Nature contents: 19 January 2012

Can't view this email? Click here to view in your browser.     Volume 481 Number 7381      nature •Visit Nature homepage •Subscribe to Nature •View Table of Contents The science that matters. Every week.                       The ORCA-Flash4.0 camera is here! This game changer in the world of scientific imaging has many features to offer. With its combination of low noise and high quantum efficiency, the ORCA-Flash4.0 delivers unprecedented sensitivity as well as high dynamic range, blazing fast speeds, large field of view, and excellent resolution simultaneously. Learn more about the ORCA-Flash4.0.             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     Earth & Environmental Sciences More Earth & Environmental sciences ▼   The Amazon basin in transition   The ecology of vast forest–river system of the Amazon basin is changing more rapidly than ever as a result of human activity. The indications are that the Amazon may even be transitioning from a net carbon sink to a net carbon source.       Physical Sciences More Physical sciences ▼   Gravitational detection of a low-mass dark satellite galaxy at cosmological distance   The observation of a dwarf satellite galaxy at the cosmological distance of redshift 0.881supports theories of galaxy formation that assume that much of the Universe consists of unobservable cold dark matter.       Earth & Environmental Sciences More Earth & Environmental sciences ▼   Kimberlite ascent by assimilation-fuelled buoyancy   Diamond-bearing kimberlites, volcanic rocks beneath the oldest portions of the Earth's crust, can rise rapidly to the Earth's surface. A novel explanation for how this might occur is presented here, involving foaming magma produced by carbon dioxide release.                   Nature Reviews Neuroscience FOCUS ON ADDICTION Read for FREE online at: www.nature.com/nrn/focus/addiction Produced with support from National Institute on Drug Abuse (NIDA) and National Institute on Alcohol Abuse and Alcoholism (NIAAA) National Institutes of Health U.S. Department of Health & Human Services                 Podcast & Video     In this week's podcast: the changing face of the Amazon, the genetics of staying sharp as you age and crowd-sourced funding. Plus, the best of the rest from this week's Nature.       Specials - Insight: Frontiers in biology     Five reviews in this issue discuss the role of innate immune signalling in tissue homeostasis and the response to infection, how understanding the DNA damage response has guided the development of inhibitors and helped to establish new principles for treating cancer, the therapeutic potential of patient-derived pluripotent stem cells, the forces that govern tumour evolution and the impact of mouse genetics on the study of bone physiology. ▼ more         News & Comment Read daily news coverage▶ ▲top             THIS WEEK           Editorials                   Antarctic Treaty is cold comfort ▶     Researchers need to cement the bond between science and the South Pole if the region is to remain one of peace and collaboration.             Face up to fraud ▶     The UK government and funding agencies must address research misconduct.             Cap in hand ▶     A word to the wise on getting that much-needed research funding.             World View                   Break down boundaries in climate research ▶     Scientists wanting to implement change must collaborate between disciplines. An ambitious Amazon study shows them how, says Paulo Artaxo.             Seven Days                   Seven days: 13–19 January 2012 ▶     The week in science: US authorities crack down on plagiarism; failed Mars probe splashes down in the Pacific; and chemical firm BASF shifts its transgenic plant operations out of Europe.           NEWS IN FOCUS           Pollutants key to climate fix ▶     Governments look to reduce methane and black carbon as a way to slow warming.             Database tallies US emissions ▶     Environment agency launches searchable public log of major greenhouse-gas emitters.             Evolution advocate turns to climate ▶     Education centre known for battling creationists aims to help science teachers convey understanding of global warming.             Murders unlikely to slow Iran's nuclear efforts ▶     Experts say international sanctions are the best way to stall the weapons programme.             Russian drug law hinders clinical trials ▶     Legislation to increase availability of new medicines has delayed approvals.             