Nature contents: 26 July 2012

Can't view this email? Click here to view in your browser.     Volume 487 Number 7408      nature •Visit Nature homepage •Subscribe to Nature •View Table of Contents The science that matters. Every week.                       Frontiers in Plant Biology: From Discovery to Applications October 3-5, 2012 - Ghent, Belgium This conference will focus on the recent breakthroughs in plant biology, enabled by the latest methodological developments. For more information and to register, visit: www.nature.com/natureconferences/fpb2012/index.html             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     Physical Sciences More Physical sciences ▼   Collective bulk carrier delocalization driven by electrostatic surface charge accumulation   In a conventional silicon transistor, the voltage-controlled switching mechanism is provided by a nanometre-sized conducting channel near the surface. This paper describes a new type of transistor in which an electric field controls the electronic properties of the whole of the device. This is made possible by using vanadium dioxide instead of silicon. Practical applications could include the remote transmission of electrical signals       Biological Sciences More Biological sciences ▼   ACE2 links amino acid malnutrition to microbial ecology and intestinal inflammation   In malnutrition, it is often the associated diarrhoea and intestinal inflammation that cause morbidity and death. A new study implicates angiotensin converting enzyme 2 (ACE2) deficiency as a cause of increased susceptibility to intestinal inflammation. Dietary tryptophan and its metabolite nicotinamide can alleviate the symptoms. This surprising finding explains nutritional effects that have been known for centuries and provides a molecular link between malnutrition and the intestinal microbiome.       Biological Sciences More Biological sciences ▼   Administration of vorinostat disrupts HIV-1 latency in patients on antiretroviral therapy   HIV infection can persist within a small population of cells without expressing any viral genes, making it a difficult target for antiviral therapies. It was previously shown in cell cultures that induction of virus gene expression in latently HIV-1 infected cells can be achieved with histone deacetylase inhibitors, such as the anticancer drug vorinostat. David Margolis and co-workers now report that proviral HIV can be 'flushed out' by vorinostat treatment in patients too. Vorinostat has toxic effects that would need to be considered when assessing the risks and benefits of attempts to eradicate HIV infection using this or similar drugs.                   Roche's X-tremeGENE Transfection Reagents Transfect efficiently with low cytotoxicity - proven in 275 different cell types...over 130 cancer cells. Free sample and protocols at www.x-tremegene.roche.com For life science research only. Not for use in diagnostic procedures                 Podcast & Video     In this week's podcast: early snake evolution, smoking out HIV and dating planets. Plus, the best of the rest from this week's Nature.         News & Comment Read daily news coverage▶ ▲top             THIS WEEK           Editorials                   Secret disservice ▶     Staff-surveillance efforts by government agencies must not contravene the rights of whistle-blowers, as the US Food and Drug Administration is accused of doing.             Protect and serve ▶     A 'health check' of protected ecological areas reveals an alarming decline in biodiversity.             Error prone ▶     Biologists must realize the pitfalls of work on massive amounts of data.             World View                   Writers should not fear jargon ▶     Researchers use complex language for a specific purpose, and science writers should be clear about what those reasons are, says Trevor Quirk.             Seven Days                   Seven days: 20–26 July 2012 ▶     The week in science: Second weight-loss drug approved; US drought hits crops; and Sally Ride — the first US woman in space — dies.           NEWS IN FOCUS           TB drugs chalk up rare win ▶     Combination therapy is just one emerging weapon in the fight against tuberculosis.             Cuts loom for US science ▶     As budget bills line up, agencies anticipate post-election panic.             End of an age for Aquarius ▶     Iconic underwater research base set to close its airlocks for the last time this year.             