A Blog Around The Clock

Is Our Self Nothing but Reward? Neuronal Overlap and Distinction between Reward and Personal Relevance and Its Relation to Human Personality:

The attribution of personal relevance, i.e. relating internal and external stimuli to establish a sense of belonging, is a common phenomenon in daily life. Although previous research demonstrated a relationship between reward and personal relevance, their exact neuronal relationship including the impact of personality traits remains unclear. Using functional magnetic resonance imaging, we applied an experimental paradigm that allowed us to explore the neural response evoked by reward and the attribution of personal relevance separately. We observed different brain regions previously reported to be active during reward and personal relevance, including the bilateral caudate nucleus and the pregenual anterior cingulate cortex (PACC). Additional analysis revealed activations in the right and left insula specific for the attribution of personal relevance. Furthermore, our results demonstrate a negative correlation between signal changes in both the PACC and the left anterior insula during the attribution of low personal relevance and the personality dimension novelty seeking. While a set of subcortical and cortical regions including the PACC is commonly involved in reward and personal relevance, other regions like the bilateral anterior insula were recruited specifically during personal relevance. Based on our correlation between novelty seeking and signal changes in both regions during personal relevance, we assume that the neuronal response to personally relevant stimuli is dependent on the personality trait novelty seeking.

A Constant Light-Genetic Screen Identifies KISMET as a Regulator of Circadian Photoresponses:

In most organisms, intracellular molecular pacemakers called circadian clocks coordinate metabolic, physiological, and behavioral processes during the course of the day. For example, they determine when animals are active or resting. Circadian clocks are self-sustained oscillators, but their free-running period does not exactly match day length. Thus, they have to be reset by environmental inputs to stay properly phased with the day:night cycle. The fruit fly Drosophila melanogaster relies primarily on CRYPTOCHROME (CRY)–a cell-autonomous blue-light photoreceptor–to synchronize its circadian clocks with the light:dark cycle. With a genetic screen, we identified over 20 candidate genes that might regulate CRY function. kismet (kis) is among them: it encodes a chromatin remodeling factor essential for the development of Drosophila. We show that, in adult flies, KIS is expressed and functions in brain neurons that control daily behavioral rhythms. KIS determines how Drosophila circadian behavior responds to light, but not its free-running period. Moreover, manipulating simultaneously kis and cry activity demonstrates that these two genes interact to control molecular and behavioral circadian photoresponses. Our work therefore reveals that KIS regulates CRY signaling and thus determines how circadian clocks respond to light input.

Emergent Patterns of Social Affiliation in Primates, a Model:

Individual primates distribute their affiliative behaviour (such as grooming) in complex patterns among their group members. For instance, they reciprocate grooming, direct it more to partners the higher the partner’s rank, use it to reconcile fights and do so in particular with partners that are more valuable. For several types of patterns (such as reconciliation and exchange), a separate theory based on specific cognitive processes has been developed (such as individual recordkeeping, a tendency to exchange, selective attraction to the former opponent, and estimation of the value of a relationship). It is difficult to imagine how these separate theories can all be integrated scientifically and how these processes can be combined in the animal’s mind. To solve this problem, we first surveyed the empirical patterns and then we developed an individual-based model (called GrooFiWorld) in which individuals group, compete and groom. The grooming rule is based on grooming out of fear of defeat and on the anxiety reducing effects of grooming. We show that in this context this rule alone can explain many of the patterns of affiliation as well as the differences between egalitarian and despotic species. Our model can be used as a null model to increase our understanding of affiliative patterns of primates.

Expanding the Paradigms of Plant Pathogen Life History and Evolution of Parasitic Fitness beyond Agricultural Boundaries:

How do pathogens, whether they parasitize plants or animals, acquire virulence to new hosts and resistance to the arms we deploy to control disease? The significance of these questions for microbiology and for society at large can be illustrated by the recent worldwide efforts to track and limit the emergence of human transmissible strains of swine and avian influenza virus and of multidrug-resistant lines of human pathogenic bacteria, and to restrain the spread of Ug99, a strain of stem rust of wheat. Recent research in medical epidemiology has elucidated the impact of pathogen ecology in environmental reservoirs on the evolution of novel or enhanced pathogen virulence. In contrast, the evolution of virulence in plant pathogens has been investigated from a predominantly agro-centric perspective, and has focused overwhelmingly on evolutionary forces related to interactions with the primary plant host. Here, we argue that current concepts from the field of medical epidemiology regarding mechanisms that lead to acquisition of novel virulence, biocide resistance, and enhanced pathogenic fitness can serve as an important foundation for novel hypotheses about the evolution of plant pathogens. We present numerous examples of virulence traits in plant pathogenic microorganisms that also have a function in their survival and growth in nonagricultural and nonplant habitats. Based on this evidence, we make an appeal to expand concepts of the life history of plant pathogens and the drivers of pathogen evolution beyond the current agro-centric perspective.

