bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tremblaya phenacola PPER: an evolutionary beta-gammaproteobacterium collage
Authors: Gil Rosario , Vargas-Chavez Carlos , López-Madrigal Sergio , Santos-García Diego , Latorre Amparo , Moya Andrés 
Published: September 2017

Abstract
Many insects rely on bacterial endosymbionts to obtain nutrients that are scarce in their highly specialized diets. The most surprising example corresponds to the endosymbiotic system found in mealybugs from subfamily Pseudococcinae in which two bacteria, the betaproteobacterium ‘Candidatus Tremblaya princeps’ and a gammaproteobacterium, maintain a nested endosymbiotic consortium. In the sister subfamily Phenacoccinae, however, a single beta-endosymbiont, ‘Candidatus Tremblaya phenacola’, has been described. In a previous study, we detected a trpB gene of gammaproteobacterial origin in ‘Ca. Tremblaya phenacola’ from two Phenacoccus species, apparently indicating an unusual case of horizontal gene transfer (HGT) in a bacterial endosymbiont. What we found by sequencing the genome of ‘Ca. Tremblaya phenacola’ PPER, single endosymbiont of Phenacoccus peruvianus, goes beyond a HGT phenomenon. It rather represents a genome fusion between a beta and a gammaproteobacterium, followed by massive rearrangements and loss of redundant genes, leading to an unprecedented evolutionary collage. Mediated by the presence of several repeated sequences, there are many possible genome arrangements, and different subgenomic sequences might coexist within the same population.
Network heterogeneity regulates steering in actin-based motility
Authors: Boujemaa-Paterski Rajaa , Suarez Cristian , Klar Tobias , Zhu Jie , Guérin Christophe , Mogilner Alex , Théry Manuel , Blanchoin Laurent 
Published: September 2017

AbstractThe growth of branched actin networks powers cell-edge protrusions and motility. A heterogeneous density of actin, which yields to a tunable cellular response, characterizes these dynamic structures. We study how actin organization controls both the rate and the steering during lamellipodium growth. We use a high-resolution surface structuration assay combined with mathematical modeling to describe the growth of a reconstituted lamellipodium. We demonstrate that local monomer depletion at the site of assembly negatively impacts the network growth rate. At the same time, network architecture tunes the protrusion efficiency, and regulates the rate of growth. One consequence of this interdependence between monomer depletion and network architecture effects is the ability of heterogeneous network to impose steering during motility. Therefore, we have established that the general principle, by which the cell can modulate the rate and the direction of a protrusion, is by varying both density and architecture of its actin network.
Modular fluorescence complementation sensors for live cell detection of epigenetic signals at endogenous genomic sites
Authors: Lungu Cristiana , Pinter Sabine , Broche Julian , Rathert Philipp , Jeltsch Albert 
Published: September 2017

AbstractInvestigation of the fundamental role of epigenetic processes requires methods for the locus-specific detection of epigenetic modifications in living cells. Here, we address this urgent demand by developing four modular fluorescence complementation-based epigenetic biosensors for live-cell microscopy applications. These tools combine engineered DNA-binding proteins with domains recognizing defined epigenetic marks, both fused to non-fluorescent fragments of a fluorescent protein. The presence of the epigenetic mark at the target DNA sequence leads to the reconstitution of a functional fluorophore. With this approach, we could for the first time directly detect DNA methylation and histone 3 lysine 9 trimethylation at endogenous genomic sites in live cells and follow dynamic changes in these marks upon drug treatment, induction of epigenetic enzymes and during the cell cycle. We anticipate that this versatile technology will improve our understanding of how specific epigenetic signatures are set, erased and maintained during embryonic development or disease onset.
Non-diffracting multi-﻿electron vortex beams balancing their electron–electron interactions
Authors: Mutzafi Maor , Kaminer Ido , Harari Gal , Segev Mordechai 
Published: September 2017

