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BMC Structural Biology - Latest Articles   [more] [xml]
 2014-07-19T00:00:00Z A simple method for finding a protein's ligand-binding pockets
Background: This paper provides a simple and rapid method for a protein-clustering strategy. The basic idea implemented here is to use computational geometry methods to predict and characterize ligand-binding pockets of a given protein structure. In addition to geometrical characteristics of the protein structure, we consider some simple biochemical properties that help recognize the best candidates for pockets in a protein's active site. Results: Our results are shown to produce good agreement with known empirical results. Conclusions: The method presented in this paper is a low-cost rapid computational method that could be used to classify proteins and other biomolecules, and furthermore could be useful in reducing the cost and time of drug discovery.


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BMC Bioinformatics - Latest Articles   [more] [xml]
 2014-07-25T00:00:00Z Enhancing HMM-based protein profile-profile alignment with structural features and evolutionary coupling information
Background: Protein sequence profile-profile alignment is an important approach to recognizing remote homologs and generating accurate pairwise alignments. It plays an important role in protein sequence database search, protein structure prediction, protein function prediction, and phylogenetic analysis. Results: In this work, we integrate predicted solvent accessibility, torsion angles and evolutionary residue coupling information with the pairwise Hidden Markov Model (HMM) based profile alignment method to improve profile-profile alignments. The evaluation results demonstrate that adding predicted relative solvent accessibility and torsion angle information improves the accuracy of profile-profile alignments. The evolutionary residue coupling information is helpful in some cases, but its contribution to the improvement is not consistent. Conclusion: Incorporating the new structural information such as predicted solvent accessibility and torsion angles into the profile-profile alignment is a useful way to improve pairwise profile-profile alignment methods.


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BMC Genomics - Latest Articles   [more] [xml]
 2014-07-25T00:00:00Z Differential gene expression and metabolomic analyses of Brachypodium distachyon infected by deoxynivalenol producing and non-producing strains of Fusarium graminearum
Background: Fusarium Head Blight (FHB) caused primarily by Fusarium graminearum (Fg) is one of the major diseases of small-grain cereals including bread wheat. This disease both reduces yields and causes quality losses due to the production of deoxynivalenol (DON), the major type B trichothecene mycotoxin. DON has been described as a virulence factor enabling efficient colonization of spikes by the fungus in wheat, but its precise role during the infection process is still elusive. Brachypodium distachyon (Bd) is a model cereal species which has been shown to be susceptible to FHB. Here, a functional genomics approach was performed in order to characterize the responses of Bd to Fg infection using a global transcriptional and metabolomic profiling of B. distachyon plants infected by two strains of F. graminearum: a wild-type strain producing DON (Fg don+) and a mutant strain impaired in the production of the mycotoxin (Fg don-). Results: Histological analysis of the interaction of the Bd21 ecotype with both Fg strains showed extensive fungal tissue colonization with the Fg don+ strain while the florets infected with the Fg don- strain exhibited a reduced hyphal extension and cell death on palea and lemma tissues. Fungal biomass was reduced in spikes inoculated with the Fg don- strain as compared with the wild-type strain. The transcriptional analysis showed that jasmonate and ethylene-signalling pathways are induced upon infection, together with genes encoding putative detoxification and transport proteins, antioxidant functions as well as secondary metabolite pathways. In particular, our metabolite profiling analysis showed that tryptophan-derived metabolites, tryptamine, serotonin, coumaroyl-serotonin and feruloyl-serotonin, are more induced upon infection by the Fg don+ strain than by the Fg don- strain. Serotonin was shown to exhibit a slight direct antimicrobial effect against Fg. Conclusion: Our results show that Bd exhibits defense hallmarks similar to those already identified in cereal crops. While the fungus uses DON as a virulence factor, the host plant preferentially induces detoxification and the phenylpropanoid and phenolamide pathways as resistance mechanisms. Together with its amenability in laboratory conditions, this makes Bd a very good model to study cereal resistance mechanisms towards the major disease FHB.


