bluuebunny/crossref_metadata_2025_split huggingface dataset:
Advanced Whole Genome Sequencing Using an Entirely PCR-free Massively Parallel Sequencing Workflow
Authors: Shen Hanjie , Liu Pengjuan , Li Zhanqing , Chen Fang , Jiang Hui , Shi Shiming , Xi Yang , Li Qiaoling , Wang Xiaojue , Zhao Jing , Liang Xinming , Xie Yinlong , Wang Lin , Tian Wenlan , Berntsen Tam , Alexeev Andrei , Luo Yinling , Gong Meihua , Li Jiguang , Xu Chongjun , Barua Nina , Drmanac Snezana , Dai Sijie , Mi Zilan , Ren Han , Lin Zhe , Chen Ao , Zhang Wenwei , Mu Feng , Xu Xun , Zhao Xia , Jiang Yuan , Drmanac Radoje 
Published: December 2019

AbstractBackgroundSystematic errors can be introduced from DNA amplification during massively parallel sequencing (MPS) library preparation and sequencing array formation. Polymerase chain reaction (PCR)-free genomic library preparation methods were previously shown to improve whole genome sequencing (WGS) quality on the Illumina platform, especially in calling insertions and deletions (InDels). We hypothesized that substantial InDel errors continue to be introduced by the remaining PCR step of DNA cluster generation. In addition to library preparation and sequencing, data analysis methods are also important for the accuracy of the output data.In recent years, several machine learning variant calling pipelines have emerged, which can correct the systematic errors from MPS and improve the data performance of variant calling.ResultsHere, PCR-free libraries were sequenced on the PCR-free DNBSEQ™ arrays from MGI Tech Co., Ltd. (referred to as MGI) to accomplish the first true PCR-free WGS which the whole process is truly not only PCR-free during library preparation but also PCR-free during sequencing. We demonstrated that PCR-based WGS libraries have significantly (about 5 times) more InDel errors than PCR-free libraries.Furthermore, PCR-free WGS libraries sequenced on the PCR-free DNBSEQ™ platform have up to 55% less InDel errors compared to the NovaSeq platform, confirming that DNA clusters contain PCR-generated errors.In addition, low coverage bias and less than 1% read duplication rate was reproducibly obtained in DNBSEQ™ PCR-free using either ultrasonic or enzymatic DNA fragmentation MGI kits combined with MGISEQ-2000. Meanwhile, variant calling performance (single-nucleotide polymorphisms (SNPs) F-score>99.94%, InDels F-score>99.6%) exceeded widely accepted standards using machine learning (ML) methods (DeepVariant or DNAscope).ConclusionsEnabled by the new PCR-free library preparation kits, ultra high-thoughput PCR-free sequencers and ML-based variant calling, true PCR-free DNBSEQ™ WGS provides a powerful solution for improving WGS accuracy while reducing cost and analysis time, thus facilitating future precision medicine, cohort studies, and large population genome projects.
Low basal expression and slow induction of IFITM3 puts immune cells at risk of influenza A infection
Authors: Wellington Dannielle , Yin Zixi , Zhang Liwei , Forbester Jessica , Kite Kerry , Laurenson-Schafer Henry , Makvandi-Nejad Shokouh , Jin Boquan , Bowes Emma , Manoharan Krishnageetha , Maldonado-Perez David , Verill Clare , Humphreys Ian , Dong Tao 
Published: December 2019

