bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbial composition of enigmatic bird parasites:WolbachiaandSpiroplasmaare the most important bacterial associates of quill mites (Acari: Syringophilidae)
Authors: Glowska Eliza , Filutowska Zuzanna K. , Dabert Miroslawa , Gerth Michael 
Published: July 2018

AbstractThe microbiome is an integral component of many animal species, potentially affecting behaviour, physiology, and other biological properties. Despite this importance, bacterial communities remain vastly understudied in many groups of invertebrates, including mites. Quill mites (Acariformes: Syringophilidae) are a poorly known group of permanent bird ectoparasites that occupy quills of feathers and feed on bird subcutaneous tissue and fluids. Most species have strongly female biased sex ratios and it was hypothesized that this is caused by endosymbiotic bacteria. Their peculiar lifestyle further makes them potential vectors for bird diseases. Previously,Anaplasma phagocytophilumand a high diversity ofWolbachiastrains were detected in quill mites via targeted PCR screens. Here, we use an unbiased 16S amplicon sequencing approach to determine other Bacteria that potentially impact quill mite biology.We performed 16S V4 amplicon sequencing of 126 quill mite individuals from eleven species parasitizing twelve bird species (four families) of passeriform birds. In addition toWolbachia, we foundSpiroplasmaas potential symbiont of quill mites. Interestingly, consistently highSpiroplasmatitres were only found in individuals of two mite species associated with finches of the genusCardfuelis, suggesting a history of horizontal transfers ofSpiroplasmavia the bird host. Furthermore, there was evidence forSpiroplasmanegatively affectingWolbachiatitres. We found no evidence for the previously reportedAnaplasmain quill mites, but detected the potential pathogensBrucellaandBartonellaat low abundances. Other amplicon sequence variants (ASVs) could be assigned to a diverse number of bacterial taxa, including several that were previously isolated from bird skin. We observed a relatively uniform distribution of these ASVs across mite taxa and bird hosts, i.e, there was a lack of host-specificity for most detected ASVs. Further, many frequently found ASVs were assigned to taxa that show a very broad distribution with no strong prior evidence for symbiotic association with animals. We interpret these findings as evidence for a scarcity or lack of resident microbial associates (other than inherited symbionts) in quill mites, or for abundances of these taxa below our detection threshold.
Social information impairs reward learning in depressive subjects: behavioral and computational characterization
Authors: Safra Lou , Chevallier Coralie , Palminteri Stefano 
Published: July 2018

AbstractDepression is characterized by a marked decrease in social interactions and blunted sensitivity to rewards. Surprisingly, despite the importance of social deficits in depression, non-social aspects have been disproportionally investigated. As a consequence, the cognitive mechanisms underlying atypical decision-making in social contexts in depression are poorly understood. In the present study, we investigate whether deficits in reward processing interact with the social context and how this interaction is affected by self-reported depression and anxiety symptoms. Two cohorts of subjects (discovery and replication sample:N= 50 each) took part in a task involving reward learning in a social context with different levels of social information (absent, partial and complete). Behavioral analyses revealed a specific detrimental effect of depressive symptoms – but not anxiety – on behavioral performance in the presence of social information, i.e. when participants were informed about the choices of another player. Model-based analyses further characterized the computational nature of this deficit as a negative audience effect, rather than a deficit in the way others’ choices and rewards are integrated in decision making. To conclude, our results shed light on the cognitive and computational mechanisms underlying the interaction between social cognition, reward learning and decision-making in depressive disorders.
Overlap graph-based generation of haplotigs for diploids and polyploids
Authors: Baaijens Jasmijn A. , Schönhuth Alexander 
Published: July 2018

