Nature contents: 18 April 2013

Can't view this email? Click here to view in your browser.     Volume 496 Number 7445      nature •Visit Nature homepage •Subscribe to Nature •View Table of Contents The science that matters. Every week.                       A*STAR Research - Highlighting the best of research at the Agency for Science, Technology and Research (A*STAR), Singapore's premier research organization Recent Highlights - Development: When fate hinges on cell-cell contact | Genomics: Sweet success with citrus | Nanotechnology: Color printing reaches new highs The new print edition of A*STAR Research is now available!             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 ▼   The African coelacanth genome provides insights into tetrapod evolution   The coelacanth (Latimeria chalumnae) became a star overnight when a specimen was netted off the South African coast in 1938. It was hailed as a 'living fossil', as it had been thought to have gone extinct 70 million years ago. Now its genome has been sequenced. Genomic analysis shows its protein-coding genes to be unusually slow to evolve, perhaps explaining why today's coelacanth looks much the same as its 300-million-year-old fossil ancestors.       Physical Sciences More Physical sciences ▼   Unexpected strain-stiffening in crystalline solids   Most materials become weaker and break when subjected to increasing strain. There are exceptions, though most commonly in complex biological systems. This study reports strain-stiffening behaviour in two crystalline solids, Fe3C (iron carbide) and (Al3BC3) aluminium borocarbide. The findings for Fe3C are of technological importance. Also known as cementite, Fe3C is a precipitate found in carbon steels and these results could contribute to models for predicting the hardness and strength of steels and other structural materials.       Earth & Environmental Sciences More Earth & Environmental sciences ▼   Earliest evidence for the use of pottery   The development of pottery paved the way for sophisticated cooking, storage and other technologies. The first known potters lived in eastern Asia long before the development of agriculture or a settled way of life, and what they did with their pots has long been a matter of conjecture. A chromatographic stable-isotope investigation of more than a hundred charred ceramic pots from the Japanese Jōmon culture, dating to 11,800 to 15,000 years old, suggests that they cooked fish in them. Lipid residues extracted from these ancient vessels are characteristic of marine and freshwater organisms.                   GRANT - Staying on the cutting edge is all about collaboration. That's why Expression Analysis & Illumina have combined forces to help fuel your research. FULLY-FUNDED GRANT - Integrated Biology Approach to Genetic Research. Apply online today or call 919-405-2248 * 866-293-6094                 Podcast & Video     In this week's podcast: eradicating polio, how rats use memory to plan future behaviour, and advice for young scientists from an ecologist with seven decades' experience.         News & Comment Read daily news coverage▶ ▲top               THIS WEEK           Editorials                   Look after the pennies ▶     Government decisions about where to spend and where to cut should be based on evidence, not ideology.             Smoke and mirrors ▶     Italy's parliament must listen to expert advice before deregulating stem-cell therapies.             Due credit ▶     Nature's podcast charts 12 landmark discoveries in the history of science.             World View                   Austerity-led brain drain is killing Greek science ▶     Lack of funding and recruitment freezes are driving young researchers out of the country, warns Varvara Trachana.             Seven Days                   Seven days: 12–18 April 2013 ▶     The week in science: IVF Nobel laureate Bob Edwards dies, Thermo Fisher Scientific buys up Life Technologies for $13.6 billion, and Romania's national research council resigns en masse.             NEWS IN FOCUS           A back seat for basic science ▶     Translational research wins in Obama's budget, but its economic value remains uncertain.             Synthetic biologists and conservationists open talks ▶     But worries persist about unintended consequences of tinkering with nature.             Photons test quantum paradox ▶     Contextuality theorem could improve secure communication.             'Living fossil' genome unlocked ▶     The genes of an ancient fish, the coelacanth, have much to reveal about our distant past.             Climate models fail to 'predict' US droughts ▶     Simulations identify past megadroughts, but at wrong times.             