Thursday, November 29, 2018

Nature contents: 29 November 2018

  journal cover  
Nature Volume 563 Issue 7733
This Week  
Beware the rise of the radical right
How some wind turbines hog the breeze
Ban bullying in science
World View  
First law of leadership: be human first, scientist second
Alison Antes
Research Highlights  
This issue's Research Highlights
Selections from the scientific literature.
Seven Days  
Chinese mega 'LHC', Scotland's research and Plan S consultation

It's Time for Precision Genomics

Current bulk NGS methods are inadequate to fully characterize cancer. Targeted single-cell DNA analysis resolves genetic heterogeneity, which has critical implications in understanding tumor evolution and the acquisition of therapeutic resistance. Read our spotlight and learn how you can use Tapestri to move precision medicine forward.

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News in Focus
Genome-edited baby claim provokes international outcry
David Cyranoski, Heidi Ledford
'Marsquake' hunter prepares to land on the red planet
Alexandra Witze
AI peer reviewers unleashed to ease publishing grind
Douglas Heaven
Can a major AI conference shed its reputation for hosting sexist behaviour?
Holly Else
Frustrated Alzheimer's researchers seek better lab mice
Sara Reardon
First sun-dimming experiment will test a way to cool Earth
Jeff Tollefson
Does science have a bullying problem?
Holly Else
Podcast: Atomic clock accuracy and wind farm worries
This week, measuring gravity's strength with clocks, and worries over wind farms' wakes.
Statistical pitfalls of personalized medicine
Stephen Senn
A 100th birthday wish: uphold academic freedom in dark times
Ehsan Masood
Books and Arts  
The secret laws of success and status
Mark Buchanan
Loop quantum gravity redux, ancient automatons, and the weirdness of tropical flora: Books in brief
Barbara Kiser
Heat and soil vie for waste to cut emissions
Karen L. Johnson, Steven A. Banwart, Caroline L. Peacock et al.
Fear holds back gene-edited crops — educate the public
Walter P. Suza, Alexander W. Kena, Richard Akromah et al.
Rat and bat hunt helped heal rift from colonial cruelty
Tyrone Lavery, Esau Kekeubata, Tommy Esau et al.
Industry is more alarmed about reproducibility than academia
Anton Bespalov, Adrian G. Barnett, C. Glenn Begley
Osamu Shimomura (1928–2018)
Georgina Ferry
Juggling research and family life: honest reflections from scientist dads
David Payne
So, one of those tiny alien spaceships has flown into your house. Now what?

