I'm away right now, and haven't had time to prepare new stuff. So, here's something from the archives again: by which I mean, something written in 2006. It's still pretty interesting (in my humble opinion), but I would definitely do some things differently were I to re-write it today [gliding sifaka below from Demes et al. (1991): read on].
Mention 'flying primate' and most zoologists will think you're referring to the well known, controversial theory of John Pettigrew of the University of ........ Read more »
Demes B, Forchap E, & Herwig H. (1991) They seem to glide. Are there aerodynamic effects in leaping prosimian primates?. Zeitschrift fur Morphologie und Anthropologie, 78(3), 373-85. PMID: 1909482
In most zoos and animal parks, polar bears (ursus maritimus) attract such a disproportionate amount of attention that they are referred to in the industry as "charismatic megafauna," or in other words, "really cool animals." Perhaps it is because it is especially rare for the average zoo-goer to happen upon a polar bear in the wild, or because they live in such an inhospitable environment. Perhaps it's just because polar bears are so damn cute.
Maybe we should just blame Coca-Cola.
Whatever........ Read more »
Renner, M., & Kelly, A. (2006) Behavioral Decisions for Managing Social Distance and Aggression in Captive Polar Bears (Ursus maritimus). Journal of Applied Animal Welfare Science, 9(3), 233-239. DOI: 10.1207/s15327604jaws0903_5
Cephalopods have quite a neat circulatory system (file that away under “dorkiest things to say at a party”.) I’m not joking, though; they do! They have a closed circulatory system, meaning that their blood is contained within blood vessels, instead of just filling their body cavity. All other molluscs have an open circulatory system, where [...]... Read more »
W.R.A. Muntz, & U. Raj. (1984) On the visual system of Nautilus Pompilus. Journal of Experimental Biology, 253-263. info:/
The emergence of next-generation sequencing has presented numerous significant challenges to the bioinformatics community. NGS instruments have given rise to a new generation of software tools for the alignment, assembly, management, and visualization of incredible amounts of data. New algorithms have also been developed to assess coverage, assess genomic copy number, call variants (SNPs/indels), and [...]... Read more »
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M.... (2010) The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome research. PMID: 20644199
During the Cretaceous, the oceans were ruled not by sharks or aquatic mammals, but by large, predatory marine reptiles. Among these, the dominant ocean predator was the Mosasaur. Mosasaurs emerged in the Early Cretaceous from a lizard-like ancestral squamate. They thrived in warm, shallow seas. Some species could reach up to 17 meters in length. [...]... Read more »
Lindgren, J., Caldwell, M., Konishi, T., & Chiappe, L. (2010) Convergent Evolution in Aquatic Tetrapods: Insights from an Exceptional Fossil Mosasaur. PLoS ONE, 5(8). DOI: 10.1371/journal.pone.0011998
Lee, M. (1997) The phylogeny of varanoid lizards and the affinities of snakes. Philosophical Transactions of the Royal Society B: Biological Sciences, 352(1349), 53-91. DOI: 10.1098/rstb.1997.0005
The newly reported Saadanius hijazensis may or may not be a "missing link" but in order for this monkey to climb onto the primate family tree, a new branch had to be sprouted. So, not only is Saadanius hijazensis a new species, but it is a member of a new taxonomic Family, Saadaniidae, which in turn is a member of a new Superfamily, Saadanioidea. Why is this important? It's complicated. But not too complicated.
