Category Archives: Science News

Do Animals Think Like Autistic Savants?:

When Temple Grandin argued that animals and autistic savants share cognitive similarities in her best-selling book Animals in Translation (2005), the idea gained steam outside the community of cognitive neuroscientists. Grandin, a professor of animal science whose best-selling books have provided an unprecedented look at the autistic mind, says her autism gives her special insight into the inner workings of the animal mind. She based her proposal on the observation that animals, like autistic humans, sense and respond to stimuli that nonautistic humans usually overlook.

Antarctic Life Hung By A Thread During Ice Ages:

Frozen in time… frozen in place… frozen solid… All of these phrases have been used to describe Antarctica, and yet they all belie the truth about this southerly point on the globe. Although the area is covered in ice and bears witness to some of the most extreme cold on the planet, this ecosystem is dynamic, not static, and change here has always been dramatic and intense. A report published in the March issue of Ecology argues that the extreme cold and environmental conditions of past Ice Ages have been even more severe than seen today and changed life at the Antarctic, forcing the migration of many animals such as penguins, whales and seals. Understanding the changes of the past may help scientists to determine how the anticipated temperature increases of the future will work to further transform this continent.

Evolutionary History Of SARS Supports Bats As Virus Source:

Scientists who have studied the genome of the virus that caused severe acute respiratory syndrome (SARS) say their comparisons to related viruses offer new evidence that the virus infecting humans originated in bats.

Fish Devastated By Sex-changing Chemicals In Municipal Wastewater:

While most people understand the dangers of flushing toxic chemicals into the ecosystem through municipal sewer systems, one potentially devastating threat to wild fish populations comes from an unlikely source: estrogen. After an exhaustive seven-year research effort, Canadian biologists found that miniscule amounts of estrogen present in municipal wastewater discharges can decimate wild fish populations living downstream.

Sleep Apnea Doubles Car Crash Risk, Study Shows:

People with sleep apnea — a breathing disorder that disrupts sleep — are at double the risk of being in a car crash, a new study by Vancouver Coastal Health Research Institute and University of British Columbia respirologists finds.

There are 50 new articles in PLoS ONE this week – here are some of my picks for you to check out (and post comments, ratings, etc.):
Clocking the Lyme Spirochete:

In order to clear the body of infecting spirochetes, phagocytic cells must be able to get hold of them. In real-time phase-contrast videomicroscopy we were able to measure the speed of Borrelia burgdorferi (Bb), the Lyme spirochete, moving back and forth across a platelet to which it was tethered. Its mean crossing speed was 1,636 µm/min (N = 28), maximum, 2800 µm/min (N = 3). This is the fastest speed recorded for a spirochete, and upward of two orders of magnitude above the speed of a human neutrophil, the fastest cell in the body. This alacrity and its interpretation, in an organism with bidirectional motor capacity, may well contribute to difficulties in spirochete clearance by the host.

Measuring the Meltdown: Drivers of Global Amphibian Extinction and Decline:

Habitat loss, climate change, over-exploitation, disease and other factors have been hypothesised in the global decline of amphibian biodiversity. However, the relative importance of and synergies among different drivers are still poorly understood. We present the largest global analysis of roughly 45% of known amphibians (2,583 species) to quantify the influences of life history, climate, human density and habitat loss on declines and extinction risk. Multi-model Bayesian inference reveals that large amphibian species with small geographic range and pronounced seasonality in temperature and precipitation are most likely to be Red-Listed by IUCN. Elevated habitat loss and human densities are also correlated with high threat risk. Range size, habitat loss and more extreme seasonality in precipitation contributed to decline risk in the 2,454 species that declined between 1980 and 2004, compared to species that were stable (n = 1,545) or had increased (n = 28). These empirical results show that amphibian species with restricted ranges should be urgently targeted for conservation.

Revealing Historic Invasion Patterns and Potential Invasion Sites for Two Non-Native Plant Species:

The historical spatio-temporal distribution of invasive species is rarely documented, hampering efforts to understand invasion dynamics, especially at regional scales. Reconstructing historical invasions through use of herbarium records combined with spatial trend analysis and modeling can elucidate spreading patterns and identify susceptible habitats before invasion occurs. Two perennial species were chosen to contrast historic and potential phytogeographies: Japanese knotweed (Polygonum cuspidatum), introduced intentionally across the US; and mugwort (Artemisia vulgaris), introduced largely accidentally to coastal areas. Spatial analysis revealed that early in the invasion, both species have a stochastic distribution across the contiguous US, but east of the 90th meridian, which approximates the Mississippi River, quickly spread to adjacent counties in subsequent decades. In contrast, in locations west of the 90th meridian, many populations never spread outside the founding county, probably a result of encountering unfavorable environmental conditions. Regression analysis using variables categorized as environmental or anthropogenic accounted for 24% (Japanese knotweed) and 30% (mugwort) of the variation in the current distribution of each species. Results show very few counties with high habitat suitability (≥80%) remain un-invaded (5 for Japanese knotweed and 6 for mugwort), suggesting these perennials are reaching the limits of large-scale expansion. Despite differences in initial introduction loci and pathways, Japanese knotweed and mugwort demonstrate similar historic patterns of spread and show declining rates of regional expansion. Invasion mitigation efforts should be concentrated on areas identified as highly susceptible that border invaded regions, as both species demonstrate secondary expansion from introduction loci.

Healthy Lifestyle Behaviour Decreasing Risks of Being Bullied, Violence and Injury:

Bullying and violence are problems of aggression in schools among adolescents. Basic daily healthy practices including nutritious diet, hygiene and physical activity are common approaches in comprehensive health promotion programs in school settings, however thier relationship to these aggressive behaviours is vague. We attempted to show the advantages of these healthy lifestyle behaviours in 9 developing countries by examining the association with being frequently bullied, violence and injury. A cross-sectional cross-national survey of 9 countries using the WHO Global School Based Student Health Survey dataset was used. Measurements included experiences of “being frequently bullied” in the preceding 30 days and violence/injury in the past 12 months. Association of risk behaviours (smoking, alcohol, sexual behaviour) and healthy lifestyle (nutrition, hygiene practices, physical activity) to being bullied, and violence/injury were assessed using multivariate logistic regression. Hygiene behaviour showed lower risks of being frequently bullied [male: RR = 0.7 (97.5CI: 0.5, 0.9); female: RR = 0.6 (0.5, 0.8)], and lower risk of experiences of violence/injury [RR = 0.7 (0.5, 0.9) for males], after controlling for risk behaviours, age, education, poverty, and country. Healthy lifestyle showed an association to decreased relative risk of being frequently bullied and violence/injury in developing countries. A comprehensive approach to risk and health promoting behaviours reducing bullying and violence is encouraged at school settings.

Shrimps Down Under: Evolutionary Relationships of Subterranean Crustaceans from Western Australia (Decapoda: Atyidae: Stygiocaris):

We investigated the large and small scale evolutionary relationships of the endemic Western Australian subterranean shrimp genus Stygiocaris (Atyidae) using nuclear and mitochondrial genes. Stygiocaris is part of the unique cave biota of the coastal, anchialine, limestones of the Cape Range and Barrow Island, most of whose nearest evolutionary relations are found in coastal caves of the distant North Atlantic. The dominance of atyids in tropical waters and their food resources suggest they are pivotal in understanding these groundwater ecosystems. Our nuclear and mitochondrial analyses all recovered the Mexican cave genus Typhlatya as the sister taxon of Stygiocaris, rather than any of the numerous surface and cave atyids from Australia or the Indo-Pacific region. The two described Stygiocaris species were recovered as monophyletic, and a third, cryptic, species was discovered at a single site, which has very different physiochemical properties from the sites hosting the two described species. Our findings suggest that Stygiocaris and Typhlatya may descend from a common ancestor that lived in the coastal marine habitat of the ancient Tethys Sea, and were subsequently separated by plate tectonic movements. This vicariant process is commonly thought to explain the many disjunct anchialine faunas, but has rarely been demonstrated using phylogenetic techniques. The Cape Range’s geological dynamism, which is probably responsible for the speciation of the various Stygiocaris species, has also led to geographic population structure within species. In particular, Stygiocaris lancifera is split into northern and southern groups, which correspond to population splits within other sympatric subterranean taxa.

Poor Reporting of Scientific Leadership Information in Clinical Trial Registers:

In September 2004, the International Committee of Medical Journal Editors (ICMJE) issued a Statement requiring that all clinical trials be registered at inception in a public register in order to be considered for publication. The World Health Organization (WHO) and ICMJE have identified 20 items that should be provided before a trial is considered registered, including contact information. Identifying those scientifically responsible for trial conduct increases accountability. The objective is to examine the proportion of registered clinical trials providing valid scientific leadership information. We reviewed clinical trial entries listing Canadian investigators in the two largest international and public trial registers, the International Standard Randomized Controlled Trial Number (ISRCTN) register, and ClinicalTrials.gov. The main outcome measures were the proportion of clinical trials reporting valid contact information for the trials’ Principal Investigator (PI)/Co-ordinating Investigator/Study Chair/Site PI, and trial e-mail contact address, stratified by funding source, recruiting status, and register. A total of 1388 entries (142 from ISRCTN and 1246 from ClinicalTrials.gov) comprised our sample. We found non-compliance with mandatory registration requirements regarding scientific leadership and trial contact information. Non-industry and partial industry funded trials were significantly more likely to identify the individual responsible for scientific leadership (OR = 259, 95% CI: 95-701) and to provide a contact e-mail address (OR = 9.6, 95% CI: 6.6-14) than were solely industry funded trials. Despite the requirements set by WHO and ICMJE, data on scientific leadership and contact e-mail addresses are frequently omitted from clinical trials registered in the two leading public clinical trial registers. To promote accountability and transparency in clinical trials research, public clinical trials registers should ensure adequate monitoring of trial registration to ensure completion of mandatory contact information fields identifying scientific leadership

Transparent Meta-Analysis of Prospective Memory and Aging:

Prospective memory (ProM) refers to our ability to become aware of a previously formed plan at the right time and place. After two decades of research on prospective memory and aging, narrative reviews and summaries have arrived at widely different conclusions. One view is that prospective memory shows large age declines, larger than age declines on retrospective memory (RetM). Another view is that prospective memory is an exception to age declines and remains invariant across the adult lifespan. The present meta-analysis of over twenty years of research settles this controversy. It shows that prospective memory declines with aging and that the magnitude of age decline varies by prospective memory subdomain (vigilance, prospective memory proper, habitual prospective memory) as well as test setting (laboratory, natural). Moreover, this meta-analysis demonstrates that previous claims of no age declines in prospective memory are artifacts of methodological and conceptual issues afflicting prior research including widespread ceiling effects, low statistical power, age confounds, and failure to distinguish between various subdomains of prospective memory (e.g., vigilance and prospective memory proper).

The Effect of Inappropriate Calibration: Three Case Studies in Molecular Ecology:

Time-scales estimated from sequence data play an important role in molecular ecology. They can be used to draw correlations between evolutionary and palaeoclimatic events, to measure the tempo of speciation, and to study the demographic history of an endangered species. In all of these studies, it is paramount to have accurate estimates of time-scales and substitution rates. Molecular ecological studies typically focus on intraspecific data that have evolved on genealogical scales, but often these studies inappropriately employ deep fossil calibrations or canonical substitution rates (e.g., 1% per million years for birds and mammals) for calibrating estimates of divergence times. These approaches can yield misleading estimates of molecular time-scales, with significant impacts on subsequent evolutionary and ecological inferences. We illustrate this calibration problem using three case studies: avian speciation in the late Pleistocene, the demographic history of bowhead whales, and the Pleistocene biogeography of brown bears. For each data set, we compare the date estimates that are obtained using internal and external calibration points. In all three cases, the conclusions are significantly altered by the application of revised, internally-calibrated substitution rates. Collectively, the results emphasise the importance of judicious selection of calibrations for analyses of recent evolutionary events.

A Non-Human Primate Model for Gluten Sensitivity:

Gluten sensitivity is widespread among humans. For example, in celiac disease patients, an inflammatory response to dietary gluten leads to enteropathy, malabsorption, circulating antibodies against gluten and transglutaminase 2, and clinical symptoms such as diarrhea. There is a growing need in fundamental and translational research for animal models that exhibit aspects of human gluten sensitivity. Using ELISA-based antibody assays, we screened a population of captive rhesus macaques with chronic diarrhea of non-infectious origin to estimate the incidence of gluten sensitivity. A selected animal with elevated anti-gliadin antibodies and a matched control were extensively studied through alternating periods of gluten-free diet and gluten challenge. Blinded clinical and histological evaluations were conducted to seek evidence for gluten sensitivity. When fed with a gluten-containing diet, gluten-sensitive macaques showed signs and symptoms of celiac disease including chronic diarrhea, malabsorptive steatorrhea, intestinal lesions and anti-gliadin antibodies. A gluten-free diet reversed these clinical, histological and serological features, while reintroduction of dietary gluten caused rapid relapse. Gluten-sensitive rhesus macaques may be an attractive resource for investigating both the pathogenesis and the treatment of celiac disease.

Colouration and Colour Changes of the Fiddler Crab, Uca capricornis: A Descriptive Study:

Colour changes in animals may be triggered by a variety of social and environmental factors and may occur over a matter of seconds or months. Crustaceans, like fiddler crabs (genus Uca), are particularly adept at changing their colour and have been the focus of numerous studies. However, few of these studies have attempted to quantitatively describe the individual variation in colour and pattern or their adaptive significance. This paper quantitatively describes the colour patterns of the fiddler crab Uca capricornis and their ability to change on a socially significant timescale. The most dramatic changes in colour pattern are associated with moulting. These ontogenetic changes result in a general reduction of the colour pattern with increasing size, although females are more colourful and variable than similarly-sized males. Uca capricornis are also capable of rapid colour changes in response to stress, but show no endogenous rhythms associated with the semilunar and tidal cycles commonly reported in other fiddler crabs. The extreme colour polymorphism and the relative stability of the colour patterns in Uca capricornis are consistent with their use in visually mediated mate recognition.

Early Development of the Central and Peripheral Nervous Systems Is Coordinated by Wnt and BMP Signals:

The formation of functional neural circuits that process sensory information requires coordinated development of the central and peripheral nervous systems derived from neural plate and neural plate border cells, respectively. Neural plate, neural crest and rostral placodal cells are all specified at the late gastrula stage. How the early development of the central and peripheral nervous systems are coordinated remains, however, poorly understood. Previous results have provided evidence that at the late gastrula stage, graded Wnt signals impose rostrocaudal character on neural plate cells, and Bone Morphogenetic Protein (BMP) signals specify olfactory and lens placodal cells at rostral forebrain levels. By using in vitro assays of neural crest and placodal cell differentiation, we now provide evidence that Wnt signals impose caudal character on neural plate border cells at the late gastrula stage, and that under these conditions, BMP signals induce neural crest instead of rostral placodal cells. We also provide evidence that both caudal neural and caudal neural plate border cells become independent of further exposure to Wnt signals at the head fold stage. Thus, the status of Wnt signaling in ectodermal cells at the late gastrula stage regulates the rostrocaudal patterning of both neural plate and neural plate border, providing a coordinated spatial and temporal control of the early development of the central and peripheral nervous systems.

Identical Twins Not As Identical As Believed:

Contrary to our previous beliefs, identical twins are not genetically identical. This surprising finding may be of great significance for research on hereditary diseases and for the development of new diagnostic methods. How can it be that one identical twin might develop Parkinson’s disease, for instance, but not the other? Until now, the reasons have been sought in environmental factors. The current study complicates the picture.

Genome Of Marine Organism Tells Of Humans’ Unicellular Ancestors:

The newly sequenced genome of a one-celled, planktonic marine organism, reported Feb. 14 in the journal Nature, is already telling scientists about the evolutionary changes that accompanied the jump from one-celled life forms to multicellular animals like ourselves.

Fruit Flies Show Surprising Sophistication In Locating Food Source:

To a fruit fly, a piece of rotting fruit or the food in your picnic basket is a little slice of heaven. It’s where the tiny animal–not much more than a speck on your fingertip can find food and a mate, the two passions of its short, two-month lifespan. But the odor plume of a food source can be very slight, subject to the vagaries of wind and other weather, in a world that looms large to this tiny bug. Yet the fly is uncanny in finding a meal. How? By using more than just its sense of smell.

Oral Contraceptives Could Work For Dogs, Cats, Pigs, Maybe Even Deer And Coyotes:

If you’re a land owner and animals such as coyotes or wild pigs are driving you hog wild, help may soon be on the way to control their numbers in a humane way — in the form of a birth control pill for animals being developed at Texas A&M University’s College of Veterinary Medicine & Biomedical Sciences. The concept would be to get it to wild animals through baited food, researchers say.

Giant Frog Jumps Continents, May Have Eaten Baby Dinosaurs:

A giant frog fossil from Madagascar dubbed Beelzebufo or ‘the frog from Hell’ has been identified by scientists from UCL (University College London) and Stony Brook University, New York. The discovery of the 70 million year-old fossil frog, of a kind once thought unique to South America, lends weight to a new theory that Madagascar, India and South America were linked until late in the Age of Dinosaurs.

Living Corals Thousands Of Years Old Hold Clues To Past Climate Changes:

New research shows that the second most diverse group of hard corals first evolved in the deep sea, and not in shallow waters. Stylasterids, or lace corals, diversified in deep waters before launching at least three successful invasions of shallow water habitats in the past 30 million years. This finding contradicts a long-established theory that suggests corals and other marine animals all evolved in shallow water before migrating into deeper habitats.

Are Animals Autistic Savants:

Do animals have privileged access to lower level sensory information before it is packaged into concepts, as Temple Grandin has argued for autistic savants? Giorgio Vallortigara and colleagues critique this perspective, and Grandin responds.

see also.
Maternal Death, Autopsy Studies, and Lessons from Pathology:

Clara Menendez and colleagues analyze 139 complete autopsies following maternal deaths in Maputo, Mozambique and find a predominance of infectious and preventable causes. Sebastian Lucas discusses the study in a related perspective.

Cheating Is Easy For The Social Amoeba:

Cheating is easy and seemingly without cost for the social amoeba known as Dictyostelium discoideum, said a team of researchers from Baylor College of Medicine and Rice University in Houston who conducted the first genome-scale search for social genes and found more than 100 mutant genes that allow cheating.

Warming Waters May Make Antarctica Hospitable To Sharks: Potentially Disastrous Consequences:

It has been 40 million years since the waters around Antarctica have been warm enough to sustain populations of sharks and most fish, but they may return this century due to the effects of global warming. If they do, the impact on Antarctic ecology could be serious, according to researchers from the University of Rhode Island.

Predicting The Perfect Predator To Control Invasive Species:

Garlic mustard has become an invasive species in temperate forests across the United States, choking out native plants on forest floors and threatening ecosystem diversity. University of Illinois ecologist Adam Davis has created a computer model that in combination with quarantined research tests he believes will be able to predict the perfect predator — a pest that can be introduced into a forested area that will help reduce the garlic mustard population.

Spider Silk: Protein’s Strength Lies In H-bond Cooperation:

Researchers in Civil and Environmental Engineering at MIT reveal that the strength of a biological material like spider silk lies in the specific geometric configuration of structural proteins, which have small clusters of weak hydrogen bonds that work cooperatively to resist force and dissipate energy.

Peptide Discovered In Scorpion Venom May Hold Key To Secretory Diseases:

Researchers have discovered a peptide in scorpion venom that may hold the key to understanding and controlling cystic fibrosis and other secretory diseases.

