bluuebunny/crossref_metadata_2025_split huggingface dataset:
Guidance of zoospores by potassium gradient sensing mediates aggregation
Authors: Galiana Eric , Cohen Celine , Thomen Philippe , Etienne Catherine , Noblin Xavier 
Published: November 2018

ABSTRACTBiflagellate zoospores of some phytopathogenic Phytophthora species spontaneously aggregate within few minutes in suspension. Depending on species auto-aggregate formation results from bioconvection or from a sequence bioconvection-positive chemotaxis. In this study, we show that P. parasitica zoospores may form aggregates upon application of a K+ gradient in particular geometric arrangements. Based on the use of macro- and microfluidic devices, in addition to time-lapse live imaging both in the vertical and horizontal planes, we defined (i) the spatiotemporal and concentration scale evolution within the gradient in correlation with (ii) cell distribution and (iii) metrics of zoospore motion (velocity, trajectory). The results indicated that K+-induced aggregates result from a single bi-phasic temporal sequence involving negative chemotaxis and then bioconvection in a K+ gradient concentration scale [0-17 mM]. Each K+-sensing cell undergoes a forward-to-backward movement within a threshold range of 1-4mM, thereby forming progressively a swarm. Once a critical population density is achieved zoospores form a plume which undergoes a downward migration leading to aggregate formation on the support surface. We discuss putative sources for K+ gradient generation in natural environment (zoospore population, microbiota, plant roots, soil particles), and implication for events preceding inoculum formation on host plant.
Plant Growth-Promoting Activity of Beta-Propeller Protein YxaL Secreted from Bacillus velezensis Strain GH1-13
Authors: Kim Yong-Hak , Choi Yunhee , Oh Yu Yeong , Ha Nam-Chul , Song Jaekyeong 
Published: November 2018

AbstractYxaL is conserved within Bacillus subtilis species complex associated with plant and soil. The mature protein YxaL contains a repeated beta-propeller domain, but the subcellular location and function of YxaL has not been determined. The gene encoding the mature YxaL protein was PCR amplified from genomic DNA of B. velezensis strain GH1-13 and used for recombinant protein production. A rabbit polyclonal antibody against the purified YxaL was generated and used for western blotting to determine the constitutive expression and secretion of YxaL, which exhibited a half-life of 1.6 h in the culture medium of strain GH1-13. In this study, we show that seed treatments of Arabidopsis thaliana and rice (Oryza sativa L) with less than 1 mg L−1 of purified YxaL in a soaking solution were effective at improving the root growth of plants. The seedlings of the treated Arabidopsis seeds markedly increased transcription of a 1-aminocyclopropane-1-carboxylate synthetase marker gene (ACS 11) but reduced expression of auxin-and abscisic acid-responsive marker genes (IAA1, GH3.3, and ABF4), especially when provided exogenous auxin. The horticulture experiments showed that pepper (Capsicum annum) seeds treated with 1 mg L−1 YxaL in soaking solution increased shoot growth and improved tolerance to drought stress. We hypothesize that YxaL secreted from plant growth-promoting Bacillus cells has a significant impact on plant roots, with the potential of improving plant growth and tolerance against stress.
Effects of High Copper Exposure on Development and Survival During Early Ontogenesis in the Common Toad
Authors: Dmitrieva ElenaV. 
Published: November 2018