Features                   Forest ecology: Splinters of the Amazon ▶     Decades after Thomas Lovejoy isolated fragments of the Brazilian rainforest in a grand experiment, researchers are building on his legacy around the world.             Public health: Polio's moving target ▶     Finding and vaccinating Nigerian nomads may be one of the last obstacles to the eradication of polio.             COMMENT           Sustainability: Choose satellites to monitor deforestation ▶     Illegal logging threatens tropical forests and carbon stocks. Governments must work together to build an early warning system, say Jim Lynch and colleagues.             Phylogenetics: Heed the father of cladistics ▶     The way Willi Hennig discovered evolutionary relationships should not be forgotten, say Quentin Wheeler, Leandro Assis and Olivier Rieppel.             Books and Arts                   Careers: A guide to the life scientific ▶     Stuart Pimm applauds eminent biologist E. O. Wilson's pragmatic and passionate career advice.             Medical history: Feeling no pain ▶     John Carmody enjoys an exhibition that charts the trajectory of anaesthesia from its botanical beginnings.             Publishing: The word on popular science ▶     To mark UNESCO's World Book and Copyright Day on 23 April, Josie Glausiusz asks science editors at leading book publishers about trends and technology.             Correspondence                   Marine ecosystems: Overfishing in west Africa by EU vessels Raül Ramos, David Grémillet | Environment: Scale of global road map is impractical Malgorzata Blicharska | Contamination: Uphold standards for lab reagents Sally Roberts, Heidi Fuller, Bruce Caterson | Technology: Crowd-sourced soil data for Europe Wayne Shelley, Russell Lawley, David A. Robinson | Intellectual property: Chinese institute clarifies patent case Li Huang, Shuang-Jiang Liu             Correction                   Correction ▶                         Grant Funding for Promising Drug Discoveries Harrington Discovery Institute at University Hospitals Case Medical Center announces its second annual Harrington Scholar-Innovator Grant competition - a nationwide search for physician-scientists seeking to accelerate promising drug discoveries into novel treatments for patients. The grant application is open to physician-scientists at accredited academic medical centers, research institutions and universities in the United States. Letters of Intent accepted through May 15, 2013. Click here to apply now.               Biological Sciences ▲top             RESEARCH           Latest Online                   Genomics: Zebrafish earns its stripes ▶     Alexander F. Schier             Neuroscience: Navigation with a cognitive map ▶     Brandy Schmidt, A. David Redish             Hippocampal place-cell sequences depict future paths to remembered goals ▶     Brad E. Pfeiffer, David J. Foster     It is known that compressed sequences of hippocampal place cells can 'replay' previous navigational trajectories in linearly constrained mazes; here, rat place-cell sequences representing two-dimensional spatial trajectories were observed before navigational decisions, and predicted the immediate navigational path.             A systematic genome-wide analysis of zebrafish protein-coding gene function ▶     Ross N. W. Kettleborough, Elisabeth M. Busch-Nentwich, Steven A. Harvey et al.     A project to identify the phenotypes of disruptive mutations in every zebrafish protein-coding gene has so far revealed potentially disruptive mutations in more than 38% of the protein-coding genes, and the phenotypic consequences of each allele can be assessed using a novel multi-allelic phenotyping scheme.             Structure of a bacterial energy-coupling factor transporter ▶     Tingliang Wang, Guobin Fu, Xiaojing Pan et al.     The crystal structure of a nucleotide-free energy-coupling factor transporter from Lactobacillus brevis at a resolution of 3.5 Å suggests a plausible working model for the transport cycle of such transporters.             Crystal structure of a folate energy-coupling factor transporter from Lactobacillus brevis  ▶     Ke Xu, Minhua Zhang, Qin Zhao et al.     The crystal structure of an inward-facing, nucleotide-free folate energy-coupling factor transporter from Lactobacillus brevis at a resolution of 3 Å suggests a transport model that involves a substantial conformational change of the substrate-specific binding protein, FolT.             A CRISPR/Cas system mediates bacterial innate immune evasion and virulence ▶     Timothy R. Sampson, Sunil D. Saroj, Anna C. Llewellyn et al.     The CRISPR/Cas system known to aid bacterial defences by targeting invading DNA can also act to evade eukaryotic defences through a different class of small RNAs downregulating an endogenous immunogenic bacterial lipoprotein.             