Sharks In Peril: Ocean’s Fiercest Predators Now Vulnerable To Extinction:

Sharks are disappearing from the world’s oceans. The numbers of many large shark species have declined by more than half due to increased demand for shark fins and meat, recreational shark fisheries, as well as tuna and swordfish fisheries, where millions of sharks are taken as bycatch each year.

‘Genetic Corridors’ Are Next Step To Saving Tigers:

The Wildlife Conservation Society and the Panthera Foundation announced plans to establish a 5,000 mile-long “genetic corridor” from Bhutan to Burma that would allow tiger populations to roam freely across landscapes. The corridor, first announced at the United Nations on January 30th, would span eight countries and represent the largest block of tiger habitat left on earth.

Direct Democracy In Science May Be Too Much Of A Good Thing:

Publicly funded science in America traditionally is accountable to the people and their government representatives. However, this arrangement raises questions regarding the effect such oversight has on science. It is a problem of particular relevance in this election year, as the nation prepares for the end of the Bush administration, which has taken strong and divisive stances on a number of scientific issues, including stem cell research and global warming.

Physics Explains Why University Rankings Won’t Change:

A Duke University researcher says that his physics theory, which has been applied to everything from global climate to traffic patterns, can also explain another trend: why university rankings tend not to change very much from year to year.

Dung Happens And Helps Scientists: Scoop On Poop And Climate Change:

When scientists around the world think of dung, they think of Jim Mead. Mead, a researcher at Northern Arizona University, is one of the world’s foremost authorities on animal dung, and he’s got the poop to prove it.

Neanderthals Moved From Place To Place, Tooth Analysis Shows:

A 40,000-year-old tooth has provided scientists with the first direct evidence that Neanderthals moved from place to place during their lifetimes. In a collaborative project involving researchers from the Germany, the United Kingdom, and Greece, Professor Michael Richards of the Max Planck institute for Evolutionary Anthropology in Leipzig, Germany and Durham University, UK, and his team used laser technology to collect microscopic particles of enamel from the tooth. By analysing strontium isotope ratios in the enamel – strontium is a naturally occurring metal ingested into the body through food and water – the scientists were able to uncover geological information showing where the Neanderthal had been living when the tooth was formed.

Hare-less: Yellowstone’s Rabbits Have Vanished, Study Says:

A new study by the Bronx Zoo-based Wildlife Conservation Society found that jack rabbits living in the Greater Yellowstone Ecosystem have apparently hopped into oblivion. The study, which appears in the journal Oryx, also speculates that the disappearance of jack rabbits may be having region-wide impacts on a variety of other prey species and their predators.

Extremophile Hunt Begins In Strange Antarctic Lake:

A team of scientists has just left the country to explore a very strange lake in Antarctica; it is filled with, essentially, extra-strength laundry detergent. No, the researchers haven’t spilled coffee on their lab coats. They are hunting for extremophiles — tough little creatures that thrive in conditions too extreme for most other living things.

Tough Breeds Of Livestock Disappearing: Saving Them Before It Is Too Late:

Phil Sponenberg, professor of pathology and genetics in the Virginia-Maryland Regional College of Veterinary Medicine, has spent more than 30 years working to make sure certain living pieces of history — some dating to the 15th century — don’t become extinct. Sponenberg’s brand of living history comes in the form of various rare strains of livestock, which were involved in events like Christopher Columbus’ discovery of the Caribbean Islands and the Spanish conquest of the Americas.

‘V-Frog’ Virtual-Reality Frog Dissection Software Offers First True Physical Simulation:

V-Frog, the world’s first virtual-reality-based frog dissection software designed for biology education — allowing not mere observation, but physically simulated dissection — has been developed and is being marketed by Tactus Technologies.

Sex Differences In The Brain’s Serotonin System:

A new thesis from he Swedish medical university Karolinska Institutet shows that the brain’s serotonin system differs between men and women. The scientists who conducted the study think that they have found one of the reasons why depression and chronic anxiety are more common in women than in men.

New Findings Contradict A Prevailing Belief About The Inner Ear:

A healthy ear emits soft sounds in response to the sounds that travel in. Detectable with sensitive microphones, these otoacoustic emissions help doctors test newborns’ hearing. A deaf ear doesn’t produce these echoes.

Probing Women’s Response To Male Odor:

A single gene determines whether a whiff of androstadienone smells pleasant or foul, or like nothing at all. But researchers who last year discovered this genetic peculiarity were left wondering about its social implications. In an effort to find out, the team has now launched a series of new studies including one that explores a different link: whether women’s perceptions of — and sensitivity to — androstadienone corresponds with their bodies’ physiological responses to it. This follow-up study, which specifically measures indices of emotional arousal and stress in ovulating women exposed to this chemical, a component of male sweat, may help the scientists better understand the role that genes play in social interaction.

Religion Colors Americans’ Views Of Nanotechnology:

Is nanotechnology morally acceptable? For a significant percentage of Americans, the answer is no, according to a recent survey of Americans’ attitudes about the science of the very small. Addressing scientists Feb. 15, 2008 at the annual meeting of the American Association for the Advancement of Science, Dietram Scheufele, a University of Wisconsin-Madison professor of life sciences communication, presented new survey results that show religion exerts far more influence on public views of technology in the United States than in Europe.

Singing In The Rainforest: Public Vs. Private Signaling By A Tropical Rainforest Bird:

According to the Chinese proverb, a bird sings because it has a song, not because it has an answer. A team of French and Brazilian researchers, however, may have the answer as to how the song of Brazilian white-browed warbler has become so well-adapted to the acoustic properties of the rainforest environment.

New Meat-eating Dinosaur Duo From Sahara Ate Like Hyenas, Sharks:

Two new 110 million-year-old dinosaurs unearthed in the Sahara Desert highlight the unusual meat-eaters that prowled southern continents during the Cretaceous Period. Named Kryptops and Eocarcharia in a paper appearing this month in the scientific journal Acta Palaeontologica Polonica, the fossils were discovered in 2000 on an expedition led by University of Chicago paleontologist Paul Sereno.

Web Sites Influence Users, Even When They Don’t Communicate Directly:

Web surfers may get more than just the music, videos and news updates they were looking for when they log onto trendy next-generation sites such as Last.fm, YouTube and Digg, according to new research by a University of Illinois business professor. Whether they know it or not, they also could be getting swayed — toward musical genres that stretch their tastes or to video and news clips they might have overlooked without an endorsement by the masses, says business administration professor Mu Xia.

Pioneering Eagle Eye Surgery Removes Cataract, Restores Vision, After Injury:

Surgeons from the University of Glasgow’s Small Animal Hospital have restored the sight of a golden eagle. The bird underwent pioneering eye surgery after it flew into electricity cables badly damaging its eyesight.

Worker Or Queen? Harvester Ant Moms Set Their Daughters’ Fates:

When it comes to deciding what harvester ant daughters will be when they grow up, mother queens hold considerable sway, according to a new study. The researchers report evidence that eggs are predetermined to become workers or queens from the moment they are lain.

Sheep In Human Clothing: Scientists Reveal Our Flock Mentality:

Have you ever arrived somewhere and wondered how you got there? Scientists at the University of Leeds believe they may have found the answer, with research that shows that humans flock like sheep and birds, subconsciously following a minority of individuals. Results from a study at the University of Leeds show that it takes a minority of just five per cent to influence a crowd’s direction – and that the other 95 per cent follow without realising it.

Thousands Of Humans Inhabited New World’s Doorstep For 20,000 Years:

The human journey from Asia to the New World was interrupted by a 20,000 -year layover in Beringia, a once-habitable region that today lies submerged under the icy waters of the Bering Strait. Furthermore, the New World was colonized by approximately 1,000 to 5,000 people – a substantially higher number than the 100 or fewer individuals of previous estimates.

New Technique Makes Tissues Transparent:

If humans had see-through skin like a jellyfish, spotting disease like cancer would be a snap: Just look, and see a tumor form or grow.

New Duck-billed Dinosaur From Mexico Offers Insights Into Ancient Life On West America:

A new species of dinosaur unearthed in Mexico is giving scientists fresh insights into the ancient history of western North America, according to an international research team led by scientists from the Utah Museum of Natural History at the University of Utah.

‘Junk DNA’ Can Explain Origin And Complexity Of Vertebrates, Study Suggests:

Dartmouth College researchers and colleagues from the University of Bristol in the U.K. have traced the beginnings of complex life, i.e. vertebrates, to microRNA, sometimes referred to as ‘junk DNA.’ The researchers argue that the evolution of microRNAs, which regulate gene expression, are behind the origin of early vertebrates.

Unique Mating Photos Of Wild Gorillas Face To Face:

Scientists from the Wildlife Conservation Society and Max Planck Institute for Evolutionary Anthropology have released the first known photographs of gorillas performing face-to-face copulation in the wild. This is the first time that western gorillas have been observed and photographed mating in such a manner.

Some Cases Of Autism May Be Traced To The Immune System Of Mothers During Pregnancy:

New research from the UC Davis M.I.N.D. Institute and Center for Children’s Environmental Health has found that antibodies in the blood of mothers of children with autism bind to fetal brain cells, potentially interrupting healthy brain development. The study authors also found that the reaction was most common in mothers of children with the regressive form of autism, which occurs when a period of typical development is followed by loss of social and/or language skills. The findings raise the possibility that the transfer of maternal antibodies during pregnancy is a risk factor for autism and, at some point, that a prenatal test and treatment could prevent the disorder for some children.

Body Part By Body Part, Sumatran Tigers Are Being Sold Into Extinction:

Laws protecting the critically endangered Sumatran Tiger have failed to prevent tiger body parts being openly sold in Indonesia, according to a new TRAFFIC report. Tiger body parts, including canine teeth, claws, skin pieces, whiskers and bones, were on sale in 10 percent of the 326 retail outlets surveyed during 2006 in 28 cities and towns across Sumatra. Outlets included goldsmiths, souvenir and traditional Chinese medicine shops, and shops selling antique and precious stones.

Dramatic Declines In Wild Salmon Populations Linked To Exposure To Farmed Salmon:

Comparing the survival of wild salmonid populations in areas near salmon farms with unexposed populations reveals a large reduction in survival in the populations reared near salmon farms. Since the late 1970s, salmon aquaculture has grown into a global industry, producing over 1 million tons of salmon per year. However, this solution to globally declining fish stocks has come under increasing fire. In a new study Jennifer Ford and Ransom Myers provide the first evidence on a global scale illustrating systematic declines in wild salmon populations that come into contact with farmed salmon.

Bats Flew First, Developed Echolocation Later, Fossilized Missing Link Shows:

The discovery of a remarkably well-preserved fossil representing the most primitive bat species known to date demonstrates that the animals evolved the ability to fly before they could echolocate. The new species, named Onychonycteris finneyi, was unearthed in 2003 in southwestern Wyoming. Bats represent one of the largest and most diverse orders of mammals, accounting for one-fifth of all living mammal species. The well-preserved condition of the new fossil permitted the scientists to take an unprecedented look at the most primitive known member of the order Chiroptera.

New Warbler-like Bird Discovered In Nepal:

Nepalese scientists have recorded a new subspecies of bird at Koshi Tappu Wildlife Reserve (KTWR) of east Nepal. The bird was identified as Rufous-vented Prinia bringing Nepal’s total bird list to 862 species. The warbler-like bird is known as Prinia burnesii to the scientific community. The new taxon from Nepal is referred to as Nepal Rufous-vented Prinia Prinia burnesii nipalensis.

There are 43 new articles in PLoS ONE this week, and these I find most interesting at first glance – you look around, comment, rate, annotate, send tracbacks….
A Three-Stage Colonization Model for the Peopling of the Americas:

We evaluate the process by which the Americas were originally colonized and propose a three-stage model that integrates current genetic, archaeological, geological, and paleoecological data. Specifically, we analyze mitochondrial and nuclear genetic data by using complementary coalescent models of demographic history and incorporating non-genetic data to enhance the anthropological relevance of the analysis. Bayesian skyline plots, which provide dynamic representations of population size changes over time, indicate that Amerinds went through two stages of growth ≈40,000 and ≈15,000 years ago separated by a long period of population stability. Isolation-with-migration coalescent analyses, which utilize data from sister populations to estimate a divergence date and founder population sizes, suggest an Amerind population expansion starting ≈15,000 years ago. These results support a model for the peopling of the New World in which Amerind ancestors diverged from the Asian gene pool prior to 40,000 years ago and experienced a gradual population expansion as they moved into Beringia. After a long period of little change in population size in greater Beringia, Amerinds rapidly expanded into the Americas ≈15,000 years ago either through an interior ice-free corridor or along the coast. This rapid colonization of the New World was achieved by a founder group with an effective population size of ≈1,000-5,400 individuals. Our model presents a detailed scenario for the timing and scale of the initial migration to the Americas, substantially refines the estimate of New World founders, and provides a unified theory for testing with future datasets and analytic methods.

Singing in the Rain Forest: How a Tropical Bird Song Transfers Information:

How information transmission processes between individuals are shaped by natural selection is a key question for the understanding of the evolution of acoustic communication systems. Environmental acoustics predict that signal structure will differ depending on general features of the habitat. Social features, like individual spacing and mating behavior, may also be important for the design of communication. Here we present the first experimental study investigating how a tropical rainforest bird, the white-browed warbler Basileuterus leucoblepharus, extracts various information from a received song: species-specific identity, individual identity and location of the sender. Species-specific information is encoded in a resistant acoustic feature and is thus a public signal helping males to reach a wide audience. Conversely, individual identity is supported by song features susceptible to propagation: this private signal is reserved for neighbors. Finally, the receivers can locate the singers by using propagation-induced song modifications. Thus, this communication system is well matched to the acoustic constraints of the rain forest and to the ecological requirements of the species. Our results emphasize that, in a constraining acoustic environment, the efficiency of a sound communication system results from a coding/decoding process particularly well tuned to the acoustic properties of this environment.

A Systematic Evaluation of the Impact of STRICTA and CONSORT Recommendations on Quality of Reporting for Acupuncture Trials:

We investigated whether there had been an improvement in quality of reporting for randomised controlled trials of acupuncture since the publication of the STRICTA and CONSORT statements. We conducted a before-and-after study, comparing ratings for quality of reporting following the publication of both STRICTA and CONSORT recommendations. Ninety peer reviewed journal articles reporting the results of acupuncture trials were selected at random from a wider sample frame of 266 papers. Papers published in three distinct time periods (1994-1995, 1999-2000 and 2004-2005) were compared. Assessment criteria were developed directly from CONSORT and STRICTA checklists. Papers were independently assessed for quality of reporting by two assessors, one of whom was blind to information which could have introduced systematic bias (e.g. date of publication). We detected a statistically significant increase in the reporting of CONSORT items for papers published in each time period measured. We did not, however, find a difference between the number of STRICTA items reported in journal articles published before and 3 to 4 years following the introduction of STRICTA recommendations. The results of this study suggest that general standards of reporting for acupuncture trials have significantly improved since the introduction of the CONSORT statement in 1996, but that quality in reporting details specific to acupuncture interventions has yet to change following the more recent introduction of STRICTA recommendations. Wider targeting and revision of the guidelines is recommended.

‘Ant’ and ‘Grasshopper’ Life-History Strategies in Saccharomyces cerevisiae:

From the evolutionary and ecological points of view, it is essential to distinguish between the genetic and environmental components of the variability of life-history traits and of their trade-offs. Among the factors affecting this variability, the resource uptake rate deserves particular attention, because it depends on both the environment and the genetic background of the individuals. In order to unravel the bases of the life-history strategies in yeast, we grew a collection of twelve strains of Saccharomyces cerevisiae from different industrial and geographical origins in three culture media differing for their glucose content. Using a population dynamics model to fit the change of population size over time, we estimated the intrinsic growth rate (r), the carrying capacity (K), the mean cell size and the glucose consumption rate per cell. The life-history traits, as well as the glucose consumption rate, displayed large genetic and plastic variability and genetic-by-environment interactions. Within each medium, growth rate and carrying capacity were not correlated, but a marked trade-off between these traits was observed over the media, with high K and low r in the glucose rich medium and low K and high r in the other media. The cell size was tightly negatively correlated to carrying capacity in all conditions. The resource consumption rate appeared to be a clear-cut determinant of both the carrying capacity and the cell size in all media, since it accounted for 37% to 84% of the variation of those traits. In a given medium, the strains that consume glucose at high rate have large cell size and low carrying capacity, while the strains that consume glucose at low rate have small cell size but high carrying capacity. These two contrasted behaviors may be metaphorically defined as “ant” and “grasshopper” strategies of resource utilization. Interestingly, a strain may be “ant” in one medium and “grasshopper” in another. These life-history strategies are discussed with regards to yeast physiology, and in an evolutionary perspective.

Oil Palm Research in Context: Identifying the Need for Biodiversity Assessment:

Oil palm cultivation is frequently cited as a major threat to tropical biodiversity as it is centered on some of the world’s most biodiverse regions. In this report, Web of Science was used to find papers on oil palm published since 1970, which were assigned to different subject categories to visualize their research focus. Recent years have seen a broadening in the scope of research, with a slight growth in publications on the environment and a dramatic increase in those on biofuel. Despite this, less than 1% of publications are related to biodiversity and species conservation. In the context of global vegetable oil markets, palm oil and soyabean account for over 60% of production but are the subject of less than 10% of research. Much more work must be done to establish the impacts of habitat conversion to oil palm plantation on biodiversity. Results from such studies are crucial for informing conservation strategies and ensuring sustainable management of plantations.

Self-Interest versus Group-Interest in Antiviral Control:

Antiviral agents have been hailed to hold considerable promise for the treatment and prevention of emerging viral diseases like H5N1 avian influenza and SARS. However, antiviral drugs are not completely harmless, and the conditions under which individuals are willing to participate in a large-scale antiviral drug treatment program are as yet unknown. We provide population dynamical and game theoretical analyses of large-scale prophylactic antiviral treatment programs. Throughout we compare the antiviral control strategy that is optimal from the public health perspective with the control strategy that would evolve if individuals make their own, rational decisions. To this end we investigate the conditions under which a large-scale antiviral control program can prevent an epidemic, and we analyze at what point in an unfolding epidemic the risk of infection starts to outweigh the cost of antiviral treatment. This enables investigation of how the optimal control strategy is moulded by the efficacy of antiviral drugs, the risk of mortality by antiviral prophylaxis, and the transmissibility of the pathogen. Our analyses show that there can be a strong incentive for an individual to take less antiviral drugs than is optimal from the public health perspective. In particular, when public health asks for early and aggressive control to prevent or curb an emerging pathogen, for the individual antiviral drug treatment is attractive only when the risk of infection has become non-negligible. It is even possible that from a public health perspective a situation in which everybody takes antiviral drugs is optimal, while the process of individual choice leads to a situation where nobody is willing to take antiviral drugs.

Phenotypic Evolutionary Models in Stem Cell Biology: Replacement, Quiescence, and Variability:

Phenotypic evolutionary models have been used with great success in many areas of biology, but thus far have not been applied to the study of stem cells except for investigations of cancer. We develop a framework that allows such modeling techniques to be applied to stem cells more generally. The fundamental modeling structure is the stochastic kinetics of stem cells in their niche and of transit amplifying and fully differentiated cells elsewhere in the organism, with positive and negative feedback. This formulation allows graded signals to be turned into all or nothing responses, and shows the importance of looking beyond the niche for understanding how stem cells behave. Using the deterministic version of this framework, we show how competition between different stem cell lines can be analyzed, and under what circumstances stem cells in a niche will be replaced by other stem cells with different phenotypic characteristics. Using the stochastic version of our framework and state dependent life history theory, we show that the optimal behavior of a focal stem cell will involve long periods of quiescence and that a population of identical stem cells will show great variability in the times at which activity occurs; we compare our results with classic ones on quiescence and variability in the hematopoietic system.

