TY - JOUR AB - Reducing defects boosts room-temperature performance of a thermoelectric device AU - Navita, Navita AU - Ibáñez, Maria ID - 15166 IS - 6688 JF - Science SN - 0036-8075 TI - Electron highways are cooler VL - 383 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 - In nature, proteins that switch between two conformations in response to environmental stimuli structurally transduce biochemical information in a manner analogous to how transistors control information flow in computing devices. Designing proteins with two distinct but fully structured conformations is a challenge for protein design as it requires sculpting an energy landscape with two distinct minima. Here we describe the design of “hinge” proteins that populate one designed state in the absence of ligand and a second designed state in the presence of ligand. X-ray crystallography, electron microscopy, double electron-electron resonance spectroscopy, and binding measurements demonstrate that despite the significant structural differences the two states are designed with atomic level accuracy and that the conformational and binding equilibria are closely coupled. AU - Praetorius, Florian M AU - Leung, Philip J. Y. AU - Tessmer, Maxx H. AU - Broerman, Adam AU - Demakis, Cullen AU - Dishman, Acacia F. AU - Pillai, Arvind AU - Idris, Abbas AU - Juergens, David AU - Dauparas, Justas AU - Li, Xinting AU - Levine, Paul M. AU - Lamb, Mila AU - Ballard, Ryanne K. AU - Gerben, Stacey R. AU - Nguyen, Hannah AU - Kang, Alex AU - Sankaran, Banumathi AU - Bera, Asim K. AU - Volkman, Brian F. AU - Nivala, Jeff AU - Stoll, Stefan AU - Baker, David ID - 14281 IS - 6659 JF - Science SN - 0036-8075 TI - Design of stimulus-responsive two-state hinge proteins VL - 381 ER - TY - JOUR AB - The hydrogen-rich outer layers of massive stars can be removed by interactions with a binary companion. Theoretical models predict that this stripping produces a population of hot helium stars of ~2 to 8 solar masses (M☉), however, only one such system has been identified thus far. We used ultraviolet photometry to identify potential stripped helium stars then investigated 25 of them using optical spectroscopy. We identified stars with high temperatures (~60,000 to 100,000 kelvin), high surface gravities, and hydrogen-depleted surfaces; 16 stars also showed binary motion. These properties match expectations for stars with initial masses of 8 to 25 M☉ that were stripped by binary interaction. Their masses fall in the gap between subdwarf helium stars and Wolf-Rayet stars. We propose that these stars could be progenitors of stripped-envelope supernovae. AU - Drout, M. R. AU - Götberg, Ylva Louise Linsdotter AU - Ludwig, B. A. AU - Groh, J. H. AU - de Mink, S. E. AU - O’Grady, A. J. G. AU - Smith, N. ID - 15085 IS - 6676 JF - Science KW - Stellar Astrophysics SN - 0036-8075 TI - An observed population of intermediate-mass helium stars that have been stripped in binaries VL - 382 ER - TY - JOUR AB - If you mix fruit syrups with alcohol to make a schnapps, the two liquids will remain perfectly blended forever. But if you mix oil with vinegar to make a vinaigrette, the oil and vinegar will soon separate back into their previous selves. Such liquid-liquid phase separation is a thermodynamically driven phenomenon and plays an important role in many biological processes (1). Although energy injection at the macroscale can reverse the phase separation—a strong shake is the normal response to a separated vinaigrette—little is known about the effect of energy added at the microscopic level on phase separation. This fundamental question has deep ramifications, notably in biology, because active processes also make the interior of a living cell different from a dead one. On page 768 of this issue, Adkins et al. (2) examine how mechanical activity at the microscopic scale affects liquid-liquid phase separation and allows liquids to climb surfaces. AU - Palacci, Jérémie A ID - 11996 IS - 6607 JF - Science SN - 0036-8075 TI - A soft active matter that can climb walls VL - 377 ER - TY - JOUR AB - Cells migrate