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Editorials

Assessing assessment p845

Transparency, education and communication are key to ensuring that appropriate metrics are used to measure individual scientific achievement.

doi:10.1038/465845a

See also: Editor's summary


A DNA education p845

Taking personal genetic testing into the classroom brings ethical and legal sensitivities to the fore.

doi:10.1038/465845b


Skyrmion makeover p846

Celebrating the treasures of topological twists.

doi:10.1038/465846a


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Research Highlights

Biology: Sniffer sharks p848

doi:10.1038/465848a


Ecology: Rise of the sources p848

doi:10.1038/465848b


Microbiology: A strain on the relationship p848

doi:10.1038/465848c


Chemistry: Potent potato power p848

doi:10.1038/465848d


Ecology: A watery grave p848

doi:10.1038/465848e


Extrasolar planets: Planets form quickly p848

doi:10.1038/465848f


Chemistry: Iodine improvement p849

doi:10.1038/465849a


Microbial ecology: Sated snakes p849

doi:10.1038/465849b


Materials science: Noodly appendages p849

doi:10.1038/465849c


Evolutionary genetics: Vive la digits p849

doi:10.1038/465849d


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Journal Club

Journal club p849

Ros Rickaby

doi:10.1038/465849e


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News

News briefing: 11–17 June 2010 p850

The week in science.

doi:10.1038/465850a


Diseased cells fail to win approval p852

Consent form signed by clinic's donors falls short of 'high ethical standards' set by the NIH.

Meredith Wadman

doi:10.1038/465852a


Intensive farming may ease climate change p853

Land saved from cultivation offsets carbon emissions.

Jeff Tollefson

doi:10.1038/465853a


MRI set to win reprieve from EU ban p854

Directive that limits workers' electromagnetic exposure aims for a compromise.

Alison Abbott

doi:10.1038/465854a


US biotech firms line up for tax credits p854

Application process begins for cash to beat the downturn.

Heidi Ledford

doi:10.1038/465854b


Mr Smits goes to Brussels p857

Enthusiastic welcome for new European research chief.

Alison Abbott

doi:10.1038/465857a


Russia woos lost scientists p858

Minister of education and science discusses plans for rebuilding the country's research base.

Quirin Schiermeier & Konstantin Severinov

doi:10.1038/465858a


UN body will assess ecosystems and biodiversity p859

Nations agree on way to keep watch on Earth's health.

Emma Marris

doi:10.1038/465859a


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Correction p859

doi:10.1038/465859b


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News Features

Metrics: Do metrics matter? p860

Many researchers believe that quantitative metrics determine who gets hired and who gets promoted at their institutions. With an exclusive poll and interviews, Nature probes to what extent metrics are really used that way.

doi:10.1038/465860a


Metrics: A profusion of measures p864

Scientific performance indicators are proliferating — leading researchers to ask afresh what they are measuring and why. Richard Van Noorden surveys the rapidly evolving ecosystem.

doi:10.1038/465864a


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Column

World view: Talking the talk p867

Without effective public engagement, there will be no synthetic biology in Europe, says Colin Macilwain.

Colin Macilwain

doi:10.1038/465867a


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Correspondence

New data system to galvanize Brazil's conservation efforts p869

Ana C. M. Malhado & Richard J. Ladle

doi:10.1038/465869a


Green development credits to foster global biodiversity p869

Alexander N. James & Francis Vorhies

doi:10.1038/465869b


Expand scientific input to address environmental effects p869

Lindsay C. Stringer, Richard J. Thomas & Mariam Akhtar-Schuster

doi:10.1038/465869c


Call for cooperation to contain damage by Chile's salmon farms p869

Heike Vester & Marc Timme

doi:10.1038/465869d


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Opinion

How to improve the use of metrics p870

Since the invention of the science citation index in the 1960s, quantitative measuring of the performance of researchers has become ever more prevalent, controversial and influential. Six commentators tell Nature what changes might ensure that individuals are assessed more fairly.

doi:10.1038/465870a

See also: Editor's summary


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Books and Arts

How the boson got Higgs's name p873

Frank Close enjoys a journalistic account of the sociology and politics of the search for the elusive particle named after physicist Peter Higgs, but cautions that the idea has deeper roots than its name implies.

