nature

THIS WEEK

Editorials

There is life after academia ▶

With high numbers of postdocs emerging from universities, prospective PhD students must be prepared for the fact that they will probably not end up with a career in research.

Heavenly homes ▶

The discovery of our Galaxy’s place in the Universe adds detail to our address.

The digital toolbox ▶

A new section of Nature examines the software and websites that make research easier.

World View

Judge research impact on a local scale ▶

Metrics that give a global overview risk sidelining science in developing nations, argues Casparus J. Crous.

Seven Days

Seven days: 29 August–4 September 2014 ▶

The week in science: Regulation on e-cigarettes, tracking space debris in Australia, and an Icelandic volcano erupts.

NEWS IN FOCUS

Ebola drug trials set to begin amid crisis ▶

Testing drugs in the middle of deadly disease outbreak is challenging but can be done.

Stalled El Niño poised to resurge ▶

Studies of brewing weather event test understanding of past and future climate.

Switzerland braces for Alpine lake tsunami ▶

Authorities in Swiss canton blaze a trail by factoring the risk into hazard planning.

California quake puts warning system in the spotlight ▶

Scientists, politicians and business leaders will discuss practicalities of a regional network.

Features

Life outside the lab: The ones who got away ▶

Sometimes, the brightest stars in science decide to leave. Nature finds out where they go.

E-cigarettes: The lingering questions ▶

In the haze of incomplete data, scientists are divided over the risks and benefits of electronic cigarettes.

COMMENT

Neuroscience: Where is the brain in the Human Brain Project? ▶

Europe's €1-billion science and technology project needs to clarify its goals and establish transparent governance, say Yves Frégnac and Gilles Laurent.

Satellites: Make Earth observations open access ▶

Freely available satellite imagery will improve science and environmental-monitoring products, say Michael A. Wulder and Nicholas C. Coops.

Books and Arts

Developmental biology: Splitting the sexes ▶

Virginia Valian ponders a study on biology, evolution and gender differences in humans.

Correspondence

Energy: Social fixes are on the up David E. Rodgers, Dustin S. Schinn | Energy: We need all hands on deck Paul C. Stern | Energy: Humanities frame the aims Noel Castree | River restoration: Better monitoring of fish in dam projects Peter Brewitt, Karen D. Holl | Antarctica: Seals collect more Southern Ocean data Clive R. McMahon, Robert Harcourt

Obituary

Yoshiki Sasai (1962–2014) ▶

Stem-cell biologist who decoded signals in embryos.

Correction

Correction ▶

RESEARCH

Latest Online

Evolutionary biology: Radiating genomes ▶

Chris D. Jiggins

Medical research: Ebola therapy protects severely ill monkeys ▶

Thomas W. Geisbert

The genomic substrate for adaptive radiation in African cichlid fish OPEN ▶

David Brawand, Catherine E. Wagner, Yang I. Li et al.

Genomes and transcriptomes of five distinct lineages of African cichlids, a textbook example of adaptive radiation, have been sequenced and analysed to reveal that many types of molecular changes contributed to rapid evolution, and that standing variation accumulated during periods of relaxed selection may have primed subsequent diversification.

Reversion of advanced Ebola virus disease in nonhuman primates with ZMapp ▶

Xiangguo Qiu, Gary Wong, Jonathan Audet et al.

A new treatment, containing an optimized cocktail of three monoclonal antibodies against Ebola virus, provided full protection and disease reversal in rhesus monkeys when given under conditions in which controls succumbed by day 8; this new therapy may be a good candidate for treating Ebola virus infection in human patients.

High-fat-diet-mediated dysbiosis promotes intestinal carcinogenesis independently of obesity ▶

Manon D. Schulz, Çiğdem Atay, Jessica Heringer et al.

A high-fat diet promotes intestinal tumorigenesis independently of obesity in a mouse model with oncogene activation, by changing the composition of the gut microbiota and altering immune regulation.

Stochasticity of metabolism and growth at the single-cell level ▶

Daniel J. Kiviet, Philippe Nghe, Noreen Walker et al.

The inherent stochasticity in metabolic reactions is a potent source of phenotypic heterogeneity in cell populations, with potentially fundamental implications for cancer research.

