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The proteome landscape of the kingdoms of life 期刊论文
NATURE, 2020
作者:  Arzi, Anat;  Rozenkrantz, Liron;  Gorodisky, Lior;  Rozenkrantz, Danit;  Holtzman, Yael;  Ravia, Aharon;  Bekinschtein, Tristan A.;  Galperin, Tatyana;  Krimchansky, Ben-Zion;  Cohen, Gal;  Oksamitni, Anna;  Aidinoff, Elena;  Sacher, Yaron;  Sobel, Noam
收藏  |  浏览/下载:15/0  |  提交时间:2020/07/03

Proteins carry out the vast majority of functions in all biological domains, but for technological reasons their large-scale investigation has lagged behind the study of genomes. Since the first essentially complete eukaryotic proteome was reported(1), advances in mass-spectrometry-based proteomics(2)have enabled increasingly comprehensive identification and quantification of the human proteome(3-6). However, there have been few comparisons across species(7,8), in stark contrast with genomics initiatives(9). Here we use an advanced proteomics workflow-in which the peptide separation step is performed by a microstructured and extremely reproducible chromatographic system-for the in-depth study of 100 taxonomically diverse organisms. With two million peptide and 340,000 stringent protein identifications obtained in a standardized manner, we double the number of proteins with solid experimental evidence known to the scientific community. The data also provide a large-scale case study for sequence-based machine learning, as we demonstrate by experimentally confirming the predicted properties of peptides fromBacteroides uniformis. Our results offer a comparative view of the functional organization of organisms across the entire evolutionary range. A remarkably high fraction of the total proteome mass in all kingdoms is dedicated to protein homeostasis and folding, highlighting the biological challenge of maintaining protein structure in all branches of life. Likewise, a universally high fraction is involved in supplying energy resources, although these pathways range from photosynthesis through iron sulfur metabolism to carbohydrate metabolism. Generally, however, proteins and proteomes are remarkably diverse between organisms, and they can readily be explored and functionally compared at www.proteomesoflife.org.


  
Detection of metastable electronic states by Penning trap mass spectrometry 期刊论文
NATURE, 2020, 581 (7806) : 42-+
作者:  Rauch, Jennifer N.;  Luna, Gabriel;  Guzman, Elmer;  Audouard, Morgane;  Challis, Collin;  Sibih, Youssef E.;  Leshuk, Carolina;  Hernandez, Israel;  Wegmann, Susanne;  Hyman, Bradley T.;  Gradinaru, Viviana;  Kampmann, Martin;  Kosik, Kenneth S.
收藏  |  浏览/下载:9/0  |  提交时间:2020/07/03

State-of-the-art optical clocks(1) achieve precisions of 10(-18) or better using ensembles of atoms in optical lattices(2,3) or individual ions in radio-frequency traps(4,5). Promising candidates for use in atomic clocks are highly charged ions(6) (HCIs) and nuclear transitions(7), which are largely insensitive to external perturbations and reach wavelengths beyond the optical range(8) that are accessible to frequency combs(9). However, insufficiently accurate atomic structure calculations hinder the identification of suitable transitions in HCIs. Here we report the observation of a long-lived metastable electronic state in an HCI by measuring the mass difference between the ground and excited states in rhenium, providing a non-destructive, direct determination of an electronic excitation energy. The result is in agreement with advanced calculations. We use the high-precision Penning trap mass spectrometer PENTATRAP to measure the cyclotron frequency ratio of the ground state to the metastable state of the ion with a precision of 10(-11)-an improvement by a factor of ten compared with previous measurements(10,11). With a lifetime of about 130 days, the potential soft-X-ray frequency reference at 4.96 x 10(16) hertz (corresponding to a transition energy of 202 electronvolts) has a linewidth of only 5 x 10(-8) hertz and one of the highest electronic quality factors (10(24)) measured experimentally so far. The low uncertainty of our method will enable searches for further soft-X-ray clock transitions(8,12) in HCIs, which are required for precision studies of fundamental physics(6).


Penning trap mass spectrometry is used to measure the electronic transition energy from a long-lived metastable state to the ground state in highly charged rhenium ions with a precision of 10(-11).