through crowded microenvironments within tissues during normal development, immune response, and cancer metastasis. Although migration through pores and tracks in the extracellular matrix (ECM) has been well studied, little is known about cellular traversal into confining cell-dense tissues. We find that embryonic tissue invasion by Drosophila macrophages requires division of an epithelial ectodermal cell at the site of entry. Dividing ectodermal cells disassemble ECM attachment formed by integrin-mediated focal adhesions next to mesodermal cells, allowing macrophages to move their nuclei ahead and invade between two immediately adjacent tissues. Invasion efficiency depends on division frequency, but reduction of adhesion strength allows macrophage entry independently of division. This work demonstrates that tissue dynamics can regulate cellular infiltration. AU - Akhmanova, Maria AU - Emtenani, Shamsi AU - Krueger, Daniel AU - György, Attila AU - Pereira Guarda, Mariana AU - Vlasov, Mikhail AU - Vlasov, Fedor AU - Akopian, Andrei AU - Ratheesh, Aparna AU - De Renzis, Stefano AU - Siekhaus, Daria E ID - 10713 IS - 6591 JF - Science SN - 0036-8075 TI - Cell division in tissues enables macrophage infiltration VL - 376 ER - TY - JOUR AB - Russia’s unprovoked attack on Ukraine has destroyed civilian infrastructure, including universities, research centers, and other academic infrastructure (1). Many Ukrainian scholars and researchers remain in Ukraine, and their work has suffered from major setbacks (2–4). We call on international scientists and institutions to support them. AU - Chhugani, Karishma AU - Frolova, Alina AU - Salyha, Yuriy AU - Fiscutean, Andrada AU - Zlenko, Oksana AU - Reinsone, Sanita AU - Wolfsberger, Walter W. AU - Ivashchenko, Oleksandra V. AU - Maci, Megi AU - Dziuba, Dmytro AU - Parkhomenko, Andrii AU - Bortz, Eric AU - Kondrashov, Fyodor AU - Łabaj, Paweł P. AU - Romero, Veronika AU - Hlávka, Jakub AU - Oleksyk, Taras K. AU - Mangul, Serghei ID - 12116 IS - 6626 JF - Science SN - 0036-8075 TI - Remote opportunities for scholars in Ukraine VL - 378 ER - TY - JOUR AB - Asymmetric multiprotein complexes that undergo subunit exchange play central roles in biology but present a challenge for design because the components must not only contain interfaces that enable reversible association but also be stable and well behaved in isolation. We use implicit negative design to generate β sheet–mediated heterodimers that can be assembled into a wide variety of complexes. The designs are stable, folded, and soluble in isolation and rapidly assemble upon mixing, and crystal structures are close to the computational models. We construct linearly arranged hetero-oligomers with up to six different components, branched hetero-oligomers, closed C4-symmetric two-component rings, and hetero-oligomers assembled on a cyclic homo-oligomeric central hub and demonstrate that such complexes can readily reconfigure through subunit exchange. Our approach provides a general route to designing asymmetric reconfigurable protein systems. AU - Sahtoe, Danny D. AU - Praetorius, Florian M AU - Courbet, Alexis AU - Hsia, Yang AU - Wicky, Basile I. M. AU - Edman, Natasha I. AU - Miller, Lauren M. AU - Timmermans, Bart J. R. AU - Decarreau, Justin AU - Morris, Hana M. AU - Kang, Alex AU - Bera, Asim K. AU - Baker, David ID - 14282 IS - 6578 JF - Science SN - 0036-8075 TI - Reconfigurable asymmetric protein assemblies through implicit negative design VL - 375 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 - 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 - 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 - 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 - 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 - Spontaneously arising channels that transport the phytohormone auxin provide positional cues for self-organizing aspects of plant development such as flexible vasculature regeneration or its patterning during leaf venation. The auxin canalization hypothesis proposes a feedback between auxin signaling and transport as the