A Blog Around The Clock

PERIOD-TIMELESS Interval Timer May Require an Additional Feedback Loop by Robert S. Kuczenski, Kevin C. Hong, Jordi García-Ojalvo and Kelvin H. Lee:

The ability of an organism to adapt to daily changes in the environment, via a circadian clock, is an inherently interesting phenomenon recently connected to several human health issues. Decades of experiments on one of the smallest model animals, the fruit fly Drosophila, has illustrated significant similarities with the mammal circadian system. Within Drosophila, the PERIOD and TIMELESS proteins are central to controlling this rhythmicity and were recently shown to have a rapid and stable association creating an “interval” timer in the cell’s cytoplasm. This interval timer creates the necessary delay between the expression and activity of these genes, and is directly opposed to the previous hypothesis of a delay created by slow association. We use several mathematical models to investigate the unknown factors controlling this timer. Using a novel positive feedback loop, we construct a circadian model consistent with the interval timer and many wild-type and mutant experimental observations. Our results suggest several novel genes and interactions to be tested experimentally.

Distributed Representations Accelerate Evolution of Adaptive Behaviours by James V. Stone:

Some behaviours are purely innate (e.g., blinking), whereas other, “apparently innate,” behaviours require a degree of learning to refine them into a useful skill (e.g., nest building). In terms of biological fitness, it matters how quickly such learning occurs, because time spent learning is time spent not eating, or time spent being eaten, both of which reduce fitness. Using artificial neural networks as model organisms, it is proven that it is possible for an organism to be born with a set of “primed” connections which guarantee that learning part of a skill induces automatic learning of other skill components, an effect known as free-lunch learning (FLL). Critically, this effect depends on the assumption that associations are stored as distributed representations. Using a genetic algorithm, it is shown that primed organisms can evolve within 30 generations. This has three important consequences. First, primed organisms learn quickly, which increases their fitness. Second, the presence of FLL effectively accelerates the rate of evolution, for both learned and innate skill components. Third, FLL can accelerate the rate at which learned behaviours become innate. These findings suggest that species may depend on the presence of distributed representations to ensure rapid evolution of adaptive behaviours.

There are 32 new papers that just went live on PLoS ONE and here are a couple of titles that got my immediate attention:
Changing Hydrozoan Bauplans by Silencing Hox-Like Genes by Wolfgang Jakob and Bernd Schierwater:

Regulatory genes of the Antp class have been a major factor for the invention and radiation of animal bauplans. One of the most diverse animal phyla are the Cnidaria, which are close to the root of metazoan life and which often appear in two distinct generations and a remarkable variety of body forms. Hox-like genes have been known to be involved in axial patterning in the Cnidaria and have been suspected to play roles in the genetic control of many of the observed bauplan changes. Unfortunately RNAi mediated gene silencing studies have not been satisfactory for marine invertebrate organisms thus far. No direct evidence supporting Hox-like gene induced bauplan changes in cnidarians have been documented as of yet. Herein, we report a protocol for RNAi transfection of marine invertebrates and demonstrate that knock downs of Hox-like genes in Cnidaria create substantial bauplan alterations, including the formation of multiple oral poles (“heads”) by Cnox-2 and Cnox-3 inhibition, deformation of the main body axis by Cnox-5 inhibition and duplication of tentacles by Cnox-1 inhibition. All phenotypes observed in the course of the RNAi studies were identical to those obtained by morpholino antisense oligo experiments and are reminiscent of macroevolutionary bauplan changes. The reported protocol will allow routine RNAi studies in marine invertebrates to be established.

Parts, Wholes, and Context in Reading: A Triple Dissociation by Denis G. Pelli and Katharine A. Tillman:

Research in object recognition has tried to distinguish holistic recognition from recognition by parts. One can also guess an object from its context. Words are objects, and how we recognize them is the core question of reading research. Do fast readers rely most on letter-by-letter decoding (i.e., recognition by parts), whole word shape, or sentence context? We manipulated the text to selectively knock out each source of information while sparing the others. Surprisingly, the effects of the knockouts on reading rate reveal a triple dissociation. Each reading process always contributes the same number of words per minute, regardless of whether the other processes are operating.

