Patchy particles made by colloidal fusion Nature (IF 40.137) Pub Date : 2017-09-18 Zhe Gong, Theodore Hueckel, Gi-Ra Yi, Stefano Sacanna
Patches on the surfaces of colloidal particles provide directional information that enables the self-assembly of the particles into higher-order structures. Although computational tools can make quantitative predictions and can generate design rules that link the patch motif of a particle to its internal microstructure and to the emergent properties of the self-assembled materials, the experimental realization of model systems of particles with surface patches (or ‘patchy’ particles) remains a challenge. Synthetic patchy colloidal particles are often poor geometric approximations of the digital building blocks used in simulations and can only rarely be manufactured in sufficiently high yields to be routinely used as experimental model systems. Here we introduce a method, which we refer to as colloidal fusion, for fabricating functional patchy particles in a tunable and scalable manner. Using coordination dynamics and wetting forces, we engineer hybrid liquid–solid clusters that evolve into particles with a range of patchy surface morphologies on addition of a plasticizer. We are able to predict and control the evolutionary pathway by considering surface-energy minimization, leading to two main branches of product: first, spherical particles with liquid surface patches, capable of forming curable bonds with neighbouring particles to assemble robust supracolloidal structures; and second, particles with a faceted liquid compartment, which can be cured and purified to yield colloidal polyhedra. These findings outline a scalable strategy for the synthesis of patchy particles, first by designing their surface patterns by computer simulation, and then by recreating them in the laboratory with high fidelity.
Neuroscience: Mum's bacteria linked to baby's behaviour Nature (IF 40.137) Pub Date : 2017-09-13 Craig M. Powell
Infection during pregnancy increases the risk of neurodevelopmental disorders, such as autism, in offspring. Mouse studies now reveal a link between gut bacteria and atypical brain-circuit connections.
Rabies screen reveals GPe control of cocaine-triggered plasticity Nature (IF 40.137) Pub Date : 2017-09-13 Kevin T. Beier, Christina K. Kim, Paul Hoerbelt, Lin Wai Hung, Boris D. Heifets, Katherine E. DeLoach, Timothy J. Mosca, Sophie Neuner, Karl Deisseroth, Liqun Luo, Robert C. Malenka
Identification of neural circuit changes that contribute to behavioural plasticity has routinely been conducted on candidate circuits that were preselected on the basis of previous results. Here we present an unbiased method for identifying experience-triggered circuit-level changes in neuronal ensembles in mice. Using rabies virus monosynaptic tracing, we mapped cocaine-induced global changes in inputs onto neurons in the ventral tegmental area. Cocaine increased rabies-labelled inputs from the globus pallidus externus (GPe), a basal ganglia nucleus not previously known to participate in behavioural plasticity triggered by drugs of abuse. We demonstrated that cocaine increased GPe neuron activity, which accounted for the increase in GPe labelling. Inhibition of GPe activity revealed that it contributes to two forms of cocaine-triggered behavioural plasticity, at least in part by disinhibiting dopamine neurons in the ventral tegmental area. These results suggest that rabies-based unbiased screening of changes in input populations can identify previously unappreciated circuit elements that critically support behavioural adaptations.
Reversing behavioural abnormalities in mice exposed to maternal inflammation Nature (IF 40.137) Pub Date : 2017-09-13 Yeong Shin Yim, Ashley Park, Janet Berrios, Mathieu Lafourcade, Leila M. Pascual, Natalie Soares, Joo Yeon Kim, Sangdoo Kim, Hyunju Kim, Ari Waisman, Dan R. Littman, Ian R. Wickersham, Mark T. Harnett, Jun R. Huh, Gloria B. Choi
Viral infection during pregnancy is correlated with increased frequency of neurodevelopmental disorders, and this is studied in mice prenatally subjected to maternal immune activation (MIA). We previously showed that maternal T helper 17 cells promote the development of cortical and behavioural abnormalities in MIA-affected offspring. Here we show that cortical abnormalities are preferentially localized to a region encompassing the dysgranular zone of the primary somatosensory cortex (S1DZ). Moreover, activation of pyramidal neurons in this cortical region was sufficient to induce MIA-associated behavioural phenotypes in wild-type animals, whereas reduction in neural activity rescued the behavioural abnormalities in MIA-affected offspring. Sociability and repetitive behavioural phenotypes could be selectively modulated according to the efferent targets of S1DZ. Our work identifies a cortical region primarily, if not exclusively, centred on the S1DZ as the major node of a neural network that mediates behavioural abnormalities observed in offspring exposed to maternal inflammation.
