A Blog Around The Clock

As always on Monday night, there are new articles published in PLoS Biology and PLoS Medicine. Here are some of the highlights:
Shedding Light on Animal Cryptochromes:

Anyone who’s neglected a houseplant for any length of time knows that plants can’t survive without light. But it’s more complicated than that; in addition to serving as an energy source, light is used by plants as a signal to sense and respond to the environment. For example, both red and blue light send the signal for maturation and flower and seed development. Depriving a plant of such light signals disrupts a variety of growth processes such as early seedling development, leaf and stem expansion, and initiation of flowering, as well as circadian clock entrainment. Cryptochromes are photoreceptor proteins used by plants to mediate the effects of blue light; they are also found in animals like flies and mice, where they help to regulate the circadian clock. In plants, exposure to blue light results in the reduction (gain of electrons) of flavin pigments that are bound by the cryptochrome. Blue light activates plant cryptochromes by reducing the flavins, but researchers weren’t sure exactly how blue light activates fly cryptochromes, or if mammalian cryptochromes even respond to light at all.

Human and Drosophila Cryptochromes Are Light Activated by Flavin Photoreduction in Living Cells:

Vision in animals is generally associated with light-sensitive rhodopsin pigments located in the eyes. However, animals ranging from flies to humans also possess ancient visual receptors known as cryptochromes in multiple cell types. In this work, we study the mechanism of light sensing in two representative animal cryptochromes: a light-sensitive Drosophila cryptochrome (Dmcry) and a presumed light-insensitive mammalian cryptochrome from humans (Hscry1). We expressed recombinant cryptochromes to high levels in living cells, irradiated the cells with blue light, and analyzed the proteins’ response to irradiation with electron paramagnetic resonance and fluorescence spectroscopic techniques. Photoreduction of protein-bound oxidized FAD cofactor to its radical form emerged as the primary cryptochrome photoreaction in living cells, and was correlated with a light-sensitive biological response in whole organisms. These results indicate that both Dmcry and Hscry1 are capable of undergoing similar light-driven reactions and suggest the possibility of an as-yet unknown photo-perception role for human cryptochromes in tissues exposed to light.

From Structure to Function: Mapping the Connection Matrix of the Human Brain:

When American architect Louis Sullivan proffered the enduring mantra of 20th century design–form follows function–he chided his peers for violating in art a law so clearly visible in the “open apple blossom” and “sweeping eagle in his flight.” The notion that the essence of things takes shape in the matter of things, first articulated in Aristotle’s philosophy, has long guided biologists’ attempts to understand the inner workings of the most complex organ known–the human brain. Fine-grained descriptions of anatomical features of the eye and ear, for example, have yielded critical insights into the neural basis of image and sound perception. But for a systems-level understanding of how the brain works, researchers look to the overall topology of network connections among neurons for answers.

Neuronal Correlates of the Set-Size Effect in Monkey Lateral Intraparietal Area:

It is well known that the brain is limited in the amount of sensory information that it can process at any given time. During an everyday task such as finding an object in a cluttered environment (known as visual search), observers take longer to find a target as the number of distractors increases. This well-known phenomenon implies that inputs from distractors interfere with the brain’s ability to perceive the target at some stage or stages of neural processing. However, the loci and mechanisms of this interference are unknown. Visual information is processed in feature-selective areas that encode the physical properties of stimuli and in higher-order areas that convey information about behavioral significance and help direct attention to individual stimuli. Here we studied a higher-order parietal area related to attention and eye movements. We found that parietal neurons selectively track the location of a search target during a difficult visual search task. However, neuronal firing rates decreased as distractors were added to the display, and the decrease in the target-related response correlated with the set-size-related increase in reaction time. This suggests that distractors trigger competitive visuo-visual interactions that limit the brain’s ability to find and focus on a task-relevant target.

Mapping the Structural Core of Human Cerebral Cortex:

In the human brain, neural activation patterns are shaped by the underlying structural connections that form a dense network of fiber pathways linking all regions of the cerebral cortex. Using diffusion imaging techniques, which allow the noninvasive mapping of fiber pathways, we constructed connection maps covering the entire cortical surface. Computational analyses of the resulting complex brain network reveal regions of cortex that are highly connected and highly central, forming a structural core of the human brain. Key components of the core are portions of posterior medial cortex that are known to be highly activated at rest, when the brain is not engaged in a cognitively demanding task. Because we were interested in how brain structure relates to brain function, we also recorded brain activation patterns from the same participant group. We found that structural connection patterns and functional interactions between regions of cortex were significantly correlated. Based on our findings, we suggest that the structural core of the brain may have a central role in integrating information across functionally segregated brain regions.

Toward a Global View of Alcohol, Tobacco, Cannabis, and Cocaine Use: Findings from the WHO World Mental Health Surveys:

Alcohol, tobacco, and illegal drug use are held responsible for considerable mortality and morbidity [1], but in the most recent World Health Organization (WHO) Global Burden of Disease estimates, the authors unanimously asserted that better epidemiological data on use were needed, particularly in less established market economies [2-4]. This paper presents data on lifetime alcohol, tobacco, cannabis, and cocaine use from rigorously conducted field surveys using a common research approach in the first 17 countries to participate in the WHO’s World Mental Health (WMH) Survey Initiative [5,6]. A number of less established market economies are included in this set of countries.

Documenting Mortality in Crises: What Keeps Us from Doing Better?:

The effects of crises (man-made or natural disasters) on physical health are ultimately quantifiable as a rise in mortality. Precise and unbiased estimates of mortality rates (deaths per person-time) or excess death tolls (deaths attributable to the presence of the crisis) are critical to grading the severity of a crisis at its onset and over time, and adjusting relief operations accordingly [1,2]. Indeed, the onset of emergencies is commonly defined as a doubling of mortality rate from the pre-crisis baseline, or the crossing of fixed thresholds, typically one death per 10,000 person-days [2]. In reality, because mortality increases only after a crisis has evolved, acute malnutrition may be a better indicator for early crisis detection [3], and data on morbidity and on the coverage of interventions against the main known risk factors for poor health outcomes (e.g., insufficient water and sanitation, lack of preventive and curative health services, etc.) are more useful to target relief programmes and minimise preventable deaths.

