bluuebunny/crossref_metadata_2025_split huggingface dataset:
Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach
Authors: von der Heyde Benedikt , Emmanouilidou Anastasia , Mazzaferro Eugenia , Vicenzi Silvia , Höijer Ida , Klingström Tiffany , Jumaa Sitaf , Dethlefsen Olga , Snieder Harold , de Geus Eco , Ameur Adam , Ingelsson Erik , Allalou Amin , Brooke Hannah L. , den Hoed Marcel 
Published: August 2018

AbstractA meta-analysis of genome-wide association studies (GWAS) identified eight loci that are associated with heart rate variability (HRV), but candidate genes in these loci remain uncharacterized. We developed an image- and CRISPR/Cas9-based pipeline to systematically characterize candidate genes for HRV in live zebrafish embryos. Nine zebrafish orthologues of six human candidate genes were targeted simultaneously in eggs from fish that transgenically express GFP on smooth muscle cells (Tg[acta2:GFP]), to visualize the beating heart. An automated analysis of repeated 30s recordings of beating atria in 381 live, intact zebrafish embryos at 2 and 5 days post-fertilization highlighted genes that influence HRV (hcn4 and si:dkey-65j6.2 [KIAA1755]); heart rate (rgs6 and hcn4); and the risk of sinoatrial pauses and arrests (hcn4). Exposure to 10 or 25µM ivabradine – an open channel blocker of HCNs – for 24h resulted in a dose-dependent higher HRV and lower heart rate at 5 days post-fertilization. Hence, our screen confirmed the role of established genes for heart rate and rhythm (RGS6 and HCN4); showed that ivabradine reduces heart rate and increases HRV in zebrafish embryos, as it does in humans; and highlighted a novel gene that plays a role in HRV (KIAA1755).
The origins and relatedness structure of mixed infections vary with local prevalence of P. falciparum malaria
Authors: Zhu Sha Joe , Hendry Jason A. , Almagro-Garcia Jacob , Pearson Richard D. , Amato Roberto , Miles Alistair , Weiss Daniel J. , Lucas Tim C.D. , Nguyen Michele , Gething Peter W. , Kwiatkowski Dominic , McVean Gil ,   for the Pf3k Project
Published: August 2018

AbstractIndividual malaria infections can carry multiple strains of Plasmodium falciparum with varying levels of relatedness. Yet, how local epidemiology affects the properties of such mixed infections remains unclear. Here, we develop an enhanced method for strain deconvolution from genome sequencing data, which estimates the number of strains, their proportions, identity-by-descent (IBD) profiles and individual haplotypes. Applying it to the Pf3k data set, we find that the rate of mixed infection varies from 29% to 63% across countries and that 51% of mixed infections involve more than two strains. Further-more, we estimate that 47% of symptomatic dual infections contain sibling strains likely to have been co-transmitted from a single mosquito, and find evidence of mixed infections propagated over successive infection cycles. Finally, leveraging data from the Malaria Atlas Project, we find that prevalence correlates within Africa, but not Asia, with both the rate of mixed infection and the level of IBD.
Systematic Analysis of Targets of Pumilio (PUM)-Mediated mRNA Decay Identifies a Role of PUM1 in Regulating DNA Damage Response Pathway
Authors: Yamada Toshimichi , Imamachi Naoto , Imamura Katsutoshi , Kawamura Takeshi , Suzuki Yutaka , Nagahama Masami , Akimitsu Nobuyoshi 
Published: August 2018

SummaryRNA-binding proteins (RBPs) play a pivotal role in gene expression by modulating the stability of transcripts; however, the identification of degradation targets of RBPs remains difficult. Here, we identified 48 target mRNAs of human Pumilio 1 (PUM1), an evolutionally conserved RBP, by combined analysis of transcriptome-wide mRNA stabilities and the binding of mRNAs to PUM1. Here, we developed an approach to identify mRNA targets of Pumilio 1 (PUM1), an evolutionally conserved RBP. By combined analysis of transcriptome-wide mRNA stabilities and the binding of mRNAs to PUM1, we identified 48 mRNAs that both bound to PUM1 and exhibited PUM1-dependent degradation. Analysis of changes in the abundance of PUM1 and its targets in RNA-seq data indicated that DNA-damaging agents negatively regulated PUM1-mediated mRNA decay. Cells exposed to cisplatin had reduced PUM1 abundance and increasedPCNAandUBE2AmRNAs, encoding proteins involved in DNA repair by translesion synthesis (TLS). Cells overexpressing PUM1 exhibited impaired DNA synthesis and TLS and increased sensitivity to the cytotoxic effect of cisplatin. Thus, our method identified targets of PUM1-mediated decay and revealed that cells respond to DNA damage by inhibiting PUM1-mediated mRNA decay to activate TLS.
Rapid Diagnosis of Lower Respiratory Infection using Nanopore-based Clinical Metagenomics
Authors: Charalampous Themoula , Richardson Hollian , Kay Gemma L. , Baldan Rossella , Jeanes Christopher , Rae Duncan , Grundy Sara , Turner Daniel J. , Wain John , Leggett Richard M. , Livermore David M. , O’Grady Justin 
Published: August 2018