Frank Close reviews Massive: The Hunt for the God Particle by Ian Sample

doi:10.1038/465873a


Books in brief p874

Joanne Baker

doi:10.1038/465874a


Earth-shaking images p874

Alexis Drahos reviews The Illustrated History of Natural Disasters by Jan Kozák & Vladimir Čermák

doi:10.1038/465874b


Nature trapped in glass p875

Colin Martin reviews Nature Transfigured: Steffen Dam

doi:10.1038/465875a


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News and Views

Biochemistry: A radically different enzyme p877

The enzyme co-substrate S-adenosylmethionine is a potential source of two different free radicals, yet only one seemed to occur in nature. The discovery of an unusual enzyme reveals that both radicals can be formed.

Joan B. Broderick

doi:10.1038/465877a

See also: Editor's summary | Article by Zhang et al.


Solar system: Blink from a remote world p878

The use of stellar occultations to disclose unknown aspects of our Solar System is not new. But the latest such event to be reported involves an object that lies beyond the orbit of Neptune — and is a first.

Bruno Sicardy

doi:10.1038/465878a

See also: Editor's summary | Letter by Elliot et al.


Genomics: The tale of our other genome p879

The groundwork for analysing the human microbiome — sequencing the collective genome of all our resident microorganisms — is now done. This work is of significance for understanding both human health and disease.

Liping Zhao

doi:10.1038/465879a


Condensed-matter physics: Single skyrmions spotted p880

Skyrmions are a special type of particle that has long been predicted to exist in many fields of physics. Direct images of these structures have now been made in a magnetic material.

Christian Pfleiderer & Achim Rosch

doi:10.1038/465880a

See also: Editor's summary | Letter by Yu et al.


Conservation biology: When an infection turns lethal p881

Losses in biodiversity and the emergence of new infectious diseases are among the greatest threats to life on the planet. The declines in amphibian populations lie at the interface between these issues.

Andrew R. Blaustein & Pieter T. J. Johnson

doi:10.1038/465881a


Structural biology: Immunity takes a heavy Toll p882

Toll receptors trigger immune responses through adaptor proteins and kinase enzymes. Structural studies reveal that hierarchical assembly of these proteins into a helical tower initiates downstream signalling events.

Steven A. Wasserman

doi:10.1038/465882a

See also: Editor's summary | Article by Lin et al.


Obituary: Martin Gardner (1914–2010) p884

'Mathemagician' who popularized maths and debunked pseudoscience.

David Singmaster

doi:10.1038/465884a


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Articles

Helical assembly in the MyD88–IRAK4–IRAK2 complex in TLR/IL-1R signalling p885

Toll-like receptors (TLRs) are crucial to innate immunity. Activation of these proteins, and of receptors for the pro-inflammatory cytokines IL-1 and IL-18, leads to the recruitment of adaptor proteins such as MyD88. These in turn interact with further proteins such as IRAK2 and IRAK4. The crystal structure of the MyD88–IRAK2–IRAK4 death domain complex is now reported, explaining how these three proteins cooperate in TLR/IL-1R signalling.

Su-Chang Lin, Yu-Chih Lo & Hao Wu

doi:10.1038/nature09121

See also: Editor's summary | News and Views by Wasserman


Diphthamide biosynthesis requires an organic radical generated by an iron–sulphur enzyme p891

Translation elongation factor 2 (EF2) from archaea and eukaryotes contains a unique, post-translationally modified histidine residue called diphthamide, which is the target of diphtheria toxin. The biosynthesis of diphthamide involves three steps; here it is shown that the first step in the archaeon Pyrococcus horikoshii requires an unusual iron–sulphur-cluster enzyme, Dph2. It catalyses unprecedented chemistry.

Yang Zhang, Xuling Zhu, Andrew T. Torelli, Michael Lee, Boris Dzikovski, Rachel M. Koralewski, Eileen Wang, Jack Freed, Carsten Krebs, Steven E. Ealick & Hening Lin

doi:10.1038/nature09138

See also: Editor's summary | News and Views by Broderick


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Letters

Size and albedo of Kuiper belt object 55636 from a stellar occultation p897

KBO 55636 (2002 TX300) is one of the Kuiper belt objects — specifically, a member of the water-ice-rich Haumea KBO collisional family. Here, observations are reported of a multi-chord stellar occultation by KBO 55636. Calculations show that KBO 55636 is smaller than previously thought and, like its parent body, is highly reflective. The dynamical age implies either that it has an active resurfacing mechanism, or that fresh water-ice in the outer Solar System can persist for gigayear timescales.

