bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamical trade-offs arise from antagonistic coevolution and decrease intraspecific diversity
Authors: Huang Weini , Traulsen Arne , Werner Benjamin , Hiltunen Teppo , Becks Lutz 
Published: December 2017

AbstractTrade-offs play an important role in evolution. Without trade-offs, evolution would maximize fitness of all traits leading to a “master of all traits”. The shape of trade-offs has been shown to determine evolutionary trajectories and is often assumed to be static and independent of the actual evolutionary process. Here we propose that coevolution leads to a dynamical trade-off. We test this hypothesis in a microbial predator–prey system and show that the bacterial growth-defense trade-off changes from concave to convex, i.e., defense is effective and cheap initially, but gets costly when predators coevolve. We further explore the impact of such dynamical trade-offs by a novel mathematical model incorporating de novo mutations for both species. Predator and prey populations diversify rapidly leading to higher prey diversity when the trade-off is concave (cheap). Coevolution results in more convex (costly) trade-offs and lower prey diversity compared to the scenario where only the prey evolves.
Coupling between oxygen redox and cation migration explains unusual electrochemistry in lithium-rich layered oxides
Authors: Gent William E. , Lim Kipil , Liang Yufeng , Li Qinghao , Barnes Taylor , Ahn Sung-Jin , Stone Kevin H. , McIntire Mitchell , Hong Jihyun , Song Jay Hyok , Li Yiyang , Mehta Apurva , Ermon Stefano , Tyliszczak Tolek , Kilcoyne David , Vine David , Park Jin-Hwan , Doo Seok-Kwang , Toney Michael F. , Yang Wanli , Prendergast David , Chueh William C. 
Published: December 2017

AbstractLithium-rich layered transition metal oxide positive electrodes offer access to anion redox at high potentials, thereby promising high energy densities for lithium-ion batteries. However, anion redox is also associated with several unfavorable electrochemical properties, such as open-circuit voltage hysteresis. Here we reveal that in Li1.17–x
Ni0.21Co0.08Mn0.54O2, these properties arise from a strong coupling between anion redox and cation migration. We combine various X-ray spectroscopic, microscopic, and structural probes to show that partially reversible transition metal migration decreases the potential of the bulk oxygen redox couple by > 1 V, leading to a reordering in the anionic and cationic redox potentials during cycling. First principles calculations show that this is due to the drastic change in the local oxygen coordination environments associated with the transition metal migration. We propose that this mechanism is involved in stabilizing the oxygen redox couple, which we observe spectroscopically to persist for 500 charge/discharge cycles.
Evolution of a flipped pathway creates metabolic innovation in tomato trichomes through BAHD enzyme promiscuity
Authors: Fan Pengxiang , Miller Abigail M. , Liu Xiaoxiao , Jones A. Daniel , Last Robert L. 
Published: December 2017

AbstractPlants produce hundreds of thousands of structurally diverse specialized metabolites via multistep biosynthetic networks, including compounds of ecological and therapeutic importance. These pathways are restricted to specific plant groups, and are excellent systems for understanding metabolic evolution. Tomato and other plants in the nightshade family synthesize protective acylated sugars in the tip cells of glandular trichomes on stems and leaves. We describe a metabolic innovation in wild tomato species that contributes to acylsucrose structural diversity. A small number of amino acid changes in two acylsucrose acyltransferases alter their acyl acceptor preferences, resulting in reversal of their order of reaction and increased product diversity. This study demonstrates how small numbers of amino acid changes in multiple pathway enzymes can lead to diversification of specialized metabolites in plants. It also highlights the power of a combined genetic, genomic and in vitro biochemical approach to identify the evolutionary mechanisms leading to metabolic novelty.
Multinational patterns of seasonal asymmetry in human movement influence infectious disease dynamics
Authors: Wesolowski Amy , zu Erbach-Schoenberg Elisabeth , Tatem Andrew J. , Lourenço Christopher , Viboud Cecile , Charu Vivek , Eagle Nathan , Engø-Monsen Kenth , Qureshi Taimur , Buckee Caroline O. , Metcalf C. J. E. 
Published: December 2017