Broad and potent HIV-1 neutralization by a human antibody that binds the gp41–gp120 interface ▶

Jinghe Huang, Byong H. Kang, Marie Pancera et al.

Molecular and structural characterization is reported for a new broad and potent monoclonal antibody against HIV that binds to an epitope bridging the gp41 and gp120 subunits — the antibody affects a step in virus entry after binding to CD4 and before engagement of CCR5.

Producing more grain with lower environmental costs ▶

Xinping Chen, Zhenling Cui, Mingsheng Fan et al.

In an experiment across China to test integrated soil–crop system management for rice, wheat and maize against current practice, improvements in grain yield are equivalent to high-input techniques, but nutrient use, nutrient loss and greenhouse gas emissions are lower than current practice.

Conditional tolerance of temperate phages via transcription-dependent CRISPR-Cas targeting ▶

Gregory W. Goldberg, Wenyan Jiang, David Bikard et al.

The Staphylococcus epidermidis CRISPR-Cas system can prevent lytic infection but tolerate lysogenization by temperate phage through a transcription-dependent DNA targeting mechanism.

Sensory-evoked LTP driven by dendritic plateau potentials in vivo ▶

Frédéric Gambino, Stéphane Pagès, Vassilis Kehayas et al.

Whole-cell recordings in mouse somatosensory cortex in vivo show that rhythmic sensory-whisker stimulation induces long-term synaptic potentiation (LTP) in layer 2/3 (L2/3) pyramidal cells, in the absence of somatic spikes, through long-lasting NMDAR-mediated depolarizations that are generated by synaptic networks originating from the posteromedial complex of the thalamus.

Structures of bacterial homologues of SWEET transporters in two distinct conformations ▶

Yan Xu, Yuyong Tao, Lily S. Cheung et al.

The X-ray crystal structures of two bacterial homologues of the SWEET sugar transporters are solved in two conformational states, and comparison of these states suggests that transport occurs via a ‘rocker-switch’ mechanism.

Transcript-RNA-templated DNA recombination and repair ▶

Havva Keskin, Ying Shen, Fei Huang et al.

Endogenous RNA transcripts are shown to mediate recombination with yeast chromosomal DNA; as the level of RNAs in the nucleus is quite high, these results may open up new understanding of the plasticity of repair and genome instability mechanisms.

Articles and Letters

Developmental plasticity and the origin of tetrapods ▶

Emily M. Standen, Trina Y. Du, Hans C. E. Larsson

The most primitive extant bony fish, Polypterus, exhibits adaptive plasticity for life on land when raised on land rather than in water, suggesting that environmentally induced phenotypic plasticity might have facilitated the macroevolutionary transition to life on land.

Alterations of the human gut microbiome in liver cirrhosis ▶

Nan Qin, Fengling Yang, Ang Li et al.

Invasion of the gut by oral bacteria in liver cirrhosis.

RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer ▶

Andrew L. Wolfe, Kamini Singh, Yi Zhong et al.

The translation of many messenger RNAs that encode important oncogenes and transcription factors depends on the eIF4A RNA helicase to resolve G-quadruplex structures, implying eIF4A inhibition as an effective cancer therapy.

RIPK1 maintains epithelial homeostasis by inhibiting apoptosis and necroptosis ▶

Marius Dannappel, Katerina Vlantis, Snehlata Kumari et al.

RIPK1 is shown to have a crucial role—independent of its known kinase function—in suppressing epithelial cell apoptosis and necroptosis in mice, thereby regulating homeostasis and preventing inflammation in barrier tissues.

RIPK1 ensures intestinal homeostasis by protecting the epithelium against apoptosis ▶

Nozomi Takahashi, Lars Vereecke, Mathieu J. M. Bertrand et al.

This study provides evidence for a critical role of RIPK1 in suppressing caspase-8-mediated cell death and maintaining intestinal homeostasis independently of its kinase activity.

Tumour-derived PTH-related protein triggers adipose tissue browning and cancer cachexia ▶

Serkan Kir, James P. White, Sandra Kleiner et al.