Age at Puberty and the Emerging Obesity Epidemic:

Recent studies have shown that puberty starts at younger ages than previously. It has been hypothesized that the increasing prevalence of childhood obesity is contributing to this trend. The purpose of this study was to analyze the association between prepubertal body mass index (BMI) and pubertal timing, as assessed by age at onset of pubertal growth spurt (OGS) and at peak height velocity (PHV), and the secular trend of pubertal timing given the prepubertal BMI. Annual measurements of height and weight were available in all children born from 1930 to 1969 who attended primary school in the Copenhagen municipality; 156,835 children fulfilled the criteria for determining age at OGS and PHV. The effect of prepubertal BMI at age seven on these markers of pubertal development within and between birth cohorts was analyzed. BMI at seven years was significantly inversely associated with age at OGS and PHV. Dividing the children into five levels of prepubertal BMI, we found a similar secular trend toward earlier maturation in all BMI groups. The heavier both boys and girls were at age seven, the earlier they entered puberty. Irrespective of level of BMI at age seven, there was a downward trend in the age at attaining puberty in both boys and girls, which suggests that the obesity epidemic is not solely responsible for the trend.

Biomedical Text Mining and Its Applications:

This tutorial is intended for biologists and computational biologists interested in adding text mining tools to their bioinformatics toolbox. As an illustrative example, the tutorial examines the relationship between progressive multifocal leukoencephalopathy (PML) and antibodies. Recent cases of PML have been associated to the administration of some monoclonal antibodies such as efalizumab [1]. Those interested in a further introduction to text mining may also want to read other reviews [2]-[4].
Understanding large amounts of text with the aid of a computer is harder than simply equipping a computer with a grammar and a dictionary. A computer, like a human, needs certain specialized knowledge in order to understand text. The scientific field that is dedicated to train computers with the right knowledge for this task (among other tasks) is called natural language processing (NLP). Biomedical text mining (henceforth, text mining) is the subfield that deals with text that comes from biology, medicine, and chemistry (henceforth, biomedical text). Another popular name is BioNLP, which some practitioners use as synonymous with text mining.
Biomedical text is not a homogeneous realm [5]. Medical records are written differently from scientific articles, sequence annotations, or public health guidelines. Moreover, local dialects are not uncommon [6]. For example, medical centers develop their own jargons and laboratories create their idiosyncratic protein nomenclatures. This variability means, in practice, that text mining applications are tailored to specific types of text. In particular, for reasons of availability and cost, many are designed for scientific abstracts in English from Medline.

There are 21 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

Continue reading →

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:

Continue reading →

There are 25 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
VitisNet: ‘Omics’ Integration through Grapevine Molecular Networks:

Genomic data release for the grapevine has increased exponentially in the last five years. The Vitis vinifera genome has been sequenced and Vitis EST, transcriptomic, proteomic, and metabolomic tools and data sets continue to be developed. The next critical challenge is to provide biological meaning to this tremendous amount of data by annotating genes and integrating them within their biological context. We have developed and validated a system of Grapevine Molecular Networks (VitisNet). The sequences from the Vitis vinifera (cv. Pinot Noir PN40024) genome sequencing project and ESTs from the Vitis genus have been paired and the 39,424 resulting unique sequences have been manually annotated. Among these, 13,145 genes have been assigned to 219 networks. The pathway sets include 88 “Metabolic”, 15 “Genetic Information Processing”, 12 “Environmental Information Processing”, 3 “Cellular Processes”, 21 “Transport”, and 80 “Transcription Factors”. The quantitative data is loaded onto molecular networks, allowing the simultaneous visualization of changes in the transcriptome, proteome, and metabolome for a given experiment. VitisNet uses manually annotated networks in SBML or XML format, enabling the integration of large datasets, streamlining biological functional processing, and improving the understanding of dynamic processes in systems biology experiments. VitisNet is grounded in the Vitis vinifera genome (currently at 8x coverage) and can be readily updated with subsequent updates of the genome or biochemical discoveries. The molecular network files can be dynamically searched by pathway name or individual genes, proteins, or metabolites through the MetNet Pathway database and web-portal at http://metnet3.vrac.iastate.edu/. All VitisNet files including the manual annotation of the grape genome encompassing pathway names, individual genes, their genome identifier, and chromosome location can be accessed and downloaded from the VitisNet tab at http://vitis-dormancy.sdstate.org.

