Yearly Archives: 2007

There are 27 new papers appearing on PLoS ONE today. A quick scan of the titles makes me want to read the following more carefully:
Plasticity of the Intrinsic Period of the Human Circadian Timing System by Frank A. J. L. Scheer, Kenneth P. Wright, Richard E. Kronauer and Charles A. Czeisler:

Human expeditions to Mars will require adaptation to the 24.65-h Martian solar day-night cycle (sol), which is outside the range of entrainment of the human circadian pacemaker under lighting intensities to which astronauts are typically exposed. Failure to entrain the circadian time-keeping system to the desired rest-activity cycle disturbs sleep and impairs cognitive function. Furthermore, differences between the intrinsic circadian period and Earth’s 24-h light-dark cycle underlie human circadian rhythm sleep disorders, such as advanced sleep phase disorder and non-24-hour sleep-wake disorders. Therefore, first, we tested whether exposure to a model-based lighting regimen would entrain the human circadian pacemaker at a normal phase angle to the 24.65-h Martian sol and to the 23.5-h day length often required of astronauts during short duration space exploration. Second, we tested here whether such prior entrainment to non-24-h light-dark cycles would lead to subsequent modification of the intrinsic period of the human circadian timing system. Here we show that exposure to moderately bright light (~450 lux; ~1.2 W/m2) for the second or first half of the scheduled wake episode is effective for entraining individuals to the 24.65-h Martian sol and a 23.5-h day length, respectively. Estimations of the circadian periods of plasma melatonin, plasma cortisol, and core body temperature rhythms collected under forced desynchrony protocols revealed that the intrinsic circadian period of the human circadian pacemaker was significantly longer following entrainment to the Martian sol as compared to following entrainment to the 23.5-h day. The latter finding of after-effects of entrainment reveals for the first time plasticity of the period of the human circadian timing system. Both findings have important implications for the treatment of circadian rhythm sleep disorders and human space exploration.

Acoel Flatworms Are Not Platyhelminthes: Evidence from Phylogenomics by Herve Philippe, Henner Brinkmann, Pedro Martinez, Marta Riutort and Jaume Baguna:

Acoel flatworms are small marine worms traditionally considered to belong to the phylum Platyhelminthes. However, molecular phylogenetic analyses suggest that acoels are not members of Platyhelminthes, but are rather extant members of the earliest diverging Bilateria. This result has been called into question, under suspicions of a long branch attraction (LBA) artefact. Here we re-examine this problem through a phylogenomic approach using 68 different protein-coding genes from the acoel Convoluta pulchra and 51 metazoan species belonging to 15 different phyla. We employ a mixture model, named CAT, previously found to overcome LBA artefacts where classical models fail. Our results unequivocally show that acoels are not part of the classically defined Platyhelminthes, making the latter polyphyletic. Moreover, they indicate a deuterostome affinity for acoels, potentially as a sister group to all deuterostomes, to Xenoturbellida, to Ambulacraria, or even to chordates. However, the weak support found for most deuterostome nodes, together with the very fast evolutionary rate of the acoel Convoluta pulchra, call for more data from slowly evolving acoels (or from its sister-group, the Nemertodermatida) to solve this challenging phylogenetic problem.

Regional Decline of Coral Cover in the Indo-Pacific: Timing, Extent, and Subregional Comparisons by John F. Bruno and Elizabeth R. Selig:

The Indo-Pacific region contains 75% of the world’s coral reefs, but little is known about ongoing changes to the level of coral cover across this region. Bruno and Selig find that levels of coral cover in the Indo-Pacific are currently much lower than expected, and that the rate of coral loss is between 1% and 2% per year.

Biometric Evidence that Sexual Selection Has Shaped the Hominin Face by Eleanor M. Weston, Adrian E. Friday and Pietro Lio:

Men and women tend to have differently shaped faces. Weston and colleagues show that these differences cannot simply be explained in terms of overall body size differences, and that some of them seem to be related to a rotation during development of the upper jaw. Some of these features may have emerged during evolution through selection for facial attractiveness.

…and many, many more. So, as always, go, read, annotate, rate and comment.

The Circadian Clock Regulates Auxin Signaling and Responses in Arabidopsis by Michael F. Covington and Stacey L. Harmer:

Most higher organisms, including plants and animals, have developed a time-keeping mechanism that allows them to anticipate daily fluctuations of environmental parameters such as light and temperature. This circadian clock efficiently coordinates plant growth and metabolism with respect to time of day by producing self-sustained rhythms of gene expression with an approximately 24-h period. One of the major contributors in specifying spatial patterns of plant growth and development is auxin, a hormone essential for nearly all stages of plant development. Auxin also helps the plant orient itself properly in response to environmental cues such as light, gravity, and water. We have now found circadian-regulated expression of components from nearly every step in the auxin-signaling pathway, from synthesis to response. We demonstrate the relevance of this observation by showing that plants have differential sensitivity to auxin at different times of day: the clock controls plant sensitivity to auxin at both the level of transcription and stem growth. Our work demonstrates an intimate connection between the clock- and auxin-signaling pathways, and suggests that other auxin-regulated processes may also be under circadian control.

Also read the synopsis by Mary Hoff:

Buried in historical scientific literature are hints that auxin might affect plants differently at different times of day. This makes sense from an adaptive standpoint: an internal clock allows plants to respond to stimuli such as sun, rain, and being eaten in the context of regular rhythms of the inescapable world around them. But how do they do it? The mechanisms tuning growth to internal rhythms, with implications for everything from growing crops to protecting biodiversity in the face of global climate change, have remained a mystery. Now, Michael Covington and Stacey Harmer have discovered clues to the roots of rhythmic growth.