Many patients with cancer experience cachexia, a wasting disorder of adipose tissue and skeletal muscle that leads to weight loss and frailty; now, tumour-derived parathyroid-hormone-related protein has been shown to stimulate the expression of genes involved in heat production in adipose tissues and to have an important role in tissue wasting.

eIF4F is a nexus of resistance to anti-BRAF and anti-MEK cancer therapies ▶

Lise Boussemart, Hélène Malka-Mahieu, Isabelle Girault et al.

BRAF mutations occur frequently in melanomas, but patients generally develop resistance to agents targeting mutant BRAF; now, the persistent formation of the translation initiation complex eIF4F has been described as an indicator of multiple mechanisms of resistance that arise in BRAF-mutated tumours and as a promising therapeutic target.

Mutant IDH inhibits HNF-4α to block hepatocyte differentiation and promote biliary cancer ▶

Supriya K. Saha, Christine A. Parachoniak, Krishna S. Ghanta et al.

Gain-of-function mutations in isocitrate dehydrogenase (IDH) are among the most common genetic alterations in intrahepatic cholangiocarcinoma (IHCC), a deadly cancer of the liver bile ducts; now mutant IDH is shown to block liver cell differentiation through the suppression of HNF-4α, a master regulator of hepatocyte identity and quiescence, leading to expansion of liver progenitor cells primed for progression to IHCC.

Dynamic and static maintenance of epigenetic memory in pluripotent and somatic cells ▶

Zohar Shipony, Zohar Mukamel, Netta Mendelson Cohen et al.

Using a new method to estimate DNA methylation turnover rate, embryonic stem cells are shown to lack clonal transmission of methylation but still maintain a stable epigenetic state, whereas somatic cells transmit methylation clonally but lose epigenetic state coherence owing to the persistence of accumulated methylation errors.

Saturation editing of genomic regions by multiplex homology-directed repair ▶

Gregory M. Findlay, Evan A. Boyle, Ronald J. Hause et al.

The authors perform saturation mutagenesis of genomic regions in their native endogenous chromosomal context by using CRISPR/Cas9 RNA-guided cleavage and multiplex homology-directed repair; its utility is demonstrated by measuring the effects of hundreds to thousands of genomic edits to BRCA1 and DBR1 on splicing and cellular fitness, respectively.

High-resolution structure of the human GPR40 receptor bound to allosteric agonist TAK-875 ▶

Ankita Srivastava, Jason Yano, Yoshihiko Hirozane et al.

The X-ray crystal structure of human GPR40 receptor in the presence of TAK-875, an orally available, potent and selective human GPR40 agonist.

News & Views

Evolutionary developmental biology: Dynasty of the plastic fish ▶

John Hutchinson

Cell biology: A guardian angel of cell integrity ▶

Francis Ka-Ming Chan

Biological techniques: Edit the genome to understand it ▶

Fyodor D. Urnov

Structural biology: How fluorescent RNA gets its glow ▶

William G. Scott

Evolutionary biology: Radiating genomes ▶

Chris D. Jiggins

Medical research: Ebola therapy protects severely ill monkeys ▶

Thomas W. Geisbert

Corrigendum

Corrigendum: Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET ▶

Toshiyuki Matsui, Danny Leung, Hiroki Miyashita et al.

Research Highlights

Fresh arguments over old data | Biochemistry: Marine enzyme can multi-task | Neuroscience: Eyes offer window on dementia | Genomics: Ebola genomes decoded

NEWS & COMMENT

Neuroscience: Where is the brain in the Human Brain Project? | Developmental biology: Splitting the sexes | River restoration: Better monitoring of fish in dam projects | Yoshiki Sasai (1962–2014) | Correction | Ebola drug trials set to begin amid crisis | E-cigarettes: The lingering questions

More Biological Sciences ▶

RESEARCH

Latest Online

Medical research: Ebola therapy protects severely ill monkeys ▶

Thomas W. Geisbert

High-fat-diet-mediated dysbiosis promotes intestinal carcinogenesis independently of obesity ▶

Manon D. Schulz, Çiğdem Atay, Jessica Heringer et al.

