Post List

  • August 5, 2010
  • 08:24 AM
  • 975 views

Foldit: Innovative Biology for Gamers

by GrrlScientist in This Scientific Life

Guessing how a protein will fold up based on its DNA sequence is often too difficult for even the most advanced computer programs. Now biochemists and computer scientists at my alma mater, the University of Washington, have collaborated to create Foldit, an online computer game where computer players do the work. ... Read more »

Cooper, S., Khatib, F., Treuille, A., Barbero, J., Lee, J., Beenen, M., Leaver-Fay, A., Baker, D., Popović, Z., & players, F. (2010) Predicting protein structures with a multiplayer online game. Nature, 466(7307), 756-760. DOI: 10.1038/nature09304  

  • August 5, 2010
  • 08:00 AM
  • 1,580 views

Do Fitness Tax Credits Only Make The Rich Richer?

by Arya M. Sharma in Dr. Sharma's Obesity Notes

Yesterday, University of Alberta’s John Spence (on faculty of the annual Canadian Obesity Network’s Student Boot Camp) together with Valerie Carson (former Bootcamper) and coworkers, published a most interesting article in BMC Public Health.
The paper looks at the uptake and effectiveness of the Children’s Fitness Tax Credit (CFTC) on Canadians. This tax credit was introduced [...]... Read more »

  • August 5, 2010
  • 08:00 AM
  • 964 views

Eyes on the edge: How archerfish see in and out of water

by Zen Faulkes in NeuroDojo

Archerfish rock.

These little sharpshooters are famous for being able to spit water at an insect, not on the surface of the water, but a good ways above it. And these insects are often camouflaged to boot. Then, they have to catch the insect when it hits the water before other fish get it, or it gets swept away by any water currents.

In other words, archerfish have to calculate, perform precision maneuvers, and anticipate the outcomes of their actions.

This paper, though, looks mainly at the visual problem. Anyone has probably noticed that light behaves differently when it moves through water than when it moves through air. The famous example that every kid has probably asked his parents about is why a spoon in a glass of water looks like the two halves are broken apart.

The authors here looked at the properties of the photoreceptors in the archerfish eyes. Something to remember is that the top of the retina looks down, which for the archerfish means into the water, and the bottom part of the retina looks up, which for the archerfish means looking up and out of the water. Now, it gets a bit sticky because fish have more complicated eyes that we primates do. We have rods and three kinds of cones. The archerfish has rods, single cones and double cones.

First, they found that the three general areas of the eye they looked at, the light-sensing cells of the ventral part of the retina had rather different light absorbing properties than the rest. This correlates with the fish’s visual task: the bottom part of the eye looks up, out of water.

As light goes through the water, the colours change. At the top of the water, the light tends to have shorter wavelengths than the light being reflected from the bottom of the water. The sensitivity of the photoreceptors in those regions matched quite well with the different kinds of light these animals would be seeing.

The highest density of cones is also right in the “sweet spot” where the fish will be looking at its target. The authors don’t use the term “fovea,” but it seems to me that is exactly what it is. And the resolution the archerfish is probably capable of is estimated to be about 8 minutes of arc; by comparison, arthropods eyes tend to be only able to resolve several degrees of arc, and I think humans in fractions of a second of arc.

They interpret these differences across the retina as adaptations to living at the interface, which is perfectly reasonable. The authors suggest that it something that other fish living near the surface have, although one might expect it to be particularly enhanced in the archerfish.

Next steps for this group is to start doing a bucket of behavioural tests to see how well the fish is able to discriminate different colours, shades, and so on. Since the fish has a nice behaviour of spitting at things they see, it should be possible to train them to spit at objects they can see, then tweak the visual stimuli until they can’t do the task any more.

