Wednesday, November 30, 2016

Nature contents: 01 December 2016

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  journal cover  
Nature Volume 540 Issue 7631
This Week  
Academia must resist political confirmation bias
It is crucial to fight discrimination in all its forms, but it is unhelpful to exclude conservative voices from debate.
Post-publication criticism is crucial, but should be constructive
In an era of online discussion, debate must remain nuanced and courteous.
Researchers serve up suggestions to reduce food waste
A change in cultural and social factors — such as overcoming a distaste for doggy bags — will be required to shift people’s behaviour.
World View  
Post-truth: a guide for the perplexed
If politicians can lie without condemnation, what are scientists to do? Kathleen Higgins offers some explanation.
Seven Days  
Chernobyl's shield, dodo skeleton and HIV vaccines
The week in science: 25 November–1 December 2016.
Research Highlights  
Immunology: Macaque social status alters immunity | Catalysts: Silicon added to life's toolbox | Cancer: 'Jet lag' increases mouse cancer risk | Seismology: Gravity changes before quake hits | Climate change: Shifting niches spell trouble | Palaeontology: Ancient reptile had a diaphragm | Quantum physics: Record set for linked photons | Materials science: Atom-thick coats for copper | Materials: Sensor detects UV exposure | Epigenetics: Gut microbes shape DNA
News in Focus
Failed Alzheimer’s trial does not kill leading theory of disease
The drug, and others based on the ‘amyloid hypothesis’, are still being tested in other, different trials.
Alison Abbott, Elie Dolgin
  UK scientists excited by surprise £2-billion government windfall
Cash to include fund modelled on DARPA, the US defence department’s research arm — but how much will go to basic research is unclear.
Elizabeth Gibney
Experimental treatments aim to prevent brain damage in babies
Advances in neuroscience are driving the development of therapies that could save thousands of the most vulnerable patients.
Erika Check Hayden
  Speedy Antarctic drills start hunt for Earth’s oldest ice
British team is first to seek site of 1.5-million-year-old sample.
Quirin Schiermeier
Weaponized antibodies use new tricks to fight cancer
Next generation of Trojan-horse drugs designed to minimize damage to healthy cells.
Heidi Ledford
  Updated: NgAgo gene-editing controversy escalates in peer-reviewed papers
String of publications describes attempts — mostly unsuccessful — to use proposed CRISPR rival.
David Cyranoski
Can old computers bring Palestinians and Israelis together?
Some of the most toxic refuse from modern society ends up in poor communities. Researchers are helping one area in the Middle East clean up its electronic-waste problem.
Josie Glausiusz
Nature Podcast: 01 December 2016
This week, CRISPR’s rival stumbles, Pluto’s icy heart, and is mitochondrial replacement ready for the clinic?
Four routes to better maritime governance
Challenges in preventing pollution from ballast water highlight reforms needed in global shipping regulation, write Zheng Wan and colleagues.
Zheng Wan, Jihong Chen, Abdel El Makhloufi et al.
A new global research agenda for food
Lawrence Haddad, Corinna Hawkes and colleagues propose ten ways to shift the focus from feeding people to nourishing them.
Lawrence Haddad, Corinna Hawkes, Patrick Webb et al.
Fix food metrics
For sustainable, equitable nutrition we must count the true global costs and benefits of food production, urge Pavan Sukhdev, Peter May and Alexander Müller.
Pavan Sukhdev, Peter May, Alexander Müller
Books and Arts  
Book publishing: University presses adapt
Roger Schonfeld analyses how the sector's scientific books are faring in the digitized, open-access era.
Roger Schonfeld
Books in brief
Barbara Kiser reviews five of the week's best science picks.
Barbara Kiser
Phylogeny: 'Tree of life' took root 150 years ago
Uwe Hossfeld, Georgy S. Levit
  Conservation: smart advocacy needs data
Douglas J. McCauley, Francis H. Joyce, Jane Lubchenco
Conservation: big data boost in China
Ruidong Wu
  Conservation: thrive on slings and arrows
David Lindenmayer
Cities: factor in their biological impact
Alexandre Antonelli, Allison Perrigo
  Cities: new fringes to act as safety nets
Pranab Chatterjee, Manish Kakkar, Tamoghna Biswas
Trump: voters show importance of SDGs
David Griggs
  Trump: offset fracking risks
Madelon Finkel
Trump: polls right, models wrong
Brandon Steelman
Susan Lee Lindquist (1949–2016)
Biologist who found unexpected power in protein folding.