Contest to sequence centenarians kicks off ▶     First entrant pins hopes on semiconductor technology.             US drug agency spied on scientists ▶     Food and Drug Administration monitored five employees, defying promises about whistle-blower protection.             A giant bid to etch tiny circuits ▶     Intel invests US$1 billion into extreme-ultraviolet light technology that will quarter the size of transistors.             US fusion in budget vice ▶     Domestic facilities struggle for survival as funding is directed to international reactor.             Feature                   Planetary science: The time machine ▶     Dating features on the Moon and Mars is guesswork. Scott Anderson is building a tool to change that.           COMMENT           Methods: Face up to false positives ▶     Scientists and journals must work together to ensure that eye-catching artefacts are not trumpeted as genomic insights, says Daniel MacArthur.             Books and Arts                   Visualization: Picturing science ▶     Katy Börner weighs up a lavish, lab-friendly guide to transforming dry data into insightful images.             Renaissance art: Puzzles beneath Dürer's paint ▶     Alison Abbott assesses an infrared analysis that could point to the artist's real ambitions.             Correspondence                   Research accountability: Mandate ethics methods in papers James A. Anderson, Marleen Eijkholt & Judy Illes | Schizophrenia: Patients' research priorities get funded Keith Lloyd, Jo White & Iain Chalmers | Astronomy: More medieval clues to cosmic-ray event Gary W. Gibbons & Marcus C. Werner | Eutrophication: Political backing to save the Baltic Sea Ragnar Elmgren | Open access: Hard on lone authors Christopher Smith           Correction                   Correction ▶             Correction ▶                 Biological Sciences ▲top             RESEARCH           Latest Online                   A transitional snake from the Late Cretaceous period of North America ▶     Nicholas R. Longrich, Bhart-Anjan S. Bhullar & Jacques A. Gauthier     Previously undescribed material from the maxilla, dentary and spine of the Cretaceous Coniophis precedens shows that it is the most primitive known snake.             Dissecting the genomic complexity underlying medulloblastoma  OPEN ▶     David T. W. Jones, Natalie Jäger, Marcel Kool, Thomas Zichner, Barbara Hutter et al.     Medulloblastoma is the most common brain tumour in children; using whole-genome sequencing of tumour samples the authors show that the clinically challenging Group 3 and 4 tumours can be tetraploid, and reveal the expression of the first medulloblastoma fusion genes identified.             Averting biodiversity collapse in tropical forest protected areas ▶     William F. Laurance, D. Carolina Useche, Julio Rendeiro, Margareta Kalka, Corey J. A. Bradshaw et al.     Analysis of changes in functional groups of species and potential drivers of environmental change for protected areas across the world’s major tropical regions reveals large variation between reserves that have been effective and those experiencing an erosion of biodiversity, and shows that environmental changes immediately outside reserves are nearly as important as those inside in determining their ecological fate.             Bacterial virulence proteins as tools to rewire kinase pathways in yeast and immune cells ▶     Ping Wei, Wilson W. Wong, Jason S. Park, Ethan E. Corcoran, Sergio G. Peisajovich et al.     Virulence factors from two bacteria are used to reprogram intracellular signalling in yeast and immune T cells, illustrating how pathogens can provide a toolkit to engineer cells for biotechnological or therapeutic applications.             Chromatin organization is a major influence on regional mutation rates in human cancer cells ▶     Benjamin Schuster-Böckler & Ben Lehner     Mutation rates in cancer genomes are closely related to chromatin organization, indicating that the arrangement of the genome into heterochromatin- and euchromatin-like domains may be a dominant influence on variation in regional mutation rate in human somatic cells.             A biophysical signature of network affiliation and sensory processing in mitral cells ▶     Kamilla Angelo, Ede A. Rancz, Diogo Pimentel, Christian Hundahl, Jens Hannibal et al.     