AbstractHaplotype aware genome assembly plays an important role in genetics, medicine, and various other disciplines, yet generation of haplotype-resolved de novo assemblies remains a major challenge. Beyond distinguishing between errors and true sequential variants, one needs to assign the true variants to the different genome copies. Recent work has pointed out that the enormous quantities of traditional NGS read data have been greatly underexploited in terms of haplotig computation so far, which reflects that methodology for reference independent haplotig computation has not yet reached maturity. We present POLYTE (POLYploid genome fitTEr) as a new approach to de novo generation of haplotigs for diploid and polyploid genomes. Our method follows an iterative scheme where in each iteration reads or contigs are joined, based on their interplay in terms of an underlying haplotype-aware overlap graph. Along the iterations, contigs grow while preserving their haplotype identity. Benchmarking experiments on both real and simulated data demonstrate that POLYTE establishes new standards in terms of error-free reconstruction of haplotype-specific sequence. As a consequence, POLYTE outperforms state-of-the-art approaches in various relevant aspects, where advantages become particularly distinct in polyploid settings. POLYTE is freely available as part of the HaploConduct package at https://github.com/HaploConduct/HaploConduct, implemented in Python and C++.
Radial Glia cell infection byToxoplasma gondiidisrupts brain microvascular endothelial cell integrity
Authors: Adesse Daniel , Marcos Anne Caroline , Siqueira Michele , Cascabulho Cynthia M. , Waghabi Mariana C. , Barbosa Helene S. , Stipursky Joice 
Published: July 2018

ABSTRACTCongenital toxoplasmosis is a parasitic disease that occurs due vertical transmission of the protozoanToxoplasma gondii(T. gondii) during pregnancy. The parasite crosses the placental barrier and reaches the developing brain, infecting progenitor, glial, neuronal and vascular cell types. Although the role of Radial glia (RG) neural stem cells in the development of the brain vasculature has been recently investigated, the impact ofT. gondiiinfection in these events is not yet understood. Herein, we studied the role ofT. gondiiinfection on RG cell function and its interaction with endothelial cells. By infecting isolated RG cells withT. gondiitachyzoites, we observed reduced cell proliferation and neurogenesis without affecting gliogenesis levels. Conditioned medium (CM) from RG control cultures increased ZO-1 and β-catenin protein levels and organization on endothelial bEnd.3 cells membranes, which was completely impaired by CM from infected RG, resulting in decreased transendothelial electrical resistance (TEER). Cytokine Bead Array and ELISA assays revealed the presence of increased levels of the pro-inflammatory cytokine IL-6 and reduced levels of anti-inflammatory cytokine TGF-β1 in CM fromT.gondii-infected RG cells. Treatment with recombinant TGF-β1 concomitantly with CM from infected RG cultures led to restoration of ZO-1 staining in bEnd.3 cells. Our results suggest that infection of RG cells byT. gondiimodulate cytokine secretion, which might contribute to endothelial loss of barrier properties, thus leading to impairment of neurovascular interaction establishment.
Local adaptation of a dominant coastal tree to freshwater availability and solar radiation suggested by genomic and ecophysiological approaches
Authors: Cruz Mariana Vargas , Mori Gustavo Maruyama , Müller Caroline Signori , da Silva Carla Cristina , Oh Dong-Ha , Dassanayake Maheshi , Zucchi Maria Imaculada , Oliveira Rafael Silva , de Souza Anete Pereira 
Published: July 2018

AbstractLocal adaptation is often a product of environmental variations in the geographical space and has implications for biodiversity conservation. We investigated the role of latitudinal heterogeneity in climate on the organization of genetic and phenotypic variation in the dominant coastal tree,Avicennia schaueriana. In a common garden experiment, samples from an equatorial region, marked by rainy/dry seasons, accumulated less biomass, showed lower stomatal conductance and transpiration, narrower xylem vessels, smaller leaves and higher reflectance of long wavelengths (red light) on the stem epidermis, than samples from a subtropical region, marked by warm/cold seasons. Transcriptome differences identified between trees sampled under field conditions at equatorial and subtropical sites, were enriched in functional categories as responses to temperature, solar radiation, water deficit, photosynthesis and cell wall biosynthesis. The diversity based on thousands of SNP loci revealed a north-south genetic structure. Remarkably, signatures of selection were identified in loci associated with photosynthesis, anthocyanin accumulation and the responses to osmotic and hypoxia stresses. Our results suggest the existence of divergence in key resource-use characteristics, likely driven by climate seasonality, based on water-deficit and solar radiation. These findings provide a basis for conservation plans and for predictions for coastal plant responses to climate change.
Infectious bursal disease virus suppresses H9N2 avian influenza viral shedding in broiler chickens
Authors: Ranjbar Vahid Reza , Mohammadi Ali , Dadras Habibollah , Bidadkosh Arash 
Published: July 2018

