Post List

  • May 21, 2010
  • 07:20 AM

Can we predict small-molecules binding affinities?

by Nir London in Macromolecular Modeling Blog

In a recent post, Derek Lowe, from "In The Pipeline", asks his readership "If we could just walk right up and calculate the free energies of binding events reliably, what would you most want such calculations to be able to do for you? What would convince you that they're actually believable? And how close to you think that we actually are to that?" We tried tobriefly answer some of these questions. How close are we to predict small molecules binding free energy?

... Read more »

Gilson, M., & Zhou, H. (2007) Calculation of Protein-Ligand Binding Affinities . Annual Review of Biophysics and Biomolecular Structure, 36(1), 21-42. DOI: 10.1146/annurev.biophys.36.040306.132550  

  • May 21, 2010
  • 06:27 AM

Attentional bias and "gaydar"

by The Neurocritic in The Neurocritic

Global or Local? Gay or Eurotrash? Navon figure flanked by two game pieces from Gay or EUROtrash? the ultimate gaydar game!Believe it or not, there's an article in the new journal Frontiers in Cognition1 entitled "Sexual orientation biases attentional control: a possible gaydar mechanism" (Colzato et al., 2010). What is "gaydar"? And why on earth would one think of studying the allocation of attention to global and local visual perceptual features in relation to gaydar? Here's why:Individuals ........ Read more »

Colzato, L., van Hooidonk, L., van den Wildenberg, W., Harinck, F., & Hommel, B. (2010) Sexual orientation biases attentional control: a possible gaydar mechanism. Frontiers in Psychology. DOI: 10.3389/fpsyg.2010.00013  

  • May 21, 2010
  • 04:48 AM

Optogenetic fMRI

by Mo in Neurophilosophy

OF all the techniques used by neuroscientists, none has captured the imagination of the general public more than functional magnetic resonance imaging (fMRI). The technique, which is also referred to as functional neuroimaging and, more commonly, "brain scanning", enables us to peer into the human brain non-invasively, observe its workings in near-real time, and correlate specific thought processes or stimuli to activity in particular regions. fMRI data affect the way in which people perceive sc........ Read more »

  • May 21, 2010
  • 04:45 AM

Opera singing in the brain scanner

by BPS Research Digest in BPS Research Digest

The idea that the brain changes and adapts according to how you use it, including through adulthood, is now widely accepted in psychology and neuroscience. Some of the most striking examples of this have come from studies of musicians. It's been shown, for instance, that string and keyboard players have more neural tissue given over to the control of the hands and fingers than do non-musicians. However, little researched until now is the brain re-organisation associated with professional singing........ Read more »

  • May 20, 2010
  • 10:10 PM

Neury Thursday: Theta Waves, Memory, Reward, and REM Sleep

by Allison in Dormivigilia

Dutch neuroscientists have elucidated theta activity in the orbitofrontal cortex that precedes and proceeds the presentation of rewarding stimuli, indicating that theta waves, which are expressed during REM sleep and memory and learning tasks, may influence the modulation of brain reward and reward pathologies such as substance abuse, binge eating, and other addictions... Read more »

van Wingerden, M., Vinck, M., Lankelma, J., & Pennartz, C. (2010) Theta-Band Phase Locking of Orbitofrontal Neurons during Reward Expectancy. Journal of Neuroscience, 30(20), 7078-7087. DOI: 10.1523/JNEUROSCI.3860-09.2010  

  • May 20, 2010
  • 05:12 PM

Greenflies clouds and networks

by Africa Gomez in BugBlog

There were raining greenflies today, whole clouds of them causing a visible effect on people, talking about them, swatting them and taking them from their clothes, glasses and skin (above). The warm weather has encouraged the winged forms of aphids (greenflies) to take to the air and search for new feeding plants. Aphids are a central part complex ecological networks. For example, a study by Muller and coworkers in an abandoned field in the south of England found:Twenty-six species of plants wer........ Read more »

Muller, C., Adriaanse, I., Belshaw, R., & Godfray, H. (1999) The structure of an aphid-parasitoid community. Journal of Animal Ecology, 68(2), 346-370. DOI: 10.1046/j.1365-2656.1999.00288.x  

  • May 20, 2010
  • 04:13 PM

Transforming Species One Genome at a Time

by avi_wener in American Biotechnologist

Gibson et. al. from the Venter Institute have just published a report in Science Express (online only) that sounds very cool, but whose implications don’t seem to be well understood yet from experts in the field. Essentially the group synthesized the genome of one bacterial species and transplanted it into another bacterial species. What resulted [...]... Read more »

