Nature contents: 10 May 2012

Can't view this email? Click here to view in your browser.     Volume 485 Number 7397      nature •Visit Nature homepage •Subscribe to Nature •View Table of Contents The science that matters. Every week.                       CBIA - 2012 China Excellence Bio Park Survey! In China, it has approximately 300 biomedical clusters/parks across 100 locations in different cities.  You will have a chance to win a free ticket to join the "CBIA - China Bio Parks Excellence Award Ceremony" in Shanghai, or the 'CBIA - The China Bio Parks White Paper 2012'. A chance to receive a USD200 gift voucher from Amazon.com Click here - Action Now! Visit to the Award website             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     Biological Sciences More Biological sciences ▼   Engineering the third wave of biocatalysis   In this review, Bornscheuer et al. survey recent advances in biocatalysis — the use of enzymes or microbes to perform synthetic chemistry. We are, they say, witnessing the 'third wave' of biocatalysis, in which dramatic new activities can now be engineered into enzymes. Applications likely to benefit include the synthesis of important commodity chemicals and advanced pharmaceutical intermediates.       Biological Sciences More Biological sciences ▼   Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq   DNA methylation is an important epigenetic modification that influences gene expression. RNA methylation also occurs, but is less well studied. This study shows that methylation at the N6 position in adenosone in mRNA (m6A) is common, and is found preferentially around stop codons and in unusually long exons.       Physical Sciences More Physical sciences ▼   Patterning by controlled cracking   A team based in South Korea has developed a technique that harnesses crack initiation, propagation and termination to create patterns in a silicon nitride thin film deposited on top of a silicon substrate. This concept opens up new possibilities for nanofabrication and patterning using fracture mechanics in applications such as nanotechnology and micro-scale fluidic devices.                   Nature Outlook: Malaria The past attempts to eradicate malaria have failed. What will it take to finally subdue this deadly disease? Access the Outlook free online for six months. Produced with support from: Medicines for Malaria Venture (MMV), Sigma-Tau, Vestergaard Frandsen New York                 Podcast & Video     In this week's podcast: what to do with plutonium stockpiles, and what happens when you eat irradiated venison. Plus, a linguistic spat and mini-mammals in the news chat.         News & Comment Read daily news coverage▶ ▲top             THIS WEEK           Editorials                   With transparency comes trust ▶     International development experts say that the Millennium Villages Project's claims of progress should be interpreted with caution.             Misplaced protest ▶     Rothamsted's genetically engineered wheat should be allowed to grow.             Price of freedom ▶     The latest mission to Jupiter highlights the benefits and pitfalls of collaboration.             World View                   Beware the creeping cracks of bias ▶     Evidence is mounting that research is riddled with systematic errors. Left unchecked, this could erode public trust, warns Daniel Sarewitz.             Seven Days                   Seven days: 4–10 May 2012 ▶     The week in science: Japan switches off its last nuclear power reactor; South Korea passes carbon-trading laws; and French-Algerian physicist Adlène Hicheur is sentenced to prison for plotting terror attacks.           NEWS IN FOCUS           War of words over tribal tongue ▶     Debate highlights pitfalls in studying minority languages.             LHC prepares for data pile-up ▶     Physicists scramble to see through fog of collisions.             A boost for quantum reality ▶     Theorists claim they can prove that wavefunctions are real states.             Development project touts health victory ▶     But critics question data and cost estimates from the Millennium Villages Project.             Drug-making plant blooms ▶     Approval of a 'biologic' manufactured in plant cells may pave the way for similar products.             Features                   Radiation risks: Raiders of the lost archive ▶     Old collections of irradiated tissues could answer modern-day questions about the dangers of radiation. Now, researchers are making a concerted effort to save the stores.             Climate forecasting: A break in the clouds ▶     Clouds and aerosol particles have bedevilled climate modellers for decades. Now researchers are starting to gain the upper hand.           