  
Electrical manipulation of a topological antiferromagnetic state 期刊论文
NATURE, 2020, 580 (7805) : 608-+
作者:  Chabon, Jacob J.;  Hamilton, Emily G.;  Kurtz, David M.;  Esfahani, Mohammad S.;  Moding, Everett J.;  Stehr, Henning;  Schroers-Martin, Joseph;  Nabet, Barzin Y.;  Chen, Binbin;  Chaudhuri, Aadel A.;  Liu, Chih Long;  Hui, Angela B.;  Jin, Michael C.;  Azad, Tej D.;  Almanza, Diego;  Jeon, Young-Jun;  Nesselbush, Monica C.;  Keh, Lyron Co Ting;  Bonilla, Rene F.;  Yoo, Christopher H.;  Ko, Ryan B.;  Chen, Emily L.;  Merriott, David J.;  Massion, Pierre P.;  Mansfield, Aaron S.;  Jen, Jin;  Ren, Hong Z.;  Lin, Steven H.;  Costantino, Christina L.;  Burr, Risa;  Tibshirani, Robert;  Gambhir, Sanjiv S.;  Berry, Gerald J.;  Jensen, Kristin C.;  West, Robert B.;  Neal, Joel W.;  Wakelee, Heather A.;  Loo, Billy W., Jr.;  Kunder, Christian A.;  Leung, Ann N.;  Lui, Natalie S.;  Berry, Mark F.;  Shrager, Joseph B.;  Nair, Viswam S.;  Haber, Daniel A.;  Sequist, Lecia V.;  Alizadeh, Ash A.;  Diehn, Maximilian
收藏  |  浏览/下载:39/0  |  提交时间:2020/07/03

Room-temperature electrical switching of a topological antiferromagnetic state in polycrystalline Mn3Sn thin films is demonstrated using the same protocol as that used for conventional ferromagnetic metals.


Electrical manipulation of phenomena generated by nontrivial band topology is essential for the development of next-generation technology using topological protection. A Weyl semimetal is a three-dimensional gapless system that hosts Weyl fermions as low-energy quasiparticles(1-4). It has various exotic properties, such as a large anomalous Hall effect (AHE) and chiral anomaly, which are robust owing to the topologically protected Weyl nodes(1-16). To manipulate such phenomena, a magnetic version of Weyl semimetals would be useful for controlling the locations of Weyl nodes in the Brillouin zone. Moreover, electrical manipulation of antiferromagnetic Weyl metals would facilitate the use of antiferromagnetic spintronics to realize high-density devices with ultrafast operation(17,18). However, electrical control of a Weyl metal has not yet been reported. Here we demonstrate the electrical switching of a topological antiferromagnetic state and its detection by the AHE at room temperature in a polycrystalline thin film(19) of the antiferromagnetic Weyl metal Mn3Sn9,10,12,20, which exhibits zero-field AHE. Using bilayer devices composed of Mn3Sn and nonmagnetic metals, we find that an electrical current density of about 10(10) to 10(11) amperes per square metre induces magnetic switching in the nonmagnetic metals, with a large change in Hall voltage. In addition, the current polarity along the bias field and the sign of the spin Hall angle of the nonmagnetic metals-positive for Pt (ref. (21)), close to 0 for Cu and negative for W (ref. (22))-determines the sign of the Hall voltage. Notably, the electrical switching in the antiferromagnet is achieved with the same protocol as that used for ferromagnetic metals(23,24). Our results may lead to further scientific and technological advances in topological magnetism and antiferromagnetic spintronics.