AbstractThe wave-like nature of electrons has been known for almost a century, but only in recent years has the ability to shape the wavefunction of EBeams (Electron-Beams) become experimentally accessible. Various EBeam wavefunctions have been demonstrated, such as vortex, self-accelerating, Bessel EBeams etc. However, none has attempted to manipulate multi-electron beams, because the repulsion between electrons rapidly alters the beam shape. Here, we show how interference effects of the quantum wavefunction describing multiple electrons can be used to exactly balance both the repulsion and diffraction-broadening. We propose non-diffracting wavepackets of multiple electrons, which can also carry orbital angular momentum. Such wavefunction shaping facilitates the use of multi-electron beams in electron microscopy with higher current without compromising on spatial resolution. Simulating the quantum evolution in three-dimensions and time, we show that imprinting such wavefunctions on electron pulses leads to shape-preserving multi-electrons ultrashort pulses. Our scheme applies to any beams of charged particles, such as protons and ion beams.
Layer- and cell type-selective co-transmission by a basal forebrain cholinergic projection to the olfactory bulb
Authors: Case Daniel T. , Burton Shawn D. , Gedeon Jeremy Y. , Williams Sean-Paul G. , Urban Nathaniel N. , Seal Rebecca P. 
Published: September 2017

AbstractCholinergic neurons in the basal forebrain project heavily to the main olfactory bulb, the first processing station in the olfactory pathway. The projections innervate multiple layers of the main olfactory bulb and strongly influence odor discrimination, detection, and learning. The precise underlying circuitry of this cholinergic input to the main olfactory bulb remains unclear, however. Here, we identify a specific basal forebrain cholinergic projection that innervates select neurons concentrated in the internal plexiform layer of the main olfactory bulb. Optogenetic activation of this projection elicits monosynaptic nicotinic and GABAergic currents in glomerular layer-projecting interneurons. Additionally, we show that the projection co-expresses markers for GABAergic neurotransmission. The data thus implicate neurotransmitter co-transmission in the basal forebrain regulation of this inhibitory olfactory microcircuit.
Optical dating in a new light: A direct, non-destructive probe of trapped electrons
Authors: Prasad Amit Kumar , Poolton Nigel R. J. , Kook Myungho , Jain Mayank 
Published: September 2017

AbstractOptical dating has revolutionized our understanding of Global climate change, Earth surface processes, and human evolution and dispersal over the last ~500 ka. Optical dating is based on an anti-Stokes photon emission generated by electron-hole recombination within quartz or feldspar; it relies, by default, on destructive read-out of the stored chronometric information. We present here a fundamentally new method of optical read-out of the trapped electron population in feldspar. The new signal termed as Infra-Red Photo-Luminescence (IRPL) is a Stokes emission (~1.30 eV) derived from NIR excitation (~1.40 eV) on samples previously exposed to ionizing radiation. Low temperature (7–295 K) spectroscopic and time-resolved investigations suggest that IRPL is generated from excited-to-ground state relaxation within the principal (dosimetry) trap. Since IRPL can be induced even in traps remote from recombination centers, it is likely to contain a stable (non-fading), steady-state component. While IRPL is a powerful tool to understand details of the electron-trapping center, it provides a novel, alternative approach to trapped-charge dating based on direct, non-destructive probing of chronometric information. The possibility of repeated readout of IRPL from individual traps will open opportunities for dating at sub-micron spatial resolution, thus, marking a step change in the optical dating technology.
Modelling compartmentalization towards elucidation and engineering of spatial organization in biochemical pathways
Authors: Menon Govind , Okeke Chinedu , Krishnan J. 
Published: September 2017

AbstractCompartmentalization is a fundamental ingredient, central to the functioning of biological systems at multiple levels. At the cellular level, compartmentalization is a key aspect of the functioning of biochemical pathways and an important element used in evolution. It is also being exploited in multiple contexts in synthetic biology. Accurate understanding of the role of compartments and designing compartmentalized systems needs reliable modelling/systems frameworks. We examine a series of building blocks of signalling and metabolic pathways with compartmental organization. We systematically analyze when compartmental ODE models can be used in these contexts, by comparing these models with detailed reaction-transport models, and establishing a correspondence between the two. We build on this to examine additional complexities associated with these pathways, and also examine sample problems in the engineering of these pathways. Our results indicate under which conditions compartmental models can and cannot be used, why this is the case, and what augmentations are needed to make them reliable and predictive. We also uncover other hidden consequences of employing compartmental models in these contexts. Or results contribute a number of insights relevant to the modelling, elucidation, and engineering of biochemical pathways with compartmentalization, at the core of systems and synthetic biology.
Population resequencing of European mitochondrial genomes highlights sex-bias in Bronze Age demographic expansions
Authors: Batini Chiara , Hallast Pille , Vågene Åshild J. , Zadik Daniel , Eriksen Heidi A. , Pamjav Horolma , Sajantila Antti , Wetton Jon H. , Jobling Mark A. 
Published: September 2017

