Similar Datasets
Project description:Genetic variants, including mobile element insertions (MEIs), are known to impact the epigenome. We hypothesized that genome graphs, which encapsulate genetic diversity, could reveal missing epigenomic signals. To test this, we sequenced the epigenome of monocyte-derived macrophages from 35 ancestrally diverse individuals before and after influenza infection, allowing us to investigate the role of MEIs in immunity. We characterized genetic variants and MEIs using linked reads and built a genome graph. Mapping epigenetic data revealed 2.3%-3% novel peaks for H3K4me1, H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq), and ATAC-seq. Additionally, the use of a genome graph modified some quantitative trait loci estimates and revealed 375 polymorphic MEIs in an active epigenomic state. Among these is an AluYh3 polymorphism whose chromatin state changed after infection and was associated with the expression of TRIM25, a gene that restricts influenza RNA synthesis. Our results demonstrate that graph genomes can reveal regulatory regions that would have been overlooked by other approaches.
| S-EPMC10203048 | biostudies-literature
Project description:Genetic variants, including mobile element insertions (MEIs), are known to impact the epigenome. We hypothesized that the use of a genome graph, which encapsulates genetic diversity, could reveal missing epigenomic signal. We tested this in a dataset obtained by sequencing the epigenome of monocyte-derived macrophages from 35 ancestrally diverse individuals before and after Influenza virus infection, which also allowed us to investigate the potential role of MEIs in immunity. After characterizing genetic variants in this cohort using linked-reads, including 5140 Alu, 316 L1, 94 SVAs and 48 ERVs, we incorporated them into a genome graph. Mapping epigenetic data to this graph revealed 2.5%, 3.0% and 2.3% novel peaks for H3K4me1 and H3K27ac ChIP-seq and ATAC-seq respectively. Notably, using a genome graph also modified quantitative trait loci estimates and we observed 375 polymorphic MEIs in active epigenomic state. For example, we found an AluYh3 polymorphism whose chromatin state changed after infection and that was associated with the expression of TRIM25, a gene that restricts influenza RNA synthesis. Our results demonstrate that graph genomes can reveal regulatory regions that would have been overlooked by other approaches.
2023-02-21 | GSE225706 | GEO
Project description:Genetic variants, including mobile element insertions (MEIs), are known to impact the epigenome. We hypothesized that the use of a genome graph, which encapsulates genetic diversity, could reveal missing epigenomic signal. We tested this in a dataset obtained by sequencing the epigenome of monocyte-derived macrophages from 35 ancestrally diverse individuals before and after Influenza virus infection, which also allowed us to investigate the potential role of MEIs in immunity. After characterizing genetic variants in this cohort using linked-reads, including 5140 Alu, 316 L1, 94 SVAs and 48 ERVs, we incorporated them into a genome graph. Mapping epigenetic data to this graph revealed 2.5%, 3.0% and 2.3% novel peaks for H3K4me1 and H3K27ac ChIP-seq and ATAC-seq respectively. Notably, using a genome graph also modified quantitative trait loci estimates and we observed 375 polymorphic MEIs in active epigenomic state. For example, we found an AluYh3 polymorphism whose chromatin state changed after infection and that was associated with the expression of TRIM25, a gene that restricts influenza RNA synthesis. Our results demonstrate that graph genomes can reveal regulatory regions that would have been overlooked by other approaches.
2023-02-21 | GSE225704 | GEO
Project description:Genome graphs detect human polymorphisms in active epigenomic state during influenza infection
| PRJNA937192 | ENA
Project description:Genome graphs detect human polymorphisms in active epigenomic state during influenza infection [ATAC-seq]
| PRJNA937198 | ENA
Project description:Genome graphs detect human polymorphisms in active epigenomic state during influenza infection [ChIP-seq]
| PRJNA937199 | ENA
Project description:Model-checking is a methodology developed in computer science to automatically assess the dynamics of discrete systems, by checking if a system modelled as a state-transition graph satisfies a dynamical property written as a temporal logic formula. The dynamics of ecosystems have been drawn as state-transition graphs for more than a century, ranging from state-and-transition models to assembly graphs. Model-checking can provide insights into both empirical data and theoretical models, as long as they sum up into state-transition graphs. While model-checking proved to be a valuable tool in systems biology, it remains largely underused in ecology apart from precursory applications. This article proposes to address this situation, through an inventory of existing ecological STGs and an accessible presentation of the model-checking methodology. This overview is illustrated by the application of model-checking to assess the dynamics of a vegetation pathways model. We select management scenarios by model-checking Computation Tree Logic formulas representing management goals and built from a proposed catalogue of patterns. In discussion, we sketch bridges between existing studies in ecology and available model-checking frameworks. In addition to the automated analysis of ecological state-transition graphs, we believe that defining ecological concepts with temporal logics could help clarify and compare them.
