bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Alternative Bioassay forSynchytrium endobioticumDemonstrates the Expression of Potato Wart Resistance in Aboveground Plant Parts
Authors: van de Vossenberg B. T. L. H. , van Gent-Pelzer M. P. E. , Boerma M. , van der Gouw L. P. , van der Lee T. A. J. , Vossen J. H. 
Published: May 2019

The obligate biotrophic chytrid species Synchytrium endobioticum is the causal agent of potato wart disease. Currently, 39 pathotypes have been described based on their interaction with a differential set of potato varieties. Wart resistance and pathotyping is performed using bioassays in which etiolated tuber sprouts are inoculated. Here, we describe an alternative method in which aboveground plant parts are inoculated. Susceptible plants produced typical wart symptoms in developing but not in fully expanded aboveground organs. Colonization of the host by S. endobioticum was verified by screening for resting spores by microscopy and by molecular techniques using TaqMan polymerase chain reaction and RNAseq analysis. When applied to resistant plants, none of these symptoms were detectable. Recognition of S. endobioticum pathotypes by differentially resistant potato varieties was identical in axillary buds and the tuber-based bioassays. This suggests that S. endobioticum resistance genes are expressed in both etiolated “belowground” sprouts and green aboveground organs. RNAseq analysis demonstrated that the symptomatic aboveground materials contain less contaminants compared with resting spores extracted from tuber-based assays. This reduced microbial contamination in the aboveground bioassay could be an important advantage to study this obligate biotrophic plant–pathogen interaction. Because wart resistance is active in both below- and aboveground organs, the aboveground bioassay can potentially speed up screening for S. endobioticum resistance in potato breeding programs because it omits the requirement for tuber formation. In addition, possibilities arise to express S. endobioticum effectors in potato leaves through agroinfiltration, thereby providing additional phenotyping tools for research and breeding.[Formula: see text] Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
Dynamic Laser Speckle Imaging
Authors: Postnov Dmitry D. , Tang Jianbo , Erdener Sefik Evren , Kılıç Kıvılcım , Boas David A. 
Published: May 2019

ABSTRACTUtilizing a high-speed camera and recording back-scattered laser light at more than 20,000 frames per second, we introduce the first wide-field dynamic laser speckle imaging (DLSI) in which we are able to quantify the laser speckleintensity temporal auto-correlation function g2(τ) for every pixel individually to obtain a quantitative image of the dynamics of the light scattering particles in the sample. The ability to directly and quantitatively measure the intensity auto-correlation function allows us to solve the problem of how to quantitatively interpret data measured by laser speckle contrast imaging (LSCI), multi-exposure laser speckle imaging (MESI) and laser Doppler flowmetry (LDF). The intensity auto-correlation function is related to the field temporal auto-correlation function g1(τ), which has been quantitatively related to the dynamics of the light scattering particles including flowing red blood cells. The form of g1(τ) depends on the amount of light scattering (i.e. single or multiple scattering) and the type of particle motion (i.e. ordered or unordered). Although these forms of the field correlation functions have been established for over 30 years, there is no agreement nor experimental support on what scattering and motion regimes are relevant for the varied biomedical applications. We thus apply DLSI to image cerebral blood flow in mouse through a cranial window and show that the generally accepted form of g1(τ), is applicable only to visible surface vessels of a specific size (20 – 200μm). We demonstrate that for flow in smaller vessels and in parenchymal regions that the proper g1(τ) form corresponds with multiple scattering light and unordered motion which was never considered to be relevant for these techniques. We show that the wrong assumption for the field auto-correlation model results in a severe underestimation of flow changes when measuring blood flow changes during ischemic stroke. Finally, we describe how DLSI can be integrated with other laser speckle methods to guide model selection, or how it can be used by itself as a quantitative blood flow imaging technique.
Fishing for mammals: landscape-level monitoring of terrestrial and semi-aquatic communities using eDNA from lotic ecosystems
Authors: Guimarães Sales Naiara , McKenzie Maisie B. , Drake Joseph , Harper Lynsey R. , Browett Samuel S. , Coscia Ilaria , Wangensteen Owen S. , Baillie Charles , Bryce Emma , Dawson Deborah A. , Ochu Erinma , Hänfling Bernd , Handley Lori Lawson , Mariani Stefano , Lambin Xavier , Sutherland Christopher , McDevitt Allan D. 
Published: May 2019

