Monthly Archives: July 2008

What’s new in PLoS Computational Biology, PLoS Genetics, PLoS Pathogens and PLoS Neglected Tropical Diseases this week? Among else, these papers that caught my eye:
Emergent Synchronous Bursting of Oxytocin Neuronal Network:

When young suckle, they are rewarded intermittently with a let-down of milk that results from reflex secretion of the hormone oxytocin. Oxytocin is a neuropeptide made by specialised neurons in the hypothalamus, and is secreted from nerve endings in the pituitary gland. During suckling, every 5 min or so, each of these neurons discharges a brief, intense burst of action potentials; these are propagated down the axons, and release a pulse of oxytocin into the circulation. Here, we have built a computational model to understand how these bursts arise and how they are synchronized. In our model, bursting is an emergent behaviour of a complex system, involving both positive and negative feedbacks, between many, sparsely connected cells. The oxytocin cells are regulated by independent afferent inputs, but they interact by local release of oxytocin and endocannabinoids. Oxytocin released from the dendrites of these cells has a positive-feedback effect, while endocannabinoids have an inhibitory effect by suppressing the afferent input to the cells. Many neurons make peptides that act as messengers within the brain, and many of these are also released from dendrites, so this model may reflect a common pattern-generating mechanism in the brain.

Genome-Wide Expression Patterns and the Genetic Architecture of a Fundamental Social Trait:

Fundamental research goals for scientists interested in social evolution are to determine the numbers and types of genes that directly regulate individual social behaviors as well as to understand how the social environment indirectly influences the expression of socially relevant traits. The fire ant Solenopsis invicta features a remarkable form of social variation in which the occurrence of two distinct social types that differ in colony queen number is associated with genetic differences at a genomic region marked by the gene Gp-9. Our analyses of gene expression profiles in fire ant workers revealed that differences in Gp-9 genotype are associated with the differential expression of an unexpectedly small number of genes, many of which are predicted to function in chemical communication relevant to the regulation of colony queen number. Surprisingly, worker gene expression profiles are more strongly influenced by indirect effects associated with the social environment within their colony than by the direct effect of their own Gp-9 genotype. These results suggest a complex genetic architecture underlying the control of colony queen number in fire ants, with a single Mendelian factor directly regulating, and the social environment indirectly influencing, the expression of the individual behaviors that, in aggregate, yield an emergent colony social organization.

Tracking the Odysseys of Juvenile Schistosomes to Understand Host Interactions:

The prospects confronting a “new-born” schistosome cercaria are formidable. That some of these microscopic helminths successfully negotiate the tortuous route from snail to human vasculature is a truly remarkable feature of adaptive biology. After escaping the birth pore of its parental sporocyst, a cercaria (at least we infer from studies of other digeneans [1]) swims and crawls through the snail body cavity before it burrows through a pre-formed escape tunnel to the aquatic environment. Once in that milieu, a cyclical suite of swimming behaviours positions the cercaria for its potential assault on the skin of an available host, should one appear. Upon skin penetration, the larva (now called a schistosomulum) sits within the skin for up to 72 hours before tracking to the lung, whereupon it re-enters a second static phase. This journey takes the organism through three distinct environments (five if we include the solid integuments of snail and human hosts), incorporates a wholesale remodelling of the surface membrane, and includes two poorly understood periods of relative immobility in the skin and the lung. Further development in the liver is required before the adults reach their ultimate destination in the vasculature of the intestine or bladder. How the juvenile stages of schistosomes negotiate these environments is of intense interest, not the least because protective immunity in schistosome infections, when it occurs, appears to be directed against the early intra-host stages, with the principal target being the lung stage schistosomulum

Dynamics of Genome Rearrangement in Bacterial Populations:

Whole-genome sequencing has revealed that organisms exhibit extreme variability in chromosome structure. One common type of chromosome structure variation is genome arrangement variation: changes in the ordering of genes on the chromosome. Not only do we find differences in genome arrangement across species, but in some organisms, members of the same species have radically different genome arrangements. We studied the evolution of genome arrangement in pathogenic bacteria from the genus Yersinia. The Yersinia exhibit substantial variation in genome arrangement both within and across species. We reconstructed the history of genome rearrangement by inversion in a group of eight Yersinia, and we statistically quantified the forces shaping their genome arrangement evolution. In particular, we discovered an excess of rearrangement activity near the origin of chromosomal replication and found evidence for a preferred configuration for the relative orientations of the origin and terminus of replication. We also found real inversions to be significantly shorter than expected. Finally, we discovered that no single reconstruction of inversion history is parsimonious with respect to the total number of inversion mutations, but on average, reconstructed genome arrangements favor “balanced” genomes–where the replication origin is positioned opposite the terminus on the circular chromosome.

Computational Biology Resources Lack Persistence and Usability:

Innovation in computational biology research is predicated on the availability of published methods and computational resources. These resources facilitate the generation of new hypotheses and observations both on the part of the creators and the scientists who use them. These methods and resources include Web servers, databases, and software, both complex and simple, that implement a specific procedure or algorithm. Usually, a resource is maintained by the laboratory in which it was initially developed. We would assert that there is a growing level of frustration among scientists who attempt to use many of these resources and find that they no longer exist or are not properly maintained. Whether you agree or disagree with this statement and the evidence that follows, we welcome your thoughts and invite you to add a Comment to this article to share your own experiences and perspectives.

New Approach Sheds Light On Ways Circadian Disruption Affects Human Health:

Growing evidence indicates that exposure to irregular patterns of light and darkness can cause the human circadian system to fall out of synchrony with the 24-hour solar day, negatively affecting human health — but scientists have been unable to effectively study the relationship between circadian disruptions and human maladies.