Lartigue, C., Vashee, S., Algire, M., Chuang, R., Benders, G., Ma, L., Noskov, V., Denisova, E., Gibson, D., Assad-Garcia, N.... (2009) Creating Bacterial Strains from Genomes That Have Been Cloned and Engineered in Yeast. Science, 325(5948), 1693-1696. DOI: 10.1126/science.1173759  

Lartigue, C., Glass, J., Alperovich, N., Pieper, R., Parmar, P., Hutchison, C., Smith, H., & Venter, J. (2007) Genome Transplantation in Bacteria: Changing One Species to Another. Science, 317(5838), 632-638. DOI: 10.1126/science.1144622  

  • May 20, 2010
  • 04:08 PM

A virtual slap in the face (isn't there an iPhone app for that?)

by NeuroKüz in NeuroKüz

Researchers from the group who recently reported the illusion of owning a virtual hand have come out with a new study on the sense of body ownership that has garnered media attention.The study, conducted by Mel Slater and colleagues, is summarized as follows at volunteers donned virtual reality goggles and took on the view of a virtual teenage girl sitting in a living room. The virtual girl's mother appeared to stroke her shoulder at the same time a real lab assistant stroke........ Read more »

Mel Slater, Bernhard Spanlang, Maria V. Sanchez-Vives, & Olaf Blanke. (2010) First Person Experience of Body Transfer in Virtual Reality. PLoS ONE. info:/

  • May 20, 2010
  • 04:05 PM

Zip up and stick together…

by Lucas in thoughtomics

… could have been a really cheesy line in an action movie. It’s also what cells in multicellular metazoans do! A little single-celled creature contains some clues about the origins of all this stickiness.
You might not realize it, but being multicellular is quite a feat! Your cells need to divide and [...]... Read more »

Abedin M, & King N. (2008) The premetazoan ancestry of cadherins. Science (New York, N.Y.), 319(5865), 946-8. PMID: 18276888  

  • May 20, 2010
  • 03:30 PM

Of mice and men – Jeff Mogil on grimacing

by Lorimer Moseley in BodyInMind

You have almost certainly noticed that we grimace when we are in pain. But have you thought about that – I mean really thought about it? Why grimace?  Well, someone who clearly thinks about such things more than most is a fellow called Jeff Mogil – Professor of Pain Type Stuff at the very pain-posh [...]... Read more »

Langford, D., Bailey, A., Chanda, M., Clarke, S., Drummond, T., Echols, S., Glick, S., Ingrao, J., Klassen-Ross, T., LaCroix-Fralish, M.... (2010) Coding of facial expressions of pain in the laboratory mouse. Nature Methods. DOI: 10.1038/nmeth.1455  

  • May 20, 2010
  • 02:57 PM

Bad Seed

by Journal Watch Online in Journal Watch Online

Some birds favor conventional over organic feed

... Read more »

McKenzie, A.J., & M.J. Whittingham. (2010) Birds select conventional over organic wheat when given free choice. Journal of the Science of Food and Agriculture. DOI: 10.1002/jsfa.4025  

  • May 20, 2010
  • 01:28 PM

Malaria in a changing world

by Aaron Berdanier in Biological Posteriors

Gething PW, Smith DL, Patil AP, Tatem AJ, Snow RW, & Hay SI (2010). Climate change and the global malaria recession. Nature, 465 (7296), 342-5 PMID: 20485434Infectious diseases straddle a fuzzy boundary between ecology and epidemiology, making the prediction of future disease dynamics difficult. Scientists need to consider how environmental change will affect the infectious organism (and sometimes the vector) as well as how humans respond to the disease. These predictions carry special weight,........ Read more »

Gething PW, Smith DL, Patil AP, Tatem AJ, Snow RW, & Hay SI. (2010) Climate change and the global malaria recession. Nature, 465(7296), 342-5. PMID: 20485434  

  • May 20, 2010
  • 01:00 PM

Everyone Rowing in the Same Direction

by Merry Youle in Small Things Considered

Is there such a thing as an obligatorily multicellular prokaryote? We presented a case for their existence before, one that fueled our evolutionary imaginations. Unlike the myxobacteria, for example, which have both unicellular and multicellular stages, some magnetotactic bacteria appeared to be multicellular throughout their lives. Their multicellular coordination is apparent from their complex swimming behavior, their...... Read more »

  • May 20, 2010
  • 11:38 AM

What controls where a species lives?

