bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary genetics of immunological supertypes reveals two faces of the Red Queen
Authors: Lighten Jackie , Papadopulos Alexander S. T. , Mohammed Ryan S. , Ward Ben J. , G. Paterson Ian , Baillie Lyndsey , Bradbury Ian R. , Hendry Andrew P. , Bentzen Paul , van Oosterhout Cock 
Published: October 2017

AbstractRed Queen host–parasite co-evolution can drive adaptations of immune genes by positive selection that erodes genetic variation (Red Queen arms race) or results in a balanced polymorphism (Red Queen dynamics) and long-term preservation of genetic variation (trans-species polymorphism). These two Red Queen processes are opposite extremes of the co-evolutionary spectrum. Here we show that both Red Queen processes can operate simultaneously by analysing the major histocompatibility complex (MHC) in guppies (Poecilia reticulata and P. obscura) and swamp guppies (Micropoecilia picta). Sub-functionalisation of MHC alleles into ‘supertypes’ explains how polymorphisms persist during rapid host–parasite co-evolution. Simulations show the maintenance of supertypes as balanced polymorphisms, consistent with Red Queen dynamics, whereas alleles within supertypes are subject to positive selection in a Red Queen arms race. Building on the divergent allele advantage hypothesis, we show that functional aspects of allelic diversity help to elucidate the evolution of polymorphic genes involved in Red Queen co-evolution.
Neuronal baseline shifts underlying boundary setting during free recall
Authors: Norman Yitzhak , Yeagle Erin M. , Harel Michal , Mehta Ashesh D. , Malach Rafael 
Published: October 2017

AbstractAsked to freely recall items from a predefined set (e.g., animals), we rarely recall a wrong exemplar (e.g., a vegetable). This capability is so powerful and effortless that it is essentially taken for granted, yet, surprisingly, the underlying neuronal mechanisms are unknown. Here we investigate this boundary setting mechanism using intracranial recordings (ECoG), in 12 patients undergoing epilepsy monitoring engaged in episodic free recall. After viewing vivid photographs from two categories (famous faces and places), patients were asked to freely recall these items, targeting each category in separate blocks. Our results reveal a rapid and sustained rise in neuronal activity (“baseline shift”) in high-order visual areas that persists throughout the free recall period and reflects the targeted category. We further show a more transient reactivation linked to individual recall events. The results point to baseline shift as a flexible top−down mechanism that biases spontaneous recall to remain within the required categorical boundaries.
Blue light and CO2 signals converge to regulate light-induced stomatal opening
Authors: Hiyama Asami , Takemiya Atsushi , Munemasa Shintaro , Okuma Eiji , Sugiyama Naoyuki , Tada Yasuomi , Murata Yoshiyuki , Shimazaki Ken-ichiro 
Published: October 2017

AbstractStomata regulate gas exchange between plants and atmosphere by integrating opening and closing signals. Stomata open in response to low CO2 concentrations to maximize photosynthesis in the light; however, the mechanisms that coordinate photosynthesis and stomatal conductance have yet to be identified. Here we identify and characterize CBC1/2 (CONVERGENCE OF BLUE LIGHT (BL) AND CO2 1/2), two kinases that link BL, a major component of photosynthetically active radiation (PAR), and the signals from low concentrations of CO2 in guard cells. CBC1/CBC2 redundantly stimulate stomatal opening by inhibition of S-type anion channels in response to both BL and low concentrations of CO2. CBC1/CBC2 function in the signaling pathways of phototropins and HT1 (HIGH LEAF TEMPERATURE 1). CBC1/CBC2 interact with and are phosphorylated by HT1. We propose that CBCs regulate stomatal aperture by integrating signals from BL and CO2 and act as the convergence site for signals from BL and low CO2.
Folding of a bacterial integral outer membrane protein is initiated in the periplasm
Authors: Sikdar Rakesh , Peterson Janine H. , Anderson D. Eric , Bernstein Harris D. 
Published: October 2017

AbstractThe Bam complex promotes the insertion of β-barrel proteins into the bacterial outer membrane, but it is unclear whether it threads β-strands into the lipid bilayer in a stepwise fashion or catalyzes the insertion of pre-folded substrates. Here, to distinguish between these two possibilities, we analyze the biogenesis of UpaG, a trimeric autotransporter adhesin (TAA). TAAs consist of three identical subunits that together form a single β-barrel domain and an extracellular coiled-coil (“passenger”) domain. Using site-specific photocrosslinking to obtain spatial and temporal insights into UpaG assembly, we show that UpaG β-barrel segments fold into a trimeric structure in the periplasm that persists until the termination of passenger-domain translocation. In addition to obtaining evidence that at least some β-barrel proteins begin to fold before they interact with the Bam complex, we identify several discrete steps in the assembly of a poorly characterized class of virulence factors.
Hot carrier cooling mechanisms in halide perovskites
Authors: Fu Jianhui , Xu Qiang , Han Guifang , Wu Bo , Huan Cheng Hon Alfred , Leek Meng Lee , Sum Tze Chien 
Published: October 2017

