Human cancers are driven by genetic and epigenetic changes to the genome of healthy cells. We often think about acquired mutations as the key drivers of tumor development and growth. Most studies empowered by next-gen sequencing have focused on identifying these changes. Yet aberrant DNA methylation - hypermethylation of tumor suppressor genes and hypomethylation of [...]... Read more »
Feber A, Wilson GA, Zhang L, Presneau N, Idowu B, Down TA, Rakyan VK, Noon LA, Lloyd AC, Stupka E.... (2011) Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors. Genome research. PMID: 21324880
Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM.... (2008) A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nature biotechnology, 26(7), 779-85. PMID: 18612301
Next generation sequencing (NGS) has heralded a new era in genomics, as the output of sequence data is now readily available for a cost that is five orders of magnitude cheaper than when the first human genome sequence was released. But one limitation of the data produced by the new sequencing technologies is that they are harder to assemble into a single contiguous sequence representing an entire chromosome, due to the short lengths of their reads and the relatively high error rates in identify........ Read more »
Liang Ye, LaDeana W Hillier, Patrick Minx, Nay Thane, Devin Locke, John C Martin, Lei Chen, Makedonka Mitreva, Jason R Miller, Kevin V Haub.... (2011) A vertebrate case study of the quality of assemblies derived from next-generation sequences. Genome Biology, 12(3). info:/doi:10.1186/gb-2011-12-3-r31
“While 2010 was celebrated as the year of ceratopsians by many,” paleontologist Dave Hone wrote at Archosaur Musings yesterday, “it should not be overlooked the huge number of tyrannosaurs that have cropped up in the last year or so.” He’s right. For a long time Albertosaurus, Gorgosaurus, Daspletosaurus, Tarbosaurus and, of course, Tyrannosaurus made up [...]... Read more »
Hone, D.; Wang, K.; Sullivan, C.; Zhao, X.; Chen, S.; Li, D.; Ji, S.; Ji, Q.; Xing, X. (2011) A new tyrannosaurine theropod, Zhuchengtyrannus magnus is named based on a maxilla and dentary . Cretaceous Research. info:/10.1016/j.cretres.2011.03.005
Occasionally, life looks like it isn’t. In the eastern forests of North America and in a thin strip along the Pacific Northwest (but sadly not in Colorado), hidden in plain sight on tree trunks you can find the gracefully named elven script lichen, Graphis scripta. With a little imagination, the lichen looks like secret writing, [...]... Read more »
New research published today in the Annals of Victus Mortuus describes a very unusual genetic mutation in Staphylococcus Rabia that results in a stark behaviour change. When the mutation was introduced the bacteria showed several changes in characteristics, including the following: Lack of fluidity of movement Spontaneous loss of soma No response to dangerous stimuli Change in … Read more... Read more »
GA Romero, D Boyle, E Wright. (2011) Missense mutation in Staphylococcus Rabia (Δ28DL) resulting behavioural changes. Annals of Victus Mortuus. info:/
Today sees the publication of what is surely the century's most significant zoological discovery. After decades of searching, Africa's mystery Congolese swamp monster, the Mokele-Mbembe, has been discovered - it is a living sauropod dinosaur, and it radically alters our understanding of archosaur phylogeny, sauropod biology and diversity, and indeed the evolutionary process as a whole.
As is fitting for the discovery of a brand new, extant, hitherto cryptic megabeast represented by complet........ Read more »
Gatesy, J., Amato, G., Norell, M., DeSalle, R., & Hayashi, C. (2003) Combined Support for Wholesale Taxic Atavism in Gavialine Crocodylians. Systematic Biology, 52(3), 403-422. DOI: 10.1080/10635150309329
I have previously written about the origins of bioinformatics as a field, starting by reposting an article I wrote in 2002, The Mythology of Bioinformatics, and subsequently introducing the first and second articles in the Roots of Bioinformatics series published in PLoS Computational Biology.