AbstractLower respiratory infections (LRIs) accounted for three million deaths worldwide in 2016, the leading infectious cause of mortality. The “gold standard” for investigation of bacterial LRIs is culture, which has poor sensitivity and is too slow to guide early antibiotic therapy. Metagenomic sequencing potentially could replace culture, providing rapid, sensitive and comprehensive results. We developed a metagenomics pipeline for the investigation of bacterial LRIs using saponin-based host DNA depletion combined with rapid nanopore sequencing. The first iteration of the pipeline was tested on respiratory samples from 40 patients. It was then refined to reduce turnaround and increase sensitivity, before testing a further 41 samples. The refined method was 96.6% concordant with culture for detection of pathogens and could accurately detect resistance genes with a turnaround time of six hours. This study demonstrates that nanopore metagenomics can rapidly and accurately characterise bacterial LRIs when combined with efficient human DNA depletion.
Systematic dissection of biases in whole-exome and whole-genome sequencing reveals major determinants of coding sequence coverage
Authors: Barbitoff Yury A. , Polev Dmitrii E. , Glotov Andrey S. , Serebryakova Elena A. , Shcherbakova Irina V. , Kiselev Artem M. , Kostareva Anna A. , Glotov Oleg S. , Predeus Alexander V. 
Published: August 2018

AbstractNext generation DNA sequencing technologies are rapidly transforming the world of human genomics. Advantages and diagnostic effectiveness of the two most widely used resequencing approaches, whole exome (WES) and whole genome (WGS) sequencing, are still frequently debated. In our study we developed a set of statistical tools to systematically assess coverage of CDS regions provided by several modern WES platforms, as well as PCR-free WGS. Using several novel metrics to characterize exon coverage in WES and WGS, we showed that some of the WES platforms achieve substantially less biased CDS coverage than others, with lower within- and between-interval variation and virtually absent GC-content bias. We discovered that, contrary to a common view, most of the coverage bias in WES stems from mappability limitations of short reads, as well as exome probe design. We identified the ~ 500 kb region of human exome that could not be effectively characterized using short read technology. We also showed that the overall power for SNP and indel discovery in CDS region is virtually indistinguishable for WGS and best WES platforms. Our results indicate that deep WES (100x) using least biased technologies provides similar effective coverage (97% of 10x q10+ bases) and CDS variant discovery to the standard 30x WGS, suggesting that WES remains an efficient alternative to WGS in many applications. Our work could serve as a guide for selection of an up-to-date resequencing approach in human genomic studies.
Mutant p63 affects epidermal cell identity through rewiring the enhancer landscape
Authors: Qu Jieqiong , Tanis Sabine , Smits Jos P.H. , Kouwenhoven Evelyn N. , Oti Martin , van den Bogaard Ellen H. , Logie Colin , Stunnenberg Hendrik G. , van Bokhoven Hans , Mulder Klaas , Zhou Huiqing 
Published: August 2018

AbstractTranscription factor p63 is a key regulator of epidermal keratinocyte proliferation and differentiation. In humans mutations in p63 cause several developmental disorders with defects of ectoderm-derived structures including the epidermis. The underlying molecular mechanisms of these mutations however remain unclear. Here we characterized the transcriptome and epigenome from EEC syndrome patients carrying mutations in the p63 DNA-binding domain. The transcriptome of p63 mutant keratinocytes deviated from the normal epidermal cell identity. Epigenomic analyses showed that the deregulated gene expression in p63 mutant keratinocytes resulted from an altered enhancer landscape contributed by loss of p63-bound active enhancers and by unexpected gain of enhancers. The gained enhancers in mutant keratinocytes were frequently bound by deregulated transcription factors such as RUNX1. Reversing RUNX1 overexpression partially rescued deregulated gene expression as well as the enhancer distribution. Our findings support the pivotal role of p63 in controlling the enhancer landscape of epidermal keratinocytes and identify a novel mechanism whereby p63 DNA-binding mutations associated with EEC syndrome rewire the enhancer landscape and affect epidermal cell identity.
Correlates of cannabinoid concentrations, real-world driving, and driving-related skills
Authors: Johnson Mark B. 
Published: August 2018