COMMENT           Nuclear proliferation: Time to bury plutonium ▶     Recycling plutonium is dangerous and costly. Britain should take the lead on direct disposal, say Frank von Hippel, Rodney Ewing, Richard Garwin and Allison Macfarlane.             Policy reform: Strengthen and stabilize the FDA ▶     The US Food and Drug Administration needs to be more independent, says Daniel Carpenter.             Books and Arts                   Natural selection: The evolutionary struggle ▶     Andrew Berry enjoys a biographical feast that turns the spotlight onto Darwin's forerunners.             Q&A: Nature's digitizer ▶     Media designer Scott Snibbe creates software apps and interactive science-museum installations, and was executive producer of the 2011 Biophilia project by singer–songwriter Björk. As he prepares to lecture at the Sónar International Festival of Advanced Music and New Media Art in São Paulo, Brazil — where his visuals will accompany Björk's performance of Biophilia — he talks about provoking wonder.             Books in brief ▶             Correspondence                   Research funding: Indian science needs alternative investors Siddhartha P. Kar | Cyprus Institute: It deserves more credit Edouard Brézin | Cyprus Institute: Improve oversight Emmanouil Lioudakis | Translational research: A UK tissue bank for breast tumours Alastair M. Thompson | History: Science sociology began before Kuhn Ulrich Lehmann           Correction                   Correction ▶                 Biological Sciences ▲top             RESEARCH           Latest Online                   Cardiac angiogenic imbalance leads to peripartum cardiomyopathy ▶     Ian S. Patten, Sarosh Rana, Sajid Shahul, Glenn C. Rowe, Cholsoon Jang et al.     Evidence from mice and humans indicates that peripartum cardiomyopathy (PPCM) is a vascular disease caused by excessive anti-angiogenic signalling in the peripartum period of pregnancy and that pre-eclampsia and multiple gestation are important risk factors for the development of PPCM.             Human gut microbiome viewed across age and geography ▶     Tanya Yatsunenko, Federico E. Rey, Mark J. Manary, Indi Trehan, Maria Gloria Dominguez-Bello et al.     The human gut microbiome from a large cohort of more than 500 indivduals living on three continents with three distinct cultures is analysed, emphasizing the effect of host age, diet and environment on the composition and functional repertoire of fecal microbiota.             Brain-wide neuronal dynamics during motor adaptation in zebrafish ▶     Misha B. Ahrens, Jennifer M. Li, Michael B. Orger, Drew N. Robson, Alexander F. Schier et al.     Neural activity is recorded at the cellular level, throughout the brain of larval zebrafish, while the animals interact with a virtual environment and adapt their motor output to changes in visual feedback; this is used to derive candidates of functional elements driving motor learning.             Accelerated speciation in colour-polymorphic birds ▶     Andrew F. Hugall & Devi Stuart-Fox     Molecular phylogenies demonstrate a link between colour polymorphism and accelerated speciation in bird families.             AMPK regulates NADPH homeostasis to promote tumour cell survival during energy stress ▶     Sang-Min Jeon, Navdeep S. Chandel & Nissim Hay     A mechanism is suggested that helps tumour cells survive energy stress conditions during early stages of tumorigenesis.             Melanoma genome sequencing reveals frequent PREX2 mutations ▶     Michael F. Berger, Eran Hodis, Timothy P. Heffernan, Yonathan Lissanu Deribe, Michael S. Lawrence et al.     Whole-genome sequencing of 25 metastatic melanomas and matched germline DNA in humans reveals that the highest mutation load is associated with chronic sun exposure, and that the PREX2 gene is mutated in approximately 14 per cent of cases             The complex of tmRNA–SmpB and EF-G on translocating ribosomes ▶     David J. F. Ramrath, Hiroshi Yamamoto, Kristian Rother, Daniela Wittek, Markus Pech et al.     Stalled bacterial ribosomes can be rescued by interaction with SmpB protein and a highly structured transfer-messenger RNA, and a cryo-electron microscopy map of this complex now shows how EF-G-dependent translocation of this non-canonical ligand is facilitated by conformational changes in the ribosome and the transfer-messenger RNA.             SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation ▶     Matthew F. Barber, Eriko Michishita-Kioi, Yuanxin Xi, Luisa Tasselli, Mitomu Kioi et al.     SIRT7 is an H3K18Ac-selective deacetylase that has a pivotal role in chromatin regulation, maintenance of cellular transformation programs and tumour formation in vivo.             