The Evolutionary History of Protein Domains Viewed by Species Phylogeny:

Protein structural domains are evolutionary units whose relationships can be detected over long evolutionary distances. The evolutionary history of protein domains, including the origin of protein domains, the identification of domain loss, transfer, duplication and combination with other domains to form new proteins, and the formation of the entire protein domain repertoire, are of great interest. A methodology is presented for providing a parsimonious domain history based on gain, loss, vertical and horizontal transfer derived from the complete genomic domain assignments of 1015 organisms across the tree of life. When mapped to species trees the evolutionary history of domains and domain combinations is revealed, and the general evolutionary trend of domain and combination is analyzed. We show that this approach provides a powerful tool to study how new proteins and functions emerged and to study such processes as horizontal gene transfer among more distant species.

High Prevalence of Multidrug-Tolerant Bacteria and Associated Antimicrobial Resistance Genes Isolated from Ornamental Fish and Their Carriage Water:

Antimicrobials are used to directly control bacterial infections in pet (ornamental) fish and are routinely added to the water these fish are shipped in to suppress the growth of potential pathogens during transport. To assess the potential effects of this sustained selection pressure, 127 Aeromonas spp. isolated from warm and cold water ornamental fish species were screened for tolerance to 34 antimicrobials. Representative isolates were also examined for the presence of 54 resistance genes by a combination of miniaturized microarray and conventional PCR. Forty-seven of 94 Aeromonas spp. isolates recovered from tropical ornamental fish and their carriage water were tolerant to ≥15 antibiotics, representing seven or more different classes of antimicrobial. The quinolone and fluoroquinolone resistance gene, qnrS2, was detected at high frequency (37% tested recent isolates were positive by PCR). Class 1 integrons, IncA/C broad host range plasmids and a range of other antibiotic resistance genes, including floR, blaTEM−1, tet(A), tet(D), tet(E), qacE2, sul1, and a number of different dihydrofolate reductase and aminoglycoside transferase coding genes were also detected in carriage water samples and bacterial isolates. These data suggest that ornamental fish and their carriage water act as a reservoir for both multi-resistant bacteria and resistance genes.

How Ebola Impacts Genetics of Western Lowland Gorilla Populations:

Emerging infectious diseases in wildlife are major threats for both human health and biodiversity conservation. Infectious diseases can have serious consequences for the genetic diversity of populations, which could enhance the species’ extinction probability. The Ebola epizootic in western and central Africa induced more than 90% mortality in Western lowland gorilla population. Although mortality rates are very high, the impacts of Ebola on genetic diversity of Western lowland gorilla have never been assessed. We carried out long term studies of three populations of Western lowland gorilla in the Republic of the Congo (Odzala-Kokoua National Park, Lossi gorilla sanctuary both affected by Ebola and Lossi’s periphery not affected). Using 17 microsatellite loci, we compared genetic diversity and structure of the populations and estimate their effective size before and after Ebola outbreaks. Despite the effective size decline in both populations, we did not detect loss in genetic diversity after the epizootic. We revealed temporal changes in allele frequencies in the smallest population. Immigration and short time elapsed since outbreaks could explain the conservation of genetic diversity after the demographic crash. Temporal changes in allele frequencies could not be explained by genetic drift or random sampling. Immigration from genetically differentiated populations and a non random mortality induced by Ebola, i.e., selective pressure and cost of sociality, are alternative hypotheses. Understanding the influence of Ebola on gorilla genetic dynamics is of paramount importance for human health, primate evolution and conservation biology.

Identifying Blood Biomarkers and Physiological Processes That Distinguish Humans with Superior Performance under Psychological Stress:

Attrition of students from aviation training is a serious financial and operational concern for the U.S. Navy. Each late stage navy aviator training failure costs the taxpayer over $1,000,000 and ultimately results in decreased operational readiness of the fleet. Currently, potential aviators are selected based on the Aviation Selection Test Battery (ASTB), which is a series of multiple-choice tests that evaluate basic and aviation-related knowledge and ability. However, the ASTB does not evaluate a person’s response to stress. This is important because operating sophisticated aircraft demands exceptional performance and causes high psychological stress. Some people are more resistant to this type of stress, and consequently better able to cope with the demands of naval aviation, than others. Although many psychological studies have examined psychological stress resistance none have taken advantage of the human genome sequence. Here we use high-throughput -omic biology methods and a novel statistical data normalization method to identify plasma proteins associated with human performance under psychological stress. We identified proteins involved in four basic physiological processes: innate immunity, cardiac function, coagulation and plasma lipid physiology. The proteins identified here further elucidate the physiological response to psychological stress and suggest a hypothesis that stress-susceptible pilots may be more prone to shock. This work also provides potential biomarkers for screening humans for capability of superior performance under stress.