underlying mechanism, but molecular players await discovery. We identified part of the machinery that routes auxin transport. The auxin-regulated receptor CAMEL (Canalization-related Auxin-regulated Malectin-type RLK) together with CANAR (Canalization-related Receptor-like kinase) interact with and phosphorylate PIN auxin transporters. camel and canar mutants are impaired in PIN1 subcellular trafficking and auxin-mediated PIN polarization, which macroscopically manifests as defects in leaf venation and vasculature regeneration after wounding. The CAMEL-CANAR receptor complex is part of the auxin feedback that coordinates polarization of individual cells during auxin canalization. AU - Hajny, Jakub AU - Prat, Tomas AU - Rydza, N AU - Rodriguez Solovey, Lesia AU - Tan, Shutang AU - Verstraeten, Inge AU - Domjan, David AU - Mazur, E AU - Smakowska-Luzan, E AU - Smet, W AU - Mor, E AU - Nolf, J AU - Yang, B AU - Grunewald, W AU - Molnar, Gergely AU - Belkhadir, Y AU - De Rybel, B AU - Friml, Jiří ID - 8721 IS - 6516 JF - Science SN - 0036-8075 TI - Receptor kinase module targets PIN-dependent auxin transport during canalization VL - 370 ER - TY - JOUR AB - Transcription factors (TFs) regulate gene expression through chromatin where nucleosomes restrict DNA access. To study how TFs bind nucleosome-occupied motifs, we focused on the reprogramming factors OCT4 and SOX2 in mouse embryonic stem cells. We determined TF engagement throughout a nucleosome at base-pair resolution in vitro, enabling structure determination by cryo–electron microscopy at two preferred positions. Depending on motif location, OCT4 and SOX2 differentially distort nucleosomal DNA. At one position, OCT4-SOX2 removes DNA from histone H2A and histone H3; however, at an inverted motif, the TFs only induce local DNA distortions. OCT4 uses one of its two DNA-binding domains to engage DNA in both structures, reading out a partial motif. These findings explain site-specific nucleosome engagement by the pluripotency factors OCT4 and SOX2, and they reveal how TFs distort nucleosomes to access chromatinized motifs. AU - Michael, Alicia Kathleen AU - Grand, Ralph S. AU - Isbel, Luke AU - Cavadini, Simone AU - Kozicka, Zuzanna AU - Kempf, Georg AU - Bunker, Richard D. AU - Schenk, Andreas D. AU - Graff-Meyer, Alexandra AU - Pathare, Ganesh R. AU - Weiss, Joscha AU - Matsumoto, Syota AU - Burger, Lukas AU - Schübeler, Dirk AU - Thomä, Nicolas H. ID - 15152 IS - 6498 JF - Science SN - 0036-8075 TI - Mechanisms of OCT4-SOX2 motif readout on nucleosomes VL - 368 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 - Although crystals of strongly correlated metals exhibit a diverse set of electronic ground states, few approaches exist for spatially modulating their properties. In this study, we demonstrate disorder-free control, on the micrometer scale, over the superconducting state in samples of the heavy-fermion superconductor CeIrIn5. We pattern crystals by focused ion beam milling to tailor the boundary conditions for the elastic deformation upon thermal contraction during cooling. The resulting nonuniform strain fields induce complex patterns of superconductivity, owing to the strong dependence of the transition temperature on the strength and direction of strain. These results showcase a generic approach to manipulating electronic order on micrometer length scales in strongly correlated matter without compromising the cleanliness, stoichiometry, or mean free path. AU - Bachmann, Maja D. AU - Ferguson, G. M. AU - Theuss, Florian AU - Meng, Tobias AU - Putzke, Carsten AU - Helm, Toni AU - Shirer, K. R. AU - Li, You-Sheng AU - Modic, Kimberly A AU - Nicklas, Michael AU - König, Markus AU - Low, D. AU - Ghosh, Sayak AU - Mackenzie, Andrew P. AU - Arnold, Frank AU - Hassinger, Elena AU - McDonald, Ross D. AU - Winter, Laurel E. AU - Bauer, Eric D. AU - Ronning, Filip AU - Ramshaw, B. J. AU - Nowack, Katja C. AU - Moll, Philip J. W. ID - 7082 IS - 6462 JF - Science SN - 0036-8075 TI - Spatial control of heavy-fermion superconductivity in CeIrIn5 VL - 366 ER - TY - JOUR AB - V (vacuolar)/A (archaeal)-type adenosine triphosphatases (ATPases), found in archaeaand eubacteria, couple ATP hydrolysis or synthesis to proton translocation across theplasma membrane using the rotary-catalysis mechanism. They belong to the V-typeATPase family, which differs from the mitochondrial/chloroplast F-type ATP synthasesin overall architecture. We solved cryo–electron microscopy structures of the intactThermus thermophilusV/A-ATPase, reconstituted into lipid nanodiscs, in three rotationalstates and two substates. These structures indicate substantial flexibility betweenV1and Voin a working enzyme, which results from mechanical competition between centralshaft rotation and resistance from the peripheral stalks. We also describedetails of adenosine diphosphate inhibition release, V1-Votorque transmission, andproton translocation, which are relevant for the entire V-type ATPase family. AU - Zhou, Long AU - Sazanov, Leonid A ID - 6859 IS - 6455 JF - Science SN - 0036-8075 TI - Structure and conformational plasticity of the intact Thermus thermophilus V/A-type ATPase VL - 365 ER - TY - JOUR AB - During corticogenesis, distinct subtypes of neurons are sequentially born from ventricular zone progenitors. How these cells are molecularly temporally patterned is poorly understood. We used single-cell RNA sequencing at high temporal resolution to trace the lineage of the molecular identities of successive generations of apical progenitors (APs) and their daughter neurons in mouse embryos. We identified a core set of evolutionarily conserved, temporally patterned genes that drive APs from internally driven to more exteroceptive states. We found that the Polycomb repressor complex 2 (PRC2) epigenetically regulates AP temporal progression. Embryonic age–dependent AP molecular states are transmitted to their progeny as successive ground states, onto which essentially conserved early postmitotic differentiation programs are applied, and are complemented by later-occurring environment-dependent signals. Thus, epigenetically regulated temporal molecular birthmarks present in progenitors act in their postmitotic progeny to seed adult neuronal diversity. AU - Telley, L AU - Agirman, G AU - Prados, J AU - Amberg, Nicole AU - Fièvre, S AU - Oberst, P AU - Bartolini, G AU - Vitali, I AU - Cadilhac, C AU - Hippenmeyer, Simon AU - Nguyen, L AU - Dayer, A AU - Jabaudon, D ID - 6455 IS - 6440 JF - Science SN - 0036-8075 TI - Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex VL - 364 ER - TY - JOUR AB - Grid cells with their rigid hexagonal firing fields are thought to provide an invariant metric to the hippocampal cognitive map, yet environmental geometrical features have recently been shown to distort the grid structure. Given that the hippocampal role goes beyond space, we tested the influence of nonspatial information on the grid organization. We trained rats to daily learn three new reward locations on a cheeseboard maze while recording from the medial entorhinal cortex and the hippocampal CA1 region. Many grid fields moved toward goal location, leading to long-lasting deformations of the entorhinal map. Therefore, distortions in the grid structure contribute to goal representation during both learning and recall, which demonstrates that grid cells participate in mnemonic coding and do not merely provide a simple metric of space. AU - Boccara, Charlotte N. AU - Nardin, Michele AU - Stella, Federico AU - O'Neill, Joseph AU - Csicsvari, Jozsef L ID - 6194 IS - 6434 JF - Science SN - 0036-8075 TI - The entorhinal cognitive map is attracted to goals VL - 363 ER - TY - JOUR AB - The anomalous metallic state in the high-temperature superconducting cuprates is masked by superconductivity near a quantum critical point. Applying high magnetic fields to suppress superconductivity has enabled detailed studies of the normal state, yet the direct effect of strong magnetic fields on the metallic state is poorly understood. We report the high-field magnetoresistance of thin-film La2–xSrxCuO4 cuprate in the vicinity of the critical doping, 0.161 ≤ p ≤ 0.190. We