Birds adapt to deforestation by growing pointier wings
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Accurate variant detection in massively parallel sequencing data is a significant bioinformatics challenge. Not only do new sequencers offer unprecedented breadth (whole genome) and depth (30x or more), but they suffer coverage biases and error rates that make variant calling difficult. Last year, we published VarScan, our in-house algorithm for SNP and indel detection on [...]... Read more »
Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, & Ding L. (2009) VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics (Oxford, England), 25(17), 2283-5. PMID: 19542151
"The beauty and mystery of life extends down to the molecular level. The more we see, the more we can appreciate the wonder of our own nature."Prof Arthur Olson, Scripps Institute Every now and then, something lands in my Google...... Read more »
Observation of reproductive isolation in finches. The road to speciation?... Read more »
Grant, P., & Grant, B. (2009) Inaugural Article: The secondary contact phase of allopatric speciation in Darwin's finches. Proceedings of the National Academy of Sciences, 106(48), 20141-20148. DOI: 10.1073/pnas.0911761106
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The sensory abilities of vertebrates and invertebrates are generally more similar than they are different: both groups can detect light, sound, pressure, and so on. One of the few cases of a sensory ability that seemed to be the domain of vertebrates alone was the ability to detect electrical signals: electroreception. Several fish have it, and use electrical signals to communicate. Platypus have it. Electroreception in fish is one of the best examples of
For a long time, people argued that in........ Read more »
Unlikely cousins? Tinamou from brunorigin @ flickr (CC BY-SA 2.0| Moa from PLoS Biology
New Zealanders often think of our unique biota as a sort of time capsule - a glimpse at lifeforms that have long since been extinguished in other parts of the world. New Zealand has been apart from the rest of the world for 85 million years. At that time the land that makes up our mini-continent split from the super-continent Gondwana, opening up the Tasman Sea and moving northward . A land apart fr........ Read more »
Phillips, M., Gibb, G., Crimp, E., & Penny, D. (2009) Tinamous and Moa Flock Together: Mitochondrial Genome Sequence Analysis Reveals Independent Losses of Flight among Ratites. Systematic Biology, 59(1), 90-107. DOI: 10.1093/sysbio/syp079
New research published in the Journal of Experimental Biology sheds light onto visual stimuli processing in arthropods. Researchers (Avargues-Weber et al., 2010) have shown that honeybees, Apis mellifera, are capable of complex visual processing and learning tasks that are commonly reserved for primates. With a small fraction of mammalian neural complexity, honeybees are [...]... Read more »
Avargues-Weber, A., Portelli, G., Benard, J., Dyer, A., & Giurfa, M. (2010) Configural processing enables discrimination and categorization of face-like stimuli in honeybees. Journal of Experimental Biology, 213(4), 593-601. DOI: 10.1242/jeb.039263
In 2008, Shozu Yokoyama et al. published a compelling paper in which they reconstructed ancestral rhodopsin proteins in order to infer specific amino acid changes that explain phenotypic differences in vertebrate dim-light vision. In doing so, the authors shed light (pun intended) on the aquatic habitat of vertebrate ancestors. Sean Carroll commented (in his book “Making of the Fittest”) that Yokoyama’s work is “the deepest body of knowledge [to date] linking differences in specific gene........ Read more »
Yokoyama S, Tada T, Zhang H, & Britt L. (2008) Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates. Proceedings of the National Academy of Sciences of the United States of America, 105(36), 13480-5. PMID: 18768804
Neural stem/progenitor cells have been co-grafted with growth factors into damaged spinal cord tissue. Prior to this, the tissue was infused with an enzyme that not only reduces chondroitin sulfate proteoglycans, which appear in the CNS following damage, but also increases the survival of the neural stem cells. The article can be found in this week's Journal of Neuroscience... Read more »
Soheila Karimi-Abdolrezaee, Eftekhar Eftekharpour, Jian Wang, Desiree Schut, and Michael G. Fehlings. (2010) Synergistic Effects of Transplanted Adult Neural Stem/Progenitor Cells, Chondroitinase, and Growth Factors Promote Functional Repair and Plasticity of the Chronically Injured Spinal Cord. Journal of Neuroscience. info:/10.1523/JNEUROSCI.3111-09.2010
The evolution of negative interactions seems like a logical consequence of natural selection. Organisms compete for resources or view one another as a resource, thus finding ways to more efficiently find and consume prey. However, to me, the natural selection of symbiotic or mutualistic interactions has never seemed as straight forward (expect maybe the case where one species provides protection for the other, such as in ant-plant mutualisms). A specific example is the rise of nitrogen-fixing pl........ Read more »
Marchetti, M., Capela, D., Glew, M., Cruveiller, S., Chane-Woon-Ming, B., Gris, C., Timmers, T., Poinsot, V., Gilbert, L., Heeb, P.... (2010) Experimental Evolution of a Plant Pathogen into a Legume Symbiont. PLoS Biology, 8(1). DOI: 10.1371/journal.pbio.1000280
If you wend your way back through the Fight Aging! archives, you'll find a lot of material on mitochondria, mitochondrial DNA, and how accumulated damage to mitochondrial DNA contributes greatly to aging. The short version is this: Mitochondria are the cell's power plants, important in the operation of metabolism, central to the mechanisms by which metabolism determines life span, and implicated as the culprit in many age-related diseases. As described in the mitochondrial free radical theory of........ Read more »
Dani MA, & Dani SU. (2010) Improving upon nature's somatic mitochondrial DNA therapies. Medical hypotheses. PMID: 20116178
Today in our journal club we have discussed the latest paper from Sabeti’s lab:
Grossman, S., Shylakhter, I., Karlsson, E., Byrne, E., Morales, S., Frieden, G., Hostetter, E., Angelino, E., Garber, M., Zuk, O., Lander, E., Schaffner, S., & Sabeti, P. (2010). A Composite of Multiple Signals Distinguishes Causal Variants in Regions of Positive Selection Science [...]
