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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]
 2014-09-03T00:00:00Z A fault-tolerant method for HLA typing with PacBio data
Background: Human leukocyte antigen (HLA) genes are critical genes involved in important biomedical aspects, including organ transplantation, autoimmune diseases and infectious diseases. The gene family contains the most polymorphic genes in humans and the difference between two alleles is only a single base pair substitution in many cases. The next generation sequencing (NGS) technologies could be used for high throughput HLA typing but in silico methods are still needed to correctly assign the alleles of a sample. Computer scientists have developed such methods for various NGS platforms, such as Illumina, Roche 454 and Ion Torrent, based on the characteristics of the reads they generate. However, the method for PacBio reads was less addressed, probably owing to its high error rates. The PacBio system has the longest read length among available NGS platforms, and therefore is the only platform capable of having exon 2 and exon 3 of HLA genes on the same read to unequivocally solve the ambiguity problem caused by the "phasing" issue. Results: We proposed a new method BayesTyping1 to assign HLA alleles for PacBio circular consensus sequencing reads using Bayes' theorem. The method was applied to simulated data of the three loci HLA-A, HLA-B and HLA-DRB1. The experimental results showed its capability to tolerate the disturbance of sequencing errors and external noise reads. Conclusions: The BayesTyping1 method could overcome the problems of HLA typing using PacBio reads, which mostly arise from sequencing errors of PacBio reads and the divergence of HLA genes, to some extent.


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BMC Genomics - Latest Articles   [more] [xml]
 2014-09-03T00:00:00Z Transcriptomic dissection of the rice - Burkholderia glumae interaction
Background: Bacterial panicle blight caused by the bacterium Burkholderia glumae is an emerging disease of rice in the United States. Not much is known about this disease, the disease cycle or any source of disease resistance. To understand the interaction between rice and Burkholderia glumae, we used transcriptomics via next-generation sequencing (RNA-Seq) and bioinformatics to identify differentially expressed transcripts between resistant and susceptible interactions and formulate a model for rice resistance to the disease. Results: Using inoculated young seedlings as sample tissues, we identified unique transcripts involved with resistance to bacterial panicle blight, including a PIF-like ORF1 and verified differential expression of some selected genes using qRT-PCR. These transcripts, which include resistance genes of the NBS-LRR type, kinases, transcription factors, transporters and expressed proteins with functions that are not known, have not been reported in other pathosystems including rice blast or bacterial blight. Further, functional annotation analysis reveals enrichment of defense response and programmed cell death (biological processes); ATP and protein binding (molecular functions); and mitochondrion-related (cell component) transcripts in the resistant interaction. Conclusion: Taken together, we formulated a model for rice resistance to bacterial panicle blight that involves an activation of previously unknown resistance genes and their activation partners upon challenge with B. glumae. Other interesting findings are that 1) though these resistance transcripts were up-regulated upon inoculation in the resistant interaction, some of them were already expressed in the water-inoculated control from the resistant genotype, but not in the water- and bacterium-inoculated samples from the susceptible genotype; 2) rice may have co-opted an ORF that was previously a part of a transposable element to aid in the resistance mechanism; and 3) resistance may have existed immediately prior to rice domestication.


