bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of whole genome sequencing for the identification and typing of Vibrio cholerae
Authors: Greig David R. , Schafer Ulf , Octavia Sophie , Hunter Ebony , Chattaway Marie A. , Dallman Timothy J. , Jenkins Claire 
Published: May 2018

AbstractEpidemiological and microbiological data on Vibrio cholerae isolated between 2004 and 2017 (n=836) and held in the Public Health England culture archive were reviewed. The traditional biochemical species identification and serological typing results were compared with the genome derived species identification and serotype for a sub-set of isolates (n=152). Of the 836 isolates, 750 (89.7%) were from faecal specimens, 206 (24.6%) belonged to serogroup O1 and seven (0.8%) were serogroup O139, and 792 (94.7%) isolates from patients reporting recent travel abroad, most commonly to India (n=209) and Pakistan (n=104). Of the 152 isolates of V. cholerae speciated by kmer identification, 149 (98.1%) were concordant with the traditional biochemical approach. Traditional serotyping results were 100% concordant with the whole genome sequencing (WGS) analysis for identification of serogroups O1 and O139 and Classical and El Tor biotypes. ctxA was detected in all isolates of V. cholerae O1 El Tor and O139 belonging to sequence type (ST) 69, and in V. cholerae O1 Classical variants belonging to ST73. A phylogeny of isolates belonging to ST69 from UK travellers clustered geographically, with isolates from India and Pakistan located on separate branches. Moving forward, WGS data from UK travellers will contribute to global surveillance programs, and the monitoring of emerging threats to public health and the global dissemination of pathogenic lineages. At the national level, these WGS data will inform the timely reinforcement of direct public health messaging to travellers and mitigate the impact of imported infections and the associated risks to public health.
Using Core Genome Alignments to Assign Bacterial Species
Authors: Chung Matthew , Munro James B. , Dunning Hotopp Julie C. 
Published: May 2018

ABSTRACTWith the exponential increase in the number of bacterial taxa with genome sequence data, a new standardized method is needed to assign bacterial species designations using genomic data that is consistent with the classically-obtained taxonomy. This is particularly acute for unculturable obligate intracellular bacteria like those in the Rickettsiales, where classical methods like DNA-DNA hybridization cannot be used to define species. Within the Rickettsiales, species designations have been applied inconsistently, often obfuscating the relationship between organisms and the context for experimental results. In this study, we generated core genome alignments for a wide range of genera with classically defined species, includingArcobacter,Caulobacter,Erwinia,Neisseria,Polaribacter,Ralstonia,Thermus, as well as genera within the Rickettsiales includingRickettsia,Orientia,Ehrlichia,Neoehrlichia,Anaplasma,eorickettsia, andWolbachia. A core genome alignment sequence identity (CGASI) threshold of 96.8% was found to maximize the prediction of classically-defined species. Using the CGASI cutoff, theWolbachiagenus can be delineated into species that differ from the currently used supergroup designations, while theRickettsiagenus is delineated into nine species, as opposed to the current 27 species. Additionally, we find that core genome alignments cannot be constructed between genomes belonging to different genera, establishing a bacterial genus cutoff that suggests the need to create new genera from theAnaplasmaandNeorickettsia. By using core genome alignments to assign taxonomic designations, we aim to provide a high-resolution, robust method for bacterial nomenclature that is aligned with classically-obtained results.
Abnormal microtubule dynamics disrupt nucleocytoplasmic transport in tau-mediated frontotemporal dementia
Authors: Paonessa F. , Evans L. , Solanki R. , Larrieu D. , Wray S. , Hardy J. , Jackson S.P. , Livesey F.J. 
Published: May 2018

