Wallpaper fermions and the nonsymmorphic Dirac insulator Science (IF 41.058) Pub Date : 2018-07-20 Benjamin J. Wieder, Barry Bradlyn, Zhijun Wang, Jennifer Cano, Youngkuk Kim, Hyeong-Seok D. Kim, Andrew M. Rappe, C. L. Kane, B. Andrei Bernevig
Materials whose gapless surface states are protected by crystal symmetries include mirror topological crystalline insulators and nonsymmorphic hourglass insulators. There exists only a very limited set of possible surface crystal symmetries, captured by the 17 “wallpaper groups.” Here we show that a consideration of symmetry-allowed band degeneracies in the wallpaper groups can be used to understand previously described topological crystalline insulators and to predict phenomenologically distinct examples. In particular, the two wallpaper groups with multiple glide lines, pgg and p4g, allow for a topological insulating phase whose surface spectrum consists of only a single, fourfold-degenerate, true Dirac fermion, representing an exception to a symmetry-enhanced fermion-doubling theorem. We theoretically predict the presence of this phase in Sr2Pb3 in space group 127 (P4/mbm).
Electrofluorochromism at the single-molecule level Science (IF 41.058) Pub Date : 2018-07-20 Benjamin Doppagne, Michael C. Chong, Hervé Bulou, Alex Boeglin, Fabrice Scheurer, Guillaume Schull
The interplay between the oxidation state and the optical properties of molecules is important for applications in displays, sensors, and molecular-based memories. The fundamental mechanisms occurring at the level of a single molecule have been difficult to probe. We used a scanning tunneling microscope (STM) to characterize and control the fluorescence of a single zinc-phthalocyanine radical cation adsorbed on a sodium chloride–covered gold (111) sample. The neutral and oxidized states of the molecule were identified on the basis of their fluorescence spectra, which revealed very different emission energies and vibronic fingerprints. The emission of the charged molecule was controlled by tuning the thickness of the insulator and the plasmons localized at the apex of the STM tip. In addition, subnanometric variations of the tip position were used to investigate the charging and electroluminescence mechanisms.
Emergence of coexisting ordered states in active matter systems Science (IF 41.058) Pub Date : 2018-07-20 L. Huber, R. Suzuki, T. Krüger, E. Frey, A. R. Bausch
Active systems can produce a far greater variety of ordered patterns than conventional equilibrium systems. In particular, transitions between disorder and either polar- or nematically ordered phases have been predicted and observed in two-dimensional active systems. However, coexistence between phases of different types of order has not been reported. We demonstrate the emergence of dynamic coexistence of ordered states with fluctuating nematic and polar symmetry in an actomyosin motility assay. Combining experiments with agent-based simulations, we identify sufficiently weak interactions that lack a clear alignment symmetry as a prerequisite for coexistence. Thus, the symmetry of macroscopic order becomes an emergent and dynamic property of the active system. These results provide a pathway by which living systems can express different types of order by using identical building blocks.
Cavity-mediated collective spin-exchange interactions in a strontium superradiant laser Science (IF 41.058) Pub Date : 2018-07-20 Matthew A. Norcia, Robert J. Lewis-Swan, Julia R. K. Cline, Bihui Zhu, Ana M. Rey, James K. Thompson
Laser-cooled and quantum degenerate atoms are being pursued as quantum simulators and form the basis of today’s most precise sensors. A key challenge toward these goals is to understand and control coherent interactions between the atoms. We observe long-range exchange interactions mediated by an optical cavity, which manifest as tunable spin-spin interactions on the pseudo spin-½ system composed of the millihertz linewidth clock transition in strontium. This leads to one-axis twisting dynamics, the emergence of a many-body energy gap, and gap protection of the optical coherence against certain sources of decoherence. Our observations will aid in the future design of versatile quantum simulators and the next generation of atomic clocks that use quantum correlations for enhanced metrology.
Torsional instability in the single-chain limit of a transition metal trichalcogenide Science (IF 41.058) Pub Date : 2018-07-20 Thang Pham, Sehoon Oh, Patrick Stetz, Seita Onishi, Christian Kisielowski, Marvin L. Cohen, Alex Zettl
The scientific bounty resulting from the successful isolation of few to single layers of two-dimensional materials suggests that related new physics resides in the few- to single-chain limit of one-dimensional materials. We report the synthesis of the quasi–one-dimensional transition metal trichalcogenide NbSe3 (niobium triselenide) in the few-chain limit, including the realization of isolated single chains. The chains are encapsulated in protective boron nitride or carbon nanotube sheaths to prevent oxidation and to facilitate characterization. Transmission electron microscopy reveals static and dynamic structural torsional waves not found in bulk NbSe3 crystals. Electronic structure calculations indicate that charge transfer drives the torsional wave instability. Very little covalent bonding is found between the chains and the nanotube sheath, leading to relatively unhindered longitudinal and torsional dynamics for the encapsulated chains.
Fault-tolerant detection of a quantum error Science (IF 41.058) Pub Date : 2018-07-20 S. Rosenblum, P. Reinhold, M. Mirrahimi, Liang Jiang, L. Frunzio, R. J. Schoelkopf
A critical component of any quantum error–correcting scheme is detection of errors by using an ancilla system. However, errors occurring in the ancilla can propagate onto the logical qubit, irreversibly corrupting the encoded information. We demonstrate a fault-tolerant error-detection scheme that suppresses spreading of ancilla errors by a factor of 5, while maintaining the assignment fidelity. The same method is used to prevent propagation of ancilla excitations, increasing the logical qubit dephasing time by an order of magnitude. Our approach is hardware-efficient, as it uses a single multilevel transmon ancilla and a cavity-encoded logical qubit, whose interaction is engineered in situ by using an off-resonant sideband drive. The results demonstrate that hardware-efficient approaches that exploit system-specific error models can yield advances toward fault-tolerant quantum computation.
The South Asian monsoon—pollution pump and purifier Science (IF 41.058) Pub Date : 2018-07-20 J. Lelieveld, E. Bourtsoukidis, C. Brühl, H. Fischer, H. Fuchs, H. Harder, A. Hofzumahaus, F. Holland, D. Marno, M. Neumaier, A. Pozzer, H. Schlager, J. Williams, A. Zahn, H. Ziereis
Air pollution is growing fastest in monsoon-affected South Asia. During the dry winter monsoon, the fumes disperse toward the Indian Ocean, creating a vast pollution haze, but their fate during the wet summer monsoon has been unclear. We performed atmospheric chemistry measurements by aircraft in the Oxidation Mechanism Observations campaign, sampling the summer monsoon outflow in the upper troposphere between the Mediterranean and the Indian Ocean. The measurements, supported by model calculations, show that the monsoon sustains a remarkably efficient cleansing mechanism by which contaminants are rapidly oxidized and deposited to Earth’s surface. However, some pollutants are lofted above the monsoon clouds and chemically processed in a reactive reservoir before being redistributed globally, including to the stratosphere.
Friction at the bed does not control fast glacier flow Science (IF 41.058) Pub Date : 2018-07-20 L. A. Stearns, C. J. van der Veen
The largest uncertainty in the ice sheet models used to predict future sea level rise originates from our limited understanding of processes at the ice/bed interface. Near glacier termini, where basal sliding controls ice flow, most predictive ice sheet models use a parameterization of sliding that has been theoretically derived for glacier flow over a hard bed. We find that this sliding relation does not apply to the 140 Greenland glaciers that we analyzed. There is no relationship between basal sliding and frictional stress at the glacier bed, contrary to theoretical predictions. There is a strong relationship between sliding speed and net pressure at the glacier bed. This latter finding is in agreement with earlier observations of mountain glaciers that have been largely overlooked by the glaciological community.
Atmospheric new particle formation from sulfuric acid and amines in a Chinese megacity Science (IF 41.058) Pub Date : 2018-07-20 Lei Yao, Olga Garmash, Federico Bianchi, Jun Zheng, Chao Yan, Jenni Kontkanen, Heikki Junninen, Stephany Buenrostro Mazon, Mikael Ehn, Pauli Paasonen, Mikko Sipilä, Mingyi Wang, Xinke Wang, Shan Xiao, Hangfei Chen, Yiqun Lu, Bowen Zhang, Dongfang Wang, Qingyan Fu, Fuhai Geng, Li Li, Hongli Wang, Liping Qiao, Xin Yang, Jianmin Chen, Veli-Matti Kerminen, Tuukka Petäjä, Douglas R. Worsnop, Markku Kulmala, Lin Wang
Atmospheric new particle formation (NPF) is an important global phenomenon that is nevertheless sensitive to ambient conditions. According to both observation and theoretical arguments, NPF usually requires a relatively high sulfuric acid (H2SO4) concentration to promote the formation of new particles and a low preexisting aerosol loading to minimize the sink of new particles. We investigated NPF in Shanghai and were able to observe both precursor vapors (H2SO4) and initial clusters at a molecular level in a megacity. High NPF rates were observed to coincide with several familiar markers suggestive of H2SO4–dimethylamine (DMA)–water (H2O) nucleation, including sulfuric acid dimers and H2SO4-DMA clusters. In a cluster kinetics simulation, the observed concentration of sulfuric acid was high enough to explain the particle growth to ~3 nanometers under the very high condensation sink, whereas the subsequent higher growth rate beyond this size is believed to result from the added contribution of condensing organic species. These findings will help in understanding urban NPF and its air quality and climate effects, as well as in formulating policies to mitigate secondary particle formation in China.