ABSTRACTExposure to environmental pollutants contributes to the global decline of amphibians. Amphibian embryos are unique models for studying the effects of various toxic agents on developmental processes. Some of the most detrimental toxic agents are heavy metals, the study of which is a priority in ecotoxicology. Copper is a microelement required in many biological systems, but it can be toxic at concentrations higher than normal physiological range. The purpose of the present study was to analyze the toxic effect of high concentrations of Cu (10, 25, and 50 mg/L) on Bufo bufo embryos. The present study shows that short-term (48 h) toxicity test can fail to register toxicological effect of Cu, whereas long-term toxicity test demonstrates that all analyzed concentrations are lethal to common toad embryos. Early stages of development (stages 4-8, Gosner 1960) are shown to be rather tolerant to copper, even at high concentrations. Effects of copper begin to manifest themselves at the blastula stage (stages 8-9, Gosner, 1960). The present study also shows that initial egg density affects copper-related mortality rate of embryos. If egg density is high, copper-related mortality rate is sometimes decreased, possibly because jelly coats of eggs bind great amounts of dissolved copper. It is also shown that clutches can differ in sensitivity to different copper concentrations. Taken together, our data demonstrate that the conditions of the experiment (such as the initial egg density) and individual sensitivity of clutches to the toxic agent considerably contribute to the results of the ecotoxicological experiment.
Title: Unravelling associations between tree-seedling performance, herbivory, competition, and facilitation in high nature value farmlands
Authors: Vaz Pedro G. , Bugalho Miguel N. , Fedriani José M. , Branco Manuela , Lecomte Xavier , Nogueira Carla , Caldeira Maria C. 
Published: November 2018

AbstractHerbivory, plant facilitation, and competition have complex impacts on tree regeneration which are seldom investigated together. Grazing exclosure experiments have allowed to quantify the effects of large herbivores on tree regeneration dynamics but have often ignored the effect of herbivorous insects. We experimentally tested how folivory (percentage of leaf damaged by insects), and microenvironment (tree-canopy cover and herbs) jointly alter performance (growth and survival) of seedlings of two dominant Mediterranean oak-species within ungulate exclosures. An agroforestry system dominated by cork oak (Quercus suber) and holm oak (Q. rotundifolia) was assessed in south-east Portugal. We aimed also to determine whether the two oak-species differ in the interdependences between folivory, microenvironment, covaring factors, and seedling performance. Unexpectedly, under the low–moderate insect defoliation occurred in our 3-year field study, growth and survival of cork and holm oak-seedlings were positively associated with herbivory damage. Herb removal increased oak folivory by 1.4 times. Herb removal was also positively associated with growth, directly and indirectly through its negative effect on oak folivory. Tree-canopy favored insect folivory upon cork oak seedlings directly and upon holm oak indirectly via decreasing light availability. Folivory was threefold greater upon cork than upon holm oak-seedlings. Our study shows that tree-canopy, herbs, and covarying factors can affect cork and holm oak-seedling performances through complex pathways, which markedly differ for the two species. The combined effect of insect herbivory and positive and negative plant-plant interactions need to be integrated into future tree regeneration efforts toward tackling the regeneration crisis of oak agroforestry systems of the Mediterranean.
How predictive can be predictions in the neurocognitive processing of auditory and audiovisual speech? A deep learning study
Authors: Hueber Thomas , Tatulli Eric , Girin Laurent , Schwartz Jean-luc 
Published: November 2018

AbstractSensory processing is increasingly conceived in a predictive framework in which neurons would constantly process the error signal resulting from the comparison of expected and observed stimuli. Surprisingly, few data exist on the amount of predictions that can be computed in real sensory scenes. Here, we focus on the sensory processing of auditory and audiovisual speech. We propose a set of computational models based on artificial neural networks (mixing deep feed-forward and convolutional networks) which are trained to predict future audio observations from 25 ms to 250 ms past audio or audiovisual observations (i.e. including lip movements). Experiments are conducted on the multispeaker NTCD-TIMIT audiovisual speech database. Predictions are efficient in a short temporal range (25-50 ms), predicting 40 to 60 % of the variance of the incoming stimulus, which could result in potentially saving up to 2/3 of the processing power. Then they quickly decrease to vanish after 100 ms. Adding information on the lips slightly improves predictions, with a 5 to 10 % increase in explained variance.Interestingly the visual gain vanishes more slowly, and the gain is maximum for a delay of 75 ms between image and predicted sound.
Inducible Lung Epithelial Resistance Requires Multisource Reactive Oxygen Species Generation to Protect against Bacterial Infections
Authors: Ware Hayden H. , Kulkarni Vikram V. , Wang Yongxing , Juarez Miguel Leiva , Kirkpatrick Carson T. , García Jezreel Pantaleón , Wali Shradha , Sikkema William K. A. , Tour James M. , Evans Scott E. 
Published: November 2018

