bluuebunny/crossref_metadata_2025_split huggingface dataset:
Timescales of water accumulation in magmas and implications for short warning times of explosive eruptions
Authors: Petrelli M. , El Omari K. , Spina L. , Le Guer Y. , La Spina G. , Perugini D. 
Published: February 2018

AbstractWater plays a key role in magma genesis, differentiation, ascent and, finally, eruption. Despite the recognized crucial function of water, there are still several issues that continue to blur our view about its role in magmatic systems. What are the timescales of H2O accumulation in crystallizing magmas? What are the ascent rates of water-rich residual melts leading to explosive eruptions? Here, we track the timescale of water accumulation in a residual melt resulting from crystallization of a hydrous CO2-bearing magmatic mass stored at mid- to deep-crustal levels in a subduction-related geodynamic setting. Our results indicate that, after a repose period ranging from few to several thousand years, water-rich melts with water concentrations larger than 6–9 wt.% can migrate towards the Earth surface in very short timescales, on the order of days or even hours, possibly triggering explosive eruptions with short warning times and devoid of long-term geophysical precursors.
Exploiting genetic variation to uncover rules of transcription factor binding and chromatin accessibility
Authors: Behera Vivek , Evans Perry , Face Carolyne J. , Hamagami Nicole , Sankaranarayanan Laavanya , Keller Cheryl A. , Giardine Belinda , Tan Kai , Hardison Ross C. , Shi Junwei , Blobel Gerd A. 
Published: February 2018

AbstractSingle-nucleotide variants that underlie phenotypic variation can affect chromatin occupancy of transcription factors (TFs). To delineate determinants of in vivo TF binding and chromatin accessibility, we introduce an approach that compares ChIP-seq and DNase-seq data sets from genetically divergent murine erythroid cell lines. The impact of discriminatory single-nucleotide variants on TF ChIP signal enables definition at single base resolution of in vivo binding characteristics of nuclear factors GATA1, TAL1, and CTCF. We further develop a facile complementary approach to more deeply test the requirements of critical nucleotide positions for TF binding by combining CRISPR-Cas9-mediated mutagenesis with ChIP and targeted deep sequencing. Finally, we extend our analytical pipeline to identify nearby contextual DNA elements that modulate chromatin binding by these three TFs, and to define sequences that impact kb-scale chromatin accessibility. Combined, our approaches reveal insights into the genetic basis of TF occupancy and their interplay with chromatin features.
Active colloids as mobile microelectrodes for unified label-free selective cargo transport
Authors: Boymelgreen Alicia M. , Balli Tov , Miloh Touvia , Yossifon Gilad 
Published: February 2018

AbstractUtilization of active colloids to transport both biological and inorganic cargo has been widely examined in the context of applications ranging from targeted drug delivery to sample analysis. In general, carriers are customized to load one specific target via a mechanism distinct from that driving the transport. Here we unify these tasks and extend loading capabilities to include on-demand selection of multiple nano/micro-sized targets without the need for pre-labelling or surface functionalization. An externally applied electric field is singularly used to drive the active cargo carrier and transform it into a mobile floating electrode that can attract (trap) or repel specific targets from its surface by dielectrophoresis, enabling dynamic control of target selection, loading and rate of transport via the electric field parameters. In the future, dynamic selectivity could be combined with directed motion to develop building blocks for bottom-up fabrication in applications such as additive manufacturing and soft robotics.
Landscape topography structures the soil microbiome in arctic polygonal tundra
Authors: Taş Neslihan , Prestat Emmanuel , Wang Shi , Wu Yuxin , Ulrich Craig , Kneafsey Timothy , Tringe Susannah G. , Torn Margaret S. , Hubbard Susan S. , Jansson Janet K. 
Published: February 2018

AbstractIn the Arctic, environmental factors governing microbial degradation of soil carbon (C) in active layer and permafrost are poorly understood. Here we determined the functional potential of soil microbiomes horizontally and vertically across a cryoperturbed polygonal landscape in Alaska. With comparative metagenomics, genome binning of novel microbes, and gas flux measurements we show that microbial greenhouse gas (GHG) production is strongly correlated to landscape topography. Active layer and permafrost harbor contrasting microbiomes, with increasing amounts of Actinobacteria correlating with decreasing soil C in permafrost. While microbial functions such as fermentation and methanogenesis were dominant in wetter polygons, in drier polygons genes for C mineralization and CH4 oxidation were abundant. The active layer microbiome was poised to assimilate N and not to release N2O, reflecting low N2O flux measurements. These results provide mechanistic links of microbial metabolism to GHG fluxes that are needed for the refinement of model predictions.
HDAC1 and HDAC2 integrate checkpoint kinase phosphorylation and cell fate through the phosphatase-2A subunit PR130
Authors: Göder Anja , Emmerich Claudia , Nikolova Teodora , Kiweler Nicole , Schreiber Maria , Kühl Toni , Imhof Diana , Christmann Markus , Heinzel Thorsten , Schneider Günter , Krämer Oliver H. 
Published: February 2018