The neuropeptide NMU amplifies ILC2-driven allergic lung inflammation Nature (IF 40.137) Pub Date : 2017-09-13 Antonia Wallrapp, Samantha J. Riesenfeld, Patrick R. Burkett, Raja-Elie E. Abdulnour, Jackson Nyman, Danielle Dionne, Matan Hofree, Michael S. Cuoco, Christopher Rodman, Daneyal Farouq, Brian J. Haas, Timothy L. Tickle, John J. Trombetta, Pankaj Baral, Christoph S. N. Klose, Tanel Mahlakõiv, David Artis, Orit Rozenblatt-Rosen, Isaac M. Chiu, Bruce D. Levy, Monika S. Kowalczyk, Aviv Regev, Vijay K. Kuchroo
Type 2 innate lymphoid cells (ILC2s) both contribute to mucosal homeostasis and initiate pathologic inflammation in allergic asthma. However, the signals that direct ILC2s to promote homeostasis versus inflammation are unclear. To identify such molecular cues, we profiled mouse lung-resident ILCs using single-cell RNA sequencing at steady state and after in vivo stimulation with the alarmin cytokines IL-25 and IL-33. ILC2s were transcriptionally heterogeneous after activation, with subpopulations distinguished by expression of proliferative, homeostatic and effector genes. The neuropeptide receptor Nmur1 was preferentially expressed by ILC2s at steady state and after IL-25 stimulation. Neuromedin U (NMU), the ligand of NMUR1, activated ILC2s in vitro, and in vivo co-administration of NMU with IL-25 strongly amplified allergic inflammation. Loss of NMU–NMUR1 signalling reduced ILC2 frequency and effector function, and altered transcriptional programs following allergen challenge in vivo. Thus, NMUR1 signalling promotes inflammatory ILC2 responses, highlighting the importance of neuro-immune crosstalk in allergic inflammation at mucosal surfaces.
cGAS senses long and HMGB/TFAM-bound U-turn DNA by forming protein–DNA ladders Nature (IF 40.137) Pub Date : 2017-09-13 Liudmila Andreeva, Björn Hiller, Dirk Kostrewa, Charlotte Lässig, Carina C. de Oliveira Mann, David Jan Drexler, Andreas Maiser, Moritz Gaidt, Heinrich Leonhardt, Veit Hornung, Karl-Peter Hopfner
Cytosolic DNA arising from intracellular pathogens triggers a powerful innate immune response. It is sensed by cyclic GMP–AMP synthase (cGAS), which elicits the production of type I interferons by generating the second messenger 2′3′-cyclic-GMP–AMP (cGAMP). Endogenous nuclear or mitochondrial DNA can also be sensed by cGAS under certain conditions, resulting in sterile inflammation. The cGAS dimer binds two DNA ligands shorter than 20 base pairs side-by-side, but 20-base-pair DNA fails to activate cGAS in vivo and is a poor activator in vitro. Here we show that cGAS is activated in a strongly DNA length-dependent manner both in vitro and in human cells. We also show that cGAS dimers form ladder-like networks with DNA, leading to cooperative sensing of DNA length: assembly of the pioneering cGAS dimer between two DNA molecules is ineffective; but, once formed, it prearranges the flanking DNA to promote binding of subsequent cGAS dimers. Remarkably, bacterial and mitochondrial nucleoid proteins HU and mitochondrial transcription factor A (TFAM), as well as high-mobility group box 1 protein (HMGB1), can strongly stimulate long DNA sensing by cGAS. U-turns and bends in DNA induced by these proteins pre-structure DNA to nucleate cGAS dimers. Our results suggest a nucleation-cooperativity-based mechanism for sensitive detection of mitochondrial DNA and pathogen genomes, and identify HMGB/TFAM proteins as DNA-structuring host factors. They provide an explanation for the peculiar cGAS dimer structure and suggest that cGAS preferentially binds incomplete nucleoid-like structures or bent DNA.
The cryo-electron microscopy structure of human transcription factor IIH Nature (IF 40.137) Pub Date : 2017-09-13 Basil J. Greber, Jie Fang, Pavel V. Afonine, Paul D. Adams, Eva Nogales
Human transcription factor IIH (TFIIH) is part of the general transcriptional machinery required by RNA polymerase II for the initiation of eukaryotic gene transcription. Composed of ten subunits that add up to a molecular mass of about 500 kDa, TFIIH is also essential for nucleotide excision repair. The seven-subunit TFIIH core complex formed by XPB, XPD, p62, p52, p44, p34, and p8 is competent for DNA repair, while the CDK-activating kinase subcomplex, which includes the kinase activity of CDK7 as well as the cyclin H and MAT1 subunits, is additionally required for transcription initiation. Mutations in the TFIIH subunits XPB, XPD, and p8 lead to severe premature ageing and cancer propensity in the genetic diseases xeroderma pigmentosum, Cockayne syndrome, and trichothiodystrophy, highlighting the importance of TFIIH for cellular physiology. Here we present the cryo-electron microscopy structure of human TFIIH at 4.4 Å resolution. The structure reveals the molecular architecture of the TFIIH core complex, the detailed structures of its constituent XPB and XPD ATPases, and how the core and kinase subcomplexes of TFIIH are connected. Additionally, our structure provides insight into the conformational dynamics of TFIIH and the regulation of its activity.
