Wednesday, June 8, 2016

Nature contents: 09 June 2016

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  journal cover  
Nature Volume 534 Issue 7606
 
This Week  
 
 
Editorials  
 
 
 
Humanity’s forgotten family
Hominin fossils discovered near the site of the ‘hobbit’ Homo floresiensis provide yet more evidence that the human lineage is more diverse than was ever imagined.
Energy hit
Germany’s decision to slow the expansion of green-energy production is a reasonable move.
Second chances
The line between compliance and misconduct is finer than you might think.
 
 
A*STAR Research - Highlighting the best of research at the Agency for Science, Technology and Research (A*STAR), Singapore's premier research organization 
 
Recent Highlights 
Biotechnology: A path away from reliance on oil | Genetics: The significance of forgetful fruit flies | Metabolomics: An effective way to explore data 
 
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World View  
 
 
 
Gene editing can drive science to openness
The fast-moving field of gene-drive research provides an opportunity to rewrite the rules of the science, says Kevin Esvelt.
 
Seven Days  
 
 
 
The week in science: 3–9 June 2016
Gravitational-wave observatory passes technology test; gunman kills engineering professor in California; and Egypt’s bullied students and professors get international recognition.
Research Highlights  
 
 
 
Glaciology: Early signs of ice retreat | Molecular biology: CRISPR tweaked to edit RNA | Geology: Magma pool under New Zealand | Ageing: Chemical extends worm lifespan | Astrophysics: Relativity passes black-hole test | Marine science: Plastic pollution hurts perch | Genomics: Ancient dog DNA shows dual origins | Evolution: Age robs monkeys of vocal control | Botany: How desert moss drinks from air | Infection: Bacterium could curb malaria
 
 

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News in Focus
 
Massive ocean-observing project launches — despite turmoil
Network of deep-water observatories streams data in real time.
Alexandra Witze
  Fairer way to distribute last-ditch drugs gets real-world trial
With drug companies’ policies hard to decipher, frustrated patients often resort to social-media campaigns and other public appeals.
Sara Reardon
Peru’s gold rush prompts public-health emergency
Gold-mining boom in southeastern Amazon is driving high levels of mercury contamination.
Barbara Fraser
  Plan to synthesize human genome triggers mixed response
Some admire project's ambition; others say that it hasn't justified its aims.
Ewen Callaway
UK government slammed for losing track of its own research
Government can't say how many policy studies it paid for or published, report reveals.
Daniel Cressey
  ‘Hobbit’ relatives found after ten-year hunt
Jaw and teeth discovered in Indonesia are triumph for team that almost gave up hope.
Ewen Callaway
Features  
 
 
 
Can Delhi save itself from its toxic air?
India’s capital city scrambles to tackle its epic pollution problems.
Meera Subramanian
The man who can map the chemicals all over your body
Pieter Dorrestein uses mass spectrometry to eavesdrop on the molecular conversations between microbes and their world.
Paul Tullis
Multimedia  
 
 
Nature Podcast: 09 June 2016
This week, researcher rehab, the hobbit’s ancestry, and Google’s quantum plans.
Correction  
 
 
Correction
Correction
 
 
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Comment
 
Misconduct: Lessons from researcher rehab
Common compliance situations can get good researchers into trouble, warn James M. DuBois and colleagues.
James M. DuBois, John T. Chibnall, Raymond Tait et al.
Books and Arts  
 
 
 
Cancer therapy: Defining stemness
Hans Clevers admires an analysis of stem-cell science that sharpens up some of the fuzziness in the field.
Hans Clevers
Books in brief
Barbara Kiser reviews five of the week's best science picks.
Barbara Kiser
Military science: Among the warriors
Sharon Weinberger finds much to amuse and disturb in Mary Roach's tour of conflict's wilder shores.
Sharon Weinberger
Correspondence  
 
 
 
Elephant poaching: Track the impact of Kenya's ivory burn
Duan Biggs
  China's primates: EU can't have it all ways
Penny Hawkins, Paul Littlefair
China's primates: preserve wild species
Alison M. Behie, Colin P. Groves
  Five-Year Plan: Supervise Chinese environment policy
Bo Zhang
Butterflies: Change of identity is not in the air
Josef Settele
 