The fossil was found while University of Michigan paleontologist Iyad Zalmout w........ Read more »
Zalmout, I., Sanders, W., MacLatchy, L., Gunnell, G., Al-Mufarreh, Y., Ali, M., Nasser, A., Al-Masari, A., Al-Sobhi, S., Nadhra, A.... (2010) New Oligocene primate from Saudi Arabia and the divergence of apes and Old World monkeys. Nature, 466(7304), 360-364. DOI: 10.1038/nature09094
Recently, I chanced upon a paper in the PLoS Genetics journal by two research groups from Brown University and the University of California San Francisco. Their findings suggest that epigenetic changes to DNA in breast cancers are related to environmental...... Read more »
Christensen, B., Kelsey, K., Zheng, S., Houseman, E., Marsit, C., Wrensch, M., Wiemels, J., Nelson, H., Karagas, M., Kushi, L.... (2010) Breast Cancer DNA Methylation Profiles Are Associated with Tumor Size and Alcohol and Folate Intake. PLoS Genetics, 6(7). DOI: 10.1371/journal.pgen.1001043
It’s a darn good time to be a meme these days, especially on the Internet. The lightning fast transmission of links and videos and funny pictures between millions of people on any number of social media outlets or email means the viral spread and replication of the latest “you’ve got to see this” thing may [...]... Read more »
Blackmore, S. (2001) EVOLUTION AND MEMES: THE HUMAN BRAIN AS A SELECTIVE IMITATION DEVICE. Cybernetics , 32(1-2), 225-255. DOI: 10.1080/019697201300001867
The destruction was epic. When the volcano Krakatau erupted on August 26, 1883 on an island in the Sunda Strait near Indonesia, molten rock flows caused the seas to boil. Layers of lava and ash up to 20 meters thick carpeted the seafloor, snuffing out all marine life within 15 kilometers of the peak. Now, […] Read More »... Read more »
Starger, C., Barber, P., Ambariyanto, ., & Baker, A. (2010) The recovery of coral genetic diversity in the Sunda Strait following the 1883 eruption of Krakatau. Coral Reefs, 29(3), 547-565. DOI: 10.1007/s00338-010-0609-2
by Mary in OpenHelix
For this week’s tip of the week we’ll be looking at the Gaggle Genome Browser. As we are seeing more and more species or individuals data coming along from high-throughput sequencing projects, metagenomics data sets, and additional annotation track types coming from various projects–we’re gonna need more visualization options. Gaggle Browser provides the foundation for a new kind of visualization and interaction with the data.
The Gaggle Browser is one piece of the Gaggl........ Read more »
Bare, J., Koide, T., Reiss, D., Tenenbaum, D., & Baliga, N. (2010) Integration and visualization of systems biology data in context of the genome. BMC Bioinformatics, 11(1), 382. DOI: 10.1186/1471-2105-11-382
There’s increasing evidence from Drosophila that genes that are important in development are not satisfied with having just one set of enhancer sequences to drive their transcription. Why is this? Sometimes, two different enhancer sequences have obviously different functions: they respond to different sets of transcription factors, for example, and create different patterns of transcription. [...]... Read more »
Frankel N, Davis GK, Vargas D, Wang S, Payre F, & Stern DL. (2010) Phenotypic robustness conferred by apparently redundant transcriptional enhancers. Nature, 466(7305), 490-3. PMID: 20512118
A major issue in human genomics over the past few years has been the case of the “missing heritability“. Roughly, we know that for many traits, such as height, most of the variation in the trait within the population is controlled by variation in the genes of the population. The height of your parents is [...]... Read more »
Boyko AR, Quignon P, Li L, Schoenebeck JJ, Degenhardt JD, & et al. (2010) A Simple Genetic Architecture Underlies Morphological Variation in Dogs. PLoS Biology. info:/10.1371/journal.pbio.1000451
The bearded goby is an ecological superhero. In less than five decades, this six-inch fish managed to revive an entire marine ecosystem—one that had careened to the brink of collapse. Now scientists are beginning to unravel how the bearded goby stabilized the communities around it and capitalized on conditions seemingly too harsh for life.... Read more »
Utne-Palm AC, Salvanes AG, Currie B, Kaartvedt S, Nilsson GE, Braithwaite VA, Stecyk JA, Hundt M, van der Bank M, Flynn B.... (2010) Trophic structure and community stability in an overfished ecosystem. Science (New York, N.Y.), 329(5989), 333-6. PMID: 20647468
Exercise correlates with a reduced risk of suffering dementia in later life, just as excess visceral fat is correlated with an increased risk of later developing dementia. The underlying mechanisms are somewhat different, but they both boil down to the quality of the blood vessels in your brain. Impaired blood vessels mean a lower blood flow or the breakages and lesions of vascular dementia - neither of which is good for you in the long term. Another issue to consider in this context is the ongo........ Read more »