AbstractCheckpoint kinases sense replicative stress to prevent DNA damage. Here we show that the histone deacetylases HDAC1/HDAC2 sustain the phosphorylation of the checkpoint kinases ATM, CHK1 and CHK2, activity of the cell cycle gatekeeper kinases WEE1 and CDK1, and induction of the tumour suppressor p53 in response to stalled DNA replication. Consequently, HDAC inhibition upon replicative stress promotes mitotic catastrophe. Mechanistically, HDAC1 and HDAC2 suppress the expression of PPP2R3A/PR130, a regulatory subunit of the trimeric serine/threonine phosphatase 2 (PP2A). Genetic elimination of PR130 reveals that PR130 promotes dephosphorylation of ATM by PP2A. Moreover, the ablation of PR130 slows G1/S phase transition and increases the levels of phosphorylated CHK1, replication protein A foci and DNA damage upon replicative stress. Accordingly, stressed PR130 null cells are very susceptible to HDAC inhibition, which abrogates the S phase checkpoint, induces apoptosis and reduces the homologous recombination protein RAD51. Thus, PR130 controls cell fate decisions upon replicative stress.
EGF receptor kinase suppresses ciliogenesis through activation of USP8 deubiquitinase
Authors: Kasahara Kousuke , Aoki Hiromasa , Kiyono Tohru , Wang Shujie , Kagiwada Harumi , Yuge Mizuki , Tanaka Toshio , Nishimura Yuhei , Mizoguchi Akira , Goshima Naoki , Inagaki Masaki 
Published: February 2018

AbstractCiliogenesis is generally inhibited in dividing cells, however, it has been unclear which signaling cascades regulate the phenomenon. Here, we report that epidermal growth factor receptor (EGFR) kinase suppresses ciliogenesis by directly phosphorylating the deubiquitinase USP8 on Tyr-717 and Tyr-810 in RPE1 cells. These phosphorylations elevate the deubiquitinase activity, which then stabilizes the trichoplein-Aurora A pathway, an inhibitory mechanism of ciliogenesis. EGFR knockdown and serum starvation result in ciliogenesis through downregulation of the USP8-trichoplein-Aurora A signal. Moreover, primary cilia abrogation, which is induced upon IFT20 or Cep164 depletion, ameliorates the cell cycle arrest of EGFR knockdown cells. The present data reveal that the EGFR-USP8-trichoplein-Aurora A axis is a critical signaling cascade that restricts ciliogenesis in dividing cells, and functions to facilitate cell proliferation. We further show that usp8 knockout zebrafish develops ciliopathy-related phenotypes including cystic kidney, suggesting that USP8 is a regulator of ciliogenesis in vertebrates.
Reshaping the phonon energy landscape of nanocrystals inside a terahertz plasmonic nanocavity
Authors: Jin Xin , Cerea Andrea , Messina Gabriele C. , Rovere Andrea , Piccoli Riccardo , De Donato Francesco , Palazon Francisco , Perucchi Andrea , Di Pietro Paola , Morandotti Roberto , Lupi Stefano , De Angelis Francesco , Prato Mirko , Toma Andrea , Razzari Luca 
Published: February 2018

AbstractPhonons (quanta of collective vibrations) are a major source of energy dissipation and drive some of the most relevant properties of materials. In nanotechnology, phonons severely affect light emission and charge transport of nanodevices. While the phonon response is conventionally considered an inherent property of a nanomaterial, here we show that the dipole-active phonon resonance of semiconducting (CdS) nanocrystals can be drastically reshaped inside a terahertz plasmonic nanocavity, via the phonon strong coupling with the cavity vacuum electric field. Such quantum zero-point field can indeed reach extreme values in a plasmonic nanocavity, thanks to a mode volume well below λ3/107. Through Raman measurements, we find that the nanocrystals within a nanocavity exhibit two new “hybridized” phonon peaks, whose spectral separation increases with the number of nanocrystals. Our findings open exciting perspectives for engineering the optical phonon response of functional nanomaterials and for implementing a novel platform for nanoscale quantum optomechanics.
Wetter summers can intensify departures from natural variability in a warming climate
Authors: Mahony Colin R. , Cannon Alex J. 
Published: February 2018