Maternal gut bacteria promote neurodevelopmental abnormalities in mouse offspring Nature (IF 40.137) Pub Date : 2017-09-13 Sangdoo Kim, Hyunju Kim, Yeong Shin Yim, Soyoung Ha, Koji Atarashi, Tze Guan Tan, Randy S. Longman, Kenya Honda, Dan R. Littman, Gloria B. Choi, Jun R. Huh
Maternal immune activation (MIA) contributes to behavioural abnormalities associated with neurodevelopmental disorders in both primate and rodent offspring. In humans, epidemiological studies suggest that exposure of fetuses to maternal inflammation increases the likelihood of developing autism spectrum disorder. In pregnant mice, interleukin-17a (IL-17a) produced by T helper 17 (TH17) cells (CD4+ T helper effector cells involved in multiple inflammatory conditions) induces behavioural and cortical abnormalities in the offspring exposed to MIA. However, it is unclear whether other maternal factors are required to promote MIA-associated phenotypes. Moreover, the underlying mechanisms by which MIA leads to T cell activation with increased IL-17a in the maternal circulation are not well understood. Here we show that MIA phenotypes in offspring require maternal intestinal bacteria that promote TH17 cell differentiation. Pregnant mice that had been colonized with mouse commensal segmented filamentous bacteria or human commensal bacteria that induce intestinal TH17 cells were more likely to produce offspring with MIA-associated abnormalities. We also show that small intestine dendritic cells from pregnant, but not from non-pregnant, females secrete IL-1β, IL-23 and IL-6 and stimulate T cells to produce IL-17a upon exposure to MIA. Overall, our data suggest that defined gut commensal bacteria with a propensity to induce TH17 cells may increase the risk of neurodevelopmental disorders in the offspring of pregnant mothers undergoing immune system activation owing to infections or autoinflammatory syndromes.
SAM-dependent enzyme-catalysed pericyclic reactions in natural product biosynthesis Nature (IF 40.137) Pub Date : 2017-09-13 Masao Ohashi, Fang Liu, Yang Hai, Mengbin Chen, Man-cheng Tang, Zhongyue Yang, Michio Sato, Kenji Watanabe, K. N. Houk, Yi Tang
Pericyclic reactions—which proceed in a concerted fashion through a cyclic transition state—are among the most powerful synthetic transformations used to make multiple regioselective and stereoselective carbon–carbon bonds. They have been widely applied to the synthesis of biologically active complex natural products containing contiguous stereogenic carbon centres. Despite the prominence of pericyclic reactions in total synthesis, only three naturally existing enzymatic examples (the intramolecular Diels–Alder reaction, and the Cope and the Claisen rearrangements) have been characterized. Here we report a versatile S-adenosyl-l-methionine (SAM)-dependent enzyme, LepI, that can catalyse stereoselective dehydration followed by three pericyclic transformations: intramolecular Diels–Alder and hetero-Diels–Alder reactions via a single ambimodal transition state, and a retro-Claisen rearrangement. Together, these transformations lead to the formation of the dihydropyran core of the fungal natural product, leporin. Combined in vitro enzymatic characterization and computational studies provide insight into how LepI regulates these bifurcating biosynthetic reaction pathways by using SAM as the cofactor. These pathways converge to the desired biosynthetic end product via the (SAM-dependent) retro-Claisen rearrangement catalysed by LepI. We expect that more pericyclic biosynthetic enzymatic transformations remain to be discovered in naturally occurring enzyme ‘toolboxes’. The new role of the versatile cofactor SAM is likely to be found in other examples of enzyme catalysis.
Hippocampal LTP and contextual learning require surface diffusion of AMPA receptors Nature (IF 40.137) Pub Date : 2017-09-13 A. C. Penn, C. L. Zhang, F. Georges, L. Royer, C. Breillat, E. Hosy, J. D. Petersen, Y. Humeau, D. Choquet
Long-term potentiation (LTP) of excitatory synaptic transmission has long been considered a cellular correlate for learning and memory. Early LTP (less than 1 h) had initially been explained either by presynaptic increases in glutamate release or by direct modification of postsynaptic AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor function. Compelling models have more recently proposed that synaptic potentiation can occur by the recruitment of additional postsynaptic AMPA receptors (AMPARs), sourced either from an intracellular reserve pool by exocytosis or from nearby extra-synaptic receptors pre-existing on the neuronal surface. However, the exact mechanism through which synapses can rapidly recruit new AMPARs during early LTP remains unknown. In particular, direct evidence for a pivotal role of AMPAR surface diffusion as a trafficking mechanism in synaptic plasticity is still lacking. Here, using AMPAR immobilization approaches, we show that interfering with AMPAR surface diffusion markedly impairs synaptic potentiation of Schaffer collaterals and commissural inputs to the CA1 area of the mouse hippocampus in cultured slices, acute slices and in vivo. Our data also identify distinct contributions of various AMPAR trafficking routes to the temporal profile of synaptic potentiation. In addition, AMPAR immobilization in vivo in the dorsal hippocampus inhibited fear conditioning, indicating that AMPAR diffusion is important for the early phase of contextual learning. Therefore, our results provide a direct demonstration that the recruitment of new receptors to synapses by surface diffusion is a critical mechanism for the expression of LTP and hippocampal learning. Since AMPAR surface diffusion is dictated by weak Brownian forces that are readily perturbed by protein–protein interactions, we anticipate that this fundamental trafficking mechanism will be a key target for modulating synaptic potentiation and learning.
