A Blog Around The Clock

New Research Alters Concept Of How Circadian Clock Functions:

Scientists from the University of Cambridge have identified a molecule that may govern how the circadian clock in plants responds to environmental changes. The researchers have discovered that a signalling molecule, known to be important for environmental stress signalling in plants, also regulates their circadian clock. They believe that the molecule may therefore incorporate information about environmental changes into the biological clock that regulates the physiology of plants. The research dramatically changes our current understanding of the circadian clock and may have important implications for the agricultural community.

Penguins In Peril As Climate Warms:

The penguin population of Antarctica is under pressure from global warming, according to a WWF report. The report, Antarctic Penguins and Climate Change, shows that the four populations of penguins that breed on the Antarctic continent — Adélie, Emperor, Chinstrap and Gentoo — are under escalating pressure. For some, global warming is taking away precious ground on which penguins raise their young. For others, food has become increasingly scarce because of warming in conjunction with overfishing.

To Catch A Panda:

Michigan State University’s panda habitat research team has spent years collecting mountains of data aimed at understanding and saving giant pandas. Now a graduate student is working to catch crucial data that’s black, white and furry. Vanessa Hull, 25, a Ph.D. candidate, is in the snowy, remote mountains of the Sichuan Province of China — which also is the heart of panda habitat. She’s hoping to capture, collar and track up to four wild pandas using advanced global positioning systems.

New, Rare And Threatened Species Discovered In Ghana:

Scientists exploring one of the largest remaining blocks of tropical forest in Western Africa discovered significant populations of new, rare and threatened species underscoring the area’s high biological diversity and value.

Genetic Differences Influence Aging Rates In The Wild:

Long-lived, wild animals harbor genetic differences that influence how quickly they begin to show their age, according to the results of a long-term study. Evidence for the existence of such genetic variation for aging rates–a central tenet in the evolutionary theory that explains why animals would show physiological declines as they grow older–had largely been lacking in natural populations until now, the researchers said.

Losses Of Long-established Genes Contribute To Human Evolution

While it is well understood that the evolution of new genes leads to adaptations that help species survive, gene loss may also afford a selective advantage. A group of scientists at the University of California, Santa Cruz led by biomolecular engineering professor David Haussler has investigated this less-studied idea, carrying out the first systematic computational analysis to identify long-established genes that have been lost across millions of years of evolution leading to the human species.

The actual paper is here
Cholesterol Fine Tunes Hearing:

Levels of cholesterol in the membranes of hair cells in the inner ear can affect your hearing, said a consortium of researchers from Baylor College of Medicine, Rice University and Purdue University in a new report in the Journal of Biological Chemistry.

Anti-drinking Campaign Ads May Be ‘Catastrophically Misconceived’:

Some anti-drinking advertising campaigns may be “catastrophically misconceived” because they play on the entertaining ‘drinking stories’ that young people use to mark their social identity, say researchers who have just completed a three year study of the subject.

Intensive Care Quality Of Sleep Improved By New Drug, Reports Study:

A new sedative drug has been shown to improve the sleep quality and comfort levels of intensive care patients, compared to the most commonly-used medication, according to research published in the journal JAMA.

On Fridays I look at the new stuff published on PLoS community journals, i.e., PLoS Pathogens, Neglected Tropical Diseases, Genetics and Computational Biology. Here are my picks for this week:
The Per2 Negative Feedback Loop Sets the Period in the Mammalian Circadian Clock Mechanism:

Network models of biological systems are appearing at an increasing rate. By encapsulating mechanistic detail of chemical and physical processes, mathematical models can successfully simulate and predict emergent network properties. However, methods are needed for analyzing the role played by individual biochemical steps in producing context-dependent system behavior, thereby linking individual molecular knowledge with network properties. Here, we apply sensitivity analysis to analyze mammalian circadian rhythms and find that a contiguous series of reactions in one of the four negative feedback loops carries primary responsibility for determining the intrinsic length of day. The key reactions, all involving the gene per2 and its products, include Per2 mRNA export and degradation, and PER2 phosphorylation, transcription, and translation. Interestingly, mutations affecting PER2 phosphorylation have previously been linked to circadian disorders. The method may be generally applicable to probe structure-function relationships in biological networks.

