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BMC Structural Biology - Latest Articles   [more] [xml]
 2014-04-15T00:00:00Z Designing and evaluating the MULTICOM protein local and global model quality prediction methods in the CASP10 experiment
Background: Protein model quality assessment is an essential component of generating and using protein structural models. During the Tenth Critical Assessment of Techniques for Protein Structure Prediction (CASP10), we developed and tested four automated methods (MULTICOM-REFINE, MULTICOM-CLUSTER, MULTICOM-NOVEL, and MULTICOM-CONSTRUCT) that predicted both local and global quality of protein structural models. Results: MULTICOM-REFINE was a clustering approach that used the average pairwise structural similarity between models to measure the global quality and the average Euclidean distance between a model and several top ranked models to measure the local quality. MULTICOM-CLUSTER and MULTICOM-NOVEL were two new support vector machine-based methods of predicting both the local and global quality of a single protein model. MULTICOM-CONSTRUCT was a new weighted pairwise model comparison (clustering) method that used the weighted average similarity between models in a pool to measure the global model quality. Our experiments showed that the pairwise model assessment methods worked better when a large portion of models in the pool were of good quality, whereas single-model quality assessment methods performed better on some hard targets when only a small portion of models in the pool were of reasonable quality. Conclusions: Since digging out a few good models from a large pool of low-quality models is a major challenge in protein structure prediction, single model quality assessment methods appear to be poised to make important contributions to protein structure modeling. The other interesting finding was that single-model quality assessment scores could be used to weight the models by the consensus pairwise model comparison method to improve its accuracy.


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BMC Bioinformatics - Latest Articles   [more] [xml]
 2014-04-17T00:00:00Z Probabilistic drug connectivity mapping
Background: The aim of connectivity mapping is to match drugs using drug-treatment gene expression profilesfrom multiple cell lines. This can be viewed as an information retrieval task, with the goal of findingthe most relevant profiles for a given query drug. We infer the relevance for retrieval by data-drivenprobabilistic modeling of the drug responses, resulting in probabilistic connectivity mapping, andfurther consider the available cell lines as different data sources. We use a special type of probabilisticmodel to separate what is shared and specific between the sources, in contrast to earlier connectivitymapping methods that have intentionally aggregated all available data, neglecting information aboutthe differences between the cell lines. Results: We show that the probabilistic multi-source connectivity mapping method is superior to alternativesin finding functionally and chemically similar drugs from the Connectivity Map data set. We alsodemonstrate that an extension of the method is capable of retrieving combinations of drugs that matchdifferent relevant parts of the query drug response profile. Conclusions: The probabilistic modeling-based connectivity mapping method provides a promising alternative toearlier methods. Principled integration of data from different cell lines helps to identify relevantresponses for specific drug repositioning applications.


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BMC Genomics - Latest Articles   [more] [xml]
 2014-04-17T10:26:48Z Deciphering gamma-decalactone biosynthesis in strawberry fruit using a combination of genetic mapping, RNA-Seq and eQTL analyses
Background: Understanding the basis for volatile organic compound (VOC) biosynthesis and regulation is of great importance for the genetic improvement of fruit flavor. Lactones constitute an essential group of fatty acid-derived VOCs conferring peach-like aroma to a number of fruits including peach, plum, pineapple and strawberry. Early studies on lactone biosynthesis suggest that several enzymatic pathways could be responsible for the diversity of lactones, but detailed information on them remained elusive. In this study, we have integrated genetic mapping and genome-wide transcriptome analysis to investigate the molecular basis of natural variation in γ-decalactone content in strawberry fruit. Results: As a result, the fatty acid desaturase FaFAD1 was identified as the gene underlying the locus at LGIII-2 that controls γ-decalactone production in ripening fruit. The FaFAD1 gene is specifically expressed in ripe fruits and its expression fully correlates with the presence of γ-decalactone in all 95 individuals of the mapping population. In addition, we show that the level of expression of FaFAH1, with similarity to cytochrome p450 hydroxylases, significantly correlates with the content of γ-decalactone in the mapping population. The analysis of expression quantitative trait loci (eQTL) suggests that the product of this gene also has a regulatory role in the biosynthetic pathway of lactones. Conclusions: Altogether, this study provides mechanistic information of how the production of γ-decalactone is naturally controlled in strawberry, and proposes enzymatic activities necessary for the formation of this VOC in plants.


