nature

THIS WEEK

Editorials

Fish have feelings too ▶

Our obligation to keep the suffering of laboratory animals to a minimum — both in life and in death — does not apply only to mammals.

Parallel lines ▶

A collaborative online mathematics project holds lessons for other disciplines.

Virgin territory ▶

Putting a private craft into space requires vision, hard work and a big dose of optimism.

World View

Scientist-versus-activist debates mislead the public ▶

The UK floods show the need to address the risks of climate change, but news teams still insist on pitching experts against sceptics, says Simon L. Lewis.

Seven Days

Seven days: 21–27 February 2014 ▶

The week in science: US bolsters patent system; $25-billion pharma deal the biggest in 5 years; and Europe picks exoplanet-hunting mission for 2024 launch.

NEWS IN FOCUS

Vietnam on high alert over flu risk ▶

H7N9 avian influenza may spread from China for first time.

Monkey brains wired to share ▶

Game-theory test exposes circuits for social interaction.

São Paulo poised to join megatelescope ▶

Brazilian state mulls support for Giant Magellan Telescope.

Einstein’s lost theory uncovered ▶

Physicist explored the idea of a steady-state Universe in 1931.

Fish-kill method questioned ▶

Common anaesthetic not the most humane option for zebrafish euthanasia, say studies.

SOFIA irons out technical kinks ▶

US–German airborne telescope slow to reach full capability.

Features

Crowd-sourcing: Strength in numbers ▶

Researchers are finding that online, crowd-sourced collaboration can speed up their work — if they choose the right problem.

Science in court: Disease detectives ▶

A powerful method for deducing microbial relationships has been edging its way into civil and criminal investigations. But courts should proceed with caution.

COMMENT

Earth science: Crystallography's journey to the deep Earth ▶

Improved methods for studying minerals at extreme pressures and temperatures promise a new era for exploring our planet's centre, says Thomas Duffy.

Books and Arts

Virology: Vanquishing HIV ▶

Sharon Lewin welcomes a book tracing how two men with HIV were functionally cured.

Physics: Inside utter strangeness ▶

David Seery applauds a primer on the incongruous world of quantum mechanics.

Arts: Eclipse of power ▶

Jay M. Pasachoff and Naomi Pasachoff appraise Alexander Borodin's solar-inspired opera.

Q&A: Melodic psychologist ▶

London-based music psychologist John Sloboda explores the subconscious connections and disjunctions between musicians and their audiences. He discusses his experiments on the 'emotional hotspots' experienced by listeners and the surprising power of improvisation.

Correspondence

University budgets: Expand fundraising by Brazil's institutes Tiago Campos Pereira | Stamina therapies: time to call a halt Silvio Garattini, Giuseppe Remuzzi, Gianluca Vago et al. | Stamina therapies: let the record stand Paolo Bianco, Elena Cattaneo, Michele De Luca et al. | Developing world: Global fund needed for STEM education Fanuel Muindi, Moytrayee Guha

Correction

Correction ▶

RESEARCH

Latest Online

Influenza: Prediction is worth a shot ▶

Katia Koelle, David A. Rasmussen

Cancer: Inflammation lights the way to metastasis ▶

Seth B. Coffelt, Karin E. de Visser

Plant science: How to switch affinity ▶

Yi-Fang Tsay

Mechanism of Tc toxin action revealed in molecular detail ▶

Dominic Meusch, Christos Gatsogiannis, Rouslan G. Efremov et al.

High-resolution structures of the Photorhabdus luminescens TcA toxin subunit and the entire Tc toxin complex reveal important new insights into Tc complex structure and function.

Crystal structure of the plant dual-affinity nitrate transporter NRT1.1 ▶

Ji Sun, John R. Bankston, Jian Payandeh et al.

A description of the crystal structure of unphosphorylated NRT1.1 provides insights into how phosphorylation switches the nitrate transporter between the low-affinity and high-affinity states.

