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BMC Structural Biology - Latest Articles   [more] [xml]
 2014-10-18T00:00:00Z A PDB-wide, evolution-based assessment of protein¿protein interfaces
Background: Thanks to the growth in sequence and structure databases, more than 50 million sequences are now available in UniProt and 100,000 structures in the PDB. Rich information about protein?protein interfaces can be obtained by a comprehensive study of protein contacts in the PDB, their sequence conservation and geometric features. Results: An automated computational pipeline was developed to run our Evolutionary Protein?Protein Interface Classifier (EPPIC) software on the entire PDB and store the results in a relational database, currently containing > 800,000 interfaces. This allows the analysis of interface data on a PDB-wide scale. Two large benchmark datasets of biological interfaces and crystal contacts, each containing about 3000 entries, were automatically generated based on criteria thought to be strong indicators of interface type. The BioMany set of biological interfaces includes NMR dimers solved as crystal structures and interfaces that are preserved across diverse crystal forms, as catalogued by the Protein Common Interface Database (ProtCID) from Xu and Dunbrack. The second dataset, XtalMany, is derived from interfaces that would lead to infinite assemblies and are therefore crystal contacts. BioMany and XtalMany were used to benchmark the EPPIC approach. The performance of EPPIC was also compared to classifications from the Protein Interfaces, Surfaces, and Assemblies (PISA) program on a PDB-wide scale, finding that the two approaches give the same call in about 85% of PDB interfaces. By comparing our safest predictions to the PDB author annotations, we provide a lower-bound estimate of the error rate of biological unit annotations in the PDB. Additionally, we developed a PyMOL plugin for direct download and easy visualization of EPPIC interfaces for any PDB entry. Both the datasets and the PyMOL plugin are available at http://www.eppic-web.org/ewui/\#downloads. Conclusions: Our computational pipeline allows us to analyze protein?protein contacts and their sequence conservation across the entire PDB. Two new benchmark datasets are provided, which are over an order of magnitude larger than existing manually curated ones. These tools enable the comprehensive study of several aspects of protein?protein contacts in the PDB and represent a basis for future, even larger scale studies of protein?protein interactions.


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BMC Bioinformatics - Latest Articles   [more] [xml]
 2014-10-22T00:00:00Z SummonChimera infers integrated viral genomes with nucleotide precision from NGS data
Background: Viral integration into a host genome is defined by two chimeric junctions that join viral and host DNA. Recently, computational tools have been developed that utilize NGS data to detect chimeric junctions. These methods identify individual viral-host junctions but do not associate chimeric pairs as an integration event. Without knowing the chimeric boundaries of an integration, its genetic content cannot be determined. Results: Summonchimera is a Perl program that associates chimera pairs to infer the complete viral genomic integration event to the nucleotide level within single or paired-end NGS data. SummonChimera integration prediction was verified on a set of single-end IonTorrent reads from a purified Salmonella bacterium with an integrated bacteriophage. Furthermore, SummonChimera predicted integrations from experimentally verified Hepatitis B Virus chimeras within a paired-end Whole Genome Sequencing hepatocellular carcinoma tumor database. Conclusions: SummonChimera identified all experimentally verified chimeras detected by current computational methods. Further, SummonChimera integration inference precisely predicted bacteriophage integration. The application of SummonChimera to cancer NGS accurately identifies deletion of host and viral sequence during integration. The precise nucleotide determination of an integration allows prediction of viral and cellular gene transcription patterns.


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BMC Genomics - Latest Articles   [more] [xml]
 2014-10-24T00:00:00Z Transcriptomic characterization of the immunogenetic repertoires of heteromyid rodents
Background: When populations evolve under disparate environmental conditions, they experience different selective pressures that shape patterns of sequence evolution and gene expression. These may be manifested in genetic and phenotypic differences such as a diverse immunogenetic repertoire in species from tropical latitudes that have greater and/or different parasite burdens than more temperate species. To test this idea, we compared the transcriptomes of one tropical species (Heteromys desmarestianus) and two species from temperate latitudes (Dipodomys spectabilis and Chaetodipus baileyi) from the Heteromyidae. We did so in a search for positive selection on sequences and/or differential expression, while controlling for phylogenetic history in our choice of species. Results: We identified 127,812 contigs and annotated 34,878 of these, identifying immune genes associated with interleukins, cytokines, and the production of mast cells. We identified 632 genes that were upregulated in H. desmarestianus (8.7% of genes tested) and 492 (6.7%) that were downregulated. Gene ontology terms including "immune response" were associated with 31 (4.9%) of the 632 upregulated genes. We found preliminary evidence for positive selection on three genes (Palmitoyltransferase ZDHHC5 Ubiquitin-conjugating enzyme E2 N, Krueppel-like factor 10, and Spindle and kinetochore-associated protein 1) along the H. desmarestianus lineage. Conclusions: Overall our findings pinpoint genes in species from disparate environments that are on different evolutionary trajectories in terms of expression levels and/or nucleotide sequence. Our data indicate there are significant differences in the expression of genes among the spleen transcriptomes of these species and that a number of these differentially expressed genes do not show the same pattern of differential expression in another tissue type. This points to the possibility of expression differences between these species specific to the spleen transcriptome.


