nature

THIS WEEK

Editorials

The price of progress ▶

A new uranium enrichment technique approved by the US Nuclear Regulatory Commission could have an impact on nuclear proliferation. This should have been taken into account.

Power cuts ▶

China’s slumping renewable-energy industry should be learnt from, not dismissed.

Life sciences ▶

Survivors of the 2010 University of Alabama shooting chose not to push for the death penalty.

World View

Gene therapies need new development models ▶

As with other medicines, the approval of gene therapies should hinge on a risk–benefit analysis for the patient, argues Fulvio Mavilio.

Seven Days

Seven days: 28 September–4 October 2012 ▶

The week in science: French research escapes cuts; fusion facility fails to ignite; and habitat for great apes is under threat.

NEWS IN FOCUS

Malaria plan under scrutiny ▶

Lack of data and donor uncertainty leave public-health experiment on the rocks.

New cures sought from old drugs ▶

Researchers to re-examine compounds shelved by industry.

The telescopes that came in from the cold ▶

Twin spy telescopes could drive US space astronomy forward, but at what cost?

Foundation opens TB lab in Africa ▶

Howard Hughes Medical Institute sets up shop at ground zero for tuberculosis: South Africa’s KwaZulu-Natal.

SARS veterans tackle coronavirus ▶

Genome sequence of new virus speeds up testing.

Misconduct is the main cause of life-sciences retractions ▶

Opaque announcements in journals can hide fraud, study finds.

Features

Plant science: The chestnut resurrection ▶

Once king of eastern forests, the American chestnut was wiped out by blight. Now it is poised to rise again.

Galaxy formation: The new Milky Way ▶

A fresh look at our Galaxy points to a chaotic past and a violent end.

COMMENT

Digital archives: Don't let copyright block data mining ▶

Matthew L. Jockers, Matthew Sag and Jason Schultz explain why humanities scholars have pitched in to the Authors Guild v. Google lawsuit.

Nobel success: What makes a great lab? ▶

William Bynum reflects on the factors that have brought nine Nobel prizes to the UK Laboratory of Molecular Biology in Cambridge.

Books and Arts

Zoonosis: Fatal exchange ▶

Nathan Wolfe applauds a tome on interspecies disease transmission that mixes research with human stories.

Mars exploration: Roving the red planet ▶

It is people who drive Curiosity and other robot missions on Mars, reminds Jim Bell.

Books in brief ▶

Network theory: The regularities of facts ▶

Carl Bergstrom assesses the power of scientometrics in predicting the shifts and shelf-life of knowledge.

Correspondence

Policy: Biodiversity needs a scientific approach David A. Westcott, Frederieke J. Kroon & Andy W. Sheppard | Nanotechnology: Change of heart on nanoparticle risks Silvia Ribeiro | Cold fusion: Fleischmann denied due credit Brian D. Josephson | Renewable energy: European biodiesel can be sustainable Rod Snowdon & Wolfgang Friedt | Publishing: Reviews turn facts into understanding Douglas B. Kell

RESEARCH

Latest Online

A map of rice genome variation reveals the origin of cultivated rice  OPEN ▶

Xuehui Huang, Nori Kurata, Xinghua Wei, Zi-Xuan Wang, Ahong Wang et al.

Whole-genome sequences of wild rice and cultivated rice varieties are used to produce a map of rice genome variation, and show that rice was probably first domesticated in southern China.

Adenoma-linked barrier defects and microbial products drive IL-23/IL-17-mediated tumour growth ▶

Sergei I. Grivennikov, Kepeng Wang, Daniel Mucida, C. Andrew Stewart, Bernd Schnabl et al.

In a mouse model of colorectal cancer, barrier deterioration results in adenoma invasion by microbial products that trigger tumour-elicited inflammation, which in turn drives IL-23-dependent tumour growth.

Dopaminergic neurons inhibit striatal output through non-canonical release of GABA ▶

Nicolas X. Tritsch, Jun B. Ding & Bernardo L. Sabatini

Activation of midbrain dopamine neurons rapidly inhibits action potential firing in both direct- and indirect-pathway striatal projection neurons through VMAT2-dependent vesicular release of the inhibitory transmitter GABA (γ-aminobutyric acid).

Black mamba venom peptides target acid-sensing ion channels to abolish pain ▶

Sylvie Diochot, Anne Baron, Miguel Salinas, Dominique Douguet, Sabine Scarzello et al.

A new class of peptides, mambalgins, is isolated from the African snake the black mamba, which can abolish pain through inhibition of particular subtypes of acid-sensing ion channels expressed either in central or peripheral neurons.