A high-fat diet promotes intestinal tumorigenesis independently of obesity in a mouse model with oncogene activation, by changing the composition of the gut microbiota and altering immune regulation.

Broad and potent HIV-1 neutralization by a human antibody that binds the gp41–gp120 interface ▶

Jinghe Huang, Byong H. Kang, Marie Pancera et al.

Molecular and structural characterization is reported for a new broad and potent monoclonal antibody against HIV that binds to an epitope bridging the gp41 and gp120 subunits — the antibody affects a step in virus entry after binding to CD4 and before engagement of CCR5.

Articles and Letters

Alterations of the human gut microbiome in liver cirrhosis ▶

Nan Qin, Fengling Yang, Ang Li et al.

Invasion of the gut by oral bacteria in liver cirrhosis.

RNA G-quadruplexes cause eIF4A-dependent oncogene translation in cancer ▶

Andrew L. Wolfe, Kamini Singh, Yi Zhong et al.

The translation of many messenger RNAs that encode important oncogenes and transcription factors depends on the eIF4A RNA helicase to resolve G-quadruplex structures, implying eIF4A inhibition as an effective cancer therapy.

Tumour-derived PTH-related protein triggers adipose tissue browning and cancer cachexia ▶

Serkan Kir, James P. White, Sandra Kleiner et al.

Many patients with cancer experience cachexia, a wasting disorder of adipose tissue and skeletal muscle that leads to weight loss and frailty; now, tumour-derived parathyroid-hormone-related protein has been shown to stimulate the expression of genes involved in heat production in adipose tissues and to have an important role in tissue wasting.

eIF4F is a nexus of resistance to anti-BRAF and anti-MEK cancer therapies ▶

Lise Boussemart, Hélène Malka-Mahieu, Isabelle Girault et al.

BRAF mutations occur frequently in melanomas, but patients generally develop resistance to agents targeting mutant BRAF; now, the persistent formation of the translation initiation complex eIF4F has been described as an indicator of multiple mechanisms of resistance that arise in BRAF-mutated tumours and as a promising therapeutic target.

Mutant IDH inhibits HNF-4α to block hepatocyte differentiation and promote biliary cancer ▶

Supriya K. Saha, Christine A. Parachoniak, Krishna S. Ghanta et al.

Gain-of-function mutations in isocitrate dehydrogenase (IDH) are among the most common genetic alterations in intrahepatic cholangiocarcinoma (IHCC), a deadly cancer of the liver bile ducts; now mutant IDH is shown to block liver cell differentiation through the suppression of HNF-4α, a master regulator of hepatocyte identity and quiescence, leading to expansion of liver progenitor cells primed for progression to IHCC.

High-resolution structure of the human GPR40 receptor bound to allosteric agonist TAK-875 ▶

Ankita Srivastava, Jason Yano, Yoshihiko Hirozane et al.

The X-ray crystal structure of human GPR40 receptor in the presence of TAK-875, an orally available, potent and selective human GPR40 agonist.

News & Views

Medical research: Ebola therapy protects severely ill monkeys ▶

Thomas W. Geisbert

NEWS & COMMENT

Ebola drug trials set to begin amid crisis | E-cigarettes: The lingering questions

More Health Sciences ▶

RESEARCH

Latest Online

Early turbulent mixing as the origin of chemical homogeneity in open star clusters ▶

Yi Feng, Mark R. Krumholz

Simulations tracing the mixing of chemical elements as star-forming clouds assemble and collapse show that turbulent mixing during cloud assembly naturally produces a scatter of stellar abundance much smaller than that in the gas, explaining why stars in the same cluster appear to be nearly identical in their chemical abundances.

Articles and Letters

The Laniakea supercluster of galaxies ▶

R. Brent Tully, Hélène Courtois, Yehuda Hoffman et al.

Examination of a three-dimensional map of galaxies and their velocities shows a surface bounding the motions of galaxies that are inward after removal of the mean cosmic expansion and long-range flows; the galaxies within this surface lie within our home supercluster.

