Development and performance of a targeted whole exome sequencing enrichment kit for the dog (Canis Familiaris Build 3.1)

Whole exome sequencing is a technique that aims to selectively sequence all exons of protein-coding genes. A canine whole exome sequencing enrichment kit was designed based on the latest canine reference genome (build 3.1.72). Its performance was tested by sequencing 2 exome captures, each consisting of 4 pre-capture pooled, barcoded Illumina libraries on an Illumina HiSeq 2500. At an average sequencing depth of 102x, 83 to 86% of the target regions were completely sequenced with a minimum coverage of five and 90% of the reads mapped on the target regions. Additionally, it is shown that the reproducibility within and between captures is high and that pooling four samples per capture is a valid option. Overall, we have demonstrated the strong performance of this WES enrichment kit and are confident it will be a valuable tool in future disease association studies

The bacterioplankton community composition and a host genotype dependent occurrence of taxa shape the Daphnia magna gut bacterial community

The assembly of host-associated bacterial communities is influenced by a multitude of biotic and abiotic factors. It is essential to gain insight in the impact and relative strength of these factors if we want to be able to predict the effects of environmental change on the assembly of host-associated bacterial communities, or deliberately modify them. The environmental pool of bacteria, from which the host is colonized, and the genetic background of the host are both considered to be important in determining the composition of host-associated bacterial communities. We experimentally assessed the relative importance of these two factors and their interaction on the composition of Daphnia magna gut bacterial communities. Bacterioplankton originating from natural ponds or a laboratory culture were used to inoculate germ-free Daphnia of different genotypes. We found that the composition of the environmental bacterial community has a major influence on the Daphnia gut bacterial community, both reflected by the presence or absence of specific taxa as well as by a correlation between abundances in the environment and on the host. Our data also indicate a consistent effect of host genotype on the occurrence of specific bacterial taxa in the gut of Daphnia over different environments

PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration

An increasing amount of studies integrate mRNA sequencing data into MS-based proteomics to complement the translation product search space. However, several factors, including extensive regulation of mRNA translation and the need for three- or six-frame-translation, impede the use of mRNA-seq data for the construction of a protein sequence search database. With that in mind, we developed the PROTEOFORMER tool that automatically processes data of the recently developed ribosome profiling method (sequencing of ribosome-protected mRNA fragments), resulting in genome-wide visualization of ribosome occupancy. Our tool also includes a translation initiation site calling algorithm allowing the delineation of the open reading frames (ORFs) of all translation products. A complete protein synthesis-based sequence database can thus be compiled for mass spectrometry-based identification. This approach increases the overall protein identification rates with 3% and 11% (improved and new identifications) for human and mouse, respectively, and enables proteome-wide detection of 5'-extended proteoforms, upstream ORF translation and near-cognate translation start sites. The PROTEOFORMER tool is available as a stand-alone pipeline and has been implemented in the galaxy framework for ease of use

Photothermally triggered endosomal escape and its influence on transfection efficiency of gold-functionalized JetPEI/pDNA nanoparticles

Plasmonic nanoparticles for drug delivery have attracted increasing interest over the last few years. Their localized surface plasmon resonance causes photothermal effects on laser irradiation, which allows for delivering drugs in a spatio-temporally controlled manner. Here, we explore the use of gold nanoparticles (AuNP) as carriers for pDNA in combination with pulsed laser irradiation to induce endosomal escape, which is currently considered to be one of the major bottlenecks in macromolecular drug delivery on the intracellular level. In particular, we evaluate nanocomplexes composed of JetPEI (polyethylenimine)pDNA and 10 nm AuNP, which do not exhibit endosomal escape by themselves. After incubating HeLa cells with these complexes, we evaluated endosomal escape and transfection efficiency using low- and high-energy laser pulses. At low laser energy heat is produced by the nanocomplexes, while, at higher laser energy, explosive vapour nanobubbles (VNB) are formed. We investigated the ability of heat transfer and VNB formation to induce endosomal escape and we examine the integrity of pDNA cargo after inducing both photothermal effects. We conclude that JetPEI/pDNA/AuNP complexes are unable to induce meaningful transfection efficiencies because laser treatment causes either dysfunctionality of the cargo when VNB are formed or forms too small pores in the endosomal membrane to allow pDNA to escape in case of heating. We conclude that laser-induced VNB is the most suitable to induce effective pDNA endosomal escape, but a different nanocomplex structure will be required to keep the pDNA intact

