1. Data from manuscript : analysis of plant and environmental samples for the quarantine fungus Phyllosticta citricarpa in four European citrus-growing areasPolona Kogovšek, Irene Vloutoglou, Valentino Bergamaschi, Neil Boonham, Maja Ferle, Sara Fišer, Eleni Kalogeropoulou, Andreas Kampletsas, Zala Kogej Zwitter, Athanasia Ligka, Roy Macarthur, Lucia Pirone, Maja Ravnikar, Luca Riccioni, Maria Teresa Valente, Darren Vella, Janja Zajc Žunič, Antonio Vicent, 2026, zaključena znanstvena zbirka raziskovalnih podatkov Povzetek: Phyllosticta citricarpa is the causal agent of citrus black spot (CBS), a disease affecting most citrus species and cultivars, particularly lemons (Citrus limon) and sweet oranges (C. sinensis). The pathogen causes fruit blemishes and premature fruit drop, leading to substantial yield and quality losses. Phyllosticta citricarpa is of global economic importance and is regulated by several citrus-growing countries, including those in the European Union (EU). The aim of this study was to develop a novel approach for early detection of P. citricarpa in environmental samples and to assess the status of P. citricarpa in selected citrus-growing areas of the EU where this species had previously been reported from leaf litter. Between 2018 and 2021, citrus plant material, air and rainwater samples were collected and analysed for the presence of Phyllosticta spp. in orchards in Greece, Italy, and Malta. Molecular analyses using qPCR assays targeting P. citricarpa were employed for the analysis of air and rainwater samples. The performance of the testing protocol was evaluated prior to sample analysis, and 1,000 conidia were determined to be the minimum number of spores required for reliable detection. No CBS symptoms were observed, and no evidence of P. citricarpa was found in collected citrus plant material, air, or rainwater samples. The only Phyllosticta species detected during this study was the endophyte P. capitalensis, isolated from citrus leaf litter in Greece. These findings support the results of official EU surveys, which indicate the current absence of P. citricarpa in the surveyed areas and demonstrate the value of integrating environmental monitoring with molecular diagnostics for plant health surveillance. The methodologies developed here offer a robust framework for early warning and rapid response, supporting efforts to prevent CBS outbreaks in Europe and can be adapted for other fungal pathogens.
Ključne besede: citrus black spot, early detection, molecular diagnostics, Phyllosticta citricarpa, spore trapping
Objavljeno v DiRROS: 30.03.2026; Ogledov: 282; Prenosov: 262
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4. Annual (2024) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota)Jens H. Kuhn, Scott Adkins, Sergey V. Alkhovsky, Wenxia An, Tatjana Avšič-Županc, María A. Ayllón, Katarina Bačnik, Justin Bahl, Anne Balkema-Buschmann, Matthew J. Ballinger, Ion Gutiérrez-Aguirre, Denis Kutnjak, Nataša Mehle, Anja Pecman, Maja Ravnikar, Ana Vučurović, 2025, izvirni znanstveni članek Povzetek: In April 2024, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was expanded by 1 new order, 1 new family, 6 new subfamilies, 34 new genera and 270 new species. One class, two orders and six species were renamed. Seven families and 12 genera were moved; ten species were renamed and moved; and nine species were abolished. This article presents the updated taxonomy of Negarnaviricota as currently accepted by the ICTV, providing an essential annual update on the classification of members of this phylum that deepen understandings of their evolution, and supports critical public health measures for virus identification and tracking.