  
Observation of topologically enabled unidirectional guided resonances 期刊论文
NATURE, 2020, 580 (7804) : 467-+
作者:  Wang, Renjing;  Wang, Shengliu;  Dhar, Ankita;  Peralta, Christopher;  Pavletich, Nikola P.
收藏  |  浏览/下载:7/0  |  提交时间:2020/07/03

Unidirectional radiation is important for various optoelectronic applications, such as lasers, grating couplers and optical antennas. However, almost all existing unidirectional emitters rely on the use of materials or structures that forbid outgoing waves-that is, mirrors, which are often bulky, lossy and difficult to fabricate. Here we theoretically propose and experimentally demonstrate a class of resonances in photonic crystal slabs that radiate only towards one side of the slab, with no mirror placed on the other side. These resonances, which we name '  unidirectional guided resonances'  , are found to be topological in nature: they emerge when a pair of half-integer topological charges(1-3) in the polarization field bounce into each other in momentum space. We experimentally demonstrate unidirectional guided resonances in the telecommunication regime by achieving single-side radiative quality factors as high as 1.6 x 10(5). We further demonstrate their topological nature through far-field polarimetry measurements. Our work represents a characteristic example of applying topological principles(4,5) to control optical fields and could lead to energy-efficient grating couplers and antennas for light detection and ranging.


Unidirectional radiation is achieved in a photonic crystal slab without the use of mirrors by merging a pair of topological defects carrying half-integer charges.


  
Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function 期刊论文
NATURE, 2020, 580 (7805) : 669-+
作者:  Kanarek, Naama;  Petrova, Boryana;  Sabatini, David M.
收藏  |  浏览/下载:11/0  |  提交时间:2020/07/03

Cryo-electron microscopy structures of the DNA-binding domains of the pioneer transcription factor SOX2 and its close homologue SOX11 elucidate the role of these factors in initiating chromatin opening and nucleosome remodelling.


'  Pioneer'  transcription factors are required for stem-cell pluripotency, cell differentiation and cell reprogramming(1,2). Pioneer factors can bind nucleosomal DNA to enable gene expression from regions of the genome with closed chromatin. SOX2 is a prominent pioneer factor that is essential for pluripotency and self-renewal of embryonic stem cells(3). Here we report cryo-electron microscopy structures of the DNA-binding domains of SOX2 and its close homologue SOX11 bound to nucleosomes. The structures show that SOX factors can bind and locally distort DNA at superhelical location 2. The factors also facilitate detachment of terminal nucleosomal DNA from the histone octamer, which increases DNA accessibility. SOX-factor binding to the nucleosome can also lead to a repositioning of the N-terminal tail of histone H4 that includes residue lysine 16. We speculate that this repositioning is incompatible with higher-order nucleosome stacking, which involves contacts of the H4 tail with a neighbouring nucleosome. Our results indicate that pioneer transcription factors can use binding energy to initiate chromatin opening, and thereby facilitate nucleosome remodelling and subsequent transcription.


  
An intestinal zinc sensor regulates food intake and developmental growth 期刊论文
NATURE, 2020, 580 (7802) : 263-+
作者:  Wu, Thomas D.;  39;Gorman, William E.
收藏  |  浏览/下载:14/0  |  提交时间:2020/07/03

Hodor, an intestinal zinc-gated chloride channel, controls systemic growth in Drosophila by promoting food intake and by modulating Tor signalling and lysosomal homeostasis within enterocytes.


In cells, organs and whole organisms, nutrient sensing is key to maintaining homeostasis and adapting to a fluctuating environment(1). In many animals, nutrient sensors are found within the enteroendocrine cells of the digestive system  however, less is known about nutrient sensing in their cellular siblings, the absorptive enterocytes(1). Here we use a genetic screen in Drosophila melanogaster to identify Hodor, an ionotropic receptor in enterocytes that sustains larval development, particularly in nutrient-scarce conditions. Experiments in Xenopus oocytes and flies indicate that Hodor is a pH-sensitive, zinc-gated chloride channel that mediates a previously unrecognized dietary preference for zinc. Hodor controls systemic growth from a subset of enterocytes-interstitial cells-by promoting food intake and insulin/IGF signalling. Although Hodor sustains gut luminal acidity and restrains microbial loads, its effect on systemic growth results from the modulation of Tor signalling and lysosomal homeostasis within interstitial cells. Hodor-like genes are insect-specific, and may represent targets for the control of disease vectors. Indeed, CRISPR-Cas9 genome editing revealed that the single hodor orthologue in Anopheles gambiae is an essential gene. Our findings highlight the need to consider the instructive contributions of metals-and, more generally, micronutrients-to energy homeostasis.


