Genome graphs detect human polymorphisms in active epigenomic state during influenza infection

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

Transposable elements are associated with the variable response to influenza infection

インフルエンザ重症度に関連する転移因子を特定: マルチオミクス解析で見えた「動く遺伝子」の新たな役割. 京都大学プレスリリース. 2023-05-11.A multiomics approach provides insights into flu severity. 京都大学プレスリリース. 2023-05-11.Influenza A virus (IAV) infections are frequent every year and result in a range of disease severity. Here, we wanted to explore the potential contribution of transposable elements (TEs) to the variable human immune response. Transcriptome profiling in monocyte-derived macrophages from 39 individuals following IAV infection revealed significant inter-individual variation in viral load post-infection. Using transposase-accessible chromatin using sequencing (ATAC-seq), we identified a set of TE families with either enhanced or reduced accessibility upon infection. Of the enhanced families, 15 showed high variability between individuals and had distinct epigenetic profiles. Motif analysis showed an association with known immune regulators (e.g., BATFs, FOSs/JUNs, IRFs, STATs, NFkBs, NFYs, and RELs) in stably enriched families and with other factors in variable families, including KRAB-ZNFs. We showed that TEs and host factors regulating TEs were predictive of viral load post-infection. Our findings shed light on the role TEs and KRAB-ZNFs may play in inter-individual variation in immunity

DESIGNING EMOTIONAL AWARENESS DEVICES: WHAT ONE SEES IS WHAT ONE FEELS DISEÑANDO DISPOSITIVOS CON AWARENESS EMOCIONAL: LO QUE UNO VE ES LO QUE UNO SIENTE

Interpersonal communication involves more than just words; it involves emotion. Emotions can be roughly seen as complex organized internal states. Awareness of those states would allow human beings to evaluate social information and develop strategic social intelligence and hence, everyday actions convey social meaning and emotion. This paper reports an experience for supporting public-emotion based dialogs, where emotions are expressed, captured and transmitted between distant participants using tangible interfaces. We also exploit the social meaning of an everyday physical object such as a portrait, in order to create affective interfaces. We describe as well, a device that allows Emotional Awareness and supports the affective interpersonal interaction among people across distance.<br>La comunicación interpersonal requiere más que solamente palabras, involucra emociones. En términos generales las emociones pueden ser vistas como estados internos complejamente organizados. El Awareness de estos estados permitiría a los seres humanos evaluar la información social y desarrollar inteligencia social estratégica y, por lo tanto, las acciones cotidianas estarían teñidas de significado social y emocional. Este artículo reporta una experiencia que busca permitir un diálogo basado en emociones expresadas, capturadas y transmitidas entre diversos participantes usando interfaces tangibles. Además, se explota el significado social de objetos físicos y cotidianos como un portarretratos, con el fin de crear interfaces afectivas entre usuarios dispersos geográficamente. En este artículo se describe un dispositivo que permite un tipo de Awareness emocional apoyando la interacción interpersonal y afectiva entre personas distantes geográficamente

Identification of coexisting indigo species in an ancient green thread using direct plasmon-enhanced raman spectroscopy

A green ancient thread sample from a Chilean mummy turban was analyzed by plasmon-enhanced Raman scattering spectroscopy using a direct drop-colloidal method. The enhanced-Raman signals in the sample are associated with biomolecules from the thread and two coexisting dyes, indigo and leuco-indigo. The presence of indigo (blue colour) was identified from its most characteristic vibrational bands. Leuco-indigo (yellow colour) was identified for the first time in an ancient textile; its SERS signals are coincident with the SERS bands of a synthesized leuco-indigo. The interconversion leuco-indigo to indigo was followed by UV-visible spectroscopy. Based on theoretical calculations it is proposed that the interconversion involves a it electron delocalization mainly around the NC-CN bridge. The mixture of both dyes (indigo and leuco-indigo) is the responsible for the green colour observed.Universidad de Playa Ancha (concurso regular de investigacion ano 2018) FONDECYT 3150222 EQM150020 FONDEQUIP CNE 10-1920 Comision Nacional de Investigacion Cientifica y Tecnologica (CONICYT) CONICYT FONDECYT 1115094

L-NIL prevents the ischemia and reperfusion injury involving TLR-4, GST, clusterin, and NFAT-5 in mice

Copyright © 2019 the American Physiological Society.—On renal ischemia-reperfusion (I/R) injury, recruitment of neutrophils during the inflammatory process promotes local generation of oxygen and nitrogen reactive species, which, in turn, are likely to exacerbate tissue damage. The mechanism by which inducible nitric oxide synthase (iNOS) is involved in I/R has not been elucidated. In this work, the selective iNOS inhibitor L-N6-(1-iminoethyl)lysine (L-NIL) and the NOS substrate L-arginine were employed to understand the role of NOS activity on the expression of particular target genes and the oxidative stress elicited after a 30-min of bilateral renal ischemia, followed by 48-h reperfusion in Balb/c mice. The main findings of the present study were that pharmacological inhibition of iNOS with L-NIL during an I/R challenge of mice kidney decreased renal injury, prevented tissue loss of integrity, and improved renal function. Several novel findings regarding the molecular mechanism by which iNOS inhibition led to these protective effects are as follows: 1) a prevention of the I/R-related increase in expression of Toll-like receptor 4 (TLR-4), and its downstream target, IL-1α; 2) reduced oxidative stress following the I/R challenge; noteworthy, this study shows the first evidence of glutathione S-transferase (GST) inactivation following kidney I/R, a phenomenon fully prevented by iNOS inhibition; 3) increased expression of clusterin, a survival autophagy component; and 4) increased expression of nuclear factor of activated T cells 5 (NFAT-5) and its target gene aquaporin-1. In conclusion, prevention of renal damage following I/R by the pharmacological inhibition of iNOS with L-NIL was associated with the inactivation of proinflammatory pathway triggered by TLR-4, oxidative stress, renoprotection (autophagy inac-tivation), and NFAT-5 signaling pathway

Genome graphs detect human polymorphisms in active epigenomic state during influenza infection

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