Table of contents
Volume 461 Number 7265 pp697-836
(this content only available online) indicates content that is available online only
Editorials
Genetics without borders p697
A UK government scheme to establish nationality through DNA testing is scientifically flawed, ethically dubious and potentially damaging to science.
doi:10.1038/461697a
Putting DNA to the test p697
Genetic-testing companies lack regulation, and a list of guiding principles does not go far enough.
doi:10.1038/461697b
How to win trust over flu p698
Mass-vaccination campaigns for the pandemic H1N1 virus must take public concerns into account.
doi:10.1038/461698a
Research Highlights
Evolution: Boys against girls p700
doi:10.1038/461700a
Cancer biology: Stem cell–cancer link p700
doi:10.1038/461700b
Ecology: Wildebeest chain reaction p700
doi:10.1038/461700c
Geoscience: Earth's magnetic personality p700
doi:10.1038/461700d
Analytical chemistry: Gloop monitor p700
doi:10.1038/461700e
Ageing: Live longer, but how? p700
doi:10.1038/461700f
Stem-cell biology: Rebooting cord blood cells p701
doi:10.1038/461701a
Microbiology: Bacteria fight back p701
doi:10.1038/461701b
Chemistry: Microwave magic p701
doi:10.1038/461701c
Materials science: No gas from glass p701
doi:10.1038/461701d
News
News briefing: 8 October 2009 p702
doi:10.1038/461702a
Fossil rewrites early human evolution p705
Ethiopian find dates back 4.4 million years.
Rex Dalton
doi:10.1038/461705a
Chromosome protection scoops Nobel p706
Prize for physiology or medicine awarded for uncovering role of telomeres.
Alison Abbott
doi:10.1038/461706a
Nobel Prize in Physics awarded to light pioneers p707
Advances in fibre optics and digital imaging are rewarded.
Geoff Brumfiel
doi:10.1038/461707a
X-ray free-electron lasers fire up p708
California's project has the lead as its facility goes live, but Europe aims for its own rapid-fire device.
Eric Hand
doi:10.1038/461708a
From plant to power p710
The last of four weekly articles looks at making liquid fuels direct from biomass.
Katharine Sanderson
doi:10.1038/461710a
Correction p711
doi:10.1038/461711a
News Features
Human genetics: Hit or miss? p712
Genome-wide association studies have identified hundreds of genetic clues to disease. Kelly Rae Chi looks at three to see just how on-target the approach seems to be.
doi:10.1038/461712a
Environment: The disappearing nutrient p716
Phosphate-based fertilizers have helped spur agricultural gains in the past century, but the world may soon run out of them. Natasha Gilbert investigates the potential phosphate crisis.
doi:10.1038/461716a
Plasmonics: Surfing the wave p720
Small oscillations of surface electrons that manipulate light on the nanoscale could be the route to applications as disparate as faster computer chips and cures for cancer. Joerg Heber reports.
doi:10.1038/461720a
Correspondence
Sanctions against scientists threaten progress p723
Bengt Gustafsson
doi:10.1038/461723a
Measures urgently required to prevent multiple submissions p723
Goudarz Molaei
doi:10.1038/461723b
Caution with claims that a species has been rediscovered p723
Richard J. Ladle, Paul Jepson, Steve Jennings & Ana C. M. Malhado
doi:10.1038/461723c
Opinion
An agenda for personalized medicine p724
Pauline C. Ng, Sarah S. Murray, Samuel Levy and J. Craig Venter find differences in results from two direct-toconsumer genetics-testing companies. They therefore give nine recommendations to improve predictions.
Pauline C. Ng, Sarah S. Murray, Samuel Levy & J. Craig Venter
doi:10.1038/461724a
Full Text | PDF (1,163K) | Supplementary information
Let's celebrate human genetic diversity p726
Science is finding evidence of genetic diversity among groups of people as well as among individuals. This discovery should be embraced, not feared, say Bruce T. Lahn and Lanny Ebenstein.
Bruce T. Lahn & Lanny Ebenstein
doi:10.1038/461726a
Books and Arts
Winning the arguments on Capitol Hill p730
Harold Varmus enjoys a guide to the inner workings of the US Congress by legislator Henry Waxman.