Dolan H, Crain B, Troncoso J, Resnick SM, Zonderman AB, & Obrien RJ. (2010) Atherosclerosis, dementia, and Alzheimer disease in the Baltimore Longitudinal Study of aging cohort. Annals of neurology, 68(2), 231-40. PMID: 20695015
I’m sure that most people know that anorexia occurs more often in women than in men, though overall in about 0.3-0.6% of the population. What a lot of people DON’T know is that anorexia nervosa is a highly heritable disease. In fact, cases of anorexia nervosa have been reported as early as the 16th century [...]... Read more »
Versini, A., Ramoz, N., Le Strat, Y., Scherag, S., Ehrlich, S., Boni, C., Hinney, A., Hebebrand, J., Romo, L., Guelfi, J.... (2010) Estrogen Receptor 1 Gene (ESR1) is Associated with Restrictive Anorexia Nervosa. Neuropsychopharmacology. DOI: 10.1038/npp.2010.49
In a comment to the previous post, Alan Reed Bishop brings up an issue closely related to the recent evidence for early maize cultivation in Chaco Canyon: the introduction of domesticated turkeys to the Southwest. A recent study of archaeological turkey remains found that the majority of the turkeys found in Southwestern archaeological sites are [...]... Read more »
Matson, R., & Chisholm, B. (1991) Basketmaker II Subsistence: Carbon Isotopes and Other Dietary Indicators from Cedar Mesa, Utah. American Antiquity, 56(3), 444. DOI: 10.2307/280894
Speller, C., Kemp, B., Wyatt, S., Monroe, C., Lipe, W., Arndt, U., & Yang, D. (2010) Ancient mitochondrial DNA analysis reveals complexity of indigenous North American turkey domestication. Proceedings of the National Academy of Sciences, 107(7), 2807-2812. DOI: 10.1073/pnas.0909724107
Jean-Louis Viovy (Universite Pierre et Marie Curie, France) and coworkers report a new technique that combines gentle cell sorting with rigorous microscopic imaging, and will revolutionize cancer diagnostics. This news feature was written on August 10, 2010.... Read more »
Saliba, A.-E., Saias, L., Psychari, E., Minc, N., Simon, D., Bidard, F.-C., Mathiot, C., Pierga, J.-Y., Fraisier, V., Salamero, J.... (2010) Microfluidic sorting and multimodal typing of cancer cells in self-assembled magnetic arrays. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1001515107
Neurodegenerative diseases (i.e. Alzheimer's and Huntington's) often involves the formation of aggregates of proteins in a patients' brain, correlated with the process of degeneration. Some of these proteins are unique to the specific disease and others are commonly found in healthy individuals but also occur intertwined with the disease-linked types. Until now, these "common proteins" were thought to be an effect of sampling the tissues and were ignored as background. A new paper out today i........ Read more »
David, D., Ollikainen, N., Trinidad, J., Cary, M., Burlingame, A., & Kenyon, C. (2010) Widespread Protein Aggregation as an Inherent Part of Aging in C. elegans. PLoS Biology, 8(8). DOI: 10.1371/journal.pbio.1000450
by thomastu in Disease Prone
Looking at protein folders A recent Nature letter looks at the properties of human protein folders and how they can design better programs to do it automatically (Photo taken by Thomas Tu) My mother was always vaguely disdainful of me playing computer games as a child (… and as an adult). But it turns out [...]... 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
A major scandal looks to be in progress involving Harvard Professor Marc Hauser, a psychologist and popular author whose research on the minds of chimpanzees and other primates is well-known and highly respected. The Boston Globe has the scoop and it's well worth a read (though you should avoid reading the comments if you react badly to stupid.)Hauser's built his career on detailed studies of the cognitive abilities of non-human primates. He's generally argued that our closest relatives are smar........ Read more »
Hauser MD, Glynn D, & Wood J. (2007) Rhesus monkeys correctly read the goal-relevant gestures of a human agent. Proceedings. Biological sciences / The Royal Society, 274(1620), 1913-8. PMID: 17540661
Wood JN, Glynn DD, Phillips BC, & Hauser MD. (2007) The perception of rational, goal-directed action in nonhuman primates. Science (New York, N.Y.), 317(5843), 1402-5. PMID: 17823353
Hauser MD, Kralik J, Botto-Mahan C, Garrett M, & Oser J. (1995) Self-recognition in primates: phylogeny and the salience of species-typical features. Proceedings of the National Academy of Sciences of the United States of America, 92(23), 10811-14. PMID: 7479889
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