Frogs With Disease-resistance Genes May Escape Extinction:

As frog populations die off around the world, researchers have identified certain genes that can help the amphibians develop resistance to harmful bacteria and disease. The discovery may provide new strategies to protect frog populations in the wild.

Men And Women May Need Different Diets:

Diet can strongly influence how long you live and your reproductive success, but now scientists have discovered that what works for males can be very different for females.

Gene That Regulates And Blocks Ovulation Discovered:

A group of Canadian and European researchers have unlocked the mystery of a gene with the potential to both regulate and block ovulation. The new study is a collaboration between the Université de Montréal in Canada and the Institut de génetique et biologie moléculaire et cellulaire of the Université de Louis Pasteur, Strasbourg, France.

From Humming Fish To Puccini: Vocal Communication Evolved With Ancient Species:

It’s a long way from the dull hums of the amorous midshipman fish to the strains of a Puccini aria — or, alas, even to the simplest Celine Dion melody. But the neural circuitry that led to the human love song — not to mention birdsongs, frog thrums and mating calls of all manner of vertebrates — was likely laid down hundreds of millions of years ago with the hums and grunts of the homely piscine.

Should We Move Species To Save Them From Climate Change?:

Many species must move to new areas to survive climate change. Often, this seems impossible. Species stranded on mountain tops in southern Europe that are becoming too hot for them, for instance, are unlikely to be able to reach northern Europe unaided. So should humans step in to help?

Fragile Antarctic Marine Life Pounded By Icebergs: Biodiversity Suffering:

Antarctic worms, sea spiders, urchins and other marine creatures living in near-shore shallow habitats are regularly pounded by icebergs. New data suggests this environment along the Antarctic Peninsula is going to get hit more frequently. This is due to an increase in the number of icebergs scouring the seabed as a result of shrinking winter sea ice.

Glimpses Of Earliest Forms Of Life On Earth: Remnant Of Ancient ‘RNA World’ Discovered:

Some bacterial cells can swim, morph into new forms and even become dangerously virulent – all without initial involvement of DNA. Yale University researchers describe July 18 in the journal Science how bacteria accomplish this amazing feat – and in doing so provide a glimpse of what the earliest forms of life on Earth may have looked like.

Birds Have A Good Sense Of Smell:

Sight and hearing are the most important senses for birds – this is at least the received wisdom. By studying bird DNA, however, researchers at the Max Planck Institute for Ornithology, along with a colleague at the Cawthron Institute in New Zealand, have now provided genetic evidence that many bird species have a well-developed sense of smell (Proceedings of the Royal Society B, 16.07.2008).

Europe’s Ancestors: Cro-Magnon 28,000 Years Old Had DNA Like Modern Humans:

Some 40,000 years ago, Cro-Magnons — the first people who had a skeleton that looked anatomically modern — entered Europe, coming from Africa. A group of geneticists, coordinated by Guido Barbujani and David Caramelli of the Universities of Ferrara and Florence, shows that a Cro-Magnoid individual who lived in Southern Italy 28,000 years ago was a modern European, genetically as well as anatomically.

Corporations Can Profit From Being Environmentally Friendly:

Though many policymakers have argued that environmental regulations can negatively impact on an organization’s bottom line, a new study by George Mason University researcher Nicole Darnall shows that companies that develop green production processes can not only offset the costs of regulations, but can also reap further benefits.

Wasps And Bumble Bees Heat Up, Fly Faster With Protein-rich Food:

Good pollen makes bees hot, biologists at UC San Diego have found. Wasps warm up too when they find protein-rich meat, a separate experiment has shown.

Over 100 Species Of Bats Found Within Several Acres Of Rainforest In Ecuador:

Bats are a remarkable evolutionary success story representing the second largest group of mammals, outnumbered only by rodents in number of species. Now, researchers of the Leibniz-Institute for Zoo and Wildlife Research in Berlin (Germany) and Boston University (U.S.A.) have discovered the place that harbours the highest number of bat species ever recorded. In a few ha* of rainforest in the Amazon basin of eastern Ecuador, the authors have found more than 100 species of bats.

There are 74 new articles in PLoS ONE today. Browse for your own choices – these are mine:
A 28,000 Years Old Cro-Magnon mtDNA Sequence Differs from All Potentially Contaminating Modern Sequences:

DNA sequences from ancient speciments may in fact result from undetected contamination of the ancient specimens by modern DNA, and the problem is particularly challenging in studies of human fossils. Doubts on the authenticity of the available sequences have so far hampered genetic comparisons between anatomically archaic (Neandertal) and early modern (Cro-Magnoid) Europeans. We typed the mitochondrial DNA (mtDNA) hypervariable region I in a 28,000 years old Cro-Magnoid individual from the Paglicci cave, in Italy (Paglicci 23) and in all the people who had contact with the sample since its discovery in 2003. The Paglicci 23 sequence, determined through the analysis of 152 clones, is the Cambridge reference sequence, and cannot possibly reflect contamination because it differs from all potentially contaminating modern sequences. The Paglicci 23 individual carried a mtDNA sequence that is still common in Europe, and which radically differs from those of the almost contemporary Neandertals, demonstrating a genealogical continuity across 28,000 years, from Cro-Magnoid to modern Europeans. Because all potential sources of modern DNA contamination are known, the Paglicci 23 sample will offer a unique opportunity to get insight for the first time into the nuclear genes of early modern Europeans.