Ključne besede: Aliusviridae, Arenaviridae, articulaviral, Articulavirales, Artoviridae, Aspiviridae, Bornaviridae, bunyaviral, Bunyavirales, Bunyaviricetes, bunyavirus, Crepuscuviridae, Discoviridae, Elliovirales, Filoviridae, Fimoviridae, Goujianvirales, Hantaviridae, Hareavirales, International Committee on Taxonomy of Viruses (ICTV), jingchuviral, Jingchuvirales, Konkoviridae, Lispiviridae, megaclassification, megataxonomy, mononegaviral, Mononegavirales, muviral, Muvirales, Mymonaviridae, Myriaviridae, naedreviral, Naedrevirales, Nairoviridae, Natareviridae, negarnaviricot, Negarnaviricota, Nyamiviridae, Orthomyxoviridae, Orthornavirae, Paramyxoviridae, Peribunyaviridae, Phasmaviridae, Phenuiviridae, Pneumoviridae, Rhabdoviridae, Riboviria, Sunviridae, Tenuivirus, Tosoviridae, Tospoviridae, Tulasviridae, virus classification, virus nomenclature, virus taxonomy, virology
Objavljeno v DiRROS: 24.06.2025; Ogledov: 935; Prenosov: 690
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5. One-step RT-droplet digital PCR : a breakthrough in the quantification of waterborne RNA virusesNejc Rački, Dany Morisset, Ion Gutiérrez-Aguirre, Maja Ravnikar, 2014, izvirni znanstveni članek Povzetek: Water contamination by viruses has an increasing worldwide impact on human health, and has led to requirements for accurate and quantitative molecular tools. Here, we report the first one-step reverse-transcription droplet digital PCR-based absolute quantification of a RNA virus (rotavirus) in different types of surface water samples. This quantification method proved to be more precise and more tolerant to inhibitory substances than the benchmarking reverse-transcription real-time PCR (RT-qPCR), and needs no standard curve. This new tool is fully amenable for the quantification of viruses in the particularly low concentrations usually found in water samples.
Ključne besede: waterborne virus, quantification, droplet digital PCR, real-time PCR, digital PCR
Objavljeno v DiRROS: 04.03.2025; Ogledov: 1191; Prenosov: 766
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6. A "crossomics" study analysing variability of different components in peripheral blood of health caucasoid individualsKristina Gruden, Matjaž Hren, Ana Herman, Andrej Blejec, Tanja Albrecht, Joachim Selbig, Chris Bauer, Jochannes Schuchardt, Michal Or-Guil, Klemen Zupančič, Urban Švajger, Borut Štabuc, Alojz Ihan, Andreja Nataša Kopitar, Maja Ravnikar, Miomir Knežević, Primož Rožman, Matjaž Jeras, 2012, izvirni znanstveni članek Povzetek: Background: Different immunotherapy approaches for the treatment of cancer andautoimmune diseases are being developed and tested in clinical studies worldwide. Their resulting complex experimental data should be properly evaluated, therefore reliable normal healthy control baseline values are indispensable. Methodology/Principal Findings: To assess intra- and inter-individual variability of various biomarkers, peripheral blood of 16 age and gender equilibrated healthy volunteers was sampled on 3 different days within a period of one month. Complex ććcrossomicsćć analyses of plasma metabolite profiles, antibody concentrations and lymphocyte subset counts as well as whole genome expression profiling in CD4+T and NK cells were performed. Some of the observed age, gender and BMI dependences are in agreement with the existing knowledge, like negative correlation between sex hormone levels and age or BMI related increase in lipids and soluble sugars. Thus we can assume that the distribution of all 39.743 analysed markers is well representing the normal Caucasoid population. All lymphocyte subsets, 20% of metabolites and less than 10% of genes, were identified as highly variable in our dataset. Conclusions/Significance: Our study shows that the intra-individual variability was at least two-fold lower compared to the inter-individual one at all investigated levels, showing the importance of personalised medicine approach from yet another perspective.
Objavljeno v DiRROS: 04.03.2025; Ogledov: 800; Prenosov: 942
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7. Dynamics of responses in compatible potato - potato virus Y interaction are modulated by salicylic acidŠpela Baebler, Katja Stare, Maja Kovač, Andrej Blejec, Nina Prezelj, Tjaša Stare, Polona Kogovšek, Maruša Pompe Novak, S. Rosahl, Maja Ravnikar, Kristina Gruden, 2011, izvirni znanstveni članek Povzetek: To investigate the dynamics of the potato – Potato virus Y (PVY) compatible interaction in relation to salicylic acid - controlled pathways we performed experiments using non-transgenic potato cv. Désirée, transgenic NahG-Désirée, cv. Igor and PVYNTN, the most aggressive strain of PVY. The importance of salicylic acid in viral multiplication and symptom development was confirmed by pronounced symptom development in NahG-Désirée, depleted in salicylic acid, and reversion of the effect after spraying with 2,6-dichloroisonicotinic acid (a salicylic acid - analogue). We have employed quantitative PCR for monitoring virus multiplication, as well as plant responses through expression of selected marker genes of photosynthetic activity, carbohydrate metabolism and the defence response. Viral multiplication was the slowest in inoculated potato of cv. Désirée, the only asymptomatic genotype in the study. The intensity of defence-related gene expression was much stronger in both sensitive genotypes (NahG-Désirée and cv. Igor) at the site of inoculation than in asymptomatic plants (cv. Désirée). Photosynthesis and carbohydrate metabolism gene expression differed between the symptomatic and asymptomatic phenotypes. The differential gene expression pattern of the two sensitive genotypes indicates that the outcome of the interaction does not rely simply on one regulatory component, but similar phenotypical features can result from distinct responses at the molecular level.