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BMC Biochemistry - Latest Articles   [more] [xml]
 2014-08-25T00:00:00Z Chemical-genetic induction of Malonyl-CoA decarboxylase in skeletal muscle
Background: Defects in skeletal muscle fatty acid oxidation have been implicated in the etiology of insulin resistance. Malonyl-CoA decarboxylase (MCD) has been a target of investigation because it reduces the concentration of malonyl-CoA, a metabolite that inhibits fatty acid oxidation. The in vivo role of muscle MCD expression in the development of insulin resistance remains unclear. Results: To determine the role of MCD in skeletal muscle of diet induced obese and insulin resistant mouse models we generated mice expressing a muscle specific transgene for MCD (Tg-fMCDSkel) stabilized posttranslationally by the small molecule, Shield-1. Tg-fMCDSkel and control mice were placed on either a high fat or low fat diet for 3.5 months. Obese and glucose intolerant as well as lean control Tg-fMCDSkel and nontransgenic control mice were treated with Shield-1 and changes in their body weight and insulin sensitivity were determined upon induction of MCD. Inducing MCD activity >5-fold in skeletal muscle over two weeks did not alter body weight or glucose intolerance of obese mice. MCD induction further potentiated the defects in insulin signaling of obese mice. In addition, key enzymes in fatty acid oxidation were suppressed following MCD induction. Conclusion: Acute induction of MCD in the skeletal muscle of obese and glucose intolerant mice did not improve body weight and decreased insulin sensitivity compared to obese nontransgenic controls. Induction of MCD in skeletal muscle resulted in a suppression of mitochondrial oxidative genes suggesting a redundant and metabolite driven regulation of gene expression.


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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]
 2014-08-29 [Editorial] Australia needs a strategy
Australians are constantly told that our economy is ‘“in transition.”’ We need to move up the global value chain, build knowledge-based industries, prepare for the Asian Century, and be the “food bowl of the world.” These are grand ambitions that we share with many other nations, in our region and beyond. The question for all of us is: How? Author: Ian Chubb
 2014-08-29 [In Brief] This week's section
A roundup of weekly science policy and related news.
 2014-08-29 [In Depth] Animal welfare accreditation called into question
PETA study finds violations more often in approved labs. Author: David Grimm
 2014-08-29 [In Depth] Genomes reveal start of Ebola outbreak
Viral sequences demonstrate how the disease spread in Sierra Leone. Author: Gretchen Vogel
 2014-08-29 [In Depth] As volcano rumbles, scientists plan for aviation alerts
Ash sensors ready to deploy on ground, planes. Author: Carolyn Gramling
 2014-08-29 [In Depth] A chocolate habit in ancient North America
Residues on pottery suggest close ties between Mesoamerica and cultures to the north. Author: Michael Bawaya
 2014-08-29 [In Depth] Why null results rarely see the light of day
“File drawer” study proposes registry for unpublished social science data. Author: Jeffrey Mervis
 2014-08-29 [In Depth] Supernova breaks the mold
A massive explosion in a nearby galaxy both confirms and confounds astronomers' expectations. Author: Daniel Clery
 2014-08-29 [Feature] In search of Green Arabia
Researchers are scouring the now-barren Arabian Peninsula to uncover its hidden role in ancient human migration. Author: Andrew Lawler
 2014-08-29 [Perspective] Glimpsing glass structure under pressure
Nuclear magnetic resonance spectroscopy of a glass under pressure adds to our understanding of network structure [Also see Report by Edwards et al.] Author: Randall E. Youngman
 2014-08-29 [Perspective] On the origin of Peter Rabbit
Domestication of rabbits led to changes across the genome, particularly in regions related to brain development [Also see Report by Carneiro et al.] Author: Kirk E. Lohmueller
 2014-08-29 [Perspective] One good cosmic measure
Radio-wave interferometry provides an accurate measurement of cosmic distances [Also see Report by Melis et al.] Author: Léo Girardi
 2014-08-29 [Perspective] Many modes of motility
Cells use a piston-driven mechanism, among others, to migrate [Also see Report by Petrie et al.] Authors: Douglas W. DeSimone, A. Rick Horwitz
 2014-08-29 [Perspective] Stories of Arctic colonization
Genetic data elucidate the population history of the North American Arctic [Also see Research Article by Raghavan et al.] Author: Robert W. Park
 2014-08-29 [Perspective] Rekindled HIV infection
What does the “Mississippi baby” tell us about curing HIV-1 infection? Authors: Janet D. Siliciano, Robert F. Siliciano
 2014-08-29 [Policy Forum] Demystifying central government R&D spending in China
Should funding focus on scientific research? Authors: Yutao Sun, Cong Cao
 2014-08-29 [Book Review] Heirloom genomes and bison conservation
Author: J. Andrew DeWoody
 2014-08-29 [Books et al.] Books Received
A listing of books received at Science during the week ending 22 August 2014.
