TY - JOUR AB - Current methods for assessing cell proliferation in 3D scaffolds rely on changes in metabolic activity or total DNA, however, direct quantification of cell number in 3D scaffolds remains a challenge. To address this issue, we developed an unbiased stereology approach that uses systematic-random sampling and thin focal-plane optical sectioning of the scaffolds followed by estimation of total cell number (StereoCount). This approach was validated against an indirect method for measuring the total DNA (DNA content); and the Bürker counting chamber, the current reference method for quantifying cell number. We assessed the total cell number for cell seeding density (cells per unit volume) across four values and compared the methods in terms of accuracy, ease-of-use and time demands. The accuracy of StereoCount markedly outperformed the DNA content for cases with ~ 10,000 and ~ 125,000 cells/scaffold. For cases with ~ 250,000 and ~ 375,000 cells/scaffold both StereoCount and DNA content showed lower accuracy than the Bürker but did not differ from each other. In terms of ease-of-use, there was a strong advantage for the StereoCount due to output in terms of absolute cell numbers along with the possibility for an overview of cell distribution and future use of automation for high throughput analysis. Taking together, the StereoCount method is an efficient approach for direct cell quantification in 3D collagen scaffolds. Its major benefit is that automated StereoCount could accelerate research using 3D scaffolds focused on drug discovery for a wide variety of human diseases. AU - Zavadakova, Anna AU - Vistejnova, Lucie AU - Belinova, Tereza AU - Tichanek, Filip AU - Bilikova, Dagmar AU - Mouton, Peter R. ID - 13033 IS - 1 JF - Scientific Reports KW - Multidisciplinary SN - 2045-2322 TI - Novel stereological method for estimation of cell counts in 3D collagen scaffolds VL - 13 ER - TY - JOUR AB - Quantum entanglement is a key resource in currently developed quantum technologies. Sharing this fragile property between superconducting microwave circuits and optical or atomic systems would enable new functionalities, but this has been hindered by an energy scale mismatch of >104 and the resulting mutually imposed loss and noise. In this work, we created and verified entanglement between microwave and optical fields in a millikelvin environment. Using an optically pulsed superconducting electro-optical device, we show entanglement between propagating microwave and optical fields in the continuous variable domain. This achievement not only paves the way for entanglement between superconducting circuits and telecom wavelength light, but also has wide-ranging implications for hybrid quantum networks in the context of modularization, scaling, sensing, and cross-platform verification. AU - Sahu, Rishabh AU - Qiu, Liu AU - Hease, William J AU - Arnold, Georg M AU - Minoguchi, Y. AU - Rabl, P. AU - Fink, Johannes M ID - 13106 IS - 6646 JF - Science KW - Multidisciplinary SN - 0036-8075 TI - Entangling microwaves with light VL - 380 ER - TY - JOUR AB - Characterizing and controlling entanglement in quantum materials is crucial for the development of next-generation quantum technologies. However, defining a quantifiable figure of merit for entanglement in macroscopic solids is theoretically and experimentally challenging. At equilibrium the presence of entanglement can be diagnosed by extracting entanglement witnesses from spectroscopic observables and a nonequilibrium extension of this method could lead to the discovery of novel dynamical phenomena. Here, we propose a systematic approach to quantify the time-dependent quantum Fisher information and entanglement depth of transient states of quantum materials with time-resolved resonant inelastic x-ray scattering. Using a quarter-filled extended Hubbard model as an example, we benchmark the efficiency of this approach and predict a light-enhanced many-body entanglement due to the proximity to a phase boundary. Our work sets the stage for experimentally witnessing and controlling entanglement in light-driven quantum materials via ultrafast spectroscopic measurements. AU - Hales, Jordyn AU - Bajpai, Utkarsh AU - Liu, Tongtong AU - Baykusheva, Denitsa Rangelova AU - Li, Mingda AU - Mitrano, Matteo AU - Wang, Yao ID - 13989 JF - Nature Communications KW - General Physics and Astronomy KW - General Biochemistry KW - Genetics and Molecular Biology KW - General Chemistry KW - Multidisciplinary TI - Witnessing light-driven entanglement using time-resolved resonant inelastic X-ray scattering VL - 14 ER - TY - JOUR AB - Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration. AU - Fäßler, Florian AU - Javoor, Manjunath AU - Datler, Julia AU - Döring, Hermann AU - Hofer, Florian AU - Dimchev, Georgi A AU - Hodirnau, Victor-Valentin AU - Faix, Jan AU - Rottner, Klemens AU - Schur, Florian KM ID - 12334 IS - 3 JF - Science Advances KW - Multidisciplinary SN - 2375-2548 TI - ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning VL - 9 ER - TY - JOUR AB - AbstractEndomembrane damage represents a form of stress that is detrimental for eukaryotic cells1,2. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis3–7. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. Here, by combining in vitro and in cellulo studies with computational modelling we uncover a biological function for stress granules whereby these biomolecular condensates form rapidly at endomembrane damage sites and act as a plug that stabilizes the ruptured membrane. Functionally, we demonstrate that stress granule formation and membrane stabilization enable efficient repair of damaged endolysosomes, through both ESCRT (endosomal sorting complex required for transport)-dependent and independent mechanisms. We also show that blocking stress granule formation in human macrophages creates a permissive environment for Mycobacterium tuberculosis, a human pathogen that exploits endomembrane damage to survive within the host. AU - Bussi, Claudio AU - Mangiarotti, Agustín AU - Vanhille-Campos, Christian Eduardo AU - Aylan, Beren AU - Pellegrino, Enrica AU - Athanasiadi, Natalia AU - Fearns, Antony AU - Rodgers, Angela AU - Franzmann, Titus M. AU - Šarić, Anđela AU - Dimova, Rumiana AU - Gutierrez, Maximiliano G. ID - 14610 JF - Nature KW - Multidisciplinary SN - 0028-0836 TI - Stress granules plug and stabilize damaged endolysosomal membranes ER - TY - JOUR AB - The next steps of deep space exploration are manned missions to Moon and Mars. For safe space missions for crew members, it is important to understand the impact of space flight on the immune system. We studied the effects of 21 days dry immersion (DI) exposure on the transcriptomes of T cells isolated from blood samples of eight healthy volunteers. Samples were collected 7 days before DI, at day 7, 14, and 21 during DI, and 7 days after DI. RNA sequencing of CD3+T cells revealed transcriptional alterations across all time points, with most changes occurring 14 days after DI exposure. At day 21, T cells showed evidence of adaptation with a transcriptional profile resembling that of 7 days before DI. At 7 days after DI, T cells again changed their transcriptional profile. These data suggest that T cells adapt by rewiring their transcriptomes in response to simulated weightlessness and that remodeling cues persist when reexposed to normal gravity. AU - Gallardo-Dodd, Carlos J. AU - Oertlin, Christian AU - Record, Julien AU - Galvani, Rômulo G. AU - Sommerauer, Christian AU - Kuznetsov, Nikolai V. AU - Doukoumopoulos, Evangelos AU - Ali, Liaqat AU - Oliveira, Mariana M. S. AU - Seitz, Christina AU - Percipalle, Mathias AU - Nikić, Tijana AU - Sadova, Anastasia A. AU - Shulgina, Sofia M. AU - Shmarov, Vjacheslav A. AU - Kutko, Olga V. AU - Vlasova, Daria D. AU - Orlova, Kseniya D. AU - Rykova, Marina P. AU - Andersson, John AU - Percipalle, Piergiorgio AU - Kutter, Claudia AU - Ponomarev, Sergey A. AU - Westerberg, Lisa S. ID - 14784 IS - 34 JF - Science Advances KW - Multidisciplinary SN - 2375-2548 TI - Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells VL - 9 ER - TY - JOUR AB - Glaciers are key components of the mountain water towers of Asia and are vital for downstream domestic, agricultural, and industrial uses. The glacier mass loss rate over the southeastern Tibetan Plateau is among the highest in Asia and has accelerated in recent decades. This acceleration has been attributed to increased warming, but the mechanisms behind these glaciers’ high sensitivity to warming remain unclear, while the influence of changes in precipitation over the past decades is poorly quantified. Here, we reconstruct glacier mass changes and catchment runoff since 1975 at a benchmark glacier, Parlung No. 4, to shed light on the drivers of recent mass losses for the monsoonal, spring-accumulation glaciers of the Tibetan Plateau. Our modeling demonstrates how a temperature increase (mean of 0.39C ⋅dec−1since 1990) has accelerated mass loss rates by altering both the ablation and accumulation regimes in a complex manner. The majority of the post-2000 mass loss occurred during the monsoon months, caused by simultaneous decreases in the solid precipitation ratio (from 0.70 to 0.56) and precipitation amount (–10%), leading to reduced monsoon accumulation (–26%). Higher solid precipitation in spring (+18%) during the last two decades was increasingly important in mitigating glacier mass loss by providing mass to the glacier and protecting it from melting in the early monsoon. With bare ice exposed to warmer temperatures for longer periods, icemelt and catchment discharge have unsustainably intensified since the start of the 21st century, raising concerns for long-term water supply and hazard occurrence in the region. AU - Jouberton, Achille AU - Shaw, Thomas E. AU - Miles, Evan AU - McCarthy, Michael AU - Fugger, Stefan AU - Ren, Shaoting AU - Dehecq, Amaury AU - Yang, Wei AU - Pellicciotti, Francesca ID - 12577 IS - 37 JF - PNAS KW - Multidisciplinary SN - 0027-8424 TI - Warming-induced monsoon precipitation phase change intensifies glacier mass loss in the southeastern Tibetan Plateau VL - 119 ER - TY - JOUR AB - Plant cell growth responds rapidly to various stimuli, adapting architecture to environmental changes. Two major endogenous signals regulating growth are the phytohormone auxin and the secreted peptides rapid alkalinization factors (RALFs). Both trigger very rapid cellular responses and also exert long-term effects [Du et al., Annu. Rev. Plant Biol. 71, 379–402 (2020); Blackburn et al., Plant Physiol. 182, 1657–1666 (2020)]. However, the way, in which these distinct signaling pathways converge to regulate growth, remains unknown. Here, using vertical confocal microscopy combined with a microfluidic chip, we addressed the mechanism of RALF action on growth. We observed correlation between RALF1-induced rapid Arabidopsis thaliana root growth inhibition and apoplast alkalinization during the initial phase of the response, and revealed that RALF1 reversibly inhibits primary root growth through apoplast alkalinization faster than within 1 min. This rapid apoplast alkalinization was the result of RALF1-induced net H+ influx and was mediated by the receptor FERONIA (FER). Furthermore, we investigated the cross-talk between RALF1 and the auxin signaling pathways during root growth regulation. The results showed that RALF-FER signaling triggered auxin signaling with a delay of approximately 1 h by up-regulating auxin biosynthesis, thus contributing to sustained RALF1-induced growth inhibition. This biphasic RALF1 action on growth allows plants to respond rapidly to environmental stimuli and also reprogram growth and development in the long term. AU - Li, Lanxin AU - Chen, Huihuang AU - Alotaibi, Saqer S. AU - Pěnčík, Aleš AU - Adamowski, Maciek AU - Novák, Ondřej AU - Friml, Jiří ID - 11723 IS - 31 JF - Proceedings of the National Academy of Sciences KW - Multidisciplinary SN - 0027-8424 TI - RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis VL - 119 ER - TY - JOUR AB - The mammalian hippocampal formation (HF) plays a key role in several higher brain functions, such as spatial coding, learning and memory. Its simple circuit architecture is often viewed as a trisynaptic loop, processing input originating from the superficial layers of the entorhinal cortex (EC) and sending it back to its deeper layers. Here, we show that excitatory neurons in layer 6b of the mouse EC project to all sub-regions comprising the HF and receive input from the CA1, thalamus and claustrum. Furthermore, their output is characterized by unique slow-decaying excitatory postsynaptic currents capable of driving plateau-like potentials in their postsynaptic targets. Optogenetic inhibition of the EC-6b pathway affects spatial coding in CA1 pyramidal neurons, while cell ablation impairs not only acquisition of new spatial memories, but also degradation of previously acquired ones. Our results provide evidence of a functional role for cortical layer 6b neurons in the adult brain. AU - Ben Simon, Yoav AU - Käfer, Karola AU - Velicky, Philipp AU - Csicsvari, Jozsef L AU - Danzl, Johann G AU - Jonas, Peter M ID - 11951 JF - Nature Communications KW - General Physics and Astronomy KW - General Biochemistry KW - Genetics and Molecular Biology KW - General Chemistry KW - Multidisciplinary SN - 2041-1723 TI - A direct excitatory projection from entorhinal layer 6b neurons to the hippocampus contributes to spatial coding and memory VL - 13 ER - TY - JOUR AB - Germline determination is essential for species survival and evolution in multicellular organisms. In most flowering plants, formation of the female germline is initiated with specification of one megaspore mother cell (MMC) in each ovule; however, the molecular mechanism underlying this key event remains unclear. Here we report that spatially restricted auxin signaling promotes MMC fate in Arabidopsis. Our results show that the microRNA160 (miR160) targeted gene ARF17 (AUXIN RESPONSE FACTOR17) is required for promoting MMC specification by genetically interacting with the SPL/NZZ (SPOROCYTELESS/NOZZLE) gene. Alterations of auxin signaling cause formation of supernumerary MMCs in an ARF17- and SPL/NZZ-dependent manner. Furthermore, miR160 and ARF17 are indispensable for attaining a normal