by Merry Youle in Small Things Considered
Like it or not, we can't shop around for a genetic code, nor do we have a choice of brand or model. We're pretty much stuck with the one we have at this point (although some researchers are modifying the code to synthesize proteins containing "designer amino acids"). The universal genetic code is just that, virtually universal. Oh, there are about 20 other "genetic codes" known but almost all of them are used only by mitochondria or else the differences are limited to start and stop codons. So h........ Read more »
So, as you have no doubt surmised from the title of this post, the cash-strapped Republican Party is going to start using their abundant frequent "flyer" points to pay their debts.
I'm kidding, of course. The GOP doesn't pay its debts!
Actually, we're going to talk about a paper just out in Genetics by Aniel Agarwal and Michael Whitlock. They provide a very thorough analysis of data on the fitness effects of homozygous and heterozygous gene deletions in yeast.
But let's back up for a minute........ Read more »
Agrawal, A., & Whitlock, M. (2010) Inferences About the Distribution of Dominance Drawn from Yeast Gene Knockout Data. Genetics. DOI: 10.1534/genetics.110.124560
As mighty as Tyrannosaurus rex was, its tiny forelimbs have also made it one of the most mocked dinosaurs of all time. The stubby arms of this predator once seemed mismatched to its enormous frame, and some of the hypotheses put forward to explain their function just made the “tyrant king” seem sillier. The ideas [...]... Read more »
Agnolin, F., & Chiarelli, P. (2009) The position of the claws in Noasauridae (Dinosauria: Abelisauroidea) and its implications for abelisauroid manus evolution. Paläontologische Zeitschrift, 84(2), 293-300. DOI: 10.1007/s12542-009-0044-2
Although some studies have found that early life environmental factors can affect our vulnerability to neurodegenerative diseases such as Alzheimer’s disease in later life, the underlying neuronal mechanisms of such vulnerability are not well understood. By looking at post mortem rhesus monkey brains, Merrill et al. (2011) finds an association between early life experience and subsequent risk of exhibiting neurodegeneration in later life. In the study, β-amyloid plaque density and synaptophys........ Read more »
Merrill DA, Masliah E, Roberts JA, McKay H, Kordower JH, Mufson EJ, & Tuszynski MH. (2011) Association of early experience with neurodegeneration in aged primates. Neurobiology of aging, 32(1), 151-6. PMID: 19321231
There is so much yet to learn about cells just sitting on a culture dish. Add cell migration to the mix, and it’s easy to be amazed at the complexity of cell function and how much there is to discover. Luckily, today’s image is from a paper that adds to our understanding of centrosome positioning and polarity in migrating cells. ... Read more »
Manneville, J., Jehanno, M., & Etienne-Manneville, S. (2010) Dlg1 binds GKAP to control dynein association with microtubules, centrosome positioning, and cell polarity. Originally published in The Journal of Cell Biology, 191(3), 585-598. DOI: 10.1083/jcb.201002151
One of the more important paradigm shifts in our understanding of the Alzheimer’s disease-causing amyloid protein in the last few years has been the recognition of differences between the well known polymer aggregates of amyloid and their smaller, soluble oligomer counterparts. For a long time it was believed that the fully formed 40-42 amino acid protein aggregate found in autopsies was the causative agent in AD, or at least the most toxic one. This understanding has radically changed in the ........ Read more »
Reinke, A., Ung, P., Quintero, J., Carlson, H., & Gestwicki, J. (2010) Chemical Probes That Selectively Recognize the Earliest Aβ Oligomers in Complex Mixtures. Journal of the American Chemical Society, 2147483647. DOI: 10.1021/ja106291e