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BMC Biochemistry - Latest Articles   [more] [xml]
 2014-10-09T00:00:00Z Alleviation effect of arbutin on oxidative stress generated through tyrosinase reaction with l-tyrosine and l-DOPA
Background: Hydroxyl radical that has the highest reactivity among reactive oxygen species (ROS) is generated through l-tyrosine-tyrosinase reaction. Thus, the melanogenesis might induce oxidative stress in the skin. Arbutin (p-hydroxyphenyl-β-d-glucopyranoside), a well-known tyrosinase inhibitor has been widely used for the purpose of skin whitening. The aim of the present study was to examine if arbutin could suppress the hydroxyl radical generation via tyrosinase reaction with its substrates, l-tyrosine and l-DOPA. Results: The hydroxyl radical, which was determined by an electron spin resonance-spin trapping technique, was generated by the addition of not only l-tyrosine but l-DOPA to tyrosinase in a concentration dependent manner. Arbutin could inhibit the hydroxyl radical generation in the both reactions. Conclusion: It is presumed that arbutin could alleviate oxidative stress derived from the melanogenic pathway in the skin in addition to its function as a whitening agent in cosmetics.


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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]
 2014-10-24 [Editorial] China's private universities
China's expansion of universities has not been on a level playing field. Earlier this year, Education Minister Guiren Yuan declared that the government must treat both public and private universities equally. As founder and president of one of China's largest private universities, I wholeheartedly agree. China's private universities can help usher in new opportunities for social and economic development, but they must be enabled to launch robust education programs and compete for research grants. Unless the government loosens restrictions on such endeavors, private universities could enter a tailspin, and such an erosion of higher education could threaten social stability. Author: Huiqing Jin
 2014-10-24 [In Brief] This week's section
A roundup of weekly science policy and related news.
 2014-10-24 [In Depth] U.S. halts two dozen risky virus studies
One-year “pause” to develop new policy on controversial research that enhances pathogens. Author: Jocelyn Kaiser
 2014-10-24 [In Depth] How we tamed ourselves—and became modern
“Self-domestication” turned humans into the cooperative species we are today. Author: Ann Gibbons
 2014-10-24 [In Depth] Epic pre-Columbian voyage suggested by genes
South American DNA found in Easter Islanders. Author: Andrew Lawler
 2014-10-24 [In Depth] Taiwan's ocean program reels from loss of ship, scientists
New vessel was sparking international collaborations. Author: Dennis Normile
 2014-10-24 [In Depth] Election stakes go beyond control of the Senate
Funding, peer review, water rules, fusion, and other science issues on tap after the vote. Author: Jeffrey Mervis
 2014-10-24 [In Depth] Does science suffer an ‘innovation deficit’?
