Just online at Genome Biology is a new paper from the Steven Salzberg lab (UMD) on searching for SNPs with cloud computing. Using $85 of computing time rented from Amazon’s EC2, Langmead et al processed an entire human genome - 3.3 billion reads totaling 38x coverage - in three hours.
The “Cloud” Can Be Nebulous
Cloud computing [...]... Read more »
Ben Langmead, Michael C. Schatz, Jimmy Lin, Mihai Pop and Steven L. Salzberg. (2009) Searching for SNPs with cloud computing. Genome Biology, 10(R134). info:/doi:10.1186/gb-2009-10-11-r134
Kuru is an acquired prion disease, transmitted through ritualistic cannibalism, that reached epidemic proportions in the Fore tribe of Papua New Guinea. In a previous post, I presented an article by John Collinge’s group on the selection process of heterozygosity at codon 129 of the prion protein gene (PRNP). The research group has gone a step further by recently describing a new polymorphism of the PRNP gene, G129V. The authors performed PRNP genotyping of 3,000 individuals from ........ Read more »
Mead S, Whitfield J, Poulter M, Shah P, Uphill J, Campbell T, Al-Dujaily H, Hummerich H, Beck J, Mein CA.... (2009) A Novel Protective Prion Protein Variant that Colocalizes with Kuru Exposure. The New England journal of medicine, 361(21), 2056-2065. PMID: 19923577
WE researchers often joke that no-one ever publishes negative results, but that doesn’t mean to say that negative results aren’t extremely useful. One one level, knowledge of such negative results can prevent you repeating the same mistakes that countless other researchers, in other labs, have undoubtedly made over the years. On the other hand, they [...]... Read more »
Smialowski, P., Pagel, P., Wong, P., Brauner, B., Dunger, I., Fobo, G., Frishman, G., Montrone, C., Rattei, T., Frishman, D.... (2009) The Negatome database: a reference set of non-interacting protein pairs. Nucleic Acids Research. DOI: 10.1093/nar/gkp1026
Stumpf, M., Thorne, T., de Silva, E., Stewart, R., An, H., Lappe, M., & Wiuf, C. (2008) From the Cover: Estimating the size of the human interactome. Proceedings of the National Academy of Sciences, 105(19), 6959-6964. DOI: 10.1073/pnas.0708078105
Venkatesan, K., Rual, J., Vazquez, A., Stelzl, U., Lemmens, I., Hirozane-Kishikawa, T., Hao, T., Zenkner, M., Xin, X., Goh, K.... (2008) An empirical framework for binary interactome mapping. Nature Methods, 6(1), 83-90. DOI: 10.1038/nmeth.1280
Huang, H., & Bader, J. (2008) Precision and recall estimates for two-hybrid screens. Bioinformatics, 25(3), 372-378. DOI: 10.1093/bioinformatics/btn640
Just released online at Biology Letters: aphid-tending ants have been observed to selectively remove sick members of their "herd" [$-a].
Most aphid species produce some sort of sweet honeydew as waste while feeding on their host plants; ant-attended aphid species use this honeydew to attract ants. In many cases, the ants "milk" the aphids by stroking them to prompt release of the honeydew. While exploiting a colony of aphids, ants defend it as a food resource, protecting the aphids from predato........ Read more »
Way, M. (1963) Mutualism between ants and honeydew-producing Homoptera. Ann. Rev. Entomology, 8(1), 307-44. DOI: 10.1146/annurev.en.08.010163.001515
A new study finds that "not all ski slopes are created equal" when it comes to impacts to fragile, high-elevation ecosystems.... Read more »
Burt, J., & Rice, K. (2009) Not all ski slopes are created equal: Disturbance intensity affects ecosystem properties. Ecological Applications, 19(8), 2242-2253. DOI: 10.1890/08-0719.1
Chocolate, like many of the things we eat regularly, is a potentially fatal poison, and so it should come as no surprise that a study by the unimaginatively-named John Johnston (at the USDA National Wildlife Research Center) shows that our favourite sweet could prove to be an effective pesticide, for use against coyotes .
