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1.
Commutators greater than a perturbation of the identity
Roman Drnovšek, Marko Kandić, 2025, original scientific article

Abstract: Let $a$ and $b$ be elements of an ordered normed algebra ${\mathcal A}$ with unit $e$. Suppose that the element $a$ is positive and that for some $\varepsilon > 0$ there exists an element $x\in {\mathcal A}$ with $\|x\|\leq \varepsilon$ such that $ab-ba \geq e+x$. If the norm on ${\mathcal A}$ is monotone, then we show $\|a\|\cdot \|b\|\geq \tfrac{1}{2} \ln \tfrac{1}{\varepsilon}$, which can be viewed as an order analog of Popa's quantitative result for commutators of operators on Hilbert spaces. We also give a relevant example of positive operators $A$ and $B$ on the Hilbert lattice $\ell^2$ such that their commutator $A B - B A$ is greater than an arbitrarily small perturbation of the identity operator.
Keywords: Banach lattices, positive operators, commutators, ordered normed algebras
Published in DiRROS: 19.09.2024; Views: 4; Downloads: 4
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2.
Ultrasound-mediated spatial and temporal control of engineered cells in vivo
Filip Ivanovski, Maja Meško, Tina Lebar, Marko Rupnik, Duško Lainšček, Miha Gradišek, Roman Jerala, Mojca Benčina, 2024, original scientific article

Published in DiRROS: 09.09.2024; Views: 145; Downloads: 3930
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3.
Report on economic justification of the project : LIFE Stop CyanoBloom
Maja Zupančič Justin, Gorazd Lakovič, Tinkara Rozina, Bojan Sedmak, Marko Gerl, 2017, final research report

Abstract: The Annexe 17 of the Final Report of the project LIFE Stop CyanoBloom, presenting the “Report on economic justification of the project” is composed of 14 chapters. The first part of the report gives a general overview of the cyanobacteria and their blooms, and species and toxicity of cyanobacterial toxins. With a literature review, economic consequences of cyanobacterial blooms on human health, commercial fishery, tourism and recreation, and lake monitoring and management have been evaluated. The chapter on phytoplankton and bacterioplankton monitoring options presents the importance of the phytoplankton for the lake ecology and evaluation of the water quality status. Traditional phytoplankton monitoring approaches are compared to the new monitoring options applied in the project. The chapter in-lake cyanobacterial control options give a broad review of available in-lake rehabilitation and remediation options, which can be compared with the electrochemical oxidation technique presented in the following chapter and applied in the project. According to the results obtained during the pilot testing activities, a cost evaluation of the approach has been performed and presented in the report. The last chapter gathers open issues and proposals for the further work in this field.
Keywords: cyanobacteria, cyanotoxins, health risk
Published in DiRROS: 05.09.2024; Views: 109; Downloads: 249
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4.
Innovative technology for cyanobacterial bloom control : LIFE Stop CyanoBloom
Maja Zupančič Justin, Marko Gerl, Gorazd Lakovič, Bojan Sedmak, Tinkara Rozina, Neža Finžgar, Maja Čič, Mario Marinovič, Luka Teslić, Jošt Grum, Maša Čater, Tina Eleršek, Andrej Meglič, Andrey Yakuntsov, Lovro Pokorn, Tomaž Kralj, Matjaž Berčon, Branko Hamiti, 2017, final research report

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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5.
Milestone M27 : user friendly data management and analysis environment for plant systems biology established and novel/improved multiomics data visualisation tool available
Luka Ausec, Barbara Jenko Bizjan, Janez Kokošar, Amrita Roy Choudhury, Miha Štajdohar, Kristina Gruden, Maja Križnik, Marko Petek, Živa Ramšak, 2018, final research report

Abstract: We present the technical report regarding the implementation of the Genialis Platform at the National Institute of Biology (NIB) within the project Hyp (J4-7636).
Published in DiRROS: 05.09.2024; Views: 98; Downloads: 78
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6.
The StPti5 ethylene response factor acts as a susceptibility factorby negatively regulating the potato immune responseto pathogens
Anna Coll Rius, Tjaša Lukan, Katja Stare, Maja Zagorščak, Tjaša Mahkovec Povalej, Špela Baebler, Salomé Prat, Núria Sánchez Coll, Marc Valls, Marko Petek, Kristina Gruden, 2024, original scientific article

