Table of contents
Volume 461 Number 7261 pp145-304
In this issue (10 September 2009)
Also this week
(this content only available online) indicates content that is available online only
Editorials
Data's shameful neglect p145
Research cannot flourish if data are not preserved and made accessible. All concerned must act accordingly.
doi:10.1038/461145a
A step too far? p145
The Obama administration must fund human space flight adequately, or stop speaking of 'exploration'.
doi:10.1038/461145b
Overrated ratings p146
Criteria for 'green buildings' need to make energy performance a priority — as do universities.
doi:10.1038/461146a
Research Highlights
Animal communication: Warning wings p148
doi:10.1038/461148a
Atmospheric chemistry: Ozone's winners and losers p148
doi:10.1038/461148b
Physics: Magnetic monopoles p148
doi:10.1038/461148c
Computational biology: A new protein subdivision p148
doi:10.1038/461148d
Microbial evolution: Cholera gene swap p148
doi:10.1038/461148e
Chemistry: Going for gold p149
doi:10.1038/461149a
Evolution and development: Genes in the mirror p149
doi:10.1038/461149b
Neuroscience: Fear net p149
doi:10.1038/461149c
Genetics: Why Y knots p149
doi:10.1038/461149d
News
News briefing p150
doi:10.1038/461150a
Cash crisis could ground NASA rocket p153
Crewed missions to the Moon are under threat, warns an expert panel.
Eric Hand
doi:10.1038/461153a
How green is your campus? p154
Universities are working to bring sustainability to their campuses and classrooms, and could serve as a model for other institutions looking to go carbon-neutral. But there's no single way to grade the initiatives.
Amanda Leigh Mascarelli
doi:10.1038/461154a
Export-control laws worry academics p156
US researchers hope planned reforms will reduce the risk of prosecution.
Sharon Weinberger
doi:10.1038/461156a
Ethics scrutiny needed for Chinese–European projects p157
Panel calls for joint advisory body to monitor research.
Daniel Cressey
doi:10.1038/461157a
Toxicity testing gets a makeover p158
Europe aims to make chemical-exposure studies more predictive while using fewer animals.
Alison Abbott
doi:10.1038/461158a
World climate services framework agreed p159
Much work remains to provide predictions to governments.
Olive Heffernan
doi:10.1038/461159a
Correction p159
doi:10.1038/461159b
News Features
Data sharing: Empty archives p160
Most researchers agree that open access to data is the scientific ideal, so what is stopping it happening? Bryn Nelson investigates why many researchers choose not to share.
doi:10.1038/461160a
Evolution: Mouth to mouth p164
Hagfish and lampreys are the only surviving fish without jaws. And they could solve an evolutionary mystery, finds Henry Nicholls.
doi:10.1038/461164a
Correspondence
Choking on carbon emissions from Greek academic paperwork p167
Costas Synolakis & Spyros Foteinis
doi:10.1038/461167a
Evolution pioneers: celebrating Lamarck at 200, Darwin 215 p167
William E. Friedman
doi:10.1038/461167b
Evolution pioneers: Lamarck's reputation saved by his zoology p167
Pietro Corsi
doi:10.1038/461167c
Religious belief and the history of science p167
Scott Goode
doi:10.1038/461167d
Opinion
Prepublication data sharing p168
Rapid release of prepublication data has served the field of genomics well. Attendees at a workshop in Toronto recommend extending the practice to other biological data sets.
Toronto International Data Release Workshop Authors
doi:10.1038/461168a
Full Text | PDF (614K) | Supplementary information
Post-publication sharing of data and tools p171
Despite existing guidelines on access to data and bioresources, good practice is not widespread. A meeting of mouse researchers in Rome proposes ways to promote a culture of sharing.
Paul N. Schofield, Tania Bubela, Thomas Weaver, Lili Portilla, Stephen D. Brown, John M. Hancock, David Einhorn, Glauco Tocchini-Valentini, Martin Hrabe de Angelis, Nadia Rosenthal & CASIMIR Rome Meeting participants
doi:10.1038/461171a
Full Text | PDF (774K) | Supplementary information
Books and Arts
Call for a climate culture shift p174
A new book describes the rapid reshaping of human priorities needed to save the planet from global warming. Some of that change is already under way at the community level, explains Robert Costanza.