The Tricarboxylic Acid Cycle, an Ancient Metabolic Network with a Novel Twist by Ranji Singh, Vasu D. Appanna, Robert D. Hamel, Ryan J. Mailloux, Joseph Lemire, Daniel R. Chénier and Robin Bériault:

The tricarboxylic acid (TCA) cycle is an essential metabolic network in all oxidative organisms and provides precursors for anabolic processes and reducing factors (NADH and FADH2) that drive the generation of energy. Here, we show that this metabolic network is also an integral part of the oxidative defence machinery in living organisms and α-ketoglutarate (KG) is a key participant in the detoxification of reactive oxygen species (ROS). Its utilization as an anti-oxidant can effectively diminish ROS and curtail the formation of NADH, a situation that further impedes the release of ROS via oxidative phosphorylation. Thus, the increased production of KG mediated by NADP-dependent isocitrate dehydrogenase (NADP-ICDH) and its decreased utilization via the TCA cycle confer a unique strategy to modulate the cellular redox environment. Activities of α-ketoglutarate dehydrogenase (KGDH), NAD-dependent isocitrate dehydrogenase (NAD-ICDH), and succinate dehydrogenase (SDH) were sharply diminished in the cellular systems exposed to conditions conducive to oxidative stress. These findings uncover an intricate link between TCA cycle and ROS homeostasis and may help explain the ineffective TCA cycle that characterizes various pathological conditions and ageing.

Rate of Decline of the Oriental White-Backed Vulture Population in India Estimated from a Survey of Diclofenac Residues in Carcasses of Ungulates by Yadvendradev Jhala, Rhys E. Green, Deborah J. Pain, Richard Cuthbert, Bindu Raghavan, Kalu Ram Senacha and Mark A. Taggart:

The non-steroidal anti-inflammatory drug diclofenac is a major cause of the rapid declines in the Indian subcontinent of three species of vultures endemic to South Asia. The drug causes kidney failure and death in vultures. Exposure probably arises through vultures feeding on carcasses of domesticated ungulates treated with the drug. However, before the study reported here, it had not been established from field surveys of ungulate carcasses that a sufficient proportion was contaminated to cause the observed declines. We surveyed diclofenac concentrations in samples of liver from carcasses of domesticated ungulates in India in 2004-2005. We estimated the concentration of diclofenac in tissues available to vultures, relative to that in liver, and the proportion of vultures killed after feeding on a carcass with a known level of contamination. We assessed the impact of this mortality on vulture population trend with a population model. We expected levels of diclofenac found in ungulate carcasses in 2004-2005 to cause oriental white-backed vulture population declines of 80-99% per year, depending upon the assumptions used in the model. This compares with an observed rate of decline, from road transect counts, of 48% per year in 2000-2003. The precision of the estimate based upon carcass surveys is low and the two types of estimate were not significantly different. Our analyses indicate that the level of diclofenac contamination found in carcasses of domesticated ungulates in 2004-2005 was sufficient to account for the observed rapid decline of the oriental white-backed vulture in India. The methods we describe could be used again to assess changes in the effect on vulture population trend of diclofenac and similar drugs. In this way, the effectiveness of the recent ban in India on the manufacture and importation of diclofenac for veterinary use could be monitored.

Intense Sweetness Surpasses Cocaine Reward by Serge H. Ahmed, Fuschia Serre, Lauriane Cantin and Magalie Lenoir:

Refined sugars (e.g., sucrose, fructose) were absent in the diet of most people until very recently in human history. Today overconsumption of diets rich in sugars contributes together with other factors to drive the current obesity epidemic. Overconsumption of sugar-dense foods or beverages is initially motivated by the pleasure of sweet taste and is often compared to drug addiction. Though there are many biological commonalities between sweetened diets and drugs of abuse, the addictive potential of the former relative to the latter is currently unknown.
Here we report that when rats were allowed to choose mutually-exclusively between water sweetened with saccharin-an intense calorie-free sweetener-and intravenous cocaine-a highly addictive and harmful substance-the large majority of animals (94%) preferred the sweet taste of saccharin. The preference for saccharin was not attributable to its unnatural ability to induce sweetness without calories because the same preference was also observed with sucrose, a natural sugar. Finally, the preference for saccharin was not surmountable by increasing doses of cocaine and was observed despite either cocaine intoxication, sensitization or intake escalation-the latter being a hallmark of drug addiction.
Our findings clearly demonstrate that intense sweetness can surpass cocaine reward, even in drug-sensitized and -addicted individuals. We speculate that the addictive potential of intense sweetness results from an inborn hypersensitivity to sweet tastants. In most mammals, including rats and humans, sweet receptors evolved in ancestral environments poor in sugars and are thus not adapted to high concentrations of sweet tastants. The supranormal stimulation of these receptors by sugar-rich diets, such as those now widely available in modern societies, would generate a supranormal reward signal in the brain, with the potential to override self-control mechanisms and thus to lead to addiction.