Meis1 regulates postnatal cardiomyocyte cell cycle arrest ▶     Ahmed I. Mahmoud, Fatih Kocabas, Shalini A. Muralidhar et al.     The neonatal heart has a high regenerative capacity that is lost in adult life; the transcription factor Meis1 has been identified as a relevant proliferative switch for this transition, providing a potential therapeutic target for adult heart regeneration.             The zebrafish reference genome sequence and its relationship to the human genome OPEN ▶     Kerstin Howe, Matthew D. Clark, Carlos F. Torroja et al.     A high-quality sequence assembly of the zebrafish genome reveals the largest gene set of any vertebrate and provides information on key genomic features, and comparison to the human reference genome shows that approximately 70% of human protein-coding genes have at least one clear zebrafish orthologue.             A role for the Perlman syndrome exonuclease Dis3l2 in the Lin28–let-7 pathway ▶     Hao-Ming Chang, Robinson Triboulet, James E. Thornton et al.     This study shows that Dis3l2 is the 3′–5′ exonuclease that mediates the degradation of uridylated precursor let-7 microRNA; this is the first physiological RNA substrate identified for this new exonuclease, which causes the Perlman syndrome of fetal overgrowth and Wilms' tumour susceptibility when mutated.             Articles and Letters                   The African coelacanth genome provides insights into tetrapod evolution OPEN ▶     Chris T. Amemiya, Jessica Alföldi, Alison P. Lee et al.     Genome sequencing and phylogenomic analysis show that the lungfish, not the coelacanth, is the closest living relative of tetrapods, that coelacanth protein-coding genes are more slowly evolving than those of tetrapods and lungfish, and that the genes and regulatory elements that underwent changes during the vertebrate transition to land reflect adaptation to a new environment.             Gating of the TrkH ion channel by its associated RCK protein TrkA ▶     Yu Cao, Yaping Pan, Hua Huang et al.     Here it is shown that ion flux through the TrkH–TrkA complex is upregulated by ATP and downregulated by ADP; solving the X-ray crystal structures of the tetrameric TrkA ring in the absence and presence of TrkH suggests a mechanism by which ATP-induced conformational changes in TrkA augment the activity of TrkH.             The structure of the KtrAB potassium transporter ▶     Ricardo S. Vieira-Pires, Andras Szollosi, João H. Morais-Cabral     This study reports the X-ray crystal structure of a Ktr K+ transporter; the structure of this KtrAB complex reveals how the dimeric membrane protein KtrB interacts with the cytosolic octameric KtrA regulatory protein.             Terrestrial water fluxes dominated by transpiration ▶     Scott Jasechko, Zachary D. Sharp, John J. Gibson et al.     An analysis of the relative effects of transpiration and evaporation, which can be distinguished by how they affect isotope ratios in water, shows that transpiration is by far the largest water flux from Earth's continents, representing 80 to 90 per cent of terrestrial evapotranspiration and using half of all solar energy absorbed by land surfaces.             Earliest evidence for the use of pottery ▶     O. E. Craig, H. Saul, A. Lucquin et al.     Chemical analysis of food residues associated with Japanese Jōmon pottery, which dates from the Late Pleistocene epoch and is the oldest pottery so far investigated, shows that most deposits were derived from high-trophic-level aquatic food.             Slower recovery in space before collapse of connected populations ▶     Lei Dai, Kirill S. Korolev, Jeff Gore     Early warning signals of systems collapse include increased recovery time after perturbations, and here spatially extended, connected yeast populations are used to identify a new warning indicator: recovery length after spatial disturbances.             Rescuing cocaine-induced prefrontal cortex hypoactivity prevents compulsive cocaine seeking ▶     Billy T. Chen, Hau-Jie Yau, Christina Hatch et al.     A study of compulsive drug-seeking behaviour in rats reveals that prolonged cocaine self-administration decreases prelimbic cortex activity resulting in increased compulsive drug-seeking actions; conversely, increasing activity in the prelimbic cortex decreases drug-seeking behaviour, a finding relevant to addiction treatment.             Visualization of an endogenous retinoic acid gradient across embryonic development ▶     Satoshi Shimozono, Tadahiro Iimura, Tetsuya Kitaguchi et al.     Genetically encoded probes for the non-peptidic morphogen retinoic acid allow the quantitative measurement of physiological RA concentration in vivo; the results support the source–sink diffusion model of morphogen dynamics proposed by Francis Crick in 1970.             