A Blog Around The Clock

‘Armored’ Fish Study Helps Strengthen Darwin’s Natural Selection Theory:

Shedding some genetically induced excess baggage may have helped a tiny fish thrive in freshwater and outsize its marine ancestors, according to a UBC study published today in Science Express. Measuring three to 10 centimetres long, stickleback fish originated in the ocean but began populating freshwater lakes and streams following the last ice age. Over the past 20,000 years – a relatively short time span in evolutionary terms – freshwater sticklebacks have lost their bony lateral plates, or “armour,” in these new environments.

Incidence Of Intestinal Parasite Coccidia Is Increasing In Broilers:

Coccidia are single-celled intestinal parasites that currently represent one of the greatest challenges to the broiler industry. To keep the level of infection low, farmers commonly add coccidia-inhibiting chemicals (coccidiostats) to broiler feed. While this does not kill the parasites, it greatly reduces the incidence of overt sickness and death from infection. While clinical coccidiosis is therefore not a problem, veterinary authorities have never been able to gauge the extent of subclinical coccidiosis and the consequences this may have for animal welfare issues and production costs.

Gray’s Reef National Marine Sanctuary In Fair Condition, Facing Emerging Threats:

A new NOAA report on the health of Gray’s Reef National Marine Sanctuary indicates that the overall condition of the sanctuary’s marine life and habitats is fair. The report also identifies several emerging threats to sanctuary resources, including non-indigenous marine species, overfishing, waterborne chemicals from human coastal activities, and increased recreational use of the site.

‘Lost World’ Beneath Caribbean To Be Explored:

Scientists at the National Oceanography Centre, Southampton, are set to explore the world’s deepest undersea volcanoes and find out what lives in a ‘lost world’ five kilometres beneath the Caribbean.

More Genes Are Controlled By Biological Clocks Than Previously Thought:

The tick-tock of your biological clock may have just gotten a little louder. Researchers at the University of Georgia report that the number of genes under control of the biological clock in a much-studied model organism is dramatically higher than previously reported. The new study implies that the clock may be much more important in living things than suspected only a few years ago.

No More Big Stink: Scent Lures Mosquitoes, But Humans Can’t Smell It:

Mosquito traps that reek like latrines may be no more. A University of California, Davis research team led by chemical ecologist Walter Leal has discovered a low-cost, easy-to-prepare attractant that lures blood-fed mosquitoes without making humans hold their noses.

Treatment For Hearing Loss? Scientists Grow Hair Cells Involved in Hearing:

Oregon Health & Science University scientists have successfully produced functional auditory hair cells in the cochlea of the mouse inner ear. The breakthrough suggests that a new therapy may be developed in the future to successfully treat hearing loss. The results of this research was recently published by the journal Nature.

Shot In The Arm For Sumatran Elephants And Tigers:

The Indonesian government is to double the size of a national park that is one of the last havens for endangered Sumatran elephants and tigers.

New Report Loosens Noose Around Albatross’s Neck:

The survival chances of the albatross, now officially the most threatened seabird family in the world, have been improved following a new report released by WWF-South Africa.

‘Fingerprinting’ Helps Make Great Grapes:

At about this time next year, nearly all of the 2,800 wild, rare and domesticated grapes in a unique northern California genebank will have had their “genetic profile” or “fingerprint” taken. These fingerprints may help grape breeders pinpoint plants in the collection that have unusual traits–ones that might appeal to shoppers in tomorrow’s supermarkets.

More Than 150,000 Species Of Flies, Gnats, Maggots, Midges, Mosquitoes Documented In Database:

Distinguishing between insect pests and partners starts with an ironclad identification. So Agricultural Research Service (ARS) entomologist Chris Thompson headed up efforts to accurately identify and name almost 157,000 flies, gnats, maggots, midges, mosquitoes and related species in the order Diptera.

Slowing Ships To Protect North Atlantic Right Whales:

NOAA’s Fisheries Service is seeking comment on the final environmental impact statement (EIS) for the Ship Strike Reduction Rule. The EIS is one of the final steps in the process to implement a final rule. The ship strike reduction rule aims to reduce the number of endangered North Atlantic right whales injured or killed by collisions with large ships.

Unexpected Large Monkey Population Discovered In Cambodia: Tens Of Thousands Of Threatened Primates:

A Wildlife Conservation Society report reveals surprisingly large populations of two globally threatened primates in a protected area in Cambodia.

