Nature contents: 28 March 2013

Can't view this email? Click here to view in your browser.     Volume 495 Number 7442      nature •Visit Nature homepage •Subscribe to Nature •View Table of Contents The science that matters. Every week.             Jump to the content that matters to you View Table of Contents ▶ ▼ News & Comment   ▼ Biological Sciences   ▼ Chemical Sciences   ▼ Physical Sciences   ▼ Earth & Environmental Sciences   ▼ Careers & Jobs       This week's highlights     Special - The future of publishing     After nearly 400 years in the slow-moving world of print, the scientific publishing industry is suddenly being thrust into a fast-paced online world of cloud computing, crowd sourcing and ubiquitous sharing. Long-established practices are being challenged by new ones – most notably, the open-access, author-pays publishing model. In this special issue, Nature takes a close look at the forces now at work in scientific publishing, and how they may play out over the coming decades. ▼ more       Chemical Sciences More Chemical sciences ▼   X-ray analysis on the nanogram to microgram scale using porous complexes   X-ray diffraction is a powerful analytical tool but it has a drawback: the target needs to be available as a crystal. This paper describes a cunning way around the problem that uses crystalline 'sponges' — called metal organic frameworks — to soak up a drop of liquid containing the target molecule. The sponges contain pores that bind the target molecules in an ordered array, so that crystal structures can be determined for both the absorbed guest and the host framework. The method is demonstrated with the absolute structure determination of a scarce natural product, miyakosyne A, using little more than a trace amount of the material.       Biological Sciences More Biological sciences ▼   Mutations in prion-like domains in hnRNPA2B1 and hnRNPA1 cause multisystem proteinopathy and ALS   Around 250 human proteins are predicted to have prion-like domains, including several RNA-binding domains that are that are associated with neurodegenerative disease. Prion-like domains are thought to have a role in RNA metabolism, but the interplay between prion-like domains and disease is poorly understood. Hong Joo Kim et al. have identified mutations in two RNA-binding proteins, hnRNPA2B1 and hnRNPA1, in families with a rare combination of inherited degenerative diseases. The mutations cause increased and dysregulated protein aggregation, and the resulting effects may initiate degenerative diseases. These findings have relevance to the pathogenesis of degenerative diseases and proteinopathies such as amyotrophic lateral sclerosis.                   Hamamatsu's NanoZoomer-XR delivers faster, worry-free scanning of up to 320 slides. Our new NDP.view2 software allows faster viewing of your slides and an improved interface. Our new NDP.analyze software, powered by Visiopharm, allows you to extract subcellular morphometric details from brightfield and fluorescent whole slide images either locally or on the Cloud.                 Biological Sciences More Biological sciences ▼   Preservation of ovarian follicles reveals early evolution of avian reproductive behaviour   A window on the evolving reproductive capacities of birds is opened by the analysis of newly discovered fossils of primitive birds from the Mesozoic of China. The specimens, more than 120 million years old, are of three mother birds and are the first in which the soft tissue of the ovaries is preserved. The fossils show that birds had only one functioning ovary from a very early stage of their evolution. The leading explanation for the loss of a functional right ovary is that it was necessary to reduce weight to assist flying. These fossil finds therefore support the hypothesis that this loss is flight related.       Podcast & Video     In this week's podcast: the future of scientific publishing, crystallography without the crystals, and how carbon dioxide escapes from the deep ocean. In our latest video feature, scientists are now able to create highly accurate three dimensional reconstructions of materials at the most fundamental scale: the atomic.           Special - The future of publishing ▲top               Editorial                   Disciplinary action ▶     How scientists share and reuse information is driven by technology but shaped by discipline.             News                   Sham journals scam authors ▶     Con artists are stealing the identities of real journals to cheat scientists out of publishing fees.             