AbstractInfectious bursal disease (Gumboro) virus causes immunosuppression in chickens, increasing their susceptibility to other viral and bacterial diseases and resulting in vaccination failure. In the present study, we investigated the immune-depressing effect of infectious bursal disease virus on H9N2 avian influenza viral infection in commercial broiler chickens. Chickens were divided into four groups. In group A, chickens were inoculated with Gumboro virus at 21 days of age and H9N2 influenza virus 5 days later. Groups B and C only received influenza virus at 26 days of age and Gumboro virus at 21 days, respectively. Chickens in the control group (D) were inoculated with normal saline at the same times.Tissue samples from different organs were collected on days 1, 3, 6, 9, and 12 after H9N2 infection. Macroscopic observation showed bursal disease lesions in groups A and C, including swollen bursa with the presence of gelatinous exudates, hemorrhages in the thigh muscle, edema, and nephritis.Reverse transcription polymerase chain reaction was used to study H9N2 influenza virus dissemination, and quantitative reverse transcription polymerase chain reaction to determine viral genome copy number in different organs. A considerable titer of avian influenza virus was found in the trachea, lungs, cecal tonsils, spleens, and feces of infected chickens. The genome copy number of the virus in the trachea and lungs of group A was significantly higher than that in group B on the first day after inoculation. However, our method did not detect the avian influenza virus genome in group A. In conclusion, we suggest that pre-exposure to Gumboro virus at 3 weeks of age reduces the replication and shedding of H9N2 in broiler chicken.
The permeabilized SecY protein-translocation channel can serve as a nonspecific sugar transporter
Authors: Mei Sen , Xie Chong , Mi Hao , Xue Chuang , Guo Qiang , Du Guang-Qing , Li Guo-Bei , Li Cai-Xia , Qu Ya-Nan , Xiong Ming-Hao , Jiang Yang , Tan Tian-Wei , Yang Shang-Tian , Fan Li-Hai 
Published: July 2018

AbstractAs the initial step in carbohydrate catabolism in cells, the substrate-specific transporters via active transport and facilitated diffusion play a decisive role in passage of sugars through the plasma membrane into the cytoplasm. The SecY complex (SecYEG) in bacteria forms a membrane channel responsible for protein translocation. This work demonstrates that weakening the sealability of the SecY channel allowed free diffusion of sugars, including glucose, fructose, mannose, xylose, arabinose, and lactose, into the engineered cells, facilitating its rapid growth on a wide spectrum of monosaccharides and bypassing/reducing stereospecificity, transport saturation, competitive inhibition, and carbon catabolite repression (CCR), which are usually encountered with the specific sugar transporters. The SecY channel is structurally conserved in prokaryotes, thus it may be engineered to serve as a unique and universal transporter for bacteria to passage sugars as demonstrated inEscherichia coliandClostridium acetobutylicum.
A novel enhancer RNA, Hmrhl, positively regulates its host gene,phkb,in Chronic Myelogenous Leukemia
Authors: Fatima Roshan , Choudhury Subhendu Roy , Divya T. R. , Bhaduri Utsa , Rao M. R. S. 
Published: July 2018