AbstractHalide perovskites exhibit unique slow hot-carrier cooling properties capable of unlocking disruptive perovskite photon–electron conversion technologies (e.g., high-efficiency hot-carrier photovoltaics, photo-catalysis, and photodetectors). Presently, the origins and mechanisms of this retardation remain highly contentious (e.g., large polarons, hot-phonon bottleneck, acoustical–optical phonon upconversion etc.). Here, we investigate the fluence-dependent hot-carrier dynamics in methylammonium lead triiodide using transient absorption spectroscopy, and correlate with theoretical modeling and first-principles calculations. At moderate carrier concentrations (around 1018 cm−3), carrier cooling is mediated by polar Fröhlich electron–phonon interactions through zone-center delayed longitudinal optical phonon emissions (i.e., with phonon lifetime τLO around 0.6 ± 0.1 ps) induced by the hot-phonon bottleneck. The hot-phonon effect arises from the suppression of the Klemens relaxation pathway essential for longitudinal optical phonon decay. At high carrier concentrations (around 1019 cm−3), Auger heating further reduces the cooling rates. Our study unravels the intricate interplay between the hot-phonon bottleneck and Auger heating effects on carrier cooling, which will resolve the existing controversy.
Quantum mechanics as classical statistical mechanics with an ontic extension and an epistemic restriction
Authors: Budiyono Agung , Rohrlich Daniel 
Published: October 2017

AbstractWhere does quantum mechanics part ways with classical mechanics? How does quantum randomness differ fundamentally from classical randomness? We cannot fully explain how the theories differ until we can derive them within a single axiomatic framework, allowing an unambiguous account of how one theory is the limit of the other. Here we derive non-relativistic quantum mechanics and classical statistical mechanics within a common framework. The common axioms include conservation of average energy and conservation of probability current. But two axioms distinguish quantum mechanics from classical statistical mechanics: an “ontic extension” defines a nonseparable (global) random variable that generates physical correlations, and an “epistemic restriction” constrains allowed phase space distributions. The ontic extension and epistemic restriction, with strength on the order of Planck’s constant, imply quantum entanglement and uncertainty relations. This framework suggests that the wave function is epistemic, yet it does not provide an ontic dynamics for individual systems.
Dense and accurate whole-chromosome haplotyping of individual genomes
Authors: Porubsky David , Garg Shilpa , Sanders Ashley D. , Korbel Jan O. , Guryev Victor , Lansdorp Peter M. , Marschall Tobias 
Published: October 2017

AbstractThe diploid nature of the human genome is neglected in many analyses done today, where a genome is perceived as a set of unphased variants with respect to a reference genome. This lack of haplotype-level analyses can be explained by a lack of methods that can produce dense and accurate chromosome-length haplotypes at reasonable costs. Here we introduce an integrative phasing strategy that combines global, but sparse haplotypes obtained from strand-specific single-cell sequencing (Strand-seq) with dense, yet local, haplotype information available through long-read or linked-read sequencing. We provide comprehensive guidance on the required sequencing depths and reliably assign more than 95% of alleles (NA12878) to their parental haplotypes using as few as 10 Strand-seq libraries in combination with 10-fold coverage PacBio data or, alternatively, 10X Genomics linked-read sequencing data. We conclude that the combination of Strand-seq with different technologies represents an attractive solution to chart the genetic variation of diploid genomes.
Strong-coupling of WSe2 in ultra-compact plasmonic nanocavities at room temperature
Authors: Kleemann Marie-Elena , Chikkaraddy Rohit , Alexeev Evgeny M. , Kos Dean , Carnegie Cloudy , Deacon Will , de Pury Alex Casalis , Große Christoph , de Nijs Bart , Mertens Jan , Tartakovskii Alexander I. , Baumberg Jeremy J. 
Published: October 2017