A third article in the series,* The Roots of Bioinformatics in Theoretical Biology, is [...]... Read more »
Hogeweg, P. (2011) The Roots of Bioinformatics in Theoretical Biology. PLoS Computational Biology, 7(3). DOI: 10.1371/journal.pcbi.1002021
One of the great things about logic is there are so many different flavours to choose from. If you thought that logic came in just one flavour (vanilla), then think again. Now, I Am Not A Logician but I can’t help but marvel at the bewildering array of logical flavours on offer including, but not limited [...]... Read more »
For today's Dose of Friday Weird Science, I thought I could do something April Fools'y, but I've always thought that day was really pretty dumb. Instead, I have something MUCH BETTER. TODAY, Sci presents to you Brian Switek, of the Laelaps Blog over at Wired! And, more pertinently, Brian is presenting you today with...HIS THIRD [...]... Read more »
Grossl NA. (2000) Supernumerary breast tissue: historical perspectives and clinical features. Southern medical journal, 93(1), 29-32. PMID: 10653061
Velanovich V. (1995) Ectopic breast tissue, supernumerary breasts, and supernumerary nipples. Southern medical journal, 88(9), 903-6. PMID: 7660204
Schmidt H. (1998) Supernumerary nipples: prevalence, size, sex and side predilection -- a prospective clinical study. European journal of pediatrics, 157(10), 821-3. PMID: 9809822
Group-living confers significant benefits in terms of protection from predation and thermoregulation, and is commonly observed in groups of herbivorous mammals. Populations of warthogs (Phacochoerus africanus) in the South African savanna live in groups; however, recent studies on group dynamics in these organisms shows that size and composition varies greatly thoughout the year. General associations [...]... Read more »
White, A., & Cameron, E. (2011) Evidence of helping behavior in a free-ranging population of communally breeding warthogs. Journal of Ethology. DOI: 10.1007/s10164-011-0268-y
In late June 2009, researchers in Rwanda noticed a female mountain gorilla coughing as she fed in her forest home. Within days, she was dead – and a new study concludes that she and an infant gorilla were killed by a virus that appears to have spread from human visitors. The news highlights the risk […] Read More »... Read more »
Gustavo Palacios et al. (2011) Human Metapneumovirus Infection in Wild Mountain Gorillas, Rwanda. Emerging Infectious Diseases. info:/
Organisms living in habitats that no sane person would call comfortable have fas...... Read more »
Fiala, G., & Stetter, K. (1986) Pyrococcus furiosus sp. nov. represents a novel genus of marine heterotrophic archaebacteria growing optimally at 100ºC. Archives of Microbiology, 56-61. DOI: 10.1007/BF00413027
Mukund, S, & Adams, M. W. (1991) The novel tungsten-iron-sulfur protein of the hyperthermophilic archaebacterium, Pyrococcus furiosus, is an aldehyde ferredoxin oxidoreductase. Evidence for its participation in a unique glycolytic pathway. The Journal of Biological Chemistry, 14208-16. PMID: 1907273
Sapra, R. et al. (2003) A simple energy-conserving system: Proton reduction coupled to proton translocation. Proceedings of the National Academy of Sciences, 100(1), 7545-7550. DOI: 10.1073/pnas.1331436100
Takai, K. et al. (2008) Cell proliferation at 122 C and isotopically heavy CH4 production by a hyperthermophilic methanogen under high-pressure cultivation. Proceedings of the National Academy of Sciences, 10949-10954. DOI: 10.1073/pnas.0712334105
Way back in November 2009 at the American Association of Cancer Research (AACR) Molecular Targets meeting in Boston, there was a fascinating poster on the early promise for nanotechnology as a new form of efficient drug delivery for cancer therapeutics … Continue reading →
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Inoue, S., Ding, H., Portilla-Arias, J., Hu, J., Konda, B., Fujita, M., Espinoza, A., Suhane, S., Riley, M., Gates, M.... (2011) Polymalic Acid-Based Nanobiopolymer Provides Efficient Systemic Breast Cancer Treatment by Inhibiting both HER2/neu Receptor Synthesis and Activity. Cancer Research, 71(4), 1454-1464. DOI: 10.1158/0008-5472.CAN-10-3093
Ljubimova, J., Fujita, M., Ljubimov, A., Torchilin, V., Black, K., & Holler, E. (2008) Poly(malic acid) nanoconjugates containing various antibodies and oligonucleotides for multitargeting drug delivery. Nanomedicine, 3(2), 247-265. DOI: 10.2217/17435822.214.171.124
Ding, H., Inoue, S., Ljubimov, A., Patil, R., Portilla-Arias, J., Hu, J., Konda, B., Wawrowsky, K., Fujita, M., Karabalin, N.... (2010) Inhibition of brain tumor growth by intravenous poly( -L-malic acid) nanobioconjugate with pH-dependent drug release. Proceedings of the National Academy of Sciences, 107(42), 18143-18148. DOI: 10.1073/pnas.1003919107
The process in which a virus causes disease and dysfunction within its host is termed viral pathogenesis; the study of which is pretty important if we are to fully understand infection, replication and transmission of pathogens as well as to develop effective antivirals and vaccines. Ebola virus (EBOV) is one such deadly virus in which there are currently no approved antivirals nor vaccines and which the study of pathogenesis is therefore ever more important.
