Today’s tip is on Genomicus. Genomicus is a great tool to visualize gene duplication, synteny and genome evolution. The search and display interfaces are quite straightforward, and there are lots of great features (viewing ancestral gene information, links out to resources, different views of phylogenies, etc) in the tool. This video is only a short introduction. You can delve deeper into the tool with the help and documentation, including an 11 minute video.
There is also a recent (adva........ Read more »
Muffato, M., Louis, A., Poisnel, C., & Roest Crollius, H. (2010) Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes. Bioinformatics. DOI: 10.1093/bioinformatics/btq079
Electronic garbage in developing countries expected to increase
... Read more »
Yu, J. et al. (2010) Forecasting global generation of obsolete personal computers. Environmental Science , 2147483647. DOI: 10.1021/es903350q
This study has nothing to do with drugs, psychotherapy, or even neuroscience. It's about Jesus' head; more specifically, it's about Jesus' head in relation to the size of the main course in 52 different depictions of the Last Supper.I know what you're all thinking, it's barely past noon, and I've hit the scotch too hard this time. From the International Journal of Obesity:"Portion sizes of foods have been noticably increasing in recent years, but when did this trend begin? If art imitates l........ Read more »
B Wansink and C S Wansink. (2010) The largest Last Supper: depictions of food portions and plate size increased over the millennium. International Journal of Obesity. info:/
I am pleased to announce the publication in PLoS ONE of Seitaad ruessi, a new sauropodomorph dinosaur from the Lower Jurassic Navajo Sandstone of southern Utah. Sauropodomorphs are (mostly) herbivorous dinosaurs that lived from the Triassic all the way until the end of the Cretaceous. Although most people know the giant quadrupedal sauropodomorphs like Brachiosaurus and Apatosaurus ("Brontosaurus"), many of the early sauropodomorphs were bipeds smaller than humans. Seitaad fits in the latter cat........ Read more »
Sertich, J.J.W., & Loewen, M. (2010) A New Basal Sauropodomorph Dinosaur from the Lower Jurassic Navajo Sandstone of Southern Utah. PLoS ONE, 5(3). DOI: 10.1371/journal.pone.0009789
Much of the discussion of the age-related decline of the immune system that can be found in the Fight Aging! archives is focused on the adaptive immune system. But the innate immune system also becomes damaged and dysfunctional with age. Here is a quick summary of the functional difference between these two components of the immune system: The immune system protects organisms from infection with layered defenses of increasing specificity. Most simply, physical barriers prevent pathogens such as ........ Read more »
Hajishengallis G. (2010) Too Old to Fight? Aging and its Toll on Innate Immunity. Molecular oral microbiology, 25(1), 25-37. PMID: 20305805
This report is a systematic review of the evidence on Exercise for overweight or obesity. It's in the form of a Cochrane Report. The Cochrane Collaboration is an international, independent, not-for-profit organisation of over 27,000 contributors from more than 100 countries, dedicated to making up-to-date, accurate information about the effects of health care readily available worldwide. It is a thorough review of the evidence in the area of obesity and exercise and it........ Read more »
“What is heritage?” sounds like the kind of essay question a lecturer might set when they run out of inspiration. It depends where you ask it. In some places it’s a question that carries a sting for the unwary. In the UK it’s almost always old buildings. Sometimes it’s very old buildings, but we build [...]... Read more »
Morrison, M., McNaughton, D., & Shiner, J. (2010) Mission-Based Indigenous Production at the Weipa Presbyterian Mission, Western Cape York Peninsula (1932–66). International Journal of Historical Archaeology, 14(1), 86-111. DOI: 10.1007/s10761-009-0096-8
Figure 1: Zooky stole his bone.
I know that I wrote about dogs yesterday. I don’t usually like to focus too much on any one particular animal two days in a row. But. This paper was too cool to put off.
Different dog growls mean different things, right? Probably. But can you tell the difference?