Mammalian Clock Protein Responds Directly To Light:

We all know that light effects the growth and development of plants, but what effect does light have on humans and animals? A new paper by Nathalie Hoang et al., published in PLoS Biology, explores this question by examining cryptochromes in flies, mice, and humans. In plants, cryptochromes are photoreceptor proteins which absorb and process blue light for functions such as growth, seedling development, and leaf and stem expansion. Cryptochromes are present in humans and animals as well and have been proven to regulate the mechanisms of the circadian clock. But how they work in humans and animals is still somewhat of a mystery.

Whales Set To Chase Shrinking Feed Zones:

Endangered migratory whales will be faced with shrinking crucial Antarctic foraging zones which will contain less food and will be further away, a new analysis of the impacts of climate change on Southern Ocean whales has found.

Watermelon May Have Viagra-effect:

A cold slice of watermelon has long been a Fourth of July holiday staple. But according to recent studies, the juicy fruit may be better suited for Valentine’s Day. That’s because scientists say watermelon has ingredients that deliver Viagra-like effects to the body’s blood vessels and may even increase libido.

Climate Change Causing Significant Shift In Composition Of Coastal Fish Communities:

A detailed analysis of data from nearly 50 years of weekly fish-trawl surveys in Narragansett Bay and adjacent Rhode Island Sound has revealed a long-term shift in species composition, which scientists attribute primarily to the effects of global warming.

Passports For Penguins: New Technology Lets Biologists ID Large Numbers Of Endangered Animals:

Ground-breaking technology that will enable biologists to identify and monitor large numbers of endangered animals, from butterflies to whales, without being captured, will be shown to the public for the first time at this year’s Royal Society Summer Science exhibition [30 June to 3 July].

Biologists Show How Eye’s Neurons Switch Functions During Metamorphosis:

Researchers at New York University’s Center for Developmental Genetics report that the photoreceptors in an insect’s eye can change their traditional functions during metamorphosis. The researchers found that when photoreceptors responsible for detecting the color green die off during metamorphosis a second class of photoreceptors–those responsible for detecting the color blue–then fill the role of detecting the color green. These rare switches, the authors speculate, are likely the result of changing life patterns.

Canine Tooth Strength Provides Clues To Behavior Of Early Human Ancestors:

Measuring and testing the teeth of living primates could provide a window into the behavior of the earliest human ancestors, based on their fossilized remains. Research funded by the National Science Foundation and led by University of Arkansas anthropologist Michael Plavcan takes us one step closer to understanding the relationship between canine teeth, body size and the lives of primates.

Thursday night – time to check in to see what is new in PLoS Genetics, PLoS Computational Biology, PLoS Pathogens and PLoS Neglected Tropical Diseases:
The Exception That Proves the Rule: An Interview with Jenny Graves:

Close to 20 years ago, I was contacted by an Australian woman who was planning to map the locations of genes that are X-linked in humans in some odd Australian critters, the monotremes. These animals comprise a distantly related branch of mammals that have hair and lactate, but additionally lay eggs. She wanted a probe from our lab, and, in exchange, little vials of DNA from spiny echidna and platypus appeared in the mail. Our lab became enamoured of these singular animals, and we followed their scientific story with great interest. The lady was Jenny Graves [Image 1], and it has taken me this long to finally meet her.

Ten Simple Rules for Organizing a Scientific Meeting:

Scientific meetings come in various flavors–from one-day focused workshops of 1-20 people to large-scale multiple-day meetings of 1,000 or more delegates, including keynotes, sessions, posters, social events, and so on. These ten rules are intended to provide insights into organizing meetings across the scale.

How To Advance Open International Scientific Exchange:

Computational biology is an international collaboration. Open scholarly exchange nurtures the development of our field. And scientists are not the only beneficiaries; international cooperation is a crucial part of any country’s diplomatic relations. Our community, by actively engaging governments, needs to promote scientific exchange.

Neglected Infections of Poverty in the United States of America:

In the United States, there is a largely hidden burden of diseases caused by a group of chronic and debilitating parasitic, bacterial, and congenital infections known as the neglected infections of poverty. Like their neglected tropical disease counterparts in developing countries, the neglected infections of poverty in the US disproportionately affect impoverished and under-represented minority populations. The major neglected infections include the helminth infections, toxocariasis, strongyloidiasis, ascariasis, and cysticercosis; the intestinal protozoan infection trichomoniasis; some zoonotic bacterial infections, including leptospirosis; the vector-borne infections Chagas disease, leishmaniasis, trench fever, and dengue fever; and the congenital infections cytomegalovirus (CMV), toxoplasmosis, and syphilis. These diseases occur predominantly in people of color living in the Mississippi Delta and elsewhere in the American South, in disadvantaged urban areas, and in the US-Mexico borderlands, as well as in certain immigrant populations and disadvantaged white populations living in Appalachia. Preliminary disease burden estimates of the neglected infections of poverty indicate that tens of thousands, or in some cases, hundreds of thousands of poor Americans harbor these chronic infections, which represent some of the greatest health disparities in the United States. Specific policy recommendations include active surveillance (including newborn screening) to ascertain accurate population-based estimates of disease burden; epidemiological studies to determine the extent of autochthonous transmission of Chagas disease and other infections; mass or targeted treatments; vector control; and research and development for new control tools including improved diagnostics and accelerated development of a vaccine to prevent congenital CMV infection and congenital toxoplasmosis.