The molecular basis of phosphate discrimination in arsenate-rich environments ▶

Mikael Elias, Alon Wellner, Korina Goldin-Azulay, Eric Chabriere, Julia A. Vorholt et al.

Ultrahigh-resolution X-ray crystallography study of a phosphate-binding protein from Pseudomonas fluorescens yields insight into how phosphate ions essential for life are discriminated from the arsenate ions inimical to it, even in arsenate-rich environments.

Androgenetic haploid embryonic stem cells produce live transgenic mice ▶

Wei Li, Ling Shuai, Haifeng Wan, Mingzhu Dong, Meng Wang et al.

Mouse androgenetic haploid ES-cell lines can be established by transferring sperm into an enucleated oocyte; the cells maintain haploidy and stable growth over 30 passages, express pluripotent markers, are able to differentiate into all three germ layers, contribute to germlines of chimaeras when injected into blastocysts and can produce fertile progeny that carry genetic modifications to the next generation.

Vaccine-induced CD8⁺ T cells control AIDS virus replication ▶

Philip A. Mudd, Mauricio A. Martins, Adam J. Ericsen, Damien C. Tully, Karen A. Power et al.

Indian rhesus macaques are vaccinated with simian immunodeficiency virus (SIV)-restricted CD8⁺ T-cell epitopes, and these vaccinated animals are shown to mediate elite control of virus replication.

Mitochondrial defect drives non-autonomous tumour progression through Hippo signalling in Drosophila ▶

Shizue Ohsawa, Yoshitaka Sato, Masato Enomoto, Mai Nakamura, Aya Betsumiya et al.

In a Drosophila imaginal epithelial disc system, mutations that lead to mitochondrial dysfunction can also promote tumorigenic growth of neighbouring cells expressing an activated Ras oncogene.

Clonal allelic predetermination of immunoglobulin-κ rearrangement ▶

Marganit Farago, Chaggai Rosenbluh, Maya Tevlin, Shira Fraenkel, Sharon Schlesinger et al.

Immunoglobulin genes are expressed from either the maternal or paternal chromosome; it is now shown that in early haematopoietic stem cells, an individual cell can choose either of the two alleles, but as they develop they become committed to only one.

Structure-based prediction of protein–protein interactions on a genome-wide scale ▶

Qiangfeng Cliff Zhang, Donald Petrey, Lei Deng, Li Qiang, Yu Shi et al.

Protein–protein interactions, essential for understanding how a cell functions, are predicted using a new method that combines protein structure with other computationally and experimentally derived clues.

Articles and Letters

The oyster genome reveals stress adaptation and complexity of shell formation  OPEN ▶

Guofan Zhang, Xiaodong Fang, Ximing Guo, Li Li, Ruibang Luo et al.

The sequencing and assembly of the highly polymorphic oyster genome through a combination of short reads and fosmid pooling, complemented with extensive transcriptome analysis of development and stress response and proteome analysis of the shell, provides new insight into oyster biology and adaptation to a highly changeable environment.

A metagenome-wide association study of gut microbiota in type 2 diabetes ▶

Junjie Qin, Yingrui Li, Zhiming Cai, Shenghui Li, Jianfeng Zhu et al.

The authors have developed a new method, metagenome-wide association study (MGWAS), to compare the combined genetic content of the faecal microbiota of healthy people versus patients with type 2 diabetes; they identify multiple microbial species and metabolic pathways that are associated with either cohort and show that some of these may be used as biomarkers.

Comprehensive molecular portraits of human breast tumours  OPEN ▶

The Cancer Genome Atlas Network

The Cancer Genome Atlas Network describe their multifaceted analyses of primary breast cancers, shedding light on breast cancer heterogeneity; although only three genes (TP53, PIK3CA and GATA3) are mutated at a frequency greater than 10% across all breast cancers, numerous subtype-associated and novel mutations were identified.

Natural and anthropogenic variations in methane sources during the past two millennia ▶

C. J. Sapart, G. Monteil, M. Prokopiou, R. S. W. van de Wal, J. O. Kaplan et al.

Centennial-scale variations in methane carbon isotope ratios are attributed to changes in pyrogenic and biogenic sources that can be correlated with anthropogenic activities, such as varying levels of biomass burning during the period of the Roman empire and the Han dynasty, and changes in natural climate variability.