Robert Costanza reviews Down to the Wire: Confronting Climate Collapse by David W. Orr
doi:10.1038/461174a
The wider lessons for finance p175
Ehsan Masood reviews Animal Spirits: How Human Psychology Drives the Economy, and Why It Matters for Global Capitalism by George A. Akerlof & Robert J. Shiller and Fool's Gold: How Unrestrained Greed Corrupted a Dream, Shattered Global Markets and Unleashed a Catastrophe by Gillian Tett
doi:10.1038/461175a
How Spain redrew the world p176
Neil Safier reviews Secret Science: Spanish Cosmography and the New World by María M. Portuondo
doi:10.1038/461176a
News and Views
Sex determination: Birds do it with a Z gene p177
The gene that determines sex in birds has eluded scientists for a decade. Now this all-important locus is revealed as a gene on the Z chromosome known for its proclivity for determining sex in all kinds of animals.
Jennifer A. Marshall Graves
doi:10.1038/461177a
See also: Editor's summary
Nanotechnology: A gentle jackhammer p178
A futuristic method of data storage depends on the 'write–read' action of a multitude of tiny silicon tips. The concept of dynamic superlubricity offers a way to avoid the wear that would otherwise cripple them.
Enrico Gnecco
doi:10.1038/461178a
Early Earth: Oxygen for heavy-metal fans p179
Chromium isotopes provide an eyebrow-raising history of oxygenation of Earth's atmosphere. Not least, it seems that oxygen might have all but disappeared half a billion years after its initial rise.
Timothy W. Lyons & Christopher T. Reinhard
doi:10.1038/461179a
See also: Editor's summary
50 & 100 years ago p180
doi:10.1038/461180a
Cell biology: Sent by the scent of death p181
Dying cells release 'find-me' factors that attract professional scavenger cells to engulf and digest them. These cellular invitations to dine can take unexpected forms.
Christopher Gregory
doi:10.1038/461181a
See also: Editor's summary
Materials chemistry: Catalysts made thinner p182
Thinner can be better, at least for the industrially useful catalysts known as zeolites. A technique that allows single layers of zeolites to assemble from solution opens up a plethora of practical applications.
Avelino Corma
doi:10.1038/461182a
See also: Editor's summary
Developmental biology: Instructions writ in blood p183
It seems that growth factors may instruct blood-cell progenitors to develop into specific mature cell types, actively determining lineage choice. But is this reductionist view of cell fate overly simplistic?
Tariq Enver & Sten Eirik W. Jacobsen
doi:10.1038/461183a
Insight: Transcribing the genome -
Insight: Transcribing the genome
Transcribing the genome p185
Alex Eccleston & Magdalena Skipper
doi:10.1038/461185a
Defining mechanisms that regulate RNA polymerase II transcription in vivo p186
Nicholas J. Fuda, M. Behfar Ardehali & John T. Lis
doi:10.1038/nature08449
Abstract | Full Text | PDF (2,417K)
The logic of chromatin architecture and remodelling at promoters p193
Bradley R. Cairns
doi:10.1038/nature08450
Abstract | Full Text | PDF (1,354K)
Genomic views of distant-acting enhancers p199
Axel Visel, Edward M. Rubin & Len A. Pennacchio
doi:10.1038/nature08451
Abstract | Full Text | PDF (1,993K)
Implications of chimaeric non-co-linear transcripts p206
Thomas R. Gingeras
doi:10.1038/nature08452
Abstract | Full Text | PDF (1,618K)
Chromosome crosstalk in three dimensions p212
Anita Göndör & Rolf Ohlsson
doi:10.1038/nature08453
Abstract | Full Text | PDF (2,340K)
Molecular networks as sensors and drivers of common human diseases p218
Eric E. Schadt
doi:10.1038/nature08454
Abstract | Full Text | PDF (3,542K)
Articles
Co-translational mRNA decay in Saccharomyces cerevisiae p225
The levels of messenger RNA are determined by the rates of RNA decay and transcription, but although the details of transcriptional regulation are increasingly understood, the mechanism(s) controlling mRNA decay remain unclear. In yeast, it is hypothesized that ribosomes must be removed from mRNA before transcripts are destroyed. However, here it is shown that decay takes place while mRNAs are associated with actively translating ribosomes, allowing the last translocating ribosome to complete translation.