In the Monod-Wyman-Changeux model for cooperative binding, proteins exist in an equilibrium of low-affinity and high-affinity states in solution, absent any ligand. In this view, although it may appear that the binding of a ligand causes a conformational transition, it actually stabilizes one conformation from a pre-existing equilibrium. In the past several years, advanced NMR techniques have yielded increasing evidence that these structural equilibria exist for a number of proteins, suggesting ........ Read more »
Farber, P., & Mittermaier, A. (2010) Concerted Dynamics Link Allosteric Sites in the PBX Homeodomain. Journal of Molecular Biology. DOI: 10.1016/j.jmb.2010.11.016
Today I bring you something extra special: A guest post from Lucas Brouwers of the world-famous blog Thoughtomics. He loves genomes, I love plankton, and you get a great story involving spaceships, genomic party crashers, and, of course, a planktonic … Continue reading →... Read more »
Denoeud F, Henriet S, Mungpakdee S, Aury JM, Da Silva C, Brinkmann H, Mikhaleva J, Olsen LC, Jubin C, Cañestro C.... (2010) Plasticity of Animal Genome Architecture Unmasked by Rapid Evolution of a Pelagic Tunicate. Science (New York, N.Y.). PMID: 21097902
Historically, perhaps due to human interest in maximizing fishing activity, we have assumed that there is a great deal of gene flow in marine populations. This assumption allowed us to maximize fishing efforts without guilt, since a large, ocean-wide population would allow fish from other parts of the world to refill populations that we had reduced by overfishing. But you know what they say about assumptions: they make an ASS out of U and ME. Thus marine biologists have taken an interest ........ Read more »
Beacham, T. (2002) Multiple stock structure of Atlantic cod (Gadus morhua) off Newfoundland and Labrador determined from genetic variation. ICES Journal of Marine Science, 59(4), 650-665. DOI: 10.1006/jmsc.2002.1253
Bradbury, I., Hubert, S., Higgins, B., Borza, T., Bowman, S., Paterson, I., Snelgrove, P., Morris, C., Gregory, R., Hardie, D.... (2010) Parallel adaptive evolution of Atlantic cod on both sides of the Atlantic Ocean in response to temperature. Proceedings of the Royal Society B: Biological Sciences, 277(1701), 3725-3734. DOI: 10.1098/rspb.2010.0985
Hellberg, M. (2009) Gene Flow and Isolation among Populations of Marine Animals. Annual Review of Ecology, Evolution, and Systematics, 40(1), 291-310. DOI: 10.1146/annurev.ecolsys.110308.120223
Have you ever cut up an apple to take for lunch, or prepared apples for a fresh fruit tray only to have them turn an unappealing shade of brown? You’re not alone. There’s nothing wrong with brown apple slices, but they certainly don’t look nice, which discourages some people from eating as many apples as they should. Apples are a healthy snack and anything that gets people to eat more fruit could be considered Continue reading...... Read more »
Herb Aldwinckle, & Mickael Malnoy. (2009) Plant Regeneration and Transformation in the Rosaceae . Transgenic Plant Journal , 1-39. info:/
Bachem, C., Speckmann, G., van der Linde, P., Verheggen, F., Hunt, M., Steffens, J., & Zabeau, M. (1994) Antisense Expression of Polyphenol Oxidase Genes Inhibits Enzymatic Browning in Potato Tubers. Bio/Technology, 12(11), 1101-1105. DOI: 10.1038/nbt1194-1101
Rommens CM, Ye J, Richael C, & Swords K. (2006) Improving potato storage and processing characteristics through all-native DNA transformation. Journal of agricultural and food chemistry, 54(26), 9882-7. PMID: 17177515
Thipyapong P, Hunt MD, & Steffens JC. (2004) Antisense downregulation of polyphenol oxidase results in enhanced disease susceptibility. Planta, 220(1), 105-17. PMID: 15300439
"Two chimps had been shut out of their shelter by mistake during a cold rain storm. They were standing dejeted, water streaming down their shivering bodies, when Professor Köhler chanced to pass." Upon opening the door for the two chimps, Dr. James Leuba recounts, "instead of scampering in without more ado, as many a child would have done, each of them delayed entering the warm shelter long enough to throw its arms around his benefactor in a frenzy of satisfaction."