AbstractClimate change can drive local climates outside the range of their historical year-to-year variability, straining the adaptive capacity of ecological and human communities. We demonstrate that dependencies between climate variables can produce larger and earlier departures from natural variability than is detectable in individual variables. Using the example of summer temperature (Tx) and precipitation (Pr), we show that this departure intensification effect occurs when the bivariate climate change trajectory is misaligned with the dominant mode of joint historical variability. Departure intensification is evident in all six CMIP5 models that we examined: 23% (9–34%) of the global land area of each model exhibits a pronounced increase in 2σ anomalies in the Tx-Pr regime relative to Tx or Pr alone. Observational data suggest that summer Tx-Pr correlations in distinct regions on all continents are sufficient to produce departure intensification. Precipitation can be an important driver of multivariate climate change signals relative to natural variability, despite typically having a much weaker univariate signal than temperature.
An ancient family of lytic polysaccharide monooxygenases with roles in arthropod development and biomass digestion
Authors: Sabbadin Federico , Hemsworth Glyn R. , Ciano Luisa , Henrissat Bernard , Dupree Paul , Tryfona Theodora , Marques Rita D. S. , Sweeney Sean T. , Besser Katrin , Elias Luisa , Pesante Giovanna , Li Yi , Dowle Adam A. , Bates Rachel , Gomez Leonardo D. , Simister Rachael , Davies Gideon J. , Walton Paul H. , Bruce Neil C. , McQueen-Mason Simon J. 
Published: February 2018

AbstractThermobia domestica belongs to an ancient group of insects and has a remarkable ability to digest crystalline cellulose without microbial assistance. By investigating the digestive proteome of Thermobia, we have identified over 20 members of an uncharacterized family of lytic polysaccharide monooxygenases (LPMOs). We show that this LPMO family spans across several clades of the Tree of Life, is of ancient origin, and was recruited by early arthropods with possible roles in remodeling endogenous chitin scaffolds during development and metamorphosis. Based on our in-depth characterization of Thermobia’s LPMOs, we propose that diversification of these enzymes toward cellulose digestion might have endowed ancestral insects with an effective biochemical apparatus for biomass degradation, allowing the early colonization of land during the Paleozoic Era. The vital role of LPMOs in modern agricultural pests and disease vectors offers new opportunities to help tackle global challenges in food security and the control of infectious diseases.
Directed gas phase formation of silicon dioxide and implications for the formation of interstellar silicates
Authors: Yang Tao , Thomas Aaron M. , Dangi Beni B. , Kaiser Ralf I. , Mebel Alexander M. , Millar Tom J. 
Published: February 2018

AbstractInterstellar silicates play a key role in star formation and in the origin of solar systems, but their synthetic routes have remained largely elusive so far. Here we demonstrate in a combined crossed molecular beam and computational study that silicon dioxide (SiO2) along with silicon monoxide (SiO) can be synthesized via the reaction of the silylidyne radical (SiH) with molecular oxygen (O2) under single collision conditions. This mechanism may provide a low-temperature path—in addition to high-temperature routes to silicon oxides in circumstellar envelopes—possibly enabling the formation and growth of silicates in the interstellar medium necessary to offset the fast silicate destruction.
Spatial organization of bacterial populations in response to oxygen and carbon counter-gradients in pore networks
Authors: Borer Benedict , Tecon Robin , Or Dani 
Published: February 2018

AbstractMicrobial activity in soil is spatially heterogeneous often forming spatial hotspots that contribute disproportionally to biogeochemical processes. Evidence suggests that bacterial spatial organization contributes to the persistence of anoxic hotspots even in unsaturated soils. Such processes are difficult to observe in situ at the microscale, hence mechanisms and time scales relevant for bacterial spatial organization remain largely qualitative. Here we develop an experimental platform based on glass-etched micrometric pore networks that mimics resource gradients postulated in soil aggregates to observe spatial organization of fluorescently tagged aerobic and facultative anaerobic bacteria. Two initially intermixed bacterial species, Pseudomonas putida and Pseudomonas veronii, segregate into preferential regions promoted by opposing gradients of carbon and oxygen (such persistent coexistence is not possible in well-mixed cultures). The study provides quantitative visualization and modeling of bacterial spatial organization within aggregate-like hotspots, a key step towards developing a mechanistic representation of bacterial community organization in soil pores.
The structure of iPLA2β reveals dimeric active sites and suggests mechanisms of regulation and localization
Authors: Malley Konstantin R. , Koroleva Olga , Miller Ian , Sanishvili Ruslan , Jenkins Christopher M. , Gross Richard W. , Korolev Sergey 
Published: February 2018

