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Duck-billed Dinosaurs Outgrew Predators To Survive:

With long limbs and a soft body, the duck-billed hadrosaur had few defenses against predators such as tyrannosaurs. But new research on the bones of this plant-eating dinosaur suggests that it had at least one advantage: It grew to adulthood much faster than its predators, giving it superiority in size.

Massive Numbers Of Critically Endangered Western Lowland Gorillas Discovered In Republic Of Congo:

The world’s population of critically endangered western lowland gorillas recently received a huge boost when the Wildlife Conservation Society released a census showing massive numbers of these secretive great apes alive and well in the Republic of Congo.

Less REM Sleep Associated With Being Overweight Among Children And Teens:

Children and teens who get less sleep, especially those who spend less time in rapid eye movement (REM) sleep, may be more likely to be overweight, according to a new report.

Why The Slow-Paced World Could Make It Difficult To Catch A Ball:

BBSRC researchers at the University of Birmingham have uncovered new information about the way that we perceive fast moving, incoming objects – such as tennis or cricket balls.

Why Some Smokers Become Addicted With Their First Cigarette:

New research from The University of Western Ontario reveals how the brain processes the ‘rewarding’ and addictive properties of nicotine, providing a better understanding of why some people seemingly become hooked with their first smoke.

Acidification Of Sea Hampers Reproduction Of Marine Species:

By absorbing carbon dioxide from the atmosphere, and from the human use of fossil fuels, the world’s seas function as a giant buffer for the Earth’s life support system. The chemical balance of the sea has long been regarded as immovable.

Next Generation Tool For Visualizing Genomic Data Introduced:

Researchers are collecting vast amounts of diverse genomic data with ever-increasing speed, but effective ways to visualize these data in an integrated manner have lagged behind the ability to generate them.

Hot Peppers Really Do Bring The Heat:

Chili peppers can do more than just make you feel hot; the active chemical in peppers can directly induce thermogenesis, the process by which cells convert energy into heat, according to a new study.

Female Guppies Risk Death To Avoid Sexual Harassment:

Sexual harassment from male guppies is so bad that long-suffering females will risk their lives to escape it, according to new research from Dr Safi Darden and Dr Darren Croft from Bangor University.

There are 69 new articles in PLoS ONE this week. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. Here are my own picks for the week – you go and look for your own favourites:
Comparison of Pattern Detection Methods in Microarray Time Series of the Segmentation Clock:

While genome-wide gene expression data are generated at an increasing rate, the repertoire of approaches for pattern discovery in these data is still limited. Identifying subtle patterns of interest in large amounts of data (tens of thousands of profiles) associated with a certain level of noise remains a challenge. A microarray time series was recently generated to study the transcriptional program of the mouse segmentation clock, a biological oscillator associated with the periodic formation of the segments of the body axis. A method related to Fourier analysis, the Lomb-Scargle periodogram, was used to detect periodic profiles in the dataset, leading to the identification of a novel set of cyclic genes associated with the segmentation clock. Here, we applied to the same microarray time series dataset four distinct mathematical methods to identify significant patterns in gene expression profiles. These methods are called: Phase consistency, Address reduction, Cyclohedron test and Stable persistence, and are based on different conceptual frameworks that are either hypothesis- or data-driven. Some of the methods, unlike Fourier transforms, are not dependent on the assumption of periodicity of the pattern of interest. Remarkably, these methods identified blindly the expression profiles of known cyclic genes as the most significant patterns in the dataset. Many candidate genes predicted by more than one approach appeared to be true positive cyclic genes and will be of particular interest for future research. In addition, these methods predicted novel candidate cyclic genes that were consistent with previous biological knowledge and experimental validation in mouse embryos. Our results demonstrate the utility of these novel pattern detection strategies, notably for detection of periodic profiles, and suggest that combining several distinct mathematical approaches to analyze microarray datasets is a valuable strategy for identifying genes that exhibit novel, interesting transcriptional patterns.