auxin maximum at the ovule apex via modulating the expression domain of PIN1 (PIN-FORMED1) auxin transporter. Our findings elucidate the mechanism by which auxin signaling promotes the acquisition of female germline cell fate in plants. AU - Huang, Jian AU - Zhao, Lei AU - Malik, Shikha AU - Gentile, Benjamin R. AU - Xiong, Va AU - Arazi, Tzahi AU - Owen, Heather A. AU - Friml, Jiří AU - Zhao, Dazhong ID - 12130 JF - Nature Communications KW - General Physics and Astronomy KW - General Biochemistry KW - Genetics and Molecular Biology KW - General Chemistry KW - Multidisciplinary SN - 2041-1723 TI - Specification of female germline by microRNA orchestrated auxin signaling in Arabidopsis VL - 13 ER - TY - JOUR AB - Complex I is the first enzyme in the respiratory chain, which is responsible for energy production in mitochondria and bacteria1. Complex I couples the transfer of two electrons from NADH to quinone and the translocation of four protons across the membrane2, but the coupling mechanism remains contentious. Here we present cryo-electron microscopy structures of Escherichia coli complex I (EcCI) in different redox states, including catalytic turnover. EcCI exists mostly in the open state, in which the quinone cavity is exposed to the cytosol, allowing access for water molecules, which enable quinone movements. Unlike the mammalian paralogues3, EcCI can convert to the closed state only during turnover, showing that closed and open states are genuine turnover intermediates. The open-to-closed transition results in the tightly engulfed quinone cavity being connected to the central axis of the membrane arm, a source of substrate protons. Consistently, the proportion of the closed state increases with increasing pH. We propose a detailed but straightforward and robust mechanism comprising a ‘domino effect’ series of proton transfers and electrostatic interactions: the forward wave (‘dominoes stacking’) primes the pump, and the reverse wave (‘dominoes falling’) results in the ejection of all pumped protons from the distal subunit NuoL. This mechanism explains why protons exit exclusively from the NuoL subunit and is supported by our mutagenesis data. We contend that this is a universal coupling mechanism of complex I and related enzymes. AU - Kravchuk, Vladyslav AU - Petrova, Olga AU - Kampjut, Domen AU - Wojciechowska-Bason, Anna AU - Breese, Zara AU - Sazanov, Leonid A ID - 12138 IS - 7928 JF - Nature KW - Multidisciplinary SN - 0028-0836 TI - A universal coupling mechanism of respiratory complex I VL - 609 ER - TY - JOUR AB - The inadequate understanding of the mechanisms that reversibly convert molecular sulfur (S) into lithium sulfide (Li2S) via soluble polysulfides (PSs) formation impedes the development of high-performance lithium-sulfur (Li-S) batteries with non-aqueous electrolyte solutions. Here, we use operando small and wide angle X-ray scattering and operando small angle neutron scattering (SANS) measurements to track the nucleation, growth and dissolution of solid deposits from atomic to sub-micron scales during real-time Li-S cell operation. In particular, stochastic modelling based on the SANS data allows quantifying the nanoscale phase evolution during battery cycling. We show that next to nano-crystalline Li2S the deposit comprises solid short-chain PSs particles. The analysis of the experimental data suggests that initially, Li2S2 precipitates from the solution and then is partially converted via solid-state electroreduction to Li2S. We further demonstrate that mass transport, rather than electron transport through a thin passivating film, limits the discharge capacity and rate performance in Li-S cells. AU - Prehal, Christian AU - von Mentlen, Jean-Marc AU - Drvarič Talian, Sara AU - Vizintin, Alen AU - Dominko, Robert AU - Amenitsch, Heinz AU - Porcar, Lionel AU - Freunberger, Stefan Alexander AU - Wood, Vanessa ID - 12208 JF - Nature Communications KW - General Physics and Astronomy KW - General Biochemistry KW - Genetics and Molecular Biology KW - General Chemistry KW - Multidisciplinary SN - 2041-1723 TI - On the nanoscale structural evolution of solid discharge products in lithium-sulfur batteries using operando scattering VL - 13 ER - TY - JOUR AB - The development dynamics and self-organization of glandular branched epithelia is of utmost importance for our understanding of diverse processes ranging from normal tissue growth to the growth of cancerous tissues. Using single primary murine pancreatic ductal adenocarcinoma (PDAC) cells embedded in a collagen matrix and adapted media supplementation, we generate organoids that self-organize into highly branched structures displaying a seamless lumen connecting terminal end buds, replicating in vivo PDAC architecture. We identify distinct morphogenesis phases, each characterized by a unique pattern of cell invasion, matrix deformation, protein expression, and respective molecular dependencies. We propose a minimal theoretical model of a branching and proliferating tissue, capturing the dynamics of the first phases. Observing the interaction of morphogenesis, mechanical environment and gene expression in vitro sets a benchmark for the understanding of self-organization processes governing complex organoid structure formation processes and branching morphogenesis. AU - Randriamanantsoa, S. AU - Papargyriou, A. AU - Maurer, H. C. AU - Peschke, K. AU - Schuster, M. AU - Zecchin, G. AU - Steiger, K. AU - Öllinger, R. AU - Saur, D. AU - Scheel, C. AU - Rad, R. AU - Hannezo, Edouard B AU - Reichert, M. AU - Bausch, A. R. ID - 12217 JF - Nature Communications KW - General Physics and Astronomy KW - General Biochemistry KW - Genetics and Molecular Biology KW - General Chemistry KW - Multidisciplinary SN - 2041-1723 TI - Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids VL - 13 ER - TY - JOUR AB - In social networks, users often engage with like-minded peers. This selective exposure to opinions might result in echo chambers, i.e., political fragmentation and social polarization of user interactions. When echo chambers form, opinions have a bimodal distribution with two peaks on opposite sides. In certain issues, where either extreme positions contain a degree of misinformation, neutral consensus is preferable for promoting discourse. In this paper, we use an opinion dynamics model that naturally forms echo chambers in order to find a feedback mechanism that bridges these communities and leads to a neutral consensus. We introduce the random dynamical nudge (RDN), which presents each agent with input from a random selection of other agents’ opinions and does not require surveillance of every person’s opinions. Our computational results in two different models suggest that the RDN leads to a unimodal distribution of opinions centered around the neutral consensus. Furthermore, the RDN is effective both for preventing the formation of echo chambers and also for depolarizing existing echo chambers. Due to the simple and robust nature of the RDN, social media networks might be able to implement a version of this self-feedback mechanism, when appropriate, to prevent the segregation of online communities on complex social issues. AU - Currin, Christopher AU - Vera, Sebastián Vallejo AU - Khaledi-Nasab, Ali ID - 12225 JF - Scientific Reports KW - Multidisciplinary SN - 2045-2322 TI - Depolarization of echo chambers by random dynamical nudge VL - 12 ER - TY - JOUR AB - Understanding the chirality of molecular reaction pathways is essential for a broad range of fundamental and applied sciences. However, the current ability to probe chirality on the time scale of primary processes underlying chemical reactions remains very limited. Here, we demonstrate time-resolved photoelectron circular dichroism (TRPECD) with ultrashort circularly polarized vacuum-ultraviolet (VUV) pulses from a tabletop source. We demonstrate the capabilities of VUV-TRPECD by resolving the chirality changes in time during the photodissociation of atomic iodine from two chiral molecules. We identify several general key features of TRPECD, which include the ability to probe dynamical chirality along the complete photochemical reaction path, the sensitivity to the local chirality of the evolving scattering potential, and the influence of electron scattering off dissociating photofragments. Our results are interpreted by comparison with high-level ab-initio calculations of transient PECDs from molecular photoionization calculations. Our experimental and theoretical techniques define a general approach to femtochirality. AU - Svoboda, Vít AU - Ram, Niraghatam Bhargava AU - Baykusheva, Denitsa Rangelova AU - Zindel, Daniel AU - Waters, Max D. J. AU - Spenger, Benjamin AU - Ochsner, Manuel AU - Herburger, Holger AU - Stohner, Jürgen AU - Wörner, Hans Jakob ID - 13992 IS - 28 JF - Science Advances KW - Multidisciplinary TI - Femtosecond photoelectron circular dichroism of chemical reactions VL - 8 ER - TY - JOUR AB - The morphology and functionality of the epithelial lining differ along the intestinal tract, but tissue renewal at all sites is driven by stem cells at the base of crypts1,2,3. Whether stem cell numbers and behaviour vary at different sites is unknown. Here we show using intravital microscopy that, despite similarities in the number and distribution of proliferative cells with an Lgr5 signature in mice, small intestinal crypts contain twice as many effective stem cells as large intestinal crypts. We find that, although passively displaced by a conveyor-belt-like upward movement, small intestinal cells positioned away from the crypt base can function as long-term effective stem cells owing to Wnt-dependent retrograde cellular movement. By contrast, the near absence of retrograde movement in the large intestine restricts cell repositioning, leading to a reduction in effective stem cell number. Moreover, after suppression of the retrograde movement in the small intestine, the number of effective stem cells is reduced, and the rate of monoclonal conversion of crypts is accelerated. Together, these results show that the number of effective stem cells is determined by active retrograde movement, revealing a new channel of stem cell regulation that can be experimentally and pharmacologically manipulated. AU - Azkanaz, Maria AU - Corominas-Murtra, Bernat AU - Ellenbroek, Saskia I. J. AU - Bruens, Lotte AU - Webb, Anna T. AU - Laskaris, Dimitrios AU - Oost, Koen C. AU - Lafirenze, Simona J. A. AU - Annusver, Karl AU - Messal, Hendrik A. AU - Iqbal, Sharif AU - Flanagan, Dustin J. AU - Huels, David J. AU - Rojas-Rodríguez, Felipe AU - Vizoso, Miguel AU - Kasper, Maria AU - Sansom, Owen J. AU - Snippert, Hugo J. AU - Liberali, Prisca AU - Simons, Benjamin D. AU - Katajisto, Pekka AU - Hannezo, Edouard B AU - van Rheenen, Jacco ID - 12274 IS - 7919 JF - Nature KW - Multidisciplinary SN - 0028-0836 TI - Retrograde movements determine effective stem cell numbers in the intestine VL - 607 ER - TY - JOUR AB - Future LEDs could be based on lead halide perovskites. A breakthrough in preparing device-compatible solids composed of nanoscale perovskite crystals overcomes a long-standing hurdle in making blue perovskite LEDs. AU - Utzat, Hendrik AU - Ibáñez, Maria ID - 14437 IS - 7941 JF - Nature KW - Multidisciplinary SN - 0028-0836 TI - Molecular engineering enables bright blue LEDs VL - 612 ER - TY - JOUR AB - Hybrid semiconductor–superconductor devices hold great promise for realizing topological quantum computing with Majorana zero modes1,2,3,4,5. However, multiple claims of Majorana detection, based on either tunnelling6,7,8,9,10 or Coulomb blockade (CB) spectroscopy11,12, remain disputed. Here we devise an experimental protocol that allows us to perform both types of measurement on the same hybrid island by adjusting its charging energy via tunable junctions to the normal leads. This method reduces ambiguities of Majorana detections by checking the consistency between CB spectroscopy and zero-bias peaks in non-blockaded transport. Specifically, we observe junction-dependent, even–odd modulated, single-electron CB peaks in InAs/Al hybrid nanowires without concomitant low-bias peaks in tunnelling spectroscopy. We provide a theoretical interpretation of the experimental observations in terms of low-energy, longitudinally confined island states rather than overlapping Majorana modes. Our results highlight the importance of combined measurements on the same device for the identification of topological Majorana zero modes. AU - Valentini, Marco AU - Borovkov, Maksim AU - Prada, Elsa AU - Martí-Sánchez, Sara AU - Botifoll, Marc AU - Hofmann, Andrea C AU - Arbiol, Jordi AU - Aguado, Ramón AU - San-Jose, Pablo AU - Katsaros, Georgios ID - 12118 IS - 7940 JF - Nature KW - Multidisciplinary SN - 0028-0836 TI - Majorana-like Coulomb spectroscopy in the absence of zero-bias peaks VL - 612 ER - TY - JOUR AB - Electrons in moiré flat band systems can spontaneously break time-reversal symmetry, giving rise to a quantized anomalous Hall effect. In this study, we use a superconducting quantum interference device to image stray magnetic fields in twisted bilayer graphene aligned to hexagonal boron nitride. We find a magnetization of several Bohr magnetons per charge carrier, demonstrating that the magnetism is primarily orbital in nature. Our measurements reveal a large change in the magnetization as the chemical potential is swept across the quantum anomalous Hall gap, consistent with the expected contribution of chiral edge states to the magnetization of an orbital Chern insulator. Mapping the spatial evolution of field-driven magnetic reversal, we find a series of reproducible micrometer-scale domains pinned to structural disorder. AU - Tschirhart, C. L. AU - Serlin, M. AU - Polshyn, Hryhoriy AU - Shragai, A. AU - Xia, Z. AU - Zhu, J. AU - Zhang, Y. AU - Watanabe, K. AU - Taniguchi, T. AU - Huber, M. E. AU - Young, A. F. ID - 10616 IS - 6548 JF - Science KW - multidisciplinary SN - 0036-8075 TI - Imaging orbital ferromagnetism in a moiré Chern insulator VL - 372 ER - TY - JOUR AB - Glaciers in High Mountain Asia generate meltwater that supports the water needs of 250 million people, but current knowledge of annual accumulation and ablation is limited to sparse field measurements biased in location and glacier size. Here, we present