A Silurian armoured aplacophoran and implications for molluscan phylogeny ▶

Mark D. Sutton, Derek E. G. Briggs, David J. Siveter, Derek J. Siveter & Julia D. Sigwart

A fossil of an aplacophoran from the Silurian of Herefordshire, England, is shown to have armour plating, supporting recent studies that have allied the worm-like, shell-less Aplacophora with the multi-shelled Polyplacophora, or chitons.

A transcriptomic hourglass in plant embryogenesis ▶

Marcel Quint, Hajk-Georg Drost, Alexander Gabel, Kristian Karsten Ullrich, Markus Bönn et al.

As it develops from a single-celled zygote to a mature plant embryo, the thale cress Arabidopsis thaliana passes through a stage during which phylogenetically very ancient genes are preferentially expressed, showing that animals and plants have independently acquired the developmental hourglass as a similar way of managing gene expression as they pass through embryogenesis, even though their morphological development is very different.

Pregnancy imprints regulatory memory that sustains anergy to fetal antigen ▶

Jared H. Rowe, James M. Ertelt, Lijun Xin & Sing Sing Way

Successful pregnancy requires immune tolerance against paternal antigens expressed by the fetus; here pregnancy is shown to stimulate the selective accumulation of maternal immune-suppressive regulatory T cells with fetal specificity that are retained post-partum, which may explain the protective benefits of prior pregnancy against pre-eclampsia and other complications in subsequent pregnancy.

Rapid induction of inflammatory lipid mediators by the inflammasome in vivo ▶

Jakob von Moltke, Norver J. Trinidad, Mahtab Moayeri, Alexander F. Kintzer, Samantha B. Wang et al.

Induction of an eicosanoid storm is shown to be an unexpected consequence of inflammasome activation in peritoneal macrophages, leading to vascular leakage and rapid death in mice.

Paramutation in Drosophila linked to emergence of a piRNA-producing locus ▶

Augustin de Vanssay, Anne-Laure Bougé, Antoine Boivin, Catherine Hermant, Laure Teysset et al.

A paramutation occurs between two alleles in the same locus, when one allele induces a heritable mutation in another allele without modifying the DNA sequence; now, in Drosophila, a paramutation is shown to be transmissible over generations.

Burkitt lymphoma pathogenesis and therapeutic targets from structural and functional genomics ▶

Roland Schmitz, Ryan M. Young, Michele Ceribelli, Sameer Jhavar, Wenming Xiao et al.

RNA sequencing of Burkitt lymphoma tumours allows identification of mutations affecting the transcription factor TCF3, its negative regulator ID3 and the cell cycle regulator CCND3; these pathways reveal new targets for potential therapeutic intervention.

Structural basis for RNA-duplex recognition and unwinding by the DEAD-box helicase Mss116p ▶

Anna L. Mallam, Mark Del Campo, Benjamin Gilman, David J. Sidote & Alan M. Lambowitz

Analysis of the yeast DEAD-box nucleic acid helicase Mss116p provides a structural model for how DEAD-box proteins recognize and unwind RNA duplexes.

Alternating-access mechanism in conformationally asymmetric trimers of the betaine transporter BetP ▶

Camilo Perez, Caroline Koshy, Özkan Yildiz & Christine Ziegler

The crystal structure of the osmotically regulated symporter BetP is reported in four new conformations, providing information about the key conformational changes that take place during the transport cycle.

News & Views

Mucosal immunology: Infection induces friendly fire ▶

David Masopust & Vaiva Vezys

Genomics: Resident risks ▶

Julia Oh & Julia A. Segre

Immunology: Tolerating pregnancy ▶

Alexander G. Betz

50 & 100 years ago ▶

Research Highlights

Animal behaviour: Feeding habits of the vampire squid | Zoology: Mother's stress slows learning | Neuroscience: Responses vary in autistic brains | Atherosclerosis: Fatty plaque link to inflammation | Cell biology: A way to catch dividing cells | Neuroscience: Zebrafish find light without eyes

NEWS & COMMENT

Gene therapies need new development models | Malaria plan under scrutiny | New cures sought from old drugs | Foundation opens TB lab in Africa | SARS veterans tackle coronavirus | Plant science: The chestnut resurrection | Zoonosis: Fatal exchange | Books in brief | Policy: Biodiversity needs a scientific approach David A. Westcott, Frederieke J. Kroon & Andy W. Sheppard

CAREERS

Higher Education: Beyond the farm | Turning point: Ethan Perlstein

More Biological Sciences ▶

RESEARCH

Articles and Letters

Natural and anthropogenic variations in methane sources during the past two millennia ▶

C. J. Sapart, G. Monteil, M. Prokopiou, R. S. W. van de Wal, J. O. Kaplan et al.

Centennial-scale variations in methane carbon isotope ratios are attributed to changes in pyrogenic and biogenic sources that can be correlated with anthropogenic activities, such as varying levels of biomass burning during the period of the Roman empire and the Han dynasty, and changes in natural climate variability.