Huge Genome-scale Phylogenetic Study Of Birds Rewrites Evolutionary Tree-of-life:

The largest ever study of bird genetics has not only shaken up but completely redrawn the avian evolutionary tree. The study challenges current classifications, alters our understanding of avian evolution, and provides a valuable resource for phylogenetic and comparative studies in birds.

Cocoa Genome To Be Sequenced: May Benefit Millions Of Farmers, Help Sustain World’s Chocolate Supply:

The United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Mars, Incorporated, and IBM intend to apply their scientific resources to sequence and analyze the entire cocoa genome. Sequencing the cocoa genome is a significant scientific step that may allow more directed breeding of cocoa plants and perhaps even enhance the quality of cocoa, the key ingredient in chocolate.

Neuroscientists Discover A Sense Of Adventure:

Wellcome Trust scientists have identified a key region of the brain which encourages us to be adventurous. The region, located in a primitive area of the brain, is activated when we choose unfamiliar options, suggesting an evolutionary advantage for sampling the unknown. It may also explain why re-branding of familiar products encourages to pick them off the supermarket shelves.

Nerve Cells Derived From Stem Cells And Transplanted Into Mice May Lead To Improved Brain Treatments:

Scientists at the Burnham Institute for Medical Research have, for the first time, genetically programmed embryonic stem (ES) cells to become nerve cells when transplanted into the brain, according to a new study published in The Journal of Neuroscience.

Women Have Not Adapted To Casual Sex, Research Shows:

The sexual and feminist revolutions were supposed to free women to enjoy casual sex just as men always had. Yet according to Professor Anne Campbell from Durham University in the UK, the negative feelings reported by women after one-night stands suggest that they are not well adapted to fleeting sexual encounters.

Salutary Pizza Spice: Oregano Helps Against Inflammations:

Oregano doesn’t only give a pizza its typical taste. Researchers at Bonn University and the ETH Zürich have discovered that this spice also contains a substance which, amongst other qualities, appears to help cure inflammations.

Diversity Among Bird Populations Found To Reduce Threat Of West Nile Virus:

A biologist and undergraduate student have discovered that what’s good for an area’s bird population is also good for people living nearby.

It’s Email, But At A Snail’s Pace:

Bournemouth University Research Fellows Vicki Isley and Paul Smith are using live snails to send emails as part of a ‘slow art’ project aimed at encouraging people to explore notions of time.

Extreme Weather Events Can Unleash A ‘Perfect Storm’ Of Infectious Diseases, Research Study Says:

An international research team, including University of Minnesota researcher Craig Packer, has found the first clear example of how climate extremes, such as the increased frequency of droughts and floods expected with global warming, can create conditions in which diseases that are tolerated individually may converge and cause mass die-offs of livestock or wildlife.

Our Genome Changes Over Lifetime, And May Explain Many ‘Late-onset’ Diseases:

Researchers at Johns Hopkins have found that epigenetic marks on DNA-chemical marks other than the DNA sequence-do indeed change over a person’s lifetime, and that the degree of change is similar among family members. The team suggests that overall genome health is heritable and that epigenetic changes occurring over one’s lifetime may explain why disease susceptibility increases with age.

Newly Identified Role For ‘Power Plants’ In Human Cells Could Lead To Targeted Therapies:

Scientists have determined that human cells are able to shift important gene products into their own mitochondria, considered the power plants of cells. The finding could eventually lead to therapies for dozens of diseases.

‘Neglected Infections Of Poverty’ In United States Disable Hundreds Of Thousands Of Americans Annually:

An analysis published June 25th in the open-access journal PLoS Neglected Tropical Diseases highlights that diseases very similar to those plaguing Africa, Asia, and Latin America are also occurring frequently among the poorest people in the United States, especially women and children. These diseases — the “neglected infections of poverty” — are caused by chronic and debilitating parasitic, bacterial, and congenital infections.

Climate Change Could Severely Impact California’s Unique Native Plants:

The native plants unique to California are so vulnerable to global climate change that two-thirds of these “endemics” could suffer more than an 80 percent reduction in geographic range by the end of the century, according to a new University of California, Berkeley, study.

No Scent, No Sex For The Japanese Beetle:

No scent. No sex. If a male Japanese beetle is unable to detect the sex pheromone released by a female, he won’t be able to locate her and reproduce.

There are 54 new articlespublished in PLoS ONE today. Here are my picks:
Climate Extremes Promote Fatal Co-Infections during Canine Distemper Epidemics in African Lions:

Extreme climatic conditions may alter historic host-pathogen relationships and synchronize the temporal and spatial convergence of multiple infectious agents, triggering epidemics with far greater mortality than those due to single pathogens. Here we present the first data to clearly illustrate how climate extremes can promote a complex interplay between epidemic and endemic pathogens that are normally tolerated in isolation, but with co-infection, result in catastrophic mortality. A 1994 canine distemper virus (CDV) epidemic in Serengeti lions (Panthera leo) coincided with the death of a third of the population, and a second high-mortality CDV epidemic struck the nearby Ngorongoro Crater lion population in 2001. The extent of adult mortalities was unusual for CDV and prompted an investigation into contributing factors. Serological analyses indicated that at least five “silent” CDV epidemics swept through the same two lion populations between 1976 and 2006 without clinical signs or measurable mortality, indicating that CDV was not necessarily fatal. Clinical and pathology findings suggested that hemoparsitism was a major contributing factor during fatal epidemics. Using quantitative real-time PCR, we measured the magnitude of hemoparasite infections in these populations over 22 years and demonstrated significantly higher levels of Babesia during the 1994 and 2001 epidemics. Babesia levels correlated with mortalities and extent of CDV exposure within prides. The common event preceding the two high mortality CDV outbreaks was extreme drought conditions with wide-spread herbivore die-offs, most notably of Cape buffalo (Syncerus caffer). As a consequence of high tick numbers after the resumption of rains and heavy tick infestations of starving buffalo, the lions were infected by unusually high numbers of Babesia, infections that were magnified by the immunosuppressive effects of coincident CDV, leading to unprecedented mortality. Such mass mortality events may become increasingly common if climate extremes disrupt historic stable relationships between co-existing pathogens and their susceptible hosts.