AbstractSeasonal variation in human mobility is globally ubiquitous and affects the spatial spread of infectious diseases, but the ability to measure seasonality in human movement has been limited by data availability. Here, we use mobile phone data to quantify seasonal travel and directional asymmetries in Kenya, Namibia, and Pakistan, across a spectrum from rural nomadic populations to highly urbanized communities. We then model how the geographic spread of several acute pathogens with varying life histories could depend on country-wide connectivity fluctuations through the year. In all three countries, major national holidays are associated with shifts in the scope of travel. Within this broader pattern, the relative importance of particular routes also fluctuates over the course of the year, with increased travel from rural to urban communities after national holidays, for example. These changes in travel impact how fast communities are likely to be reached by an introduced pathogen.
PEPD is a pivotal regulator of p53 tumor suppressor
Authors: Yang Lu , Li Yun , Bhattacharya Arup , Zhang Yuesheng 
Published: December 2017

Abstractp53 tumor suppressor responds to various cellular stresses and regulates cell fate. Here, we show that peptidase D (PEPD) binds and suppresses over half of nuclear and cytoplasmic p53 under normal conditions, independent of its enzymatic activity. Eliminating PEPD causes cell death and tumor regression due to p53 activation. PEPD binds to the proline-rich domain in p53, which inhibits phosphorylation of nuclear p53 and MDM2-mediated mitochondrial translocation of nuclear and cytoplasmic p53. However, the PEPD-p53 complex is critical for p53 response to stress, as stress signals doxorubicin and H2O2 each must free p53 from PEPD in order to achieve robust p53 activation, which is mediated by reactive oxygen species. Thus, PEPD stores p53 for the stress response, but this also renders cells dependent on PEPD for survival, as it suppresses p53. This finding provides further understanding of p53 regulation and may have significant implications for the treatment of cancer and other diseases.
Prodigious submarine landslides during the inception and early growth of volcanic islands
Authors: Hunt James E. , Jarvis Ian 
Published: December 2017

AbstractVolcanic island inception applies large stresses as the ocean crust domes in response to magma ascension and is loaded by eruption of lavas. There is currently limited information on when volcanic islands are initiated on the seafloor, and no information regarding the seafloor instabilities island inception may cause. The deep sea Madeira Abyssal Plain contains a 43 million year history of turbidites among which many originate from mass movements in the Canary Islands. Here, we investigate the composition and timing of a distinctive group of turbidites that we suggest represent a new unique record of large-volume submarine landslides triggered during the inception, submarine shield growth, and final subaerial emergence of the Canary Islands. These slides are predominantly multi-stage and yet represent among the largest mass movements on the Earth’s surface up to three or more-times larger than subaerial Canary Islands flank collapses. Thus whilst these deposits provide invaluable information on ocean island geodynamics they also represent a significant, and as yet unaccounted, marine geohazard.
Comprehensive phase diagram of two-dimensional space charge doped Bi2Sr2CaCu2O8+x
Authors: Sterpetti Edoardo , Biscaras Johan , Erb Andreas , Shukla Abhay 
Published: December 2017

AbstractThe phase diagram of hole-doped high critical temperature superconductors as a function of doping and temperature has been intensively studied with chemical variation of doping. Chemical doping can provoke structural changes and disorder, masking intrinsic effects. Alternatively, a field-effect transistor geometry with an electrostatically doped, ultra-thin sample can be used. However, to probe the phase diagram, carrier density modulation beyond 1014 cm−2 and transport measurements performed over a large temperature range are needed. Here we use the space charge doping method to measure transport characteristics from 330 K to low temperature. We extract parameters and characteristic temperatures over a large doping range and establish a comprehensive phase diagram for one-unit-cell-thick BSCCO-2212 as a function of doping, temperature and disorder.
Global unleashing of transcription elongation waves in response to genotoxic stress restricts somatic mutation rate
Authors: Lavigne Matthieu D. , Konstantopoulos Dimitris , Ntakou-Zamplara Katerina Z. , Liakos Anastasios , Fousteri Maria 
Published: December 2017