A 400-solar-mass black hole in the galaxy M82 ▶

Dheeraj R. Pasham, Tod E. Strohmayer, Richard F. Mushotzky

The discovery of two stable peaks at frequencies with a ratio of 3:2 in the power spectrum of X-ray emission from the brightest X-ray source in galaxy M82 suggests that, if the relationship between frequency and mass that holds for stellar-mass black holes can be extended to intermediate masses, the black hole believed to be the source of the emission has a mass approximately 400 times that of the Sun.

Hierarchical organization of chiral rafts in colloidal membranes ▶

Prerna Sharma, Andrew Ward, T. Gibaud et al.

Inclusions dissolved in a colloidal membrane assemble into highly uniform finite-sized liquid droplets or rafts consisting of thousands of molecules.

News & Views

50 & 100 Years Ago ▶

Cosmology: Meet the Laniakea supercluster ▶

Elmo Tempel

Research Highlights

Materials science: Flexible solar cells work both ways

NEWS & COMMENT

Heavenly homes | Energy: Social fixes are on the up | Energy: We need all hands on deck | Energy: Humanities frame the aims | River restoration: Better monitoring of fish in dam projects

More Physical Sciences ▶

RESEARCH

Articles and Letters

Temperature sensitivity of soil respiration rates enhanced by microbial community response ▶

Kristiina Karhu, Marc D. Auffret, Jennifer A. J. Dungait et al.

Microbial community responses in soils from the Arctic to the Amazon often enhance the longer-term temperature sensitivity of respiration, particularly in soils with high carbon-to-nitrogen ratios and in soils from cold regions, suggesting that carbon stored in Arctic and boreal soils could be more vulnerable to climate warming than currently predicted.

Asymmetric three-dimensional topography over mantle plumes ▶

Evgueni Burov, Taras Gerya

Three-dimensional numerical models of the interaction of a mantle plume with a rheologically realistic lithosphere predict complex surface evolution very different from the smooth, radially symmetric patterns usually assumed to be the signature of a mantle upwelling, with strongly asymmetric small-scale three-dimensional features such as rifts and linear fault structures.

Reviews and Perspectives

Migrations and dynamics of the intertropical convergence zone ▶

Tapio Schneider, Tobias Bischoff, Gerald H. Haug

The intertropical convergence zone, where global rainfall is greatest, is a narrow belt of clouds usually centred about six degrees north of the Equator; this Review links its migrations on various timescales to the atmospheric energy balance.

News & Views

Geodynamics: How plumes help to break plates ▶

Susanne Buiter

Research Highlights

Geology: Mobile rocks explained | Anthropology: Sahara stopped human mixing

NEWS & COMMENT

Switzerland braces for Alpine lake tsunami | Antarctica: Seals collect more Southern Ocean data | Stalled El Niño poised to resurge | Satellites: Make Earth observations open access | California quake puts warning system in the spotlight

More Earth & Environmental Sciences ▶

How to tame the flood of literature ▶

Recommendation services claim to help researchers keep up with the most important papers without becoming overwhelmed.

Interviews: The all-important job talk ▶

How people present their research and aspirations during interviews for academic positions can make or break their career.

Turning point: Shingo Kajimura ▶

Brown-fat research helps one-time fish scientist to make waves in obesity field.

Careers related news & comment

Neuroscience: Where is the brain in the Human Brain Project? Yves Frégnac, Gilles Laurent | There is life after academia | Seven days: 29 August–4 September 2014 | Life outside the lab: The ones who got away Ewen Callaway | Energy: We need all hands on deck Paul C. Stern | River restoration: Better monitoring of fish in dam projects Peter Brewitt, Karen D. Holl | Judge research impact on a local scale Casparus J Crous

Bioinformatics Position (m / f)

Fraunhofer Gesellschaft FhG, Institute for Molecular Biology and Applied Ecology (IME) 

Postdoctoral Position in Behavioral Neuroscience

University of Gothenburg (GU) 

POSTDOC : Organic Memory Devices and their Implementation in Neuromorphic Circuits

CEA French Atomic and Alternative Energies Commission 

Tenure Track Faculty Positions

The Department of Genetics Washington University School of Medicine, St. Louis 

The 6th Annual Personalized Medicine Conference

29.-30.10.14 San Francisco, US