Left Hemisphere Specialization for Oro-Facial Movements of Learned Vocal Signals by Captive Chimpanzees:

The left hemisphere of the human brain is dominant in the production of speech and signed language. Whether similar lateralization of function for communicative signal production is present in other primates remains a topic of considerable debate. In the current study, we examined whether oro-facial movements associated with the production of learned attention-getting sounds are differentially lateralized compared to facial expressions associated with the production of species-typical emotional vocalizations in chimpanzees. Still images captured from digital video were used to quantify oro-facial asymmetries in the production of two attention-getting sounds and two species-typical vocalizations in a sample of captive chimpanzees. Comparisons of mouth asymmetries during production of these sounds revealed significant rightward biased asymmetries for the attention-getting sounds and significant leftward biased asymmetries for the species-typical sounds. These results suggest that the motor control of oro-facial movements associated with the production of learned sounds is lateralized to the left hemisphere in chimpanzees. Furthermore, the findings suggest that the antecedents for lateralization of human speech may have been present in the common ancestor of chimpanzees and humans ~5 mya and are not unique to the human lineage.

Mapping Health Literacy Research in the European Union: A Bibliometric Analysis:

To examine and compare the research productivity on selected fields related to health literacy of the current members of the European Union, the four candidate countries waiting to join the EU, Norway, Switzerland, and the United States. A bibliometric analysis (1991-2005). Data sources included papers published by authors from each country separately. The 25 European countries produce less than 1/3 health literacy research when compared to the U.S. (13,710 and 49,523 articles were published by authors with main affiliation in the European Union and the four candidate countries, and the U.S., respectively). The Netherlands and Sweden (followed by Germany, Italy, and France) are the European countries with the highest number of research published in fields related to health literacy. After adjustment for population Sweden, Finland, and Norway, were on the top of the relevant list. In addition, Sweden, Finland, and Ireland, were on the top of the list of countries regarding research productivity on the selected fields after adjustment for gross domestic product (GDP). Inequalities in research published on the topic of health literacy exist among Europe, Norway, Switzerland, and the U.S. More research may need to be done in all areas of health literacy in Europe and the potential detrimental effects of this gap should be further investigated.

Climate Change and the Future of California’s Endemic Flora:

The flora of California, a global biodiversity hotspot, includes 2387 endemic plant taxa. With anticipated climate change, we project that up to 66% will experience >80% reductions in range size within a century. These results are comparable with other studies of fewer species or just samples of a region’s endemics. Projected reductions depend on the magnitude of future emissions and on the ability of species to disperse from their current locations. California’s varied terrain could cause species to move in very different directions, breaking up present-day floras. However, our projections also identify regions where species undergoing severe range reductions may persist. Protecting these potential future refugia and facilitating species dispersal will be essential to maintain biodiversity in the face of climate change.

Increased Avian Diversity Is Associated with Lower Incidence of Human West Nile Infection: Observation of the Dilution Effect:

Recent infectious disease models illustrate a suite of mechanisms that can result in lower incidence of disease in areas of higher disease host diversity-the ‘dilution effect’. These models are particularly applicable to human zoonoses, which are infectious diseases of wildlife that spill over into human populations. As many recent emerging infectious diseases are zoonoses, the mechanisms that underlie the ‘dilution effect’ are potentially widely applicable and could contribute greatly to our understanding of a suite of diseases. The dilution effect has largely been observed in the context of Lyme disease and the predictions of the underlying models have rarely been examined for other infectious diseases on a broad geographic scale. Here, we explored whether the dilution effect can be observed in the relationship between the incidence of human West Nile virus (WNV) infection and bird (host) diversity in the eastern US. We constructed a novel geospatial contrasts analysis that compares the small differences in avian diversity of neighboring US counties (where one county reported human cases of WNV and the other reported no cases) with associated between-county differences in human disease. We also controlled for confounding factors of climate, regional variation in mosquito vector type, urbanization, and human socioeconomic factors that are all likely to affect human disease incidence. We found there is lower incidence of human WNV in eastern US counties that have greater avian (viral host) diversity. This pattern exists when examining diversity-disease relationships both before WNV reached the US (in 1998) and once the epidemic was underway (in 2002). The robust disease-diversity relationships confirm that the dilution effect can be observed in another emerging infectious disease and illustrate an important ecosystem service provided by biodiversity, further supporting the growing view that protecting biodiversity should be considered in public health and safety plans.

Cortical Plasticity Induced by Transcranial Magnetic Stimulation during Wakefulness Affects Electroencephalogram Activity during Sleep:

Sleep electroencephalogram (EEG) brain oscillations in the low-frequency range show local signs of homeostatic regulation after learning. Such increases and decreases of slow wave activity are limited to the cortical regions involved in specific task performance during wakefulness. Here, we test the hypothesis that reorganization of motor cortex produced by long-term potentiation (LTP) affects EEG activity of this brain area during subsequent sleep. By pairing median nerve stimulation with transcranial magnetic stimulation over the contralateral motor cortex, one can potentiate the motor output, which is presumed to reflect plasticity of the neural circuitry. This paired associative stimulation increases M1 cortical excitability at interstimulus intervals of 25 ms. We compared the scalp distribution of sleep EEG power following paired associative stimulation at 25 ms to that following a control paradigm with 50 ms intervals. It is shown that the experimental manipulation by paired associative stimulation at 25 ms induces a 48% increase in amplitude of motor evoked potentials. This LTP-like potentiation, induced during waking, affects delta and theta EEG power in both REM and non-REM sleep, measured during the following night. Slow-wave activity increases in some frontal and prefrontal derivations and decreases at sites neighboring and contralateral to the stimulated motor cortex. The magnitude of increased amplitudes of motor evoked potentials by the paired associative stimulation at 25 ms predicts enhancements of slow-wave activity in prefrontal regions. An LTP-like paradigm, presumably inducing increased synaptic strength, leads to changes in local sleep regulation, as indexed by EEG slow-wave activity. Enhancement and depression of slow-wave activity are interpreted in terms of a simultaneous activation of both excitatory and inhibitory circuits consequent to the paired associative stimulation at 25 ms.