J. L. Elliot, M. J. Person, C. A. Zuluaga, A. S. Bosh, E. R. Adams, T. C. Brothers, A. A. S. Gulbis, S. E. Levine, M. Lockhart, A. M. Zangari, B. A. Babcock, K. DuPré, J. M. Pasachoff, S. P. Souza, W. Rosing, N. Secrest, L. Bright, E. W. Dunham, S. S. Sheppard, M. Kakkala, T. Tilleman, B. Berger, J. W. Briggs, G. Jacobson, P. Valleli, B. Volz, S. Rapoport, R. Hart, M. Brucker, R. Michel, A. Mattingly, L. Zambrano-Marin, A. W. Meyer, J. Wolf, E. V. Ryan, W. H. Ryan, K. Morzinski, B. Grigsby, J. Brimacombe, D. Ragozzine, H. G. Montano & A. Gilmore

doi:10.1038/nature09109

See also: Editor's summary | News and Views by Sicardy


Real-space observation of a two-dimensional skyrmion crystal p901

Skyrmions are stable topological textures with particle-like properties — a mathematical concept that was originally used to describe nuclear particles but has since turned up at all scales. Last year, the presence of skyrmions in the magnetic compounds MnSi and Fe1−xCoxSi was confirmed with neutron-scattering experiments. Here, real-space images are presented of a two-dimensional skyrmion lattice in a thin film of the latter compound. The observed nanometre-scale spin topology might reveal new magneto-transport effects.

X. Z. Yu, Y. Onose, N. Kanazawa, J. H. Park, J. H. Han, Y. Matsui, N. Nagaosa & Y. Tokura

doi:10.1038/nature09124

See also: Editor's summary | News and Views by Pfleiderer & Rosch


Visualizing and controlling vibrational wave packets of single molecules p905

Over the past few decades, two techniques in particular have opened up new avenues for probing molecular processes: ultrafast spectroscopy and single-molecule detection. The two approaches have now been combined, enabling not only the observation but also the manipulation of vibrational wave-packet interference at ambient conditions. The technique could help to unravel details of molecular function and dynamics in systems as diverse as light-harvesting complexes, photoactive proteins and conjugated polymers.

Daan Brinks, Fernando D. Stefani, Florian Kulzer, Richard Hildner, Tim H. Taminiau, Yuri Avlasevich, Klaus Müllen & Niek F. van Hulst

doi:10.1038/nature09110

See also: Editor's summary


Massive volcanic SO2 oxidation and sulphate aerosol deposition in Cenozoic North America p909

Volcanic eruptions release a large amount of sulphur dioxide. This is oxidized to sulphate and can then form sulphate aerosol, which can affect the Earth's radiation balance. Here, past volcanic eruptions and atmospheric conditions are investigated by using sulphur and triple oxygen isotope measurements of atmospheric sulphate preserved in the rock record. The results show that seven eruption-related sulphate aerosol deposition events occurred in the mid-Cenozoic era in the northern High Plains of North America.

Huiming Bao, Shaocai Yu & Daniel Q. Tong

doi:10.1038/nature09100

See also: Editor's summary


The importance of rift history for volcanic margin formation p913

Rifting and magmatism are fundamental geological processes that shape our planet's surface, but the nature of the relationship between these processes has been controversial. Here a numerical model that explicitly accounts for the effects of earlier episodes of extension has been applied to compare magmatism generated at different locations during continental rifting. The findings show that the volume of rift-related magmatism generated depends not only on the mantle temperature but also on the rift history.

John J. Armitage, Jenny S. Collier & Tim A. Minshull

doi:10.1038/nature09063

See also: Editor's summary


Ecological interactions are evolutionarily conserved across the entire tree of life p918

It is expected that closely related organisms are more likely to show similar ecological interactions than less related ones. But this has been tested only for certain types of interaction, and in a restricted set of taxa. Now interaction networks have been constructed for 116 different clades of related organisms, across the entire tree of life, and including all types of interaction. The results reveal significant conservatism across the board, including both specialist and generalist species.

José M. Gómez, Miguel Verdú & Francisco Perfectti

doi:10.1038/nature09113

See also: Editor's summary


Sequence space and the ongoing expansion of the protein universe p922

The need to maintain the structural and functional integrity of an evolving protein limits the range of acceptable amino-acid substitutions — but to what extent does this constrain how far homologous protein sequences can diverge? Here, sequence divergence data are used to explore the limits of protein evolution, and to conclude that ancient proteins are continuing to diverge from one another, indicating that the protein sequence universe is slowly expanding.

