Epigenetic effects of stress and corticosteroids in the brain

Stress is a common life event with potentially long lasting effects on health and behavior. Stress, and the corticosteroid hormones that mediate many of its effects, are well known for their ability to alter brain function and plasticity. While genetic susceptibility may influence the impact of stress on the brain, it does not provide us with a complete understanding of the capacity of stress to produce long lasting perturbations on the brain and behavior. The growing science of epigenetics, however, shows great promise of deepening our understanding of the persistent impacts of stress and corticosteroids on health and disease. Epigenetics, broadly defined, refers to influences on phenotype operating above the level of the genetic code itself. At the molecular level, epigenetic events belong to three major classes: DNA methylation, covalent histone modification and non-coding RNA. This review will examine the bi-directional interactions between stress and corticosteroids and epigenetic mechanisms in the brain and how the novel insights, gleaned from recent research in neuro-epigenetics, change our understanding of mammalian brain function and human disease states

Jellyfish on the menu: mtDNA assay reveals scyphozoan predation in the Irish Sea

Localized outbreaks of jellyfish, known as blooms, cause a variety of adverse ecological and economic effects. However, fundamental aspects of their ecology remain unknown. Notably, there is scant information on the role jellyfish occupy in food webs: in many ecosystems, few or no predators are known. To identify jellyfish consumers in the Irish Sea, we conducted a molecular gut content assessment of 50 potential predators using cnidarian-specific mtDNA primers and sequencing. We show that jellyfish predation may be more common than previously acknowledged: uncovering many previously unknown jellyfish predators. A substantial proportion of herring and whiting were found to have consumed jellyfish. Rare ingestion was also detected in a variety of other species. Given the phenology of jellyfish in the region, we suggest that the predation was probably targeting juvenile stages of the jellyfish life cycle

How quantitative is metabarcoding: a meta-analytical approach

Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis, and the analysis of environmental DNA. However, after a decade of use in these applications there is little consensus on the extent to which proportions of reads generated corresponds to the original proportions of species in a community. To quantify our current understanding we conducted a structured review and meta‐analysis. The analysis suggests that a weak quantitative relationship may exist between the biomass and sequences produced (slope = 0.52 ±0.34, p<0.01), albeit it with a large degree of uncertainty. None of the tested moderators: sequencing platform type, the number of species used in a trial, or the source of DNA were able to explain the variance. Our current understanding of the factors affecting the quantitative performance of metabarcoding is still limited: additional research is required before metabarcoding can be confidently utilised for quantitative applications. Until then, we advocate the inclusion of mock communities when metabarcoding as this facilitates direct assessment of the quantitative ability of any given study

Dynamic changes in 5-hydroxymethylation signatures underpin early and late events in drug exposed liver

Aberrant DNA methylation is a common feature of neoplastic lesions, and early detection of such changes may provide powerful mechanistic insights and biomarkers for carcinogenesis. Here, we investigate dynamic changes in the mouse liver DNA methylome associated with short (1 day) and prolonged (7, 28 and 91 days) exposure to the rodent liver non-genotoxic carcinogen, phenobarbital (PB). We find that the distribution of 5mC/5hmC is highly consistent between untreated individuals of a similar age; yet, changes during liver maturation in a transcriptionally dependent manner. Following drug treatment, we identify and validate a series of differentially methylated or hydroxymethylated regions: exposure results in staged transcriptional responses with distinct kinetic profiles that strongly correlate with promoter proximal region 5hmC levels. Furthermore, reciprocal changes for both 5mC and 5hmC in response to PB suggest that active demethylation may be taking place at each set of these loci via a 5hmC intermediate. Finally, we identify potential early biomarkers for non-genotoxic carcinogenesis, including several genes aberrantly expressed in liver cancer. Our work suggests that 5hmC profiling can be used as an indicator of cell states during organ maturation and drug-induced responses and provides novel epigenetic signatures for non-genotoxic carcinogen exposur

FieldML: concepts and implementation

The field modelling language FieldML is being developed as a standard for modelling and interchanging field descriptions in software, suitable for a wide range of computation techniques. It comprises a rich set of operators for defining generalized fields as functions of other fields, starting with basic domain fields including sets of discrete objects and coordinate systems. It is extensible by adding new operators and by their arbitrary combination in expressions, making it well suited for describing the inherent complexity of biological materials and organ systems. This paper describes the concepts behind FieldML, including a simple example of a spatially varying finite-element field. It outlines current implementations in established, open source computation and visualization software, both drawing on decades of bioengineering modelling software development experience