Ključne besede: plant viruses, plant diseases
Objavljeno v DiRROS: 04.03.2025; Ogledov: 964; Prenosov: 617
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8. Odkrivanje in z vodo povezana epidemiologija porajajočih se tobamovirusov, ki okužujejo kmetijske rastlineNataša Mehle, Denis Kutnjak, Ana Vučurović, Ion Gutiérrez-Aguirre, Katarina Bačnik, Luka Kranjc, Irena Bajde, Jakob Brodarič, Maja Ravnikar, Olivera Maksimović, Mark Paul Selda Rivarez, Tomaž Curk, Neža Pajek Arambašić, Rok Štravs, 2024, končno poročilo o rezultatih raziskav Ključne besede: diagnostika, rastlinski virusi, ToBRFV, ToMMV, tobamovirusi, epidemiologija, voda kot vir okužb, poročila
Objavljeno v DiRROS: 20.02.2025; Ogledov: 1105; Prenosov: 400
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9. Odkrivanje in z vodo povezana epidemiologija porajajočih se tobamovirusov, ki okužujejo kmetijske rastline : aplikativni raziskovalni projekt L4-3179Nataša Mehle, Denis Kutnjak, Tomaž Curk, Neža Pajek Arambašić, Ion Gutiérrez-Aguirre, Rok Štravs, Katarina Bačnik, Luka Kranjc, Irena Bajde, Jakob Brodarič, Miha Kitek, Maja Ravnikar, Olivera Maksimović, Mark Paul Selda Rivarez, Ana Vučurović, 2024, končno poročilo o rezultatih raziskav Ključne besede: ToBRFV, ToMMV, tobamovirusi, epidemiologija, voda kot vir okužb, poročila
Objavljeno v DiRROS: 28.11.2024; Ogledov: 1385; Prenosov: 898
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10. Cold plasma within a stable supercavitation bubble - a breakthrough technology for efficient inactivation of viruses in waterArijana Filipić, David Dobnik, Ion Gutiérrez-Aguirre, Maja Ravnikar, Tamara Košir, Špela Baebler, Alja Štern, Bojana Žegura, Martin Petkovšek, Matevž Dular, Miran Mozetič, Rok Zaplotnik, Gregor Primc, 2023, izvirni znanstveni članek Povzetek: Water scarcity, one of the most pressing challenges we face today, has developed for many reasons, including the increasing number of waterborne pollutants that affect the safety of the water environment. Waterborne human, animal and plant viruses represent huge health, environmental, and financial burden and thus it is important to efficiently inactivate them. Therefore, the main objective of this study was to construct a unique device combining plasma with supercavitation and to evaluate its efficiency for water decontamination with the emphasis on inactivation of viruses. High inactivation (>5 log10 PFU/mL) of bacteriophage MS2, a human enteric virus surrogate, was achieved after treatment of 0.43 L of recirculating water for up to 4 min. The key factors in the inactivation were short-lived reactive plasma species that damaged viral RNA. Water treated with plasma for a short time required for successful virus inactivation did not cause cytotoxic effects in the in vitro HepG2 cell model system or adverse effects on potato plant physiology. Therefore, the combined plasma-supercavitation device represents an environmentally-friendly technology that could provide contamination-free and safe water.
Ključne besede: cold plasma, hydrodynamic cavitation, supercavitation, virus inactivation, water decontamination, toxicity assays
Objavljeno v DiRROS: 28.11.2024; Ogledov: 1523; Prenosov: 1183
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