Features                   The future of publishing: A new page ▶     A special issue of Nature looks at the transformation taking place in scientific publishing.             Open access: The true cost of science publishing ▶     Cheap open-access journals raise questions about the value publishers add for their money.             Publishing frontiers: The library reboot ▶     As scientific publishing moves to embrace open data, libraries and researchersare trying to keep up.             Investigating journals: The dark side of publishing ▶     The explosion in open-access publishing has fuelled the rise of questionable operators.             Comment                   Scholarship: Beyond the paper ▶     The journal and article are being superseded by algorithms that filter, rate and disseminate scholarship as it happens, argues Jason Priem.             Licence restrictions: A fool's errand ▶     Objections to the Creative Commons attribution licence are straw men raised by parties who want open access to be as closed as possible, warns John Wilbanks.             Advocacy: How to hasten open access ▶     Three advocates for a universally free scholarly literature give their prescriptions for the movement's next push, from findability to translations.             Books and Arts                   Q&A: Knowledge liberator ▶     Robert Darnton heads the world's largest collection of academic publications, the Harvard University Library system. He is also a driver behind the new Digital Public Library of America. Ahead of its launch in April, he talks about Google, science journals and the open-access debate.             Naturejobs                   Publishing: Open to possibilities ▶     Opting for open access means considering costs, journal prestige and career implications.               News & Comment Read daily news coverage▶ ▲top               THIS WEEK           Editorials                   Under the gun ▶     A ban on advocacy and promotion of gun control is keeping US agencies from conducting research that is sorely needed to inform policy on firearms and prevent shootings.             Push the boat out ▶     The latest private research vessel to be launched could open up the world of marine science.             World View                   H5N1 viral-engineering dangers will not go away ▶     Governments, funders and regulatory authorities must urgently address the risks posed by gain-of-function research, says Simon Wain-Hobson.             Seven Days                   Seven days: 22–28 March 2013 ▶     The week in science: US science agencies get funding boost; UK edges towards approving IVF techniques to avoid some genetic diseases; and Australia gets fourth science minister in less than 16 months.             NEWS IN FOCUS           Planck snaps infant Universe ▶     Space telescope culls exotic creation theories with ultra-precise microwave map.             Stem-cell ruling riles researchers ▶     Italian health minister's support for a controversial treatment appals the country's scientists.             Drug-company data vaults to be opened ▶     European agency will publish firms' clinical-trial results.             Private research ship makes waves ▶     Falkor plots a fresh course for ocean studies with Google cash.             Higgs physics on the cheap ▶     Tabletop Higgs particles may illuminate cosmic cousin.             COMMENT           Military history: Dinner at the Fission Chips ▶     Mark Peplow assesses a chronicle of the blighted US and Soviet communities that fuelled the nuclear arms race.             Books in brief ▶             Gastroenterology: Down the hatch ▶     David Katz savours a guided tour of the ins and outs of the gastrointestinal tract.             Correspondence                   Research conduct: Online integrity training falls short Kenneth D. Pimple | Research ethics: Too much reliance on anonymous tip-offs Gilberto Corbellini | Health metrics: Standardize records of place of death Barbara Gomes | Radioactive dumping: Nuclear-waste site geology is paramount David Smythe             Obituary                   Robert Richardson (1937-2013) ▶     Discoverer of superfluidity in helium-3.             