Response Properties of the Auditory Telencephalon in Songbirds Change with Recent Experience and Season:

The caudomedial nidopallium (NCM) is a telencephalic auditory area that is selectively activated by conspecific vocalizations in zebra finches and canaries. We recently demonstrated that temporal and spectral dynamics of auditory tuning in NCM differ between these species [1]. In order to determine whether these differences reflect recent experience, we exposed separate groups of each species and sex to different housing conditions. Adult birds were housed either in an aviary with conspecifics (NORM), with heterospecifics (canary subjects in a zebra finch aviary, and vice versa: (CROSS)), or in isolation (ISO) for 9 days prior to testing. We then recorded extracellular multi-unit electrophysiological responses to simple pure tone stimuli (250-5000 Hz) in awake birds from each group and analyzed auditory tuning width using methods from our earlier studies. Relative to NORM birds, tuning was narrower in CROSS birds, and wider in ISO birds. The trend was greater in canaries, especially females. The date of recording was also included as a covariate in ANCOVAs that analyzed a larger set of the canary data, including data from birds tested outside of the breeding season, and treated housing condition and sex as independent variables. These tests show that tuning width was narrower early in the year and broader later. This effect was most pronounced in CROSS males. The degree of the short-term neural plasticity described here differs across sexes and species, and may reflect differences in NCM’s anatomical and functional organization related to species differences in song characteristics, adult plasticity and/or social factors. More generally, NCM tuning is labile and may be modulated by recent experience to reflect the auditory processing required for behavioral adaptation to the current acoustic, social or seasonal context.

Consumption of Bt Maize Pollen Expressing Cry1Ab or Cry3Bb1 Does Not Harm Adult Green Lacewings, Chrysoperla carnea (Neuroptera: Chrysopidae):

Adults of the common green lacewing, Chrysoperla carnea (Stephens) (Neuroptera: Chrysopidae), are prevalent pollen-consumers in maize fields. They are therefore exposed to insecticidal proteins expressed in the pollen of insect-resistant, genetically engineered maize varieties expressing Cry proteins derived from Bacillus thuringiensis (Bt). Laboratory experiments were conducted to evaluate the impact of Cry3Bb1 or Cry1Ab-expressing transgenic maize (MON 88017, Event Bt176) pollen on fitness parameters of adult C. carnea. Adults were fed pollen from Bt maize varieties or their corresponding near isolines together with sucrose solution for 28 days. Survival, pre-oviposition period, fecundity, fertility and dry weight were not different between Bt or non-Bt maize pollen treatments. In order to ensure that adults of C. carnea are not sensitive to the tested toxins independent from the plant background and to add certainty to the hazard assessment, adult C. carnea were fed with artificial diet containing purified Cry3Bb1 or Cry1Ab at about a 10 times higher concentration than in maize pollen. Artificial diet containing Galanthus nivalis agglutinin (GNA) was included as a positive control. No differences were found in any life-table parameter between Cry protein containing diet treatments and control diet. However, the pre-oviposition period, daily and total fecundity and dry weight of C. carnea were significantly negatively affected by GNA-feeding. In both feeding assays, the stability and bioactivity of Cry proteins in the food sources as well as the uptake by C. carnea was confirmed. These results show that adults of C. carnea are not affected by Bt maize pollen and are not sensitive to Cry1Ab and Cry3Bb1 at concentrations exceeding the levels in pollen. Consequently, Bt maize pollen consumption will pose a negligible risk to adult C. carnea.