Alternative evolutionary histories in the sequence space of an ancient protein Nature (IF 40.137) Pub Date : 2017-09-13 Tyler N. Starr, Lora K. Picton, Joseph W. Thornton
To understand why molecular evolution turned out as it did, we must characterize not only the path that evolution followed across the space of possible molecular sequences but also the many alternative trajectories that could have been taken but were not. A large-scale comparison of real and possible histories would establish whether the outcome of evolution represents an optimal state driven by natural selection or the contingent product of historical chance events; it would also reveal how the underlying distribution of functions across sequence space shaped historical evolution. Here we combine ancestral protein reconstruction with deep mutational scanning to characterize alternative histories in the sequence space around an ancient transcription factor, which evolved a novel biological function through well-characterized mechanisms. We find hundreds of alternative protein sequences that use diverse biochemical mechanisms to perform the derived function at least as well as the historical outcome. These alternatives all require prior permissive substitutions that do not enhance the derived function, but not all require the same permissive changes that occurred during history. We find that if evolution had begun from a different starting point within the network of sequences encoding the ancestral function, outcomes with different genetic and biochemical forms would probably have resulted; this contingency arises from the distribution of functional variants in sequence space and epistasis between residues. Our results illuminate the topology of the vast space of possibilities from which history sampled one path, highlighting how the outcome of evolution depends on a serial chain of compounding chance events.
The Apostasia genome and the evolution of orchids Nature (IF 40.137) Pub Date : 2017-09-13 Guo-Qiang Zhang, Ke-Wei Liu, Zhen Li, Rolf Lohaus, Yu-Yun Hsiao, Shan-Ce Niu, Jie-Yu Wang, Yao-Cheng Lin, Qing Xu, Li-Jun Chen, Kouki Yoshida, Sumire Fujiwara, Zhi-Wen Wang, Yong-Qiang Zhang, Nobutaka Mitsuda, Meina Wang, Guo-Hui Liu, Lorenzo Pecoraro, Hui-Xia Huang, Xin-Ju Xiao, Min Lin, Xin-Yi Wu, Wan-Lin Wu, You-Yi Chen, Song-Bin Chang, Shingo Sakamoto, Masaru Ohme-Takagi, Masafumi Yagi, Si-Jin Zeng, Ching-Yu Shen, Chuan-Ming Yeh, Yi-Bo Luo, Wen-Chieh Tsai, Yves Van de Peer, Zhong-Jian Liu
Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth. Here we report the draft genome sequence of Apostasia shenzhenica, a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution. In addition, we present transcriptome data for representatives of Vanilloideae, Cypripedioideae and Orchidoideae, and novel third-generation genome data for two species of Epidendroideae, covering all five orchid subfamilies. A. shenzhenica shows clear evidence of a whole-genome duplication, which is shared by all orchids and occurred shortly before their divergence. Comparisons between A. shenzhenica and other orchids and angiosperms also permitted the reconstruction of an ancestral orchid gene toolkit. We identify new gene families, gene family expansions and contractions, and changes within MADS-box gene classes, which control a diverse suite of developmental processes, during orchid evolution. This study sheds new light on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms.
Support Ismail Serageldin Nature (IF 40.137) Pub Date : 2017-09-13
Egypt’s courts must listen to dozens of Nobel prizewinners who have defended the founder of the Alexandria Library.
Pregnant mice illuminate risk factors that could lead to autism Nature (IF 40.137) Pub Date : 2017-09-13
Studies highlight link between immune response and unusual neural wiring.
Giraffes could have evolved long necks to keep cool Nature (IF 40.137) Pub Date : 2017-09-12
Another explanation offered for one of animal kingdom’s most distinctive features.
Faculty promotion must assess reproducibility Nature (IF 40.137) Pub Date : 2017-09-12 Jeffrey Flier
Research institutions should explicitly seek job candidates who can be frankly self-critical of their work, says Jeffrey Flier.
Hurricane havoc, deep-ocean floats and Mexico’s fatal quake Nature (IF 40.137) Pub Date : 2017-09-13
The week in science: 8–14 September 2017.
Geneticists pan paper that claims to predict a person's face from their DNA Nature (IF 40.137) Pub Date : 2017-09-08 Sara Reardon
Reviewers and a co-author of a paper by genomics entrepreneur Craig Venter claim that it misrepresents the risks of public access to genome data.
Researchers riled by lack of detail in Brexit science plans Nature (IF 40.137) Pub Date : 2017-09-06 Daniel Cressey
UK government document fails to extinguish concerns over funding and migration.
South Korean researchers lobby government to lift human-embryo restrictions Nature (IF 40.137) Pub Date : 2017-09-08 Mark Zastrow
Regulations are deterring research that could lead to disease treatments, say scientists.
Jordan seeks to become an oasis of water-saving technology Nature (IF 40.137) Pub Date : 2017-09-12 Amy Maxmen
As strains on the desert nation’s supply increase, scientists collaborate on projects to keep water flowing.
UK gender-equality scheme spreads across the world Nature (IF 40.137) Pub Date : 2017-09-13 Elizabeth Gibney
The United States is set to trial a version that will also cover race and disability, while other countries have already embraced the voluntary rating system.
The new economy of excrement Nature (IF 40.137) Pub Date : 2017-09-13 Chelsea Wald
Entrepreneurs are finding profits turning human waste into fertiliser, fuel and even food.
First quantum computers need smart software Nature (IF 40.137) Pub Date : 2017-09-13 Will Zeng, Blake Johnson, Robert Smith, Nick Rubin, Matt Reagor, Colm Ryan, Chad Rigetti
Early devices must solve real-world problems, urge Will Zeng and colleagues.
Insurance companies should collect a carbon levy Nature (IF 40.137) Pub Date : 2017-09-13 Anthony J. Webster, Richard H. Clarke
A surcharge on energy producers would fund climate adaptation and the low-carbon transition, suggest Anthony J. Webster and Richard H. Clarke.