AbstractComplex molecular responses preserve gene expression accuracy and genome integrity in the face of environmental perturbations. Here we report that, in response to UV irradiation, RNA polymerase II (RNAPII) molecules are dynamically and synchronously released from promoter-proximal regions into elongation to promote uniform and accelerated surveillance of the whole transcribed genome. The maximised influx of de novo released RNAPII correlates with increased damage-sensing, as confirmed by RNAPII progressive accumulation at dipyrimidine sites and by the average slow-down of elongation rates in gene bodies. In turn, this transcription elongation ‘safe’ mode guarantees efficient DNA repair regardless of damage location, gene size and transcription level. Accordingly, we detect low and homogenous rates of mutational signatures associated with UV exposure or cigarette smoke across all active genes. Our study reveals a novel advantage for transcription regulation at the promoter-proximal level and provides unanticipated insights into how active transcription shapes the mutagenic landscape of cancer genomes.
Balancing mcr-1 expression and bacterial survival is a delicate equilibrium between essential cellular defence mechanisms
Authors: Yang Qiue , Li Mei , Spiller Owen B. , Andrey Diego O. , Hinchliffe Philip , Li Hui , MacLean Craig , Niumsup Pannika , Powell Lydia , Pritchard Manon , Papkou Andrei , Shen Yingbo , Portal Edward , Sands Kirsty , Spencer James , Tansawai Uttapoln , Thomas David , Wang Shaolin , Wang Yang , Shen Jianzhong , Walsh Timothy 
Published: December 2017

AbstractMCR-1 is a lipid A modifying enzyme that confers resistance to the antibiotic colistin. Here, we analyse the impact of MCR-1 expression on E. coli morphology, fitness, competitiveness, immune stimulation and virulence. Increased expression of mcr-1 results in decreased growth rate, cell viability, competitive ability and significant degradation in cell membrane and cytoplasmic structures, compared to expression of catalytically inactive MCR-1 (E246A) or MCR-1 soluble component. Lipopolysaccharide (LPS) extracted from mcr-1 strains induces lower production of IL-6 and TNF, when compared to control LPS. Compared to their parent strains, high-level colistin resistance mutants (HLCRMs) show reduced fitness (relative fitness is 0.41–0.78) and highly attenuated virulence in a Galleria mellonella infection model. Furthermore, HLCRMs are more susceptible to most antibiotics than their respective parent strains. Our results show that the bacterium is challenged to find a delicate equilibrium between expression of MCR-1-mediated colistin resistance and minimalizing toxicity and thus ensuring cell survival.
Identification and characterization of two functional variants in the human longevity gene FOXO3
Authors: Flachsbart Friederike , Dose Janina , Gentschew Liljana , Geismann Claudia , Caliebe Amke , Knecht Carolin , Nygaard Marianne , Badarinarayan Nandini , ElSharawy Abdou , May Sandra , Luzius Anne , Torres Guillermo G. , Jentzsch Marlene , Forster Michael , Häsler Robert , Pallauf Kathrin , Lieb Wolfgang , Derbois Céline , Galan Pilar , Drichel Dmitriy , Arlt Alexander , Till Andreas , Krause-Kyora Ben , Rimbach Gerald , Blanché Hélène , Deleuze Jean-François , Christiansen Lene , Christensen Kaare , Nothnagel Michael , Rosenstiel Philip , Schreiber Stefan , Franke Andre , Sebens Susanne , Nebel Almut 
Published: December 2017

AbstractFOXO3 is consistently annotated as a human longevity gene. However, functional variants and underlying mechanisms for the association remain unknown. Here, we perform resequencing of the FOXO3 locus and single-nucleotide variant (SNV) genotyping in three European populations. We find two FOXO3 SNVs, rs12206094 and rs4946935, to be most significantly associated with longevity and further characterize them functionally. We experimentally validate the in silico predicted allele-dependent binding of transcription factors (CTCF, SRF) to the SNVs. Specifically, in luciferase reporter assays, the longevity alleles of both variants show considerable enhancer activities that are reversed by IGF-1 treatment. An eQTL database search reveals that the alleles are also associated with higher FOXO3 mRNA expression in various human tissues, which is in line with observations in long-lived model organisms. In summary, we present experimental evidence for a functional link between common intronic variants in FOXO3 and human longevity.
Mating system manipulation and the evolution of sex-biased gene expression in Drosophila
Authors: Veltsos Paris , Fang Yongxiang , Cossins Andrew R. , Snook Rhonda R. , Ritchie Michael G. 
Published: December 2017