Absence of 2009 Pandemic H1N1 Influenza A Virus in Fresh Pork:

The emergence of the pandemic 2009 H1N1 influenza A virus in humans and subsequent discovery that it was of swine influenza virus lineages raised concern over the safety of pork. Pigs experimentally infected with pandemic 2009 H1N1 influenza A virus developed respiratory disease; however, there was no evidence for systemic disease to suggest that pork from pigs infected with H1N1 influenza would contain infectious virus. These findings support the WHO recommendation that pork harvested from pandemic influenza A H1N1 infected swine is safe to consume when following standard meat hygiene practices.

Calculating Evolutionary Dynamics in Structured Populations:

Evolution is shaping the world around us. At the core of every evolutionary process is a population of reproducing individuals. The outcome of an evolutionary process depends on population structure. Here we provide a general formula for calculating evolutionary dynamics in a wide class of structured populations. This class includes the recently introduced “games in phenotype space” and “evolutionary set theory.” There can be local interactions for determining the relative fitness of individuals, but we require global updating, which means all individuals compete uniformly for reproduction. We study the competition of two strategies in the context of an evolutionary game and determine which strategy is favored in the limit of weak selection. We derive an intuitive formula for the structure coefficient, σ, and provide a method for efficient numerical calculation.

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

Motion-defined form can seem to persist briefly after motion ceases, before seeming to gradually disappear into the background. Here we investigate if this subjective persistence reflects a signal capable of improving objective measures of sensitivity to static form. We presented a sinusoidal modulation of luminance, masked by a background noise pattern. The sinusoidal luminance modulation was usually subjectively invisible when static, but visible when moving. We found that drifting then stopping the waveform resulted in a transient subjective persistence of the waveform in the static display. Observers’ objective sensitivity to the position of the static waveform was also improved after viewing moving waveforms, compared to viewing static waveforms for a matched duration. This facilitation did not occur simply because movement provided more perspectives of the waveform, since performance following pre-exposure to scrambled animations did not match that following pre-exposure to smooth motion. Observers did not simply remember waveform positions at motion offset, since removing the waveform before testing reduced performance. Motion processing therefore interacts with subsequent static visual inputs in a way that can improve performance in objective sensitivity measures. We suggest that the brief subjective persistence of motion-defined forms that can occur after motion offsets is a consequence of the decay of a static form signal that has been transiently enhanced by motion processing.

Vector Field Embryogeny:

We present a novel approach toward evolving artificial embryogenies, which omits the graph representation of gene regulatory networks and directly shapes the dynamics of a system, i.e., its phase space. We show the feasibility of the approach by evolving cellular differentiation, a basic feature of both biological and artificial development. We demonstrate how a spatial hierarchy formulation can be integrated into the framework and investigate the evolution of a hierarchical system. Finally, we show how the framework allows the investigation of allometry, a biological phenomenon, and its role for evolution. We find that direct evolution of allometric change, i.e., the evolutionary adaptation of the speed of system states on transient trajectories in phase space, is advantageous for a cellular differentiation task.

There are 25 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:
The Secret Life of Oilbirds: New Insights into the Movement Ecology of a Unique Avian Frugivore:

Steatornis caripensis (the oilbird) is a very unusual bird. It supposedly never sees daylight, roosting in huge aggregations in caves during the day and bringing back fruit to the cave at night. As a consequence a large number of the seeds from the fruit they feed upon germinate in the cave and spoil. Here we use newly developed GPS/acceleration loggers with remote UHF readout to show that several assumptions about the behaviour of Steatornis caripensis need to be revised. On average, they spend only every 3rd day in a cave, individuals spent most days sitting quietly in trees in the rainforest where they regurgitate seeds. This provides new data on the extent of seed dispersal and the movement ecology of Steatornis caripensis. It suggests that Steatornis caripensis is perhaps the most important long-distance seed disperser in Neotropical forests. We also show that colony-living comes with high activity costs to individuals.

Cranial Anatomy of the Earliest Marsupials and the Origin of Opossums:

The early evolution of living marsupials is poorly understood in part because the early offshoots of this group are known almost exclusively from jaws and teeth. Filling this gap is essential for a better understanding of the phylogenetic relationships among living marsupials, the biogeographic pathways that led to their current distribution as well as the successive evolutionary steps that led to their current diversity, habits and various specializations that distinguish them from placental mammals. Here we report the first skull of a 55 million year old peradectid marsupial from the early Eocene of North America and exceptionally preserved skeletons of an Oligocene herpetotheriid, both representing critical groups to understand early marsupial evolution. A comprehensive phylogenetic cladistic analysis of Marsupialia including the new findings and close relatives of marsupials show that peradectids are the sister group of living opossums and herpetotheriids are the sister group of all living marsupials. The results imply that North America played an important role in early Cenozoic marsupial evolutionary history and may have even been the center of origin of living marsupials and opossums. New data from the herpetotheriid postcranium support the view that the ancestral morphotype of Marsupialia was more terrestrial than opossums are. The resolution of the phylogenetic position of peradectids reveals an older calibration point for molecular estimates of divergence times among living marsupials than those currently used.