James Shorter, Aaron D. Gitler
Metabolomics: Small molecules, single cells
Sensitive mass spectrometry and innovative cell-sampling techniques allow researchers to profile metabolites in single cells, but the field is still in its infancy.
Marissa Fessenden
Stat-checking software stirs up psychology
Researchers debate whether using a program to automatically detect inconsistencies in papers improves the literature, or raises false alarms.
Monya Baker
Outlook: Multiple sclerosis  
Multiple sclerosis
Brian Owens
  Biology: A degenerative affliction
Charles Schmidt
Aetiology: Neighbourhood watch
Carolyn Brown
  Therapies: Progressive steps
Elie Dolgin
Perspective: Who dares, wins
Bibi Bielekova
  Stem cells: Stemming the tide
Asher Mullard
Diet: Changing the recipe
Sujata Gupta
Grant provider
Biomedicine: Replacing the cell's power plants
Nuclear DNA from human eggs that harbour mutations in the DNA of organelles called mitochondria has been successfully transferred to donor eggs, bringing the prospect of therapy for mitochondrial diseases a step closer.
Stem cells: Aspiring to naivety
Human stem cells that can give rise to every cell type in the body are major players in biomedical research. A molecular analysis of human embryos might help to make these cultured cells more authentic imitations of their in vivo counterparts.
Stem cells: Cause and consequence in aged-muscle decline
Activation of aged muscle stem cells induces changes in DNA packaging that lead to expression of the gene Hoxa9. This reactivates embryonic signalling pathways, restricting the cells' ability to repair injured muscle.
Biomedicine: An eye on retinal recovery
Retinal-cell transplants restore vision in mouse models of retinal degeneration. It emerges that the transplant leads to an exchange of material between donor and host cells — not to donor-cell integration into the retina, as had been presumed.
Safikhani et al. reply
Safeguarding pollinators and their values to human well-being
Wild and managed pollinators are threatened by pressures such as environmental changes and pesticides, leading to risks for pollinator-dependent crop production, meaning more research and better policies are needed to safeguard pollinators and their services.
m6A modulates neuronal functions and sex determination in Drosophila
One of the most abundant modifications found in messenger RNAs is N6-methyladenosine (m6A); here, this modification is shown to alter gene expression during sex determination and affect neuronal functions and behaviour in Drosophila via the m6A reader protein YT521-B.
Persistent microbiome alterations modulate the rate of post-dieting weight regain
Extensive degeneracy, Coulomb phase and magnetic monopoles in artificial square ice
All of the characteristics of the square-ice model are observed in an artificial square-ice system in which the two sublattices of nanomagnets are slightly vertically separated.
Capturing pairwise and multi-way chromosomal conformations using chromosomal walks
A conformation capture sequencing method is developed to link multiple genomic loci into three-dimensional proximity chains called chromosomal walks (C-walks), adding to our understanding of how higher-order chromosomal structures participate in genome regulation.
Intronic polyadenylation of PDGFRα in resident stem cells attenuates muscle fibrosis
Changes in intronic polyadenylation of the Pdgfra in fibro/adipogenic progenitors lead to increased expression of a shorter variant with a truncated kinase domain, which modulates pro-fibrotic pathways to reduce tissue fibrosis in muscle.
Land-use intensification causes multitrophic homogenization of grassland communities
Analysis of a large grassland biodiversity dataset shows that increases in local land-use intensity cause biotic homogenization at landscape scale across microbial, plant and animal groups, both above- and belowground, that is largely independent of changes in local diversity.
m6A potentiates Sxl alternative pre-mRNA splicing for robust Drosophila sex determination
Two complementary studies describe how the pervasive N 6-methyladenosine modification in mRNA can affect Drosophila sex determination, neuronal function and behaviour.
Mitochondrial replacement in human oocytes carrying pathogenic mitochondrial DNA mutations
Analysis of mitochondrial replacement therapy shows, even with efficient mutant mitochondrial DNA replacement and maintenance in embryonic stem cells, a gradual loss of donor mitochondrial DNA in some lines owing to a polymorphism in the D-loop, potentially causing preferential replication of specific mitochondrial DNA haplotypes.
