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Nature contents: 16 November 2017

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  journal cover  
Nature Volume 551 Issue 7680
This Week  
Graduate students face alarming tax hike
Adding to PhD students’ woes will undermine US research and economy.
Chemists get faster on the draw
A Nature journals guide to drawing the structures of molecules should aid expert and casual chemists alike.
How China could make the most of its beamlines
More international collaboration could build capacity at big physics facilities especially in the south.

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How you can protect genetically engineered models against genetic drift — and catastrophic loss.

World View  
Immunization needs a technology boost
Tracking who receives vaccines is essential, but will be impossible without innovations in digital technologies, says Seth Berkley.
Seven Days  
New Delhi smog, death-sentence appeal and a porpoise setback
The week in science: 11–16 November 2017.
Research Highlights  
This issue's Research Highlights
Selections from the scientific literature.
News in Focus
Archaeologists say human-evolution study used stolen bone
Bizarre tale of theft and suspicious packages casts doubt on claims for early-human occupation in northern Europe.
Ewen Callaway
  Lab mice's ancestral ‘Eve’ gets her genome sequenced
Effort aims to help scientists understand how generations of inbreeding have altered the genetics of research rodents.
Sara Reardon
UK government appoints next chief scientific adviser
A former pharmaceutical boss will help navigate the UK’s exit from the European Union.
Elizabeth Gibney
  Puerto Rico struggles to assess hurricane’s health effects
While dealing with their own losses, public-health researchers are regrouping to study the aftermath of Hurricane Maria.
Sara Reardon
World’s carbon emissions set to spike by 2% in 2017
Increased coal use in China appears to be driving the first increase in global greenhouse-gas output since 2014.
Jeff Tollefson
  China fires up next-generation neutron-science facility
Beam generator puts country in elite company for doing experiments in materials science and other fields.
David Cyranoski
Biology’s beloved amphibian — the axolotl — is racing towards extinction
Although abundant in captivity, the salamander has nearly disappeared from its natural habitat, and that’s a problem.
Erik Vance
Nature Podcast: 16 November 2017
This week, a bacterial communication system, and ancient houses illuminate inequality.

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Ideas must be novel, bold and potentially transformative in order to warrant the creation of a long-term, interdisciplinary and collaborative research program. Proposals are welcome from all areas of research.