Gemini's twin telescopes reboot ▶     Adaptive optics put the observatory at the cutting edge.             Features                   Finding philanthropy: Like it? Pay for it ▶     With conventional sources of money drying up, some scientists are turning to crowd-funding.             Alternative funding: Sponsor my science ▶     Philanthropists will sometimes give large sums of money to support science — but researchers have to learn how to sell themselves first.           COMMENT           Preventing pandemics: The fight over flu ▶     A proposal to restrict the planned publication of research on a potentially deadly avian influenza virus is causing a furore. Ten experts suggest ways to proceed.             Philanthropy: The price of charity ▶     Philanthropists should pay their fair share of research costs, says Patrick Aebischer.             Books and Arts                   Public health: Biodefence built on teamwork ▶     The golden era of US vaccine research holds beneficial lessons for today, finds John Grabenstein.             Fiction: Cosmic creation ▶     Pedro Ferreira explores Alan Lightman's latest novel — a magical-reality take on the origins of the Universe.             Books in brief ▶             Antarctica: Scientists to the end ▶     Colin Martin celebrates a London exhibition revealing the research legacy of Robert Scott's final journey.             Correspondence                   Leap year: Rare day to highlight rare diseases Susan M. Gasser, James R. Lupski, Yann Le Cam & Olivier Menzel | Asian medicine: Small species at risk Vincent Nijman, K. Anne-Isole Nekaris & David P. Bickford | Overfishing: Call to split fisheries at home and abroad U. Rashid Sumaila | Pharmaceutical industry: Investors unfazed by drug-patent expiry David Brindley, Brock Reeve & Chris Mason           Obituary                   Paul Mead Doty (1920–2011) ▶     Chemist and arms-control advocate who unravelled the structures of biomolecules.               Specials - Insight: Frontiers in Biology ▲top               Frontiers in biology ▶     Alex Eccleston, Angela Eggleston, Marie-Thérèse Heemels, Barbara Marte & Ursula Weiss             Inflammasomes in health and disease ▶     Till Strowig, Jorge Henao-Mejia, Eran Elinav & Richard Flavell             The DNA damage response and cancer therapy ▶     Christopher J. Lord & Alan Ashworth             The promise of induced pluripotent stem cells in research and therapy ▶     Daisy A. Robinton & George Q. Daley             Clonal evolution in cancer ▶     Mel Greaves & Carlo C. Maley             The contribution of bone to whole-organism physiology ▶     Gérard Karsenty & Mathieu Ferron                           Don't miss out on $3 million in research funding seeking immediate proposals for projects focused on modulation of: •B cells •Glial cells, including microglia, macrophages, astrocytes •CNS ion channels, exchangers, transporters Apply TODAY at www.FastForward.org Deadline 05/01/12               Biological Sciences ▲top             RESEARCH           Latest Online                   Genome-wide structure and organization of eukaryotic pre-initiation complexes ▶     Ho Sung Rhee & B. Franklin Pugh     Ultra-high-resolution mapping of the eukaryotic transcription machinery across the yeast genome reveals several unifying principles of pre-initiation complexes at coding and non-coding genes.             DNA breaks and chromosome pulverization from errors in mitosis ▶     Karen Crasta, Neil J. Ganem, Regina Dagher, Alexandra B. Lantermann, Elena V. Ivanova et al.     Chromosomes within micronuclei are shown to be damaged during S phase and become highly fragmented, and the damaged pieces can be reincorporated into the genome.             Neuron-type-specific signals for reward and punishment in the ventral tegmental area ▶     Jeremiah Y. Cohen, Sebastian Haesler, Linh Vong, Bradford B. Lowell & Naoshige Uchida     Dopaminergic neurons in the mouse ventral tegmental area signal the difference between received and expected reward, whereas GABAergic neurons signal expected reward.             Exercise-induced BCL2-regulated autophagy is required for muscle glucose homeostasis ▶     Congcong He, Michael C. Bassik, Viviana Moresi, Kai Sun, Yongjie Wei et al.     Acute exercise is shown to induce autophagy in skeletal muscle of fed mice, indicating a possible mechanism for the beneficial metabolic effects of exercise.             