Functional heterogeneity within a class of neurons is investigated by comparing the intrinsic properties of pairs of mitral cells belonging to either the same or different glomerular circuits; this shows that neuronal excitability is stereotypic for mitral cells from the same olfactory network indicating that local circuits are functionally adapted to process subtly distinct information.             Heterodimeric JAK–STAT activation as a mechanism of persistence to JAK2 inhibitor therapy ▶     Priya Koppikar, Neha Bhagwat, Outi Kilpivaara, Taghi Manshouri, Mazhar Adli et al.     Chronic exposure to JAK2 inhibitors leads to reactivation of downstream signalling through the formation of heterodimers between JAK2 and other JAK kinases in myeloproliferative neoplasms, which can be overcome with Hsp90 inhibitors.             Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations ▶     Trevor J. Pugh, Shyamal Dilhan Weeraratne, Tenley C. Archer, Daniel A. Pomeranz Krummel, Daniel Auclair et al.     Medulloblastoma is the most common brain tumour in children; using exome sequencing of tumour samples the authors show that these cancers have low mutation rates and identify 12 significantly mutated genes, among them the gene encoding RNA helicase DDX3X.             Articles and Letters                   Oligodendroglia metabolically support axons and contribute to neurodegeneration ▶     Youngjin Lee, Brett M. Morrison, Yun Li, Sylvain Lengacher, Mohamed H. Farah et al.     Disruption of the lactate transporter monocarboxylate transporter 1 (MCT1), which is highly enriched within oligodendroglia and reduced in patients with amyotrophic lateral sclerosis (ALS), causes axon damage and neurodegeneration in animal and cell culture models, suggesting a fundamental role for MCT1 in metabolic support of axons and ALS pathogenesis.             Reconciling the temperature dependence of respiration across timescales and ecosystem types ▶     Gabriel Yvon-Durocher, Jane M. Caffrey, Alessandro Cescatti, Matteo Dossena, Paul del Giorgio et al.     The sensitivity of ecosystem respiration to seasonal changes in temperature is shown to be remarkably similar for a wide range of ecosystem types spanning the globe; however, terrestrial and aquatic ecosystems differ markedly in their temperature sensitivity over annual timescales.             ACE2 links amino acid malnutrition to microbial ecology and intestinal inflammation ▶     Tatsuo Hashimoto, Thomas Perlot, Ateequr Rehman, Jean Trichereau, Hiroaki Ishiguro et al.     Mutations in angiotensin-converting enzyme 2 are shown to predispose mice to colitis as a consequence of neutral amino acid malabsorption and a change in the resident microbiota; these results could explain how protein malnutrition — affecting up to one billion people — leads to intestinal inflammation.             Administration of vorinostat disrupts HIV-1 latency in patients on antiretroviral therapy ▶     N. M. Archin, A. L. Liberty, A. D. Kashuba, S. K. Choudhary, J. D. Kuruc et al.     The latent HIV-1 reservoir represents a major barrier to curing patients with HIV-1 infection, and now in vivo evidence is presented that vorinostat can disrupt proviral latency of HIV-1.             Viral immune modulators perturb the human molecular network by common and unique strategies ▶     Andreas Pichlmair, Kumaran Kandasamy, Gualtiero Alvisi, Orla Mulhern, Roberto Sacco et al.     A systems approach provides a global perspective of the different strategies that viruses use to modulate the cellular innate immune response; this may be useful in the design of future viral intervention strategies.             Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins ▶     Orit Rozenblatt-Rosen, Rahul C. Deo, Megha Padi, Guillaume Adelmant, Michael A. Calderwood et al.     Combining analysis of host proteome and transcriptome perturbations induced by tumour virus proteins with ongoing genome-wide studies of cancer facilitates the prioritization of cancer genes.             Live imaging of stem cell and progeny behaviour in physiological hair-follicle regeneration ▶     Panteleimon Rompolas, Elizabeth R. Deschene, Giovanni Zito, David G. Gonzalez, Ichiko Saotome et al.     A non-invasive method is used to study and manipulate hair-follicle regeneration over time in live mice, and shows that hair growth involves spatially regulated cell divisions, cellular reorganization and migration of epithelial cells, and that the mesenchyme is required for hair growth.             