  
Ball-and-chain inactivation in a calcium-gated potassium channel 期刊论文
NATURE, 2020, 580 (7802) : 288-+
作者:  Peron, Simon;  Pancholi, Ravi;  Voelcker, Bettina;  Wittenbach, Jason D.;  olafsdottir, H. Freyja;  Freeman, Jeremy;  Svoboda, Karel
收藏  |  浏览/下载:23/0  |  提交时间:2020/07/03

Cryo-electron microscopy structures and molecular dynamics simulations of the calcium-activated potassium channel MthK from Methanobacterium thermoautotrophicum are used to show that gating of this channel involves a ball-and-chain inactivation mechanism mediated by a previously unresolved N-terminal peptide.


Inactivation is the process by which ion channels terminate ion flux through their pores while the opening stimulus is still present(1). In neurons, inactivation of both sodium and potassium channels is crucial for the generation of action potentials and regulation of firing frequency(1,2). A cytoplasmic domain of either the channel or an accessory subunit is thought to plug the open pore to inactivate the channel via a '  ball-and-chain'  mechanism(3-7). Here we use cryo-electron microscopy to identify the molecular gating mechanism in calcium-activated potassium channels by obtaining structures of the MthK channel from Methanobacterium thermoautotrophicum-a purely calcium-gated and inactivating channel-in a lipid environment. In the absence of Ca2+, we obtained a single structure in a closed state, which was shown by atomistic simulations to be highly flexible in lipid bilayers at ambient temperature, with large rocking motions of the gating ring and bending of pore-lining helices. In Ca2+-bound conditions, we obtained several structures, including multiple open-inactivated conformations, further indication of a highly dynamic protein. These different channel conformations are distinguished by rocking of the gating rings with respect to the transmembrane region, indicating symmetry breakage across the channel. Furthermore, in all conformations displaying open channel pores, the N terminus of one subunit of the channel tetramer sticks into the pore and plugs it, with free energy simulations showing that this is a strong interaction. Deletion of this N terminus leads to functionally non-inactivating channels and structures of open states without a pore plug, indicating that this previously unresolved N-terminal peptide is responsible for a ball-and-chain inactivation mechanism.


  
Mott and generalized Wigner crystal states in WSe2/WS2 moire superlattices 期刊论文
NATURE, 2020, 579 (7799) : 359-+
作者:  Yuan, Jie;  Chang, Si-Yuan;  Yin, Shi-Gang;  Liu, Zhi-Yang;  Cheng, Xiu;  Liu, Xi-Juan;  Jiang, Qiang;  Gao, Ge;  Lin, De-Ying;  Kang, Xin-Lei;  Ye, Shi-Wei;  Chen, Zheng;  Yin, Jiang-An;  Hao, Pei;  Jiang, Lubin;  Cai, Shi-Qing
收藏  |  浏览/下载:51/0  |  提交时间:2020/07/03

Strongly correlated insulating Mott and generalized Wigner phases are detected in WSe2/WS2 moire superlattices, and their electrical properties and excited spin states are studied using an optical technique.


Moire superlattices can be used to engineer strongly correlated electronic states in two-dimensional van der Waals heterostructures, as recently demonstrated in the correlated insulating and superconducting states observed in magic-angle twisted-bilayer graphene and ABC trilayer graphene/boron nitride moire superlattices(1-4). Transition metal dichalcogenide moire heterostructures provide another model system for the study of correlated quantum phenomena(5) because of their strong light-matter interactions and large spin-orbit coupling. However, experimental observation of correlated insulating states in this system is challenging with traditional transport techniques. Here we report the optical detection of strongly correlated phases in semiconducting WSe2/WS2 moire superlattices. We use a sensitive optical detection technique and reveal a Mott insulator state at one hole per superlattice site and surprising insulating phases at 1/3 and 2/3 filling of the superlattice, which we assign to generalized Wigner crystallization on the underlying lattice(6-11). Furthermore, the spin-valley optical selection rules(12-14) of transition metal dichalcogenide heterostructures allow us to optically create and investigate low-energy excited spin states in the Mott insulator. We measure a very long spin relaxation lifetime of many microseconds in the Mott insulating state, orders of magnitude longer than that of charge excitations. Our studies highlight the value of using moire superlattices beyond graphene to explore correlated physics.