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BMC Biochemistry - Latest Articles   [more] [xml]
 2014-07-09T00:00:00Z Application of Gaussia luciferase in bicistronic and non-conventional secretion reporter constructs
Background: Secreted luciferases are highly useful bioluminescent reporters for cell-based assays and drug discovery. A variety of secreted luciferases from marine organisms have been described that harbor an N-terminal signal peptide for release along the classical secretory pathway. Here, we have characterized the secretion of Gaussia luciferase in more detail. Results: We describe three basic mechanisms by which GLUC can be released from cells: first, classical secretion by virtue of the N-terminal signal peptide; second, internal signal peptide-mediated secretion and third, non-conventional secretion in the absence of an N-terminal signal peptide. Non-conventional release of dNGLUC is not stress-induced, does not require autophagy and can be enhanced by growth factor stimulation. Furthermore, we have identified the golgi-associated, gamma adaptin ear containing, ARF binding protein 1 (GGA1) as a suppressor of release of dNGLUC. Conclusions: Due to its secretion via multiple secretion pathways GLUC can find multiple applications as a research tool to study classical and non-conventional secretion. As GLUC can also be released from a reporter construct by internal signal peptide-mediated secretion it can be incorporated in a novel bicistronic secretion system.


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Nature   [more] [xml]
 2005-01-19 Einstein is dead
Until its next revolution, much of the glory of physics will be in engineering. It is a shame that the physicists who do so much of it keep so quiet about it.

Einstein is dead

Nature 433, 179 (2005). doi:10.1038/433179a

Until its next revolution, much of the glory of physics will be in engineering. It is a shame that the physicists who do so much of it keep so quiet about it.