Engineering: Reclusive genius who connected the world Nature (IF 40.137) Pub Date : 2017-09-13 W. Bernard Carlson
W. Bernard Carlson relishes a biography of a self-taught engineer who revolutionized telecommunications.
Q&A: The AI composer Nature (IF 40.137) Pub Date : 2017-09-13 Laura Spinney
Computer scientist Luc Steels uses artificial intelligence to explore the origins and evolution of language. He is best known for his 1999–2001 Talking Heads Experiment, in which robots had to construct a language from scratch to communicate with each other. Now Steels, who works at the Free University of Brussels (VUB), has composed an opera based on the legend of Faust, with a twenty-first-century twist. He talks about Mozart as a nascent computer programmer, how music maps onto language, and the blurred boundaries of a digitized world.
History of technology: How China sidestepped QWERTY Nature (IF 40.137) Pub Date : 2017-09-13 Raja Adal
Raja Adal investigates the 150-year history of a typewriter able to reproduce thousands of characters.
Statues: a mother of gynaecology Nature (IF 40.137) Pub Date : 2017-09-13 Monica H. Green
I have often walked past the statue of J. Marion Sims (see Editorial, correction and apology: Nature549, 5–6; 10.1038/549005b2017). It seems to say to me: “Go away, woman. You have no authority here,” and: “Go away, woman of
Statues: learn from mistakes Nature (IF 40.137) Pub Date : 2017-09-13 Kim M. Cobb
I am disheartened that Nature has apparently joined the chorus of tone-deaf statements on race and racism in science, technology, engineering and mathematics (see Editorial, correction and apology: Nature549, 5–6; 10.1038/549005b2017). Your unsigned article may have done
Statues: for those deserving respect Nature (IF 40.137) Pub Date : 2017-09-13 Katherine E. Gould
We should reserve statuaries for people who deserve our respect — not just for their discoveries, but also for their methods (see Editorial, correction and apology: Nature549, 5–6; 10.1038/549005b2017). Sims' discoveries will not be forgotten. Sims himself will
Units: Don't tamper with SI-unit consistency Nature (IF 40.137) Pub Date : 2017-09-13 Michael C. Wendl
I disagree with your suggestion to promote the radian to the International System of Units (SI units) to address the confusion over dimensionless numbers (Nature548, 135; 10.1038/548135b2017). On the contrary, this could perpetrate the mistaken view that everything in
Correction Nature (IF 40.137) Pub Date : 2017-09-13
The Nature Index article 'Game changers' (Nature548, S9–S11; 10.1038/548S9a2017) gave the wrong affiliation for David Lipman. He was at the US National Institute of Arthritis, Diabetes, and Digestive and Kidney Diseases.
Outside the lab: Side jobs for scientists Nature (IF 40.137) Pub Date : 2017-09-13 Elie Dolgin
Paid work beyond the bench can offer a welcome source of income to cash-strapped junior researchers and provide opportunities for career development.
Students: Immigration targets Nature (IF 40.137) Pub Date : 2017-09-13
UK report investigates whether international students remain illegally after graduating.
Universities: Low diversity levels Nature (IF 40.137) Pub Date : 2017-09-13
US universities fall short in hiring women and under-represented minorities.
Roads towards fault-tolerant universal quantum computation Nature (IF 40.137) Pub Date : 2017-09-13 Earl T. Campbell, Barbara M. Terhal, Christophe Vuillot
A practical quantum computer must not merely store information, but also process it. To prevent errors introduced by noise from multiplying and spreading, a fault-tolerant computational architecture is required. Current experiments are taking the first steps toward noise-resilient logical qubits. But to convert these quantum
Quantum software Nature (IF 40.137) Pub Date : 2017-09-13 Leonie Mueck
Decades have passed since the great minds of physics, including Richard Feynman and David Deutsch, predicted that the laws of quantum mechanics could give rise to a computing paradigm that — for certain tasks — is superior to classical computing. But controlling fragile quantum systems
Programming languages and compiler design for realistic quantum hardware Nature (IF 40.137) Pub Date : 2017-09-13 Frederic T. Chong, Diana Franklin, Margaret Martonosi
Quantum computing sits at an important inflection point. For years, high-level algorithms for quantum computers have shown considerable promise, and recent advances in quantum device fabrication offer hope of utility. A gap still exists, however, between the hardware size and reliability requirements of quantum computing
Post-quantum cryptography Nature (IF 40.137) Pub Date : 2017-09-13 Daniel J. Bernstein, Tanja Lange
Cryptography is essential for the security of online communication, cars and implanted medical devices. However, many commonly used cryptosystems will be completely broken once large quantum computers exist. Post-quantum cryptography is cryptography under the assumption that the attacker has a large quantum computer; post-quantum cryptosystems
Quantum machine learning Nature (IF 40.137) Pub Date : 2017-09-13 Jacob Biamonte, Peter Wittek, Nicola Pancotti, Patrick Rebentrost, Nathan Wiebe, Seth Lloyd
Fuelled by increasing computer power and algorithmic advances, machine learning techniques have become powerful tools for finding patterns in data. Quantum systems produce atypical patterns that classical systems are thought not to produce efficiently, so it is reasonable to postulate that quantum computers may outperform
Quantum computational supremacy Nature (IF 40.137) Pub Date : 2017-09-13 Aram W. Harrow, Ashley Montanaro
The field of quantum algorithms aims to find ways to speed up the solution of computational problems by using a quantum computer. A key milestone in this field will be when a universal quantum computer performs a computational task that is beyond the capability of
Planet of the five rings Nature (IF 40.137) Pub Date : 2017-09-13 Marissa Lingen
It's a dream come true.
