Similar Datasets
Project description:Caves as Reservoirs of Novel and Re-emerging Zoonoses: Ecological Monitoring and Real-Time Metagenomic Analysis Metagenome
| PRJNA1215671 | ENA
Project description:Zoonotic viruses are an omnipresent threat to global health. Influenza A virus (IAV) transmits between birds, livestock, and humans. Proviral host factors involved in the cross-species interface are well known, less is known about antiviral mechanisms that suppress IAV zoonoses. We observed CpG dinucleotide depletion in human IAV relative to avian IAV. Notably, human ZAP selectively depletes CpG-enriched viral RNAs with its cofactor KHNYN. ZAP is conserved in tetrapods but we uncovered that avian species lack KHNYN. We found that chicken ZAP does not affect IAV (PR8) or CpG enriched IAV. Human ZAP or KHNYN independently restricted CpG enriched IAV by overexpression in chicken cells or knockout in human cells. Additionally, mammalian ZAP-L and KHNYN also independently restricted an avian retrovirus (ROSV). Curiously, platypus KHNYN, the most divergent from eutherian mammals, was also capable of direct restriction of multiple diverse viruses. We suggest that mammalian KHNYN may be a bona fide restriction factor with cell-autonomous activity. Furthermore, we speculate that through repeated contact between avian viruses and mammalian hosts, protein changes may accompany CpG-biased mutations or reassortment to evade mammalian ZAP and KHNYN.
2025-12-11 | GSE286989 | GEO
Project description:Study of Swine Workers and Their Pigs for Influenza Viruses and Porcine Rotaviruses for Evidence of Zoonoses in South Africa
| PRJNA543217 | ENA
Project description:Background. Leptospirosis is among the most widespread zoonoses worldwide. Severe pulmonary hemorrhagic syndrome (SPHS) represents a serious complication of leptospirosis, with poor understanding of its underlying mechanisms and an urgent need for identification of effective biomarkers. Methods. A nested case-control analysis of the blood specimens obtained from two previous multi-center cohorts was conducted. Candidate microRNAs were initially discovered through a global profiling of 800 serum microRNAs, then validated using real-time polymerase-chain reactions. We further conducted a multi-omics analysis incorporating transcriptomic and proteomic data to identify enriched pathways through which the newly identified microRNAs could regulate. Findings. A total of 28 SPHS and 140 non-SPHS patients were evaluated by serum microRNA profiling, revealing distinct expression patterns between the two phenotypes. From the top 81 significantly expressed microRNAs, seven were selected for validation. Among these, miR-5010-3p and miR-147b-3p had area under the curve (AUC) values of 0.72 (95% CI: 0·62–0·81) and 0·66 (95% CI: 0·55–0·76) for discriminating SPHS. Notably, the two microRNAs could detect SPHS in patients who were yet to manifest chest radiograph shadows at the time of sample collection, and in a subgroup of patients who were recruited on day 2 of illness or earlier, with consistent AUC values. Integrated gene-protein pathway enrichment analysis revealed numerous pathways involving host immune responses. Among these, the tumor necrosis factor signaling pathway was the most significant with many of its member genes being targeted by miR-5010-3p or miR-147b-3p.
2026-02-09 | PXD052319 | Pride
Project description:Brucellosis is one of the most widespread bacterial zoonoses worldwide. Here, our aim was to identify the effector mechanisms controlling the early stages of intranasal infection with Brucella in C57BL/6 mice. During the first 48 hours of infection, alveolar macrophages (AMs) are the main cells infected in the lungs. Using RNA sequencing, we identified the aconitate decarboxylase 1 gene (Acod1; also known as Immune responsive gene 1), as one of the genes most upregulated in murine AMs in response to B. melitensis infection at 24 hours post-infection. Upregulation of Acod1 was confirmed by RT-qPCR in lungs infected with B. melitensis and B. abortus. We observed that Acod1-/- C57BL/6 mice display a higher bacterial load in their lungs than wild-type (wt) mice following B. melitensis or B. abortus infection, demonstrating that Acod1 participates in the control of pulmonary Brucella infection. The ACOD1 enzyme is mostly produced in mitochondria of macrophages, and converts cis-aconitate, a metabolite in the Krebs cycle, into itaconate. Dimethyl itaconate (DMI), a chemically-modified membrane permeable form of itaconate, has a dose-dependent inhibitory effect on Brucella growth in vitro. Interestingly, modelling studies suggest the binding of itaconate into the binding site of isocitrate lyase. DMI does not inhibit multiplication of the isocitrate lyase deletion mutant ∆aceA B. abortus in vitro. Finally, we observed that, unlike the wt strain, the ∆aceA B. abortus strain multiplies similarly in wt and Acod1-/- C57BL/6 mice. These data suggest that bacterial isocitrate lyase might be a target of itaconate in AMs.
2021-09-21 | GSE180699 | GEO
Project description:The white-footed deermouse Peromyscus leucopus is a primary reservoir for the agents of Lyme disease and other zoonoses in North America. These and other species of Peromyscus are tolerant of the infection by the bacteria, protozoa, and viruses they host. This is mainly by mitigating the damaging effects of the innate immune response. In previous studies we demonstrated differences between P. leucopus and either inbred or outbred M. musculus in the degree of sickness and profiles of biomarkers after exposure to bacterial lipopolysaccharide, a TLR4 agonist. With the objective of developing a method for broadly assessing of innate immunity of capture-release mammals in nature, we evaluated using bulk and single cell RNA-seq primary dermal fibroblast cultures of P. leucopus and M. musculus in their short-term responses to a lipopeptide that is a TLR2 agonist. As we had observed for experimental animals, the fibroblast cultures of the two species displayed both similarities and differences in their responses to the agonist. The notable differences included the greater magnitude of an anti-viral profile of cytokines and other effectors in the deermouse fibroblasts and the occurrence of an interleukin-11 response in the mouse cultures but not deermouse. We also observed in both species' cultures an increased transcription of several types of endogenous retrovirus (ERV) elements after exposure of the cells to the agonist. The P. leucopus cells were distinguished from M. musculus cells in the generally shorter retroviral open reading frames among the differentially expressed sequences. This was consistent with previous findings about ERV transcription in P. leucopus and M. musculus and suggests a greater suppression of ERV activity in P. leuocopus. The results affirm the feasibility of this in vitro model for both laboratory- and field-based studies without need for euthanasia and that inherent differences between deermice and mice in innate immune responses can be demonstrated in primary fibroblasts as well as the animals themselves.
2025-10-22 | GSE302225 | GEO
Project description:This study aims to investigate the DNA methylation patterns at transcription factor binding regions and their evolutionary conservation with respect to binding activity divergence. We combined newly generated bisulfite-sequencing experiments in livers of five mammals (human, macaque, mouse, rat and dog) and matched publicly available ChIP-sequencing data for five transcription factors (CEBPA, HNF4a, CTCF, ONECUT1 and FOXA1). To study the chromatin contexts of TF binding subjected to distinct evolutionary pressures, we integrated publicly available active promoter, active enhancer and primed enhancer calls determined by profiling genome wide patterns of H3K27ac, H3K4me3 and H3K4me1.
2022-10-20 | E-MTAB-11946 | biostudies-arrayexpress
Project description:Whole genome sequencing of the Arabidopsis thaliana dot5-1 transposon insertion line described in Petricka et al 2008 The Plant Journal 56(2): 251-263.
2022-08-07 | E-MTAB-12010 | biostudies-arrayexpress