AbstractInterpretations of genetic data concerning the prehistory of Europe have long been a subject of great debate, but increasing amounts of ancient and modern DNA data are now providing new and more informative evidence. Y-chromosome resequencing studies in Europe have highlighted the prevalence of recent expansions of male lineages, and focused interest on the Bronze Age as a period of cultural and demographic change. These findings contrast with phylogeographic studies based on mitochondrial DNA (mtDNA), which have been interpreted as supporting expansions from glacial refugia. Here we have undertaken a population-based resequencing of complete mitochondrial genomes in Europe and the Middle East, in 340 samples from 17 populations for which Y-chromosome sequence data are also available. Demographic reconstructions show no signal of Bronze Age expansion, but evidence of Paleolithic expansions in all populations except the Saami, and with an absence of detectable geographical pattern. In agreement with previous inference from modern and ancient DNA data, the unbiased comparison between the mtDNA and Y-chromosome population datasets emphasizes the sex-biased nature of recent demographic transitions in Europe.
Functional neural networks of honesty and dishonesty in children: Evidence from graph theory analysis
Authors: Ding Xiao Pan , Wu Si Jia , Liu Jiangang , Fu Genyue , Lee Kang 
Published: September 2017

AbstractThe present study examined how different brain regions interact with each other during spontaneous honest vs. dishonest communication. More specifically, we took a complex network approach based on the graph-theory to analyze neural response data when children are spontaneously engaged in honest or dishonest acts. Fifty-nine right-handed children between 7 and 12 years of age participated in the study. They lied or told the truth out of their own volition. We found that lying decreased both the global and local efficiencies of children’s functional neural network. This finding, for the first time, suggests that lying disrupts the efficiency of children’s cortical network functioning. Further, it suggests that the graph theory based network analysis is a viable approach to study the neural development of deception.
Electrophysiological Studies in Thyroid Associated Orbitopathy: A Systematic Review
Authors: Iao Tiara W. U. , Rong Shi Song , Ling An Ni , Brelén Mårten E. , Young Alvin Lerrmann , Chong Kelvin K. L. 
Published: September 2017

AbstractDysthyroid optic neuropathy (DON) is the commonest cause of blindness in thyroid associated orbitopathy (TAO). While diagnosis remains clinical, objective tests for eyes with early or equivocal findings are lacking. Various electrophysiological studies (EPS) have been reported, yet the types and parameters useful for DON remain inconclusive. We performed a systematic literature search in MEDLINE, EMBASE and the Cochrane databases via the OVID platform up to August 20, 2017. 437 records were identified for screening and 16 original studies (1327 eyes, 787 patients) were eligible for review. Pattern visual evoked potential (pVEP) was the most frequently studied EPS. Eyes of TAO patients with DON showed delayed P100 latencies, decreased P100 amplitudes or delayed N75 latencies during pVEP, compared to those without or healthy controls. Due to study heterogeneity, no quantitative analysis was possible. This review highlights the most common type (pVEP) and useful parameters (P100 latency and amplitude) of EPS, and supports further research on them using standardized testing conditions.
Whole genome sequencing, molecular typing and in vivo virulence of OXA-48-producing Escherichia coli isolates including ST131 H30-Rx, H22 and H41 subclones
Authors: de Toro María , Fernández Javier , García Vanesa , Mora Azucena , Blanco Jorge , de la Cruz Fernando , Rodicio M. Rosario 
Published: September 2017