AbstractStrong coupling of monolayer metal dichalcogenide semiconductors with light offers encouraging prospects for realistic exciton devices at room temperature. However, the nature of this coupling depends extremely sensitively on the optical confinement and the orientation of electronic dipoles and fields. Here, we show how plasmon strong coupling can be achieved in compact, robust, and easily assembled gold nano-gap resonators at room temperature. We prove that strong-coupling is impossible with monolayers due to the large exciton coherence size, but resolve clear anti-crossings for greater than 7 layer devices with Rabi splittings exceeding 135 meV. We show that such structures improve on prospects for nonlinear exciton functionalities by at least 104, while retaining quantum efficiencies above 50%, and demonstrate evidence for superlinear light emission.
Genomic structural variation-mediated allelic suppression causes hybrid male sterility in rice
Authors: Shen Rongxin , Wang Lan , Liu Xupeng , Wu Jiang , Jin Weiwei , Zhao Xiucai , Xie Xianrong , Zhu Qinlong , Tang Huiwu , Li Qing , Chen Letian , Liu Yao-Guang 
Published: October 2017

AbstractHybrids between divergent populations commonly show hybrid sterility; this reproductive barrier hinders hybrid breeding of the japonica and indica rice (Oryza sativa L.) subspecies. Here we show that structural changes and copy number variation at the Sc locus confer japonica–indica hybrid male sterility. The japonica allele, Sc-j, contains a pollen-essential gene encoding a DUF1618-domain protein; the indica allele, Sc-i, contains two or three tandem-duplicated ~ 28-kb segments, each carrying an Sc-j-homolog with a distinct promoter. In Sc-j/Sc-i hybrids, the high-expression of Sc-i in sporophytic cells causes suppression of Sc-j expression in pollen and selective abortion of Sc-j-pollen, leading to transmission ratio distortion. Knocking out one or two of the three Sc-i copies by CRISPR/Cas9 rescues Sc-j expression and male fertility. Our results reveal the gene dosage-dependent allelic suppression as a mechanism of hybrid incompatibility, and provide an effective approach to overcome the reproductive barrier for hybrid breeding.
Structural basis for mutually exclusive co-transcriptional nuclear cap-binding complexes with either NELF-E or ARS2
Authors: Schulze Wiebke Manuela , Cusack Stephen 
Published: October 2017

AbstractPol II transcribes diverse classes of RNAs that need to be directed into the appropriate nuclear maturation pathway. All nascent Pol II transcripts are 5′-capped and the cap is immediately sequestered by the nuclear cap-binding complex (CBC). Mutually exclusive interactions of CBC with different partner proteins have been implicated in transcript fate determination. Here, we characterise the direct interactions between CBC and NELF-E, a subunit of the negative elongation factor complex, ARS2 and PHAX. Our biochemical and crystal structure results show that the homologous C-terminal peptides of NELF-E and ARS2 bind identically to CBC and in each case the affinity is enhanced when CBC is bound to a cap analogue. Furthermore, whereas PHAX forms a complex with CBC and ARS2, NELF-E binding to CBC is incompatible with PHAX binding. We thus define two mutually exclusive complexes CBC–NELF–E and CBC–ARS2–PHAX, which likely act in respectively earlier and later phases of transcription.
Strategies for feeding the world more sustainably with organic agriculture
Authors: Muller Adrian , Schader Christian , El-Hage Scialabba Nadia , Brüggemann Judith , Isensee Anne , Erb Karl-Heinz , Smith Pete , Klocke Peter , Leiber Florian , Stolze Matthias , Niggli Urs 
Published: October 2017

AbstractOrganic agriculture is proposed as a promising approach to achieving sustainable food systems, but its feasibility is also contested. We use a food systems model that addresses agronomic characteristics of organic agriculture to analyze the role that organic agriculture could play in sustainable food systems. Here we show that a 100% conversion to organic agriculture needs more land than conventional agriculture but reduces N-surplus and pesticide use. However, in combination with reductions of food wastage and food-competing feed from arable land, with correspondingly reduced production and consumption of animal products, land use under organic agriculture remains below the reference scenario. Other indicators such as greenhouse gas emissions also improve, but adequate nitrogen supply is challenging. Besides focusing on production, sustainable food systems need to address waste, crop–grass–livestock interdependencies and human consumption. None of the corresponding strategies needs full implementation and their combined partial implementation delivers a more sustainable food future.
Pink-beam serial crystallography
Authors: Meents A. , Wiedorn M. O. , Srajer V. , Henning R. , Sarrou I. , Bergtholdt J. , Barthelmess M. , Reinke P. Y. A. , Dierksmeyer D. , Tolstikova A. , Schaible S. , Messerschmidt M. , Ogata C. M. , Kissick D. J. , Taft M. H. , Manstein D. J. , Lieske J. , Oberthuer D. , Fischetti R. F. , Chapman H. N. 
Published: October 2017