Sustained Post-Mating Response in Drosophila melanogaster Requires Multiple Seminal Fluid Proteins:

In sexually reproducing organisms, sperm enter the female in combination with seminal proteins that are critical for fertility. These proteins can activate sperm or enhance sperm storage within the female, and can improve the chance that sperm will fertilize eggs. Understanding the action of seminal proteins has potential utility in insect pest control and in the diagnosis of certain human infertilities. However, the precise function of very few seminal proteins is known. To address this, we knocked down the levels of 25 seminal proteins individually in male fruit flies, and tested the males’ abilities to modulate egg production, sperm storage/release, or behavior of their mates. We found five seminal proteins that are necessary to elevate offspring production in mated females. Four of these proteins are needed for efficient release of sperm from storage to fertilize eggs, a function that had not been previously assigned to any seminal protein. All four are in biochemical classes that are conserved in seminal fluid from insects to humans, suggesting they may play similar sperm-related roles in other animals. In addition to assigning functions to particular seminal proteins, our results suggest that fruit flies can serve as a model with which to dissect the functions of conserved protein classes in seminal fluid.

A Bacterial Kind of Aging:

Bacteria are sometimes honored with a few lines in books and reviews on aging as an example of organisms that do not age. This is because binary fission of bacteria has been assumed to proceed with a nonconservative dispersion of both undamaged and damaged constituents, such that there are no adult forms of bacterial cells and the bacterial population is not age structured. However, some authors have expressed different views; for example, Partridge and Barton [1] consider asymmetry in simple unicellular systems and how this might develop into aging, and Tom Kirkwood [2] argues, on theoretical grounds, that damage segregation could be selected for in simple unicellular systems dividing by binary fission, and that sibling-specific deterioration may confer a selective advantage. Indeed, recent reports lend experimental support to this notion and point to mandatory aging also being a part of the life history of bacteria.

Blind Humans Lacking Rods And Cones Retain Normal Responses To Non-visual Effects Of Light:

In addition to allowing us to see, the mammalian eye also detects light for a number of “non-visual” phenomena. A prime example of this is the timing of the sleep/wake cycle, which is synchronized by the effects of light on the circadian pacemaker in the hypothalamus. Researchers have identified two totally blind humans whose non-visual responses to light remain intact, suggesting that visual and non-visual responses to light are functionally distinct. Indeed, this separation was suggested by earlier studies in mice that demonstrated that circadian rhythms and other non-visual responses remain sensitive to light in the absence of rods and cones, the two photoreceptor types that are responsible for vision.

Related: Compared to your pet iguana, you are practically blind
Melanopsin
Semen Ingredient ‘Drastically’ Enhances HIV Infection:

A plentiful ingredient found in human semen drastically enhances the ability of the human immunodeficiency virus (HIV) to cause infection, according to a report in the December 14, 2007, issue of the journal Cell. The findings help to understand the sexual transmission of HIV and suggest a potential new target for preventing the spread of AIDS, the researchers said.

Mom’s Personality Means Survival For Her Squirrel Pups:

A recent study indicates that mother squirrels have personalities, and they are essential for the growth rate and survival of her pups. Researchers at the Kluane Red Squirrel Project found that red squirrels have a range of personalities, from exploratory and aggressive to careful and passive. Both kinds of squirrels persist in the population because neither personality type offers an exclusive advantage for survival.

Andean Highlands In Chile Yield Ancient South American Armored Mammal Fossil:

A paleontological dig in Chile at an altitude of more than 14,000 feet in the Andes has yielded fossils of an 18-million-year-old armored mammal. It appears to be one of the most primitive members of a family of extinct mammals known as “glyptodonts,” a group closely related to the modern-day armadillo.

Present-day Species Of Piranha Resulted From Marine Incursion Into Amazon Basin:

Piranhas inhabit exclusively the fresh waters of South America. Their geographical distribution extends from the Orinoco River basin (Venezuela) to the North, down to that of the Paraná (Argentina) to the South. Over this whole area, which also embraces the entire Amazon Basin, biologists have recorded 28 carnivorous species of these fish (2). In spite of the evolutionary success of this subfamily of fish, the mechanisms that generated the species richness of this group are still insufficiently known.

Massive Dinosaur Discovered In Antarctica Sheds Light On Life, Distribution Of Sauropodomorphs:

A new genus and species of dinosaur from the Early Jurassic has been discovered in Antarctica. The massive plant-eating primitive sauropodomorph is called Glacialisaurus hammeri and lived about 190 million years ago.