AbstractEnvironmental DNA (eDNA) metabarcoding has revolutionised biomonitoring in both marine and freshwater ecosystems. However, for semi-aquatic and terrestrial animals, the application of this technique remains relatively untested.We first assess the efficiency of eDNA metabarcoding in detecting semi-aquatic and terrestrial mammals in natural lotic ecosystems in the UK by comparing sequence data recovered from water and sediment samples to the mammalian communities expected from historical data. Secondly, we evaluate the detection efficiency of eDNA samples compared to multiple conventional non-invasive survey methods (latrine surveys and camera trapping) using occupancy modelling.eDNA metabarcoding detected a large proportion of the expected mammalian community within each area. Common species in the areas were detected at the majority of sites. Several key species of conservation concern in the UK were detected by eDNA in areas where authenticated records do not currently exist, but potential false positives were also identified for several non-native species.Water-based eDNA samples provided comparable results to conventional survey methods in per unit of survey effort for three species (water vole, field vole, and red deer) using occupancy models. The comparison between survey ‘effort’ to reach a detection probability of ≥0.95 revealed that 3-6 water replicates would be equivalent to 3-5 latrine surveys and 5-30 weeks of single camera deployment, depending on the species.Synthesis and Applications. eDNA metabarcoding represents an extremely promising tool for monitoring mammals, allowing for the detection of multiple species simultaneously, and provides comparable results to widely-used conventional survey methods. eDNA from freshwater systems delivers a ‘terrestrial dividend’ by detecting both semi-aquatic and terrestrial mammalian communities, and provides a basis for future monitoring at a landscape level over larger spatial and temporal scales (i.e. long-term monitoring at national levels).
Rainfall as a significant contributing factor to butterfly seasonality along a climatic gradient in the neotropics
Authors: Checa María F. , Levy Elisa , Rodriguez Jaqueline , Willmott Keith 
Published: May 2019

AbstractWe analyzed the dynamics of multi-species butterfly communities along a climatic gradient with varying precipitation regimes for three consecutive years, and determine how climatic variables associate with observed butterfly seasonality. To provide a baseline for future studies of how climate change might affect these butterfly populations, we additionally explored the role of butterfly seasonality as a potential contributing factor for their susceptibility to climate variation. As far as we know, this represents the first study that simultaneously sampled and described seasonality patterns of tropical butterfly communities across ecosystems with varying climatic seasonality. A 3-year survey was carried out at three sites (i.e., wet, transition and dry forests) across a climatic gradient in western Ecuador. Butterflies were sampled using traps baited with rotting banana and prawn every two months from Nov 2010 to Sep 2013. Traps were set up at two heights, in the understory and canopy. In total, 7046 individuals of 212 species were sampled over 180 sampling days.Butterfly communities exhibited conspicuous intra and inter-annual variation in temporal dynamics with certain elements (e.g., maximum abundance recorded) of seasonality patterns likely synchronized in seasonal forests (i.e., transition and dry forest) across years but not in aseasonal forests (i.e., wet forest). In addition, the highest numbers of species and individuals occurred during the wet season across all study sites and years; indeed, rainfall was significantly positively associated with temporal abundance. Likewise, butterfly species displaying stronger seasonality were significantly associated with higher rainfall periods in seasonal forests. Variation in precipitation regimes might significantly affect more seasonal species.
Aggregation of nontuberculous mycobacteria is regulated by carbon:nitrogen balance
Authors: DePas William H. , Bergkessel Megan , Newman Dianne K. 
Published: May 2019