An oxygen-regulated switch in the protein synthesis machinery ▶     James Uniacke, Chet E. Holterman, Gabriel Lachance, Aleksandra Franovic, Mathieu D. Jacob et al.     Hypoxia activates a translation initiation pathway that escapes global inhibition of protein synthesis.             Articles and Letters                   ZNRF3 promotes Wnt receptor turnover in an R-spondin-sensitive manner ▶     Huai-Xiang Hao, Yang Xie, Yue Zhang, Olga Charlat, Emma Oster et al.     ZNRF3 and RNF43 are identified as negative feedback regulators of Wnt signalling; the stem-cell growth factor R-spondin is shown to potentiate Wnt signalling by inhibiting ZNRF3.             Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq ▶     Dan Dominissini, Sharon Moshitch-Moshkovitz, Schraga Schwartz, Mali Salmon-Divon, Lior Ungar et al.     N6-methyladenosine (m6A) is the most prevalent internal modification in messenger RNA; here the human and mouse m6A modification landscape is presented in a transcriptome-wide manner, providing insights into this epigenetic modification.             Molecular mechanism of ATP binding and ion channel activation in P2X receptors ▶     Motoyuki Hattori & Eric Gouaux     The X-ray crystal structure of the zebrafish P2X4 receptor in the presence and absence of ATP is determined, revealing an ATP-binding site and an open ion channel pore.             Selective cortical representation of attended speaker in multi-talker speech perception ▶     Nima Mesgarani & Edward F. Chang     The neural correlates of how attended speech is internally represented are described, shedding light on the ‘cocktail party problem’.             De novo mutations revealed by whole-exome sequencing are strongly associated with autism ▶     Stephan J. Sanders, Michael T. Murtha, Abha R. Gupta, John D. Murdoch, Melanie J. Raubeson et al.     Rare de novo single nucleotide variants in brain-expressed genes are found to be associated with autism spectrum disorders and to carry large effects.             Patterns and rates of exonic de novo mutations in autism spectrum disorders ▶     Benjamin M. Neale, Yan Kou, Li Liu, Avi Ma’ayan, Kaitlin E. Samocha et al.     Exome sequencing of 175 autism spectrum disorder parent–child trios reveals that few de novo point mutations have a role in autism spectrum disorder and those that do are distributed across many genes and are incompletely penetrant, further supporting extreme genetic heterogeneity of this spectrum disorder.             Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations ▶     Brian J. O’Roak, Laura Vives, Santhosh Girirajan, Emre Karakoc, Niklas Krumm et al.     Exome sequencing on a large cohort of parent–child trios with sporadic autism spectrum disorders shows that de novo point mutations are mainly paternal in origin and positively correlate with paternal age, and identifies a highly interconnected network formed from the products of the most severe mutations.             Mitochondrial DNA that escapes from autophagy causes inflammation and heart failure ▶     Takafumi Oka, Shungo Hikoso, Osamu Yamaguchi, Manabu Taneike, Toshihiro Takeda et al.     Mitochondrial DNA escaping from the autophagy pathway can trigger inflammation through Toll-like receptor (TLR) 9, leading to abnormalities in cardiac structure and function, and increased mortality.             Cell attachment protein VP8* of a human rotavirus specifically interacts with A-type histo-blood group antigen ▶     Liya Hu, Sue E. Crawford, Rita Czako, Nicolas W. Cortes-Penfield, David F. Smith et al.     This crystallographic study shows the attachment of human rotavirus VP8* to histo blood group A antigen, and suggests how changes within the structure of VP8* could allow switching from sialylated to non-sialylated glycan receptor.             Validation of ITD mutations in FLT3 as a therapeutic target in human acute myeloid leukaemia ▶     Catherine C. Smith, Qi Wang, Chen-Shan Chin, Sara Salerno, Lauren E. Damon et al.     Internal tandem duplication mutations in FLT3, known to be associated with a poor prognosis in acute myeloid leukaemia, are now shown to be a valid therapeutic target for the disease.             Systematic discovery of structural elements governing stability of mammalian messenger RNAs ▶     Hani Goodarzi, Hamed S. Najafabadi, Panos Oikonomou, Todd M. Greco, Lisa Fish et al.     Secondary structures, or pairing of complementary sequences within RNA, can regulate the binding of proteins that affect transcript stability, splicing, localization, and translation; a computational approach has now been used to discover secondary structures that affect global RNA stability through the binding of specific RNA binding proteins.             