Three-Dimensional Analysis of Vascular Development in the Mouse Embryo:

Key vasculogenic (de-novo vessel forming) and angiogenic (vessel remodelling) events occur in the mouse embryo between embryonic days (E) 8.0 and 10.0 of gestation, during which time the vasculature develops from a simple circulatory loop into a complex, fine structured, three-dimensional organ. Interpretation of vascular phenotypes exhibited by signalling pathway mutants has historically been hindered by an inability to comprehensively image the normal sequence of events that shape the basic architecture of the early mouse vascular system. We have employed Optical Projection Tomography (OPT) using frequency distance relationship (FDR)-based deconvolution to image embryos immunostained with the endothelial specific marker PECAM-1 to create a high resolution, three-dimensional atlas of mouse vascular development between E8.0 and E10.0 (5 to 30 somites). Analysis of the atlas has provided significant new information regarding normal development of intersomitic vessels, the perineural vascular plexus, the cephalic plexus and vessels connecting the embryonic and extraembryonic circulation. We describe examples of vascular remodelling that provide new insight into the mechanisms of sprouting angiogenesis, vascular guidance cues and artery/vein identity that directly relate to phenotypes observed in mouse mutants affecting vascular development between E8.0 and E10.0. This atlas is freely available at http://www.mouseimaging.ca/research/mouse_atlas.html and will serve as a platform to provide insight into normal and abnormal vascular development.

Characterization of a Nonclassical Class I MHC Gene in a Reptile, the Galápagos Marine Iguana (Amblyrhynchus cristatus):

Squamates are a diverse order of vertebrates, representing more than 7,000 species. Yet, descriptions of full-length major histocompatibility complex (MHC) genes in this group are nearly absent from the literature, while the number of MHC studies continues to rise in other vertebrate taxa. The lack of basic information about MHC organization in squamates inhibits investigation into the relationship between MHC polymorphism and disease, and leaves a large taxonomic gap in our understanding of amniote MHC evolution. Here, we use both cDNA and genomic sequence data to characterize a class I MHC gene (Amcr-UA) from the Galápagos marine iguana, a member of the squamate subfamily Iguaninae. Amcr-UA appears to be functional since it is expressed in the blood and contains many of the conserved peptide-binding residues that are found in classical class I genes of other vertebrates. In addition, comparison of Amcr-UA to homologous sequences from other iguanine species shows that the antigen-binding portion of this gene is under purifying selection, rather than balancing selection, and therefore may have a conserved function. A striking feature of Amcr-UA is that both the cDNA and genomic sequences lack the transmembrane and cytoplasmic domains that are necessary to anchor the class I receptor molecule into the cell membrane, suggesting that the product of this gene is secreted and consequently not involved in classical class I antigen-presentation. The truncated and conserved character of Amcr-UA lead us to define it as a nonclassical gene that is related to the few available squamate class I sequences. However, phylogenetic analysis placed Amcr-UA in a basal position relative to other published classical MHC genes from squamates, suggesting that this gene diverged near the beginning of squamate diversification.

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Novel Kind Of Learning Gene Discovered:

Scientists at the Freie Universität Berlin have come one step closer to unraveling the molecular basis of learning. A team led by neurobiologist Björn Brembs has discovered the first gene for operant conditioning in the fruit fly Drosophila.

Family Type Has Less-than-expected Impact On Parental Involvement, Study Finds:

Children in step-families and in other non-traditional families get just as much quality time with their parents as those in traditional families, with only a few exceptions, according to research to be presented at the annual meeting of the American Sociological Association today.

Homeownership In Disadvantaged Neighborhoods Linked To Increased Political Participation:

Homeowners in disadvantaged neighborhoods are more likely to vote than renters and those who own homes in more privileged communities, according to research to be presented at the annual meeting of the American Sociological Association (ASA).

Teacher-student Relationships Key To Learning Health And Sex Education:

When it comes to learning life-changing behaviors in high school health classes, the identity of the person teaching may be even more important than the curriculum, a new study suggests.

Paradox Of Higher Education, Crime: Male College Students More Likely Than Less-educated Peers To Commit Property Crimes, Study Finds:

Men who attend college are more likely to commit property crimes during their college years than their non-college-attending peers, according to research to be presented at the annual meeting of the American Sociological Association.

