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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]
 2014-09-22T00:00:00Z Prediction of nucleosome rotational positioning in yeast and human genomes based on sequence-dependent DNA anisotropy
Background: An organism's DNA sequence is one of the key factors guiding the positioning of nucleosomes within a cell's nucleus. Sequence-dependent bending anisotropy dictates how DNA is wrapped around a histone octamer. One of the best established sequence patterns consistent with this anisotropy is the periodic occurrence of AT-containing dinucleotides (WW) and GC-containing dinucleotides (SS) in the nucleosomal locations where DNA is bent in the minor and major grooves, respectively. Although this simple pattern has been observed in nucleosomes across eukaryotic genomes, its use for prediction of nucleosome positioning was not systematically tested. Results: We present a simple computational model, termed the W/S scheme, implementing this pattern, without using any training data. This model accurately predicts the rotational positioning of nucleosomes both in vitro and in vivo, in yeast and human genomes. About 65 - 75% of the experimentally observed nucleosome positions are predicted with the precision of one to two base pairs. The program is freely available at http://people.rit.edu/fxcsbi/WS_scheme/. We also introduce a simple and efficient way to compare the performance of different models predicting the rotational positioning of nucleosomes. Conclusions: This paper presents the W/S scheme to achieve accurate prediction of rotational positioning of nucleosomes, solely based on the sequence-dependent anisotropic bending of nucleosomal DNA. This method successfully captures DNA features critical for the rotational positioning of nucleosomes, and can be further improved by incorporating additional terms related to the translational positioning of nucleosomes in a species-specific manner.


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BMC Genomics - Latest Articles   [more] [xml]
 2014-09-22T00:00:00Z Genome-wide identification and analysis of the growth-regulating factor family in Chinese cabbage (Brassica rapa L. ssp. pekinensis)
Background: Growth regulating factors (GRFs) have been shown to play important roles in plant growth and development. GRF genes represent a large multigene family in plants. Recently, genome-wide structural and evolutionary analyses of the GRF gene families in Arabidopsis, rice, and maize have been reported. Chinese cabbage (Brassica rapa L. ssp. pekinensis) is one of the most important vegetables for agricultural production, and a full genome assembly for this plant has recently been released. However, to our knowledge, the GRF gene family from Chinese cabbage has not been characterized in detail. Results: In this study, genome-wide analysis was carried out to identify all the GRF genes in Chinese cabbage. Based on the complete Chinese cabbage genome sequence, 17 nonredundant GRF genes, named BrGRFs, were identified and classified into six groups. Phylogenetic analysis of the translated GRF protein sequences from Chinese cabbage, Arabidopsis, and rice indicated that the Chinese cabbage GRF proteins were more closely related to the GRF proteins of Arabidopsis than to those of rice. Expression profile analysis showed that the BrGRF genes had uneven transcript levels in different organs or tissues, and the transcription of most BrGRF genes was induced by gibberellic acid (GA3) treatment. Additionally, over-expression of BrGRF8 in transgenic Arabidopsis plants increased the sizes of the leaves and other organs by regulation of cell proliferation. Conclusions: The data obtained from this investigation will contribute to a better understanding of the characteristics of the GRF gene family in Chinese cabbage, and provide a basis for further studies to investigate GRF protein function during development as well as for Chinese cabbage-breeding programs to improve yield and/or head size.


