Post List

  • March 11, 2010
  • 07:11 AM

Review of Towards pharmacogenomics knowledge discovery with the semantic web

by UUCJC in Uppsala University Cheminformatics Journal Club

The article, Towards pharmacogenomics knowledge discovery with the semantic web, written by Michael Dumontier and Natalia Villanueva-Rosales attempts to demonstrate the importance of pharmacogenomics and how the data should be structured in the best possible way. Their strategy towards knowledge discovery involves ontology design, population and question answering. In a more specific manner this was established with Web Ontology Language OWL-DL, Protégé and Manchester OWL Syntax.With the SO-Ph........ Read more »

Dumontier, M., & Villanueva-Rosales, N. (2009) Towards pharmacogenomics knowledge discovery with the semantic web. Briefings in Bioinformatics, 10(2), 153-163. DOI: 10.1093/bib/bbn056  

  • March 11, 2010
  • 05:34 AM

"Why do we believe", and are atheists really more intelligent?

by Daniel in Ego sum Daniel editor Dave Munger has written an article for SEED magazine entitled "Why do we believe". The article summarizes recent blog entries regarding studies on the origins of religiosity. It's really worth reading to get a good overview of the subject, and what do you know he links my entry on god's will and beliefs in it.

Among the studies that are mentioned is a controversial study entitled "Why Liberals and Atheists Are More Intelligent" (link at the end of this post).

Medic........ Read more »

  • March 11, 2010
  • 05:30 AM

The Common Genetic Causes of Celiac Disease

by Rick Scavetta in DNA Dude

Celiac disease is characterized by an immune response to glutin and similar proteins found in wheat, rye and barley. For individuals with celiac disease, eating glutin results in an inflammed small intestine, diarrhea and fatigue, among other symptoms. It’s estimated that about 1% of all Americans suffer from celiac disease. Given the heritability of [...]... Read more »

Dubois, P., Trynka, G., Franke, L., Hunt, K., Romanos, J., Curtotti, A., Zhernakova, A., Heap, G., Ádány, R., Aromaa, A.... (2010) Multiple common variants for celiac disease influencing immune gene expression. Nature Genetics. DOI: 10.1038/ng.543  

  • March 11, 2010
  • 05:30 AM

Will booze make you skinny?

by Yoni Freedhoff in Weighty Matters

Roll out the barrel because if you believe the news reports alcohol contains magical negative calories!Yup a recent study is making waves in the media and blogosphere and the gist of the reporting is that a few alcoholic drinks a day may help control your weight - though of course that's not the whole story.The study's a big one. It looked at 19,220 American women aged 38.9 years or older who had a baseline normal BMI and followed them for 12.9 years and tracked alcohol consumption and self rep........ Read more »

  • March 11, 2010
  • 05:00 AM

Delimiting the boundaries of a species invasion (with no prior info)

by Rob Goldstein in Conservation Maven

When it comes to successfully controlling invasive species, managers face the critically important step of figuring out the extent of the invasion. Researchers have developed and tested an innovative approach for accomplishing this challenging task...... Read more »

  • March 11, 2010
  • 03:05 AM

Fossil testate amoebae

by Psi Wavefunction in Skeptic Wonder

There's something about the idea of fossilised single-celled organisms that's just pure awesome. Even if it's just their shells.For example, take a look at these past relatives of Centropyxis and Leptochlamys from Schmidt et al. 2010 JEM, AOP:Testate amoebae from 100mya amber in France. The arrow in 1 points to what the authors believe may be fossilised cytoplasm flowing out of the cell. 2) four ventral pores visible. 4-7) holotype of modern Leptochlamys, optical sections. 8-11 potential resting........ Read more »

  • March 10, 2010
  • 11:10 PM

The way the worm wiggles

by sandygautam in The Mouse Trap

Image via Wikipedia

Once in a while you come across a study article that is so elegant and lucid that you have to blog about it. A not-son recent, but new to me  article in PLOS computational biology by Stephens et al is just such an awesome and well written article that despite being outside my More >Rating: 0.0/10 (0 votes cast)

Related posts:The 33rd edition of Encephelon online now! the 33rd edition of neuroscience carnival encephalon is now online....
Now I see it, now I ........ Read more »

Stephens, G., Johnson-Kerner, B., Bialek, W., & Ryu, W. (2008) Dimensionality and Dynamics in the Behavior of C. elegans. PLoS Computational Biology, 4(4). DOI: 10.1371/journal.pcbi.1000028  

