Background: Adverse outcome pathway (AOP) networks are versatile tools in toxicology and risk assessment that capture and visualize mechanisms driving toxicity originating from various data sources. They share a common structure consisting of a set of molecular initiating events and key events, connected by key event relationships, leading to the actual adverse outcome. AOP networks are to be considered living documents that should be frequently updated by feeding in new data. Such iterative optimization exercises are typically done manually, which not only is a time-consuming effort, but also bears the risk of overlooking critical data. The present study introduces a novel approach for AOP network optimization of a previously published AOP network on chemical-induced cholestasis using artificial intelligence to facilitate automated data collection followed by subsequent quantitative confidence assessment of molecular initiating events, key events, and key event relationships. Methods: Artificial intelligence-assisted data collection was performed by means of the free web platform Sysrev. Confidence levels of the tailored Bradford-Hill criteria were quantified for the purpose of weight-of-evidence assessment of the optimized AOP network. Scores were calculated for biological plausibility, empirical evidence, and essentiality, and were integrated into a total key event relationship confidence value. The optimized AOP network was visualized using Cytoscape with the node size representing the incidence of the key event and the edge size indicating the total confidence in the key event relationship. Results: This resulted in the identification of 38 and 135 unique key events and key event relationships, respectively. Transporter changes was the key event with the highest incidence, and formed the most confident key event relationship with the adverse outcome, cholestasis. Other important key events present in the AOP network include: nuclear receptor changes, intracellular bile acid accumulation, bile acid synthesis changes, oxidative stress, inflammation and apoptosis. Conclusions: This process led to the creation of an extensively informative AOP network focused on chemical-induced cholestasis. This optimized AOP network may serve as a mechanistic compass for the development of a battery of in vitro assays to reliably predict chemical-induced cholestatic injury.
We review over 10 years of research at Elsevier and various Dutch academic institutions on establishing a new format for the scientific research article. Our work rests on two main theoretical principles: the concept of modular documents, consisting of content elements that can exist and be published independently and are linked by meaningful relations, and the use of semantic data standards allowing access to heterogeneous data. We discuss the application of these concepts in five different projects: a modular format for physics articles, an XML encyclopedia in pharmacology, a semantic data integration project, a modular format for computer science proceedings papers, and our current work on research articles in cell biology.
Control of plant growth is an important aspect of crop productivity and yield in agriculture. Overexpression of the At CHR12/ 23 genes in Arabidopsis thaliana reduced growth habit without other morphological changes. These two genes encode Snf2 chromatin remodelling ATPases. Here, we translate this approach to the horticultural crop tomato ( Solanum lycopersicum). We identified and cloned the single tomato ortholog of the two Arabidopsis Snf2 genes, designated Sl CHR1. Transgenic tomato plants (cv. Micro-Tom) that constitutively overexpress the coding sequence of Sl CHR1 show reduced growth in all developmental stages of tomato. This confirms that Sl CHR1 combines the functions of both Arabidopsis genes in tomato. Compared to the wild type, the transgenic seedlings of tomato have significantly shorter roots, hypocotyls and reduced cotyledon size. Transgenic plants have a much more compact growth habit with markedly reduced plant height, severely compacted reproductive structures with smaller flowers and smaller fruits. The results indicate that either GMO-based or non- GMO-based approaches to modulate the expression of chromatin remodelling ATPase genes could develop into methods to control plant growth, for example to replace the use of chemical growth retardants. This approach is likely to be applicable and attractive for any crop for which growth habit reduction has added value.
To treat microbial infections, antibiotics are life-saving but the increasing antimicrobial resistance is a World-wide problem. Therefore, there is a great need for novel antimicrobial substances. Fruit and flower anthocyanins have been recognized as promising alternatives to traditional antibiotics. How-ever, for future application as innovative alternative antibiotics, the full potential of anthocyanins should be further investigated. The antimicrobial potential of anthocyanin mixtures against different bacterial species has been demonstrated in literature. Preliminary experiments performed by our laboratories, using grape, rose and red cabbage anthocyanins against S. aureus and E. coli confirmed the antimicrobial potential of these substances. Hundreds of different anthocyanin entities have been described. However, which of these entities hold antimicrobial effects is currently unknown. Our preliminary data show that an-thocyanins extracted from grape, rose and red cabbage contain different collections of anthocyanin entities with differential antimicrobial efficacies. Our focus is on the extraction and characterization of anthocyanins from various crop residues. Grape peels are residues in the production of wine, while red rose and tulip leaves are residues in the production of tulip bulbs and regular horticulture. The presence of high-grade substances for pharmacological purposes in these crops may provide an innovative strategy to add value to other-wise invaluable crop residues. This project will be performed by the collaborative effort of our institute together with the Medi-cal Microbiology department of the University Medical Center Groningen (UMCG), 'Wijnstaete', a small-scale wine-producer (Lemelerveld) and Imenz Bioengineering (Groningen), a company that develops processes to improve the production of biobased chemicals from waste products. Within this project, we will focus on the antimicrobial efficacy of anthocyanin-mixtures from sources that are abundantly and locally available as a residual waste product. The project is part of a larger re-search effect to further characterize, modify and study the antimicrobial effects of specific anthocy-anin entities.