AbstractCalcium-independent phospholipase A2β (iPLA2β) regulates important physiological processes including inflammation, calcium homeostasis and apoptosis. It is genetically linked to neurodegenerative disorders including Parkinson’s disease. Despite its known enzymatic activity, the mechanisms underlying iPLA2β-induced pathologic phenotypes remain poorly understood. Here, we present a crystal structure of iPLA2β that significantly revises existing mechanistic models. The catalytic domains form a tight dimer. They are surrounded by ankyrin repeat domains that adopt an outwardly flared orientation, poised to interact with membrane proteins. The closely integrated active sites are positioned for cooperative activation and internal transacylation. The structure and additional solution studies suggest that both catalytic domains can be bound and allosterically inhibited by a single calmodulin. These features suggest mechanisms of iPLA2β cellular localization and activity regulation, providing a basis for inhibitor development. Furthermore, the structure provides a framework to investigate the role of neurodegenerative mutations and the function of iPLA2β in the brain.
A regulatory circuit of two lncRNAs and a master regulator directs cell fate in yeast
Authors: Moretto Fabien , Wood N. Ezgi , Kelly Gavin , Doncic Andreas , van Werven Folkert J. 
Published: February 2018

AbstractTranscription of long noncoding RNAs (lncRNAs) regulates local gene expression in eukaryotes. Many examples of how a single lncRNA controls the expression of an adjacent or nearby protein-coding gene have been described. Here we examine the regulation of a locus consisting of two contiguous lncRNAs and the master regulator for entry into yeast meiosis, IME1. We find that the cluster of two lncRNAs together with several transcription factors form a regulatory circuit by which IME1 controls its own promoter and thereby promotes its own expression. Inhibition or stimulation of this unusual feedback circuit affects timing and rate of IME1 accumulation, and hence the ability for cells to enter meiosis. Our data demonstrate that orchestrated transcription through two contiguous lncRNAs promotes local gene expression and determines a critical cell fate decision.
Sumoylation regulates FMRP-mediated dendritic spine elimination and maturation
Authors: Khayachi Anouar , Gwizdek Carole , Poupon Gwénola , Alcor Damien , Chafai Magda , Cassé Frédéric , Maurin Thomas , Prieto Marta , Folci Alessandra , De Graeve Fabienne , Castagnola Sara , Gautier Romain , Schorova Lenka , Loriol Céline , Pronot Marie , Besse Florence , Brau Frédéric , Deval Emmanuel , Bardoni Barbara , Martin Stéphane 
Published: February 2018

AbstractFragile X syndrome (FXS) is the most frequent inherited cause of intellectual disability and the best-studied monogenic cause of autism. FXS results from the functional absence of the fragile X mental retardation protein (FMRP) leading to abnormal pruning and consequently to synaptic communication defects. Here we show that FMRP is a substrate of the small ubiquitin-like modifier (SUMO) pathway in the brain and identify its active SUMO sites. We unravel the functional consequences of FMRP sumoylation in neurons by combining molecular replacement strategy, biochemical reconstitution assays with advanced live-cell imaging. We first demonstrate that FMRP sumoylation is promoted by activation of metabotropic glutamate receptors. We then show that this increase in sumoylation controls the homomerization of FMRP within dendritic mRNA granules which, in turn, regulates spine elimination and maturation. Altogether, our findings reveal the sumoylation of FMRP as a critical activity-dependent regulatory mechanism of FMRP-mediated neuronal function.
Mutant p53 cancers reprogram macrophages to tumor supporting macrophages via exosomal miR-1246
Authors: Cooks Tomer , Pateras Ioannis S. , Jenkins Lisa M. , Patel Keval M. , Robles Ana I. , Morris James , Forshew Tim , Appella Ettore , Gorgoulis Vassilis G. , Harris Curtis C. 
Published: February 2018