SUMMARYThe neuronal microtubule-associated protein tau (MAPT) is central to the pathogenesis of many dementias, including Alzheimer’s disease. Autosomal dominant mutations inMAPTcause inherited frontotemporal dementia (FTD), but the underlying pathogenic mechanisms are unclear. Using human stem cell models of FTD due toMAPTmutations, we find that tau becomes hyperphosphorylated and mislocalises to neuronal cell bodies and dendrites in cortical neurons, recapitulating a key early event in FTD. Mislocalised tau in the cell body leads to abnormal microtubule dynamics in FTD-MAPT neurons that grossly deform the nuclear membrane, resulting in defective nucleocytoplasmic transport. Neurons in the post-mortem human FTD-MAPT cortex have a high incidence of nuclear deformation, indicating that tau-mediated nuclear membrane dysfunction is an important pathogenic process in FTD. Defects in nucleocytoplasmic transport in FTD point to important commonalities in the pathogenic mechanisms of both tau-mediated dementias and ALS-FTD due to TDP-43 and C9orf72 mutations.
Practical bioinstrumentation developments for AC magnetic field-mediated magnetic nanoparticle heating applications
Authors: Subramanian Mahendran , Miaskowski Arkadiusz , Mahapatro Ajit K. , Hovorka Ondrej , Dobson Jon 
Published: May 2018

AbstractHeat dissipation during magnetization reversal processes in magnetic nanoparticles (MNP), upon exposure to alternating magnetic fields (AMF), has been extensively studied in relation to applications in magnetic fluid hyperthermia (MFH). This current paper demonstrates the design, fabrication, and evaluation of an efficient instrument, operating on this principle, for use as (i) a non-contact, in vitro, real-time temperature monitor; (ii) a drug release analysis system (DRAS); (iii) a high flux density module for AMF-mediated MNP studies; and (iv) an in vivo coil setup for real-time, whole body thermal imaging. The proposed DRAS is demonstrated by an AMF-mediated drug release proof-of-principle experiment. Also, the technique described facilitates non-contact temperature measurements of specific absorption rate (SAR) as accurately as temperature measurements using a probe in contact with the sample. Numerical calculations estimating the absolute and root mean squared flux densities, and other MNP – AMF studies suggest that the proposed stacked planar coil module could be employed for calorimetry. Even though the proposed in vivo coil setup could be used for real-time, whole body thermal imaging (within the limitations due to issues of penetration depth), further design effort is required in order to enhance the energy transfer efficiency.
A survey of public attitudes towards third-party reproduction in Japan in 2014
Authors: Yamamoto Naoko , Hirata Tetsuya , Izumi Gentaro , Nakazawa Akari , Fukuda Shinya , Neriishi Kazuaki , Arakawa Tomoko , Takamura Masashi , Harada Miyuki , Hirota Yasushi , Koga Kaori , Wada-Hiraike Osamu , Fujii Tomoyuki , Irahara Minoru , Osuga Yutaka 
Published: May 2018

AbstractObjective: The objective of this study was to examine public attitudes towards third-party reproduction and the disclosure of conception through third-party reproduction.Methods: We conducted the web-based survey for the public attitude towards third-party reproduction in February 2014. Twenty-five hundred people were recruited with equal segregation of age (20s, 30s, 40s, and 50s) and gender. We analyzed the association between gender, age, infertility, and ethical view using a questionnaire regarding donor sperm, donor oocyte, donor embryo, gestational surrogacy, and disclosure to offspring.Results: Of the respondents, 36.2% approved and 26.6% disapproved with gamete or embryo donation. The frequency of those who approved was the lowest in females in the 50-59 years age group, and was significantly higher in males or females with infertility. Secondly, 40.9% approved and 21.8% disapproved with gestational surrogacy. The frequency of those who approved gestational surrogacy was higher in males or females with infertility. Thirdly, 46.3% of respondents agreed and 20.4% disagreed with “offspring have the right to know their origin”. Those who disagreed were primarily in the 50-59 age group of both genders, and disagreement was significantly higher in the infertility group compared with non-infertility group.Conclusion: In this study, public attitudes were affected by gender, age, and experience of infertility. These study findings are important in understanding the attitude towards third-party reproduction and disclosure to the offspring. Respondents having indecisive attitudes were >30%, which might indicate an increased requirement for information and education to enhance the discussion on the ethical consensus on third-party reproduction in Japan.
Single-fluorescent protein reporters allow parallel quantification of NK cell-mediated granzyme and caspase activities in single target cells
Authors: Liesche Clarissa , Sauer Patricia , Claus Maren , Eils Roland , Beaudouin Joël , Watzl Carsten 
Published: May 2018

