71. Cold atmospheric plasma as a novel method for inactivation of potato virus Y in water samplesArijana Filipić, Gregor Primc, Rok Zaplotnik, Nataša Mehle, Ion Gutiérrez-Aguirre, Maja Ravnikar, Miran Mozetič, Jana Žel, David Dobnik, 2019, original scientific article Abstract: While one of the biggest problems we are facing today is water scarcity, enormous quantities of water are still being used in irrigation. If contaminated, this water can act as an effective pathway for the spread of disease-causing agents, like viruses. Here, we present a novel, environmentally friendly method known as cold atmospheric plasma for inactivation of viruses in water used in closed irrigation systems. We measured the plasma-mediated viral RNA degradation as well as the plasma-induced loss of viral infectivity using potato virus Y as a model virus due to its confirmed water transmissibility and economic as well as biological importance. We showed that only 1 min of plasma treatment is sufficient for successful inactivation of viruses in water samples with either high or low organic background. The plasma-mediated inactivation was efficient even at markedly higher virus concentrations than those expected in irrigation waters. Obtained results point to reactive oxygen species as the main mode of viral inactivation. Our laboratory-scale experiments confirm for the first time that plasma has an excellent potential as the eukaryotic virus inactivation tool for water sources and could thus provide a cost-effective solution for irrigation mediated plant virus transmission. The outstanding inactivation efficiency demonstrated by plasma treatments in water samples offers further expansions of its application to other water sources such as reused wastewater or contaminated drinking waters, as well as other plant, animal, and human waterborne viruses, ultimately leading to the prevention of water scarcity and numerous human, animal, and plant infections worldwide.
Keywords: cold atmospheric plasma, potato virus Y, virus inactivation, water decontamination
Published in DiRROS: 23.07.2024; Views: 201; Downloads: 150
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72. Bacteria associated with moon jellyfish during bloom and post-bloom periods in the Gulf of Trieste (northern Adriatic)Maja Kos Kramar, Tinkara Tinta, Davor Lučić, Alenka Malej, Valentina Turk, 2019, original scientific article Abstract: Jellyfish are a prominent component of the plankton community. They frequently form conspicuous blooms which may interfere with different human enterprises. Among the aspects that remain understudied are jellyfish associations with microorganisms having potentially important implications for organic matter cycling. To the best of our knowledge, this study is the first to investigate the bacterial community associated with live moon jellyfish (Aurelia solida, Scyohozoa) in the Adriatic Sea. Using 16S rRNA clone libraries and culture-based methods, we have analyzed the bacterial community composition of different body parts: the exumbrella surface, oral arms, and gastric cavity, and investigated possible differences in medusa-associated bacterial community structure at the time of the jellyfish population peak, and during the senescent phase at the end of bloom. Microbiota associated with moon jellyfish was different from ambient seawater bacterial assemblage and varied between different body parts. Betaproteobacteria (Burkholderia, Cupriavidus and Achromobacter) dominated community in the gastral cavity of medusa, while Alphaproteobacteria (Phaeobacter, Ruegeria) and Gammaproteobacteria (Stenotrophomonas, Alteromonas, Pseudoalteromonas and Vibrio) prevailed on ‘outer’ body parts. Bacterial community structure changed during senescent phase, at the end of the jellyfish bloom, showing an increased abundance of Gammaproteobacteria, exclusively Vibrio. The results of cultured bacterial isolates showed the dominance of Gammaproeteobacteria, especially Vibrio and Pseudoalteromonas in all body parts. Our results suggest that jellyfish associated bacterial community might have an important role for the host, and that anthropogenic pollution in the Gulf of Trieste might affect their community structure.
