bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of early life glucocorticoid exposure on metabolism in zebrafish (Danio rerio) larvae
Authors: van den Bos Ruud 
Published: December 2019

AbstractIn this study we assessed the effects of increased cortisol levels during early embryonic development (0-6 hours post-fertilisation (hpf)), thereby mimicking maternal stress, on metabolism in zebrafish (Danio rerio) larvae. In two series of experiments fertilized eggs were exposed to a cortisol-containing, a dexamethasone-containing (to stimulate the glucocorticoid receptor (GR) specifically) or a control medium for 6 hours post-fertilisation (0-6 hpf). In the first series we measured oxygen consumption as a proxy for metabolism, in the second series gene-expression of genes related to gluconeogenesis and glucose transport. Previously we have found that at 5 days post-fertilisation (dpf) baseline cortisol levels are increased following cortisol pre-treatment but not following dexamethasone pre-treatment, suggesting a higher hypothalamus-pituitary-interrenal cells (HPI-axis) activity. Hence, we hypothesized that oxygen consumption and gene-expression were stronger in cortisol-treated than in dexamethasone-treated and control-treated subjects at 5 dpf. Indeed, we observed increased oxygen consumption in cortisol-treated subjects compared to dexamethasone-treated or control-treated subjects. However, gene-expression levels were not different between treatments, which may have been due to a developmental delay in this second series. We also reasoned that both cortisol-treated and dexamethasone-treated subjects would show a higher metabolism at 1 dpf than control-treated subjects as the HPI-axis is not functional as yet and more general processes are being stimulated by cortisol through GR stimulation. Indeed, we observed increased oxygen consumption and increased expression of genes related to gluconeogenesis and glucose transport in cortisol-treated and dexamethasone-treated subjects than control-treated subjects. These data show that early-life exposure to cortisol, mimicking thereby maternal stress, increased metabolism at different life stages, i.e. 1 and 5 dpf, involving the GR.
Opening the black box of high resolution fish tracking using yaps
Authors: Baktoft Henrik , Gjelland Karl Ø. , Økland Finn , Rehage Jennifer S. , Rodemann Jonathan R. , Corujo Rolando Santos , Viadero Natasha , Thygesen Uffe H. 
Published: December 2019

AbstractThe R packageyapswas introduced in 2017 as a transparent open source alternative to closed source manufacturer-provided solutions to estimate positions of fish (and other aquatic animals) tagged with acoustic transmitters.Althoughyapsis open source and transparent, the process from raw detections to final tracks has proved to be challenging for many potential users, effectively preventing most users from accessing the benefits of usingyaps. Especially, the very important process of synchronizing the hydrophone arrays have proven to be an obstacle for many potential users.To makeyapsmore approachable to the wider fish tracking community, we have developed and added user-friendly functions assisting users in the complex process of synchronizing the data.Here, we introduce these functions and a six-step protocol intended to provide users with an example workflow that can be used as a template enabling users to applyyapsto their own data. Using example data collected by an array of Vemco VR2 hydrophones, the protocol walks the user through the entire process from raw data to final tracks. Example data sets and complete code for reproducing results are provided.
How do backward walking ants (Cataglyphis velox) cope with navigational uncertainty?
Authors: Schwarz Sebastian , Clement Leo , Gkanias Evripides , Wystrach Antoine 
Published: December 2019

ABSTRACTCurrent opinion in insect navigation assumes that animals need to align with the goal direction to recognise familiar views and approach it. Yet, ants sometimes drag heavy food items backward to the nest and it is still unclear to what extent they rely on visual memories while doing so. In this study displacement experiments and alterations of the visual scenery reveal that ants do indeed recognise and use the learnt visual scenery to guide their path while walking backward. In addition, the results show that backward homing ants estimate their directional certainty by combining visual familiarity with other cues such as their path integrator and the time spent backward. A simple model that combines path integration with repulsive and attractive visual memories captures the results.
Ancient microRNA profiles of a 14,300-year-old canid are taxonomically informative and give glimpses into gene regulation from the Pleistocene
Authors: Fromm Bastian , Tarbier Marcel , Smith Oliver , Dalén Love , Gilbert M. T. P. , Friedländer Marc R. 
Published: December 2019