Shorter Telomeres May Mark Early Risk of Dementia: Preliminary Analysis of 62 Participants from the Nurses’ Health Study:

Dementia takes decades to develop, and effective prevention will likely require early intervention. Thus, it is critical to identify biomarkers of preclinical disease, allowing targeting of high-risk subjects for preventive efforts. Since telomeres shorten with age and oxidative stress, both of which are important contributors to the onset of dementia, telomere length might be a valuable biomarker. Among 62 participants of the Nurses’ Health Study, we conducted neurologic evaluations, including patient and caregiver interviews, physical exam, neurologic exam, and neuropsychologic testing. We also conducted magnetic resonance imaging (MRI) in a sample of 29 of these women. In these preliminary data, after adjustment for numerous health and lifestyle factors, we found that truncated telomeres in peripheral blood leukocytes segregate with preclinical dementia states, including mild cognitive impairment (MCI); the odds of MCI were 12-fold higher (odds ratio = 12.00, 95% confidence interval 1.24-116.5) for those with shorter telomere length compared to longer telomere length. In addition, decreasing telomere length was strongly related to decreasing hippocampal volume (p = 0.038). These preliminary data suggest that telomere length may be a possible early marker of dementia risk, and merits further study in large, prospective investigations.

Coordination of Cell Polarity during Xenopus Gastrulation:

Cell polarity is an essential feature of animal cells contributing to morphogenesis. During Xenopus gastrulation, it is known that chordamesoderm cells are polarized and intercalate each other allowing anterior-posterior elongation of the embryo proper by convergent extension (CE). Although it is well known that the cellular protrusions at both ends of polarized cells exert tractive force for intercalation and that PCP pathway is known to be essential for the cell polarity, little is known about what triggers the cell polarization and what the polarization causes to control intracellular events enabling the intercalation that leads to the CE. In our research, we used EB3 (end-binding 3), a member of +TIPs that bind to the plus end of microtubule (MT), to visualize the intracellular polarity of chordamesoderm cells during CE to investigate the trigger of the establishment of cell polarity. We found that EB3 movement is polarized in chordamesoderm cells and that the notochord-somite tissue boundary plays an essential role in generating the cell polarity. This polarity was generated before the change of cell morphology and the polarized movement of EB3 in chordamesoderm cells was also observed near the boundary between the chordamesoderm tissue and naïve ectoderm tissue or lateral mesoderm tissues induced by a low concentration of nodal mRNA. These suggest that definitive tissue separation established by the distinct levels of nodal signaling is essential for the chordamesodermal cells to acquire mediolateral cell polarity.

The Evolution of Norovirus, the ‘Gastric Flu’ and Mechanisms of GII.4 Norovirus Persistence in Human Populations:

Noroviruses are the leading cause of viral acute gastroenteritis in humans, noted for causing epidemic outbreaks in communities, the military, cruise ships, hospitals, and assisted living communities. The evolutionary mechanisms governing the persistence and emergence of new norovirus strains in human populations are unknown. Primarily organized by sequence homology into two major human genogroups defined by multiple genoclusters, the majority of norovirus outbreaks are caused by viruses from the GII.4 genocluster, which was first recognized as the major epidemic strain in the mid-1990s. Previous studies by our laboratory and others indicate that some noroviruses readily infect individuals who carry a gene encoding a functional alpha-1,2-fucosyltransferase (FUT2) and are designated “secretor-positive” to indicate that they express ABH histo-blood group antigens (HBGAs), a highly heterogeneous group of related carbohydrates on mucosal surfaces. Individuals with defects in the FUT2 gene are termed secretor-negative, do not express the appropriate HBGA necessary for docking, and are resistant to Norwalk infection. These data argue that FUT2 and other genes encoding enzymes that regulate processing of the HBGA carbohydrates function as susceptibility alleles. However, secretor-negative individuals can be infected with other norovirus strains, and reinfection with the GII.4 strains is common in human populations. In this article, we analyze molecular mechanisms governing GII.4 epidemiology, susceptibility, and persistence in human populations.

Can Farmed and Wild Salmon Coexist? and A Global Assessment of Salmon Aquaculture Impacts on Wild Salmonids:

The impact of salmon farming on wild salmon and trout is a hotly debated issue in all countries where salmon farms and wild salmon coexist. Studies have clearly shown that escaped farm salmon breed with wild populations to the detriment of the wild stocks, and that diseases and parasites are passed from farm to wild salmon. An understanding of the importance of these impacts at the population level, however, has been lacking. In this study, we used existing data on salmon populations to compare survival of salmon and trout that swim past salmon farms early in their life cycle with the survival of nearby populations that are not exposed to salmon farms. We have detected a significant decline in survival of populations that are exposed to salmon farms, correlated with the increase in farmed salmon production in five regions. Combining the regional estimates statistically, we find a reduction in survival or abundance of wild populations of more than 50% per generation on average, associated with salmon farming. Many of the salmon populations we investigated are at dramatically reduced abundance, and reducing threats to them is necessary for their survival. Reducing impacts of salmon farming on wild salmon should be a high priority.

No Place for Predators?:

Time and again, advancing civilization has set people against large carnivores. On the front lines of Washington State, wildlife biologists hope that knowledge can trump fear, and ultimately lead to detente.

Seymour Benzer 1921-2007 The Man Who Took Us from Genes to Behaviour:

Seymour Benzer died suddenly in December 2007. William Harris pays tribute to Benzer’s pioneering work in solid state physics, molecular biology, and neurogenetics.

Fast Learning Bumblebees Reap Greater Nectar Rewards:

The speed with which bees learn affects their ability to collect food from flowers, according to a new study from Queen Mary, University of London. As nectar levels in flowers change from minute-to-minute, faster learning bees are more likely to keep track of which blooms are most rewarding, and thrive as a result.

Living On ‘The Red Edge’: Rare Form Of Chlorophyll Discovered In Newly Sequenced Bacterium:

Researchers at Washington University in St. Louis and Arizona State University have sequenced the genome of a rare bacterium that harvests light energy by making an even rarer form of chlorophyll, chlorophyll d. Chlorophyll d absorbs “red edge,” near infrared, long wave length light, invisible to the naked eye.

The Way A Protein Is Folded Affects The Molecular Dance Of Water:

Scientists from Bochum, Illinois, and Nevada were able to prove with terahertz (THz) spectroscopy that proteins do modify water molecules in their environment to a long range extent: The water molecules, which generally move around like disco dancers in their collective network motions behave more like in a neat minuet under protein influence.

Quality Schooling Has Little Impact On Teenage Sexual Activity; Socioeconomic Status Does:

A report shows that socio-economic situation and the local high school catchment area have a more powerful influence on reported sexual experience among 15 and 16 year olds than classroom discipline or the quality of relationships within schools.

How Did Huge Dinosaurs Find Enough Food? Did Bacteria Aid Their Digestion?:

Scientists from the University of Bonn are researching which plants giant dinosaurs could have lived off more than 100 million years ago. They want to find out how the dinosaurs were able to become as large as they did. In fact such gigantic animals should not have existed according to general rules of ecology.

Birds, Bats And Insects Hold Secrets For Aerospace Engineers:

Natural flyers like birds, bats and insects outperform man-made aircraft in aerobatics and efficiency. University of Michigan engineers are studying these animals as a step toward designing flapping-wing planes with wingspans smaller than a deck of playing cards.

Intersex Fish Linked To Population And Agriculture In Potomac River Watershed:

For several years, scientists have been working to determine why so many male smallmouth bass in the Potomac River basin have immature female egg cells in their testes – a form of intersex. They are closer to finding an answer.

Quick Feather Test Determines Sex Of Chicks:

Scientists in Germany are reporting development of test that can answer one of the most frustrating questions in the animal kingdom: Is that bird a boy or a girl? Their study is a potential boon to poultry farmers and bird breeders.

Neural Basis Of ‘Number Sense’ In Young Infants:

Behavioral experiments indicate that infants aged 4½ months or older possess an early “number sense” that allows them to detect changes in the number of objects. However, the neural basis of this ability was previously unknown.

Nurses As ‘Soft Targets’ Of Drug Company Promotion:

Nursing education fails to prepare graduates to deal with the pharmaceutical industry’s promotional tactics, and many nurses appear to accept promotional materials uncritically, according to an analysis of the nursing literature recently published.

Transparent Adult Zebra Fish Will Make Human Biology Even Clearer:

Zebrafish are genetically similar to humans and are good models for human biology and disease. Now, researchers at Children’s Hospital Boston have created a zebrafish that is transparent throughout its life. The new fish allows scientists to directly view its internal organs, and observe processes like tumor metastasis and blood production after bone-marrow transplant in a living organism.

Oldest Horseshoe Crab Fossil Found, 100 Million Years Old:

Few modern animals are as deserving of the title “living fossil” as the lowly horseshoe crab. Seemingly unchanged since before the Age of Dinosaurs, these venerable sea creatures can now claim a history that reaches back almost half-a billion years.

Coral Reefs May Be Protected By Natural Ocean Thermostat:

Natural processes may prevent oceans from warming beyond a certain point, helping protect some coral reefs from the impacts of climate change, new research finds. The study, by scientists at the National Center for Atmospheric Research (NCAR) and Australian Institute of Marine Science (AIMS), finds evidence that an ocean “thermostat” appears to be helping to regulate sea-surface temperatures in a biologically diverse region of the western Pacific.

Did Birds Originate When Dinosaurs Went Extinct, Or Have They Been Around Far Longer?:

Did modern birds originate around the time of the dinosaurs’ demise, or have they been around far longer? The question is at the center of a sometimes contentious “rocks versus clocks” debate between paleontologists, whose estimates are based on the fossil record, and scientists who use “molecular clock” methods to study evolutionary history.

Beaked Whales Actually Hear Through Their Throats:

Researchers from San Diego State University and the University of California have been using computer models to mimic the effects of underwater noise on an unusual whale species and have discovered a new pathway for sound entering the head and ears.

Pygmy Dinosaur Inhabited Tropical Islands In Britain’s Prehistoric Past:

The celebrated Bristol Dinosaur, Thecodontosaurus, has now been shown to live on subtropical islands around Bristol, instead of in a desert on the mainland as previously thought.

There are some interesting articles published in PLoS Genetics, Computational Biology, Pathogens and Neglected Tropical Diseases and these got my attention at the first glance – you look around for stuff you may be interested in:
Comparing Patterns of Natural Selection across Species Using Selective Signatures:

Natural selection promotes the survival of the fittest individuals within a species. Over many generations, this may result in the maintenance of ancestral traits (conservation through purifying selection), or the emergence of newly beneficial traits (adaptation through positive selection). At the genetic level, long-term purifying or positive selection can cause genes to evolve more slowly, or more rapidly, providing a way to identify these evolutionary forces. While some genes are subject to consistent purifying or positive selection in most species, other genes show unexpected levels of selection in a particular species or group of species–a pattern we refer to as the “selective signature” of the gene. In this work, we demonstrate that these patterns of natural selection can be mined for information about gene function and species ecology. In the future, this method could be applied to any set of related species with fully sequenced genomes to better understand the genetic basis of ecological divergence.

Evolution of Complex Modular Biological Networks:

The modular organization of cells is not immediately obvious from the network of interacting genes, proteins, and molecules. A new window into cellular modularity is opened up by genetic data that identifies pairs of genes that interact either directly or indirectly to provide robustness to cellular function. Such pairs can map out the modular nature of a network if we understand how they relate to established mathematical clustering methods applied to networks to identify putative modules. We can test the relationship between genetically interacting pairs and modules on artificial data: large networks of interacting proteins and molecules that were evolved within an artificial chemistry and genetics, and that pass the standard tests for biological networks. Modularity evolves in these networks in order to deal with a multitude of functional goals, with a degree depending on environmental variability. Relationships between genetically interacting pairs and modules similar to those displayed by the artificial gene networks are found in the protein-protein interaction network of baker’s yeast. The evolution of complex functional biological networks in silico provides an opportunity to develop and test new methods and tools to understand the complexity of biological systems at the network level.

Social Exclusion Modifies Climate and Deforestation Impacts on a Vector-Borne Disease:

American Cutaneous Leishmaniasis emergence has been associated with changes in the interaction between people and forests. The association between outbreaks and forest clearance, higher risk for populations living close to forests, and the absence of this disease from urban settings has led to the proposal that it will disappear with the destruction of primary forests. This view ignores the complex nature of deforestation as a product of socioeconomic inequities. Our study shows that such inequities, as measured by a marginalization index, may ultimately determine risk within the country, with socially excluded populations most affected by the disease. Contrary to the established view, living close to the forest edge can diminish the risk provided other factors are taken into account. Additionally, differences in vulnerability to climatic variability appear to interact with forest cover to influence risk across counties where the disease has its largest burden. Incidence exacerbation associated with El Niño Southern Oscillation is observed in counties with larger proportions of deforestation. Our study calls for control efforts targeted to socially excluded populations and for more localized ecological studies of transmission in vectors and reservoirs in order to understand the role of biodiversity changes in driving the emergence of this disease.

Gene Variants May Help To Distribute The Work Of Evolution Between Men And Women:

Scientists from deCODE genetics have discovered two common, single-letter variants in the sequence of the human genome (SNPs) that regulate one of the principle motors of evolution.

Key ‘Impact Hunters’ Catalyze Hunting Among Male Chimpanzees:

While hunting among chimpanzees is a group effort, key males, known as “impact hunters” are highly influential within the group. They are more likely to initiate a hunt, and hunts rarely occur in their absence, according to a new study. The findings shed light on how and why some animals cooperate to hunt for food, and how individual variation among chimpanzees contributes to collective predation.

Globetrotting Black Rat Genes Reveal Spread Of Humans And Diseases:

DNA of the common Black Rat has shed light on the ancient spread of rats, people and diseases around the globe. Studying the mitochondrial DNA of 165 Black Rat specimens from 32 countries around the world, an international team of scientists has identified six distinct lineages in the Black Rat’s family tree, each originating from a different part of Asia.

Baboon Dads Have Surprising Influence On Daughters’ Fitness:

Polygamous baboon fathers get more grandchildren if they spend a little time with their children during their juvenile years, according to research directed by scientists at Duke and Princeton universities.

Gotta Have Heart: Crocodilians Bypass Their Lungs To Improve Digestion:

As perhaps confirmed by their ubiquity on nature cable channels, crocodiles are among nature’s most fearsome predators. When the opportunity arises, crocodilians will gorge, voluntarily consuming meals weighing 23% of their own body weight. This is analogous to a 130 -pound woman eating, at one sitting, a hamburger weighing 30 pounds. But what to do with all of that food? If they do not digest their meal quickly, crocodilians risk death from within, or if they are young, by predators.

Barnacles Go To Great Lengths To Mate:

Compelled to mate, yet firmly attached to the rock, barnacles have evolved the longest penis of any animal for their size – up to 8 times their body length – so they can find and fertilize distant neighbours.

Broiler Chickens Bred For Fast Growth Are Having Difficulty Walking:

The huge increase in growth rates of broiler chickens means more than a quarter of these intensively-reared birds have difficulty walking, according to a comprehensive survey carried out by the University of Bristol. The study identifies a range of management factors that could be altered to reduce leg health problems but warns that implementation of these changes would be likely to reduce growth rate and production.

Tons of new stuff in PLoS ONE this week. Some titles that caught my eye:
Comparative Bacterial Proteomics: Analysis of the Core Genome Concept:

While comparative bacterial genomic studies commonly predict a set of genes indicative of common ancestry, experimental validation of the existence of this core genome requires extensive measurement and is typically not undertaken. Enabled by an extensive proteome database developed over six years, we have experimentally verified the expression of proteins predicted from genomic ortholog comparisons among 17 environmental and pathogenic bacteria. More exclusive relationships were observed among the expressed protein content of phenotypically related bacteria, which is indicative of the specific lifestyles associated with these organisms. Although genomic studies can establish relative orthologous relationships among a set of bacteria and propose a set of ancestral genes, our proteomics study establishes expressed lifestyle differences among conserved genes and proposes a set of expressed ancestral traits.

Leg Disorders in Broiler Chickens: Prevalence, Risk Factors and Prevention:

Broiler (meat) chickens have been subjected to intense genetic selection. In the past 50 years, broiler growth rates have increased by over 300% (from 25 g per day to 100 g per day). There is growing societal concern that many broiler chickens have impaired locomotion or are even unable to walk. Here we present the results of a comprehensive survey of commercial flocks which quantifies the risk factors for poor locomotion in broiler chickens. We assessed the walking ability of 51,000 birds, representing 4.8 million birds within 176 flocks. We also obtained information on approximately 150 different management factors associated with each flock. At a mean age of 40 days, over 27.6% of birds in our study showed poor locomotion and 3.3% were almost unable to walk. The high prevalence of poor locomotion occurred despite culling policies designed to remove severely lame birds from flocks. We show that the primary risk factors associated with impaired locomotion and poor leg health are those specifically associated with rate of growth. Factors significantly associated with high gait score included the age of the bird (older birds), visit (second visit to same flock), bird genotype, not feeding whole wheat, a shorter dark period during the day, higher stocking density at the time of assessment, no use of antibiotic, and the use of intact feed pellets. The welfare implications are profound. Worldwide approximately 2×1010 broilers are reared within similar husbandry systems. We identify a range of management factors that could be altered to reduce leg health problems, but implementation of these changes would be likely to reduce growth rate and production. A debate on the sustainability of current practice in the production of this important food source is required.

Reverse Genetics in Ecological Research:

By precisely manipulating the expression of individual genetic elements thought to be important for ecological performance, reverse genetics has the potential to revolutionize plant ecology. However, untested concerns about possible side-effects of the transformation technique, caused by Agrobacterium infection and tissue culture, on plant performance have stymied research by requiring onerous sample sizes. We compare 5 independently transformed Nicotiana attenuata lines harboring empty vector control (EVC) T-DNA lacking silencing information with isogenic wild types (WT), and measured a battery of ecologically relevant traits, known to be important in plant-herbivore interactions: phytohormones, secondary metabolites, growth and fitness parameters under stringent competitive conditions, and transcriptional regulation with microarrays. As a positive control, we included a line silenced in trypsin proteinase inhibitor gene (TPI) expression, a potent anti-herbivore defense known to exact fitness costs in its expression, in the analysis. The experiment was conducted twice, with 10 and 20 biological replicates per genotype. For all parameters, we detected no difference between any EVC and WT lines, but could readily detect a fitness benefit of silencing TPI production. A statistical power analyses revealed that the minimum sample sizes required for detecting significant fitness differences between EVC and WT was 2-3 orders of magnitude larger than the 10 replicates required to detect a fitness effect of TPI silencing. We conclude that possible side-effects of transformation are far too low to obfuscate the study of ecologically relevant phenotypes.

Self-Consistent Estimation of Mislocated Fixations during Reading:

During reading, we generate saccadic eye movements to move words into the center of the visual field for word processing. However, due to systematic and random errors in the oculomotor system, distributions of within-word landing positions are rather broad and show overlapping tails, which suggests that a fraction of fixations is mislocated and falls on words to the left or right of the selected target word. Here we propose a new procedure for the self-consistent estimation of the likelihood of mislocated fixations in normal reading. Our approach is based on iterative computation of the proportions of several types of oculomotor errors, the underlying probabilities for word-targeting, and corrected distributions of landing positions. We found that the average fraction of mislocated fixations ranges from about 10% to more than 30% depending on word length. These results show that fixation probabilities are strongly affected by oculomotor errors.