Keywords: bacteria, moon jellyfish, Gulf of Trieste, Adriatic sea
Published in DiRROS: 23.07.2024; Views: 212; Downloads: 151
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73. MitomiRs: their roles in mitochondria and importance in cancer cell metabolismAndrej Renčelj, Nada Gvozdenović, Maja Čemažar, 2021, review article Abstract: Background. MicroRNAs (miRNAs) are short non-coding RNAs that play important roles in almost all biological path- ways. They regulate post-transcriptional gene expression by binding to the 3%untranslated region (3%UTR) of messenger RNAs (mRNAs). MitomiRs are miRNAs of nuclear or mitochondrial origin that are localized in mitochondria and have a crucial role in regulation of mitochondrial function and metabolism. In eukaryotes, mitochondria are the major sites of oxidative metabolism of sugars, lipids, amino acids, and other bio-macromolecules. They are also the main sites of adenosine triphosphate (ATP) production. Conclusions. In the review, we discuss the role of mitomiRs in mitochondria and introduce currently well studied mito- miRs, their target genes and functions. We also discuss their role in cancer initiation and progression through the regu- lation of mRNA expression in mitochondria. MitomiRs directly target key molecules such as transporters or enzymes in cell metabolism and regulate several oncogenic signaling pathways. They also play an important role in the Warburg effect, which is vital for cancer cells to maintain their proliferative potential. In addition, we discuss how they indirectly upregulate hexokinase 2 (HK2), an enzyme involved in glucose phosphorylation, and thus may affect energy metabo- lism in breast cancer cells. In tumor tissues such as breast cancer and head and neck tumors, the expression of one of the mitomiRs (miR-210) correlates with hypoxia gene signatures, suggesting a direct link between mitomiR expression and hypoxia in cancer. The miR-17/92 cluster has been shown to act as a key factor in metabolic reprogramming of tumors by regulating glycolytic and mitochondrial metabolism. This cluster is deregulated in B-cell lymphomas, B-cell chronic lymphocytic leukemia, acute myeloid leukemia, and T-cell lymphomas, and is particularly overexpressed in several other cancers. Based on the current knowledge, we can conclude that there is a large number of miRNAs present in mitochondria, termed mitomiR, and that they are important regulators of mitochondrial function. Therefore, mitomiRs are important players in the metabolism of cancer cells, which need to be further investigated in order to develop a potential new therapies for cancer.
Keywords: microRNAs, mitomiR, mitochondria, cancer cell metabolism
Published in DiRROS: 22.07.2024; Views: 243; Downloads: 89
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74. Simvastatin is effective in killing the radioresistant breast carcinoma cellsBertram Aschenbrenner, Giulia Negro, Dragana Savic, Maxim Sorokin, Anton A. Buzdin, Ute Maria Ganswindt, Maja Čemažar, Gregor Serša, Sergej Skvortsov, Ira Skvortsova, 2021, original scientific article Abstract: Background. Statins, small molecular 3-hydroxy-3-methylglutaryl-coenzyme A reductase inhibitors, are widely used to lower cholesterol levels in lipid-metabolism disorders. Recent preclinical and clinical studies have shown that statins exert beneficial effects in the management of breast cancer by increasing recurrence free survival. Unfortunately, the underlying mechanisms remain elusive. Materials and methods. Simvastatin, one of the most widely prescribed lipophilic statins was utilized to investigate potential radiosensitizing effects and an impact on cell survival and migration in radioresistant breast cancer cell lines. Results. Compared to parental cell counterparts, radioresistant MDA-MB-231-RR, T47D-RR andAu565-RR cells were characterized by upregulation of 3-hydroxy-3-methylglutharyl-coenzyme A reductase (HMGCR) expression accom-panied by epithelial-to-mesenchymal transition (EMT) activation. Radioresistant breast cancer cells can be killed by simvastatin via mobilizing of a variety of pathways involved in apoptosis and autophagy. In the presence of simvasta-tin migratory abilities and vimentin expression is diminished while E-cadherin expression is increased. Conclusions. The present study suggests that simvastatin may effectively eradicate radioresistant breast carcinoma cells and diminish their mesenchymal phenotypes.
Keywords: radiotherapy, breast cancer, radioresistant cells
Published in DiRROS: 22.07.2024; Views: 245; Downloads: 193
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75. Morphological features of breast cancer circulating tumor cells in blood after physical and biological type of isolationTanja Jesenko, Živa Pišljar, Cvetka Grašič-Kuhar, Maja Čemažar, Urška Matkovič, Simona Miceska, Jerneja Varl, Anamarija Kuhar, Veronika Kloboves-Prevodnik, 2021, original scientific article Abstract: Background. Circulating tumor cells (CTCs) have become an important biomarker in breast cancer. Different iso-lation tech-niques based on their biological or physical features were established. Currently, the most widely used methods for visualization after their separation are based on immunofluorescent staining, which does not provide the information on the morphology.Materials and methods. The aim of this study was to evaluate how two different separation techniques affect cell morphology and to analyse cell morphology with techniques used in routine cytopathological laboratory. A direct side-by-side comparison of physical (Parsortix%) and biological (MACS%) separation technique was performed.Results. In the preclinical setting, both isolation techniques retained the viability and antigenic characteristics of MCF7 breast cancer cells. Some signs of degeneration such as cell swelling, cytoplasmic blebs, villous projections and vacuolization were observed. In metastatic breast cancer patient cohort, morphological features of isolated CTCs were dependent on the separation technique. After physical separation, CTCs with preserved cell morphology were detected. After biological separation the majority of the isolated CTCs were so degenerated that their identity was difficult to confirm.Conclusions. Taken together, physical separation is a suitable technique for detection of CTCs with preserved cell morphology for the use in a routine cytopathological laboratory.