‘Pristine’ Amazonian Region Hosted Large, Urban Civilization:

They aren’t the lost cities early explorers sought fruitlessly to discover. But ancient settlements in the Amazon, now almost entirely obscured by tropical forest, were once large and complex enough to be considered “urban” as the term is commonly applied to both medieval European and ancient Greek communities.

Scientists Discover Why Flies Are So Hard To Swat:

Over the past two decades, Michael Dickinson has been interviewed by reporters hundreds of times about his research on the biomechanics of insect flight. One question from the press has always dogged him: Why are flies so hard to swat?

Why Did The Squirrel Cross The Road?:

A study has shown that red squirrels can and do make use of special crossings set up over busy roads. A researcher from the University of Leeds’ Faculty of Biological Sciences conducted a survey to discover whether red squirrels living in Loch Lomond and the Trossachs National Park were using rope bridges installed by a local wildlife group.

Diversity Among Parasitic Wasps Is Even Greater Than Suspected:

A tiny wasp that lays its eggs under the skin of unwitting caterpillars belongs to one of the most diverse groups of insects on Earth. Now researchers report that its diversity is even higher than previously thought.

There are 12 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. Here are my own picks for the week – you go and look for your own favourites:
Urochordate Histoincompatible Interactions Activate Vertebrate-Like Coagulation System Components:

The colonial ascidian Botryllus schlosseri expresses a unique allorecognition system. When two histoincompatible Botryllus colonies come into direct contact, they develop an inflammatory-like rejection response. A surprising high number of vertebrates’ coagulation genes and coagulation-related domains were disclosed in a cDNA library of differentially expressed sequence tags (ESTs), prepared for this allorejection process. Serine proteases, especially from the trypsin family, were highly represented among Botryllus library ortholgues and its “molecular function” gene ontology analysis. These, together with the built-up clot-like lesions in the interaction area, led us to further test whether a vertebrate-like clotting system participates in Botryllus innate immunity. Three morphologically distinct clot types (points of rejection; POR) were followed. We demonstrated the specific expression of nine coagulation orthologue transcripts in Botryllus rejection processes and effects of the anti-coagulant heparin on POR formation and heartbeats. In situ hybridization of fibrinogen and von Willebrand factor orthologues elucidated enhanced expression patterns specific to histoincompatible reactions as well as common expressions not augmented by innate immunity. Immunohistochemistry for fibrinogen revealed, in naïve and immune challenged colonies alike, specific antibody binding to a small population of Botryllus compartment cells. Altogether, molecular, physiological and morphological outcomes suggest the involvement of vertebrates-like coagulation elements in urochordate immunity, not assigned with vasculature injury.

Changes in Cognition and Mortality in Relation to Exercise in Late Life: A Population Based Study:

On average, cognition declines with age but this average hides considerable variability, including the chance of improvement. Here, we investigate how exercise is associated with cognitive change and mortality in older people and, particularly, whether exercise might paradoxically increase the risk of dementia by allowing people to live longer. In the Canadian Study of Health and Aging (CSHA), of 8403 people who had baseline cognition measured and exercise reported at CSHA-1, 2219 had died and 5376 were re-examined at CSHA-2. We used a parametric Markov chain model to estimate the probabilities of cognitive improvement, decline, and death, adjusted for age and education, from any cognitive state as measured by the Modified Mini-Mental State Examination. High exercisers (at least three times per week, at least as intense as walking, n = 3264) had more frequent stable or improved cognition (42.3%, 95% confidence interval: 40.6-44.0) over 5 years than did low/no exercisers (all other exercisers and non exercisers, n = 4331) (27.8% (95% CI 26.4-29.2)). The difference widened as baseline cognition worsened. The proportion whose cognition declined was higher amongst the high exercisers but was more similar between exercise groups (39.4% (95% CI 37.7-41.1) for high exercisers versus 34.8% (95% CI 33.4-36.2) otherwise). People who did not exercise were also more likely to die (37.5% (95% CI 36.0-39.0) versus 18.3% (95% CI 16.9-19.7)). Even so, exercise conferred its greatest mortality benefit to people with the highest baseline cognition. Exercise is strongly associated with improving cognition. As the majority of mortality benefit of exercise is at the highest level of cognition, and declines as cognition declines, the net effect of exercise should be to improve cognition at the population level, even with more people living longer.