AbstractAncient DNA sequencing is the key technology for paleogenomic studies and today a routine method in many laboratories. Recent analyses have shown that, under favoring conditions, also RNA can be sequenced from historical and even ancient samples. We have re-analyzed ancient RNA data from a Pleistocene canid and find - in addition to the previously described messenger RNA fragments - intact microRNAs, which are short transcripts with important gene regulatory functions. With an extraordinary age of 14,300 years, the canid microRNA profiles are the oldest ever reported. Despite their age, we show that the microRNA profiles are conclusive of taxonomic origin, tissue identity with organ- and cell-type specific signatures, and that they yield glimpses into gene regulatory activity and biological processes from the Pleistocene. In summary, we here show that straightforward microRNA analyses hold great promise for deeper insights into gene regulation in extinct animals.
Separating Functions of the Phage-Encoded Quorum-Sensing-Activated Antirepressor Qtip
Authors: Silpe Justin E. , Bridges Andrew A. , Huang Xiuliang , Coronado Daniela R. , Duddy Olivia P. , Bassler Bonnie L. 
Published: December 2019

SummaryQuorum sensing is a process of chemical communication that bacteria use to track cell density and coordinate gene expression across a population. Bacteria-infecting viruses, called phages, can encode quorum-sensing components that enable them to integrate host cell density information into the lysis-lysogeny decision. Vibriophage VP882 is one such phage, and activation of its quorum-sensing pathway leads to the production of an antirepressor called Qtip. Qtip interferes with the prophage repressor (cIVP882), leading to host-cell lysis. Here, we show that Qtip interacts with the N-terminus of cIVP882, inhibiting both cIVP882DNA-binding and cIVP882autoproteolysis. Qtip also sequesters cIVP882, localizing it to the poles. Qtip can localize to the poles independently of cIVP882. Alanine-scanning mutagenesis of Qtip shows that its localization and interference with cIVP882activities are separable. Comparison of Qtip to a canonical phage antirepressor reveals that, despite both proteins interacting with their partner repressors, only Qtip drives polar localization.
Enhancing vs. inhibiting semantic performance with repetitive transcranial magnetic stimulation over the anterior temporal lobe: frequency- and task- specific effects
Authors: Jung JeYoung , Lambon Ralph Matthew A. 
Published: December 2019

AbstractAccumulating, converging evidence indicates that the anterior temporal lobe (ATL) appears to be the transmodal hub for semantic representation. A series of repetitive transcranial magnetic stimulation (rTMS) investigations utilizing the ‘virtual lesion’ approach have established the brain-behavioural relationship between the ATL and semantic processing by demonstrating that inhibitory rTMS over the ATL induced impairments in semantic performance in healthy individuals. However, a growing body of rTMS studies suggest that rTMS might also be a tool for cognitive enhancement and rehabilitation, though there has been no previous exploration in semantic cognition. Here, we explored a potential role of rTMS in enhancing and inhibiting semantic performance with contrastive rTMS protocols (1Hz vs. 20Hz) by controlling practice effects. Our results demonstrated that it is possible to modulate semantic performance positively or negatively depending on the ATL stimulation frequency: 20Hz rTMS was optimal for facilitating cortical processing (faster RT in a semantic task) contrasting with diminished semantic performance after 1Hz rTMS. In addition to cementing the importance of the ATL to semantic representation, our findings suggest that 20Hz rTMS leads to semantic enhancement in healthy individuals and potentially could be used for patients with semantic impairments as a therapeutic tool.
Cleavage of a pathogen apoplastic protein by plant subtilases activates immunity
Authors: Wang Shuaishuai , Xing Rongkang , Wang Yan , Shu Haidong , Fu Shenggui , Paulus Judith K. , Schuster Mariana , Saunders Diane G.O. , Win Joe , Vleeshouwers Vivianne , Zheng Xiaobo , van der Hoorn Renier A. L. , Kamoun Sophien , Dong Suomeng 
Published: December 2019