Reference

Temple, S., Hart, N., Marshall, N., & Collin, S. (2010). A spitting image: specializations in archerfish eyes for vision at the interface between air and water Proceedings of the Royal Society B: Biological Sciences, 277 (1694), 2607-2615 DOI: 10.1098/rspb.2010.0345... Read more »

  • August 5, 2010
  • 06:56 AM
  • 722 views

A Practical Approach to MIQE for the Bench Scientist

by aviwener in Canadian Biotechnologist 2.0

In a groundbreaking review published in February 2009, Bustin et al bemoaned the lack of standardization in Quantitative Real-Time PCR (qPCR) experimentation and data analysis. In their critique the authors cite the use of diverse reagents, protocols, analysis methods and reporting formats which has negatively impacted on the acceptance of qPCR as a robust quantitative [...]... Read more »

Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL.... (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clinical chemistry, 55(4), 611-22. PMID: 19246619  

  • August 5, 2010
  • 06:14 AM
  • 1,653 views

The good old days, revisited

by iayork in Mystery Rays from Outer Space

As a general remark, the Measles were mild, while on the contrary, the Mumps were almost invariably severe, and frequently attended with metastasis to the testicles. Some cases of the latter were attended with enormous swelling and high inflammatory excitement, requiring the lancet and other antiphlogistic remedies. … As a local application to the scrotum none appeared to afford [...]... Read more »

Quinlisk, M. (2010) Mumps Control Today. The Journal of Infectious Diseases, 2147483647. DOI: 10.1086/655395  

  • August 5, 2010
  • 03:38 AM
  • 557 views

1 in 200 men direct descendants of Genghis Khan

by Razib Khan in Gene Expression

In 2003 a groundbreaking historical genetics paper reported results which indicated that a substantial proportion of men in the world are direct line descendants of Genghis Khan. By direct line, I mean that they carry Y chromosomes which seem to have come down from an individual who lived approximately 1,000 years ago. As Y chromosomes [...]... Read more »

ZERJAL, T. (2003) The Genetic Legacy of the Mongols. The American Journal of Human Genetics, 72(3), 717-721. DOI: 10.1086/367774  

  • August 5, 2010
  • 12:16 AM
  • 1,380 views

Language and inflation

by Ingrid Piller in Language on the Move

Some Language-on-the-Movers based here in Sydney had the opportunity to attend Professor Masaki Oda’s lecture about the current state of the English language in Japan yesterday. With major Japanese companies announcing a switch to English as their official company language … Continue reading →... Read more »

  • August 5, 2010
  • 12:00 AM
  • 947 views

Close encounters with outer shells

by Joerg Heber in All That Matters

If you look at the image of an atom in a text book, it looks rather quiet and peaceful. There is a nucleus in the center made from a number of protons and neutrons. Around the nucleus the electrons typically are shown to orbit the core like planets around the sun. The reality, however, is far more complicated. First of all, the electrons don’t look like small planets, but are smeared out in complex shapes known as orbitals. The energy states of the different orbitals correspond to the electron shells in atomic physics. And secondly the electron motion is extremely fast, on the timescale of a femtosecond (fs), which is 10-15 seconds. [...]... Read more »

Goulielmakis, E., Loh, Z., Wirth, A., Santra, R., Rohringer, N., Yakovlev, V., Zherebtsov, S., Pfeifer, T., Azzeer, A., Kling, M.... (2010) Real-time observation of valence electron motion. Nature, 466(7307), 739-743. DOI: 10.1038/nature09212  

  • August 4, 2010
  • 10:55 PM
  • 483 views

A Clinically Useful Fluorescence Microscope for $240 USD

by Michael Long in Phased

Andrew Miller (Rice University, United States) and coworkers have developed a remarkably cheap microscope with both the portability and imaging capabilites required for routine slide-based medical diagnostics, an extremely useful development for health professionals in remote regions of the world. This news feature was written on August 4, 2010.... Read more »