An Update on MyoD Evolution in Teleosts and a Proposed Consensus Nomenclature to Accommodate the Tetraploidization of Different Vertebrate Genomes:

MyoD is a muscle specific transcription factor that is essential for vertebrate myogenesis. In several teleost species, including representatives of the Salmonidae and Acanthopterygii, but not zebrafish, two or more MyoD paralogues are conserved that are thought to have arisen from distinct, possibly lineage-specific duplication events. Additionally, two MyoD paralogues have been characterised in the allotetraploid frog, Xenopus laevis. This has lead to a confusing nomenclature since MyoD paralogues have been named outside of an appropriate phylogenetic framework. Here we initially show that directly depicting the evolutionary relationships of teleost MyoD orthologues and paralogues is hindered by the asymmetric evolutionary rate of Acanthopterygian MyoD2 relative to other MyoD proteins. Thus our aim was to confidently position the event from which teleost paralogues arose in different lineages by a comparative investigation of genes neighbouring myod across the vertebrates. To this end, we show that genes on the single myod-containing chromosome of mammals and birds are retained in both zebrafish and Acanthopterygian teleosts in a striking pattern of double conserved synteny. Further, phylogenetic reconstruction of these neighbouring genes using Bayesian and maximum likelihood methods supported a common origin for teleost paralogues following the split of the Actinopterygii and Sarcopterygii. Our results strongly suggest that myod was duplicated during the basal teleost whole genome duplication event, but was subsequently lost in the Ostariophysi (zebrafish) and Protacanthopterygii lineages. We propose a sensible consensus nomenclature for vertebrate myod genes that accommodates polyploidization events in teleost and tetrapod lineages and is justified from a phylogenetic perspective.

A Proposed Mechanism for the Interaction of the Segmentation Clock and the Determination Front in Somitogenesis:

Recent discoveries in the field of somitogenesis have confirmed, for the most part, the feasibility of the clock and wavefront model. There are good candidates for both the clock (various genes expressed cyclically in the tail bud of vertebrate embryos have been discovered) and the wavefront (there are at least three different substances, whose expression levels vary along the presomitic mesoderm [PSM], that have important effects on the formation of somites). Nevertheless, the mechanisms through which the wavefront interacts with the clock to arrest the oscillations and induce somite formation have not yet been fully elucidated. In this work, we propose a gene regulatory network which is consistent with all known experimental facts in embryonic mice, and whose dynamic behaviour provides a potential explanation for the periodic aggregation of PSM cells into blocks: the first step leading to the formation of somites. To our knowledge, this is the first proposed mechanism that fully explains how a block of PSM cells can stop oscillating simultaneously, and how this process is repeated periodically, via the interaction of the segmentation clock and the determination front.

The Citius End: World Records Progression Announces the Completion of a Brief Ultra-Physiological Quest:

World records (WR) in sports illustrate the ultimate expression of human integrated muscle biology, through speed or strength performances. Analysis and prediction of man’s physiological boundaries in sports and impact of external (historical or environmental) conditions on WR occurrence are subject to scientific controversy. Based on the analysis of 3263 WR established for all quantifiable official contests since the first Olympic Games, we show here that WR progression rate follows a piecewise exponential decaying pattern with very high accuracy (mean adjusted r2 values = 0.91±0.08 (s.d.)). Starting at 75% of their estimated asymptotic values in 1896, WR have now reached 99%, and, present conditions prevailing, half of all WR will not be improved by more than 0,05% in 2027. Our model, which may be used to compare future athletic performances or assess the impact of international antidoping policies, forecasts that human species’ physiological frontiers will be reached in one generation. This will have an impact on the future conditions of athlete training and on the organization of competitions. It may also alter the Olympic motto and spirit.

There’s some cool new stuff in PLoS Biology and PLoS Medicine this week. Here are my picks and you look around and see what you are interested in….
The Evolutionary and Developmental Foundations of Mathematics:

Understanding the evolutionary precursors of human mathematical ability is a highly active area of research in psychology and biology with a rich and interesting history. At one time, numerical abilities, like language, tool use, and culture, were thought to be uniquely human. However, at the turn of the 20th century, scientists showed more interest in the numerical abilities of animals. The earliest research was focused on whether animals could count in any way that approximated the counting skills of humans [1,2], though many early studies lacked the necessary scientific controls to truly prove numerical abilities in animals. In addition, both the public and many in the scientific community too readily accepted cases of “genius” animals, including those that performed amazing mathematical feats. One such animal still lends its name to the phenomenon of inadvertent cuing of animals by humans: Clever Hans. Hans was a horse that seemed to calculate solutions to all types of numerical problems. In reality, the horse was highly attuned to the subtle and inadvertent bodily movements that people would make when Hans had reached the correct answer (by tapping his hoof) and should have stopped responding [3]. One consequence of this embarrassing realization was a backlash for the better part of the 20th century against the idea that animals could grasp numerical concepts. The second, more positive consequence, however, was that future researchers would include appropriate controls to account for such cues.

Fish Invasions in the World’s River Systems: When Natural Processes Are Blurred by Human Activities:

As one of the major threats to biodiversity, the detrimental consequences of biological invasions are widely recognised. Despite this, a global view of invasion patterns and their determinants is still lacking in aquatic ecosystems, reducing our ability to initiate practical actions. Here we report the global patterns of freshwater fish invasion in 1,055 river basins covering more than 80% of Earth’s continental surface. This allows us to identify six major invasion hotspots where non-native species represent more than a quarter of the total number of species. According to the World Conservation Union, these areas are also characterised by the highest proportion of threatened fish species. We also show that the natural factors controlling global biodiversity do not influence the number of non-native species in a given river basin. Instead, human activity-related factors, and particularly economic activity, explain why some river basins host more non-native species. In view of our findings, we fear massive invasions in developing countries with a growing economy as already experienced in developed countries. This constitutes a serious threat to global biodiversity.

Human Activity, not Ecosystem Characters, Drives Potential Species Invasions:

From the Asian tiger mosquito in the American South, to the Eurasian zebra mussel in the Great Lakes, to European quackgrass throughout the United States, invasions of non-native species can disrupt ecosystems, cause havoc with local economies, and even threaten health. A new study shows that, at least for freshwater fishes, the major driver of successful invasion is human development, not intrinsic ecological factors, suggesting that in the future, many more newcomers will be making their homes in foreign lands.
Competing hypotheses have been proposed to account for the establishment of non-native species. Human activities, from disrupting ecosystems to transporting exotic species, have clearly contributed to many invasions. But do ecosystems themselves play a part? The “biotic resistance” hypothesis suggests that species-rich environments can deter newcomers, while the “biotic acceptance” hypothesis suggests the opposite, that if it’s good for the locals, it’s good for the invaders.

Does Preventing Obesity Lead to Reduced Health-Care Costs:

In a study in this issue of PLoS Medicine, Pieter van Baal and colleagues used data from The Netherlands to simulate the annual and lifetime medical costs attributable to obesity [1]. They also compared these costs to those attributable to smoking as well as to the medical costs associated with healthy, living persons (defined as non-smokers with a body mass index in the range of 18.5 to less than 25 kg/m2). The researchers explored the question of whether reducing obesity would lead to reduced or increased health-care costs

Lifetime Medical Costs of Obesity: Prevention No Cure for Increasing Health Expenditure:

Background.
Since the mid 1970s, the proportion of people who are obese (people who have an unhealthy amount of body fat) has increased sharply in many countries. One-third of all US adults, for example, are now classified as obese, and recent forecasts suggest that by 2025 half of US adults will be obese. A person is overweight if their body mass index (BMI, calculated by dividing their weight in kilograms by their height in meters squared) is between 25 and 30, and obese if BMI is greater than 30. Compared to people with a healthy weight (a BMI between 18.5 and 25), overweight and obese individuals have an increased risk of developing many diseases, such as diabetes, coronary heart disease and stroke, and tend to die younger. People become unhealthily fat by consuming food and drink that contains more energy than they need for their daily activities. In these circumstances, the body converts the excess energy into fat for use at a later date. Obesity can be prevented, therefore, by having a healthy diet and exercising regularly.
Why Was This Study Done?
Because obesity causes so much illness and premature death, many governments have public-health policies that aim to prevent obesity. Clearly, the improvement in health associated with the prevention of obesity is a worthwhile goal in itself but the prevention of obesity might also reduce national spending on medical care. It would do this, the argument goes, by reducing the amount of money spent on treating the diseases for which obesity is a risk factor. However, some experts have suggested that these short-term savings might be offset by spending on treating the diseases that would occur during the extra lifespan experienced by non-obese individuals. In this study, therefore, the researchers have used a computer model to calculate yearly and lifetime medical costs associated with obesity in The Netherlands.
What Did the Researchers Do and Find?
The researchers used their model to estimate the number of surviving individuals and the occurrence of various diseases for three hypothetical groups of men and women, examining data from the age of 20 until the time when the model predicted that everyone had died. The “obese” group consisted of never-smoking people with a BMI of more than 30; the “healthy-living” group consisted of never-smoking people with a healthy weight; the “smoking” group consisted of lifetime smokers with a healthy weight. Data from the Netherlands on the costs of illness were fed into the model to calculate the yearly and lifetime health-care costs of all three groups. The model predicted that until the age of 56, yearly health costs were highest for obese people and lowest for healthy-living people. At older ages, the highest yearly costs were incurred by the smoking group. However, because of differences in life expectancy (life expectancy at age 20 was 5 years less for the obese group, and 8 years less for the smoking group, compared to the healthy-living group), total lifetime health spending was greatest for the healthy-living people, lowest for the smokers, and intermediate for the obese people.
What Do These Findings Mean?
As with all mathematical models such as this, the accuracy of these findings depend on how well the model reflects real life and the data fed into it. In this case, the model does not take into account varying degrees of obesity, which are likely to affect lifetime health-care costs, nor indirect costs of obesity such as reduced productivity. Nevertheless, these findings suggest that although effective obesity prevention reduces the costs of obesity-related diseases, this reduction is offset by the increased costs of diseases unrelated to obesity that occur during the extra years of life gained by slimming down.

Soft Targets: Nurses and the Pharmaceutical Industry:

The nursing literature has yet to pay much attention to the expansive reach of the pharmaceutical industry into the nursing profession. In this article, we examine some of the key literature on the influence of drug companies upon nurses, consider the limitations of this literature, and define a strategy for heightening awareness and strengthening the skills of nurses to manage the impact of commercial interests.

Anna’s Hummingbird Chirps With Its Tail During Display Dives:

The beeps, chirps and whistles made by some hummingbirds and thought to be vocal are actually created by the birds’ tail feathers, according to a study by two students at the University of California, Berkeley.

Why Don’t Chimpanzees Like To Barter Food?:

For thousands of years, human beings have relied on commodity barter as an essential aspect of their lives. It is the behavior that allows specialized professions, as one individual gives up some of what he has reaped to exchange with another for something different. In this way, both individuals end up better off. Despite the importance of this behavior, little is known about how barter evolved and developed.

Black Death Selective In Its Wrath: Plague Targeted The Weak, Frail:

Despite the long-held assumption by historians that Europe’s Black Death of 1347 to 1351 killed indiscriminately, a new report by University at Albany anthropologist Sharon DeWitte and Pennsylvania State University researcher James Wood finds that the deadly plaque targeted the already ill and weak.

Ecological Genetics Of Freshwater Bacteria Surveyed:

Novel molecular techniques have been responsible for major strides in microbial ecology and are addressing broadly important scientific questions about the variety and distribution of microbial life, according to a new article.

Revolution In Understanding Of Ion Channel Regulation:

A study at Rush University Medical Center in Chicago proposes that bubbles may control the opening and closing of ion channels. This new understanding of the channels that control much of life in health and disease provides a vital piece of the molecular puzzle.

Lost City Pumps Life-essential Chemicals At Rates Unseen At Typical Deep Ocean Hydrothermal Vents:

Hydrocarbons — molecules critical to life — are being generated by the simple interaction of seawater with the rocks under the Lost City hydrothermal vent field in the mid-Atlantic Ocean.

You Are What You Eat: Some Differences Between Humans And Chimpanzees Traced To Diet:

Using mice as models, researchers at the Max Planck Institute for Evolutionary Anthropology traced some of the differences between humans and chimpanzees to differences in our diet.

Migrating Birds Detect Latitude And Longitude, But How Remains A Mystery:

Eurasian reed warblers captured during their spring migrations and released after being flown 1,000 kilometers to the east can correct their travel routes and head for their original destinations, researchers report.

Conspicuous Social Signaling Drives Evolution Of Chameleon Color Change:

What drove the evolution of color change in chameleons? Chameleons can use color change to camouflage and to signal to other chameleons, but a new paper shows that the need to rapidly signal to other chameleons, and not the need to camouflage from predators, has driven the evolution of this characteristic trait.

Why Scratching Relieves An Itch:

In the first study to use imaging technology to see what goes on in the brain when we scratch, researchers at Wake Forest University Baptist Medical Center have uncovered new clues about why scratching may be so relieving — and why it can be hard to stop.

Destined To Cheat? New Research Finds Free Will Can Keep Us Honest:

With the start of the New Year millions of Americans have resolved to lie less, cheat less, put the holiday hangovers behind them, or otherwise better their lives. Some will moderate their bad habits; others may make significant changes and become shining examples of integrity. But most of those well-intended New Year’s resolutions are destined to fail. In an age where cheating scandals plague elite universities and major corporations are brought down by unethical actions, the debate about the origins and nature of our decisions play into a larger debate about genetic determinism and free will.

New Species Of Giant Elephant-shrew Discovered:

When Francesco Rovero first saw the image captured by one of his automatic cameras in a remote Tanzanian forest, he knew he’d never seen anything quite like it. It was the size of a small dog, covered in orange and gray fur, and had a long snout like an elephant. Its markings and general appearance suggested it was a member of the elephant-shrew family, called a sengi in Swahili. Today, the Journal of Zoology reports that Rovero discovered a new species of giant elephant-shrew.

Anne-Marie has more.
Cats’ Family Tree Rooted In Fertile Crescent, Study Confirms:

The Fertile Crescent of the Middle East has long been identified as a “cradle of civilization” for humans. In a new genetic study, researchers at the University of California, Davis, have concluded that all ancestral roads for the modern day domestic cat also lead back to the same locale.

Greg Laden has more.
Blue-eyed Humans Have A Single, Common Ancestor:

New research shows that people with blue eyes have a single, common ancestor. A team at the University of Copenhagen have tracked down a genetic mutation which took place 6-10,000 years ago and is the cause of the eye colour of all blue-eyed humans alive on the planet today.

Which became obvious once Larry shaved off his mustache.
Lusty Voles, Mindless Of Danger, Mate Like Rabbits:

Forgetful Casanovas are lucky in love. At least that’s how University of Florida researchers interpret the results of new research on the mating habits and nervous systems of prairie voles. An article about the research, which examined both the voles’ behavior and their brains, appeared recently in the Proceedings of the National Academy of Sciences.

Hmmm, this is something I expect Kate will blog about soon…that’s right up her alley.

The Eyes Have It: Researchers Can Now Determine When A Human Was Born By Looking Into The Eyes Of The Dead:

Using the radiocarbon dating method and special proteins in the lens of the eye, researchers at the University of Copenhagen and Aarhus can now establish, with relatively high precision, when a person was born. This provides a useful tool for forensic scientists who can use it to establish the date of birth of an unidentified body and could also have further consequences for health science research.

Cats’ Family Tree Rooted In Fertile Crescent, Study Confirms:

The Fertile Crescent of the Middle East has long been identified as a “cradle of civilization” for humans. In a new genetic study, researchers at the University of California, Davis, have concluded that all ancestral roads for the modern day domestic cat also lead back to the same locale.

Microbes As Climate Engineers:

We might think we control the climate but unless we harness the powers of our microbial co-habitants on this planet we might be fighting a losing battle, according to an article in the February 2008 issue of Microbiology Today.

In Nature, And Maybe The Corner Office, Scientists Find That Generalists Can Thrive:

The assignment of duties in a single cell, ocean life or even a small business does not have to be defined by a division of labor where every individual has a specific role, according to biologists at Ohio State University.

Developing Better Forage For Feeding Hungry Cattle Year Round:

A herd of hungry cattle isn’t a pretty sight. So scientists with the Agricultural Research Service (ARS) are developing forage grasses that provide nutritious forage to livestock in the southern Great Plains throughout the year.

Today’s crop of new articles published in PLoS ONE is an emebarassment of riches. It’s hard to make just a couple of picks out of 39 papers, but I’ll try to restrain myself and you go and look around for the rest of them….
Chimpanzee Autarky:

Economists believe that barter is the ultimate cause of social wealth–and even much of our human culture–yet little is known about the evolution and development of such behavior. It is useful to examine the circumstances under which other species will or will not barter to more fully understand the phenomenon. Chimpanzees (Pan troglodytes) are an interesting test case as they are an intelligent species, closely related to humans, and known to participate in reciprocal interactions and token economies with humans, yet they have not spontaneously developed costly barter. Although chimpanzees do engage in noncostly barter, in which otherwise value-less tokens are exchanged for food, this lack of risk is not typical of human barter. Thus, we systematically examined barter in chimpanzees to ascertain under what circumstances chimpanzees will engage in costly barter of commodities, that is, trading food items for other food items with a human experimenter. We found that chimpanzees do barter, relinquishing lower value items to obtain higher value items (and not the reverse). However, they do not trade in all beneficial situations, maintaining possession of less preferred items when the relative gains they stand to make are small. Two potential explanations for this puzzling behavior are that chimpanzees lack ownership norms, and thus have limited opportunity to benefit from the gains of trade, and that chimpanzees’ risk of defection is sufficiently high that large gains must be imminent to justify the risk. Understanding the conditions that support barter in chimpanzees may increase understanding of situations in which humans, too, do not maximize their gains.

Prelude to Passion: Limbic Activation by ‘Unseen’ Drug and Sexual Cues:

The human brain responds to recognizable signals for sex and for rewarding drugs of abuse by activation of limbic reward circuitry. Does the brain respond in similar way to such reward signals even when they are “unseen”, i.e., presented in a way that prevents their conscious recognition? Can the brain response to “unseen” reward cues predict the future affective response to recognizable versions of such cues, revealing a link between affective/motivational processes inside and outside awareness? We exploited the fast temporal resolution of event-related functional magnetic resonance imaging (fMRI) to test the brain response to “unseen” (backward-masked) cocaine, sexual, aversive and neutral cues of 33 milliseconds duration in male cocaine patients (n = 22). Two days after scanning, the affective valence for visible versions of each cue type was determined using an affective bias (priming) task. We demonstrate, for the first time, limbic brain activation by “unseen” drug and sexual cues of only 33 msec duration. Importantly, increased activity in an large interconnected ventral pallidum/amygdala cluster to the “unseen” cocaine cues strongly predicted future positive affect to visible versions of the same cues in subsequent off-magnet testing, pointing both to the functional significance of the rapid brain response, and to shared brain substrates for appetitive motivation within and outside awareness. These findings represent the first evidence that brain reward circuitry responds to drug and sexual cues presented outside awareness. The results underscore the sensitivity of the brain to “unseen” reward signals and may represent the brain’s primordial signature for desire. The limbic brain response to reward cues outside awareness may represent a potential vulnerability in disorders (e.g., the addictions) for whom poorly-controlled appetitive motivation is a central feature.