Harold Varmus reviews The Waxman Report: How Congress Really Works by Henry Waxman & Joshua Green
doi:10.1038/461730a
China's unofficial democracy p731
Li Gong reviews The Power of the Internet in China: Citizen Activism Online by Guobin Yang
doi:10.1038/461731a
Darwin's legacy down under p732
Mark A. Elgar reviews Reframing Darwin: Evolution and Art in Australia
doi:10.1038/461732a
A creative celebration of evolution p733
Jason Hodin, Cory D. Bishop, Fred A. Sharpe & Ruben E. Valas review Burning Man 2009: Evolution
doi:10.1038/461733a
News and Views
Human genetics: Sharp focus on the variable genome p735
Copy-number variation — deleted or duplicated regions of DNA — is widespread in the human genome. A systematic population survey of the common variants provides an invaluable resource for further studies.
John A. L. Armour
doi:10.1038/461735a
Quantum mechanics: Passage through chaos p736
A quantum system can undergo tunnelling even without a barrier to tunnel through. The latest experiments visualize this process in exquisite detail, completely reconstructing the state of the evolving system.
Daniel A. Steck
doi:10.1038/461736a
See also: Editor's summary
Vision: Gene therapy in colour p737
Replacing a missing gene in adult colour-blind monkeys restores normal colour vision. How the new photoreceptor cells produced by this therapy lead to colour vision is a fascinating question.
Robert Shapley
doi:10.1038/461737a
See also: Editor's summary
Cosmology: Dark is the new black p740
Rival experimental methods to determine the Universe's expansion are contending to become the fashionable face of cosmology. Fresh theoretical calculations make one of them the hot tip for next season.
Richard Massey
doi:10.1038/461740a
Microbiology: Life on leaves p741
The surface of plant leaves — the phyllosphere — is home to many microbes. A 'community proteogenomics' approach offers a fresh look at what it takes to survive and thrive in this unique habitat.
Johan Leveau
doi:10.1038/461741a
Structural biology: Tracing Argonaute binding p743
Argonaute proteins inhibit gene expression by binding to messenger RNA via a small nucleic-acid guide. Structures of the Argonaute complex bound to target RNA reveal snapshots of a silencing machine at work.
Samir Bouasker & Martin J. Simard
doi:10.1038/461743a
See also: Editor's summary
Photonics: One-way road for light p744
The transmission of information from one place to another by light waves sent through waveguides is hampered by light attenuation and scattering loss. Magnetic photonic crystals could provide a solution to such problems.
Eli Yablonovitch
doi:10.1038/461744a
See also: Editor's summary
Brief Communications Arising
Gal4 turnover and transcription activation pE7
Galen A. Collins, J. Russell Lipford, Raymond J. Deshaies & William P. Tansey
doi:10.1038/nature08406
First paragraph | Full Text | PDF (116K)
Nalley et al. reply pE8
Kip Nalley, Stephen Albert Johnston & Thomas Kodadek
doi:10.1038/nature08407
First paragraph | Full Text | PDF (116K)
Review
Finding the missing heritability of complex diseases p747
Teri A. Manolio, Francis S. Collins, Nancy J. Cox, David B. Goldstein, Lucia A. Hindorff, David J. Hunter, Mark I. McCarthy, Erin M. Ramos, Lon R. Cardon, Aravinda Chakravarti, Judy H. Cho, Alan E. Guttmacher, Augustine Kong, Leonid Kruglyak, Elaine Mardis, Charles N. Rotimi, Montgomery Slatkin, David Valle, Alice S. Whittemore, Michael Boehnke, Andrew G. Clark, Evan E. Eichler, Greg Gibson, Jonathan L. Haines, Trudy F. C. Mackay, Steven A. McCarroll & Peter M. Visscher
doi:10.1038/nature08494
First paragraph | Full Text | PDF (242K)
See also: Editor's summary
Articles
Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes p754
The Argonaute (Ago) family of proteins provides the slicer activity of the RNA-induced silencing complex, with the Ago component of the complex providing the catalytic residues governing guide-strand mediated site-specific cleavage of target RNA. Here, the crystal structures of ternary complexes of Thermus thermophilus Ago catalytic mutants are reported and analysed.
