A Blog Around The Clock

Navigation: Using Geometry To Navigate Is Innate, At Least For Fish:

Many animals, including humans, frequently face the task of getting from one place to another. Although many navigational strategies exist, all vertebrate species readily use geometric cues; things such as walls and corners to determine direction within an enclosed space. Moreover, some species such as rats and human children are so influenced by these geometric cues that they often ignore more reliable features such as a distinctive object or colored wall.
This surprising reliance on geometry has led researchers to suggest the existence of a geometric module in the brain. However, since both humans and laboratory animals typically grow up in environments not entirely made up of right angles and straight lines, the prevalent use of geometry could reflect nurture rather than nature. A new study published in the July issue of Psychological Science, a journal of the Association for Psychological Science, is the first attempt to examine whether early exposure to strong geometric cues influences navigational strategy.

Unravelling New Complexity In The Genome:

A major surprise emerging from genome sequencing projects is that humans have a comparable number of protein-coding genes as significantly less complex organisms such as the minute nematode worm Caenorhabditis elegans. Clearly something other than gene count is behind the genetic differences between simpler and more complex life forms.

Rainforest Biodiversity Shows Differing Patterns:

Rainforests are the world’s treasure houses of biodiversity, but all rainforests are not the same. Biodiversity may be more evenly distributed in some forests than in others and, therefore, may require different management and preservation strategies. That is one of the conclusions of a large-scale Smithsonian study of a lowland rainforest in New Guinea, published in the Aug. 9 issue of the journal Nature.

Evolution Is Driven By Gene Regulation:

It is not just what’s in your genes, it’s how you turn them on that accounts for the difference between species — at least in yeast — according to a report by Yale researchers in this week’s issue of Science.

Gene Regulation, Not Just Genes, Is What Sets Humans Apart:

The striking differences between humans and chimps aren’t so much in the genes we have, which are 99 percent the same, but in the way those genes are used, according to new research from a Duke University team. It’s rather like the same set of notes being played in very different ways.

Which Came First, The Moth Or The Cactus?:

It’s not a good idea to put all your eggs in one basket… unless you’re a senita moth. Found in the parched Sonoran desert of southern Arizona and northern Mexico, the senita moth depends on a single plant species — the senita cactus — both for its food and for a place to lay eggs. The senita cactus is equally dependent upon the moth, the only species that pollinates its flowers. Senita cacti and senita moths have a rare, mutually dependent relationship, one of only three known dependencies in which an insect actively pollinates flowers for the purpose of assuring a food resource for its offspring.

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.