Chronic Cigarette Smoke Causes Oxidative Damage and Apoptosis to Retinal Pigmented Epithelial Cells in Mice:

The purpose of this study was to determine whether mice exposed to chronic cigarette smoke develop features of early age-related macular degeneration (AMD). Two month old C57Bl6 mice were exposed to either filtered air or cigarette smoke in a smoking chamber for 5 h/day, 5 days/week for 6 months. Eyes were fixed in 2.5% glutaraldehyde/2% paraformaldehyde and examined for ultrastructural changes by transmission electron microscopy. The contralateral eye was fixed in 2% paraformaldehyde and examined for oxidative injury to the retinal pigmented epithelium (RPE) by 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-OHdG) immunolabeling and apoptosis by TUNEL labeling. Mice exposed to cigarette smoke had immunolabeling for 8-OHdG in 85±3.7% of RPE cells counted compared to 9.5±3.9% in controls (p<0.00001). Bruch membrane was thicker in mice exposed to smoke (1086±332 nm) than those raised in air (543±132 nm; p = 0.0069). The two most pronounced ultrastructural changes (severity grading scale from 0-3) seen were a loss of basal infoldings (mean difference in grade = 1.98; p<0.0001), and an increase in intracellular vacuoles (mean difference in grade = 1.7; p<0.0001). Ultrastructural changes to Bruch membrane in cigarette-smoke exposed mice were smaller in magnitude but consistently demonstrated significantly higher grade injury in cigarette-exposed mice, including basal laminar deposits (mean difference in grade = 0.54; p<0.0001), increased outer collagenous layer deposits (mean difference in grade = 0.59; p = 0.002), and increased basal laminar deposit continuity (mean difference in grade = 0.4; p<0.0001). TUNEL assay showed a higher percentage of apoptotic RPE from mice exposed to cigarette smoke (average 8.0±1.1%) than room air (average 0±0%; p = 0.043). Mice exposed to chronic cigarette smoke develop evidence of oxidative damage with ultrastructural degeneration to the RPE and Bruch membrane, and RPE cell apoptosis. This model could be useful for studying the mechanism of smoke induced changes during early AMD.

Eyes Evolved For ‘X-Ray Vision’: Forward-facing Eyes Allow Animals To ‘See Through’ Clutter In The World:

The advantage of using two eyes to see the world around us has long been associated solely with our capacity to see in 3-D. Now, a new study from a scientist at Rensselaer Polytechnic Institute has uncovered a truly eye-opening advantage to binocular vision: our ability to see through things.

Sticks And Stones: A New Study On Social And Physical Pain:

We all know the famous saying: “Sticks and stones may break my bones, but words will never hurt me,” but is this proverb actually true? According to some researchers, words may pack a harder punch that we realize. Psychologists Zhansheng Chen and Kipling D. Williams of Purdue University, Julie Fitness of Macquarie University, and Nicola C. Newton of the University of New South Wales found that the pain of physical events may fade with time, while the pain of social occurrences can be re-instantiated through memory retrievals.

Linguistic Tools Used To Analyze Human Language Applied To Conversation Between Scientist And Bonobo:

What happens when linguistic tools used to analyze human language are applied to a conversation between a language-competent bonobo and a human? The findings, published this month in the Journal of Integrative Psychological and Behavioral Science, indicate that bonobos may exhibit larger linguistic competency in ordinary conversation than in controlled experimental settings.

Economic And Social Disadvantage Can Affect Young Citizens’ Voter Turnout:

A study recently published in the Journal of Social Issues illustrates how certain disadvantages experienced in adolescence, such as early pregnancy, dropping out of high school, being arrested, or going to an underprivileged school, contribute to lower voter turnout in young adulthood. In addition, the types of disadvantage vary across racial groups.