Analysis of Expressed Sequence Tags of the Cyclically Parthenogenetic Rotifer Brachionus plicatilis by Atsushi Hagiwara, David Mark Welch, Yukari Tanaka, Koushirou Suga and Yoshitaka Sakakura:

Rotifers are among the most common non-arthropod animals and are the most experimentally tractable members of the basal assemblage of metazoan phyla known as Gnathifera. The monogonont rotifer Brachionus plicatilis is a developing model system for ecotoxicology, aquatic ecology, cryptic speciation, and the evolution of sex, and is an important food source for finfish aquaculture. However, basic knowledge of the genome and transcriptome of any rotifer species has been lacking.
We generated and partially sequenced a cDNA library from B. plicatilis and constructed a database of over 2300 expressed sequence tags corresponding to more than 450 transcripts. About 20% of the transcripts had no significant similarity to database sequences by BLAST; most of these contained open reading frames of significant length but few had recognized Pfam motifs. Sixteen transcripts accounted for 25% of the ESTs; four of these had no significant similarity to BLAST or Pfam databases. Putative up- and downstream untranslated regions are relatively short and AT rich. In contrast to bdelloid rotifers, there was no evidence of a conserved trans-spliced leader sequence among the transcripts and most genes were single-copy.
Despite the small size of this EST project it revealed several important features of the rotifer transcriptome and of individual monogonont genes. Because there is little genomic data for Gnathifera, the transcripts we found with no known function may represent genes that are species-, class-, phylum- or even superphylum-specific; the fact that some are among the most highly expressed indicates their importance. The absence of trans-spliced leader exons in this monogonont species contrasts with their abundance in bdelloid rotifers and indicates that the presence of this phenomenon can vary at the subphylum level. Our EST database provides a relatively large quantity of transcript-level data for B. plicatilis, and more generally of rotifers and other gnathiferan phyla, and can be browsed and searched at gmod.mbl.edu.

Flip Of Genetic Switch Causes Cancers In Mice To Self-destruct:

Killing cancerous tumors isn’t easy, as anyone who has suffered through chemotherapy can attest. But a new study in mice shows that switching off a single malfunctioning gene can halt the limitless division of tumor cells and turn them back to the path of their own planned obsolescence.

Zebrafish Research Provides Answers About Neurological Development:

Zebrafish cost about a dollar at the pet store. They grow from eggs to hunting their own food in three days. Adults can lay up to 500 eggs at once… and you have more in common with them than you think. “For all their differences, humans and zebrafish aren’t that dissimilar,” said Rice University zebrafish expert Mary Ellen Lane. “For every zebrafish gene we isolate, there is a related gene in humans.”
In her most recent work, Lane, graduate students Catherine McCollum and Shivas Amin, and undergraduate Philip Pauerstein zeroed in on a gene called LMO4 that’s known to play roles in both cell reproduction and in breast cancer. Using the tools of biotechnology, the team studied zebrafish that couldn’t transcribe the LMO4 gene, and they observed marked enlargement in both the forebrain and optical portions of the embryos.

Rare Example Of Darwinism Seen In Action:

A research team, including UC Riverside biologists, has found experimental evidence that supports a controversial theory of genetic conflict in the reproduction of those animals that support their developing offspring through a placenta.

Coelacanth Fossil Sheds Light On Fin-to-limb Evolution:

A 400 million-year-old fossil of a coelacanth fin, the first finding of its kind, fills a shrinking evolutionary gap between fins and limbs. University of Chicago scientists describe the finding in the July/August 2007 issue of Evolution & Development.

Chickens Dieting To Help Delaware Waterways:

Millions of chickens in Delaware–one of the nation’s top poultry producers–have been on a diet to reduce their impact on the environment and improve the health of the state’s waterways, and it appears to be working.

