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Povzetek: Cyanobacteria are adaptable and dominant organisms that exist in many harsh and extreme environments due to their great ecological tolerance. They produce various secondary metabolites, including cyanotoxins. While cyanobacteria are well studied in surface waters and some aerial habitats, numerous other habitats and niches remain underexplored. We collected 61 samples of: (i) biofilms from springs, (ii) aerial microbial mats from buildings and subaerial mats from caves, and (iii) water from borehole wells, caves, alkaline, saline, sulphidic, thermal, and iron springs, rivers, seas, and melted cave ice from five countries (Croatia, Georgia, Italy, Serbia, and Slovenia). We used (q)PCR to detect cyanobacteria (phycocyanin intergenic spacer—PC-IGS and cyanobacteria-specific 16S rRNA gene) and cyanotoxin genes (microcystins—mcyE, saxitoxins—sxtA, cylindrospermopsins—cyrJ), as well as amplicon sequencing and morphological observations for taxonomic identification. Cyanobacteria were detected in samples from caves, a saline spring, and an alkaline spring. While mcyE or sxtA genes were not observed in any sample, cyrJ results showed the presence of a potential cylindrospermopsin producer in a biofilm from a sulphidic spring in Slovenia. This study contributes to our understanding of cyanobacteria occurrence in diverse habitats, including rare and extreme ones, and provides relevant methodological considerations for future research in such environments.
Ključne besede: extreme environments, cylindrospermopsin, sulphidic springs, caves, qPCR, PC-IGS
Objavljeno v DiRROS: 01.09.2026; Ogledov: 84; Prenosov: 70
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Povzetek: Monitoring airborne inoculum of pathogens is important for plant disease surveillance. Here, we evaluate spider webs as passive environmental DNA (eDNA) samplers for detecting the pathogenic fungus Hymenoscyphus fraxineus, the causal agent of ash dieback, in a forest environment. In a temperate mixed forest, we compared two types of spider webs (orb and sheet webs) with a conventional passive sampler (filter paper) over matched day (orb) and week (sheet) deployments. Laboratory validation confirmed that webs exposed to airborne spores from apothecia yield positive qPCR signals. Across seven field sampling campaigns, both a species-specific qPCR (Hfrax) and a broad fungal assay (FQ) detected fungal eDNA on spider webs more reliably and at higher relative quantities than on filter paper. In daily and weekly pairs, orb and sheet web vs. filters, the median ΔCq (filter − web) was above 4 for both qPCR assays (Wilcoxon paired, p < 0.05), which corresponds to more than a 10-fold difference in the amount of target DNA. This study provides proof of concept for using spider webs as scalable, low-cost tools suitable for targeted (qPCR) surveillance to complement aerobiological networks.
Ključne besede: airborne eDNA, ash dieback, forest pathogens, Hymenoscyphus fraxineus, passive sampling, qPCR, spider webs, forest health
Objavljeno v DiRROS: 03.06.2026; Ogledov: 364; Prenosov: 452
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Povzetek: Tomato mottle mosaic virus (ToMMV) poses a growing threat to tomato and pepper crops, yet its epidemiology remains largelyunexplored. This study aimed to investigate water- and soil-mediated transmission of ToMMV under controlled conditions. Theexperiment involved mechanical inoculation of tomato plants, which demonstrated that infectious ToMMV particles remainedviable in water up to 27 weeks at a 10−2 dilution. In hydroponic systems, ToMMV present in the nutrient solution caused systemicinfection in bait plants within 5–17 weeks, depending on the severity of root injury, while infection was not observed in plantswith intact roots even after 38 weeks of exposure. The transmission of the pathogen via irrigation was also confirmed in an ex-periment where seedlings and seed-derived plants grown in substrate (roots were not deliberately injured) were irrigated withToMMV-contaminated water, resulting in infection 6 and 10 weeks after the start of exposure, respectively. The soil-mediatedtransmission process was further verified by planting healthy seedlings and seeds into previously contaminated substrate, re-sulting in infection within a period of 3–18 weeks. These findings emphasise the need for upgrading integrated managementstrategies, including water quality monitoring and reliable, rapid diagnostics, to mitigate the spread of ToMMV in greenhouseproduction systems. To support the development of effective monitoring strategies, the study also assessed the performance oftwo isothermal amplification assays for potential on-site detection of ToMMV in water. A recombinase-polymerase amplification(RPA) assay exhibited sensitivity comparable to that of reverse transcription-quantitative PCR and reliably detected ToMMV incrude water samples without RNA extraction.
Ključne besede: RPA assay, RT- qPCR, survival, tomato, tomato mottle mosaic virus, water-linked epidemiology
Objavljeno v DiRROS: 22.01.2026; Ogledov: 629; Prenosov: 475
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Povzetek: Measurement of RNA can be used to study and monitor a range of infectious and non-communicable diseases, with profiling of multiple gene expression mRNA transcripts being increasingly applied to cancer stratification and prognosis. An international comparison study (Consultative Committee for Amount of Substance (CCQM)-P103.1) was performed in order to evaluate the comparability of measurements of RNA copy number ratio for multiple gene targets between two samples. Six exogenous synthetic targets comprising of External RNA Control Consortium (ERCC) standards were measured alongside transcripts for three endogenous gene targets present in the background of human cell line RNA. The study was carried out under the auspices of the Nucleic Acids (formerly Bioanalysis) Working Group of the CCQM. It was coordinated by LGC (United Kingdom) with the support of National Institute of Standards and Technology (USA) and results were submitted from thirteen National Metrology Institutes and Designated Institutes. The majority of laboratories performed RNA measurements using RT-qPCR, with datasets also being submitted by two laboratories based on reverse transcription digital polymerase chain reaction and one laboratory using a next-generation sequencing method. In RT-qPCR analysis, the RNA copy number ratios between the two samples were quantified using either a standard curve or a relative quantification approach. In general, good agreement was observed between the reported results of ERCC RNA copy number ratio measurements. Measurements of the RNA copy number ratios for endogenous genes between the two samples were also consistent between the majority of laboratories. Some differences in the reported values and confidence intervals (‘measurement uncertainties’) were noted which may be attributable to choice of measurement method or quantification approach. This highlights the need for standardised practices for the calculation of fold change ratios and uncertainties in the area of gene expression profiling.
Ključne besede: RNA copy number ratio, RT-qPCR, gene expression, normalisation, standardisation, molecular diagnostic, transcriptomics, cancer, diagnostics, biomarker identification and validation
Objavljeno v DiRROS: 04.03.2025; Ogledov: 1248; Prenosov: 673
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Ključne besede: varstvo gozdov, morfološke analize, Geosmithia morbida, bolezen tisočerih rakov, qPCR, Juglans, program preiskav
Objavljeno v DiRROS: 30.08.2024; Ogledov: 1288; Prenosov: 0
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