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BMC Biochemistry - Latest Articles   [more] [xml]
 2014-04-03T00:00:00Z Plasmodium falciparum UvrD activities are downregulated by DNA-interacting compounds and its dsRNA inhibits malaria parasite growth
Background: Human malaria parasite infection and its control is a global challenge which is responsible for ~0.65 million deaths every year globally. The emergence of drug resistant malaria parasite is another challenge to fight with malaria. Enormous efforts are being made to identify suitable drug targets in order to develop newer classes of drug. Helicases play crucial roles in DNA metabolism and have been proposed as therapeutic targets for cancer therapy as well as viral and parasitic infections. Genome wide analysis revealed that Plasmodium falciparum possesses UvrD helicase, which is absent in the human host. Results: Recently the biochemical characterization of P. falciparum UvrD helicase revealed that N-terminal UvrD (PfUDN) hydrolyses ATP, translocates in 3’ to 5’ direction and interacts with MLH to modulate each other’s activity. In this follow up study, further characterization of P. falciparum UvrD helicase is presented. Here, we screened the effect of various DNA interacting compounds on the ATPase and helicase activity of PfUDN. This study resulted into the identification of daunorubicin (daunomycin), netropsin, nogalamycin, and ethidium bromide as the potential inhibitor molecules for the biochemical activities of PfUDN with IC50 values ranging from ~3.0 to ~5.0 μM. Interestingly etoposide did not inhibit the ATPase activity but considerable inhibition of unwinding activity was observed at 20 μM. Further study for analyzing the importance of PfUvrD enzyme in parasite growth revealed that PfUvrD is crucial/important for its growth ex-vivo. Conclusions: As PfUvrD is absent in human hence on the basis of this study we propose PfUvrD as suitable drug target to control malaria. Some of the PfUvrD inhibitors identified in the present study can be utilized to further design novel and specific inhibitor molecules.


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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]
 2014-04-18 [Errata] Erratum for the Research Article: “Total Synthesis of a Functional Designer Eukaryotic Chromosome” by N. Annaluru, H. Muller, L. A. Mitchell, S. Ramalingam, G. Stracquadanio, S. M. Richardson, J. S. Dymond, Z. Kuang, L. Z. Scheifele, E. M. Cooper, Y. Cai, K. Zeller, N. Agmon, J. S. Han, M. Hadjithomas, J. Tullman, K. Caravelli, K. Cirelli, Z. Guo, V. London, A. Yeluru, S. Murugan, K. Kandavelou, N. Agier, G. Fischer, K. Yang, J. A. Martin, M. Bilgel, P. Bohutskyi, K. M. Boulier, B. J. Capaldo, J. Chang, K. Charoen, W. J. Choi, P. Deng, J. E. DiCarlo, J. Doong, J. Dunn, J. I. Feinberg, C. Fernandez, C. E. Floria, D. Gladowski, P. Hadidi, I. Ishizuka, J. Jabbari, C. Y. L. Lau, P. A. Lee, S. Li, D. Lin, M. E. Linder, J. Ling, J. Liu, J. Liu, M. London, H. Ma, J. Mao, J. E. McDade, A. McMillan, A. M. Moore, W. C. Oh, Y. Ouyang, R. Patel, M. Paul, L. C. Paulsen, J. Qiu, A. Rhee, M. G. Rubashkin, I. Y. Soh, N. E. Sotuyo, V. Srinivas, A. Suarez, A. Wong, R. Wong, W. R. Xie, Y. Xu, A. T. Yu, R. Koszul, J. S. Bader, J. D. Boeke, S. Chandrasegaran
 2014-04-18 This Week in Science
Patchy Insulation | Sleep Tight, Fly | Smoothing Graphene | On a Zeppelin | Starry Brightness | Changing Assemblages | Resilient Hyperpolarization | Hope for SUSY? | Strained Superconductor | Thin and Selective Outpourings | How Tight? | Resisting the Chop | Universal Immune Function | L[i]nc to Dendritic Cell Activation
 2014-04-18 [Editorial] Influenza and the Live Poultry Trade
Live poultry trade at local markets has long been a part of China's national identity. From small villages to big cities, the gathering and selling of different birds in this vibrant atmosphere is at the heart of the country's cuisine culture. Unfortunately, the backdrop to this tradition has changed. Last year, the H7N9 virus, a new strain of influenza A, jumped from birds to humans, causing 144 cases of human infection and 47 deaths in China. Now a second wave of this flu is coursing through the country, with 258 confirmed cases and 99 deaths as of 8 April 2014. Scientific evidence points to a connection between the conditions at these live markets and the spread of flu, suggesting that until other means are found to prevent the transmission of or effectively treat the illness, China must shut down live poultry markets to prevent further spread of the virus and a possible global pandemic. Author: George F. Gao
 2014-04-18 Editors' Choice
It's All in the Timing | Dead But Not Dangerous | Seeing Signaling | Disrupted Development | Doing Better Caged | On the Wall | Lead-Free Film
 2014-04-18 [News of the Week] This Week's Section
Follow the links below for a roundup of the week's top stories in science, or download a PDF of the entire section. Around the WorldFindingsNewsmakersRandom Samples
 2014-04-18 [News of the Week] Around the World
In science news around the world, the National Park Service decides not to introduce mainland wolves to rescue the declining wolf population on Lake Superior's Isle Royale, Japanese researchers plan to resume controversial whaling in 2015, Australia's Antarctic research program faces budget cuts, and more.