by Aaron Berdanier in Biological Posteriors

Pigot AL, Owens IP, & Orme CD (2010). The environmental limits to geographic range expansion in birds. Ecology letters PMID: 20412281Or, what prevents that species from expanding further?  Generally, we assume that the environment has something to do with controlling a species' distribution.  But, our understanding of this topic is surprisingly limited, given centuries of scientists prodding the question.  Part of the problem has been:a limited number of species analyzed with smal........ Read more »

  • May 20, 2010
  • 10:09 AM

A Closer Look at Ankylosaur Armor

by Brian Switek in Dinosaur Tracking

Many dinosaurs were adorned with spikes, horns and plates, but it was the ankylosaurs that took armor to the extreme. These dinosaurs were covered in bony armor from snout to tail-tip, yet, as a new study suggests, there may have been more to some of these structures than just attack and defense.
As reviewed by paleontologists [...]... Read more »

  • May 20, 2010
  • 09:39 AM

Tiny treasures - 100 million year old mammal hairs trapped in amber

by Laelaps in Laelaps

Mammal hairs preserved in amber specimen ARC2-A1-3. a - First fragment; b - Line drawing of first fragment; c - Second fragment; d - Line drawing of second fragment; e - Close-up of second fragment to show the cuticular surface.

About 100 million years ago, in a coastal forest located in what is today southwestern France, a small mammal skittered up the trunk of a conifer tree. As it did so it lost a few of its hairs, and this minor event would have been entirely unremarkable if two of tho........ Read more »

Vullo, R., Girard, V., Azar, D., & Néraudeau, D. (2010) Mammalian hairs in Early Cretaceous amber. Naturwissenschaften. DOI: 10.1007/s00114-010-0677-8  

  • May 20, 2010
  • 08:00 AM

Study links spearfishing with reef fish crisis

by Rob Goldstein in Conservation Maven

... Read more »

Godoy, N., Gelcich, S., Vasquez, J., & Castilla, J. (2010) Spearfishing to depletion: Evidence from temperate reef fishes in Chile. Ecological Applications, 2147483647. DOI: 10.1890/09-1806  

  • May 20, 2010
  • 08:00 AM

Women Are Fat - Men Are Just Big And Strong?

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

Being overweight or obese has been associated with a poor body image and a lower quality of life specially in females, but the impact on males is less clear.
This relationship was now examined by Saloumi and Plourde from McGill University, Montreal, in a paper just published in Psychology, Health & Medicine.
The analysis was based on [...]... Read more »

  • May 20, 2010
  • 08:00 AM

Clinical Psychologists’ Perceptions of Persons with Mental Illness

by Shaheen Lakhan in Brain Blogger

Many people have fabulous relationships with their psychologists. They feel supported, understood, well-liked. But there are also those who feel a little uneasy. Research by Lynn Servais and Stephen Saunders of Marquette University in Milwaukee, Wisconsin may have unearthed one of the reasons why.
Some psychologists have a hard time connecting with people with mental illness, [...]... Read more »

Servais, L., & Saunders, S. (2007) Clinical psychologists' perceptions of persons with mental illness. Professional Psychology: Research and Practice, 38(2), 214-219. DOI: 10.1037/0735-7028.38.2.214  

  • May 20, 2010
  • 07:58 AM

Excessive Daytime Sleepiness - Can be a Big Issue predictor.

by mc in begin to dig (b2d)

Sleep is so important. Sleepiness during the day may likewise be a really critical health marker. Sleepiness itself is usually taken as a sign that we just didn't get enough kip. Sometimes figuring out why is easy, and we can fix it; sometimes figuring out why is a little more elusive, and getting some knowledgable help is a great idea. But no matter what, we know chronic sleepiness"older adults"... Read more »

Baldwin CM, Ervin AM, Mays MZ, Robbins J, Shafazand S, Walsleben J, & Weaver T. (2010) Sleep disturbances, quality of life, and ethnicity: the Sleep Heart Health Study. Journal of clinical sleep medicine : JCSM : official publication of the American Academy of Sleep Medicine, 6(2), 176-83. PMID: 20411696  

Boulos MI, & Murray BJ. (2010) Current evaluation and management of excessive daytime sleepiness. The Canadian journal of neurological sciences. Le journal canadien des sciences neurologiques, 37(2), 167-76. PMID: 20437926  

Chokroverty S. (2010) Overview of sleep . The Indian journal of medical research, 126-40. PMID: 20308738  

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