1. Stress knowledge map : a knowledge graph resource for systems biology analysis of plant stress responsesCarissa Bleker, Živa Ramšak, Andras Bittner, Vid Podpečan, Maja Zagorščak, Bernhard Wurzinger, Špela Baebler, Marko Petek, Maja Križnik, Anže Županič, Kristina Gruden, 2024, izvirni znanstveni članek Povzetek: Stress Knowledge Map (SKM; https://skm.nib.si) is a publicly available resource containing two complementary knowledge graphs that describe the current knowledge of biochemical, signaling, and regulatory molecular interactions in plants: a highly curated model of plant stress signaling (PSS; 543 reactions) and a large comprehensive knowledge network (488 390 interactions). Both were constructed by domain experts through systematic curation of diverse literature and database resources. SKM provides a single entry point for investigations of plant stress response and related growth trade-offs, as well as interactive explorations of current knowledge. PSS is also formulated as a qualitative and quantitative model for systems biology and thus represents a starting point for a plant digital twin. Here, we describe the features of SKM and show, through two case studies, how it can be used for complex analyses, including systematic hypothesis generation and design of validation experiments, or to gain new insights into experimental observations in plant biology.
Ključne besede: Stress knowledge map, knowledge graph, knowledge network, entry point, plant digital twin, plant stress responses, plant signaling, systems biology
Objavljeno v DiRROS: 11.06.2024; Ogledov: 115; Prenosov: 67
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2. pISA-tree : a data management framework for life science research projects using a standardised directory treeMarko Petek, Maja Zagorščak, Andrej Blejec, Živa Ramšak, Anna Coll Rius, Špela Baebler, Kristina Gruden, 2022, izvirni znanstveni članek Ključne besede: pISA-tree, ISA model, data management, research data, metadata
Objavljeno v DiRROS: 05.06.2024; Ogledov: 144; Prenosov: 114
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3. Transcriptome-informed identification and characterization of Planococcus citri cis- and trans-isoprenyl diphosphate synthase genesMojca Juteršek, Iryna Gerasymenko, Marko Petek, Kristina Gruden, Špela Baebler, 2024, izvirni znanstveni članek Povzetek: Insect physiology and reproduction depend on several terpenoid compounds, whose biosynthesis is mainly unknown. One enigmatic group of insect monoterpenoids are mealybug sex pheromones, presumably resulting from the irregular coupling activity of unidentified isoprenyl diphosphate synthases (IDSs). Here, we performed a comprehensive search for IDS coding sequences of the pest mealybug Planococcus citri. We queried the available genomic and newly generated short- and long-read P. citri transcriptomic data and identified 18 putative IDS genes, whose phylogenetic analysis indicates several gene family expansion events. In vitro testing confirmed regular short-chain coupling activity with five gene products. With the candidate with highest IDS activity, we also detected low amounts of irregular coupling products, and determined amino acid residues important for chain-length preference and irregular coupling activity. This work therefore provides an important foundation for deciphering terpenoid biosynthesis in mealybugs, including the sex pheromone biosynthesis in P. citri.
Ključne besede: insect pheromones, isoprenyl diphosphate synthase, monoterpenes, phylogenetic analysis
Objavljeno v DiRROS: 29.03.2024; Ogledov: 299; Prenosov: 141
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4. Chloroplast redox state changes mark cell-to-cell signaling in the hypersensitive responseTjaša Lukan, Anže Županič, Tjaša Mahkovec Povalej, Jacob O. Brunkard, Mirjam Kmetič, Mojca Juteršek, Špela Baebler, Kristina Gruden, 2023, izvirni znanstveni članek Povzetek: Bisphenol A (BPA) is one of the most commonly used substances in the manufacture ofvarious everyday products. Growing concerns about its hazardous properties, including endocrinedisruption and genotoxicity, have led to its gradual replacement by presumably safer analogues inmanufacturing plastics. The widespread use of BPA and, more recently, its analogues has increasedtheir residues in the environment. However, our knowledge of their toxicological profiles is limitedand their combined effects are unknown. In the present study, we investigated the toxic effectscaused by single bisphenols and by the combined exposure of BPA and its two analogues, BPAP andBPC, after short (24-h) and prolonged (96-h) exposure in HepG2 spheroids. The results showed thatBPA did not reduce cell viability in HepG2 spheroids after 24-h exposure. In contrast, BPAP andBPC affected cell viability in HepG2 spheroids. Both binary mixtures (BPA/BPAP and BPA/BPC)decreased cell viability in a dose-dependent manner, but the significant difference was only observedfor the combination of BPA/BPC (both at 40μM). After 96-h exposure, none of the BPs studiedaffected cell viability in HepG2 spheroids. Only the combination of BPA/BPAP decreased cellviability in a dose-dependent manner that was significant for the combination of 4μM BPA and 4μMBPAP. None of the BPs and their binary mixtures studied affected the surface area and growth ofspheroids as measured by planimetry. In addition, all BPs and their binary mixtures studied triggeredoxidative stress, as measured by the production of reactive oxygen species and malondialdehyde,at both exposure times. Overall, the results suggest that it is important to study the effects of BPsas single compounds. It is even more important to study the effects of combined exposures, as thecombined effects may differ from those induced by single compounds.
Ključne besede: chloroplast redox state, hypersensitive response (HR)-conferred resistance, immune signaling, live cell imaging, Solanum tuberosum (potato), spatiotemporal analysis, stromules, virus resistance
Objavljeno v DiRROS: 13.04.2023; Ogledov: 494; Prenosov: 240
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8. 7th Slovenian Symposium on Plant Biology with International Participation, Biotechnical Faculty, University of Ljubljana, September 17-18, 2018, Ljubljana, Slovenia2018, druge monografije in druga zaključena dela Povzetek: Publikacija je zbirka povzetkov predavanj in posterskih predstavitev v okviru simpozija
Ključne besede: rastline, sistemska biologija, molekularna biologija, rastlinska ekologija, interakcije, rastlinska biotehnologija, zborniki, povzetki, elektronske knjige
Objavljeno v DiRROS: 25.09.2018; Ogledov: 5118; Prenosov: 1942
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