1.AbstractNatural killer (NK) cells eliminate infected and tumorigenic cells through delivery of granzymes via perforin pores or by activation of caspases via death receptors. In order to understand how NK cells combine different cell death mechanisms it is important to quantify target cell responses on a single cell level. However, currently existing reporters do not allow the measurement of several protease activities inside the same cell. Here we present a strategy for the comparison of two different proteases at a time inside individual target cells upon engagement by NK cells. We developed single-fluorescent protein reporters containing the RIEAD or the VGPD cleavage site for the measurement of granzyme B activity. We show that these two granzyme B reporters can be applied in combination with caspase-8 or caspase-3 reporters. While we did not find that caspase-8 was activated by granzyme B, our method revealed that caspase-3 activity follows granzyme B activity with a delay of about 6 minutes. Finally, we illustrate the comparison of several different reporters for granzyme A, M, K and H. The here presented approach is a valuable means for the investigation of the temporal evolution of cell death mediated by cytotoxic lymphocytes.
Antimicrobial peptides modulate long-term memory
Authors: Barajas Azpeleta Raquel , Wu Jianping , Gill Jason , Welte Ryan , Seidel Chris , Si Kausik 
Published: May 2018

AbstractAntimicrobial peptides act as a host defense mechanism and regulate the commensal microbiome. To obtain a comprehensive view of genes contributing to long-term memory we performed mRNA sequencing from singleDrosophilaheads following behavioral training that produces long-lasting memory. Surprisingly, we find that two immune peptides with antimicrobial activity, Diptericin B and Gram-Negative Bacteria Binding Protein like 3, regulate long-term but not short-term memory or instinctive behavior inDrosophila. The cellular requirement of these two peptides is distinct: head fat body for DptB, and neurons for GNBP-like3. That antimicrobial peptides influence memory provides a novel example of the emerging link between the immune and nervous systems and reveals that some immune peptides may have been repurposed in the nervous system.
An intermittent hypercaloric diet alters gut microbiota, prefrontal cortical gene expression and social behaviours in rats
Authors: Reichelt Amy C , Loughman Amy , Bernard Ashton , Raipuria Mukesh , Abott Kirsten N , Dachtler James , Van Thi Thu Hao , Moore Robert J 
Published: May 2018

AbstractExcessive consumption of high fat and high sugar (HFHS) diets are known to alter reward processing and aspects of behaviour, and change microbiota profiles. Studies in gnotobiotic mice also provide evidence that gut microorganisms influence social behaviour. To further investigate these interactions, the impact of intermittent access to a HFHS diet on social behaviour, gene expression and microbiota composition was examined. Rats were permitted intermittent daily access (2h / day) to a palatable HFHS diet for 28 days across the adolescent period. Social interaction, social memory and novel object recognition were assessed during this period. Following testing, RT-PCR was conducted on hippocampal and prefrontal cortex (PFC) samples. 16S ribosomal RNA amplicon sequencing was used for identification and relative quantification of bacterial taxa. Reduced social interaction behaviours, and impaired social memory and novel object recognition were observed in HFHS diet rats. Reduced levels of monoamine oxidase A (Maoa), catechol-O-methyltransferase (Comt) and brain derived neurotrophic factor (Bdnf) mRNA were observed in the PFC of HFHS diet rats. The relative abundance of a number of specific taxa differed significantly between the two diet groups, in particular,LachnospiraceaeandRuminoccoceaebacteria, which also predicted social behaviours, novel object recognition performance and Maoa expression. This is the first study to show that limited daily access to HFHS diet alters social behaviour and cognition in rats. Furthermore, behavioural changes are associated with alterations to cortical gene expression of enzymes involved in monoamine synthesis and neuroplasticity, and microbiota profiles predicted diet-induced changes to behaviour and gene expression.
Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells
Authors: Saikia Mridusmita , Burnham Philip , Keshavjee Sara H. , Wang Michael F. Z. , Heyang Michael , Moral-Lopez Pablo , Hinchman Meleana M. , Danko Charles G. , Parker John S. L. , Vlaminck Iwijn De 
Published: May 2018