Structural basis for RNA-duplex recognition and unwinding by the DEAD-box helicase Mss116p ▶

Anna L. Mallam, Mark Del Campo, Benjamin Gilman, David J. Sidote & Alan M. Lambowitz

Analysis of the yeast DEAD-box nucleic acid helicase Mss116p provides a structural model for how DEAD-box proteins recognize and unwind RNA duplexes.

Alternating-access mechanism in conformationally asymmetric trimers of the betaine transporter BetP ▶

Camilo Perez, Caroline Koshy, Özkan Yildiz & Christine Ziegler

The crystal structure of the osmotically regulated symporter BetP is reported in four new conformations, providing information about the key conformational changes that take place during the transport cycle.

NEWS & COMMENT

New cures sought from old drugs | Network theory: The regularities of facts

More Chemical Sciences ▶

RESEARCH

Latest Online

Delayed build-up of Arctic ice sheets during 400,000-year minima in insolation variability ▶

Qingzhen Hao, Luo Wang, Frank Oldfield, Shuzhen Peng, Li Qin et al.

An East Asian winter monsoon proxy record using grain size variations in Chinese loess over the past 900,000 years shows that for up to 20,000 years after the interglacials at 400,000-year intervals, the weak monsoon winds maintain a mild, non-glacial climate at high northern latitudes.

Probing graphene grain boundaries with optical microscopy ▶

Dinh Loc Duong, Gang Hee Han, Seung Mi Lee, Fethullah Gunes, Eun Sung Kim et al.

A simple method to observe grain boundaries in graphene is reported, using ultraviolet irradiation in humid conditions followed by optical microscopy.

Articles and Letters

Two stellar-mass black holes in the globular cluster M22 ▶

Jay Strader, Laura Chomiuk, Thomas J. Maccarone, James C. A. Miller-Jones & Anil C. Seth

Two flat-spectrum radio sources in the Milky Way globular cluster M22 are thought to be accreting stellar-mass black holes; the identification of two black holes in one cluster shows that the ejection of black holes from clusters is not as efficient as predicted by most models.

Comet-like mineralogy of olivine crystals in an extrasolar proto-Kuiper belt ▶

B. L. de Vries, B. Acke, J. A. D. L. Blommaert, C. Waelkens, L. B. F. M. Waters et al.

Analysis of the 69-micrometre spectral band of olivine crystals in the β Pictoris planetary system shows that they can be associated with an extrasolar proto-Kuiper belt, are rich in magnesium and make up about 3.6 per cent of the dust mass in the system — properties remarkably similar to those of olivine crystals from primitive comets in the Solar System.

Stabilizing Rabi oscillations in a superconducting qubit using quantum feedback ▶

R. Vijay, C. Macklin, D. H. Slichter, S. J. Weber, K. W. Murch et al.

Real-time quantum feedback based on weak measurement of the quantum state is used to stabilize the oscillation phase of a driven quantum bit.

Sulphate–climate coupling over the past 300,000 years in inland Antarctica ▶

Yoshinori Iizuka, Ryu Uemura, Hideaki Motoyama, Toshitaka Suzuki, Takayuki Miyake et al.

Profiles of sulphate fluxes over the past 300,000 years from an Antarctic ice core show that, whereas the flux of sulphate-adhered dust has remained almost constant, that of sulphate salts correlates inversely with temperature, suggesting a coupling between particulate sulphur and temperature.

Natural and anthropogenic variations in methane sources during the past two millennia ▶

C. J. Sapart, G. Monteil, M. Prokopiou, R. S. W. van de Wal, J. O. Kaplan et al.

Centennial-scale variations in methane carbon isotope ratios are attributed to changes in pyrogenic and biogenic sources that can be correlated with anthropogenic activities, such as varying levels of biomass burning during the period of the Roman empire and the Han dynasty, and changes in natural climate variability.

Dynamical similarity of geomagnetic field reversals ▶

Jean-Pierre Valet, Alexandre Fournier, Vincent Courtillot & Emilio Herrero-Bervera

Volcanic records of the reversals of the geomagnetic field can be well matched under the assumption of a common reversal duration, and imply that the reversal process comprises three phases—a precursor, a fast polarity switch and a rebound—the properties of which have remained unchanged for about 180 million years.