altitudinally-resolved specific mass balances (surface, internal, and basal combined) for 5527 glaciers in High Mountain Asia for 2000–2016, derived by correcting observed glacier thinning patterns for mass redistribution due to ice flow. We find that 41% of glaciers accumulated mass over less than 20% of their area, and only 60% ± 10% of regional annual ablation was compensated by accumulation. Even without 21st century warming, 21% ± 1% of ice volume will be lost by 2100 due to current climatic-geometric imbalance, representing a reduction in glacier ablation into rivers of 28% ± 1%. The ablation of glaciers in the Himalayas and Tien Shan was mostly unsustainable and ice volume in these regions will reduce by at least 30% by 2100. The most important and vulnerable glacier-fed river basins (Amu Darya, Indus, Syr Darya, Tarim Interior) were supplied with >50% sustainable glacier ablation but will see long-term reductions in ice mass and glacier meltwater supply regardless of the Karakoram Anomaly. AU - Miles, Evan AU - McCarthy, Michael AU - Dehecq, Amaury AU - Kneib, Marin AU - Fugger, Stefan AU - Pellicciotti, Francesca ID - 12585 JF - Nature Communications KW - General Physics and Astronomy KW - General Biochemistry KW - Genetics and Molecular Biology KW - General Chemistry KW - Multidisciplinary SN - 2041-1723 TI - Health and sustainability of glaciers in High Mountain Asia VL - 12 ER - TY - JOUR AB - Genomes of germ cells present an existential vulnerability to organisms because germ cell mutations will propagate to future generations. Transposable elements are one source of such mutations. In the small flowering plant Arabidopsis, Long et al. found that genome methylation in the male germline is directed by small interfering RNAs (siRNAs) imperfectly transcribed from transposons (see the Perspective by Mosher). These germline siRNAs silence germline transposons and establish inherited methylation patterns in sperm, thus maintaining the integrity of the plant genome across generations. AU - Long, Jincheng AU - Walker, James AU - She, Wenjing AU - Aldridge, Billy AU - Gao, Hongbo AU - Deans, Samuel AU - Vickers, Martin AU - Feng, Xiaoqi ID - 12187 IS - 6550 JF - Science KW - Multidisciplinary SN - 0036-8075 TI - Nurse cell--derived small RNAs define paternal epigenetic inheritance in Arabidopsis VL - 373 ER - TY - JOUR AB - The control of nonequilibrium quantum dynamics in many-body systems is challenging because interactions typically lead to thermalization and a chaotic spreading throughout Hilbert space. We investigate nonequilibrium dynamics after rapid quenches in a many-body system composed of 3 to 200 strongly interacting qubits in one and two spatial dimensions. Using a programmable quantum simulator based on Rydberg atom arrays, we show that coherent revivals associated with so-called quantum many-body scars can be stabilized by periodic driving, which generates a robust subharmonic response akin to discrete time-crystalline order. We map Hilbert space dynamics, geometry dependence, phase diagrams, and system-size dependence of this emergent phenomenon, demonstrating new ways to steer complex dynamics in many-body systems and enabling potential applications in quantum information science. AU - Bluvstein, D. AU - Omran, A. AU - Levine, H. AU - Keesling, A. AU - Semeghini, G. AU - Ebadi, S. AU - Wang, T. T. AU - Michailidis, Alexios AU - Maskara, N. AU - Ho, W. W. AU - Choi, S. AU - Serbyn, Maksym AU - Greiner, M. AU - Vuletić, V. AU - Lukin, M. D. ID - 9618 IS - 6536 JF - Science KW - Multidisciplinary SN - 0036-8075 TI - Controlling quantum many-body dynamics in driven Rydberg atom arrays VL - 371 ER - TY - JOUR AB - Ferromagnetism is most common in transition metal compounds but may also arise in low-density two-dimensional electron systems, with signatures observed in silicon, III-V semiconductor systems, and graphene moiré heterostructures. Here we show that gate-tuned van Hove singularities in rhombohedral trilayer graphene drive the spontaneous ferromagnetic polarization of the electron system into one or more spin- and valley flavors. Using capacitance measurements on graphite-gated van der Waals heterostructures, we find a cascade of density- and electronic displacement field tuned phase transitions marked by negative electronic compressibility. The transitions define the boundaries between phases where quantum oscillations have either four-fold, two-fold, or one-fold degeneracy, associated with a spin and valley degenerate normal metal, spin-polarized `half-metal', and spin and valley polarized `quarter metal', respectively. For electron doping, the salient features are well captured by a phenomenological Stoner model with a valley-anisotropic Hund's coupling, likely arising from interactions at the lattice scale. For hole filling, we observe a richer phase diagram featuring a delicate interplay of broken symmetries and transitions in the Fermi surface topology. Finally, by rotational alignment of a hexagonal boron nitride substrate to induce a moiré superlattice, we find that the superlattice perturbs the preexisting isospin order only weakly, leaving the basic phase diagram intact while catalyzing the formation of topologically nontrivial gapped states whenever itinerant half- or quarter metal states occur at half- or quarter superlattice band filling. Our results show that rhombohedral trilayer graphene is an ideal platform for well-controlled tests of many-body theory and reveal magnetism in moiré materials to be fundamentally itinerant in nature. AU - Zhou, Haoxin AU - Xie, Tian AU - Ghazaryan, Areg AU - Holder, Tobias AU - Ehrets, James R. AU - Spanton, Eric M. AU - Taniguchi, Takashi AU - Watanabe, Kenji AU - Berg, Erez AU - Serbyn, Maksym AU - Young, Andrea F. ID - 10025 JF - Nature KW - condensed matter - mesoscale and nanoscale physics KW - condensed matter - strongly correlated electrons KW - multidisciplinary SN - 0028-0836 TI - Half and quarter metals in rhombohedral trilayer graphene ER - TY - JOUR AB - Turbulence generally arises in shear flows if velocities and hence, inertial forces are sufficiently large. In striking contrast, viscoelastic fluids can exhibit disordered motion even at vanishing inertia. Intermediate between these cases, a state of chaotic motion, “elastoinertial turbulence” (EIT), has been observed in a narrow Reynolds number interval. We here determine the origin of EIT in experiments and show that characteristic EIT structures can be detected across an unexpectedly wide range of parameters. Close to onset, a pattern of chevron-shaped streaks emerges in qualitative agreement with linear and weakly nonlinear theory. However, in experiments, the dynamics remain weakly chaotic, and the instability can be traced to far lower Reynolds numbers than permitted by theory. For increasing inertia, the flow undergoes a transformation to a wall mode composed of inclined near-wall streaks and shear layers. This mode persists to what is known as the “maximum drag reduction limit,” and overall EIT is found to dominate viscoelastic flows across more than three orders of magnitude in Reynolds number. AU - Choueiri, George H AU - Lopez Alonso, Jose M AU - Varshney, Atul AU - Sankar, Sarath AU - Hof, Björn ID - 10299 IS - 45 JF - Proceedings of the National Academy of Sciences KW - multidisciplinary KW - elastoinertial turbulence KW - viscoelastic flows KW - elastic instability KW - drag reduction SN - 0027-8424 TI - Experimental observation of the origin and structure of elastoinertial turbulence VL - 118 ER - TY - JOUR AB - Thermoelectric materials are engines that convert heat into an electrical current. Intuitively, the efficiency of this process depends on how many electrons (charge carriers) can move and how easily they do so, how much energy those moving electrons transport, and how easily the temperature gradient is maintained. In terms of material properties, an excellent thermoelectric material requires a high electrical conductivity σ, a high Seebeck coefficient S (a measure of the induced thermoelectric voltage as a function of temperature gradient), and a low thermal conductivity κ. The challenge is that these three properties are strongly interrelated in a conflicting manner (1). On page 722 of this issue, Roychowdhury et al. (2) have found a way to partially break these ties in silver antimony telluride (AgSbTe2) with the addition of cadmium (Cd) cations, which increase the ordering in this inherently disordered thermoelectric material. AU - Liu, Yu AU - Ibáñez, Maria ID - 10809 IS - 6530 JF - Science KW - multidisciplinary SN - 0036-8075 TI - Tidying up the mess VL - 371 ER - TY - JOUR AB - Shape resonances play a central role in many areas of science, but the real-time measurement of the associated many-body dynamics remains challenging. Here, we present measurements of recoil frame angle-resolved photoionization delays in the vicinity of shape resonances of CF4. This technique provides insights into the spatiotemporal photoionization dynamics of molecular shape resonances. We find delays of up to ∼600 as in the ionization out of the highest occupied molecular orbital (HOMO) with a strong dependence on the emission direction and a pronounced asymmetry along the dissociation axis. Comparison with quantum-scattering calculations traces the asymmetries to the interference of a small subset of partial waves at low kinetic energies and, additionally, to the interference of two overlapping shape resonances in the HOMO-1 channel. Our experimental and theoretical results establish a broadly applicable approach to space- and time-resolved photoionization dynamics in the molecular frame. AU - Heck, Saijoscha AU - Baykusheva, Denitsa Rangelova AU - Han, Meng AU - Ji, Jia-Bao AU - Perry, Conaill AU - Gong, Xiaochun AU - Wörner, Hans Jakob ID - 13995 IS - 49 JF - Science Advances KW - Multidisciplinary TI - Attosecond interferometry of shape resonances in the recoil frame of CF4 VL - 7 ER - TY - JOUR AB - Growth regulation tailors development in plants to their environment. A prominent example of this is the response to gravity, in which shoots bend up and roots bend down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phosphoproteomics in Arabidopsis thaliana, we advance understanding of how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on rapid regulation of apoplastic pH, a causative determinant of growth. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+ influx, causing apoplast alkalinization. Simultaneous activation of these two counteracting mechanisms poises roots for rapid, fine-tuned growth modulation in navigating complex soil environments. AU - Li, Lanxin AU - Verstraeten, Inge AU - Roosjen, Mark AU - Takahashi, Koji AU - Rodriguez Solovey, Lesia AU - Merrin, Jack AU - Chen, Jian AU - Shabala, Lana AU - Smet, Wouter AU - Ren, Hong AU - Vanneste, Steffen AU - Shabala, Sergey AU - De Rybel, Bert AU - Weijers, Dolf AU - Kinoshita, Toshinori AU - Gray, William M. AU - Friml, Jiří ID - 10223 IS - 7884 JF - Nature KW - Multidisciplinary SN - 00280836 TI - Cell surface and intracellular auxin signalling for H+ fluxes in root growth VL - 599 ER - TY - JOUR AB - Indirect reciprocity is a mechanism for the evolution of cooperation based on social norms. This mechanism requires that individuals in a population observe and judge each other’s behaviors. Individuals with a good reputation are more likely to receive help from others. Previous work suggests that indirect reciprocity is only effective when all relevant information is reliable and publicly available. Otherwise, individuals may disagree on how to assess others, even if they all apply the same social norm. Such disagreements can lead to a breakdown of cooperation. Here we explore whether the predominantly studied ‘leading eight’ social norms of indirect reciprocity can be made more robust by equipping them with an element of generosity. To this end, we distinguish between two kinds of generosity. According to assessment generosity, individuals occasionally assign a good reputation to group members who would usually be regarded as bad. According to action generosity, individuals occasionally cooperate with group members with whom they would usually defect. Using individual-based simulations, we show that the two kinds of generosity have a very different effect on the resulting reputation dynamics. Assessment generosity tends to add to the overall noise and allows defectors to invade. In contrast, a limited amount of action generosity can be beneficial in a few cases. However, even when action generosity is beneficial, the respective simulations do not result in full cooperation. Our results suggest that while generosity can favor cooperation when individuals use the most simple strategies of reciprocity, it is disadvantageous when individuals use more complex social norms. AU - Schmid, Laura AU - Shati, Pouya AU - Hilbe, Christian AU - Chatterjee, Krishnendu ID - 9997 IS - 1 JF - Scientific Reports KW - Multidisciplinary TI - The evolution of indirect reciprocity under action and assessment generosity VL - 11 ER - TY - JOUR AB - The blood-brain barrier is made of polarized brain endothelial cells (BECs) phenotypically conditioned by the central nervous system (CNS). Although transport across BECs is of paramount importance for nutrient uptake as well as ridding the brain of waste products, the intracellular sorting mechanisms that regulate successful receptor-mediated transcytosis in BECs remain to be elucidated. Here, we used a synthetic multivalent system with tunable avidity to the low-density lipoprotein receptor–related protein 1 (LRP1) to investigate the mechanisms of transport across BECs. We used a combination of conventional and super-resolution microscopy, both in vivo and in vitro, accompanied with biophysical modeling of transport kinetics and membrane-bound interactions to elucidate the role of membrane-sculpting protein syndapin-2 on fast transport via tubule formation. We show that high-avidity cargo biases the LRP1 toward internalization associated with fast degradation, while mid-avidity augments the formation of syndapin-2 tubular carriers promoting a fast shuttling across. AU - Tian, Xiaohe AU - Leite, Diana M. AU - Scarpa, Edoardo AU - Nyberg, Sophie AU - Fullstone, Gavin AU - Forth, Joe AU - Matias, Diana AU - Apriceno, Azzurra AU - Poma, Alessandro AU - Duro-Castano, Aroa AU - Vuyyuru, Manish AU - Harker-Kirschneck, Lena AU - Šarić, Anđela AU - Zhang, Zhongping AU - Xiang, Pan AU - Fang, Bin AU - Tian, Yupeng AU - Luo, Lei AU - Rizzello, Loris AU - Battaglia, Giuseppe ID - 10342 IS - 48 JF - Science Advances KW - multidisciplinary SN - 2375-2548 TI - On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias VL - 6 ER - TY - JOUR AB - Sulfolobus acidocaldarius is the closest experimentally tractable archaeal relative of eukaryotes and, despite lacking obvious cyclin-dependent kinase and cyclin homologs, has an ordered eukaryote-like cell cycle with distinct phases of DNA replication and division. Here, in exploring the mechanism of cell division in S. acidocaldarius, we identify a role for the archaeal proteasome in regulating the transition from the end of one cell cycle to the beginning of the next. Further, we identify the archaeal ESCRT-III homolog, CdvB, as a key target of the proteasome and show that its degradation triggers division by allowing constriction of the CdvB1:CdvB2 ESCRT-III division ring. These findings offer a minimal mechanism for ESCRT-III–mediated membrane remodeling and point to a conserved role for the proteasome in eukaryotic and archaeal cell cycle control. AU - Tarrason Risa, Gabriel AU - Hurtig, Fredrik AU - Bray, Sian AU - Hafner, Anne E. AU - Harker-Kirschneck, Lena AU - Faull, Peter AU - Davis, Colin AU - Papatziamou, Dimitra AU - Mutavchiev, Delyan R. AU - Fan, Catherine AU - Meneguello, Leticia AU - Arashiro Pulschen, Andre AU - Dey, Gautam AU - Culley, Siân AU - Kilkenny, Mairi AU - Souza, Diorge P. AU - Pellegrini, Luca AU - de Bruin, Robertus A. M. AU - Henriques, Ricardo AU - Snijders, Ambrosius P. AU - Šarić, Anđela AU - Lindås, Ann-Christin AU - Robinson, Nicholas P. AU - Baum, Buzz ID - 10349 IS - 6504 JF - Science KW - multidisciplinary SN - 0036-8075 TI - The proteasome controls ESCRT-III–mediated cell division in an archaeon VL - 369 ER - TY - JOUR AB - Understanding the mechanism of action of compounds capable of inhibiting amyloid-fibril formation is critical to the development of potential therapeutics against protein-misfolding diseases. A fundamental challenge for progress is the range of possible target species and the disparate timescales involved, since the aggregating proteins are simultaneously the reactants, products, intermediates, and catalysts of the reaction. It is a complex problem, therefore, to choose the states of the aggregating proteins that should be bound by the compounds to achieve the most potent inhibition. We present here a comprehensive kinetic theory of amyloid-aggregation inhibition that reveals the fundamental thermodynamic and kinetic signatures characterizing effective inhibitors by identifying quantitative relationships between the aggregation and binding rate constants. These results provide general physical laws to guide the design and optimization of inhibitors of amyloid-fibril formation, revealing in particular the important role of on-rates in the binding of the inhibitors. AU - Michaels, Thomas C. T. AU - Šarić, Anđela AU - Meisl, Georg AU - Heller, Gabriella T. AU - Curk, Samo AU - Arosio, Paolo AU - Linse, Sara AU - Dobson, Christopher M. AU - Vendruscolo, Michele AU - Knowles, Tuomas P. J. ID - 10347 IS - 39 JF - Proceedings of the National Academy of Sciences KW - multidisciplinary SN - 0027-8424 TI - Thermodynamic and kinetic design principles for amyloid-aggregation inhibitors VL - 117 ER - TY - JOUR AB - Magnetism typically arises from the joint effect of Fermi statistics and repulsive Coulomb interactions, which favours ground states with non-zero electron spin. As a result, controlling spin magnetism with electric fields—a longstanding technological goal in spintronics and multiferroics1,2—can be achieved only indirectly. Here we experimentally demonstrate direct electric-field control of magnetic states in an orbital Chern insulator3,4,5,6, a magnetic system in which non-trivial band topology favours long-range order of orbital angular momentum but the spins are thought to remain disordered7,8,9,10,11,12,13,14. We use van der Waals heterostructures consisting of a graphene monolayer rotationally faulted with respect to a Bernal-stacked bilayer to realize narrow and topologically non-trivial valley-projected moiré minibands15,16,17. At fillings of one and three electrons per moiré unit cell within these bands, we observe quantized anomalous Hall effects18 with transverse resistance approximately equal to h/2e2 (where h is Planck’s constant and e is the charge on the electron), which is indicative of spontaneous polarization of the system into a single-valley-projected band with a Chern number equal to two. At a filling of three electrons per moiré unit cell, we find that the sign of the quantum anomalous Hall effect can be reversed via field-effect control of the chemical potential; moreover, this transition is hysteretic, which we use to demonstrate non-volatile electric-field-induced reversal of the magnetic state. A theoretical analysis19 indicates that the effect arises from the topological edge states, which drive a change in sign of the magnetization and thus a reversal in the favoured magnetic state. Voltage control of magnetic states can be used to electrically pattern non-volatile magnetic-domain structures hosting chiral edge states, with applications ranging from reconfigurable microwave circuit elements to ultralow-power magnetic memories. AU - Polshyn, Hryhoriy AU - Zhu, J. AU - Kumar, M. A. AU - Zhang, Y. AU - Yang, F. AU - Tschirhart, C. L. AU - Serlin, M. AU - Watanabe, K. AU - Taniguchi, T. AU - MacDonald, A. H. AU - Young, A. F. ID - 10618 IS - 7836 JF - Nature KW - multidisciplinary SN - 0028-0836 TI - Electrical switching of magnetic order in an orbital Chern insulator VL - 588 ER - TY - JOUR AB - From rock salt to nanoparticle superlattices, complex structure can emerge from simple building blocks that attract each other through Coulombic forces1-4. On the micrometre scale, however, colloids in water defy the intuitively simple idea of forming crystals from oppositely charged partners, instead forming non-equilibrium structures such as clusters and gels5-7. Although various systems have been engineered to grow binary crystals8-11, native surface charge in aqueous conditions has not been used to assemble crystalline materials. Here we form ionic colloidal crystals in water through an approach that we refer to as polymer-attenuated Coulombic self-assembly. The key to crystallization is the use of a neutral polymer to keep particles separated by well defined distances, allowing us to tune the attractive overlap of electrical double layers, directing particles to disperse, crystallize or become permanently fixed on demand. The nucleation and growth of macroscopic single crystals is demonstrated by using the Debye screening length to fine-tune assembly. Using a variety of colloidal particles and commercial polymers, ionic colloidal crystals isostructural to caesium chloride, sodium chloride, aluminium diboride and K4C60 are selected according to particle size ratios. Once fixed by simply diluting out solution salts, crystals are pulled out of the water for further manipulation, demonstrating an accurate translation from solution-phase assembly to dried solid structures. In contrast to other assembly approaches, in which particles must be carefully engineered to encode binding information12-18, polymer-attenuated Coulombic self-assembly enables conventional colloids to be used as model colloidal ions, primed for crystallization. AU - Hueckel, Theodore AU - Hocky, Glen M. AU - Palacci, Jérémie A AU - Sacanna, Stefano ID - 9059 IS - 7804 JF - Nature KW - Multidisciplinary SN - 0028-0836 TI - Ionic solids from common colloids VL - 580 ER - TY - JOUR AB - Molecular mechanisms enabling the switching and maintenance of epigenetic states are not fully understood. Distinct histone modifications are often associated with ON/OFF epigenetic states, but how these states are stably maintained through DNA replication, yet in certain situations switch from one to another remains unclear. Here, we address this problem through identification of Arabidopsis INCURVATA11 (ICU11) as a Polycomb Repressive Complex 2 accessory protein. ICU11 robustly immunoprecipitated in vivo with PRC2 core components and the accessory proteins, EMBRYONIC FLOWER 1 (EMF1), LIKE HETEROCHROMATIN PROTEIN1 (LHP1), and TELOMERE_REPEAT_BINDING FACTORS (TRBs). ICU11 encodes a 2-oxoglutarate-dependent dioxygenase, an activity associated with histone demethylation in other organisms, and mutant plants show defects in multiple aspects of the Arabidopsis epigenome. To investigate its primary molecular function we identified the Arabidopsis FLOWERING LOCUS C (FLC) as a direct target and found icu11 disrupted the cold-induced, Polycomb-mediated silencing underlying vernalization. icu11 prevented reduction in H3K36me3 levels normally seen during the early cold phase, supporting a role for ICU11 in H3K36me3 demethylation. This was coincident with an attenuation of H3K27me3 at the internal nucleation site in FLC, and reduction in H3K27me3 levels across the body of the gene after plants were returned to the warm. Thus, ICU11 is required for the cold-induced epigenetic switching between the mutually exclusive chromatin states at FLC, from the active H3K36me3 state to the silenced H3K27me3 state. These data support the importance of physical coupling of histone modification activities to promote epigenetic switching between opposing chromatin states. AU - Bloomer, Rebecca H. AU - Hutchison, Claire E. AU - Bäurle, Isabel AU - Walker, James AU - Fang, Xiaofeng AU - Perera, Pumi AU - Velanis, Christos N. AU - Gümüs, Serin AU - Spanos, Christos AU - Rappsilber, Juri AU - Feng, Xiaoqi AU - Goodrich, Justin AU - Dean, Caroline ID - 12188 IS - 28 JF - Proceedings of the National Academy of Sciences KW - Multidisciplinary SN - 0027-8424 TI - The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2 VL - 117 ER - TY - JOUR AB - Animal development entails the organization of specific cell types in space and time, and spatial patterns must form in a robust manner. In the zebrafish spinal cord, neural progenitors form stereotypic patterns despite noisy morphogen signaling and large-scale cellular rearrangements during morphogenesis and growth. By directly measuring adhesion forces and preferences for three types of endogenous neural progenitors, we provide evidence for the differential adhesion model in which differences in intercellular adhesion mediate cell sorting. Cell type–specific combinatorial expression of different classes of cadherins (N-cadherin, cadherin 11, and protocadherin 19) results in homotypic preference ex vivo and patterning robustness in vivo. Furthermore, the differential adhesion code is regulated by the sonic hedgehog morphogen gradient. We propose that robust patterning during tissue morphogenesis results from interplay between adhesion-based self-organization and morphogen-directed patterning. AU - Tsai, Tony Y.-C. AU - Sikora, Mateusz K AU - Xia, Peng AU - Colak-Champollion, Tugba AU - Knaut, Holger AU - Heisenberg, Carl-Philipp J AU - Megason, Sean G. ID - 8680 IS - 6512 JF - Science KW - Multidisciplinary SN - 0036-8075 TI - An adhesion code ensures robust pattern formation during tissue morphogenesis VL - 370 ER - TY - JOUR AB - The discovery of superconductivity and exotic insulating phases in twisted bilayer graphene has established this material as a model system of strongly correlated electrons. To achieve superconductivity, the two layers of graphene need to be at a very precise angle with respect to each other. Yankowitz et al. now show that another experimental knob, hydrostatic pressure, can be used to tune the phase diagram of twisted bilayer graphene (see the Perspective by Feldman). Applying pressure increased the coupling between the layers, which shifted the superconducting transition to higher angles and somewhat higher temperatures. AU - Yankowitz, Matthew AU - Chen, Shaowen AU - Polshyn, Hryhoriy AU - Zhang, Yuxuan AU - Watanabe, K. AU - Taniguchi, T. AU - Graf, David AU - Young, Andrea F. AU - Dean, Cory R. ID - 10625 IS - 6431 JF - Science KW - multidisciplinary SN - 0036-8075 TI - Tuning superconductivity in twisted bilayer graphene VL - 363 ER - TY - JOUR AB - The quantum anomalous Hall (QAH) effect combines topology and magnetism to produce precisely quantized Hall resistance at zero magnetic field. We report the observation of a QAH effect in twisted bilayer graphene aligned to hexagonal boron nitride. The effect is driven by intrinsic strong interactions, which polarize the electrons into a single spin- and valley-resolved moiré miniband with Chern number C = 1. In contrast to magnetically doped systems, the measured transport energy gap is larger than the Curie temperature for magnetic ordering, and quantization to within 0.1% of the von Klitzing constant persists to temperatures of several kelvin at zero magnetic field. Electrical currents as small as 1 nanoampere controllably switch the magnetic order between states of opposite polarization, forming an electrically rewritable magnetic memory. AU - Serlin, M. AU - Tschirhart, C. L. AU - Polshyn, Hryhoriy AU - Zhang, Y. AU - Zhu, J. AU - Watanabe, K. AU - Taniguchi, T. AU - Balents, L. AU - Young, A. F. ID - 10619 IS - 6480 JF - Science KW - multidisciplinary SN - 0036-8075 TI - Intrinsic quantized anomalous Hall effect in a moiré heterostructure VL - 367 ER - TY - JOUR AB - Epigenetic reprogramming is required for proper regulation of gene expression in eukaryotic organisms. In Arabidopsis, active DNA demethylation is crucial for seed viability, pollen function, and successful reproduction. The DEMETER (DME) DNA glycosylase initiates localized DNA demethylation in vegetative and central cells, so-called companion cells that are adjacent to sperm and egg gametes, respectively. In rice, the central cell genome displays local DNA hypomethylation, suggesting that active DNA demethylation also occurs in rice; however, the enzyme responsible for this process is unknown. One candidate is the rice REPRESSOR OF SILENCING 1a (ROS1a) gene, which is related to DME and is essential for rice seed viability and pollen