AbstractThe interferon-induced transmembrane protein, IFITM3, has been shown to restrict influenza virus infection in murine andin vitrosettings for ten years, but no explanation has been found to explain why this virus infection is so highly contagious and infects most individuals it comes in contact with. We confirm that the expression level of IFITM3 plays a role in determining the level of viral infection through manipulation of IFITM3 levels with interferon (IFN) stimulation and overexpression systems. Low basal expression may put some immune cells, including lymphocytes and lung-resident macrophages, at risk of influenza virus infection. Investigating the induction of IFITM3 by IFN, we find a strong preference for Type I IFN in IFITM3 induction in both cell lines and primary human cells. While myeloid cells can increase expression following stimulation by Type I IFN, lymphocytes show minimal induction of IFITM3 following IFN stimulation, suggesting that they are always at risk of viral infection. Surprisingly, we found that the time it takes for maximal induction of IFITM3 is relatively slow for an interferon-stimulated gene at around 36 hours. Low basal expression and slow induction of IFITM3 could increase the risk of influenza virus infection in selected immune cells.ImportanceInfluenza virus infection remains one of the top ten threats to global health, causing significant deaths and hospitalisations across the world each year. Understanding mechanisms for controlling influenza virus infection remain a priority. The interferon-induced transmembrane protein IFITM3 can restrict influenza infection by limiting replication of the virus. The precise mechanisms of how IFITM3 reduced replication of influenza are unknown, although it is predicted to prevent release of viral contents into the cytosol by preventing pore formation on the endosomal compartments where it is suggested to reside. Here we have shown that the expression level of IFITM3 is important in determining the control of influenza virus infection. We find an expression pattern for IFITM3 that varies based on cell type, tissue locality, differentiation state and cell naivety, all of which highlights cells that may be at the highest risk of influenza infection.
A single-cell atlas of the human healthy airways
Authors: Deprez Marie , Zaragosi Laure-Emmanuelle , Truchi Marin , Garcia Sandra Ruiz , Arguel Marie-Jeanne , Lebrigand Kevin , Paquet Agnès , Pee’r Dana , Marquette Charles-Hugo , Leroy Sylvie , Barbry Pascal 
Published: December 2019

AbstractRationaleThe respiratory tract constitutes an elaborated line of defense based on a unique cellular ecosystem. Single-cell profiling methods enable the investigation of cell population distributions and transcriptional changes along the airways.MethodsWe have explored cellular heterogeneity of the human airway epithelium in 10 healthy living volunteers by single-cell RNA profiling. 77,969 cells were collected by bronchoscopy at 35 distinct locations, from the nose to the 12thdivision of the airway tree.ResultsThe resulting atlas is composed of a high percentage of epithelial cells (89.1%), but also immune (6.2%) and stromal (4.7%) cells with peculiar cellular proportions in different sites of the airways. It reveals differential gene expression between identical cell types (suprabasal, secretory, and multiciliated cells) from the nose (MUC4,PI3,SIX3) and tracheobronchial (SCGB1A1,TFF3) airways. By contrast, cell-type specific gene expression was stable across all tracheobronchial samples. Our atlas improves the description of ionocytes, pulmonary neuro-endocrine (PNEC) and brush cells, which are likely derived from a common population of precursor cells. We also report a population ofKRT13positive cells with a high percentage of dividing cells which are reminiscent of “hillock” cells previously described in mouse.ConclusionsRobust characterization of this unprecedented large single-cell cohort establishes an important resource for future investigations. The precise description of the continuum existing from nasal epithelium to successive divisions of lung airways and the stable gene expression profile of these regions better defines conditions under which relevant tracheobronchial proxies of human respiratory diseases can be developed.
Transcriptomic responses to hypoxia in endometrial and decidual stromal cells
Authors: Rytkönen Kalle T. , Heinosalo Taija , Mahmoudian Mehrad , Ma Xinghong , Perheentupa Antti , Elo Laura L. , Poutanen Matti , Wagner Günter P. 
Published: December 2019

AbstractHuman reproductive success depends on a properly decidualized uterine endometrium that allows implantation and the formation of the placenta. At the core of the decidualization process are endometrial stromal fibroblasts (ESF) that differentiate to decidual stromal cells (DSC). As variations in oxygen levels are functionally relevant in endometrium both upon menstruation and during placentation, we assessed the transcriptomic responses to hypoxia in ESF and DSC. In both cell types hypoxia upregulated genes in classical hypoxia pathways such as glycolysis and the epithelial mesenchymal transition. In DSC hypoxia restored an ESF like transcriptional state for a subset of transcription factors that are known targets of the progesterone receptor, suggesting that hypoxia partially interferes with progesterone signaling. In both cell types hypoxia modified transcription of several inflammatory transcription factors that are known regulators of decidualization, including decreased transcription ofSTATsand increased transcription ofCEBPs. We observed that hypoxia upregulated genes had a significant overlap with genes previously detected to be upregulated in endometriotic stromal cells. Promoter analysis of the genes in this overlap suggested the hypoxia upregulated Jun/Fos and CEBP transcription factors as potential drivers of endometriosis-associated transcription. Using immunohistochemistry we observed increased expression of JUND and CEBPD in endometriosis lesions compared to healthy endometria. Overall the findings suggest that hypoxic stress establishes distinct transcriptional states in ESF and DSC, and that hypoxia influences the expression of genes that contribute to the core gene regulation of endometriotic stromal cells.
OBERON3 and SUPPRESSOR OF MAX2 1-LIKE proteins form a regulatory module specifying phloem identity
Authors: Wallner Eva-Sophie , Tonn Nina , Shi Dongbo , Luzzietti Laura , Wanke Friederike , Hunziker Pascal , Xu Yingqiang , Jung Ilona , Lopéz-Salmerón Vadir , Gebert Michael , Wenzl Christian , Lohmann Jan U. , Harter Klaus , Greb Thomas 
Published: December 2019