"Chimpanzees," primatolog........ Read more »
Krisin E. Bonnie, & Frans B. M. de Waal. (2004) Primate Social Reciprocity and the Origin of Gratitude. in Robert A. Emmons , 213-229. info:/
DEWAAL, F. (1997) The Chimpanzee's service economy: Food for grooming. Evolution and Human Behavior, 18(6), 375-386. DOI: 10.1016/S1090-5138(97)00085-8
HART, B., & HART, L. (1992) Reciprocal allogrooming in impala, Aepyceros melampus. Animal Behaviour, 44(6), 1073-1083. DOI: 10.1016/S0003-3472(05)80319-7
Seyfarth RM, & Cheney DL. (1984) Grooming, alliances and reciprocal altruism in vervet monkeys. Nature, 308(5959), 541-3. PMID: 6709060
Recently, at the NY Chemotherapy Foundation symposium, Dr Phil Kantoff from Dana Farber gave a lecture on new therapeutic strategies in prostate cancer. Despite the unsociably early hour (7.30am), the room was almost packed. While waiting for the session to … Continue reading →... Read more »
Gattinoni, L., Ji, Y., & Restifo, N. (2010) Wnt/ -Catenin Signaling in T-Cell Immunity and Cancer Immunotherapy. Clinical Cancer Research, 16(19), 4695-4701. DOI: 10.1158/1078-0432.CCR-10-0356
Staal, F., Luis, T., & Tiemessen, M. (2008) WNT signalling in the immune system: WNT is spreading its wings. Nature Reviews Immunology, 8(8), 581-593. DOI: 10.1038/nri2360
Fleming HE, Janzen V, Lo Celso C, Guo J, Leahy KM, Kronenberg HM, & Scadden DT. (2008) Wnt signaling in the niche enforces hematopoietic stem cell quiescence and is necessary to preserve self-renewal in vivo. Cell stem cell, 2(3), 274-83. PMID: 18371452
An article was released online Monday in Environmental Health Perspectives which surprised me. For the last five or six years I’ve been enthusiastically extolling the evils of triclosan in the environment, but the connection with human immune dysfunction really caught me by surprise, most likely because I’m a microbiologist (this is probably not news to [...]... Read more »
Clayton, E., Todd, M., Dowd, J., & Aiello, A. (2010) The Impact of Bisphenol A and Triclosan on Immune Parameters in the US Population, NHANES 2003-2006. Environmental Health Perspectives. DOI: 10.1289/ehp.1002883
Pycke, B., Crabbe, A., Verstraete, W., & Leys, N. (2010) Characterization of Triclosan-Resistant Mutants Reveals Multiple Antimicrobial Resistance Mechanisms in Rhodospirillum rubrum S1H. Applied and Environmental Microbiology, 76(10), 3116-3123. DOI: 10.1128/AEM.02757-09
A surprising new model for studying muscle function was unveiled this week: the couch potato mouse. While these mice maintain normal activity and body weight, they don’t have the energy to exercise. In the December 1 issue of the journal Cell Metabolism, Dr. Daniel Kelly, Dr. Christoph Zechner and their colleagues report what happens when [...]... Read more »
Zechner C, Lai L, Zechner JF, Geng T, Yan Z, Rumsey JW, Collia D, Chen Z, Wozniak DF, Leone TC.... (2010) Total Skeletal Muscle PGC-1 Deficiency Uncouples Mitochondrial Derangements from Fiber Type Determination and Insulin Sensitivity. Cell metabolism, 12(6), 633-42. PMID: 21109195
Fossilized dinosaur tracks can be exceptionally informative traces of prehistoric life, but figuring out what dinosaur made a particular set of footprints can be tricky. Unless an animal literally dies in its tracks, the best we can do is to match the skeletal anatomy of dinosaur feet with the anatomical clues left in the impressions [...]... Read more »
Romilio, A., & Salisbury, S. (2010) A reassessment of large theropod dinosaur tracks from the mid-Cretaceous (late Albian–Cenomanian) Winton Formation of Lark Quarry, central-western Queensland, Australia: A case for mistaken identity. Cretaceous Research. DOI: 10.1016/j.cretres.2010.11.003
Yesterday I was out with my running group, and chatting with an acquaintance. She was saying that someone at her office had accused her of “eating her feelings” when she was stressed. Her: She accused me of eating my feelings! I’m kind of upset she would say that…so I had a cookie, and then a [...]... Read more »
Ulrich-Lai YM, Christiansen AM, Ostrander MM, Jones AA, Jones KR, Choi DC, Krause EG, Evanson NK, Furay AR, Davis JF.... (2010) Pleasurable behaviors reduce stress via brain reward pathways. Proceedings of the National Academy of Sciences of the United States of America, 107(47), 20529-34. PMID: 21059919
Quick! How many dots?