AbstractNontuberculous mycobacteria (NTM) are emerging opportunistic pathogens that form biofilms in environmental reservoirs such as household water systems and aggregate into phagocytosis-resistant clusters during infection. NTM constitutively aggregatein vitro, a phenotype typically considered to be a by-product of the mycolic-acid-rich cell wall. While culturing a model NTM,Mycobacterium smegmatis, in rich medium, we fortuitously discovered that planktonic cells accumulated in the culture after ∼3 days. By providing selective pressure for bacteria that disperse earlier, we isolated a strain with two mutations in the oligopeptide permease operon (opp). A mutant lacking theoppoperon (Δopp) dispersed earlier and more completely than wildtype (WT). We show that Δopp’s aggregation defect was nutrient related; aggregation was restored by non-peptide carbon sources. Experiments with WTM. smegmatisrevealed that growth as aggregates is favored when carbon is replete, while dispersal can be induced by carbon starvation. In addition, under conditions of low available carbon relative to available nitrogen,M. smegmatisgrows as planktonic cells. By adjusting carbon and nitrogen sources in defined medium, we tuned the cellular C:N ratio such thatM. smegmatisgrows either as aggregates or planktonic cells. Lastly, we tested the effect of C:N balance on aggregation in clinically relevant NTM. Altogether, we show that NTM aggregation is a controlled process that is regulated by the relative availability of carbon and nitrogen for metabolism. Because NTM aggregation is correlated with increased virulence, these results may contribute to targeted anti-biofilm therapeutics.ImportanceFree-living bacteria can assemble into multicellular aggregates called biofilms. Biofilms help bacteria tolerate multiple stresses, including antibiotics and the host immune system. Differing environmental pressures have resulted in biofilm architecture and regulation varying among bacterial species and strains. Nontuberculous mycobacteria are a group of emerging opportunistic pathogens that utilize biofilms to adhere to household plumbing and showerheads and to avoid phagocytosis by host immune cells. Mycobacteria harbor a unique cell wall built chiefly of long chain mycolic acids that confers hydrophobicity and has been thought to cause constitutive aggregation in liquid media. Here we show that aggregation is instead a regulated process dictated by the balance of available carbon and nitrogen. Understanding that mycobacteria utilize metabolic cues to regulate the transition between planktonic and aggregated cells reveals an inroad to controlling aggregation through targeted therapeutics.
Multi-resolution localization of causal variants across the genome
Authors: Sesia Matteo , Katsevich Eugene , Bates Stephen , Candès Emmanuel , Sabatti Chiara 
Published: May 2019

AbstractWe presentKnockoffZoom, a flexible method for the genetic mapping of complex traits at multiple resolutions.KnockoffZoomlocalizes causal variants by testing the conditional associations of genetic segments of decreasing width while provably controlling the false discovery rate using artificial genotypes as negative controls. Our method is equally valid for quantitative and binary phenotypes, making no assumptions about their genetic architectures. Instead, we rely on well-established genetic models of linkage disequilibrium. We demonstrate that our method can detect more associations than mixed effects models and achieve fine-mapping precision, at comparable computational cost. Lastly, we applyKnockoffZoomto data from 350k subjects in the UK Biobank and report many new findings.
CENP-A drives asymmetric cell division and maintains stem identity
Authors: Dattoli Anna A. , Carty Ben L. , Kochendoerfer Antje M. , Walshe Annie E. , Dunleavy Elaine M. 
Published: May 2019

SUMMARYCentromeres, chromosomal loci essential for genome integrity, are epigenetically defined by CENP-A-containing chromatin. Recent studies suggest that parental CENP-A is asymmetrically distributed upon stem cell asymmetric division. However, a direct link between centromeres and stem cell identity has not been demonstrated. We show thatDrosophilafemale germline stem cells (GSCs) and neuroblasts assemble centromeres between G2-phase and prophase, requiring CYCLIN A. Intriguingly, chromosomes that will be inherited by GSCs incorporate more CENP-A and capture more spindle fibers at pro-metaphase. Furthermore, over-expression of CAL1 (DrosophilaCENP-A assembly factor) causes GSC-like tumours, while over-expression of both CENP-A and CAL1 promotes stem cell self-renewal. Finally, once centromeres have been assembled in GSCs, continued CENP-A assembly is not required in differentiating cells outside of the niche and CAL1 becomes dispensable. According to our results CENP-A regulates stem cell identity/maintenance. Moreover, crucial centromere assembly occurs in the niche prior to oocyte meiosis.
Fluorescence assay for simultaneous quantification of CFTR ion-channel function and plasma membrane proximity
Authors: Prins Stella , Langron Emily , Hastings Cato , Hill Emily J. , Stefan Andra C. , Griffin Lewis D. , Vergani Paola 
Published: May 2019