Miller, A. R., Davis, G. L., Oden, Z. M., Razavi, M. R., Fateh, A., Ghazanfari, M., Abdolrahimi, F., Poorazar, S., Sakhaie, F., Olsen, R. J.... (2010) Portable, Battery-Operated, Low-Cost, Bright Field and Fluorescence Microscope. PLoS ONE, 5(8). DOI: 10.1371/journal.pone.0011890  

  • August 4, 2010
  • 09:51 PM
  • 673 views

Pharmacy Customers Perception of Complementary and Alternative Medicine in Pharmacies

by Darcy Cowan in Skepticon

Going through the papers cluttering my inbox I found this survey of Australian pharmacy customers relating to their use of CAM and their impressions of how pharmacists should approach the subject. Regular readers of Sciblogs may remember a kerfuffle earlier in the year regarding the sale of homeopathic remedies in pharmacies, I and others were [...]... Read more »

Braun, L., Tiralongo, E., Wilkinson, J., Spitzer, O., Bailey, M., Poole, S., & Dooley, M. (2010) Perceptions, use and attitudes of pharmacy customers on complementary medicines and pharmacy practice. BMC Complementary and Alternative Medicine, 10(1), 38. DOI: 10.1186/1472-6882-10-38  

  • August 4, 2010
  • 09:25 PM
  • 469 views

Don’t Bite: The Defenestration of Cookie

by Jason Goldman in Child's Play

III. Whither the Cookie Task? WARNING: What you are about to read may contain graphic statistical content.  Side effects may include: contagious yawning, inappropriate arousal, and / or spontaneous combustion, depending on how you like your math cooked… darling. Psychologists often think about the cookie task as a test of cognitive control, and in keeping [...]... Read more »

Eigsti, I., Zayas, V., Mischel, W., Shoda, Y., Ayduk, O., Dadlani, M., Davidson, M., Aber, J., & Casey, B. (2006) Predicting Cognitive Control From Preschool to Late Adolescence and Young Adulthood. Psychological Science, 17(6), 478-484. DOI: 10.1111/j.1467-9280.2006.01732.x  

Mischel, W., Shoda, Y., & Rodriguez, M. (1989) Delay of gratification in children. Science, 244(4907), 933-938. DOI: 10.1126/science.2658056  

  • August 4, 2010
  • 06:05 PM
  • 1,021 views

More on maternal spiders

by Africa Gomez in BugBlog

I posted recently on maternal behaviour in spiders, but I when I came across this I knew another post was in order. The photo above shows what is is most likely a Gnaphosidae spider with her eggs in her nest on the 19th of July. The spider has wrapped herself inside a silken nest she has made for her eggs, and she will remain there until they hatch and the spiderlings disperse. This behaviour, called 'egg guarding' is present in many spiders. Why would a spider do this? Do the eggs benefit in a any way from their mothers behaviour? There is anecdotal evidence in related species that unattended eggs are predated, but little information was available on who the predators are until Simon Pollard carried out some experiments on Clubiona cambridgei, an endemic species from New Zealand displaying this egg guarding behaviour, and the results were surprising.  Simon had noticed that sometimes Clubiona spiders were found inside or just outside nests with eaten eggs and suspected that individuals from the same species were actually the egg predators. Egg predation seems an unusual behaviour for spiders, who are considered hunters of active organisms. He wanted to test the hypotheses that (1) spiders eat eggs from their own species - a form of cannibalism - and (2) egg guarding represents a defensive mechanism that decreases the chances of conspecific predation. He carried out simple experiments with egg nests - easily collected in this species as it is abundant and nests in folded out flax leaves. His results were conclusive. Nests where mothers had been carefully removed (therefore, unattended) and then were exposed to non-breeding females were all predated, with all eggs eaten within 16 h. Males or breeding females did not eat unatended eggs. When nests were attended, males and non-breeding females quickly retreated when noticing the activity of the guarding mother and no egg predation took place. Therefore egg guarding in Clubiona is indeed a strategy to protect the eggs from other spiders predation. More recently, cannibalistic egg predation has been documented in 12 spider families - including Gnaphosidae -, and therefore, egg guarding behaviour is likely to have the same defensive function in these spiders against cannibalistic predation.My spider successfully defended her eggs, and yesterday, I could see the pale, tiny spiderlings through the nest walls.More informationPollard, S.D. (1984). Egg guarding by Clubiona cambridgei (Araneae, Clubionidae) against conspecific predators Journal of Arachnology, 11, 323-326Nyffeler, M., Breene, R., Dean, D., & Sterling, W. (1990). Spiders as predators of arthropod eggs Journal of Applied Entomology, 109 (1-5), 490-501 DOI: 10.1111/j.1439-0418.1990.tb00080.x... Read more »