A pathogenic picornavirus acquires an envelope by hijacking cellular membranes ▶     Zongdi Feng, Lucinda Hensley, Kevin L. McKnight et al.     Hepatitis A virus particles released from cells can hijack and become wrapped in host-derived membranes by using proteins that facilitate the budding of many enveloped viruses, calling into question the traditional distinction between enveloped and non-enveloped viruses.             Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization ▶     Shireen A. Sarraf, Malavika Raman, Virginia Guarani-Pereira et al.     PARKIN, a protein involved in mitochondria clearance by autophagy, is often mutated in early-onset familial Parkinson's disease; here the cellular repertoire of PARKIN targets is identified by quantitative proteomics.             A conformational switch in HP1 releases auto-inhibition to drive heterochromatin assembly ▶     Daniele Canzio, Maofu Liao, Nariman Naber et al.     The Schizosaccharomyces pombe HP1 protein, Swi6, is shown to exist in an auto-inhibited state when unbound to chromatin, switching to a spreading-competent state upon binding to the HK9 methyl mark; disrupting this switch affects heterochromatin assembly and gene silencing.             Structural basis of kynurenine 3-monooxygenase inhibition ▶     Marta Amaral, Colin Levy, Derren J. Heyes et al.     Inhibition of kynurenine 3-monooxygenase (KMO) leads to amelioration of Huntington's-disease-relevant phenotypes in yeast, fruitfly and mouse models; here the crystal structures of free and inhibitor-bound yeast KMO are presented, which could aid the development of targeted therapies for human neurodegenerative diseases.             News & Views                   Archaeology: A potted history of Japan ▶     Simon Kaner             Sensory biology: A whiff of genome ▶     Thomas Boehm             Complex systems: Spatial signatures of resilience ▶     Stephen R. Carpenter             Genomics: Zebrafish earns its stripes ▶     Alexander F. Schier             Neuroscience: Navigation with a cognitive map ▶     Brandy Schmidt, A. David Redish             Corrigenda                   Corrigendum: Serine is a natural ligand and allosteric activator of pyruvate kinase M2 ▶     Barbara Chaneton, Petra Hillmann, Liang Zheng et al.             Corrigendum: Mitochondrial Atpif1 regulates haem synthesis in developing erythroblasts ▶     Dhvanit I. Shah, Naoko Takahashi-Makise, Jeffrey D. Cooney et al.             Research Highlights                   Climate change: Desert plants reap no rewards | Neuroscience: Brain signature for thermal pain | Symbiosis: Roots spur on helpful biofilms | Conservation biology: Old evidence for fewer fish | Biomaterials: Leafy trap for bedbugs' legs | Cell biology: Super-enhancers rule genes | Ecology: Symbionts set squid's clock | Immunology: Proteins that rouse also quash         NEWS & COMMENT           Due credit | 'Living fossil' genome unlocked | Forest ecology: Splinters of the Amazon | Public health: Polio's moving target | Phylogenetics: Heed the father of cladistics | Careers: A guide to the life scientific | Medical history: Feeling no pain | Marine ecosystems: Overfishing in west Africa by EU vessels | Correction | Smoke and mirrors | Synthetic biologists and conservationists open talks             More Biological Sciences ▶                         FREE FOCUS: Traumatic brain injury Traumatic brain injury is known as a silent epidemic as few people are aware that each year, in the US alone, around 1.7 million people sustain a TBI, resulting in 52,000 deaths. This Nature Reviews Neurology Focus provides an overview of recent advances in our knowledge of causes, consequences, pathologies and diagnosis of brain injury, as well as issues that remain to be addressed in future research. FREE online for a limited time.               Chemical Sciences ▲top             RESEARCH           News & Views                   Physical chemistry: Molecular motion watched ▶     Bradley Siwick, Eric Collet             Corrigendum                   Corrigendum: Serine is a natural ligand and allosteric activator of pyruvate kinase M2 ▶     Barbara Chaneton, Petra Hillmann, Liang Zheng et al.             More Chemical Sciences ▶               Physical Sciences ▲top             RESEARCH           Latest Online                   Experimental realization of non-Abelian non-adiabatic geometric gates ▶     A. A. Abdumalikov, J. M. Fink, K. Juliusson et al.     Microwave stimulation of a superconducting artificial three-level atom is used to demonstrate high-fidelity, non-Abelian geometric transformations, the results of which depend on the order in which they are performed.             