Genetic contributions to stability and change in intelligence from childhood to old age ▶     Ian J. Deary, Jian Yang, Gail Davies, Sarah E. Harris, Albert Tenesa et al.     Using a unique and rich data set of lifetime cognitive measures, the contribution of genetics to differences in cognitive ageing is explored.             Multi-isotope imaging mass spectrometry quantifies stem cell division and metabolism ▶     Matthew L. Steinhauser, Andrew P. Bailey, Samuel E. Senyo, Christelle Guillermier, Todd S. Perlstein et al.     Multi-isotope imaging mass spectrometry is used to investigate the ‘immortal strand hypothesis’, Drosophila lipid metabolism and human lymphopoiesis.             Galectin 8 targets damaged vesicles for autophagy to defend cells against bacterial invasion ▶     Teresa L. M. Thurston, Michal P. Wandel, Natalia von Muhlinen, Ágnes Foeglein & Felix Randow     Galectin 8, a cytosolic lectin, is shown to function as a danger receptor that detects damaged vesicles and protects cells from bacterial infection by inducing autophagy.             Multi-isotope imaging mass spectrometry reveals slow protein turnover in hair-cell stereocilia ▶     Duan-Sun Zhang, Valeria Piazza, Benjamin J. Perrin, Agnieszka K. Rzadzinska, J. Collin Poczatek et al.     Multi-isotope imaging mass spectrometry is used to quantify protein turnover in animal stereocilia, showing that rapid turnover occurs only in stereocilia tips.             A novel sensor to map auxin response and distribution at high spatio-temporal resolution ▶     Géraldine Brunoud, Darren M. Wells, Marina Oliva, Antoine Larrieu, Vincent Mirabet et al.     A new auxin sensor is used to reveal complex dynamic patterns of hormone distribution in development.             Articles and Letters                   A novel retinoblastoma therapy from genomic and epigenetic analyses ▶     Jinghui Zhang, Claudia A. Benavente, Justina McEvoy, Jacqueline Flores-Otero, Li Ding et al.     The retinoblastoma genome is shown to be stable, but multiple cancer pathways are identified that are epigenetically deregulated, providing potential new therapeutic targets.             Structure of HDAC3 bound to co-repressor and inositol tetraphosphate ▶     Peter J. Watson, Louise Fairall, Guilherme M. Santos & John W. R. Schwabe     The crystal structure of histone deacetylase HDAC3 bound to the co-repressor SMRT is reported, and suggests that inositol tetraphosphate could act as a regulator of HDAC3; this has therapeutic implications, because HDACs are emerging targets of anti-cancer drugs.             Recovery rates reflect distance to a tipping point in a living system ▶     Annelies J. Veraart, Elisabeth J. Faassen, Vasilis Dakos, Egbert H. van Nes, Miquel Lürling et al.     Decreased rates of recovery from perturbations, or critical slowing down, are demonstrated in a living system, indicating that recovery rates can be used to probe the resilience of complex systems.             Evolution of increased complexity in a molecular machine ▶     Gregory C. Finnigan, Victor Hanson-Smith, Tom H. Stevens & Joseph W. Thornton     Increased complexity in an essential molecular machine evolved through simple, high-probability genetic mechanisms.             Global landscape of HIV–human protein complexes ▶     Stefanie Jäger, Peter Cimermancic, Natali Gulbahce, Jeffrey R. Johnson, Kathryn E. McGovern et al.     Affinity tagging, mass spectroscopy and a tailor-made scoring system are used to identify 497 high-confidence interactions between human proteins and human immunodeficiency virus proteins.             Vif hijacks CBF-β to degrade APOBEC3G and promote HIV-1 infection ▶     Stefanie Jäger, Dong Young Kim, Judd F. Hultquist, Keisuke Shindo, Rebecca S. LaRue et al.     The transcription cofactor CBF-β is shown to regulate the ability of HIV-1 to evade host restriction mediated by the deaminase APOBEC3; it acts by interacting with the HIV protein Vif, so disrupting the Vif–CBF-β interaction could provide a new therapeutic target against HIV-1 infection.             T-cell differentiation factor CBF-β regulates HIV-1 Vif-mediated evasion of host restriction ▶     Wenyan Zhang, Juan Du, Sean L. Evans, Yunkai Yu & Xiao-Fang Yu     CBF-β is shown to regulate the ability of HIV-1 to evade host restriction mediated by the deaminase APOBEC3.             Reductive glutamine metabolism by IDH1 mediates lipogenesis under hypoxia ▶     Christian M. Metallo, Paulo A. Gameiro, Eric L. Bell, Katherine R. Mattaini, Juanjuan Yang et al.             