 2014-04-18 [News of the Week] Newsmakers
Molecular biologist Feng Zhang wins the National Science Foundation's Alan T. Waterman Award for young researchers, President Barack Obama nominates White House budget office director Sylvia Mathews Burwell to replace outgoing Health and Human Services head Kathleen Sebelius, physicist Stuart Parkin wins the 2014 Millennium Technology Prize, and more.
 2014-04-18 [News of the Week] Random Sample
The winners of the Science, Play and Research Kit Competition reimagine the childhood chemistry set—on a microfluidic chip.
 2014-04-18 Findings
Hunter-Gatherers Don't Need Probiotics
 2014-04-18 [News & Analysis] U.S. Support for ITER Wavers as Costs Spiral
Soaring cost estimates are jeopardizing the U.S. contribution to ITER, the massive international fusion energy project. Author: Adrian Cho
 2014-04-18 [News & Analysis] 'Humanized' Mouse Detects Deadly Drug Side Effects
A chimeric mouse with a humanized liver offers a novel window into drug toxicity. Author: Jon Cohen
 2014-04-18 [News & Analysis] Ancient DNA Holds Clues to Gene Activity in Extinct Humans
Researchers have harnessed the chemical degradation of fossil DNA to determine methylation patterns that may reveal which genes were turned on, or off, in ancient human species. Author: Elizabeth Pennisi
 2014-04-18 [News & Analysis] More Sophisticated Forecasts Yield Glimmer of Hope in Climate Gloom
The latest Intergovernmental Panel on Climate Change report, on mitigating emissions, finds a few glimmers of hope amid gloomy projections. Author: Eli Kintisch
 2014-04-18 [News & Analysis] Almost-Earth Tantalizes Astronomers With Promise of Worlds to Come
A new find from NASA's Kepler orbiting observatory is the first Earth-sized planet to be detected in the habitable zone of a star. Author: Yudhijit Bhattacharjee
 2014-04-18 [News Focus] Into the Maelstrom
Jennifer Francis has made waves linking the melting Arctic to extreme weather around the world. But a storm of criticism has forced the climate scientist to defend her hypothesis. Author: Eli Kintisch
 2014-04-18 [Letter] Climate Discussion Echoes Tobacco Debate
Authors: Robert J. Gould, Edward Maibach
 2014-04-18 [Letter] Integrating Psychological Treatment Approaches
Author: Brendan D. Kelly
 2014-04-18 [Letter] Uganda Homosexuality Report in Context
Author: Misaki Wayengera
 2014-04-18 [Correction] Corrections and Clarifications
 2014-04-18 [Letter] Weeds Making Waves
Author: David Samuel Johnson
 2014-04-18 [Book Review] On Scientists and Advocacy
Howe considers how researchers, environmentalists, and the public have interpreted and responded to the problem of global warming. Author: Gavin A. Schmidt
 2014-04-18 [Books et al.] Books Received
A listing of books received at Science during the week ending 11 April 2014.