AbstractSpatial specificity of cell fate decisions is central for organismal development. The phloem tissue mediates long-distance transport of energy metabolites along plant bodies and is characterized by an exceptional degree of cellular specialization. How a phloem-specific developmental program is implemented is, however, unknown. Here we reveal that the ubiquitously expressed PHD-finger protein OBE3 forms a central module with the phloem- specific SMXL5 protein for establishing phloem identity inArabidopsis thaliana. By protein interaction studies and phloem-specific ATAC-seq analyses, we show that OBE3 and SMXL5 proteins form a complex in nuclei of phloem stem cells where they establish a phloem-specific chromatin profile. This profile allows expression ofOPS,BRX,BAM3, andCVP2genes acting as mediators of phloem differentiation. Our findings demonstrate that OBE3/SMXL5 protein complexes establish nuclear features essential for determining phloem cell fate and highlight how a combination of ubiquitous and local regulators generate specificity of developmental decisions in plants.
Disentangling microbial associations from hidden environmental and technical factors via latent graphical models
Authors: Kurtz Zachary D. , Bonneau Richard , Müller Christian L. 
Published: December 2019

AbstractDetecting community-wide statistical relationships from targeted amplicon-based and metagenomic profiling of microbes in their natural environment is an important step toward understanding the organization and function of these communities. We present a robust and computationally tractable latent graphical model inference scheme that allows simultaneous identification of parsimonious statistical relationships among microbial species and unobserved factors that influence the prevalence and variability of the abundance measurements. Our method comes with theoretical performance guarantees and is available within the SParse InversE Covariance estimation for Ecological ASsociation Inference (SPIEC-EASI) framework (‘SpiecEasi’ R-package). Using simulations, as well as a comprehensive collection of amplicon-based gut microbiome datasets, we illustrate the method’s ability to jointly identify compositional biases, latent factors that correlate with observed technical covariates, and robust statistical microbial associations that replicate across different gut microbial data sets.
Analysis of human mitochondrial genome co-occurrence networks of Asian population at varying altitudes
Authors: Verma Rahul K , Kalyakulina Alena , Giuliani Cristina , Shinde Pramod , Kachhvah Ajay Deep , Ivanchenko Mikhail , Jalan Sarika 
Published: December 2019

ABSTRACTNetworks have been established as an extremely powerful framework to understand and predict the behavior of many large-scale complex systems. We have studied network motifs, the basic structural elements of networks, to describe the possible role of co-occurrence of genomic variations behind high altitude adaptation in the Asian human population. Mitochondrial DNA (mt-DNA) variations have been acclaimed as one of the key players in understanding the biological mechanisms behind adaptation to extreme conditions. To explore the cumulative effects and variations in the mitochondrial genome with the variation in the altitude, we investigated human mt-DNA sequences from the NCBI database at different altitudes under the co-occurrence motifs framework. Analysis of the co-occurrence motifs using similarity clusteringrevealed a clear distinction between lower and higher altitude regions. In addition, the previously known high altitude markers 3394 and 7697 (which are definitive sites of haplogroup M9a1a1c1b) were found to co-occur within their own gene complexes indicating the impact of intra-genic constraint on co-evolution of nucleotides. Furthermore, an ancestral ‘RSRS50’ variant 10398 was found to co-occur only at higher altitudes supporting the fact that a separate route of colonization at these altitudes might have taken place. Overall, our analysis revealed the presence of co-occurrence interactions specific to high altitude at a whole mitochondrial genome level. This study, combined with the classical haplogroups analysis is useful in understanding the role of co-occurrence of mitochondrial variations in high altitude adaptation.
Competition for access to mates predicts female-specific ornamentation and polyandry
Authors: Murray Rosalind L. , Herridge Elizabeth J. , Ness Rob W. , Wiberg R. Axel W. , Bussière Luc F. 
Published: December 2019