AbstractCarbapenem-resistant Enterobacteriaceae, including the increasingly reported OXA-48 Escherichia coli producers, are an emerging public health threat worldwide. Due to their alarming detection in our healthcare setting and their possible presence in the community, seven OXA-48-producing, extraintestinal pathogenic E. coli were analysed by whole genome sequencing as well as conventional tools, and tested for in vivo virulence. As a result, five E. coli OXA-48-producing subclones were detected (O25:H4-ST131/PST43-fimH30-virotype E; O25:H4-ST131/PST9-fimH22-virotype D5, O16:H5-ST131/PST506-fimH41; O25:H5-ST83/PST207 and O9:H25-ST58/PST24). Four ST131 and one ST83 isolates satisfied the ExPEC status, and all except the O16:H5 ST131 isolate were UPEC. All isolates exhibited local inflammatory response with extensive subcutaneous necrosis but low lethality when tested in a mouse sepsis model. The blaOXA-48 gene was located in MOBP131/IncL plasmids (four isolates) or within the chromosome (three ST131 H30-Rx isolates), carried by Tn1999-like elements. All, except the ST83 isolate, were multidrug-resistant, with additional plasmids acting as vehicles for the spread of various resistance genes. This is the first study to analyse the whole genome sequences of blaOXA-48-positive ST131, ST58 and ST83 E. coli isolates in conjunction with experimental data, and to evaluate the in vivo virulence of blaOXA-48 isolates, which pose an important challenge to patient management.
Resilience of the larval slipper limpet Crepidula onyx to direct and indirect-diet effects of ocean acidification
Authors: Maboloc Elizaldy A. , Chan Kit Yu Karen 
Published: September 2017

AbstractOcean acidification (OA) is known to directly impact larval physiology and development of many marine organisms. OA also affects the nutritional quality and palatability of algae, which are principal food sources for many types of planktonic larvae. This potential indirect effect of OA via trophic interactions, however, has not been fully explored. In this study, veligers of Crepidula onyx were exposed to different pH levels representing the ambient (as control) and low pH values (pH 7.7 and pH 7.3) for 14 days, and were fed with Isochrysis galbana cultured at these three respective pHs. pH, diet, nor their interactions had no effect on larval mortality. Decrease in pH alone had a significant effect on growth rate and shell size. Structural changes (increased porosity) in larval shells were also observed in the low pH treatments. Interactions between acidification and reduced diet quality promoted earlier settlement. Unlike other calcifying molluscs, this population of slipper limpets introduced to Hong Kong in 1960s appeared to be resilient to OA and decreased algal nutritional value. If this robustness observed in the laboratory applies to the field, competition with native invertebrates may intensify and this non-native snail could flourish in acidified coastal ecosystems.
Trap diversity and character evolution in carnivorous bladderworts (Utricularia, Lentibulariaceae)
Authors: Westermeier Anna Sofia , Fleischmann Andreas , Müller Kai , Schäferhoff Bastian , Rubach Carmen , Speck Thomas , Poppinga Simon 
Published: September 2017

AbstractBladderworts (Utricularia, Lentibulariaceae, Lamiales) constitute the largest genus of carnivorous plants but only aquatic species (about one fifth of the genus) have so far been thoroughly studied as to their suction trap functioning. In this study, we comparatively investigated trap biomechanics in 19 Utricularia species to examine correlations between life-forms, trapping mechanisms, and functional-morphological traits. Our investigations show the existence of two functional trap principles (passive trap in U. multifida vs. active suction traps), and – in active suction traps – three main trapdoor movement types (with several subtypes). The trapdoor movement types and their corresponding functional-morphological features most presumably represent adaptations to the respective habitat. We furthermore give insights into fluid dynamics during suction in three representatives of the main types of trapdoor movement. The results on functional morphology and trapdoor movement were mapped onto a new phylogenetic reconstruction of the genus, derived from the rapidly evolving chloroplast regions trnK, rps16 and trnQ-rps16 and a sampling of 105 Utricularia species in total. We discuss potential scenarios of trap character evolution and species radiation, highlighting possible key innovations that enable such a unique carni﻿vorous lifestyle in different habitats.
Polarization-entangled photon generation using partial spatially coherent pump beam
Authors: Ismail Yaseera , Joshi Stuti , Petruccione Francesco 
Published: September 2017