Wenqian Hu, Thomas J. Sweet, Sangpen Chamnongpol, Kristian E. Baker & Jeff Coller
doi:10.1038/nature08265
Abstract | Full Text | PDF (584K) | Supplementary information
See also: Editor's summary
An RNA-dependent RNA polymerase formed by TERT and the RMRP RNA p230
Accumulating evidence suggests that the human telomerase reverse transcriptase catalytic subunit (TERT) has a role in cell physiology independent to that of elongating telomeres. Here it is shown to interact with RMRP, a gene that is mutated in the syndrome cartilage–hair hypoplasia, to form a distinct ribonucleoprotein complex that has RNA-dependent RNA polymerase (RdRP) activity and produces double-stranded RNAs that can be processed into small interfering RNAs.
Yoshiko Maida, Mami Yasukawa, Miho Furuuchi, Timo Lassmann, Richard Possemato, Naoko Okamoto, Vivi Kasim, Yoshihide Hayashizaki, William C. Hahn & Kenkichi Masutomi
doi:10.1038/nature08283
Abstract | Full Text | PDF (663K) | Supplementary information
See also: Editor's summary
Letters
The global distribution of pure anorthosite on the Moon p236
It has long been thought that the lunar highland crust was formed by the crystallization and floatation of plagioclase from a global magma ocean, but the exact mechanism by which such a crust formed remains debated. Data from the Japanese SELENE spacecraft are now used to produce a clear and high spatial resolution view of the composition of the lunar crust. The existence of widely distributed crustal rocks with compositions approaching 100 per cent (by volume) plagioclase is revealed.
Makiko Ohtake, Tsuneo Matsunaga, Junichi Haruyama, Yasuhiro Yokota, Tomokatsu Morota, Chikatoshi Honda, Yoshiko Ogawa, Masaya Torii, Hideaki Miyamoto, Tomoko Arai, Naru Hirata, Akira Iwasaki, Ryosuke Nakamura, Takahiro Hiroi, Takamitsu Sugihara, Hiroshi Takeda, Hisashi Otake, Carle M. Pieters, Kazuto Saiki, Kohei Kitazato, Masanao Abe, Noriaki Asada, Hirohide Demura, Yasushi Yamaguchi, Sho Sasaki, Shinsuke Kodama, Junya Terazono, Motomaro Shirao, Atsushi Yamaji, Shigeyuki Minami, Hiroaki Akiyama & Jean-Luc Josset
doi:10.1038/nature08317
First paragraph | Full Text | PDF (1,050K) | Supplementary information
See also: Editor's summary
Coherent optical pulse sequencer for quantum applications p241
Precise and arbitrary control of an optical field that preserves optical coherence is an important requisite for many proposed photonic technologies. Here, a coherent optical memory based on photon echoes induced through controlled reversible inhomogeneous broadening is presented. The scheme allows storage of multiple pulses of light which can be arbitrarily recalled, time-stretched or split.
Mahdi Hosseini, Ben M. Sparkes, Gabriel Hétet, Jevon J. Longdell, Ping Koy Lam & Ben C. Buchler
doi:10.1038/nature08325
First paragraph | Full Text | PDF (654K)
See also: Editor's summary
Stable single-unit-cell nanosheets of zeolite MFI as active and long-lived catalysts p246
Zeolites — microporous crystalline aluminosilicates — are widely used in industry as size- and shape-selective catalysts, but the micropores that enable this catalytic activity also cause diffusion limitations that adversely affect it. This can be overcome by reducing the thickness of the zeolite crystals and thus improving molecular diffusion. Here it is shown that bifunctional surfactants can direct the formation of zeolite structures that are only one unit cell thick.