Corrections                   Correction ▶             Correction ▶                         October 21 - 22 2013 The Royal Society, London Alfred Russel Wallace and his legacy This report assesses the potential of new supergenerics in the setting of specific therapeutic classes. The report identifies the drivers and resistors for developing supergenerics in different countries and regions, and evaluates regulatory issues that hamper or encourage the development of supergenerics. Contact: discussion.meetings@royalsociety.org               Biological Sciences ▲top             RESEARCH           Latest Online                   Microbiology: Intraterrestrial lifestyles ▶     David L. Valentine             Succinate is an inflammatory signal that induces IL-1β through HIF-1α ▶     G. M. Tannahill, A. M. Curtis, J. Adamik et al.     Succinate is identified as a metabolite in innate immune signalling, which leads to enhanced interleukin-1β production during inflammation.             A solution to release twisted DNA during chromosome replication by coupled DNA polymerases ▶     Isabel Kurth, Roxana E. Georgescu, Mike E. O'Donnell     During chromosome replication, coupled polymerases introduce topological changes that cause lower processivity and transient lagging-strand polymerase dissociation from DNA.             Structures of protein–protein complexes involved in electron transfer ▶     Svetlana V. Antonyuk, Cong Han, Robert R. Eady et al.     Structures of a newly characterized three-domain haem-c-Cu nitrite reductase are reported at 1.01 Å resolution, indicating how electron transfer may occur in protein–protein complexes.             Draft genome of the wheat A-genome progenitor Triticum urartu  ▶     Hong-Qing Ling, Shancen Zhao, Dongcheng Liu et al.     The genome sequence and its analysis of the diploid wild wheat Triticum urartu (progenitor of the wheat A genome) represent a tool for studying the complex, polyploid wheat genomes and should be a valuable resource for the genetic improvement of wheat.             Proteolytic elimination of N-myristoyl modifications by the Shigella virulence factor IpaJ ▶     Nikolay Burnaevskiy, Thomas G. Fox, Daniel A. Plymire et al.     An irreversible mechanism of protein demyristoylation catalysed by invasion plasmid antigen J (IpaJ), a Shigella flexneri type III effector protein with cysteine protease activity, is described.             Structural basis for the drug extrusion mechanism by a MATE multidrug transporter ▶     Yoshiki Tanaka, Christopher J. Hipolito, Andrés D. Maturana et al.     Several X-ray crystal structures of an H+-driven multidrug and toxic compound extrusion (MATE) transporter from Pyrococcus furiosus are presented, whose complex structure with macrocyclic peptides may help facilitate the discovery of efficient inhibitors of MATE transporters.             Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation OPEN ▶     Jizeng Jia, Shancen Zhao, Xiuying Kong et al.     Sequencing and analysing the diploid genome and transcriptome of Aegilops tauschii provide new insights into the role of this genome in enabling the adaptation of bread wheat and are a step towards understanding the very large and complicated hexaploid genomes of wheat species.             Predominant archaea in marine sediments degrade detrital proteins ▶     Karen G. Lloyd, Lars Schreiber, Dorthe G. Petersen et al.     Miscellaneous crenarchaeotal group (MCG) and marine benthic group-D (MBG-D) are among the most numerous archaea in sea-floor sediments; single-cell genomics reveals that these archaea belong to new branches of the archaeal tree and probably have a role in protein remineralization in anoxic marine sediments.             Glutamine supports pancreatic cancer growth through a KRAS-regulated metabolic pathway ▶     Jaekyoung Son, Costas A. Lyssiotis, Haoqiang Ying et al.     Pancreatic cancers use a novel glutamine metabolism pathway, regulated by oncogenic KRAS, to maintain redox balance; these findings add to the understanding of the mechanisms by which oncogenic alterations reprogram cellular metabolism to promote tumour growth.             Articles and Letters                   X-ray analysis on the nanogram to microgram scale using porous complexes ▶     Yasuhide Inokuma, Shota Yoshioka, Junko Ariyoshi et al.     Absorption of target molecules into a porous matrix permits single-crystal X-ray diffraction analysis of the 'guest' molecules, avoiding the need to obtain them in single-crystal form and making analysis possible using as little as 80 nanograms of sample.             Mutations in prion-like domains in hnRNPA2B1 and hnRNPA1 cause multisystem proteinopathy and ALS ▶     Hong Joo Kim, Nam Chul Kim, Yong-Dong Wang et al.     