Project description:Understanding natural defence mechanisms against parasites can be a valuable tool for the development of innovative therapies. In this study, we investigated the interplay between the gill mucus metabolome and microbiome of Chaetodon lunulatus, a butterflyfish known to avoid gill monogeneans whilst living amongst closely related parasitized species. In an attempt to identify metabolites and OTUs potentially involved in parasite defence mechanisms, we studied the metabolome (LC-MS/MS) and microbiome of several sympatric butterflyfish species, including the only non-parasitized species C. lunulatus. After observing significant differences between the metabolome and microbiome of parasitized versus non-parasitized fish (PCoA, ANOSIM), we obtained the discriminant metabolites and OTUs using a supervised analysis. Some of the most important discriminant metabolites were identified as peptides, and three new β-subunit haemoblogin-derived peptides from C. lunulatus (CLHbβ-1, CLHbβ-2 and CLHbβ-3) were purified, characterised and synthesised. We also identified specific bacterial families and OTUs typical from low-oxygen habitats in C. lunulatus gill mucus. By using a correlation network between the two datasets, we found a Fusobacteriaceae strain exclusively present in C. lunulatus highly correlated to the peptides. Finally, we discuss the possible involvement of these peptides and Fusobacteriaceae in monogenean avoidance by this fish species.
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.
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.