| S-EPMC9203009 | biostudies-literature
Project description:Influenza A virus (IAV) is a major respiratory pathogen of both humans and animals. The lung is protected from pathogens by alveolar epithelial cells, tissue-resident alveolar macrophages, dendritic cells, and mast cells. The role of alveolar epithelial cells, endothelial cells, and alveolar macrophages during IAV infection has been studied previously. In this study, we address the role of mast cells during IAV infection. Respiratory infection with A/WSN/33 causes significant disease and immunopathology in C57BL/6 mice but not in B6.Cg-Kit(W-sh) mice, which lack mast cells. During in vitro coculture, A/WSN/33 caused mast cells to release histamine, secrete cytokines and chemokines, and produce leukotrienes. Moreover, when mast cells were infected with IAV, the virus did not replicate within mast cells. Importantly, human H1N1, H3N2, and influenza B virus isolates also could activate mast cells in vitro. Mast cell production of cytokines and chemokines occurs in a RIG-I/MAVS-dependent mechanism; in contrast, histamine production occurred through a RIG-I/MAVS-independent mechanism. Our data highlight that, following IAV infection, the response of mast cells is controlled by multiple receptors. In conclusion, we identified a unique inflammatory cascade activated during IAV infection that could potentially be targeted to limit morbidity following IAV infection.
| S-EPMC3633673 | biostudies-literature
Project description:Cell-based assays can monitor virus infection at a single-cell level with high sensitivity and cost-efficiency. For this purpose, it is crucial to develop molecular probes that respond selectively to physiological changes in live cells. We report stimuli-responsive light-emitters built on a T-shaped benzimidazole platform, and consecutive borylation reactions to produce a library of homologs displaying systematic changes in fluorescence quantum yield and environmental sensitivity. We find that certain fluorophores localize selectively at the endoplasmic reticulum, and interact with proteins involved in the stress signaling pathways. Notably, the mono-borylated compound responds selectively to the stress conditions by enhancing fluorescence, and detects avian influenza virus infection at the single-cell level. Our findings demonstrate the unprecedented practical utility of the stress-responsive molecular probes to differentiate cellular states for early diagnosis. Methods to detect and distinguish the early stage of viral infection often involve complicated and time-consuming protocols. Here, the authors disclose a class of fluorescent molecules that enable fast detection of avian influenza virus infection by selectively localizing at the endoplasmic reticulum in the cell.
| S-EPMC9529605 | biostudies-literature
Project description:BackgroundCertain hand activities cause deformation and displacement of the median nerve at the carpal tunnel due to the gliding motion of tendons surrounding it. As smartphone usage escalates, this raises the public's concern whether hand activities while using smartphones can lead to median nerve problems.ObjectiveThe aims of this study were to 1) develop kinematic graphs and 2) investigate the associated deformation and rotational information of median nerve in the carpal tunnel during hand activities.MethodsDominant wrists of 30 young adults were examined with ultrasonography by placing a transducer transversely on their wrist crease. Ultrasound video clips were recorded when the subject performing 1) thumb opposition with the wrist in neutral position, 2) thumb opposition with the wrist in ulnar deviation and 3) pinch grip with the wrist in neutral position. Six still images that were separated by 0.2-second intervals were then captured from the ultrasound video for the determination of 1) cross-sectional area (CSA), 2) flattening ratio (FR), 3) rotational displacement (RD) and 4) translational displacement (TD) of median nerve in the carpal tunnel, and these collected information of deformation, rotational and displacement of median nerve were compared between 1) two successive time points during a single hand activity and 2) different hand motions at the same time point. Finally, kinematic graphs were constructed to demonstrate the mobility of median nerve during different hand activities.ResultsPerforming different hand activities during this study led to a gradual reduction in CSA of the median nerve, with thumb opposition together with the wrist in ulnar deviation causing the greatest extent of deformation of the median nerve. Thumb opposition with the wrist in ulnar deviation also led to the largest extent of TD when compared to the other two hand activities of this study. Kinematic graphs showed that the motion pathways of median nerve during different hand activities were complex.ConclusionWe observed that the median nerve in the carpal tunnel was rotated, deformed and displaced during the hand activities that people may be performed when using a smartphone, suggesting an increased risk of carpal tunnel syndrome (CTS). In addition, the kinematic graphs of median nerve developed in the present study provide new clues for further studies on the pathophysiology of CTS, and alerting smartphone users to establish proper postural habits when using handheld electronic devices.
| S-EPMC4930216 | biostudies-literature