AbstractSex differences in dioecious animals are pervasive and result from gene expression differences. Elevated sexual selection has been predicted to increase the number and expression of male-biased genes, and experimentally imposing monogamy onDrosophila melanogasterhas led to a relative feminisation of the transcriptome. Here, we test this hypothesis further by subjecting another polyandrous species,D. pseudoobscura, to 150 generations of experimental monogamy or elevated polyandry. We find that sex-biased genes do change in expression but, contrary to predictions, there is usually masculinisation of the transcriptome under monogamy, although this depends on tissue and sex. We also identify and describe gene expression changes following courtship experience. Courtship often influences gene expression, including patterns in sex-biased gene expression. Our results confirm that mating system manipulation disproportionately influences sex-biased gene expression but show that the direction of change is dynamic and unpredictable.
An oomycete plant pathogen reprograms host pre-mRNA splicing to subvert immunity
Authors: Huang Jie , Gu Lianfeng , Zhang Ying , Yan Tingxiu , Kong Guanghui , Kong Liang , Guo Baodian , Qiu Min , Wang Yang , Jing Maofeng , Xing Weiman , Ye Wenwu , Wu Zhe , Zhang Zhengguang , Zheng Xiaobo , Gijzen Mark , Wang Yuanchao , Dong Suomeng 
Published: December 2017

AbstractThe process of RNA splicing influences many physiological processes, including plant immunity. However, how plant parasites manipulate host RNA splicing process remains unknown. Here we demonstrate that PsAvr3c, an avirulence effector from oomycete plant pathogen Phytophthora sojae, physically binds to and stabilizes soybean serine/lysine/arginine-rich proteins GmSKRPs. The SKRPs are novel proteins that associate with a complex that contains plant spliceosome components, and are negative regulators of plant immunity. Analysis by RNA-seq data indicates that alternative splicing of pre-mRNAs from 401 soybean genes, including defense-related genes, is altered in GmSKRP1 and PsAvr3c overexpressing lines compared to control plants. Representative splicing events mediated by GmSKRP1 and PsAvr3c are tested by infection assays or by transient expression in soybean plants. Our results show that plant pathogen effectors can reprogram host pre-mRNA splicing to promote disease, and we propose that pathogens evolved such strategies to defeat host immune systems.
Controlling supercurrents and their spatial distribution in ferromagnets
Authors: Lahabi Kaveh , Amundsen Morten , Ouassou Jabir Ali , Beukers Ewout , Pleijster Menno , Linder Jacob , Alkemade Paul , Aarts Jan 
Published: December 2017

AbstractSpin-triplet Cooper pairs induced in ferromagnets form the centrepiece of the emerging field of superconducting spintronics. Usually the focus is on the spin-polarization of the triplets, potentially enabling low-dissipation magnetization switching. However, the magnetic texture which provides the fundamental mechanism for generating triplets also permits control over the spatial distribution of supercurrent. Here we demonstrate the tailoring of distinct supercurrent pathways in the ferromagnetic barrier of a Josephson junction. We combine micromagnetic simulations with three-dimensional supercurrent calculations to design a disk-shaped structure with a ferromagnetic vortex which induces two transport channels across the junction. By using superconducting quantum interferometry, we show the existence of two channels. Moreover, we show how the supercurrent can be controlled by moving the vortex with a magnetic field. This approach paves the way for supercurrent paths to be dynamically reconfigured in order to switch between different functionalities in the same device.
Voltage-gated sodium channels assemble and gate as dimers
Authors: Clatot Jérôme , Hoshi Malcolm , Wan Xiaoping , Liu Haiyan , Jain Ankur , Shinlapawittayatorn Krekwit , Marionneau Céline , Ficker Eckhard , Ha Taekjip , Deschênes Isabelle 
Published: December 2017