AbstractWe describe Droplet Assisted RNA Targeting by single cell sequencing (DART-seq), a versatile technology that enables multiplexed amplicon sequencing and transcriptome profiling in single cells. We applied DART-seq to simultaneously characterize the non-A-tailed transcripts of a segmented dsRNA virus and the transcriptome of the infected cell. In addition, we used DART-seq to simultaneously determine the natively paired, variable region heavy and light chain amplicons and the transcriptome of B lymphocytes.
Description and charactrization of the Amazonian entomopathogenic bacteriumPhotorhabdus luminescensMN7
Authors: Kamitani Fernando L. , Almenara Daniela P. , Rossi Carolina , Camargo Neves Maira R. , Müller Lissandra M. A. , Gruber Arthur , Alves João M. P. , Yamaguchi Lydia F. , Yoshida Nídia C. , Kato Massuo J. , Winter Carlos E. 
Published: May 2018

AbstractMany isolates of the genusPhotorhabdushave been reported around the world. Here we describe the first BrazilianPhotorhabdusisolate, found in association with the entomopathogenic nematodeHeterorhabditis baujardiLPP7, from the Amazonian forest in Monte Negro (RO, Brazil). The new isolate can be grouped with the Hb-Hm clade ofP. luminescenssubsp.luminescens, close to the new subspeciesP. luminescenssubsp.sonorensis. P. luminescensMN7 has several characteristics expected of variant form I cells, such as the presence of intracellular crystals, secretion of hydrolytic enzymes (lipases and proteases) and bioluminescence. AlthoughH. baujardiLPP7 is not prolific when compared toH. bacteriophoraHP88,P. luminescensMN7 is clearly pathogenic and probably secretes the same toxins asP. luminescenssubsp.luminescensW14, when fed to larvae of the greater wax mothGalleria mellonella. This behavior is different from what is found inPhotorhabdus luminescenssubsp.laumondiiHP88, which was used as a control in our experiments, andP. l. subsp.laumondiiTT01. Besides the toxin secretion,P. luminescensMN7 secretes proteolytic polypeptides that have molecular masses different from those found inP. l. subsp.laumondiiTT01. Finally, the crude extract from spent culture medium was shown to contain 3,5-dihydroxy-4-isopropyl-cis-stilbene and 1,3,8-trihydroxy-9,10-anthraquinone as the major compounds, similarly to otherPhotorhabdus luminescensstrains.
Capturing single-cell heterogeneity via data fusion improves image-based profiling
Authors: Rohban Mohammad H. , Singh Shantanu , Carpenter Anne E. 
Published: May 2018

AbstractSingle-cell resolution technologies warrant computational methods that capture cell heterogeneity while allowing efficient comparisons of populations. Here, we summarize cell populations by adding features’ dispersion and covariances to population averages, in the context of image-based profiling. We find that data fusion is critical for these metrics to improve results over the prior state-of-the-art, providing at least ~20% better performance in predicting a compound’s mechanism of action (MoA) and a gene’s pathway.
Exploring the impact of inoculum dose on host immunity and morbidity to inform model-based vaccine design
Authors: Handel Andreas , Li Yan , McKay Brian , Pawelek Kasia A. , Zarnitsyna Veronika , Antia Rustom 
Published: May 2018