Mesophotic coral ecosystems are threatened and ecologically distinct from shallow water reefs Science (IF 41.058) Pub Date : 2018-07-20 Luiz A. Rocha, Hudson T. Pinheiro, Bart Shepherd, Yannis P. Papastamatiou, Osmar J. Luiz, Richard L. Pyle, Pim Bongaerts
The rapid degradation of coral reefs is one of the most serious biodiversity problems facing our generation. Mesophotic coral reefs (at depths of 30 to 150 meters) have been widely hypothesized to provide refuge from natural and anthropogenic impacts, a promise for the survival of shallow reefs. The potential role of mesophotic reefs as universal refuges is often highlighted in reef conservation research. This hypothesis rests on two assumptions: (i) that there is considerable overlap in species composition and connectivity between shallow and deep populations and (ii) that deep reefs are less susceptible to anthropogenic and natural impacts than their shallower counterparts. Here we present evidence contradicting these assumptions and argue that mesophotic reefs are distinct, impacted, and in as much need of protection as shallow coral reefs.
Domain-focused CRISPR screen identifies HRI as a fetal hemoglobin regulator in human erythroid cells Science (IF 41.058) Pub Date : 2018-07-20 Jeremy D. Grevet, Xianjiang Lan, Nicole Hamagami, Christopher R. Edwards, Laavanya Sankaranarayanan, Xinjun Ji, Saurabh K. Bhardwaj, Carolyne J. Face, David F. Posocco, Osheiza Abdulmalik, Cheryl A. Keller, Belinda Giardine, Simone Sidoli, Ben A. Garcia, Stella T. Chou, Stephen A. Liebhaber, Ross C. Hardison, Junwei Shi, Gerd A. Blobel
Increasing fetal hemoglobin (HbF) levels in adult red blood cells provides clinical benefit to patients with sickle cell disease and some forms of β-thalassemia. To identify potentially druggable HbF regulators in adult human erythroid cells, we employed a protein kinase domain–focused CRISPR-Cas9–based genetic screen with a newly optimized single-guide RNA scaffold. The screen uncovered the heme-regulated inhibitor HRI (also known as EIF2AK1), an erythroid-specific kinase that controls protein translation, as an HbF repressor. HRI depletion markedly increased HbF production in a specific manner and reduced sickling in cultured erythroid cells. Diminished expression of the HbF repressor BCL11A accounted in large part for the effects of HRI depletion. Taken together, these results suggest HRI as a potential therapeutic target for hemoglobinopathies.
VHL substrate transcription factor ZHX2 as an oncogenic driver in clear cell renal cell carcinoma Science (IF 41.058) Pub Date : 2018-07-20 Jing Zhang, Tao Wu, Jeremy Simon, Mamoru Takada, Ryoichi Saito, Cheng Fan, Xian-De Liu, Eric Jonasch, Ling Xie, Xian Chen, Xiaosai Yao, Bin Tean Teh, Patrick Tan, Xingnan Zheng, Mingjie Li, Cortney Lawrence, Jie Fan, Jiang Geng, Xijuan Liu, Lianxin Hu, Jun Wang, Chengheng Liao, Kai Hong, Giada Zurlo, Joel S. Parker, J. Todd Auman, Charles M. Perou, W. Kimryn Rathmell, William Y. Kim, Marc W. Kirschner, William G. Kaelin, Albert S. Baldwin, Qing Zhang
Inactivation of the von Hippel-Lindau (VHL) E3 ubiquitin ligase protein is a hallmark of clear cell renal cell carcinoma (ccRCC). Identifying how pathways affected by VHL loss contribute to ccRCC remains challenging. We used a genome-wide in vitro expression strategy to identify proteins that bind VHL when hydroxylated. Zinc fingers and homeoboxes 2 (ZHX2) was found as a VHL target, and its hydroxylation allowed VHL to regulate its protein stability. Tumor cells from ccRCC patients with VHL loss-of-function mutations usually had increased abundance and nuclear localization of ZHX2. Functionally, depletion of ZHX2 inhibited VHL-deficient ccRCC cell growth in vitro and in vivo. Mechanistically, integrated chromatin immunoprecipitation sequencing and microarray analysis showed that ZHX2 promoted nuclear factor κB activation. These studies reveal ZHX2 as a potential therapeutic target for ccRCC.
Meat consumption, health, and the environment Science (IF 41.058) Pub Date : 2018-07-20 H. Charles J. Godfray, Paul Aveyard, Tara Garnett, Jim W. Hall, Timothy J. Key, Jamie Lorimer, Ray T. Pierrehumbert, Peter Scarborough, Marco Springmann, Susan A. Jebb
Both the global average per capita consumption of meat and the total amount of meat consumed are rising, driven by increasing average individual incomes and by population growth. The consumption of different types of meat and meat products has substantial effects on people’s health, and livestock production can have major negative effects on the environment. Here, we explore the evidence base for these assertions and the options policy-makers have should they wish to intervene to affect population meat consumption. We highlight where more research is required and the great importance of integrating insights from the natural and social sciences.
Modeling the ecology and evolution of biodiversity: Biogeographical cradles, museums, and graves Science (IF 41.058) Pub Date : 2018-07-20 Thiago F. Rangel, Neil R. Edwards, Philip B. Holden, José Alexandre F. Diniz-Filho, William D. Gosling, Marco Túlio P. Coelho, Fernanda A. S. Cassemiro, Carsten Rahbek, Robert K. Colwell
Individual processes shaping geographical patterns of biodiversity are increasingly understood, but their complex interactions on broad spatial and temporal scales remain beyond the reach of analytical models and traditional experiments. To meet this challenge, we built a spatially explicit, mechanistic simulation model implementing adaptation, range shifts, fragmentation, speciation, dispersal, competition, and extinction, driven by modeled climates of the past 800,000 years in South America. Experimental topographic smoothing confirmed the impact of climate heterogeneity on diversification. The simulations identified regions and episodes of speciation (cradles), persistence (museums), and extinction (graves). Although the simulations had no target pattern and were not parameterized with empirical data, emerging richness maps closely resembled contemporary maps for major taxa, confirming powerful roles for evolution and diversification driven by topography and climate.
Human influence on the seasonal cycle of tropospheric temperature Science (IF 41.058) Pub Date : 2018-07-20 Benjamin D. Santer, Stephen Po-Chedley, Mark D. Zelinka, Ivana Cvijanovic, Céline Bonfils, Paul J. Durack, Qiang Fu, Jeffrey Kiehl, Carl Mears, Jeffrey Painter, Giuliana Pallotta, Susan Solomon, Frank J. Wentz, Cheng-Zhi Zou
We provide scientific evidence that a human-caused signal in the seasonal cycle of tropospheric temperature has emerged from the background noise of natural variability. Satellite data and the anthropogenic “fingerprint” predicted by climate models show common large-scale changes in geographical patterns of seasonal cycle amplitude. These common features include increases in amplitude at mid-latitudes in both hemispheres, amplitude decreases at high latitudes in the Southern Hemisphere, and small changes in the tropics. Simple physical mechanisms explain these features. The model fingerprint of seasonal cycle changes is identifiable with high statistical confidence in five out of six satellite temperature datasets. Our results suggest that attribution studies with the changing seasonal cycle provide powerful evidence for a significant human effect on Earth’s climate.
Optical skyrmion lattice in evanescent electromagnetic fields Science (IF 41.058) Pub Date : 2018-07-19 S. Tsesses, E. Ostrovsky, K. Cohen, B. Gjonaj, N. Lindner, G. Bartal
Topological defects play a key role in a variety of physical systems, ranging from high-energy to solid state physics. A skyrmion is a type of topological defect that has shown promise for applications in the fields of magnetic storage and spintronics. We show that optical skyrmion lattices can be generated using evanescent electromagnetic fields and demonstrate this using surface plasmon polaritons, imaged by phase-resolved near-field optical microscopy. We show how the optical skyrmion lattice exhibits robustness to imperfections while the topological domain walls in the lattice can be continuously tuned, changing the spatial structure of the skyrmions from bubble-type to Néel-type. Extending the generation of skyrmions to photonic systems provides various possibilities for applications in optical information processing, transfer and storage.