  • March 10, 2010
  • 11:08 PM

Global pollinator declines

by CJA Bradshaw in ConservationBytes

Mention anything about ecosystem services – those ecological functions arising from the interactions between species that provide some benefit (source of food/clean water, health, etc.) to humanity1 – and one of the most cited examples is pollination.
It’s really a no-brainer, hence its popularity as an example. Pollinators (mainly insects, but birds, bats and other assorted [...]... Read more »

Potts, S., Biesmeijer, J., Kremen, C., Neumann, P., Schweiger, O., & Kunin, W. (2010) Global pollinator declines: trends, impacts and drivers. Trends in Ecology . DOI: 10.1016/j.tree.2010.01.007  

  • March 10, 2010
  • 09:53 PM

CNiFERS of Acetylcholine and Attention

by AndrewHires in Brain Windows

Nguyen et al demonstrate a mammalian cell based system for optically measuring ACh levels in an intact brain. They coexpressed M1 muscarinic receptors with the genetically-encoded calcium indicator TN-XXL in HEK293 cells. ACh binding to the M1 receptor induced IP3-mediated calcium influx. This calcium rise was then picked up by the TN-XXL and reported as a change in CFP/YFP fluorescence. The crazy part is that they took this cell culture assay and implanted the cells into the brains of livin........ Read more »

Nguyen, Q., Schroeder, L., Mank, M., Muller, A., Taylor, P., Griesbeck, O., & Kleinfeld, D. (2009) An in vivo biosensor for neurotransmitter release and in situ receptor activity. Nature Neuroscience, 13(1), 127-132. DOI: 10.1038/nn.2469  

  • March 10, 2010
  • 09:40 PM

Natural climate factors unlikely to put the brakes on greenhouse-gas-driven sea level rise this century

by Phil Camill in Global Change: Intersection of Nature and Culture

The IPCC 2007 report projected a conservative sea level rise of about 18-59 cm by the year 2100.
Why conservative?  Because it mainly accounted for things we know are happening and can measure well—like thermal expansion of the ocean and melting of land glaciers (see here for a discussion of the Kilimanjaro example).  What it doesn’t [...]... Read more »

Jevrejeva, S., J. C. Moore, and A. Grinsted. (2010) How will sea level respond to changes in natural and anthropogenic forcings by 2100?. Geophysical Research Letters. info:/10.1029/2010GL042947

  • March 10, 2010
  • 05:41 PM

Prehistoric DNA reveals the story of a Pleistocene survivor, the muskox

by Laelaps in Laelaps

A muskox (Ovibos moschatus), photographed in Alaska. From Flickr user drurydrama.

Of all the mass extinctions that have occurred during earth's history, among the most hotly debated is the one which wiped out mammoths, saber-toothed cats, giant ground sloths, and the other peculiar members of the Pleistocene megafauna around 12,000 years ago. It was not the most severe mass extinction, not by a long shot, but unlike the end-Cretaceous catastrophe 65 million years ago there is no single "sm........ Read more »

Campos, P., Willerslev, E., Sher, A., Orlando, L., Axelsson, E., Tikhonov, A., Aaris-Sorensen, K., Greenwood, A., Kahlke, R., Kosintsev, P.... (2010) Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.0907189107  

  • March 10, 2010
  • 05:10 PM

Can We Rely on fMRI?

by Neuroskeptic in Neuroskeptic

Craig Bennett (of and Michael Miller, of dead fish brain scan fame, have a new paper out: How reliable are the results from functional magnetic resonance imaging?Tal over at the [citation needed] blog has an excellent in-depth discussion of the paper, and Mind Hacks has a good summary, but here's my take on what it all means in practical terms.Suppose you scan someone's brain while they're looking at a picture of a cat. You find that certain parts of their brain are activated to ........ Read more »

Bennett CM, Miller MB. (2010) How reliable are the results from functional magnetic resonance imaging?. Annals of the New York Academy of Sciences. info:/

  • March 10, 2010
  • 05:00 PM

Disease hunting with whole genome sequences: the good news, and the bad news

by dgmacarthur in Genetic Future

Lupski, J.R., et al. (2010). Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. New England Journal of Medicine advance online 10.1056/nejmoa0908094Roach, J.C., & et al. (2010). Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science : 10.1126/science.1186802[Note that links to the papers may not yet be active.]Two new papers out today - the first ever studies to employ whole-genome sequencing for disease gene discovery - ........ Read more »

Lupski, J.R. (2010) Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. New England Journal of Medicine. info:/10.1056/nejmoa0908094

Roach, J.C., & et al. (2010) Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science. info:/10.1126/science.1186802

  • March 10, 2010
  • 03:50 PM

Ancient DNA Isolated from Fossil Eggshells May Provide Clues to Eggstinction of Giant Birds

by GrrlScientist in Living the Scientific Life (Scientist, Interrupted)

tags: evolution, evolutionary biology, ancient DNA, aDNA, molecular biology, molecular ecology, archaeology, paleontology, fossil eggshell, extinct birds, giant moa, Dinornis robustus, elephant birds, Aepyornis maximus, Mullerornis, Thunderbirds, Genyornis,,peer-reviewed research, peer-reviewed paper, journal club

Elephant bird, Aepyornis maximus, egg
compared to a human hand with a hummingbird egg balanced on a fingertip.