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BMC Biochemistry - Latest Articles   [more] [xml]
 2014-09-10T00:00:00Z Importance of extended protease substrate recognition motifs in steering BNIP-2 cleavage by human and mouse granzymes B
Background: Previous screening of the substrate repertoires and substrate specificity profiles of granzymes resulted in long substrate lists highly likely containing bystander substrates. Here, a recently developed degradomics technology that allows distinguishing efficiently from less efficiently cleaved substrates was applied to study the degradome of mouse granzyme B (mGrB). Results: In vitro kinetic degradome analysis resulted in the identification of 37 mGrB cleavage events, 9 of which could be assigned as efficiently targeted ones. Previously, cleavage at the IEAD75 tetrapeptide motif of Bid was shown to be efficiently and exclusively targeted by human granzyme B (hGrB) and thus not by mGrB. Strikingly, and despite holding an identical P4-P1 human Bid (hBid) cleavage motif, mGrB was shown to efficiently cleave the BCL2/adenovirus E1B 19 kDa protein-interacting protein 2 or BNIP-2 at IEAD28. Like Bid, BNIP-2 represents a pro-apoptotic Bcl-2 protein family member and a potential regulator of GrB induced cell death. Next, in vitro analyses demonstrated the increased efficiency of human and mouse BNIP-2 cleavage by mGrB as compared to hGrB indicative for differing Bid/BNIP-2 substrate traits beyond the P4-P1 IEAD cleavage motif influencing cleavage efficiency. Murinisation of differential primed site residues in hBNIP-2 revealed that, although all contributing, a single mutation at the P3′ position was found to significantly increase the mGrB/hGrB cleavage ratio, whereas mutating the P1′ position from I29 > T yielded a 4-fold increase in mGrB cleavage efficiency. Finally, mutagenesis analyses revealed the composite BNIP-2 precursor patterns to be the result of alternative translation initiation at near-cognate start sites within the 5′ leader sequence (5′UTR) of BNIP-2. Conclusions: Despite their high sequence similarity, and previously explained by their distinct tetrapeptide specificities observed, the substrate repertoires of mouse and human granzymes B only partially overlap. Here, we show that the substrate sequence context beyond the P4-P1 positions can influence orthologous granzyme B cleavage efficiencies to an unmatched extent. More specifically, in BNIP-2, the identical and hGrB optimal IEAD tetrapeptide substrate motif is targeted highly efficiently by mGrB, while this tetrapeptide motif is refractory towards mGrB cleavage in Bid.


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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]
 2014-09-19 [Errata] Erratum for the Report: “Observation of the transition state for pressure-induced BO3→ BO4 conversion in glass” by T. Edwards, T. Endo, J. H. Walton, S. Sen
 2014-09-19 [Editorial] Be one of the first
On 3 July 1880, “a weekly journal of scientific progress” published its first research articles under the banner Science. From that original print medium, the inaugural set of papers has been reprinted, photocopied, posted online, converted to PDF, and even etched in glass blocks to serve as special gifts. Being part of the vanguard is indeed a privilege, and opportunities to be one of the first are rare. For that reason, I proudly announce that Science Advances, a new open-access journal for all of the sciences, officially joins the Science family of journals (Science, Science Translational Medicine, and Science Signaling) and is now accepting submissions (go to www.scienceadvances.org). In February 2015, the inaugural papers will be released, heralding the start of something big in scope, reach, and influence. Author: Marcia McNutt
 2014-09-19 [Editorial] The Pope tackles sustainability
The war on environmental degradation has a powerful new ally: Pope Francis. Prompted by a Joint Workshop of the Pontifical Academy of Sciences and the Pontifical Academy of Social Sciences on sustainability that was convened in May 2014, the Vatican has articulated some of its strongest environmental statements to date, calling for all of us to take personal responsibility and redirect our relationship with nature to ensure the future habitability and sustainability of this planet (see the Perspective on p. 1457). The problems that motivate the Vatican are no different from those that concern the scientific community: depletion of nonrenewable resources, loss of ecosystem services, and risks from changing climate. But what the Vatican contributes is the rationale for taking action: because it is our moral responsibility to bequeath a habitable planet to future generations. Author: Marcia McNutt
 2014-09-19 [In Brief] This week's section
A roundup of weekly science policy and related news.
 2014-09-19 [In Depth] All eyes on shooting stars
By tracking meteorite falls, camera and radar networks help searchers find precious fragments. Author: Eric Hand
 2014-09-19 [In Depth] Harmful mutations can fly under the radar
With more sensitive genetic tests, researchers are hunting the roots of disease in the human “mosaic.” Author: Kelly Servick
 2014-09-19 [In Depth] Who are the science stars of Twitter?