ABSTRACTPneumonia remains a global health threat, in part due to expanding categories of susceptible individuals and increasing prevalence of antibiotic resistant pathogens. However, therapeutic stimulation of the lungs’ mucosal defenses by inhaled exposure to a synergistic combination of Toll-like receptor (TLR) agonists known as Pam2-ODN promotes mouse survival of pneumonia caused by a wide array of pathogens. This inducible resistance to pneumonia relies on intact lung epithelial TLR signaling, and inducible protection against viral pathogens has recently been shown to require increased production of epithelial reactive oxygen species (ROS) from multiple epithelial ROS generators. To determine whether similar mechanisms contribute to inducible antibacterial responses, the current work investigates the role of ROS in therapeutically-stimulated protection against Pseudomonas aerugnosa challenges. Inhaled Pam2-ODN treatment one day before infection prevented hemorrhagic lung cytotoxicity and mouse death in a manner that correlated with reduction in bacterial burden. The bacterial killing effect of Pam2-ODN was recapitulated in isolated mouse and human lung epithelial cells, and the protection correlated with inducible epithelial generation of ROS. Scavenging or targeted blockade of ROS production from either dual oxidase or mitochondrial sources resulted in near complete loss of Pam2-ODN-induced bacterial killing, whereas deficiency of induced antimicrobial peptides had little effect. These findings support a central role for multisource epithelial ROS in inducible resistance against bacterial pathogens and provide mechanistic insights into means to protect vulnerable patients against lethal infections.
Genome-wide association studies for yield-related traits in soft red winter wheat grown in Virginia
Authors: Ward Brian P. , Brown-Guedira Gina , Kolb Frederic L. , Van Sanford David A. , Tyagi Priyanka , Sneller Clay H. , Griffey Carl A. 
Published: November 2018

AbstractGrain yield is a trait of paramount importance in the breeding of all cereals. In wheat (Triticum aestivumL.), yield has steadily increased since the Green Revolution, though the current rate of increase is not forecasted to keep pace with demand due to growing world population and affluence. While several genome-wide association studies (GWAS) on yield and related component traits have been performed in wheat, the previous lack of a reference genome has made comparisons between studies difficult. In this study, a GWAS for yield and yield-related traits was carried out on a population of 324 soft red winter wheat lines across a total of four rain-fed environments in the state of Virginia using single-nucleotide polymorphism (SNP) marker data generated by a genotyping-by-sequencing (GBS) protocol. Two separate mixed linear models were used to identify significant marker-trait associations (MTAs). The first was a single-locus model utilizing a leave-one-chromosome-out approach to estimating kinship. The second was a sub-setting kinship multi-locus method (FarmCPU). The single-locus model identified nine significant MTAs for various yield-related traits, while the FarmCPU model identified 74 significant MTAs. The availability of the wheat reference genome allowed for the description of MTAs in terms of both genetic and physical positions, and enabled more extensive post-GWAS characterization of significant MTAs. The results indicate promising avenues for increasing grain yield by exploiting variation in traits relating to the number of grains per unit area, as well as phenological traits influencing grain-filling duration of genotypes.
Radtools: R utilities for smooth navigation of medical image data
Authors: Russell Pamela H , Ghosh Debashis 
Published: November 2018