AbstractResearch on the relationship between cannabis use and safe driving has produced mixed results. Most studies have focused exclusively on the presence or concentration of delta-9-tetrahydrocannabinol (THC), the primary psychoactive ingredient in the drug. However, cannabis is a complex substance, and both toxicological research and user experience suggests that some cannabis strains—often those with at least moderate levels of cannabidiol (CBD)— produce a different, more sedating “high” than cannabis strains with no or low levels of CBD. We hypothesize that the sedating properties of some high-CBD cannabis strains has potential to impair driving and driving-related skills above and beyond the effects of THC intoxication. Three studies—one instrumented vehicle driving study and two laboratory-style epidemiological studies—examined real driving and computerized task performance as a function THC and CBD concentrations (and their interactions). In all three studies, higher CBD levels predicted greater impairment. There was relatively little evidence of impairment when CBD was zero, even at high THC levels. The results suggest that THC concentrations alone are not sufficient to predict impairment due to cannabis use. Results are interpreted in the context of drug tolerance.
SyngenicDNA: stealth-based evasion of restriction-modification barriers during bacterial genetic engineering
Authors: Johnston Christopher D. , Cotton Sean , Rittling Susan R. , Starr Jacqueline R. , Borisy Gary , Dewhirst Floyd E. , Lemon Katherine P. 
Published: August 2018

AbstractRestriction-modification (RM) systems hinder the use of genetic approaches in the vast majority of bacteria. Here, we describe a systematic approach to adapt genetic tools for use in bacteria that are genetically intractable or poorly tractable owing to active RM defenses. In this process, we determine the genome and methylome of a bacterial strain and use this information to define the bacterium’s RM target motifs. We then synonymously eliminate RM targets from the nucleotide sequence of a genetic toolin silico,synthesize an RM-silent ‘SyngenicDNA’ tool and propagate the tool as novel minicircle plasmids, termed SyMPL tools, before transformation. Using SyngenicDNA and SyMPL tools, we achieved a profound, >100,000- fold, improvement in the transformation of a clinically relevant USA300 strain ofStaphylococcus aureusdemonstrating the efficacy of these approaches for evading RM systems. The SyngenicDNA and SyMPL approaches are effective, flexible, and should be broadly applicable in microbial genetics. We expect these will facilitate a new era of microbial genetics free of the restraints of restriction-modification barriers.
Transcriptome analysis of mycorrhizal and non-mycorrhizal soybean plantlets upon infection withFusarium virguliforme, one causal agent of sudden death syndrome
Authors: Marquez N. , Giachero M. L. , Gallou A. , Debat H. J. , Declerck S. , Ducasse D. A. 
Published: August 2018

ABSTRACTSoilborne pathogens represent a threat to agriculture causing important yield losses. The “Sudden Death Syndrome” (SDS), a severe disease in soybean is caused by a complex ofFusariumspecies. This pathosystem has been widely investigated and several strategies were proposed to manage SDS. Although a decrease in symptoms and in the level of root tissue infection particularly byF. virguliformewas observed in presence of arbuscular mycorrhizal fungi (AMF), biological control based on AMF has received less attention. Here we report the results, under strictin vitroculture experimental conditions, a transcriptional analysis in mycorrhizal versus non-mycorrhizal soybean plantlets upon infection byF. virguliforme.An important transcriptional reprogramming was detected following infection by the pathogen. Results revealed 1768 and 967 differentially expressed genes in the AMF-colonized (+AMF+Fv) and non-colonized (−AMF+Fv) plants, respectively. Major transcriptional changes, corresponded to defence response related genes belonging to secondary metabolism, stress and signalling categories. The +AMF+Fv treatment showed the largest number of upregulated genes related to defence, as those encoding for disease resistance proteins, WRKY transcription factors, auxins, receptors kinases, and proteases. Only few genes had primed expression in +AMF+Fv treatment, as those coding for a thaumatin-like protein (TLP) and a pleiotropic drug resistance (PDR) protein. Moreover, +AMF+Fv showed a significant number of downregulated genes related to cell wall modification and peroxidases than – AMF+Fv treatment. This detailed insight increases our knowledge on the transcriptional changes and the potential metabolic pathways involved in the enhanced resistance/tolerance of mycorrhizal plants upon infection withF. virguliforme.
Measuring Illumina Size Bias Using REcount: A Novel Method for Highly Accurate Quantification of Engineered Genetic Constructs
Authors: Gohl Daryl M. , Becker Aaron , Johnson Darrell , Anderson Shea , Billstein Bradley , McDevitt Shana L. , Beckman Kenneth B. 
Published: August 2018

