–over many generations. Counter adaptations in fish are not expected, as tentacled snakes are rare predators exploiting fish responses that are usually adaptive.

Coupling of a Core Post-Translational Pacemaker to a Slave Transcription/Translation Feedback Loop in a Circadian System:

Many organisms from bacteria to humans have evolved circadian mechanisms for regulating biological processes on a daily time scale. In cyanobacteria, a minimal system for such cyclical regulation can be reconstituted in vitro from three proteins, called KaiA, KaiB, and KaiC. This three-protein oscillator is believed to regulate the cyclical activities in vivo through a post-translational mechanism that involves rhythmic phosphorylation of KaiC. Although this post-translational oscillator (PTO) is sufficient for generating rhythms in vitro, the cyanobacterial circadian system in vivo also includes a transcriptional/translational feedback loop (TTFL). The precise roles of the PTO and the TTFL and their interdependence in forming the complete clock system in vivo are unclear. By manipulating wild-type and mutant clock protein expression in vivo, we here show that the cyanobacterial circadian system is dependent upon the biochemical oscillator provided by the PTO and that suppression of the PTO leads to a residual damped (slave) oscillation that results from the TTFL. Mathematical modeling shows that the experimental data are compatible with a mechanism in which the PTO acts as a pacemaker to drive the activity of the TTFL. Moreover, our analyses suggest a mechanism by which the TTFL can feed back into the PTO such that new synthesis of the Kai proteins entrains the core PTO pacemaker. Therefore, the PTO and TTFL appear to have a definite hierarchical interdependency: the PTO is a self-sustained core pacemaker that can oscillate independently of the TTFL, but the TTFL is a slave oscillator that damps when the phosphorylation status of KaiC in the PTO is clamped. The core circadian pacemaker in eukaryotes is thought to be a TTFL, but our results with cyanobacteria have important implications for eukaryotic clock systems in that they can explain how a TTFL could appear to be the core clock when in fact the true pacemaker is an embedded biochemical oscillator.

Neural Processing of Short-Term Recurrence in Songbird Vocal Communication:

Many situations involving animal communication are dominated by recurring, stereotyped signals. How do receivers optimally distinguish between frequently recurring signals and novel ones? Cortical auditory systems are known to be pre-attentively sensitive to short-term delivery statistics of artificial stimuli, but it is unknown if this phenomenon extends to the level of behaviorally relevant delivery patterns, such as those used during communication. We recorded and analyzed complete auditory scenes of spontaneously communicating zebra finch (Taeniopygia guttata) pairs over a week-long period, and show that they can produce tens of thousands of short-range contact calls per day. Individual calls recur at time scales (median interval 1.5 s) matching those at which mammalian sensory systems are sensitive to recent stimulus history. Next, we presented to anesthetized birds sequences of frequently recurring calls interspersed with rare ones, and recorded, in parallel, action and local field potential responses in the medio-caudal auditory forebrain at 32 unique sites. Variation in call recurrence rate over natural ranges leads to widespread and significant modulation in strength of neural responses. Such modulation is highly call-specific in secondary auditory areas, but not in the main thalamo-recipient, primary auditory area. Our results support the hypothesis that pre-attentive neural sensitivity to short-term stimulus recurrence is involved in the analysis of auditory scenes at the level of delivery patterns of meaningful sounds. This may enable birds to efficiently and automatically distinguish frequently recurring vocalizations from other events in their auditory scene.