Bell violation using entangled photons without the fair-sampling assumption ▶     Marissa Giustina, Alexandra Mech, Sven Ramelow et al.     The fair-sampling loophole is closed in a Bell inequality violation experiment with entangled photons, making the photon the first physical system for which all the main loopholes have been closed.             Articles and Letters                   A dust-obscured massive maximum-starburst galaxy at a redshift of 6.34 ▶     Dominik A. Riechers, C. M. Bradford, D. L. Clements et al.     A massive starburst galaxy with 100 billion solar masses of gas is identified at a redshift of 6.34; a 'maximum starburst' converts the gas into stars at a rate more than 2,000 times that of the Milky Way.             High-fidelity readout and control of a nuclear spin qubit in silicon ▶     Jarryd J. Pla, Kuan Y. Tan, Juan P. Dehollain et al.     Electrical detection and coherent manipulation of a single 31P nuclear spin qubit is reported; the high fidelities are promising for fault-tolerant nuclear-spin-based quantum computing using silicon.             Unexpected strain-stiffening in crystalline solids ▶     Chao Jiang, Srivilliputhur G. Srinivasan     Quantum mechanical calculations reveal a surprising strain-stiffening phenomenon in two crystalline solids, one of which is cementite, a precipitate found in carbon steels.             Mapping molecular motions leading to charge delocalization with ultrabright electrons ▶     Meng Gao, Cheng Lu, Hubert Jean-Ruel et al.     An ultrabright femtosecond electron source is used to monitor the molecular motions in the organic salt (EDO-TTF)2PF6 as it undergoes its photo-induced insulator-to-metal phase transition.             News & Views                   Astronomy: A cosmic growth spurt in an infant galaxy ▶     Desika Narayanan, Chris Carilli             Physical chemistry: Molecular motion watched ▶     Bradley Siwick, Eric Collet             Research Highlights                   Biomaterials: Leafy trap for bedbugs' legs | Photovoltaics: Cheap, colourful solar cells         NEWS & COMMENT           Photons test quantum paradox             More Physical Sciences ▶               Earth & Environmental Sciences ▲top             RESEARCH           Articles and Letters                   Terrestrial water fluxes dominated by transpiration ▶     Scott Jasechko, Zachary D. Sharp, John J. Gibson et al.     An analysis of the relative effects of transpiration and evaporation, which can be distinguished by how they affect isotope ratios in water, shows that transpiration is by far the largest water flux from Earth's continents, representing 80 to 90 per cent of terrestrial evapotranspiration and using half of all solar energy absorbed by land surfaces.             News & Views                   Biogeochemistry: Nitrogen deposition and forest carbon ▶     Beverly Law             Complex systems: Spatial signatures of resilience ▶     Stephen R. Carpenter             Research Highlights                   Climate change: Desert plants reap no rewards | Conservation biology: Old evidence for fewer fish         NEWS & COMMENT           Forest ecology: Splinters of the Amazon | Sustainability: Choose satellites to monitor deforestation | Environment: Scale of global road map is impractical | Synthetic biologists and conservationists open talks | Climate models fail to 'predict' US droughts             More Earth & Environmental Sciences ▶                         Ludwig Institute for Cancer Research, Nature Genetics, and Nature Reviews Cancer present: Nuclear Reprogramming and the Cancer Genome St. Catherine's College, University of Oxford, Oxford, UK September 25-27, 2013 Click here for more information or to register for this conference.               Careers & Jobs ▲top               Regulatory science: Researchers in the pipeline ▶     Prospects are starting to look bright in the growing field of science intended to aid regulation of food safety and drug development.                   Turning point: Adam de la Zerda ▶     Former engineer takes up structural biology to help to develop cancer treatments.             Careers related news & comment                   Seven days: 12–18 April 2013 | Austerity-led brain drain is killing Greek science Varvara Trachana | Careers: A guide to the life scientific Stuart Pimm | Look after the pennies               naturejobs.com Science jobs of the week       Research Associate     Centre for Molecular Medicine and Therapeuitcs/UBC            Research Fellows     University of St Andrews            Research Officer / Research Fellow     The University of Queensland          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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