New catch phrase represents a two-edged sword for research community. Author: Jeffrey Mervis
 2014-10-24 [In Depth] Searching for science in India's traditional medicine
Critics say ayurgenomics is at best a quixotic quest. Author: Priyanka Pulla
 2014-10-24 [Feature] Show me the money
A bitter dispute lays bare questionable practices in China's foreign-talent programs. Author: Mara Hvistendahl
 2014-10-24 [Perspective] Beyond the rainbow
Dinosaur color vision may have been key to the evolution of bird feathers Authors: Marie-Claire Koschowitz, Christian Fischer, Martin Sander
 2014-10-24 [Perspective] Terminating the replisome
Multiple proteins modify and dismantle a key enzyme after DNA replication terminates [Also see Research Article by Maric et al. and Report by Priego Moreno et al.] Author: Stephen P. Bell
 2014-10-24 [Perspective] Boundless no more
Ending illegal, unregulated, and unreported fishing would bring hope for ocean wildlife Authors: Amanda C. J. Vincent, Jean M. Harris
 2014-10-24 [Perspective] Harnessing chirality for valleytronics
Artificial magnetic fields bend electron trajectories in gapped graphene [Also see Report by Gorbachev et al.] Authors: Mark B. Lundeberg, Joshua A. Folk
 2014-10-24 [Perspective] Sex and the single fern
Separation of the synthesis and sensing of a signaling molecule controls sex in ferns [Also see Report by Tanaka et al.] Author: Tai-ping Sun
 2014-10-24 [Perspective] Breathing the unbreathable
A crystal structure reveals how some bacteria break down organohalide pollutants [Also see Report by Bommer et al.] Author: Elizabeth Anne Edwards
 2014-10-24 [Perspective] Ratcheting the evolution of multicellularity
Traits that entrench cells in a group lifestyle may pave the way for complexity Authors: Eric Libby, William C. Ratcliff
 2014-10-24 [Perspective] Unanchored ubiquitin in virus uncoating
Components of a cellular degradation system are exploited by influenza virus during infection [Also see Report by Banerjee et al.] Authors: Ricardo Rajsbaum, Adolfo García-Sastre
 2014-10-24 [Policy Forum] Coping with the curse of freshwater variability
Institutions, infrastructure, and information for adaptation Authors: J. W. Hall, D. Grey, D. Garrick, F. Fung, C. Brown, S. J. Dadson, C. W. Sadoff
 2014-10-24 [Book Review] The rise and fall of the nation's doctor
Author: Jonathan M. Samet
 2014-10-24 [Book Review] Science on the silver screen
Author: Caroline Ash
 2014-10-24 [Books et al.] Books Received
A listing of books received at Science during the week ending 17 October 2014.
 2014-10-24 [Letter] Ebola: Mobility data
Authors: M. Elizabeth Halloran, Alessandro Vespignani, Nita Bharti, Leora R. Feldstein, K. A. Alexander, Matthew Ferrari, Jeffrey Shaman, John M. Drake, Travis Porco, Joseph N. S. Eisenberg, Sara Y. Del Valle, Eric Lofgren, Samuel V. Scarpino, Marisa C. Eisenberg, Daozhou Gao, James M. Hyman, Stephen Eubank, Ira M. Longini
 2014-10-24 [Letter] Ebola: Public-private partnerships
Authors: L. A. Reperant, L. H. M. van de Burgwal, E. Claassen, A. D. M. E. Osterhaus
 2014-10-24 [Letter] Ebola: Social research overlooked
Author: Gilles Guerrier
 2014-10-24 [Technical Comment] Comment on “A Jurassic ornithischian dinosaur from Siberia with both feathers and scales”
Godefroit et al. (Reports, 25 July 2014, p. 451) reported scales and feathers, including “basal plates,” in an ornithischian dinosaur. Their arguments against the filaments being collagen fibers are not supported because of a fundamental misinterpretation of such structures and underestimation of their size. The parsimonious explanation is that the filaments are support fibers in association with badly degraded scales and that they do not represent early feather stages. Author: Theagarten Lingham-Soliar
 2014-10-24 [Technical Response] Response to Comment on “A Jurassic ornithischian dinosaur from Siberia with both feathers and scales”
Lingham-Soliar questions our interpretation of integumentary structures in the Middle-Late Jurassic ornithischian dinosaur Kulindadromeus as feather-like appendages and alternatively proposes that the compound structures observed around the humerus and femur of Kulindadromeus are support fibers associated with badly degraded scales. We consider this hypothesis highly unlikely because of the taphonomy and morphology of the preserved structures. Authors: Pascal Godefroit, Sofia M. Sinitsa, Danielle Dhouailly, Yuri L. Bolotsky, Alexander V. Sizov, Maria E. McNamara, Michael J. Benton, Paul Spagna