AbstractThe generation of two photon fields, to date, has been demonstrated utilizing a fully coherent pump beam. In this paper we demonstrate, the theoretical and experimental generation of polarization entangled single photon pairs by varying the spatial coherence of the pump beam. The effect of the pump beam spatial coherence on the visibility of a polarization-entangled single photon source is investigated. A comparison of the visibility measurements using a fully coherent and partially coherent pump beam is performed. It is shown that the partial coherence of the pump beam contributes to an increase in the visibility. The coherence properties of the beam are significant for free-space optical transmission in particular for long range free-space quantum communication.
Process signatures in glatiramer acetate synthesis: structural and functional relationships
Authors: Campos-García Víctor R. , Herrera-Fernández Daniel , Espinosa-de la Garza Carlos E. , González German , Vallejo-Castillo Luis , Avila Sandra , Muñoz-García Leslie , Medina-Rivero Emilio , Pérez Néstor O. , Gracia-Mora Isabel , Pérez-Tapia Sonia Mayra , Salazar-Ceballos Rodolfo , Pavón Lenin , Flores-Ortiz Luis F. 
Published: September 2017

AbstractGlatiramer Acetate (GA) is an immunomodulatory medicine approved for the treatment of multiple sclerosis, whose mechanisms of action are yet to be fully elucidated. GA is comprised of a complex mixture of polypeptides with different amino acid sequences and structures. The lack of sensible information about physicochemical characteristics of GA has contributed to its comprehensiveness complexity. Consequently, an unambiguous determination of distinctive attributes that define GA is of highest relevance towards dissecting its identity. Herein we conducted a study of characteristic GA heterogeneities throughout its manufacturing process (process signatures), revealing a strong impact of critical process parameters (CPPs) on the reactivity of amino acid precursors; reaction initiation and polymerization velocities; and peptide solubility, susceptibility to hydrolysis, and size-exclusion properties. Further, distinctive GA heterogeneities were correlated to defined immunological and toxicological profiles, revealing that GA possesses a unique repertoire of active constituents (epitopes) responsible of its immunological responses, whose modification lead to altered profiles. This novel approach established CPPs influence on intact GA peptide mixture, whose physicochemical identity cannot longer rely on reduced properties (based on complete or partial GA degradation), providing advanced knowledge on GA structural and functional relationships to ensure a consistent manufacturing of safe and effective products.
Differentially expressed genes and canonical pathways in the ascending thoracic aortic aneurysm – The Tampere Vascular Study
Authors: Sulkava Miska , Raitoharju Emma , Mennander Ari , Levula Mari , Seppälä Ilkka , Lyytikäinen Leo-Pekka , Järvinen Otso , Illig Thomas , Klopp Norman , Mononen Nina , Laaksonen Reijo , Kähönen Mika , Oksala Niku , Lehtimäki Terho 
Published: September 2017

AbstractAscending thoracic aortic aneurysm (ATAA) is a multifactorial disease with a strong inflammatory component. Surgery is often required to prevent aortic rupture and dissection. We performed gene expression analysis (Illumina HumanHT-12 version 3 Expression BeadChip) for 32 samples from ATAA (26 without/6 with dissection), and 28 left internal thoracic arteries (controls) collected in Tampere Vascular study. We compared expression profiles and conducted pathway analysis using Ingenuity Pathway Analysis (IPA) to reveal differences between ATAA and a healthy artery wall. Almost 5000 genes were differentially expressed in ATAA samples compared to controls. The most downregulated gene was homeobox (HOX) A5 (fold change, FC = −25.3) and upregulated cadherin-2 (FC = 12.6). Several other HOX genes were also found downregulated (FCs between -25.3 and -1.5, FDR < 0.05). 43, mostly inflammatory, canonical pathways in ATAA were found to be significantly (p < 0.05, FDR < 0.05) differentially expressed. The results remained essentially the same when the 6 dissected ATAA samples were excluded from the analysis. We show for the first time on genome level that ATAA is an inflammatory process, revealing a more detailed molecular pathway level pathogenesis. We propose HOX genes as potentially important players in maintaining aortic integrity, altered expression of which might be important in the pathobiology of ATAA.