AbstractBackgroundVaccination is an effective method to protect against infectious diseases. An important consideration in any vaccine formulation is the inoculum dose, i.e., amount of antigen or live attenuated pathogen that is used. Higher levels generally lead to better stimulation of the immune response but might cause more severe side effects and allow for less population coverage in the presence of vaccine shortages. Determining the optimal amount of inoculum dose is an important component of rational vaccine design. A combination of mathematical models with experimental data can help determine the impact of the inoculum dose.MethodsWe designed mathematical models and fit them to data from influenza A virus (IAV) infection of mice and human parainfluenza virus (HPIV) of cotton rats at different inoculum doses. We used the model to predict the level of immune protection and morbidity for different inoculum doses and to explore what an optimal inoculum dose might be.ResultsWe show how a framework that combines mathematical models with experimental data can be used to study the impact of inoculum dose on important outcomes such as immune protection and morbidity. We find that the impact of inoculum dose on immune protection and morbidity depends on the pathogen and both protection and morbidity do not always increase with increasing inoculum dose. An intermediate inoculum dose can provide the best balance between immune protection and morbidity, though this depends on the specific weighting of protection and morbidity.ConclusionsOnce vaccine design goals are specified with required levels of protection and acceptable levels of morbidity, our proposed framework which combines data and models can help in the rational design of vaccines and determination of the optimal amount of inoculum.
Within-species phylogenetic relatedness of a common mycorrhizal fungus affects evenness in plant communities through effects on dominant species
Authors: Savary Romain , Villard Lucas , Sanders Ian R. 
Published: May 2018

AbstractArbuscular mycorrhizal fungi (AMF) have been shown to influence plant community structure and diversity. Studies based on single plant - single AMF isolate experiments show that within AMF species variation leads to large differential growth responses of different plant species. Because of these differential effects, genetic differences among isolates of an AMF species could potentially have strong effects on the structure of plant communities.We tested the hypothesis that within species variation in the AMF R. irregularis significantly affects plant community structure and plant co-existence. We took advantage of a recent genetic characterization of several isolates using double-digest restriction-site associated DNA sequencing (ddRADseq). This allowed us to test not only for the impact of within AMF species variation on plant community structure but also for the role of the R. irregularis phylogeny on plant community metrics. Nine isolates of R. irregularis, belonging to three different genetic groups (Gp1, Gp3 and Gp4), were used as either single inoculum or as mixed diversity inoculum. Plants in a mesocosm representing common species that naturally co-exist in European grasslands were inoculated with the different AMF treatments.We found that within-species differences in R. irregularis did not strongly influence the performance of individual plants or the structure of the overall plant community. However, the evenness of the plant community was affected by the phylogeny of the fungal isolates, where more closely-related AMF isolates were more likely to affect plant community evenness in a similar way compared to more genetically distant isolates.This study underlines the effect of within AMF species variability on plant community structure. While differential effects of the AMF isolates were not strong, a single AMF species had enough functional variability to change the equilibrium of a plant community in a way that is associated with the evolutionary history of the fungus.
Belowground plant functional ecology: Towards an integrated perspective
Authors: Klimešová Jitka , Martínková Jana , Ottaviani Gianluigi 
Published: May 2018

Abstract

In recent years, belowground plant ecology has experienced a booming interest. This has resulted in major advances towards a greater understanding of belowground plant and ecosystem functioning focused on fine roots, mycorrhizal associations and nutrient acquisition.

Despite this, other important functions (e.g., on‐spot persistence, space occupancy, resprouting after biomass removal) exerted by different belowground plant organs (e.g., roots, rhizomes, bulbs) remain largely unexplored.

Here, we propose a framework providing a comprehensive perspective on the entire set of belowground plant organs and functions. We suggest a compartment‐based approach. We identify two major belowground compartments, that is, acquisitive and nonacquisitive, associated with biomass allocation into these functions. Also, we recommend the nonacquisitive compartment to be divided into structural (e.g., functional roles carried out by rhizomes, such as sharing of resources, space occupancy) and nonstructural (e.g., functional roles exerted by carbohydrates reserve affecting resprouting ability, protection against climate adversity) subcompartments. We discuss methodological challenges—and their possible solutions—posed by changes in biomass allocation across growth forms and ontogenetic stages, and in relation to biomass partitioning and turnover.

We urge the implementation of methods and approaches considering all the belowground plant compartments. This way, we would make sure that key, yet less‐studied functions would be incorporated into the belowground plant ecology research agenda. The framework has potential to advance the understanding of belowground plant and ecosystem functioning by considering relations and trade‐offs between different plant functions and organs. At last, we identify four major areas where using the proposed compartment‐based approach would be particularly important, namely (a) biomass scaling, (b) clonality‐resource acquisition relations, (c) linkages between resprouting and changing environmental conditions and (d) carbon sequestration.

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