AbstractQuantification of DNA sequence tags associated with engineered genetic constructs underlies many genomics measurements. Typically, such measurements are done using PCR to enrich sequence tags and add adapters, followed by next-generation sequencing (NGS). However, PCR amplification can introduce significant quantitative error into these measurements. Here we describe REcount, a novel PCR-free direct counting method for NGS-based quantification of engineered genetic constructs. By comparing measurements of defined plasmid pools to droplet digital PCR data, we demonstrate that this method is highly accurate and reproducible. We further demonstrate that the REcount approach is amenable to multiplexing through the use of orthogonal restriction enzymes. Finally, we use REcount to provide new insights into clustering biases due to molecule length across different Illumina sequencing platforms.
Virus-inclusive single cell RNA sequencing reveals molecular signature predictive of progression to severe dengue infection
Authors: Zanini Fabio , Robinson Makeda L. , Croote Derek , Sahoo Malaya Kumar , Sanz Ana Maria , Ortiz-Lasso Eliana , Albornoz Ludwig Luis , Suarez Fernando Rosso , Montoya Jose G. , Pinsky Benjamin A. , Quake Stephen R. , Einav Shirit 
Published: August 2018

AbstractDengue virus (DENV) infection can result in severe complications. Yet, the understanding of the molecular correlates of severity is limited, partly due to difficulties in defining the peripheral blood mononuclear cells (PBMCs) that are associated with DENV in vivo. Additionally, there are currently no biomarkers predictive of progression to severe dengue (SD). Bulk transcriptomics data are difficult to interpret because blood consists of multiple cell types that may react differently to infection. Here we applied virus-inclusive single cell RNA-seq approach (viscRNA-Seq) to profile transcriptomes of thousands of single PBMCs derived early in the course of disease from six dengue patients and four healthy controls, and to characterize distinct DENV-associated leukocytes. Multiple genes, particularly interferon response genes, were upregulated in a cell-specific manner prior to progression to SD. Expression of MX2 in naive B cells and CD163 in CD14+ CD16+ monocytes was predictive of SD. The majority of DENV-associated cells in the blood of two patients who progressed to SD were naive IgM B cells expressing the CD69 and CXCR4 receptors and antiviral genes, followed by monocytes. Bystander uninfected B cells also demonstrated immune activation, and plasmablasts from two patients exhibited antibody lineages with convergently hypermutated heavy chain sequences. Lastly, assembly of the DENV genome revealed diversity at unexpected genomic sites. This study presents a multi-faceted molecular elucidation of natural dengue infection in humans and proposes biomarkers for prediction of SD, with implications for profiling any tissue and viral infection, and for the development of a dengue prognostic assay.SignificanceA fraction of the 400 million people infected with dengue annually progresses to severe dengue (SD). Yet, there are currently no biomarkers to effectively predict disease progression. We profiled the landscape of host transcripts and viral RNA in thousands of single blood cells from dengue patients prior to progressing to SD. We discovered cell-type specific immune activation and candidate predictive biomarkers. We also revealed preferential virus association with specific cell populations, particularly naive B cells and monocytes. We then explored immune activation of bystander cells, clonality and somatic evolution of adaptive immune repertoires, and viral genomics. This multi-faceted approach could advance understanding of pathogenesis of any viral infection, map an atlas of infected cells and promote the development of prognostics.
Efficiency and precision of miRNA biogenesis modes in plants
Authors: Moro Belén , Chorostecki Uciel , Arikit Siwaret , Suarez Irina P. , Höbartner Claudia , Rasia Rodolfo M. , Meyers Blake C. , Palatnik Javier F. 
Published: August 2018

