Post List

  • August 5, 2010
  • 06:52 PM

R and Google Earth ~ comparing tuna tracks vs. Gulf of Mexico oil spill extent

by apeescape in mind of a Markov chain

There is a lot of interest in how the Gulf of Mexico oil gusher will affect the ecosystem and its marine species. One such species is the Western Atlantic bluefin tuna that holds the Gulf of Mexico as one of its major spawning grounds. Recent tag data show that the location of the gusher is [...]... Read more »

  • August 5, 2010
  • 05:21 PM

by Cristy at Living Donor 101 in Living Donors Are People Too

I hardly even know where to begin with Aaron Spital, MD. He is so pro-living donation that he concocts justifications for opinions not based on fact or logic, and refuses to acknowledge that living donors are vulnerable human beings with the same rights as the sick recipient and the almighty surgeon. In his 2001 article, he addresses Informed Consent (not necessary) and the Right to Donate (doesn't exist; a surgeon's rights come first). "Sometimes even competent people make rash decisions or are........ Read more »

  • August 5, 2010
  • 05:00 PM

Fosmid cloning enables new techniques in synthetic biology

by epibio in EpiCentral

In a recent functional genomics study, Sommer et al. cite the use of the CopyControl™ Fosmid Library Production Kit to create a library from plant biomass DNA. Plant biomass is being explored for use in new biofuel development, in an effort to discover genetic functionalities that will allow growth improvement in key microbes by overcoming toxic/inhibitory compounds that are byproducts of biofuel conversions. Clones harboring these fosmids were tested against seven known growth inhibitors from........ Read more »

  • August 5, 2010
  • 04:57 PM

Neury Thursday: Neural Mechanisms of Song Learning

by Allison in Dormivigilia

Researchers at Duke have elucidated the neural mechanisms of song learning and recall in swamp sparrows. Using neurophysiology, it was observed that songs learned during juvenile years are more strongly encoded and surprisingly, there was no difference between those songs sung and simply heard. This is remarkably different from human speech learning.... Read more »

Jonathan F. Prather, Susan Peters, Stephen Nowicki,and Richard Mooney. (2010) Persistent Representation of Juvenile Experience in the Adult Songbird Brain. Journal of Neuroscience, 30(31). info:/10.1523/JNEUROSCI.6042-09.2010

  • August 5, 2010
  • 03:51 PM

The Context for Early Maize at Chaco

by teofilo in Gambler's House

In my earlier post about Stephen Hall‘s recent paper reporting on maize pollen at Chaco Canyon dating as early as 2500 BC, I said briefly that this really shouldn’t be surprising to anyone who’s been following this kind of research closely, and also that I would discuss the context for it later.  Basically, the context [...]... Read more »

Merrill, W., Hard, R., Mabry, J., Fritz, G., Adams, K., Roney, J., & MacWilliams, A. (2009) The diffusion of maize to the southwestern United States and its impact. Proceedings of the National Academy of Sciences, 106(50), 21019-21026. DOI: 10.1073/pnas.0906075106  

  • August 5, 2010
  • 01:00 PM

Fine Reading: The Sex Habits of Fungi

by Moselio Schaechter in Small Things Considered

by Elio
As luck would have it, two pieces of writing on the sex habits of fungi appeared within days of each other. One is light reading, a post in the admirable Cornell Mushroom Blog entitled A Fungus Walks Into a Singles Bar. This is a précis into the complex story of fungal sexuality. It takes you...... Read more »

  • August 5, 2010
  • 12:35 PM

Memory, observation, and consciousness in Octopus Vulgaris

by Mike Mike in Cephalove

          A while back, I wrote a post about short and long term memory processes in cephalopods.  I wrote then that there is good evidence for a dissociation of short and long term memory process in cephalopods, but that this isn't a good basis (alone) for inferring the presence of consciousness, or in the case of arguments about animal's rights, the capacity to suffer (which, I guess, usually comes along with being conscious.)  I stand by ........ Read more »

  • August 5, 2010
  • 12:11 PM

Trees that farm bacteria

by Lab Rat in Lab Rat

One of the factors that is occasionally (rather inaccurately) used to separate plants from animals is that plants generally don't move. Some have fast moving parts, such as the venus fly trap, but they are still usually stuck in one place in the ground. Which means that once they've decided to grow they are totally dependent on their immediate surroundings for nutrients.As nutrients are not always plentiful many trees form symbiotic relationships with bacteria, for example nitrogen fixing bacte........ Read more »