Possible Fruit Protein Effects on Primate Communities in Madagascar and the Neotropics:

The ecological factors contributing to the evolution of tropical vertebrate communities are still poorly understood. Primate communities of the tropical Americas have fewer folivorous but more frugivorous genera than tropical regions of the Old World and especially many more frugivorous genera than Madagascar. Reasons for this phenomenon are largely unexplored. We developed the hypothesis that Neotropical fruits have higher protein concentrations than fruits from Madagascar and that the higher representation of frugivorous genera in the Neotropics is linked to high protein concentrations in fruits. Low fruit protein concentrations in Madagascar would restrict the evolution of frugivores in Malagasy communities. We reviewed the literature for nitrogen concentrations in fruits from the Neotropics and from Madagascar, and analyzed fruits from an additional six sites in the Neotropics and six sites in Madagascar. Fruits from the Neotropical sites contain significantly more nitrogen than fruits from the Madagascar sites. Nitrogen concentrations in New World fruits are above the concentrations to satisfy nitrogen requirements of primates, while they are at the lower end or below the concentrations to cover primate protein needs in Madagascar. Fruits at most sites in the Neotropics contain enough protein to satisfy the protein needs of primates. Thus, selection pressure to develop new adaptations for foods that are difficult to digest (such as leaves) may have been lower in the Neotropics than in Madagascar. The low nitrogen concentrations in fruits from Madagascar may contribute to the almost complete absence of frugivorous primate species on this island.

Culture Modulates Eye-Movements to Visual Novelty:

When viewing complex scenes, East Asians attend more to contexts whereas Westerners attend more to objects, reflecting cultural differences in holistic and analytic visual processing styles respectively. This eye-tracking study investigated more specific mechanisms and the robustness of these cultural biases in visual processing when salient changes in the objects and backgrounds occur in complex pictures. Chinese Singaporean (East Asian) and Caucasian US (Western) participants passively viewed pictures containing selectively changing objects and background scenes that strongly captured participants’ attention in a data-driven manner. We found that although participants from both groups responded to object changes in the pictures, there was still evidence for cultural divergence in eye-movements. The number of object fixations in the US participants was more affected by object change than in the Singapore participants. Additionally, despite the picture manipulations, US participants consistently maintained longer durations for both object and background fixations, with eye-movements that generally remained within the focal objects. In contrast, Singapore participants had shorter fixation durations with eye-movements that alternated more between objects and backgrounds. The results demonstrate a robust cultural bias in visual processing even when external stimuli draw attention in an opposite manner to the cultural bias. These findings also extend previous studies by revealing more specific, but consistent, effects of culture on the different aspects of visual attention as measured by fixation duration, number of fixations, and saccades between objects and backgrounds.

Rhodopsin Molecular Evolution in Mammals Inhabiting Low Light Environments:

The ecological radiation of mammals to inhabit a variety of light environments is largely attributed to adaptive changes in their visual systems. Visual capabilities are conferred by anatomical features of the eyes as well as the combination and properties of their constituent light sensitive pigments. To test whether evolutionary switches to different niches characterized by dim-light conditions coincided with molecular adaptation of the rod pigment rhodopsin, we sequenced the rhodopsin gene in twenty-two mammals including several bats and subterranean mole-rats. We compared these to thirty-seven published mammal rhodopsin sequences, from species with divergent visual ecologies, including nocturnal, diurnal and aquatic groups. All taxa possessed an intact functional rhodopsin; however, phylogenetic tree reconstruction recovered a gene tree in which rodents were not monophyletic, and also in which echolocating bats formed a monophyletic group. These conflicts with the species tree appear to stem from accelerated evolution in these groups, both of which inhabit low light environments. Selection tests confirmed divergent selection pressures in the clades of subterranean rodents and bats, as well as in marine mammals that live in turbid conditions. We also found evidence of divergent selection pressures among groups of bats with different sensory modalities based on vision and echolocation. Sliding window analyses suggest most changes occur in transmembrane domains, particularly obvious within the pinnipeds; however, we found no obvious pattern between photopic niche and predicted spectral sensitivity based on known critical amino acids. This study indicates that the independent evolution of rhodopsin vision in ecologically specialised groups of mammals has involved molecular evolution at the sequence level, though such changes might not mediate spectral sensitivity directly.