Goats’ Milk Is More Beneficial To Health Than Cows’ Milk, Study Suggests:

Researchers have carried out a comparative study on the properties of goats’ milk compared to those of cows’ milk. They found reason to believe that goats’ milk could help prevent diseases such as anemia and bone demineralization. Goats’ milk was found to help with the digestive and metabolic utilization of minerals such as iron, calcium, phosphorus and magnesium.

Is there a new Tuberculosis vaccine in the making?
Another movie is being made about Ivory-Bill woodpeckers.
A new astronomical explanation for the cycles of extinctions.

Sleep-Wake Controls Identified: Implications For Coma Patients And Those Under Anesthesia:

How do we wake up? How do we shift from restful sleep to dreaming? Researchers at the University of Arkansas for Medical Sciences (UAMS) have discovered a new brain mechanism that just might explain how we do that. This new mechanism also may help us understand how certain anesthetics put us to sleep and how certain stimulants wake us up. In their first published study on this topic, researchers in the UAMS Center for Translational Neuroscience found that some neurons in the reticular activating system, a region of the brain that controls sleep-wake states, are electrically coupled.

Infant Hearing Test Results May Predict Sudden Infant Death Syndrome:

One of the greatest medical mysteries of our time has taken a leap forward in medical understanding with new study results announced by Dr. Daniel D. Rubens of Children’s Hospital and Regional Medical Center in Seattle. Rubens’ study published in July, 2007 in Early Human Development found all babies in a Rhode Island study group who died of Sudden Infant Death Syndrome (SIDS) universally shared the same distinctive difference in their newborn hearing test results for the right inner ear, when compared to infants who did not have SIDS.

Low Literacy Equals Early Death Sentence:

Not being able to read doesn’t just make it harder to navigate each day. Low literacy impairs people’s ability to obtain critical information about their health and can dramatically shorten their lives.

Obesity Is ‘Socially Contagious’:

Are your friends making you fat? Or keeping you slender? According to new research from Harvard and the University of California, San Diego, the short answer on both counts is “yes.” Appearing in the July 26 issue of the New England Journal of Medicine, a study coauthored by Nicholas Christakis of Harvard Medical School and James Fowler of UC San Diego suggests that obesity is “socially contagious,” spreading from person to person in a social network.

Hearing Colors And Seeing Sounds: How Real Is Synesthesia?:

In the psychological phenomenon known as “synesthesia,” individuals’ sensory systems are a bit more intertwined than usual. Some people, for example, report seeing colors when musical notes are played. One of the most common forms is grapheme-color synesthesia, in which letters or numbers (collectively called “graphemes”) are highlighted with particular colors. Although synesthesia has been well documented, it is unknown whether these experiences, reported as vivid and realistic, are actually being perceived or if they are a byproduct of some other psychological mechanism such as memory.

Context Affects Opinion About Novel Energy Sources:

Opinions people have about innovations are influenced by the context in which they form their opinion. For example, opinions about a novel energy source like biomass are influenced by thoughts regarding other energy sources. The less knowledge, interest or time people have, the stronger this effect. Sustainable energy options must therefore be promoted in the right context says Dutch researcher Wouter van den Hoogen.

Prenatal Stress Keeps Infants, Toddlers Up At Night, Study Says:

Anxious or depressed mothers-to-be are at increased risk of having children who will experience sleep problems in infancy and toddlerhood, finds a study that published this month in Early Human Development.

Resisting Peer Pressure: New Findings Shed Light On Adolescent Decision-making:

The capacity to resist peer pressure in early adolescence may depend on the strength of connections between certain areas of the brain, according to a study carried out by University of Nottingham researchers.

Humanitarians, You’re Not As Generous As You Think:

A new study out of Carnegie Mellon University reveals that people who regard themselves as humanitarians are even more likely than others to base donations to the poor on whether they believe poverty is a result of bad luck or bad choices.

Anger, Depression Much Higher Among Jailed Teen Girls Than Boys:

A new study reveals that girls in juvenile detention centers face surprisingly different psychological issues than average teen girls and, in some ways, more severe problems than incarcerated boys.

Learning A Second Language: Is It All In Your Head?:

Think you haven’t got the aptitude to learn a foreign language? New research led by Northwestern University neuroscientists suggests that the problem, quite literally, could be in your head. … Based on the size of Heschl’s Gyrus (HG), a brain structure that typically accounts for no more than 0.2 percent of entire brain volume, the researchers found they could predict — even before exposing study participants to an invented language — which participants would be more successful in learning 18 words in the “pseudo” language.