find that the metallic state exposed by suppressing superconductivity is characterized by magnetoresistance that is linear in magnetic fields up to 80 tesla. The magnitude of the linear-in-field resistivity mirrors the magnitude and doping evolution of the well-known linear-in-temperature resistivity that has been associated with quantum criticality in high-temperature superconductors. AU - Giraldo-Gallo, P. AU - Galvis, J. A. AU - Stegen, Z. AU - Modic, Kimberly A AU - Balakirev, F. F. AU - Betts, J. B. AU - Lian, X. AU - Moir, C. AU - Riggs, S. C. AU - Wu, J. AU - Bollinger, A. T. AU - He, X. AU - Božović, I. AU - Ramshaw, B. J. AU - McDonald, R. D. AU - Boebinger, G. S. AU - Shekhter, A. ID - 7060 IS - 6401 JF - Science SN - 0036-8075 TI - Scale-invariant magnetoresistance in a cuprate superconductor VL - 361 ER - TY - JOUR AB - Flores Island, Indonesia, was inhabited by the small-bodied hominin species Homo floresiensis, which has an unknown evolutionary relationship to modern humans. This island is also home to an extant human pygmy population. Here we describe genome-scale single-nucleotide polymorphism data and whole-genome sequences from a contemporary human pygmy population living on Flores near the cave where H. floresiensis was found. The genomes of Flores pygmies reveal a complex history of admixture with Denisovans and Neanderthals but no evidence for gene flow with other archaic hominins. Modern individuals bear the signatures of recent positive selection encompassing the FADS (fatty acid desaturase) gene cluster, likely related to diet, and polygenic selection acting on standing variation that contributed to their short-stature phenotype. Thus, multiple independent instances of hominin insular dwarfism occurred on Flores. AU - Tucci, Serena AU - Vohr, Samuel H. AU - McCoy, Rajiv C. AU - Vernot, Benjamin AU - Robinson, Matthew Richard AU - Barbieri, Chiara AU - Nelson, Brad J. AU - Fu, Wenqing AU - Purnomo, Gludhug A. AU - Sudoyo, Herawati AU - Eichler, Evan E. AU - Barbujani, Guido AU - Visscher, Peter M. AU - Akey, Joshua M. AU - Green, Richard E. ID - 7718 IS - 6401 JF - Science SN - 0036-8075 TI - Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia VL - 361 ER - TY - JOUR AB - Cuprate superconductors have long been thought of as having strong electronic correlations but negligible spin-orbit coupling. Using spin- and angle-resolved photoemission spectroscopy, we discovered that one of the most studied cuprate superconductors, Bi2212, has a nontrivial spin texture with a spin-momentum locking that circles the Brillouin zone center and a spin-layer locking that allows states of opposite spin to be localized in different parts of the unit cell. Our findings pose challenges for the vast majority of models of cuprates, such as the Hubbard model and its variants, where spin-orbit interaction has been mostly neglected, and open the intriguing question of how the high-temperature superconducting state emerges in the presence of this nontrivial spin texture. AU - Gotlieb, Kenneth AU - Lin, Chiu-Yun AU - Serbyn, Maksym AU - Zhang, Wentao AU - Smallwood, Christopher L. AU - Jozwiak, Christopher AU - Eisaki, Hiroshi AU - Hussain, Zahid AU - Vishwanath, Ashvin AU - Lanzara, Alessandra ID - 5767 IS - 6420 JF - Science SN - 0036-8075 TI - Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor VL - 362 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 - 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 - We describe an approach to bottom-up fabrication that allows integration of the functional diversity of proteins into designed three-dimensional structural frameworks. A set of custom staple proteins based on transcription activator–like effector proteins folds a double-stranded DNA template into a user-defined shape. Each staple protein is designed to recognize and closely link two distinct double-helical DNA sequences at separate positions on the template. We present design rules for constructing megadalton-scale DNA-protein hybrid shapes; introduce various structural motifs, such as custom curvature, corners, and