Risks for Acquisition of Bacterial Vaginosis Among Women Who Report Sex with Women: A Cohort Study:

Bacterial vaginosis (BV) is common in women who have sex with women. While cross-sectional data support a role for sexual transmission, risks for incident BV have not been prospectively studied in this group. We studied risks for BV acquisition in a prospective cohort study of women (age 16-35 years) who reported sex with other women (≥1 partner, prior year). Women were followed for one year with examinations at quarterly visits and for genital symptoms at any time. Species-specific 16S rRNA gene PCRs for BV-associated bacteria (BVAB) were applied to vaginal fluid obtained at enrollment. Sexual behaviors were ascertained by computer-assisted interview. Of 335 participants, 239 had no BV at baseline; 199 were seen in follow-up (median follow-up 355 days, 4.0 visits/subject). Forty women experienced ≥1 BV episode. Risks for incident BV were presentation ≤14 days since onset of menses (hazard ratio (HR) 2.3 (95% CI, 1.2-4.7), report of new sex partner with BV history (HR 3.63 (1.1-11.9)), change in vaginal discharge (HR 2.6 (1.3-5.2)) and detection of any of several BVAB in vaginal fluid at enrollment, including BVAB1 (HR 6.3 (1.4-28.1)), BVAB2 (HR 18.2 (6.4-51.8)), BVAB3 (HR 12.6 (2.7-58.4)), G. vaginalis (HR 3.9 (1.5-10.4)), Atopobium vaginae (HR 4.2 (1.9-9.3)), Leptotrichia spp (9.3 (3.0-24.4)), and Megasphaera-1 (HR 11.5 (5.0-26.6)). Detection of Lactobacillus crispatus at enrollment conferred reduced risk for subsequent BV (HR 0.18 (0.08-0.4)). Detailed analysis of behavioral data suggested a direct dose-response relationship with increasing number of episodes of receptive oral-vulvovaginal sex (HR 1.02 (95% CI, 1.00-1.04). Vaginal detection of several BVAB in BV-negative women predicted subsequent BV, suggesting that changes in vaginal microbiota precede BV by weeks or months. BV acquisition was associated with report of new partner with BV; associations with sexual practices – specifically, receptive oral sex – require further investigation.

Effects of Enriched Physical and Social Environments on Motor Performance, Associative Learning, and Hippocampal Neurogenesis in Mice:

We have studied the motor abilities and associative learning capabilities of adult mice placed in different enriched environments. Three-month-old animals were maintained for a month alone (AL), alone in a physically enriched environment (PHY), and, finally, in groups in the absence (SO) or presence (SOPHY) of an enriched environment. The animals’ capabilities were subsequently checked in the rotarod test, and for classical and instrumental learning. The PHY and SOPHY groups presented better performances in the rotarod test and in the acquisition of the instrumental learning task. In contrast, no significant differences between groups were observed for classical eyeblink conditioning. The four groups presented similar increases in the strength of field EPSPs (fEPSPs) evoked at the hippocampal CA3-CA1 synapse across classical conditioning sessions, with no significant differences between groups. These trained animals were pulse-injected with bromodeoxyuridine (BrdU) to determine hippocampal neurogenesis. No significant differences were found in the number of NeuN/BrdU double-labeled neurons. We repeated the same BrdU study in one-month-old mice raised for an additional month in the above-mentioned four different environments. These animals were not submitted to rotarod or conditioned tests. Non-trained PHY and SOPHY groups presented more neurogenesis than the other two groups. Thus, neurogenesis seems to be related to physical enrichment at early ages, but not to learning acquisition in adult mice.

Variation within and between Closely Related Species Uncovers High Intra-Specific Variability in Dispersal:

Mounting evidence shows that contrasting selection pressures generate variability in dispersal patterns among individuals or populations of the same species, with potential impacts on both species dynamics and evolution. However, this variability is hardly considered in empirical works, where a single dispersal function is considered to adequately reflect the species-specific dispersal ability, suggesting thereby that within-species variation is negligible as regard to inter-specific differences in dispersal abilities. We propose here an original method to make the comparison of intra- and inter-specific variability in dispersal, by decomposing the diversity of that trait along a phylogeny of closely related species. We used as test group European butterflies that are classic study organisms in spatial ecology. We apply the analysis separately to eight metrics that reflect the dispersal propensity, the dispersal ability or the dispersal efficiency of populations and species. At the inter-specific level, only the dispersal ability showed the signature of a phylogenetic signal while neither the dispersal propensity nor the dispersal efficiency did. At the within-species level, the partitioning of dispersal diversity showed that dispersal was variable or highly variable among populations: intra-specific variability represented from 11% to 133% of inter-specific variability in dispersal metrics. This finding shows that dispersal variation is far from negligible in the wild. Understanding the processes behind this high within-species variation should allow us to properly account for dispersal in demographic models. Accordingly, to encompass the within species variability in life histories the use of more than one value per trait per species should be encouraged in the construction of databases aiming at being sources for modelling purposes.

