bluuebunny/crossref_metadata_2025_split huggingface dataset:
phyloFlash – Rapid SSU rRNA profiling and targeted assembly from metagenomes
Authors: Gruber-Vodicka Harald R. , Seah Brandon K. B. , Pruesse Elmar 
Published: January 2019

ABSTRACTThe SSU rRNA gene is the key marker in molecular ecology for all domains of life, but is largely absent from metagenome-assembled genomes that often are the only resource available for environmental microbes. Here we present phyloFlash, a pipeline to overcome this gap with rapid, SSU rRNA-centered taxonomic classification, targeted assembly, and graph-based binning of full metagenomic assemblies. We show that a cleanup of artifacts is pivotal even with a curated reference database. With such a filtered database, the general-purpose mapper BBmap extracts SSU rRNA reads five times faster than the rRNA-specialized tool SortMeRNA with similar sensitivity and higher selectivity on simulated metagenomes. Reference-based targeted assemblers yielded either highly fragmented assemblies or high levels of chimerism, so we employ the general-purpose genomic assembler SPAdes. Our optimized implementation is independent of reference database composition and has satisfactory levels of chimera formation. Using the phyloFlash workflow we could recover the first complete genomes of several enigmatic taxa, including Marinamargulisbacteria from surface ocean seawater. phyloFlash quickly processes Illumina (meta)genomic data, is straightforward to use, even as part of high-throughput quality control, and has user-friendly output reports. The software is available at https://github.com/HRGV/phyloFlash (GPL3 license) and is documented with an online manual.
Bacteriophage to Combat Biofilms in Hospital Drains
Authors: Huang Jenny Yijian 
Published: January 2019

AbstractBackgroundAccording to the World Health Organization, nearly 15% of all hospitalized patients worldwide acquire nosocomial infections. A particular area of concern for bacterial build up in hospitals is sink drains. The moist, microbiologically active environment of drains promotes the formation of biofilms that are difficult to target with standard chemical disinfectants. Bacteriophages, however, show potential to be used as disinfecting agents in hospital drains. Not only do bacteriophages increase in titer as they infect, spreading to hard-to-reach surfaces, phages have been shown to degrade the extracellular matrix of biofilms and gain access to underlying bacteria. This research explores the potential of bacteriophages to eradicate biofilms in an environment modeling a sink drain by comparing the efficacy, range, and durability of bacteriophage to a chemical disinfectant.MethodsE. coli biofilms were grown in M9 minimal media placed in sink P-traps assigned one of three treatments: chemical disinfectant, bacteriophage, or deionized water (control). Biofilms were quantified at five time points -- 1, 12, 24, 36, and 48 hours -- using the crystal violet assay.ResultsBoth chemical disinfectant and bacteriophage significantly decreased the optical densities of biofilms (p < 0.001***). P-traps treated with bacteriophages showed more uniform destruction of biofilm across P-trap compared to chemical disinfectant (p < 0.01**). A trend may suggest that over time bacteriophage became more effective at reducing biofilm than chemical disinfectant.ConclusionThis work highlights the potential of bacteriophage as an alternative to conventional chemical disinfectants for biofilm control in settings such as hospital drains.ImportanceNosocomial infections prolong hospital stay, costing the U.S. healthcare system $5-10 billion annually. An increasing number of reports demonstrate that sink drains -- reservoirs for multidrug resistant bacteria -- may be a source of hospital-related outbreaks. Recent studies have elucidated the mechanism of dispersal of bacteria from contaminated sinks to patients, but limited data are available identifying disinfecting methods for hospital drains. Not only did this study demonstrate that bacteriophages could reduce biofilms on sink drains just as effectively as a commercial disinfectant, it showed that phages tended to spread more thoroughly across P-traps and may work for longer. With hand-washing an imperative activity for disease prevention, hospital sinks should remain clean. This work explores an alternative disinfecting method for hospital sink drains.
EphA7 functions as a receptor for cell-to-cell transmission of Kaposi’s sarcoma-associated herpesvirus into BJAB B cells and for cell-free virus infection by the related rhesus monkey rhadinovirus
Authors: Großkopf Anna K. , Schlagowski Sarah , Hörnich Bojan F. , Fricke Thomas , Desrosiers Ronald C. , Hahn Alexander S. 
Published: January 2019