The identification of pathogenic mutations within prion-like domains (PrLDs) of the RNA-binding proteins hnRNPA2B1 and hnRNPA1 add to our understanding of how mutations in these proteins lead to degenerative disease, and highlight the potential importance of PrLDs in degenerative diseases of the nervous system, muscle and bone.             CLP1 links tRNA metabolism to progressive motor-neuron loss ▶     Toshikatsu Hanada, Stefan Weitzer, Barbara Mair et al.     Inactivating the CLP1 RNA kinase in mice leads to a progressive loss of motor neurons, through a mechanism related to the accumulation of a novel set of small RNA fragments derived from aberrant processing of tyrosine pre-transfer RNA.             Structural visualization of key steps in human transcription initiation ▶     Yuan He, Jie Fang, Dylan J. Taatjes et al.     Cryo-electron microscopy structures of key intermediates during the sequential assembly of the pre-initiation complex are presented; structures of the closed and open-promoter complexes allow insights into the process of promoter melting.             Tubicolous enteropneusts from the Cambrian period ▶     Jean-Bernard Caron, Simon Conway Morris, Christopher B. Cameron     Examination of a fossil enteropneust, Spartobranchus tenuis (Walcott, 1911), from the Cambrian-period Burgess Shale shows that they looked similar to modern enteropneusts but lived in tubes, like modern pterobranchs; the findings shed light on the common ancestor of enteropneusts and pterobranchs, and hence the origin of chordates.             Preservation of ovarian follicles reveals early evolution of avian reproductive behaviour ▶     Xiaoting Zheng, Jingmai O'Connor, Fritz Huchzermeyer et al.     Newly discovered fossils of primitive birds from China, preserved with ovarian follicles intact, show that birds only had one functioning ovary at any given time from a very early date, but that other features, such as skeletal and sexual maturity, remained very dinosaur-like.             Accelerated gene evolution through replication–transcription conflicts ▶     Sandip Paul, Samuel Million-Weaver, Sujay Chattopadhyay et al.     Bacteria promote faster evolution of individual genes through orientation-dependent encounters between DNA replication and transcription.             A central role for TFIID in the pluripotent transcription circuitry ▶     W. W. M. Pim Pijnappel, Daniel Esch, Marijke P. A. Baltissen et al.     High levels of TFIID, a basal transcription factor, are found to be essential to induce and maintain the transcriptional program of pluripotent cells.             A syringe-like injection mechanism in Photorhabdus luminescens toxins ▶     Christos Gatsogiannis, Alexander E. Lang, Dominic Meusch et al.     The TcA component of Photorhabdus luminescens ABC-type toxin complexes forms a transmembrane pore and injects TcC, the functional component of the toxin, into the target cell by means of a syringe-like mechanism.             Critical role of Trib1 in differentiation of tissue-resident M2-like macrophages ▶     Takashi Satoh, Hiroyasu Kidoya, Hisamichi Naito et al.     Haematopoietic expression of the adaptor protein Trib1 is shown to be required for the presence of adipose-tissue-resident macrophages with an M2-like phenotype; Trib1 deficiency leads to aberrant expression of C/EBPα and impaired adipose tissue function.             CLASP-mediated cortical microtubule organization guides PIN polarization axis ▶     Klementina Kakar, Hongtao Zhang, Ben Scheres et al.     The microtubule orientation regulators CLASP and MAP65 are shown to control the distribution of the polarity regulator PINOID kinase by controlling its retention at the plasma membrane, providing a mechanism for how polarity is established in plants.             Conformational biosensors reveal GPCR signalling from endosomes ▶     Roshanak Irannejad, Jin C. Tomshine, Jon R. Tomshine et al.     Conformation-specific antibodies capable of monitoring the activation state of a G-protein-coupled seven-transmembrane receptor, the β2-adrenoceptor, reveals receptor and G-protein activation not only in the plasma membrane, but also in the endosome.             News & Views                   Global health: Persuasive evidence on HIV policy ▶     Grace John-Stewart             Cell biology: Receptor signals come in waves ▶     Martin J. Lohse & Davide Calebiro             Palaeontology: Tubular worms from the Burgess Shale ▶     Henry Gee             Microbiology: Intraterrestrial lifestyles ▶     David L. Valentine             Brief Communications Arising                   Is the ocean food provision index biased? ▶     Trevor A. Branch, Daniel J. Hively, Ray Hilborn             Halpern et al. reply ▶     Benjamin S. Halpern, Steven D. Gaines, Kristin Kleisner et al.             