EBOV particle. www.accessex........ Read more »
Wauquier N, Becquart P, Padilla C, Baize S, & Leroy EM. (2010) Human fatal zaire ebola virus infection is associated with an aberrant innate immunity and with massive lymphocyte apoptosis. PLoS neglected tropical diseases, 4(10). PMID: 20957152
Every two years, the German society for developmental biology (Gesellschaft für Entwicklungsbiologie - GfE) hands out an award for the best PhD thesis of the previous two years. At their society meeting last week, this award went to Marion Silies, for her PhD thesis on glial cell migration. I met up with Marion after her [...]... Read more »
Silies M, & Klämbt C. (2010) APC/C(Fzr/Cdh1)-dependent regulation of cell adhesion controls glial migration in the Drosophila PNS. Nature neuroscience, 13(11), 1357-64. PMID: 20890296
Stem cell research has made leaps and bounds the past few years, and it’s no wonder why…they hold amazing therapeutic potential and teach us so much about development. A recent paper makes another leap for the stem cell community and shows some amazing things that stem cells can do.Stem cells have the ability to differentiate into many cell types, and this ability requires that stem cells respond to different cues depending on the resulting cell type. Biologists have been able to induce di........ Read more »
Spence, J., Mayhew, C., Rankin, S., Kuhar, M., Vallance, J., Tolle, K., Hoskins, E., Kalinichenko, V., Wells, S., Zorn, A.... (2010) Directed differentiation of human pluripotent stem cells into intestinal tissue in vitro. Nature, 470(7332), 105-109. DOI: 10.1038/nature09691
How does one go about selling a sabercat skeleton? This was the question the Argentinean naturalist Francisco Javier Muñiz asked Charles Darwin in a letter sent on August 30, 1846.
Almost one year previously, in the pages of the Gaceta Mercantil, Muñiz published a detailed description of a nearly-complete saber-toothed cat skeleton. The article’s title proclaimed [...]... Read more »
Rincon, A., Prevosti, F., & Parra, G. (2011) New saber-toothed cat records (Felidae: Machairodontinae) for the Pleistocene of Venezuela, and the Great American Biotic Interchange. Journal of Vertebrate Paleontology, 31(2), 468-478. DOI: 10.1080/02724634.2011.550366
by Vincent Racaniello in virology blog
Last week we discussed the second known virophage, but we didn’t have any explanation of why such viruses might evolve. This week we have the discovery of a third virophage, hints of many more, and a hypothesis for what they might be doing in the global ecosystem. The newest virus eater is called Organic Lake [...]... Read more »
Yau S, Lauro FM, Demaere MZ, Brown MV, Thomas T, Raftery MJ, Andrews-Pfannkoch C, Lewis M, Hoffman JM, Gibson JA.... (2011) Virophage control of antarctic algal host-virus dynamics. Proceedings of the National Academy of Sciences of the United States of America. PMID: 21444812
So, if you're an evolutionary biologist, or really if you follow the biology literature at all, you have probably heard about the paper published last fall in Nature by Martin Nowak, Corina Tarnita, and E. O. Wilson. The paper claims that all theories based on kin selection and inclusive fitness are fundamentally flawed and unsupported by any empirical evidence.
Recently, responses to the paper were published in Nature, and the original article has been criticized on a number of counts.&n........ Read more »
Abbot, P., Abe, J., Alcock, J., Alizon, S., Alpedrinha, J., Andersson, M., Andre, J., van Baalen, M., Balloux, F., Balshine, S.... (2011) Inclusive fitness theory and eusociality. Nature, 471(7339). DOI: 10.1038/nature09831
Boomsma, J., Beekman, M., Cornwallis, C., Griffin, A., Holman, L., Hughes, W., Keller, L., Oldroyd, B., & Ratnieks, F. (2011) Only full-sibling families evolved eusociality. Nature, 471(7339). DOI: 10.1038/nature09832
Most people reading this blog will have heard of the "selfish gene" - the idea, formally defined by Hamilton and popularised by Dawkins, that what matters from the perspective of evolution is not organisms, but genes.
Those genes that maximise their chances of survival - regardless of what happens to individuals - will be the ones that come to predominate.
It comes in for a lot of flack, mostly from people who wrongly equate selfish genes with selfish people. To be fair, there also a lot of co........ Read more »
West, S., El Mouden, C., & Gardner, A. (2010) Sixteen common misconceptions about the evolution of cooperation in humans. Evolution and Human Behavior. DOI: 10.1016/j.evolhumbehav.2010.08.001
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