Why Do People Love Horror Movies? They Enjoy Being Scared:

A bedrock assumption in theories that explain and predict human behavior is people’s motivation to pursue pleasure and avoid pain. How can this be reconciled with the decision to engage in experiences known to elicit negative feelings, such as horror movies” It certainly seems counterintuitive that so many people would voluntarily immerse themselves in almost two hours of fear, disgust and terror. “Why do people pay for this?” “How is this enjoyable?”

How To Manipulate Perceptual Focus In Advertisements:

In a new study from the August issue of the Journal of Consumer Research, researchers from Northwestern University demonstrate how advertisements can be manipulated to cause overemphasis of a particular feature and increase the likelihood that a certain product is chosen. Their finding runs contrary to economic models, which assume that choices are based on stable preferences and should not be influenced by the inclusion of inferior options.

College Science Success Linked To Math And Same-subject Preparation:

Researchers at Harvard University and the University of Virginia have found that high school coursework in one of the sciences generally does not predict better college performance in other scientific disciplines. But there’s one notable exception: Students with the most rigorous high school preparation in mathematics perform significantly better in college courses in biology, chemistry, and physics.

Relational Uncertainty Sparks Negativity In Marital Conversations:

Spouses who experience doubts about their marriage, even weak doubts, make pessimistic judgments about their partner’s behavior in conversation. That’s the conclusion of researchers who have conducted the first study to examine the link between relational uncertainty and conversation within marriage.

Why We May Feel Guilty:

Guilt plays a vital role in the regulation of social behavior. That worried feeling in our gut often serves as the impetus for our stab at redemption. However, psychologists have trouble agreeing on the function of this complex emotion.

Electronic Eggs Used To Help Save Threatened African Bird:

This is an important summer for kori bustards at the Smithsonian’s National Zoo. Four chicks of this threatened African bird have hatched in June and July. Along with the bumper crop of baby birds is a bumper crop of new information for scientists working to preserve the species, thanks to an electronic egg that transmits real-time incubation data from the nest.

Reef Corals: How To Structure A Complex Body Plan:

Phenotypic flexibility enables multicellular organisms to adjust morphologies to variable environmental challenges. Such plastic variations are also documented in reef corals. Coral colonies are made of multiple genetically identical physiologically integrated modules (polyps).

Fossils Older Than Dinosaurs Reveal Pattern Of Early Animal Evolution On Earth:

The abundant diversity of characteristics within species likely helped fuel the proliferation and evolution of an odd-looking creature that emerged from an unprecedented explosion of life on Earth more than 500 million years ago. University of Chicago paleontologist Mark Webster reports this finding in the July 27 issue of the journal Science.

Curiosities: Why Do Flowers Smell, And Why Do Plants Smell, Too?:

The luscious aroma of flowers attracts lovers, and the biological role of that smell is similar: to attract pollinators. “Plants need to attract insects, bats and hummingbirds to transfer the pollen and create fertile seeds,” says Hugh Iltis, professor emeritus of botany at UW-Madison.

Mystery Of Mammalian Ears Solved:

A 30-year scientific debate over how specialized cells in the inner ear amplify sound in mammals appears to have been settled more in favor of bouncing cell bodies rather than vibrating, hair-like cilia, according to investigators at St. Jude Children’s Research Hospital.

In A Bug-eat-bug World, Researchers Use Unique Chinese Wasp To Battle Soybean Aphids:

The days of soybean aphids feasting on soybean fields may be numbered, thanks to a unique import from China. University of Minnesota scientists are field testing a beneficial insect, a stingless wasp from China also known as Binodoxys communis, that kills soybean aphids. A successful field test would be a major breakthrough in controlling a damaging crop pest. The U of M received permission from the federal government to conduct this test and is the leading institution in the testing.

Surprising New Species Of Light-harvesting Bacterium Discovered In Yellowstone:

In the hot springs of Yellowstone National Park, a team of researchers has discovered a novel bacterium that transforms light into chemical energy. The researchers also discovered that the new genus and species belongs to a new phylum, Acidobacteria — only the third time in the past 100 years that a new bacterial phylum has been added to the list of those with chlorophyll-producing members, of which there are now only six.

Humboldt Squid On The Move:

Over the last five years, large, predatory Humboldt squid have moved north from equatorial waters and invaded the sea off Central California, where they may be decimating populations of Pacific hake, an important commercial fish.