A recycler’s perspective on the implications of REACH and food contact material (FCM) regulations for the mechanical recycling of FCM plastics

This manuscript provides an overview of the legislative requirements for the use of mechanical recycled plastics in articles placed on the EU market, as seen from the perspective of a plastics recycler. The first part reviews the main principles included in the overarching legislation on Registration, Evaluation, Authorisation and Restrictions of Chemicals (REACH) and to what extent these are applicable for mechanical recyclers of plastics. The interactions between REACH and the Waste Framework Directive (WFD) is discussed, as well as the difficulties for recyclers to comply with certain REACH requirements. In a second part, the focus is moved to the use of recycled plastics as Food Contact Material (FCM). The scope of the different applicable EU FCM regulations is inventorised as well as the key legislative principles involved. A final section is dedicated to the discussion on the authorisation of recycling processes under the FCM regulation and the practical challenges involved for the effective introduction of FCMs containing recycled plastics. Altogether it could be concluded that the complexity of the different legal perspectives, a lack of communication and transparency within the plastic value chain together with technical challenges related to recycling processes have been hindering the effective uptake of recycled plastic FCM (with the exception for bottle PET). The development of targeted solutions across the entire valuechain, taking into account different perspectives in terms of legislation and health protection, economic growth and technical innovations, will be crucial in achieving a circular economy for plastics, including recycled plastics for FCM

Distinct transcriptome signatures of Helicobacter suis and Helicobacter heilmannii strains upon adherence to human gastric epithelial cells

The porcine Helicobacter suis and canine-feline H. heilmannii are gastric Helicobacter species with zoonotic potential. However, little is known about the pathogenesis of human infections with these Helicobacter species. To gain more insight into the interactions of both zoonotic Helicobacter species with human gastric epithelial cells, we investigated bacterial genes that are differentially expressed in a H. suis and H. heilmannii strain after adhesion to the human gastric epithelial cell line MKN7. In vitro Helicobacter-MKN7 binding assays were performed to obtain bacterial RNA for sequencing analysis. H. suis and H. heilmannii bacteria attached to the gastric epithelial cells (i.e. cases) as well as unbound bacteria (i.e. controls) were isolated, after which prokaryotic RNA was purified and sequenced. Differentially expressed genes were identified using the DESeq2 package and SARTools pipeline in R. A list of 134 (83 up-regulated and 51 down-regulated) and 143 (60 up-regulated and 83 down-regulated) differentially expressed genes (p(adj)= 2) were identified for the adherent H. suis and H. heilmannii strains, respectively. According to BLASTp analyses, only 2 genes were commonly up-regulated and 4 genes commonly down-regulated in both pathogens. Differentially expressed genes of the H. suis and H. heilmannii strains belonged to multiple functional classes, indicating that adhesion of both strains to human gastric epithelial cells evokes pleiotropic adaptive responses. Our results suggest that distinct pathways are involved in human gastric colonization of H. suis and H. heilmannii. Further research is needed to elucidate the clinical significance of these findings

Chytrid epidemics may increase genetic diversity of a diatom spring-bloom

Contrary to expectation, populations of clonal organisms are often genetically highly diverse. In phytoplankton, this diversity is maintained throughout periods of high population growth (that is, blooms), even though competitive exclusion among genotypes should hypothetically lead to the dominance of a few superior genotypes. Genotype-specific parasitism may be one mechanism that helps maintain such high-genotypic diversity of clonal organisms. Here, we present a comparison of population genetic similarity by estimating the beta-dispersion among genotypes of early and peak bloom populations of the diatom Asterionella formosa for three spring-blooms under high or low parasite pressure. The Asterionella population showed greater beta-dispersion at peak bloom than early bloom in the 2 years with high parasite pressure, whereas the within group dispersion did not change under low parasite pressure. Our findings support that high prevalence parasitism can promote genetic diversification of natural populations of clonal hosts