Here’s a dog [...]... Read more »
Farago, T., Pongracz, P., Range, F., Viranyi, Z., & Miklosi, A. (2010) ‘The bone is mine’: affective and referential aspects of dog growls. Animal Behaviour, 917-925. info:/10.1016/j.anbehav.2010.01.005
A protein has several different levels of structure. The primary structure is the arrangements of atoms and bonds, and it is formed in the ribosome by the assembly of amino acids as directed by an RNA template. The secondary structure is the local topology, the helices and strands, and this forms mostly because of the release of energy through the formation of hydrogen bonds. The tertiary structure is the actual fold of the protein, the way helices, strands, and loops are arranged in space. The ........ Read more »
Babu, C., Hilser, V., & Wand, A. (2004) Direct access to the cooperative substructure of proteins and the protein ensemble via cold denaturation. Nature Structural , 11(4), 352-357. DOI: 10.1038/nsmb739
Shan, B., McClendon, S., Rospigliosi, C., Eliezer, D., & Raleigh, D. (2010) The Cold Denatured State of the C-terminal Domain of Protein L9 Is Compact and Contains Both Native and Non-native Structure. Journal of the American Chemical Society, 2147483647. DOI: 10.1021/ja908104s
Research team finds brain abnormalities.
When it came to babies born to crack-addicted mothers, the media went overboard, creating a crisis in the form of an epidemic that never quite was. By contrast, when it came to babies born to alcoholic mothers, Fetal Alcohol Syndrome went unrecognized in the science and medical community until 1968.
Now comes a study on prenatal methamphetamine exposure in The Journal of Neuroscience, headed up by Elizabeth Sowell of the University of California, Los ........ Read more »
Sowell, E., Leow, A., Bookheimer, S., Smith, L., O'Connor, M., Kan, E., Rosso, C., Houston, S., Dinov, I., & Thompson, P. (2010) Differentiating Prenatal Exposure to Methamphetamine and Alcohol versus Alcohol and Not Methamphetamine using Tensor-Based Brain Morphometry and Discriminant Analysis. Journal of Neuroscience, 30(11), 3876-3885. DOI: 10.1523/JNEUROSCI.4967-09.2010
Smith, L., LaGasse, L., Derauf, C., Grant, P., Shah, R., Arria, A., Huestis, M., Haning, W., Strauss, A., Grotta, S.... (2006) The Infant Development, Environment, and Lifestyle Study: Effects of Prenatal Methamphetamine Exposure, Polydrug Exposure, and Poverty on Intrauterine Growth. PEDIATRICS, 118(3), 1149-1156. DOI: 10.1542/peds.2005-2564
The NEJM just posted this entry that clearly shows that when clinicians report side effects of the drugs that their patient is taking, their reports don’t agree with what patients report. Interestingly, clinicians are doing the reporting of these side effects as part of their participation in clinical trials, and the clinical trials are almost [...]... Read more »
Basch, E. (2010) The Missing Voice of Patients in Drug-Safety Reporting. New England Journal of Medicine, 362(10), 865-869. DOI: 10.1056/NEJMp0911494
Ren'an Wu, Hanfa Zou (Chinese Academy of Sciences), and coworkers have used carbon nanotubes to kill the cancer cells that commonly linger after chemotherapy, which are a major threat to successful treatment. This news feature was written on March 23, 2010.... Read more »
Li, R., Wu, R., Zhao, L., Wu, M., Yang, L., & Zou, H. (2010) P-Glycoprotein Antibody Functionalized Carbon Nanotube Overcomes the Multidrug Resistance of Human Leukemia Cells. ACS Nano, 4(3), 1399-1408. DOI: 10.1021/nn9011225
I can’t remember a time when people working in health were told ‘Go and spend as much as you like to help people get well’ – in fact, in over 20 years I can only recall being told ‘there is less money in the kitty, we need to look for efficiencies, tighten your belts’!