  
Observations of grain-boundary phase transformations in an elemental metal 期刊论文
NATURE, 2020, 579 (7799) : 375-+
作者:  Valente, Luis;  Phillimore, Albert B.;  Melo, Martim;  Warren, Ben H.;  Clegg, Sonya M.;  Havenstein, Katja;  Tiedemann, Ralph;  Illera, Juan Carlos;  Thebaud, Christophe;  Aschenbach, Tina;  Etienne, Rampal S.
收藏  |  浏览/下载:17/0  |  提交时间:2020/07/03

Atomic-resolution observations combined with simulations show that grain boundaries within elemental copper undergo temperature-induced solid-state phase transformation to different structures  grain boundary phases can also coexist and are kinetically trapped structures.


The theory of grain boundary (the interface between crystallites, GB) structure has a long history(1) and the concept of GBs undergoing phase transformations was proposed 50 years ago(2,3). The underlying assumption was that multiple stable and metastable states exist for different GB orientations(4-6). The terminology '  complexion'  was recently proposed to distinguish between interfacial states that differ in any equilibrium thermodynamic property(7). Different types of complexion and transitions between complexions have been characterized, mostly in binary or multicomponent systems(8-19). Simulations have provided insight into the phase behaviour of interfaces and shown that GB transitions can occur in many material systems(20-24). However, the direct experimental observation and transformation kinetics of GBs in an elemental metal have remained elusive. Here we demonstrate atomic-scale GB phase coexistence and transformations at symmetric and asymmetric [111 over bar ] tilt GBs in elemental copper. Atomic-resolution imaging reveals the coexistence of two different structures at sigma 19b GBs (where sigma 19 is the density of coincident sites and b is a GB variant), in agreement with evolutionary GB structure search and clustering analysis(21,25,26). We also use finite-temperature molecular dynamics simulations to explore the coexistence and transformation kinetics of these GB phases. Our results demonstrate how GB phases can be kinetically trapped, enabling atomic-scale room-temperature observations. Our work paves the way for atomic-scale in situ studies of metallic GB phase transformations, which were previously detected only indirectly(9,15,27-29), through their influence on abnormal grain growth, non-Arrhenius-type diffusion or liquid metal embrittlement.


  
Probing the core of the strong nuclear interaction 期刊论文
NATURE, 2020, 578 (7796) : 540-+
作者:  Bialas, Allison R.;  Presumey, Jessy;  Das, Abhishek;  van der Poel, Cees E.;  Lapchak, Peter H.;  Mesin, Luka;  Victora, Gabriel;  Tsokos, George C.;  Mawrin, Christian;  Herbst, Ronald;  Carroll, Michael C.
收藏  |  浏览/下载:16/0  |  提交时间:2020/07/03

High-energy electron scattering that can isolate pairs of nucleons in high-momentum configurations reveals a transition to spin-independent scalar forces at small separation distances, supporting the use of point-like nucleon models to describe dense nuclear systems.


The strong nuclear interaction between nucleons (protons and neutrons) is the effective force that holds the atomic nucleus together. This force stems from fundamental interactions between quarks and gluons (the constituents of nucleons) that are described by the equations of quantum chromodynamics. However, as these equations cannot be solved directly, nuclear interactions are described using simplified models, which are well constrained at typical inter-nucleon distances(1-5) but not at shorter distances. This limits our ability to describe high-density nuclear matter such as that in the cores of neutron stars(6). Here we use high-energy electron scattering measurements that isolate nucleon pairs in short-distance, high-momentum configurations(7-9), accessing a kinematical regime that has not been previously explored by experiments, corresponding to relative momenta between the pair above 400 megaelectronvolts per c (c, speed of light in vacuum). As the relative momentum between two nucleons increases and their separation thereby decreases, we observe a transition from a spin-dependent tensor force to a predominantly spin-independent scalar force. These results demonstrate the usefulness of using such measurements to study the nuclear interaction at short distances and also support the use of point-like nucleon models with two- and three-body effective interactions to describe nuclear systems up to densities several times higher than the central density of the nucleus.