Science communicators and some highly cited researchers, but few women, make top 50 most followed list. Author: Jia You
 2014-09-19 [In Depth] Ebola vaccine: Little and late
Scaling up production of Ebola vaccines and treatments will take many months. Author: Jon Cohen
 2014-09-19 [In Depth] Play it again, Uncle Sam
Prominent academics recommend growth in federal basic research budget that matches previous golden era Author: Jeffrey Mervis
 2014-09-19 [Feature] No miracles
Biologist Russell Gray uses evolutionary ideas to probe the origin of languages and complex thinking. Author: Virginia Morell
 2014-09-19 [Feature] Outsmarting the placebo effect
Can a genetic test to predict a person's level of placebo response help new drugs win approval? Author: Kelly Servick
 2014-09-19 [Perspective] Biomimetics and evolution
Linking biomechanical and evolutionary analysis helps to create viable biomimetic products Author: S. N. Patek
 2014-09-19 [Perspective] Manipulating spin in organic spintronics
Probing the interplay between the electronic and nuclear spins in organic semiconductors [Also see Report by Malissa et al.] Author: Peter A. Bobbert
 2014-09-19 [Perspective] Superheavy carbonyls
The radioactive superheavy element seaborgium can form a carbonyl compound during its short lifetime [Also see Report by Even et al.] Author: Walter Loveland
 2014-09-19 [Perspective] Cascading into focus
Structures of a multisubunit protein-RNA complex reveal how the CRISPR system recognizes DNA targets [Also see Research Articles by Jackson et al. and Mulepati et al.] Authors: Yan Zhang, Erik J. Sontheimer
 2014-09-19 [Perspective] Tracking antibiotic resistance
Sequencing plasmids can reveal the transmission of resistance among bacteria from patients in a clinical setting Authors: Scott A. Beatson, Mark J. Walker
 2014-09-19 [Perspective] Making strong nanomaterials ductile with gradients
Microstructures that increase metal crystallite size from nanoscale with surface depth are both strong and ductile Author: K. Lu
 2014-09-19 [Policy Forum] Pursuit of the common good
Religious institutions may mobilize public opinion and action Authors: Partha Dasgupta, Veerabhadran Ramanathan
 2014-09-19 [Book Review] Ode to fine wines and rocks
Author: Lawrence D. Meinert
 2014-09-19 [Book Review] Understanding and saving big predators
Author: Matthew E. Gompper
 2014-09-19 [Books et al.] Books Received
A listing of books received at Science during the week ending 12 September 2014.
 2014-09-19 [Letter] Island outlook: Warm and swampy
Authors: Dennis Hubbard, Eberhard Gischler, Peter Davies, Lucien Montaggioni, Gilbert Camoin, Wolf-Christian Dullo, Curt Storlazzi, Michael Field, Charles Fletcher, Eric Grossman, Charles Sheppard, Halard Lescinsky, Douglas Fenner, John McManus, Sander Scheffers
 2014-09-19 [Letter] Lab animal protection overdue
Author: Aysha Akhtar
 2014-09-19 [Letter] Prenatal prevention
Author: Philippe Grandjean
 2014-09-19 This Week in Science
Rings of ocean upwelling | A carbonyl compound that tips the scales | Cancer immunotherapy expands T cell attack | Aligning a magnetic atomic gas | The file drawer is full. Should we worry? | Human adult stem cell expansion | Building connections by gene therapy | One protein smothers other deadly ones | Establishing memory of gene repression | Regulating DNA building blocks | Studying magnetism with cold atoms | Organic semiconductors go out for a spin | A pathway that controls our mood | A foreign-DNA–destroying machine
 2014-09-19 Editors' Choice
Biting into Big Data in the Big Apple | Simpler coating of silica surfaces | Clone wars: Let's pick out the superbugs | Signaling back and forth for cartilage | Gut bugs may boost flu shots' effects | Getting by with a little help from eel friends | Magnetism leads to superconductivity | Reservoir assembly drives super-eruptions
 2014-09-19 [Review] Metabolic control of cell death
