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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]
 2014-07-29T00:00:00Z A continuous optimization approach for inferring parameters in mathematical models of regulatory networks
Background: The advances of systems biology have raised a large number of sophisticated mathematical models for describing the dynamic property of complex biological systems. One of the major steps in developing mathematical models is to estimate unknown parameters of the model based on experimentally measured quantities. However, experimental conditions limit the amount of data that is available for mathematical modelling. The number of unknown parameters in mathematical models may be larger than the number of observation data. The imbalance between the number of experimental data and number of unknown parameters makes reverse-engineering problems particularly challenging. Results: To address the issue of inadequate experimental data, we propose a continuous optimization approach for making reliable inference of model parameters. This approach first uses a spline interpolation to generate continuous functions of system dynamics as well as the first and second order derivatives of continuous functions. The expanded dataset is the basis to infer unknown model parameters using various continuous optimization criteria, including the error of simulation only, error of both simulation and the first derivative, or error of simulation as well as the first and second derivatives. We use three case studies to demonstrate the accuracy and reliability of the proposed new approach. Compared with the corresponding discrete criteria using experimental data at the measurement time points only, numerical results of the ERK kinase activation module show that the continuous absolute-error criteria using both function and high order derivatives generate estimates with better accuracy. This result is also supported by the second and third case studies for the G1/S transition network and the MAP kinase pathway, respectively. This suggests that the continuous absolute-error criteria lead to more accurate estimates than the corresponding discrete criteria. We also study the robustness property of these three models to examine the reliability of estimates. Simulation results show that the models with estimated parameters using continuous fitness functions have better robustness properties than those using the corresponding discrete fitness functions. Conclusions: The inference studies and robustness analysis suggest that the proposed continuous optimization criteria are effective and robust for estimating unknown parameters in mathematical models.


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BMC Genomics - Latest Articles   [more] [xml]
 2014-07-29T00:00:00Z Endogenous small-noncoding RNAs and their roles in chilling response and stress acclimation in Cassava
Background: Small noncoding RNA (sncRNA), including microRNAs (miRNAs) and endogenous small-interfering RNAs (endo-siRNAs) are key gene regulators in eukaryotes, playing critical roles in plant development and stress tolerance. Trans-acting siRNAs (ta-siRNAs), which are secondary siRNAs triggered by miRNAs, and siRNAs from natural antisense transcripts (nat-siRNAs) are two well-studied classes of endo-siRNAs. Results: In order to understand sncRNAs' roles in plant chilling response and stress acclimation, we performed a comprehensive study of miRNAs and endo-siRNAs in Cassava (Manihot esculenta), a major source of food for the world populations in tropical regions. Combining Next-Generation sequencing and computational and experimental analyses, we profiled and characterized sncRNA species and mRNA genes from the plants that experienced severe and moderate chilling stresses, that underwent further severe chilling stress after chilling acclimation at moderate stress, and that grew under the normal condition. We also included castor bean (Ricinus communis) in our study to understand conservation of sncRNAs. In addition to known miRNAs, we identified 32 (22 and 10) novel miRNAs as well as 47 (26 and 21) putative secondary siRNA-yielding and 8 (7 and 1) nat-siRNA-yielding candidate loci in Cassava and castor bean, respectively. Among the expressed sncRNAs, 114 miRNAs, 12 ta-siRNAs and 2 nat-siRNAs showed significant expression changes under chilling stresses. Conclusion: Systematic and computational analysis of microRNAome and experimental validation collectively showed that miRNAs, ta-siRNAs, and possibly nat-siRNAs play important roles in chilling response and chilling acclimation in Cassava by regulating stress-related pathways, e.g. Auxin signal transduction. The conservation of these sncRNA might shed lights on the role of sncRNA-mediated pathways affected by chilling stress and stress acclimation in Euphorbiaceous plants.


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BMC Biochemistry - Latest Articles   [more] [xml]
 2014-07-28T00:00:00Z Extraction, purification, kinetic and thermodynamic properties of urease from germinating Pisum Sativum L. seeds
Background: Urease, one of the highly efficient known enzymes, catalyzes the hydrolysis of urea into ammonia and carbon dioxide. The present study aimed to extract urease from pea seeds (Pisum Sativum L). The enzyme was then purified in three consequence steps: acetone precipitation, DEAE-cellulose ion-exchange chromatography, and gel filtration chromatography (Sephacryl S-200 column). Results: The purification fold was 12.85 with a yield of 40%. The molecular weight of the isolated urease was estimated by chromatography to be 269,000 Daltons. Maximum urease activity (190 U/g) was achieved at the optimum conditions of 40[degree sign]C and pH of 7.5 after 5 min of incubation. The kinetic parameters,Km and Vmax, were estimated by Lineweaver-Burk fits and found to be 500 mM and 333.3 U/g, respectively. The thermodynamic constants of activation, DeltaH, Ea, and DeltaS, were determined using Arrhenius plot and found to be 21.20 kJ/mol, 23.7 kJ/mol, and 1.18 kJ/mol/K, respectively. Conclusions: Urease was purified from germinating Pisum Sativum L. seeds. The purification fold, yield, and molecular weight were determined. The effects of pH, concentration of enzyme, temperature, concentration of substrate, and storage period on urease activity were examined. This may provide an insight on the various aspects of the property of the enzyme. The significance of extracting urease from different sources could play a good role in understanding the metabolism of urea in plants.


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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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