A molecular mechanism for Wnt ligand-specific signaling Science (IF 41.058) Pub Date : 2018-07-19 Marie Eubelen, Naguissa Bostaille, Pauline Cabochette, Anne Gauquier, Patricia Tebabi, Andra C. Dumitru, Melanie Koehler, Philipp Gut, David Alsteens, Didier Y. R. Stainier, Abel Garcia-Pino, Benoit Vanhollebeke
Wnt signaling is key to many developmental, physiological and disease processes, in which cells seem able to discriminate between multiple Wnt ligands. This selective Wnt recognition or “decoding” capacity has remained enigmatic as Wnt/Frizzled interactions are largely incompatible with mono-specific recognition. Gpr124 and Reck enable brain endothelial cells to selectively respond to Wnt7. We show that Reck binds with low micromolar affinity to the intrinsically disordered linker region of Wnt7. Availability of Reck-bound Wnt7 for Frizzled signaling relies on the interaction between Gpr124 and Dishevelled. By polymerization, Dishevelled recruits Gpr124 and the associated Reck-bound Wnt7 into dynamic Wnt/Frizzled/Lrp5/6 signalosomes, resulting in increased local concentrations of Wnt7 available for Frizzled signaling. This work provides mechanistic insights into the Wnt decoding capacities of vertebrate cells and unravels structural determinants of the functional diversification of Wnt family members.
Large-scale ocean deoxygenation during the Paleocene-Eocene Thermal Maximum Science (IF 41.058) Pub Date : 2018-07-19 Weiqi Yao, Adina Paytan, Ulrich G. Wortmann
The consequences of global warming for fisheries are not well understood, but the geological record demonstrates that carbon cycle perturbations are frequently associated with ocean deoxygenation. Of particular interest is the Paleocene-Eocene Thermal Maximum (PETM) where the CO2 input into the atmosphere was similar to the IPCC RCP8.5 emission scenario. Here we present sulfur-isotope data which record a positive 1 ‰ excursion during the PETM. Modeling suggests that significant parts of the ocean must have become sulfidic. The toxicity of hydrogen sulfide will render two of the largest and least explored ecosystems on Earth, the mesopelagic and bathypelagic zones, uninhabitable by multi-cellular organisms. This will affect many marine species whose eco-zones stretch into the deep ocean.
Abrupt cloud clearing of marine stratocumulus in the subtropical southeast Atlantic Science (IF 41.058) Pub Date : 2018-07-19 Sandra E. Yuter, John D. Hader, Matthew A. Miller, David. B. Mechem
We document rapid and dramatic clearings of large portions of the subtropical marine low cloud deck that have implications for the global radiation balance and climate sensitivity. Over the southeast Atlantic, large areas of stratocumulus are rapidly eroded, yielding partial or complete clearing along sharp transitions hundreds to thousands of kilometers in length that move westward at 8 to 12 meters per second and travel as far as 1000+ kilometers from the African coast. The westward-moving cloudiness reductions have an annual peak in occurrence in April-May-June. The cloud erosion boundaries reduce cloud at ≈10-kilometer scale in less than 15 minutes, move approximately perpendicular to the mean flow, and are often accompanied by small-scale wave features. Observations suggest that the cloud erosion is caused by atmospheric gravity waves.
Biallelic RIPK1 mutations in humans cause severe immunodeficiency, arthritis, and intestinal inflammation Science (IF 41.058) Pub Date : 2018-07-19 Delphine Cuchet-Lourenço, Davide Eletto, Changxin Wu, Vincent Plagnol, Olivier Papapietro, James Curtis, Lourdes Ceron-Gutierrez, Chris M. Bacon, Scott Hackett, Badr Alsaleem, Mailis Maes, Miguel Gaspar, Ali Alisaac, Emma Goss, Eman AlIdrissi, Daniela Siegmund, Harald Wajant, Dinakantha Kumararatne, Mofareh S. AlZahrani, Peter D. Arkwright, Mario Abinun, Rainer Doffinger, Sergey Nejentsev
Receptor Interacting Serine/Threonine Kinase 1 (RIPK1) is a master regulator of signaling pathways leading to inflammation and cell death and is of medical interest as a drug target. Here, we report four patients from three unrelated families with complete RIPK1 deficiency caused by rare homozygous mutations. The patients suffered from recurrent infections, early-onset inflammatory bowel disease and progressive polyarthritis. They had immunodeficiency with lymphopenia and altered production of various cytokines revealed by whole-blood assays. In vitro, RIPK1-deficient cells showed impaired MAPK activation and cytokine secretion and were prone to necroptosis. Hematopoietic stem cell transplantation reversed cytokine production defects and resolved clinical symptoms in one patient. Thus, RIPK1 plays a critical role in the human immune system.
Mixed tailing by TENT4A and TENT4B shields mRNA from rapid deadenylation Science (IF 41.058) Pub Date : 2018-07-19 Jaechul Lim, Dongwan Kim, Young-suk Lee, Minju Ha, Mihye Lee, Jinah Yeo, Hyeshik Chang, Jaewon Song, Kwangseog Ahn, V. Narry Kim
RNA tails play integral roles in the regulation of mRNA translation and decay. Guanylation of poly(A) tail was discovered recently, yet the enzymology and function remain obscure. Here we identify TENT4A (PAPD7) and TENT4B (PAPD5) as the enzymes responsible for mRNA guanylation. Purified TENT4 proteins generate a mixed poly(A) tail with intermittent non-adenosine residues, favoring guanosine. A single guanosine is sufficient to impede deadenylase CCR4-NOT which trims the tail and exposes guanosine at the 3′ end. Consistently, depletion of TENT4A/B leads to a decrease in mRNA half-life and abundance in cells. Thus, TENT4A/B produce a mixed tail which shields mRNA from rapid deadenylation. Our study unveils the role of mixed tailing and expands the complexity of post-transcriptional gene regulation.
Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser Science (IF 41.058) Pub Date : 2018-07-13 Przemyslaw Nogly, Tobias Weinert, Daniel James, Sergio Carbajo, Dmitry Ozerov, Antonia Furrer, Dardan Gashi, Veniamin Borin, Petr Skopintsev, Kathrin Jaeger, Karol Nass, Petra Båth, Robert Bosman, Jason Koglin, Matthew Seaberg, Thomas Lane, Demet Kekilli, Steffen Brünle, Tomoyuki Tanaka, Wenting Wu, Christopher Milne, Thomas White, Anton Barty, Uwe Weierstall, Valerie Panneels, Eriko Nango, So Iwata, Mark Hunter, Igor Schapiro, Gebhard Schertler, Richard Neutze, Jörg Standfuss
Ultrafast isomerization of retinal is the primary step in photoresponsive biological functions including vision in humans and ion transport across bacterial membranes. We used an x-ray laser to study the subpicosecond structural dynamics of retinal isomerization in the light-driven proton pump bacteriorhodopsin. A series of structural snapshots with near-atomic spatial resolution and temporal resolution in the femtosecond regime show how the excited all-trans retinal samples conformational states within the protein binding pocket before passing through a twisted geometry and emerging in the 13-cis conformation. Our findings suggest ultrafast collective motions of aspartic acid residues and functional water molecules in the proximity of the retinal Schiff base as a key facet of this stereoselective and efficient photochemical reaction.
Neutrino emission from the direction of the blazar TXS 0506+056 prior to the IceCube-170922A alert Science (IF 41.058) Pub Date : 2018-07-13 IceCube Collaboration
A high-energy neutrino event detected by IceCube on 22 September 2017 was coincident in direction and time with a gamma-ray flare from the blazar TXS 0506+056. Prompted by this association, we investigated 9.5 years of IceCube neutrino observations to search for excess emission at the position of the blazar. We found an excess of high-energy neutrino events, with respect to atmospheric backgrounds, at that position between September 2014 and March 2015. Allowing for time-variable flux, this constitutes 3.5σ evidence for neutrino emission from the direction of TXS 0506+056, independent of and prior to the 2017 flaring episode. This suggests that blazars are identifiable sources of the high-energy astrophysical neutrino flux.
Metal-free three-dimensional perovskite ferroelectrics Science (IF 41.058) Pub Date : 2018-07-13 Heng-Yun Ye, Yuan-Yuan Tang, Peng-Fei Li, Wei-Qiang Liao, Ji-Xing Gao, Xiu-Ni Hua, Hu Cai, Ping-Ping Shi, Yu-Meng You, Ren-Gen Xiong
Inorganic perovskite ferroelectrics are widely used in nonvolatile memory elements, capacitors, and sensors because of their excellent ferroelectric and other properties. Organic ferroelectrics are desirable for their mechanical flexibility, low weight, environmentally friendly processing, and low processing temperatures. Although almost a century has passed since the first ferroelectric, Rochelle salt, was discovered, examples of highly desirable organic perovskite ferroelectrics are lacking. We found a family of metal-free organic perovskite ferroelectrics with the characteristic three-dimensional structure, among which MDABCO (N-methyl-N'-diazabicyclo[2.2.2]octonium)–ammonium triiodide has a spontaneous polarization of 22 microcoulombs per square centimeter [close to that of barium titanate (BTO)], a high phase transition temperature of 448 kelvins (above that of BTO), and eight possible polarization directions. These attributes make it attractive for use in flexible devices, soft robotics, biomedical devices, and other applications.