Aging In Salmon Depends On Choosy Bears:

According to George Bernard Shaw: “We don’t stop playing because we grow old; we grow old because we stop playing.” But how fast does that aging occur once started? In the case of populations of salmon in Alaska studied by Stephanie Carlson and colleagues at the University of Washington and McGill University and reported on in this week’s PLoS ONE, it all depends on how choosy are the bears which feed on them.

When She’s Turned On, Some Of Her Genes Turn Off, Fish Study Shows:

When a female is attracted to a male, entire suites of genes in her brain turn on and off, show biologists from The University of Texas at Austin studying swordtail fish.

The Effect Of ‘In Your Face’ Political Television On Democracy:

Television can encourage awareness of political perspectives among Americans, but the incivility and close-up camera angles that characterize much of today’s “in your face” televised political debate also causes audiences to react more emotionally and think of opposing views as less legitimate.

Different Areas Of The Brain Respond To Belief, Disbelief And Uncertainty:

The human mind is a prolific generator of beliefs about the world. The capacity of our minds to believe or disbelieve linguistic propositions is a powerful force for controlling both behavior and emotion, but the basis of this process in the brain is not yet understood.

There are 30 new articles published in PLoS ONE today. My personal picks:
Genetic Impact of a Severe El Nino Event on Galápagos Marine Iguanas (Amblyrhynchus cristatus):

El Nino is an ocean-atmosphere phenomenon occurring in the Pacific Basin which is responsible for extreme climate variation in the Southern hemisphere. In this study, the authors investigated whether a severe El Nino event affected the genetic make-up of Galapagos marine iguanas. No strong influence of El Nino on genetic diversity in the iguana populations was uncovered; however, the data suggest that future studies of this type also need to consider the potential effect of other biological and environmental changes on genetic diversity.

What Are You Feeling? Using Functional Magnetic Resonance Imaging to Assess the Modulation of Sensory and Affective Responses during Empathy for Pain:

Previous research suggests that empathy for pain activates similar pathways in the brain as first-hand painful experiences. However, the extent of similarity between empathy for pain and experienced pain is thought to depend on social factors and personality traits. Here, Lamm and colleagues studied the brain activity of participants who were shown photographs depicting painful or non-painful procedures on the hand of another participant. The results demonstrate that through emotional and bodily awareness people are able to evaluate the sensory and affective states of others.

Predation by Bears Drives Senescence in Natural Populations of Salmon:

Pacific salmon do not feed during their breeding period; they physically deteriorate very quickly once they start breeding and then die several weeks later. In this population-based study, the authors studied salmon and brown bears in southwest Alaska to find out whether the rate of aging in salmon was driven primarily by the rate of predation by bears, or by the tendency of the bears to prey on salmon with less evidence of aging. The results show that the main factor affecting the rate of aging in salmon populations was the tendency of bears to choose salmon with less evidence of aging.

Cross-Attraction between an Exotic and a Native Pine Bark Beetle: A Novel Invasion Mechanism?:

Aside from the ecological impacts, invasive species fascinate ecologists because of the unique opportunities that invasives offer in the study of community ecology. Some hypotheses have been proposed to illustrate the mechanisms that allow exotics to become invasive. However, positive interactions between exotic and native insects are rarely utilized to explain invasiveness of pests. Here, we present information on a recently formed association between a native and an exotic bark beetle on their shared host, Pinus tabuliformis, in China. In field examinations, we found that 35-40% of P. tabuliformis attacked by an exotic bark beetle, Dendroctonus valens, were also attacked by a native pine bark beetle, Hylastes parallelus. In the laboratory, we found that the antennal and walking responses of H. parallelus to host- and beetle-produced compounds were similar to those of the exotic D. valens in China. In addition, D. valens was attracted to volatiles produced by the native H. parallelus. We report, for the first time, facilitation between an exotic and a native bark beetle seems to involve overlap in the use of host attractants and pheromones, which is cross-attraction. The concept of this interspecific facilitation could be explored as a novel invasive mechanism which helps explain invasiveness of not only exotic bark beetles but also other introduced pests in principle. The results reported here also have particularly important implications for risk assessments and management strategies for invasive species.

