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Salmon rickettsial septicaemia (SRS), caused by the bacteria Piscirickettsia salmonis (P. salmonis), is responsible for significant mortality in farmed Atlantic salmon in Chile. Currently there are no effective treatments or preventive measures for this disease, although genetic selection or genome engineering to increase salmon resistance to SRS are promising strategies. The accuracy and efficiency of these strategies are usually influenced by the available biological background knowledge of the disease. The aim of this study was to investigate DNA methylation changes in response to P. salmonis infection in the head kidney and liver tissue of Atlantic salmon, and the interaction between gene expression and DNA methylation in the same tissues. The head kidney and liver methylomes of 66 juvenile salmon were profiled using reduced representation bisulphite sequencing (RRBS), and compared between P. salmonis infected animals (3 and 9 days post infection) and uninfected controls, and between SRS resistant and susceptible fish. Methylation was correlated with matching RNA-Seq data from the same animals, revealing that methylation in the first exon leads to an important repression of gene expression. Head kidney methylation showed a clear response to the infection, associated with immunological processes such as actin cytoskeleton regulation, phagocytosis, endocytosis and pathogen associated pattern receptor signaling. Our results contribute to the growing understanding of the role of methylation in regulation of gene expression and response to infectious diseases and could inform the incorporation of epigenetic markers into genomic selection for disease resistant and the design of diagnostic epigenetic markers to better manage fish health in salmon aquaculture. • Methylation plays a role in the interaction between Atlantic salmon and P. salmonis. • The actin cytoskeleton pathway is regulated via methylation during infection. • Specific CpG sites can be associated with genetic resistance to P. salmonis. • Methylation in promoter-TSS and first exon strongly represses gene expression. [ABSTRACT FROM AUTHOR]

Abstract: On the basis of stable carbon and nitrogen isotope analysis of human remains, this paper provides evidence for the retention of hunter–gatherer economies among coastal inhabitants in northern Chile during the late Holocene – at the same time that inland populations were adopting agricultural economies. Coastal diets from the Caleta Vitor region of the Atacama Desert were dominated by marine-based foods, predominantly from upper trophic levels. The focus on reliable marine food resources is interpreted as a risk minimisation strategy in this marginal arid environment. Although these coastal hunter–gatherers adopted other goods and traditions from agricultural populations, their participation in this larger interregional exchange network did not affect their basic subsistence economies. Associated new radiocarbon dates from the site are also discussed. Skeletal remains and artefacts associated with the Caleta Vitor shell middens generally originate from sites with dates ranging from c. 9000–476 BP. However, the human remains that are the subject of this research cover the time period c. 4000–476 BP. [Copyright &y& Elsevier]