Potential Effects of Oilseed Rape Expressing Oryzacystatin-1 (OC-1) and of Purified Insecticidal Proteins on Larvae of the Solitary Bee Osmia bicornis:

Despite their importance as pollinators in crops and wild plants, solitary bees have not previously been included in non-target testing of insect-resistant transgenic crop plants. Larvae of many solitary bees feed almost exclusively on pollen and thus could be highly exposed to transgene products expressed in the pollen. The potential effects of pollen from oilseed rape expressing the cysteine protease inhibitor oryzacystatin-1 (OC-1) were investigated on larvae of the solitary bee Osmia bicornis ( = O. rufa). Furthermore, recombinant OC-1 (rOC-1), the Bt toxin Cry1Ab and the snowdrop lectin Galanthus nivalis agglutinin (GNA) were evaluated for effects on the life history parameters of this important pollinator. Pollen provisions from transgenic OC-1 oilseed rape did not affect overall development. Similarly, high doses of rOC-1 and Cry1Ab as well as a low dose of GNA failed to cause any significant effects. However, a high dose of GNA (0.1%) in the larval diet resulted in significantly increased development time and reduced efficiency in conversion of pollen food into larval body weight. Our results suggest that OC-1 and Cry1Ab expressing transgenic crops would pose a negligible risk for O. bicornis larvae, whereas GNA expressing plants could cause detrimental effects, but only if bees were exposed to high levels of the protein. The described bioassay with bee brood is not only suitable for early tier non-target tests of transgenic plants, but also has broader applicability to other crop protection products.

Molecular Characterization of the Gastrula in the Turtle Emys orbicularis: An Evolutionary Perspective on Gastrulation:

Due to the presence of a blastopore as in amphibians, the turtle has been suggested to exemplify a transition form from an amphibian- to an avian-type gastrulation pattern. In order to test this hypothesis and gain insight into the emergence of the unique characteristics of amniotes during gastrulation, we have performed the first molecular characterization of the gastrula in a reptile, the turtle Emys orbicularis. The study of Brachyury, Lim1, Otx2 and Otx5 expression patterns points to a highly conserved dynamic of expression with amniote model organisms and makes it possible to identify the site of mesoderm internalization, which is a long-standing issue in reptiles. Analysis of Brachyury expression also highlights the presence of two distinct phases, less easily recognizable in model organisms and respectively characterized by an early ring-shaped and a later bilateral symmetrical territory. Systematic comparisons with tetrapod model organisms lead to new insights into the relationships of the blastopore/blastoporal plate system shared by all reptiles, with the blastopore of amphibians and the primitive streak of birds and mammals. The biphasic Brachyury expression pattern is also consistent with recent models of emergence of bilateral symmetry, which raises the question of its evolutionary significance.

Female Dominance over Males in Primates: Self-Organisation and Sexual Dimorphism:

The processes that underlie the formation of the dominance hierarchy in a group are since long under debate. Models of self-organisation suggest that dominance hierarchies develop by the self-reinforcing effects of winning and losing fights (the so-called winner-loser effect), but according to ‘the prior attribute hypothesis’, dominance hierarchies develop from pre-existing individual differences, such as in body mass. In the present paper, we investigate the relevance of each of these two theories for the degree of female dominance over males. We investigate this in a correlative study in which we compare female dominance between groups of 22 species throughout the primate order. In our study female dominance may range from 0 (no female dominance) to 1 (complete female dominance). As regards ‘the prior attribute hypothesis’, we expected a negative correlation between female dominance over males and species-specific sexual dimorphism in body mass. However, to our surprise we found none (we use the method of independent contrasts). Instead, we confirm the self-organisation hypothesis: our model based on the winner-loser effect predicts that female dominance over males increases with the percentage of males in the group. We confirm this pattern at several levels in empirical data (among groups of a single species and between species of the same genus and of different ones). Since the winner-loser effect has been shown to work in many taxa including humans, these results may have broad implications.

Diversity and Evolution of Coral Fluorescent Proteins:

GFP-like fluorescent proteins (FPs) are the key color determinants in reef-building corals (class Anthozoa, order Scleractinia) and are of considerable interest as potential genetically encoded fluorescent labels. Here we report 40 additional members of the GFP family from corals. There are three major paralogous lineages of coral FPs. One of them is retained in all sampled coral families and is responsible for the non-fluorescent purple-blue color, while each of the other two evolved a full complement of typical coral fluorescent colors (cyan, green, and red) and underwent sorting between coral groups. Among the newly cloned proteins are a “chromo-red” color type from Echinopora forskaliana (family Faviidae) and pink chromoprotein from Stylophora pistillata (Pocilloporidae), both evolving independently from the rest of coral chromoproteins. There are several cyan FPs that possess a novel kind of excitation spectrum indicating a neutral chromophore ground state, for which the residue E167 is responsible (numeration according to GFP from A. victoria). The chromoprotein from Acropora millepora is an unusual blue instead of purple, which is due to two mutations: S64C and S183T. We applied a novel probabilistic sampling approach to recreate the common ancestor of all coral FPs as well as the more derived common ancestor of three main fluorescent colors of the Faviina suborder. Both proteins were green such as found elsewhere outside class Anthozoa. Interestingly, a substantial fraction of the all-coral ancestral protein had a chromohore apparently locked in a non-fluorescent neutral state, which may reflect the transitional stage that enabled rapid color diversification early in the history of coral FPs. Our results highlight the extent of convergent or parallel evolution of the color diversity in corals, provide the foundation for experimental studies of evolutionary processes that led to color diversification, and enable a comparative analysis of structural determinants of different colors.