Laura Pearlman
Location matters for insulin-producing cells
Intrinsic and extrinsic cues drive dynamic processes that control cell fate during organ development. A study of mouse and human cells reveals how these inputs affect cells that make the essential hormone insulin.
Francesca M. Spagnoli
CDK12 regulates DNA repair genes by suppressing intronic polyadenylation
The kinase CDK12 suppresses usage of intronic polyadenylation sites and thereby promotes the expression of genes involved in homologous recombination DNA repair.
Sara J. Dubbury, Paul L. Boutz, Phillip A. Sharp
Extreme-ultraviolet refractive optics
A refractive lens and a refractive prism for extreme-ultraviolet radiation have been developed that use the deflection of the radiation in an inhomogeneous jet of atoms.
L. Drescher, O. Kornilov, T. Witting et al.
FBXO38 mediates PD-1 ubiquitination and regulates anti-tumour immunity of T cells
PD-1 undergoes internalization, FBXO38-mediated ubiquitination and proteasome degradation in activated T cells, and inhibition of this pathway dampens anti-tumour immunity of T cells.
Xiangbo Meng, Xiwei Liu, Xingdong Guo et al.
Metabolic reprogramming by the S-nitroso-CoA reductase system protects against kidney injury
AKR1A1-regulated protein S-nitrosylation protects against kidney injury through PKM2-mediated metabolic reprogramming.
Hua-Lin Zhou, Rongli Zhang, Puneet Anand et al.
Stella safeguards the oocyte methylome by preventing de novo methylation mediated by DNMT1
Stella, a factor essential for female fertility, protects the oocyte methylome in mice by suppressing de novo DNA methylation mediated by the DNA methyltransferase DNMT1.
Yingfeng Li, Zhuqiang Zhang, Jiayu Chen et al.
How cells hush a viral invader
Viruses can insert a copy of their genetic sequence into a host cell's genome. If the insertion fails, gene expression of unintegrated viral DNA in the nucleus is silenced. How this process occurs has now been uncovered.
Parinaz Fozouni, Melanie Ott
PtdIns4P on dispersed trans-Golgi network mediates NLRP3 inflammasome activation
Recruitment of NLRP3 to the dispersed trans-Golgi network via binding to PtdIns4P is required for activation of the NLRP3 inflammasome by diverse stimuli.
Jueqi Chen, Zhijian J. Chen
Atomic clock performance enabling geodesy below the centimetre level
Improved techniques allow the measurement of a frequency difference with an uncertainty of the order of 10–19 between two independent atomic optical lattice clocks, suggesting that they may be able to improve state-of-the-art geodetic techniques.
W. F. McGrew, X. Zhang, R. J. Fasano et al.
Mechanosignalling via integrins directs fate decisions of pancreatic progenitors
Single-cell analysis reveals that interactions with the extracellular matrix via integrin α5 and mechanotransducer YAP1 determine whether pancreatic progenitors develop along the duct or endocrine lineages.
Anant Mamidi, Christy Prawiro, Philip A. Seymour et al.
Metabolism reprogrammed by the nitric oxide signalling molecule
The signalling molecule nitric oxide protects the kidneys by reprogramming metabolism, and its levels are regulated by a two-component system in mice. These findings identify new targets for drug discovery.
Charles J. Lowenstein
NP220 mediates silencing of unintegrated retroviral DNA
In mammalian cells, NP220 is a key protein that recruits the HUSH complex, SETDB1 and the histone deacetylases HDAC1 and HDAC4 to silence unintegrated retroviral DNA.
Yiping Zhu, Gary Z. Wang, Oya Cingöz et al.
Trophoblast organoids as a model for maternal–fetal interactions during human placentation
An in vitro system that generates three-dimensional cultures of extraembryonic fetal trophoblast cells that differentiate into the two main types of trophoblast can be used to study human placental development.
Margherita Y. Turco, Lucy Gardner, Richard G. Kay et al.
Reversible superdense ordering of lithium between two graphene sheets
Using a double-aberration-corrected transmission electron microscope, intercalation of lithium between two graphene sheets is found to produce a dense, multilayer lithium phase, rather than the expected single layer.
Matthias Kühne, Felix Börrnert, Sven Fecher et al.
Darwin's finches choose parent lookalikes as mates
A preference for mating with similar individuals can have a key role in speciation. Research on Darwin's finches suggests that individuals might use the likeness of their parents as a guide for choosing mates.
Lewis G. Spurgin, Tracey Chapman
Reward behaviour is regulated by the strength of hippocampus–nucleus accumbens synapses
Dopamine-independent induction of long-term potentiation at hippocampal synapses onto the nucleus accumbens modulates reward-related behaviour.
Tara A. LeGates, Mark D. Kvarta, Jessica R. Tooley et al.
News & Views  
Past warming events in the Arctic linked to shifting winds in the Antarctic
Nerilie J. Abram
A newly discovered mechanism driving neuronal mutations in Alzheimer's disease
Guoliang Chai, Joseph G. Gleeson
From the archive
A spotlight on bacterial mutations for 75 years
Manoshi S. Datta, Roy Kishony
The not-so-dangerous lives of Neanderthals
Marta Mirazón Lahr
A glimpse into the heart of a quasar
Erin Kara
A bacterium's enemy isn't your friend
Michael S. Gilmore, Ona K. Miller
Somatic APP gene recombination in Alzheimer's disease and normal neurons
The gene for the amyloid precursor protein (APP) shows somatic gene recombination in neurons, and the abundance and diversity of APP variants is increased in neurons from individuals with Alzheimer's disease.
Ming-Hsiang Lee, Benjamin Siddoway, Gwendolyn E. Kaeser et al.
Predictable and precise template-free CRISPR editing of pathogenic variants