 2014-04-18 [Policy Forum] Particulate Matter Matters
Quasi-experimental evidence is needed on the relations between human health and airborne particulate matter. Authors: Francesca Dominici, Michael Greenstone, Cass R. Sunstein
 2014-04-18 [Perspective] Avoiding (Re)extinction
Alternative methods of identification should be used to avoid collection of voucher specimens of threatened or rediscovered species. Authors: Ben A. Minteer, James P. Collins, Karen E. Love, Robert Puschendorf
 2014-04-18 [Perspective] Exploring the Interface of Graphene and Biology
To take advantage of the properties of graphene in biomedical applications, well-defined materials need to be matched with intended applications. Authors: Kostas Kostarelos, Kostya S. Novoselov
 2014-04-18 [Perspective] Refractory Plasmonics
Stable at high temperatures, refractory plasmonic materials could boost existing optoelectronic technologies. Authors: Urcan Guler, Alexandra Boltasseva, Vladimir M. Shalaev
 2014-04-18 [Perspective] Myelin—More than Insulation
Unusual features of myelin in the mammalian cerebral cortex permit more complex forms of network integration. [Also see Report by Tomassy et al.] Author: R. Douglas Fields
 2014-04-18 [Perspective] Novelty Trumps Loss in Global Biodiversity
Although global biodiversity is declining, local ecosystems are not systematically losing diversity, but rather experiencing rapid turnover in species. [Also see Report by Dornelas et al.] Authors: John M. Pandolfi, Catherine E. Lovelock
 2014-04-18 [Perspective] Paired Plant Immune Receptors
The ability of plant cell immune sensors to combine in different pairs could expand the host's defense against pathogens. [Also see Report by Williams et al.] Authors: Marc T. Nishimura, Jeffery L. Dangl
 2014-04-18 [Research Article] A Critical Period of Sleep for Development of Courtship Circuitry and Behavior in Drosophila
Young flies need their sleep, too. Authors: Matthew S. Kayser, Zhifeng Yue, Amita Sehgal
 2014-04-18 [Report] KOI-3278: A Self-Lensing Binary Star System
A white dwarf that eclipses a Sun-like star enhances, rather than dims, its brightness through relativistic effects. Authors: Ethan Kruse, Eric Agol
 2014-04-18 [Report] An Earth-Sized Planet in the Habitable Zone of a Cool Star
NASA’s Kepler mission revealed that the fifth and outermost planet orbiting Kepler-186 is capable of hosting liquid water. Authors: Elisa V. Quintana, Thomas Barclay, Sean N. Raymond, Jason F. Rowe, Emeline Bolmont, Douglas A. Caldwell, Steve B. Howell, Stephen R. Kane, Daniel Huber, Justin R. Crepp, Jack J. Lissauer, David R. Ciardi, Jeffrey L. Coughlin, Mark E. Everett, Christopher E. Henze, Elliott Horch, Howard Isaacson, Eric B. Ford, Fred C. Adams, Martin Still, Roger C. Hunter, Billy Quarles, Franck Selsis
 2014-04-18 [Report] Emergent Space-Time Supersymmetry at the Boundary of a Topological Phase
An elusive symmetry is predicted to emerge at the boundary of an exotic condensed matter system. Authors: Tarun Grover, D. N. Sheng, Ashvin Vishwanath
 2014-04-18 [Report] Strong Increase of Tc of Sr2RuO4 Under Both Tensile and Compressive Strain
An apparatus that can apply both tensile and compressive strain is used to study an unconventional superconductor. Authors: Clifford W. Hicks, Daniel O. Brodsky, Edward A. Yelland, Alexandra S. Gibbs, Jan A. N. Bruin, Mark E. Barber, Stephen D. Edkins, Keigo Nishimura, Shingo Yonezawa, Yoshiteru Maeno, Andrew P. Mackenzie
 2014-04-18 [Report] Wafer-Scale Growth of Single-Crystal Monolayer Graphene on Reusable Hydrogen-Terminated Germanium
Wafer-scale single-crystal monolayer graphene can be repeatedly grown on a hydrogen-terminated germanium (110) surface. Authors: Jae-Hyun Lee, Eun Kyung Lee, Won-Jae Joo, Yamujin Jang, Byung-Sung Kim, Jae Young Lim, Soon-Hyung Choi, Sung Joon Ahn, Joung Real Ahn, Min-Ho Park, Cheol-Woong Yang, Byoung Lyong Choi, Sung-Woo Hwang, Dongmok Whang
 2014-04-18 [Report] Ultimate Permeation Across Atomically Thin Porous Graphene