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Science: Current Issue   [more] [xml]
 2014-07-25 [Editorial] Ghosts from the past
2014 marks the centennial of the commencement of World War I. One connection between today and that seemingly long-ago war is how we make choices when the future seems obvious only in retrospect, in what former U.S. Secretary of State George P. Shultz refers to as a world “awash in change.” Max Hastings, in Catastrophe 1914: Europe Goes to War, summarizes his views on how the rulers of Europe allowed World War I to start, then continue with a loss of over 8.6 million soldiers: “It is more appropriate to call them deniers, who preferred to persist with supremely dangerous policies and strategies….” Author: David Titley
 2014-07-25 [In Brief] This week's section
A roundup of weekly science policy and related news.
 2014-07-25 [In Depth] Ebola drugs still stuck in lab
Experts discussed—and rejected—bringing experimental vaccines and therapies to West Africa. Author: Martin Enserink
 2014-07-25 [In Depth] Road hazards threaten rover
To limit wheel damage from sharp rocks, the Curiosity Mars rover detours into sandy valleys. Author: Eric Hand
 2014-07-25 [In Depth] NIH institute considers broad shift to ‘people’ awards
Approach promises freedom from grant writing but could favor established researchers. Author: Jocelyn Kaiser
 2014-07-25 [In Depth] Dengue vaccine trial poses public health quandary
Experimental vaccine fell short against key strain. Author: Dennis Normile
 2014-07-25 [In Depth] Oil sands fight heats up in U.S.
Environmentalists oppose federal lease in Utah. Author: David Malakoff
 2014-07-25 [Feature] Fusion's restless pioneers
Startups with novel technologies are taking on fusion's Goliaths. Author: Daniel Clery
 2014-07-25 [Policy Forum] Wildlife decline and social conflict
Policies aimed at reducing wildlife-related conflict must address the underlying causes Authors: Justin S. Brashares, Briana Abrahms, Kathryn J. Fiorella, Christopher D. Golden, Cheryl E. Hojnowski, Ryan A. Marsh, Douglas J. McCauley, Tristan A. Nuñez, Katherine Seto, Lauren Withey
 2014-07-25 [Perspective] Ribosome rescue and neurodegeneration
A mutation in a brain-specific tRNA reveals the link between ribosome maintenance and neuronal cell death [Also see Report by Ishimura et al.] Author: Jennifer C. Darnell
 2014-07-25 [Perspective] Ultraslow relaxation of confined DNA
DNA dynamics in tight spaces challenge nature's nanomachines Authors: Yann R. Chemla, Taekjip Ha
 2014-07-25 [Perspective] Self-control tames the coupling of reactive radicals
Iridium complexes use two points of contact to control carbon-carbon bond formation [Also see Reports by Tellis et al. and Zuo et al.] Authors: Guy C. Lloyd-Jones, Liam T. Ball
 2014-07-25 [Perspective] Why are plant-pollinator networks nested?
Mutualistic communities maximize their structural stability [Also see Research Article by Rohr et al.] Author: Samraat Pawar
 2014-07-25 [Perspective] A cloaking coating for murky media
Objects shrouded in fog disappear entirely with simple coating [Also see Report by Schittny et al.] Author: David R. Smith
 2014-07-25 [Perspective] Astrocytes eyeball axonal mitochondria
Retinal neurons transfer mitochondria to astrocytes for rapid turnover to meet energy demands Authors: Thomas C. Burdett, Marc R. Freeman
 2014-07-25 [Book Review] Who guards the guardians?
Authors: Kieron O'Hara, Nigel Shadbolt
 2014-07-25 [Book Review] Repairing ecosystems
Author: William E. Stutz
 2014-07-25 [Books et al.] Books Received
A listing of books received at Science during the week ending 18 July 2014.
 2014-07-25 [Letter] In defense of fences
Authors: M. Pfeifer, C. Packer, A. C. Burton, S. T. Garnett, A. J. Loveridge, D. MacNulty, P. J. Platts
 2014-07-25 [Letter] In defense of fences—Response
Authors: Rosie Woodroffe, Simon Hedges, Sarah Durant
 2014-07-25 [Letter] Early Americans: Misstated results
Authors: Douglas J. Kennett, Yemane Asmerom, Brian M. Kemp, Victor Polyak, Deborah A. Bolnick, Ripan S. Malhi, Brendan J. Culleton
 2014-07-25 [Letter] Early Americans: Respecting ancestors
Authors: D. K. Grayson, D. J. Meltzer, J. E. Buikstra, K. V. Flannery, C. S. Fowler, J. Marcus, J. F. O'Connell, D. R. Piperno, J. A. Sabloff, B. D. Smith, D. H. Thomas, E. Willerslev, M. A. Zeder
 2014-07-25 [Letter] Early Americans: Respecting ancestors—Response
Author: James C. Chatters
 2014-07-25 [Association Affairs] AAAS news and notes
A monthly roundup of recent news and projects of Science's publisher, the American Association for the Advancement of Science.