To conduct my avian research, I've isolated and........ Read more »

Charlotte L. Oskam, James Haile, Emma McLay, Paul Rigby, Morten E. Allentoft, Maia E. Olsen, Camilla Bengtsson, Gifford H. Miller, Jean-Luc Schwenninger, Chris Jacomb, Richard Walter, Alexander Baynes, Joe Dortch, Michael Parker-Pearson, M. Thomas P. Gilb. (2010) Fossil avian eggshell preserves ancient DNA. Proc. R. Soc. B. info:/10.1098/rspb.2009.2019

  • March 10, 2010
  • 12:50 PM

Spent Hydrogen Regeneration in Ammonia Borane Derivatives

by Michael Long in Phased

Shin-Yuan Liu (University of Oregon, United States) and coworkers have addressed a challenge that is often brushed aside in hydrogen fuel cell research, but which is absolutely critical for practical, real-world applications. This news feature was written on March 10, 2010.... Read more »

Campbell, P. G., Zakharov, L. N., Grant, D. J., Dixon, D. A., & Liu, S.-Y. (2010) Hydrogen Storage by Boron−Nitrogen Heterocycles: A Simple Route for Spent Fuel Regeneration. Journal of the American Chemical Society, 132(10), 3289-3291. DOI: 10.1021/ja9106622  

  • March 10, 2010
  • 12:20 PM

Immune response to brain infection may trigger Alzheimer's

by Mo in Neurophilosophy

ALZHEIMER'S Disease is the most common form of dementia, affecting an estimated 30 million people worldwide. The cause of the condition is unknown, but the prime suspect is amyloid-beta (Aβ), a 42-amino acid peptide which accumulates within neurons to form insoluble structures called senile plaques that are thought to be toxic. Aβ is synthesized in all neurons; it is associated with the cell membrane, and is thought to be involved in cell-to-cell signalling, but its exact role has eluded resea........ Read more »

Soscia, S., Kirby, J., Washicosky, K., Tucker, S., Ingelsson, M., Hyman, B., Burton, M., Goldstein, L., Duong, S., Tanzi, R.... (2010) The Alzheimer's Disease-Associated Amyloid β-Protein Is an Antimicrobial Peptide. PLoS ONE, 5(3). DOI: 10.1371/journal.pone.0009505  

  • March 10, 2010
  • 12:04 PM

Nitrogen, Phosphorus and Organic Carbon (The Big Three)

by JL in Analyze Everything

I'm a stoichiometry kind of guy (even if I've been relatively unsuccessful lately), and stoichiometry seems to revolve around N, P and C. And really, mostly just N&P. As a result, I've been thinking a lot about how the terrestrial and upstream watershed affects the N, P, and C in receiving waters. So, for instance, if you change the proportion of wetlands, how is the ratio of these nutrients ... Read more »

  • March 10, 2010
  • 12:00 PM

Path Integration in Humans

by Jason Goldman in The Thoughtful Animal

I know you’ve all been waiting for it. We’ve talked about putting ants on stilts, kidnapping baby gerbils, and hijacking a truck full of geese. All in the name of science. Ants and gerbils taught us about the limitations of the path integration system, but also how amazingly cool it is. The geese suggested that [...]... Read more »

Landau, B., Spelke, E., & Gleitman, H. (1984) Spatial knowledge in a young blind child. Cognition, 16(3), 225-260. DOI: 10.1016/0010-0277(84)90029-5  

  • March 10, 2010
  • 11:42 AM

Environmental news round up

by Elements Science in Elements Science

Find out how climate change is affecting malaria, how ocean bacteria could be the key to producing clean fuels, how a tree purifies dirty water and more.... Read more »

  • March 10, 2010
  • 11:40 AM

Body mass index (BMI) as a measure of obesity and health: a critical appraisal

by Travis Saunders, MSc in Obesity Panacea

If you go to your physician's office and inquire about your weight status, he or she will measure your height and weight to derive your BMI (weight in kg divided by height in m squared). Then they will compare your BMI to that of established criteria to decide whether you are underweight (30 kg/m2) . Often times, this measure alone determines whether or not you receive lifestyle treatment. But how useful is this measure anyways? What does it tell you about your health? And finally, how helpful i........ Read more »

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