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  • May 8, 2017
  • 05:45 PM
  • 202 views

Let those who never smelled bad cast the first stone

by Aurametrix team in Aurametrix Blog

Analysis of our metabolism is crucial to comprehending the responses of our genes and microbes to the stresses of daily life, and to elucidating the causes and consequences of health and disease. And measurement of urinary metabolites - small molecules produced from foods, drinks, drugs, environmental contaminants, bodily waste products and bacterial by-products - is key to the analysis. We applied this approach to an elusive condition that has always evaded diagnosis: s........ Read more »

Bouatra, S., Aziat, F., Mandal, R., Guo, A., Wilson, M., Knox, C., Bjorndahl, T., Krishnamurthy, R., Saleem, F., Liu, P.... (2013) The Human Urine Metabolome. PLoS ONE, 8(9). DOI: 10.1371/journal.pone.0073076  

Irene S. Gabashvili. (2017) Raw Data from Clinical Trial NCT02692495. Mendeley Data. info:/DOI: 10.17632/8bk6h6bmkr.1

  • April 12, 2017
  • 10:59 AM
  • 309 views

Flyfocals: Vision and Vectors Help Hunting Robber Flies

by Melissa Chernick in Science Storiented

Image credit: Thomas ShahanRobber flies (Asilidae family) are not your typical house flies. They are small, predatory insects that feed on a vast array of other arthropods. While they are small in size (10 times smaller than a dragonfly), these guys are serious hunters. For example, Mallophora omboides is known as the “Florida bee killer” for its taste for honey bees. Other robber flies hunt down wasps, dragonflies, spiders, or grasshoppers, just to name a few. Perhaps almost as impressive a........ Read more »

Wardill, T., Fabian, S., Pettigrew, A., Stavenga, D., Nordström, K., & Gonzalez-Bellido, P. (2017) A Novel Interception Strategy in a Miniature Robber Fly with Extreme Visual Acuity. Current Biology, 27(6), 854-859. DOI: 10.1016/j.cub.2017.01.050  

  • April 4, 2017
  • 12:49 AM
  • 248 views

A clue towards understanding intrinsically disordered proteins

by ragothamanyennamalli in Getting to know Structural Bioinformatics

ntrinsically disordered proteins are thought to be fully functional, yet do not confirm to a single conformation, thereby identifying their structure via crystallography becomes problematic. Many intrinsically disordered proteins have been studied and analyzed using NMR methods, however the question as to why proteins are intrinsically disordered is still debatable.... Read more »

  • March 3, 2017
  • 11:05 PM
  • 251 views

All-Atom Molecular Dynamics Simulations

by ragothamanyennamalli in Getting to know Structural Bioinformatics

With increasing computational power (aka GPU) that can be accessed these days, it is no wonder that performing all-atom molecular dynamics simulation for a longer time, with duplicates and/or triplicates, has become easier.... Read more »

  • November 27, 2016
  • 04:16 PM
  • 394 views

Interview with Tunca Doğan, OMA Visiting Fellow 2016

by Christophe Dessimoz in Open Reading Frame

Note: the “Life in the Lab” series features interviews of interns and visitors. This post is by our second 2016 OMA Visiting Fellow Tunca Doğan, who spent a month with us earlier this year. You can follow Tunca on Twitter at @tuncadogan. —Christophe



Please introduce yourself in a few sentences.

My name is Tunca Doğan. I received my PhD in 2013 with a thesis study in the fields of bioinformatics and computational biology where we developed methods for the clustering........ Read more »

  • July 7, 2016
  • 09:09 AM
  • 932 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
  • 733 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  

  • June 15, 2016
  • 08:05 AM
  • 766 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
  • 931 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 »

  • March 23, 2016
  • 07:25 AM
  • 1,110 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 »

  • March 16, 2016
  • 06:45 AM
  • 944 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 »

  • March 6, 2016
  • 11:51 PM
  • 867 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
  • 615 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  

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  

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  

  • January 28, 2016
  • 09:29 AM
  • 746 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
  • 788 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 »

  • December 21, 2015
  • 07:45 AM
  • 1,017 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
  • 958 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
  • 742 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
  • 731 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
  • 770 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  

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