AbstractThe radiology community has adopted several widely used standards for medical image files, including the popular DICOM (Digital Imaging and Communication in Medicine) and NIfTI (Neuroimaging Informatics Technology Initiative) standards. These file formats include image intensities as well as potentially extensive metadata. The NIfTI standard specifies a particular set of header fields describing the image and minimal information about the scan. DICOM headers can include any of over 4,000 available metadata attributes spanning a variety of topics. NIfTI files contain all slices for an image series, while DICOM files capture single slices and image series are typically organized into a directory. Each DICOM file contains metadata for the image series as well as the individual image slice.The programming environment R is popular for data analysis due to its free and open code, active ecosystem of tools and users, and excellent system of contributed packages. Currently, many published radiological image analyses are performed with proprietary software or custom unpublished scripts. However, R is increasing in popularity in this area due to several packages for processing and analysis of image files. While these R packages handle image import and processing, no existing package makes image metadata conveniently accessible. Extracting image metadata, combining across slices, and converting to useful formats can be prohibitively cumbersome, especially for DICOM files.We present radtools, an R package for smooth navigation of medical image data. Radtools makes the problem of extracting image metadata trivially simple, providing simple functions to explore and return information in familiar R data structures. Radtools also facilitates extraction of image data and viewing of image slices. The package is freely available under the MIT license at https://github.com/pamelarussell/radtools and is easily installable from the Comprehensive R Archive Network (https://cran.r-project.org/package=radtools).
Validation of a Miniaturized Permeability Assay Compatible with CRISPR-Mediated Genome-Wide Screen
Authors: Simonneau Claire , Yang Junning , Kong Xianguo , Kilker Robert , Edelstein Leonard , Fortina Paolo , Londin Eric , Horowitz Arie 
Published: November 2018

ABSTRACTThe impermeability of the luminal endothelial cell monolayer is crucial for the normal performance of the vascular and lymphatic systems. A key to this function is the integrity of the monolayer’s intercellular junctions. The known repertoire of junction-regulating genes is incomplete. Current permeability assays are incompatible with high-throughput genome-wide screens that could identify these genes. To overcome these limitations, we designed a new permeability assay that consists of cell monolayers grown on ∼150 μm microcarriers. Each microcarrier functions as a miniature individual assay of permeability (MAP). We demonstrate that false-positive results can be minimized, and that MAP sensitivity to thrombin-induced increase in monolayer permeability is similar to the sensitivity of the measurement of impedance. We validate the assay by showing that the expression of single guide RNAs (sgRNAs) that target genes encoding known thrombin signaling proteins blocks effectively thrombin-induced junction disassembly, and that MAPs carrying such cells can be separated effectively by a fluorescent probe from those that carry cells expressing non-targeting sgRNAs. These results indicate that MAPs are suitable for high-throughput experimentation and for genome-wide screens for genes that mediate the disruptive effect of thrombin on endothelial cell junctions.
Maternally inherited differences within mitochondrial Complex I control murine healthspan
Authors: Hirose Misa , Schilf Paul , Zarse Kim , Busch Hauke , Füllen Georg , Jöhren Olaf , Köhling Rüdiger , König Inke R , Richer Barbara , Rupp Jan , Schwaninger Markus , Seeger Karsten , Sina Christian , Ristow Michael , Ibrahim Saleh M 
Published: November 2018

AbstractMitochondrial complex I, the largest enzyme complex of the mitochondrial oxidative phosphorylation machinery, has been proposed to contribute to a variety of age-related pathological alterations as well as longevity. The enzyme complex-consisting proteins are encoded by both nuclear (nDNA) and mitochondrial DNA (mtDNA). While some association studies of mtDNA-encoded complex I genes and lifespan in humans have been reported, experimental evidence and the functional consequence of such variants is limited to studies using invertebrate models. Here, we present experimental evidence that a homoplasmic mutation in the mitochondrially encoded complex I gene mt-Nd2 modulates lifespan by altering cellular tryptophan levels and, consequently, ageing-related pathways in mice. A conplastic mouse strain carrying a mutation at m.4738C>A in mt-Nd2 lived significantly shorter than the controls did. The same mutation led to a higher susceptibility to glucose intolerance induced by high-fat diet feeding. These phenotypes were not observed in mice carrying a mutation in another mtDNA-encoded complex I gene, mt-Nd5, suggesting the functional relevance of particular mutations in complex I to ageing and age-related diseases.
Laboratory Methods Supporting Measles surveillance in Queensland, Australia, 2010 – 2017
Authors: McMahon Jamie L. , Northill Judy , Finger Mitchell , Lyon Michael , Lambert Stephen B. , Mackay Ian M. 
Published: November 2018