AbstractMany evolutionary conserved microRNAs (miRNAs) in plants regulate transcription factors with key functions in development. Hence, mutations in the core components of the miRNA biogenesis machinery cause strong growth defects. An essential aspect of miRNA biogenesis is the precise excision of the small RNA from its precursor. In plants, miRNA precursors are largely variable in size and shape and can be processed by different modes. Here, we optimized an approach to detect intermediates during miRNA biogenesis. We characterized a miRNA whose processing is triggered by a terminal branched loop. Plant miRNA processing can be initiated by internal bubbles, small terminal loops or branched loops followed by dsRNA segments of 15-17 bp. Interestingly, precision and efficiency vary with the processing modes. Despite the various potential structural determinants present in a single a miRNA precursor, DCL1 is mostly guided by a predominant structural region in each precursor in wild-type plants. However, our studies in fiery1, hyl1 and se mutants revealed the existence of cleavage signatures consistent with the recognition of alternative processing determinants. The results provide a general view of the mechanisms underlying the specificity of miRNA biogenesis in plants.
bin3C : Exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes (MAGs)
Authors: DeMaere Matthew Z. , Darling Aaron E. 
Published: August 2018

AbstractMost microbes inhabiting the planet cannot be easily grown in the lab. Metagenomic techniques provide a means to study these organisms, and recent advances in the field have enabled the resolution of individual genomes from metagenomes, so-called Metagenome Assembled Genomes (MAGs). In addition to expanding the catalog of known microbial diversity, the systematic retrieval of MAGs stands as a tenable divide and conquer reduction of metagenome analysis to the simpler problem of single genome analysis. Many leading approaches to MAG retrieval depend upon time-series or transect data, whose effectiveness is a function of community complexity, target abundance and depth of sequencing. Without the need for time-series data, promising alternative methods are based upon the high-throughput sequencing technique called Hi-C.The Hi-C technique produces read-pairs which capture in-vivo DNA-DNA proximity interactions (contacts). The physical structure of the community modulates the signal derived from these interactions and a hierarchy of interaction rates exists (īntra-chromosomal > Inter-chromosomal > Inter-cellular).We describe an unsupervised method that exploits the hierarchical nature of Hi-C interaction rates to resolve MAGs from a single time-point. As a quantitative demonstration, next, we validate the method against the ground truth of a simulated human faecal microbiome. Lastly, we directly compare our method against a recently announced proprietary service ProxiMeta, which also performs MAG retrieval using Hi-C data.bin3C has been implemented as a simple open-source pipeline and makes use of the unsupervised community detection algorithm Infomap (https://github.com/cerebis/bin3C).
Positive Selection and Adaptation of Novel Inner Ear Genes in the Mammalian Lineage
Authors: Pisciottano Francisco , Cinalli Alejandro R. , Stopiello Matías , Castagna Valeria C. , Belén Elgoyhen Ana , Rubinstein Marcelo , Gómez-Casati María Eugenia , Franchini Lucía F. 
Published: August 2018

AbstractThe mammalian inner ear possesses functional and morphological innovations that contribute to its unique hearing capacities. The genetic bases underlying the evolution of this mammalian landmark are poorly understood. We propose that the emergence of morphological and functional innovations in the mammalian inner ear could have been driven by adaptive molecular evolution.In this work, we analyzed the complete inner ear transcriptome in order to identify genes that show signatures of adaptive evolution in this lineage. We analyzed approximately 1,300 inner ear expressed genes and found that 13 % show signatures of positive selection in the mammalian lineage. Several of these genes are known to play an important function in the inner ear. In addition, we identified that a significant proportion of genes showing signatures of adaptive evolution in mammals have not been previously reported to participate in inner ear development and/or physiology. We focused our analysis in two of these novel genes:STRIP2andABLIM2by generating null mutant mice and analyzed their auditory function. We found that mice lackingStrip2displayed a decrease in neural response amplitudes. In addition, we observed a reduction in the number of afferent synapses, suggesting a potential cochlear neuropathy.Thus, this study shows the usefulness of pursuing a high-throughput evolutionary approach followed by functional studies to track down novel genes that are important for inner ear function. Moreover, this approach sheds light on the genetic basis underlying the evolution of the mammalian inner ear.