Open Access

For specific primary modes of action (MoA) in environmental non-target organisms, EU legislation restricts the usage of active substances of pesticides or biocides. Corresponding regulatory hazard assessments are costly, time consuming and require large numbers of non-human animal studies. Currently, predictive toxicology of development compounds relies on their chemical structure and provides little insights into toxicity mechanisms that precede adverse effects. Using the zebrafish embryo model, we characterized transcriptomic responses to a range of sublethal concentrations of six nerve- and muscle-targeting insecticides with different MoA (abamectin, carbaryl, chlorpyrifos, fipronil, imidacloprid & methoxychlor). Our aim was to identify affected biological processes and suitable biomarker candidates for MoA-specific signatures. Abamectin showed the most divergent signature among the tested insecticides, linked to lipid metabolic processes. Differentially expressed genes (DEGs) after imidacloprid exposure were primarily associated with immune system and inflammation. In total, 222 early responsive genes to either MoA were identified, many related to three major processes: (1) cardiac muscle cell development and functioning (tcap, desma, bag3, hspb1, hspb8, flnca, myoz3a, mybpc2b, actc2, tnnt2c), (2) oxygen transport and hypoxic stress (alas2, hbbe1.1, hbbe1.3, hbbe2, hbae3, igfbp1a, hif1al) and (3) neuronal development and plasticity (npas4a, egr1, btg2, ier2a, vgf). The thyroidal function related gene dio3b was upregulated by chlorpyrifos and downregulated by higher abamectin concentrations. Important regulatory genes for cardiac muscle (tcap) and forebrain development (npas4a) were the most frequently ifferentially expressed across all insecticide treatments. We consider the identified gene sets as useful early warning biomarker candidates, i.e. for developmental toxicity targeting heart and brain in aquatic vertebrates. Our findings provide a better understanding about early molecular events in response to the analyzed MoA. Perceptively, this promotes the development for sensitive and informative biomarker-based in vitro assays for toxicological MoA prediction and AOP refinement, without the suffering of adult fish.

Wood-inhabiting fungi play an integral role in wood degradation and the cycle of matter in the ecological system. They are considered a ʻkey playerʼ in wood decomposition because of their ability to produce all kinds of enzymes that break down lignin, cellulose and hemicellulose. In this study, some wood-inhabiting mushrooms were collected from the Yunnan-Guizhou Plateau, Asia, and based on the morphological and molecular evidence, they are introduced as Punctochaete murina J.H.Dong & C.L.Zhao gen. et sp. nov. Punctochaete J.H.Dong & C.L.Zhao gen. nov. is characterized by resupinate basidiomata with a punctate hymenial surface, a monomitic hyphal system and generative hyphae bearing clamp connections, and cylindrical to allantoid, thin-walled, smooth, slightly curved basidiospores. Sequences of the internal transcribed spacer (ITS) and large subunit (nLSU) markers of the studied samples were generated, and phylogenetic analyses were performed with maximum likelihood, maximum parsimony and Bayesian inference methods. Phylogenetic analyses of ITS+nLSU nuclear RNA gene regions showed that Punctochaete forms a monophyletic lineage within the order Auriculariales in which it is sister to a clade comprising two closely related genera: Exidiopsis and Tremellochaete.

The broad global distribution of freshwater clams belonging to the genus Corbicula is driven by multiple hermaphroditic lineages. These lineages, characterized by shared morphological traits and phenotypic plasticity, pose challenges to morphological identification. Genetic markers, such as the mitochondrial COI gene, play a crucial role in delineating these lineages and their ranges. Morphotypes represent observed phenotypic variations, while lineages are defined based on genetic markers. Here, we comprehensively review Corbicula’s distribution in Argentina, discriminate extant lineages based on both morphological and genetic (COI) data, and describe variations in internal and external morphologies using 15 Argentine populations. Genetic analyses identified two mitochondrial lineages: the AR morphotype (FW5 haplotype) and CS morphotype (FW17 haplotype). Strikingly, despite having similar vectors, origins, and invasive stages, Corbicula lineages exhibit virtually segregated distributions. However, mitochondrial haplotypes are found in sympatry mainly in northeastern Argentina where individuals with intermediate morphotypes exist, suggesting the presence of hybrids due to maternal genome retention. These findings contribute to the clarification of the identity and distribution of Corbicula lineages in Argentina, where the genus has been found for over half a century. Similar studies are needed in other areas to better understand the invasion patterns of this successful and adaptable group.