AbstractNoncoding RNAs are increasingly being accredited with key roles in gene regulation during development and disease. Here we report the discovery and characterization of a novel long noncoding RNA, Hmrhl, which shares synteny and partial sequence similarity with the mouse lncRNA, Mrhl. The human homolog, Hmrhl, transcribed from intron 14 ofphkbgene, is 5.5kb in size, expressed in all tissues examined and has acquired additional repeat elements. Analysis of Hmrhl locus using ENCODE database revealed that it is associated with hallmarks of enhancers like the open chromatin configuration, binding of transcription factors, enhancer specific histone signature etc. in the K562 Chronic Myelogenous Leukemia (CML) cells. We compared the expression of Hmrhl in the normal lymphoblast cell line, GM12878, with that of K562 cells and lymphoma samples and show that it is highly upregulated in leukemia as well as several cases of lymphoma. We validated the enhancer properties of Hmrhl locus in K562 cells with the help of Luciferase assay. Moreover, siRNA mediated down-regulation of Hmrhl in K562 cells leads to a concomitant down regulation of its parent gene,phkb, showing that Hmrhl functions as an enhancer RNA and positively regulates its host gene,phkb,in chronic myelogenous leukemia.
A Cytoplasmic GOLD Protein Controls Cell Polarity
Authors: Omnus Deike J. , Cadou Angela , Chung Gary H.C. , Bader Jakob M. , Stefan Christopher J. 
Published: July 2018

AbstractPhosphoinositide lipids provide spatial landmarks during polarized secretion. Here, we elucidate a role for phosphatidylinositol 4-phosphate (PI4P) metabolism in the control of cell polarity. In budding yeast, PI4P is enriched at the plasma membrane of growing daughter cells. Upon heat shock however, PI4P rapidly increases at the plasma membrane in mother cells resulting in a more uniform PI4P distribution. Rather than phosphoinositide kinase activation, PI4P hydrolysis is impaired to generate the heat-induced PI4P signal in mother cells. This fine tune control of PI4P metabolism is mediated through attenuation of the Osh3 protein that binds and presents PI4P to a phosphoinositide phosphatase. Importantly, Osh3 undergoes phase transitions upon environmental stress conditions, resulting in intracellular aggregates and reduced cortical localization. The chaperone Hsp104 co-assembles with intracellular Osh3 granules, but is not required for their formation. Interestingly, the Osh3 GOLD domain, also present in the ER-localized p24 cargo adaptor family, is sufficient to form stress granules. Accordingly, GOLD-mediated phase transitions may provide a general mechanism to modulate secretion and growth upon transient changes in physiological and environmental conditions.
Neurons of the inferior olive respond to broad classes of sensory input while subject to homeostatic control
Authors: Ju Chiheng , Bosman Laurens W.J. , Hoogland Tycho M. , Velauthapillai Arthiha , Murugesan Pavithra , Warnaar Pascal , van Genderen Romano M. , Negrello Mario , De Zeeuw Chris I. 
Published: July 2018

AbstractCerebellar Purkinje cells integrate sensory information with motor efference copies to adapt movements to behavioural and environmental requirements. They produce complex spikes that are triggered by the activity of climbing fibres originating in neurons of the inferior olive. These complex spikes can shape the onset, amplitude and direction of movements as well as the adaptation of such movements to sensory feedback. Clusters of nearby inferior olive neurons project to parasagittally aligned stripes of Purkinje cells, referred to as “microzones”. It is currently unclear to what extent individual Purkinje cells within a single microzone integrate climbing fibre inputs from multiple sources of different sensory origins, and to what extent sensory-evoked climbing fibre responses depend on the strength and recent history of activation. Here we imaged complex spike responses in cerebellar lobule crus 1 to various types of sensory stimulation in awake mice. We find that different sensory modalities and receptive fields have a mild, but consistent, tendency to converge on individual Purkinje cells. Purkinje cells encoding the same stimulus show increased events with coherent complex spike firing and tend to lie close together. Moreover, whereas complex spike firing is only mildly affected by variations in stimulus strength, it strongly depends on the recent history of climbing fibre activity. Our data point towards a mechanism in the olivo-cerebellar system that regulates complex spike firing during mono- or multisensory stimulation around a relatively low set-point, highlighting an integrative coding scheme of complex spike firing under homeostatic control.
Probing the Modularity of Megasynthases by Rational Engineering of a Fatty Acid Synthase (FAS) Type I
Authors: Rittner Alexander , Paithankar Karthik S. , Drexler David , Himmler Aaron , Grininger Martin 
Published: July 2018