Yanli Wang, Stefan Juranek, Haitao Li, Gang Sheng, Greg S. Wardle, Thomas Tuschl & Dinshaw J. Patel
doi:10.1038/nature08434
Abstract | Full Text | PDF (1,894K) | Supplementary information
See also: Editor's summary | News and Views by Bouasker & Simard
Role of the polycomb protein EED in the propagation of repressive histone marks p762
Polycomb group proteins are involved in the epigenetic maintenance of repressive chromatin states, with the gene-silencing activity of the Polycomb repressive complex 2 (PRC2) dependent on its ability to trimethylate lysine 27 of histone H3. The carboxy-terminal domain of the EED subunit of the complex is now shown to specifically bind to histone tails carrying trimethyl-lysine residues associated with repressive chromatin marks, leading to activation of the methyltransferase activity of PRC2.
Raphael Margueron, Neil Justin, Katsuhito Ohno, Miriam L. Sharpe, Jinsook Son, William J. Drury III, Philipp Voigt, Stephen R. Martin, William R. Taylor, Valeria De Marco, Vincenzo Pirrotta, Danny Reinberg & Steven J. Gamblin
doi:10.1038/nature08398
Abstract | Full Text | PDF (772K) | Supplementary information
See also: Editor's summary
Letters
Quantum signatures of chaos in a kicked top p768
There has been a long-standing search for quantum signatures of classical chaos. Here, an atomic system that can be used to study quantum chaos — the quantum kicked top — is experimentally realized and directly observed to reveal dynamics in quantum phase space that have a chaotic classical counterpart. Clear differences are noted in the sensitivity to perturbation in chaotic versus regular regimes and dynamical entanglement is proposed as a signature of chaos.
S. Chaudhury, A. Smith, B. E. Anderson, S. Ghose & P. S. Jessen
doi:10.1038/nature08396
First paragraph | Full Text | PDF (829K) | Supplementary information
See also: Editor's summary | News and Views by Steck
Observation of unidirectional backscattering-immune topological electromagnetic states p772
The quantum Hall effect arises in two-dimensional electron systems and is characterized by current being carried by electrons along the edges of the system, in so-called chiral edge states (CESs), as a consequence of nontrivial topological properties of the bulk electronic band structure. Recently, it was theoretically predicted that electromagnetic analogues of CESs could be observed in photonic crystals; here, this is experimentally demonstrated.
Zheng Wang,
Yidong Chong,
J. D. Joannopoulos
&
Marin Solja
i
doi:10.1038/nature08293
First paragraph | Full Text | PDF (698K) | Supplementary information
See also: Editor's summary | News and Views by Yablonovitch
Early Palaeogene temperature evolution of the southwest Pacific Ocean p776
About 34 million years ago, the first major Antarctic ice sheets appeared, suggesting that major cooling had taken place; however, the global transition into this icehouse climate remains poorly constrained. A new, continuous record of sea surface temperature (SST) from an ocean sediment core in the East Tasman Plateau now suggests that there was almost no latitudinal SST gradient between subequatorial and subpolar regions during the Early Eocene age (55–50 million years ago).
Peter K. Bijl, Stefan Schouten, Appy Sluijs, Gert-Jan Reichart, James C. Zachos & Henk Brinkhuis
doi:10.1038/nature08399
First paragraph | Full Text | PDF (2,249K) | Supplementary information
See also: Editor's summary
Rapid ascent of rhyolitic magma at Chaitén volcano, Chile p780
Although rhyolite magma has fuelled some of the Earth's largest explosive volcanic eruptions, our understanding of these events is incomplete due to the previous lack of direct observation of these eruptions. On 1 May 2008, Chaitén volcano in Chile erupted rhyolite magma unexpectedly and explosively. Here, petrological and experimental data are presented that indicate that the hydrous rhyolite magma at Chaitén ascended very rapidly from storage depth to near-surface, with velocities of the order of one metre per second.
Jonathan M. Castro & Donald B. Dingwell
doi:10.1038/nature08458
First paragraph | Full Text | PDF (857K) | Supplementary information
See also: Editor's summary
Gene therapy for red–green colour blindness in adult primates p784
Red–green colour blindness is the most common single locus genetic disorder. Gene therapy is now used in adult monkeys, colour blind since birth, to provide the receptoral basis for trichromatic colour vision. Despite the expectation from classic visual deprivation experiments that neural connections established during development are incapable of processing an input not present from birth, treated monkeys displayed trichromatic colour vision behaviour.