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Grossman, S., Shylakhter, I., Karlsson, E., Byrne, E., Morales, S., Frieden, G., Hostetter, E., Angelino, E., Garber, M., Zuk, O.... (2010) A Composite of Multiple Signals Distinguishes Causal Variants in Regions of Positive Selection. Science. DOI: 10.1126/science.1183863
This post contributed by Nadine Lymn, ESA Director of Public Affairs
Personality traits that lead an individual to want to avoid crowds could actually be playing a role in biological invasions, says a recent study that appeared in the Proceedings of the Royal Society Biological Sciences. Julien Cote and colleagues at the University of California at [...]
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Cote, J., Fogarty, S., Weinersmith, K., Brodin, T., & Sih, A. (2010) Personality traits and dispersal tendency in the invasive mosquitofish (Gambusia affinis). Proceedings of the Royal Society B: Biological Sciences. DOI: 10.1098/rspb.2009.2128
Yes, years after I left the lab, I published a scientific paper. How did that happen?
Back in 2000, I published a paper on the way circadian clock controls the time of day when the eggs are laid in Japanese quail. Several years later, I wrote a blog post about that paper, trying to explain in lay terms what I did, why I did it, what I found, and how it fits into the broader context of this line of research. The paper was a physiology paper, and my blog post also focused on the physiological asp........ Read more »
Cooper, C., Voss, M., & Zivkovic, B. (2009) Extended Laying Interval of Ultimate Eggs of the Eastern Bluebird. The Condor, 111(4), 752-755. DOI: 10.1525/cond.2009.090061
This is a picture of a small cyanobacteria under red light:And this is a picture of exactly the same organism under blue-green light:Some cyanobacteria (both freshwater, marine and soil varieties) have the ability to change their colour depending out external conditions. The reason they do this is because they photosynthesise and therefore require light for energy. The light is harvested by the bacteria using special protein complexes called phycobilisomes which contain (among other things) two ........ Read more »
Kehoe, D., & Gutu, A. (2006) RESPONDING TO COLOR: The Regulation of Complementary Chromatic Adaptation. Annual Review of Plant Biology, 57(1), 127-150. DOI: 10.1146/annurev.arplant.57.032905.105215
Eureka has come out with a list of the 30 best science blogs, including greats like Not Exactly Rocket Science and Neurotopia. Congrats! Everyone should go check out the top 30!
While you're at it, though, be sure to tell Eureka YOUR favorites - they're looking for a top 100, and they want to know which ones they missed. Just send an e-mail to eureka [at] thetimes [dot] co [dot] uk with "Best Blogs" in the subject to submit observations of a nerd your picks for the best science blogs not on tha........ Read more »
Larval eel jaw diversity from Michael Miller 2009 ASMB 2(4): 1-94.
There are all sort of eels in this world. Big ones, small ones, gulper eels, morays. But the most tastiest are the Japanese freshwater eel. Nothing says Ohayo Gozaimasu like fresh eel sushi topped with a mountain of pickled ginger and lightly spackled with sweet [...]... Read more »
In recent surveys, researchers have shown that the number of individual pandas has increased due to conservation efforts in the country, but the populations remain disparate. A recent study published in the Journal of Biogeography takes a look at how exactly these pandas are distributed in the forests of Southwest China, in relation to the level of fragmentation.... Read more »
Wang, T., Ye, X., Skidmore, A., & Toxopeus, A. (2010) Characterizing the spatial distribution of giant pandas ( ) in fragmented forest landscapes . Journal of Biogeography. DOI: 10.1111/j.1365-2699.2009.02259.x
A restoration of Titanoboa (foreground) and Cerrejonisuchus improcerus (background, left) in their natural setting. (By Jason Bourque, image from Wikipedia.)
When I was growing up I used to spend hours poring over the Time/Life series of nature books in my little library, absolutely enthralled by images of strange creatures from all over the world, but one photograph was particularly arresting. A grainy black-and-white double-page spread showed an anaconda that had wrapped its crushing coi........ Read more »
Alexander K. Hastings; Jonathan I. Bloch; Edwin A. Cadena; Carlos A. Jaramillo. (2010) A new small short-snouted dyrosaurid (Crocodylomorpha, Mesoeucrocodylia) from the Paleocene of northeastern Colombia. Journal of Verterbrate Paleontology, 30(1), 139-162. info:/10.1080/02724630903409204
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