Post List

  • May 21, 2010
  • 12:09 PM

A non-post about Craig Venter’s new bug

by Iddo Friedberg in Byte Size Biology

In case you have been vacationing in a parallel universe in the past two days, you should have heard about the new synthetic bacterium created at the J Craig Venter Institute. In a nutshell, the scientific team synthesized an artificial chromosome of the bacterium Mycoplasma mycoides and transferred it to another bacterium, Mycoplasma capricolum. The [...]... Read more »

Gibson, D., Glass, J., Lartigue, C., Noskov, V., Chuang, R., Algire, M., Benders, G., Montague, M., Ma, L., Moodie, M.... (2010) Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome. Science. DOI: 10.1126/science.1190719  

  • May 21, 2010
  • 11:28 AM

myExperiment: The Videos

by Duncan Hull in O'Really?

myExperiment is a research project that is exploring models, techniques and infrastructure for sharing digital items associated with  research , especially scientific workflows. The project is funded by the Joint Information Standards Committee (JISC) as part of a series of projects building Virtual Research Environments (VRE’s) and is run by Dave De Roure and Carole [...]... Read more »

David De Roure, Carole Goble, & Robert Stevens. (2007) Designing the myExperiment Virtual Research Environment for the Social Sharing of Workflows. IEEE International Conference on e-Science and Grid Computing, 603-610. DOI: 10.1109/E-SCIENCE.2007.29  

David De Roure, Carole Goble, Jiten Bhagat, Don Cruickshank, Antoon Goderis, Danius Michaelides, & David Newman. (2008) myExperiment: Defining the Social Virtual Research Environment. IEEE Fourth International Conference on eScience, 2008. eScience '08., 182-189. DOI: 10.1109/eScience.2008.86  

  • May 21, 2010
  • 10:52 AM

Inner Life of Mesoorganisms

by Arunn in nOnoScience (a.k.a. Unruled Notebook)

The title of both this note and the paper it discusses is inspired by a 1970s classic paper by Nobel Laureate Edward Purcell on Life at low Reynolds number. With simple physics, that paper gave insights about micro-organisms (bacteria, sperms … Continue reading →... Read more »

  • May 21, 2010
  • 10:30 AM

Physical Features in Autism

by William Yates, M.D. in Brain Posts

Social and language issues dominate most of the discussion about the features of autism spectrum disorder (ASD). A neglected area of study are the physical feature characteristics that have been known to be associated with ASD. Unlike some of the diagnostic physical changes in disorders such as Down Syndrome, physical features found in ASD are often subtle and missed by most clinicians.Ozgen and colleagues from the Netherlands, UCLA and the UK recently published a case-control study of physica........ Read more »

Ozgen, H., Hellemann, G., Stellato, R., Lahuis, B., Daalen, E., Staal, W., Rozendal, M., Hennekam, R., Beemer, F., & Engeland, H. (2010) Morphological Features in Children with Autism Spectrum Disorders: A Matched Case–Control Study. Journal of Autism and Developmental Disorders. DOI: 10.1007/s10803-010-1018-7  

  • May 21, 2010
  • 10:28 AM

On synthesis

by Richard Grant in Confessions of a (former) Lab Rat

Oh my God, we're all going to die, exclaimed the Daily Mail today. Well, we are all going to die some day, but not because of the paper from the J. Craig Venter Institute, published in Science. I'm having a...... Read more »

Gibson, D., Glass, J., Lartigue, C., Noskov, V., Chuang, R., Algire, M., Benders, G., Montague, M., Ma, L., Moodie, M.... (2010) Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome. Science. DOI: 10.1126/science.1190719  

  • May 21, 2010
  • 10:18 AM

Azendohsaurus, the Dinosaur That Wasn’t

by Brian Switek in Dinosaur Tracking

Parsing the origins and early history of dinosaurs is a challenging task. A number of prehistoric creatures were a lot like some of the earliest dinosaurs, and sometimes evolutionary cousins of early dinosaurs have been mistaken for dinosaurs on the basis of fragmentary material. As a study published in Palaeontology now shows, this was the [...]... Read more »

  • May 21, 2010
  • 10:00 AM

Proteomics Refined

by avi_wener in American Biotechnologist

As a proteomics fan in general and a 2D Gel Electrophoresis fan specifically, I have been following the Ludesi Blog which I have found to be a resource rich in 2D information including a knowledgebase, webinars and an great tool that pulls together all proteomics related tweets from twitter. For those of you who [...]... Read more »

  • May 21, 2010
  • 09:24 AM

Pulling the Wool Back: Studying the Biochemical Properties of Mammoth Hemoglobin

by Kelly Grooms in Promega Connections

What do you do with the DNA sequence of an animal that has been extinct for tens of thousands of years? Well, if you are on the team of Professor Kevin Campbell (University of Manitoba, Canada), you go for the blood; specifically, the hemoglobin. In a study published in Nature Genetics (1), Professor Campbell’s team reports [...]... Read more »

Campbell KL, Roberts JE, Watson LN, Stetefeld J, Sloan AM, Signore AV, Howatt JW, Tame JR, Rohland N, Shen TJ.... (2010) Substitutions in woolly mammoth hemoglobin confer biochemical properties adaptive for cold tolerance. Nature genetics. PMID: 20436470  

  • May 21, 2010
  • 09:22 AM

Tomatoes On My Mind

by Jennifer in OpenHelix

I’ve got tomatoes on my mind, so summer must be coming. It seems every where I turn, I’m being reminded of tomatoes. Not the grocery store/hot house kind, but the fresh farmer’s market/back yard-grown kind with juice and flavor so plentiful that it runs down your arms and onto the sunny porch floor where [...]... Read more »

Ruzicka, D., Barrios-Masias, F., Hausmann, N., Jackson, L., & Schachtman, D. (2010) Tomato root transcriptome response to a nitrogen-enriched soil patch. BMC Plant Biology, 10(1), 75. DOI: 10.1186/1471-2229-10-75  

  • May 21, 2010
  • 08:00 AM

On the recent systematic food allergy review

by Colby in

All over the media last week were reports that the prevalence of food allergies is grossly overestimated.  That is indeed good news, let’s have a quick look at the systematic review that led to these statements (1).
The review focused on foods which account for over 50% of food allergies: cow’s milk, hen’s egg, peanut, tree [...]... Read more »

Chafen, J., Newberry, S., Riedl, M., Bravata, D., Maglione, M., Suttorp, M., Sundaram, V., Paige, N., Towfigh, A., Hulley, B.... (2010) Diagnosing and Managing Common Food Allergies: A Systematic Review. JAMA: The Journal of the American Medical Association, 303(18), 1848-1856. DOI: 10.1001/jama.2010.582  

  • 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  

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