Katherine Mancuso, William W. Hauswirth, Qiuhong Li, Thomas B. Connor, James A. Kuchenbecker, Matthew C. Mauck, Jay Neitz & Maureen Neitz
doi:10.1038/nature08401
First paragraph | Full Text | PDF (1,102K)
See also: Editor's summary | News and Views by Shapley
STING regulates intracellular DNA-mediated, type I interferon-dependent innate immunity p788
Although the innate immune system is known to be critical for the early detection of invading pathogens and for initiating host defence systems, little is known about how it is galvanized to respond to DNA-based microbes. STING (stimulator of interferon genes) is now shown to be necessary for the initiation of effective type I interferon production and, accordingly, there is an increase in the susceptibility of Sting-knockout mice to infection by the DNA virus HSV-1.
Hiroki Ishikawa, Zhe Ma & Glen N. Barber
doi:10.1038/nature08476
First paragraph | Full Text | PDF (757K) | Supplementary information
See also: Editor's summary
Prohibitin couples diapause signalling to mitochondrial metabolism during ageing in C. elegans p793
Prohibitins are ubiquitous, evolutionarily conserved proteins, which form a ring-like complex at the inner membrane of the mitochondria. Here, the mitochondrial prohibitin complex is shown to promote longevity by modulating mitochondrial function and fat metabolism in the nematode Caenorhabditis elegans, with its deficiency shortening the lifespan of otherwise wild-type animals. However, under conditions of dietary restriction, knockdown of prohibitin promotes longevity.
Marta Artal-Sanz & Nektarios Tavernarakis
doi:10.1038/nature08466
First paragraph | Full Text | PDF (518K) | Supplementary information
See also: Editor's summary
Genetic variation in IL28B and spontaneous clearance of hepatitis C virus p798
There are approximately 170 million people infected with hepatitis C virus (HCV) worldwide. About 30% of individuals with persistent HCV infection develop chronic liver disease, with various epidemiological, viral and host factors having been implicated in the differences in HCV clearance or persistence. Here, a single nucleotide polymorphism recently shown to be strongly associated with a difference in response to HCV drug treatment is also shown to be associated with viral clearance.
David L. Thomas, Chloe L. Thio, Maureen P. Martin, Ying Qi, Dongliang Ge, Colm O'hUigin, Judith Kidd, Kenneth Kidd, Salim I. Khakoo, Graeme Alexander, James J. Goedert, Gregory D. Kirk, Sharyne M. Donfield, Hugo R. Rosen, Leslie H. Tobler, Michael P. Busch, John G. McHutchison, David B. Goldstein & Mary Carrington
doi:10.1038/nature08463
First paragraph | Full Text | PDF (377K) | Supplementary information
See also: Editor's summary
A genome-wide linkage and association scan reveals novel loci for autism p802
Autism is a highly heritable neurodevelopmental disorder, and yet few specific susceptibility genes have been identified to date. A linkage and association mapping study using half a million genome-wide single nucleotide polymorphisms is now described in a common set of 1,031 multiplex autism families. The linkage regions identified provide targets for rare variation screening whereas the discovery of a single novel association, SEMA5A, demonstrates the action of common variants.
Lauren A. Weiss, Dan E. Arking & The Gene Discovery Project of Johns Hopkins & the Autism Consortium
doi:10.1038/nature08490
First paragraph | Full Text | PDF (483K) | Supplementary information
See also: Editor's summary
Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution p809
Advances in next generation sequencing have made it possible to precisely characterize the coding mutations that occur during the development and progression of individual cancers. Here, this technique is used to sequence the genomes and transcriptomes of an oestrogen-receptor-
-positive metastatic lobular breast cancer; significant evolution is found to occur with disease progression.
