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Abstract: The last decade has seen the adverse outcome pathways (AOP) framework become one of the most powerful tools in chemical risk assessment, but the development of new AOPs remains a slow and manually intensive process. Here, we present a faster approach for AOP generation, based on manually curated causal toxicological networks. As a case study, we took a recently published zebrafish developmental neurotoxicity network, which contains causally connected molecular events leading to neuropathologies, and developed two new adverse outcome pathways: Inhibition of Fyna (Src family tyrosine kinase A) leading to increased mortality via decreased eye size (AOP 399 on AOP-Wiki) and GSK3beta (Glycogen synthase kinase 3 beta) inactivation leading to increased mortality via defects in developing inner ear (AOP 410). The approach consists of an automatic separation of the toxicological network into candidate AOPs, filtering the AOPs according to available evidence and length as well as manual development of new AOPs and weight-of-evidence evaluation. The semiautomatic approach described here provides a new opportunity for fast and straightforward AOP development based on large network resources.
Keywords: systems toxicology, adverse outcome pathway, casual network, toxicological network, neurotoxicity
Published in DiRROS: 16.07.2024; Views: 257; Downloads: 174
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Abstract: Tobamovirus species represent a threat to solanaceous crops worldwide, due to their extreme stability and because they are seed borne. In particular, recent outbreaks of tomato brown rugose fruit virus in tomato and pepper crops led to the establishment of prompt control measures, and the need for reliable diagnosis was urged. Another member of the genus, tomato mottle mosaic virus, has recently gained attention due to reports in different continents and its common features with tomato brown rugose fruit virus. In this study, a new real-time RT-PCR detection system was developed for tomato brown rugose fruit virus and tomato mottle mosaic virus on tomato leaves and seeds using TaqMan chemistry. This test was designed to detect tomato mottle mosaic virus by amplifying the movement protein gene in a duplex assay with the tomato brown rugose fruit virus target on the CP-3’NTR region, which was previously validated as a single assay. The performance of this test was evaluated, displaying analytical sensitivity 10−5–10−6-fold dilution for seeds and leaves, respectively, and good analytical specificity, repeatability, and reproducibility. Using the newly developed and validated test, tomato brown rugose fruit virus detection was 100% concordant with previously performed analyses on 106 official samples collected in 2021 from different continents.
Keywords: real-time PCR, tomato mottle mosaic virus, tomato brown rugose fruit virus, leaves detection, seeds detections, performance criteria
Published in DiRROS: 16.07.2024; Views: 280; Downloads: 223
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Abstract: Colour polymorphism may be accompanied by alternative expressions of phenotypic traits that are directly or indirectly related to fitness, and selection forces may act on the traits separately or concurrently. In polymorphic species, natural selection may act through frequency- or density-dependent mechanisms and maintain polymorphism through interactions among morphs. We used an integrative approach to examine functionally relevant and interrelated life history traits in the context of colour polymorphism in the European wall lizard (Podarcis muralis). Body, head and limb morphology, bite and locomotor performance, and physiology, particularly metabolic and antioxidant capacity, were analysed in the three pure colour morphs (yellow, orange, white) and the two mosaic morphs (yellow-orange and white-orange). Morphological differences between morphs were present but subtle and consisted mainly of variations in head length. Head size and bite force were strongly associated between and within morphs. Limb and boot morphology and locomotor performance (sprinting and climbing) were variably associated among morphs. Finally, variation in biochemical indicators of cellular metabolism and antioxidant capacity appeared to be largely independent of morphology and performance. The results provide evidence for existing and non-existing relationships between colour and morphology, performance, and physiology that could have short- and long-term effects on selection.
Keywords: colour morphs, sprint speed, climbing, bite force, physiology
Published in DiRROS: 16.07.2024; Views: 273; Downloads: 197
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Abstract: Amphibole asbestos is related to lung fibrosis and several types of lung tumors. The disease-triggering mechanisms still challenge our diagnostic capabilities and are still far from being fully understood. The literature focuses primarily on the role and formation of asbestos bodies in lung tissues, but there is a distinct lack of studies on amphibole particles that have been internalized by alveolar epithelial cells (AECs). These internalized particles may directly interact with the cell nucleus and the organelles, exerting a synergistic action with asbestos bodies (AB) from a different location. Here we document the near-atomic- to nano-scale transformations induced by, and taking place within, AECs of three distinct amphiboles (anthophyllite, grunerite, “amosite”) with different Fe-content and morphologic features. We show that: (i) an Fe-rich layer is formed on the internalized particles, (ii) particle grain boundaries are transformed abiotically by the internal chemical environment of AECs and/or by a biologically induced mineralization mechanism, (iii) the Fe-rich material produced on the particle surface does not contain large amounts of P, in stark contrast to extracellular ABs, and (iv) the iron in the Fe-rich layer is derived from the particle itself. Internalized particles and ABs follow two distinct formation mechanisms reaching different physicochemical end-states.
Keywords: amphiboles, human alveolar epithelial cells, asbestos, lung cancer, nanoscale investigation, acS/TEM-EDXS, dual-EELS, asbestos-related tumors
Published in DiRROS: 16.07.2024; Views: 367; Downloads: 211
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Abstract: Planetary extinction of biodiversity underscores the need for taxonomy. Here, we scrutinizespider taxonomy over the last decade (2008–2018), compiling 2083 published accounts of newlydescribed species. We evaluated what type of data were used to delineate species, whether data weremade freely available, whether an explicit species hypothesis was stated, what types of media wereused, the sample sizes, and the degree to which species constructs were integrative. The findings wereport reveal that taxonomy remains largely descriptive, not integrative, and provides no explicitconceptual framework. Less than 4% of accounts explicitly stated a species concept and over one-thirdof all new species described were based on 1–2 specimens or only one sex. Only ~5% of studies madedata freely available, and only ~14% of all newly described species employed more than one line ofevidence, with molecular data used in ~6% of the studies. These same trends have been discovered inother animal groups, and therefore we find it logical that taxonomists face an uphill challenge whenjustifying the scientific rigor of their field and securing the needed resources. To move taxonomyforward, we make recommendations that, if implemented, will enhance its rigor, repeatability, andscientific standards.
Keywords: taxonomy, taxonomic crisis, species concepts, data management, monographic research
Published in DiRROS: 16.07.2024; Views: 268; Downloads: 139
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