AbstractFast opening and closing of voltage-gated sodium channels are crucial for proper propagation of the action potential through excitable tissues. Unlike potassium channels, sodium channel α-subunits are believed to form functional monomers. Yet, an increasing body of literature shows inconsistency with the traditional idea of a single α-subunit functioning as a monomer. Here we demonstrate that sodium channel α-subunits not only physically interact with each other but they actually assemble, function and gate as a dimer. We identify the region involved in the dimerization and demonstrate that 14-3-3 protein mediates the coupled gating. Importantly we show conservation of this mechanism among mammalian sodium channels. Our study not only shifts conventional paradigms in regard to sodium channel assembly, structure, and function but importantly this discovery of the mechanism involved in channel dimerization and biophysical coupling could open the door to new approaches and targets to treat and/or prevent sodium channelopathies.
p16Ink4a and p21Cip1/Waf1 promote tumour growth by enhancing myeloid-derived suppressor cells chemotaxis
Authors: Okuma Atsushi , Hanyu Aki , Watanabe Sugiko , Hara Eiji 
Published: December 2017

Abstractp16Ink4aand p21Cip1/Waf1act as tumour suppressors through induction of cellular senescence. However, senescence-independent roles of these CDK inhibitors are not well understood. Here, we report an unexpected function of p16Ink4and p21Cip1/Waf1, namely, tumour promotion through chemotaxis. In monocytic myeloid-derived suppressor cells (Mo-MDSCs), p16Ink4and p21Cip1/Waf1are highly expressed and stimulate CX3CR1 chemokine receptor expression by preventing CDK-mediated phosphorylation and inactivation of SMAD3. Thus, deletion ofp16Ink4andp21Cip1/Waf1reduces CX3CR1 expression, thereby inhibiting Mo-MDSC accumulation in tumours expressing CX3CL1 and suppressing the tumour progression in mice. Notably, blockade of the CX3CL1/CX3CR1 axis suppresses tumour growth, whereas inactivation of CDKs elicits the opposite effect. These findings reveal an unexpected function ofp16Ink4aandp21Waf1/Cip1and indicate that regulation of Mo-MDSCs chemotaxis is a valuable potential strategy for control of tumour development.
Forming quasicrystals by monodisperse soft core particles
Authors: Zu Mengjie , Tan Peng , Xu Ning 
Published: December 2017

AbstractIn traditional approaches to form quasicrystals, multiple competing length scales involved in particle size, shape, or interaction potential are believed to be necessary. It is unexpected that quasicrystals can be formed by monodisperse, isotropic particles interacting via a simple potential that does not contain explicit multiple length scales to stabilize quasicrystals. Here, we report the surprising finding of the formation of such quasicrystals in high-density systems of soft-core particles. Although there are length scales naturally introduced in our model systems, they do not establish the quasicrystalline order. In two dimensions, we find not only dodecagonal but also octagonal quasicrystals, which have not been found yet in soft quasicrystals. In such unexpected quasicrystals, particles tend to form pentagons, which are essential elements to develop the quasicrystalline order. Our findings thus pave an unexpected and simple way to form quasicrystals and pose a challenge for theoretical understanding of quasicrystals.
High-Resolution Single Particle Zeta Potential Characterisation of Biological Nanoparticles using Tunable Resistive Pulse Sensing
Authors: Vogel Robert , Pal Anoop K. , Jambhrunkar Siddharth , Patel Pragnesh , Thakur Sachin S. , Reátegui Eduardo , Parekh Harendra S. , Saá Paula , Stassinopoulos Adonis , Broom Murray F. 
Published: December 2017

AbstractPhysicochemical properties of nanoparticles, such as size, shape, surface charge, density, and porosity play a central role in biological interactions and hence accurate determination of these characteristics is of utmost importance. Here we propose tunable resistive pulse sensing for simultaneous size and surface charge measurements on a particle-by-particle basis, enabling the analysis of a wide spectrum of nanoparticles and their mixtures. Existing methodologies for measuring zeta potential of nanoparticles using resistive pulse sensing are significantly improved by including convection into the theoretical model. The efficacy of this methodology is demonstrated for a range of biological case studies, including measurements of mixed anionic, cationic liposomes, extracellular vesicles in plasma, and in situ time study of DNA immobilisation on the surface of magnetic nanoparticles. The high-resolution single particle size and zeta potential characterisation will provide a better understanding of nano-bio interactions, positively impacting nanomedicine development and their regulatory approval.