Programming self-organizing multicellular structures with synthetic cell-cell signaling Science (IF 41.058) Pub Date : 2018-07-13 Satoshi Toda, Lucas R. Blauch, Sindy K. Y. Tang, Leonardo Morsut, Wendell A. Lim
A common theme in the self-organization of multicellular tissues is the use of cell-cell signaling networks to induce morphological changes. We used the modular synNotch juxtacrine signaling platform to engineer artificial genetic programs in which specific cell-cell contacts induced changes in cadherin cell adhesion. Despite their simplicity, these minimal intercellular programs were sufficient to yield assemblies with hallmarks of natural developmental systems: robust self-organization into multidomain structures, well-choreographed sequential assembly, cell type divergence, symmetry breaking, and the capacity for regeneration upon injury. The ability of these networks to drive complex structure formation illustrates the power of interlinking cell signaling with cell sorting: Signal-induced spatial reorganization alters the local signals received by each cell, resulting in iterative cycles of cell fate branching. These results provide insights into the evolution of multicellularity and demonstrate the potential to engineer customized self-organizing tissues or materials.
Phase transitions in a programmable quantum spin glass simulator Science (IF 41.058) Pub Date : 2018-07-13 R. Harris, Y. Sato, A. J. Berkley, M. Reis, F. Altomare, M. H. Amin, K. Boothby, P. Bunyk, C. Deng, C. Enderud, S. Huang, E. Hoskinson, M. W. Johnson, E. Ladizinsky, N. Ladizinsky, T. Lanting, R. Li, T. Medina, R. Molavi, R. Neufeld, T. Oh, I. Pavlov, I. Perminov, G. Poulin-Lamarre, C. Rich, A. Smirnov, L. Swenson, N. Tsai, M. Volkmann, J. Whittaker, J. Yao
Understanding magnetic phases in quantum mechanical systems is one of the essential goals in condensed matter physics, and the advent of prototype quantum simulation hardware has provided new tools for experimentally probing such systems. We report on the experimental realization of a quantum simulation of interacting Ising spins on three-dimensional cubic lattices up to dimensions 8 × 8 × 8 on a D-Wave processor (D-Wave Systems, Burnaby, Canada). The ability to control and read out the state of individual spins provides direct access to several order parameters, which we used to determine the lattice’s magnetic phases as well as critical disorder and one of its universal exponents. By tuning the degree of disorder and effective transverse magnetic field, we observed phase transitions between a paramagnetic, an antiferromagnetic, and a spin-glass phase.
The rise, collapse, and compaction of Mt. Mantap from the 3 September 2017 North Korean nuclear test Science (IF 41.058) Pub Date : 2018-07-13 Teng Wang, Qibin Shi, Mehdi Nikkhoo, Shengji Wei, Sylvain Barbot, Douglas Dreger, Roland Bürgmann, Mahdi Motagh, Qi-Fu Chen
Surveillance of clandestine nuclear tests relies on a global seismic network, but the potential of spaceborne monitoring has been underexploited. We used satellite radar imagery to determine the complete surface displacement field of up to 3.5 meters of divergent horizontal motion with 0.5 meters of subsidence associated with North Korea’s largest underground nuclear test. Combining insight from geodetic and seismological remote sensing, we found that the aftermath of the initial explosive deformation involved subsidence associated with subsurface collapse and aseismic compaction of the damaged rocks of the test site. The explosive yield from the nuclear detonation with best-fitting source parameters for 450-meter depth was 191 kilotonnes of TNT equivalent. Our results demonstrate the capability of spaceborne remote sensing to help characterize large underground nuclear tests.
Deconstructive fluorination of cyclic amines by carbon-carbon cleavage Science (IF 41.058) Pub Date : 2018-07-13 Jose B. Roque, Yusuke Kuroda, Lucas T. Göttemann, Richmond Sarpong
Deconstructive functionalizations involving scission of carbon-carbon double bonds are well established. In contrast, unstrained C(sp3)–C(sp3) bond cleavage and functionalization have less precedent. Here we report the use of deconstructive fluorination to access mono- and difluorinated amine derivatives by C(sp3)–C(sp3) bond cleavage in saturated nitrogen heterocycles such as piperidines and pyrrolidines. Silver-mediated ring-opening fluorination using Selectfluor highlights a strategy for cyclic amine functionalization and late-stage skeletal diversification, establishing cyclic amines as synthons for amino alkyl radicals and providing synthetic routes to valuable building blocks.
Late inception of a resiliently oxygenated upper ocean Science (IF 41.058) Pub Date : 2018-07-13 Wanyi Lu, Andy Ridgwell, Ellen Thomas, Dalton S. Hardisty, Genming Luo, Thomas J. Algeo, Matthew R. Saltzman, Benjamin C. Gill, Yanan Shen, Hong-Fei Ling, Cole T. Edwards, Michael T. Whalen, Xiaoli Zhou, Kristina M. Gutchess, Li Jin, Rosalind E. M. Rickaby, Hugh C. Jenkyns, Timothy W. Lyons, Timothy M. Lenton, Lee R. Kump, Zunli Lu
Rising oceanic and atmospheric oxygen levels through time have been crucial to enhanced habitability of surface Earth environments. Few redox proxies can track secular variations in dissolved oxygen concentrations around threshold levels for metazoan survival in the upper ocean. We present an extensive compilation of iodine-to-calcium ratios (I/Ca) in marine carbonates. Our record supports a major rise in the partial pressure of oxygen in the atmosphere at ~400 million years (Ma) ago and reveals a step change in the oxygenation of the upper ocean to relatively sustainable near-modern conditions at ~200 Ma ago. An Earth system model demonstrates that a shift in organic matter remineralization to greater depths, which may have been due to increasing size and biomineralization of eukaryotic plankton, likely drove the I/Ca signals at ~200 Ma ago.
Sensitivity to “sunk costs” in mice, rats, and humans Science (IF 41.058) Pub Date : 2018-07-13 Brian M. Sweis, Samantha V. Abram, Brandy J. Schmidt, Kelsey D. Seeland, Angus W. MacDonald, Mark J. Thomas, A. David Redish
Sunk costs are irrecoverable investments that should not influence decisions, because decisions should be made on the basis of expected future consequences. Both human and nonhuman animals can show sensitivity to sunk costs, but reports from across species are inconsistent. In a temporal context, a sensitivity to sunk costs arises when an individual resists ending an activity, even if it seems unproductive, because of the time already invested. In two parallel foraging tasks that we designed, we found that mice, rats, and humans show similar sensitivities to sunk costs in their decision-making. Unexpectedly, sensitivity to time invested accrued only after an initial decision had been made. These findings suggest that sensitivity to temporal sunk costs lies in a vulnerability distinct from deliberation processes and that this distinction is present across species.
Ethylene-gibberellin signaling underlies adaptation of rice to periodic flooding Science (IF 41.058) Pub Date : 2018-07-13 Takeshi Kuroha, Keisuke Nagai, Rico Gamuyao, Diane R. Wang, Tomoyuki Furuta, Masanari Nakamori, Takuya Kitaoka, Keita Adachi, Anzu Minami, Yoshinao Mori, Kiyoshi Mashiguchi, Yoshiya Seto, Shinjiro Yamaguchi, Mikiko Kojima, Hitoshi Sakakibara, Jianzhong Wu, Kaworu Ebana, Nobutaka Mitsuda, Masaru Ohme-Takagi, Shuichi Yanagisawa, Masanori Yamasaki, Ryusuke Yokoyama, Kazuhiko Nishitani, Toshihiro Mochizuki, Gen Tamiya, Susan R. McCouch, Motoyuki Ashikari
Most plants do poorly when flooded. Certain rice varieties, known as deepwater rice, survive periodic flooding and consequent oxygen deficiency by activating internode growth of stems to keep above the water. Here, we identify the gibberellin biosynthesis gene, SD1 (SEMIDWARF1), whose loss-of-function allele catapulted the rice Green Revolution, as being responsible for submergence-induced internode elongation. When submerged, plants carrying the deepwater rice–specific SD1 haplotype amplify a signaling relay in which the SD1 gene is transcriptionally activated by an ethylene-responsive transcription factor, OsEIL1a. The SD1 protein directs increased synthesis of gibberellins, largely GA4, which promote internode elongation. Evolutionary analysis shows that the deepwater rice–specific haplotype was derived from standing variation in wild rice and selected for deepwater rice cultivation in Bangladesh.
