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Published in DiRROS: 09.09.2024; Views: 145; Downloads: 3930
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Abstract: Despite the efforts invested into measures to prevent water eutrophication, like prevention and treatment of point and dispersed discharges, the eutrophication still occurs. One of the unwanted consequences of eutrophic water state is the occurrence of excessive cyanobacterial blooms. Mass occurrence of cyanobacteria is a significant health risk related to surface waters in EU and worldwide since most of the cyanobacterial genera produce cyanotoxins. Besides toxicity, cyanobacterial blooms cause an increase in the turbidity of water and create taste and odour problems. All mentioned represents substantial economic losses in sectors like aquaculture, tourism, drinking water facilities and indirect losses due to increased healthcare expenditures and environmental degradation. It is, therefore, necessary to find appropriate solutions for rapid detection and also in-lake prevention of bloom occurrence despite, for example, existing high eutrophic conditions in the water body. The proposed project represents such a solution. In the frame of the LIFE Stop CyanoBloom project, we have designed two solar powered robotic vessels for the in-lake detection and control of cyanobacterial proliferation. Each vessel is capable of three-dimensional localisation of cyanobacteria by measuring fluorescence of pigments involved in the process of photosynthesis. The vessels are additionally equipped with electrochemical cells using boron doped diamond electrodes fixed on board, producing short-lived hydroxyl radicals, which prevent cyanobacterial proliferation as well as cyanotoxins inactivation. Hydroxyl radicals cause different levels of damages to cyanobacterial cells as well as stress, that may also result in phage induced cyanobacterial lysis. Natural control of cyanobacterial density by lytic cyanophages is known for several years. The mixing of water during the electrolytic cell operation also increases the potential contacts of cyanobacteria with cyanophages, disturbs cyanobacterial buoyancy and generates additional nutrients for nontoxic phytoplankton population. Additional newly developed equipment of the vessel allows advanced automated navigation (automatic docking, avoiding obstacles, maintaining the position in windy conditions, etc.), sampling from different depths, real-time data transfer, statistical analysis and graphical presentation using the adequate software.
Keywords: cyanobacteria, cyanobacterial blooms, cyanotoxins, health risk
Published in DiRROS: 05.09.2024; Views: 89; Downloads: 668
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Abstract: Ethylene response factors (ERFs) have been associated with biotic stress in Arabidopsis, while their function in non-model plants is still poorly understood. Here we investigated the role of potato ERF StPti5 in plant immunity. We show that StPti5 acts as a susceptibility factor. It negatively regulates potato immunity against potato virus Y and Ralstonia solanacearum, pathogens with completely different modes of action, and thereby has a different role than its orthologue in tomato. Remarkably, StPti5 is destabilised in healthy plants via the autophagy pathway and accumulates exclusively in the nucleus upon infection. We demonstrate that StEIN3 and StEIL1 directly bind the StPti5 promoter and activate its expression, while synergistic activity of the ethylene and salicylic acid pathways is required for regulated StPti expression. To gain further insight into the mode of StPti5 action in attenuating potato defence responses, we investigated transcriptional changes in salicylic acid deficient potato lines with silenced StPti5 expression. We show that StPti5 regulates the expression of other ERFs and downregulates the ubiquitin-proteasome pathway as well as several proteases involved in directed proteolysis. This study adds a novel element to the complex puzzle of immune regulation, by deciphering a two-level regulation of ERF transcription factor activity in response to pathogens.
Keywords: ethylene response factor, immune signalling, potato virus Y, Pti5, Ralstonia solanacearum, Solanum tuberosum, susceptibility factor
Published in DiRROS: 29.08.2024; Views: 136; Downloads: 587
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Abstract: The global impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its companion disease, COVID-19, has reminded us of the importance of basic coronaviral research. In this study, a comprehensive approach using molecular docking, in vitro assays, and molecular dynamics simulations was applied to identify potential inhibitors for SARS-CoV-2 papain-like protease (PLpro), a key and underexplored viral enzyme target. A focused protease inhibitor library was initially created and molecular docking was performed using CmDock software (v0.2.0), resulting in the selection of hit compounds for in vitro testing on the isolated enzyme. Among them, compound 372 exhibited promising inhibitory properties against PLpro, with an IC50 value of 82 ± 34 μM. The compound also displayed a new triazolopyrimidinyl scaffold not yet represented within protease inhibitors. Molecular dynamics simulations demonstrated the favorable binding properties of compound 372. Structural analysis highlighted its key interactions with PLpro, and we stress its potential for further optimization. Moreover, besides compound 372 as a candidate for PLpro inhibitor development, this study elaborates on the PLpro binding site dynamics and provides a valuable contribution for further efforts in pan-coronaviral PLpro inhibitor development.
Keywords: drug design, protease inhibitor, SARS-CoV-2, papain-like protease, PLpro, antiviral design, in silico drug design, CADD, virtual screening, HTVS, structure-based design
Published in DiRROS: 07.08.2024; Views: 215; Downloads: 178
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Abstract: Background In experimental data analysis, bioinformatics researchers increasingly rely on tools that enable the composition and reuse of scientific workflows. The utility of current bioinformatics workflow environments can be significantly increased by offering advanced data mining services as workflow components. Such services can support, for instance, knowledge discovery from diverse distributed data and knowledge sources (such as GO, KEGG, PubMed, and experimental databases). Specifically, cutting-edge data analysis approaches, such as semantic data mining, link discovery, and visualization, have not yet been made available to researchers investigating complex biological datasets. Results We present a new methodology, SegMine, for semantic analysis of microarray data by exploiting general biological knowledge, and a new workflow environment, Orange4WS, with integrated support for web services in which the SegMine methodology is implemented. The SegMine methodology consists of two main steps. First, the semantic subgroup discovery algorithm is used to construct elaborate rules that identify enriched gene sets. Then, a link discovery service is used for the creation and visualization of new biological hypotheses. The utility of SegMine, implemented as a set of workflows in Orange4WS, is demonstrated in two microarray data analysis applications. In the analysis of senescence in human stem cells, the use of SegMine resulted in three novel research hypotheses that could improve understanding of the underlying mechanisms of senescence and identification of candidate marker genes. Conclusions Compared to the available data analysis systems, SegMine offers improved hypothesis generation and data interpretation for bioinformatics in an easy-to-use integrated workflow environment.
Published in DiRROS: 05.08.2024; Views: 188; Downloads: 140
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