The authors use a machine-learning algorithm to predict the spectrum of CRISPR–Cas9-nuclease-mediated DNA repair outcomes at human genomic target sites.
Max W. Shen, Mandana Arbab, Jonathan Y. Hsu et al.
Structural plasticity of D3–D14 ubiquitin ligase in strigolactone signalling
The plant F-box protein D3 has a C-terminal α-helix that switches between two conformational states, allowing the α/β hydrolase D14 to recruit the transcription repressor D53 for strigolactone-dependent degradation.
Nitzan Shabek, Fabrizio Ticchiarelli, Haibin Mao et al.
Spatially resolved rotation of the broad-line region of a quasar at sub-parsec scale
High-angular-resolution observations of the quasar 3C 273 reveal that it has a relatively small but thick disk, viewed nearly face-on, in which material is orbiting the central supermassive black hole.
GRAVITY Collaboration
Quantum control of surface acoustic-wave phonons
A non-classical superposition of zero- and one-phonon mechanical Fock states is generated and measured by strongly coupling a surface acoustic-wave resonator to a superconducting qubit.
K. J. Satzinger, Y. P. Zhong, H.-S. Chang et al.
Creation and control of multi-phonon Fock states in a bulk acoustic-wave resonator
Circuit quantum acoustodynamics is used to achieve controlled generation of multi-phonon Fock states in a bulk acoustic-wave resonator, which are demonstrated to have a quantum nature.
Yiwen Chu, Prashanta Kharel, Taekwan Yoon et al.
Superfluorescence from lead halide perovskite quantum dot superlattices
Cooperative quantum effects in superlattices of quantum dots made of caesium lead halide perovskite give rise to superfluorescence, with the individual emitters interacting coherently to give intense bursts of light.
Gabriele Rainò, Michael A. Becker, Maryna I. Bodnarchuk et al.
A structural transition in physical networks
A modelling framework is presented to determine the optimal layout and physical properties of networks in which the nodes and links have physical sizes and intersections between components is prohibited.
Nima Dehmamy, Soodabeh Milanlouei, Albert-László Barabási
Abrupt ice-age shifts in southern westerly winds and Antarctic climate forced from the north
The position of the Southern Hemisphere westerly winds responds immediately to abrupt North Atlantic climate events of the last ice age, with a spatially heterogeneous impact on Antarctic climate.
Christo Buizert, Michael Sigl, Mirko Severi et al.
Similar cranial trauma prevalence among Neanderthals and Upper Palaeolithic modern humans
Neanderthals and Upper Palaeolithic modern humans exhibit similar overall incidences of cranial trauma that are higher for males of both taxa; however, there are species-specific, age-related variations in trauma prevalence.
Judith Beier, Nils Anthes, Joachim Wahl et al.
Trans-differentiation of outer hair cells into inner hair cells in the absence of INSM1
Conditional deletion of Insm1 in mice demonstrates that INSM1 is the key switch that causes the maturation of outer hair cells in the cochlea, with its absence resulting in an increase in inner hair cells instead.
Teerawat Wiwatpanit, Sarah M. Lorenzen, Jorge A. Cantú et al.
Helios is a key transcriptional regulator of outer hair cell maturation
Ikzf2, which encodes the transcription factor Helios, is identified as a crucial regulator of gene expression in maturing cochlear outer hair cells, and overexpression of Ikzf2 in inner hair cells induces prestin expression and electromotility.
Lauren Chessum, Maggie S. Matern, Michael C. Kelly et al.
Linking a cell-division gene and a suicide gene to define and improve cell therapy safety
Introduction of a suicide gene together with a linked cell-division gene to generate a safe-cell system enables the selective elimination of proliferating cells after cell transplantation in mouse models of cell therapy.
Qin Liang, Claudio Monetti, Maria V. Shutova et al.
Methicillin-resistant Staphylococcus aureus alters cell wall glycosylation to evade immunity
Strains of methicillin-resistant Staphylococcus aureus use a prophage-encoded glycosyltransferase to alter the glycosylation of their wall teichoic acid and thereby evade antibody-mediated immune responses.
David Gerlach, Yinglan Guo, Cristina De Castro et al.
Cryptic connections illuminate pathogen transmission within community networks
Cryptic connections facilitate the community-wide spread of disease both within and among species.
Joseph R. Hoyt, Kate E. Langwig, J. Paul White et al.
Efferocytosis induces a novel SLC program to promote glucose uptake and lactate release
Distinct transcriptional programs are activated during different stages of apoptotic cell engulfment, including a unique program of genes coding for solute carrier proteins and enzymes in the glycolytic pathway.
Sho Morioka, Justin S. A. Perry, Michael H. Raymond et al.
Mannose impairs tumour growth and enhances chemotherapy
Mannose reduces the growth of tumour cells by impairing the metabolism of glucose, and enhances cell death when used in combination with conventional chemotherapy.
Pablo Sierra Gonzalez, James O'Prey, Simone Cardaci et al.
Amendments & Corrections
Author Correction: Phosphocode-dependent functional dichotomy of a common co-receptor in plant signalling

Artemis Perraki, Thomas A. DeFalco, Paul Derbyshire et al.
Author Correction: Nearly all the sky is covered by Lyman-α emission around high-redshift galaxies

L. Wisotzki, R. Bacon, J. Brinchmann et al.
Publisher Correction: The NORAD lncRNA assembles a topoisomerase complex critical for genome stability

Mathias Munschauer, Celina T. Nguyen, Klara Sirokman et al.
Publisher Correction: Evidence that CD32a does not mark the HIV-1 latent reservoir

Christa E. Osuna, So-Yon Lim, Jessica L. Kublin et al.
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