function. Here, we report genome-wide analyses of DNA methylation in wild-type and ros1a mutant sperm and vegetative cells. We find that the rice vegetative cell genome is locally hypomethylated compared with sperm by a process that requires ROS1a activity. We show that many ROS1a target sequences in the vegetative cell are hypomethylated in the rice central cell, suggesting that ROS1a also demethylates the central cell genome. Similar to Arabidopsis, we show that sperm non-CG methylation is indirectly promoted by DNA demethylation in the vegetative cell. These results reveal that DNA glycosylase-mediated DNA demethylation processes are conserved in Arabidopsis and rice, plant species that diverged 150 million years ago. Finally, although global non-CG methylation levels of sperm and egg differ, the maternal and paternal embryo genomes show similar non-CG methylation levels, suggesting that rice gamete genomes undergo dynamic DNA methylation reprogramming after cell fusion. AU - Kim, M. Yvonne AU - Ono, Akemi AU - Scholten, Stefan AU - Kinoshita, Tetsu AU - Zilberman, Daniel AU - Okamoto, Takashi AU - Fischer, Robert L. ID - 9460 IS - 19 JF - Proceedings of the National Academy of Sciences KW - Multidisciplinary SN - 0027-8424 TI - DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm VL - 116 ER - TY - JOUR AB - Chiral molecules interact and react differently with other chiral objects, depending on their handedness. Therefore, it is essential to understand and ultimately control the evolution of molecular chirality during chemical reactions. Although highly sophisticated techniques for the controlled synthesis of chiral molecules have been developed, the observation of chirality on the natural femtosecond time scale of a chemical reaction has so far remained out of reach in the gas phase. Here, we demonstrate a general experimental technique, based on high-harmonic generation in tailored laser fields, and apply it to probe the time evolution of molecular chirality during the photodissociation of 2-iodobutane. These measurements show a change in sign and a pronounced increase in the magnitude of the chiral response over the first 100 fs, followed by its decay within less than 500 fs, revealing the photodissociation to achiral products. The observed time evolution is explained in terms of the variation of the electric and magnetic transition-dipole moments between the lowest electronic states of the cation as a function of the reaction coordinate. These results open the path to investigations of the chirality of molecular-reaction pathways, light-induced chirality in chemical processes, and the control of molecular chirality through tailored laser pulses. AU - Baykusheva, Denitsa Rangelova AU - Zindel, Daniel AU - Svoboda, Vít AU - Bommeli, Elias AU - Ochsner, Manuel AU - Tehlar, Andres AU - Wörner, Hans Jakob ID - 14001 IS - 48 JF - Proceedings of the National Academy of Sciences KW - Multidisciplinary SN - 0027-8424 TI - Real-time probing of chirality during a chemical reaction VL - 116 ER - TY - JOUR AB - Idealized simulations of tropical moist convection have revealed that clouds can spontaneously clump together in a process called self-aggregation. This results in a state where a moist cloudy region with intense deep convection is surrounded by extremely dry subsiding air devoid of deep convection. Because of the idealized settings of the simulations where it was discovered, the relevance of self-aggregation to the real world is still debated. Here, we show that self-aggregation feedbacks play a leading-order role in the spontaneous genesis of tropical cyclones in cloud-resolving simulations. Those feedbacks accelerate the cyclogenesis process by a factor of 2, and the feedbacks contributing to the cyclone formation show qualitative and quantitative agreement with the self-aggregation process. Once the cyclone is formed, wind-induced surface heat exchange (WISHE) effects dominate, although we find that self-aggregation feedbacks have a small but nonnegligible contribution to the maintenance of the mature cyclone. Our results suggest that self-aggregation, and the framework developed for its study, can help shed more light into the physical processes leading to cyclogenesis and cyclone intensification. In particular, our results point out the importance of the longwave radiative cooling outside the cyclone. AU - Muller, Caroline J AU - Romps, David M. ID - 9135 IS - 12 JF - Proceedings of the National Academy of Sciences KW - Multidisciplinary SN - 0027-8424 TI - Acceleration of tropical cyclogenesis by self-aggregation feedbacks VL - 115 ER - TY - JOUR AB - The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation and is required for endosperm genomic imprinting and embryo viability. Targets of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons and at the boundaries of large transposons, but how DME interacts with these diverse chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1) subunit of the chromatin remodeler FACT (facilitates chromatin transactions), was previously shown to be involved in the DME-dependent regulation of genomic imprinting in Arabidopsis endosperm. Therefore, to investigate the interaction between DME and chromatin, we focused on the activity of the two FACT subunits, SSRP1 and SUPPRESSOR of TY16 (SPT16), during reproduction in Arabidopsis. We found that FACT colocalizes with nuclear DME in vivo, and that DME has two classes of target sites, the first being euchromatic and accessible to DME, but the second, representing over half of DME targets, requiring the action of FACT for DME-mediated DNA demethylation genome-wide. Our results show that the FACT-dependent DME targets are GC-rich heterochromatin domains with high nucleosome occupancy enriched with H3K9me2 and H3K27me1. Further, we demonstrate that heterochromatin-associated linker histone H1 specifically mediates the requirement for FACT at a subset of DME-target loci. Overall, our results demonstrate that FACT is required for DME targeting by facilitating its access to heterochromatin. AU - Frost, Jennifer M. AU - Kim, M. Yvonne AU - Park, Guen Tae AU - Hsieh, Ping-Hung AU - Nakamura, Miyuki AU - Lin, Samuel J. H. AU - Yoo, Hyunjin AU - Choi, Jaemyung AU - Ikeda, Yoko AU - Kinoshita, Tetsu AU - Choi, Yeonhee AU - Zilberman, Daniel AU - Fischer, Robert L. ID - 9471 IS - 20 JF - Proceedings of the National Academy of Sciences KW - Multidisciplinary SN - 0027-8424 TI - FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis VL - 115 ER - TY - JOUR AB - Efficient molecular switching in confined spaces is critical for the successful development of artificial molecular machines. However, molecular switching events often entail large structural changes and therefore require conformational freedom, which is typically limited under confinement conditions. Here, we investigated the behavior of azobenzene—the key building block of light-controlled molecular machines—in a confined environment that is flexible and can adapt its shape to that of the bound guest. To this end, we encapsulated several structurally diverse azobenzenes within the cavity of a flexible, water-soluble coordination cage, and investigated their light-responsive behavior. Using UV/Vis absorption spectroscopy and a combination of NMR methods, we showed that each of the encapsulated azobenzenes exhibited distinct switching properties. An azobenzene forming a 1:1 host–guest inclusion complex could be efficiently photoisomerized in a reversible fashion. In contrast, successful switching in inclusion complexes incorporating two azobenzene guests was dependent on the availability of free cages in the system, and it involved reversible trafficking of azobenzene between the cages. In the absence of extra cages, photoswitching was either suppressed or it involved expulsion of azobenzene from the cage and consequently its precipitation from the solution. This finding was utilized to develop an information storage medium in which messages could be written and erased in a reversible fashion using light. AU - Samanta, Dipak AU - Gemen, Julius AU - Chu, Zonglin AU - Diskin-Posner, Yael AU - Shimon, Linda J. W. AU - Klajn, Rafal ID - 13376 IS - 38 JF - Proceedings of the National Academy of Sciences KW - Multidisciplinary SN - 0027-8424 TI - Reversible photoswitching of encapsulated azobenzenes in water VL - 115 ER - TY - JOUR AB - Confining molecules to volumes only slightly larger than the molecules themselves can profoundly alter their properties. Molecular switches—entities that can be toggled between two or more forms upon exposure to an external stimulus—often require conformational freedom to isomerize. Therefore, placing these switches in confined spaces can render them non-operational. To preserve the switchability of these species under confinement, we work with a water-soluble coordination cage that is flexible enough to adapt its shape to the conformation of the encapsulated guest. We show that owing to its flexibility, the cage is not only capable of accommodating—and solubilizing in water—several light-responsive spiropyran-based molecular switches, but, more importantly, it also provides an environment suitable for the efficient, reversible photoisomerization of the bound guests. Our findings pave the way towards studying various molecular switching processes in confined environments. AU - Samanta, Dipak AU - Galaktionova, Daria AU - Gemen, Julius AU - Shimon, Linda J. W. AU - Diskin-Posner, Yael AU - Avram, Liat AU - Král, Petr AU - Klajn, Rafal ID - 13374 JF - Nature Communications KW - General Physics and Astronomy KW - General Biochemistry KW - Genetics and Molecular Biology KW - General Chemistry KW - Multidisciplinary TI - Reversible chromism of spiropyran in the cavity of a flexible coordination cage VL - 9 ER - TY - JOUR AB - The reversibly switchable fluorescent proteins (RSFPs) commonly used for RESOLFT nanoscopy have been developed from fluorescent proteins of the GFP superfamily. These proteins are bright, but exhibit several drawbacks such as relatively large size, oxygen-dependence, sensitivity to low pH, and limited switching speed. Therefore, RSFPs from other origins with improved properties need to be explored. Here, we report the development of two RSFPs based on the LOV domain of the photoreceptor protein YtvA from Bacillus subtilis. LOV domains obtain their fluorescence by association with the abundant cellular cofactor flavin mononucleotide (FMN). Under illumination with blue and ultraviolet light, they undergo a photocycle, making these proteins inherently photoswitchable. Our first improved variant, rsLOV1, can be used for RESOLFT imaging, whereas rsLOV2 proved useful for STED nanoscopy of living cells with a resolution of down to 50 nm. In addition to their smaller size compared to GFP-related proteins (17 kDa instead of 27 kDa) and their usability at low pH, rsLOV1 and rsLOV2 exhibit faster switching kinetics, switching on and off 3 times faster than rsEGFP2, the fastest-switching RSFP reported to date. Therefore, LOV-domain-based RSFPs have potential for applications where the switching speed of GFP-based proteins is limiting. AU - Gregor, Carola AU - Sidenstein, Sven C. AU - Andresen, Martin AU - Sahl, Steffen J. AU - Danzl, Johann G AU - Hell, Stefan W. ID - 8618 JF - Scientific Reports KW - Multidisciplinary SN - 2045-2322 TI - Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA VL - 8 ER - TY - JOUR AB - Pore-forming toxins (PFT) are virulence factors that transform from soluble to membrane-bound states. The Yersinia YaxAB system represents a family of binary α-PFTs with orthologues in human, insect, and plant pathogens, with unknown structures. YaxAB was shown to be cytotoxic and likely involved in pathogenesis, though the molecular basis for its two-component lytic mechanism remains elusive. Here, we present crystal structures of YaxA and YaxB, together with a cryo-electron microscopy map of the YaxAB complex. Our structures reveal a pore predominantly composed of decamers of YaxA–YaxB heterodimers. Both subunits bear membrane-active moieties, but only YaxA is capable of binding to membranes by itself. YaxB can subsequently be recruited to membrane-associated YaxA and induced to present its lytic transmembrane helices. Pore formation can progress by further oligomerization of YaxA–YaxB dimers. Our results allow for a comparison between pore assemblies belonging to the wider ClyA-like family of α-PFTs, highlighting diverse pore architectures. AU - Bräuning, Bastian AU - Bertosin, Eva AU - Praetorius, Florian M AU - Ihling, Christian AU - Schatt, Alexandra AU - Adler, Agnes AU - Richter, Klaus AU - Sinz, Andrea AU - Dietz, Hendrik AU - Groll, Michael ID - 14284 JF - Nature Communications KW - General Physics and Astronomy KW - General Biochemistry KW - Genetics and Molecular Biology KW - General Chemistry KW - Multidisciplinary SN - 2041-1723 TI - Structure and mechanism of the two-component α-helical pore-forming toxin YaxAB VL - 9 ER - TY - JOUR AB - Electric charges are conserved. The same would be expected to hold for magnetic charges, yet magnetic monopoles have never been observed. It is therefore surprising that the laws of nonequilibrium thermodynamics, combined with Maxwell’s equations, suggest that colloidal particles heated or cooled in certain polar or paramagnetic solvents may behave as if they carry an electric/magnetic charge. Here, we present numerical simulations that show that the field distribution around a pair of such heated/cooled colloidal particles agrees quantitatively with the theoretical predictions for a pair of oppositely charged electric or magnetic monopoles. However, in other respects, the nonequilibrium colloidal particles do not behave as monopoles: They cannot be moved by a homogeneous applied field. The numerical evidence for the monopole-like fields around heated/cooled colloidal particles is crucial because the experimental and numerical determination of forces between such colloidal particles would be complicated by the presence of other effects, such as thermophoresis. AU - Wirnsberger, Peter AU - Fijan, Domagoj AU - Lightwood, Roger A. AU - Šarić, Anđela AU - Dellago, Christoph AU - Frenkel, Daan ID - 10373 IS - 19 JF - Proceedings of the National Academy of Sciences KW - multidisciplinary SN - 0027-8424 TI - Numerical