Does Sex-Selective Predation Stabilize or Destabilize Predator-Prey Dynamics?:

Little is known about the impact of prey sexual dimorphism on predator-prey dynamics and the impact of sex-selective harvesting and trophy hunting on long-term stability of exploited populations. We review the quantitative evidence for sex-selective predation and study its long-term consequences using several simple predator-prey models. These models can be also interpreted in terms of feedback between harvesting effort and population size of the harvested species under open-access exploitation. Among the 81 predator-prey pairs found in the literature, male bias in predation is 2.3 times as common as female bias. We show that long-term effects of sex-selective predation depend on the interplay of predation bias and prey mating system. Predation on the ‘less limiting’ prey sex can yield a stable predator-prey equilibrium, while predation on the other sex usually destabilizes the dynamics and promotes population collapses. For prey mating systems that we consider, males are less limiting except for polyandry and polyandrogyny, and male-biased predation alone on such prey can stabilize otherwise unstable dynamics. On the contrary, our results suggest that female-biased predation on polygynous, polygynandrous or monogamous prey requires other stabilizing mechanisms to persist. Our modelling results suggest that the observed skew towards male-biased predation might reflect, in addition to sexual selection, the evolutionary history of predator-prey interactions. More focus on these phenomena can yield additional and interesting insights as to which mechanisms maintain the persistence of predator-prey pairs over ecological and evolutionary timescales. Our results can also have implications for long-term sustainability of harvesting and trophy hunting of sexually dimorphic species.

Influenza Virus in Human Exhaled Breath: An Observational Study:

Recent studies suggest that humans exhale fine particles during tidal breathing but little is known of their composition, particularly during infection. We conducted a study of influenza infected patients to characterize influenza virus and particle concentrations in their exhaled breath. Patients presenting with influenza-like-illness, confirmed influenza A or B virus by rapid test, and onset within 3 days were recruited at three clinics in Hong Kong, China. We collected exhaled breath from each subject onto Teflon filters and measured exhaled particle concentrations using an optical particle counter. Filters were analyzed for influenza A and B viruses by quantitative polymerase chain reaction (qPCR). Twelve out of thirteen rapid test positive patients provided exhaled breath filter samples (7 subjects infected with influenza B virus and 5 subjects infected with influenza A virus). We detected influenza virus RNA in the exhaled breath of 4 (33%) subjects-three (60%) of the five patients infected with influenza A virus and one (14%) of the seven infected with influenza B virus. Exhaled influenza virus RNA generation rates ranged from <3.2 to 20 influenza virus RNA particles per minute. Over 87% of particles exhaled were under 1 µm in diameter. These findings regarding influenza virus RNA suggest that influenza virus may be contained in fine particles generated during tidal breathing, and add to the body of literature suggesting that fine particle aerosols may play a role in influenza transmission.

Major Histocompatibility Complex Based Resistance to a Common Bacterial Pathogen of Amphibians:

Given their well-developed systems of innate and adaptive immunity, global population declines of amphibians are particularly perplexing. To investigate the role of the major histocompatibilty complex (MHC) in conferring pathogen resistance, we challenged Xenopus laevis tadpoles bearing different combinations of four MHC haplotypes (f, g, j, and r) with the bacterial pathogen Aeromonas hydrophila in two experiments. In the first, we exposed ff, fg, gg, gj, and jj tadpoles, obtained from breeding MHC homozygous parents, to one of three doses of A. hydrophila or heat-killed bacteria as a control. In the second, we exposed ff, fg, fr, gg, rg, and rr tadpoles, obtained from breeding MHC heterozygous parents and subsequently genotyped by PCR, to A. hydrophila, heat-killed bacteria or media alone as controls. We thereby determined whether the same patterns of MHC resistance emerged within as among families, independent of non-MHC heritable differences. Tadpoles with r or g MHC haplotypes were more likely to die than were those with f or j haplotypes. Growth rates varied among MHC types, independent of exposure dose. Heterozygous individuals with both susceptible and resistant haplotypes were intermediate to either homozygous genotype in both size and survival. The effect of the MHC on growth and survival was consistent between experiments and across families. MHC alleles differentially confer resistance to, or tolerance of, the bacterial pathogen, which affects tadpoles’ growth and survival.

Evaluating the Influence of Epidemiological Parameters and Host Ecology on the Spread of Phocine Distemper Virus through Populations of Harbour Seals:

Outbreaks of phocine distemper virus (PDV) in Europe during 1988 and 2002 were responsible for the death of around 23,000 and 30,000 harbour seals, respectively. These epidemics, particularly the one in 2002, provided an unusual opportunity to estimate epidemic parameters for a wildlife disease. There were marked regional differences in the values of some parameters both within and between epidemics. We used an individual-based model of seal movement that allowed us to incorporate realistic representations of space, time and animal behaviour into a traditional epidemiological modelling framework. We explored the potential influence of a range of ecological (foraging trip duration, time of epidemic onset, population size) and epidemiological (length of infectious period, contact rate between infectious and susceptible individuals, case mortality) parameters on four readily-measurable epidemic characteristics (number of dead individuals, duration of epidemic, peak mortality date and prevalence) and on the probability that an epidemic would occur in a particular region. We analysed the outputs as if they were the results of a series of virtual experiments, using Generalised Linear Modelling. All six variables had a significant effect on the probability that an epidemic would be recognised as an unusual mortality event by human observers. Regional and temporal variation in contact rate was the most likely cause of the observed differences between the two epidemics. This variation could be a consequence of differences in the way individuals divide their time between land and sea at different times of the year.

