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  • July 7, 2016
  • 09:09 AM
  • 591 views

Are animals (and AI’s) people too?

by gdw in FictionalFieldwork

Charles gets up and balances on his short legs. During the brief ungainly walk to the dais, he fights the urge to scratch his arms. The vest that has been tailor-made for him itches. But it will help focus the committee on his purpose, focus on him as a person. He squats on the low […]... Read more »

Perring C. (1997) Degrees of personhood. The Journal of medicine and philosophy, 22(2), 173-97. PMID: 9186928  

Windrem MS, Schanz SJ, Morrow C, Munir J, Chandler-Militello D, Wang S, & Goldman SA. (2014) A competitive advantage by neonatally engrafted human glial progenitors yields mice whose brains are chimeric for human glia. The Journal of neuroscience : the official journal of the Society for Neuroscience, 34(48), 16153-61. PMID: 25429155  

  • June 29, 2016
  • 06:20 AM
  • 469 views

Birdsong Babel: Different birds use different grammar rules

by gdw in FictionalFieldwork

Zizou listens carefully. She ignores her confines and tries to focus on the intruder’s song. There’s something odd about it. Something she can’t quite put her feather on. It’s familiar, yet… not familiar. The intruder is strong. He or she keeps signing incessantly. There’s no sight of him or her, though. She has to make a […]... Read more »

Olkowicz S, Kocourek M, Lučan RK, Porteš M, Fitch WT, Herculano-Houzel S, & Němec P. (2016) Birds have primate-like numbers of neurons in the forebrain. PNAS, 113(26), 7255-60. PMID: 27298365  

Spierings, M., & ten Cate, C. (2016) Budgerigars and zebra finches differ in how they generalize in an artificial grammar learning experiment. Proceedings of the National Academy of Sciences, 113(27). DOI: 10.1073/pnas.1600483113  

  • June 15, 2016
  • 08:05 AM
  • 524 views

Tricky Little Buggers

by Mark Lasbury in As Many Exceptions As Rules

Evolution brings wisdom with age – and bacteria are ancient. Bacteria have evolved defenses ranging from evasion or inhibition of immune systems to protecting crucial functions from environmental injury. New studies have identified spring-loaded spikes that can be assembled and disassembled for puncturing other bacteria and delivering toxins, while other work is focused on using those same toxins to kill antibiotic resistant organisms, with E. coli have been engineered to produce toxins ag........ Read more »

Basler, M., Pilhofer, M., Henderson, G., Jensen, G., & Mekalanos, J. (2012) Type VI secretion requires a dynamic contractile phage tail-like structure. Nature, 483(7388), 182-186. DOI: 10.1038/nature10846  

Saeidi, N., Wong, C., Lo, T., Nguyen, H., Ling, H., Leong, S., Poh, C., & Chang, M. (2011) Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen. Molecular Systems Biology. DOI: 10.1038/msb.2011.55  

  • April 13, 2016
  • 07:10 AM
  • 688 views

Ivy League Climber

by Mark Lasbury in As Many Exceptions As Rules

English ivy doesn’t send out entwining tendrils, it doesn’t burrow into cracks as an anchor. It doesn’t have hooked thorns like a climbing rose – no, English ivy can grow up the side of Wrigley Field because its millions of adventitious roots secrete the strongest glue in the world. However, it doesn’t work like most glues – it works like a gecko’s feet. Oh, and it will help protect you from skin cancer too!... Read more »

Lijin Xia, Scott C Lenaghan, Mingjun Zhang, Zhili Zhang and Quanshui Li. (2010) Naturally occurring nanoparticles from English ivy: an alternative to metal-based nanoparticles for UV protection. Journal of Nanbiotechnology. DOI: 10.1186/1477-3155-8-12  

  • March 23, 2016
  • 07:25 AM
  • 813 views

Leaves Suck!

by Mark Lasbury in As Many Exceptions As Rules

People need the power of an elevator or our legs to rise high in a building, so how does water get from the roots of a tree to the very top leaves? Hint, it isn’t capillary action – even capillary tubes can move water only a few centimeters. The key is evaporation. But if water evaporates off plants, how do they survive during droughts? They have tricks to retain water, including developing big leaves and little leaves. Look carefully at some trees, you’ll find that they have t........ Read more »

von Caemmerer, S., & Baker, N. (2006) The Biology of Transpiration. From Guard Cells to Globe. PLANT PHYSIOLOGY, 143(1), 3-3. DOI: 10.1104/pp.104.900213  

Terashima, I. (2005) Irradiance and phenotype: comparative eco-development of sun and shade leaves in relation to photosynthetic CO2 diffusion. Journal of Experimental Botany, 57(2), 343-354. DOI: 10.1093/jxb/erj014  