Protecting Biodiversity when Money Matters: Maximizing Return on Investment:

Conventional wisdom identifies biodiversity hotspots as priorities for conservation investment because they capture dense concentrations of species. However, density of species does not necessarily imply conservation ‘efficiency’. Here we explicitly consider conservation efficiency in terms of species protected per dollar invested. We apply a dynamic return on investment approach to a global biome and compare it with three alternate priority setting approaches and a random allocation of funding. After twenty years of acquiring habitat, the return on investment approach protects between 32% and 69% more species compared to the other priority setting approaches. To correct for potential inefficiencies of protecting the same species multiple times we account for the complementarity of species, protecting up to three times more distinct vertebrate species than alternate approaches. Incorporating costs in a return on investment framework expands priorities to include areas not traditionally highlighted as priorities based on conventional irreplaceability and vulnerability approaches.

Shark Attacks in Dakar and the Cap Vert Peninsula, Senegal: Low Incidence despite High Occurrence of Potentially Dangerous Species:

The International Shark Attack File mentions only four unprovoked shark attacks on the coast of West Africa during the period 1828-2004, an area where high concentrations of sharks and 17 species potentially dangerous to man have been observed. To investigate if the frequency of shark attacks could be really low and not just under-reported and whether there are potentially sharks that might attack in the area, a study was carried out in Dakar and the Cap Vert peninsula, Senegal. Personnel of health facilities, administrative services, traditional authorities and groups of fishermen from the region of Dakar were interviewed about the occurrence of shark attacks, and visual censuses were conducted along the coastline to investigate shark communities associated with the coasts of Dakar and the Cap Vert peninsula. Six attacks were documented for the period 1947-2005, including two fatal ones attributed to the tiger shark Galeocerdo cuvieri. All attacks concerned fishermen and only one occurred after 1970. Sharks were observed year round along the coastline in waters 3-15 m depth. Two species potentially dangerous for man, the nurse shark Ginglymostoma cirratum and the blacktip shark Carcharhinus limbatus, represented together 94% of 1,071 sharks enumerated during 1,459 hours of observations. Threatening behaviour from sharks was noted in 12 encounters (1.1%), including 8 encounters with C. limbatus, one with Galeocerdo cuvieri and 3 with unidentified sharks. These findings suggest that the frequency of shark attacks on the coast of West Africa is underestimated. However, they also indicate that the risk is very low despite the abundance of sharks. In Dakar area, most encounters along the coastline with potentially dangerous species do not result in an attack. Compared to other causes of water related deaths, the incidence of shark attack appears negligible, at least one thousand fold lower.

Human and Chimpanzee Gene Expression Differences Replicated in Mice Fed Different Diets:

Although the human diet is markedly different from the diets of closely related primate species, the influence of diet on phenotypic and genetic differences between humans and other primates is unknown. In this study, we analyzed gene expression in laboratory mice fed diets typical of humans and of chimpanzees. The effects of human diets were found to be significantly different from that of a chimpanzee diet in the mouse liver, but not in the brain. Importantly, 10% of the genes that differ in their expression between humans and chimpanzee livers differed also between the livers of mice fed the human and chimpanzee diets. Furthermore, both the promoter sequences and the amino acid sequences of these diet-related genes carry more differences between humans and chimpanzees than random genes. Our results suggest that the mouse can be used to study at least some aspects of human-specific traits.

Transmissibility of the Influenza Virus in the 1918 Pandemic:

With a heightened increase in concern for an influenza pandemic we sought to better understand the 1918 Influenza pandemic, the most devastating epidemic of the previous century. We use data from several communities in Maryland, USA as well as two ships that experienced well-documented outbreaks of influenza in 1918. Using a likelihood-based method and a nonparametric method, we estimate the serial interval and reproductive number throughout the course of each outbreak. This analysis shows the basic reproductive number to be slightly lower in the Maryland communities (between 1.34 and 3.21) than for the enclosed populations on the ships (R0 = 4.97, SE = 3.31). Additionally the effective reproductive number declined to sub epidemic levels more quickly on the ships (within around 10 days) than in the communities (within 30-40 days). The mean serial interval for the ships was consistent (3.33, SE = 5.96 and 3.81, SE = 3.69), while the serial intervals in the communities varied substantially (between 2.83, SE = 0.53 and 8.28, SE = 951.95). These results illustrate the importance of considering the population dynamics when making statements about the epidemiological parameters of Influenza. The methods that we employ for estimation of the reproductive numbers and the serial interval can be easily replicated in other populations and with other diseases.

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Synthesis Of Natural Molecule Could Lead To Better Anti-cancer Drugs:

In early 2007, Northwestern University chemist Karl Scheidt’s interest was piqued when marine chemist Amy Wright reported in the Journal of Natural Products that a new natural compound derived from an uncommon deep-sea sponge was extremely effective at inhibiting cancer cell growth.

Ants And Avalanches: Insects On Coffee Plants Follow Widespread Natural Tendency:

Ever since a forward-thinking trio of physicists identified the phenomenon known as self-organized criticality—a mechanism by which complexity arises in nature—scientists have been applying its concepts to everything from economics to avalanches. Now, researchers at the University of Michigan and the University of Toledo have shown that clusters of ant nests on a coffee farm in Mexico also adhere to the model. Their work, which has implications for controlling coffee pests, appears in the Jan. 24 issue of the journal Nature.

Vets Focus On Neurological Disorders In Dogs, Humans:

Parkinson’s disease and epilepsy strike millions of people each year. They also affect countless dogs, and veterinarians at the University of Missouri are working to find ways to treat these and other neurological diseases in both species.

Lessons From Evolution Applied To National Security And Other Threats:

Could lessons learned from Mother Nature help airport security screening checkpoints better protect us from terror threats? The authors of a new book, Natural Security: A Darwinian Approach to a Dangerous World, believe they can — if governments are willing to think outside the box and pay heed to some of nature’s most successful evolutionary strategies for species adaptation and survival.

Tasmanian Devils’ Existence Threatened By Rapidly Spreading Cancer:

Researchers are working toward an understanding a unique transmissible and rapidly spreading cancer that threatens the very existence of Tasmanian devils. To combat this particularly aggressive disease, a Cold Spring Harbor Laboratory research team in collaboration with 454 Lifesciences is committing resources to sequence parts of the devil’s genome in an effort to increase the odds of saving them from extinction.

Scientists Call For Urgent Research Into ‘Real’ Impacts Of Invasive Species:

Scientists warn that unless more research is carried out to highlight the damage caused by invasive species, more livelihoods and natural ecosystems will be ruined as a consequence of their effects. Invasive alien species are those that occur outside their natural range and threaten the existence of native plants and animals. They can be plants, animals or microorganisms that are introduced intentionally for economic or agricultural purposes, or accidentally, through tourism, travel or trade, or when domestic animals become feral.

There is lots of cool new stuff in PLoS Biology this week. Take a look:
Conspicuous Chameleons is a synopsis/summary of this article:
Selection for Social Signalling Drives the Evolution of Chameleon Colour Change:

The ability to change colour has evolved in numerous vertebrate and invertebrate groups, the most well-known of which are chameleons and cephalopods (octopuses and their relatives). There is great variation among species, however, in the apparent capacity for colour change, ranging from limited changes in brightness to dramatic changes in hue. What drives the evolution of this remarkable strategy? We addressed this question by using a combination of field-based behavioural trials in which we quantified colour change, models of colour perception, and our knowledge of phylogenetic relationships for 21 distinct lineages of southern African dwarf chameleons. We show that evolutionary changes in the capacity for colour change are consistently associated with the use of social signals that are highly conspicuous to the visual system of chameleons. Moreover, capacity for colour change is unrelated to variation in the environmental backgrounds that chameleons must match in order to be camouflaged. Overall, our results suggest that the evolution of the ability to exhibit striking changes in colour evolved as a strategy to facilitate social signalling and not, as popularly believed, camouflage.

There are types of pain that naked mole-rats do not feel – Selective Inflammatory Pain Insensitivity in the African Naked Mole-Rat (Heterocephalus glaber):

Chemicals such as capsaicin and acid are considered noxious because they cause irritation and pain when applied to the skin. Acid is, for example, a very noxious stimulus and can cause intense pain. Indeed, acid is both noxious and painful to all animals including amphibians and fish. Here we describe a member of the rodent family, the African naked mole-rat (Heterocephalus glaber), that is behaviorally completely oblivious to capsaicin and acid. Tissue injury and inflammation increase sensitivity to normally non painful stimuli, a phenomenon called hyperalgesia. Here we show that the naked mole-rat does not experience hyperalgesia to painful thermal stimuli after inflammation. To our knowledge, no other mammal has so far been described that is selectively insensitive to chemical pain or that lacks thermal hyperalgesia. Naked mole-rats live in very large subterranean social groups and are remarkably tolerant to low-oxygen and high-carbon dioxide conditions. We hypothesize that naked mole-rats are selectively pain insensitive partly because of selection pressure arising from the extremity of their normal habitat.

The Evolution of Quorum Sensing in Bacterial Biofilms:

Bacteria are increasingly recognized as highly interactive organisms with complex social lives, which are critical to their capacity to cause disease. In particular, many species inhabit dense, surface-bound communities, termed biofilms, within which they communicate and respond to local cell density through a process known as quorum sensing. Enormous effort has been devoted to understanding the genetics and biochemistry of biofilm formation and quorum sensing, but how and why they evolve remain virtually unexplored. Many bacteria use quorum sensing to regulate the secretion of sticky extracellular slime, an integral feature of biofilm life. Intriguingly, however, some pathogenic species turn on slime production at high cell density, whereas others turn it off. Using an individual-based model of biofilm growth, we investigated why different species use quorum sensing to control slime production in opposite ways. The secret underlying this variation appears to reside in the nature of infections. Turning slime on at high cell density can allow one strain to suffocate another when competition is intense, as occurs in long-lived chronic infections. Meanwhile, turning slime secretion off at high cell density can benefit a strain causing an acute infection by allowing rapid growth before departing the host.

Riders of a Modern-Day Ark:

Amphibians may not seem the hardiest of creatures, but they have roamed Earth for 360 million years–a span including at least two major Ice Ages and four warming, interglacial periods. Yet their ability to evolve in concert with an ever-changing environment may not be enough to survive a world now dominated by human activity. Over 1,800 amphibian species, one-third of all known species, are threatened with extinction, according to the Global Amphibian Assessment [1]. Countless other, yet-undescribed, species may never have their place on Earth documented. Of all amphibians–toads, salamanders, newts, and caecilians–the frog’s prevalence renders it at greatest risk.

EDGE Amphibians: World’s Weirdest Creatures Just Got Weirder:

A gigantic, ancient relative of the newt, a drawing-pin sized frog, a limbless, tentacled amphibian and a blind see-through salamander have all made it onto a list of the world’s weirdest and most endangered creatures.

Scientists Look At Those In Evolutionary Race Who Don’t Make It ‘Out Of The Gate’:

In the race of evolution, scientists until now have only looked at winners and losers. Now, they’ve come up with a way to look at the contenders who never made it out of the gate. It’s the organisms — in this case lizards — that die early in life, before scientists can even assess what they might bring to the reproduction game, and that have gone uncounted in the effort to quantify genetic fitness. This group has been dubbed the “invisible fraction.” Andrew McAdam, assistant professor of fisheries and wildlife and zoology at Michigan State University, has co-authored a paper in the Jan. 23 Proceedings of the Royal Society which brings that elusive fraction to light.

World’s Aging Population To Defuse War On Terrorism:

Changing demographic trends will impact the future of international relations, according to the latest issue of Public Policy & Aging Report (PP&AR). Several hotbed areas in the world that offer the motive and opportunity for political violence are due to stabilize by the year 2030.

How Much You’re Willing To Pay Depends On What You Were Just Doing:

Your shopping buddy turns to you and asks, “Which one of these would you get?” Or, you’re talking with your spouse about which candidate you’d like to vote for before switching on the nightly news. Turns out simply being asked to make a choice– especially if you’re in a hurry or have something on your mind — will make you like the next thing you see more, says a new study from the Journal of Consumer Research. The researchers found that asking people to choose among things primed them to think about positive attributes — and caused them to be in a positive frame of mind when evaluating the next item they saw.

Extinct Marsupial Lion Tops African Lion In Fight To Death:

Pound for pound, Australia’s extinct marsupial lion (Thylacoleo carnifex) would have made mince meat of today’s African lion (Panthera leo) had the two big hyper-carnivores ever squared off in a fight to the death, according to an Australian scientist.

Secret Of Scottish Sheep Evolution Discovered:

Researchers from the University of Sheffield, as part of an international team, have discovered the secret of why dark sheep on a remote Scottish Island are mysteriously declining, seemingly contradicting Darwin’s evolutionary theory. Dr Jacob Gratten and Dr Jon Slate, from the University’s Department of Animal and Plant Sciences, led the team, which found that the gene responsible for dark coat colour is linked to other genes that reduce an animal’s fitness.

Friday – time to take a look at the new articles in PLoS Computational Biology, Genetics and Pathogens – check them all out, but here are a couple of picks:
Exploration of Small RNAs:

There is substantial interest in noncoding RNAs (ncRNAs), which play an essential role in complex biological systems without encoding for proteins. Only a limited number of ncRNAs, such as ribosomal RNA (rRNA) and transfer RNA (tRNA), have previously been characterized in any depth. Recent studies revealed many novel ncRNAs, covering a wide range of sizes [1]. RNA molecules have several functions including catalytic activity and ability to act as a structural component. Of these functions, the ability to specify a nucleic acid sequence is superior compared to proteins. A common way in which ncRNA contributes to biological processes is through the ribonucleoprotein (RNP) complex, where its role is to guide recognition of nucleic acid target sequences relying upon sequence complementarity [2]. Small RNA molecules are widely utilized in this type of machinery, and are involved in important biological processes [3]. Exploration of novel small RNA species and their functions attracts substantial interest. The advent of recent technologies to profile cellular RNAs, such as high-throughput sequencing and microarray, coupled with computational analysis, has contributed to rapid progress in this field. Here, we review the recently discovered small RNA species and their pathways in a view of conservations and differences between higher eukaryotes. We also summarize recent exploration efforts of novel small RNAs based on devised technologies to provide a perspective for the future.

Why is Real-World Visual Object Recognition Hard?:

The ease with which we recognize visual objects belies the computational difficulty of this feat. At the core of this challenge is image variation–any given object can cast an infinite number of different images onto the retina, depending on the object’s position, size, orientation, pose, lighting, etc. Recent computational models have sought to match humans’ remarkable visual abilities, and, using large databases of “natural” images, have shown apparently impressive progress. Here we show that caution is warranted. In particular, we found that a very simple neuroscience “toy” model, capable only of extracting trivial regularities from a set of images, is able to outperform most state-of-the-art object recognition systems on a standard “natural” test of object recognition. At the same time, we found that this same toy model is easily defeated by a simple recognition test that we generated to better span the range of image variation observed in the real world. Together these results suggest that current “natural” tests are inadequate for judging success or driving forward progress. In addition to tempering claims of success in the machine vision literature, these results point the way forward and call for renewed focus on image variation as a central challenge in object recognition.

Getting Started in Text Mining:

Text mining is the use of automated methods for exploiting the enormous amount of knowledge available in the biomedical literature. There are at least as many motivations for doing text mining work as there are types of bioscientists. Model organism database curators have been heavy participants in the development of the field due to their need to process large numbers of publications in order to populate the many data fields for every gene in their species of interest. Bench scientists have built biomedical text mining applications to aid in the development of tools for interpreting the output of high-throughput assays and to improve searches of sequence databases (see [1] for a review). Bioscientists of every stripe have built applications to deal with the dual issues of the double-exponential growth in the scientific literature over the past few years and of the unique issues in searching PubMed/MEDLINE for genomics-related publications. A surprising phenomenon can be noted in the recent history of biomedical text mining: although several systems have been built and deployed in the past few years–Chilibot, Textpresso, and PreBIND (see Text S1 for these and most other citations), for example–the ones that are seeing high usage rates and are making productive contributions to the working lives of bioscientists have been built not by text mining specialists, but by bioscientists. We speculate on why this might be so below.

Seismic Images Show Dinosaur-killing Meteor Made Bigger Splash:

The most detailed three-dimensional seismic images yet of the Chicxulub crater, a mostly submerged and buried impact crater on the Mexico coast, may modify a theory explaining the extinction of 70 percent of life on Earth 65 million years ago.

Jacky Dragons Are Born When The Temperature Is Right For Their Sex:

An Iowa State University researcher spent four years in Australia studying reptiles. Dan Warner, a researcher in the ecology, evolution and organismal biology department, has been working with the jacky dragon, a lizard found in Australia, to discover if egg incubation temperature and sex affects the viability of the lizards.

Adaptive Functional Evolution Of Leptin In Cold-adaptive Pika Family:

Researchers at the Northwest Institute of Plateau Biology, Chinese Academy of Sciences have put forward the viewpoint for the first time that adaptive functional evolution may occur in the leptin protein of the pika (Ochotona) family, a typical cold-adaptive mammal. They speculated that the cold, rather than hypoxia, may be the primary environmental factor that drives the adaptive evolution of pika leptin.

Forests Could Benefit When Fall Color Comes Late:

Do those fall colors seem to show up later and later–if at all? Scientists say we can blame increasing amounts of carbon dioxide in the atmosphere for prolonging the growing season of the trees. And that may actually be good news for forestry industries.

Changing Fashions Govern Mating Success In Lark Buntings, Study Finds:

A study of how female lark buntings choose their mates, published in Science, adds a surprising new twist to the evolutionary theory of sexual selection. Researchers at the University of California, Santa Cruz, discovered that female lark buntings show strong preferences for certain traits in the males, but those preferences change from year to year.

There is a lot of new stuff published this week in PLoS Biology, PLoS Medicine, PLoS Neglected Tropical Diseases and PLoS ONE.
Molecular Studies in Treponema pallidum Evolution: Toward Clarity? is an Expert Commentary on last week’s (widely reported) study On the Origin of the Treponematoses: A Phylogenetic Approach (the paper that suggests that Columbus brought syphilis from the New World back to Europe).
Looking at the 33 new articles on PLoS ONE, here are a few titles I found intriguing:
Seasonal Changes in Mood and Behavior Are Linked to Metabolic Syndrome:

Obesity is a major public health problem worldwide. Metabolic syndrome is a risk factor to the cardiovascular diseases. It has been reported that disruptions of the circadian clockwork are associated with and may predispose to metabolic syndrome. 8028 individuals attended a nationwide health examination survey in Finland. Data were collected with a face-to-face interview at home and during an individual health status examination. The waist circumference, height, weight and blood pressure were measured and samples were taken for laboratory tests. Participants were assessed using the ATP-III criteria for metabolic syndrome and with the Seasonal Pattern Assessment Questionnaire for their seasonal changes in mood and behavior. Seasonal changes in weight in particular were a risk factor of metabolic syndrome, after controlling for a number of known risk and potential confounding factors. Metabolic syndrome is associated with high global scores on the seasonal changes in mood and behavior, and with those in weight in particular. Assessment of these changes may serve as a useful indicator of metabolic syndrome, because of easy assessment. Abnormalities in the circadian clockwork which links seasonal fluctuations to metabolic cycles may predispose to seasonal changes in weight and to metabolic syndrome.

