Gene body methylation patterns in Daphnia are associated with gene family size

The relation between gene body methylation and gene function remains elusive. Yet, our understanding of this relationship can contribute significant knowledge on how and why organisms target specific gene bodies for methylation. Here, we studied gene body methylation patterns in two Daphnia species. We observed both highly methylated genes and genes devoid of methylation in a background of low global methylation levels. A small but highly significant number of genes was highly methylated in both species. Remarkably, functional analyses indicate that variation in methylation within and between Daphnia species is primarily targeted to small gene families whereas large gene families tend to lack variation. The degree of sequence similarity could not explain the observed pattern. Furthermore, a significant negative correlation between gene family size and the degree of methylation suggests that gene body methylation may help regulate gene family expansion and functional diversification of gene families leading to phenotypic variation

Exposure of microplastic at levels relevant for human health : cytotoxicity and cellular localization of polystyrene microparticles in four human cell lines

Microplastics (MPs), which are ubiquitous in our living environment, can enter into human body via diverse pathways such as food packaging, contaminated food and bottled mineral water. Therefore, it is essential to assess the risk of MPs daily human intake. Up to date, almost all of related publications used concentrations that are much higher than likely present in these sources. Thus, investigation at levels of MPs relevant for human health exposure can help us rationally understand the threats of MPs. This study is aimed to evaluate cytotoxicity and quantify the cellular uptake and localization of MPs within the concentration range reported in bottled mineral water in human cell lines. To this aim, four types of human cell lines derived from colon (Caco-2), liver (HepG2) and lung (A549 and BEAS-2B) were exposed to 2-µm fluorescent PS microspheres (1E+3-1E+7 particles/L). A series of cellular and biochemical assays (intracellular reactive oxygen species, mitochondrial membrane potential, sulforhodamine B and MTT assay) were conducted. To confirm the cellular uptake, the fluorescent cells containing PS were counted by flow cytometry to evaluate the probability of cells embedded PS under different concentrations. Furthermore, laser confocal scanning microscopy was used to observe the distribution and count the number of PS microspheres in four cell lines

The effect of emerging pollutants in the North Sea on fish growth : an in silico-in vitro approach

Environmental risk assessment is of extreme importance to assure a safe, balanced and sustainable use of chemicals, while playing a key role in environmental regulation. However, it currently relies on ethically controversial, expensive and time-costly methods and experiments (e.g. animal testing). Moreover, quantification of chemical toxicity is commonly based on external concentrations in water, soil or air, even though it is the internal concentration in the organism that gives raise to the biological effect. Recently, a combination of in vitro and in silico has been put forward as a viable alternative to the conventional in vivo testing. In this study, we have applied this concept to emerging pollutants detected in the North Sea, particularly pharmaceuticals and pesticides. We assessed the effect of these chemicals on growth impairment in fish through in silico methods, using predicted internal concentrations of these chemicals, based on environmental concentrations. In particular, we exposed gill cells of rainbow trout (Oncorhynchus mykiss), RTgill-W1 cell line, to the predicted internal concentrations of each chemical and then used the in vitro cell growth to predict in vivo growth. It is our believe that the adopted methodology allows the tackling of the previously described issues related to chemical risk assessment and encourages a shift of the current paradigm

Metatranscriptome of a marine pelagic crustacean community using nanopore sequencing

Due to their rapid responses to environmental variation, planktonic organisms are used as bio-indicators of ecosystem changes. Most zooplankton monitoring studies focus mainly on variability in biodiversity, densities and biomass. Advances in practical, cost-effective molecular approaches can help overcome the issues with morphology-based biomonitoring. While molecular studies are growing in popularity, a fundamental challenge remains the transport of biological material to a laboratory for DNA/RNA extractions and sequencing. The MinION™, a portable nanopore-based DNA/RNA sequencing platform (Oxford Nanopore Technologies), offers big potential advantages in the context of biodiversity research, i.e. portability and low costs of instrument and reagents. It weighs less than 100 g, is therefore easily transportable and is powered to sequence RNA using the USB port on a standard laptop, hence making it suitable for mobile research setups and real time monitoring campaigns onsite. In a first step, we wanted to understand how the gene expression in zooplankton fluctuates over the course of a short time period. Therefore, we monitored the gene expression of the dominant zooplankter, the calanoid copepod Temora longicornis, over a short time span (one day), making use of the infrastructure of the research vessel Simon Stevin. We compared gene expression results with in situ determined biotic and abiotic patterns. Moreover, due to the recent development of the VolTRAX, a small device designed to perform library preparation automatically, for the first time we were able to prepare a biological sample for analysis in situ and hands-free, making in-field, molecular monitoring of marine life possible

Metabarcoding of marine zooplankton communities in the North Sea using nanopore sequencing

Zooplankton are crucial organisms both in terms of biodiversity and their unique position in aquatic food webs. As such, it is crucial that we improve our insights into how anthropogenic and natural factors may affect these pelagic organisms. Although easily collected in large numbers, the subsequent processing and identification of specimens has usually been a barrier to large-scale biodiversity assessments. DNA barcoding, the use of standardized short gene regions to discriminate species, has been increasingly used by non-taxonomists to identify species. Here, we measured the diversity and community composition of zooplankton in the Belgian part of the North Sea over the course of one year. We identified zooplankton using both a traditional approach, based on morphological characteristics, and by metabarcoding of a 650 bp fragment of the 18S rRNA gene using the MinION™, a portable nanopore-based DNA sequencing platform. We established a method for characterizing zooplankton communities in marine samples using nanopore sequencing. We were able to identify several taxa at the species level, across a broad taxonomic scale and we thus could obtain several diversity metrics, allowing comparisons of diversity and community composition