vertices; and describe principles for creating multilayer DNA-protein objects with enhanced rigidity. We demonstrate self-assembly of our hybrid nanostructures in one-pot mixtures that include the genetic information for the designed proteins, the template DNA, RNA polymerase, ribosomes, and cofactors for transcription and translation. AU - Praetorius, Florian M AU - Dietz, Hendrik ID - 14287 IS - 6331 JF - Science SN - 0036-8075 TI - Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes VL - 355 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 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 - 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 - 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 rechargeable nonaqueous lithium-air (Li-O2) battery is receiving a great deal of interest because, theoretically, its specific energy far exceeds the best that can be achieved with lithium-ion cells. Operation of the rechargeable Li-O2 battery depends critically on repeated and highly reversible formation/decomposition of lithium peroxide (Li2O2) at the cathode upon cycling. Here, we show that this process is possible with the use of a dimethyl sulfoxide electrolyte and a porous gold electrode (95% capacity retention from cycles 1 to 100), whereas previously only partial Li2O2 formation/decomposition and limited cycling could occur. Furthermore, we present data indicating that the kinetics of Li2O2 oxidation on charge is approximately 10 times faster than on carbon electrodes. AU - Peng, Z. AU - Freunberger, Stefan Alexander AU - Chen, Y. AU - Bruce, P. G. ID - 7310 IS - 6094 JF - Science SN - 0036-8075 TI - A reversible and higher-rate Li-O2 battery VL - 337 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 - 9451 IS - 6100 JF - Science SN - 0036-8075 TI - Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes VL - 337 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 - Cortical neurons receive balanced excitatory and inhibitory synaptic currents. Such a balance could be established and maintained in an experience-dependent manner by synaptic plasticity at inhibitory synapses. We show that this mechanism provides an explanation for the sparse firing patterns observed in response to natural stimuli and fits well with a recently observed interaction of excitatory and inhibitory receptive field plasticity. The introduction of inhibitory plasticity in suitable recurrent networks provides a homeostatic mechanism that leads to asynchronous irregular network states. Further, it can accommodate synaptic memories with activity patterns that become indiscernible from the background state but can be reactivated by external stimuli. Our results suggest an essential role of inhibitory plasticity in the formation and maintenance of functional cortical circuitry. AU - Vogels, Tim P AU - Sprekeler, H. AU - Zenke, F. AU - Clopath, C. AU - Gerstner, W. ID - 8074 IS - 6062 JF - Science SN - 0036-8075 TI - Inhibitory plasticity balances excitation and inhibition in sensory pathways and memory networks VL - 334 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 - About 20% of the world's population uses the Web, and a large majority thereof uses Web search engines to find information. As a result, many Web researchers are devoting much effort to improving the speed and capability of search technology. AU - Henzinger, Monika H ID - 11884 IS - 5837 JF - Science SN - 0036-8075 TI - Search technologies for the internet VL - 317 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 - The Sir2 deacetylase modulates organismal life-span in various species. However, the molecular mechanisms by which Sir2 increases longevity are largely unknown. We show that in mammalian cells, the Sir2 homolog SIRT1 appears to control the cellular response to stress by regulating the FOXO family of Forkhead transcription factors, a family of proteins that function as sensors of the insulin signaling pathway and as regulators of organismal longevity. SIRT1 and the FOXO transcription factor FOXO3 formed a complex in cells in response to oxidative stress, and