Molecular Exploration of the First-Century Tomb of the Shroud in Akeldama, Jerusalem:

The Tomb of the Shroud is a first-century C.E. tomb discovered in Akeldama, Jerusalem, Israel that had been illegally entered and looted. The investigation of this tomb by an interdisciplinary team of researchers began in 2000. More than twenty stone ossuaries for collecting human bones were found, along with textiles from a burial shroud, hair and skeletal remains. The research presented here focuses on genetic analysis of the bioarchaeological remains from the tomb using mitochondrial DNA to examine familial relationships of the individuals within the tomb and molecular screening for the presence of disease. There are three mitochondrial haplotypes shared between a number of the remains analyzed suggesting a possible family tomb. There were two pathogens genetically detected within the collection of osteological samples, these were Mycobacterium tuberculosis and Mycobacterium leprae. The Tomb of the Shroud is one of very few examples of a preserved shrouded human burial and the only example of a plaster sealed loculus with remains genetically confirmed to have belonged to a shrouded male individual that suffered from tuberculosis and leprosy dating to the first-century C.E. This is the earliest case of leprosy with a confirmed date in which M. leprae DNA was detected.

An Information Gap in DNA Evidence Interpretation:

Forensic DNA evidence often contains mixtures of multiple contributors, or is present in low template amounts. The resulting data signals may appear to be relatively uninformative when interpreted using qualitative inclusion-based methods. However, these same data can yield greater identification information when interpreted by computer using quantitative data-modeling methods. This study applies both qualitative and quantitative interpretation methods to a well-characterized DNA mixture and dilution data set, and compares the inferred match information. The results show that qualitative interpretation loses identification power at low culprit DNA quantities (below 100 pg), but that quantitative methods produce useful information down into the 10 pg range. Thus there is a ten-fold information gap that separates the qualitative and quantitative DNA mixture interpretation approaches. With low quantities of culprit DNA (10 pg to 100 pg), computer-based quantitative interpretation provides greater match sensitivity.

Testosterone Administration Decreases Generosity in the Ultimatum Game:

How do human beings decide when to be selfish or selfless? In this study, we gave testosterone to 25 men to establish its impact on prosocial behaviors in a double-blind within-subjects design. We also confirmed participants’ testosterone levels before and after treatment through blood draws. Using the Ultimatum Game from behavioral economics, we find that men with artificially raised T, compared to themselves on placebo, were 27% less generous towards strangers with money they controlled (95% CI placebo: (1.70, 2.72); 95% CI T: (.98, 2.30)). This effect scales with a man’s level of total-, free-, and dihydro-testosterone (DHT). Men in the lowest decile of DHT were 560% more generous than men in the highest decile of DHT. We also found that men with elevated testosterone were more likely to use their own money punish those who were ungenerous toward them. Our results continue to hold after controlling for altruism. We conclude that elevated testosterone causes men to behave antisocially.

Quantifying the Extent of North American Mammal Extinction Relative to the Pre-Anthropogenic Baseline:

Earth has experienced five major extinction events in the past 450 million years. Many scientists suggest we are now witnessing a sixth, driven by human impacts. However, it has been difficult to quantify the real extent of the current extinction episode, either for a given taxonomic group at the continental scale or for the worldwide biota, largely because comparisons of pre-anthropogenic and anthropogenic biodiversity baselines have been unavailable. Here, we compute those baselines for mammals of temperate North America, using a sampling-standardized rich fossil record to reconstruct species-area relationships for a series of time slices ranging from 30 million to 500 years ago. We show that shortly after humans first arrived in North America, mammalian diversity dropped to become at least 15%-42% too low compared to the “normal” diversity baseline that had existed for millions of years. While the Holocene reduction in North American mammal diversity has long been recognized qualitatively, our results provide a quantitative measure that clarifies how significant the diversity reduction actually was. If mass extinctions are defined as loss of at least 75% of species on a global scale, our data suggest that North American mammals had already progressed one-fifth to more than halfway (depending on biogeographic province) towards that benchmark, even before industrialized society began to affect them. Data currently are not available to make similar quantitative estimates for other continents, but qualitative declines in Holocene mammal diversity are also widely recognized in South America, Eurasia, and Australia. Extending our methodology to mammals in these areas, as well as to other taxa where possible, would provide a reasonable way to assess the magnitude of global extinction, the biodiversity impact of extinctions of currently threatened species, and the efficacy of conservation efforts into the future.