  • August 5, 2010
  • 11:46 AM

Somatic mutations and pathway alterations in cancer

by Sally Church in Pharma Strategy Blog

"The systematic characterization of somatic mutations in cancer genomes is essential for understanding the disease and for developing targeted therapeutics." So began today's journal article from a letter to Nature (link below) from scientists at Genentech. They went on to...... Read more »

Kan, Z., Jaiswal, B., Stinson, J., Janakiraman, V., Bhatt, D., Stern, H., Yue, P., Haverty, P., Bourgon, R., Zheng, J.... (2010) Diverse somatic mutation patterns and pathway alterations in human cancers. Nature. DOI: 10.1038/nature09208  

  • August 5, 2010
  • 11:21 AM

Bacteria force wasps to leave sex behind

by Lucas in thoughtomics

An end to the blogging hiatus at last! I hope to entertain you with the fascinating story on how female wasps got rid of their men and sex in return for bacterial endosymbionts..
Despite the obvious benefits of pleasure and procreation, sex has other advantages. The genetic material of both parents gets mixed in [...]... Read more »

  • August 5, 2010
  • 11:21 AM

Inevitability and oil, Pt. 2: the “end of oil” and human empathy

by Hannah Waters in Culturing Science – biology as relevant to us earthly beings

Never thought I’d actually get around to a Pt. 2, eh?  Well, I’ve shown you!  Here’s the first part: Inevitability and Oil, Pt. 1: the inherent risk for accidents in complex technology For decades now economists and scientists have predicted the “end of oil:” the day when we use up our oil reserves, potentially resulting [...]... Read more »

  • August 5, 2010
  • 10:13 AM

Publication Bias: Not Dead Yet

by Neuroskeptic in Neuroskeptic

Suppose you do two clinical trials of a drug, and only one of them shows it to work. It would be entirely misleading to only tell people about that one, and sweep the negative result under the carpet - but it happens.That's publication bias. A simple but powerful remedy is to require everyone to publically announce their trials before the data comes in. The USA has led the way in this, with the public database, and for several years it's been a legal requirement that all clini........ Read more »

Bourgeois FT, Murthy S, & Mandl KD. (2010) Outcome Reporting Among Drug Trials Registered in Annals of internal medicine, 153(3), 158-66. PMID: 20679560  

  • August 5, 2010
  • 10:04 AM

Humans beat computers in predicting protein structures

by The Curious Wavefunction in The Curious Wavefunction

I was going to first describe Rosetta in a post, but a rather cool paper related to the program which appeared in Nature yesterday makes me jump the gun.In a nutshell, Rosetta tries to predict the structure of proteins from amino acid sequence by inserting fragments from known protein structures and doing many rounds of side chain torsional angle and rigid-body energy optimization. It uses a scoring function to rank the resulting structures that uses empirically derived hydrogen bonding, hydroph........ 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
  • 10:00 AM

Fructose and pancreatic cancer

by Orac in Respectful Insolence

I hate science press releases.

Well, not exactly. I hate science press releases that hype a study beyond its importance. I hate it even more when the investigators who published the study make statements not justified by the study and use the study as a jumping off point to speculate wildly. True, it's not always the fault of the investigators, particularly if they don't have much experience dealing with the press, but all too often scientists fall prey to the tendency to gab glibly and give th........ Read more »

Liu, H., Huang, D., McArthur, D., Boros, L., Nissen, N., & Heaney, A. (2010) Fructose Induces Transketolase Flux to Promote Pancreatic Cancer Growth. Cancer Research, 70(15), 6368-6376. DOI: 10.1158/0008-5472.CAN-09-4615  

  • August 5, 2010
  • 08:42 AM

‘Personalising’ autoimmune disease treatments

by Wellcome Trust in Wellcome Trust Blog

Researchers have identified biomarkers that could save patients with severe autoimmune disease from having to take potentially toxic drug treatments for too long. The biomarkers predict how different patients will react following initial treatment – opening the door to more personalised therapies. Researchers from the University of Cambridge and colleagues found a pattern of gene [...]... Read more »

McKinney EF, Lyons PA, Carr EJ, Hollis JL, Jayne DR, Willcocks LC, Koukoulaki M, Brazma A, Jovanovic V, Kemeny DM.... (2010) A CD8 T cell transcription signature predicts prognosis in autoimmune disease. Nature medicine, 16(5), 586. PMID: 20400961  

  • August 5, 2010
  • 08:24 AM

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

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

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 ........ Read more »

  • August 5, 2010
  • 06:56 AM

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

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  

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