 2014-08-29 [Letter] Is it time to destroy the smallpox virus?
Authors: Isao Arita, Donald Francis
 2014-08-29 [Letter] Gene drives raise dual-use concerns
Author: David Gurwitz
 2014-08-29 [Letter] Gene drives raise dual-use concerns—Response
Authors: Kenneth A. Oye, Kevin M. Esvelt
 2014-08-29 [Technical Comment] Comment on “The hologenomic basis of speciation: Gut bacteria cause hybrid lethality in the genus Nasonia”
Brucker and Bordenstein (Reports, 9 August 2013, p. 667) claim that adaptive codivergence of gut bacteria with hosts contributes to hybrid lethality. Yet, they provide no evidence for coadaptation of bacteria and Nasonia hosts. Their data on hybrid viability suggest that bacteria contribute to inviability only because intrinsic hybrid dysfunction increases susceptibility to free-living bacteria. Hologenomic speciation remains testable speculation without experimental support. Authors: James Angus Chandler, Michael Turelli
 2014-08-29 [Technical Response] Response to Comment on “The hologenomic basis of speciation: Gut bacteria cause hybrid lethality in the genus Nasonia”
Chandler and Turelli postulate that intrinsic hybrid dysfunction underscores hybrid lethality in Nasonia. Although it is a suitable conception for examining hybrid incompatibilities, their account of the evidence is factually inaccurate and leaves out the evolutionary process for why lethality became conditional on nuclear-microbe interactions. Hybrid incompatibilities in the context of phylosymbiosis are resolved by hologenomic principles and exemplify this emerging postmodern synthesis. Authors: Robert M. Brucker, Seth R. Bordenstein
 2014-08-29 [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.
 2014-08-29 This Week in Science
Cost-effective conservation on private land | Signature microbes follow you from house to house | Distance score settled for Seven Sisters | Strong yet creeping megathrust faults | Rabbits softly swept to domestication | Cutting out a kinase for T cell survival | Push me, pull you, that's the way to move | An enzyme offers a new path to pain control | A cosmic dust storm that came and went | Making a superfluid lithium mixture | Catching changing boron coordination | Arctic genetics comes in from the cold | Activating a receptor to excite a neuron | Brain stimulation to improve human memory | Chromatin mutations disrupt development | T and B cells' intricate molecular dance | Oxidizing hydrogen in place of nitrite | El Niño shifted between the center and the East
 2014-08-29 Editors' Choice
Need proteasomes? Make some! | Incentives work on economists, too! | Eliminating the effects of the pesky bulk | Making mantle melt analogs more accurate | Cleaving RNA dials down inflammation | Moving from one novelty to the next | Seals infected early Americans with TB | Interior design with nanoparticles
 2014-08-29 [Research Article] The genetic prehistory of the New World Arctic
Early Arctic humans differed from both present-day Inuit and Native Americans. [Also see Perspective by Park] Authors: Maanasa Raghavan, Michael DeGiorgio, Anders Albrechtsen, Ida Moltke, Pontus Skoglund, Thorfinn S. Korneliussen, Bjarne Grønnow, Martin Appelt, Hans Christian Gulløv, T. Max Friesen, William Fitzhugh, Helena Malmström, Simon Rasmussen, Jesper Olsen, Linea Melchior, Benjamin T. Fuller, Simon M. Fahrni, Thomas Stafford, Vaughan Grimes, M. A. Priscilla Renouf, Jerome Cybulski, Niels Lynnerup, Marta Mirazon Lahr, Kate Britton, Rick Knecht, Jette Arneborg, Mait Metspalu, Omar E. Cornejo, Anna-Sapfo Malaspinas, Yong Wang, Morten Rasmussen, Vibha Raghavan, Thomas V. O. Hansen, Elza Khusnutdinova, Tracey Pierre, Kirill Dneprovsky, Claus Andreasen, Hans Lange, M. Geoffrey Hayes, Joan Coltrain, Victor A. Spitsyn, Anders Götherström, Ludovic Orlando, Toomas Kivisild, Richard Villems, Michael H. Crawford, Finn C. Nielsen, Jørgen Dissing, Jan Heinemeier, Morten Meldgaard, Carlos Bustamante, Dennis H. O’Rourke, Mattias Jakobsson, M. Thomas P. Gilbert, Rasmus Nielsen, Eske Willerslev