evidence for thermally induced monopoles VL - 114 ER - TY - JOUR AB - Self-assembly of inorganic nanoparticles has been used to prepare hundreds of different colloidal crystals, but almost invariably with the restriction that the particles must be densely packed. Here, we show that non–close-packed nanoparticle arrays can be fabricated through the selective removal of one of two components comprising binary nanoparticle superlattices. First, a variety of binary nanoparticle superlattices were prepared at the liquid-air interface, including several arrangements that were previously unknown. Molecular dynamics simulations revealed the particular role of the liquid in templating the formation of superlattices not achievable through self-assembly in bulk solution. Second, upon stabilization, all of these binary superlattices could be transformed into distinct “nanoallotropes”—nanoporous materials having the same chemical composition but differing in their nanoscale architectures. AU - Udayabhaskararao, Thumu AU - Altantzis, Thomas AU - Houben, Lothar AU - Coronado-Puchau, Marc AU - Langer, Judith AU - Popovitz-Biro, Ronit AU - Liz-Marzán, Luis M. AU - Vuković, Lela AU - Král, Petr AU - Bals, Sara AU - Klajn, Rafal ID - 13381 IS - 6362 JF - Science KW - Multidisciplinary SN - 0036-8075 TI - Tunable porous nanoallotropes prepared by post-assembly etching of binary nanoparticle superlattices VL - 358 ER - TY - JOUR AB - Although methane is a volatile gas, it can be efficiently trapped in ice, which can then be readily set on fire. Beyond the curiosity of this “burning ice,” caged methane is of great importance as one of the world's largest natural gas resources. In these materials, known as clathrates, methane molecules are tightly bound in nanometer-sized, regularly interspaced cages. Other inorganic materials, such as the silica mineral chibaite, can similarly encapsulate methane and higher hydrocarbons. Simple organic compounds have also been found to trap various organic molecules upon crystallization. AU - Samanta, Dipak AU - Klajn, Rafal ID - 13384 IS - 6328 JF - Science KW - Multidisciplinary SN - 0036-8075 TI - Clathrates grow up VL - 355 ER - TY - JOUR AB - Strong-field photoelectron holography and laser-induced electron diffraction (LIED) are two powerful emerging methods for probing the ultrafast dynamics of molecules. However, both of them have remained restricted to static systems and to nuclear dynamics induced by strong-field ionization. Here we extend these promising methods to image purely electronic valence-shell dynamics in molecules using photoelectron holography. In the same experiment, we use LIED and photoelectron holography simultaneously, to observe coupled electronic-rotational dynamics taking place on similar timescales. These results offer perspectives for imaging ultrafast dynamics of molecules on femtosecond to attosecond timescales. AU - Walt, Samuel G. AU - Bhargava Ram, Niraghatam AU - Atala, Marcos AU - Shvetsov-Shilovski, Nikolay I AU - von Conta, Aaron AU - Baykusheva, Denitsa Rangelova AU - Lein, Manfred AU - Wörner, Hans Jakob ID - 14005 JF - Nature Communications KW - General Physics and Astronomy KW - General Biochemistry KW - Genetics and Molecular Biology KW - General Chemistry KW - Multidisciplinary TI - Dynamics of valence-shell electrons and nuclei probed by strong-field holography and rescattering VL - 8 ER - TY - JOUR AB - Time-resolved x-ray absorption spectroscopy (TR-XAS) has so far practically been limited to large-scale facilities, to subpicosecond temporal resolution, and to the condensed phase. We report the realization of TR-XAS with a temporal resolution in the low femtosecond range by developing a tabletop high-harmonic source reaching up to 350 electron volts, thus partially covering the spectral region of 280 to 530 electron volts, where water is transmissive. We used this source to follow previously unexamined light-induced chemical reactions in the lowest electronic states of isolated CF4+ and SF6+ molecules in the gas phase. By probing element-specific core-to-valence transitions at the carbon K-edge or the sulfur L-edges, we characterized their reaction paths and observed the effect of symmetry breaking through the splitting of absorption bands and Rydberg-valence mixing induced by the geometry changes. AU - Pertot, Yoann AU - Schmidt, Cédric AU - Matthews, Mary AU - Chauvet, Adrien AU - Huppert, Martin AU - Svoboda, Vit AU - von Conta, Aaron AU - Tehlar, Andres AU - Baykusheva, Denitsa Rangelova AU - Wolf, Jean-Pierre AU - Wörner, Hans Jakob ID - 14008 IS - 6322 JF - Science KW - Multidisciplinary SN - 0036-8075 TI - Time-resolved x-ray absorption spectroscopy with a water window high-harmonic source VL - 355 ER - TY - JOUR AB - The basic helix–loop–helix PAS domain (bHLH-PAS) transcription factor CLOCK:BMAL1 (brain and muscle Arnt-like protein 1) sits at the core of the mammalian circadian transcription/translation feedback loop. Precise control of CLOCK:BMAL1 activity by coactivators and repressors establishes the ∼24-h periodicity of gene expression. Formation of a repressive complex, defined by the core clock proteins cryptochrome 1 (CRY1):CLOCK:BMAL1, plays an important role controlling the switch from repression to activation each day. Here we show that CRY1 binds directly to the PAS domain core of CLOCK:BMAL1, driven primarily by interaction with the CLOCK PAS-B domain. Integrative modeling and solution X-ray scattering studies unambiguously position a key loop of the CLOCK PAS-B domain in the secondary pocket of CRY1, analogous to the antenna chromophore-binding pocket of photolyase. CRY1 docks onto the transcription factor alongside the PAS domains, extending above the DNA-binding bHLH domain. Single point mutations at the interface on either CRY1 or CLOCK disrupt formation of the ternary complex, highlighting the importance of this interface for direct regulation of CLOCK:BMAL1 activity by CRY1. AU - Michael, Alicia Kathleen AU - Fribourgh, Jennifer L. AU - Chelliah, Yogarany AU - Sandate, Colby R. AU - Hura, Greg L. AU - Schneidman-Duhovny, Dina AU - Tripathi, Sarvind M. AU - Takahashi, Joseph S. AU - Partch, Carrie L. ID - 15157 IS - 7 JF - Proceedings of the National Academy of Sciences KW - Multidisciplinary SN - 0027-8424 TI - Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1 VL - 114 ER - TY - JOUR AB - Circadian clocks are ubiquitous timing systems that induce rhythms of biological activities in synchrony with night and day. In cyanobacteria, timing is generated by a posttranslational clock consisting of KaiA, KaiB, and KaiC proteins and a set of output signaling proteins, SasA and CikA, which transduce this rhythm to control gene expression. Here, we describe crystal and nuclear magnetic resonance structures of KaiB-KaiC,KaiA-KaiB-KaiC, and CikA-KaiB complexes. They reveal how the metamorphic properties of KaiB, a protein that adopts two distinct folds, and the post–adenosine triphosphate hydrolysis state of KaiC create a hub around which nighttime signaling events revolve, including inactivation of KaiA and reciprocal regulation of the mutually antagonistic signaling proteins, SasA and CikA. AU - Tseng, Roger AU - Goularte, Nicolette F. AU - Chavan, Archana AU - Luu, Jansen AU - Cohen, Susan E. AU - Chang, Yong-Gang AU - Heisler, Joel AU - Li, Sheng AU - Michael, Alicia Kathleen AU - Tripathi, Sarvind AU - Golden, Susan S. AU - LiWang, Andy AU - Partch, Carrie L. ID - 15156 IS - 6330 JF - Science KW - Multidisciplinary SN - 0036-8075 TI - Structural basis of the day-night transition in a bacterial circadian clock VL - 355 ER - TY - JOUR AB - The interplay of membrane proteins is vital for many biological processes, such as cellular transport, cell division, and signal transduction between nerve cells. Theoretical considerations have led to the idea that the membrane itself mediates protein self-organization in these processes through minimization of membrane curvature energy. Here, we present a combined experimental and numerical study in which we quantify these interactions directly for the first time. In our experimental model system we control the deformation of a lipid membrane by adhering colloidal particles. Using confocal microscopy, we establish that these membrane deformations cause an attractive interaction force leading to reversible binding. The attraction extends over 2.5 times the particle diameter and has a strength of three times the thermal energy (−3.3 kBT). Coarse-grained Monte-Carlo simulations of the system are in excellent agreement with the experimental results and prove that the measured interaction is independent of length scale. Our combined experimental and numerical results reveal membrane curvature as a common physical origin for interactions between any membrane-deforming objects, from nanometre-sized proteins to micrometre-sized particles. AU - van der Wel, Casper AU - Vahid, Afshin AU - Šarić, Anđela AU - Idema, Timon AU - Heinrich, Doris AU - Kraft, Daniela J. ID - 10377 IS - 1 JF - Scientific Reports KW - multidisciplinary SN - 2045-2322 TI - Lipid membrane-mediated attraction between curvature inducing objects VL - 6 ER - TY - JOUR AB - Mountain ranges are the world’s natural water towers and provide water resources for millions of people. However, their hydrological balance and possible future changes in river flow remain poorly understood because of high meteorological variability, physical inaccessibility, and the complex interplay between climate, cryosphere, and hydrological processes. Here, we use a state-of-the art glacio-hydrological model informed by data from high-altitude observations and the latest climate change scenarios to quantify the climate change impact on water resources of two contrasting catchments vulnerable to changes in the cryosphere. The two study catchments are located in the Central Andes of Chile and in the Nepalese Himalaya in close vicinity of densely populated areas. Although both sites reveal a strong decrease in glacier area, they show a remarkably different hydrological response to projected climate change. In the Juncal catchment in Chile, runoff is likely to sharply decrease in the future and the runoff seasonality is sensitive to projected climatic changes. In the Langtang catchment in Nepal, future water availability is on the rise for decades to come with limited shifts between seasons. Owing to the high spatiotemporal resolution of the simulations and process complexity included in the modeling, the response times and the mechanisms underlying the variations in glacier area and river flow can be well constrained. The projections indicate that climate change adaptation in Central Chile should focus on dealing with a reduction in water availability, whereas in Nepal preparedness for flood extremes should be the policy priority. AU - Ragettli, Silvan AU - Immerzeel, Walter W. AU - Pellicciotti, Francesca ID - 12618 IS - 33 JF - PNAS KW - Multidisciplinary SN - 0027-8424 TI - Contrasting climate change impact on river flows from high-altitude catchments in the Himalayan and Andes Mountains VL - 113 ER - TY - JOUR AB - Cytosine methylation is a DNA modification with important regulatory functions in eukaryotes. In flowering plants, sexual reproduction is accompanied by extensive DNA demethylation, which is required for proper gene expression in the endosperm, a nutritive extraembryonic seed tissue. Endosperm arises from a fusion of a sperm cell carried in the pollen and a female central cell. Endosperm DNA demethylation is observed specifically on the chromosomes inherited from the central cell in Arabidopsis thaliana, rice, and maize, and requires the DEMETER DNA demethylase in Arabidopsis. DEMETER is expressed in the central cell before fertilization, suggesting that endosperm demethylation patterns are inherited from the central cell. Down-regulation of the MET1 DNA methyltransferase has also been proposed to contribute to central cell demethylation. However, with the exception of three maize genes, central cell DNA methylation has not been directly measured, leaving the origin and mechanism of endosperm demethylation uncertain. Here, we report genome-wide analysis of DNA methylation in the central cells of Arabidopsis and rice—species that diverged 150 million years ago—as well as in rice egg cells. We find that DNA demethylation in both species is initiated in central cells, which requires DEMETER in Arabidopsis. However, we do not observe a global reduction of CG methylation that would be indicative of lowered MET1 activity; on the contrary, CG methylation efficiency is elevated in female gametes compared with nonsexual tissues. Our results demonstrate that locus-specific, active DNA demethylation in the central cell is the origin of maternal chromosome hypomethylation in the endosperm. AU - Park, Kyunghyuk AU - Kim, M. Yvonne AU - Vickers, Martin AU - Park, Jin-Sup AU - Hyun, Youbong AU - Okamoto, Takashi AU - Zilberman, Daniel AU - Fischer, Robert L. AU - Feng, Xiaoqi AU - Choi, Yeonhee AU - Scholten, Stefan ID - 9477 IS - 52 JF - Proceedings of the National Academy of Sciences KW - Multidisciplinary SN - 0027-8424 TI - DNA demethylation is initiated in the central cells of Arabidopsis and rice VL - 113 ER - TY - JOUR AB - All attosecond time-resolved measurements have so far relied on the use of intense near-infrared laser pulses. In particular, attosecond streaking, laser-induced electron diffraction and high-harmonic generation all make use of non-perturbative light–matter interactions. Remarkably, the effect of the strong laser field on the studied sample has often been neglected in previous studies. Here we use high-harmonic spectroscopy to measure laser-induced modifications of the electronic structure of molecules. We study high-harmonic spectra of spatially oriented CH3F and CH3Br as generic examples of polar polyatomic molecules. We accurately measure intensity ratios of even and odd-harmonic orders, and of the emission from aligned and unaligned molecules. We show that these robust observables reveal a substantial modification of the molecular electronic structure by the external laser field. Our insights offer new challenges and opportunities for a range of emerging strong-field attosecond spectroscopies. AU - Kraus, P. M. AU - Tolstikhin, O. I. AU - Baykusheva, Denitsa