 2014-07-25 [Introduction to Special Issue] Vanishing fauna
Author: Sacha Vignieri
 2014-07-25 [Special Issue News] The empty forest
A beleaguered national park in Borneo hints at what can happen when animals disappear. Author: Erik Stokstad
 2014-07-25 [Editorial] An animal-rich future
The rate at which animals are vanishing from this planet is one of the signatures of this age, as sure a sign of human dominance as our impact on Earth's nitrogen, phosphorus, and carbon cycles. This disappearance of animals from the world's ecosystems is generally a by-product of human activity, not an intentional act. Animals do matter to people, but on balance, they matter less than food, jobs, energy, money, and development. As long as we continue to view animals in ecosystems as irrelevant to these basic demands, animals will lose. Authors: Joshua J. Tewksbury, Haldre S. Rogers
 2014-07-25 [Special Issue Review] Defaunation in the Anthropocene
We live amid a global wave of anthropogenically driven biodiversity loss: species and population extirpations and, critically, declines in local species abundance. Particularly, human impacts on animal biodiversity are an under-recognized form of global environmental change. Among terrestrial vertebrates, 322 species have become extinct since 1500, and populations of the remaining species show 25% average decline in abundance. Invertebrate patterns are equally dire: 67% of monitored populations show 45% mean abundance decline. Such animal declines will cascade onto ecosystem functioning and human well-being. Much remains unknown about this “Anthropocene defaunation”; these knowledge gaps hinder our capacity to predict and limit defaunation impacts. Clearly, however, defaunation is both a pervasive component of the planet’s sixth mass extinction and also a major driver of global ecological change. Authors: Rodolfo Dirzo, Hillary S. Young, Mauro Galetti, Gerardo Ceballos, Nick J. B. Isaac, Ben Collen
 2014-07-25 [Special Issue Review] Reversing defaunation: Restoring species in a changing world
The rate of biodiversity loss is not slowing despite global commitments, and the depletion of animal species can reduce the stability of ecological communities. Despite this continued loss, some substantial progress in reversing defaunation is being achieved through the intentional movement of animals to restore populations. We review the full spectrum of conservation translocations, from reinforcement and reintroduction to controversial conservation introductions that seek to restore populations outside their indigenous range or to introduce ecological replacements for extinct forms. We place the popular, but misunderstood, concept of rewilding within this framework and consider the future role of new technical developments such as de-extinction. Authors: Philip J. Seddon, Christine J. Griffiths, Pritpal S. Soorae, Doug P. Armstrong
 2014-07-25 This Week in Science
Feathers, not just for the birds? | Problems making proteins kills nerve cells | In CF, two drugs are no better than one | To cast no shadow in a murky medium | Changing skin cells in development with TGF-β | Subtle entanglement in an atomic cloud | Tricky star plays sleight-of-light | Wastewater disposal linked to earthquakes | A membrane-activated switch to bind clathrin | A structural approach to species interactions | A bright outlook for carbon coupling | How to benchmark a quantum computer | Toward the control of light with light | Characterization of a quantum simulator | Climates conspire together to make big changes | Making tropomodulin find the right point
 2014-07-25 Editors' Choice
Marmoset DNA shows why it's small | Stealthy spying on a moving target | TRF2 gets transcription started, too | A vitamin's dark side in liver disease | Avoiding instabilities while creating wires | Warming waters create new bedfellows | Springtime sighting at Titan's coastline | Making protection of biodiversity count
 2014-07-25 [Research Article] On the structural stability of mutualistic systems
In ecology, structural stability influences the range of perturbations mutualistic networks can withstand. [Also see Perspective by Pawar] Authors: Rudolf P. Rohr, Serguei Saavedra, Jordi Bascompte
 2014-07-25 [Report] Ultrafast optical control by few photons in engineered fiber
Ultrafast photon-photon control is achieved in an engineered optic fiber. Authors: R. Nissim, A. Pejkic, E. Myslivets, B. P. Kuo, N. Alic, S. Radic
 2014-07-25 [Report] Defining and detecting quantum speedup