Obituary  
 
 
 
Ilkka Hanski (1953–2016)
Population ecologist who modelled how species cope with habitat loss.
Anna-Liisa Laine
 
 
Research
 
NEW ONLINE  
 
 
 
Cell reprogramming: Brain versus brawn
The mechanisms that underlie enforced transitions between mature cell lineages are poorly understood. Profiling single skin cells that are induced to become neurons reveals that, unexpectedly, they often become muscle.
Genomics: The language of flowers
The complete DNA sequences of the two wild parents of the garden petunia provide valuable genetic insights into this model plant, and will improve the optimization of other crop plants for agriculture.
Selective spider toxins reveal a role for the Nav1.1 channel in mechanical pain
Two spider toxins are shown to target the Nav1.1 subtype of sodium channel specifically, shedding light on the role of these channels in mechanical pain signalling.
Dual targeting of p53 and c-MYC selectively eliminates leukaemic stem cells
Leukaemic stem cells (LSCs) are responsible for BCR–ABL-driven chronic myeloid leukaemia relapse; here, p53 and MYC signalling networks are shown to regulate LSCs concurrently, and targeting both these pathways has a synergistic effect in managing the disease.
Pore-forming activity and structural autoinhibition of the gasdermin family
The N-terminal domains of gasdermin proteins cause pyroptotic cell death by oligomerizing to form membrane pores.
Solid-state harmonics beyond the atomic limit
A direct comparison of high harmonic generation in the solid and gas phases of Ar and Kr reveals higher harmonics in these rare-gas solids caused by strong interband couplings; evidence of recollisions implies that gas-phase techniques for attosecond pulse generation and orbital tomography could be adapted for solids.
Synthetic Landau levels for photons
It is an long-standing goal to produce a photonic quantum Hall effect, analogous to the well-known quantum Hall effect for electrons; now an artificial magnetic field for a continuum of photons has been produced, making it possible to observe photonic Landau levels in a photonic quantum Hall material.
Self-assembly of microcapsules via colloidal bond hybridization and anisotropy
The self-assembly of colloidal particles into hollow micrometre-scale capsules is achieved through the combination of anisotropic particle morphology, deformable surface ligands that re-distribute on binding and the mutual attraction between particles, suggesting a design strategy for colloidal self-assembly
The bacterial DnaA-trio replication origin element specifies single-stranded DNA initiator binding
The bacterial chromosome replication origin contains an indispensable element composed of a repeating trinucleotide motif, termed the DnaA-trio, that stabilizes DnaA binding on single-stranded DNA.
Controlled fragmentation of multimaterial fibres and films via polymer cold-drawing
Cold-drawing of multimaterial fibres consisting of a brittle core embedded in a ductile polymer cladding results in controllable fragmentation of the core to produce uniformly sized rods parallel to the drawing direction for cylindrical geometries and narrow, parallel strips perpendicular to the drawing direction for flat geometries.
Image-based detection and targeting of therapy resistance in pancreatic adenocarcinoma
The stem cell determinant Musashi (Msi) is a key mediator of pancreatic cancer progression and therapy resistance.
Co-repressor CBFA2T2 regulates pluripotency and germline development
A co-repressor protein, CBFA2T2, oligomerizes to stabilize its binding partner PRDM14 and the pluripotency factor OCT4 on chromatin, thus facilitating the transcriptional landscape underpinning the germline and pluripotent fate.
Towards clinical application of pronuclear transfer to prevent mitochondrial DNA disease
Preclinical evaluation and optimization of mitochondrial replacement therapy reveals that a modified form of pronuclear transfer is likely to give rise to normal pregnancies with a reduced risk of mitochondrial DNA disease, but may need further modification to eradicate the disease in all cases.
Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq
The transcriptome changes driving the conversion of fibroblasts to neurons at the single-cell level are reported, revealing that early neuronal reprogramming steps are homogenous, driven by the proneural pioneer factor Ascl1; the expression of myogenic genes then has a dampening effect on efficiency, which needs to be counteracted by the neuronal factors Myt1l and Brn2 for more efficient reprogramming.
News and Views  
 
 
 
Host-microbe interaction: Rules of the game for microbiota
Karoline Faust, Jeroen Raes
Geochemistry: Hydrogen and oxygen in the deep Earth
Takehiko Yagi
Evolutionary biology: To mimicry and back again
David W. Pfennig
 
Nature Outlook: Research commercialization

Universities need to deliver more value for research outlay. Companies are facing competition in the search for the next business-sustaining product. These sectors have their own objectives, but are locked in a synergistic embrace that is fuelling a push to extract commercial value from academic research.