Molecular basis of nitrate uptake by the plant nitrate transporter NRT1.1 ▶

Joanne L. Parker, Simon Newstead

In Arabidopsis thaliana the phosphorylation state of the ‘dual affinity’ transporter, NRT1.1, allows the uptake of nitrate over a wide concentration range; the crystal structure and molecular basis for this is described in this study.

A transcriptional switch underlies commitment to sexual development in malaria parasites ▶

Björn F. C. Kafsack, Núria Rovira-Graells, Taane G. Clark et al.

The DNA-binding protein PfAP2-G is found to be a master regulator of sexual development in the malaria parasite; this protein appears to regulate early gametocytogenesis and is epigenetically silenced in the majority of blood-stage parasites.

A cascade of DNA-binding proteins for sexual commitment and development in Plasmodium  ▶

Abhinav Sinha, Katie R. Hughes, Katarzyna K. Modrzynska et al.

Malaria parasites must produce gametocytes for transmission to the mosquito vector, although the molecular mechanisms underlying commitment to gametocyte production remain unclear; here this process is found to be controlled by PbAP2-G, a member of the ApiAP2 family of DNA-binding proteins, in the rodent-infecting Plasmodium berghei parasite.

IL-35-producing B cells are critical regulators of immunity during autoimmune and infectious diseases ▶

Ping Shen, Toralf Roch, Vicky Lampropoulou et al.

B cells can secrete IL-35 upon activation, and subsequently contribute negatively to the regulation of immunity, such as T-cell-mediated autoimmunity or anti-microbial immunity, and a characterization of these cells raises new questions about possible independent roles for IL-10- and IL-35-expressing plasma cells as regulatory cells.

A dedicated circuit links direction-selective retinal ganglion cells to the primary visual cortex ▶

Alberto Cruz-Martín, Rana N. El-Danaf, Fumitaka Osakada et al.

Using a combination of viral-tracing and in vivo imaging techniques, the authors show that there are several parallel pathways in the mouse visual system and that directional and orientation selectivity in the cortex may arise from the specialized tuning of retinal circuits.

Detection and replication of epistasis influencing transcription in humans ▶

Gibran Hemani, Konstantin Shakhbazov, Harm-Jan Westra et al.

Epistasis has rarely been shown among natural polymorphisms in human traits; this research using advanced computation and gene expression data reveals many instances of epistasis between common single nucleotide polymorphisms in humans, with epistasis and the direction of its effect replicating in independent cohorts.

Mouse liver repopulation with hepatocytes generated from human fibroblasts ▶

Saiyong Zhu, Milad Rezvani, Jack Harbell et al.

Human fibroblasts can be converted into hepatocytes capable of repopulating mouse livers by shortcutting reprogramming to pluripotency with factors promoting endoderm and hepatocyte differentiation.

The hippocampal CA2 region is essential for social memory ▶

Frederick L. Hitti, Steven A. Siegelbaum

CA2 neuron inactivation leads to a severe deficit in social memory, while having little effect on other well-known hippocampal functions such as contextual or spatial memory.

Ultraviolet-radiation-induced inflammation promotes angiotropism and metastasis in melanoma ▶

Tobias Bald, Thomas Quast, Jennifer Landsberg et al.

Mouse experiments show that ultraviolet radiation can promote tumour metastasis in melanoma by enhancing the expansion of tumour cells on blood vessel surfaces in a process linked to inflammation and requiring neutrophils and the proteins HMGB1 and TLR4.

A predictive fitness model for influenza ▶

Marta Łuksza & Michael Lässig

The seasonal human influenza A/H3N2 virus undergoes rapid evolution, which produces significant year-to-year sequence turnover in the population of circulating strains. This fitness model maps the adaptive history of influenza A and suggests a principled method for vaccine selection.

Articles and Letters

Epigenomic alterations define lethal CIMP-positive ependymomas of infancy ▶

S. C. Mack, H. Witt, R. M. Piro et al.

Although genetically bland, the posterior fossa group A subgroup of ependymomas, found often in infants and associated with poor prognosis, exhibit widespread epigenetic alterations, namely a CpG island methylator phenotype; these tumours are shown to be susceptible both in vitro and in vivo to various compounds that target epigenetic modifications, such as DNA methylation and H3K27 tri-methylation.