Pollard, S.D. (1984) Egg guarding by Clubiona cambridgei (Araneae, Clubionidae) against conspecific predators. Journal of Arachnology, 323-326. info:/

Nyffeler, M., Breene, R., Dean, D., & Sterling, W. (1990) Spiders as predators of arthropod eggs. Journal of Applied Entomology, 109(1-5), 490-501. DOI: 10.1111/j.1439-0418.1990.tb00080.x  

  • August 4, 2010
  • 05:12 PM
  • 708 views

The Palin Effect

by Bob O'Hara in This Scientific Life

As attentive readers of the New York Times are aware, science bloggers are all about being noisy and shouting at people we don’t like. As most of us have liberal leanings, that means we can be obnoxious towards people on the political right. And this week we’ve got great fodder, in the shape of a [...]... Read more »

  • August 4, 2010
  • 03:51 PM
  • 1,111 views

The genetics of dystonia in CRPS – not what we were expecting

by Lorimer Moseley in BodyInMind

The genetics of dystonia in CRPS - genes don't seem to predispose or cause dystonia in CRPS. This doesn’t mean that there is no genetic contribution, but it does mean that the genes that underpin familial dystonia are not important in CRPS-dystonia.... Read more »

[1] Fahn S. (1988) Concept and classification of dystonia. Advances in neurology, 1-8. PMID: 3041755  

[2] van Rijn MA, Marinus J, Putter H, & van Hilten JJ. (2007) Onset and progression of dystonia in complex regional pain syndrome. Pain, 130(3), 287-93. PMID: 17499924  

  • August 4, 2010
  • 03:44 PM
  • 842 views

Real Time fMRI

by Neuroskeptic in Neuroskeptic

Wouldn't it be cool if you could measure brain activation with fMRI... right as it happens?You could lie there in the scanner and watch your brain light up. Then you could watch your brain light up some more in response to seeing your brain light up, and watch it light up even more upon seeing your brain light up in response to seeing itself light up... like putting your brain between two mirrors and getting an infinite tunnel of activations.Ok, that would probably get boring, eventually. But there'd be some useful applications too. Apart from the obvious research interest, it would allow you to attempt fMRI neurofeedback: training yourself to be able to activate or deactivate parts of your brain. Neurofeedback has a long (and controversial) history, but so far it's only been feasible using EEG because that's the only neuroimaging method that gives real-time results. EEG is unfortunately not very good at localizing activity to specific areas.Now MIT neuroscientists Hinds et al present a new way of doing right-now fMRI: Computing moment to moment BOLD activation for real-time neurofeedback. It's not in fact the first such method, but they argue that it's the only one that provides reliable, truly real-time signals.Essentially the approach is closely related to standard fMRI analysis processes, except instead of waiting for all of the data to come in before starting to analyze it, it incrementally estimates neural activation every time a new scan of the brain arrives, while accounting for various forms of noise. They first show that it works well on some simulated data, and then discuss the results of a real experiment in which 16 people were asked to alternately increase or decrease their own neural response to hearing the noise of the MRI scanner (they are very noisy). Neurofeedback was given by showing them a "thermometer" representing activity in their auditory cortex.The real-time estimates of activation turned out to be highly correlated with the estimates given by conventional analysis after the experiment was over - though we're not told how well people were able to use the neurofeedback to regulate their own brains.Unfortunately, we're not given all of the technical details of the method, so you won't be able to jump into the nearest scanner and look into your brain quite yet, though they do promise that "this method will be made publicly available as part of a real-time functional imaging software package."Hinds, O., Ghosh, S., Thompson, T., Yoo, J., Whitfield-Gabrieli, S., Triantafyllou, C., & Gabrieli, J. (2010). Computing moment to moment BOLD activation for real-time neurofeedback NeuroImage DOI: 10.1016/j.neuroimage.2010.07.060... Read more »