Enhanced Caenorhabditis elegans Locomotion in a Structured Microfluidic Environment:

Behavioral studies of Caenorhabditis elegans traditionally are done on the smooth surface of agar plates, but the natural habitat of C. elegans and other nematodes is the soil, a complex and structured environment. In order to investigate how worms move in such environments, we have developed a technique to study C. elegans locomotion in microstructures fabricated from agar. When placed in open, liquid-filled, microfluidic chambers containing a square array of posts, we discovered that worms are capable of a novel mode of locomotion, which combines the fast gait of swimming with the more efficient movements of crawling. When the wavelength of the worms matched the periodicity of the post array, the microstructure directed the swimming and increased the speed of C. elegans ten-fold. We found that mutants defective in mechanosensation (mec-4, mec-10) or mutants with abnormal waveforms (unc-29) did not perform this enhanced locomotion and moved much more slowly than wild-type worms in the microstructure. These results show that the microstructure can be used as a behavioral screen for mechanosensory and uncoordinated mutants. It is likely that worms use mechanosensation in the movement and navigation through heterogeneous environments.

A Vaccine against Nicotine for Smoking Cessation: A Randomized Controlled Trial:

Tobacco dependence is the leading cause of preventable death and disabilities worldwide and nicotine is the main substance responsible for the addiction to tobacco. A vaccine against nicotine was tested in a 6-month randomized, double blind phase II smoking cessation study in 341 smokers with a subsequent 6-month follow-up period. 229 subjects were randomized to receive five intramuscular injections of the nicotine vaccine and 112 to receive placebo at monthly intervals. All subjects received individual behavioral smoking cessation counseling. The vaccine was safe, generally well tolerated and highly immunogenic, inducing a 100% antibody responder rate after the first injection. Point prevalence of abstinence at month 2 showed a statistically significant difference between subjects treated with Nicotine-Qβ (47.2%) and placebo (35.1%) (P = 0.036), but continuous abstinence between months 2 and 6 was not significantly different. However, in subgroup analysis of the per-protocol population, the third of subjects with highest antibody levels showed higher continuous abstinence from month 2 until month 6 (56.6%) than placebo treated participants (31.3%) (OR 2.9; P = 0.004) while medium and low antibody levels did not increase abstinence rates. After 12 month, the difference in continuous abstinence rate between subjects on placebo and those with high antibody response was maintained (difference 20.2%, P = 0.012). Whereas Nicotine-Qβ did not significantly increase continuous abstinence rates in the intention-to-treat population, subgroup analyses of the per-protocol population suggest that such a vaccination against nicotine can significantly increase continuous abstinence rates in smokers when sufficiently high antibody levels are achieved. Immunotherapy might open a new avenue to the treatment of nicotine addiction.

Inverse Correlation of Population Similarity and Introduction Date for Invasive Ascidians:

The genomes of many marine invertebrates, including the purple sea urchin and the solitary ascidians Ciona intestinalis and Ciona savignyi, show exceptionally high levels of heterozygosity, implying that these populations are highly polymorphic. Analysis of the C. savignyi genome found little evidence to support an elevated mutation rate, but rather points to a large population size contributing to the polymorphism level. In the present study, the relative genetic polymorphism levels in sampled populations of ten different ascidian species were determined using a similarity index generated by AFLP analysis. The goal was to determine the range of polymorphism within the populations of different species, and to uncover factors that may contribute to the high level of polymorphism. We observe that, surprisingly, the levels of polymorphism within these species show a negative correlation with the reported age of invasive populations, and that closely related species show substantially different levels of genetic polymorphism. These findings show exceptions to the assumptions that invasive species start with a low level of genetic polymorphism that increases over time and that closely related species have similar levels of genetic polymorphism.

The Prehistory of Potyviruses: Their Initial Radiation Was during the Dawn of Agriculture:

Potyviruses are found world wide, are spread by probing aphids and cause considerable crop damage. Potyvirus is one of the two largest plant virus genera and contains about 15% of all named plant virus species. When and why did the potyviruses become so numerous? Here we answer the first question and discuss the other. We have inferred the phylogenies of the partial coat protein gene sequences of about 50 potyviruses, and studied in detail the phylogenies of some using various methods and evolutionary models. Their phylogenies have been calibrated using historical isolation and outbreak events: the plum pox virus epidemic which swept through Europe in the 20th century, incursions of potyviruses into Australia after agriculture was established by European colonists, the likely transport of cowpea aphid-borne mosaic virus in cowpea seed from Africa to the Americas with the 16th century slave trade and the similar transport of papaya ringspot virus from India to the Americas. Our studies indicate that the partial coat protein genes of potyviruses have an evolutionary rate of about 1.15×10−4 nucleotide substitutions/site/year, and the initial radiation of the potyviruses occurred only about 6,600 years ago, and hence coincided with the dawn of agriculture. We discuss the ways in which agriculture may have triggered the prehistoric emergence of potyviruses and fostered their speciation.

Single Insecticide Application Can Kill Three Cockroach Generations:

One dose of an insecticide can kill three generations of cockroaches as they feed off of each other and transfer the poison, according to Purdue University entomologists who tested the effectiveness of a specific gel bait.

To Find Out What’s Eating Bats, Biologist Takes To Barn Rooftops:

Bloodsucking pests like bat fleas and bat flies may not sound very appealing to the rest of us, but to University at Buffalo biologist Katharina Dittmar de la Cruz, Ph.D., they are among the most successful creatures evolution has ever produced.