Minkee Choi, Kyungsu Na, Jeongnam Kim, Yasuhiro Sakamoto, Osamu Terasaki & Ryong Ryoo
doi:10.1038/nature08288
First paragraph | Full Text | PDF (1,421K) | Supplementary information
See also: Editor's summary | News and Views by Corma
Fluctuations in Precambrian atmospheric oxygenation recorded by chromium isotopes p250
It is thought that oxygenation of the Earth's atmosphere occurred in two broad steps, but details of the evolution of atmospheric oxygenation remain uncertain. Chromium (Cr) stable isotopes from banded iron formations are now used to track the presence of Cr(VI) in Precambrian oceans, providing a time-resolved picture of the oxygenation history of the Earth's atmosphere–hydrosphere system.
Robert Frei, Claudio Gaucher, Simon W. Poulton & Don E. Canfield
doi:10.1038/nature08266
First paragraph | Full Text | PDF (388K) | Supplementary information
See also: Editor's summary | News and Views by Lyons & Reinhard
The importance of niches for the maintenance of species diversity p254
If organisms are involved in a perpetual struggle for existence, how is it that communities are so diverse? The traditional answer is the ecological niche but this has recently been challenged by the neutral theory of biodiversity, which explains coexistence with the equivalence of competitors. Here, theory and experimentation are integrated in order to explore this problem; the results show that diversity declines when niches are removed.
Jonathan M. Levine & Janneke HilleRisLambers
doi:10.1038/nature08251
First paragraph | Full Text | PDF (451K) | Supplementary information
See also: Editor's summary
Photosystem I gene cassettes are present in marine virus genomes p258
Cyanobacteria are important contributors to photosynthetic productivity in the open oceans. Functional photosystem II components are known to be encoded in cyanophage genomes and are suggested to provide a fitness advantage to the virus by boosting host performance. It is now shown that photosystem I components can also be detected in cyanophages.
Itai Sharon, Ariella Alperovitch, Forest Rohwer, Matthew Haynes, Fabian Glaser, Nof Atamna-Ismaeel, Ron Y. Pinter, Frédéric Partensky, Eugene V. Koonin, Yuri I. Wolf, Nathan Nelson & Oded Béjà
doi:10.1038/nature08284
PDB code
3D view
First paragraph | Full Text | PDF (780K) | Supplementary information
See also: Editor's summary
Changes of mind in decision-making p263
How do we change our minds? Here, subjects were asked to make decisions about a noisy visual stimulus, which they indicated by moving a handle. By following hand trajectories, it was possible to determine the rare occasions when subjects changed their minds halfway through a trial. The authors extend a model developed to account for the timing and accuracy of the initial decision to explain these subsequent changes of mind.
Arbora Resulaj, Roozbeh Kiani, Daniel M. Wolpert & Michael N. Shadlen
doi:10.1038/nature08275
First paragraph | Full Text | PDF (438K) | Supplementary information
See also: Editor's summary
The avian Z-linked gene DMRT1 is required for male sex determination in the chicken p267
Although sex determination in birds, as in mammals, is chromosomally based, its mechanism has been a long-standing mystery. In birds, the homogametic sex is male (ZZ) and the heterogametic sex is female (ZW); one hypothesis is that two doses of a Z-linked gene are required for male development. Here it is shown that reducing expression of the conserved Z-linked gene DMRT1 feminizes the embryonic gonads in genetically male (ZZ) chicken embryos.
Craig A. Smith, Kelly N. Roeszler, Thomas Ohnesorg, David M. Cummins, Peter G. Farlie, Timothy J. Doran & Andrew H. Sinclair
doi:10.1038/nature08298
First paragraph | Full Text | PDF (966K) | Supplementary information
See also: Editor's summary | News and Views by Marshall Graves
Targeted capture and massively parallel sequencing of 12 human exomes p272
Although DNA sequencing costs have fallen dramatically, they are still too high for whole genome sequencing to be used to routinely identify rare and novel variants in large cohorts. The targeted capture and massively parallel sequencing of the exomes of 12 humans is now reported. Freeman–Sheldon syndrome is used as a proof-of-concept that candidate genes for monogenic disorders can be identified by exome sequencing of a small number of unrelated, affected individuals.