Epigenetic stress responses induce muscle stem-cell ageing by Hoxa9 developmental signals
Changes in active chromatin marks in old activated satellite cells lead to Hoxa9 activation, which induces the expression of developmental pathway genes with a known inhibitory effect on satellite cell function and muscle regeneration in aged mice.
Designed proteins induce the formation of nanocage-containing extracellular vesicles
Autonomously produced hybrid biological nanomaterials termed ‘enveloped protein nanocages’ incorporate features for membrane binding, self-assembly, and ESCRT recruitment for cellular release.
Corrigendum: Lens regeneration using endogenous stem cells with gain of visual function
Brief Communications Arising  
Consistency in large pharmacogenomic studies
Paul Geeleher, Eric R. Gamazon, Cathal Seoighe et al.
Safikhani et al. reply
Zhaleh Safikhani, Nehme El-Hachem, Petr Smirnov et al.
Consistency in drug response profiling
John Patrick Mpindi, Bhagwan Yadav, Päivi Östling et al.
Safikhani et al. reply
Zhaleh Safikhani, Nehme El-Hachem, Petr Smirnov et al.
Drug response consistency in CCLE and CGP
Mehdi Bouhaddou, Matthew S. DiStefano, Eric A. Riesel et al.
Safikhani et al. reply
Zhaleh Safikhani, Nehme El-Hachem, Petr Smirnov et al.
News and Views  
Quantum computing: Efficient fault tolerance
Daniel Gottesman
Cell biology: Double agents for mitochondrial division
Heidi M. McBride, Adam Frost
Cell Biology: Sort of unexpected
Martin R. Pool
Astronomy: A black hole changes its feeding habits
Stephanie LaMassa
Biological rhythms: Wild times
C. Loren Buck
Planetary science: Pluto's telltale heart
Amy C. Barr
Biogeochemistry: Projections of the soil-carbon deficit
Eric A. Davidson
Stem cells and interspecies chimaeras
A comprehensive review into mammalian interspecies chimaeras, documenting the advances that have occurred alongside developments in stem-cell biology and assessing the future of the field, including any possible ethical and legal issues.
Jun Wu, Henry T. Greely, Rudolf Jaenisch et al.
Organization and functions of mGlu and GABAB receptor complexes
This Review discusses current knowledge of the structure, function and interactions of the metabotropic glutamate and GABAB receptors and the potential to target receptor subunits for future therapeutic intervention in neurological and mental health disorders.
Jean-Philippe Pin, Bernhard Bettler
Correcting mitochondrial fusion by manipulating mitofusin conformations
Specific intramolecular interactions of mitofusin 2 amino acid sequences either constrain or permit mitochondrial fusion and the addition of short peptides matching these sequences stabilize the fusion-constrained or fusion-permissive form, thus inhibiting or promoting mitochondrial fusion.
Antonietta Franco, Richard N. Kitsis, Julie A. Fleischer et al.
The genomic basis of circadian and circalunar timing adaptations in a midge OPEN
Genomic and molecular analyses of Clunio marinus timing strains suggest that modulation of alternative splicing of Ca2+/calmodulin-dependent kinase II represents a mechanism for evolutionary adaptation of circadian timing.
Tobias S. Kaiser, Birgit Poehn, David Szkiba et al.
The pathway to GTPase activation of elongation factor SelB on the ribosome
The structures of several states on the pathway of SelB-mediated delivery of selenocysteine-specific tRNA to the ribosome in Escherichia coli reveal the mechanism of UGA stop codon recoding to selenocysteine and show how codon recognition triggers activation of translational GTPases.
Niels Fischer, Piotr Neumann, Lars V. Bock et al.
Observed glacier and volatile distribution on Pluto from atmosphere–topography processes
Simulations of the levels of nitrogen, methane and carbon monoxide over thousands of years confirm the existence of a nitrogen glacier in Sputnik Planitia, Pluto’s deepest basin.
Tanguy Bertrand, François Forget
Reorientation and faulting of Pluto due to volatile loading within Sputnik Planitia
The location of Sputnik Planitia on Pluto is shown to result from volatiles sequestered within the basin forcing the reorientation of the dwarf planet, as supported by the planet-wide fault network.
James T. Keane, Isamu Matsuyama, Shunichi Kamata et al.
Reorientation of Sputnik Planitia implies a subsurface ocean on Pluto
To explain the position of the Sputnik Planitia basin on Pluto, the feature would need to have formed via impact and Pluto would need to have a subsurface ocean.