Life On The Edge: To Disperse, Or Become Extinct?:

The hardiest plants and those most likely to survive the climatic shifts brought about by global warming are now easier to identify, thanks to new research findings by a team from Queen’s University. Plants existing at the edges of their natural habitats may enhance survival of the species during global warming, says Queen’s University professor.

From The Egg, Baby Crocodiles Call To Each Other And To Mom:

For the first time, researchers have shown that the pre-hatching calls of baby Nile crocodiles actually mean something to their siblings and to their mothers. The calls–which are perfectly audible to humans and sound like “umph! umph! umph!”–tell the others in the nest that it’s time to hatch, according to the report in the June 23rd issue of Current Biology. Those cries also tell the mother croc to start digging up the nest.

Exploited Fish Make Rapid Comeback In World’s Largest No-take Marine Reserve Network:

No-take marine reserves, in which fishing is completely banned, can lead to very rapid comebacks of the fish species most prized by commercial and recreational fisheries, reveals a new study of Australia’s Great Barrier Reef published in the June 24th issue of Current Biology.

It’s Monday night – time for new articles in PLoS Biology and PLoS Medicine:
On the Emergence and Awareness of Auditory Objects:

Anyone who has walked into a crowded reverberant nightclub, with a hubbub of multiple conversations amidst blaring music, will recall the initial impression of the sound as loud and undifferentiated noise. In short order, however, different sound streams begin to emerge as one attends to individual speakers, listens to the melody from the band, or even hears one instrument in it. Humans perform this remarkable feat effortlessly. Our extraordinary abilities to extract signal from noise have evolved in natural environments that are often extremely auditorily cluttered. Many animals have developed abilities to navigate their complex auditory scenes in order to mate, locate prey, feed their young, and avoid predators. It is likely that these abilities are mediated by similar mechanisms that have evolved in many animals and include a mix of “bottom-up” automatic processes with complex “top-down” behaviors involving attention, expectation, learning, and memory (as illustrated schematically in Figure 1). However, little is known about the underlying computational details, or the manner in which these diverse processes interact to give rise to this auditory ability. And it is therefore no coincidence that we still lack engineering systems that can recognize speech robustly in realistic environments, or reliably transcribe polyphonic music.

Beyond Competition: Incorporating Positive Interactions between Species to Predict Ecosystem Invasibility:

One of the many unintended consequences of global commerce has been the translocation of countless plants and animals to new regions, continents, and oceans [1,2]. Such “exotic” species have colonized nearly every habitat on Earth, and modern ecosystems are now made up largely of species originating from geographically distinct regions [3-5]. Most exotic species have negligible or no negative effects, but a small handful have had substantial impacts on native species and ecosystem processes [3,6]. For example, the introduction of the Nile perch (Lates niloticus) into Lake Victoria has not only caused the extinction of two-thirds of the endemic fish fauna, but has changed the entire food web of the lake by reducing the grazing by phytoplanktivores [7,8].
Given the sizable ecological and economic costs of species invasions [9], understanding the environmental factors that regulate them has become a major goal for basic and applied ecologists. One major research theme is the investigation of the relationship between native species richness (the number of local native species) and the ability of exotic species to colonize and thrive in new habitats (termed community “invasibility”) [10,11]. A longstanding concept in ecology is that habitats with high levels of diversity are difficult to invade (the biotic resistance hypothesis–see Glossary) [11-15]. This is because, in theory, a more diverse assemblage of plants or animals can utilize resources more fully than a less diverse community, thus increasing the intensity of competition and making it harder for new species to become established. Predictions from this model are, however, based on the assumption that natural communities are largely structured by competitive interactions and that the effects of native species on invaders are predominantly negative.

Drug Development for Maternal Health Cannot Be Left to the Whims of the Market:

In an essay published in this month’s PLoS Medicine, Nicholas White and colleagues [1] lament that an insufficient understanding of even well-established drugs has led to a lack of effective treatments in pregnancy. They conclude that “we do not know how best to treat most tropical infectious diseases in pregnancy”–an alarming and shameful situation–and lay out causes of this ignorance. For example, concern about teratogenicity has led to the exclusion of pregnant women from clinical trials regardless of their stage of pregnancy, resulting in a crucial lack of evidence even in late pregnancy, when teratogenicity is not a concern. Gaps in the evidence on pharmacokinetics of some antimalarial drugs have often led to under-dosing of pregnant women, and in some cases the erroneous conclusion that such drugs are not effective in pregnancy. The authors note that “‘better safe than sorry’ is the mantra of our risk-averse age.” But since severe malaria has a mortality approaching 50% in late pregnancy, we concur with the authors that this mantra has actually produced harm.

Guidelines for Reporting Health Research: The EQUATOR Network’s Survey of Guideline Authors:

Scientific publications are one of the most important outputs of any research, as they are the primary means of sharing the findings with the broader research community. The quality and relevance of research is mostly judged through the published report, which is often the only public record that the research was done. Unclear reporting of a study’s methodology and findings prevents critical appraisal of the study and limits effective dissemination. Inadequate reporting of medical research carries with it an additional risk of inadequate and misleading study results being used by patients and health care providers. Patients may be harmed and scarce health care resources may be expended on ineffective health care treatments through such inadequate reporting. There is a wealth of evidence that much of published medical research is reported poorly [1-12]. Yet a good report is an essential component of good research.

Effect of a Brief Video Intervention on Incident Infection among Patients Attending Sexually Transmitted Disease Clinics:

In the US alone there are 19 million new cases of sexually transmitted diseases (STDs) every year. STDs are infections that pass between people during sexual activity (through semen, vaginal fluids, blood, or skin-to-skin contact). Some STDs are caused by bacteria (for example, chlamydia, gonorrhea, and syphilis). Others are caused by parasites (for example, trichomoniasis) or viruses (for example, herpes simplex virus and HIV). Symptoms vary among STDs but may include sores, unusual lumps and itching in the genital region, pain when urinating, and unusual genital discharge. While symptoms are generally more common in men than women, many STDs cause no symptoms. Untreated STDs are more serious for women and may include pelvic inflammatory disease (PID), ectopic pregnancy, infertility, and chronic pain. Bacterial and parasitic STDs can be cured with various drugs; STDs caused by viruses cannot be cured although they can be treated with antiviral drugs.