Reductive carboxylation supports growth in tumour cells with defective mitochondria ▶     Andrew R. Mullen, William W. Wheaton, Eunsook S. Jin, Pei-Hsuan Chen, Lucas B. Sullivan et al.     Tumour cells with defective mitochondria are found to use glutamine-dependent reductive carboxylation, rather than oxidative metabolism, as the major pathway of citrate and lipid formation.             Differential oestrogen receptor binding is associated with clinical outcome in breast cancer ▶     Caryn S. Ross-Innes, Rory Stark, Andrew E. Teschendorff, Kelly A. Holmes, H. Raza Ali et al.     Genome-wide mapping of oestrogen receptor-α binding sites in primary breast cancer tissues shows that oestrogen receptor binding is dynamically regulated and that the expression of genes near differentially bound regulatory regions is associated with clinical outcome.             Natural killer cells act as rheostats modulating antiviral T cells ▶     Stephen N. Waggoner, Markus Cornberg, Liisa K. Selin & Raymond M. Welsh     Natural killer cells can act as rheostats, or ‘master regulators’, controlling antiviral T-cell responses.             Reviews and Perspectives                   The Amazon basin in transition ▶     Eric A. Davidson, Alessandro C. de Araújo, Paulo Artaxo, Jennifer K. Balch, I. Foster Brown et al.     A synthesis of recent research shows that the effects of human actions have already altered the regional hydrology and energy balance of parts of the Amazon basin, and that interactions between deforestation, fire and climate change are likely to further alter carbon storage, precipitation patterns and river discharge.             News & Views                   Genomics: The path to retinoblastoma ▶     Julien Sage & Michael L. Cleary             Evolutionary biology: A ratchet for protein complexity ▶     W. Ford Doolittle             50 & 100 years ago ▶             Cell cycle: A division duet ▶     Curt Wittenberg             Cancer: Reprogramming clinical outcome ▶     Geneviève Deblois & Vincent Giguère             Research Highlights                   Evolution: Social life shapes primate faces | Microbiology: Bacterial weapon: inflammation | Biochemistry: Fungi munch on lead | Botany: Plant gobbles buried worms | Microbiology: How parasites get sticky | Developmental biology: Watching cells die in real time         NEWS & COMMENT           Russian drug law hinders clinical trials | Preventing pandemics: The fight over flu | Public health: Biodefence built on teamwork | Books in brief | Antarctica: Scientists to the end | Leap year: Rare day to highlight rare diseases Susan M. Gasser, James R. Lupski, Yann Le Cam & Olivier Menzel | Asian medicine: Small species at risk Vincent Nijman, K. Anne-Isole Nekaris & David P. Bickford | Pharmaceutical industry: Investors unfazed by drug-patent expiry David Brindley, Brock Reeve & Chris Mason | Paul Mead Doty (1920–2011)           CAREERS           Jackson Lab to expand             More Biological Sciences ▶                         Nature Outlook: Traditional Asian Medicine Using scientific techniques to investigate the claims of traditional medicine as practised in countries such as China and Japan can help sort effective treatments from unfounded superstitions. Access the Outlook free online for six months. Produced with support from: Saishunkan Pharmaceutical               Chemical Sciences ▲top             RESEARCH           Latest Online                   Genome-wide structure and organization of eukaryotic pre-initiation complexes ▶     Ho Sung Rhee & B. Franklin Pugh     Ultra-high-resolution mapping of the eukaryotic transcription machinery across the yeast genome reveals several unifying principles of pre-initiation complexes at coding and non-coding genes.             Pathway complexity in supramolecular polymerization ▶     Peter A. Korevaar, Subi J. George, Albert J. Markvoort, Maarten M. J. Smulders, Peter A. J. Hilbers et al.     Kinetic control of the self-assembly of the π-conjugated oligomer S-chiral oligo(p-phenylenevinylene) (SOPV) reveals two competing pathways, leading to a kinetically favoured metastable product and a thermodynamically favoured stable product with opposite helicity, but the addition of a chiral tartaric acid changes the assembly process to produce only the desired metastable product.             