Research Highlights                   Ecology: Primates hunting leaves forest scar | Behavioural neuroscience: Male mice cut out for fathering | Palaeontology: Trilobite fossil spotted | Structural biology: Serotonin signalling secrets | Neuroimaging: Single cells seen in whole brains | Obesity: Fat cells use immune signal | Development: Origins of the ear lining | Chemistry: Long DNA-like chains assemble         NEWS & COMMENT           H5N1 viral-engineering dangers will not go away | Drug-company data vaults to be opened | Books in brief | Gastroenterology: Down the hatch | Health metrics: Standardize records of place of death | Correction | Stem-cell ruling riles researchers             More Biological Sciences ▶                         Nature Outlook: Gold Gold nanoparticles can help pinpoint a tumour - and then carry drugs to it. Gold also holds promise for making extremely efficient solar cells, among other photonic applications. Nature Outlook: Gold reports on what's driving the twenty-first-century gold rush. Access the Outlook free online for six months. Produced with support from: World Gold Council               Chemical Sciences ▲top             RESEARCH           Articles and Letters                   X-ray analysis on the nanogram to microgram scale using porous complexes ▶     Yasuhide Inokuma, Shota Yoshioka, Junko Ariyoshi et al.     Absorption of target molecules into a porous matrix permits single-crystal X-ray diffraction analysis of the 'guest' molecules, avoiding the need to obtain them in single-crystal form and making analysis possible using as little as 80 nanograms of sample.             News & Views                   Materials science: Nanoparticle structures served up on a tray ▶     Simon Billinge             X-ray crystallography: One size fits most ▶     Pierre Stallforth, Jon Clardy             Research Highlights                   Chemistry: Long DNA-like chains assemble           More Chemical Sciences ▶               Physical Sciences ▲top             RESEARCH           Latest Online                   Techniques: 3D imaging of crystal defects ▶     Patrick J. McNally             Three-dimensional imaging of dislocations in a nanoparticle at atomic resolution ▶     Chien-Chun Chen, Chun Zhu, Edward R. White et al.     A new combination of established techniques is used to produce three-dimensional (3D) images and a video of almost all the atoms in a platinum nanoparticle, revealing the 3D core structure of edge and screw dislocations and 3D twin boundaries in the nanoparticle at atomic resolution.             Articles and Letters                   X-ray analysis on the nanogram to microgram scale using porous complexes ▶     Yasuhide Inokuma, Shota Yoshioka, Junko Ariyoshi et al.     Absorption of target molecules into a porous matrix permits single-crystal X-ray diffraction analysis of the 'guest' molecules, avoiding the need to obtain them in single-crystal form and making analysis possible using as little as 80 nanograms of sample.             Carbon monoxide in clouds at low metallicity in the dwarf irregular galaxy WLM ▶     Bruce G. Elmegreen, Monica Rubio, Deidre A. Hunter et al.     New and archival observations of the low-metallicity dwarf irregular galaxy WLM show that it contains carbon monoxide, the main tracer for interstellar clouds capable of forming stars, and suggest that in small galaxies both star-forming cores and carbon monoxide become increasingly rare as the metallicity decreases.             Evidence for sympathetic vibrational cooling of translationally cold molecules ▶     Wade G. Rellergert, Scott T. Sullivan, Steven J. Schowalter et al.     The vibrational motion of trapped BaCl+ molecules can be quenched by collisions with ultracold calcium atoms at a rate comparable to the classical scattering rate; this method is over four orders of magnitude more efficient than traditional sympathetic cooling schemes and should be applicable to many different types of molecule.             