AbstractSerial X-ray crystallography allows macromolecular structure determination at both X-ray free electron lasers (XFELs) and, more recently, synchrotron sources. The time resolution for serial synchrotron crystallography experiments has been limited to millisecond timescales with monochromatic beams. The polychromatic, “pink”, beam provides a more than two orders of magnitude increased photon flux and hence allows accessing much shorter timescales in diffraction experiments at synchrotron sources. Here we report the structure determination of two different protein samples by merging pink-beam diffraction patterns from many crystals, each collected with a single 100 ps X-ray pulse exposure per crystal using a setup optimized for very low scattering background. In contrast to experiments with monochromatic radiation, data from only 50 crystals were required to obtain complete datasets. The high quality of the diffraction data highlights the potential of this method for studying irreversible reactions at sub-microsecond timescales using high-brightness X-ray facilities.
Two missense mutations in KCNQ1 cause pituitary hormone deficiency and maternally inherited gingival fibromatosis
Authors: Tommiska Johanna , Känsäkoski Johanna , Skibsbye Lasse , Vaaralahti Kirsi , Liu Xiaonan , Lodge Emily J. , Tang Chuyi , Yuan Lei , Fagerholm Rainer , Kanters Jørgen K. , Lahermo Päivi , Kaunisto Mari , Keski-Filppula Riikka , Vuoristo Sanna , Pulli Kristiina , Ebeling Tapani , Valanne Leena , Sankila Eeva-Marja , Kivirikko Sirpa , Lääperi Mitja , Casoni Filippo , Giacobini Paolo , Phan-Hug Franziska , Buki Tal , Tena-Sempere Manuel , Pitteloud Nelly , Veijola Riitta , Lipsanen-Nyman Marita , Kaunisto Kari , Mollard Patrice , Andoniadou Cynthia L. , Hirsch Joel A. , Varjosalo Markku , Jespersen Thomas , Raivio Taneli 
Published: October 2017

AbstractFamilial growth hormone deficiency provides an opportunity to identify new genetic causes of short stature. Here we combine linkage analysis with whole-genome resequencing in patients with growth hormone deficiency and maternally inherited gingival fibromatosis. We report that patients from three unrelated families harbor either of two missense mutations, c.347G>T p.(Arg116Leu) or c.1106C>T p.(Pro369Leu), in KCNQ1, a gene previously implicated in the long QT interval syndrome. Kcnq1 is expressed in hypothalamic GHRH neurons and pituitary somatotropes. Co-expressing KCNQ1 with the KCNE2 β-subunit shows that both KCNQ1 mutants increase current levels in patch clamp analyses and are associated with reduced pituitary hormone secretion from AtT-20 cells. In conclusion, our results reveal a role for the KCNQ1 potassium channel in the regulation of human growth, and show that growth hormone deficiency associated with maternally inherited gingival fibromatosis is an allelic disorder with cardiac arrhythmia syndromes caused by KCNQ1 mutations.
Towards visible soliton microcomb generation
Authors: Lee Seung Hoon , Oh Dong Yoon , Yang Qi-Fan , Shen Boqiang , Wang Heming , Yang Ki Youl , Lai Yu-Hung , Yi Xu , Li Xinbai , Vahala Kerry 
Published: October 2017

AbstractFrequency combs have applications that extend from the ultra-violet into the mid-infrared bands. Microcombs, a miniature and often semiconductor-chip-based device, can potentially access most of these applications, but are currently more limited in spectral reach. Here, we demonstrate mode-locked silica microcombs with emission near the edge of the visible spectrum. By using both geometrical and mode-hybridization dispersion control, devices are engineered for soliton generation while also maintaining optical Q factors as high as 80 million. Electronics-bandwidth-compatible (20 GHz) soliton mode locking is achieved with low pumping powers (parametric oscillation threshold powers as low as 5.4 mW). These are the shortest wavelength soliton microcombs demonstrated to date and could be used in miniature optical clocks. The results should also extend to visible and potentially ultra-violet bands.
Structure and functional dynamics of the mitochondrial Fe/S cluster synthesis complex
Authors: Boniecki Michal T. , Freibert Sven A. , Mühlenhoff Ulrich , Lill Roland , Cygler Miroslaw 
Published: October 2017