AbstractThe plant apoplast is a harsh environment in which hydrolytic enzymes, especially proteases, accumulate during pathogen infection. However, the defense functions of most apoplastic proteases remains largely elusive. Here, we show that a newly identified small cysteine-rich secreted protein PC2 from the potato late blight pathogenPhytophthora infestansinduces immunity in Solanum plant species only after cleavage by plant apoplastic subtilisin-like proteases, such as tomato P69B. A minimal 61-amino-acid core peptide carrying two key cysteines and widely conserved among most oomycete species is sufficient for PC2 activity. Kazal-like protease inhibitors, such as EPI1 produced byP. infestanscan prevent PC2 cleavage and dampen PC2 elicited host immunity. This study reveals that cleavage of pathogen proteins to release immunogenic peptides is an important function of apoplastic proteases but that pathogens interfere with these functions using protease inhibitor effectors.
Simulation-based comprehensive study of batch effects in metabolomics studies
Authors: Yu Miao , Roszkowska Anna , Pawliszyn Janusz 
Published: December 2019

AbstractBatch effects will influence the interpretation of metabolomics data. In order to avoid misleading results, batch effects should be corrected and normalized prior to statistical analysis. Metabolomics studies are usually performed without targeted compounds (e.g., internal standards) and it is a challenging task to validate batch effects correction methods. In addition, statistical properties of metabolomics data are quite different from genomics data (where most of the currently used batch correction methods have originated from). In this study, we firstly analyzed already published metabolomics datasets so as to summarize and discuss their statistical properties. Then, based on available datasets, we developed novel statistical properties-basedin silicosimulations of metabolomics peaks’ intensity data so as to analyze the influence of batch effects on metabolomic data with the use of currently available batch correction strategies. Overall, 252000 batch corrections on 14000 differentin silicosimulated datasets and related differential analyses were performed in order to evaluate and validate various batch correction methods. The obtained results indicate that log transformations strongly influence the performance of all investigated batch correction methods. False positive rates increased after application of batch correction methods with almost no improvement on true positive rates among the analyzed batch correction methods. Hence, in metabolomic studies it is recommended to implement preliminary experiments to simulate batch effects from real data in order to select adequate batch correction method, based on a given distribution of peaks intensity. The presented study is reproducible and related R package mzrtsim software can be found online (https://github.com/yufree/mzrtsim).
Serum biochemistry suggests grey squirrels (Sciurus carolinensis) have poorer physiological condition in urban settings
Authors: Schmidt Chloé , Treberg Jason R , Kinnunen Riikka P , Garroway Colin J 
Published: December 2019

AbstractHuman food waste in cities presents urban wildlife with predictable, easily accessible high-calorie food sources, but this can be both beneficial and harmful for individual health. We analyzed body condition and serum chemistry (electrolyte levels, markers of kidney and liver function, protein, glucose, and cholesterol) in an urban and rural population of eastern grey squirrels (Sciurus carolinensis) to assess whether proximity to the human food waste that is associated with urban habitats had ill effects on health. We found no differences in body condition between habitats and no evidence of malnutrition at either site. However, urban squirrels had higher blood glucose, lower potassium, phosphorus, chloride, and albumin:globulin ratios. These results align with previous findings of increased dietary sugar in cities, and suggest that urban populations of grey squirrels are under greater environmental stress than rural populations.
Dynamic rotation of the protruding domain enhances the infectivity of norovirus
Authors: Song Chihong , Takai-Todaka Reiko , Miki Motohiro , Haga Kei , Fujimoto Akira , Ishiyama Ryoka , Oikawa Kazuki , Yokoyama Masaru , Miyazaki Naoyuki , Iwasaki Kenji , Murakami Kosuke , Katayama Kazuhiko , Murata Kazuyoshi 
Published: December 2019