Cognitive Control in Auditory Working Memory Is Enhanced in Musicians:

Musical competence may confer cognitive advantages that extend beyond processing of familiar musical sounds. Behavioural evidence indicates a general enhancement of both working memory and attention in musicians. It is possible that musicians, due to their training, are better able to maintain focus on task-relevant stimuli, a skill which is crucial to working memory. We measured the blood oxygenation-level dependent (BOLD) activation signal in musicians and non-musicians during working memory of musical sounds to determine the relation among performance, musical competence and generally enhanced cognition. All participants easily distinguished the stimuli. We tested the hypothesis that musicians nonetheless would perform better, and that differential brain activity would mainly be present in cortical areas involved in cognitive control such as the lateral prefrontal cortex. The musicians performed better as reflected in reaction times and error rates. Musicians also had larger BOLD responses than non-musicians in neuronal networks that sustain attention and cognitive control, including regions of the lateral prefrontal cortex, lateral parietal cortex, insula, and putamen in the right hemisphere, and bilaterally in the posterior dorsal prefrontal cortex and anterior cingulate gyrus. The relationship between the task performance and the magnitude of the BOLD response was more positive in musicians than in non-musicians, particularly during the most difficult working memory task. The results confirm previous findings that neural activity increases during enhanced working memory performance. The results also suggest that superior working memory task performance in musicians rely on an enhanced ability to exert sustained cognitive control. This cognitive benefit in musicians may be a consequence of focused musical training.

Lacrimal Hypofunction as a New Mechanism of Dry Eye in Visual Display Terminal Users:

Dry eye has shown a marked increase due to visual display terminal (VDT) use. It remains unclear whether reduced blinking while focusing can have a direct deleterious impact on the lacrimal gland function. To address this issue that potentially affects the life quality, we conducted a large-scale epidemiological study of VDT users and an animal study. Cross sectional survey carried out in Japan. A total of 1025 office workers who use VDT were enrolled. The association between VDT work duration and changes in tear film status, precorneal tear stability, lipid layer status and tear secretion were analyzed. For the animal model study, the rat VDT user model, placing rats onto a balance swing in combination with exposure to an evaporative environment was used to analyze lacrimal gland function. There was no positive relationship between VDT working duration and change in tear film stability and lipid layer status. The odds ratio for decrease in Schirmer score, index of tear secretion, were significantly increased with VDT working year (P = 0.012) and time (P = 0.005). The rat VDT user model, showed chronic reduction of tear secretion and was accompanied by an impairment of the lacrimal gland function and morphology. This dysfunction was recovered when rats were moved to resting conditions without the swing. These data suggest that lacrimal gland hypofunction is associated with VDT use and may be a critical mechanism for VDT-associated dry eye. We believe this to be the first mechanistic link to the pathogenesis of dry eye in office workers.

Ecological Adaptation of Diverse Honey Bee (Apis mellifera) Populations:

Honey bees are complex eusocial insects that provide a critical contribution to human agricultural food production. Their natural migration has selected for traits that increase fitness within geographical areas, but in parallel their domestication has selected for traits that enhance productivity and survival under local conditions. Elucidating the biochemical mechanisms of these local adaptive processes is a key goal of evolutionary biology. Proteomics provides tools unique among the major ‘omics disciplines for identifying the mechanisms employed by an organism in adapting to environmental challenges. Through proteome profiling of adult honey bee midgut from geographically dispersed, domesticated populations combined with multiple parallel statistical treatments, the data presented here suggest some of the major cellular processes involved in adapting to different climates. These findings provide insight into the molecular underpinnings that may confer an advantage to honey bee populations. Significantly, the major energy-producing pathways of the mitochondria, the organelle most closely involved in heat production, were consistently higher in bees that had adapted to colder climates. In opposition, up-regulation of protein metabolism capacity, from biosynthesis to degradation, had been selected for in bees from warmer climates. Overall, our results present a proteomic interpretation of expression polymorphisms between honey bee ecotypes and provide insight into molecular aspects of local adaptation or selection with consequences for honey bee management and breeding. The implications of our findings extend beyond apiculture as they underscore the need to consider the interdependence of animal populations and their agro-ecological context.

How Are the Interests of Incapacitated Research Participants Protected through Legislation? An Italian Study on Legal Agency for Dementia Patients:

Patients with dementia may have limited capacity to give informed consent to participate in clinical research. One possible way to safeguard the patients’ interests in research is the involvement of a proxy in the recruitment process. In Italy, the system of proxy is determined by the courts. In this study we evaluate the timing for appointment of a legal proxy in Italy and identify predictive variables of appointment. Subjects were recruited among the outpatients seeking medical advice for cognitive complaints at the Centre for Research and Treatment of Cognitive Dysfunctions, University of Milan, “Luigi Sacco” Hospital. The Centre was participating to the AdCare Study, a no-profit randomised clinical trial coordinated by the Italian National Institute of Health. The requirement that informed consent be given by a legal representative dramatically slowed down the recruitment process in AdCare, which was prematurely interrupted. The Centre for Research and Treatment of Cognitive Dysfunctions collected data on the timing required to appoint the legal representatives. Patients diagnosed with dementia and their caregivers were provided information on the Italian law on legal agency (law 6/2004). At each scheduled check-up the caregiver was asked whether she/he had applied to appoint a legal proxy for the patient and the time interval between the presentation of the law, the registration of the application at the law court chancellery and the sentence of appointment was registered. The study involved 169 demented patients. Seventy-eight patients (46.2%) applied to appoint a legal proxy. These subjects were usually younger, had been suffering from dementia for a longer time, had less than two children and made more use of memantine. The mean interval time between the presentation of the law and the patients’ application to the law court chancellery was two months. The mean interval time between the patient’s application to the law court chancellery and the sentence of appointment was four months. In Italy the requirement that legal representatives be appointed by the courts slows down subjects’ participation in research. Other procedures for legal agency of the incapacitated patients may be adopted, taking as examples other EU countries’ systems.

Gene Flow and Genetic Diversity of a Broadcast-Spawning Coral in Northern Peripheral Populations:

Recently, reef-building coral populations have been decreasing worldwide due to various disturbances. Population genetic studies are helpful for estimating the genetic connectivity among populations of marine sessile organisms with metapopulation structures such as corals. Moreover, the relationship between latitude and genetic diversity is informative when evaluating the fragility of populations. In this study, using highly variable markers, we examined the population genetics of the broadcast-spawning coral Acropora digitifera at 19 sites in seven regions along the 1,000 km long island chain of Nansei Islands, Japan. This area includes both subtropical and temperate habitats. Thus, the coral populations around the Nansei Islands in Japan are northern peripheral populations that would be subjected to environmental stresses different from those in tropical areas. The existence of high genetic connectivity across this large geographic area was suggested for all sites (FST≤0.033) although small but significant genetic differentiation was detected among populations in geographically close sites and regions. In addition, A. digitifera appears to be distributed throughout the Nansei Islands without losing genetic diversity. Therefore, A. digitifera populations in the Nansei Islands may be able to recover relatively rapidly even when high disturbances of coral communities occur locally if populations on other reefs are properly maintained.