Keywords: circulating tumor cells, breast cancer, morphology
Published in DiRROS: 22.07.2024; Views: 237; Downloads: 192
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76. Radiotherapy-associated angiosarcoma in the breast reconstructed by autologous free-flap and treated with electrochemotherapyRomi Cencelj-Arnež, Jerica Novak, Andreja Klevišar Ivančič, Maša Omerzel, Maja Čemažar, Marko Snoj, 2021, original scientific article Abstract: Radiotherapy-associated angiosarcoma (RAA) of the breast is a rare complication of radiotherapy, which is often difficult to identify and has poor prognosis. It usually presents as violaceous skin, erythema or rapidly growing palpable firm mass that can be confused with other benign skin lesions. Patients and methods After reviewing the literature, we found only four cases with RAA after mastectomy and autologous breast reconstruction. The presented case is the first that was treated by electrochemotherapy. The patient presented with secondary angiosarcoma of the breast five years after mastectomy, immediate breast reconstruction with deep inferior epigastric artery perforator free flap and adjuvant radiotherapy. Results Electrochemotherapy was feasible, safe and effective in treatment of radiation induced sarcoma. Most of the treated lesions in several consecutive electrochemotherapy sessions responded with complete response, but multiple recurrences occurred in non-treated areas. Conclusions Patients with breast cancer after skin-sparing mastectomy and immediate breast reconstruction, who receive radiotherapy, need regular long-term follow up and low threshold for biopsy of any suspicious lesions is mandatory. Electrochemotherapy proved as one of feasible modalities of treatment for RAA.
Keywords: angiosarcoma, breast reconstruction, breast cancer, electrochemotherapy
Published in DiRROS: 22.07.2024; Views: 311; Downloads: 93
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77. Heavy metals in the Adriatic-Ionian Seas : a case study to illustrate the challenges in data management when dealing with regional datasetsMaria-Eugenia Molina Jack, Rigers Bakiu, Ana Castelli, Branko Čermelj, Maja Fafanđel, Christina Georgopoulou, Giordano Giorgi, Athanassia Iona, Damir Ivankovic, Martina Kralj, Elena Partescano, Alice Rotini, Melita Velikonja, Marina Lipizer, 2020, original scientific article Abstract: Harmonization of monitoring protocols and analytical methods is a crucial issue for transnational marine environmental status assessment, yet not the only one. Coherent data management and quality control become very relevant when environmental status is assessed at regional or subregional scale (e.g., for the Mediterranean or the Adriatic Sea), thus requiring data from different sources. Heavy metals are among the main targets of monitoring activities. Significant efforts have been dedicated to share best practices for monitoring and assessment of ecosystem status and to strengthen the network of national, regional and European large data infrastructures in order to facilitate the access to data among countries. Data comparability and interoperability depend not only on sampling and analytical protocols but also on how data and metadata are managed, quality controlled and made accessible. Interoperability is guaranteed by using common metadata and data formats, and standard vocabularies to assure homogeneous syntax and semantics. Data management of contaminants is complex and challenging due to the high number of information required on sampling and analytical procedures, high heterogeneity in matrix characteristics, but also to the large and increasing number of pollutants. Procedures for quality control on heterogeneous datasets provided by multiple sources are not yet uniform and consolidated. Additional knowledge and reliable long time-series of data are needed to evaluate typical ranges of contaminant concentration. The analysis of a coherent and harmonized regional dataset can provide the basis for a multi-step quality control procedure, which can be further improved as knowledge increases during data validation process.
Keywords: contaminants, data management, harmonization, Adriatic Sea, Ionian Sea, pollution, assessment, heavy metals
Published in DiRROS: 22.07.2024; Views: 250; Downloads: 186
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78. Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potatoMarko Petek, Maja Zagorščak, Živa Ramšak, Sheri Sanders, Špela Tomaž, Elizabeth Tseng, Mohamed Zouine, Anna Coll Rius, Kristina Gruden, 2020, original scientific article Abstract: Although the reference genome of Solanum tuberosum Group Phureja double-monoploid (DM) clone is available, knowledge on the genetic diversity of the highly heterozygous tetraploid Group Tuberosum, representing most cultivated varieties, remains largely unexplored. This lack of knowledge hinders further progress in potato research. In conducted investigation, we first merged and manually curated the two existing partially-overlapping DM genome-based gene models, creating a union of genes in Phureja scaffold. Next, we compiled available and newly generated RNA-Seq datasets (cca. 1.5 billion reads) for three tetraploid potato genotypes (cultivar Désirée, cultivar Rywal, and breeding clone PW363) with diverse breeding pedigrees. Short-read transcriptomes were assembled using several de novo assemblers under different settings to test for optimal outcome. For cultivar Rywal, PacBio Iso-Seq full-length transcriptome sequencing was also performed. EvidentialGene redundancy-reducing pipeline complemented with in-house developed scripts was employed to produce accurate and complete cultivar-specific transcriptomes, as well as to attain the pan-transcriptome. The generated transcriptomes and pan-transcriptome represent a valuable resource for potato gene variability exploration, high-throughput omics analyses, and breeding programmes.