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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7.
Oxytetracycline hyper-production through targeted genome reduction of Streptomyces rimosus
Alen Pšeničnik, Lucija Slemc, Martina Avbelj, Miha Tome, Martin Šala, Paul R. Herron, Maksym Shmatkov, Marko Petek, Špela Baebler, Peter Mrak, Daslav Hranueli, Antonio Starcevic, Iain S. Hunter, Hrvoje Petković, 2024, original scientific article

Abstract: Most biosynthetic gene clusters (BGC) encoding the synthesis of important microbial secondary metabolites, such as antibiotics, are either silent or poorly expressed; therefore, to ensure a strong pipeline of novel antibiotics, there is a need to develop rapid and efficient strain development approaches. This study uses comparative genome analysis to instruct rational strain improvement, using Streptomyces rimosus, the producer of the important antibiotic oxytetracycline (OTC) as a model system. Sequencing of the genomes of two industrial strains M4018 and R6-500, developed independently from a common ancestor, identified large DNA rearrangements located at the chromosome end. We evaluated the effect of these genome deletions on the parental S. rimosus Type Strain (ATCC 10970) genome where introduction of a 145 kb deletion close to the OTC BGC in the Type Strain resulted in massive OTC overproduction, achieving titers that were equivalent to M4018 and R6-500. Transcriptome data supported the hypothesis that the reason for such an increase in OTC biosynthesis was due to enhanced transcription of the OTC BGC and not due to enhanced substrate supply. We also observed changes in the expression of other cryptic BGCs; some metabolites, undetectable in ATCC 10970, were now produced at high titers. This study demonstrated for the first time that the main force behind BGC overexpression is genome rearrangement. This new approach demonstrates great potential to activate cryptic gene clusters of yet unexplored natural products of medical and industrial value.
Keywords: genome reduction, antibiotic biosynthesis, oxytetracycline, cryptic metabolites
Published in DiRROS: 07.08.2024; Views: 193; Downloads: 180
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8.
Identification of triazolopyrimidinyl scaffold SARS-CoV-2 papain-like protease (PLpro) inhibitor
Sebastjan Kralj, Marko Jukič, Miha Bahun, Luka Kranjc, Anja Kolarič, Milan Hodošček, Nataša Poklar Ulrih, Urban Bren, 2024, original scientific article

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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9.
Insect pest management in the age of synthetic biology
Rubèn Mateos Fernández, Marko Petek, Mojca Juteršek, Iryna Gerasymenko, Špela Baebler, Kalyani Kallam, Elena Moreno Gimenéz, Janine Gondolf, Alfred Nordmann, Kristina Gruden, Diego Orzaez, Nicola Patron, 2022, review article

Abstract: Arthropod crop pests are responsible for 20% of global annual crop losses, a figure predicted to increase in a changing climate where the ranges of numerous species are projected to expand. At the same time, many insect species are beneficial, acting as pollinators and predators of pest species. For thousands of years, humans have used increasingly sophisticated chemical formulations to control insect pests but, as the scale of agriculture expanded to meet the needs of the global population, concerns about the negative impacts of agricultural practices on biodiversity have grown. While biological solutions, such as biological control agents and pheromones, have previously had relatively minor roles in pest management, biotechnology has opened the door to numerous new approaches for controlling insect pests. In this review, we look at how advances in synthetic biology and biotechnology are providing new options for pest control. We discuss emerging technologies for engineering resistant crops and insect populations and examine advances in biomanufacturing that are enabling the production of new products for pest control.
Keywords: biotechnology, insect pest management, synthetic biology
Published in DiRROS: 05.08.2024; Views: 174; Downloads: 263
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10.
SegMine workflows for semantic microarray data analysis in Orange4WS
Vid Podpečan, Nada Lavrač, Igor Mozetič, Petra Kralj Novak, Igor Trajkovski, Laura Langohr, Kimmo Kulovesi, Hannu Toivonen, Marko Petek, Helena Motaln, Kristina Gruden, 2011, original scientific article

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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