AbstractIron–sulfur (Fe/S) clusters are essential protein cofactors crucial for many cellular functions including DNA maintenance, protein translation, and energy conversion. De novo Fe/S cluster synthesis occurs on the mitochondrial scaffold protein ISCU and requires cysteine desulfurase NFS1, ferredoxin, frataxin, and the small factors ISD11 and ACP (acyl carrier protein). Both the mechanism of Fe/S cluster synthesis and function of ISD11-ACP are poorly understood. Here, we present crystal structures of three different NFS1-ISD11-ACP complexes with and without ISCU, and we use SAXS analyses to define the 3D architecture of the complete mitochondrial Fe/S cluster biosynthetic complex. Our structural and biochemical studies provide mechanistic insights into Fe/S cluster synthesis at the catalytic center defined by the active-site Cys of NFS1 and conserved Cys, Asp, and His residues of ISCU. We assign specific regulatory rather than catalytic roles to ISD11-ACP that link Fe/S cluster synthesis with mitochondrial lipid synthesis and cellular energy status.
Cell-permeable organic fluorescent probes for live-cell long-term super-resolution imaging reveal lysosome-mitochondrion interactions
Authors: Han Yubing , Li Meihua , Qiu Fengwu , Zhang Meng , Zhang Yu-Hui 
Published: October 2017

AbstractCharacterizing the long-term nanometer-scale interactions between lysosomes and mitochondria in live cells is essential for understanding their functions but remains challenging due to limitations of the existing fluorescent probes. Here, we develop cell-permeable organic fluorescent probes for lysosomes with excellent specificity and high photostability. We also use an existing Atto 647N dye with high brightness and excellent photostability to achieve specific labeling of mitochondria in live cells. Using these probes, we obtain dual-color structured illumination microscopy (SIM) images of dynamic physical lysosome-mitochondrion interactions in live cells at an ~90-nm resolution over a long time course of ~13 min. We successfully record the consecutive dynamic processes of lysosomal fusion and fission, as well as four types of physical lysosome-mitochondrion interactions by super-resolution imaging. Our probes provide an avenue for understanding the functions and the dynamic interplay of lysosomes and mitochondria in live cells.
Programmed cell senescence in skeleton during late puberty
Authors: Li Changjun , Chai Yu , Wang Lei , Gao Bo , Chen Hao , Gao Peisong , Zhou Feng-Quan , Luo Xianghang , Crane Janet L. , Yu Bin , Cao Xu , Wan Mei 
Published: October 2017

AbstractMesenchymal stem/progenitor cells (MSPCs) undergo rapid self-renewal and differentiation, contributing to fast skeletal growth during childhood and puberty. It remains unclear whether these cells change their properties during late puberty to young adulthood, when bone growth and accrual decelerate. Here we show that MSPCs in primary spongiosa of long bone in mice at late puberty undergo normal programmed senescence, characterized by loss of nestin expression. MSPC senescence is epigenetically controlled by the polycomb histone methyltransferase enhancer of zeste homolog 2 (Ezh2) and its trimethylation of histone H3 on Lysine 27 (H3K27me3) mark. Ezh2 maintains the repression of key cell senescence inducer genes through H3K27me3, and deletion of Ezh2 in early pubertal mice results in premature cellular senescence, depleted MSPCs pool, and impaired osteogenesis as well as osteoporosis in later life. Our data reveals a programmed cell fate change in postnatal skeleton and unravels a regulatory mechanism underlying this phenomenon.
Direct observation of valley-polarized topological edge states in designer surface plasmon crystals
Authors: Wu Xiaoxiao , Meng Yan , Tian Jingxuan , Huang Yingzhou , Xiang Hong , Han Dezhuan , Wen Weijia 
Published: October 2017

AbstractThe extensive research of two-dimensional layered materials has revealed that valleys, as energy extrema in momentum space, could offer a new degree of freedom for carrying information. Based on this concept, researchers have predicted valley-Hall topological insulators that could support valley-polarized edge states at non-trivial domain walls. Recently, several kinds of photonic and sonic crystals have been proposed as classical counterparts of valley-Hall topological insulators. However, direct experimental observation of valley-polarized edge states in photonic crystals has remained difficult until now. Here, we demonstrate a designer surface plasmon crystal comprising metallic patterns deposited on a dielectric substrate, which can become a valley-Hall photonic topological insulator by exploiting the mirror-symmetry-breaking mechanism. Topological edge states with valley-dependent transport are directly visualized in the microwave regime. The observed edge states are confirmed to be fully valley-polarized through spatial Fourier transforms. Topological protection of the edge states at sharp corners is also experimentally demonstrated.