ABSTRACTAustralia was officially recognised as having eliminated endemic measles circulation in 2014. Maintaining laboratory support for surveillance of vaccine-preventable diseases such as measles is an essential component of reaching and maintaining circulation-free status. Between 2010 and 2017 over 13,700 specimens were tested in our laboratory by real-time RT-PCR (RT-rPCR). Positive extracts from travellers were sequenced as required. Sequences were uploaded to GenBank and demonstrated the wide genetic variation expected from detection of MeV among virus introductions due to global travel. We describe the laboratory workflow employed in our laboratory between 2010 and 2017 for the sensitive detection of MeV infection, supporting high-quality surveillance.
C. elegansgranulins promote an age-associated decline in protein homeostasis via lysosomal protease inhibition
Authors: Butler Victoria J. , Cortopassi Wilian A. , Argouarch Andrea R. , Pierce M. Olivia , Vohra Mihir , Oses-Prieto Juan A. , Gao Fuying , Caballero Benjamin , Chand Shreya , Seeley William W. , Miller Bruce L. , Coppola Giovanni , Burlingame Alma L. , Ashrafi Kaveh , Cuervo Ana Maria , Jacobson Matthew P. , Kao Aimee W. 
Published: November 2018

AbstractThe progressive failure of protein homeostasis is a hallmark of aging and a common feature in neurodegenerative disease. As the enzymes executing the final stages of autophagy, lysosomal proteases (or cathepsins) are key contributors to maintenance of protein homeostasis with age. Here, we identify the cysteine-rich granulin peptides as a new class of regulators of lysosomal aspartyl protease activity. Granulins are produced in an age and stress-dependent manner through cleavage of the neurodegenerative disease protein, progranulin. Once liberated, granulins selectively interact with the aspartyl protease ASP-3/cathepsin D to impair enzymatic activity. Consequently, protein homeostasis and lysosome function is disrupted, prompting cells to activate a compensatory transcriptional program. Our results support a model in which granulin production modulates a critical transition between the normal, physiological regulation of protease activity and the impairment of lysosomal function that can occur with age and disease.
Development of three-dimensional articular cartilage construct using silica nano-patterned substrate
Authors: Park In-Su , Choi Ye Ji , Song Bo Ram , Kim Hyo-Sop , Park Sang-Hyug , Choi Byung Hyune , Kim Jae-Ho , Min Byoung-Hyun 
Published: November 2018

AbstractCurrent strategies for cartilage cell therapy are mostly based on the use of autologous chondrocytes or mesenchymal stem cells (MSCs). However, these cells have limitations of a small number of cells available and of low chondrogenic ability, respectively. Many studies now suggest that fetal stem cells are more plastic than adult stem cells and can therefore more efficiently differentiate into target tissues. This study introduces, efficiency chondrogenic differentiation of fetal cartilage-derived progenitor cells (FCPCs) to adult cells can be achieved using a three-dimensional (3D) spheroid culture method based on silica nanopatterning techniques. In evaluating the issue of silica nano-particle size (Diameter of 300, 750, 1200 nm), each particle size was coated into the well of a 6-well tissue culture plate. FCPCs (2 x 105 cells/well in 6-well plate) were seeded in each well with chondrogenic medium. In this studys, the 300 nm substrate that formed multi-spheroids and the 1200 nm substrate that showed spreading were due to the cell-cell adhesion force(via N-cadherin) and cell-substrate(via Integrin) force, the 750 nm substrate that formed the mass-aggregation can be interpreted as the result of cell monolayer formation through cell-substrate force followed by cell-cell contact force contraction. We conclude that our 3D spheroid culture system contributes to an optimization for efficient differentiation of FCPC, offers insight into the mechanism of efficient differentiation of engineered 3D culture system, and has promise for wide applications in regeneration medicine and drug discovery fields.