AbstractNorovirus is the major cause of epidemic nonbacterial gastroenteritis worldwide. Lack of structural information on infection and replication mechanisms hampers the development of effective vaccines and remedies. Here, using cryo-electron microscopy, we show that the capsid structure of murine noroviruses changes in response to aqueous conditions. By twisting the flexible hinge connecting two domains, the protruding (P) domain reversibly rises off the shell (S) domain in solutions of higher pH, but rests on the S domain in solutions of lower pH. Metal ions help to stabilize the latter conformation in this process. Furthermore, in the resting conformation, the cellular receptor CD300lf is readily accessible, and thus infection efficiency is significantly enhanced. Two P domain conformations were also found in the human norovirus GII.3 capsid. These results provide new insights into the infection mechanisms of the non-envelope viruses that function in dramatic environmental changes such as the digestive tract.Significance StatementThe capsid structures of caliciviruses have been reported to be classified into two different types, according to species and genotype. One is the rising P domain type as shown in human norovirus GII.10 and rabbit hemorrhagic disease virus, where the P domain rises from the S domain surface. The other is the resting P domain type as shown in human norovirus GI.1, sapovirus and San Miguel sea lion virus, where the P domain rests upon the S domain. Here, we demonstrate that the P domain of the murine norovirus infectious particles changes reversibly between the rising and resting P domain types in response to aqueous conditions. Our findings provide new insights into the mechanisms of viral infection of caliciviruses.
Homoeologous gene expression and co-expression network analyses and evolutionary inference in allopolyploids
Authors: Hu Guanjing , Grover Corrinne E. , Arick Mark A. , Liu Meiling , Peterson Daniel G. , Wendel Jonathan F. 
Published: December 2019

ABSTRACTPolyploidy is a widespread phenomenon throughout eukaryotes. Due to the coexistence of duplicated genomes, polyploids offer unique challenges for estimating gene expression levels, which is essential for understanding the massive and various forms of transcriptomic responses accompanying polyploidy. Although previous studies have explored the bioinformatics of polyploid transcriptomic profiling, the causes and consequences of inaccurate quantification of transcripts from duplicated gene copies have not been addressed. Using transcriptomic data from the cotton genus (Gossypium) as an example, we present an analytical workflow to evaluate a variety of bioinformatic method choices at different stages of RNA-seq analysis, from homoeolog expression quantification to downstream analysis used to infer key phenomena of polyploid expression evolution. In general, GSNAP-PolyCat outperforms other quantification pipelines tested, and its derived expression dataset best represents the expected homoeolog expression and co-expression divergence. The performance of co-expression network analysis was less affected by homoeolog quantification than by network construction methods, where weighted networks outperformed binary networks. By examining the extent and consequences of homoeolog read ambiguity, we illuminate the potential artifacts that may affect our understanding of duplicate gene expression, including an over-estimation of homoeolog co-regulation and the incorrect inference of subgenome asymmetry in network topology. Taken together, our work points to a set of reasonable practices that we hope are broadly applicable to the evolutionary exploration of polyploids.
Genome-wide functional analysis of hot pepper immune receptors reveals an autonomous NLR cluster in seed plants
Authors: Lee Hye-Young , Mang Hyunggon , Choi Eun-Hye , Seo Ye-Eun , Kim Myung-Shin , Oh Soohyun , Kim Saet-Byul , Choi Doil 
Published: December 2019

AbstractPlants possess hundreds of intracellular immune receptors encoding nucleotide-binding domain and leucine-rich repeat (NLR) proteins. Autoactive NLRs, in some cases a specific NLR domain, induce plant cell death in the absence of pathogen infection. In this study, we identified a group of NLRs (G10) carrying autoactive coiled-coil (CC) domains in pepper (Capsicum annuum L. cv. CM334) by genome-wide transient expression analysis. The G10-CC-mediated cell death mimics hypersensitive response (HR) cell death triggered by interaction between NLR and effectors derived from pathogens. Sequence alignment and mutagenesis analyses revealed that the intact α1 helix of G10-CCs is critical for both G10-CC- and R gene-mediated HR cell death. The cell death induced by G10-CCs does not require known helper NLRs, suggesting G10-NLRs are novel singleton NLRs. We also found that G10-CCs localize in the plasma membrane as Arabidopsis singleton NLR ZAR1. Extended studies revealed that autoactive G10-CCs are well conserved in other Solanaceae plants, including tomato, potato, and tobacco, as well as a monocot plant, rice. Furthermore, G10-NLR is an ancient form of NLR that present in all tested seed plants (spermatophytes). Our studies not only uncover the autonomous NLR cluster in plants but also provide powerful resources for dissecting the underlying molecular mechanism of NLR-mediated cell death in plants.
Improving characterization of understudied human microbiomes using targeted phylogenetics
Authors: Rosa Bruce A , Mihindukulasuriya Kathie , Hallsworth-Pepin Kymberlie , Wollam Aye , Martin John , Snowden Caroline , Dunne Wm. Michael , Weinstock George , Burnham Carey-Ann D. , Mitreva Makedonka 
Published: December 2019