Seventeen New Complete mtDNA Sequences Reveal Extensive Mitochondrial Genome Evolution within the Demospongiae:

Two major transitions in animal evolution-the origins of multicellularity and bilaterality-correlate with major changes in mitochondrial DNA (mtDNA) organization. Demosponges, the largest class in the phylum Porifera, underwent only the first of these transitions and their mitochondrial genomes display a peculiar combination of ancestral and animal-specific features. To get an insight into the evolution of mitochondrial genomes within the Demospongiae, we determined 17 new mtDNA sequences from this group and analyzing them with five previously published sequences. Our analysis revealed that all demosponge mtDNAs are 16- to 25-kbp circular molecules, containing 13-15 protein genes, 2 rRNA genes, and 2-27 tRNA genes. All but four pairs of sampled genomes had unique gene orders, with the number of shared gene boundaries ranging from 1 to 41. Although most demosponge species displayed low rates of mitochondrial sequence evolution, a significant acceleration in evolutionary rates occurred in the G1 group (orders Dendroceratida, Dictyoceratida, and Verticillitida). Large variation in mtDNA organization was also observed within the G0 group (order Homosclerophorida) including gene rearrangements, loss of tRNA genes, and the presence of two introns in Plakortis angulospiculatus. While introns are rare in modern-day demosponge mtDNA, we inferred that at least one intron was present in cox1 of the common ancestor of all demosponges. Our study uncovered an extensive mitochondrial genomic diversity within the Demospongiae. Although all sampled mitochondrial genomes retained some ancestral features, including a minimally modified genetic code, conserved structures of tRNA genes, and presence of multiple non-coding regions, they vary considerably in their size, gene content, gene order, and the rates of sequence evolution. Some of the changes in demosponge mtDNA, such as the loss of tRNA genes and the appearance of hairpin-containing repetitive elements, occurred in parallel in several lineages and suggest general trends in demosponge mtDNA evolution.

Willingness of Men Who Have Sex with Men (MSM) in the United States to Be Circumcised as Adults to Reduce the Risk of HIV Infection:

Circumcision reduces HIV acquisition among heterosexual men in Africa, but it is unclear if circumcision may reduce HIV acquisition among men who have sex with men (MSM) in the United States, or whether MSM would be willing to be circumcised if recommended. We interviewed presumed-HIV negative MSM at gay pride events in 2006. We asked uncircumcised respondents about willingness to be circumcised if it were proven to reduce risk of HIV among MSM and perceived barriers to circumcision. Multivariate logistic regression was used to identify covariates associated with willingness to be circumcised. Of 780 MSM, 133 (17%) were uncircumcised. Of these, 71 (53%) were willing to be circumcised. Willingness was associated with black race (exact odds ratio [OR]: 3.4, 95% confidence interval [CI]: 1.3-9.8), non-injection drug use (OR: 6.1, 95% CI: 1.8-23.7) and perceived reduced risk of penile cancer (OR: 4.7, 95% CI: 2.0-11.9). The most commonly endorsed concerns about circumcision were post-surgical pain and wound infection. Over half of uncircumcised MSM, especially black MSM, expressed willingness to be circumcised. Perceived risks and benefits of circumcision should be a part of educational materials if circumcision is recommended for MSM in the United States.

Forty Years Trends in Timing of Pubertal Growth Spurt in 157,000 Danish School Children:

Entering puberty is an important milestone in reproductive life and secular changes in the timing of puberty may be an important indicator of the general reproductive health in a population. Too early puberty is associated with several psychosocial and health problems. The aim of our study was to determine if the age at onset of pubertal growth spurt (OGS) and at peak height velocity (PHV) during puberty show secular trends during four decades in a large cohort of school children. Annual measurements of height were available in all children born from 1930 to 1969 who attended primary school in the Copenhagen Municipality. 135,223 girls and 21,612 boys fulfilled the criteria for determining age at OGS and age at PHV. These physiological events were used as markers of pubertal development in our computerized method in order to evaluate any secular trends in pubertal maturation during the study period (year of birth 1930 to 1969). In this period, age at OGS declined statistically significantly by 0.2 and 0.4 years in girls and boys, respectively, whereas age at PHV declined statistically significantly by 0.5 and 0.3 years in girls and boys, respectively. The decline was non-linear with a levelling off in the children born between 1940 and 1955. The duration of puberty, as defined by the difference between age at OGS and age at PHV, increased slightly in boys, whereas it decreased in girls. Our finding of declining age at OGS and at PHV indicates a secular trend towards earlier sexual maturation of Danish children born between 1930 and 1969. Only minor changes were observed in duration of puberty assessed by the difference in ages at OGS and PHV.

Two Extinct Flying Reptiles Compared: One Was A Glider, The Other A Parachutist:

Archaeopteryx is famous as the world’s oldest bird, but reptiles were flying about some 50 million years earlier than that (225 million years ago), even before large dinosaurs roamed the Earth. A new study of extinct reptiles called kuehneosaurs, by scientists from the University of Bristol, England, shows that these early flyers used extraordinary extensions of their ribs to form large gliding surfaces on the side of the body.

Marsupials And Humans Share Same Genetic Imprinting That Evolved 150 Million Years Ago:

Research published in Nature Genetics by a team of international scientists including the University of Melbourne, Department of Zoology, has established an identical mechanism of genetic imprinting, a process involved in marsupial and human fetal development, which evolved 150 million years ago.

Men And Women Are Programmed Differently When It Comes To Temptation:

Temptation may be everywhere, but it’s how the different sexes react to flirtation that determines the effect it will have on their relationships. In a new study, psychologists determined men tend to look at their partners in a more negative light after meeting a single, attractive woman. On the other hand, women are likelier to work to strengthen their current relationships after meeting an available, attractive man.

Snake Venom Tells Tales About Geography:

Just as people give away their origins by that southern drawl or New England twang, poisonous snakes produce venom that differs distinctly from one geographic area to another, the first study of the “snake venomics” of one of the most common pit vipers in Latin America has found.

