1. 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: 145; Downloads: 39 Full text (142,90 KB) |
2. 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: 442; Downloads: 135 Full text (1,17 MB) This document has many files! More... |
3. 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: 282; Downloads: 85 Full text (737,50 KB) |
4. 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: 292; Downloads: 172 Full text (2,68 MB) This document has many files! More... |
5. 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: 327; Downloads: 0 |
6. 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: 364; Downloads: 0 |
7. 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: 528; Downloads: 240 Full text (6,32 MB) This document has many files! More... |
8. 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: 476; Downloads: 249 Full text (5,84 MB) This document has many files! More... |
9. 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: 470; Downloads: 258 Full text (1,89 MB) This document has many files! More... |
10. In vitro and in vivo correlation of skin and cellular responses to nucleic acid deliveryMaša Omerzel, Katarina Žnidar, A. Sales Conniff, Tanja Jesenko, Boštjan Markelc, Jared Tur, Nina Semenova, Kristopher Kohena, Simona Kranjc Brezar, Loree C. Heller, Maja Čemažar, 2022, original scientific article Abstract: Skin, the largest organ in the body, provides a passive physical barrier against infection and contains elements of the innate and adaptive immune systems. Skin consists of various cells, including keratinocytes, fibroblasts, endothelial cells and immune cells. This diversity of cell types could be important to gene therapies because DNA transfection could elicit different responses in different cell types. Previously, we observed the upregulation and activation of cytosolic DNA sensing pathways in several non-tumor and tumor cell types as well in tumors after the electroporation (electrotransfer) of plasmid DNA (pDNA). Based on this research and the innate immuno- genicity of skin, we correlated the effects of pDNA electrotransfer to fibroblasts and keratinocytes to mouse skin using reverse transcription real-time PCR (RT-qPCR) and several types of protein quantification. After pDNA electrotransfer, the mRNAs of the putative DNA sensors DEAD (AspGlu-Ala-Asp) box polypeptide 60 (Ddx60), absent in melanoma 2 (Aim2), Z-DNA binding protein 1 (Zbp1), interferon activated gene 202 (Ifi202), and interferon-inducible protein 204 (Ifi204) were upregulated in keratinocytes, while Ddx60, Zbp1 and Ifi204 were upregulated in fibroblasts. Increased levels of the mRNAs and proteins of several cytokines and chemokines were detected and varied based on cell type. Mouse skin experiments in vivo confirmed our in vitro results with increased expression of putative DNA sensor mRNAs and of the mRNAs and proteins of several cytokines and chemokines. Keywords: DNA sensors, cytokines, electrotransfer, skin Published in DiRROS: 06.09.2022; Views: 592; Downloads: 303 Full text (7,72 MB) This document has many files! More... |