New Role Found For A ‘Foxy Old Gene’:

Researchers at the University of Pennsylvania School of Medicine have discovered that a protein called FOXA2 controls genes that maintain the proper level of bile in the liver. FOXA2 may become the focus for new therapies to treat diseases that involve the regulation of bile salts. The study was published online this week in Nature Medicine.

Extinction Threat To Monkeys And Other Primates Due To Habitat Loss, Hunting:

Mankind’s closest relatives – the world’s monkeys, apes and other primates – are disappearing from the face of the Earth, with some literally being eaten into extinction.

Memory, Depression, Insomnia — And Worms?:

Researchers have spent decades probing the causes of depression, schizophrenia and insomnia in humans. But a new study may have uncovered key insights into the origins of these and other conditions by examining a most unlikely research subject: worms.

Little Teeth Suggest Big Jump In Primate Timeline:

Tiny fossilized teeth excavated from an Indian open-pit coal mine could be the oldest Asian remains ever found of anthropoids, the primate lineage of today’s monkeys, apes and humans, say researchers from Duke University and the Indian Institute of Technology.

It’s Monday afternoon, time to take a look at the brand new articles in PLoS Medicine and PLoS Biology:
Tasting the Bitter Sunlight:

Have you ever had that gut reaction to your surroundings, some physical sensation that something isn’t quite right? Maybe a squirmy, uneasy feeling in your stomach or an acrid taste on your tongue that makes you want to leave the scene? When the nematode C. elegans encounters an offensive sensation–whether a pungent, potentially dangerous odor (such as those associated with fungal parasites), extreme temperature, or the poking probe of a researcher–it wastes no time in making a hasty retreat. Researchers have elucidated the mechanisms of avoidance in these tiny worms to remarkable molecular and cellular detail (a much clearer picture than the often mysterious avoidance behaviors of humans).
In a new study, Stacey L. Edwards, Kenneth G. Miller, and colleagues expand the level of our understanding by describing a striking new behavior and mechanism of sensory detection for these microscopic animals. They demonstrate that short-wavelength light, such as blue-violet and ultraviolet (UV), is a potent avoidance cue, stimulating a robust acceleration of locomotion when the tail or body is illuminated, while head illumination drives reversal locomotion. After identifying and characterizing this new behavior, Edwards et al. used classic forward genetics (whereby animals are mutagenized and screened for defective phenotypes) to identify mutants that are unresponsive to UV light. Surprisingly, the mutations mapped to a gene that encodes a protein unrelated to any of the known phototransduction systems in nature. The authors named this new protein LITE-1 and showed that it functions as a UV light receptor. Interestingly, LITE-1 is related to the large family of insect Gustatory receptors that mediate taste responses. The closest homology is to that of fly Gustatory receptors, which detect water-soluble sugars and carbon dioxide.

Can a Topical Microbicide Prevent Rectal HIV Transmission?:

Animal models are critical tools for the preclinical evaluation of drugs. Yet in the HIV field, the value of such models for predicting the success of preventive drug and vaccination strategies in humans has been disappointing. For example, animal models were unable to predict the failure of vaginal microbicides in large clinical trials in humans [1,2]. However, two recently published studies have provided encouraging results. Using a repeat, low-dose exposure macaque model, Walid Heneine and colleagues found that systemic pre-exposure prophylaxis (PrEP), using a combination of the nucleoside analogue reverse transcriptase inhibitors emtricitabine and tenofovir, protected macaques against rectal challenge with simian HIV [3]. Most prior macaque studies used single high-dose virus challenges, which are less representative of viral exposure in humans. Another study by J. Victor Garcia and colleagues introduced an improved mouse model of vaginal HIV transmission [4]. Mice engineered to stably exhibit extensive infiltration of organs and tissues, including the female reproductive tract, with a broad range of human blood cells were protected from intravaginal HIV infection by PrEP with emtricitabine/tenofovir. This mouse model opened the way for larger-scale comparative assessments in vivo, which is impossible in macaques due to the prohibitively high costs.
A third key study by Martin Cranage and colleagues is published in this issue of PLoS Medicine [5]. The researchers investigated whether rectal simian immunodeficiency virus (SIV) transmission in macaques could be prevented by the topical pre-exposure application of tenofovir gel. Rectal SIV or HIV challenge bears a much higher transmission probability than vaginal challenge. With some caveats, as discussed further below, successful prevention of rectal transmission is therefore likely to have a better predictive value for human trials than vaginal challenge models. Moreover, anal intercourse in heterosexual populations has been underestimated in the past, and means to prevent rectal HIV transmission are thus urgently needed for both women and men who have unprotected anal intercourse.