F. Nimmo, D. P. Hamilton, W. B. McKinnon et al.
Ghost imaging with atoms
Ghost imaging is demonstrated using beams of correlated pairs of ultracold helium atoms, rather than photons, yielding a reconstructed image with submillimetre resolution.
R. I. Khakimov, B. M. Henson, D. K. Shin et al.
Quantifying global soil carbon losses in response to warming
A compilation of global soil carbon data from field experiments provides empirical evidence that warming-induced net losses of soil carbon could accelerate climate change.
T. W. Crowther, K. E. O. Todd-Brown, C. W. Rowe et al.
Inhibition of mTOR induces a paused pluripotent state
Inhibition of mechanistic target of rapamycin (mTOR) suspends mouse blastocyst development and the cells remain ‘paused’ in a reversible pluripotent state, allowing prolonged culture.
Aydan Bulut-Karslioglu, Steffen Biechele, Hu Jin et al.
RIPK1 counteracts ZBP1-mediated necroptosis to inhibit inflammation
The enzyme RIPK1 functions through its RHIM domain to prevent ZBP1-mediated activation of RIPK3–MLKL-dependent necroptosis, thus preventing perinatal lethality and skin inflammation in adult mice.
Juan Lin, Snehlata Kumari, Chun Kim et al.
The SND proteins constitute an alternative targeting route to the endoplasmic reticulum
Experiments in yeast cells show that three proteins—Snd1, Snd2 and Snd3—provide an alternative pathway for targeting of cellular proteins to the endoplasmic reticulum.
Naama Aviram, Tslil Ast, Elizabeth A. Costa et al.
Multiple dynamin family members collaborate to drive mitochondrial division
The classical dynamin Dyn2 is required for mitochondrial division.
Jason E. Lee, Laura M. Westrate, Haoxi Wu et al.
RIPK1 inhibits ZBP1-driven necroptosis during development
In the absence of RIPK1, ZBP1 engages RIPK3 in a RHIM-dependent manner and acts as a critical activator of RIPK3/MLKL-dependent necroptosis.
Kim Newton, Katherine E. Wickliffe, Allie Maltzman et al.
The rapid formation of Sputnik Planitia early in Pluto’s history
Modelling suggests that the icy region on Pluto known as Sputnik Planitia formed shortly after Charon did and has since been stable, with its latitude corresponding to a minimum in annual solar illumination and its longitude determined by tidal forces from Charon.
Douglas P. Hamilton, S. A. Stern, J. M. Moore et al.
Unexpected diversity in socially synchronized rhythms of shorebirds
Socially synchronized rhythms in shorebirds were assessed during biparental incubation under natural circumstances and were exceptionally diverse, often not following the 24-h day, whereby risk of predation, not starvation, determined some of the variation in incubation rhythms.
Martin Bulla, Mihai Valcu, Adriaan M. Dokter et al.
Genomic evolution and chemoresistance in germ-cell tumours
Genomic analyses show that primary germ-cell tumours are highly enriched for chromosomal reciprocal loss of heterozygosity, mutations in KRAS and have high mitochondrial priming, providing insight into chemosensitivity and the evolution of chemoresistance in this disease.
Amaro Taylor-Weiner, Travis Zack, Elizabeth O’Donnell et al.
In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration
A method for CRISPR-based genome editing that harnesses cellular non-homologous end joining activity to achieve targeted DNA knock-in in non-dividing tissues.
Keiichiro Suzuki, Yuji Tsunekawa, Reyna Hernandez-Benitez et al.
Corrigendum: Design of a hyperstable 60-subunit protein icosahedron
Yang Hsia, Jacob B. Bale, Shane Gonen et al.
Corrigendum: Fumarate is an epigenetic modifier that elicits epithelial-to-mesenchymal transition
Marco Sciacovelli, Emanuel Gonçalves, Timothy Isaac Johnson et al.
Erratum: Pancreatic stellate cells support tumour metabolism through autophagic alanine secretion
Cristovão M. Sousa, Douglas E. Biancur, Xiaoxu Wang et al.
Erratum: Pore-forming activity and structural autoinhibition of the gasdermin family
Jingjin Ding, Kun Wang, Wang Liu et al. webcasts - watch the free webinar available on-demand:


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