C11orf95–RELA fusions drive oncogenic NF-κB signalling in ependymoma ▶

Matthew Parker, Kumarasamypet M. Mohankumar, Chandanamali Punchihewa et al.

At least two-thirds of supratentorial ependymomas contain oncogenic fusions between RELA, the principal effector of nuclear factor-κB (NF-κB) signalling, and uncharacterized gene C11orf95; C11orf95–RELA fusion proteins translocate spontaneously to the nucleus to activate NF-κB target genes, and rapidly transform neural stem cells to form tumours in mice

A Crohn's disease variant in Atg16l1 enhances its degradation by caspase 3 ▶

Aditya Murthy, Yun Li, Ivan Peng et al.

The Crohn’s disease risk-conferring T300A variant in the autophagy protein ATG16L1 increases its sensitivity to caspase-3-mediated cleavage; this decreases the induction of autophagy in response to metabolic stress or pathogen infection, leading to increased secretion of inflammatory cytokines.

Skin pigmentation provides evidence of convergent melanism in extinct marine reptiles ▶

Johan Lindgren, Peter Sjövall, Ryan M. Carney et al.

Dark melanin pigment was detected in the fossilized skin of three distantly related marine reptiles (a leatherback turtle, mosasaur and ichthyosaur); benefits of thermoregulation and/or crypsis may have contributed to this melanisation, which therefore has implications for our understanding of how these animals may have lived.

Sequential evolution of bacterial morphology by co-option of a developmental regulator ▶

Chao Jiang, Pamela J. B. Brown, Adrien Ducret et al.

A developmental regulator in Caulobacter evolved to specify the location of cell envelope morphogenesis in a related genus.

Genetics of single-cell protein abundance variation in large yeast populations ▶

Frank W. Albert, Sebastian Treusch, Arthur H. Shockley et al.

A new method for identifying genetic loci that influence protein expression in budding yeast reveals considerable complexity in how genetic variation shapes the proteome.

A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes ▶

Johan Larsbrink, Theresa E. Rogers, Glyn R. Hemsworth et al.

A genetic locus from the gut symbiont Bacteroides ovatus is identified and described that encodes a cohort of enzymes and carbohydrate-binding proteins necessary for the metabolism of xyloglucans—a predominant component of dietary fibre.

Sessile alveolar macrophages communicate with alveolar epithelium to modulate immunity ▶

Kristin Westphalen, Galina A. Gusarova, Mohammad N. Islam et al.

Tissue-resident macrophages are shown to stop lipopolysaccharide-induced inflammation by spreading an anti-inflammatory calcium signal to alveolar epithelial cells through connexin-43-positive gap junction channels.

A new metabolic cell-wall labelling method reveals peptidoglycan in Chlamydia trachomatis  ▶

G. W. Liechti, E. Kuru, E. Hall et al.

Peptidoglycan is an essential structural component of the cell wall in the majority of bacteria, but the obligate intracellular human pathogen Chlamydia trachomatis was thought to be one of the few exceptions; here a click chemistry approach is used to label peptidoglycan in replicating C. trachomatis with novel d-amino acid dipeptide probes.

Broadly permissive intestinal chromatin underlies lateral inhibition and cell plasticity ▶

Tae-Hee Kim, Fugen Li, Isabel Ferreiro-Neira et al.

A study investigating the mechanisms underlying lateral inhibition and lineage plasticity in the mouse small intestine crypts in vivo finds that crypt cells maintain a permissive chromatin state upon which a transcription factor acts to determine lineage specification, and this is the basis of lateral inhibition.

News & Views

Tuberculosis: Drug discovery goes au naturel ▶

Clifton E. Barry

Cancer: Tumours outside the mutation box ▶

Rogier Versteeg

Conservation: Wind blown ▶

Andrew Mitchinson

Cell biology: Stressful genetics in Crohn's disease ▶

Arthur Kaser, Richard S. Blumberg

Brief Communications Arising

Is SIRT2 required for necroptosis? ▶

Kim Newton, Joanne M. Hildebrand, Zhirong Shen et al.