Natural Selection and Adaptive Evolution of Leptin in the Ochotona Family Driven by the Cold Environmental Stress:

Environmental stress can accelerate the evolutionary rate of specific stress-response proteins and create new functions specialized for different environments, enhancing an organism’s fitness to stressful environments. Pikas (order Lagomorpha), endemic, non-hibernating mammals in the modern Holarctic Region, live in cold regions at either high altitudes or high latitudes and have a maximum distribution of species diversification confined to the Qinghai-Tibet Plateau. Variations in energy metabolism are remarkable for them living in cold environments. Leptin, an adipocyte-derived hormone, plays important roles in energy homeostasis. To examine the extent of leptin variations within the Ochotona family, we cloned the entire coding sequence of pika leptin from 6 species in two regions (Qinghai-Tibet Plateau and Inner Mongolia steppe in China) and the leptin sequences of plateau pikas (O. curzonia) from different altitudes on Qinghai-Tibet Plateau. We carried out both DNA and amino acid sequence analyses in molecular evolution and compared modeled spatial structures. Our results show that positive selection (PS) acts on pika leptin, while nine PS sites located within the functionally significant segment 85-119 of leptin and one unique motif appeared only in pika lineages-the ATP synthase α and β subunit signature site. To reveal the environmental factors affecting sequence evolution of pika leptin, relative rate test was performed in pikas from different altitudes. Stepwise multiple regression shows that temperature is significantly and negatively correlated with the rates of non-synonymous substitution (Ka) and amino acid substitution (Aa), whereas altitude does not significantly affect synonymous substitution (Ks), Ka and Aa. Our findings support the viewpoint that adaptive evolution may occur in pika leptin, which may play important roles in pikas’ ecological adaptation to extreme environmental stress. We speculate that cold, and probably not hypoxia, may be the primary environmental factor for driving adaptive evolution of pika leptin.

Mammalian Cells Change Volume during Mitosis:

Using single cell-imaging methods we have found that the volume of adherent cells grown in culture decreases as the cells rounds when it enters mitosis. A minimal volume is reached at metaphase. Rapid volume recovery initiates before abscission as cells make the transition from metaphase to cytokinesis. These volume changes are simultaneous with the rapid surface area decrease and recovery observed in mitotic cells.

A Technique for Characterizing the Development of Rhythms in Bird Song:

The developmental trajectory of nervous system dynamics shows hierarchical structure on time scales spanning ten orders of magnitude from milliseconds to years. Analyzing and characterizing this structure poses significant signal processing challenges. In the context of birdsong development, we have previously proposed that an effective way to do this is to use the dynamic spectrum or spectrogram, a classical signal processing tool, computed at multiple time scales in a nested fashion. Temporal structure on the millisecond timescale is normally captured using a short time Fourier analysis, and structure on the second timescale using song spectrograms. Here we use the dynamic spectrum on time series of song features to study the development of rhythm in juvenile zebra finch. The method is able to detect rhythmic structure in juvenile song in contrast to previous characterizations of such song as unstructured. We show that the method can be used to examine song development, the accuracy with which rhythm is imitated, and the variability of rhythms across different renditions of a song. We hope that this technique will provide a standard, automated method for measuring and characterizing song rhythm.

The Epidemics of Donations: Logistic Growth and Power-Laws:

This paper demonstrates that collective social dynamics resulting from individual donations can be well described by an epidemic model. It captures the herding behavior in donations as a non-local interaction between individual via a time-dependent mean field representing the mass media. Our study is based on the statistical analysis of a unique dataset obtained before and after the tsunami disaster of 2004. We find a power-law behavior for the distributions of donations with similar exponents for different countries. Even more remarkably, we show that these exponents are the same before and after the tsunami, which accounts for some kind of universal behavior in donations independent of the actual event. We further show that the time-dependent change of both the number and the total amount of donations after the tsunami follows a logistic growth equation. As a new element, a time-dependent scaling factor appears in this equation which accounts for the growing lack of public interest after the disaster. The results of the model are underpinned by the data analysis and thus also allow for a quantification of the media influence.

Deconstructing Insight: EEG Correlates of Insightful Problem Solving:

Cognitive insight phenomenon lies at the core of numerous discoveries. Behavioral research indicates four salient features of insightful problem solving: (i) mental impasse, followed by (ii) restructuring of the problem representation, which leads to (iii) a deeper understanding of the problem, and finally culminates in (iv) an “Aha!” feeling of suddenness and obviousness of the solution. However, until now no efforts have been made to investigate the neural mechanisms of these constituent features of insight in a unified framework. In an electroencephalographic study using verbal remote associate problems, we identified neural correlates of these four features of insightful problem solving. Hints were provided for unsolved problems or after mental impasse. Subjective ratings of the restructuring process and the feeling of suddenness were obtained on trial-by-trial basis. A negative correlation was found between these two ratings indicating that sudden insightful solutions, where restructuring is a key feature, involve automatic, subconscious recombination of information. Electroencephalogram signals were analyzed in the space×time×frequency domain with a nonparametric cluster randomization test. First, we found strong gamma band responses at parieto-occipital regions which we interpreted as (i) an adjustment of selective attention (leading to a mental impasse or to a correct solution depending on the gamma band power level) and (ii) encoding and retrieval processes for the emergence of spontaneous new solutions. Secondly, we observed an increased upper alpha band response in right temporal regions (suggesting active suppression of weakly activated solution relevant information) for initially unsuccessful trials that after hint presentation led to a correct solution. Finally, for trials with high restructuring, decreased alpha power (suggesting greater cortical excitation) was observed in right prefrontal area. Our results provide a first account of cognitive insight by dissociating its constituent components and potential neural correlates.

The Sorcerer II Global Ocean Sampling Expedition: Metagenomic Characterization of Viruses within Aquatic Microbial Samples:

Viruses are the most abundant biological entities on our planet. Interactions between viruses and their hosts impact several important biological processes in the world’s oceans such as horizontal gene transfer, microbial diversity and biogeochemical cycling. Interrogation of microbial metagenomic sequence data collected as part of the Sorcerer II Global Ocean Expedition (GOS) revealed a high abundance of viral sequences, representing approximately 3% of the total predicted proteins. Cluster analyses of the viral sequences revealed hundreds to thousands of viral genes encoding various metabolic and cellular functions. Quantitative analyses of viral genes of host origin performed on the viral fraction of aquatic samples confirmed the viral nature of these sequences and suggested that significant portions of aquatic viral communities behave as reservoirs of such genetic material. Distributional and phylogenetic analyses of these host-derived viral sequences also suggested that viral acquisition of environmentally relevant genes of host origin is a more abundant and widespread phenomenon than previously appreciated. The predominant viral sequences identified within microbial fractions originated from tailed bacteriophages and exhibited varying global distributions according to viral family. Recruitment of GOS viral sequence fragments against 27 complete aquatic viral genomes revealed that only one reference bacteriophage genome was highly abundant and was closely related, but not identical, to the cyanomyovirus P-SSM4. The co-distribution across all sampling sites of P-SSM4-like sequences with the dominant ecotype of its host, Prochlorococcus supports the classification of the viral sequences as P-SSM4-like and suggests that this virus may influence the abundance, distribution and diversity of one of the most dominant components of picophytoplankton in oligotrophic oceans. In summary, the abundance and broad geographical distribution of viral sequences within microbial fractions, the prevalence of genes among viral sequences that encode microbial physiological function and their distinct phylogenetic distribution lend strong support to the notion that viral-mediated gene acquisition is a common and ongoing mechanism for generating microbial diversity in the marine environment.

What Happens in Between? Human Oscillatory Brain Activity Related to Crossmodal Spatial Cueing:

Previous studies investigated the effects of crossmodal spatial attention by comparing the responses to validly versus invalidly cued target stimuli. Dynamics of cortical rhythms in the time interval between cue and target might contribute to cue effects on performance. Here, we studied the influence of spatial attention on ongoing oscillatory brain activity in the interval between cue and target onset. In a first experiment, subjects underwent periods of tactile stimulation (cue) followed by visual stimulation (target) in a spatial cueing task as well as tactile stimulation as a control. In a second experiment, cue validity was modified to be 50%, 75%, or else 25%, to separate effects of exogenous shifts of attention caused by tactile stimuli from that of endogenous shifts. Tactile stimuli produced: 1) a stronger lateralization of the sensorimotor beta-rhythm rebound (15-22 Hz) after tactile stimuli serving as cues versus not serving as cues; 2) a suppression of the occipital alpha-rhythm (7-13 Hz) appearing only in the cueing task (this suppression was stronger contralateral to the endogenously attended side and was predictive of behavioral success); 3) an increase of prefrontal gamma-activity (25-35 Hz) specifically in the cueing task. We measured cue-related modulations of cortical rhythms which may accompany crossmodal spatial attention, expectation or decision, and therefore contribute to cue validity effects. The clearly lateralized alpha suppression after tactile cues in our data indicates its dependence on endogenous rather than exogenous shifts of visuo-spatial attention following a cue independent of its modality.

Lots of cool stuff at PLoS lately….
First, there is a great review in PLoS Medicine, that should be of interest to scienceblogs.com readers: Plague: Past, Present, and Future:

The causative bacterium (Yersinia pestis) was discovered by Yersin in 1894 [11] (see also [63]). Case-fatality ratio varies from 30% to 100%, if left untreated. Plague is endemic in many countries in the Americas, Asia, and Africa. More than 90% of cases are currently being reported from Africa.
Clinical presentation: After an incubation period of 3-7 days, patients typically experience a sudden onset of fever, chills, headaches, body aches, weakness, vomiting, and nausea. Clinical plague infection manifests itself in three forms, depending on the route of infection: bubonic, septicaemic, and pneumonic. The bubonic form is the most common, resulting from the bite of an infected flea. The pneumonic form initially is directly transmitted from human to human via inhalation of infected respiratory droplets.
Treatment: Rapid diagnosis and treatment are essential to reduce the risk of complications and death. Streptomycin, tetracyclines, and sulfonamides are the standard treatment. Gentamicin and fluoroquinolones may represent alternatives when the above antibiotics are not available. Patients with pneumonic plague must be isolated to avoid respiratory transmission.
Challenges ahead: Biological diagnosis of plague remains a challenge because most human cases appear in remote areas with scarce laboratory resources. So far, the main confirmation techniques were based on the isolation of Y. pestis (requiring a minimum of 4 days). The recent development of rapid diagnostic tests, now considered a confirmation method in endemic areas, opens new possibilities in terms of surveillance and case management.

A number of sciencebloggers are writing about the Plague these days, most notably Shelley Batts and Tara Smith so check out their posts as well.
Second, there is an exciting new article in PLoS Neglected Tropical Diseases, arguing that Columbus brought syphilis from the New World back to the Old World:
On the Origin of the Treponematoses: A Phylogenetic Approach:

Since the first recorded epidemic of syphilis in 1495, controversy has surrounded the origins of the bacterium Treponema pallidum subsp. pallidum and its relationship to the pathogens responsible for the other treponemal diseases: yaws, endemic syphilis, and pinta. Some researchers have argued that the syphilis-causing bacterium, or its progenitor, was brought from the New World to Europe by Christopher Columbus and his men, while others maintain that the treponematoses, including syphilis, have a much longer history on the European continent. We applied phylogenetics to this problem, using data from 21 genetic regions examined in 26 geographically disparate strains of pathogenic Treponema. Of all the strains examined, the venereal syphilis-causing strains originated most recently and were more closely related to yaws-causing strains from South America than to other non-venereal strains. Old World yaws-causing strains occupied a basal position on the tree, indicating that they arose first in human history, and a simian strain of T. pallidum was found to be indistinguishable from them. Our results lend support to the Columbian theory of syphilis’s origin while suggesting that the non-sexually transmitted subspecies arose earlier in the Old World. This study represents the first attempt to address the problem of the origin of syphilis using molecular genetics, as well as the first source of information regarding the genetic make-up of non-venereal strains from the Western hemisphere.

Tara Smith and Greg Laden have posted thoughtful reviews of this paper yesterday – check them out.
Third, there are 26 new articles on PLoS ONE this week, including:
Potential Impacts of Climatic Change on European Breeding Birds:

Climatic change is expected to lead to changes in species’ geographical ranges. Adaptation strategies for biodiversity conservation require quantitative estimates of the magnitude, direction and rates of these potential changes. Such estimates are of greatest value when they are made for large ensembles of species and for extensive (sub-continental or continental) regions. For six climate scenarios for 2070-99 changes have been estimated for 431 European breeding bird species using models relating species’ distributions in Europe to climate. Mean range centroid potentially shifted 258-882 km in a direction between 341° (NNW) and 45° (NE), depending upon the climate scenario considered. Potential future range extent averaged 72-89% of the present range, and overlapped the present range by an average of 31-53% of the extent of the present range. Even if potential range changes were realised, the average number of species breeding per 50×50 km grid square would decrease by 6·8-23·2%. Many species endemic or near-endemic to Europe have little or no overlap between their present and potential future ranges; such species face an enhanced extinction risk as a consequence of climatic change. Although many human activities exert pressures upon wildlife, the magnitude of the potential impacts estimated for European breeding birds emphasises the importance of climatic change. The development of adaptation strategies for biodiversity conservation in the face of climatic change is an urgent need; such strategies must take into account quantitative evidence of potential climatic change impacts such as is presented here.

Climate Influence on Deep Sea Populations:

Dynamics of biological processes on the deep-sea floor are traditionally thought to be controlled by vertical sinking of particles from the euphotic zone at a seasonal scale. However, little is known about the influence of lateral particle transport from continental margins to deep-sea ecosystems. To address this question, we report here how the formation of dense shelf waters and their subsequent downslope cascade, a climate induced phenomenon, affects the population of the deep-sea shrimp Aristeus antennatus. We found evidence that strong currents associated with intense cascading events correlates with the disappearance of this species from its fishing grounds, producing a temporary fishery collapse. Despite this initial negative effect, landings increase between 3 and 5 years after these major events, preceded by an increase of juveniles. The transport of particulate organic matter associated with cascading appears to enhance the recruitment of this deep-sea living resource, apparently mitigating the general trend of overexploitation. Because cascade of dense water from continental shelves is a global phenomenon, we anticipate that its influence on deep-sea ecosystems and fisheries worldwide should be larger than previously thought.

Antibiotics Threaten Wildlife: Circulating Quinolone Residues and Disease in Avian Scavengers:

Antibiotic residues that may be present in carcasses of medicated livestock could pass to and greatly reduce scavenger wildlife populations. We surveyed residues of the quinolones enrofloxacin and its metabolite ciprofloxacin and other antibiotics (amoxicillin and oxytetracycline) in nestling griffon Gyps fulvus, cinereous Aegypius monachus and Egyptian Neophron percnopterus vultures in central Spain. We found high concentrations of antibiotics in the plasma of many nestling cinereous (57%) and Egyptian (40%) vultures. Enrofloxacin and ciprofloxacin were also found in liver samples of all dead cinereous vultures. This is the first report of antibiotic residues in wildlife. We also provide evidence of a direct association between antibiotic residues, primarily quinolones, and severe disease due to bacterial and fungal pathogens. Our results indicate that, by damaging the liver and kidney and through the acquisition and proliferation of pathogens associated with the depletion of lymphoid organs, continuous exposure to antibiotics could increase mortality rates, at least in cinereous vultures. If antibiotics ingested with livestock carrion are clearly implicated in the decline of the vultures in central Spain then it should be considered a primary concern for conservation of their populations.

Auditory ERPs to Stimulus Deviance in an Awake Chimpanzee (Pan troglodytes): Towards Hominid Cognitive Neurosciences:

For decades, the chimpanzee, phylogenetically closest to humans, has been analyzed intensively in comparative cognitive studies. Other than the accumulation of behavioral data, the neural basis for cognitive processing in the chimpanzee remains to be clarified. To increase our knowledge on the evolutionary and neural basis of human cognition, comparative neurophysiological studies exploring endogenous neural activities in the awake state are needed. However, to date, such studies have rarely been reported in non-human hominid species, due to the practical difficulties in conducting non-invasive measurements on awake individuals. We measured auditory event-related potentials (ERPs) of a fully awake chimpanzee, with reference to a well-documented component of human studies, namely mismatch negativity (MMN). In response to infrequent, deviant tones that were delivered in a uniform sound stream, a comparable ERP component could be detected as negative deflections in early latencies. The present study reports the MMN-like component in a chimpanzee for the first time. In human studies, various ERP components, including MMN, are well-documented indicators of cognitive and neural processing. The results of the present study validate the use of non-invasive ERP measurements for studies on cognitive and neural processing in chimpanzees, and open the way for future studies comparing endogenous neural activities between humans and chimpanzees. This signifies an essential step in hominid cognitive neurosciences.

Distortions of Subjective Time Perception Within and Across Senses:

The ability to estimate the passage of time is of fundamental importance for perceptual and cognitive processes. One experience of time is the perception of duration, which is not isomorphic to physical duration and can be distorted by a number of factors. Yet, the critical features generating these perceptual shifts in subjective duration are not understood. We used prospective duration judgments within and across sensory modalities to examine the effect of stimulus predictability and feature change on the perception of duration. First, we found robust distortions of perceived duration in auditory, visual and auditory-visual presentations despite the predictability of the feature changes in the stimuli. For example, a looming disc embedded in a series of steady discs led to time dilation, whereas a steady disc embedded in a series of looming discs led to time compression. Second, we addressed whether visual (auditory) inputs could alter the perception of duration of auditory (visual) inputs. When participants were presented with incongruent audio-visual stimuli, the perceived duration of auditory events could be shortened or lengthened by the presence of conflicting visual information; however, the perceived duration of visual events was seldom distorted by the presence of auditory information and was never perceived shorter than their actual durations. These results support the existence of multisensory interactions in the perception of duration and, importantly, suggest that vision can modify auditory temporal perception in a pure timing task. Insofar as distortions in subjective duration can neither be accounted for by the unpredictability of an auditory, visual or auditory-visual event, we propose that it is the intrinsic features of the stimulus that critically affect subjective time distortions.

And don’t forget that the Journal Club is ongoing on this article so join in the discussion….

Culture Influences Brain Function, Study Shows:

People from different cultures use their brains differently to solve the same visual perceptual tasks, MIT researchers and colleagues report in the first brain imaging study of its kind.

Aroma Of Chocolate Chip Cookies Prompts Splurging On Expensive Sweaters:

Exposure to something that whets the appetite, such as a picture of a mouthwatering dessert, can make a person more impulsive with unrelated purchases, finds a study from the February 2008 issue of the Journal of Consumer Research. For example, the researchers reveal in one experiment that the aroma of chocolate chip cookies can prompt women on a tight budget to splurge on a new item of clothing.

Teens Getting Help For Suicidal Behavior From An Online Community:

It’s a topic people often don’t want to talk about, but suicide is a serious issue that needs serious attention. According to a University of Alberta researcher, teens are difficult to reach and there have traditionally been few services that directly target adolescent suicidal behavior. Elaine Greidanus says many teens aren’t picking up a phone, or seeing a counsellor, they’re more likely logging on for emotional support.

Is An Aspirin A Day Good For You?:

Is an aspirin a day good for you, and how much should you take? Ten years after the FDA issued recommendations about the use of aspirin for people who have had heart attacks or are at risk for them, it may be a good time to talk to your doctor about the aspirin you’re taking.

Millions Of Young People Have Used Cough Syrup To Get High:

About 3.1 million people in the United States aged 12 to 25 (5.3 percent of this age group) have used over-the-counter (non-prescription) cough and cold medicines to get high at least once in their lifetimes, according to a report by the Substance Abuse and Mental Health Services Administration (SAMHSA). The level is comparable to LSD, and more than the reported use of methamphetamines, among those aged 12 to 25. White youths were more than three times as likely as Black youths to have misused these drugs during the past year.

