Thursday, August 2, 2018

Nature contents: 02 August 2018

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  journal cover  
Nature Volume 560 Issue 7716
This Week  
How lizards got their big feet
Pinning extreme weather on climate change is now routine and reliable science
World View  
Wildfire science is at a loss for comprehensive data
David Bowman
Research Highlights  
This issue's Research Highlights
Selections from the scientific literature.
Seven Days  
Volcano threat, Parkinson’s trial and harassment lawsuits
News in Focus
There’s water on Mars! Signs of buried lake tantalize scientists
Alexandra Witze
Chinese vaccine scandal unlikely to dent childhood immunization rates
Nicky Phillips
CRISPR plants now subject to tough GM laws in European Union
Ewen Callaway
Milky Way’s black hole provides long-sought test of Einstein’s general relativity
Alexandra Witze
Push to weaken US Endangered Species Act runs into roadblocks
Jeremy Rehm
Droughts, heatwaves and floods: How to tell when climate change is to blame
Quirin Schiermeier
Nature Podcast 02 August 2018
This week, how a bird sees colour, modifying Mars, and linking extreme weather to our changing climate.
Set road charges in real time to ease traffic
Peter Cramton, R. Richard Geddes, Axel Ockenfels
Books and Arts  
The band of biologists who redrew the tree of life
John Archibald
Ebola from the front lines, US aviation’s female high-fliers, and a history of science journals: Books in brief
Barbara Kiser
Ideal witness: a physicist takes on the world
Robert P. Crease
Make research-paper databases multilingual
Daniel Prieto
Resist calls for replicability in the humanities
Sarah de Rijcke, Bart Penders
Solar power brings money to rural areas
Yang Zhou, Yansui Liu
Colombia’s rural development must honour peace agreement
Luca Eufemia, Michelle Bonatti, Marcos A. Lana
Rectify biased interpretation of science history
Aiza Kabeer, Jessica W. Tsai
Why it is not a ‘failure’ to leave academia
Philipp Kruger
The tail of Danny Whiskers
It's not easy being smart.
Fawaz Al-Matrouk
Birds perceive colours in categories
Humans perceive colours in categories such as red, even though we can discern red hues including ruby and crimson. It emerges that birds also categorize colours and this affects their colour-discrimination ability.
Almut Kelber
Creating a functional single-chromosome yeast
Successive fusion of yeast chromosomes is used to produce a single-chromosome strain that is viable, albeit with slightly reduced fitness.
Yangyang Shao, Ning Lu, Zhenfang Wu et al.
Structure and function of the global topsoil microbiome
Metagenomic, chemical and biomass analyses of topsoil samples from around the world reveal spatial and environmental trends in microbial community composition and genetic diversity.
Mohammad Bahram, Falk Hildebrand, Sofia K. Forslund et al.
A revised airway epithelial hierarchy includes CFTR-expressing ionocytes
Single-cell RNA sequencing analysis identifies cell types and lineages in airway epithelium, including the pulmonary ionocyte, a new cell type predominantly expressing the cystic fibrosis gene CFTR.
Daniel T. Montoro, Adam L. Haber, Moshe Biton et al.
Human glioblastoma arises from subventricular zone cells with low-level driver mutations
Human neural stem cells from the subventricular zone are identified as the cells of origin that contain the driver mutations for glioblastomas.
Joo Ho Lee, Jeong Eun Lee, Jee Ye Kahng et al.
Extensive loss of past permafrost carbon but a net accumulation into present-day soils
Comparing the northern permafrost region of the Last Glacial Maximum with the same area today shows that the soil carbon stock has now increased, suggesting that permafrost carbon made no net contribution to preindustrial atmospheric carbon.
Amelie Lindgren, Gustaf Hugelius, Peter Kuhry
Categorical perception of colour signals in a songbird
Female zebra finches exhibited categorical perception of colour signals, as they categorized colour stimuli that varied along a continuous scale and showed increased discrimination between colours from opposite sides of the category boundary compared to equally different colours from within a category.
Eleanor M. Caves, Patrick A. Green, Matthew N. Zipple et al.
Inositol phosphates are assembly co-factors for HIV-1
Inositol hexakisphosphate, which is found in all mammalian cells, binds to two separate sites to promote the assembly and maturation of HIV-1 virus particles.
Robert A. Dick, Kaneil K. Zadrozny, Chaoyi Xu et al.
CRISPR-guided DNA polymerases enable diversification of all nucleotides in a tunable window
A system that targets DNA polymerase activity with CRISPR-guided nickases to provide genetic diversification at user-defined loci enables forward genetic approaches.
Shakked O. Halperin, Connor J. Tou, Eric B. Wong et al.
Inhibitors of histone acetyltransferases KAT6A/B induce senescence and arrest tumour growth
Selective inhibitors of KAT6A and KAT6B inhibit MYST-catalysed histone acetylation, induce cell cycle exit and cellular senescence without causing DNA damage, and arrest lymphoma progression in mouse models.