AbstractSexually selected ornaments are highly variable and the factors that drive variation in ornament expression are not always clear. Rare instances of female-specific ornament evolution (such as in some dance fly species) are particularly puzzling. While some evidence suggests that such rare instances represent straightforward reversals of sexual selection intensity, the distinct nature of trade-offs between ornaments and offspring pose special constraints in females. To examine whether competition for access to mates generally favours heightened ornament expression, we built a phylogeny and conducted a comparative analysis of Empidinae dance fly taxa that display ornate female-specific ornaments. We show that species with more female-biased operational sex ratios in lek-like mating swarms have greater female ornamentation, and in taxa with more ornate females, polyandry is increased. These findings support the hypothesis that ornament diversity in dance flies depends on female receptivity, which is associated with contests for nutritious nuptial gifts provided by males. Moreover, our results suggest that increases in female receptivity lead to higher levels of polyandry and sperm competition among males. The incidence of both heightened pre-mating sexual selection on females and post-mating selection on males contradicts assertions that sex-roles are straightforwardly reversed in dance flies.
XACT-seq comprehensively defines the promoter-position and promoter-sequence determinants for initial-transcription pausing
Authors: Winkelman Jared T. , Pukhrambam Chirangini , Vvedenskaya Irina O. , Zhang Yuanchao , Taylor Deanne M. , Shah Premal , Ebright Richard H. , Nickels Bryce E. 
Published: December 2019

AbstractPausing by RNA polymerase (RNAP) during transcription elongation, in which a translocating RNAP uses a “stepping” mechanism, has been studied extensively, but pausing by RNAP during initial transcription, in which a promoter-anchored RNAP uses a “scrunching” mechanism, has not. We report a method that directly defines RNAP-active-center position relative to DNAin vivowith single-nucleotide resolution (XACT-seq; crosslink-between-active-center-and-template sequencing). We apply this method to detect and quantify pausing in initial transcription at 411(∼4,000,000) promoter sequencesin vivo, inEscherichia coli. The results show initial-transcription pausing can occur in each nucleotide addition during initial transcription, particularly the first 4-5 nucleotide additions. The results further show initial-transcription pausing occurs at sequences that resemble the consensus sequence element for transcription-elongation pausing. Our findings define the positional and sequence determinants for initial-transcription pausing and establish initial-transcription pausing is hard-coded by sequence elements similar to those for transcription-elongation pausing.
Spatiotemporal analysis of host cell modification during herpes simplex virus 1 replication
Authors: Scherer Katharina M. , Manton James D. , Soh Timothy K. , Mascheroni Luca , Connor Viv , Crump Colin M. , Kaminski Clemens F. 
Published: December 2019

AbstractHerpesviruses are large and complex viruses, and have a long evolutionary history with their host species. One poorly understood, but important, area in virus-host interaction is the extensive remodelling of intracellular organelles and morphology that occurs during active viral replication. We have constructed a recombinant reporter virus that allowed us to classify four distinct stages in the infection cycle of herpes simplex virus 1. Single-cell analysis of the impact of the viral load on replication dynamics demonstrates the utility of this times-tamping method for tracking the infection cycle. High-resolution microscopy analysis of cellular structures in live and fixed cells in concert with our dual-fluorescent reporter virus have enabled us to generate a detailed overview over the spatial and temporal organisation of the cytoskeleton and organelles during viral replication. This provides the first systems-level analysis of the morphological changes involved in viral replication.
GABA signalling in guard cells acts as a ‘stress memory’ to optimise plant water loss
Authors: Xu Bo , Long Yu , Feng Xueying , Zhu Xujun , Sai Na , Chirkova Larissa , Herrmann Johannes , Okamoto Mamoru , Hedrich Rainer , Gilliham Matthew 
Published: December 2019