Big Predatory Mammals Such As Felines Need Between 5 And 7 Different Types Of Prey To Meet Their Dietary Needs:

Faced with earlier studies stating that the big predators such as tigers, lions, and lynxes fulfil their dietary needs by eating one or two types of prey, scientists from the University of Malaga assure us now that felines need from 5 to 7 different types of prey to fulfil their dietary needs, although they may be more specialised anatomically than the canines (wolves, dogs) who can obtain 100% ingested biomass by eating three types of prey.

Mystery Insect Found In London’s Natural History Museum’s Wildlife Garden:

An insect, not seen in the UK before, has been discovered living in the Natural History Museum’s Wildlife Garden. The tiny bug is baffling insect experts at the Museum who are still trying to identify the mystery newcomer.

Understanding Hearing, Molecule By Molecule:

Berkeley Lab scientists have for the first time pieced together the three-dimensional structure of one of nature’s most exquisite pieces of machinery, a gossamer-like filament of proteins in the inner ear that enables the sense of hearing and balance.

Marine Worm’s Jaws Say ‘Cutting-edge New Aerospace Materials’:

Researchers in California and New Hampshire report the first detailed characterization of the protein composition of the hard, fang-like jaws of a common marine worm. Their work could lead to the design of a new class of super-strong, lightweight materials for use as construction and repair materials for spacecraft, airplanes, and other applications.

Apples And Pears Contain Pathways To ‘Breathe’:

Pears and apples contain air pathways to “breathe”. The pathways are microscopically small structures for oxygen supply and are key elements in determining the fruit’s health. Researchers from the Catholic University of Leuven in Belgium and the European Synchrotron Radiation Facility (ESRF) have visualized them for the first time, therefore proving their hypothesized existence.

Scientists Discover Key Patterns In The Packaging Of Genes:

Although every cell of our bodies contains the same genetic instructions, specific genes typically act only in specific cells at particular times. Other genes are “silenced” in a variety of ways. One mode of gene silencing depends upon the way DNA, the genetic material, is packed in the nucleus of cells.

Monday – the day when PLoS Medicine and PLoS Biology publish new articles, among others, these:
Persistent Leatherback Turtle Migrations Present Opportunities for Conservation :

Highly migratory marine animals routinely cross international borders during extensive migrations over thousands of kilometers, thus requiring conservation strategies with information about habitat use and movement patterns. Critically endangered leatherback turtles (Dermochelys coriacea) in the eastern Pacific have suffered a severe population decline in recent years. In this study, we present the largest multi-year satellite tracking data set for leatherback turtles (n = 46 turtles, 12,095 days) to describe the migrations, habitats, and dispersal of female leatherbacks tagged at Playa Grande, Costa Rica. Leatherbacks followed a migration corridor southward from Costa Rica into the South Pacific Gyre in each year of our study. In the equatorial region, leatherbacks experienced strong ocean currents that influenced the direction of their movements; leatherbacks responded to current deflection with rapid, directed movements to maintain their southward heading. After passing through this equatorial current field, turtles dispersed broadly within a low-energy, low-productivity region of the South Pacific. Our analyses revealed that ocean currents shaped the migration corridor and influenced the scope of turtle dispersal in the South Pacific–results that provide a biological rationale for the development of multi-scale conservation strategies. These strategies could involve improved and enhanced monitoring of leatherback-fisheries interactions as well as dynamic time-area fisheries closures and protected area designations within the high seas of the South Pacific.

Next Stop, Don’t Block the Doors: Opening Up Access to Clinical Trials Results:

2008 has been a good year for access to research. Effective New Year’s Day, both the Canadian Institutes of Health Research [1] and the Howard Hughes Medical Institute [2] require publicly accessible archiving of papers published by their grantees. Also in January, the European Research Council announced its European Union-wide open-access mandate [3]. In February, the Harvard Faculty of Arts and Sciences voted to give the University a worldwide license to exercise copyright in each faculty member’s scholarly articles for the purpose of making these articles freely available [4]; Harvard Law School committed to mandatory free access in May [5]. In March, the European University Association endorsed open-access repositories [6], and in April the United States National Institutes of Health Public Access Policy [7] took effect, bringing America’s leading sponsor of biomedical research into the impressive circle of agencies that require archiving of papers resulting from the research they fund. Judging by the ever-increasing number of submissions to PLoS journals, authors appear to be voting with their manuscripts for open access to research.

Controlling Size in Multicellular Organs: Focus on the Leaf:

Leaf size depends on cell number and size. However, leaves are not simply the sum of cell size and number; rather, they are under the control of an unknown, organ-wide integration system. The existence of such a system is strongly suggested by two mysterious phenomena: compensation and high-ploidy syndrome. Compensation is characterized by cell enlargement triggered by a significant decrease in cellular proliferation, while plants with high-ploidy syndrome have more than eight sets of homologous chromosomes (8C), resulting in an increase in cell volume, but smaller leaves. Determining the mechanisms underlying these phenomena will provide important insight into the mechanism of multicellular organogenesis.

Considering the First Steps toward a Stable and Orderly Way of Bacterial Life:

Bacteria are small unicellular organisms who could well enjoy a bohemian life–moving independently wherever and whenever they want to and existing with no regard for conventional rules of behavior. In spite of this apparent freedom, most bacteria abandon their footloose lifestyle as soon as they come into contact with a surface. Irrespective of whether the surface is of biotic or abiotic origin, they clinch to it, forgoing independence in favor of settling down. Similar to animals that gather in flocks and people who live in societies, surface-attached microbes can form networks as multicellular communities called biofilms. Bacterial biofilms are heterogeneous structures of increasing complexity that consist of differently specialized cells enclosed in a self-produced polymeric matrix associated with the surface.