Reviews and Perspectives                   Engineering the third wave of biocatalysis ▶     U. T. Bornscheuer, G. W. Huisman, R. J. Kazlauskas, S. Lutz, J. C. Moore et al.     Over the past ten years, protein engineering has established biocatalysis as a practical and environmentally friendly alternative to traditional forms of catalysis both in the laboratory and in industry.             News & Views                   Cardiovascular Biology: Escaped DNA inflames the heart ▶     Klitos Konstantinidis & Richard N. Kitsis             Stem Cells: One step closer to gut repair ▶     Anisa Shaker & Deborah C. Rubin             Research Highlights                   Neuroscience: BOLD strides in brain imaging | Physiology: Bladder under circadian control | Evolution: Gene duplication for bigger brains | Nanobiotechnology: Radio remote control of genes | Biophysics: High-throughput cell stretcher | Evolution: Cheating cuts offspring fitness | Drug Delivery: On-demand drug release         NEWS & COMMENT           Misplaced protest | Beware the creeping cracks of bias | War of words over tribal tongue | Development project touts health victory | Drug-making plant blooms | Radiation risks: Raiders of the lost archive | Policy reform: Strengthen and stabilize the FDA | Natural selection: The evolutionary struggle | Translational research: A UK tissue bank for breast tumours Alastair M. Thompson             More Biological Sciences ▶                         Gut Microbiota Web Collection A growing number of conditions are now linked to dysbiosis of the gut microbiota (such as IBD, cancer and obesity). This Nature Reviews Gastroenterology & Hepatology collection considers the gut microbiota's role in health and disease as well as innovative health-care approaches that target this microbial 'organ'. FREE online for a limited time.               Chemical Sciences ▲top             RESEARCH           Latest Online                   The complex of tmRNA–SmpB and EF-G on translocating ribosomes ▶     David J. F. Ramrath, Hiroshi Yamamoto, Kristian Rother, Daniela Wittek, Markus Pech et al.     Stalled bacterial ribosomes can be rescued by interaction with SmpB protein and a highly structured transfer-messenger RNA, and a cryo-electron microscopy map of this complex now shows how EF-G-dependent translocation of this non-canonical ligand is facilitated by conformational changes in the ribosome and the transfer-messenger RNA.             An oxygen-regulated switch in the protein synthesis machinery ▶     James Uniacke, Chet E. Holterman, Gabriel Lachance, Aleksandra Franovic, Mathieu D. Jacob et al.     Hypoxia activates a translation initiation pathway that escapes global inhibition of protein synthesis.             Articles and Letters                   Molecular mechanism of ATP binding and ion channel activation in P2X receptors ▶     Motoyuki Hattori & Eric Gouaux     The X-ray crystal structure of the zebrafish P2X4 receptor in the presence and absence of ATP is determined, revealing an ATP-binding site and an open ion channel pore.             Systematic discovery of structural elements governing stability of mammalian messenger RNAs ▶     Hani Goodarzi, Hamed S. Najafabadi, Panos Oikonomou, Todd M. Greco, Lisa Fish et al.     Secondary structures, or pairing of complementary sequences within RNA, can regulate the binding of proteins that affect transcript stability, splicing, localization, and translation; a computational approach has now been used to discover secondary structures that affect global RNA stability through the binding of specific RNA binding proteins.             Reviews and Perspectives                   Engineering the third wave of biocatalysis ▶     U. T. Bornscheuer, G. W. Huisman, R. J. Kazlauskas, S. Lutz, J. C. Moore et al.     Over the past ten years, protein engineering has established biocatalysis as a practical and environmentally friendly alternative to traditional forms of catalysis both in the laboratory and in industry.           NEWS & COMMENT           Climate forecasting: A break in the clouds             More Chemical Sciences ▶               Physical Sciences ▲top             RESEARCH           Articles and Letters                   The suppression of star formation by powerful active galactic nuclei ▶     M. J. Page, M. Symeonidis, J. D. Vieira, B. Altieri, A. Amblard et al.     Observations at submillimetre and X-ray wavelengths show that rapid star formation was common in the host galaxies of active galactic nuclei when the Universe was 2–6 Gyr old, but that the most vigorous star formation is not observed around powerful black holes, thereby confirming a key prediction of models in which an active galactic nucleus expels the interstellar medium of its host galaxy.             