Available free online
Physiology: Microbial signals to the brain control weight
Mirko Trajkovski, Claes B. Wollheim
 
Chemistry: No turning back for motorized molecules
Jonathan Clayden
Palaeoanthropology: The dawn of Homo floresiensis
Aida Gómez-Robles
 
Perspectives  
 
 
 
Accounting for reciprocal host–microbiome interactions in experimental science
This work highlights the critical challenges in experimental design and interpretation due to important combinatorial effects of host and microbial genes, and calls for the development of minimal reporting requirements to improve the interpretation and reproducibility of experimental biology.
Thaddeus S. Stappenbeck, Herbert W. Virgin
Articles  
 
 
 
Midbrain circuits for defensive behaviour
A combination of optogenetic, electrophysiological and neuroanatomical tracing methods defines midbrain periaqueductal grey circuits for specific defensive behaviours.
Philip Tovote, Maria Soledad Esposito, Paolo Botta et al.
The genetic history of Ice Age Europe
Analysis of ancient genomic data of 51 humans from Eurasia dating from 45,000 to 7,000 years ago provides insight into the population history of pre-Neolithic Europe and support for recurring migration and population turnover in Europe during this period.
Qiaomei Fu, Cosimo Posth, Mateja Hajdinjak et al.
Acetate mediates a microbiome–brain–β-cell axis to promote metabolic syndrome
Increased acetate production by an altered gut microbiota in rats fed a high-fat diet activates the parasympathetic nervous system, which in turn promotes increased insulin secretion, increased food intake, obesity and related changes.
Rachel J. Perry, Liang Peng, Natasha A. Barry et al.
Letters  
 
 
 