Tumour micro-environment elicits innate resistance to RAF inhibitors through HGF secretion ▶     Ravid Straussman, Teppei Morikawa, Kevin Shee, Michal Barzily-Rokni, Zhi Rong Qian et al.     The secretion of hepatocyte growth factor by stromal cells in the tumour micro-environment can make melanoma resistant to RAF inhibitors, through the activation of the MET signalling pathway, but a combination of RAF and MET inhibitors can overcome this resistance.             Widespread potential for growth-factor-driven resistance to anticancer kinase inhibitors ▶     Timothy R. Wilson, Jane Fridlyand, Yibing Yan, Elicia Penuel, Luciana Burton et al.     The efficacy of kinase inhibitors in treating cancer is limited by drug resistance; here it is shown that most human tumour cells can develop drug resistance through being exposed to one or more receptor tyrosine kinase ligands.             RNA sequencing of pancreatic circulating tumour cells implicates WNT signalling in metastasis ▶     Min Yu, David T. Ting, Shannon L. Stott, Ben S. Wittner, Fatih Ozsolak et al.     A new method allows the collection of circulating tumour cells (CTCs) despite their rarity; transcriptome sequencing of CTCs could allow identification of pathways involved in metastasis.             Structural insights into electron transfer in caa3-type cytochrome oxidase ▶     Joseph A. Lyons, David Aragão, Orla Slattery, Andrei V. Pisliakov, Tewfik Soulimane et al.     The caa3-type cytochrome oxidase structure described here provides insight into the coupling of energy transduction to the complete reduction of oxygen.             News & Views                   Neuroscience: The wrap that feeds neurons ▶     Johanne E. Rinholm & Linda H. Bergersen             Immunology: Malnutrition promotes rogue bacteria ▶     Ana Izcue & Fiona Powrie             HIV: Shock and kill ▶     Steven G. Deeks             Vision: Looking to develop sight ▶     Eileen Birch             Research Highlights                   Bioengineering: Engineered 'jellyfish' | Cancer immunology: Pathway from breast to bone | Microbiology: Recycling at root of arsenic 'life' | HIV: Human response in model mice | Animal behaviour: Squid 'fly' faster than they swim | Cancer: New target for melanoma fight | Ecology: Toxins for cane-toad control         NEWS & COMMENT           Secret disservice | Protect and serve | Error prone | TB drugs chalk up rare win | Contest to sequence centenarians kicks off | Methods: Face up to false positives | Schizophrenia: Patients' research priorities get funded Keith Lloyd, Jo White & Iain Chalmers           CAREERS           Germany: Excellence revisited             More Biological Sciences ▶                         Eppendorf Award for Young European Investigators Nature is the partner for the Eppendorf Award for Young European Investigators. Listen to a podcast with this year's winner Elizabeth Murchison, Ph.D. (Wellcome Trust Sanger Institute, Cambridge, United Kingdom) to learn more about her work, and read excerpts from the interview in a Q&A feature article               Chemical Sciences ▲top             RESEARCH           Latest Online                   Bacterial virulence proteins as tools to rewire kinase pathways in yeast and immune cells ▶     Ping Wei, Wilson W. Wong, Jason S. Park, Ethan E. Corcoran, Sergio G. Peisajovich et al.     Virulence factors from two bacteria are used to reprogram intracellular signalling in yeast and immune T cells, illustrating how pathogens can provide a toolkit to engineer cells for biotechnological or therapeutic applications.             Articles and Letters                   Viral immune modulators perturb the human molecular network by common and unique strategies ▶     Andreas Pichlmair, Kumaran Kandasamy, Gualtiero Alvisi, Orla Mulhern, Roberto Sacco et al.     A systems approach provides a global perspective of the different strategies that viruses use to modulate the cellular innate immune response; this may be useful in the design of future viral intervention strategies.             Structural insights into electron transfer in caa3-type cytochrome oxidase ▶     Joseph A. Lyons, David Aragão, Orla Slattery, Andrei V. Pisliakov, Tewfik Soulimane et al.     The caa3-type cytochrome oxidase structure described here provides insight into the coupling of energy transduction to the complete reduction of oxygen.             