Articles and Letters                   Structure of HDAC3 bound to co-repressor and inositol tetraphosphate ▶     Peter J. Watson, Louise Fairall, Guilherme M. Santos & John W. R. Schwabe     The crystal structure of histone deacetylase HDAC3 bound to the co-repressor SMRT is reported, and suggests that inositol tetraphosphate could act as a regulator of HDAC3; this has therapeutic implications, because HDACs are emerging targets of anti-cancer drugs.             Global landscape of HIV–human protein complexes ▶     Stefanie Jäger, Peter Cimermancic, Natali Gulbahce, Jeffrey R. Johnson, Kathryn E. McGovern et al.     Affinity tagging, mass spectroscopy and a tailor-made scoring system are used to identify 497 high-confidence interactions between human proteins and human immunodeficiency virus proteins.             Vif hijacks CBF-β to degrade APOBEC3G and promote HIV-1 infection ▶     Stefanie Jäger, Dong Young Kim, Judd F. Hultquist, Keisuke Shindo, Rebecca S. LaRue et al.     The transcription cofactor CBF-β is shown to regulate the ability of HIV-1 to evade host restriction mediated by the deaminase APOBEC3; it acts by interacting with the HIV protein Vif, so disrupting the Vif–CBF-β interaction could provide a new therapeutic target against HIV-1 infection.             Reductive glutamine metabolism by IDH1 mediates lipogenesis under hypoxia ▶     Christian M. Metallo, Paulo A. Gameiro, Eric L. Bell, Katherine R. Mattaini, Juanjuan Yang et al.             News & Views                   Cell cycle: A division duet ▶     Curt Wittenberg             Organic chemistry: Stabilizers cause instability ▶     Jonathan Clayden             Research Highlights                   Biochemistry: Fungi munch on lead         NEWS & COMMENT           Paul Mead Doty (1920–2011)             More Chemical Sciences ▶               Physical Sciences ▲top             RESEARCH           Latest Online                   Pathway complexity in supramolecular polymerization ▶     Peter A. Korevaar, Subi J. George, Albert J. Markvoort, Maarten M. J. Smulders, Peter A. J. Hilbers et al.     Kinetic control of the self-assembly of the π-conjugated oligomer S-chiral oligo(p-phenylenevinylene) (SOPV) reveals two competing pathways, leading to a kinetically favoured metastable product and a thermodynamically favoured stable product with opposite helicity, but the addition of a chiral tartaric acid changes the assembly process to produce only the desired metastable product.             Articles and Letters                   Gravitational detection of a low-mass dark satellite galaxy at cosmological distance ▶     S. Vegetti, D. J. Lagattuta, J. P. McKean, M. W. Auger, C. D. Fassnacht et al.     The discovery of a distant, low-mass satellite galaxy helps to constrain the mass function for substructure beyond the local Universe to a form that agrees at the 95 per cent confidence level with predictions based on cold dark matter.             Coherent singlet-triplet oscillations in a silicon-based double quantum dot ▶     B. M. Maune, M. G. Borselli, B. Huang, T. D. Ladd, P. W. Deelman et al.     Exploiting the weak interactions between electron spins and nuclear spins in silicon-based quantum dots leads to a dephasing time two orders of magnitude greater than in analogous gallium-arsenide-based devices, demonstrating the potential of silicon as a host material for quantum information processing.             Reconfigurable self-assembly through chiral control of interfacial tension ▶     Thomas Gibaud, Edward Barry, Mark J. Zakhary, Mir Henglin, Andrew Ward et al.     Molecular chirality can be used to control interfacial tension in multi-component mixtures of chiral molecules, and tuning the chirality makes it possible to produce and manipulate self-assembling complex chiral structures.             Evolution of increased complexity in a molecular machine ▶     Gregory C. Finnigan, Victor Hanson-Smith, Tom H. Stevens & Joseph W. Thornton     Increased complexity in an essential molecular machine evolved through simple, high-probability genetic mechanisms.             Global landscape of HIV–human protein complexes ▶     Stefanie Jäger, Peter Cimermancic, Natali Gulbahce, Jeffrey R. Johnson, Kathryn E. McGovern et al.     Affinity tagging, mass spectroscopy and a tailor-made scoring system are used to identify 497 high-confidence interactions between human proteins and human immunodeficiency virus proteins.             Reviews and Perspectives                   The Amazon basin in transition ▶     Eric A. Davidson, Alessandro C. de Araújo, Paulo Artaxo, Jennifer K. Balch, I. Foster Brown et al.     