  • March 16, 2016
  • 06:45 AM
  • 702 views

How Fast Is Fast

by Mark Lasbury in As Many Exceptions As Rules

What’s the fastest organism in the world? The cheetah s fast on land, and the white throated needle tail is fast in the air, but there are bacteria faster than these animals. It all depends on how you measure speed. The fastest? A beetle from down under – it’s confirmed by science!... Read more »

Penny E. Hudson, Sandra A. Corr and Alan M. Wilson. (2012) High speed galloping in the cheetah (Acinonyx jubatus) and the racing greyhound (Canis familiaris): spatio-temporal and kinetic characteristics. J Exp Biol. DOI: 10.1242/​jeb.066720  

Wilson RP, Griffiths IW, Mills MG, Carbone C, Wilson JW, & Scantlebury DM. (2015) Mass enhances speed but diminishes turn capacity in terrestrial pursuit predators. eLife. PMID: 26252515  

  • March 6, 2016
  • 11:51 PM
  • 569 views

From evolutionary morphology to Godzilla

by adam phillips in It Ain't Magic

I recently spoke with Chief Scientist Shigeru Kuratani about evolutionary morphology, sci-fi monsters, the genius of Alien, and more.... Read more »

Sugahara, F., Pascual-Anaya, J., Oisi, Y., Kuraku, S., Aota, S., Adachi, N., Takagi, W., Hirai, T., Sato, N., Murakami, Y.... (2016) Evidence from cyclostomes for complex regionalization of the ancestral vertebrate brain. Nature, 531(7592), 97-100. DOI: 10.1038/nature16518  

  • February 2, 2016
  • 05:14 AM
  • 420 views

Computational Tools from Biophysical Journal

by ragothamanyennamalli in Getting to know Structural Bioinformatics

Biophysical Journal has created a collection of papers that describe tools and software that can be routinely used in biological research. Editor Prof. Leslie Loew mentions that the full-text of articles in this collection will be freely available until February 25, 2016.... Read more »

Qi Y, Cheng X, Lee J, Vermaas JV, Pogorelov TV, Tajkhorshid E, Park S, Klauda JB, & Im W. (2015) CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model. Biophysical journal, 109(10), 2012-22. PMID: 26588561  

McGibbon RT, Beauchamp KA, Harrigan MP, Klein C, Swails JM, Hernández CX, Schwantes CR, Wang LP, Lane TJ, & Pande VS. (2015) MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories. Biophysical journal, 109(8), 1528-32. PMID: 26488642  

Ribeiro AA, & Ortiz V. (2015) MDN: A Web Portal for Network Analysis of Molecular Dynamics Simulations. Biophysical journal, 109(6), 1110-6. PMID: 26143656  

Hertig S, Goddard TD, Johnson GT, & Ferrin TE. (2015) Multidomain Assembler (MDA) Generates Models of Large Multidomain Proteins. Biophysical journal, 108(9), 2097-102. PMID: 25954868  

Leonarski F, & Trylska J. (2015) RedMDStream: Parameterization and Simulation Toolbox for Coarse-Grained Molecular Dynamics Models. Biophysical journal, 108(8), 1843-7. PMID: 25902423  

de Vries SJ, Schindler CE, Chauvot de Beauchêne I, & Zacharias M. (2015) A web interface for easy flexible protein-protein docking with ATTRACT. Biophysical journal, 108(3), 462-5. PMID: 25650913  

Biedermann J, Ullrich A, Schöneberg J, & Noé F. (2015) ReaDDyMM: Fast interacting particle reaction-diffusion simulations using graphical processing units. Biophysical journal, 108(3), 457-61. PMID: 25650912  

Holmes WR, Mata MA, & Edelstein-Keshet L. (2015) Local perturbation analysis: a computational tool for biophysical reaction-diffusion models. Biophysical journal, 108(2), 230-6. PMID: 25606671  

  • January 28, 2016
  • 09:29 AM
  • 526 views

Help me, neighbor!

by ragothamanyennamalli in Getting to know Structural Bioinformatics

We all have neighbors who help us in our hour of need. Some go out of the way as well. In enzymes too, it seems, that neighbors play a crucial role. Lafond et al in their recent publication in the Journal of Biological Chemistry report the invovlement of neighboring chains of the same enzyme, lichenase. Apart from the role of stabilizing the quarternary structure (a trimer), they are also invovled in the enzymatic activity.... Read more »

Lafond M, Sulzenbacher G, Freyd T, Henrissat B, Berrin JG, & Garron ML. (2016) the quaternary structure of a glycoside hydrolase dictates specificity towards beta-glucans. The Journal of biological chemistry. PMID: 26755730  

  • December 29, 2015
  • 05:02 AM
  • 613 views

Mosquitoes like it hot!