Assessment of methane emissions from the U.S. oil and gas supply chain Science (IF 41.058) Pub Date : 2018-07-13 Ramón A. Alvarez, Daniel Zavala-Araiza, David R. Lyon, David T. Allen, Zachary R. Barkley, Adam R. Brandt, Kenneth J. Davis, Scott C. Herndon, Daniel J. Jacob, Anna Karion, Eric A. Kort, Brian K. Lamb, Thomas Lauvaux, Joannes D. Maasakkers, Anthony J. Marchese, Mark Omara, Stephen W. Pacala, Jeff Peischl, Allen L. Robinson, Paul B. Shepson, Colm Sweeney, Amy Townsend-Small, Steven C. Wofsy, Steven P. Hamburg
Methane emissions from the U.S. oil and natural gas supply chain were estimated by using ground-based, facility-scale measurements and validated with aircraft observations in areas accounting for ~30% of U.S. gas production. When scaled up nationally, our facility-based estimate of 2015 supply chain emissions is 13 ± 2 teragrams per year, equivalent to 2.3% of gross U.S. gas production. This value is ~60% higher than the U.S. Environmental Protection Agency inventory estimate, likely because existing inventory methods miss emissions released during abnormal operating conditions. Methane emissions of this magnitude, per unit of natural gas consumed, produce radiative forcing over a 20-year time horizon comparable to the CO2 from natural gas combustion. Substantial emission reductions are feasible through rapid detection of the root causes of high emissions and deployment of less failure-prone systems.
Dual-spindle formation in zygotes keeps parental genomes apart in early mammalian embryos Science (IF 41.058) Pub Date : 2018-07-13 Judith Reichmann, Bianca Nijmeijer, M. Julius Hossain, Manuel Eguren, Isabell Schneider, Antonio Z. Politi, M. Julia Roberti, Lars Hufnagel, Takashi Hiiragi, Jan Ellenberg
At the beginning of mammalian life, the genetic material from each parent meets when the fertilized egg divides. It was previously thought that a single microtubule spindle is responsible for spatially combining the two genomes and then segregating them to create the two-cell embryo. We used light-sheet microscopy to show that two bipolar spindles form in the zygote and then independently congress the maternal and paternal genomes. These two spindles aligned their poles before anaphase but kept the parental genomes apart during the first cleavage. This spindle assembly mechanism provides a potential rationale for erroneous divisions into more than two blastomeric nuclei observed in mammalian zygotes and reveals the mechanism behind the observation that parental genomes occupy separate nuclear compartments in the two-cell embryo.
Multimessenger observations of a flaring blazar coincident with high-energy neutrino IceCube-170922A Science (IF 41.058) Pub Date : 2018-07-13 The IceCube Collaboration, Fermi-LAT, MAGIC, AGILE, ASAS-SN, HAWC, H.E.S.S., INTEGRAL, Kanata, Kiso, Kapteyn, Liverpool Telescope, Subaru, Swift/NuSTAR, VERITAS, VLA/17B-403 teams
Previous detections of individual astrophysical sources of neutrinos are limited to the Sun and the supernova 1987A, whereas the origins of the diffuse flux of high-energy cosmic neutrinos remain unidentified. On 22 September 2017, we detected a high-energy neutrino, IceCube-170922A, with an energy of ~290 tera–electron volts. Its arrival direction was consistent with the location of a known γ-ray blazar, TXS 0506+056, observed to be in a flaring state. An extensive multiwavelength campaign followed, ranging from radio frequencies to γ-rays. These observations characterize the variability and energetics of the blazar and include the detection of TXS 0506+056 in very-high-energy γ-rays. This observation of a neutrino in spatial coincidence with a γ-ray–emitting blazar during an active phase suggests that blazars may be a source of high-energy neutrinos.
Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis Science (IF 41.058) Pub Date : 2018-07-13 Maximilian Griesmann, Yue Chang, Xin Liu, Yue Song, Georg Haberer, Matthew B. Crook, Benjamin Billault-Penneteau, Dominique Lauressergues, Jean Keller, Leandro Imanishi, Yuda Purwana Roswanjaya, Wouter Kohlen, Petar Pujic, Kai Battenberg, Nicole Alloisio, Yuhu Liang, Henk Hilhorst, Marco G. Salgado, Valerie Hocher, Hassen Gherbi, Sergio Svistoonoff, Jeff J. Doyle, Shixu He, Yan Xu, Shanyun Xu, Jing Qu, Qiang Gao, Xiaodong Fang, Yuan Fu, Philippe Normand, Alison M. Berry, Luis G. Wall, Jean-Michel Ané, Katharina Pawlowski, Xun Xu, Huanming Yang, Manuel Spannagl, Klaus F. X. Mayer, Gane Ka-Shu Wong, Martin Parniske, Pierre-Marc Delaux, Shifeng Cheng
The root nodule symbiosis of plants with nitrogen-fixing bacteria affects global nitrogen cycles and food production but is restricted to a subset of genera within a single clade of flowering plants. To explore the genetic basis for this scattered occurrence, we sequenced the genomes of 10 plant species covering the diversity of nodule morphotypes, bacterial symbionts, and infection strategies. In a genome-wide comparative analysis of a total of 37 plant species, we discovered signatures of multiple independent loss-of-function events in the indispensable symbiotic regulator NODULE INCEPTION in 10 of 13 genomes of nonnodulating species within this clade. The discovery that multiple independent losses shaped the present-day distribution of nitrogen-fixing root nodule symbiosis in plants reveals a phylogenetically wider distribution in evolutionary history and a so-far-underestimated selection pressure against this symbiosis.
Single-crystal x-ray diffraction structures of covalent organic frameworks Science (IF 41.058) Pub Date : 2018-07-06 Tianqiong Ma, Eugene A. Kapustin, Shawn X. Yin, Lin Liang, Zhengyang Zhou, Jing Niu, Li-Hua Li, Yingying Wang, Jie Su, Jian Li, Xiaoge Wang, Wei David Wang, Wei Wang, Junliang Sun, Omar M. Yaghi
The crystallization problem is an outstanding challenge in the chemistry of porous covalent organic frameworks (COFs). Their structural characterization has been limited to modeling and solutions based on powder x-ray or electron diffraction data. Single crystals of COFs amenable to x-ray diffraction characterization have not been reported. Here, we developed a general procedure to grow large single crystals of three-dimensional imine-based COFs (COF-300, hydrated form of COF-300, COF-303, LZU-79, and LZU-111). The high quality of the crystals allowed collection of single-crystal x-ray diffraction data of up to 0.83-angstrom resolution, leading to unambiguous solution and precise anisotropic refinement. Characteristics such as degree of interpenetration, arrangement of water guests, the reversed imine connectivity, linker disorder, and uncommon topology were deciphered with atomic precision—aspects impossible to determine without single crystals.
Atmospheric blocking as a traffic jam in the jet stream Science (IF 41.058) Pub Date : 2018-07-06 Noboru Nakamura, Clare S. Y. Huang
Atmospheric blocking due to anomalous, persistent meandering of the jet stream often causes weather extremes in the mid-latitudes. Despite the ubiquity of blocking, the onset mechanism is not well understood. Here we demonstrate a close analogy between blocking and traffic congestion on a highway by using meteorological data and show that blocking and traffic congestion can be described by a common mathematical theory. The theory predicts that the jet stream has a capacity for the flux of wave activity (a measure of meandering), just as the highway has traffic capacity, and when the capacity is exceeded, blocking manifests as congestion. Stationary waves modulate the jet stream’s capacity for transient waves and localize block formation. Climate change likely affects blocking frequency by modifying the jet stream’s proximity to capacity.
Seeded growth of single-crystal two-dimensional covalent organic frameworks Science (IF 41.058) Pub Date : 2018-07-06 Austin M. Evans, Lucas R. Parent, Nathan C. Flanders, Ryan P. Bisbey, Edon Vitaku, Matthew S. Kirschner, Richard D. Schaller, Lin X. Chen, Nathan C. Gianneschi, William R. Dichtel
Polymerization of monomers into periodic two-dimensional networks provides structurally precise, layered macromolecular sheets that exhibit desirable mechanical, optoelectronic, and molecular transport properties. Two-dimensional covalent organic frameworks (2D COFs) offer broad monomer scope but are generally isolated as powders comprising aggregated nanometer-scale crystallites. We found that 2D COF formation could be controlled using a two-step procedure in which monomers are added slowly to preformed nanoparticle seeds. The resulting 2D COFs are isolated as single-crystalline, micrometer-sized particles. Transient absorption spectroscopy of the dispersed COF nanoparticles revealed improvement in signal quality by two to three orders of magnitude relative to polycrystalline powder samples, and suggests exciton diffusion over longer length scales than those obtained through previous approaches. These findings should enable a broad exploration of synthetic 2D polymer structures and properties.
A single-photon switch and transistor enabled by a solid-state quantum memory Science (IF 41.058) Pub Date : 2018-07-06 Shuo Sun, Hyochul Kim, Zhouchen Luo, Glenn S. Solomon, Edo Waks
Single-photon switches and transistors generate strong photon-photon interactions that are essential for quantum circuits and networks. However, the deterministic control of an optical signal with a single photon requires strong interactions with a quantum memory, which has been challenging to achieve in a solid-state platform. We demonstrate a single-photon switch and transistor enabled by a solid-state quantum memory. Our device consists of a semiconductor spin qubit strongly coupled to a nanophotonic cavity. The spin qubit enables a single 63-picosecond gate photon to switch a signal field containing up to an average of 27.7 photons before the internal state of the device resets. Our results show that semiconductor nanophotonic devices can produce strong and controlled photon-photon interactions that could enable high-bandwidth photonic quantum information processing.