Some Birds Can Communicate About Behavior Of Predators:

With the aid of various alarm calls the Siberian jay bird species tells other members of its group what their main predators-¬hawks¬-are doing. The alarm calls are sufficient for Siberian jays to evince situation-specific fleeing behaviors, which enhances their chances of survival. This discovery, being published by Uppsala University researcher Michael Griesser in the journal Current Biology, shows for the first time that animals can assess and communicate about the behavior of predators.

High Degree Of Antibiotic Resistance Found In Wild Arctic Birds:

Swedish researchers report that birds captured in the hyperboreal tundra, in connection with the tundra expedition “Beringia 2005,” were carriers of antibiotics-resistant bacteria. These findings indicate that resistance to antibiotics has spread into nature, which is an alarming prospect for future health care.

Down To Earth Remedies For Chimps: Eat Mud:

The deliberate ingestion of soil, or ‘geophagy’, has important health benefits for chimpanzees, according to Sabrina Krief and her colleagues from the Muséum National d’Histoire Naturelle in Paris, France. Far from being a dysfunctional behavior, geophagy has evolved as a practice for maintaining health amongst chimpanzees. In this particular study geophagy is shown to increase the potency of ingested plants with anti-malarial properties.

When Tsetse Flies Fall For A Host, They Keep Coming Back For More:

If you like a restaurant first time around, you’re likely to go back, aren’t you? Well the same goes, more or less, for tsetse flies, as researchers from CIRAD, CIRDES and the University of Neuchâtel have recently demonstrated.

Snoozing Worms Help Explain The Evolution Of Sleep:

The roundworm C. elegans, a staple of laboratory research, may be key in unlocking one of the central biological mysteries: why we sleep. Researchers at the University of Pennsylvania School of Medicine report in the January 11 advanced online edition of Nature that the round worm has a sleep-like state, joining most of the animal kingdom in displaying this physiology. This research has implications for explaining the evolution and purpose of sleep and sleep-like states in animals.

Ancient Cave Bears Were As Omnivorous As Modern Bears:

Rather than being gentle giants, new research reveals that Pleistocene cave bears ate both plants and animals and competed for food with the other contemporary large carnivores of the time: hyaenas, lions, wolves, and our own human ancestors.

More
Chimpanzees May Build Their ‘Cultures’ In A Similar Way To Humans:

Socially-learned cultural behaviour thought to be unique to humans is also found among chimpanzees colonies, scientists at the University of Liverpool have found. Historically, scientists believed that behavioural differences between colonies of chimpanzees were due to variations in genetics. A team at Liverpool, however, has now discovered that variations in behaviour are down to chimpanzees migrating to other colonies, proving that they build their ‘cultures’ in a similar way to humans.

Where Do The Buffalo And Elk Still Roam?:

Less than twenty-one percent of the earth’s terrestrial surface still contains all of the large mammals that used to occur there 500 years ago, according to a new study. Authored by a team of scientists from the World Wildlife Fund (WWF) and Princeton University, the study is the first of its kind to offer an ecologically based measurement of human impacts on biodiversity based on the absence of native, large mammals.

Four Health Behaviors Can Add 14 Extra Years Of Life:

People who adopt four healthy behaviours — not smoking; taking exercise; moderate alcohol intake; and eating five servings of fruit and vegetables a day — live on average an additional fourteen years of life compared with people who adopt none of these behaviours, according to a new study.

480-million-year-old Fossil Sheds Light On 150-year-old Paleontological Mystery:

Discovery of an exceptional fossil specimen in southeastern Morocco that preserves evidence of the animal’s soft tissues has solved a paleontological puzzle about the origins of an extinct group of bizarre slug-like animals with rows of mineralized armor plates on their backs, according to a paper in Nature.

24 new article got published on PLoS ONE last night. Here are some interesting titles for you to check out (and then look around at others, add comments, annotations and ratings, and blog about them):
Self Assessment in Insects: Honeybee Queens Know Their Own Strength:

Contests mediate access to reproductive opportunities in almost all species of animals. An important aspect of the evolution of contests is the reduction of the costs incurred during intra-specific encounters to a minimum. However, escalated fights are commonly lethal in some species like the honeybee, Apis mellifera. By experimentally reducing honeybee queens’ fighting abilities, we demonstrate that they refrain from engaging in lethal contests that typically characterize their reproductive dominance behavior and coexist peacefully within a colony. This suggests that weak queens exploit an alternative reproductive strategy and provides an explanation for rare occurrences of queen cohabitation in nature. Our results further indicate that self-assessment, but not mutual assessment of fighting ability occurs prior to and during the agonistic encounters.

Paracellular Absorption: A Bat Breaks the Mammal Paradigm:

Bats tend to have less intestinal tissue than comparably sized nonflying mammals. The corresponding reduction in intestinal volume and hence mass of digesta carried is advantageous because the costs of flight increase with load carried and because take-off and maneuverability are diminished at heavier masses. Water soluble compounds, such as glucose and amino acids, are absorbed in the small intestine mainly via two pathways, the transporter-mediated transcellular and the passive, paracellular pathways. Using the microchiropteran bat Artibeus literatus (mean mass 80.6±3.7 g), we tested the predictions that absorption of water-soluble compounds that are not actively transported would be extensive as a compensatory mechanism for relatively less intestinal tissue, and would decline with increasing molecular mass in accord with sieve-like paracellular absorption. Using a standard pharmacokinetic technique, we fed, or injected intraperitonealy the metabolically inert carbohydrates L-rhamnose (molecular mass = 164 Da) and cellobiose (molecular mass = 342 Da) which are absorbed only by paracellular transport, and 3-O-methyl-D-glucose (3OMD-glucose) which is absorbed via both mediated (active) and paracellular transport. As predicted, the bioavailability of paracellular probes declined with increasing molecular mass (rhamnose, 90±11%; cellobiose, 10±3%, n = 8) and was significantly higher in bats than has been reported for laboratory rats and other mammals. In addition, absorption of 3OMD-glucose was high (96±11%). We estimated that the bats rely on passive, paracellular absorption for more than 70% of their total glucose absorption, much more than in non-flying mammals. Although possibly compensating for less intestinal tissue, a high intestinal permeability that permits passive absorption might be less selective than a carrier-mediated system for nutrient absorption and might permit toxins to be absorbed from plant and animal material in the intestinal lumen.

A Meta-Analysis of Effects of Bt Crops on Honey Bees (Hymenoptera: Apidae):

Honey bees (Apis mellifera L.) are the most important pollinators of many agricultural crops worldwide and are a key test species used in the tiered safety assessment of genetically engineered insect-resistant crops. There is concern that widespread planting of these transgenic crops could harm honey bee populations. We conducted a meta-analysis of 25 studies that independently assessed potential effects of Bt Cry proteins on honey bee survival (or mortality). Our results show that Bt Cry proteins used in genetically modified crops commercialized for control of lepidopteran and coleopteran pests do not negatively affect the survival of either honey bee larvae or adults in laboratory settings. Although the additional stresses that honey bees face in the field could, in principle, modify their susceptibility to Cry proteins or lead to indirect effects, our findings support safety assessments that have not detected any direct negative effects of Bt crops for this vital insect pollinator.

Life Depends upon Two Kinds of Water:

Many well-documented biochemical processes lack a molecular mechanism. Examples are: how ATP hydrolysis and an enzyme contrive to perform work, such as active transport; how peptides are formed from amino acids and DNA from nucleotides; how proteases cleave peptide bonds, how bone mineralises; how enzymes distinguish between sodium and potassium; how chirality of biopolymers was established prebiotically. It is shown that involvement of water in all these processes is mandatory, but the water must be of the simplified configuration in which there are only two strengths of water-water hydrogen bonds, and in which these two types of water coexist as microdomains throughout the liquid temperature range. Since they have different strengths of hydrogen bonds, the microdomains differ in all their physical and chemical properties. Solutes partition asymmetrically, generating osmotic pressure gradients which must be compensated for or abolished. Displacement of the equilibrium between high and low density waters incurs a thermodynamic cost which limits solubility, depresses ionisation of water, drives protein folding and prevents high density water from boiling at its intrinsic boiling point which appears to be below 0°C. Active processes in biochemistry take place in sequential partial reactions, most of which release small amounts of free energy as heat. This ensures that the system is never far from equilibrium so that efficiency is extremely high. Energy transduction is neither possible and nor necessary. Chirality was probably established in prebiotic clays which must have carried stable populations of high density and low density water domains. Bioactive enantiomorphs partition into low density water in which they polymerise spontaneously. The simplified model of water has great explanatory power.

Size Doesn’t Matter To Fighting Fiddler Crabs:

A person’s home may be their castle and in the world of the fiddler crabs having the home advantage makes it a near certainty that you’ll win a battle against an intruder – regardless of your opponent’s size. That’s one of the findings of a new study by a research team from The Australian National University. The team, working from the University’s Darwin research station, set out to discover why male fiddler crabs have an ‘owner advantage’ when defending their burrow that equates to a 92 per cent success rate.

Related
Researchers Use Magnetic Fields, Rather Than Drugs, To Control Cellular Signaling:

Researchers at Children’s Hospital Boston have developed a new “nanobiotechnology” that enables magnetic control of events at the cellular level. They describe the technology, which could lead to finely-tuned but noninvasive treatments for disease, in the January issue of Nature Nanotechnology (published online January 3).

Progeny Of Blind Cavefish Can ‘Regain’ Their Sight:

Blind cavefish whose eyes have withered while living in complete darkness over the course of evolutionary time can be made to see again. In some cases, the offspring of mated pairs originating from distinct cave populations regain vision, researchers found. The result shows that mutations in different genes are responsible for eye loss in separate cavefish lineages that may not have been exposed to light for the last one million years.

Molecular Basis Of Monarch Butterfly Migration Discovered:

Since its discovery, the annual migration of eastern North American monarch butterflies has captivated the human imagination and spirit. That millions of butterflies annually fly a few thousand miles to reach a cluster of pine groves in central Mexico comprising just 70 square miles is, for many, an awesome and mysterious occurrence. However, over the past two decades, scientists have begun to unveil the journey for what it is: a spectacular result of biology, driven by an intricate molecular mechanism in a tiny cluster of cells in the butterfly brain.

Does Biology Matter When Predicting How Animals Will Respond To Climate Change?:

Most predictions of how animals will move in changing climates rely on statistically relating an animal’s current location to environmental conditions. This approach ignores potentially important aspects of an animal’s biology including size, physiology, and behavior.

Related
Evolution Of Male-female Differences Within A Shared Genome:

One of the major components of the world’s biological diversity are the differences between males and females in traits related to mating, including weapons used when competing for mates and display traits used to seduce them. Such gender differences are thought to arise because selection acts differently on each sex. The conflicting interests of males and females in reproduction are thought to be a key source of sex-specific selection on such traits.

Smell-wars Between Butterflies And Ants:

Among humans, making yourself smell more alluring than you really are is a fairly harmless, socially accepted habit that maintains a complete perfume industry. However, it is a matter of life and death for caterpillars of large blue butterflies that dupe ant workers into believing them to be one of the ant’s own larvae.

Big Predators May Need Large Size To Conquer Prey, But Not True For Bacteria:

Ecologists generally observe a positive relationship between sizes of predators and their prey, mainly because predators need to be large to eat a larger prey. But does this positive relationship hold for sizes of bacteria and their food molecules? Using a mathematical model, scientists at Michigan State University predict the opposite, an inverse relationship between sizes of bacteria and their resource molecules.

Sexual Conflict Resolution? Mating Frequency And Fitness In Fruit Flies:

In the gene’s eye view, female mating frequency is difficult to understand. A substantial body of evidence, taken throughout the animal kingdom, demonstrates that females mate frequently, even when bouts of mating decrease offspring production. This finding is counterintuitive because we would expect natural selection to remove mating behaviors which decrease fitness. However, new research suggests that frequent mating females receive fitness benefits from an unexpected source: their daughters.

Why Are Chickens Getting So Fat?:

Obesity is a problem for many American consumers–and now, even our chickens are getting fat! In all animals, obesity results from an energy imbalance that occurs when more food energy (calories) is consumed than the body actually needs. The excess energy is stored mostly as fat. Over the years, poultry breeders have bred chickens that grow faster and produce more meat in response to a growing worldwide consumer demand. But modern broiler/breeder chickens don’t adequately balance their feed consumption to match their energy requirements. When these birds are given unrestricted access to feed, they will overeat and become obese.

From Theory to Practice: Translating Research into Health Outcomes:

A research article by Kay-Tee Khaw and colleagues in this issue of PLoS Medicine [1] quantifies the benefits of adopting not just one but four healthy forms of behavior. Compared with people who do not engage in any of these behaviors, people in this United Kingdom study who drank in moderation, did not smoke, took exercise, and ate an adequate amount of fruit and vegetables were calculated to live an additional 14 years. Clearly, these striking findings are of relevance, not only for health researchers and public policy makers but for the entire population. If everyone in the UK adopted these four behaviors, the public health impact would be substantial. What does it take for such research findings to be turned into actual public health outcomes?

Bright Light Therapy Eases Bipolar Depression For Some:

Bright light therapy can ease bipolar depression in some patients, according to a study published in the journal Bipolar Disorders. Researchers from the University of Pittsburgh School of Medicine’s Western Psychiatric Institute and Clinic studied nine women with bipolar disorder to examine the effects of light therapy in the morning or at midday on mood symptoms.

Insect Attack May Have Finished Off Dinosaurs:

Asteroid impacts or massive volcanic flows might have occurred around the time dinosaurs became extinct, but a new arguemet is that the mightiest creatures the world has ever known may have been brought down by a tiny, much less dramatic force — biting, disease-carrying insects.

Predator Pressures Maintain Bees’ Social Life:

The complex organisation of some insect societies is thought to have developed to such a level that these animals can no longer survive on their own. New research suggests that rather than organisational, genetic, or biological complexity defining a ‘point of no return’ for social living, pressures of predation create advantages to not living alone.

Two Explosive Evolutionary Events Shaped Early History Of Multicellular Life:

Scientists have known for some time that most major groups of complex animals appeared in the fossils record during the Cambrian Explosion, a seemingly rapid evolutionary event that occurred 542 million years ago. Now Virginia Tech paleontologists, using rigorous analytical methods, have identified another explosive evolutionary event that occurred about 33 million years earlier among macroscopic life forms unrelated to the Cambrian animals. They dubbed this earlier event the “Avalon Explosion.”

Why Do Some Animals Live Longer Than Others?:

Why do some live longer than others? Researchers from Leiden University, the Netherlands, turned to tropical African butterflies to find the answer. “The definitive answer is still not known, but our results give an interesting new insight into the evolution of lifespan,” says Jeroen Pijpe, first author of a new article.

New Model Of Competitive Speciation Unifies Insights From Earlier Work:

Under which circumstances is sympatric speciation possible? An answer to this long-standing question of evolutionary biology has turned out to be challenging. In particular, models for the evolution of assortative mating under frequency-dependent disruptive selection necessarily depend on a large number of ecological and genetic factors.

Insects’ ‘Giant Leap’ Reconstructed By Founder Of Sociobiology:

The January 2008 issue of BioScience includes an article by biologist Edward O. Wilson that argues for a new perspective on the evolution of advanced social organization in some ants, bees, and wasps (Hymenoptera).

Fresh Fossil Evidence Of Eye Forerunner Uncovered:

Ancient armoured fish fossils from Australia present some of the first definite fossil evidence of a forerunner to the human eye, a scientist from The Australian National University says.

Parents Show Bias In Sibling Rivalry, Says Study:

Most parents would hotly deny favouring one child over another but new research suggests they may have little choice in the matter.

Lack Of Deep Sleep May Increase Risk Of Type 2 Diabetes:

Suppression of slow-wave sleep in healthy young adults significantly decreases their ability to regulate blood-sugar levels and increases the risk of type 2 diabetes, report researchers at the University of Chicago Medical Center.

Giraffes And Frogs Provide More Evidence Of New Species Hidden In Plain Sight:

Two new articles provide further evidence that we have hugely underestimated the number of species with which we share our planet. Today sophisticated genetic techniques mean that superficially identical animals previously classed as members of a single species, including the frogs and giraffes in these studies, could in fact come from several distinct ‘cryptic’ species.

Violent Sex Acts Boost Insect’s Immunity System:

The long-held idea that only vertebrates have sophisticated adaptive immune systems that can protect them for life against many pathogens after being infected by them just once has been revised in recent years. It turns out that many insects also have a form of immune memory that protects them against reinvasion by a pathogen they have previously encountered. This research was discussed at a conference on Innate Immunity and the Environment.

Nurses Working Extended Shifts, Are Tired At Work And Sleep Little Likely To Drive Drowsy:

Hospital staff nurses who work extended hours, work at night, struggle to remain awake at work, or obtain less sleep are more likely to experience a drowsy driving episode, according to a study published in the December 1 issue of the journal SLEEP.

Childhood Sleep-disordered Breathing Disproportionately Affects Obese And African-Americans:

As the obesity epidemic grows in the U.S., doctors are discovering more and more far reaching health concerns for overweight children. Sleep-disordered breathing (SDB), which can include various sleep behaviors ranging in severity from snoring to obstructive sleep apnea (OSA), disproportionately affects children who are overweight and African- American, according to a new study published in the December 2007 edition of Otolaryngology — Head and Neck Surgery. Obstructive sleep apnea (OSA) can pose serious health threats, including hypertension and higher risk for cardiac disease.

Restless Legs Syndrome Doubles Risk Of Stroke And Heart Disease, Study Shows:

People with restless legs syndrome (RLS) are twice as likely to have a stroke or heart disease compared to people without RLS, and the risk is greatest in those with the most frequent and severe symptoms, according to new research.

Holidays slightly altered the publication dates at PLoS this week, so I had to wait until Wednesday to bring you my picks from PLoS Biology, PLoS Medicine and PLoS ONE. Of course, look beyond my own picks and look at all the new articles to see what you are interested in:
Recurring Ethanol Exposure Induces Disinhibited Courtship in Drosophila:

Alcohol has a strong causal relationship with sexual arousal and disinhibited sexual behavior in humans; however, the physiological support for this notion is largely lacking and thus a suitable animal model to address this issue is instrumental. We investigated the effect of ethanol on sexual behavior in Drosophila. Wild-type males typically court females but not males; however, upon daily administration of ethanol, they exhibited active intermale courtship, which represents a novel type of behavioral disinhibition. The ethanol-treated males also developed behavioral sensitization, a form of plasticity associated with addiction, since their intermale courtship activity was progressively increased with additional ethanol experience. We identified three components crucial for the ethanol-induced courtship disinhibition: the transcription factor regulating male sex behavior Fruitless, the ABC guanine/tryptophan transporter White and the neuromodulator dopamine. fruitless mutant males normally display conspicuous intermale courtship; however, their courtship activity was not enhanced under ethanol. Likewise, white males showed negligible ethanol-induced intermale courtship, which was not only reinstated but also augmented by transgenic White expression. Moreover, inhibition of dopamine neurotransmission during ethanol exposure dramatically decreased ethanol-induced intermale courtship. Chronic ethanol exposure also affected a male’s sexual behavior toward females: it enhanced sexual arousal but reduced sexual performance. These findings provide novel insights into the physiological effects of ethanol on sexual behavior and behavioral plasticity.