Increased Litterfall in Tropical Forests Boosts the Transfer of Soil CO2 to the Atmosphere:

Aboveground litter production in forests is likely to increase as a consequence of elevated atmospheric carbon dioxide (CO2) concentrations, rising temperatures, and shifting rainfall patterns. As litterfall represents a major flux of carbon from vegetation to soil, changes in litter inputs are likely to have wide-reaching consequences for soil carbon dynamics. Such disturbances to the carbon balance may be particularly important in the tropics because tropical forests store almost 30% of the global soil carbon, making them a critical component of the global carbon cycle; nevertheless, the effects of increasing aboveground litter production on belowground carbon dynamics are poorly understood. We used long-term, large-scale monthly litter removal and addition treatments in a lowland tropical forest to assess the consequences of increased litterfall on belowground CO2 production. Over the second to the fifth year of treatments, litter addition increased soil respiration more than litter removal decreased it; soil respiration was on average 20% lower in the litter removal and 43% higher in the litter addition treatment compared to the controls but litter addition did not change microbial biomass. We predicted a 9% increase in soil respiration in the litter addition plots, based on the 20% decrease in the litter removal plots and an 11% reduction due to lower fine root biomass in the litter addition plots. The 43% measured increase in soil respiration was therefore 34% higher than predicted and it is possible that this ‘extra’ CO2 was a result of priming effects, i.e. stimulation of the decomposition of older soil organic matter by the addition of fresh organic matter. Our results show that increases in aboveground litter production as a result of global change have the potential to cause considerable losses of soil carbon to the atmosphere in tropical forests.

A Novel Interhemispheric Interaction: Modulation of Neuronal Cooperativity in the Visual Areas:

The cortical representation of the visual field is split along the vertical midline, with the left and the right hemi-fields projecting to separate hemispheres. Connections between the visual areas of the two hemispheres are abundant near the representation of the visual midline. It was suggested that they re-establish the functional continuity of the visual field by controlling the dynamics of the responses in the two hemispheres. To understand if and how the interactions between the two hemispheres participate in processing visual stimuli, the synchronization of responses to identical or different moving gratings in the two hemi-fields were studied in anesthetized ferrets. The responses were recorded by multiple electrodes in the primary visual areas and the synchronization of local field potentials across the electrodes were analyzed with a recent method derived from dynamical system theory. Inactivating the visual areas of one hemisphere modulated the synchronization of the stimulus-driven activity in the other hemisphere. The modulation was stimulus-specific and was consistent with the fine morphology of callosal axons in particular with the spatio-temporal pattern of activity that axonal geometry can generate. These findings describe a new kind of interaction between the cerebral hemispheres and highlight the role of axonal geometry in modulating aspects of cortical dynamics responsible for stimulus detection and/or categorization.

What Causes Partial F1 Hybrid Viability? Incomplete Penetrance versus Genetic Variation:

Interspecific hybrid crosses often produce offspring with reduced but non-zero survivorship. In this paper we ask why such partial inviability occurs. This partial inviability could arise from incomplete penetrance of lethal Dobzhansky-Muller incompatibilities (DMIs) shared by all members of a hybrid cross. Alternatively, siblings may differ with respect to the presence or number of DMIs, leading to genotype-dependent variation in viability and hence non-Mendelian segregation of parental alleles in surviving F1 hybrids. We used amplified fragment length polymorphisms (AFLPs) to test for segregation distortion in one hybrid cross between green and longear sunfish (Lepomis cyanellus and L. megalotis). Hybrids showed partial viability, and twice as much segregation distortion (36.8%) of AFLPs as an intraspecific control cross (18.8%). Incomplete penetrance of DMIs, which should cause genotype-independent mortality, is insufficient to explain the observed segregation distortion. We conclude that F1 hybrid sunfish are polymorphic for DMIs, either due to sex-linked DMI loci (causing Haldane’s Rule), or polymorphic autosomal DMI loci. Because few AFLP markers were sex-linked (2%), the most parsimonious conclusion is that parents may have been heterozygous for loci causing hybrid inviability.