Observation of an environmentally insensitive solid-state spin defect in diamond Science (IF 41.058) Pub Date : 2018-07-06 Brendon C. Rose, Ding Huang, Zi-Huai Zhang, Paul Stevenson, Alexei M. Tyryshkin, Sorawis Sangtawesin, Srikanth Srinivasan, Lorne Loudin, Matthew L. Markham, Andrew M. Edmonds, Daniel J. Twitchen, Stephen A. Lyon, Nathalie P. de Leon
Engineering coherent systems is a central goal of quantum science. Color centers in diamond are a promising approach, with the potential to combine the coherence of atoms with the scalability of a solid-state platform. We report a color center that shows insensitivity to environmental decoherence caused by phonons and electric field noise: the neutral charge state of silicon vacancy (SiV0). Through careful materials engineering, we achieved >80% conversion of implanted silicon to SiV0. SiV0 exhibits spin-lattice relaxation times approaching 1 minute and coherence times approaching 1 second. Its optical properties are very favorable, with ~90% of its emission into the zero-phonon line and near–transform-limited optical linewidths. These combined properties make SiV0 a promising defect for quantum network applications.
Imaging CF3I conical intersection and photodissociation dynamics with ultrafast electron diffraction Science (IF 41.058) Pub Date : 2018-07-06 Jie Yang, Xiaolei Zhu, Thomas J. A. Wolf, Zheng Li, J. Pedro F. Nunes, Ryan Coffee, James P. Cryan, Markus Gühr, Kareem Hegazy, Tony F. Heinz, Keith Jobe, Renkai Li, Xiaozhe Shen, Theodore Veccione, Stephen Weathersby, Kyle J. Wilkin, Charles Yoneda, Qiang Zheng, Todd J. Martinez, Martin Centurion, Xijie Wang
Conical intersections play a critical role in excited-state dynamics of polyatomic molecules because they govern the reaction pathways of many nonadiabatic processes. However, ultrafast probes have lacked sufficient spatial resolution to image wave-packet trajectories through these intersections directly. Here, we present the simultaneous experimental characterization of one-photon and two-photon excitation channels in isolated CF3I molecules using ultrafast gas-phase electron diffraction. In the two-photon channel, we have mapped out the real-space trajectories of a coherent nuclear wave packet, which bifurcates onto two potential energy surfaces when passing through a conical intersection. In the one-photon channel, we have resolved excitation of both the umbrella and the breathing vibrational modes in the CF3 fragment in multiple nuclear dimensions. These findings benchmark and validate ab initio nonadiabatic dynamics calculations.
Tandem catalysis for asymmetric coupling of ethylene and enynes to functionalized cyclobutanes Science (IF 41.058) Pub Date : 2018-07-06 Vinayak Vishnu Pagar, T. V. RajanBabu
Transformation of simple precursors into structurally complex cyclobutanes, present in many biologically important natural products and pharmaceuticals, is of considerable interest in medicinal chemistry. Starting from 1,3-enynes and ethylene, both exceptionally inexpensive starting materials, we report a cobalt-catalyzed route to vinylcyclobutenes, as well as the further enantioselective addition of ethylene to these products to form complex cyclobutanes with all-carbon quaternary centers. These reactions can proceed in discrete stages or in a tandem fashion to achieve three highly selective carbon-carbon bond formations in one pot using a single chiral cobalt catalyst.
Biological uptake and reversible scavenging of zinc in the global ocean Science (IF 41.058) Pub Date : 2018-07-06 Thomas Weber, Seth John, Alessandro Tagliabue, Tim DeVries
Zinc (Zn) is a key micronutrient for marine phytoplankton, with a global distribution that is similar to silicic acid. The processes that govern this relationship, despite the very different biological cycling of Zn and silica, remain poorly understood. Here, we use diagnostic and mechanistic models to show that only a combination of Southern Ocean biological uptake and reversible scavenging of Zn onto sinking particles can explain the observations. The distinction between organic and adsorbed Zn can also reconcile the vertical distribution and mass balance of Zn isotopes, which previously appeared at odds. This holistic understanding explains the Zn deficiencies observed throughout the low-latitude ocean and implies a greater sensitivity of the marine Zn cycle to climate-driven changes in organic matter cycling than previously recognized.
Regulation of feeding by somatostatin neurons in the tuberal nucleus Science (IF 41.058) Pub Date : 2018-07-06 Sarah Xinwei Luo, Ju Huang, Qin Li, Hasan Mohammad, Chun-Yao Lee, Kumar Krishna, Alison Maun-Yeng Kok, Yu Lin Tan, Joy Yi Lim, Hongyu Li, Ling Yun Yeow, Jingjing Sun, Miao He, Joanes Grandjean, Sreedharan Sajikumar, Weiping Han, Yu Fu
The tuberal nucleus (TN) is a surprisingly understudied brain region. We found that somatostatin (SST) neurons in the TN, which is known to exhibit pathological or cytological changes in human neurodegenerative diseases, play a crucial role in regulating feeding in mice. GABAergic tuberal SST (TNSST) neurons were activated by hunger and by the hunger hormone, ghrelin. Activation of TNSST neurons promoted feeding, whereas inhibition reduced it via projections to the paraventricular nucleus and bed nucleus of the stria terminalis. Ablation of TNSST neurons reduced body weight gain and food intake. These findings reveal a previously unknown mechanism of feeding regulation that operates through orexigenic TNSST neurons, providing a new perspective for understanding appetite changes.
The evolutionary history of dogs in the Americas Science (IF 41.058) Pub Date : 2018-07-06 Máire Ní Leathlobhair, Angela R. Perri, Evan K. Irving-Pease, Kelsey E. Witt, Anna Linderholm, James Haile, Ophelie Lebrasseur, Carly Ameen, Jeffrey Blick, Adam R. Boyko, Selina Brace, Yahaira Nunes Cortes, Susan J. Crockford, Alison Devault, Evangelos A. Dimopoulos, Morley Eldridge, Jacob Enk, Shyam Gopalakrishnan, Kevin Gori, Vaughan Grimes, Eric Guiry, Anders J. Hansen, Ardern Hulme-Beaman, John Johnson, Andrew Kitchen, Aleksei K. Kasparov, Young-Mi Kwon, Pavel A. Nikolskiy, Carlos Peraza Lope, Aurélie Manin, Terrance Martin, Michael Meyer, Kelsey Noack Myers, Mark Omura, Jean-Marie Rouillard, Elena Y. Pavlova, Paul Sciulli, Mikkel-Holger S. Sinding, Andrea Strakova, Varvara V. Ivanova, Christopher Widga, Eske Willerslev, Vladimir V. Pitulko, Ian Barnes, M. Thomas P. Gilbert, Keith M. Dobney, Ripan S. Malhi, Elizabeth P. Murchison, Greger Larson, Laurent A. F. Frantz
Dogs were present in the Americas before the arrival of European colonists, but the origin and fate of these precontact dogs are largely unknown. We sequenced 71 mitochondrial and 7 nuclear genomes from ancient North American and Siberian dogs from time frames spanning ~9000 years. Our analysis indicates that American dogs were not derived from North American wolves. Instead, American dogs form a monophyletic lineage that likely originated in Siberia and dispersed into the Americas alongside people. After the arrival of Europeans, native American dogs almost completely disappeared, leaving a minimal genetic legacy in modern dog populations. The closest detectable extant lineage to precontact American dogs is the canine transmissible venereal tumor, a contagious cancer clone derived from an individual dog that lived up to 8000 years ago.
Ancient goat genomes reveal mosaic domestication in the Fertile Crescent Science (IF 41.058) Pub Date : 2018-07-06 Kevin G. Daly, Pierpaolo Maisano Delser, Victoria E. Mullin, Amelie Scheu, Valeria Mattiangeli, Matthew D. Teasdale, Andrew J. Hare, Joachim Burger, Marta Pereira Verdugo, Matthew J. Collins, Ron Kehati, Cevdet Merih Erek, Guy Bar-Oz, François Pompanon, Tristan Cumer, Canan Çakırlar, Azadeh Fatemeh Mohaseb, Delphine Decruyenaere, Hossein Davoudi, Özlem Çevik, Gary Rollefson, Jean-Denis Vigne, Roya Khazaeli, Homa Fathi, Sanaz Beizaee Doost, Roghayeh Rahimi Sorkhani, Ali Akbar Vahdati, Eberhard W. Sauer, Hossein Azizi Kharanaghi, Sepideh Maziar, Boris Gasparian, Ron Pinhasi, Louise Martin, David Orton, Benjamin S. Arbuckle, Norbert Benecke, Andrea Manica, Liora Kolska Horwitz, Marjan Mashkour, Daniel G. Bradley
Current genetic data are equivocal as to whether goat domestication occurred multiple times or was a singular process. We generated genomic data from 83 ancient goats (51 with genome-wide coverage) from Paleolithic to Medieval contexts throughout the Near East. Our findings demonstrate that multiple divergent ancient wild goat sources were domesticated in a dispersed process that resulted in genetically and geographically distinct Neolithic goat populations, echoing contemporaneous human divergence across the region. These early goat populations contributed differently to modern goats in Asia, Africa, and Europe. We also detect early selection for pigmentation, stature, reproduction, milking, and response to dietary change, providing 8000-year-old evidence for human agency in molding genome variation within a partner species.