SIRT1 deacetylated FOXO3 in vitro and within cells. SIRT1 had a dual effect on FOXO3 function: SIRT1 increased FOXO3's ability to induce cell cycle arrest and resistance to oxidative stress but inhibited FOXO3's ability to induce cell death. Thus, one way in which members of the Sir2 family of proteins may increase organismal longevity is by tipping FOXO-dependent responses away from apoptosis and toward stress resistance. AU - Brunet, Anne AU - Sweeney, Lora Beatrice Jaeger AU - Sturgill, J Fitzhugh AU - Chua, Katrin AU - Greer, Paul AU - Lin, Yingxi AU - Tran, Hien AU - Ross, Sarah AU - Mostoslavsky, Raul AU - Cohen, Haim AU - Hu, Linda AU - Chen, Hwei-Ling AU - Jedrychowski, Mark AU - Gygi, Steven AU - Sinclair, David AU - Alt, Frederick AU - Greenberg, Michael ID - 7706 IS - 5666 JF - Science SN - 0036-8075 TI - Stress-dependent regulation of FOXO transcription factors by the SIRT1 deacetylase VL - 303 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 - Humans and their closest evolutionary relatives, the chimpanzees, differ in ∼1.24% of their genomic DNA sequences. The fraction of these changes accumulated during the speciation processes that have separated the two lineages may be of special relevance in understanding the basis of their differences. We analyzed human and chimpanzee sequence data to search for the patterns of divergence and polymorphism predicted by a theoretical model of speciation. According to the model, positively selected changes should accumulate in chromosomes that present fixed structural differences, such as inversions, between the two species. Protein evolution was more than 2.2 times faster in chromosomes that had undergone structural rearrangements compared with colinear chromosomes. Also, nucleotide variability is slightly lower in rearranged chromosomes. These patterns of divergence and polymorphism may be, at least in part, the molecular footprint of speciation events in the human and chimpanzee lineages. AU - Navarro, Arcadio AU - Barton, Nicholas H ID - 4255 IS - 5617 JF - Science SN - 0036-8075 TI - Chromosomal speciation and molecular divergence -- Accelerated evolution in rearranged chromosomes VL - 300 ER - TY - JOUR AB - A central problem in biology is determining how genes interact as parts of functional networks. Creation and analysis of synthetic networks, composed of well-characterized genetic elements, provide a framework for theoretical modeling. Here, with the use of a combinatorial method, a library of networks with varying connectivity was generated in Escherichia coli. These networks were composed of genes encoding the transcriptional regulators Lacl, TetR, and lambda Cl, as well as the corresponding promoters. They displayed phenotypic behaviors resembling binary logical circuits, with two chemical “inputs” and a fluorescent protein “output.” Within this simple system, diverse computational functions arose through changes in network connectivity. Combinatorial synthesis provides an alternative approach for studying biological networks, as well as an efficient method for producing diverse phenotypes in vivo. AU - Guet, Calin C AU - Elowitz, Michael AU - Hsing, Weihong AU - Leibler, Stanislas ID - 3757 IS - 5572 JF - Science SN - 0036-8075 TI - Combinatorial synthesis of genetic networks VL - 296 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 - TY - JOUR AB - As a discipline, phylogenetics is becoming transformed by a flood of molecular data. These data allow broad questions to be asked about the history of life, but also present difficult statistical and computational problems. Bayesian inference of phylogeny brings a new perspective to a number of outstanding issues in evolutionary biology, including the analysis of large phylogenetic trees and complex evolutionary models and the detection of the footprint of natural selection in DNA sequences. AU - Huelsenbeck, John AU - Ronquist, Fredrik AU - Nielsen, Rasmus AU - Bollback, Jonathan P ID - 3438 IS - 5550 JF - Science SN - 0036-8075 TI - Bayesian inference of phylogeny and its impact on evolutionary biology VL - 294 ER -