Does Time Really Slow Down during a Frightening Event?:

Observers commonly report that time seems to have moved in slow motion during a life-threatening event. It is unknown whether this is a function of increased time resolution during the event, or instead an illusion of remembering an emotionally salient event. Using a hand-held device to measure speed of visual perception, participants experienced free fall for 31 m before landing safely in a net. We found no evidence of increased temporal resolution, in apparent conflict with the fact that participants retrospectively estimated their own fall to last 36% longer than others’ falls. The duration dilation during a frightening event, and the lack of concomitant increase in temporal resolution, indicate that subjective time is not a single entity that speeds or slows, but instead is composed of separable subcomponents. Our findings suggest that time-slowing is a function of recollection, not perception: a richer encoding of memory may cause a salient event to appear, retrospectively, as though it lasted longer.

Researchers Can Read Thoughts To Decipher What A Person Is Actually Seeing:

Following ground-breaking research showing that neurons in the human brain respond in an abstract manner to particular individuals or objects, University of Leicester researchers have now discovered that, from the firing of this type of neuron, they can tell what a person is actually seeing.

Are Humans Evolving Faster? Findings Suggest We Are Becoming More Different, Not Alike:

Researchers have discovered genetic evidence that human evolution is speeding up — and has not halted or proceeded at a constant rate, as had been thought — indicating that humans on different continents are becoming increasingly different.

Eating More Red And Processed Meats Linked To Greater Risk For Bowel And Lung Cancer, Findings Suggest:

New findings provide evidence that people who eat a lot of red and processed meats have greater risk of developing bowel and lung cancer than people who eat small quantities. The research by Amanda Cross and colleagues at the US National Cancer Institute is published in the latest issue of PLoS Medicine.

For The Fruit Fly, Everything Changes After Sex:

Barry Dickson, director of the Research Institute of Molecular Pathology (IMP) in Austria, and his group are interested in the genetic basis of innate behaviour. They focus on the reproductive behaviour of the fruit fly Drosophila melanogaster. Two years ago, the team was able to identify the fruitless gene as a key regulator of mating behaviour.

Threatened Birds May Be Rarer Than Geographic Range Maps Suggest:

Geographic range maps that allow conservationists to estimate the distribution of birds may vastly overestimate the actual population size of threatened species and those with specific habitats, according to a study published online this week in the journal Conservation Biology.

On Monday nights, it is time to see what is new in PLoS Medicine and PLoS Biology:
Meat Consumption and Cancer Risk:

Meat consumption in relation to cancer risk has been reported in over a hundred epidemiological studies from many countries with diverse diets. The association between meat intake and cancer risk has been evaluated by looking both at broad groupings of total meat intake, and also at finer categorizations, particularly intakes of red meat, which includes beef, lamb, pork, and veal, and also more specifically processed meats, which includes meats preserved by salting, smoking, or curing.

A Prospective Study of Red and Processed Meat Intake in Relation to Cancer Risk:

Background.
Every year, there are more than 10 million new cases of cancer around the world. These cases are not spread evenly across the globe. The annual incidence of cancer (the number of new cases divided by the population size) and the type of cancer most commonly diagnosed varies widely among countries. Much of the global variation in cancer incidence and type is thought to be due to environmental influences. These include exposure to agents in the air or water that cause cancer, and lifestyle factors such as smoking and diet. Researchers identify environmental factors that affect cancer risk by measuring the exposure of a large number of individuals to a specific environmental factor and then monitoring these people for several years to see who develops cancer. The hope is that by identifying the environmental factors that cause or prevent cancer, the global burden of cancer can be reduced.
Why Was This Study Done?
Diet is thought to influence the incidence of several cancers but it is very difficult to unravel which aspects of diet are important. Being overweight, for example, is strongly associated with an increased risk of developing several types of cancer, but the evidence that the intake of red meat (beef, pork, and lamb) and of processed meat (for example, bacon, ham, and sausages) is linked to cancer risk is much weaker. Although several studies have linked a high intake of red meat and processed meat to an increased risk of colorectal cancer (the colon is the large bowel; the rectum is the final few inches of the large bowel before the anus), whether this aspect of diet affects the risk of other types of cancer is unclear. In this prospective study, the researchers have examined the association between meat intake and the incidence of a wide range of cancers.
What Did the Researchers Do and Find?
In 1995-1996, nearly half a million US men and women aged 50-71 y joined the NIH-AARP Diet and Health Study. The participants in this study–none of whom had had cancer previously–completed a questionnaire about their dietary habits over the previous year and provided other personal information such as their age, weight, and smoking history. The researchers used these data and information from state cancer registries to look for associations between the intake of red and processed meat and the incidence of various cancers. They found that people whose red meat intake was in the top fifth of the range of intakes recorded in the study (the highest quintile of consumption) had an increased risk of developing colorectal, liver, lung, and esophageal cancer when compared with people in the lowest quintile of consumption. People in the highest quintile of processed meat intake had an increased risk of developing colorectal and lung cancer. The incidences of other cancers were largely unaffected by meat intake.
What Do These Findings Mean?
These findings provide strong evidence that people who eat a lot of red and processed meats have greater risk of developing colorectal and lung cancer than do people who eat small quantities. They also indicate that a high red meat intake is associated with an increased risk of esophageal and liver cancer, and that one in ten colorectal and one in ten lung cancers could be avoided if people reduced their red and processed meat intake to the lowest quintile. However, although the researchers allowed for factors such as smoking history that might have affected cancer incidences, some of the effects they ascribe to meat intake might be caused by other lifestyle factors. Furthermore, because the study’s definitions of red meat and processed meat overlapped–bacon and ham, for example, were included in both categories–exactly which type of meat is related to cancer remains unclear. Finally, most of the study participants were non-Hispanic white, so these findings may not apply to people with different genetic backgrounds. Nevertheless, they add to the evidence that suggests that decreased consumption of red and processed meats could reduce the incidence of several types of cancer.