Kisspeptin Signalling in the Hypothalamic Arcuate Nucleus Regulates GnRH Pulse Generator Frequency in the Rat:

Kisspeptin and its G protein-coupled receptor (GPR) 54 are essential for activation of the hypothalamo-pituitary-gonadal axis. In the rat, the kisspeptin neurons critical for gonadotropin secretion are located in the hypothalamic arcuate (ARC) and anteroventral periventricular (AVPV) nuclei. As the ARC is known to be the site of the gonadotropin-releasing hormone (GnRH) pulse generator we explored whether kisspeptin-GPR54 signalling in the ARC regulates GnRH pulses. We examined the effects of kisspeptin-10 or a selective kisspeptin antagonist administration intra-ARC or intra-medial preoptic area (mPOA), (which includes the AVPV), on pulsatile luteinizing hormone (LH) secretion in the rat. Ovariectomized rats with subcutaneous 17β-estradiol capsules were chronically implanted with bilateral intra-ARC or intra-mPOA cannulae, or intra-cerebroventricular (icv) cannulae and intravenous catheters. Blood samples were collected every 5 min for 5-8 h for LH measurement. After 2 h of control blood sampling, kisspeptin-10 or kisspeptin antagonist was administered via pre-implanted cannulae. Intranuclear administration of kisspeptin-10 resulted in a dose-dependent increase in circulating levels of LH lasting approximately 1 h, before recovering to a normal pulsatile pattern of circulating LH. Both icv and intra-ARC administration of kisspeptin antagonist suppressed LH pulse frequency profoundly. However, intra-mPOA administration of kisspeptin antagonist did not affect pulsatile LH secretion. These data are the first to identify the arcuate nucleus as a key site for kisspeptin modulation of LH pulse frequency, supporting the notion that kisspeptin-GPR54 signalling in this region of the mediobasal hypothalamus is a critical neural component of the hypothalamic GnRH pulse generator.

Brownie, a Gene Involved in Building Complex Respiratory Devices in Insect Eggshells:

Insect eggshells must combine protection for the yolk and embryo with provisions for respiration and for the entry of sperm, which are ensured by aeropyles and micropyles, respectively. Insects which oviposit the eggs in an egg-case have a double problem of respiration as gas exchange then involves two barriers. An example of this situation is found in the cockroach Blattella germanica, where the aeropyle and the micropyle are combined in a complex structure called the sponge-like body. The sponge-like body has been well described morphologically, but nothing is known about how it is built up. In a library designed to find genes expressed during late chorion formation in B. germanica, we isolated the novel sequence Bg30009 (now called Brownie), which was outstanding due to its high copy number. In the present work, we show that Brownie is expressed in the follicle cells localized in the anterior pole of the oocyte in late choriogenesis. RNA interference (RNAi) of Brownie impaired correct formation of the sponge-like body and, as a result, the egg-case was also ill-formed and the eggs were not viable. Results indicate that the novel gene Brownie plays a pivotal role in building up the sponge-like body. Brownie is the first reported gene involved in the construction of complex eggshell respiratory structures.

Refuge or Reservoir? The Potential Impacts of the Biofuel Crop Miscanthus x giganteus on a Major Pest of Maize:

Interest in the cultivation of biomass crops like the C4 grass Miscanthus x giganteus (Miscanthus) is increasing as global demand for biofuel grows. In the US, Miscanthus is promoted as a crop well-suited to the Corn Belt where it could be cultivated on marginal land interposed with maize and soybean. Interactions (direct and indirect) of Miscanthus, maize, and the major Corn Belt pest of maize, the western corn rootworm, (Diabrotica virgifera virgifera LeConte, WCR) are unknown. Adding a perennial grass/biomass crop to this system is concerning since WCR is adapted to the continuous availability of its grass host, maize (Zea mays). In a greenhouse and field study, we investigated WCR development and oviposition on Miscanthus. The suitability of Miscanthus for WCR development varied across different WCR populations. Data trends indicate that WCR populations that express behavioural resistance to crop rotation performed as well on Miscanthus as on maize. Over the entire study, total adult WCR emergence from Miscanthus (212 WCR) was 29.6% of that from maize (717 WCR). Adult dry weight was 75-80% that of WCR from maize; female emergence patterns on Miscanthus were similar to females developing on maize. There was no difference in the mean no. of WCR eggs laid at the base of Miscanthus and maize in the field. Field oviposition and significant WCR emergence from Miscanthus raises many questions about the nature of likely interactions between Miscanthus, maize and WCR and the potential for Miscanthus to act as a refuge or reservoir for Corn Belt WCR. Responsible consideration of the benefits and risks associated with Corn Belt Miscanthus are critical to protecting an agroecosystem that we depend on for food, feed, and increasingly, fuel. Implications for European agroecosystems in which Miscanthus is being proposed are also discussed in light of the WCR’s recent invasion into Europe.