Beyond their contribution to basic metabolism, the major cellular organelles, in particular mitochondria, can determine whether cells respond to stress in an adaptive or suicidal manner. Thus, mitochondria can continuously adapt their shape to changing bioenergetic demands as they are subjected to quality control by autophagy, or they can undergo a lethal permeabilization process that initiates apoptosis. Along similar lines, multiple proteins involved in metabolic circuitries, including oxidative phosphorylation and transport of metabolites across membranes, may participate in the regulated or catastrophic dismantling of organelles. Many factors that were initially characterized as cell death regulators are now known to physically or functionally interact with metabolic enzymes. Thus, several metabolic cues regulate the propensity of cells to activate self-destructive programs, in part by acting on nutrient sensors. This suggests the existence of “metabolic checkpoints” that dictate cell fate in response to metabolic fluctuations. Here, we discuss recent insights into the intersection between metabolism and cell death regulation that have major implications for the comprehension and manipulation of unwarranted cell loss. Authors: Douglas R. Green, Lorenzo Galluzzi, Guido Kroemer
 2014-09-19 [Research Article] Spectroscopic observation of SU(N)-symmetric interactions in Sr orbital magnetism
An unusual symmetry is observed in an array of pancake-shaped atomic clouds of strontium-87. Authors: X. Zhang, M. Bishof, S. L. Bromley, C. V. Kraus, M. S. Safronova, P. Zoller, A. M. Rey, J. Ye
 2014-09-19 [Research Article] Crystal structure of the CRISPR RNA– guided surveillance complex from Escherichia coli
The structure of the Cascade complex reveals how the bacterial CRISPR immune system targets foreign DNA. [Also see Perspective by Zhang and Sontheimer] Authors: Ryan N. Jackson, Sarah M. Golden, Paul B. G. van Erp, Joshua Carter, Edze R. Westra, Stan J. J. Brouns, John van der Oost, Thomas C. Terwilliger, Randy J. Read, Blake Wiedenheft
 2014-09-19 [Research Article] Crystal structure of a CRISPR RNA– guided surveillance complex bound to a ssDNA target
The structure of the Cascade complex reveals how the bacterial CRISPR immune system targets foreign DNA. [Also see Perspective by Zhang and Sontheimer] Authors: Sabin Mulepati, Annie Héroux, Scott Bailey
 2014-09-19 [Report] Observation of Fermi surface deformation in a dipolar quantum gas
Erbium atoms with high magnetic dipole moments interact anisotropically, causing the Fermi surface to deform. Authors: K. Aikawa, S. Baier, A. Frisch, M. Mark, C. Ravensbergen, F. Ferlaino
 2014-09-19 [Report] Room-temperature coupling between electrical current and nuclear spins in OLEDs
Magnetic resonance spectroscopy enables detection and manipulation of subtle spin interactions in organic semiconductors. [Also see Perspective by Bobbert] Authors: H. Malissa, M. Kavand, D. P. Waters, K. J. van Schooten, P. L. Burn, Z. V. Vardeny, B. Saam, J. M. Lupton, C. Boehme
 2014-09-19 [Report] Synthesis and detection of a seaborgium carbonyl complex
A special apparatus enables synthesis of a compound with carbon bonds to a short-lived element produced via nuclear reaction. [Also see Perspective by Loveland] Authors: J. Even, A. Yakushev, Ch. E. Düllmann, H. Haba, M. Asai, T. K. Sato, H. Brand, A. Di Nitto, R. Eichler, F. L. Fan, W. Hartmann, M. Huang, E. Jäger, D. Kaji, J. Kanaya, Y. Kaneya, J. Khuyagbaatar, B. Kindler, J. V. Kratz, J. Krier, Y. Kudou, N. Kurz, B. Lommel, S. Miyashita, K. Morimoto, K. Morita, M. Murakami, Y. Nagame, H. Nitsche, K. Ooe, Z. Qin, M. Schädel, J. Steiner, T. Sumita, M. Takeyama, K. Tanaka, A. Toyoshima, K. Tsukada, A. Türler, I. Usoltsev, Y. Wakabayashi, Y. Wang, N. Wiehl, S. Yamaki
 2014-09-19 [Report] GABA/glutamate co-release controls habenula output and is modified by antidepressant treatment
The relative level of excitation and inhibition controls activity of a brain region that is linked to depression. Authors: Steven J. Shabel, Christophe D. Proulx, Joaquin Piriz, Roberto Malinow