So it’s [...]... Read more »
Lamb, S., Hansen, Z., Lall, R., Castelnuovo, E., Withers, E., Nichols, V., Potter, R., & Underwood, M. (2010) Group cognitive behavioural treatment for low-back pain in primary care: a randomised controlled trial and cost-effectiveness analysis. The Lancet, 375(9718), 916-923. DOI: 10.1016/s0140-6736(09)62164-4
Allcock N, Elkan R, & Williams J. (2007) Patients referred to a pain management clinic: beliefs, expectations and priorities. Journal of advanced nursing, 60(3), 248-56. PMID: 17908123
Gene sequences evolve at different rates due to different constraints, either due to chromosome position, functional constraint, and status as a single-copy or multi-copy gene. In a recent paper, Allen Rodrigo (the new NESCent director by the, way, congrats!) the authors hypothesize that correlation in branch lengths of gene trees suggest they operate in the [...]... Read more »
Li WL, & Rodrigo AG. (2009) Covariation of branch lengths in phylogenies of functionally related genes. PloS one, 4(12). PMID: 20041191
Click to enlarge images
ARTISTS employ a number of different techniques to represent implied motion in two-dimensional works. One of these, commonly used in posters, comics and animation, is the affine shear effect, whereby a moving object is depicted as leaning into the direction of movement. Cartoonists also use action lines to depict movement and speed, with straight lines conveying fast movements and wavy lines conveying slower ones. Motion can also be conveyed by superimposing several imag........ Read more »
Osaka, N., Matsuyoshi, D., Ikeda, T., & Osaka, M. (2010) Implied motion because of instability in Hokusai Manga activates the human motion-sensitive extrastriate visual cortex: an fMRI study of the impact of visual art. NeuroReport, 21(4), 264-267. DOI: 10.1097/WNR.0b013e328335b371
Bhut jolokia is now confirmed to be the world’s spiciest chili and is being used to create natural, nontoxic weapons.... Read more »
Liu Y, & Nair MG. (2010) Capsaicinoids in the hottest pepper Bhut Jolokia and its antioxidant and antiinflammatory activities. Natural product communications, 5(1), 91-4. PMID: 20184029
A comparison of three-dimensional scans of hominin footprints. Top) A footprint made by an experimental subject using a normal, "extended" gait. Middle) A footprint made by an experimental subject using a "bent-knee, bent-hip" gait. Bottom) A Laetoli footprints. From Raichlen et al., 2010.
About 3.6 million years ago, at a spot now in Laetoli, Tanzania, a pair of hominins trudged through the ashfall dumped onto the landscape by a nearby volcano. We don't know for certain what they looked l........ Read more »
Raichlen, D., Gordon, A., Harcourt-Smith, W., Foster, A., & Haas, W. (2010) Laetoli Footprints Preserve Earliest Direct Evidence of Human-Like Bipedal Biomechanics. PLoS ONE, 5(3). DOI: 10.1371/journal.pone.0009769
0Last year was the year of the acai berry. Mangosteen, noni, goji, and others also proliferate on the juice and supplement market. Some are predicting what will be next. Are these so called “superfruits” any better than “regular” fruit?
Let’s look at a few lines of evidence.
What makes a fruit “super”?
First of all, we have to [...]... Read more »
Prior RL, & Cao G. (1999) In vivo total antioxidant capacity: comparison of different analytical methods. Free radical biology , 27(11-12), 1173-81. PMID: 10641708
Seeram NP, Aviram M, Zhang Y, Henning SM, Feng L, Dreher M, & Heber D. (2008) Comparison of antioxidant potency of commonly consumed polyphenol-rich beverages in the United States. Journal of agricultural and food chemistry, 56(4), 1415-22. PMID: 18220345
Stem cells are a little like teenagers, full of potential but not sure what they’re going to be when they grow up. It’s that uncertain destiny that makes stem cells so exciting to scientists and physicians, who hope to someday use them for everything from spinal cord repair to organ regeneration. But corralling the uncertain [...]... Read more »
Kilian, K., Bugarija, B., Lahn, B., & Mrksich, M. (2010) Geometric cues for directing the differentiation of mesenchymal stem cells. Proceedings of the National Academy of Sciences, 107(11), 4872-4877. DOI: 10.1073/pnas.0903269107
The first time I heard someone discuss using shock collars as a control technique for wild wolves, I thought it must be a really bad joke. Only, it wasn’t. It fell squarely under the heading of “aversive conditioning” a school of thought aimed at devising ways to keep wolves where we humans want them to [...]... Read more »
Hawley, J., Gehring, T., Schultz, R., Rossler, S., & Wydeven, A. (2009) Assessment of Shock Collars as Nonlethal Management for Wolves in Wisconsin. Journal of Wildlife Management, 73(4), 518-525. DOI: 10.2193/2007-066
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