AbstractCFTR, a plasma membrane anion channel, plays a key role in controlling transepithelial fluid movement. Excessive activation results in intestinal fluid loss during secretory diarrhoeas, while CFTR mutations underlie cystic fibrosis (CF). Anion permeability depends both on how well CFTR channels work (permeation/gating) and on how many are present at the membrane (reflecting folding, trafficking, metabolic stability). Recently, treatments with two drug classes targeting CFTR – one boosting ion-channel function (potentiators), the other increasing plasma membrane density (correctors) – have provided significant health benefits to CF patients.Here we present an image-based fluorescence assay that can rapidly and simultaneously estimate both CFTR ion-channel function and the protein’s proximity to the membrane. We monitor F508del-CFTR, the most common CF-causing variant, and confirm rescue by low temperature, CFTR-targeting drugs and second-site revertant mutation R1070W. In addition, we characterize a panel of 62 CF-causing mutations. Our measurements correlate well with published data (electrophysiology and biochemistry), further confirming validity of the assay.Finally, we profile effects of acute treatment with approved potentiator drug VX-770 on the rare-mutation panel. Mapping the potentiation profile on CFTR structures raises mechanistic hypotheses on drug action, suggesting that VX-770 might allow an open-channel conformation with an alternative arrangement of domain interfaces around site 1.The assay is a valuable tool for investigation of CFTR molecular mechanisms, allowing accurate inferences on gating/permeation. In addition, by providing a two-dimensional characterization of the CFTR protein, it could better inform development of single-drug and precision therapies addressing the root cause of CF disease.
Multiplex RNA single molecule FISH of inducible mRNAs in single yeast cells
Authors: Li Guoliang , Neuert Gregor 
Published: May 2019

AbstractTranscript levels powerfully influence cell behavior and phenotype and are carefully regulated at several steps. Recently developed single cell approaches such as RNA single molecule fluorescence in-situ hybridization (smFISH) have produced advances in our understanding of how these steps work within the cell. In comparison to single-cell sequencing, smFISH provides more accurate quantification of RNA levels. Additionally, transcript subcellular localization is directly visualized, enabling the analysis of transcription (initiation and elongation), RNA export and degradation. As part of our efforts to investigate how this type of analysis can generate improved models of gene expression, we used smFISH to quantify the kinetic expression of STL1 and CTT1 mRNAs in single Saccharomyces cerevisiae cells upon 0.2 and 0.4M NaCl osmotic stress. In this Data Descriptor, we outline our procedure along with our data in the form of raw images and processed mRNA counts. We discuss how these data can be used to develop single cell modelling approaches, to study fundamental processes in transcription regulation and develop single cell image processing approaches.
Daily rhythms in lactate metabolism in the medial prefrontal cortex of mouse: Effects of light and aging
Authors: Wallace Naomi K. , Pollard Felicity , Savenkova Marina , Karatsoreos Ilia N. 
Published: May 2019

AbstractAging is associated with reduced circadian (daily) rhythm amplitude in physiology and behavior, and decreased function of the prefrontal cortex (PFC). Similar effects are seen in younger mice experiencing circadian desynchrony (CD) caused by exposure to 20h light-dark cycles (T20). Given changes in PFC structure/function, underlying metabolic functioning of the PFC may also occur. We aimed to determine whether there are similarities in neurometabolism between Aged and CD mice. Using enzymatic amperometric biosensors, we recorded lactate concentration changes in the medial PFC in freely-behaving mice. Young mice displayed a circadian rhythm of lactate, which was severely blunted by CD, while Aging only changed the rhythm in constant conditions. We simultaneously probed the relationship between arousal state and PFC lactate rhythms, showing relationships between arousal state and lactate concentration, and documenting changes that occurred in CD and aging. Finally, using RT-qPCR, we found changes in genes related to metabolism and plasticity in both Aged and CD mice. Together, these data suggest both Aging and light cycle manipulation can disrupt mPFC neurometabolism.HighlightsLactate recordings were taken in Aged and circadian desynchronized (CD) mice.Lactate displayed a circadian rhythm in Control mice which was blunted in CD mice.The sleep state/lactate relationship was influenced by Aging, CD, and light.Both Aging and CD changed the expression of genes related to neurometabolism.
Phylogeography and Molecular Species Delimitation Reveal Cryptic and Incipient Speciation in Synchronous Flashing Fireflies (Coleoptera: Lampyridae) of Southeast Asia
Authors: Jusoh Wan F. A. , Ballantyne Lesley , Onn Chan Kin 
Published: May 2019