 2014-09-19 [Report] Six centuries of variability and extremes in a coupled marine-terrestrial ecosystem
Winter upwelling along the Pacific coast of North America became unusually variable during the 20th century. Authors: Bryan A. Black, William J. Sydeman, David C. Frank, Daniel Griffin, David W. Stahle, Marisol García-Reyes, Ryan R. Rykaczewski, Steven J. Bograd, William T. Peterson
 2014-09-19 [Report] Publication bias in the social sciences: Unlocking the file drawer
Fully half of peer-reviewed and implemented social science experiments are not published. Authors: Annie Franco, Neil Malhotra, Gabor Simonovits
 2014-09-19 [Report] DOK7 gene therapy benefits mouse models of diseases characterized by defects in the neuromuscular junction
Supersizing neuromuscular junctions by gene therapy ameliorates muscle weakness in mice. Authors: Sumimasa Arimura, Takashi Okada, Tohru Tezuka, Tomoko Chiyo, Yuko Kasahara, Toshiro Yoshimura, Masakatsu Motomura, Nobuaki Yoshida, David Beeson, Shin’ichi Takeda, Yuji Yamanashi
 2014-09-19 [Report] Pyrimidoindole derivatives are agonists of human hematopoietic stem cell self-renewal
The self-renewal of human hematopoietic stem cells in vitrois enhanced by the pyrimidoindole derivative UM171. Authors: Iman Fares, Jalila Chagraoui, Yves Gareau, Stéphane Gingras, Réjean Ruel, Nadine Mayotte, Elizabeth Csaszar, David J. H. F. Knapp, Paul Miller, Mor Ngom, Suzan Imren, Denis-Claude Roy, Kori L. Watts, Hans-Peter Kiem, Robert Herrington, Norman N. Iscove, R. Keith Humphries, Connie J. Eaves, Sandra Cohen, Anne Marinier, Peter W. Zandstra, Guy Sauvageau
 2014-09-19 [Report] IRBIT is a novel regulator of ribonucleotide reductase in higher eukaryotes
A regulator of the enzyme that makes the building blocks of DNA provides a new target for anticancer drugs. Authors: Alexei Arnaoutov, Mary Dasso
 2014-09-19 [Report] H3K27me and PRC2 transmit a memory of repression across generations and during development
Repression is perpetuated across generations and cell divisions via methylated histones and methylating enzymes. Authors: Laura J. Gaydos, Wenchao Wang, Susan Strome
 2014-09-19 [Business Office Feature] What's next in 'omics: The metabolome
Chris Tachibana
 2014-09-19 [New Products] New Products
A weekly roundup of information on newly offered instrumentation, apparatus, and laboratory materials of potential interest to researchers.
 2014-09-19 [Podcast] Science Podcast: 19 September Show
On this week's show: Capturing a 600-year record for a coastal ecosystem.
 2014-09-19 [Business Office Feature] Human performance in space: Advancing astronautics research in China
As we pursue bolder initiatives in space, and as China moves towards launching a permanently manned space station, gaining a clearer understanding of the impact of long-term space travel becomes essential to maintain the well-being of astronauts. Serious consideration has been given to human travel beyond low Earth orbit—where the International Space Station resides—and beyond the moon, possibly to Mars or the moons of Jupiter. Examples of groundbreaking space research currently underway in China are collected in this booklet, providing the reader with a taste of what future space exploration might look like. As Chinese scientists learn about the effects on the body and mind, they are applying their knowledge to modify equipment, improve astronaut training, and fine-tune the selection process for astronauts. Other scientists and engineers around the world will benefit, and can apply the new information to space programs in their own countries. Human Performance in Space (PDF, 18 MB)Human Performance in Space (PDF, low resolution version, 6 MB)Read the e-bookletThis booklet brought to you by the Science/AAAS Custom Publishing Office.DOI: 10.1126/science.opms.sb0002
 2014-09-19 [Working Life] Rhubarb pie and science
Author: Sandy Becker

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