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Chemists can help to solve the air-pollution health crisis
Learning more about how pollutants enter and damage the body would reduce disease and deaths, say Jos Lelieveld and Ulrich Pöschl.
Jos Lelieveld, Ulrich Pöschl
Boycott products from states with dirty energy
Consumer pressure could encourage regions to switch from fossil fuels to cleaner sources of electricity, argues Christopher Kennedy.
Christopher Kennedy
Books and Arts  
Bioethics: Justice in genomics
Rosario Isasi examines a study on the societal impact of grand sequencing projects.
Rosario Isasi
Economics: How science got a golden ticket
Ehsan Masood hails an account of the mixed implications of governments valuing research as an investment.
Ehsan Masood
Computer science: Visionary of virtual reality
Aldo Faisal explores the immersive journey of technology pioneer Jaron Lanier.
Aldo Faisal
Preclinical research: Meet patients to sharpen up research
Mark Yarborough, Ulrich Dirnagl
  Research reports: An open market for scientific verbiage?
Kevin B. Marvel
Fires: degree courses for fire professionals
Victor Resco de Dios, Domingo Molina-Terrén
  Fires: fund research for citizen safety
Georgios Boustras, Enrico Ronchi, Guillermo Rein
International funding: Empower Africa’s electricity sector
Philipp Trotter, Sabah Abdullah
Need a paper? Get a plug-in
A collection of web-browser plug-ins is making the scholarly literature more discoverable.
Dalmeet Singh Chawla
Archaeology: Inequality has deep roots in Eurasia
A study of 64 archaeological sites across four continents shows that the growth of agricultural and political systems provoked economic disparities, more so in Eurasia than in North America.
Cancer immunotherapy: The dark side of PD-1 receptor inhibition
Inhibiting the protein PD-1 can activate T cells that trigger immune responses against tumour cells. But it emerges that, in mice, this immunotherapy exacerbates a cancer that involves the T cells themselves.
Microbiota: A high-pressure situation for bacteria
Analyses in mice suggest that dietary salt increases blood pressure partly by affecting some of the microbes that inhabit the gut. The implications of this work for hypertension warrant further study in humans.
Visualization of chemical modifications in the human 80S ribosome structure
A high-resolution structure of the human ribosome determined by cryo-electron microscopy visualizes numerous RNA modifications that are concentrated at functional sites with an extended shell, and suggests the possibility of designing more specific ribosome-targeting drugs.
A Jurassic gliding euharamiyidan mammal with an ear of five auditory bones
The fossil of a gliding mammal from the Jurassic period sheds light on both the evolution of gliding and the development of the middle ear, as it has a previously unseen five-ossicle auditory system.
Salt-responsive gut commensal modulates TH17 axis and disease
High salt intake changed the gut microbiome and increased TH17 cell numbers in mice, and reduced intestinal survival of Lactobacillus species, increased the number of TH17 cells and increased blood pressure in humans.
Solar abundance ratios of the iron-peak elements in the Perseus cluster
High-resolution X-ray spectra show near-solar abundances of chromium, manganese and nickel with respect to iron in the Perseus cluster, suggesting that the progenitors of type Ia supernovae could be near- and sub-Chandrasekhar-mass white dwarfs.
Quantitative microbiome profiling links gut community variation to microbial load
Quantitive microbiome profiling reveals that total microbial load is an important determinant of enterotypes and may be a key driver of microbiota alterations in patients with Crohn’s disease.
Structural basis of nucleotide sugar transport across the Golgi membrane
Crystal structures of the nucleotide sugar transporter Vrg4 are reported in both the substrate-free and the bound states.
Genome sequence of the progenitor of the wheat D genome Aegilops tauschii OPEN
A combination of advanced sequencing and mapping techniques is used to produce a reference genome of Aegilops tauschii, progenitor of the wheat D genome, providing a valuable resource for comparative genetic studies.
Greater post-Neolithic wealth disparities in Eurasia than in North America and Mesoamerica
Analyses of house-size distributions in the Old and New World showed that wealth disparities increased with the domestication of plants and animals and with increased sociopolitical scale.
PD-1 is a haploinsufficient suppressor of T cell lymphomagenesis
Loss of the PD-1 receptor promotes the development of T cell non-Hodgkin lymphomas by modulating oncogenic signalling pathways, and blocking these pathways reduces tumourigenesis.
IL11 is a crucial determinant of cardiovascular fibrosis
A non-canonical Notch complex regulates adherens junctions and vascular barrier function
Erratum: The neuropeptide NMU amplifies ILC2-driven allergic lung inflammation
Corrigendum: RNA m6A methylation regulates the ultraviolet-induced DNA damage response
News and Views  
Microbiology: Bacteria disarm host-defence proteins
John D. MacMicking
Planetary science: Haze cools Pluto's atmosphere
Robert A. West
50 & 100 Years Ago