Chocolate, or rather the theobromine and caffiene it contains, is potentially fatal to many creatures, but of course "the poison is the dose." Humans are particularly ef........ Read more »
Johnston, J. (2005) Evaluation of Cocoa- and Coffee-Derived Methylxanthines as Toxicants for the Control of Pest Coyotes. Journal of Agricultural and Food Chemistry, 53(10), 4069-4075. DOI: 10.1021/jf050166p
Another week has gone by and some very interesting molbio blog posts have been aggregated to Researchblogging.org. Every week [see my opening post on the matter], I'll select some blog posts I consider particularly interesting in the field of molecular biology [see here to get a sense of the criteria that will be used], briefly describe them and list them here for you to check out.Note that I'm ... Read more »
Hase, K., Kawano, K., Nochi, T., Pontes, G., Fukuda, S., Ebisawa, M., Kadokura, K., Tobe, T., Fujimura, Y., Kawano, S.... (2009) Uptake through glycoprotein 2 of FimH bacteria by M cells initiates mucosal immune response. Nature, 462(7270), 226-230. DOI: 10.1038/nature08529
A deep-sea crab walks into a pub and asked, ”Where’s the bar tender?”
Few deep-sea organisms rely on food originally from land. Most deep-sea dwellers rely on marine snow (detritus raining from the surface), large food falls like dead whales, or chemosynthetic pathways like those at hot vents and cold seeps. This makes sense. How much land [...]... Read more »
Hoyoux, C., Zbinden, M., Samadi, S., Gaill, F., & Compère, P. (2009) Wood-based diet and gut microflora of a galatheid crab associated with Pacific deep-sea wood falls. Marine Biology, 156(12), 2421-2439. DOI: 10.1007/s00227-009-1266-2
Apparently, the author is under the impression that the world’s evolutionary biologists can be dichotomously classified as either ‘adaptationists’ or ‘pluarlists.’ And further, that those classified in the former category should seek reincarnation as enlightened members of the latter... the argument begins (predictably) with Stephen J. Gould and Richard C. Lewontin’s ‘The Spandrels of San Marco,’ an article originally published by the Royal Society in 1979. The broad point of the........ Read more »
The amount of arthroscopic rotator cuff repairs being performed has skyrocketed in recent years. The last 20 years or so have seen the transition from a full open approach, to a combined arthroscopic and mini-open technique, to the current all-arthroscopic technique. The implications on rehabilitation are enormous, as patients are recovering faster with less pain and surrounding tissue involvement. Initially, the strength of these arthroscopic rotator cuff repairs was in question a........ Read more »
Nho SJ, Adler RS, Tomlinson DP, Allen AA, Cordasco FA, Warren RF, Altchek DW, & MacGillivray JD. (2009) Arthroscopic rotator cuff repair: prospective evaluation with sequential ultrasonography. The American journal of sports medicine, 37(10), 1938-45. PMID: 19531660
Scary lab exam in 9h, so this one will be another 'protist appreciation' compilation rather than anything particularly informative. Today this maltreatment will be inflicted upon some poor ciliates, which deserve much more than just a simple appreciation post. Ciliates ARE the higher eukaryotes, the most advanced and awesome organisms on earth. What god created in his/her/its image wasn't the ugly naked humans, it was, in fact, Spirotrich ciliates. Everything else is just basal offshoots, failed........ Read more »
CAMERON, S. (2002) The ultrastructure of and revised diagnosis of the Macropodiniidae (Litostomatea: Trichostomatia). European Journal of Protistology, 38(2), 179-194. DOI: 10.1078/0932-4739-00861
FURNESS, D., & BUTLER, R. (1983) The Cytology of Sheep Rumen Ciliates. I. Ultrastructure of Epidinium caudatum Crawley. The Journal of Eukaryotic Microbiology, 30(4), 676-687. DOI: 10.1111/j.1550-7408.1983.tb05343.x
Furness, D., & Butler, R. (1985) The Cytology of Sheep Rumen Ciliates. II. Ultrastructure of Eudiplodinium maggii. The Journal of Eukaryotic Microbiology, 32(1), 205-214. DOI: 10.1111/j.1550-7408.1985.tb03041.x
LYNN, D. (2003) Morphology or molecules: How do we identify the major lineages of ciliates (Phylum Ciliophora). European Journal of Protistology, 39(4), 356-364. DOI: 10.1078/0932-4739-00004
STRUDERKYPKE, M., KORNILOVA, O., & LYNN, D. (2007) Phylogeny of trichostome ciliates (Ciliophora, Litostomatea) endosymbiotic in the Yakut horse (Equus caballus). European Journal of Protistology, 43(4), 319-328. DOI: 10.1016/j.ejop.2007.06.005
Attention all chameleon fans! It's official: there is now one more species of chameleon known to science. Meet the Magombera chameleon, aka Kinyongia magomberae, a small chameleon with a long tail and a delicate spattering of colors. Although most of its body scales are a soft grey-brown hue, this little lizard is far from dull.