Applied Climate-Change Analysis: The Climate Wizard Tool:

Although the message of “global climate change” is catalyzing international action, it is local and regional changes that directly affect people and ecosystems and are of immediate concern to scientists, managers, and policy makers. A major barrier preventing informed climate-change adaptation planning is the difficulty accessing, analyzing, and interpreting climate-change information. To address this problem, we developed a powerful, yet easy to use, web-based tool called Climate Wizard (http://ClimateWizard.org) that provides non-climate specialists with simple analyses and innovative graphical depictions for conveying how climate has and is projected to change within specific geographic areas throughout the world. To demonstrate the Climate Wizard, we explored historic trends and future departures (anomalies) in temperature and precipitation globally, and within specific latitudinal zones and countries. We found the greatest temperature increases during 1951-2002 occurred in northern hemisphere countries (especially during January-April), but the latitude of greatest temperature change varied throughout the year, sinusoidally ranging from approximately 50°N during February-March to 10°N during August-September. Precipitation decreases occurred most commonly in countries between 0-20°N, and increases mostly occurred outside of this latitudinal region. Similarly, a quantile ensemble analysis based on projections from 16 General Circulation Models (GCMs) for 2070-2099 identified the median projected change within countries, which showed both latitudinal and regional patterns in projected temperature and precipitation change. The results of these analyses are consistent with those reported by the Intergovernmental Panel on Climate Change, but at the same time, they provide examples of how Climate Wizard can be used to explore regionally- and temporally-specific analyses of climate change. Moreover, Climate Wizard is not a static product, but rather a data analysis framework designed to be used for climate change impact and adaption planning, which can be expanded to include other information, such as downscaled future projections of hydrology, soil moisture, wildfire, vegetation, marine conditions, disease, and agricultural productivity.

On the ‘Duel’ Nature of History: Revisiting Contingency versus Determinism:

What is the relationship between external–physical and biological–influences on increasingly complex matter over billions of years? In his most recent book, Islands in the Cosmos: the Evolution of Life on Land, Dale Russell attempts to answer this question. Russell is the senior curator of paleontology at the North Carolina Museum of Natural Sciences and, among other things, is well known for proposing in 1971 an extraterrestrial cause for the Cretaceous-Tertiary extinction that wiped out the non-avian dinosaurs [2]. This places Russell among the first paleontologists to consider this extinction as a relatively sudden event in Earth’s history. Dale Russell has spent his lifetime pondering grand evolutionary questions, and it is a quest that Islands in the Cosmos well illustrates.

School Playground Surfacing and Arm Fractures in Children: A Cluster Randomized Trial Comparing Sand to Wood Chip Surfaces:

Playgrounds and outdoor play equipment provide children with a place to let steam off, play creatively, socialize, and learn new skills. And, in a world where childhood obesity is a burgeoning problem, playgrounds provide a place where children can be encouraged to exercise. But playgrounds are not without hazards. Even in well-maintained and well-run facilities, children can hurt themselves by falling off climbing frames, monkey bars, and other equipment or by falling from standing height during playground games such as tag. In the US alone, more than 200,000 children are treated in emergency departments for injuries sustained in playgrounds every year and about 6,400 children are admitted to hospitals because of playground injuries, most of which are bone fractures (broken bones). In fact, playground injuries in the US are more severe and have a higher hospital admission rate than any other sort of child injury except those involving vehicles.

Structural Basis for the Aminoacid Composition of Proteins from Halophilic Archea:

Life on earth exhibits an enormous adaptive capacity and living organisms can be found even in extreme environments. The halophilic archea are a group of microorganisms that grow best in highly salted lakes (with KCl concentrations between 2 and 6 molar). To avoid osmotic shock, halophilic archea have the same ionic strength inside their cells as outside. All their macromolecules, including the proteins, have therefore adapted to remain folded and functional under such ionic strength conditions. As a result, the amino acid composition of proteins adapted to a hypersaline environment is very characteristic: they have an abundance of negatively charged residues combined with a low frequency of lysines. In this study, we have investigated the relationship between this biased amino-acid composition and protein stability. Three model proteins – one from a strict halophile, its homolog from a mesophile and a totally unrelated protein from a mesophile – have been largely redesigned by site-directed mutagenesis, and the resulting mutants have been characterized structurally and thermodynamically. Our results show that amino acids with short side-chains (like aspartic and glutamic acid) are preferred to the longer lysine because they succeed in reducing the interaction surface between the protein and the solvent, which is beneficial in an environment where water is in limited availability because it also has to hydrate the salt ions.

Surviving Salt: How Do Extremophiles Do It?:

Immersed in waters saltier than chicken soup, salt-tolerant “halophilic” microorganisms are able to thrive in conditions that would reduce a less-adapted organism to a shriveled remnant. One way halophilic archaea avoid this fate is by bathing their molecular machinery in a similarly salty intracellular environment that would cause ordinary proteins to lose their shape. How do the proteins inside these cells survive?