A detailed look at structural variation in the human genome

Structural variant types, their contribution to disease & detection methods
Biogeochemistry: Ocean hotspots of nitrogen loss
Katja Fennel
Gene therapy: Transgenic stem cells replace skin
Mariaceleste Aragona, Cédric Blanpain
Geophysics: The buoyancy of Earth's deep mantle
Barbara Romanowicz
Ecology: The effect of conservation spending
Hugh P. Possingham, Leah R. Gerber
Influenza: A broadly protective antibody
Peter Palese
Progress in and promise of bacterial quorum sensing research
A Review of the genetics, biochemistry, ecology and evolution of bacterial quorum sensing.
Marvin Whiteley, Stephen P. Diggle, E. Peter Greenberg
Tidal tomography constrains Earth’s deep-mantle buoyancy
An estimate of Earth’s deep-mantle buoyancy is derived from GPS-based measurements of body tide deformation and shown to be dominated by dense material possibly related to subducted oceanic plates or primordial rock.
Harriet C. P. Lau, Jerry X. Mitrovica, James L. Davis et al.
Regeneration of the entire human epidermis using transgenic stem cells
Autologous transgenic epidermal stem cell cultures are used to reconstitute almost the entire epidermis of a patient with severe junctional epidermolysis bullosa.
Tobias Hirsch, Tobias Rothoeft, Norbert Teig et al.
A single-cell survey of the small intestinal epithelium
Profiling of 53,193 individual epithelial cells from the mouse small intestine identifies previously unknown cell subtypes and corresponding gene markers, providing insight into gut homeostasis and response to pathogens.
Adam L. Haber, Moshe Biton, Noga Rogel et al.
Dynamics of P-type ATPase transport revealed by single-molecule FRET
Single-molecule fluorescence resonance energy transfer is used to identify the rate-limiting step and new intermediates in the conformational cycle of the Listeria monocytogenes calcium transporter LMCA1.
Mateusz Dyla, Daniel S. Terry, Magnus Kjaergaard et al.
Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity
IgA+ B cells expressing programmed death ligand 1 (PD-L1) and interleukin 10 accumulate in the inflamed livers of humans and mice with non-alcoholic fatty liver disease where they promote the progression to hepatocellular carcinoma by limiting the local activation of PD-1-expressing CD8+ T cells.
Shabnam Shalapour, Xue-Jia Lin, Ingmar N. Bastian et al.
Haze heats Pluto’s atmosphere yet explains its cold temperature
Modelling results find that the temperature of Pluto’s atmosphere is regulated by haze particles rather than gas molecules, suggesting that Pluto should be brighter than previously thought at mid-infrared wavelengths.
Xi Zhang, Darrell F. Strobel, Hiroshi Imanaka
Granular materials flow like complex fluids
The relaxation dynamics of granular materials is more like that of complex fluids than that of thermal glass-forming systems, owing to the absence of the ‘cage effect’.
Binquan Kou, Yixin Cao, Jindong Li et al.
Reductions in global biodiversity loss predicted from conservation spending
Empirical two-part models describe the relationship between conservation spending, human development pressures and biodiversity loss and can inform sustainable development strategies by predicting the effects of financing decisions on future biodiversity losses.
Anthony Waldron, Daniel C. Miller, Dave Redding et al.
Parallel palaeogenomic transects reveal complex genetic history of early European farmers
In European Neolithic populations, the arrival of farmers prompted admixture with local hunter-gatherers over many centuries, resulting in distinct signatures in each region due to a complex series of interactions.
Mark Lipson, Anna Szécsényi-Nagy, Swapan Mallick et al.
Ubiquitination and degradation of GBPs by a Shigella effector to suppress host defence
A Shigella flexneri type III secretion system effector targets cellular proteins for degradation via the ubiquitin/proteasome pathway, suggesting that such effectors help to overcome defences against bacterial infection.
Peng Li, Wei Jiang, Qin Yu et al.
Collective emission of matter-wave jets from driven Bose–Einstein condensates
Sufficiently strong modulation of the interaction strength in a Bose–Einstein condensate induces inelastic atom–atom scattering and causes collective emission of matter-wave jets from the condensate.
Logan W. Clark, Anita Gaj, Lei Feng et al.
Locomotor speed control circuits in the caudal brainstem
In the mouse caudal brainstem, functionally distinct neuronal subpopulations, which are distinguishable by neurotransmitter identity, connectivity and location, regulate locomotion parameters.
Paolo Capelli, Chiara Pivetta, Maria Soledad Esposito et al.
BCAT1 restricts αKG levels in AML stem cells leading to IDHmut-like DNA hypermethylation
The mechanistic basis for the role of the metabolic enzyme BCAA transaminase 1 (BCAT1) in acute myeloid leukaemias.
Simon Raffel, Mattia Falcone, Niclas Kneisel et al.
A ubiquitin-dependent signalling axis specific for ALKBH-mediated DNA dealkylation repair
A signalling mechanism in human cells for sensing DNA damage induced by alkylation involves ubiquitin-dependent recruitment of the alkylation repair complex ASCC to the vicinity of the damage and co-localization with transcription and splicing factors.
Joshua R. Brickner, Jennifer M. Soll, Patrick M. Lombardi et al.
Structure and assembly of the Ebola virus nucleocapsid
Application of cryo-electron tomography and subtomogram averaging to determine the structure of the Ebola virus nucleocapsid within intact viruses and recombinant nucleocapsid-like assemblies.
William Wan, Larissa Kolesnikova, Mairi Clarke et al.
Corrigendum: Superparamagnetic enhancement of thermoelectric performance
Wenyu Zhao, Zhiyuan Liu, Zhigang Sun et al.
Corrigendum: High-throughput discovery of novel developmental phenotypes
Mary E. Dickinson, Ann M. Flenniken, Xiao Ji et al.
Erratum: Non-homeostatic body weight regulation through a brainstem-restricted receptor for GDF15
Jer-Yuan Hsu, Suzanne Crawley, Michael Chen et al.


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Survival stories: science endures
Virginia Gewin
Turning point: Gourmet investigator
Virginia Gewin
Those who favour fire
A final farewell.
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