... Read more »
MICHELE MENEGON, KRYSTAL A. TOLLEY, TREVOR JONES,, FRANCES COROVERO, ANDREW R. MARSHALL, & . (2009) A new species of chameleon (Sauria: Chamaeleonidae: Kinyongia) from the Magombera forest and the Udzungwa Mountains National Park, Tanzania. African Journal of Herpetology, 58(2), 59-70. info:/
Based on the results from functional neuroimaging studies, lesion patient studies and brain stimulation studies two important brain areas play an important role in the pathophysiology of depression. These two brain area s are the ventromedial prefrontal cortex and the dorsolateral prefrontal cortex. The ventromedial prefrontal cortex is depicted in red on the picture above [...]
Related posts:New Kind of Brain Stimulation for Treatment Resistant Depression In a recent online publication abou........ Read more »
Koenigs, M., & Grafman, J. (2009) The functional neuroanatomy of depression: Distinct roles for ventromedial and dorsolateral prefrontal cortex. Behavioural Brain Research, 201(2), 239-243. DOI: 10.1016/j.bbr.2009.03.004
Lui, S., Parkes, L., Huang, X., Zou, K., Chan, R., Yang, H., Zou, L., Li, D., Tang, H., Zhang, T.... (2009) Depressive Disorders: Focally Altered Cerebral Perfusion Measured with Arterial Spin-labeling MR Imaging. Radiology, 251(2), 476-484. DOI: 10.1148/radiol.2512081548
Costafreda, S., Chu, C., Ashburner, J., & Fu, C. (2009) Prognostic and Diagnostic Potential of the Structural Neuroanatomy of Depression. PLoS ONE, 4(7). DOI: 10.1371/journal.pone.0006353
A nice complement to the one paper (Ng et al) I detailed last week is a paper that actually came out just before hand (Choi et al). Whereas the Ng paper used whole exome targeted sequencing to find the mutation for a previously unexplained rare genetic disease, the Choi et al paper used a similar scheme (though with a different choice of targeting platform) to find a known mutation in a patient, thereby diagnosing the patient.The patient in question has a tightly interlocked pedigree (Figure 2)........ Read more »
Choi M, Scholl UI, Ji W, Liu T, Tikhonova IR, Zumbo P, Nayir A, Bakkaloğlu A, Ozen S, Sanjad S.... (2009) Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proceedings of the National Academy of Sciences of the United States of America, 106(45), 19096-101. PMID: 19861545
A new take on the evolutionary history of the moa was published in PNAS this week. Mike Bunce from Murdoch University in Perth and researchers from Alan Cooper’s lab at University of Adelaide have combined genetic data from over 260 moa bones with anatomical, geological and ecological information, to revise species relationships among moa and suggest a timeframe and origin for [...]... Read more »
Bunce, M., Worthy, T., Phillips, M., Holdaway, R., Willerslev, E., Haile, J., Shapiro, B., Scofield, R., Drummond, A., Kamp, P.... (2009) The evolutionary history of the extinct ratite moa and New Zealand Neogene paleogeography. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.0906660106
Tree plantations can drain soil of nutrients
... Read more »
Berthrong, S., Jobbágy, E., & Jackson, R. (2009) A global meta-analysis of soil exchangeable cations, pH, carbon, and nitrogen with afforestation. Ecological Applications, 19(8), 2228-2241. DOI: 10.1890/08-1730.1