Who Dares Sings, And Who Sings Wins: Bold Birds Get The Girl:

Humans often choose partners based on behavioural keys that are displayed during social interactions. The way we behave in different social contexts can reflect personality traits or temperament that may inspire long-term love. Behavioural norms that we perceive as sexually attractive are not culturally or evolutionarily arbitrary.

Disproving Conventional Wisdom On Diversity Of Marine Fossils And Extinction Rates:

It took a decade of painstaking study, the cooperation of hundreds of researchers, and a database of more than 200,000 fossil records, but John Alroy thinks he’s disproved much of the conventional wisdom about the diversity of marine fossils and extinction rates.

New Mode Of Gene Regulation Discovered In Mammals:

Researchers at the University of California, Santa Cruz, have discovered a type of gene regulation never before observed in mammals — a “ribozyme” that controls the activity of an important family of genes in several different species.

RNA Emerges From DNA’s Shadow:

RNA, the transporter of genetic information within the cell, has emerged from the shadow of DNA to become one of the hottest research areas of molecular biology, with implications for many diseases as well as understanding of evolution. But the field is complex, requiring access to the latest equipment and techniques of imaging, gene expression analysis and bioinformatics, as well as cross-pollination between multiple scientific disciplines.

Biodiversity Defensing Against Climate Change:

Climate change is happening, and we must develop ways for all life to be able to cope, environmental advocates urge. WWF Vietnam Programme is looking at this through the development of resilient multifunctional landscapes that also work as forest corridors, assisting with species dispersal and adaptation, by changes in land-use practices.

Will Our Future Brains Be Smaller?:

The speed at which we react to threatening situations can have life or death implications. In the more primitive past, it could have meant escaping a wild animal; today it might mean swerving to avoid a head-on car crash. It has been thought for some years that mammals have two decision-making systems in their brains which operate at different speeds to cope with different situations. New research from the University of Bristol supports this theory and has shown that the evolutionary pressures arising from the older, faster, but less accurate, part of the brain may have shaped the more recent development of the slower-acting but more precise cortex, found in humans and higher animals.

I was busy, so I did not have time to take a look until now at what is new this week in PLoS Genetics, Computational Biology, Pathogens and Neglected Tropical Diseases. Go take a look at these papers and others:
Evolution of Evolvability in Gene Regulatory Networks:

A cell receives signals both from its internal and external environment and responds by changing the expression of genes. In this manner the cell adjusts to heat, osmotic pressures and other circumstances during its lifetime. Over long timescales, the network of interacting genes and its regulatory actions also undergo evolutionary adaptation. Yet how do such networks evolve and become adapted?
In this paper we describe the study of a simple model of gene regulatory networks, focusing solely on evolutionary adaptation. We let a population of individuals evolve, while the external environment changes through time. To ensure evolution is the only source of adaptation, we do not provide the individuals with a sensor to the environment. We show that the interplay between the long-term process of evolution and short-term gene regulation dynamics leads to a striking increase in the efficiency of creating well-adapted offspring. Beneficial mutations become more frequent, nevertheless robustness to the majority of mutations is maintained. Thus we demonstrate a clear example of the evolution of evolvability.

Domestic Pigs Have Low Susceptibility to H5N1 Highly Pathogenic Avian Influenza Viruses:

Highly pathogenic avian influenza A viruses of H5N1 subtype have spread through Eurasia and Africa with continuing cases of human infection, suggesting the potential to become a pandemic influenza virus. Pigs which are susceptible to infection with both human and avian influenza A viruses are one of the natural hosts where a pandemic virus could be produced. In this study, we characterized in a pig model the infection caused by four H5N1 virus strains isolated from humans, poultry and wild birds. We demonstrated that exposure of pigs through the nose with H5N1 viruses or consumption of meat from infected chickens resulted in infection with mild weight loss. In contrast to mouse and ferret animal models where some of viruses were highly pathogenic and replicated in multiple organs, replication of H5N1 viruses in pigs was restricted to the respiratory tract, mainly to the lungs, and tonsils. Mild to moderate bronchiolitis and pneumonia were observed in the lungs of infected animals. Our results demonstrated that domestic pigs had low susceptibility to infection and disease with highly pathogenic H5N1 influenza A viruses.

Zebrafish Whole-Adult-Organism Chemogenomics for Large-Scale Predictive and Discovery Chemical Biology:

To understand chemical-induced biological responses/effects, it is important to have large-scale and rapid capacity to investigate gene expression changes caused by chemical compounds at genome-wide scale in an adult vertebrate model; this capability is essential for drug development and toxicology. Small aquarium fish with vast genomic resources, such as zebrafish, will probably be the only vertebrate models that allow for cost-effective, large-scale, genome-wide determination of gene expression net changes in the entire adult organism in response to a chemical compound. Presently, such a whole adult organism approach is only feasible in invertebrate models such as the worm and fly, and not in rodent models, hence the usefulness of such an approach has not been demonstrated in a vertebrate. By using two classes of chemicals with wide implications to human health, we showed that capturing net changes of gene expression at a genome-wide scale in an entire adult zebrafish is useful for predicting toxicity and chemical classes, for discovering biomarkers and major signaling pathways, as well as for inferring human health risk and new biological insights. Our study provides a new approach for genome-wide investigation of chemical-induced biological responses/effects in a whole adult vertebrate that can benefit the drug discovery process and chemical toxicity testing for environmental health risk inference.