by ragothamanyennamalli in Getting to know Structural Bioinformatics

We all know how pesky mosquitoes can be. Did you know that the ability of a mosquito to find a suitable host to feed is due to thermotaxis? This behavior, being attracted/repelled due to high/low temperature, is seen in other organisms as well such as Drosophila melanogaster and Caenorhabditis elegans. ... Read more »

Corfas RA, & Vosshall LB. (2015) The cation channel TRPA1 tunes mosquito thermotaxis to host temperatures. eLife. PMID: 26670734  

  • December 21, 2015
  • 07:45 AM
  • 828 views

Music of the Macromolecules

by Shane Caldwell in Helical Translations

A molecule is like an instrument in an orchestra. Find out about the symphony inside your own cells.... Read more »

C. Wilson, R. V. Agafonov, M. Hoemberger, S. Kutter, A. Zorba, J. Halpin, V. Buosi, R. Otten, D. Waterman, D. L. Theobald, D. Kern. (2015) Using ancient protein kinases to unravel a modern cancer drug’s mechanism. Science, 882-886. info:/10.1126/science.aaa1823

  • December 10, 2015
  • 11:52 PM
  • 757 views

Alternate conformations

by ragothamanyennamalli in Getting to know Structural Bioinformatics

In the 90s morphing of two unrelated images was popular and mostly it was used for entertainment purposes. For example: the famous video of Michael Jackson’s pop hit “Black or White”.... Read more »

Narunsky A, Nepomnyachiy S, Ashkenazy H, Kolodny R, & Ben-Tal N. (2015) ConTemplate Suggests Possible Alternative Conformations for a Query Protein of Known Structure. Structure (London, England : 1993), 23(11), 2162-70. PMID: 26455800  

  • November 27, 2015
  • 09:28 AM
  • 548 views

Designer proteins helping biomedicine

by ragothamanyennamalli in Getting to know Structural Bioinformatics

Professor Meiering and her colleagues were able to incorporate both structure and function into the design process by using bioinformatics to leverage information from nature. They then analyzed what they made and measured how long it took for the folded, functional protein to unfold and breakdown... Read more »

Broom A, Ma SM, Xia K, Rafalia H, Trainor K, Colón W, Gosavi S, & Meiering EM. (2015) Designed protein reveals structural determinants of extreme kinetic stability. Proceedings of the National Academy of Sciences of the United States of America, 112(47), 14605-10. PMID: 26554002  

  • October 16, 2015
  • 06:28 AM
  • 562 views

Mutations that identify Thermostability

by ragothamanyennamalli in Getting to know Structural Bioinformatics

In protein engineering studies, mutating a residue to increase thermostability without affecting the activity of the protein/enzyme is a major consideration for researchers. The laborious method is list the number of possible mutations and then finding out the stability and activity for each mutant, one after another.... Read more »

Mancusso R, Karpowich NK, Czyzewski BK, & Wang DN. (2011) Simple screening method for improving membrane protein thermostability. Methods (San Diego, Calif.), 55(4), 324-9. PMID: 21840396  

Sauer DB, Karpowich NK, Song JM, & Wang DN. (2015) Rapid Bioinformatic Identification of Thermostabilizing Mutations. Biophysical journal, 109(7), 1420-8. PMID: 26445442  

  • September 23, 2015
  • 07:39 AM
  • 594 views

What about Lignin?

by ragothamanyennamalli in Getting to know Structural Bioinformatics

Biofuel prodcution involves removing Lignin from the biomass, in fact efficient removal so that Lignin and its by-products do not inhibit the enzymatic process that follows. But, what happens to the Lignin? ... Read more »

Bourzac, K. (2015) Inner Workings: Paving with plants. Proceedings of the National Academy of Sciences, 112(38), 11743-11744. DOI: 10.1073/pnas.1509010112  

  • September 17, 2015
  • 07:30 AM
  • 1,023 views

A Tuberculosis Enzyme Decapitates Vital Energy Molecules to Kill Cells

by Shane Caldwell in Helical Translations

UAB researchers determine how M. tb kills immune cells with an enzyme toxin... Read more »

Sun, J., Siroy, A., Lokareddy, R., Speer, A., Doornbos, K., Cingolani, G., & Niederweis, M. (2015) The tuberculosis necrotizing toxin kills macrophages by hydrolyzing NAD. Nature Structural , 22(9), 672-678. DOI: 10.1038/nsmb.3064  