Rangelova AU - Rupenyan, A. AU - Schneider, J. AU - Bisgaard, C. Z. AU - Morishita, T. AU - Jensen, F. AU - Madsen, L. B. AU - Wörner, H. J. ID - 14016 JF - Nature Communications KW - General Physics and Astronomy KW - General Biochemistry KW - Genetics and Molecular Biology KW - General Chemistry KW - Multidisciplinary TI - Observation of laser-induced electronic structure in oriented polyatomic molecules VL - 6 ER - TY - JOUR AB - The ultrafast motion of electrons and holes after light-matter interaction is fundamental to a broad range of chemical and biophysical processes. We advanced high-harmonic spectroscopy to resolve spatially and temporally the migration of an electron hole immediately after ionization of iodoacetylene while simultaneously demonstrating extensive control over the process. A multidimensional approach, based on the measurement and accurate theoretical description of both even and odd harmonic orders, enabled us to reconstruct both quantum amplitudes and phases of the electronic states with a resolution of ~100 attoseconds. We separately reconstructed quasi-field-free and laser-controlled charge migration as a function of the spatial orientation of the molecule and determined the shape of the hole created by ionization. Our technique opens the prospect of laser control over electronic primary processes. AU - Kraus, P. M. AU - Mignolet, B. AU - Baykusheva, Denitsa Rangelova AU - Rupenyan, A. AU - Horný, L. AU - Penka, E. F. AU - Grassi, G. AU - Tolstikhin, O. I. AU - Schneider, J. AU - Jensen, F. AU - Madsen, L. B. AU - Bandrauk, A. D. AU - Remacle, F. AU - Wörner, H. J. ID - 14013 IS - 6262 JF - Science KW - Multidisciplinary SN - 0036-8075 TI - Measurement and laser control of attosecond charge migration in ionized iodoacetylene VL - 350 ER - TY - JOUR AB - Protein oligomers have been implicated as toxic agents in a wide range of amyloid-related diseases. However, it has remained unsolved whether the oligomers are a necessary step in the formation of amyloid fibrils or just a dangerous byproduct. Analogously, it has not been resolved if the amyloid nucleation process is a classical one-step nucleation process or a two-step process involving prenucleation clusters. We use coarse-grained computer simulations to study the effect of nonspecific attractions between peptides on the primary nucleation process underlying amyloid fibrillization. We find that, for peptides that do not attract, the classical one-step nucleation mechanism is possible but only at nonphysiologically high peptide concentrations. At low peptide concentrations, which mimic the physiologically relevant regime, attractive interpeptide interactions are essential for fibril formation. Nucleation then inevitably takes place through a two-step mechanism involving prefibrillar oligomers. We show that oligomers not only help peptides meet each other but also, create an environment that facilitates the conversion of monomers into the β-sheet–rich form characteristic of fibrils. Nucleation typically does not proceed through the most prevalent oligomers but through an oligomer size that is only observed in rare fluctuations, which is why such aggregates might be hard to capture experimentally. Finally, we find that the nucleation of amyloid fibrils cannot be described by classical nucleation theory: in the two-step mechanism, the critical nucleus size increases with increases in both concentration and interpeptide interactions, which is in direct contrast with predictions from classical nucleation theory. AU - Šarić, Anđela AU - Chebaro, Yassmine C. AU - Knowles, Tuomas P. J. AU - Frenkel, Daan ID - 10382 IS - 50 JF - Proceedings of the National Academy of Sciences KW - multidisciplinary SN - 0027-8424 TI - Crucial role of nonspecific interactions in amyloid nucleation VL - 111 ER - TY - JOUR AB - Nanoporous frameworks are polymeric materials built from rigid molecules, which give rise to their nanoporous structures with applications in gas sorption and storage, catalysis and others. Conceptually new applications could emerge, should these beneficial properties be manipulated by external stimuli in a reversible manner. One approach to render nanoporous frameworks responsive to external signals would be to immobilize molecular switches within their nanopores. Although the majority of molecular switches require conformational freedom to isomerize, and switching in the solid state is prohibited, the nanopores may provide enough room for the switches to efficiently isomerize. Here we describe two families of nanoporous materials incorporating the spiropyran molecular switch. These materials exhibit a variety of interesting properties, including reversible photochromism and acidochromism under solvent-free conditions, light-controlled capture and release of metal ions, as well reversible chromism induced by solvation/desolvation. AU - Kundu, Pintu K. AU - Olsen, Gregory L. AU - Kiss, Vladimir AU - Klajn, Rafal ID - 13402 JF - Nature Communications KW - General Physics and Astronomy KW - General Biochemistry KW - Genetics and Molecular Biology KW - General Chemistry KW - Multidisciplinary TI - Nanoporous frameworks exhibiting multiple stimuli responsiveness VL - 5 ER - TY - JOUR AB - Organizing inorganic nanocrystals into complex architectures is challenging and typically relies on preexisting templates, such as properly folded DNA or polypeptide chains. We found that under carefully controlled conditions, cubic nanocrystals of magnetite self-assemble into arrays of helical superstructures in a template-free manner with >99% yield. Computer simulations revealed that the formation of helices is determined by the interplay of van der Waals and magnetic dipole-dipole interactions, Zeeman coupling, and entropic forces and can be attributed to spontaneous formation of chiral nanocube clusters. Neighboring helices within their densely packed ensembles tended to adopt the same handedness in order to maximize packing, thus revealing a novel mechanism of symmetry breaking and chirality amplification. AU - Singh, Gurvinder AU - Chan, Henry AU - Baskin, Artem AU - Gelman, Elijah AU - Repnin, Nikita AU - Král, Petr AU - Klajn, Rafal ID - 13400 IS - 6201 JF - Science KW - Multidisciplinary SN - 0036-8075 TI - Self-assembly of magnetite nanocubes into helical superstructures VL - 345 ER - TY - JOUR AB - Spontaneous formation of colonies of bacteria or flocks of birds are examples of self-organization in active living matter. Here, we demonstrate a form of self-organization from nonequilibrium driving forces in a suspension of synthetic photoactivated colloidal particles. They lead to two-dimensional "living crystals," which form, break, explode, and re-form elsewhere. The dynamic assembly results from a competition between self-propulsion of particles and an attractive interaction induced respectively by osmotic and phoretic effects and activated by light. We measured a transition from normal to giant-number fluctuations. Our experiments are quantitatively described by simple numerical simulations. We show that the existence of the living crystals is intrinsically related to the out-of-equilibrium collisions of the self-propelled particles. AU - Palacci, Jérémie A AU - Sacanna, S. AU - Steinberg, A. P. AU - Pine, D. J. AU - Chaikin, P. M. ID - 9055 IS - 6122 JF - Science KW - Multidisciplinary SN - 0036-8075 TI - Living crystals of light-activated colloidal surfers VL - 339 ER - TY - JOUR AB - Arabidopsis thaliana endosperm, a transient tissue that nourishes the embryo, exhibits extensive localized DNA demethylation on maternally inherited chromosomes. Demethylation mediates parent-of-origin–specific (imprinted) gene expression but is apparently unnecessary for the extensive accumulation of maternally biased small RNA (sRNA) molecules detected in seeds. Endosperm DNA in the distantly related monocots rice and maize is likewise locally hypomethylated, but whether this hypomethylation is generally parent-of-origin specific is unknown. Imprinted expression of sRNA also remains uninvestigated in monocot seeds. Here, we report high-coverage sequencing of the Kitaake rice cultivar that enabled us to show that localized hypomethylation in rice endosperm occurs solely on the maternal genome, preferring regions of high DNA accessibility. Maternally expressed imprinted genes are enriched for hypomethylation at putative promoter regions and transcriptional termini and paternally expressed genes at promoters and gene bodies, mirroring our recent results in A. thaliana. However, unlike in A. thaliana, rice endosperm sRNA populations are dominated by specific strong sRNA-producing loci, and imprinted 24-nt sRNAs are expressed from both parental genomes and correlate with hypomethylation. Overlaps between imprinted sRNA loci and imprinted genes expressed from opposite alleles suggest that sRNAs may regulate genomic imprinting. Whereas sRNAs in seedling tissues primarily originate from small class II (cut-and-paste) transposable elements, those in endosperm are more uniformly derived, including sequences from other transposon classes, as well as genic and intergenic regions. Our data indicate that the endosperm exhibits a unique pattern of sRNA expression and suggest that localized hypomethylation of maternal endosperm DNA is conserved in flowering plants. AU - Rodrigues, Jessica A. AU - Ruan, Randy AU - Nishimura, Toshiro AU - Sharma, Manoj K. AU - Sharma, Rita AU - Ronald, Pamela C AU - Fischer, Robert L. AU - Zilberman, Daniel ID - 9481 IS - 19 JF - Proceedings of the National Academy of Sciences KW - Multidisciplinary SN - 0027-8424 TI - Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm VL - 110 ER - TY - JOUR AB - To combat the functional decline of the proteome, cells use the process of protein turnover to replace potentially impaired polypeptides with new functional copies. We found that extremely long-lived proteins (ELLPs) did not turn over in postmitotic cells of the rat central nervous system. These ELLPs were associated with chromatin and the nuclear pore complex, the central transport channels that mediate all molecular trafficking in and out of the nucleus. The longevity of these proteins would be expected to expose them to potentially harmful metabolites, putting them at risk of accumulating damage over extended periods of time. Thus, it is possible that failure to maintain proper levels and functional integrity of ELLPs in nonproliferative cells might contribute to age-related deterioration in cell and tissue function. AU - Savas, Jeffrey N. AU - Toyama, Brandon H. AU - Xu, Tao AU - Yates, John R. AU - HETZER, Martin W ID - 11092 IS - 6071 JF - Science KW - Multidisciplinary SN - 0036-8075 TI - Extremely long-lived nuclear pore proteins in the rat brain VL - 335 ER - TY - JOUR AB - The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes DNA demethylation before fertilization, but the targeting preferences, mechanism, and biological significance of this process remain unclear. Here, we show that active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for all of the demethylation in the central cell and preferentially targets small, AT-rich, and nucleosome-depleted euchromatic transposable elements. The vegetative cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation of similar sequences, and lack of DEMETER in vegetative cells causes reduced small RNA–directed DNA methylation of transposons in sperm. Our results demonstrate that demethylation in companion cells reinforces transposon methylation in plant gametes and likely contributes to stable silencing of transposable elements across generations. AU - Ibarra, Christian A. AU - Feng, Xiaoqi AU - Schoft, Vera K. AU - Hsieh, Tzung-Fu AU - Uzawa, Rie AU - Rodrigues, Jessica A. AU - Zemach, Assaf AU - Chumak, Nina AU - Machlicova, Adriana AU - Nishimura, Toshiro AU - Rojas, Denisse AU - Fischer, Robert L. AU - Tamaru, Hisashi AU - Zilberman, Daniel ID - 12198 IS - 6100 JF - Science KW - Multidisciplinary SN - 0036-8075 TI - Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes VL - 337 ER - TY - JOUR AB - Understanding the mechanism of protein folding requires a detailed knowledge of the structural properties of the barriers separating unfolded from native conformations. The S-peptide from ribonuclease S forms its α-helical structure only upon binding to the folded S-protein. We characterized the transition state for this binding-induced folding reaction at high resolution by determining the effect of site-specific backbone thioxylation and side-chain modifications on the kinetics and thermodynamics of the reaction, which allows us to monitor formation of backbone hydrogen bonds and side-chain interactions in the transition state. The experiments reveal that α-helical structure in the S-peptide is absent in the transition state of binding. Recognition between the unfolded S-peptide and the S-protein is mediated by loosely packed hydrophobic side-chain interactions in two well defined regions on the S-peptide. Close packing and helix formation occurs rapidly after binding. Introducing hydrophobic residues at positions outside the recognition region can drastically slow down association. AU - Bachmann, Annett AU - Wildemann, Dirk AU - Praetorius, Florian M AU - Fischer, Gunter AU - Kiefhaber, Thomas ID - 14305 IS - 10 JF - PNAS KW - Multidisciplinary SN - 0027-8424 TI - Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction VL - 108 ER - TY - JOUR AB - Eukaryotic cytosine methylation represses transcription but also occurs in the bodies of active genes, and the extent of methylation biology conservation is unclear. We quantified DNA methylation in 17 eukaryotic genomes and found that gene body methylation is conserved between plants and animals, whereas selective methylation of transposons is not. We show that methylation of plant transposons in the CHG context extends to green algae and that exclusion of histone H2A.Z from methylated DNA is conserved between plants and animals, and we present evidence for RNA-directed DNA methylation of fungal genes. Our data demonstrate that extant DNA methylation systems are mosaics of conserved and derived features, and indicate that gene body methylation is an ancient property of eukaryotic genomes. AU - Zemach, Assaf AU - McDaniel, Ivy E. AU - Silva, Pedro AU - Zilberman, Daniel