How Well Do Clinical Pain Assessment Tools Reflect Pain in Infants?:

Pain is a sensory and emotional experience. It is normally triggered by messages transmitted from specialized receptors (nociceptors) in the body to integrative centers in the spinal cord and brainstem and on to the brain, where it undergoes higher sensory and cognitive analysis, allowing the body to respond appropriately to the stimuli. While the experience of pain may be considered to be unpleasant, it is a useful tool in communicating to us and to others that there is something wrong with our bodies. Ultimately, these responses help restrict further damage to the body and start the process of healing.
In a clinical setting, the ability to communicate about pain allows an individual to seek strategies to ease the pain, such as taking analgesics. Being unable to effectively communicate one’s experience of pain leaves the individual vulnerable to prolonged suffering. One such vulnerable group is infants.
Ignored and untreated pain in infants has been shown to have immediate and long-term effects as a result of structural and physiological changes within the nervous system. For example, the body responds to untreated pain by increased release of stress hormones, which may be associated with increased morbidity and mortality in the short term. Long-term effects of pain may include altered pain perception, chronic pain syndromes, and somatic complaints such as sleep disturbances, feeding problems, and inability to self-regulate in response to internal and external stressors. It has been proposed that attention deficit disorders, learning disorders, and behavioral problems in later childhood may be linked to repetitive pain in the preterm infant.

Britain’s Last Neanderthals Were More Sophisticated Than We Thought:

An archaeological excavation at a site near Pulborough, West Sussex, has thrown remarkable new light on the life of northern Europe’s last Neanderthals. It provides a snapshot of a thriving, developing population – rather than communities on the verge of extinction.

Microscopic ‘Clutch’ Puts Flagellum In Neutral:

A tiny but powerful engine that propels the bacterium Bacillus subtilis through liquids is disengaged from the corkscrew-like flagellum by a protein clutch, Indiana University Bloomington and Harvard University scientists have learned. Their report appears in Science on June 20.

DNA Study Unlocks Mystery To Diverse Traits In Dogs:

What makes a pointer point, a sheep dog herd, and a retriever retrieve? Why do Yorkshire terriers live longer than Great Danes? And how can a tiny Chihuahua possibly be related to a Great Dane?

New Findings On Immune System In Amphibians:

Major Histocompatibility Complex (MHC) genes produce proteins that are crucial in fighting pathogen assault. Researchers from the Jagiellonian University in Krakow and from the Helmholtz Centre for Environmental Research (UFZ) characterized genetic variation and detected more than one MHC class II locus in a tailed amphibian. Unlike mammals, not much has been known until now about the immune defence of amphibians.

World’s Only Captive Hairy-nosed Otter Gets New Home:

Dara, the world’s only captive hairy-nosed otter, is one of the rarest of otter species. He was recently released into his new home in a wildlife center in…

Unlocking Genome Of World’s Worst Insect Pest:

Scientists from CSIRO and the University of Melbourne in Australia, and the Baylor College of Medicine in Houston, Texas, are on the brink of a discovery which will facilitate the development of new, safe, more sustainable ways of controlling the world’s worst agricultural insect pest – the moth, Helicoverpa armigera.

Infant Play Drives Chimpanzee Respiratory Disease Cycles:

The signature boom-bust cycling of childhood respiratory diseases was long attributed to environmental cycling. However, the effect of school holidays on rates of social contact amongst children is increasingly seen as another major driver. New research on chimpanzees suggests that this effect of social connectivity on disease cycling may long predate attendance of children at schools, with chimpanzee infant mortality rates cycling in phase with rates of social play amongst infants.

High Hormone Levels In Seabird Chicks Prepare Them To Kill Their Siblings:

The Nazca booby, a Galápagos Island seabird, emerges from its shell ready to kill its brother or sister. Wake Forest University biologists and their colleagues have linked the murderous behavior to high levels of testosterone and other male hormones found in the hatchlings.

Desert Plant May Hold Key To Surviving Food Shortage:

Scientists at the University of Liverpool are investigating how a Madagascan plant could be used to help produce crops in harsh environmental conditions. The plant, Kalanchoe fedtschenkoi, is unique because, unlike normal plants, it captures most of its carbon dioxide at night when the air is cooler and more humid, making it 10 times more water-efficient than major crops such as wheat. Scientists will use the latest next-generation DNA sequencing to analyse the plant’s genetic code and understand how these plants function at night.

Birds Migrate Earlier, But Some May Be Left Behind As The Climate Warms Rapidly:

Many birds are arriving earlier each spring as temperatures warm along the East Coast of the United States. However, the farther those birds journey, the less likely they are to keep pace with the rapidly changing climate. Scientists at Boston University and the Manomet Center for Conservation Sciences analyzed changes in the timing of spring migrations of 32 species of birds along the coast of eastern Massachusetts since 1970. Researchers at Manomet gathered this data by capturing birds in mist nets, attaching bands to their legs, and then releasing them. Their findings show that eight out of 32 bird species are passing by Cape Cod significantly earlier on their annual trek north than they were 38 years ago. The reason? Warming temperatures. Temperatures in eastern Massachusetts have risen by 1.5 degrees Celsius (2.7 degrees Fahrenheit) since 1970.

When It Comes To Female Red Squirrels, It Seems Any Male Will Do, Even Close Relatives:

Researchers have found that female red squirrels showed high levels of multimale mating and would even mate with males that had similar genetic relatedness, basically mating with their relatives.