Retraction

Retraction: The NAD-dependent deacetylase SIRT2 is required for programmed necrosis ▶

Nisha Narayan, In Hye Lee, Ronen Borenstein et al.

Addendum

Addendum: Enterotypes of the human gut microbiome ▶

Manimozhiyan Arumugam, Jeroen Raes, Eric Pelletier et al.

Research Highlights

Conservation biology: Bears use animal bridges to breed | Neuroscience: Carbon dating spots new neurons | Zoology: Farming shifts bird reproduction | Archaeology: Ancient artists' gender is a mystery | Regenerative biology: Altered proteins boost healing | Vision: Molecule makes blind mice see light

NEWS & COMMENT

Vietnam on high alert over flu risk | Science in court: Disease detectives | Virology: Vanquishing HIV | Q&A: Melodic psychologist | Stamina therapies: time to call a halt | Stamina therapies: let the record stand | Fish have feelings too | Monkey brains wired to share | Fish-kill method questioned

More Biological Sciences ▶

RESEARCH

Articles and Letters

Epigenomic alterations define lethal CIMP-positive ependymomas of infancy ▶

S. C. Mack, H. Witt, R. M. Piro et al.

Although genetically bland, the posterior fossa group A subgroup of ependymomas, found often in infants and associated with poor prognosis, exhibit widespread epigenetic alterations, namely a CpG island methylator phenotype; these tumours are shown to be susceptible both in vitro and in vivo to various compounds that target epigenetic modifications, such as DNA methylation and H3K27 tri-methylation.

C11orf95–RELA fusions drive oncogenic NF-κB signalling in ependymoma ▶

Matthew Parker, Kumarasamypet M. Mohankumar, Chandanamali Punchihewa et al.

At least two-thirds of supratentorial ependymomas contain oncogenic fusions between RELA, the principal effector of nuclear factor-κB (NF-κB) signalling, and uncharacterized gene C11orf95; C11orf95–RELA fusion proteins translocate spontaneously to the nucleus to activate NF-κB target genes, and rapidly transform neural stem cells to form tumours in mice

News & Views

Tuberculosis: Drug discovery goes au naturel ▶

Clifton E. Barry

Cancer: Tumours outside the mutation box ▶

Rogier Versteeg

Cell biology: Stressful genetics in Crohn's disease ▶

Arthur Kaser, Richard S. Blumberg

Research Highlights

Vision: Molecule makes blind mice see light

NEWS & COMMENT

Vietnam on high alert over flu risk | Science in court: Disease detectives | Virology: Vanquishing HIV | Stamina therapies: time to call a halt | Stamina therapies: let the record stand | Fish-kill method questioned

More Health Sciences ▶

RESEARCH

Latest Online

The remnant of a merger between two dwarf galaxies in Andromeda II ▶

N. C. Amorisco, N. W. Evans, G. van de Ven

At the lowest galactic mass scales, evidence of a merger between two galaxies is provided by the kinematic detection of a stellar stream — indicative of an accretion event — in the dwarf spheroidal galaxy Andromeda II, one of the satellite galaxies of Andromeda.

Articles and Letters

A single low-energy, iron-poor supernova as the source of metals in the star SMSS J031300.36−670839.3 ▶

S. C. Keller, M. S. Bessell, A. Frebel et al.

The optical spectrum of the star SMSS J031300.36−670839.3 shows no evidence of iron; this, together with comparisons of the star’s observed element abundance pattern with those of models, means that SMSS J031300.36−670839.3 must have been seeded with material from a single supernova with an original mass about 60 times that of the Sun.

High-precision measurement of the atomic mass of the electron ▶

S. Sturm, F. Köhler, J. Zatorski et al.

A very precise measurement of the magnetic moment of a single electron bound to a carbon nucleus, combined with a state-of-the-art calculation in the framework of bound-state quantum electrodynamics, gives a new value of the atomic mass of the electron that is more precise than the currently accepted one by a factor of 13.

