1. Identification of epigenetically regulated genes involved in plant-virus interaction and their role in virus-triggered induced resistanceRégis L. Corrêa, Denis Kutnjak, Silvia Ambrós, Mónica Bustos, Santiago F. Elena, 2024, original scientific article Abstract: Background: Plant responses to a wide range of stresses are known to be regulated by epigenetic mechanisms. Path-ogen-related investigations, particularly against RNA viruses, are however scarce. It has been demonstrated that Arabi-dopsis thaliana plants defective in some members of the RNA-directed DNA methylation (RdDM) or histone modi-fication pathways presented differential susceptibility to the turnip mosaic virus. In order to identify genes directly targeted by the RdDM-related RNA Polymerase V (POLV ) complex and the histone demethylase protein JUMONJI14 (JMJ14) during infection, the transcriptomes of infected mutant and control plants were obtained and integrated with available chromatin occupancy data for various epigenetic proteins and marks. Results: A comprehensive list of virus-responsive gene candidates to be regulated by the two proteins was obtained. Twelve genes were selected for further characterization, confirming their dynamic regulation during the course of infection. Several epigenetic marks on their promoter sequences were found using in silico data, raising confidence that the identified genes are actually regulated by epigenetic mechanisms. The altered expression of six of these genes in mutants of the methyltransferase gene CURLY LEAF and the histone deacetylase gene HISTONE DEACETYLASE 19 suggests that some virus-responsive genes may be regulated by multiple coordinated epigenetic complexes. A temporally separated multiple plant virus infection experiment in which plants were transiently infected with one virus and then infected by a second one was designed to investigate the possible roles of the identified POLV- and JMJ14-regulated genes in wild-type (WT ) plants. Plants that had previously been stimulated with viruses were found to be more resistant to subsequent virus challenge than control plants. Several POLV- and JMJ14-regulated genes were found to be regulated in virus induced resistance in WT plants, with some of them poisoned to be expressed in early infection stages. Conclusions: A set of confident candidate genes directly regulated by the POLV and JMJ14 proteins during virus infection was identified, with indications that some of them may be regulated by multiple epigenetic modules. A sub-set of these genes may also play a role in the tolerance of WT plants to repeated, intermittent virus infections.Keywords Biotic stress, Defense priming, Epigenetics, Histone modifications, Induced resistance, Potyvirus, RNA-directed DNA methylation.
Keywords: biotic stress, defense priming, epigenetics, histone modifications, induced resistance, Potyvirus, RNA-directed DNA methylation
Published in DiRROS: 17.05.2024; Views: 27; Downloads: 11
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2. Subchronic exposure of rats to sublethal dose of microcystin-YR induces DNA damage in multiple organsMetka Filipič, Bojana Žegura, Bojan Sedmak, Irena Horvat-Žnidaršič, Aleksandra Milutinović Živin, Dušan Šuput, 2007, original scientific article Abstract: Background. Microcystins (MCs) are cyclic heptapeptides that are considered tobe liver specific toxins. They are potent tumour promoters and recent studies indicate that they are also genotoxic. In this study we measured DNA damage in lymphocytes, liver, kidney (cortex and medulla), lung, spleen and brain cells of male Fisher F344 rats that were exposed to sublethal dose (every second day 10 Ugžkg b.w.č i.p) of microeysrin-YR (MCYR) for one month. Methods. At the end of exposure the animals were sacrificed, the lymphocytes were isolated from blood taken from jugular vein, liver cells were obtained byperfusion with collagenase A and the cells from other organs were isolated by incubating small tissue pieces with eollagenase A. The DNA damage in isolated cells was measured with the single cells gel electrophoresis (SCGE) also called the comet assay. Results. A significant increase of the % tail DNAin MCYR-exposed animals compared to the nonexposed control ones was observed in brain (2.5 fold), liver (2.1 fold), kidney medulla (1.9 fold), kidney cortex (1.8 fold) and lung (1.7 fold) cells, while the DNA from lymphocytes and spleen cells was not affected. Conclusion. This study demonstrated that subehronic exposure to sublethal doses of MCs can induce systemicgenotoxicity in mammals, and it affects not only the liver but also other vital organs.
Keywords: DNA damage, comet assay, cyanobacteria, bacterial toxins, rats, inbred F344
Published in DiRROS: 20.02.2024; Views: 156; Downloads: 40
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3. The influence of storage conditions and DNA extraction protocol on the results of molecular analysis of the European spruce bark beetle (Ips typographus L.)Zina Devetak, Andreja Kavčič, Maarten De Groot, Barbara Piškur, 2023, original scientific article Abstract: One of the key steps of the molecular identification of bark beetles is obtaining a sufficient quantity of high-quality DNA extract. In this study, we investigated the influence of different storage procedures for Ips typographus (L.) specimens and various DNA extraction protocols on the quantity and quality of DNA intended for use in molecular diagnostics. Adult beetles were frozen at -20 °C, either dry or in ethanol. We tested four different protocols for DNA extraction. We compared the quantity of extracted DNA and assessed its quality with PCR and Sanger sequencing. Different storage protocols had no significant effect on the quantity of DNA extracted. However, freezing specimens in ethanol provided higher-quality DNA for molecular applications. Only two of the extraction protocols produced sequenceable amplicons, and the difference in the amount of extracted DNA between them was not significant. We propose the optimal combination of storing specimens in ethanol at -20°C and using the Nucleospin Insect DNA extraction kit from Macherey Nagel, enabling a timeefficient identification process.