Sarah B. Ng, Emily H. Turner, Peggy D. Robertson, Steven D. Flygare, Abigail W. Bigham, Choli Lee, Tristan Shaffer, Michelle Wong, Arindam Bhattacharjee, Evan E. Eichler, Michael Bamshad, Deborah A. Nickerson & Jay Shendure
doi:10.1038/nature08250
First paragraph | Full Text | PDF (285K) | Supplementary information
See also: Editor's summary
Modification of CO2 avoidance behaviour in Drosophila by inhibitory odorants p277
Fruitflies instinctively avoid CO2, for example that produced by stressed fellow flies, but they overcome this avoidance response in some environments that contain CO2, such as ripening fruits. Here, a new class of odorants present in food is identified that directly inhibit CO2-sensitive neurons in the antenna — not, as one would expect, indirectly via other olfactory pathways.
Stephanie Lynn Turner & Anandasankar Ray
doi:10.1038/nature08295
First paragraph | Full Text | PDF (549K) | Supplementary information
See also: Editor's summary
Nucleotides released by apoptotic cells act as a find-me signal to promote phagocytic clearance p282
The efficient removal of apoptotic cells in vivo is thought to be due to the release of 'find-me' signals by apoptotic cells that recruit motile phagocytes. Here, the caspase-dependent release of ATP and UTP during the early stages of apoptosis is demonstrated. ATP and UTP are found to act as chemoattractants in a process mediated through the ATP/UTP receptor P2Y2, which is present on monocytes and macrophages.
Michael R. Elliott, Faraaz B. Chekeni, Paul C. Trampont, Eduardo R. Lazarowski, Alexandra Kadl, Scott F. Walk, Daeho Park, Robin I. Woodson, Marina Ostankovich, Poonam Sharma, Jeffrey J. Lysiak, T. Kendall Harden, Norbert Leitinger & Kodi S. Ravichandran
doi:10.1038/nature08296
First paragraph | Full Text | PDF (589K) | Supplementary information
See also: Editor's summary | News and Views by Gregory
ErbB2 resembles an autoinhibited invertebrate epidermal growth factor receptor p287
The tyrosine kinase receptor ErbB2 has been implicated in cancer, particularly breast cancer. It has been suggested that its oncogenic signalling properties result from the absence of a key 'tether' in the extracellular region that autoinhibits other human ErbB receptors. ErbB2 is now shown to be the closest structural relative of the dEGFR receptor in Drosophila; although dEGFR also lacks a tether, a distinct set of autoinhibitory interactions keep it inactive.
Diego Alvarado, Daryl E. Klein & Mark A. Lemmon
doi:10.1038/nature08297
First paragraph | Full Text | PDF (957K) | Supplementary information
See also: Editor's summary
Structure of the BK potassium channel in a lipid membrane from electron cryomicroscopy p292
Electron cryomicroscopy (cryo-EM) is an increasingly powerful method for looking at the structures of large soluble proteins that does not require crystallization of the proteins. Here, the first single-particle cryo-EM study of a membrane protein is reported — the human large-conductance calcium- and voltage-activated potassium channel (BK) — in a lipid environment.
Liguo Wang & Fred J. Sigworth
doi:10.1038/nature08291
First paragraph | Full Text | PDF (700K) | Supplementary information
See also: Editor's summary
Erratum
MicroRNA-mediated switching of chromatin-remodelling complexes in neural development p296
Andrew S. Yoo, Brett T. Staahl, Lei Chen & Gerald R. Crabtree
doi:10.1038/nature08359
Naturejobs
NewsBusiness skills for postdocs p299
Master's programme recognizes need for bridge into industry.
Virginia Gewin
doi:10.1038/nj7261-299a
Postdoc journal
Finding the perfect match p299
Applying for jobs can be like finding the perfect date.
Julia Boughner
doi:10.1038/nj7261-299b
In Brief
Foreign admissions fall p299
Foreign admissions down at US graduate schools.
doi:10.1038/nj7261-299c
Data manager for Europe p299
Colossal data management effort could open up bioinformatics opportunities.
doi:10.1038/nj7261-299d
IT sector takes a hit p299
IT sector hurting but industry will remain a magnet for venture-capital investment.
doi:10.1038/nj7261-299e
Region
Eyeing the underdog p300
Can Philadelphia's biotechnology industry absorb the jobs lost from pharmaceutical companies? Kerry Grens investigates.
Kerry Grens
doi:10.1038/nj7261-300a
Spotlight
Spotlight on Philadelphia
doi:10.1038/nj0259