 2014-10-24 This Week in Science
Making adjustments for a new neighborhood | Digital amplification of T cell receptor signals | Mountain dwellers of the Pleistocene | Flu mimics damaged proteins during entry | Making use of graphene's valleys | Layering on solar cell power and stability | Building with alphahelical coiled coils | Anticancer drug coming out on TOPK | How bacteria break down organohalides | Experimental platforms for probing bacteria | From single molecules to embryos in living color | How to stop after copying the genome | How to make vanadium dioxide metallic | Ensuring handedness when breaking C-H bonds | Identifying the workhorse of working memory | Sex determination driven by community cooperation | Addressing fishing threats to ocean wildlife | Dinosaur color vision and the evolution of feathers
 2014-10-24 Editors' Choice
Actin reins in plant cell division | When winter snowfall trumps summer melting | A primate model of Alzheimer's disease | Helping palladium atoms stand apart | For radiotherapy, less can be more | Blending polymers with Janus particles | A microRNA for retinal regeneration
 2014-10-24 [Review] Zooming in to see the bigger picture: Microfluidic and nanofabrication tools to study bacteria
The spatial structure of natural habitats strongly affects bacterial life, ranging from nanoscale structural features that individual cells exploit for surface attachment, to micro- and millimeter-scale chemical gradients that drive population-level processes. Nanofabrication and microfluidics are ideally suited to manipulate the environment at those scales and have emerged as powerful tools with which to study bacteria. Here, we review the new scientific insights gained by using a diverse set of nanofabrication and microfluidic techniques to study individual bacteria and multispecies communities. This toolbox is beginning to elucidate disparate bacterial phenomena—including aging, electron transport, and quorum sensing—and enables the dissection of environmental communities through single-cell genomics. A more intimate integration of microfluidics, nanofabrication, and microbiology will enable further exploration of bacterial life at the smallest scales. Authors: Felix J. H. Hol, Cees Dekker
 2014-10-24 [Research Article] Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution
A new microscope allows three-dimensional imaging of living systems at very high resolution in real time. Authors: Bi-Chang Chen, Wesley R. Legant, Kai Wang, Lin Shao, Daniel E. Milkie, Michael W. Davidson, Chris Janetopoulos, Xufeng S. Wu, John A. Hammer, Zhe Liu, Brian P. English, Yuko Mimori-Kiyosue, Daniel P. Romero, Alex T. Ritter, Jennifer Lippincott-Schwartz, Lillian Fritz-Laylin, R. Dyche Mullins, Diana M. Mitchell, Joshua N. Bembenek, Anne-Cecile Reymann, Ralph Böhme, Stephan W. Grill, Jennifer T. Wang, Geraldine Seydoux, U. Serdar Tulu, Daniel P. Kiehart, Eric Betzig
 2014-10-24 [Research Article] Cdc48 and a ubiquitin ligase drive disassembly of the CMG helicase at the end of DNA replication
DNA replication machinery stably encircles replicating DNA and is actively disassembled once replication is complete. [Also see Perspective by Bell] Authors: Marija Maric, Timurs Maculins, Giacomo De Piccoli, Karim Labib
 2014-10-24 [Report] Fulleropyrrolidine interlayers: Tailoring electrodes to raise organic solar cell efficiency
A polar fullerene derivative layered on the cathode of a polymer solar cell fosters simultaneous stability and efficiency. Authors: Zachariah A. Page, Yao Liu, Volodimyr V. Duzhko, Thomas P. Russell, Todd Emrick
 2014-10-24 [Report] A photoinduced metal-like phase of monoclinic VO2 revealed by ultrafast electron diffraction
Simultaneous measurements of structural and optical properties are used to study optically excited vanadium dioxide. Authors: Vance R. Morrison, Robert. P. Chatelain, Kunal L. Tiwari, Ali Hendaoui, Andrew Bruhács, Mohamed Chaker, Bradley J. Siwick
 2014-10-24 [Report] Detecting topological currents in graphene superlattices
Graphene is aligned with a layer of hexagonal boron nitride to achieve the valley Hall effect. [Also see Perspective by Lundeberg and Folk] Authors: R. V. Gorbachev, J. C. W. Song, G. L. Yu, A. V. Kretinin, F. Withers, Y. Cao, A. Mishchenko, I. V. Grigorieva, K. S. Novoselov, L. S. Levitov, A. K. Geim
 2014-10-24 [Report] Room-temperature enantioselective C–H iodination via kinetic resolution