Correction Nature (IF 40.137) Pub Date : 2017-09-13
The Editorial ‘Made of stone’ (Nature549, 5–6; 2017) appeared online with a poorly worded and offensive headline and standfirst. Taken together with some of the article’s text, this implied that Nature supports retaining statues of historical figures whose work harmed
Microbiology: A fight for scraps of ammonia Nature (IF 40.137) Pub Date : 2017-09-13 Marcel M. M. Kuypers
Bacteria that can oxidize both ammonia to nitrite and nitrite to nitrate seem to be better adapted to ammonia-limited environments than most cultured microbes that oxidize ammonia to nitrite only, contrary to expectations. See Letter p.269
Optical physics: A laser model for cosmology Nature (IF 40.137) Pub Date : 2017-09-13 Stefan Rotter
Experiments reveal that the laws governing the immediate aftermath of the Big Bang also apply to the behaviour of coupled lasers. The findings could be used to solve complex computational problems.
Cancer: Division hierarchy leads to cell heterogeneity Nature (IF 40.137) Pub Date : 2017-08-30 Joan Seoane
Cellular diversity can hamper cancer treatment. Analysis of tumour cell-division patterns now reveals how such heterogeneity can arise by a hierarchical pattern of stem-cell divisions yielding a mosaic of different cells. See Article p.227
Climate science: The future of Asia's glaciers Nature (IF 40.137) Pub Date : 2017-09-13 J. Graham Cogley
Glaciers in the high mountains of Asia are a crucial water resource, but are at risk from global warming. Modelling suggests that the glaciers will shed mass in direct proportion to the warming to which they are exposed. See Letter p.257
Palaeontology: Plenty of fish in the tree Nature (IF 40.137) Pub Date : 2017-09-13 Michael Coates
Polypterid fish were considered to be archaic outliers of the bony-fish grouping. Fossil analysis now places them at the heart of early ray-finned fishes, a radical change that transforms the timing of their evolution. See Letter p.265
50 & 100 Years Ago Nature (IF 40.137) Pub Date : 2017-09-13
50 Years AgoIn this paper we describe the synthesis from hydrogen cyanide of yet a further class of compounds—polymers that are readily converted by water to peptide like solids ... In the reducing atmosphere of primeval times direct synthesis of polypeptides would have been
Materials science: Nanomagnets boost thermoelectric output Nature (IF 40.137) Pub Date : 2017-09-13 Stephen R. Boona
The direct conversion of heat into electricity — a reversible process known as the thermoelectric effect — can be greatly enhanced in some materials by embedding them with a small number of magnetic nanoparticles. See Letter p.247
Detecting recovery of the stratospheric ozone layer Nature (IF 40.137) Pub Date : 2017-09-13 Martyn P. Chipperfield, Slimane Bekki, Sandip Dhomse, Neil R. P. Harris, Birgit Hassler, Ryan Hossaini, Wolfgang Steinbrecht, Rémi Thiéblemont, Mark Weber
As a result of the 1987 Montreal Protocol and its amendments, the atmospheric loading of anthropogenic ozone-depleting substances is decreasing. Accordingly, the stratospheric ozone layer is expected to recover. However, short data records and atmospheric variability confound the search for early signs of recovery, and climate change is masking ozone recovery from ozone-depleting substances in some regions and will increasingly affect the extent of recovery. Here we discuss the nature and timescales of ozone recovery, and explore the extent to which it can be currently detected in different atmospheric regions.
The 4D nucleome project Nature (IF 40.137) Pub Date : 2017-09-13 Job Dekker, Andrew S. Belmont, Mitchell Guttman, Victor O. Leshyk, John T. Lis, Stavros Lomvardas, Leonid A. Mirny, Clodagh C. O’Shea, Peter J. Park, Bing Ren, Joan C. Ritland Politz, Jay Shendure, Sheng Zhong
The 4D Nucleome Network aims to develop and apply approaches to map the structure and dynamics of the human and mouse genomes in space and time with the goal of gaining deeper mechanistic insights into how the nucleus is organized and functions. The project will
Fate mapping of human glioblastoma reveals an invariant stem cell hierarchy Nature (IF 40.137) Pub Date : 2017-08-30 Xiaoyang Lan, David J. Jörg, Florence M. G. Cavalli, Laura M. Richards, Long V. Nguyen, Robert J. Vanner, Paul Guilhamon, Lilian Lee, Michelle M. Kushida, Davide Pellacani, Nicole I. Park, Fiona J. Coutinho, Heather Whetstone, Hayden J. Selvadurai, Clare Che, Betty Luu, Annaick Carles, Michelle Moksa, Naghmeh Rastegar, Renee Head, Sonam Dolma, Panagiotis Prinos, Michael D. Cusimano, Sunit Das, Mark Bernstein, Cheryl H. Arrowsmith, Andrew J. Mungall, Richard A. Moore, Yussanne Ma, Marco Gallo, Mathieu Lupien, Trevor J. Pugh, Michael D. Taylor, Martin Hirst, Connie J. Eaves, Benjamin D. Simons, Peter B. Dirks
Human glioblastomas harbour a subpopulation of glioblastoma stem cells that drive tumorigenesis. However, the origin of intratumoural functional heterogeneity between glioblastoma cells remains poorly understood. Here we study the clonal evolution of barcoded glioblastoma cells in an unbiased way following serial xenotransplantation to define their individual fate behaviours. Independent of an evolving mutational signature, we show that the growth of glioblastoma clones in vivo is consistent with a remarkably neutral process involving a conserved proliferative hierarchy rooted in glioblastoma stem cells. In this model, slow-cycling stem-like cells give rise to a more rapidly cycling progenitor population with extensive self-maintenance capacity, which in turn generates non-proliferative cells. We also identify rare ‘outlier’ clones that deviate from these dynamics, and further show that chemotherapy facilitates the expansion of pre-existing drug-resistant glioblastoma stem cells. Finally, we show that functionally distinct glioblastoma stem cells can be separately targeted using epigenetic compounds, suggesting new avenues for glioblastoma-targeted therapy.