Jonathan B. Baell, David J. Leaver, Stefan J. Hermans et al.
Karyotype engineering by chromosome fusion leads to reproductive isolation in yeast
Yeast chromosomes have been fused to produce viable strains with only two chromosomes that are reproductively isolated from the sixteen-chromosome wild type, but otherwise show high fitness in mitosis and meiosis.
Jingchuan Luo, Xiaoji Sun, Brendan P. Cormack et al.
A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte
Single-cell RNA sequencing analysis is used to identify cell types in the tracheal epithelium, including previously unidentified ionocytes, which express high levels of the cystic fibrosis transmembrane conductance regulator, CFTR.
Lindsey W. Plasschaert, Rapolas Žilionis, Rayman Choo-Wing et al.
Yeast chromosome numbers minimized using genome editing
Genome-editing approaches have been used to fuse 16 yeast chromosomes to produce yeast strains with only 1 or 2 chromosomes. Surprisingly, this fusion has little effect on cell fitness.
Gianni Liti
Cryo-EM of the dynamin polymer assembled on lipid membrane
A cryo-electron microscopy structure of human dynamin-1 demonstrates conformational changes and sheds light on the fission of membranes during endocytosis.
Leopold Kong, Kem A. Sochacki, Huaibin Wang et al.
Profile of an unknown airway cell
RNA sequencing of single cells in the mammalian trachea reveals a previously unknown airway cell that expresses genes involved in fluid and solute balance, and that might play a part in cystic fibrosis.
Kyle J. Travaglini, Mark A. Krasnow
Shared evolutionary origin of vertebrate neural crest and cranial placodes
Similarities between the patterning of the lateral plate in Ciona and of the neural plate ectoderm in vertebrates indicate that compartmentalization of the lateral plate ectoderm preceded the advent of vertebrates.
Ryoko Horie, Alex Hazbun, Kai Chen et al.
Stable and switchable electric polarization in two dimensions
The electric polarization of materials called ferroelectrics is often suppressed by an internal electric field, limiting uses for these materials. The discovery of a thin-film ferroelectric that is resistant to this field represents a major advance.
Turan Birol
Building C(sp3)-rich complexity by combining cycloaddition and C–C cross-coupling reactions
Combining cycloaddition and carbon–carbon cross-coupling offers a way of simplifying the enantioselective preparation of chemical building blocks, natural products and medicines such as the antipsychotic asenapine.
Tie–Gen Chen, Lisa M. Barton, Yutong Lin et al.
News & Views  
Hyperactive soil microbes might weaken the terrestrial carbon sink
Kiona Ogle
Peptide secretion triggers diabetes
Jiajie Wei, Jonathan W. Yewdell
The origin of blue diamonds
Andrew Mitchinson

Cell Culture Media Analysis Platform
A fully automated and integrated sample preparation workstation, the C2MAP system measures changes of 95 components in a culture supernatant as culturing progresses using LC-MS/MS to improve antibody production and accelerate process optimization.
Learn more
Leukaemia follows a blood-vessel track to enter the nervous system
Frank Winkler
Reflection forbidden and refraction reversed in an artificial crystal
Baile Zhang
From the archive
An unexpected trigger for calorie burning in brown fat
Sheng Hui, Joshua D. Rabinowitz
Developing neurons are innately inclined to learn on the job
Christian Mayer, Gord Fishell
Machine learning at the energy and intensity frontiers of particle physics
The application and development of machine-learning methods used in experiments at the frontiers of particle physics (such as the Large Hadron Collider) are reviewed, including recent advances based on deep learning.
Alexander Radovic, Mike Williams, David Rousseau et al.
Genome-centric view of carbon processing in thawing permafrost
Analysis of more than 1,500 microbial genomes sheds light on the processing of carbon released as permafrost thaws.
Ben J. Woodcroft, Caitlin M. Singleton, Joel A. Boyd et al.
Leukaemia hijacks a neural mechanism to invade the central nervous system
Expression of α6 integrin enables acute lymphoblastic leukaemia cells to use neural migratory pathways to invade the central nervous system and metastasize to the brain.
Hisayuki Yao, Trevor T. Price, Gaia Cantelli et al.
Topological negative refraction of surface acoustic waves in a Weyl phononic crystal
Sound waves in a specially designed crystal undergo ‘topologically protected’ negative refraction, whereby no reflection is allowed, at certain facets of the crystal and positive refraction at others.
Hailong He, Chunyin Qiu, Liping Ye et al.
Photoswitching topology in polymer networks with metal–organic cages as crosslinks
Using topology-switching metal–ligand cages to crosslink polymer networks produces gels whose chemical and mechanical properties can be radically and reversibly switched on irradiation.
Yuwei Gu, Eric A. Alt, Heng Wang et al.