ABSTRACTKaposi’s sarcoma-associated herpesvirus (KSHV) is the causative agent of Kaposi’s sarcoma and is associated with two B cell malignancies, primary effusion lymphoma and the plasmablastic variant of multicentric Castleman’s disease. EphA2 functions as a cellular receptor for the gH/gL glycoprotein complex of KSHV for several adherent cell types. KSHV gH/gL was previously shown to also weakly interact with other members of the Eph family of receptors. Whether these interactions are of functional consequence remained unclear so far, even if other A-type Ephs were shown to be able to compensate for absence of EphA2 in overexpression systems. Here, we demonstrate for the first time that endogenously expressed EphA7 in BJAB B cells is critical for the cell-to-cell transmission of KSHV from producer iSLK cells to BJAB target cells. The BJAB lymphoblastoid cell line often serves as a model for B cell infection and expresses only low levels of all Eph family receptors other than EphA7. Endogenous EphA7 could be precipitated from the cellular lysate of BJAB cells using recombinant gH/gL, and knockout of EphA7 significantly reduced transmission of KSHV into BJAB target cells by over 80%. Finally, we demonstrate that receptor function of EphA7 is conserved between cell-to-cell transmission of KSHV and cell-free infection by the related rhesus monkey rhadinovirus (RRV), which is relatively even more dependent on EphA7 for infection of BJAB cells.IMPORTANCEInfection of B cells is biologically relevant for two KSHV-associated malignancies, the plasmablastic variant of multicentric Castleman’s disease (MCD) and primary effusion lymphoma (PEL). Elucidating the process of B cell infection is therefore important to understand the pathogenesis of these diseases. For various types of adherent cells, EphA2 has been shown by several groups to function as an entry receptor that is engaged by the gH/gL glycoprotein complex. Our previous findings indicate that KSHV does not only interact with EphA2, but can also bind to other members of the Eph family of receptor tyrosine kinases with comparatively lower avidity. We now analyzed the requirement of Eph interactions for infection of the BJAB B cell line, a model for infection of B cells by KSHV. We identify EphA7 as the principal Eph receptor for infection of this model B cell line by both KSHV and the related rhesus monkey rhadinovirus.
Early steps in the evolution of vertical transmission revealed by a plant-bacterium symbiosis
Authors: De Meyer Frédéric , Danneels Bram , Acar Tessa , Rasolomampianina Rado , Rajaonah Mamy Tiana , Jeannoda Vololoniaina , Carlier Aurelien 
Published: January 2019

ABSTRACTVarious plant species establish intimate symbioses with bacteria within their aerial organs. The bacteria are contained within nodules or glands often present in distinctive patterns on the leaves in what is commonly referred to as leaf nodule symbiosis. We describe here a highly specific symbiosis between a wild yam species from Madagascar,Dioscorea sansibarensisand bacteria of the speciesOrrella dioscoreae. Using whole genome sequencing of plastid and bacteria from wild-collected samples, we show phylogenetic patterns consistent with a vertical transmission of the symbionts. Unique among leaf nodule symbioses, the bacteria can be cultured and are amenable to comparative transcriptomics and phenotypic characterization, revealing a potential role in complementing the host’s arsenal of secondary metabolites. We propose a very recent acquisition of the vertical mode of transmission in this symbiosis which, together with a large effective populations size explain the cultivability and remarkable lack of genome reductive evolution inO. dioscoreae. We leverage these unique features to reveal pathways and functions under positive selection in these specialized endophytes, highlighting the mechanisms enabling a permanent association in the phyllosphere.
Cell Autonomous Neuroprotection by the Mitochondrial Uncoupling Protein 2 in a Mouse Model of Glaucoma
Authors: Hass Daniel T. , Barnstable Colin J. 
Published: January 2019