AbstractWhole genome bacterial sequences are required to better understand microbial functions, niches-pecific bacterial metabolism, and disease states. Although genomic sequences are available for many of the human-associated bacteria from commonly tested body habitats (e.g. stool), as few as 13% of bacterial-derived reads from other sites such as the skin map to known bacterial genomes. To facilitate a better characterization of metagenomic shotgun reads from under-represented body sites, we collected over 10,000 bacterial isolates originating from 14 human body habitats, identified novel taxonomic groups based on full length 16S rRNA sequences, clustered the sequences to ensure that no individual taxonomic group was over-selected for sequencing, prioritized bacteria from under-represented body sites (such as skin, respiratory and urinary tract), and sequenced and assembled genomes for 665 new bacterial strains. Here we show that addition of these genomes improved read mapping rates of HMP metagenomic samples by nearly 30% for the previously under-represented phylumFusobacteria, and 27.5% of the novel genomes generated here had high representation in at least one of the tested HMP samples, compared to 12.5% of the sequences in the public databases, indicating an enrichment of useful novel genomic sequences resulting from the prioritization procedure. As our understanding of the human microbiome continues to improve and to enter the realm of therapy developments, targeted approaches such as this to improve genomic databases will increase in importance from both an academic and clinical perspective.ImportanceThe human microbiome plays a critically important role in health and disease, but current understanding of the mechanisms underlying the interactions between the varying microbiome and the different host environments is lacking. Having access to a database of fully sequenced bacterial genomes provides invaluable insights into microbial functions, but currently sequenced genomes for the human microbiome have largely come from a limited number of body sites (primarily stool), while other sites such as the skin, respiratory tract and urinary tracts are under-represented, resulting in as little as 13% of bacterial-derived reads mapping to known bacterial genomes. Here, we sequenced and assembled 665 new bacterial genomes, prioritized from a larger database to select under-represented body sites and bacterial taxa in the existing databases. As a result, we substantially improve mapping rates for samples from the Human Microbiome Project and provide an important contribution to human bacterial genomic databases for future studies.
SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework
Authors: Lewinski Martin , Bramkamp Yannik , Köster Tino , Staiger Dorothee 
Published: December 2019

AbstractBackgroundRNA-binding proteins interact with their target RNAs at specific sites. These binding sites can be determined genome-wide through individual nucleotide resolution crosslinking immunoprecipitation (iCLIP). Subsequently, the binding sites have to be visualized. So far, no visualization tool exists that is easily accessible but also supports restricted access so that data can be shared among collaborators.ResultsHere we present SEQing, a customizable interactive dashboard to visualize crosslink sites on target genes of RNA-binding proteins that have been obtained by iCLIP. Moreover, SEQing supports RNA-seq data that can be displayed in a diffrerent window tab. This allows, e.g. crossreferencing the iCLIP data with genes differentially expressed in mutants of the RBP and thus obtain some insights into a potential functional relevance of the binding sites. Additionally, detailed information on the target genes can be incorporated in another tab.ConclusionSEQing is written in Python3 and runs on Linux. The web-based access makes iCLIP data easily accessible, even with mobile devices. SEQing is customizable in many ways and has also the option to be secured by a password. The source code is available athttps://github.com/malewins/SEQing.