Sohrab P. Shah, Ryan D. Morin, Jaswinder Khattra, Leah Prentice, Trevor Pugh, Angela Burleigh, Allen Delaney, Karen Gelmon, Ryan Guliany, Janine Senz, Christian Steidl, Robert A. Holt, Steven Jones, Mark Sun, Gillian Leung, Richard Moore, Tesa Severson, Greg A. Taylor, Andrew E. Teschendorff, Kane Tse, Gulisa Turashvili, Richard Varhol, René L. Warren, Peter Watson, Yongjun Zhao, Carlos Caldas, David Huntsman, Martin Hirst, Marco A. Marra & Samuel Aparicio
doi:10.1038/nature08489
First paragraph | Full Text | PDF (166K) | Supplementary information
See also: Editor's summary
Direct RNA sequencing p814
Understanding the functional output of the genome — the transcriptome — is an essential step on the way to understanding human biology and disease. Current transcriptome analysis methods are indirect, typically requiring RNA to be converted to complementary DNA (cDNA) before measurements. Single molecule RNA sequencing without prior conversion of RNA to cDNA is now reported.
Fatih Ozsolak, Adam R. Platt, Dan R. Jones, Jeffrey G. Reifenberger, Lauryn E. Sass, Peter McInerney, John F. Thompson, Jayson Bowers, Mirna Jarosz & Patrice M. Milos
doi:10.1038/nature08390
First paragraph | Full Text | PDF (1,525K) | Supplementary information
See also: Editor's summary
JAK2 phosphorylates histone H3Y41 and excludes HP1
from chromatin p819
The activation of Janus kinase 2 (JAK2), a non-receptor tyrosine kinase that regulates several cellular processes by inducing cytoplasmic signalling cascades, is a frequent event in haematological malignancies. Here, human JAK2 is shown to be present in the nucleus of haematopoietic cells, where it directly phosphorylates Tyr 41 on histone H3, thus preventing the binding of heterochromatin protein I.
Mark A. Dawson, Andrew J. Bannister, Berthold Göttgens, Samuel D. Foster, Till Bartke, Anthony R. Green & Tony Kouzarides
doi:10.1038/nature08448
First paragraph | Full Text | PDF (662K) | Supplementary information
See also: Editor's summary
Structural insights into mechanisms of the small RNA methyltransferase HEN1 p823
Some of the small RNAs involved in RNA silencing require the addition of a 2'-O-methyl group on the 3' terminal nucleotide in order for the precursor RNA to be correctly processed. This modification is performed by the HEN1 RNA methyltransferase, the crystal structure of which — from Arabidopsis — is now solved.
Ying Huang, Lijuan Ji, Qichen Huang, Dmitry G. Vassylyev, Xuemei Chen & Jin-Biao Ma
doi:10.1038/nature08433
PDB code
3D view
First paragraph | Full Text | PDF (1,610K) | Supplementary information
See also: Editor's summary
Errata
Dense packings of the Platonic and Archimedean solids p828
S. Torquato & Y. Jiao
doi:10.1038/nature08492
Stable single-unit-cell nanosheets of zeolite MFI as active and long-lived catalysts p828
Minkee Choi, Kyungsu Na, Jeongnam Kim, Yasuhiro Sakamoto, Osamu Terasaki & Ryong Ryoo
doi:10.1038/nature08493
Corrigendum
Genotypic sex determination enabled adaptive radiations of extinct marine reptiles p828
Chris L. Organ, Daniel E. Janes, Andrew Meade & Mark Pagel
doi:10.1038/nature08523
Naturejobs
Careers Q&ARobert Margolskee p831
An expert in the molecular mechanisms of taste, Margolskee recently accepted a faculty position at the Monell Chemical Senses Center in Philadelphia, Pennsylvania.
Virginia Gewin
doi:10.1038/nj7265-831a
Postdoc journal
Communicating science p831
A science-communication programme has taught me how to talk science.
Julia Boughner
doi:10.1038/nj7265-831b
In Brief
Endangered papers p831
Conservation biologists' government jobs preclude speedy publishing.
doi:10.1038/nj7265-831c
Bridges to biotechnology p831
Stimulus funds support biotech retraining programme in Oregon.
doi:10.1038/nj7265-831d
Gender imbalance persists p831
Survey shows men still hold most positions in US science and engineering.
doi:10.1038/nj7265-831e
Region
Rising star? p832
The Japanese city of Nagoya is aiming to turn a history of manufacturing success into fertile ground for science applications. David Cyranoski surveys its potential.
David Cyranoski
doi:10.1038/nj7265-832a