Research Highlights                   Microbiology: Recycling at root of arsenic 'life'           More Chemical Sciences ▶               Physical Sciences ▲top             RESEARCH           Latest Online                   Quantum optics: Strongly interacting photons ▶     Thad G. Walker             Quantum nonlinear optics with single photons enabled by strongly interacting atoms ▶     Thibault Peyronel, Ofer Firstenberg, Qi-Yu Liang, Sebastian Hofferberth, Alexey V. Gorshkov et al.     A cold, dense atomic gas is found to be optically nonlinear at the level of individual quanta, thereby opening possibilities for quantum-by-quantum control of light fields, including single-photon switching and deterministic quantum logic.             Articles and Letters                   Alignment of the stellar spin with the orbits of a three-planet system ▶     Roberto Sanchis-Ojeda, Daniel C. Fabrycky, Joshua N. Winn, Thomas Barclay, Bruce D. Clarke et al.     An analysis of transits of planets over starspots on the Sun-like star Kepler-30 shows that the orbits of the three planets are aligned with the stellar equator; this configuration is similar to that of our Solar System, and suggests that high obliquities are confined to systems that experienced disruptive dynamical interactions.             The ‘Higgs’ amplitude mode at the two-dimensional superfluid/Mott insulator transition ▶     Manuel Endres, Takeshi Fukuhara, David Pekker, Marc Cheneau, Peter Schauβ et al.     A ‘Higgs’ mode, signifying the breaking of a continuous symmetry in a model with emergent Lorentz invariance, is found close to the transition to the Mott insulating phase in a two-dimensional neutral superfluid.             Collective bulk carrier delocalization driven by electrostatic surface charge accumulation ▶     M. Nakano, K. Shibuya, D. Okuyama, T. Hatano, S. Ono et al.     A conceptually new type of transistor, based on a strongly correlated material, allows external control of a macroscopic electronic phase transition, and gives rise to a non-volatile memory effect.             Structured spheres generated by an in-fibre fluid instability ▶     Joshua J. Kaufman, Guangming Tao, Soroush Shabahang, Esmaeil-Hooman Banaei, Daosheng S. Deng et al.     Uniformly sized, structured spherical particles can be made in large quantities and across a wide range of sizes by an ingenious technique involving heating and drawing out multi-component fibres.             Inland thinning of West Antarctic Ice Sheet steered along subglacial rifts ▶     Robert G. Bingham, Fausto Ferraccioli, Edward C. King, Robert D. Larter, Hamish D. Pritchard et al.     Estimates of ice loss from the West Antarctic Ice Sheet depend on accurate modelling of dynamic thinning, for which knowledge of basal topography is needed; here, ice-penetrating radar, gravity and magnetic measurements reveal a subglacial rift basin that acts as a conduit between the Bellingshausen Sea and the ice-sheet interior.             News & Views                   Astronomy: Planets on the spot ▶     Drake Deming             Device physics: Put the pedal to the metal ▶     Jochen Mannhart & Wilfried Haensch             Materials science: The abilities of instabilities ▶     Ali Passian & Thomas Thundat             Quantum optics: Strongly interacting photons ▶     Thad G. Walker             Research Highlights                   Materials: Rolling out data storage         NEWS & COMMENT           A giant bid to etch tiny circuits | US fusion in budget vice | Planetary science: The time machine | Visualization: Picturing science | Astronomy: More medieval clues to cosmic-ray event Gary W. Gibbons & Marcus C. Werner           CAREERS           Germany: Excellence revisited | Turning point: Robert Gregg             More Physical Sciences ▶               Earth & Environmental Sciences ▲top             RESEARCH           Latest Online                   Averting biodiversity collapse in tropical forest protected areas ▶     William F. Laurance, D. Carolina Useche, Julio Rendeiro, Margareta Kalka, Corey J. A. Bradshaw et al.     Analysis of changes in functional groups of species and potential drivers of environmental change for protected areas across the world’s major tropical regions reveals large variation between reserves that have been effective and those experiencing an erosion of biodiversity, and shows that environmental changes immediately outside reserves are nearly as important as those inside in determining their ecological fate.             