So, let’s see what’s new in PLoS Genetics, PLoS Computational Biology, PLoS Pathogens and PLoS Neglected Tropical Diseases this week. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. Here are my own picks for the week – you go and look for your own favourites:
Strategies for Aspiring Biomedical Researchers in Resource-Limited Environments:

Countries struggling with global health challenges desperately need local biomedical researchers to find health care solutions to address the deadly diseases that affect their populations. Building the scientific capacity of resource-limited countries is a clear priority among the scientific community [1]-[3].
As the Global Forum for Health Research Report stated [4], “Strengthening research capacity in developing countries is one of the most effective and sustainable ways of advancing health and development in these countries and of helping correct the 10/90 gap in health research.” The 10/90 gap refers to the statistical finding of the Global Forum for Health Research that only 10% of all global health research funding is directed to research on the health problems that affect 90% of the world’s population [5].
Great efforts are now being made to correct this gap, and some call it the golden age of global health. Many researchers in resource-limited environments have the opportunity to train outside their country and are offered scholarships to do so, with the goal that they will return and help their country. For researchers willing to deal with developing world challenges (poor infrastructure and support), there are exciting opportunities to solve a nation’s most pressing health problems and make a name for themselves along the way.

Training the Next Generation of Global Health Scientists: A School of Appropriate Technology for Global Health:

In March of 2008, the Bill & Melinda Gates Foundation made the impressive announcement that it will accept proposals for a new Grand Challenges Explorations program [1]. Grand Challenges Explorations will provide $100 million for global health scientists to identify new ways to protect against infectious diseases (including neglected tropical diseases [NTDs]), to create new drugs or delivery systems, to prevent or cure HIV/AIDS, and to explore the basis of latency in tuberculosis [1]. In so doing, the Gates Foundation will build on its long-standing multibillion dollar commitments to develop and test new drugs, diagnostics, and vaccines for NTDs, as well as the better known “big three” diseases, HIV/AIDS, tuberculosis, and malaria, and to fund critically needed operational research in support of large-scale control programs for these conditions [1]. The Gates Foundation is not alone–the United Kingdom’s Wellcome Trust has a £15 billion investment portfolio of which a significant amount is devoted to global infectious diseases [2], while the United States National Institutes of Health (NIH) also devotes a significant amount of funding towards global health [3]. Therefore, in the coming decade we can expect that these initiatives will contribute significantly towards reducing the so-called 10/90 gap, a term coined by the Global Forum for Health Research to refer to the finding that only 10% or less of the global expenditure on medical research and development is directed towards neglected health problems that disproportionately affect the poorest people in developing regions of sub-Saharan Africa, Asia, and tropical regions of the Americas.

A Tribute to Evgenii V. Ananiev, 1947-2008:

This article is a tribute to Dr. Evgenii Ananiev, who passed away on January 10, 2008, after a year-long battle with a brain tumor. It is nearly impossible for me to comprehend this loss, as Evgenii (Image 1) was always larger than life–full of ideas, vitality, and joy. I first met Evgenii more than 30 years ago, when I started working on my senior thesis in the laboratory of Roman Khesin in the legendary Radiobiology Department of the Atomic Energy Institute in Moscow. Evgenii was a postdoctoral fellow in the lab next door headed by Vladimir Gvozdev. From day one, it was hard not to notice this energetic, well-built young man with a broad, charismatic smile and engaging manners. He would bump into you in the corridor to share his excitement about his most recent observations made using DNA hybridization in situ with the polytene chromosomes of Drosophila. Admittedly, he had every reason to get excited, as his data provided the first molecular evidence for the existence of mobile elements in eukaryotes–a discovery of foremost significance. The paper describing these striking results came out in Science, an unprecedented success for Soviet molecular biology.

Sweating the Details: An Interview with Jamie Thomson:

If you had to name the most controversial scientific achievement of the past decade, you’d be hard pressed to top the development of human embryonic stem [ES] cells. Human ES cells followed on the heels of another major technological advance–Dolly, the cloned ewe. Together, these remarkable breakthroughs have stimulated great public interest and have ushered in a new era in the exploration of human biology. At the center of the ES maelstrom is a soft-spoken and intensely private scientist from the Genome Center at the University of Wisconsin. Jamie Thomson (Image 1), who is also Director of Regenerative Biology at the new Morgridge Institute for Research and the founder of two companies, is purposeful, with an obvious knack for a difficult experiment, yet seems a bit uncomfortable in the limelight his work has generated.