Sleep Apnea Linked To Increased Risk Of Death:

Sleep-disordered breathing (also known as sleep apnea) is associated with an increased risk of death, according to new results from the Wisconsin Sleep Cohort, an 18-year observational study supported by the National Heart, Lung, and Blood Institute (NHLBI) of the National Institutes of Health.

World’s Smallest Snake Found In Barbados:

The world’s smallest species of snake, with adults averaging just under four inches in length, has been identified on the Caribbean island of Barbados. The species — which is as thin as a spaghetti noodle and small enough to rest comfortably on a U.S. quarter –was discovered by Blair Hedges, an evolutionary biologist at Penn State.

Long Work Hours Widen The Gender Gap:

Working overtime has a disproportionate impact on women in dual-earner households, exacerbating gender inequality and supporting the “separate sphere” phenomenon in which men are the breadwinners while women tend to the home, according to research to be presented at the annual meeting of the American Sociological Association.

Australian Bird Research Could Rewrite ‘Ring Theory’ Of Speciation:

New research has uncovered how different populations of the bird crimson rosella are related to each other – a discovery which has important implications for research into how climate change may affect Australia’s biodiversity.

Plant Parasite ‘Wiretaps’ Host:

A parasitic plant that sucks water and nutrients from its plant host also taps into its communications traffic, a new report finds. The research could lead to new ways to combat parasites that attack crop plants.

Fungi Expert Finds New Species In Aberdeen City Centre, Scotland:

A leading fungi expert has accidentally stumbled upon a new species in Scotland – as he walked home from work.

Cellular Symmetry: What Cues Tell A Cell To Divide At The Center:

Cells are intrinsically artistic. When the right signals tell a cell to divide, it usually splits down the middle, resulting in two identical daughter cells. (Stem cells are the exception to the rule.) This natural symmetry is visible on the macroscopic scale as well. All living creatures, be they mushrooms or humans, are visibly symmetric, a product of our cells’ preference for equilibrium.

Emerging Scientific Discipline Of Aeroecology:

Aeroecology is the emerging discipline for studying how airborne organisms — birds, bats, arthropods and microbes — depend on the support of the lower atmosphere that is closest to the Earth’s surface.

Fruit-fly Study Adds Weight To Theories About Another Type Of Adult Stem Cell:

It turns out that an old dog – or at least an old fruit-fly cell – can learn new tricks. Researchers at the Stanford University School of Medicine have found that mature, specialized cells naturally regress to serve as a kind of de facto stem cell during the fruit-fly life cycle.

Brain Plays Key Role In Appetite By Regulating Free Radicals:

Researchers at Yale School of Medicine have found the brain’s appetite center uses fat for fuel by involving oxygen free radicals–molecules associated with aging and neurodegeneration. The findings, reported in the journal Nature, suggest that antioxidants could play a role in weight control.

How ‘Hidden Mutations’ Contribute To HIV Drug Resistance:

One of the major reasons that treatment for HIV/AIDS often doesn’t work as well as it should is resistance to the drugs involved. Now, scientists at McGill University have revealed how mutations hidden in previously ignored parts of the HIV genome play an important role in the development of drug resistance in AIDS patients.