Using fMRI Brain Activation to Identify Cognitive States Associated with Perception of Tools and Dwellings:

Previous studies have succeeded in identifying the cognitive state corresponding to the perception of a set of depicted categories, such as tools, by analyzing the accompanying pattern of brain activity, measured with fMRI. The current research focused on identifying the cognitive state associated with a 4s viewing of an individual line drawing (1 of 10 familiar objects, 5 tools and 5 dwellings, such as a hammer or a castle). Here we demonstrate the ability to reliably (1) identify which of the 10 drawings a participant was viewing, based on that participant’s characteristic whole-brain neural activation patterns, excluding visual areas; (2) identify the category of the object with even higher accuracy, based on that participant’s activation; and (3) identify, for the first time, both individual objects and the category of the object the participant was viewing, based only on other participants’ activation patterns. The voxels important for category identification were located similarly across participants, and distributed throughout the cortex, focused in ventral temporal perceptual areas but also including more frontal association areas (and somewhat left-lateralized). These findings indicate the presence of stable, distributed, communal, and identifiable neural states corresponding to object concepts.

Recognizing Student Misconceptions through Ed’s Tools and the Biology Concept Inventory:

Over the past decade, workers in physics education research have developed effective instructional methods and materials (e.g., workshop physics [1]; lecture demonstrations [2]; tutorials in introductory physics [3]) based on research into student thinking. A Socratic process of questioning and careful analysis of responses can reveal students’ thinking on a subject area, including misconceptions, prior conceptions, and conceptual lacunae. Applying this approach to biological concepts, we have built a software system, called Ed’s Tools, to capture and analyze student responses. Both instructors and researchers can use this system to obtain a more complete and nuanced picture of student understanding, which can then serve as the foundation on which to base subsequent instruction and the construction of concept inventories. We illustrate the value of the data obtained through this analysis by showing how it helped us trace the conceptual problems that students have in two subject areas, molecular biology and evolutionary biology, to a common cause: a fundamental misunderstanding of random processes.

In the Era of Systematic Reviews, Does the Size of an Individual Trial Still Matter:

Background to the debate: Systematic reviews that combine high-quality evidence from several trials are now widely considered to be at the top of the hierarchy of clinical evidence. Given the primacy of systematic reviews–and the fact that individual clinical trials rarely provide definitive answers to a clinical research question–some commentators question whether the sample size calculation for an individual trial still matters. Others point out that small trials can still be potentially misleading.

Adult Male Chimpanzees Don’t Stray Far From The Home:

When it comes to choosing a place to live, male chimpanzees in the wild don’t stray far from home, according to a new report. The researchers found that adult male chimps out on their own tend to follow in their mother’s footsteps, spending their days in the same familiar haunts where they grew up. Male chimpanzees are generally very social, but how they use space when they are alone might be critical to their survival, the researchers said.

Solving Another Mystery Of An Amazing Water Walker:

Walking on water may seem like a miracle to humans, but it is a ho-hum for the water strider and scientists who already solved the mystery of that amazing ability. Now researchers in Korea are reporting a long-sought explanation for the water strider’s baffling ability to leap onto a liquid surface without sinking.

Innovative Model Connects Circuit Theory To Wildlife Corridors:

Scientists at Northern Arizona University and the National Center for Ecological Analysis and Synthesis have developed a model that borrows from electronic circuit theory to predict gene flow across complex landscapes . Their approach could help biologists design better wildlife corridors, which are crucial to protecting threatened plant and animal populations.

Smelly Sounds: One Person Out Of Every 1,000 Has Synesthesia:

Surprising as it may seem, there are people who can smell sounds, see smells or hear colours. One person out of every thousand has synesthesia, a psychological phenomenon in which an individual can smell a sound or hear a color. Most of these people are not aware they are synesthetes: they think the way they experience the world is normal.

Sleep Chemical Central To Effectiveness Of Deep Brain Stimulation:

A brain chemical that makes us sleepy also appears to play a central role in the success of deep brain stimulation to ease symptoms in patients with Parkinson’s disease and other brain disorders. The surprising finding is outlined in a paper published online Dec. 23 in Nature Medicine. The work shows that adenosine, a brain chemical most widely known as the cause of drowsiness, is central to the effect of deep brain stimulation, or DBS. The technique is used to treat people affected by Parkinson’s disease and who have severe tremor, and it’s also being tested in people who have severe depression or obsessive-compulsive disorder.

On Fridays, I take a look at what’s new in PLoS Neglected Tropical Diseases, Pathogens, Computational Biology and Genetics. Here are some of my picks for this week:
Neglected Diseases and Poverty in “The Other America”: The Greatest Health Disparity in the United States?:

Large numbers of the poorest Americans living in the United States are suffering from some of the same parasitic infections that affect the poor in Africa, Asia, and Latin America.

The Long and Thorny Road to Publication in Quality Journals:

Within the “Ten Simple Rules” series in PLoS Computational Biology, Dr. Bourne suggests that for younger investigators it is better to publish one paper in a quality journal rather than having multiple papers in lesser journals [1]. While this is certainly advisable, it can be very difficult. Indeed, for young scientists or, more to the point, for researchers with a short record of publications, it may be almost impossible to make their work and themselves visible to a larger scientific community via higher impact journals. A not-too-small share of “seasoned” scientists will argue without malignity that “we experienced similar or the same” and “good researchers will eventually be recognized.” What they imply is that those who continue to provide good science shall be rewarded later, i.e., their papers will eventually find a home in quality journals, thus yielding better chances that the work will have impact. And yet, a much-cited case study ([2]; cited 264 times as of November 18, 2007, according to http://isiwebofknowledge.com/) may illustrate that the road to publication and recognition can be thorny and long for younger and less-recognized scientists.

Computational Biology in Argentina:

Sebastian Bassi and colleagues from the Universidad Nacional de Quilmes, Buenos Aires, reflect on the identity of the interdisciplinary field of computational biology both generally and specifically in their country, Argentina.

A Tribute to Marcy Carlson Speer, 1959-2007:

It is with great sadness that we say goodbye to Marcy Carlson Speer, who died on August 4, 2007, at the age of 47 after a two-year battle with breast cancer. Marcy was an extremely accomplished scientist who, at the time of her death, was the director of the Duke Center for Human Genetics and chief of the Division of Medical Genetics. During her career, she published 124 articles and 16 book chapters; the topics of her scholarly scientific work ranged from gene mapping and identification to method development in genetic epidemiology and authoritative book chapters on linkage analysis. Over her scientific career, Marcy was the recipient of 24 National Institutes of Health (NIH) grants; of these, she was principal investigator of 18.

There are 30 new articles in PLoS ONE this week. Here are my picks:
Ultrasonic Communication in Rats: Can Playback of 50-kHz Calls Induce Approach Behavior?:

Rats emit distinct types of ultrasonic vocalizations, which differ depending on age, the subject’s current state and environmental factors. Since it was shown that 50-kHz calls can serve as indices of the animal’s positive subjective state, they have received increasing experimental attention, and have successfully been used to study neurobiological mechanisms of positive affect. However, it is likely that such calls do not only reflect a positive affective state, but that they also serve a communicative purpose. Actually, rats emit the highest rates of 50-kHz calls typically during social interactions, like reproductive behavior, juvenile play and tickling. Furthermore, it was recently shown that rats emit 50-kHz calls after separation from conspecifics. The aim of the present study was to test the communicative value of such 50-kHz calls. In a first experiment, conducted in juvenile rats situated singly on a radial maze apparatus, we showed that 50-kHz calls can induce behavioral activation and approach responses, which were selective to 50-kHz signals, since presentation of 22-kHz calls, considered to be aversive or threat signals, led to behavioral inhibition. In two other experiments, we used either natural 50-kHz calls, which had been previously recorded from other rats, or artificial sine wave stimuli, which were identical to these calls with respect to peak frequency, call length and temporal appearance. These signals were presented to either juvenile (Exp. 2) or adult (Exp. 3) male rats. Our data clearly show that 50-kHz signals can induce approach behavior, an effect, which was more pronounced in juvenile rats and which was not selective to natural calls, especially in adult rats. The recipient rats also emitted some 50-kHz calls in response to call presentation, but this effect was observed only in adult subjects. Together, our data show that 50-kHz calls can serve communicative purposes, namely as a social signal, which increases the likelihood of approach in the recipient conspecific.

An Animal Model of Emotional Blunting in Schizophrenia:

Schizophrenia is often associated with emotional blunting–the diminished ability to respond to emotionally salient stimuli–particularly those stimuli representative of negative emotional states, such as fear. This disturbance may stem from dysfunction of the amygdala, a brain region involved in fear processing. The present article describes a novel animal model of emotional blunting in schizophrenia. This model involves interfering with normal fear processing (classical conditioning) in rats by means of acute ketamine administration. We confirm, in a series of experiments comprised of cFos staining, behavioral analysis and neurochemical determinations, that ketamine interferes with the behavioral expression of fear and with normal fear processing in the amygdala and related brain regions. We further show that the atypical antipsychotic drug clozapine, but not the typical antipsychotic haloperidol nor an experimental glutamate receptor 2/3 agonist, inhibits ketamine’s effects and retains normal fear processing in the amygdala at a neurochemical level, despite the observation that fear-related behavior is still inhibited due to ketamine administration. Our results suggest that the relative resistance of emotional blunting to drug treatment may be partially due to an inability of conventional therapies to target the multiple anatomical and functional brain systems involved in emotional processing. A conceptual model reconciling our findings in terms of neurochemistry and behavior is postulated and discussed.

The Oral Cavity and Age: A Site of Chronic Inflammation?:

Aging may be accompanied by a low grade chronic up-regulation of inflammatory mediators. A variety of endogenous locally released mediators as well as inflammatory cells have been reported in the human oral cavity. The aim of this investigation was to determine the presence of different classes of inflammatory mediators in human saliva and correlate the levels with age. Unstimulated whole buccal salivary samples were obtained in the morning from 94 healthy volunteers within 30 minutes after waking. None of the participants had taken aspirin in the week prior to the saliva collection. Lysozyme activity, eicosanoid levels (prostaglandin E2 and leukotriene B4) and MMP-9 activity were measured. The antimicrobial activity (lysozyme activity) was not correlated with age whereas PGE2 levels were markedly correlated with age (r = 0.29; P40 years) demonstrated a significant increase in the mean values for PGE2 and MMP-9 activity with age. In addition, significant correlations were observed between LTB4 and PGE2 (r = 0.28; P<0.05; n = 56) and between LTB4 levels and MMP-9 activity in smokers (r = 0.78; P<0.001; n = 15). The presence of significant levels and activity of inflammatory mediators in saliva suggests that the oral cavity of healthy subjects may be in a constant low state of inflammation associated with age.

Songbirds Offer Clues To Highly Practiced Motor Skills In Humans:

The melodious sound of a songbird may appear effortless, but his elocutions are actually the result of rigorous training undergone in youth and maintained throughout adulthood. His tune has virtually “crystallized” by maturity. The same control is seen in the motor performance of top athletes and musicians. Yet, subtle variations in highly practiced skills persist in both songbirds and humans. Now, scientists think they know why.

Scientist On Quest For Disappearing Eel:

A Queen’s environmental scientist will head a new international study to determine whether American eels – the slimy, snake-like fish considered worldwide to be a food delicacy – are dying from chemical pollution in Lake Ontario.

Photo-monitoring Whale Sharks: Largest Fish In The Sea Appear To Thrive Under Regulated Ecotourism:

Up to 20 meters long and weighing as much as 20 tons, its enormous size gives the whale shark (Rhincodon typus) its name. Known as the ‘gentle giant’ for its non-predatory behavior, this fish, with its broad, flattened head and minute teeth, eats tiny zooplankton, sieving them through a fine mesh of gill-rakers. Listed as a rare species, relatively little is known about whale sharks, which live in tropical and warm seas, including the western Atlantic and southern Pacific.

Two ‘Noses’ Are Necessary For Flies To Navigate Well:

Animals and insects communicate through an invisible world of scents. By exploiting infrared technology, researchers at Rockefeller University just made that world visible. With the ability to see smells, these scientists now show that when fly larvae detect smells with both olfactory organs they find their way toward a scented target more accurately than when they detect them with one.

Lots of good stuff in PLoS Biology this week:
Cognitive Dimensions of Predator Responses to Imperfect Mimicry:

Many palatable animals, for example hoverflies, deter predators by mimicking well-defended insects such as wasps. However, for human observers, these flies often seem to be little better than caricatures of wasps–their visual appearance and behaviour are easily distinguishable from those which they are attempting to mimic. This imperfect mimicry baffles evolutionary biologists, because one might expect natural selection to do a more thorough job. Here we discuss two types of cognitive processes that might explain why distinguishable mimics could enjoy increased protection from predation. Speed-accuracy tradeoffs in predator decision making might give imperfect mimics sufficient time to escape, and predators under time constraint might avoid time-consuming discriminations between well-defended models and inaccurate edible mimics and instead adopt a “safety first” policy of avoiding insects with similar appearance. Categorisation of prey types by predators could mean that wholly dissimilar mimics may be protected, provided they share some common property with noxious prey. If predators use experience with multiple prey types to learn rules rather than just memorising the appearance of individual prey types, it follows that different individual predators should form different categories, each including separate types of novel prey. Experimental studies to test these hypotheses should be straightforward, because we can use the relatively simple signals (e.g., striped patterns) with which prey manipulate predator behaviour as tools for investigating cognitive processes that underlie decision making and object recognition in animals’ daily lives.

Going against the Grain:

The data that would change the course of Jonathan Tilly’s career and cause an uproar in the field of ovarian biology almost never saw the light of day. In Tilly’s cell death lab, postdoctoral fellow Tomoko Kaneko had twice repeated her experiments to kill off mouse egg cells, but something was wrong because the egg cell numbers were still high after treatment with a chemotherapy drug. Kaneko consulted another postdoc in the lab, Josh Johnson, and together they tried to determine if she had made a technical mistake or perhaps switched her control and experimental groups.
“All of us ‘knew’ that egg regeneration couldn’t be occurring,” says Johnson, referring to the long-held view that adult female mammals are born with a fixed pool of oocytes, or egg cells, which gradually declines in number with age. The work appeared to be an anomaly, but Johnson prodded Kaneko to take it to their advisor’s office. That 2002 meeting was the birth of an ongoing controversy that has shaken up the field of reproductive biology, with Tilly’s laboratory publishing data they interpret as evidence of egg regeneration occurring in adult mice.

Sex, Dose, and Equality:

As a rule, genes and chromosomes come in pairs. Sex chromosomes are an exception to this rule. Males of many species have only one X chromosome, a male-specific Y chromosome, and a set of autosomes (AA). Individuals with two X chromosomes and a set of autosomes (XX;AA) are female. Sex chromosomes were first noticed for this distinct unpaired morphology and are now known to have substantially different gene content [1]. These unusual cases have attracted a great deal of attention over the years, not only because of the role they often play in sex determination, but also as windows into more basic features of genes and gene networks. One such feature is the relationship between gene function and dose. Sex chromosomes allow us to question the importance of having a pair of each gene. With current knowledge of gene regulation, one can make an argument that gene dose should not matter. In textbooks and manuscripts, one often finds figures showing the relationship between genes in a pathway or network, replete with elegant feed-back and feed-forward regulatory interactions, parallel pathways, etc. At the transcript level, it seems logical that any inherent 2-fold quantitative difference due to gene dose should be dwarfed, or even nullified, by the high-magnitude changes resulting from transcriptional regulation by proteins that are arrayed at enhancers or silencers. Basic textbook knowledge of genetics also suggests that dose is not very important. Having a single copy of most genes is not deleterious–there are few dominant alleles due to haploinsufficiency. These observations suggest that genes come in pairs to facilitate reproduction, and perhaps to provide a backup in case of spontaneous mutations occurring during the course of somatic development. It seems likely that the dose of most genes is unimportant because of robustness in gene networks, which buffers against noise and mutation [2].

Male or Female? The Answer Depends on When You Ask:

Akey decision in the life of an organism is whether to be male or female. In Drosophila, each cell makes this choice independently of its neighbors such that diploid cells with one X chromosome (XY) are male and those with two chromosomes (XX) are female. In classic experiments carried out more than 80 years ago, Calvin Bridges made two important conclusions about how sex is determined in flies [1-3]. He showed that the Y chromosome is not a factor and suggested that sex is determined not simply by counting X chromosomes, but by calculating the ratio of X chromosomes to the number of sets of autosomes (known as the X:A ratio). The concept that sex is determined by a mechanism that evaluates the number of X chromosomes relative to autosomes was invoked to explain the observation that animals with two X chromosomes and three sets of autosomes (XX; AAA) develop as sexual mosaics rather than females. According to this model, animals with the same number of X chromosomes as autosome sets (ratio of 1) are female, animals with half as many X chromosomes as sets of autosomes are male (ratio of 0.5), and those with an intermediate ratio (XX; AAA; ratio of 0.67) are sexual mosaics. With the finding that haploid cells (X; A; ratio of 1) are female [4,5], the idea that sex is determined by the X:A ratio became enshrined in the literature.

A Neural Computation for Visual Acuity in the Presence of Eye Movements:

Like a camera, the eye projects an image of the world onto our retina. But unlike a camera, the eye continues to execute small, random movements, even when we fix our gaze. Consequently, the projected image jitters over the retina. In a camera, such jitter leads to a blurred image on the film. Interestingly, our visual acuity is many times sharper than expected from the motion blur. Apparently, the brain uses an active process to track the image through its jittering motion across the retina. Here, we propose an algorithm for how this can be accomplished. The algorithm uses realistic spike responses of optic nerve fibers to reconstruct the visual image, and requires no knowledge of the eye movement trajectory. Its performance can account for human visual acuity. Furthermore, we show that this algorithm could be implemented biologically by the neural circuits of primary visual cortex.

Study Of Bear Hair Will Reveal Genetic Diversity Of Yellowstone’s Grizzlies:

Locks of hair from more than 400 grizzly bears are stored at Montana State University, waiting to tell the tale of genetic diversity in the Yellowstone Ecosystem.

My friend Tim Langer has done a very similar study here in North Carolina.
Squirrels Use Old Snake Skins To Mask Their Scent From Predators:

California ground squirrels and rock squirrels chew up rattlesnake skin and smear it on their fur to mask their scent from predators, according to a new study by researchers at UC Davis.

Anne-Marie has more.
Pinot Noir Grape Sequenced:

Viticulture, the growing of grapes (Vitis vinifera) chiefly to make wine, is an ancient form of agriculture, evidence of which has been found from the Neolithic and Early Bronze Ages. We have a detailed understanding of how nurture affects the qualities of a grape harvest leading to the concept of terroir (the range of local influences that carry over into a wine). The nature of the grapes themselves has been less well understood but our knowledge of this is substantially increased by the publication of a high quality draft genome sequence of a Pinot Noir grape by an Italian-based multinational consortium.

Success Of Invasive Argentine Ants Linked To Diet Shifts:

The Argentine ant, Linepithema humile, is one of the most successful invasive species in the world, having colonized parts of five continents in addition to its native range in South America. A new study sheds light on the secrets of its success.

Snake Venoms Share Similar Ingredients:

Venoms from different snake families may have many deadly ingredients in common, more than was previously thought. A study published in the online open access journal BMC Molecular Biology has unexpectedly discovered three-finger toxins in a subspecies of the Massasauga Rattlesnake, as well as evidence for a novel toxin genes resulting from gene fusion.

Dolphin ‘Therapy’ A Dangerous Fad, Researchers Warn:

People suffering from chronic mental or physical disabilities should not resort to a dolphin “healing” experience, warn two researchers from Emory University. Lori Marino, senior lecturer in the Neuroscience and Behavioral Biology Program, has teamed with Scott Lilienfeld, professor in the Department of Psychology, to launch an educational campaign countering claims made by purveyors of what is known as dolphin-assisted therapy (DAT).