AbstractGlaucoma is a group of disorders associated with retinal ganglion cell (RGC) degeneration and death. There is a clear contribution of mitochondrial dysfunction and oxidative stress toward glaucomatous RGC death. Mitochondrial uncoupling protein 2 (Ucp2) is a well-known regulator of oxidative stress that increases cell survival in acute models of oxidative damage. The impact of Ucp2 on cell survival during sub-acute and chronic neurodegenerative conditions however is not yet clear. Herein, we test the hypothesis that increased Ucp2 expression will improve retinal ganglion cell survival in a mouse model of glaucoma. We show that increasing retinal ganglion cell but not glial Ucp2 expression in transgenic animals decreases glaucomatous RGC death, but also that the PPAR-γ agonist rosiglitazone, an endogenous transcriptional activator of Ucp2, does not significantly alter RGC loss during glaucoma. Together, these data support a model whereby increased Ucp2 expression mediates neuroprotection during a long-term oxidative stressor, but that transcriptional activation alone is insufficient to elicit a neuroprotective effect, motivating further research in to the post-transcriptional regulation of Ucp2.
NWB:N 2.0: An Accessible Data Standard for Neurophysiology
Authors: Rübel Oliver , Tritt Andrew , Dichter Benjamin , Braun Thomas , Cain Nicholas , Clack Nathan , Davidson Thomas J. , Dougherty Max , Fillion-Robin Jean-Christophe , Graddis Nile , Grauer Michael , Kiggins Justin T. , Niu Lawrence , Ozturk Doruk , Schroeder William , Soltesz Ivan , Sommer Friedrich T. , Svoboda Karel , Lydia Ng , Frank Loren M. , Bouchard Kristofer 
Published: January 2019

ABSTRACTNeurodata Without Borders: Neurophysiology (NWB:N) is a data standard for neurophysiology, providing neuroscientists with a common standard to share, archive, use, and build common analysis tools for neurophysiology data. With NWB:N version 2.0 (NWB:N 2.0) we made significant advances towards creating a usable standard, software ecosystem, and vibrant community for standardizing neurophysiology data. In this manuscript we focus in particular on the NWB:N data standard schema and present advances towards creating an accessible data standard for neurophysiology.
Consistency of SVDQuartets and Maximum Likelihood for Coalescent-based Species Tree Estimation
Authors: Wascher Matthew , Kubatko Laura 
Published: January 2019

AbtractNumerous methods for inferring species-level phylogenies under the coalescent model have been proposed within the last 20 years, and debates continue about the relative strengths and weaknesses of these methods. One desirable property of a phylogenetic estimator is that of statistical consistency, which means intuitively that as more data are collected, the probability that the estimated tree has the same topology as the true tree goes to 1. To date, consistency results for species tree inference under the multispecies coalescent have been derived only for summary statistics methods, such as ASTRAL and MP-EST. These methods have been found to be consistent given true gene trees, but may be inconsistent when gene trees are estimated from data for loci of finite length (Roch et al., 2019). Here we consider the question of statistical consistency for four taxa for SVDQuartets for general data types, as well as for the maximum likelihood (ML) method in the case in which the data are a collection of sites generated under the multispecies coalescent model such that the sites are conditionally independent given the species tree (we call these data Coalescent Independent Sites (CIS) data). We show that SVDQuartets is statistically consistent for all data types (i.e., for both CIS data and for multilocus data), and we derive its rate of convergence. We additionally show that ML is consistent for CIS data under the JC69 model, and discuss why a proof for the more general multilocus case is difficult. Finally, we compare the performance of maximum likelihood and SDVQuartets using simulation for both data types.
Genome rearrangements induce biofilm formation inEscherichia coliC – an old model organism with a new application in biofilm research
Authors: Król Jarosław E. , Hall Donald C. , Balashov Sergey , Pastor Steven , Siebert Justin , McCaffrey Jennifer , Lang Steven , Ehrlich Rachel L. , Earl Joshua , Mell Joshua C. , Xiao Ming , Ehrlich Garth D. 
Published: January 2019