Metabolic State Alters Economic Decision Making under Risk in Humans:

Animals’ attitudes to risk are profoundly influenced by metabolic state (hunger and baseline energy stores). Specifically, animals often express a preference for risky (more variable) food sources when below a metabolic reference point (hungry), and safe (less variable) food sources when sated. Circulating hormones report the status of energy reserves and acute nutrient intake to widespread targets in the central nervous system that regulate feeding behaviour, including brain regions strongly implicated in risk and reward based decision-making in humans. Despite this, physiological influences per se have not been considered previously to influence economic decisions in humans. We hypothesised that baseline metabolic reserves and alterations in metabolic state would systematically modulate decision-making and financial risk-taking in humans. We used a controlled feeding manipulation and assayed decision-making preferences across different metabolic states following a meal. To elicit risk-preference, we presented a sequence of 200 paired lotteries, subjects’ task being to select their preferred option from each pair. We also measured prandial suppression of circulating acyl-ghrelin (a centrally-acting orexigenic hormone signalling acute nutrient intake), and circulating leptin levels (providing an assay of energy reserves). We show both immediate and delayed effects on risky decision-making following a meal, and that these changes correlate with an individual’s baseline leptin and changes in acyl-ghrelin levels respectively. We show that human risk preferences are exquisitely sensitive to current metabolic state, in a direction consistent with ecological models of feeding behaviour but not predicted by normative economic theory. These substantive effects of state changes on economic decisions perhaps reflect shared evolutionarily conserved neurobiological mechanisms. We suggest that this sensitivity in human risk-preference to current metabolic state has significant implications for both real-world economic transactions and for aberrant decision-making in eating disorders and obesity.

MicroRNAs and Developmental Robustness: A New Layer Is Revealed:

It does not happen often that an entirely novel gene regulatory mechanism is revealed. The discovery of microRNAs (miRNAs) is one such finding that revolutionized our understanding of cellular events and of the intricacy of developmental processes [1],[2]. These small (~22 nucleotide), single-stranded RNA molecules act through binding in a sequence-specific manner to the 3′UTR of mRNA targets, an event that leads to facilitated mRNA degradation or translational inhibition [3]. With a very short recognition sequence determining its specificity for target mRNAs, each miRNA can potentially regulate hundreds of transcripts, though in many cases the physiological effects of miRNA targeting can be attributed to its binding to one major mRNA transcript. Each genome encodes hundreds of potential miRNA genes, and their expression is often widespread within the tissues of an organism. Although miRNAs lurked undetected until only relatively recently, it is now well established that miRNAs play an essential role in the regulation of many cellular processes [4].

Sympatric and Allopatric Divergence of MHC Genes in Threespine Stickleback:

Parasites can strongly affect the evolution of their hosts, but their effects on host diversification are less clear. In theory, contrasting parasite communities in different foraging habitats could generate divergent selection on hosts and promote ecological speciation. Immune systems are costly to maintain, adaptable, and an important component of individual fitness. As a result, immune system genes, such as those of the Major Histocompatability Complex (MHC), can change rapidly in response to parasite-mediated selection. In threespine stickleback (Gasterosteus aculeatus), as well as in other vertebrates, MHC genes have been linked with female mating preference, suggesting that divergent selection acting on MHC genes might influence speciation. Here, we examined genetic variation at MHC Class II loci of sticklebacks from two lakes with a limnetic and benthic species pair, and two lakes with a single species. In both lakes with species pairs, limnetics and benthics differed in their composition of MHC alleles, and limnetics had fewer MHC alleles per individual than benthics. Similar to the limnetics, the allopatric population with a pelagic phenotype had few MHC alleles per individual, suggesting a correlation between MHC genotype and foraging habitat. Using a simulation model we show that the diversity and composition of MHC alleles in a sympatric species pair depends on the amount of assortative mating and on the strength of parasite-mediated selection in adjacent foraging habitats. Our results indicate parallel divergence in the number of MHC alleles between sympatric stickleback species, possibly resulting from the contrasting parasite communities in littoral and pelagic habitats of lakes.