The prehistoric peopling of Southeast Asia Science (IF 41.058) Pub Date : 2018-07-06 Hugh McColl, Fernando Racimo, Lasse Vinner, Fabrice Demeter, Takashi Gakuhari, J. Víctor Moreno-Mayar, George van Driem, Uffe Gram Wilken, Andaine Seguin-Orlando, Constanza de la Fuente Castro, Sally Wasef, Rasmi Shoocongdej, Viengkeo Souksavatdy, Thongsa Sayavongkhamdy, Mohd Mokhtar Saidin, Morten E. Allentoft, Takehiro Sato, Anna-Sapfo Malaspinas, Farhang A. Aghakhanian, Thorfinn Korneliussen, Ana Prohaska, Ashot Margaryan, Peter de Barros Damgaard, Supannee Kaewsutthi, Patcharee Lertrit, Thi Mai Huong Nguyen, Hsiao-chun Hung, Thi Minh Tran, Huu Nghia Truong, Giang Hai Nguyen, Shaiful Shahidan, Ketut Wiradnyana, Hiromi Matsumae, Nobuo Shigehara, Minoru Yoneda, Hajime Ishida, Tadayuki Masuyama, Yasuhiro Yamada, Atsushi Tajima, Hiroki Shibata, Atsushi Toyoda, Tsunehiko Hanihara, Shigeki Nakagome, Thibaut Deviese, Anne-Marie Bacon, Philippe Duringer, Jean-Luc Ponche, Laura Shackelford, Elise Patole-Edoumba, Anh Tuan Nguyen, Bérénice Bellina-Pryce, Jean-Christophe Galipaud, Rebecca Kinaston, Hallie Buckley, Christophe Pottier, Simon Rasmussen, Tom Higham, Robert A. Foley, Marta Mirazón Lahr, Ludovic Orlando, Martin Sikora, Maude E. Phipps, Hiroki Oota, Charles Higham, David M. Lambert, Eske Willerslev
The human occupation history of Southeast Asia (SEA) remains heavily debated. Current evidence suggests that SEA was occupied by Hòabìnhian hunter-gatherers until ~4000 years ago, when farming economies developed and expanded, restricting foraging groups to remote habitats. Some argue that agricultural development was indigenous; others favor the “two-layer” hypothesis that posits a southward expansion of farmers giving rise to present-day Southeast Asian genetic diversity. By sequencing 26 ancient human genomes (25 from SEA, 1 Japanese Jōmon), we show that neither interpretation fits the complexity of Southeast Asian history: Both Hòabìnhian hunter-gatherers and East Asian farmers contributed to current Southeast Asian diversity, with further migrations affecting island SEA and Vietnam. Our results help resolve one of the long-standing controversies in Southeast Asian prehistory.
Ancient genomes document multiple waves of migration in Southeast Asian prehistory Science (IF 41.058) Pub Date : 2018-07-06 Mark Lipson, Olivia Cheronet, Swapan Mallick, Nadin Rohland, Marc Oxenham, Michael Pietrusewsky, Thomas Oliver Pryce, Anna Willis, Hirofumi Matsumura, Hallie Buckley, Kate Domett, Giang Hai Nguyen, Hoang Hiep Trinh, Aung Aung Kyaw, Tin Tin Win, Baptiste Pradier, Nasreen Broomandkhoshbacht, Francesca Candilio, Piya Changmai, Daniel Fernandes, Matthew Ferry, Beatriz Gamarra, Eadaoin Harney, Jatupol Kampuansai, Wibhu Kutanan, Megan Michel, Mario Novak, Jonas Oppenheimer, Kendra Sirak, Kristin Stewardson, Zhao Zhang, Pavel Flegontov, Ron Pinhasi, David Reich
Southeast Asia is home to rich human genetic and linguistic diversity, but the details of past population movements in the region are not well known. Here, we report genome-wide ancient DNA data from 18 Southeast Asian individuals spanning from the Neolithic period through the Iron Age (4100 to 1700 years ago). Early farmers from Man Bac in Vietnam exhibit a mixture of East Asian (southern Chinese agriculturalist) and deeply diverged eastern Eurasian (hunter-gatherer) ancestry characteristic of Austroasiatic speakers, with similar ancestry as far south as Indonesia providing evidence for an expansive initial spread of Austroasiatic languages. By the Bronze Age, in a parallel pattern to Europe, sites in Vietnam and Myanmar show close connections to present-day majority groups, reflecting substantial additional influxes of migrants.
Structure basis for RNA-guided DNA degradation by Cascade and Cas3 Science (IF 41.058) Pub Date : 2018-07-06 Yibei Xiao, Min Luo, Adam E. Dolan, Maofu Liao, Ailong Ke
Type I CRISPR-Cas system features a sequential target-searching and degradation process on double-stranded DNA by the RNA-guided Cascade (CRISPR associated complex for antiviral defense) complex and the nuclease-helicase fusion enzyme Cas3, respectively. Here, we present a 3.7-angstrom-resolution cryo–electron microscopy (cryo-EM) structure of the Type I-E Cascade/R-loop/Cas3 complex, poised to initiate DNA degradation. Cas3 distinguishes Cascade conformations and only captures the R-loop–forming Cascade, to avoid cleaving partially complementary targets. Its nuclease domain recruits the nontarget strand (NTS) DNA at a bulged region for the nicking of single-stranded DNA. An additional 4.7-angstrom-resolution cryo-EM structure captures the postnicking state, in which the severed NTS retracts to the helicase entrance, to be threaded for adenosine 5′-triphosphate–dependent processive degradation. These snapshots form the basis for understanding RNA-guided DNA degradation in Type I-E CRISPR-Cas systems.
High thermal conductivity in cubic boron arsenide crystals Science (IF 41.058) Pub Date : 2018-07-05 Sheng Li, Qiye Zheng, Yinchuan Lv, Xiaoyuan Liu, Xiqu Wang, Pinshane Y. Huang, David G. Cahill, Bing Lv
The high density of heat generated in power electronics and optoelectronic devices is a critical bottleneck in their application. New, high thermally-conducting materials are needed to effectively dissipate heat and thereby enable enhanced performance of power controls, solid-state lighting, communication, and security systems. We report our experimental discovery of high thermal conductivity of 1000 ± 90 W/m/K at room temperature in cubic boron arsenide (BAs) grown through modified chemical vapor transport technique. Such thermal conductivity is a factor of 3 higher than that of silicon carbide and surpassed only by diamond and the basal plane value of graphite. This work establishes BAs as the first realization of a new class of ultrahigh thermal conductivity materials predicted by a recent theory, and a potential revolutionary thermal management material.
Unusual high thermal conductivity in boron arsenide bulk crystals Science (IF 41.058) Pub Date : 2018-07-05 Fei Tian, Bai Song, Xi Chen, Navaneetha K. Ravichandran, Yinchuan Lv, Ke Chen, Sean Sullivan, Jaehyun Kim, Yuanyuan Zhou, Te-Huan Liu, Miguel Goni, Zhiwei Ding, Jingying Sun, Geethal Amila Gamage Udalamatta Gamage, Haoran Sun, Hamidreza Ziyaee, Shuyuan Huyan, Liangzi Deng, Jianshi Zhou, Aaron J. Schmidt, Shuo Chen, Ching-Wu Chu, Pinshane Y. Huang, David Broido, Li Shi, Gang Chen, Zhifeng Ren
Conventional theory predicts that ultrahigh lattice thermal conductivity can only occur in crystals composed of strongly-bonded light elements, and that it is limited by anharmonic three-phonon processes. We report experimental evidence that is a departure from these long-held criteria. We measured a local room-temperature thermal conductivity exceeding 1000 W m−1 K−1 and an average bulk value reaching 900 W m−1 K−1 in bulk boron arsenide (BAs) crystals, where boron and arsenic are light and heavy elements, respectively. The high values are consistent with a proposal for phonon band engineering and can only be explained with higher order phonon processes. These findings yield new insight into the physics of heat conduction in solids and show BAs to be the first known semiconductor with ultrahigh thermal conductivity.
A liquid phase of synapsin and lipid vesicles Science (IF 41.058) Pub Date : 2018-07-05 Dragomir Milovanovic, Yumei Wu, Xin Bian, Pietro De Camilli
Neurotransmitter containing synaptic vesicles (SVs) form tight clusters at synapses. These clusters act as a reservoir from which SVs are drawn for exocytosis during sustained activity. Several components associated with synaptic vesicles likely to help forming such clusters have been reported, including synapsin. Here we found that synapsin can form a distinct liquid phase in an aqueous environment. Other scaffolding proteins could co-assemble into this condensate, but were not necessary for its formation. Importantly, the synapsin phase could capture small lipid vesicles. The synapsin phase rapidly disassembled upon phosphorylation by calcium/calmodulin-dependent protein kinase II (CaMKII), mimicking the dispersion of synapsin 1 that occurs at presynaptic sites upon stimulation. Thus, principles of liquid-liquid phase separation may apply to the clustering of SVs at synapses.