Hinds, O., Ghosh, S., Thompson, T., Yoo, J., Whitfield-Gabrieli, S., Triantafyllou, C., & Gabrieli, J. (2010) Computing moment to moment BOLD activation for real-time neurofeedback. NeuroImage. DOI: 10.1016/j.neuroimage.2010.07.060  

  • August 4, 2010
  • 03:30 PM
  • 892 views

The Genetics of Being Lean: Thyrotropin Releasing Hormone Receptor

by William Yates, M.D. in Brain Posts

Research addressing genetic factors in obesity grows each year.  However, there has been limited attention to the other side of the coin, the genetics of thinness and a related body composition variable lean body mass.  Some might say, why bother, isn't being thin a good thing?Thinness does confer some advantages with reduced risk of hypertension, diabetes, osteoarthritis and some types of cancer.  However, there are some disorders (i.e. osteoporosis) increased in those underweight.  And there is some epidemiological data that suggests increased mortality rates for middle-aged and older aged individuals.Additionally, low weight is a hallmark of the eating disorder anorexia nervosa.  Anorexia nervosa is likely to have unique risks and mechanisms in producing low weight.  Nevertheless, understanding the genetics and mechanisms for low weight in community may provide some insight into eating disorders as well as obesity.  For example, a gene found to produce low weight in the general population might provide a clue for the site of a drug target for obesity.A collaborative group from China and the U.S. recently published a genome-wide association study looking for genes important for lean body mass.  The primary measure of lean body mass was measured by dual energy X-ray absorption (DXA).  This study included three replication studies using independent samples. The primary sample and replication samples all found an association between lean body mass and the TRHR gene.  TRHR is thyrotropin-releasing hormone receptor. The TRHR is:Located in the pituitaryResponds to thyrotropin releasing hormone (TRH) produced in the hypothalamusModulates thyroid stimulating hormone (TSH) and therefore thyroid hormone metabolismBelongs to the G protein-coupled receptor 1 familyThyroid hormone is required for the anabolic (muscle building) effect of human growth hormone.  Growth hormone acts through insulin-like growth factor 1 in controlling muscle growth.  This association may explain some of the effect of TRHR in lean body mass.The authors note lean body mass accounts for about 60% of body weight and significantly contributes to body mass index (BMI).  Future genetic studies of lean body mass, leanness and obesity will need to examine thyroid and growth factor pathways.Photo of Lean Triathlete Courtesy of Yates PhotographyLiu XG, Tan LJ, Lei SF, Liu YJ, Shen H, Wang L, Yan H, Guo YF, Xiong DH, Chen XD, Pan F, Yang TL, Zhang YP, Guo Y, Tang NL, Zhu XZ, Deng HY, Levy S, Recker RR, Papasian CJ, & Deng HW (2009). Genome-wide association and replication studies identified TRHR as an important gene for lean body mass. American journal of human genetics, 84 (3), 418-23 PMID: 19268274... Read more »

Liu XG, Tan LJ, Lei SF, Liu YJ, Shen H, Wang L, Yan H, Guo YF, Xiong DH, Chen XD.... (2009) Genome-wide association and replication studies identified TRHR as an important gene for lean body mass. American journal of human genetics, 84(3), 418-23. PMID: 19268274  

  • August 4, 2010
  • 03:14 PM
  • 710 views

Sensitivity and Specialization in the Occipitatemporal Region: Differences in Dyslexic Children

by Livia in Reading and Word Recognition Research

Accessibility: Advanced/intermediate



Early research on the role of the occipitotemporal region in reading often focused on characterizing a single region in the mid fusiform, commonly called the visual word form area. Since then, focus has gradually...