 2014-08-29 [Research Article] X-ray structures of AMPA receptor–cone snail toxin complexes illuminate activation mechanism
X-ray structures provide insight into how an ion channel involved in activation of neurons is gated. Authors: Lei Chen, Katharina L. Dürr, Eric Gouaux
 2014-08-29 [Report] Observation of the transition state for pressure-induced BO3→ BO4 conversion in glass
Boron atoms move out of plane with pressure as they transition from threefold to fourfold coordination in borosilicate glass. [Also see Perspective by Youngman] Authors: Trenton Edwards, Takatsugu Endo, Jeffrey H. Walton, Sabyasachi Sen
 2014-08-29 [Report] A VLBI resolution of the Pleiades distance controversy
A highly accurate and precise radio measurement overrules a contrary result from the Hipparcos satellite. [Also see Perspective by Girardi] Authors: Carl Melis, Mark J. Reid, Amy J. Mioduszewski, John R. Stauffer, Geoffrey C. Bower
 2014-08-29 [Report] Large impacts around a solar-analog star in the era of terrestrial planet formation
Variations in the brightness of warm dust indicate recent destructive collisions among protoplanets. Authors: Huan Y. A. Meng, Kate Y. L. Su, George H. Rieke, David J. Stevenson, Peter Plavchan, Wiphu Rujopakarn, Carey M. Lisse, Saran Poshyachinda, Daniel E. Reichart
 2014-08-29 [Report] A mixture of Bose and Fermi superfluids
An ultracold gas mixture of two lithium isotopes, one bosonic and the other fermionic, manifests superfluidity. Authors: I. Ferrier-Barbut, M. Delehaye, S. Laurent, A. T. Grier, M. Pierce, B. S. Rem, F. Chevy, C. Salomon
 2014-08-29 [Report] Strength of stick-slip and creeping subduction megathrusts from heat flow observations
Megathrusts subducting rugged sea floor have high fault strength but do not unleash great earthquakes. Authors: Xiang Gao, Kelin Wang
 2014-08-29 [Report] Using ecological thresholds to evaluate the costs and benefits of set-asides in a biodiversity hotspot
A small portion of Brazil’s agricultural subsidies would be enough to preserve private land in the Brazilian Atlantic Forest. Authors: Cristina Banks-Leite, Renata Pardini, Leandro R. Tambosi, William D. Pearse, Adriana A. Bueno, Roberta T. Bruscagin, Thais H. Condez, Marianna Dixo, Alexandre T. Igari, Alexandre C. Martensen, Jean Paul Metzger
 2014-08-29 [Report] Holocene history of ENSO variance and asymmetry in the eastern tropical Pacific
El Niño–Southern Oscillation warming of the sea surface was strongly skewed toward the central Pacific in the Mid-Holocene. Authors: Matthieu Carré, Julian P. Sachs, Sara Purca, Andrew J. Schauer, Pascale Braconnot, Rommel Angeles Falcón, Michèle Julien, Danièle Lavallée
 2014-08-29 [Report] Longitudinal analysis of microbial interaction between humans and the indoor environment
Microbes colonize not only our guts, but also our homes. Authors: Simon Lax, Daniel P. Smith, Jarrad Hampton-Marcell, Sarah M. Owens, Kim M. Handley, Nicole M. Scott, Sean M. Gibbons, Peter Larsen, Benjamin D. Shogan, Sophie Weiss, Jessica L. Metcalf, Luke K. Ursell, Yoshiki Vázquez-Baeza, Will Van Treuren, Nur A. Hasan, Molly K. Gibson, Rita Colwell, Gautam Dantas, Rob Knight, Jack A. Gilbert