AbstractEscherichia coliC forms more robust biofilms than the other laboratory strains. Biofilm formation and cell aggregation under a high shear force depends on temperature and salt concentrations. It is the last of fiveE. colistrains (C, K12, B, W, Crooks) designated as safe for laboratory purposes whose genome has not been sequenced. Here we present the complete genomic sequence of this strain in which we utilized both long-read PacBio-based sequencing and high resolution optical mapping to confirm a large inversion in comparison to the other laboratory strains. Notably, DNA sequence comparison revealed the absence of several genes thought to be involved in biofilm formation, including antigen 43,waaSBOJYZULfor LPS synthesis, andcpsBfor curli synthesis. The first main difference we identified that likely affects biofilm formation is the presence of an IS3-like insertion sequence in front of the carbon storage regulatorcsrAgene. This insertion is located 86 bp upstream of thecsrAstart codon inside the −35 region of P4 promoter and blocks the transcription from the sigma32and sigma70promoters P1-P3 located further upstream. The second is the presence of an IS5/IS1182 in front of thecsgDgene, which may drive its overexpression in biofilm. And finally,E. coliC encodes an additional sigma70subunit overexpressed in biofilm and driven by the same IS3-like insertion sequence. Promoter analyses using GFP gene fusions and total expression profiles using RNA-seq analyses comparing planktonic and biofilm envirovars provided insights into understanding this regulatory pathway inE. coli.IMPORTANCEBiofilms are crucial for bacterial survival, adaptation, and dissemination in natural, industrial, and medical environments. Most laboratory strains ofE. coligrown for decadesin vitrohave evolved and lost their ability to form biofilm, while environmental isolates that can cause infections and diseases are not safe to work with. Here, we show that the historic laboratory strain ofE. coliC produces a robust biofilm and can be used as a model organism for multicellular bacterial research. Furthermore, we ascertained the full genomic sequence as well as gene expression profiles of both the biofilm and planktonic envirovars of this classic strain, which provide for a base level of characterization and make it useful for many biofilm-based applications.
Relating growth potential and biofilm formation of ShigatoxigenicEscherichia colitoin plantacolonisation and the metabolome of ready-to-eat crops
Authors: Merget Bernhard , Forbes Ken J. , Brennan Fiona , McAteer Sean , Shepherd Tom , Strachan Norval J.C. , Holden Nicola J. 
Published: January 2019

AbstractContamination of fresh produce with pathogenicEscherichia coli,including ShigatoxigenicE. coli(STEC), represents a serious risk to human health. Colonisation is governed by multiple bacterial and plant factors that can impact on the probability and suitability of bacterial growth. Thus, we aimed to determine whether the growth potential of STEC for plants associated with foodborne outbreaks (two leafy vegetables and two sprouted seed species), is predictive for colonisation of living plants as assessed from growth kinetics and biofilm formation in plant extracts. Fitness of STEC was compared to environmentalE. coli, at temperatures relevant to plant growth. Growth kinetics in plant extracts varied in a plant-dependent and isolate-dependent manner for all isolates, with spinach leaf lysates supporting the fastest rates of growth. Spinach extracts also supported the highest levels of biofilm formation. Saccharides were identified as the major driver of bacterial growth, although no single metabolite could be correlated with growth kinetics. The highest level ofin plantacolonisation occurred on alfalfa sprouts, though internalisation was 10-times more prevalent in the leafy vegetables than in sprouted seeds. Marked differences inin plantagrowth meant that growth potential could only be inferred for STEC for sprouted seeds. In contrast, biofilm formation in extracts related to spinach colonisation. Overall, the capacity ofE. colito colonise, grow and internalise within plants or plant-derived matrices were influenced by the isolate type, plant species, plant tissue type and temperature, complicating any straight-forward relationship betweenin vitroandin plantabehaviours.ImportanceFresh produce is an important vehicle for STEC transmission and experimental evidence shows that STEC can colonise plants as secondary hosts, but differences in the capacity to colonise occur between different plant species and tissues. Therefore, an understanding of the impact of these plant factors have on the ability of STEC to grow and establish is required for food safety considerations and risk assessment. Here, we determined whether growth and the ability of STEC to form biofilms in plants extracts could be related to specific plant metabolites or could predict the ability of the bacteria to colonise living plants. Growth rates for sprouted seeds (alfalfa and fenugreek) exhibited a positive relationship between plant extracts and living plants, but not for leafy vegetables (lettuce and spinach). Therefore, the detailed variations at the level of the bacterial isolate, plant species and tissue type all need to be considered in risk assessment.
Identification of regulatory genes through global gene expression analysis of aHelicobacter pylorico-culture system
Authors: Tubau-Juni Nuria , Bassaganya-Riera Josep , Leber Andrew , Zoccoli-Rodriguez Victoria , Kronsteiner Barbara , Viladomiu Monica , Abedi Vida , Hontecillas Raquel 
Published: January 2019