New Discovery Proves ‘Selfish Gene’ Exists:

In studying genomes, the word ‘selfish’ does not refer to the human-describing adjective of self-centered behavior but rather to the blind tendency of genes wanting to continue their existence into the next generation. Ironically, this ‘selfish’ tendency can appear anything but selfish when the gene does move ahead for selfless and even self-sacrificing reasons. For instance, in the honey bee colony, a complex social breeding system described as a ‘super-organism,’ the female worker bees are sterile. The adult queen bee, selected and developed by the worker bees, is left to mate with the male drones.

Mechanism Contributing To Appropriate Formation Of The Spine Discovered:

The Stowers Institute’s Pourquié Lab has shed light on the mechanism causing animals to develop the appropriate number of vertebrae. Vertebrae are formed from their embryonic precursors, called somites. The number of somites is consistent within a species, but varies significantly across species. By comparing the developing embryos of zebrafish, chicken, mice, and corn snakes, the team established an understanding of how an organism regulates the number of somites formed.

It’s All In Your Head – The Effect Of Metaphor On Web Navigation:

In the internet world of sites, pages, lounges and whatever else is out there, most of us have found ourselves ‘lost in hyperspace’, a frustrating experience of having lost track of where we are, where we’re going, or where to find what we’re looking for. However, hope is at hand, through a recent study by a PhD Student at the University of Leicester, Kine Dorum. Based on the notion that people create images or maps in their heads to represent the world around them, designers and developers often attempt to help people find their way by working on the principle that virtual environments should be made to look and feel as similar to the real world as possible. One example is the computer desktop with its files, folders, and ‘trash can’.

It’s Friday – and time for new articles in PLoS Computational Biology, PLoS Pathogens and PLoS Genetics:
An Evolutionarily Conserved Sexual Signature in the Primate Brain:

The contribution of genetics versus environment to behavioral differences between the sexes is a fundamental question in neuroscience. We hypothesized that some differences between the sexes might be partially explained by sexually dependent gene expression differences in the brain. We further speculated that if differences in gene expression between males and females are functionally important, they may be conserved in the evolution of primates. To test these hypotheses, we measured gene expression in the brains of male and female primates from three species: humans (Homo sapiens), macaques (Macaca fascicularis), and marmosets (Callithrix jacchus). Our results point to a conserved signature of sexual gene expression dimorphism in the brains of primates. Interestingly, we found that genes with conserved sexual gene expression dimorphism in the brain also evolve under more evolutionary constraint, compared with other genes, suggesting that they may have important roles during evolution of sex in primates. Moreover, we found higher evolutionary constrains in the coding regions of female-biased genes as compared to both male-biased and non sex-biased brain expressed genes. The study of sex dimorphic genes may in the future shed light on the basis of psychiatric diseases with differences in prevalence between the sexes.

How To Record a Million Synaptic Weights in a Hippocampal Slice:

The circuitry of the brain is defined by the connections (synapses) between its cells. Synapses are very small, so it is difficult to identify more than a few at a time using standard methods like electron microscopy or high-precision electrical recordings from cells. This study shows that it is possible to measure single synapses using low-precision methods such as optical recordings from neuronal cell bodies. I model optical or electrical stimulation of many inputs to trigger a visible response from neurons, and find single synapses by testing how this response is modulated when a single additional input synapse is triggered as well. I predict that it should be possible to record from as many as a million synapses using new optical recording and stimulation methods. It is believed that memories are encoded in synaptic connection patterns, so such connectivity data may give us a picture of how memories are encoded. We now know a great deal about how individual neurons behave, so a synapse-level wiring diagram would go a long way to fill out the picture of how neurons work together in the brain to interpret sensory information and plan actions.

Quorum Sensing Coordinates Brute Force and Stealth Modes of Infection in the Plant Pathogen Pectobacterium atrosepticum:

Many Gram-negative bacteria use a population density-dependent regulatory mechanism called quorum sensing (QS) to control the production of virulence factors during infection. In the bacterial plant pathogen Pectobacterium atrosepticum (formerly Erwinia carotovora subsp. atroseptica), an important model for QS, this mechanism regulates production of enzymes that physically attack the host plant cell wall. This study used a whole genome microarray-based approach to investigate the entire QS regulon during plant infection. Results demonstrate that QS regulates a much wider set of essential virulence factors than was previously appreciated. These include virulence factors similar to those in other plant and animal pathogens that have not previously been associated with QS, e.g., a Type VI secretion system (and its potential substrates), shown for the first time to be required for virulence in a plant pathogen; and the plant toxin coronafacic acid, known in other pathogens to play a role in manipulating plant defences. This study provides the first evidence that Pectobacterium may target host defences simultaneously with a physical attack on the plant cell wall. Moreover, the study demonstrates that a wide range of previously known and unknown virulence regulators lie within the QS regulon, revealing it to be the master regulator of virulence.

Real-Time High Resolution 3D Imaging of the Lyme Disease Spirochete Adhering to and Escaping from the Vasculature of a Living Host:

Pathogenic spirochetes are bacteria that cause a number of emerging and re-emerging diseases worldwide, including syphilis, leptospirosis, relapsing fever, and Lyme disease. They exhibit an unusual form of motility and can infect many different tissues; however, the mechanism by which they disseminate from the blood to target sites is unknown. Direct visualization of bacterial pathogens at the single cell level in living hosts is an important goal of microbiology, since this approach is likely to yield critical insight into disease processes. We engineered a fluorescent strain of Borrelia burgdorferi, a Lyme disease pathogen, and used conventional and spinning disk confocal intravital microscopy to directly visualize these bacteria in real time and 3D in living mice. We found that spirochete interaction with and dissemination out of the vasculature was a multi-stage process of unexpected complexity and that spirochete movement appeared to play an integral role in dissemination. To our knowledge, this is the first report of high resolution 3D visualization of dissemination of a bacterial pathogen in a living mammalian host, and provides the first direct insight into spirochete dissemination in vivo.