Palladium catalysis produces benzylamine derivatives of interest in medicinal chemistry. Authors: Ling Chu, Kai-Jiong Xiao, Jin-Quan Yu
 2014-10-24 [Report] Structural basis for organohalide respiration
The crystal structure of a reductive dehalogenase shows how bacteria break down organohalide contaminants. [Also see Perspective by Edwards] Authors: Martin Bommer, Cindy Kunze, Jochen Fesseler, Torsten Schubert, Gabriele Diekert, Holger Dobbek
 2014-10-24 [Report] Medial prefrontal activity during delay period contributes to learning of a working memory task
Optogenetic manipulation of neuronal activity as memories form can impair acquisition of working memory. Authors: Ding Liu, Xiaowei Gu, Jia Zhu, Xiaoxing Zhang, Zhe Han, Wenjun Yan, Qi Cheng, Jiang Hao, Hongmei Fan, Ruiqing Hou, Zhaoqin Chen, Yulei Chen, Chengyu T. Li
 2014-10-24 [Report] Rapid evolution of a native species following invasion by a congener
On small islands in Florida, native lizards adapt to higher perches following invasion by a related species. Authors: Y. E. Stuart, T. S. Campbell, P. A. Hohenlohe, R. G. Reynolds, L. J. Revell, J. B. Losos
 2014-10-24 [Report] Paleoindian settlement of the high-altitude Peruvian Andes
Artifacts and rock shelters indicate hunter-gatherer presence at ~4500 meters above sea level, 12.8 to 11.5 thousand years ago. Authors: Kurt Rademaker, Gregory Hodgins, Katherine Moore, Sonia Zarrillo, Christopher Miller, Gordon R. M. Bromley, Peter Leach, David A. Reid, Willy Yépez Álvarez, Daniel H. Sandweiss
 2014-10-24 [Report] Antheridiogen determines sex in ferns via a spatiotemporally split gibberellin synthesis pathway
A biosynthetic pathway split between young and old individual ferns controls hormonal signaling that regulates sex determination. [Also see Perspective by Sun] Authors: Junmu Tanaka, Kenji Yano, Koichiro Aya, Ko Hirano, Sayaka Takehara, Eriko Koketsu, Reynante Lacsamana Ordonio, Seung-Hyun Park, Masatoshi Nakajima, Miyako Ueguchi-Tanaka, Makoto Matsuoka
 2014-10-24 [Report] Influenza A virus uses the aggresome processing machinery for host cell entry
A flu virus mimics misfolded protein aggregates and hijacks associated cellular machinery early during infection. [Also see Perspective by Rajsbaum and García-Sastre] Authors: Indranil Banerjee, Yasuyuki Miyake, Samuel Philip Nobs, Christoph Schneider, Peter Horvath, Manfred Kopf, Patrick Matthias, Ari Helenius, Yohei Yamauchi
 2014-10-24 [Report] Polyubiquitylation drives replisome disassembly at the termination of DNA replication
DNA replication machinery stably encircles replicating DNA and is actively disassembled once replication is complete. [Also see Perspective by Bell] Authors: Sara Priego Moreno, Rachael Bailey, Nicholas Campion, Suzanne Herron, Agnieszka Gambus
 2014-10-24 [Report] High thermodynamic stability of parametrically designed helical bundles
Protein design expands the repertoire of coiled-coil structures to α-helical barrels and hyperstable helical bundles. Authors: Po-Ssu Huang, Gustav Oberdorfer, Chunfu Xu, Xue Y. Pei, Brent L. Nannenga, Joseph M. Rogers, Frank DiMaio, Tamir Gonen, Ben Luisi, David Baker
 2014-10-24 [Report] Computational design of water-soluble α-helical barrels
Protein design expands the repertoire of coiled-coil structures to α-helical barrels and hyperstable helical bundles. Authors: Andrew R. Thomson, Christopher W. Wood, Antony J. Burton, Gail J. Bartlett, Richard B. Sessions, R. Leo Brady, Derek N. Woolfson
 2014-10-24 [New Products] New Products
A weekly roundup of information on newly offered instrumentation, apparatus, and laboratory materials of potential interest to researchers.
 2014-10-24 [Podcast] Science Podcast: 24 October Show
On this week's show: The earliest high-altitude humans.
 2014-10-24 [Business Office Feature] Innovations in light sheet microscopy: Strategies and new applications
Thai Truong
 2014-10-24 [Association Affairs] AAAS 2015 Annual Meeting Program
This issue of Science includes the program of the 2015 AAAS Annual Meeting. The theme of the AAAS Annual Meeting in San Jose, CA, 12 to 16 February 2015, is Innovations, Information, and Imaging.A PDF of the program as it appears in this issue is available here; for more information on the meeting (including registration forms and information on accommodations), please visit www.aaas.org/meetings/.
 2014-10-24 [Working Life] A double dose of advice
Author: Huan Wang

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