Quantum droplets of electrons and holes ▶

A. E. Almand-Hunter, H. Li, S. T. Cundiff et al.

Fast optical pulses create a plasma of electrons and holes in a semiconductor in which excitons (pairs of holes and electrons) and combinations of two excitons emerge; now a stable liquid-like droplet of electrons and holes has been detected and called a ‘dropleton’.

News & Views

Applied physics: Optical trapping for space mirrors ▶

David McGloin

50 & 100 Years Ago ▶

Fundamental constants: The teamwork of precision ▶

Edmund G. Myers

Erratum

Erratum: Asymmetric synthesis from terminal alkenes by cascades of diboration and cross-coupling ▶

Scott N. Mlynarski, Christopher H. Schuster, James P. Morken

Research Highlights

Materials: Muscles made from thread | Materials: Patterns make circuits stretchy

NEWS & COMMENT

Parallel lines | Crowd-sourcing: Strength in numbers | Earth science: Crystallography's journey to the deep Earth | Physics: Inside utter strangeness | Arts: Eclipse of power | Virgin territory | São Paulo poised to join megatelescope | Einstein’s lost theory uncovered | SOFIA irons out technical kinks

More Physical Sciences ▶

RESEARCH

Latest Online

Earth science: Missing link in mantle dynamics ▶

Greg Hirth

Disclinations provide the missing mechanism for deforming olivine-rich rocks in the mantle ▶

Patrick Cordier, Sylvie Demouchy, Benoît Beausir et al.

Using electron backscattering diffraction maps of deformed olivine to resolve the disclinations at grain boundaries, combined with a disclination-based model of a high-angle tilt boundary in olivine, reveals the missing mechanism for describing plastic flow in polycrystalline olivine: an applied shear induces grain-boundary migration through disclination motion.

Articles and Letters

A large source of low-volatility secondary organic aerosol ▶

Mikael Ehn, Joel A. Thornton, Einhard Kleist et al.

The link between biogenic volatile organic compounds in the atmosphere and their conversion to aerosol particles is unclear, but a direct reaction pathway is now described by which volatile organic compounds lead to low-volatility vapours that can then condense onto aerosol surfaces, producing secondary organic aerosol.

Rapid remobilization of magmatic crystals kept in cold storage ▶

Kari M. Cooper, Adam J. R. Kent

We lack thermal histories for magma reservoirs, but here the magma under Mount Hood (Oregon, USA) is shown to have been too cold to mobilize for most of the time it has been stored, which implies that magma mobilizes (at which point it can be imaged geophysically) very quickly prior to eruption.

News & Views

50 & 100 Years Ago ▶

Conservation: Wind blown ▶

Andrew Mitchinson

Atmospheric science: Involatile particles from rapid oxidation ▶

Gordon McFiggans

Research Highlights

Climate change: Permafrost grows thanks to plants | Geology: Plate tectonics got an early start

NEWS & COMMENT

Scientist-versus-activist debates mislead the public | Earth science: Crystallography's journey to the deep Earth

More Earth & Environmental Sciences ▶

Computer science: Hacking into the cyberworld ▶

Scientists are well placed to enter the growing, under-supplied cybersecurity workforce.

Minority support ▶

University consortium aims to boost diversity using NSF funds.

Canada needs managers ▶

Government grant will use fellowships to increase the number of research managers.

Race obstacle ▶

Race presents major barrier to advancement in the behavioural sciences, says study.

Careers related news & comment

Parallel lines | Seven days: 21–27 February 2014 | Crowd-sourcing: Strength in numbers Philip Ball | Physics: Inside utter strangeness David Seery | University budgets: Expand fundraising by Brazil's institutes Tiago Campos Pereira | Developing world: Global fund needed for STEM education Fanuel Muindi, Moytrayee Guha

Research Technician

King's College London 

Research Associate

Moffitt Cancer Center & Research Institute 

Research Fellow

The University of Nottingham 

PhD Position

Otto-Von-Guericke University Magdeburg 

A Celebration of Organic Chemistry 2014

22.09.14 Surrey, UK