AbstractHelicobacter pyloriis a gram-negative bacterium that establishes life-long infections by inducing immunoregulatory responses. We have developed a novelex vivo H. pylorico-culture system to identify new regulatory genes based on expression kinetics overlapping with that of genes with known regulatory functions. Using this novel experimental platform, in combination with global transcriptomic analysis, we have identified five lead candidates, validated them using mouse models ofH. pyloriinfection andin vitroco-cultures under pro-inflammatory conditions. Plexin domain containing 2(Plxdc2)was selected as the top lead immunoregulatory target. Gene silencing and ligand-induced activation studies confirmed its predicted regulatory function. Our integrated bioinformatics analyses and experimental validation platform has enabled the discovery of new immunoregulatory genes. This pipeline can be used for the identification of genes with therapeutic applications for treating infectious, inflammatory, and autoimmune diseases.
Disharmony of the world’s island floras
Authors: König Christian , Weigelt Patrick , Taylor Amanda , Stein Anke , Dawson Wayne , Essl Franz , Pergl Jan , Pyšek Petr , van Kleunen Mark , Winter Marten , Chatelain Cyrille , Wieringa Jan J. , Krestov Pavel , Kreft Holger 
Published: January 2019

AbstractAimDisharmony is a key concept in island biology that describes the imbalance in the representation of higher taxa on islands compared to their mainland source regions. Although there are strong theoretical arguments for the differential colonization success of different taxa on islands, the empirical evidence for disharmony remains largely anecdotal. Here, we develop a novel method for delineating island source regions and present the first global quantitative assessment of island disharmony.LocationGlobal.Time periodRecent.Major taxa studiedVascular plants.MethodsWe developed a generalizable method for estimating the source regions of an island flora based on statistical predictions of species turnover. We then designed two metrics to investigate disharmony from an island- and a taxon-centered perspective. First, we used linear mixed effects models to analyse the overall taxonomic bias of 305 island floras (compositional disharmony) as a function of geographical and climatic island features. Second, we applied linear models to examine the over- or under-representation of 450 vascular plant families on islands (representational disharmony) as a function of family size, age, higher taxonomic group and family-specific functional traits.ResultsWe found that compositional disharmony scales positively with island isolation and negatively with island area, and is strongly modulated by climatic variables. In contrast, the relationship between representational disharmony and family-specific characteristics was weaker. We found significant effects of family species richness and pollination syndrome, whereas family age and all other tested functional traits remained without effect.ConclusionsThe taxonomic scope of the disharmony concept has historically limited its wider applicability, because higher taxa are inconsistent ecological proxies. However, our results provide a strong foundation for integrating disharmony with quantitative functional and phylogenetic approaches in order to gain a deeper understanding of assembly processes on islands.
Development of an ELISA-Based Method for Testing Aflatoxigenicity and Aflatoxigenic Variability among Aspergillus species in Culture
Authors: Micah Lagat Kipkemboi , Toroitich Faith Jebet , Obonyo Meshack Amos 
Published: January 2019

AbstractAflatoxins contaminate foodstuff posing a severe threat to human health because chronic exposure is linked to liver cancer while acute exposure may cause death. Therefore, it is of interest to reduce the contamination of crops by aflatoxins in the field and post-harvest. Among the current technologies being developed is the deployment of non-aflatoxigenic strains of Aspergillus species to competitively exclude aflatoxigenic conspecifics from crops in the field thereby curtailing aflatoxin production by the former. The success in this endeavor makes the non-aflatoxigenic fungi good candidates for biological control programs. However, the current techniques for segregating non-aflatoxigenic from aflatoxigenic fungi suffer two main drawbacks: they are based on morphological and chemical tests with a combination of visual color changes detected in a culture plate which suffer some degree of inaccuracy. Secondly, the existing methods are incapable of accurately quantifying aflatoxin production by fungi in culture. We developed a culture system for inducing aflatoxin production by Aspergillus using maize kernels as growth substrate followed by quantification using ELISA. The method was compared to the Dichlorvos-Ammonia (DV-AM) method for determining aflatoxigenicity. Our findings encapsulate a method more robust than the currently used DV-AM approach because, for the first time, we are able to assess aflatoxigenicity and aflatoxigenic variability among Aspergillus species earlier classified as non-aflatoxigenic by the DV-AM method. Furthermore, the new method presents an opportunity to attribute toxin production by actively growing fungal cultures. We believe this method when further developed presents a chance to study and predict fungal behavior prior to field trials for biological control programs.