Spatial Learning Depends on Both the Addition and Removal of New Hippocampal Neurons by David Dupret, Annabelle Fabre, Màtè Dàniel Döbrössy, Aude Panatier, José Julio Rodríguez, Stéphanie Lamarque, Valerie Lemaire, Stephane H. R. Oliet, Pier-Vincenzo Piazza, and Djoher Nora Abrous:

The birth of adult hippocampal neurons is associated with enhanced learning and memory performance. In particular, spatial learning increases the survival and the proliferation of newborn cells, but surprisingly, it also decreases their number. Here, we hypothesized that spatial learning also depends upon the death of newborn hippocampal neurons. We examined the effect of spatial learning in the water maze on cell birth and death in the rodent hippocampus. We then determined the influence of an inhibitor of cell death on memory abilities and learning-induced changes in cell death, cell proliferation, and cell survival. We show that learning increases the elimination of the youngest newborn cells during a specific developmental period. The cell-death inhibitor impairs memory abilities and blocks the learning-induced cell death, the survival-promoting effect of learning on older newly born neurons, and the subsequent learning-induced proliferation of neural precursors. These results show that spatial learning induces cell death in the hippocampus, a phenomenon that subserves learning and is necessary for both the survival of older newly born neurons and the proliferation of neural precursors. These findings suggest that during learning, neuronal networks are sculpted by a tightly regulated selection of newly born neurons and reveal a novel mechanism mediating learning and memory in the adult brain.

Glia Play An Important Role In Circadian Timing:

Glial cells of the nervous system, once thought to function strictly as support cells for neurons, are now thought to actively modulate them. Providing further evidence in support of this theory, researchers at the Department of Neuroscience and the Center for Neuroscience Research (CNR) at Tufts University School of Medicine (TUSM) recently identified a specific population of glial cells that is required for the control of circadian behavior in Drosophila (the fruit fly). Their findings, which confirm and extend their earlier work, are published in the August 2, 2007, issue of Neuron.

Why Were Prehistoric Insects Huge?:

Alexander Kaiser, Ph.D., of Midwestern University’s Department of Physiology, Division of Basic Sciences, was the lead author in a recent study to help determine why insects, once dramatically larger than they are today, have seen such a remarkable reduction in size over the course of history.

Old McDonald’s Has A Hold On Kids’ Taste Buds, Study Finds:

Asked to sample two identical foods from the fast-food giant McDonald’s, children preferred the taste of the version branded with the restaurant’s familiar “Golden Arches” to one extracted from unmarked paper packaging, say researchers at the Stanford University School of Medicine and Lucile Packard Children’s Hospital.

Lost Forest Yields Several New Species:

An expedition led by the Wildlife Conservation Society (WCS) to a remote corner of the eastern Democratic Republic of Congo has uncovered unique forests which, so far, have been found to contain six animal species new to science: a bat, a rodent, two shrews, and two frogs.

First Giant Anteater Born At The National Zoo:

A giant anteater was born at the Smithsonian’s National Zoo the morning of Tuesday, July 24–a first in the Zoo’s 118-year history.

Immunity In Social Amoeba Suggests Ancient Beginnings:

Finding an immune system in the social amoeba (Dictyostelium discoideum) is not only surprising but it also may prove a clue as to what is necessary for an organism to become multicellular, said the Baylor College of Medicine researcher who led the research that appears in the journal Science.

Penguin Guano Shows Problem Of Pollution:

Penguin guano in the Antarctic is adding to organic pollutant problems there, according to a report to be featured in a Royal Society of Chemistry publication.

Tipping Points: Exploring How Agriculture Contributes To Global Change:

Growing food and fiber entails the use of fertilizer and irrigation systems and results in land clearing. These ‘side effects’ of agriculture can lead to regime shifts–or ‘tipping points’ which include desertification, salinisation, water degradation, and changes in climate due to altered water flows from land to atmosphere.

Source Of Fever Identified:

With the finding that fever is produced by the action of a hormone on a specific site in the brain, scientists have answered a key question as to how this adaptive function helps to protect the body during bacterial infection and other types of illness.

Fruit Bats Discovered To Have Menstrual Cycles:

Scientists have discovered that a type of fruit bat menstruate in a similar way to women.

Community-supported Agriculture Serves As Counterexample To Market Demands Of Globalization:

A compelling new paper from the August issue of the Journal of Consumer Research explores the community-supported agriculture movement and its survival in the face of economic globalization. Organic food was once an economic haven for small farms who distributed their goods predominantly through local channels such as farmers’ markets and food co-ops. In the contemporary marketplace, however, the vast majority of organic food production occurs on large-scale, industrial farms whose goods flow through global supply chains. In the United States, more than eighty percent of all sales in the organic category hail from brands owned by corporate conglomerates.

Secret Life Of Elephant Seals Not Secret Anymore!:

The measurements reveal in detail where the seals go on their winter feeding trips, where they find food and where they don’t, and help explain why some populations have remained stable since 1950 while others have declined.

Sensory Organ, Not Brain, Differentiates Male And Female Behavior In Some Mammals:

For years, scientists have searched in vain for slivers of the brain that might drive the dramatic differences between male and female behavior. Now biologists at Harvard University say these efforts may have fallen flat because such differences may not arise in the brain at all.

‘Convenience’ Foods Save Little Time For Working Families At Dinner:

Two-income families in Los Angeles don’t live so much in a fast food nation as they do in a Hamburger Helper hamlet on the edge of a packaged lettuce greenbelt, according to the first academic study to track American families moment by moment as they make dinner.

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.