A synthesis of recent research shows that the effects of human actions have already altered the regional hydrology and energy balance of parts of the Amazon basin, and that interactions between deforestation, fire and climate change are likely to further alter carbon storage, precipitation patterns and river discharge.             News & Views                   Materials science: A fresh twist for self-assembly ▶     Volker Schaller & Andreas R. Bausch             Galaxy formation: Distant dwarfs ▶     Robert W. Schmidt             Research Highlights                   Physics: Not so ice-free materials | Applied physics: Magnetic switch for memory         NEWS & COMMENT           Pollutants key to climate fix | Database tallies US emissions | Evolution advocate turns to climate | Murders unlikely to slow Iran's nuclear efforts | Gemini's twin telescopes reboot | Fiction: Cosmic creation | Books in brief             More Physical Sciences ▶               Earth & Environmental Sciences ▲top             RESEARCH           Articles and Letters                   Kimberlite ascent by assimilation-fuelled buoyancy ▶     James K. Russell, Lucy A. Porritt, Yan Lavallée & Donald B. Dingwell     Assimilation of mantle minerals is proposed as a cause of deep-seated exsolution of dissolved volatiles and the driver of kimberlite magma ascent.             Recovery rates reflect distance to a tipping point in a living system ▶     Annelies J. Veraart, Elisabeth J. Faassen, Vasilis Dakos, Egbert H. van Nes, Miquel Lürling et al.     Decreased rates of recovery from perturbations, or critical slowing down, are demonstrated in a living system, indicating that recovery rates can be used to probe the resilience of complex systems.             Reviews and Perspectives                   The Amazon basin in transition ▶     Eric A. Davidson, Alessandro C. de Araújo, Paulo Artaxo, Jennifer K. Balch, I. Foster Brown et al.     A synthesis of recent research shows that the effects of human actions have already altered the regional hydrology and energy balance of parts of the Amazon basin, and that interactions between deforestation, fire and climate change are likely to further alter carbon storage, precipitation patterns and river discharge.             News & Views                   50 & 100 years ago ▶             Research Highlights                   Atmospheric science: More aerosols, more rain         NEWS & COMMENT           Break down boundaries in climate research | Pollutants key to climate fix | Database tallies US emissions | Evolution advocate turns to climate | Books in brief | Antarctica: Scientists to the end | Overfishing: Call to split fisheries at home and abroad U. Rashid Sumaila             More Earth & Environmental Sciences ▶                         Announcing Principles of Biology, a textbook for the 21st century from Nature Publishing Group Principles of Biology is a peer-reviewed, affordable textbook solution for university-level Introductory Biology courses, featuring 200+ customizable learning modules, 175+ interactive exercises, 3,000+ assessment questions, and access from laptops, smartphones, or tablets. Learn more.               Careers & Jobs ▲top               Outreach: Field hospitality ▶     Hosting guests on research trips can give scientists a chance to showcase their work — but it can also cause distractions.                   British prospects grim ▶     Job security for junior academics set to fall.                   Jackson Lab to expand ▶     Biomedical institute finalizes plans to open facility in Connecticut.                   Scientists miss their peak ▶     The average age of US researchers getting their first grant is on the rise.                   Careers related news & comment                   Face up to fraud | Break down boundaries in climate research | Evolution advocate turns to climate | Philanthropy: The price of charity | Leap year: Rare day to highlight rare diseases Susan M. Gasser, James R. Lupski, Yann Le Cam & Olivier Menzel | Pharmaceutical industry: Investors unfazed by drug-patent expiry David Brindley, Brock Reeve & Chris Mason             naturejobs.com Science jobs of the week       2 Research Associates in Evolutionary Anthropology     UCL            Assistant Professor in Mircobial Ecology     University of Warwick            Assistant Professor     University of Tsukuba            Postdoctoral Fellow Cell Biology     University College Dublin          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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