AbstractModularity is an aspect of a decomposable system with a coordinating authority that acts as a glue which holds the loosely held components. These multi-component entities (“modules”) facilitate rewiring into different designs allowing for change. Such modular character is a fundamental property of many biological entities, especially the family of megasynthases such as polyketide synthases (PKSs). The ability of these PKSs to produce diverse product spectra is strongly coupled to their broad architectural modularity. Decoding the molecular basis of modularity, i.e. identifying the folds and domains that comprise the modules as well as understanding constrains of the assembly of modules, is of utmost importance for harnessing megasynthases for the synthesis of designer compounds. In this study, we exploit the close semblance between PKSs and animal FAS to re-engineer animal FAS to probe the modularity of the FAS/PKS family. Guided by structural and sequence information, we truncate and dissect animal FAS into its components, and reassemble them to generate new PKS-like modules as well as bimodular constructs. The novel engineered modules resemble all four common module types of PKSs and demonstrate that this approach can be a powerful tool to create higher catalytic efficiency. Our data exemplify the inherent plasticity and robustness of the overall FAS/PKS fold, and open new avenues to explore FAS-based biosynthetic pathways for custom compound design.
Signal propagation in metal-rich railway environment
Authors: Nikolic Bojana , Dimitrijevic Bojan , Hutschenreuther Tino , Toepfer Hannes 
Published: July 2018

Purpose
The purpose of this paper is to analyze a signal propagation in highly metalized environments, which has not been extensively studied in the literature. Having in mind a large number of such applications, better understanding and possibly finding a way of improving communication in these conditions would be highly beneficial.

Design/methodology/approach
The analysis is performed in a simulation environment developed by the authors, based on finite difference time domain (FDTD) method, to identify effects that have decisive influence on electromagnetic (EM) wave propagation in the aforementioned conditions. The analysis of the EM field at the reception is modified so that a multiple-field sampling is performed, and maximal values are further used. In practical realizations, this procedure could be implemented by using multiple antennas and selective combining at the reception.

Findings
Results show that the existence of metal objects (in the observed case, these are railway tracks), in combination with the appropriate choice of antenna parameters, can be favorably used to improve signal reception. The contribution is manifested through the reduction of the pathloss.

Research limitations/implications
In the performed analysis, one should be aware of the limitations that the FDTD method brings. Those limitations are related to the size of the computational domain and discretization mesh refinement (possibility of modeling geometry in fine details).

Originality/value
Originality of this paper consists of the introduced modification in the analysis of signal propagation in heavily metalized environment. Namely, a multiple-field sampling in the reception zone (in one plane, dimensions λ × λ = 12.5 cm X 12.5 cm) is performed using several probes in simulation environment. In this way, a qualitative analysis is performed more efficiently, which made it is possible to distinguish and identify different propagation mechanisms.
Radio spectrum regulation as a matter of international affairs: discussing the effectiveness of the European Union at World Radiocommunication Conferences
Authors: Massaro Maria 
Published: July 2018

PurposeThis paper aims to discuss the effectiveness of the European Union (EU) at World Radiocommunication Conferences (WRCs) by comparing EU objectives prior to and outcomes of recent WRCs.Design/methodology/approachA thematic analysis of qualitative data extracted from documents is conducted. The effectiveness of the EU is discussed by using the concepts of agenda-setting and coalition-building, borrowed from international relations literature.FindingsA clear conclusion on EU effectiveness could not be drawn based on the degree of match between EU objectives and WRC outcomes. Other factors need to be included in the analysis, such as relevance of the EU’s participation at WRCs to the EU member states and availability and allocation of EU resources to the various stages of the WRC process.Research limitations/implicationsFurther research is encouraged to investigate the role of the EU at WRCs. In particular, interviews with experts involved in the WRC process may help gather relevant information on EU relevance and EU resource availability and allocation.Originality/valueThis paper contributes to existing research on international radio spectrum regulation by drawing attention to the role of the EU as an international actor.