Contour Drawing Rating Scale (Thompson & Gray, 1995) - established as a reliable and valid measure of body size perception.Anorexia nervosa, an obsessive and unrelenting quest for thinness, is one of the most deadly psychiatric disorders. The documented mortality rate ranges from 3.3% to 18% in different studies (Herzog et al., 2000), and those with the disorder are ten times more likely to die from their illness than a comparable healthy population. A severe distortion of body image is a ca........ Read more »
Suchan, B., Busch, M., Schulte, D., Grönermeyer, D., Herpertz, S., & Vocks, S. (2010) Reduction of gray matter density in the extrastriate body area in women with anorexia nervosa. Behavioural Brain Research, 206(1), 63-67. DOI: 10.1016/j.bbr.2009.08.035
We know that physical sullying, immorality and shame can all be associated with feelings of literal and mental dirtiness, but it's not entirely clear how all these things interact. For example, for a heterosexual woman, which is worse: having a kiss forced on you by an otherwise moral man, or having a consensual kiss with an immoral man? Corinna Elliott and Adam Radomsky have investigated and they say their findings could prove useful to therapists treating people with obsessive compulsive disor........ Read more »
ELLIOTT, C. (2009) Analyses of mental contamination: Part I, experimental manipulations of morality. Behaviour Research and Therapy, 47(12), 995-1003. DOI: 10.1016/j.brat.2009.03.004
As part of my course last year, I wrote an extended long essay concerning the use of bacteria in biorefineries. As I've had a very lazy weekend (and to celebrate crossing the hundred post mark) I've decided to reproduce some of it here. More may be forthcoming at some point, depending on the laziness of my weekends.Second Generation BiofuelsSecond generation biofuels consist of lignocellulose material, which is broken down into simple sugars via enzymatic reactions and then fermented to produce ........ Read more »
Gilbert, H. (2007) Cellulosomes: microbial nanomachines that display plasticity in quaternary structure. Molecular Microbiology, 63(6), 1568-1576. DOI: 10.1111/j.1365-2958.2007.05640.x
Blumer-Schuette, S., Kataeva, I., Westpheling, J., Adams, M., & Kelly, R. (2008) Extremely thermophilic microorganisms for biomass conversion: status and prospects. Current Opinion in Biotechnology, 19(3), 210-217. DOI: 10.1016/j.copbio.2008.04.007
Zhang, Y. (2005) Cellulose utilization by Clostridium thermocellum: Bioenergetics and hydrolysis product assimilation. Proceedings of the National Academy of Sciences, 102(20), 7321-7325. DOI: 10.1073/pnas.0408734102
Today I was going to blog this paper, which says that you can predict which kids will grow up and be criminals by measuring their Pavlovian fear conditioning at age 8. In Mauritius. But The Last Psychiatrist already said everything I was going to.Luckily, there's another article in the American Journal of Psychiatry about crime in a tropical country for me to write about - Randomized, Double-Blind, Placebo-Controlled Trial of Vigabatrin for the Treatment of Cocaine Dependence in Mexican Parolees........ Read more »
Brodie, J., Case, B., Figueroa, E., Dewey, S., Robinson, J., Wanderling, J., & Laska, E. (2009) Randomized, Double-Blind, Placebo-Controlled Trial of Vigabatrin for the Treatment of Cocaine Dependence in Mexican Parolees. American Journal of Psychiatry, 166(11), 1269-1277. DOI: 10.1176/appi.ajp.2009.08121811
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