ID - 9452 IS - 5980 JF - Science KW - Multidisciplinary SN - 0036-8075 TI - Genome-wide evolutionary analysis of eukaryotic DNA methylation VL - 328 ER - TY - JOUR AB - Parent-of-origin-specific (imprinted) gene expression is regulated in Arabidopsis thaliana endosperm by cytosine demethylation of the maternal genome mediated by the DNA glycosylase DEMETER, but the extent of the methylation changes is not known. Here, we show that virtually the entire endosperm genome is demethylated, coupled with extensive local non-CG hypermethylation of small interfering RNA–targeted sequences. Mutation of DEMETER partially restores endosperm CG methylation to levels found in other tissues, indicating that CG demethylation is specific to maternal sequences. Endosperm demethylation is accompanied by CHH hypermethylation of embryo transposable elements. Our findings demonstrate extensive reconfiguration of the endosperm methylation landscape that likely reinforces transposon silencing in the embryo. AU - Hsieh, Tzung-Fu AU - Ibarra, Christian A. AU - Silva, Pedro AU - Zemach, Assaf AU - Eshed-Williams, Leor AU - Fischer, Robert L. AU - Zilberman, Daniel ID - 9453 IS - 5933 JF - Science KW - Multidisciplinary SN - 0036-8075 TI - Genome-wide demethylation of Arabidopsis endosperm VL - 324 ER - TY - JOUR AB - In traditional photoconductors1,2,3, the impinging light generates mobile charge carriers in the valence and/or conduction bands, causing the material’s conductivity to increase4. Such positive photoconductance is observed in both bulk and nanostructured5,6 photoconductors. Here we describe a class of nanoparticle-based materials whose conductivity can either increase or decrease on irradiation with visible light of wavelengths close to the particles’ surface plasmon resonance. The remarkable feature of these plasmonic materials is that the sign of the conductivity change and the nature of the electron transport between the nanoparticles depend on the molecules comprising the self-assembled monolayers (SAMs)7,8 stabilizing the nanoparticles. For SAMs made of electrically neutral (polar and non-polar) molecules, conductivity increases on irradiation. If, however, the SAMs contain electrically charged (either negatively or positively) groups, conductivity decreases. The optical and electrical characteristics of these previously undescribed inverse photoconductors can be engineered flexibly by adjusting the material properties of the nanoparticles and of the coating SAMs. In particular, in films comprising mixtures of different nanoparticles or nanoparticles coated with mixed SAMs, the overall photoconductance is a weighted average of the changes induced by the individual components. These and other observations can be rationalized in terms of light-induced creation of mobile charge carriers whose transport through the charged SAMs is inhibited by carrier trapping in transient polaron-like states9,10. The nanoparticle-based photoconductors we describe could have uses in chemical sensors and/or in conjunction with flexible substrates. AU - Nakanishi, Hideyuki AU - Bishop, Kyle J. M. AU - Kowalczyk, Bartlomiej AU - Nitzan, Abraham AU - Weiss, Emily A. AU - Tretiakov, Konstantin V. AU - Apodaca, Mario M. AU - Klajn, Rafal AU - Stoddart, J. Fraser AU - Grzybowski, Bartosz A. ID - 13418 IS - 7253 JF - Nature KW - Multidisciplinary SN - 0028-0836 TI - Photoconductance and inverse photoconductance in films of functionalized metal nanoparticles VL - 460 ER - TY - JOUR AB - We present a miniaturized pull-down method for the detection of protein-protein interactions using standard affinity chromatography reagents. Binding events between different proteins, which are color-coded with quantum dots (QDs), are visualized on single affinity chromatography beads by fluorescence microscopy. The use of QDs for single molecule detection allows the simultaneous analysis of multiple protein-protein binding events and reduces the amount of time and material needed to perform a pull-down experiment. AU - Schulte, Roberta AU - Talamas, Jessica AU - Doucet, Christine AU - HETZER, Martin W ID - 11114 IS - 4 JF - PLoS ONE KW - Multidisciplinary SN - 1932-6203 TI - Single bead affinity detection (SINBAD) for the analysis of protein-protein interactions VL - 3 ER - TY - JOUR AB - Eukaryotic chromatin is separated into functional domains differentiated by posttranslational histone modifications, histone variants, and DNA methylation1–6. Methylation is associated with repression of transcriptional initiation in plants and animals, and is frequently found in transposable elements. Proper methylation patterns are critical for eukaryotic development4,5, and aberrant methylation-induced silencing of tumor suppressor genes is a common feature of human cancer7. In contrast to methylation, the histone variant H2A.Z is preferentially deposited by the Swr1 ATPase complex near 5′ ends of genes where it promotes transcriptional competence8–20. How DNA methylation and H2A.Z influence transcription remains largely unknown. Here we show that in the plant Arabidopsis thaliana, regions of DNA methylation are quantitatively deficient in H2A.Z. Exclusion of H2A.Z is seen at sites of DNA methylation in the bodies of actively transcribed genes and in methylated transposons. Mutation of the MET1 DNA methyltransferase, which causes both losses and gains of DNA methylation4,5, engenders opposite changes in H2A.Z deposition, while mutation of the PIE1 subunit of the Swr1 complex that deposits H2A.Z17 leads to genome-wide hypermethylation. Our findings indicate that DNA methylation can influence chromatin structure and effect gene silencing by excluding H2A.Z, and that H2A.Z protects genes from DNA methylation. AU - Zilberman, Daniel AU - Coleman-Derr, Devin AU - Ballinger, Tracy AU - Henikoff, Steven ID - 9457 IS - 7218 JF - Nature KW - Multidisciplinary SN - 0028-0836 TI - Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks VL - 456 ER - TY - JOUR AB - Atom-resolved real-time studies of kinetic processes in proteins have been hampered in the past by the lack of experimental techniques that yield sufficient temporal and atomic resolution. Here we present band-selective optimized flip-angle short transient (SOFAST) real-time 2D NMR spectroscopy, a method that allows simultaneous observation of reaction kinetics for a large number of nuclear sites along the polypeptide chain of a protein with an unprecedented time resolution of a few seconds. SOFAST real-time 2D NMR spectroscopy combines fast NMR data acquisition techniques with rapid sample mixing inside the NMR magnet to initiate the kinetic event. We demonstrate the use of SOFAST real-time 2D NMR to monitor the conformational transition of α-lactalbumin from a molten globular to the native state for a large number of amide sites along the polypeptide chain. The kinetic behavior observed for the disappearance of the molten globule and the appearance of the native state is monoexponential and uniform along the polypeptide chain. This observation confirms previous findings that a single transition state ensemble controls folding of α-lactalbumin from the molten globule to the native state. In a second application, the spontaneous unfolding of native ubiquitin under nondenaturing conditions is characterized by amide hydrogen exchange rate constants measured at high pH by using SOFAST real-time 2D NMR. Our data reveal that ubiquitin unfolds in a gradual manner with distinct unfolding regimes. AU - Schanda, Paul AU - Forge, V. AU - Brutscher, B. ID - 8483 IS - 27 JF - Proceedings of the National Academy of Sciences KW - Multidisciplinary SN - 0027-8424 TI - Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy VL - 104 ER - TY - JOUR AB - Nanoparticles (NPs) decorated with ligands combining photoswitchable dipoles and covalent cross-linkers can be assembled by light into organized, three-dimensional suprastructures of various types and sizes. NPs covered with only few photoactive ligands form metastable crystals that can be assembled and disassembled “on demand” by using light of different wavelengths. For higher surface concentrations, self-assembly is irreversible, and the NPs organize into permanently cross-linked structures including robust supracrystals and plastic spherical aggregates. AU - Klajn, Rafal AU - Bishop, Kyle J. M. AU - Grzybowski, Bartosz A. ID - 13425 IS - 25 JF - Proceedings of the National Academy of Sciences KW - Multidisciplinary SN - 0027-8424 TI - Light-controlled self-assembly of reversible and irreversible nanoparticle suprastructures VL - 104 ER - TY - JOUR AB - Deformable, spherical aggregates of metal nanoparticles connected by long-chain dithiol ligands self-assemble into nanostructured materials of macroscopic dimensions. These materials are plastic and moldable against arbitrarily shaped masters and can be thermally hardened into polycrystalline metal structures of controllable porosity. In addition, in both plastic and hardened states, the assemblies are electrically conductive and exhibit Ohmic characteristics down to ∼20 volts per meter. The self-assembly method leading to such materials is applicable both to pure metals and to bimetallic structures of various elemental compositions. AU - Klajn, Rafal AU - Bishop, Kyle J. M. AU - Fialkowski, Marcin AU - Paszewski, Maciej AU - Campbell, Christopher J. AU - Gray, Timothy P. AU - Grzybowski, Bartosz A. ID - 13427 IS - 5822 JF - Science KW - Multidisciplinary SN - 0036-8075 TI - Plastic and moldable metals by self-assembly of sticky nanoparticle aggregates VL - 316 ER - TY - JOUR AB - Nuclear pore complexes are multiprotein channels that span the double lipid bilayer of the nuclear envelope. How new pores are inserted into the intact nuclear envelope of proliferating and differentiating eukaryotic cells is unknown. We found that the Nup107-160 complex was incorporated into assembly sites in the nuclear envelope from both the nucleoplasmic and the cytoplasmic sides. Nuclear pore insertion required the generation of Ran guanosine triphosphate in the nuclear and cytoplasmic compartments. Newly formed nuclear pore complexes did not contain structural components of preexisting pores, suggesting that they can form de novo. AU - D'Angelo, Maximiliano A. AU - Anderson, Daniel J. AU - Richard, Erin AU - HETZER, Martin W ID - 11118 IS - 5772 JF - Science KW - Multidisciplinary SN - 0036-8075 TI - Nuclear pores form de novo from both sides of the nuclear envelope VL - 312 ER - TY - JOUR AU - Chan, Simon W.-L. AU - Zilberman, Daniel AU - Xie, Zhixin AU - Johansen, Lisa K. AU - Carrington, James C. AU - Jacobsen, Steven E. ID - 9454 IS - 5662 JF - Science KW - Multidisciplinary SN - 0036-8075 TI - RNA silencing genes control de novo DNA methylation VL - 303 ER - TY - JOUR AB - In metazoa, the nuclear envelope breaks down and reforms during each cell cycle. Nuclear pore complexes (NPCs), which serve as channels for transport between the nucleus and cytoplasm1, assemble into the reforming nuclear envelope in a sequential process involving association of a subset of NPC proteins, nucleoporins, with chromatin followed by the formation of a closed nuclear envelope fenestrated by NPCs2,3,4,5,6,7. How chromatin recruitment of nucleoporins and NPC assembly are regulated is unknown. Here we demonstrate that RanGTP production is required to dissociate nucleoporins Nup107, Nup153 and Nup358 from Importin β, to target them to chromatin and to induce association between separate NPC subcomplexes. Additionally, either an excess of RanGTP or removal of Importin β induces formation of NPC-containing membrane structures—annulate lamellae—both in vitro in the absence of chromatin and in vivo. Annulate lamellae formation is strongly and specifically inhibited by an excess of Importin β. The data demonstrate that RanGTP triggers distinct steps of NPC assembly, and suggest a mechanism for the spatial restriction of NPC assembly to the surface of chromatin. AU - Walther, Tobias C. AU - Askjaer, Peter AU - Gentzel, Marc AU - Habermann, Anja AU - Griffiths, Gareth AU - Wilm, Matthias AU - Mattaj, Iain W. AU - HETZER, Martin W ID - 11121 IS - 6949 JF - Nature KW - Multidisciplinary SN - 0028-0836 TI - RanGTP mediates nuclear pore complex assembly VL - 424 ER - TY - JOUR AB - Proteins of the ARGONAUTE family are important in diverse posttranscriptional RNA-mediated gene-silencing systems as well as in transcriptional gene silencing in Drosophila and fission yeast and in programmed DNA elimination in Tetrahymena. We cloned ARGONAUTE4 (AGO4) from a screen for mutants that suppress silencing of the Arabidopsis SUPERMAN(SUP) gene. The ago4-1 mutant reactivated silentSUP alleles and decreased CpNpG and asymmetric DNA methylation as well as histone H3 lysine-9 methylation. In addition,ago4-1 blocked histone and DNA methylation and the accumulation of 25-nucleotide small interfering RNAs (siRNAs) that correspond to the retroelement AtSN1. These results suggest that AGO4 and long siRNAs direct chromatin modifications, including histone methylation and non-CpG DNA methylation. AU - Zilberman, Daniel AU - Cao, Xiaofeng AU - Jacobsen, Steven E. ID - 9455 IS - 5607 JF - Science KW - Multidisciplinary SN - 0036-8075 TI - ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation VL - 299 ER - TY - JOUR AB - Epigenetic silenced alleles of the Arabidopsis SUPERMANlocus (the clark kent alleles) are associated with dense hypermethylation at noncanonical cytosines (CpXpG and asymmetric sites, where X = A, T, C, or G). A genetic screen for suppressors of a hypermethylated clark kent mutant identified nine loss-of-function alleles of CHROMOMETHYLASE3(CMT3), a novel cytosine methyltransferase homolog. These cmt3 mutants display a wild-type morphology but exhibit decreased CpXpG methylation of the SUP gene and of other sequences throughout the genome. They also show reactivated expression of endogenous retrotransposon sequences. These results show that a non-CpG DNA methyltransferase is responsible for maintaining epigenetic gene silencing. AU - Lindroth, A. M. AU - Cao, Xiaofeng AU - Jackson, James P. AU - Zilberman, Daniel AU - McCallum, Claire M. AU - Henikoff, Steven AU - Jacobsen, Steven E. ID - 9444 IS - 5524 JF - Science KW - Multidisciplinary SN - 0036-8075 TI - Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation VL - 292 ER -