Keywords: early detection, specimen storage, total DNA extraction, PCR, polymerase chain reaction, Sanger sequencing, molecular diagnostics
Published in DiRROS: 02.02.2024; Views: 481; Downloads: 152
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4. Chemotherapy for hürthle cell carcinoma based on sequential DNA measurementsMarija Auersperg, Ruda Zorc-Pleskovič, Marija Us-Krašovec, Ana Pogačnik, Gabrijela Petrič, Olga Vraspir-Porenta, 1988, original scientific article Keywords: rak (medicina), karcinom, zdravljenje, kemoterapija, DNA
Published in DiRROS: 15.09.2023; Views: 306; Downloads: 87
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5. Insight into tetramolecular DNA G-quadruplexes associated with ALS and FTLD : cation interactions and formation of higher-ordered structureMatja Zalar, Baifan Wang, Janez Plavec, Primož Šket, 2023, original scientific article Keywords: ALS, FTLD, DNA, c9orf7, NMR, quadruplex, cations
Published in DiRROS: 06.09.2023; Views: 311; Downloads: 181
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6. Verifikacijsko poročilo - LVG POS 021Zina Devetak, 2023, treatise, preliminary study, study Keywords: Ceratocystis platani, platanov obarvani rak, diagnostični protokol, molekularna analiza, ekstrakcija DNA, PCR v realnem času, verifikacija
Published in DiRROS: 07.06.2023; Views: 347; Downloads: 0 |
7. Verifikacijsko poročilo - LVG POS 020Zina Devetak, 2023, treatise, preliminary study, study Keywords: Geosmithia morbida, bolezen tisočerih rakov, diagnostični protokol, molekularna analiza, ekstrakcija DNA, PCR v realnem času, verifikacija
Published in DiRROS: 07.06.2023; Views: 379; Downloads: 0 |
8. Use of an arboretum and DNA barcoding for the detection and identification of leaf-mining insects on alien woody plantsNatalia I. Kirichenko, Stanislav Gomboc, Barbara Piškur, Maarten De Groot, 2023, original scientific article Abstract: Arboreta serve as effective tools for identifying alien insect pests and novel trophic associations. In this study, we used an arboretum in Slovenia to survey woody plants and identify both alien and native leaf miners. The leaves and twigs of 50 woody plant species and their cultivars were examined for characteristic damage. We used an integrative approach that combined identification based on leaf mines and DNA barcoding of the larvae and pupae found in the mines. In total, 62 leaf-mining species were identified, including eight alien species, of which the heliozelid Coptodisca lucifluella (Clemens, 1860) and the agromyzid Cerodontha unisetiorbita Zlobin, 1992 were documented for Slovenia for the first time. Additionally, three presumably native Gracillariidae moths Phyllocnistis labyrinthella (Bjerkander, 1790), P. ramulicola Langmaid & Corley, 2007 and P. saligna (Zeller, 1839) represented the first record for Slovenia. Furthermore, we documented 23 novel-to-science trophic associations, 20 of which involved native insects and alien woody plants, primarily from Asia. This study highlights the importance of arboreta and botanical gardens for the interception of invasive alien insects and the early detection of trophic shifts of native insects to alien plants, which can aid in predicting their potential spread.
Keywords: botanical garden, sentinels, leaf miners, alien species, non-native trees, novel trophic associations, DNA barcoding, Slovenia
Published in DiRROS: 24.03.2023; Views: 558; Downloads: 250
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9. Radiation induced upregulation of DNA Sensing pathways is cell-type dependent and can mediate the off-target effectsTanja Jesenko, Maša Omerzel, Boštjan Markelc, Gregor Serša, Katarina Žnidar, Loree C. Heller, Maja Čemažar, 2020, original scientific article Keywords: DNA sensors, irradiation, immunostimulation
Published in DiRROS: 10.10.2022; Views: 490; Downloads: 255
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10. New approach for detection of normal alternative splicing events and aberrant spliceogenic transcripts with long-range PCR and deep RNA sequencingVita Šetrajčič Dragoš, Vida Stegel, Ana Blatnik, Gašper Klančar, Mateja Krajc, Srdjan Novaković, 2021, original scientific article Abstract: RNA sequencing is a promising technique for detecting normal and aberrant RNA isoforms. Here, we present a new single-gene, straightforward 1-day hands-on protocol for detection of splicing alterations with deep RNA sequencing from blood. We have validated our method%s accuracy by detecting previously published normal splicing isoforms of STK11 gene. Additionally, the same technique was used to provide the first comprehensive catalogue of naturally occurring alternative splicing events of the NBN gene in blood. Furthermore, we demonstrate that our approach can be used for detection of splicing impairment caused by genetic variants. Therefore, we were able to reclassify three variants of uncertain significance: NBN:c.584G>A, STK11:c.863-5_863-3delCTC and STK11:c.615G>A. Due to the simplicity of our approach, it can be incorporated into any molecular diagnostics laboratory for determination of variant%s impact on splicing.
Keywords: RNA sequencing, DNA variant, splicing
Published in DiRROS: 21.09.2022; Views: 474; Downloads: 260
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