What makes a quantum machine quantum? Authors: Troels F. Rønnow, Zhihui Wang, Joshua Job, Sergio Boixo, Sergei V. Isakov, David Wecker, John M. Martinis, Daniel A. Lidar, Matthias Troyer
 2014-07-25 [Report] Fisher information and entanglement of non-Gaussian spin states
An unconventional entangled state is created out of a mesoscopic number of ultracold rubidium atoms. Authors: Helmut Strobel, Wolfgang Muessel, Daniel Linnemann, Tilman Zibold, David B. Hume, Luca Pezzè, Augusto Smerzi, Markus K. Oberthaler
 2014-07-25 [Report] Invisibility cloaking in a diffusive light scattering medium
A core-shell structure provides a cloak for objects within a diffusive medium. [Also see Perspective by Smith] Authors: Robert Schittny, Muamer Kadic, Tiemo Bückmann, Martin Wegener
 2014-07-25 [Report] Coherent imaging spectroscopy of a quantum many-body spin system
A method for validating quantum simulations is based on interrogating the system with a modulated magnetic field. Authors: C. Senko, J. Smith, P. Richerme, A. Lee, W. C. Campbell, C. Monroe
 2014-07-25 [Report] Single-electron transmetalation in organoboron cross-coupling by photoredox/nickel dual catalysis
Combining two catalysts, one light-activated, facilitates bond formation between saturated and unsaturated carbons. [Also see Perspective by Lloyd-Jones an Ball] Authors: John C. Tellis, David N. Primer, Gary A. Molander
 2014-07-25 [Report] Merging photoredox with nickel catalysis: Coupling of α-carboxyl sp3-carbons with aryl halides
Combining two catalysts, one light-activated, facilitates bond formation between saturated and unsaturated carbons. [Also see Perspective by Lloyd-Jones an Ball] Authors: Zhiwei Zuo, Derek T. Ahneman, Lingling Chu, Jack A. Terrett, Abigail G. Doyle, David W. C. MacMillan
 2014-07-25 [Report] Stellar activity masquerading as planets in the habitable zone of the M dwarf Gliese 581
Reexamination of the radial velocity signals from a famous exoplanet system demands demotion of terrestrial candidates. Authors: Paul Robertson, Suvrath Mahadevan, Michael Endl, Arpita Roy
 2014-07-25 [Report] Synchronization of North Pacific and Greenland climates preceded abrupt deglacial warming
The North Pacific and Greenland cause big climate changes when they act together. Authors: Summer K. Praetorius, Alan C. Mix
 2014-07-25 [Report] Sharp increase in central Oklahoma seismicity since 2008 induced by massive wastewater injection
The recent surge in central U.S. seismicity is likely attributable to injection of wastewater at a small number of wells. Authors: K. M. Keranen, M. Weingarten, G. A. Abers, B. A. Bekins, S. Ge
 2014-07-25 [Report] A Jurassic ornithischian dinosaur from Siberia with both feathers and scales
A fossil dinosaur with primitive feathers and scales suggests that feathers may have been present across dinosaur clades. Authors: Pascal Godefroit, Sofia M. Sinitsa, Danielle Dhouailly, Yuri L. Bolotsky, Alexander V. Sizov, Maria E. McNamara, Michael J. Benton, Paul Spagna
 2014-07-25 [Report] Ribosome stalling induced by mutation of a CNS-specific tRNA causes neurodegeneration
Mutations in a transfer RNA expressed in the nervous system stall ribosomes and can cause cell death if ribosome recycling fails. [Also see Perspective by Darnell] Authors: Ryuta Ishimura, Gabor Nagy, Ivan Dotu, Huihao Zhou, Xiang-Lei Yang, Paul Schimmel, Satoru Senju, Yasuharu Nishimura, Jeffrey H. Chuang, Susan L. Ackerman
 2014-07-25 [Report] AP2 controls clathrin polymerization with a membrane-activated switch
An autoinhibitory mechanism prevents clathrin recruitment by cytosolic AP2. Authors: Bernard T. Kelly, Stephen C. Graham, Nicole Liska, Philip N. Dannhauser, Stefan Höning, Ernst J. Ungewickell, David J. Owen
 2014-07-25 [Report] Mechanism of actin filament pointed-end capping by tropomodulin
The actin-capping protein tropomodulin achieves high-affinity binding through several discrete low-affinity interactions. Authors: Jampani Nageswara Rao, Yadaiah Madasu, Roberto Dominguez
 2014-07-25 [Business Office Feature] LIFE SCIENCE TECHNOLOGIES: DIGITAL LAB MANAGEMENT
Chris Tachibana
 2014-07-25 [New Products] New Products
A weekly roundup of information on newly offered instrumentation, apparatus, and laboratory materials of potential interest to researchers.
 2014-07-25 [Podcast] Science Podcast: 25 July Show
On this week's show: NIH funding for people not projects and a roundup of stories from our daily news site.
 2014-07-25 [Business Office Feature] Western blot tips and tricks: Filling the gap between art and science
Pier Giorgio Righetti
 2014-07-25 [Working Life] A scientific partnership
Author: Jim Austin

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