Unraveling Protein Networks with Power Graph Analysis:

Networks play a crucial role in biology and are often used as a way to represent experimental results. Yet, their analysis and representation is still an open problem. Recent experimental and computational progress yields networks of increased size and complexity. There are, for example, small- and large-scale interaction networks, regulatory networks, genetic networks, protein-ligand interaction networks, and homology networks analyzed and published regularly. A common way to access the information in a network is though direct visualization, but this fails as it often just results in “fur balls” from which little insight can be gathered. On the other hand, clustering techniques manage to avoid the problems caused by the large number of nodes and even larger number of edges by coarse-graining the networks and thus abstracting details. But these also fail, since, in fact, much of the biology lies in the details. This work presents a novel methodology for analyzing and representing networks. Power Graphs are a lossless representation of networks, which reduces network complexity by explicitly representing re-occurring network motifs. Moreover, power graphs can be clearly visualized: they compress up to 90% of the edges in biological networks and are applicable to all types of networks such as protein interaction, regulatory networks, or homology networks.

Children Are Naturally Prone To Be Empathic And Moral:

Children between the ages of seven and 12 appear to be naturally inclined to feel empathy for others in pain, according to researchers at the University of Chicago, who used functional Magnetic Resonance Imaging (fMRI) scans to study responses in children.

Scientists Identify Genetic Basis For The Black Sheep Of The Family:

Coat color of wild and domestic animals is a critical trait that has significant biological and economic impact. Researchers have now identified the genetic basis for black coat color, and white, in a breed of domestic sheep.

Insect Warning Colors Aid Cancer And Tropical Disease Drug Discovery:

Brightly colored beetles or butterfly larvae nibbling on a plant may signal the presence of chemical compounds active against cancer cell lines and tropical parasitic diseases, according to researchers at Smithsonian’s Tropical Research Institute in Panama. Such clues could speed drug discovery and provide insight into the ecological relationships between tropical-forest plants and insects that feed on them.

Molecular Motor Works By Detecting Minute Changes In Force:

Researchers at the University of Pennsylvania School of Medicine discovered that the activity of a specific family of nanometer-sized molecular motors called myosin-I is regulated by force. The motor puts tension on cellular springs that allow vibrations to be detected within the body. This finely tuned regulation has important implications for understanding a wide variety of basic cellular processes, including hearing and balance and glucose uptake in response to insulin. The findings appear in the most recent issue of Science.

Weight Gain In Adolescent Girls: Role Of Internet, Alcohol And Sleep:

Girls moving through adolescence may experience unhealthy levels of weight gain, but the reasons for this are not always clear. In fact, many potential causes of weight gain are easily overlooked. A new study analyzes the effect of Internet usage, sleep, and alcohol and coffee consumption on weight gain in adolescent girls.

Verbally Aggressive Mothers Direct Their Children’s Behavior:

A new study reveals that verbally aggressive (VA) mothers tend to control their children’s choice of activities as well as use physical negative touch, along with directives, when trying to alter their child’s actions.

Report Calls For Expansion Of Professional Science Master’s Degree Programs:

Policymakers, universities, and employers should work together to speed the development of professionally oriented master’s degree programs in the natural sciences, says a new report from the National Research Council. Graduates of these programs — which build both scientific knowledge and practical workplace skills — can make a strong contribution to the nation’s competitiveness, said the committee that wrote the report.

Decadent, Convenient Banana Dessert Débuted At Food Expo:

Who doesn’t like a banana split? Fresh fruit, three flavors of ice cream and chocolate syrup. Yum. That vision was the subjective basis for a new product developed by a team of Virginia Tech students – frozen bite-sized slices of banana filled with creamy chocolate, vanilla, or strawberry non-fat frozen yogurt and enrobed in dark chocolate. Called “Banana Splitters,” the new confection is packaged as nine individual pieces – three of each flavor – in a sleeve, six sleeves in a package to be available next to the ice cream and other frozen goodies. And, get this, an entire sleeve is a serving.

Superfast Vocal Muscles In Songbirds: Hundred Times Faster Than Blink Of An Eye:

Certain songbirds can contract their vocal muscles 100 times faster than humans can blink an eye — placing the birds with a handful of animals that have evolved superfast muscles, University of Utah researchers found.

Reducing Global Warming And Working For Common Good: What Inspires Collective Cooperation?:

No one enjoys paying taxes. Even so, we need taxes if we want our streets clean, a proper public health care system, an educated population or the maintenance of Earth’s climate within habitable boundaries. This is what scientists commonly refer as public goods — benefits that everyone receives whether or not they contribute to them. The missing link between paying and benefiting from a public good creates an obvious dilemma and temptation to cheat (not to cooperate): Why shouldn’t I let the others pay for it?

Avatars As Communicators Of Emotions:

Current interactive systems enable users to communicate with computers in many ways, but not taking into account emotional communication. A PhD thesis presented at the University of the Basque Country puts forward the use of avatars or virtual Internet personages as an efficient form of non-verbal communication, principally focusing on emotional aspects.

Why Musicians Make Us Weep And Computers Don’t:

Music can soothe the savage breast much better if played by musicians rather than clever computers, according to a new University of Sussex-led study.

Scientists Generally Happy With Their Media Interaction:

Scientists and journalists get along much better than the anecdotal ‘horror stories’ would lead us to believe, according to new research published today in the journal Science, which has found that 57% of researchers were ‘mostly pleased’ with their media interaction, while only 6% percent were ‘mostly dissatisfied’.

Learning To Talk To Teens About Sex — While At Work:

Sex is one of the most difficult topics a parent can bring up with an adolescent, but a new study finds that parents who are taught specific communication skills can more readily tackle these conversations and sustain them over time.

Gender, Time Of Day Affect Response To Vaccination:

A new study reveals that men, but not women, vaccinated in the morning produced a better peak antibody response to both hepatitis A and the influenza strain. ———- Men vaccinated in the morning showed the strongest immune response. Almost twice as many men showed a twofold increase in antibody response when vaccinated in the morning as opposed to the afternoon.