Inna S. Povolotskaya & Fyodor A. Kondrashov

doi:10.1038/nature09105

See also: Editor's summary


Fine-tuning of pre-balanced excitation and inhibition during auditory cortical development p927

To build a representation of the auditory world, neuronal circuits in neonatal rodents exhibit plasticity, allowing sensitivity to the pattern of sensory inputs. At this time, neurons construct a receptive field, which relies on a balance of excitatory and inhibitory inputs. Here, excitation and inhibition were not found to be co-tuned upon hearing onset, but later an adjustment in the excitatory input strength occurred. Thus a fine adjustment in synaptic inputs, rather than more radical changes such as input pruning, may refine mature receptive fields.

Yujiao J. Sun, Guangying K. Wu, Bao-hua Liu, Pingyang Li, Mu Zhou, Zhongju Xiao, Huizhong W. Tao & Li I. Zhang

doi:10.1038/nature09079

See also: Editor's summary


Developmental sensory experience balances cortical excitation and inhibition p932

To build a representation of the auditory world, neuronal circuits in neonatal rodents exhibit plasticity, allowing sensitivity to the pattern of sensory inputs. At this time, neurons construct a receptive field, which relies on a balance of excitatory and inhibitory inputs. Here, excitation and inhibition were not found to be co-tuned upon hearing onset, but an experience-dependent refinement of inhibition later occurred. Thus a fine adjustment in synaptic inputs, rather than more radical changes such as input pruning, may refine mature receptive fields.

Anja L. Dorrn, Kexin Yuan, Alison J. Barker, Christoph E. Schreiner & Robert C. Froemke

doi:10.1038/nature09119

See also: Editor's summary


TLR recognition of self nucleic acids hampers glucocorticoid activity in lupus p937

Glucocorticoids are widely used to treat patients with autoimmune diseases such as systemic lupus erythematosus (SLE), but many treatment regimens cannot maintain disease control in SLE patients. Here it is shown that the stimulation of plasmacytoid dendritic cells through toll-like receptors TLR7 and TLR9 can account for the reduced activity of glucocorticoids to inhibit the type I interferon pathway in SLE patients. Thus inhibitors of TLR7 and TLR9 signalling might prove to be effective corticosteroid-sparing drugs.

Cristiana Guiducci, Mei Gong, Zhaohui Xu, Michelle Gill, Damien Chaussabel, Thea Meeker, Jean H. Chan, Tracey Wright, Marilynn Punaro, Silvia Bolland, Vassili Soumelis, Jacques Banchereau, Robert L. Coffman, Virginia Pascual & Franck J. Barrat

doi:10.1038/nature09102

See also: Editor's summary


Termination of autophagy and reformation of lysosomes regulated by mTOR p942

When cells are starved, the enzyme TOR is inhibited, inducing autophagy. In this process, autophagosomes sequester intracellular components and then fuse with lysosomes, producing autolysosomes in which cargo is degraded to regenerate nutrients. Now, a mechanism is revealed by which lysosomes are re-formed. When starvation conditions are prolonged, mTOR is re-activated; this attenuates autophagy and results in tubules and vesicles extruding from the autolysosome and maturing into functional lysosomes.

Li Yu, Christina K. McPhee, Lixin Zheng, Gonzalo A. Mardones, Yueguang Rong, Junya Peng, Na Mi, Ying Zhao, Zhihua Liu, Fengyi Wan, Dale W. Hailey, Viola Oorschot, Judith Klumperman, Eric H. Baehrecke & Michael J. Lenardo

doi:10.1038/nature09076

See also: Editor's summary


Principles of stop-codon reading on the ribosome p947

Stop codons in messenger RNA define when a protein sequence has been completely synthesized; such codons bind release factors (RFs), which cause the newly made protein to be released. Structures of RFs alone and in combination with the ribosome have been reported, but the energetics of the reaction in the presence of codons had not been determined. Here, molecular dynamics simulations of 14 termination complexes are used to define how termination is achieved and how the RFs distinguish different sequences.

Johan Sund, Martin Andér & Johan Åqvist

doi:10.1038/nature09082

See also: Editor's summary


Ubiquitin-dependent DNA damage bypass is separable from genome replication p951

Post-replicative repair (PRR) enables cells to bypass or overcome DNA damage during DNA replication. In eukaryotes, ubiquitylation of the replication clamp PCNA by components of the RAD6 pathway activates damage bypass. When this occurs has been debated. It is now shown that PRR can be postponed until much of the undamaged genome is replicated. Moreover, it seems that PRR occurs mainly by an error-prone process, with error-free bypass playing a minor role.