  • August 21, 2015
  • 09:00 AM
  • 529 views

TDP-43 differentially splices FNIP1

by Joana Guedes in BHD Research Blog

Folliculin interaction protein 1 (FNIP1), through interactions with FLCN, plays a role in a range of cellular processes (Baba et al., 2006). Alternative splicing of FNIP1, under the control of MBNL1, was previously reported in late mesenchymal differentiation (Venables et al., 2013). New research from De Conti et al., (2015) has identified FNIP1 as also being differentially spliced by TDP-43 – a protein associated with neurodegeneration in ALS and fronto-temporal dementia (Neumann et al., ........ Read more »

De Conti L, Akinyi MV, Mendoza-Maldonado R, Romano M, Baralle M, & Buratti E. (2015) TDP-43 affects splicing profiles and isoform production of genes involved in the apoptotic and mitotic cellular pathways. Nucleic acids research. PMID: 26261209  

  • August 20, 2015
  • 02:09 PM
  • 959 views

Falling with Style: Controlled Gliding in Spiders

by Melissa Chernick in Science Storiented

Sometimes I read a paper because the methods catch my eye. I can just imagine some scientists sitting around a table with a beer and saying, “I wonder what would happen if we just dropped a bunch of spiders from the tops of trees.” An article published online yesterday did just that.Barro Colorado Island is a man-made island is located in Gatun Lake, created by filling of the Panama Canal. It is covered in tropical rainforests, and its inhabitants have been studied extensively. It would be a........ Read more »

Stephen P. Yanoviak, Yonatan Munk, & Robert Dudley. (2015) Arachnid aloft: directed aerial descent in neotropical canopy spiders. J. R. Soc. Interface. info:/10.1098/rsif.2015.0534

  • June 10, 2015
  • 08:00 AM
  • 1,001 views

Everybody Is Just A Little Twisted

by Mark Lasbury in As Many Exceptions As Rules

You may have your head on straight, but your brain is still twisted. Everyone’s is. The symmetry of the brain is not absolute and the two halves are shaped differently, this results in your brain torquing (not twerking) inside your skull. The reasons are many, but one is gender: boy brains and girl brains really are different!... Read more »

Maller, J., Anderson, R., Thomson, R., Rosenfeld, J., Daskalakis, Z., & Fitzgerald, P. (2015) Occipital bending (Yakovlevian torque) in bipolar depression. Psychiatry Research: Neuroimaging, 231(1), 8-14. DOI: 10.1016/j.pscychresns.2014.11.008  

Maller, J., Thomson, R., Rosenfeld, J., Anderson, R., Daskalakis, Z., & Fitzgerald, P. (2014) Occipital bending in depression. Brain, 137(6), 1830-1837. DOI: 10.1093/brain/awu072  

Mock, J., Zadina, J., Corey, D., Cohen, J., Lemen, L., & Foundas, A. (2012) Atypical Brain Torque in Boys With Developmental Stuttering. Developmental Neuropsychology, 37(5), 434-452. DOI: 10.1080/87565641.2012.661816  

Savic, I. (2014) Asymmetry of cerebral gray and white matter and structural volumes in relation to sex hormones and chromosomes. Frontiers in Neuroscience. DOI: 10.3389/fnins.2014.00329  

Witelson, S., Kigar, D., & Harvey, T. (1999) The exceptional brain of Albert Einstein. The Lancet, 353(9170), 2149-2153. DOI: 10.1016/S0140-6736(98)10327-6  

  • March 18, 2015
  • 08:00 AM
  • 1,097 views

The Search For The Unicorn - Slightly Off Center

by Mark Lasbury in As Many Exceptions As Rules

One of the most amazing animals is one of the least often seen. It has one tooth that grows into a tusk that’s off center. The tusk is basically inside out, with the inside of the tooth exposed to the world. This animal also has the world’s only spiraled tooth, for strength and because that’s what keeps it growing straight. Finally, this animal spends an amazing amount of time on its back. Why do we care about these animal…..because they are so awesome!... Read more »

Christen AG, & Christen JA. (2011) The unicorn and the narwhal: a tale of the tooth. Journal of the history of dentistry, 59(3), 135-42. PMID: 22372187  

Kingsley, M., & Ramsay, M. (1988) The Spiral in the Tusk of the Narwhal. ARCTIC, 41(3). DOI: 10.14430/arctic1723  

Nweeia, M., Eichmiller, F., Hauschka, P., Donahue, G., Orr, J., Ferguson, S., Watt, C., Mead, J., Potter, C., Dietz, R.... (2014) Sensory ability in the narwhal tooth organ system. The Anatomical Record, 297(4), 599-617. DOI: 10.1002/ar.22886  

Dietz, R., Shapiro, A., Bakhtiari, M., Orr, J., Tyack, P., Richard, P., Eskesen, I., & Marshall, G. (2007) Upside-down swimming behaviour of free-ranging narwhals. BMC Ecology, 7(1), 14. DOI: 10.1186/1472-6785-7-14  

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