Atomically thin nanoporous graphene membranes can sustain ultimate permeation in mass transport. Authors: Kemal Celebi, Jakob Buchheim, Roman M. Wyss, Amirhossein Droudian, Patrick Gasser, Ivan Shorubalko, Jeong-Il Kye, Changho Lee, Hyung Gyu Park
 2014-04-18 [Report] Missing Gas-Phase Source of HONO Inferred from Zeppelin Measurements in the Troposphere
The tropospheric production of HONO from a light-dependent gas-phase source raises questions about its impact on OH. Authors: Xin Li, Franz Rohrer, Andreas Hofzumahaus, Theo Brauers, Rolf Häseler, Birger Bohn, Sebastian Broch, Hendrik Fuchs, Sebastian Gomm, Frank Holland, Julia Jäger, Jennifer Kaiser, Frank N. Keutsch, Insa Lohse, Keding Lu, Ralf Tillmann, Robert Wegener, Glenn M. Wolfe, Thomas F. Mentel, Astrid Kiendler-Scharr, Andreas Wahner
 2014-04-18 [Report] Assemblage Time Series Reveal Biodiversity Change but Not Systematic Loss
Ecological communities are experiencing changes in species composition rather than unidirectional loss. [Also see Perspective by Pandolfi and Lovelock] Authors: Maria Dornelas, Nicholas J. Gotelli, Brian McGill, Hideyasu Shimadzu, Faye Moyes, Caya Sievers, Anne E. Magurran
 2014-04-18 [Report] Structural Basis for Assembly and Function of a Heterodimeric Plant Immune Receptor
A heterodimer stands at the ready; a homodimer responds with action. [Also see Perspective by Nishimura and Dangl] Authors: Simon J. Williams, Kee Hoon Sohn, Li Wan, Maud Bernoux, Panagiotis F. Sarris, Cecile Segonzac, Thomas Ve, Yan Ma, Simon B. Saucet, Daniel J. Ericsson, Lachlan W. Casey, Thierry Lonhienne, Donald J. Winzor, Xiaoxiao Zhang, Anne Coerdt, Jane E. Parker, Peter N. Dodds, Bostjan Kobe, Jonathan D. G. Jones
 2014-04-18 [Report] Crystal Structure of a Claudin Provides Insight into the Architecture of Tight Junctions
The structure of a mammalian claudin suggests how extracellular domains may form paracellular ion pathways. Authors: Hiroshi Suzuki, Tomohiro Nishizawa, Kazutoshi Tani, Yuji Yamazaki, Atsushi Tamura, Ryuichiro Ishitani, Naoshi Dohmae, Sachiko Tsukita, Osamu Nureki, Yoshinori Fujiyoshi
 2014-04-18 [Report] The Structural Basis of Pathogenic Subgenomic Flavivirus RNA (sfRNA) Production
A pseudoknot in a flavivirus RNA resists efforts by a host nuclease to untangle it. Authors: Erich G. Chapman, David A. Costantino, Jennifer L. Rabe, Stephanie L. Moon, Jeffrey Wilusz, Jay C. Nix, Jeffrey S. Kieft
 2014-04-18 [Report] The STAT3-Binding Long Noncoding RNA lnc-DC Controls Human Dendritic Cell Differentiation
A long noncoding RNA regulates dendritic cell differentiation and function. Authors: Pin Wang, Yiquan Xue, Yanmei Han, Li Lin, Cong Wu, Sheng Xu, Zhengping Jiang, Junfang Xu, Qiuyan Liu, Xuetao Cao
 2014-04-18 [Report] Enhancing Depression Mechanisms in Midbrain Dopamine Neurons Achieves Homeostatic Resilience
Intensifying pathogenic changes paradoxically ameliorate depressive symptoms in mice. Authors: Allyson K. Friedman, Jessica J. Walsh, Barbara Juarez, Stacy M. Ku, Dipesh Chaudhury, Jing Wang, Xianting Li, David M. Dietz, Nina Pan, Vincent F. Vialou, Rachael L. Neve, Zhenyu Yue, Ming-Hu Han
 2014-04-18 [Report] Distinct Profiles of Myelin Distribution Along Single Axons of Pyramidal Neurons in the Neocortex
Mouse neurons display different and distinctive patterns of myelination. [Also see Perspective by Fields] Authors: Giulio Srubek Tomassy, Daniel R. Berger, Hsu-Hsin Chen, Narayanan Kasthuri, Kenneth J. Hayworth, Alessandro Vercelli, H. Sebastian Seung, Jeff W. Lichtman, Paola Arlotta
 2014-04-18 [New Products] New Products
A weekly roundup of information on newly offered instrumentation, apparatus, and laboratory materials of potential interest to researchers.
 2014-04-18 [Podcast] Science Podcast: 18 April Show
On this week's show: observation of a distinctive binary-star system that includes a white dwarf and a roundup of stories from our daily news site.

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