AbstractThe non-protein amino acid γ-aminobutyric acid (GABA) has been proposed to be an ancient messenger for cellular communication conserved across biological kingdoms. GABA has well-defined signalling roles in animals; however, whilst GABA accumulates in plants under stress it has not been determined if, how, where and when GABA acts as an endogenous plant signalling molecule. Here, we establish that endogenous GABA is abona fideplant signal, acting via a mechanism not found in animals. GABA antagonises stomatal movement in response to opening and closing stimuli in multiple plant families including dicot and monocot crops. UsingArabidopsis thaliana, we show guard cell GABA production is necessary and sufficient to influence stomatal aperture, transpirational water loss and drought tolerance via inhibition of stomatal guard cell plasma membrane and tonoplast-localised anion transporters. This study proposes a novel role for GABA – as a ‘stress memory’ – opening new avenues for improving plant stress tolerance.
Microglial homeostasis requires balanced CSF-1/CSF-2 receptor signaling
Authors: Chitu Violeta , Biundo Fabrizio , Shlager Gabriel G. L. , Park Eun S. , Wang Ping , Gulinello Maria E. , Gokhan Solen , Ketchum Harmony C. , Saha Kusumika , DeTure Michael A. , Dickson Dennis W. , Wszolek Zbignew K. , Zheng Deyou , Croxford Andrew L. , Becher Burkhard , Sun Daqian , Mehler Mark F. , Stanley E. Richard 
Published: December 2019

SummaryCSF-1Rhaploinsufficiency causes adult-onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP). Previous studies in theCsf1r+/-mouse model of ALSP hypothesized a central role of elevated cerebralCsf2expression. Here we show that monoallelic deletion ofCsf2rescues most behavioral deficits and histopathological changes inCsf1r+/-mice by preventing microgliosis and eliminating most microglial transcriptomic alterations, including those indicative of oxidative stress and demyelination. We also show elevation ofCsf2transcripts and of several CSF-2 downstream targets in the brains of ALSP patients, demonstrating that the mechanisms identified in the mouse model are functional in man. Our data provide new insights into the mechanisms underlying ALSP. Since both increasedCSF2levels and decreased microglialCsf1rexpression have also been reported in Alzheimer’s disease and multiple sclerosis, we suggest that the unbalanced CSF-1R/CSF-2 signaling we describe in the present study may contribute to the pathogenesis of other neurodegenerative conditions.HighlightsALSP is aCSF1R-deficiency dementia associated with increasedCSF2expressionInCsf1r+/-ALSP mice CSF-2 promotes microgliosis by direct signaling in microgliaTargetingCsf2improves cognition, myelination and normalizes microglial functionCSF-2 is a therapeutic target in ALSP
Fluorescent secreted bacterial effectors reveal active intravacuolar proliferation ofListeria monocytogenesin epithelial cells
Authors: Peron-Cane Caroline , Fernandez José-Carlos , Leblanc Julien , Wingertsmann Laure , Gautier Arnaud , Desprat Nicolas , Lebreton Alice 
Published: December 2019

AbstractReal-time imaging of bacterial virulence factor dynamics is hampered by the limited number of fluorescent tools suitable for tagging secreted effectors. Here, we demonstrated that the fluorogenic reporter FAST could be used to tag secreted proteins, and we implemented it to monitor infection dynamics in epithelial cells exposed to the human pathogenListeria monocytogenes(Lm). By tracking individual FAST-labelled vacuoles afterLminternalisation into cells, we unveiled the heterogeneity of residence time inside entry vacuoles. Although half of the bacterial population escaped within 13 minutes after entry, 12% of bacteria remained entrapped over an hour inside long term vacuoles, and sometimes much longer, regardless of the secretion of the pore-forming toxin listeriolysin O (LLO). We imaged LLO-FAST in these long-term vacuoles, and showed that LLO enabledLmto proliferate inside these compartments, reminiscent of what had been previously observed for SpaciousListeria-containing phagosomes (SLAPs). Unexpectedly, inside epithelial SLAP-like vacuoles (eSLAPs),Lmproliferated as fast as in the host cytosol. eSLAPs thus constitute an alternative replication niche in epithelial cells that might promote the colonization of host tissues.Author summaryBacterial pathogens secrete virulence factors to subvert their hosts; however, monitoring bacterial secretion in real-time remains challenging. Here, we developed a convenient method that enabled fluorescent imaging of secreted proteins in live microscopy, and applied it to the human pathogenListeria monocytogenes.Listeriahas been described to invade cells and proliferate in their cytosol; it is first internalized inside vacuoles, from where it escapes thanks to the secretion of virulence factors that disrupt membranes. Our work revealed the existence, in human epithelial cells, of a population ofListeriathat failed to escape vacuoles but instead multiplied efficiently therein, despite -and in fact, thanks to— the active secretion of a toxin that permeates membranes. This intravacuolar niche may provideListeriawith an alternative strategy to colonize its host.