ABSTRACTSynchronous flashing fireflies of the genusPteroptyxare ubiquitous throughout Southeast Asia, yet, knowledge on its biodiversity and evolutionary history remains lacking. Recent studies have revealed notable population-level phylogeographic structure within theP. tenerandP. bearnigroups in Malaysia, suggesting that cryptic species may exist. Additionally, the close morphological and genetic affinity of the recently described speciesP. balingianatoP. malaccaehas raised questions about its validity. In this study, we assembled the most densely sampled genetic dataset onPteroptyxto-date to estimate a comprehensive phylogeny using mitochondrial and nuclear DNA and subsequently implemented a suite of distance-, phylogeny-, and coalescent-based species delimitation methods to characterize species boundaries within theP. tener,P. bearni, andP. balingiana/P. malaccaegroups. Using a total evidence approach from multiple lines of evidence, we showed that populations ofP. teneralong the west coast of Peninsular Malaysia are sufficiently divergent from populations from the east coast and Borneo to warrant specific recognition, despite the absence of morphological differentiation. Conversely, divergence ofP. bearnifrom Borneo and eastern Peninsular Malaysia, as well asP. balingianafromP. malaccaewere modest and their distinction as separate species were ambiguous; consistent with incipient species in the gray zone of speciation. Overall, this study contributes to the limited but growing body of genetic work on Southeast Asian fireflies and underscores the urgent need to increase the breadth and depth of geographic, taxonomic, and genetic sampling to provide a deeper understanding of their biodiversity and evolutionary history.
Analysis host-recognition mechanism of staphylococcal kayvirus ɸSA039 reveals a novel strategy that protects Staphylococcus aureus against infection by Staphylococcus pseudintermedius Siphoviridae phages
Authors: Azam Aa Haeruman , Kadoi Kenji , Miyanaga Kazuhiko , Usui Masaru , Tamura Yutaka , Cui Longzhu , Tanji Yasunori 
Published: May 2019

AbstractFollowing the emergence of antibiotic resistant bacteria such as methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant Staphylococcus pseudintermedius (MRSP), phage therapy has attracted significant attention as an alternative to antibiotic treatment. Bacteriophages belonging to kayvirus (previously known as Twort-like phages) have broad host range and are strictly lytic in Staphylococcus spp. Previous work revealed that kayvirus ɸSA039 has a host-recognition mechanism distinct from those of other known kayviruses: most of kayviruses use the backbone of wall teichoic acid (WTA) as their receptor; by contrast, ɸSA039 uses the β-N-acetylglucosamine (β-GlcNAc) residue in WTA. In this study, we found that ɸSA039 could switch its receptor to be able to infect S. aureus lacking the β-GlcNAc residue by acquiring a spontaneous mutation in open reading frame (ORF) 100 and ORF102. Moreover, ɸSA039 could infect S. pseudintermedius, which has a different WTA structure than S. aureus. By comparison with newly isolated S. pseudintermedius–specific phage (SP phages), we determined that glycosylation in WTA of S. pseudintermedius is essential for adsorption of SP phages, but not ɸSA039. Finally, we describe a novel strategy of S. aureus which protects the bacteria from infection of SP phages. Notably, glycosylation of ribitol phosphate (RboP) WTA by TarM or/and TarS prevents infection of S. aureus by SP phages. These findings could help to establish a new strategy for treatment of S. aureus and S. pseudintermedius infection, as well as provide valuable insights into the biology of phage–host interactions.