AbstractTP53 mutants (mutp53) are involved in the pathogenesis of most human cancers. Specific mutp53 proteins gain oncogenic functions (GOFs) distinct from the tumor suppressor activity of the wild-type protein. Tumor-associated macrophages (TAMs), a hallmark of solid tumors, are typically correlated with poor prognosis. Here, we report a non-cell-autonomous mechanism, whereby human mutp53 cancer cells reprogram macrophages to a tumor supportive and anti-inflammatory state. The colon cancer cells harboring GOF mutp53 selectively shed miR-1246-enriched exosomes. Uptake of these exosomes by neighboring macrophages triggers their miR-1246-dependent reprogramming into a cancer-promoting state. Mutp53-reprogammed TAMs favor anti-inflammatory immunosuppression with increased activity of TGF-β. These findings, associated with poor survival in colon cancer patients, strongly support a microenvironmental GOF role for mutp53 in actively engaging the immune system to promote cancer progression and metastasis.
A quantum causal discovery algorithm
Authors: Giarmatzi Christina , Costa Fabio 
Published: February 2018

AbstractFinding a causal model for a set of classical variables is now a well-established task—but what about the quantum equivalent? Even the notion of a quantum causal model is controversial. Here, we present a causal discovery algorithm for quantum systems. The input to the algorithm is a process matrix describing correlations between quantum events. Its output consists of different levels of information about the underlying causal model. Our algorithm determines whether the process is causally ordered by grouping the events into causally ordered non-signaling sets. It detects if all relevant common causes are included in the process, which we label Markovian, or alternatively if some causal relations are mediated through some external memory. For a Markovian process, it outputs a causal model, namely the causal relations and the corresponding mechanisms, represented as quantum states and channels. Our algorithm opens the route to more general quantum causal discovery methods.
Superior memory efficiency of quantum devices for the simulation of continuous-time stochastic processes
Authors: Elliott Thomas J. , Gu Mile 
Published: February 2018

AbstractContinuous-time stochastic processes pervade everyday experience, and the simulation of models of these processes is of great utility. Classical models of systems operating in continuous-time must typically track an unbounded amount of information about past behaviour, even for relatively simple models, enforcing limits on precision due to the finite memory of the machine. However, quantum machines can require less information about the past than even their optimal classical counterparts to simulate the future of discrete-time processes, and we demonstrate that this advantage extends to the continuous-time regime. Moreover, we show that this reduction in the memory requirement can be unboundedly large, allowing for arbitrary precision even with a finite quantum memory. We provide a systematic method for finding superior quantum constructions, and a protocol for analogue simulation of continuous-time renewal processes with a quantum machine.
Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat
Authors: Zepeda Mendoza M. Lisandra , Xiong Zijun , Escalera-Zamudio Marina , Runge Anne Kathrine , Thézé Julien , Streicker Daniel , Frank Hannah K. , Loza-Rubio Elizabeth , Liu Shengmao , Ryder Oliver A. , Samaniego Castruita Jose Alfredo , Katzourakis Aris , Pacheco George , Taboada Blanca , Löber Ulrike , Pybus Oliver G. , Li Yang , Rojas-Anaya Edith , Bohmann Kristine , Carmona Baez Aldo , Arias Carlos F. , Liu Shiping , Greenwood Alex D. , Bertelsen Mads F. , White Nicole E. , Bunce Michael , Zhang Guojie , Sicheritz-Pontén Thomas , Gilbert M. P. Thomas 
Published: February 2018

AbstractAdaptation to specialized diets often requires modifications at both genomic and microbiome levels. We applied a hologenomic approach to the common vampire bat (Desmodus rotundus), one of the only three obligate blood-feeding (sanguivorous) mammals, to study the evolution of its complex dietary adaptation. Specifically, we assembled its high-quality reference genome (scaffold N50 = 26.9 Mb, contig N50 = 36.6 kb) and gut metagenome, and compared them against those of insectivorous, frugivorous and carnivorous bats. Our analyses showed a particular common vampire bat genomic landscape regarding integrated viral elements, a dietary and phylogenetic influence on gut microbiome taxonomic and functional profiles, and that both genetic elements harbour key traits related to the nutritional (for example, vitamin and lipid shortage) and non-nutritional (for example, nitrogen waste and osmotic homeostasis) challenges of sanguivory. These findings highlight the value of a holistic study of both the host and its microbiota when attempting to decipher adaptations underlying radical dietary lifestyles.