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... Read more »

van der Mark S, Bucher K, Maurer U, Schulz E, Brem S, Buckelmüller J, Kronbichler M, Loenneker T, Klaver P, Martin E.... (2009) Children with dyslexia lack multiple specializations along the visual word-form (VWF) system. NeuroImage, 47(4), 1940-9. PMID: 19446640  

  • August 4, 2010
  • 03:00 PM
  • 1,120 views

SHARK WEEK!

by EcoPhysioMichelle in C6-H12-O6

In case you hadn't heard, it's Shark Week, and Michelle is here to teach you a little bit of shark physiology. In the interest of full disclosure, sharks are not my forte. I am a tetrapod girl, but I know just enough about sharks to know that they have a really, really cool electrosensory system that helps them catch prey.... Read more »

Bullock, T. (1982) Electroreception. Annual Review of Neuroscience, 5(1), 121-170. DOI: 10.1146/annurev.ne.05.030182.001005  

Montgomery, J., Coombs, S., & Halstead, M. (1995) Biology of the mechanosensory lateral line in fishes. Reviews in Fish Biology and Fisheries, 5(4), 399-416. DOI: 10.1007/BF01103813  

  • August 4, 2010
  • 01:32 PM
  • 780 views

Y Chromsome V: The Ampliconic Sequence Class

by Kele in Kele's Science Blog

If you recall from Y Chromosome II, the ampliconic class displays extraordinarily high sequence similarity to other sequences of the same region, has higher gene density than the X-degenerate class, and its genes are found in multiple copies and are expressed almost exclusively in the testes. The ampliconic class just doesn’t show the signs of [...]... Read more »

Skaletsky H, Kuroda-Kawaguchi T, Minx PJ, Cordum HS, Hillier L, Brown LG, Repping S, Pyntikova T, Ali J, Bieri T.... (2003) The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature, 423(6942), 825-37. PMID: 12815422  

  • August 4, 2010
  • 01:30 PM
  • 625 views

The Scientist and the Anarchist - Part I

by Eric Michael Johnson in The Primate Diaries

The latest stop in the #PDEx tour is being hosted by Jennifer Ouellette at her wonderful blog Cocktail Party Physics.If the city is an ecosystem, Huxley embodies the phrase “survival of the fittest.” Lanky and high-strung, estranged from his father at an early age, and the youngest of six children, Huxley was primed from birth to view life as a struggle. Born on May 4, 1825 above a butcher’s shop on London’s outskirts, Huxley was the son of a poor schoolteacher and a member of England’s newly emerging middle class (in culture though not in wealth). As such he was determined to separate himself from the ranks of the working poor. In the years to come he would claw his way out of obscurity and establish himself as a celebrated anatomist, President of the Royal Academy of Sciences, and evolutionary theorist widely hailed as “Darwin’s bulldog.” He would forge a path of his own and create a revolution in the way science was practiced. As his biographer, Adrian Desmond, would later put it:The young hothead scrambled to the top of his profession; indeed he made a profession of science. With him the ‘scientist’ was born.Read the rest of the post here and stay tuned for Part II next week at Skulls in the Stars.Adrian Desmond (1997). Huxley: From Devil's Disciple to Evolution's High Priest. Massachusettes: Addison-Wesley.... Read more »

Adrian Desmond. (1997) Huxley:. From Devil's Disciple to Evolution's High Priest. info:other/

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