News & Views                   Materials science: Nanoparticle structures served up on a tray ▶     Simon Billinge             X-ray crystallography: One size fits most ▶     Pierre Stallforth, Jon Clardy             Techniques: 3D imaging of crystal defects ▶     Patrick J. McNally             Research Highlights                   Planetary science: Migrating planets sped up collisions | Chemistry: Long DNA-like chains assemble         NEWS & COMMENT           Publishing frontiers: The library reboot | Military history: Dinner at the Fission Chips | Q&A: Knowledge liberator | Robert Richardson (1937-2013) | Planck snaps infant Universe | Higgs physics on the cheap             More Physical Sciences ▶               Earth & Environmental Sciences ▲top             RESEARCH           Latest Online                   Microbiology: Intraterrestrial lifestyles ▶     David L. Valentine             Predominant archaea in marine sediments degrade detrital proteins ▶     Karen G. Lloyd, Lars Schreiber, Dorthe G. Petersen et al.     Miscellaneous crenarchaeotal group (MCG) and marine benthic group-D (MBG-D) are among the most numerous archaea in sea-floor sediments; single-cell genomics reveals that these archaea belong to new branches of the archaeal tree and probably have a role in protein remineralization in anoxic marine sediments.             Articles and Letters                   Deglacial pulses of deep-ocean silicate into the subtropical North Atlantic Ocean ▶     A. N. Meckler, D. M. Sigman, K. A. Gibson et al.     Records of biogenic opal export in the North Atlantic Ocean show pronounced maxima during each glacial termination over the past 550,000 years, consistent with a strong deglacial reduction in the formation of silicate-poor glacial North Atlantic intermediate water and a consequent increase in upward silicate transport.             Electrical image of passive mantle upwelling beneath the northern East Pacific Rise ▶     Kerry Key, Steven Constable, Lijun Liu et al.     Sea-floor magnetotelluric soundings along a portion of the East Pacific Rise reveal a symmetric, high-conductivity triangular region at depths of 20–90 kilometres that is consistent with partial melting of passively upwelling mantle.             News & Views                   Earth science: How the ocean exhales ▶     Elisabeth Sikes             Palaeontology: Tubular worms from the Burgess Shale ▶     Henry Gee             Microbiology: Intraterrestrial lifestyles ▶     David L. Valentine           NEWS & COMMENT           Push the boat out | Private research ship makes waves | Military history: Dinner at the Fission Chips | Radioactive dumping: Nuclear-waste site geology is paramount             More Earth & Environmental Sciences ▶                         For many years, science in the Asia-Pacific region has been dominated by Japan. However, as seen through the lens of the Nature Publishing Index (NPI), the fastest growth in high-quality research is now coming from other countries — in particular China and Singapore. The 2012 NPI Asia-Pacific presents an analysis of the dynamic changes in the region’s scientific publishing record. www.natureasia.com/en/publishing-index/asia-pacific/               Careers & Jobs ▲top               Publishing: Open to possibilities ▶     Opting for open access means considering costs, journal prestige and career implications.                   Turning point: Kate Rubins ▶     Virologist decides to follow her dream and become an astronaut.             Careers related news & comment                   Disciplinary action | Seven days: 22–28 March 2013 | Sham journals scam authors Declan Butler | The future of publishing: A new page | Open access: The true cost of science publishing Richard Van Noorden | Investigating journals: The dark side of publishing Declan Butler | Push the boat out | Scholarship: Beyond the paper Jason Priem | Licence restrictions: A fool's errand John Wilbanks | Advocacy: How to hasten open access | Research conduct: Online integrity training falls short Kenneth D. Pimple | Research ethics: Too much reliance on anonymous tip-offs Gilberto Corbellini | Planck snaps infant Universe Mark Peplow               naturejobs.com Science jobs of the week       Staff Associate     Columbia University - Department of Biological Sciences            6 Doctoral Positions     Helmholtz Center for Environmental Research - UFZ            Research Associate     Imperial College London - Faculty of Medicine            Associate / Assistant Professors     National University of Singapore, Department of Microbiology          No matter what your career stage, student, postdoc or senior scientist, you will find articles on naturejobs.com to help guide you in your science career. 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