Yasukazu Daigaku, Adelina A. Davies & Helle D. Ulrich

doi:10.1038/nature09097

See also: Editor's summary


TFIIA and the transactivator Rap1 cooperate to commit TFIID for transcription initiation p956

Here, the early steps of activator-dependent transcription in yeast are examined by using cryo-electron microscopy to study the transcription activator Rap1 in complex with the general transcription factors TFIID and TFIIA and with yeast enhancer–promoter DNA. A model is proposed whereby interactions between Rap1 and TFIIA convey activating signals to TFIID. Moreover, a Rap1-dependent DNA loop is visualized between the enhancer and the promoter.

Gabor Papai, Manish K. Tripathi, Christine Ruhlmann, Justin H. Layer, P. Anthony Weil & Patrick Schultz

doi:10.1038/nature09080

See also: Editor's summary


Structure of the bifunctional isocitrate dehydrogenase kinase/phosphatase p961

The Escherichia coli isocitrate dehydrogenase kinase/phosphatase (AceK) is a bifunctional enzyme that can phosphorylate or dephosphorylate isocitrate dehydrogenase (ICDH) to either inactivate or activate it in response to environmental changes. Now the structures of AceK and the AceK–ICDH complex have been solved, revealing the conformational changes that occur when AceK changes from a kinase to a phosphatase and vice versa.

Jimin Zheng & Zongchao Jia

doi:10.1038/nature09088

See also: Editor's summary


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Addendum

Cancer-associated IDH1 mutations produce 2-hydroxyglutarate p966

Lenny Dang, David W. White, Stefan Gross, Bryson D. Bennett, Mark A. Bittinger, Edward M. Driggers, Valeria R. Fantin, Hyun Gyung Jang, Shengfang Jin, Marie C. Keenan, Kevin M. Marks, Robert M. Prins, Patrick S. Ward, Katharine E. Yen, Linda M. Liau, Joshua D. Rabinowitz, Lewis C. Cantley, Craig B. Thompson, Matthew G. Vander Heiden & Shinsan M. Su

doi:10.1038/nature09132


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Erratum

B-cell-derived lymphotoxin promotes castration-resistant prostate cancer p966

Massimo Ammirante, Jun-Li Luo, Sergei Grivennikov, Sergei Nedospasov & Michael Karin

doi:10.1038/nature09133


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Corrigenda

Surface hydrophobin prevents immune recognition of airborne fungal spores p966

Vishukumar Aimanianda, Jagadeesh Bayry, Silvia Bozza, Olaf Kniemeyer, Katia Perruccio, Sri Ramulu Elluru, Cécile Clavaud, Sophie Paris, Axel A. Brakhage, Srini V. Kaveri, Luigina Romani & Jean-Paul Latgé

doi:10.1038/nature09134


International network of cancer genome projects p966

The International Cancer Genome Consortium

doi:10.1038/nature09167


Sphingosine-1-phosphate mobilizes osteoclast precursors and regulates bone homeostasis p966

Masaru Ishii, Jackson G. Egen, Frederick Klauschen, Martin Meier-Schellersheim, Yukihiko Saeki, Jean Vacher, Richard L. Proia & Ronald N. Germain

doi:10.1038/nature09193


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Naturejobs

Careers Q&A

Gustavo Ayala p969

Pathologist Gustavo Ayala of Baylor College of Medicine in Houston, Texas, won a Creativity Award in May from the Prostate Cancer Foundation, Santa Monica, California, for his work on how nerve toxins affect tumours.

Virginia Gewin

doi:10.1038/nj7300-969a


In Brief

Female students scarcer p969

US enrolment rates come under focus.

doi:10.1038/nj7300-969b


RNA Institute launched p969

New York facility plans new building and seeks faculty members.

doi:10.1038/nj7300-969c


Particle physics exodus p969

Tenure proves troublesome in United States.

doi:10.1038/nj7300-969d


Special Report

Extra credit p970

In Britain, organizations award 'chartered status', which claims to validate a scientist's professional credentials. But what are such designations really worth? Nadya Anscombe reports.

Nadya Anscombe

doi:10.1038/nj7300-970a


Correction

Correction p971

doi:10.1038/nj7300-971a


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Futures

IRC p974

A helping hand.

Julian Tang

doi:10.1038/465974a


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