Articles and Letters                   Alignment of the stellar spin with the orbits of a three-planet system ▶     Roberto Sanchis-Ojeda, Daniel C. Fabrycky, Joshua N. Winn, Thomas Barclay, Bruce D. Clarke et al.     An analysis of transits of planets over starspots on the Sun-like star Kepler-30 shows that the orbits of the three planets are aligned with the stellar equator; this configuration is similar to that of our Solar System, and suggests that high obliquities are confined to systems that experienced disruptive dynamical interactions.             Inland thinning of West Antarctic Ice Sheet steered along subglacial rifts ▶     Robert G. Bingham, Fausto Ferraccioli, Edward C. King, Robert D. Larter, Hamish D. Pritchard et al.     Estimates of ice loss from the West Antarctic Ice Sheet depend on accurate modelling of dynamic thinning, for which knowledge of basal topography is needed; here, ice-penetrating radar, gravity and magnetic measurements reveal a subglacial rift basin that acts as a conduit between the Bellingshausen Sea and the ice-sheet interior.             Reconciling the temperature dependence of respiration across timescales and ecosystem types ▶     Gabriel Yvon-Durocher, Jane M. Caffrey, Alessandro Cescatti, Matteo Dossena, Paul del Giorgio et al.     The sensitivity of ecosystem respiration to seasonal changes in temperature is shown to be remarkably similar for a wide range of ecosystem types spanning the globe; however, terrestrial and aquatic ecosystems differ markedly in their temperature sensitivity over annual timescales.             News & Views                   Astronomy: Planets on the spot ▶     Drake Deming             Brief Communications Arising                   Atmospheric oxygenation and volcanism ▶     James F. Kasting, David C. Catling & Kevin Zahnle             Gaillard et al. reply ▶     Fabrice Gaillard, Bruno Scaillet & Nicholas T. Arndt             Research Highlights                   Geology: Greenland's ancient impact         NEWS & COMMENT           Protect and serve | End of an age for Aquarius | Planetary science: The time machine | Eutrophication: Political backing to save the Baltic Sea Ragnar Elmgren             More Earth & Environmental Sciences ▶                         Scientific Reports publishes 457 open access papers in its first year Publishing technically sound research articles, Scientific Reports is Nature Publishing Group’s fastest growing journal. Given the speed and visibility offered, no wonder 93% of our authors said that they are “likely” or “very likely” to submit again. Keep your research moving. Submit to Scientific Reports               Careers & Jobs ▲top               Germany: Excellence revisited ▶     The second phase of the German Excellence Initiative is helping scientists and universities. But sustaining its gains in the long term could be a challenge.                   Turning point: Robert Gregg ▶     Father's illness spurs engineer to pursue medical advances through robotics and prosthetics.                   Careers related news & comment                   Error prone | Schizophrenia: Patients' research priorities get funded Keith Lloyd, Jo White & Iain Chalmers             naturejobs.com Science jobs of the week       Director - Tumor Immunology (full-time position)     iTeos Therapeutics             Post-doc Research Associate - Ecosystem Service Analyses (f / m)     University of Hamburg, Biocentre Klein Flottbek and Botanical Gardens             Doctoral candidate (PhD student) in Physics (M / F)     Universite du Luxembourg            Postdoctoral Scientist (m / f)     Deutsches Krebsforschungszentrum (DKFZ)          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. Keep up-to-date with the latest sector trends, vote in our reader poll and sign-up to receive the monthly Naturejobs newsletter.           • Nature events featured events           natureevents featured events         Earth Science - 2012     21.-22.08.12 Chicago, US         Nature events is the premier resource for scientists looking for the latest scientific conferences, courses, meetings and symposia. Featured across Nature Publishing Group journals and centrally at natureevents.com it is an essential reference guide to scientific events worldwide.               Futures                   Lifeboat ▶     David Carr                 Your email address is in the Nature mailing list. You have been sent this Table of Contents Alert because you have opted in to receive it. 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