Experimental observation of high thermal conductivity in boron arsenide Science (IF 41.058) Pub Date : 2018-07-05 Joon Sang Kang, Man Li, Huan Wu, Huuduy Nguyen, Yongjie Hu
Improving thermal management of small scale devices requires developing materials with high thermal conductivities. The semiconductor boron arsenide (BAs) is an attractive target due to ab initio calculation indicating single crystals have an ultrahigh thermal conductivity. We synthesized BAs single crystals with undetectable defects, and measured a room temperature thermal conductivity of 1300 W/mK. Our spectroscopy study in conjunction with atomistic theory reveals that the unique band structure of BAs allows for very long phonon mean free paths and strong high-order anharmonicity through the four-phonon process. The single-crystal BAs has better thermal properties than other metals and semiconductors. Our study establishes BAs as a benchmark material for thermal management applications, and exemplifies the power of combing experiments and ab initio theory in new materials discovery.
Juno observations of spot structures and a split tail in Io-induced aurorae on Jupiter Science (IF 41.058) Pub Date : 2018-07-05 A. Mura, A. Adriani, J. E. P. Connerney, S. Bolton, F. Altieri, F. Bagenal, B. Bonfond, B.M. Dinelli, J-C. Gérard, T. Greathouse, D. Grodent, S. Levin, B. Mauk, M.L. Moriconi, J. Saur, J. H. Waite, M. Amoroso, A. Cicchetti, F. Fabiano, G. Filacchione, D. Grassi, A. Migliorini, R. Noschese, A. Olivieri, G. Piccioni, C. Plainaki, G. Sindoni, R. Sordini, F. Tosi, D. Turrini
Jupiter’s aurorae are produced in its upper atmosphere when incoming high-energy electrons precipitate along the planet's magnetic field lines. A northern and a southern main auroral oval are visible, surrounded by small emission features associated with the Galilean moons. We present infrared observations, obtained with the Juno spacecraft, showing that in the case of Io, this emission exhibits a swirling pattern that is similar in appearance to a von Kármán vortex street. Well downstream of the main auroral spots the extended tail is split in two. Both of Ganymede’s footprints also appear as a pair of emission features, which may provide a remote measure of Ganymede’s magnetosphere. These features suggest that magnetohydrodynamic interaction between Jupiter and its moon is more complex than previously anticipated.
DNA-induced liquid phase condensation of cGAS activates innate immune signaling Science (IF 41.058) Pub Date : 2018-07-05 Mingjian Du, Zhijian J. Chen
The binding of DNA to cyclic GMP-AMP synthase (cGAS) leads to the production of the secondary messenger cyclic GMP-AMP (cGAMP), which activates innate immune responses. Here, we show that DNA binding to cGAS robustly induced the formation of liquidlike droplets in which cGAS was activated. The disordered and positively charged cGAS N terminus enhanced cGAS-DNA phase separation by increasing the valencies of DNA binding. Long DNA was more efficient in promoting cGAS liquid phase separation and cGAS enzyme activity than short DNA. Moreover, free zinc ion enhanced cGAS enzyme activity both in vitro and in cells by promoting cGAS-DNA phase separation. These results demonstrated that the DNA-induced phase transition of cGAS promotes cGAMP production and innate immune signaling.
Structures of the fully assembled Saccharomyces cerevisiae spliceosome before activation Science (IF 41.058) Pub Date : 2018-06-29 Rui Bai, Ruixue Wan, Chuangye Yan, Jianlin Lei, Yigong Shi
The precatalytic spliceosome (B complex) is preceded by the pre-B complex. Here we report the cryo–electron microscopy structures of the Saccharomyces cerevisiae pre-B and B complexes at average resolutions of 3.3 to 4.6 and 3.9 angstroms, respectively. In the pre-B complex, the duplex between the 5′ splice site (5′SS) and U1 small nuclear RNA (snRNA) is recognized by Yhc1, Luc7, and the Sm ring. In the B complex, U1 small nuclear ribonucleoprotein is dissociated, the 5′-exon–5′SS sequences are translocated near U6 snRNA, and three B-specific proteins may orient the precursor messenger RNA. In both complexes, U6 snRNA is anchored to loop I of U5 snRNA, and the duplex between the branch point sequence and U2 snRNA is recognized by the SF3b complex. Structural analysis reveals the mechanism of assembly and activation for the yeast spliceosome.
Second Chern number of a quantum-simulated non-Abelian Yang monopole Science (IF 41.058) Pub Date : 2018-06-29 Seiji Sugawa, Francisco Salces-Carcoba, Abigail R. Perry, Yuchen Yue, I. B. Spielman
Topological order is often quantified in terms of Chern numbers, each of which classifies a topological singularity. Here, inspired by concepts from high-energy physics, we use quantum simulation based on the spin degrees of freedom of atomic Bose-Einstein condensates to characterize a singularity present in five-dimensional non-Abelian gauge theories—a Yang monopole. We quantify the monopole in terms of Chern numbers measured on enclosing manifolds: Whereas the well-known first Chern number vanishes, the second Chern number does not. By displacing the manifold, we induce and observe a topological transition, where the topology of the manifold changes to a trivial state.
Multivalent counterions diminish the lubricity of polyelectrolyte brushes Science (IF 41.058) Pub Date : 2018-06-29 J. Yu, N. E. Jackson, X. Xu, Y. Morgenstern, Y. Kaufman, M. Ruths, J. J. de Pablo, M. Tirrell
Polyelectrolyte brushes provide wear protection and lubrication in many technical, medical, physiological, and biological applications. Wear resistance and low friction are attributed to counterion osmotic pressure and the hydration layer surrounding the charged polymer segments. However, the presence of multivalent counterions in solution can strongly affect the interchain interactions and structural properties of brush layers. We evaluated the lubrication properties of polystyrene sulfonate brush layers sliding against each other in aqueous solutions containing increasing concentrations of counterions. The presence of multivalent ions (Y3+, Ca2+, Ba2+), even at minute concentrations, markedly increases the friction forces between brush layers owing to electrostatic bridging and brush collapse. Our results suggest that the lubricating properties of polyelectrolyte brushes in multivalent solution are hindered relative to those in monovalent solution.
Carbonyl catalysis enables a biomimetic asymmetric Mannich reaction Science (IF 41.058) Pub Date : 2018-06-29 Jianfeng Chen, Xing Gong, Jianyu Li, Yingkun Li, Jiguo Ma, Chengkang Hou, Guoqing Zhao, Weicheng Yuan, Baoguo Zhao
Chiral amines are widely used as catalysts in asymmetric synthesis to activate carbonyl groups for α-functionalization. Carbonyl catalysis reverses that strategy by using a carbonyl group to activate a primary amine. Inspired by biological carbonyl catalysis, which is exemplified by reactions of pyridoxal-dependent enzymes, we developed an N-quaternized pyridoxal catalyst for the asymmetric Mannich reaction of glycinate with aryl N-diphenylphosphinyl imines. The catalyst exhibits high activity and stereoselectivity, likely enabled by enzyme-like cooperative bifunctional activation of the substrates. Our work demonstrates the catalytic utility of the pyridoxal moiety in asymmetric catalysis.
Enhanced photovoltage for inverted planar heterojunction perovskite solar cells Science (IF 41.058) Pub Date : 2018-06-29 Deying Luo, Wenqiang Yang, Zhiping Wang, Aditya Sadhanala, Qin Hu, Rui Su, Ravichandran Shivanna, Gustavo F. Trindade, John F. Watts, Zhaojian Xu, Tanghao Liu, Ke Chen, Fengjun Ye, Pan Wu, Lichen Zhao, Jiang Wu, Yongguang Tu, Yifei Zhang, Xiaoyu Yang, Wei Zhang, Richard H. Friend, Qihuang Gong, Henry J. Snaith, Rui Zhu
The highest power conversion efficiencies (PCEs) reported for perovskite solar cells (PSCs) with inverted planar structures are still inferior to those of PSCs with regular structures, mainly because of lower open-circuit voltages (Voc). Here we report a strategy to reduce nonradiative recombination for the inverted devices, based on a simple solution-processed secondary growth technique. This approach produces a wider bandgap top layer and a more n-type perovskite film, which mitigates nonradiative recombination, leading to an increase in Voc by up to 100 millivolts. We achieved a high Voc of 1.21 volts without sacrificing photocurrent, corresponding to a voltage deficit of 0.41 volts at a bandgap of 1.62 electron volts. This improvement led to a stabilized power output approaching 21% at the maximum power point.
Some contents have been Reproduced by permission of The Royal Society of Chemistry.
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