The Dynamic Brain: From Spiking Neurons to Neural Masses and Cortical Fields:

The cortex is a complex system, characterized by its dynamics and architecture, which underlie many functions such as action, perception, learning, language, and cognition. Its structural architecture has been studied for more than a hundred years; however, its dynamics have been addressed much less thoroughly. In this paper, we review and integrate, in a unifying framework, a variety of computational approaches that have been used to characterize the dynamics of the cortex, as evidenced at different levels of measurement. Computational models at different space-time scales help us understand the fundamental mechanisms that underpin neural processes and relate these processes to neuroscience data. Modeling at the single neuron level is necessary because this is the level at which information is exchanged between the computing elements of the brain; the neurons. Mesoscopic models tell us how neural elements interact to yield emergent behavior at the level of microcolumns and cortical columns. Macroscopic models can inform us about whole brain dynamics and interactions between large-scale neural systems such as cortical regions, the thalamus, and brain stem. Each level of description relates uniquely to neuroscience data, from single-unit recordings, through local field potentials to functional magnetic resonance imaging (fMRI), electroencephalogram (EEG), and magnetoencephalogram (MEG). Models of the cortex can establish which types of large-scale neuronal networks can perform computations and characterize their emergent properties. Mean-field and related formulations of dynamics also play an essential and complementary role as forward models that can be inverted given empirical data. This makes dynamic models critical in integrating theory and experiments. We argue that elaborating principled and informed models is a prerequisite for grounding empirical neuroscience in a cogent theoretical framework, commensurate with the achievements in the physical sciences.

There are 11 new articles in PLoS ONE today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. Here are my own picks for the week – you go and look for your own favourites:
Systems Biology of the Clock in Neurospora crassa:

A model-driven discovery process, Computing Life, is used to identify an ensemble of genetic networks that describe the biological clock. A clock mechanism involving the genes white-collar-1 and white-collar-2 (wc-1 and wc-2) that encode a transcriptional activator (as well as a blue-light receptor) and an oscillator frequency (frq) that encodes a cyclin that deactivates the activator is used to guide this discovery process through three cycles of microarray experiments. Central to this discovery process is a new methodology for the rational design of a Maximally Informative Next Experiment (MINE), based on the genetic network ensemble. In each experimentation cycle, the MINE approach is used to select the most informative new experiment in order to mine for clock-controlled genes, the outputs of the clock. As much as 25% of the N. crassa transcriptome appears to be under clock-control. Clock outputs include genes with products in DNA metabolism, ribosome biogenesis in RNA metabolism, cell cycle, protein metabolism, transport, carbon metabolism, isoprenoid (including carotenoid) biosynthesis, development, and varied signaling processes. Genes under the transcription factor complex WCC ( = WC-1/WC-2) control were resolved into four classes, circadian only (612 genes), light-responsive only (396), both circadian and light-responsive (328), and neither circadian nor light-responsive (987). In each of three cycles of microarray experiments data support that wc-1 and wc-2 are auto-regulated by WCC. Among 11,000 N. crassa genes a total of 295 genes, including a large fraction of phosphatases/kinases, appear to be under the immediate control of the FRQ oscillator as validated by 4 independent microarray experiments. Ribosomal RNA processing and assembly rather than its transcription appears to be under clock control, suggesting a new mechanism for the post-transcriptional control of clock-controlled genes.

Leptin Replacement Improves Cognitive Development:

Background
Leptin changes brain structure, neuron excitability and synaptic plasticity. It also regulates the development and function of feeding circuits. However, the effects of leptin on neurocognitive development are unknown.
Objective
To evaluate the effect of leptin on neurocognitive development.
Methodology
A 5-year-old boy with a nonconservative missense leptin gene mutation (Cys-to-Thr in codon 105) was treated with recombinant methionyl human leptin (r-metHuLeptin) at physiologic replacement doses of 0.03 mg/kg/day. Cognitive development was assessed using the Differential Ability Scales (DAS), a measure of general verbal and nonverbal functioning; and selected subtests from the NEPSY, a measure of neuropsychological functioning in children.
Principal Findings
Prior to treatment, the patient was morbidly obese, hypertensive, dyslipidemic, and hyperinsulinemic. Baseline neurocognitive tests revealed slower than expected rates of development (developmental age lower than chronological age) in a majority of the areas assessed. After two years, substantial increases in the rates of development in most neurocognitive domains were apparent, with some skills at or exceeding expectations based on chronological age. We also observed marked weight loss and resolution of hypertension, dyslipidemia and hyperinsulinemia.
Conclusions
We concluded that replacement with r-metHuLeptin is associated with weight loss and changes in rates of development in many neurocognitive domains, which lends support to the hypothesis that, in addition to its role in metabolism, leptin may have a cognitive enhancing role in the developing central nervous system.