Improving Science Education for Sustainable Development:

In recent issues of noteworthy journals, natural scientists have argued for the improvement of science education. Such pleas reflect the growing awareness that high-quality science education is required not only for sustaining a lively scientific community that is able to address global problems like global warming and pandemics, but also to bring about and maintain a high level of scientific literacy in the general population. There is no doubt that effective education can serve as a vehicle for solving global problems. The problem centers on how to achieve more effective education.

Generosity May Be Genetically Programmed:

Are those inclined towards generosity genetically programmed to behave that way? A team of researchers, including Dr. Ariel Knafo of the Psychology Department at the Hebrew University of Jerusalem, believes that this could very well be the case.

Like Humans, Monkey See, Monkey Plan, Monkey Do:

How many times a day do you grab objects such as a pencil or a cup? We perform these tasks without thinking, however the motor planning necessary to grasp an object is quite complex. The way human adults grasp objects is typically influenced more by their knowledge of what they intend to do with the objects than the objects’ immediate appearance. Psychologists call this the “end-state comfort effect,” when we adopt initially unusual, and perhaps uncomfortable, postures to make it easier to actually use an object.

In Fruit Flies, Homosexuality Is Biological But Not Hard-wired, Study Shows:

While the biological basis for homosexuality remains a mystery, a team of neurobiologists reports they may have closed in on an answer — by a nose.

Bacteria Employ Type Of DNA Modification Never Before Seen In Nature:

A team of MIT researchers and others has discovered that bacteria employ a type of DNA modification never before seen in nature.

‘Smart’ Flower Bulbs Pull Themselves To Deeper Ground:

Confused about the right planting depth for flower bulbs? Trust the bulbs! Researchers have discovered that some flower bulbs are actually “smart” enough to adjust themselves to the right planting depth. A recent study published in the Journal of the American Society for Horticultural Science proved that bulbs can adjust their planting position by moving deeper into the ground, apparently in search of moister, more conducive growing conditions.

Young Chimps Top Adult Humans In Numerical Memory:

Young chimpanzees have an “extraordinary” ability to remember numerals that is superior to that of human adults, researchers report.

Artificial Jellyfish, Explosives Sensor Among Projects Being Developed At Undersea Technology Center:

Artificial jellyfish, explosives sensors and seabed batteries are among the diverse research projects under way just nine months after the creation of a Center of Excellence in Undersea Technology in collaboration with the Naval Undersea Warfare Center in Rhode Island.

Heads Or Tails? Scientists Identify Gene That Regulates Polarity In Regenerating Flatworms:

When cut, a planarian flatworm can use a population of stem cells called neoblasts to regenerate new heads, new tails or even entire new organisms from a tiny fragment of its body. Mechanisms have been sought to explain this process of regeneration polarity for over 100 years, but until now, little was known about how planaria can regenerate heads and tails at their proper sites.