Structural basis of MsbA-mediated lipopolysaccharide transport Nature (IF 40.137) Pub Date : 2017-09-06 Wei Mi, Yanyan Li, Sung Hwan Yoon, Robert K. Ernst, Thomas Walz, Maofu Liao
Lipopolysaccharide (LPS) in the outer membrane of Gram-negative bacteria is critical for the assembly of their cell envelopes. LPS synthesized in the cytoplasmic leaflet of the inner membrane is flipped to the periplasmic leaflet by MsbA, an ATP-binding cassette transporter. Despite substantial efforts, the structural mechanisms underlying MsbA-driven LPS flipping remain elusive. Here we use single-particle cryo-electron microscopy to elucidate the structures of lipid-nanodisc-embedded MsbA in three functional states. The 4.2 Å-resolution structure of the transmembrane domains of nucleotide-free MsbA reveals that LPS binds deep inside MsbA at the height of the periplasmic leaflet, establishing extensive hydrophilic and hydrophobic interactions with MsbA. Two sub-nanometre-resolution structures of MsbA with ADP-vanadate and ADP reveal an unprecedented closed and an inward-facing conformation, respectively. Our study uncovers the structural basis for LPS recognition, delineates the conformational transitions of MsbA to flip LPS, and paves the way for structural characterization of other lipid flippases.
Detection of titanium oxide in the atmosphere of a hot Jupiter Nature (IF 40.137) Pub Date : 2017-09-13 Elyar Sedaghati, Henri M. J. Boffin, Ryan J. MacDonald, Siddharth Gandhi, Nikku Madhusudhan, Neale P. Gibson, Mahmoudreza Oshagh, Antonio Claret, Heike Rauer
As an exoplanet transits its host star, some of the light from the star is absorbed by the atoms and molecules in the planet’s atmosphere, causing the planet to seem bigger; plotting the planet’s observed size as a function of the wavelength of the light produces a transmission spectrum. Measuring the tiny variations in the transmission spectrum, together with atmospheric modelling, then gives clues to the properties of the exoplanet’s atmosphere. Chemical species composed of light elements—such as hydrogen, oxygen, carbon, sodium and potassium—have in this way been detected in the atmospheres of several hot giant exoplanets, but molecules composed of heavier elements have thus far proved elusive. Nonetheless, it has been predicted that metal oxides such as titanium oxide (TiO) and vanadium oxide occur in the observable regions of the very hottest exoplanetary atmospheres, causing thermal inversions on the dayside. Here we report the detection of TiO in the atmosphere of the hot-Jupiter planet WASP-19b. Our combined spectrum, with its wide spectral coverage, reveals the presence of TiO (to a confidence level of 7.7σ), a strongly scattering haze (7.4σ) and sodium (3.4σ), and confirms the presence of water (7.9σ) in the atmosphere.
Hardware-efficient variational quantum eigensolver for small molecules and quantum magnets Nature (IF 40.137) Pub Date : 2017-09-13 Abhinav Kandala, Antonio Mezzacapo, Kristan Temme, Maika Takita, Markus Brink, Jerry M. Chow, Jay M. Gambetta
Quantum computers can be used to address electronic-structure problems and problems in materials science and condensed matter physics that can be formulated as interacting fermionic problems, problems which stretch the limits of existing high-performance computers. Finding exact solutions to such problems numerically has a computational cost that scales exponentially with the size of the system, and Monte Carlo methods are unsuitable owing to the fermionic sign problem. These limitations of classical computational methods have made solving even few-atom electronic-structure problems interesting for implementation using medium-sized quantum computers. Yet experimental implementations have so far been restricted to molecules involving only hydrogen and helium. Here we demonstrate the experimental optimization of Hamiltonian problems with up to six qubits and more than one hundred Pauli terms, determining the ground-state energy for molecules of increasing size, up to BeH2. We achieve this result by using a variational quantum eigenvalue solver (eigensolver) with efficiently prepared trial states that are tailored specifically to the interactions that are available in our quantum processor, combined with a compact encoding of fermionic Hamiltonians and a robust stochastic optimization routine. We demonstrate the flexibility of our approach by applying it to a problem of quantum magnetism, an antiferromagnetic Heisenberg model in an external magnetic field. In all cases, we find agreement between our experiments and numerical simulations using a model of the device with noise. Our results help to elucidate the requirements for scaling the method to larger systems and for bridging the gap between key problems in high-performance computing and their implementation on quantum hardware.