Micro RNAs (miRNAs) are important post-translational regulators of gene expression that occur in both plants and animals. They inhibit gene expression by promoting translational inhibition and decay of messenger RNAs (mRNAs). One miRNA can have thousands of different target mRNAs in any given cell and usually slightly decreases translation of a plethora of genes. An important example of this is the miRNA family miR-181 during T-cell development. Thymic progenitor cells travel to the thymus, where they develop through several distinct stages into mature T cells of every type. One of these stages is the CD4/CD8 double positive (DP) stage, where miR-181 is particularly highly expressed and important for the cells to proceed through TCR repertoire selection. While miRNAs have been extensively studied in vitro, their effects within whole organisms are not completely understood. Even extremely abundant miRNAs are vastly outnumbered by their potential target sites, which begs the question of a targeting hierarchy. Therefore, in this study, we set out to analyse miR-181 in thymocytes as a representative model for overall miRNA function in vivo. To assess the role of miR-181 on a global level, we chose a multi-omics approach on DP thymocytes from wild type (WT) and miR-181 knock-out (KO) mice, including a ribosome profiling experiment and quantitative mass spectrometry (MS) to visualize the effects of miR-181 on translation, and enhanced crosslinking immunoprecipitation (miR-eCLIP) to find true miR-181 binding sites. The combination of these experiments enables us to stratify effects on expression by the binding site information. Secondly, we investigate the maturation of miR-181 and its regulation to understand the life cycle of miR-181, particularly because of the extensive length of the miR-181 progenitor, pri-miR-181, as its only known function is the production of two miRNAs. Our analysis of the targetome first confirmed known and predicted targets and secondly found additional targets that were previously not described. We analysed target mRNAs depending on their miRNA response elements (MREs). When assigning the target mRNAs to categories based on the target information obtained in the miR-eCLIP, we could stratify the functional effects by the mRNA’s attributes. Most effects could be observed in both RNAseq and ribosome footprint (RF). However, the quantitative MS was not able to visualize the often small effects of miRNA repression. The largest effects could be attributed to the number of MREs in any given mRNA, the position and the type of an MRE. We were able to show a hierarchy in the strength of repression between different types of MREs. Effect strength correlates with the length of the miRNA-mRNA pairing sequence. Furthermore, we showed that more miRNA binding sites in a single mRNA provided stronger effects than fewer binding sites. We found that binding sites in the 3’ untranslated region (3’UTR) mediate the strongest effect, but binding sites located in the coding sequence (CDS) also have repressive functions. Interestingly, most of these effects were achieved by mRNA decay and not through translational repression, except for a group of MREs located in satellite repeat elements in CDS, leading to significant changes in translational efficiency (TE). Additionally, we showed that an alternative seed match exists in some miR-181 MREs which contains an A-U switch but still shows repressive capacity. To further investigate miR-181 function in thymocytes, we created a mouse with a pri-miR-181 ablation caused by a premature poly-A signal. The preliminary investigation of miRNA expression and cell types could mostly reproduce the results to the mature miR-181 KO mouse, but further analysis is required. With this study, we deepened the knowledge of how miRNAs act in complex in vivo systems. We were able to confirm many predicted targets but furthermore, found large amounts of non-canonical target sites not yet described. We detected a new mechanism of regulation for a group of zinc finger proteins, which are in turn described to have role in T-cell function. We shed light on the way miR-181 regulates TCR signalling and leads to the depletion of non-conventional T cells upon KO. So far, the extensive length of the pri-miR-181 transcripts lacks explanation, but we created a pri-miR-181 ablation model that will be useful for further analysis of miR-181 development.

Natural History institutes hold an immense number of specimens and artefacts. For years these collections were not accessible online, remaining inaccessible to researchers from far away and hidden from the general public. Large digitisation projects and cross-institutional agreements aim to bring their collections into the digital era, such as the SYNTHESYS+ project and the Distributed System of Scientific Collections (DiSSCo) Research Infrastructure. As specimens are 3D physical objects with different characteristics many techniques are available to 3D digitise them. For inexperienced users this can be quite overwhelming. Which techniques are already well tested in other institutions and are suitable for a specific specimen or collection? To investigate this, we have set up a dichotomous identification key for digitisation techniques: DIGIT-KEY, (https://digit.naturalheritage.be/digit-key). For each technique, examples used in SYNTHESYS+ Institutions are visualised and training manuals provided. All information can be easily updated and representatives can be contacted if necessary to request more information about a certain technique. This key can be helpful to achieve comparable results across institutions when digitising collections on demand in future DiSSCo research initiatives coordinated through the European Loans and Visits System (ELViS) for Virtual and Transnational Access.