You can do that fast, right? You don’t even have to count.
In comparison, as fast as you can, how many dots?
That’s much trickier, isn’t it? Slower. You have to count.
The first, “at a glance” way of determining the number of things is called subitizing.
A new paper by Bisazza and colleagues takes a look at these abilities in guppies. Guppies, like many other fish, have a behaviour that is sensitive to numbers of things: joining a school of other fish. Bisa........ Read more »
Being able to see your unborn child is truly an amazing experience. Ultrasound (diagnostic sonography) is a common diagnostic tool for, among other things, imaging the foetus to determine its age, look for abnormalities and observe blood flow in the umbilical cord. But possibly its most memorable effect is seeing your baby's heart beat - and in 3D/4D ultrasounds, seeing your baby's face.
The term "ultrasound" applies to acoustic energy (sound) with a frequency above the audible range of human h........ Read more »
Kurjak, A., Miskovic, B., Andonotopo, W., Stanojevic, M., Azumendi, G., & Vrcic, H. (2007) How useful is 3D and 4D ultrasound in perinatal medicine?. Journal of Perinatal Medicine, 35(1), 10-27. DOI: 10.1515/JPM.2007.002
Carrera, J.M. (2006) Donald School Atlas of Clin. Application of Ultrasound in Obs/ Gyn. www.jaypeebrothers.com. DOI: 10.5005/jp/books/10226
Recently I featured a piece about how turtle hatchlings change their movement strategy several times in just the first few hours of life in order to suit their changing needs as they move across different types of sand. Well, to go from the sublime to the ridiculous (or rather, just from the really small to the truly gargantuan) there’s a new paper out that shows that whale sharks, too, adjust the way they move according to their needs. This new work follow........ Read more »
Gleiss, A., Norman, B., & Wilson, R. (2010) Moved by that sinking feeling: variable diving geometry underlies movement strategies in whale sharks. Functional Ecology. DOI: 10.1111/j.1365-2435.2010.01801.x
Brunnschweiler, J., Baensch, H., Pierce, S., & Sims, D. (2009) Deep-diving behaviour of a whale shark during long-distance movement in the western Indian Ocean . Journal of Fish Biology, 74(3), 706-714. DOI: 10.1111/j.1095-8649.2008.02155.x
The following post is what I wrote for the first 2-day essay in my developmental biology course. It covers the potential limitations of mathematical modeling in developmental biology – specfically, the reaction-diffusion systems of the computer scientist, Alan Turing. Perhaps the larger point I try to make is that ideas that are initially and blatantly [...]... Read more »
Kondo S, & Miura T. (2010) Reaction-diffusion model as a framework for understanding biological pattern formation. Science (New York, N.Y.), 329(5999), 1616-20. PMID: 20929839
Maini PK, Baker RE, & Chuong CM. (2006) Developmental biology. The Turing model comes of molecular age. Science (New York, N.Y.), 314(5804), 1397-8. PMID: 17138885
Madzvamuse A, Gaffney EA, & Maini PK. (2010) Stability analysis of non-autonomous reaction-diffusion systems: the effects of growing domains. Journal of mathematical biology, 61(1), 133-64. PMID: 19727733
Sick, S., Reinker, S., Timmer, J., & Schlake, T. (2006) WNT and DKK Determine Hair Follicle Spacing Through a Reaction-Diffusion Mechanism. Science, 314(5804), 1447-1450. DOI: 10.1126/science.1130088
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