An ultraviolet–optical flare from the tidal disruption of a helium-rich stellar core ▶     S. Gezari, R. Chornock, A. Rest, M. E. Huber, K. Forster et al.     The observation of a flare of radiation from the centre of an inactive galaxy fits a model of the tidal disruption of a helium-rich stellar core and its accretion onto a black hole of about three million solar masses.             Patterning by controlled cracking ▶     Koo Hyun Nam, Il H. Park & Seung Hwan Ko     Propagating cracks—normally associated with material failure and viewed as undesirable—can be controlled in a film/substrate system, opening up new possibilities for nanofabrication and atomic-scale patterning.             Twenty-first-century warming of a large Antarctic ice-shelf cavity by a redirected coastal current ▶     Hartmut H. Hellmer, Frank Kauker, Ralph Timmermann, Jürgen Determann & Jamie Rae     The redirection of warm water under the Filchner–Ronne Ice Shelf during the second half of this century could cause the ice-shelf base to melt at a rate 20 times higher than at present.             News & Views                   Materials science: Cracks tamed ▶     Antonio J. Pons             Climate science: A grip on ice-age ocean circulation ▶     Jochem Marotzke             Black holes: Star ripped to shreds ▶     Giuseppe Lodato             Brief Communications Arising                   Nanostructure-enhanced atomic line emission ▶     M. Sivis, M. Duwe, B. Abel & C. Ropers             Kim et al. reply ▶     Seungchul Kim, Jonghan Jin, Young-Jin Kim, In-Yong Park, Yunseok Kim et al.             Research Highlights                   Climate science: A check on speeding glaciers         NEWS & COMMENT           LHC prepares for data pile-up | A boost for quantum reality | Climate forecasting: A break in the clouds | Nuclear proliferation: Time to bury plutonium | Q&A: Nature's digitizer             More Physical Sciences ▶               Earth & Environmental Sciences ▲top             RESEARCH           Latest Online                   Planetary science: Martian sand blowing in the wind ▶     Jasper Kok             Earth-like sand fluxes on Mars ▶     N. T. Bridges, F. Ayoub, J-P. Avouac, S. Leprince, A. Lucas et al.     Satellite images of a Martian dune field reveal unexpectedly high sand fluxes, suggesting rates of landscape modification similar to those on Earth.             Articles and Letters                   Twenty-first-century warming of a large Antarctic ice-shelf cavity by a redirected coastal current ▶     Hartmut H. Hellmer, Frank Kauker, Ralph Timmermann, Jürgen Determann & Jamie Rae     The redirection of warm water under the Filchner–Ronne Ice Shelf during the second half of this century could cause the ice-shelf base to melt at a rate 20 times higher than at present.             Comparing the yields of organic and conventional agriculture ▶     Verena Seufert, Navin Ramankutty & Jonathan A. Foley     A meta-analysis assessing the relative yields of organic and conventional agriculture shows that organic yields are on average lower, but that the magnitude of the difference is dependent on context.             News & Views                   Agriculture: Comparing apples with oranges ▶     John P. Reganold & Achim Dobermann             Climate science: A grip on ice-age ocean circulation ▶     Jochem Marotzke             Planetary science: Martian sand blowing in the wind ▶     Jasper Kok             Research Highlights                   Climate science: A check on speeding glaciers | Geochemistry: North Sea starved of oxygen         NEWS & COMMENT           Price of freedom | Climate forecasting: A break in the clouds             More Earth & Environmental Sciences ▶                         Nature Genetics and the Wellcome Trust present: The Genomics of Common Diseases 2012 September 19-22, 2012 • Potomac, MD, USA For more information and to register, visit: www.nature.com/natureconferences/gcd2012 Abstract submission deadline - June 28, 2012               Careers & Jobs ▲top               Enterprising science ▶     Graduate students and postdocs are often best placed to turn basic research into entrepreneurial gold, argues Peter Fiske.                   Mobility boost ▶     European student group calls for funding to support mobility.                   Best practice ▶     Agreement to improve UK research careers yields some positives.                   More US success ▶     Technology-transfer model best for inventors who need commercialization support.                   Careers related news & comment                   Price of freedom | War of words over tribal tongue | Research funding: Indian science needs alternative investors Siddhartha P. 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