Direct arylation of strong aliphatic C–H bonds
Direct coupling of aliphatic C–H nucleophiles to aryl electrophiles is described, through the combination of light-driven polyoxometalate hydrogen atom transfer and nickel catalysis.
Ian B. Perry, Thomas F. Brewer, Patrick J. Sarver et al.
A two-million-year-long hydroclimatic context for hominin evolution in southeastern Africa
A multiple-proxy reconstruction for the catchment of the Limpopo River and of sea surface temperatures in the Indian Ocean provides evidence for hydroclimatic changes that may have been important in hominin evolution.
Thibaut Caley, Thomas Extier, James A. Collins et al.
Globally rising soil heterotrophic respiration over recent decades
Global soil respiration is rising, probably in response to environmental changes, suggesting that climate-driven losses of soil carbon are occurring worldwide.
Ben Bond-Lamberty, Vanessa L. Bailey, Min Chen et al.
Blue boron-bearing diamonds from Earth’s lower mantle
Mineral inclusions in blue boron-bearing diamonds reveal that such diamonds are among the deepest diamonds ever found and indicate a viable pathway for the deep-mantle recycling of crustal elements.
Evan M. Smith, Steven B. Shirey, Stephen H. Richardson et al.
Hurricane-induced selection on the morphology of an island lizard
Two populations of Anolis lizards that survived Hurricanes Irma and Maria had larger toepads, longer forelimbs and shorter hindlimbs relative to the pre-hurricane populations, which suggests hurricane-induced natural selection.
Colin M. Donihue, Anthony Herrel, Anne-Claire Fabre et al.
Ecosystem restructuring along the Great Barrier Reef following mass coral bleaching
Fish and invertebrate communities transformed across the span of the Great Barrier Reef following the 2016 bleaching event due to a decline in coral-feeding fishes resulting from coral loss, and because of different regional responses of key trophic groups to the direct effect of temperature.
Rick D. Stuart-Smith, Christopher J. Brown, Daniela M. Ceccarelli et al.
Differential tuning of excitation and inhibition shapes direction selectivity in ferret visual cortex
Inhibition to the null direction of motion has a critical role in the direction selectivity of neurons in ferret primary visual cortex.
Daniel E. Wilson, Benjamin Scholl, David Fitzpatrick
Accumulation of succinate controls activation of adipose tissue thermogenesis
A comparative metabolomics approach is used to identify succinate as a key activator of thermogenesis in brown adipose tissue.
Evanna L. Mills, Kerry A. Pierce, Mark P. Jedrychowski et al.
Pancreatic islets communicate with lymphoid tissues via exocytosis of insulin peptides
A sensitive T cell tracking assay reveals immunogenic activity of specific catabolized peptide fragments of insulin and their effects on T cell activity in lymph nodes, highlighting communication between pancreatic islets and lymphoid tissue.
Xiaoxiao Wan, Bernd H. Zinselmeyer, Pavel N. Zakharov et al.
53BP1–RIF1–shieldin counteracts DSB resection through CST- and Polα-dependent fill-in
53BP1 and shieldin recruit the CTC1–STN1–TEN1 complex and polymerase-α to sites of DNA damage to help control the repair of double-strand breaks.
Zachary Mirman, Francisca Lottersberger, Hiroyuki Takai et al.
The shieldin complex mediates 53BP1-dependent DNA repair
The 53BP1 effector complex shieldin is involved in non-homologous end-joining and immunoglobulin class switching, and acts to protect DNA ends to facilitate the repair of DNA by 53BP1.
Sylvie M. Noordermeer, Salomé Adam, Dheva Setiaputra et al.
53BP1 cooperation with the REV7–shieldin complex underpins DNA structure-specific NHEJ
The specificity of 53BP1 and its co-factors for particular DNA substrates during non-homologous end joining (NHEJ) derives from REV7–shieldin, a four-subunit DNA-binding complex that is required for REV7-dependent NHEJ but not for REV7-dependent DNA interstrand cross-link repair.
Hind Ghezraoui, Catarina Oliveira, Jordan R. Becker et al.
Structures of human Patched and its complex with native palmitoylated sonic hedgehog
High-resolution structures of the human plasma membrane protein patched 1 alone and in complex with the native form of the ligand sonic hedgehog are determined.
Xiaofeng Qi, Philip Schmiege, Elias Coutavas et al.
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Amendments & Corrections
Author Correction: Crowther et al. reply
T. W. Crowther, M. B. Machmuller, J. C. Carey et al.
Author Correction: Inflammatory memory sensitizes skin epithelial stem cells to tissue damage
Shruti Naik, Samantha B. Larsen, Nicholas C. Gomez et al.
Author Correction: A molecular atlas of cell types and zonation in the brain vasculature
Michael Vanlandewijck, Liqun He, Maarja Andaloussi Mäe et al.
Publisher Correction: Integrating photonics with silicon nanoelectronics for the next generation of systems on a chip
Amir H. Atabaki, Sajjad Moazeni, Fabio Pavanello et al.
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