 2014-08-29 [Report] Growth of nitrite-oxidizing bacteria by aerobic hydrogen oxidation
Bacteria thought to rely on the oxidation of nitrite for energy can, in fact, do just fine by oxidizing hydrogen instead. Authors: Hanna Koch, Alexander Galushko, Mads Albertsen, Arno Schintlmeister, Christiane Gruber-Dorninger, Sebastian Lücker, Eric Pelletier, Denis Le Paslier, Eva Spieck, Andreas Richter, Per H. Nielsen, Michael Wagner, Holger Daims
 2014-08-29 [Report] Targeted enhancement of cortical-hippocampal brain networks and associative memory
Noninvasive stimulation of the brain can improve memories for episodes by boosting the connectivity between cortical regions. Authors: Jane X. Wang, Lynn M. Rogers, Evan Z. Gross, Anthony J. Ryals, Mehmet E. Dokucu, Kelly L. Brandstatt, Molly S. Hermiller, Joel L. Voss
 2014-08-29 [Report] Dynamic signaling by T follicular helper cells during germinal center B cell selection
Live-cell imaging in mice reveals the molecular details of B cell selection in germinal centers. Authors: Ziv Shulman, Alexander D. Gitlin, Jason S. Weinstein, Begoña Lainez, Enric Esplugues, Richard A. Flavell, Joseph E. Craft, Michel C. Nussenzweig
 2014-08-29 [Report] Generation of compartmentalized pressure by a nuclear piston governs cell motility in a 3D matrix
Human fibroblast migration in a physiological extracellular matrix relies on a polarized intracellular pressure gradient. [Also see Perspective by DeSimone and Horwitz] Authors: Ryan J. Petrie, Hyun Koo, Kenneth M. Yamada
 2014-08-29 [Report] Histone H3 lysine-to-methionine mutants as a paradigm to study chromatin signaling
Mutations in the DNA packaging material disrupt fruit fly development and reveal epigenetic regulatory pathways. Authors: Hans-Martin Herz, Marc Morgan, Xin Gao, Jessica Jackson, Ryan Rickels, Selene K. Swanson, Laurence Florens, Michael P. Washburn, Joel C. Eissenberg, Ali Shilatifard
 2014-08-29 [Report] Structure of an agonist-bound ionotropic glutamate receptor
X-ray structures provide insight into how an ion channel involved in activation of neurons is gated. Authors: Maria V. Yelshanskaya, Minfen Li, Alexander I. Sobolevsky
 2014-08-29 [Report] Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication
The domestication of rabbits primarily shifted the frequencies of alleles represented, rather than creating new genes. [Also see Perspective by Lohmueller] Authors: Miguel Carneiro, Carl-Johan Rubin, Federica Di Palma, Frank W. Albert, Jessica Alföldi, Alvaro Martinez Barrio, Gerli Pielberg, Nima Rafati, Shumaila Sayyab, Jason Turner-Maier, Shady Younis, Sandra Afonso, Bronwen Aken, Joel M. Alves, Daniel Barrell, Gerard Bolet, Samuel Boucher, Hernán A. Burbano, Rita Campos, Jean L. Chang, Veronique Duranthon, Luca Fontanesi, Hervé Garreau, David Heiman, Jeremy Johnson, Rose G. Mage, Ze Peng, Guillaume Queney, Claire Rogel-Gaillard, Magali Ruffier, Steve Searle, Rafael Villafuerte, Anqi Xiong, Sarah Young, Karin Forsberg-Nilsson, Jeffrey M. Good, Eric S. Lander, Nuno Ferrand, Kerstin Lindblad-Toh, Leif Andersson
 2014-08-29 [New Products] New Products
A weekly roundup of information on newly offered instrumentation, apparatus, and laboratory materials of potential interest to researchers.
 2014-08-29 [Podcast] Science Podcast: 29 August Show
On this week's show: Our microbial housemates and a news roundup.
 2014-08-29 [Working Life] Having it all
Author: Jyoti Mishra

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