News & Views

Climate science: The aerosol effect ▶

Bjorn Stevens & Olivier Boucher

Quantum physics: Cruise control for a qubit ▶

Howard M. Wiseman

Astrophysics: Two black holes found in a star cluster ▶

Stefan Umbreit

Research Highlights

Astronomy: Missing Galactic baryons spotted | Astronomy: Homing in on a black hole's jets | Electronics: Bendable battery yields flexible LED

NEWS & COMMENT

The telescopes that came in from the cold | Galaxy formation: The new Milky Way | Books in brief | Network theory: The regularities of facts | Cold fusion: Fleischmann denied due credit Brian D. Josephson

More Physical Sciences ▶

RESEARCH

Latest Online

Delayed build-up of Arctic ice sheets during 400,000-year minima in insolation variability ▶

Qingzhen Hao, Luo Wang, Frank Oldfield, Shuzhen Peng, Li Qin et al.

An East Asian winter monsoon proxy record using grain size variations in Chinese loess over the past 900,000 years shows that for up to 20,000 years after the interglacials at 400,000-year intervals, the weak monsoon winds maintain a mild, non-glacial climate at high northern latitudes.

Articles and Letters

Comet-like mineralogy of olivine crystals in an extrasolar proto-Kuiper belt ▶

B. L. de Vries, B. Acke, J. A. D. L. Blommaert, C. Waelkens, L. B. F. M. Waters et al.

Analysis of the 69-micrometre spectral band of olivine crystals in the β Pictoris planetary system shows that they can be associated with an extrasolar proto-Kuiper belt, are rich in magnesium and make up about 3.6 per cent of the dust mass in the system — properties remarkably similar to those of olivine crystals from primitive comets in the Solar System.

Sulphate–climate coupling over the past 300,000 years in inland Antarctica ▶

Yoshinori Iizuka, Ryu Uemura, Hideaki Motoyama, Toshitaka Suzuki, Takayuki Miyake et al.

Profiles of sulphate fluxes over the past 300,000 years from an Antarctic ice core show that, whereas the flux of sulphate-adhered dust has remained almost constant, that of sulphate salts correlates inversely with temperature, suggesting a coupling between particulate sulphur and temperature.

Natural and anthropogenic variations in methane sources during the past two millennia ▶

C. J. Sapart, G. Monteil, M. Prokopiou, R. S. W. van de Wal, J. O. Kaplan et al.

Centennial-scale variations in methane carbon isotope ratios are attributed to changes in pyrogenic and biogenic sources that can be correlated with anthropogenic activities, such as varying levels of biomass burning during the period of the Roman empire and the Han dynasty, and changes in natural climate variability.

Dynamical similarity of geomagnetic field reversals ▶

Jean-Pierre Valet, Alexandre Fournier, Vincent Courtillot & Emilio Herrero-Bervera

Volcanic records of the reversals of the geomagnetic field can be well matched under the assumption of a common reversal duration, and imply that the reversal process comprises three phases—a precursor, a fast polarity switch and a rebound—the properties of which have remained unchanged for about 180 million years.

News & Views

Climate science: The aerosol effect ▶

Bjorn Stevens & Olivier Boucher

NEWS & COMMENT

Mars exploration: Roving the red planet | Books in brief | Policy: Biodiversity needs a scientific approach David A. Westcott, Frederieke J. Kroon & Andy W. Sheppard | Renewable energy: European biodiesel can be sustainable Rod Snowdon & Wolfgang Friedt

More Earth & Environmental Sciences ▶

Higher Education: Beyond the farm ▶

Veterinary expertise is an advantage for researchers hoping to stem disease outbreaks and bolster food safety.

Turning point: Ethan Perlstein ▶

Evolutionary pharmacologist reaches out online.

People power ▶

Crowd-funding gains traction as a way to support research.

Relationship advice ▶

Report proposes guidelines for navigating academic-industrial partnerships.

Careers related news & comment

New cures sought from old drugs | Nobel success: What makes a great lab? | Mars exploration: Roving the red planet | Publishing: Reviews turn facts into understanding Douglas B. Kell

Faculty Position-NYU Center for Genomics & Systems Biology

New York University 

Research Assistant

University of Bristol 

Research Laboratory Manager

Imperial College London 

Postdoctoral Opportunity In Cell-Cell Adhesion And Communication

Northwestern Univeristy Feinberg School of Medicine 

International Conference on Microelectronics, Optoelectronics, and Nanoelectronics

28.-30.11.12 Paris, France