Superparamagnetic enhancement of thermoelectric performance Nature (IF 40.137) Pub Date : 2017-09-13 Wenyu Zhao, Zhiyuan Liu, Zhigang Sun, Qingjie Zhang, Ping Wei, Xin Mu, Hongyu Zhou, Cuncheng Li, Shifang Ma, Danqi He, Pengxia Ji, Wanting Zhu, Xiaolei Nie, Xianli Su, Xinfeng Tang, Baogen Shen, Xiaoli Dong, Jihui Yang, Yong Liu, Jing Shi
The ability to control chemical and physical structuring at the nanometre scale is important for developing high-performance thermoelectric materials. Progress in this area has been achieved mainly by enhancing phonon scattering and consequently decreasing the thermal conductivity of the lattice through the design of either interface structures at nanometre or mesoscopic length scales or multiscale hierarchical architectures. A nanostructuring approach that enables electron transport as well as phonon transport to be manipulated could potentially lead to further enhancements in thermoelectric performance. Here we show that by embedding nanoparticles of a soft magnetic material in a thermoelectric matrix we achieve dual control of phonon- and electron-transport properties. The properties of the nanoparticles—in particular, their superparamagnetic behaviour (in which the nanoparticles can be magnetized similarly to a paramagnet under an external magnetic field)—lead to three kinds of thermoelectromagnetic effect: charge transfer from the magnetic inclusions to the matrix; multiple scattering of electrons by superparamagnetic fluctuations; and enhanced phonon scattering as a result of both the magnetic fluctuations and the nanostructures themselves. We show that together these effects can effectively manipulate electron and phonon transport at nanometre and mesoscopic length scales and thereby improve the thermoelectric performance of the resulting nanocomposites.
Real-space imaging of non-collinear antiferromagnetic order with a single-spin magnetometer Nature (IF 40.137) Pub Date : 2017-09-13 I. Gross, W. Akhtar, V. Garcia, L. J. Martínez, S. Chouaieb, K. Garcia, C. Carrétéro, A. Barthélémy, P. Appel, P. Maletinsky, J.-V. Kim, J. Y. Chauleau, N. Jaouen, M. Viret, M. Bibes, S. Fusil, V. Jacques
Although ferromagnets have many applications, their large magnetization and the resulting energy cost for switching magnetic moments bring into question their suitability for reliable low-power spintronic devices. Non-collinear antiferromagnetic systems do not suffer from this problem, and often have extra functionalities: non-collinear spin order may break space-inversion symmetry and thus allow electric-field control of magnetism, or may produce emergent spin–orbit effects that enable efficient spin–charge interconversion. To harness these traits for next-generation spintronics, the nanoscale control and imaging capabilities that are now routine for ferromagnets must be developed for antiferromagnetic systems. Here, using a non-invasive, scanning single-spin magnetometer based on a nitrogen–vacancy defect in diamond, we demonstrate real-space visualization of non-collinear antiferromagnetic order in a magnetic thin film at room temperature. We image the spin cycloid of a multiferroic bismuth ferrite (BiFeO3) thin film and extract a period of about 70 nanometres, consistent with values determined by macroscopic diffraction. In addition, we take advantage of the magnetoelectric coupling present in BiFeO3 to manipulate the cycloid propagation direction by an electric field. Besides highlighting the potential of nitrogen–vacancy magnetometry for imaging complex antiferromagnetic orders at the nanoscale, these results demonstrate how BiFeO3 can be used in the design of reconfigurable nanoscale spin textures.
Impact of a global temperature rise of 1.5 degrees Celsius on Asia’s glaciers Nature (IF 40.137) Pub Date : 2017-09-13 P. D. A. Kraaijenbrink, M. F. P. Bierkens, A. F. Lutz, W. W. Immerzeel
Glaciers in the high mountains of Asia (HMA) make a substantial contribution to the water supply of millions of people, and they are retreating and losing mass as a result of anthropogenic climate change at similar rates to those seen elsewhere. In the Paris Agreement of 2015, 195 nations agreed on the aspiration to limit the level of global temperature rise to 1.5 degrees Celsius ( °C) above pre-industrial levels. However, it is not known what an increase of 1.5 °C would mean for the glaciers in HMA. Here we show that a global temperature rise of 1.5 °C will lead to a warming of 2.1 ± 0.1 °C in HMA, and that 64 ± 7 per cent of the present-day ice mass stored in the HMA glaciers will remain by the end of the century. The 1.5 °C goal is extremely ambitious and is projected by only a small number of climate models of the conservative IPCC’s Representative Concentration Pathway (RCP)2.6 ensemble. Projections for RCP4.5, RCP6.0 and RCP8.5 reveal that much of the glacier ice is likely to disappear, with projected mass losses of 49 ± 7 per cent, 51 ± 6 per cent and 64 ± 5 per cent, respectively, by the end of the century; these projections have potentially serious consequences for regional water management and mountain communities.
Some contents have been Reproduced by permission of The Royal Society of Chemistry.
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