Digitized adiabatic quantum computing with a superconducting circuit
A digitized approach to adiabatic quantum computing, combining the generality of the adiabatic algorithm with the universality of the digital method, is implemented using a superconducting circuit to find the ground states of arbitrary Hamiltonians.
R. Barends, A. Shabani, L. Lamata et al.
Overcoming mTOR resistance mutations with a new-generation mTOR inhibitor
Inhibitors of the mTOR kinase are in clinical trials for the treatment of cancer; here, mutations in mTOR that can lead to drug resistance are investigated and the results are used to design a new class of mTOR inhibitors that can overcome this resistance.
Vanessa S. Rodrik-Outmezguine, Masanori Okaniwa, Zhan Yao et al.
Development of the gut microbiota and mucosal IgA responses in twins and gnotobiotic mice
The relationship between assembly of the gut community and gut mucosal immunoglobulin A responses during the first 24–36 months of postnatal life in a cohort of 40 twin pairs is defined and modelled in gnotobiotic mice.
Joseph D. Planer, Yangqing Peng, Andrew L. Kau et al.
FeO2 and FeOOH under deep lower-mantle conditions and Earth’s oxygen–hydrogen cycles
First-principles calculations and experiments are used to identify a stable, pyrite-structured iron oxide at 76 gigapascals and 1,800 kelvin that holds an excessive amount of oxygen and to show that goethite (rust) decomposes under these deep lower-mantle conditions to form an iron oxide and release hydrogen; this process provides another way to interpret the origin of seismic and geochemical anomalies in the deep lower mantle of Earth.
Qingyang Hu, Duck Young Kim, Wenge Yang et al.
Homofloresiensis-like fossils from the early Middle Pleistocene of Flores
Remains of what appears to be Homo floresiensis have now been found at another site in Flores in Indonesia; these 700,000-year-old fossils are older and slightly smaller than the first fossils identified as Homo floresiensis.
Gerrit D. van den Bergh, Yousuke Kaifu, Iwan Kurniawan et al.
The Brazilian Zika virus strain causes birth defects in experimental models
The Zika virus can cross the placenta and cause intrauterine growth restriction, including microcephaly, in the SJL strain of mice; the virus can also infect human brain organoids, inducing cell death by apoptosis and disrupting cortical layers.
Fernanda R. Cugola, Isabella R. Fernandes, Fabiele B. Russo et al.
Cold, clumpy accretion onto an active supermassive black hole
The so-called accretion flow that powers the growth of supermassive black holes in galaxy centres is assumed to be dominated by a smooth, steady flow of very hot plasma, but now observations instead reveal a clumpy accretion of very cold molecular clouds onto a supermassive black hole in the nucleus of a nearby giant elliptical galaxy.
Grant R. Tremblay, J. B. Raymond Oonk, Françoise Combes et al.
Metastable high-entropy dual-phase alloys overcome the strength–ductility trade-off
An alloy design strategy that aims for phase metastability, rather than phase stability, is described that will lead to the development of transformation-induced plasticity-assisted, dual-phase high-entropy alloys, which exhibit a rare combined increase in strength and ductility.
Zhiming Li, Konda Gokuldoss Pradeep, Yun Deng et al.
Strongly correlated perovskite fuel cells
A fundamentally different approach to designing solid oxide electrolytes is presented, using a phase transition to suppress electronic conduction in a correlated perovskite nickelate; this yields ionic conductivity comparable to the best-performing solid electrolytes in the same temperature range.
You Zhou, Xiaofei Guan, Hua Zhou et al.
An autonomous chemically fuelled small-molecule motor
A system is described in which a small macrocycle is continuously transported directionally around a cyclic molecular track when powered by irreversible reactions of a chemical fuel; such autonomous chemically fuelled molecular motors should find application as engines in molecular nanotechnology.
Miriam R. Wilson, Jordi Solà, Armando Carlone et al.
Age and context of the oldest known hominin fossils from Flores
Stratigraphic, chronological, environmental and faunal context are provided to the newly discovered fossils of hominins that lived in the So’a Basin in Flores, Indonesia, 700,000 years ago; the stone tools recovered with the fossils are similar to those associated with the much younger Homo floresiensis from Flores, discovered in Liang Bua to the west.
Adam Brumm, Gerrit D. van den Bergh, Michael Storey et al.
Environmental Breviatea harbour mutualistic Arcobacter epibionts
The cultivation of Lenisia limosa, a newly discovered breviate protist, symbiotically colonized by relatives of the animal-associated bacterium Arcobacter.
Emmo Hamann, Harald Gruber-Vodicka, Manuel Kleiner et al.
Universality of human microbial dynamics
A new computational method to characterize the dynamics of human-associated microbial communities is applied to data from two large-scale metagenomic studies, and suggests that gut and mouth microbiomes of healthy individuals are subjected to universal (that is, host-independent) dynamics, whereas skin microbiomes are shaped by the host environment; the method paves the way to designing general microbiome-based therapies.
Amir Bashan, Travis E. Gibson, Jonathan Friedman et al.
Ribosome-dependent activation of stringent control
The structure of a bacterial ribosome–RelA complex reveals that RelA, a protein recruited to the ribosome in the case of scarce amino acids, binds in a different location to translation factors, and that this binding event suppresses auto-inhibition to activate synthesis of the (p)ppGpp secondary messenger, thus initiating stringent control.
Alan Brown, Israel S. Fernández, Yuliya Gordiyenko et al.
Charge-density analysis of an iron–sulfur protein at an ultra-high resolution of 0.48 Å
The ultra-high-resolution structure of the high-potential iron–sulfur protein at 0.48 Å, the highest-resolution X-ray crystal structure of a protein reported so far.
Yu Hirano, Kazuki Takeda, Kunio Miki
 
 

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Careers & Jobs
 
Feature  
 
 
 
Science illustration: Picture perfect
Jyoti Madhusoodanan
Q&AS  
 
 
 
Trade talk: College 'mayor'
Monya Baker
Correction
Futures  
 
 
The Memory Ward
Forgive and forget?
Wendy Nikel
 
 
 
 
 

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