Published in DiRROS: 22.07.2024; Views: 222; Downloads: 146
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79. Challenges in harmonized environmental impact assessment (EIA), monitoring and decommissioning procedures of offshore platforms in Adriatic-Ionian (ADRION) regionLoredana Manfra, Claudia Virno Lamberti, Silvia Ceracchi, Giordano Giorgi, Daniela Berto, Marina Lipizer, Michele Giani, Oliver Bajt, Maja Fafanđel, Magdalena Cara, Slavica Matijević, Milena Mitrić, Stefanos Papazisimou, Mateja Poje, Christina Zeri, Benedetta Trabucco, 2020, original scientific article Abstract: A harmonized and integrated approach for monitoring and assessment of contamination, including hydrocarbon exploitation one, is required both by Marine Strategy Framework Directive (MSFD) at EU level and by the Ecosystem Approach (EcAp) program of the Barcelona Convention at Mediterranean level. A broad review of protocols of environmental impact assessment (EIA) procedures, monitoring and decommissioning of offshore platforms adopted by EU and non-EU countries along the Adriatic-Ionian seas was carried out in the framework of the Interreg offshore platforms in Adriatic-Ionian (ADRION) project HarmoNIA (Harmonization and networking for contaminant assessment in the Ionian and Adriatic Seas). The comparison of information provided by six ADRION countries and the application of a harmonized and integrated approach has highlighted specific challenges for managing offshore platform impacts emerged at ADRION level: (i) need of the same legislative level (the Offshore Protocol of Barcelona Convention is not ratified by all countries); (ii) set up of a task force of ADRION experts for discussing critical issues related to impacts of offshore platforms; (iii) harmonization, at the regional level, of EIA procedures, monitoring and decommissioning; (iv) need of an agreed and common list of recommended parameters to monitor in water, sediment and biota for the assessment of impacts due to platform installations and PFW discharges.
Keywords: harmonized protocols, environmental impact assessment, monitoring, decommissioning, offshore platforms, Adriatic-Ionian Sea region, MSFD, Barcelona Convention
Published in DiRROS: 22.07.2024; Views: 329; Downloads: 111
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80. Precision transcriptomics of viral foci reveals the spatial regulation of immune-signaling genes and identifies RBOHD as an important player in the incompatible interaction between potato virus Y and potatoTjaša Lukan, Maruša Pompe Novak, Špela Baebler, Magda Tušek-Žnidarič, Aleš Kladnik, Maja Križnik, Andrej Blejec, Maja Zagorščak, Katja Stare, Barbara Dušak, Anna Coll Rius, Stephan Pollmann, Karolina Morgiewicz, Jacek Hennig, Kristina Gruden, 2020, original scientific article Abstract: Whereas the activation of resistance (R) proteins has been intensively studied, the downstream signaling mechanisms leading to the restriction of the pathogen remain mostly unknown. We studied the immunity network response conditioned by the potato Ny-1 gene against potato virus Y. We analyzed the processes in the cell death zone and surrounding tissue on the biochemical and gene expression levels in order to reveal the spatiotemporal regulation of the immune response. We show that the transcriptional response in the cell death zone and surrounding tissue is dependent on salicylic acid (SA). For some genes the spatiotemporal regulation is completely lost in the SA-deficient line, whereas other genes show a different response, indicating multiple connections between hormonal signaling modules. The induction of NADPH oxidase RBOHD expression occurs specifically on the lesion border during the resistance response. In plants with silenced RBOHD, the functionality of the resistance response is perturbed and the spread of the virus is not arrested at the site of infection. RBOHD is required for the spatial accumulation of SA, and conversely RBOHD is under the transcriptional regulation of SA. Using spatially resolved RNA-seq, we also identified spatial regulation of an UDP-glucosyltransferase, another component in feedback activation of SA biosynthesis, thus deciphering a novel aspect of resistance signaling.
Keywords: immune signaling network, NADPH oxidase RBOHD, reactive oxygen species, salicylic acid, Sola-num tuberosum (potato), spatiotemporal response analysis, virus resistance, Potyvirus
Published in DiRROS: 22.07.2024; Views: 207; Downloads: 155
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