81. Načrtovanje ravnanja z raziskovalnimi podatkiPeter Čerče, Branimir Leskošek, Miro Pušnik, 2024, other monographs and other completed works Keywords: Nacionalni portal odprte znanosti, odprta znanost, institucionalni repozitoriji, projekt Spoznaj, načela odprte znanosti, znanost, odprti podatki
Published in DiRROS: 04.03.2025; Views: 72; Downloads: 22
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82. Nacionalna infrastruktura odprte znanosti : predstavitev v okviru izobraževanja podatkovnih strokovnjakov, Ljubljana, 17. 10. 2024Milan Ojsteršek, 2024, other monographs and other completed works Keywords: Nacionalni portal odprte znanosti, odprta znanost, institucionalni repozitoriji, projekt Spoznaj, načela odprte znanosti, znanost, odprti podatki
Published in DiRROS: 04.03.2025; Views: 64; Downloads: 16
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83. Perspectives and pitfalls in preserving subterranean biodiversity through protected areasStefano Mammola, Florian Altermatt, Roman Alther, Isabel R. Amorim, Raluca I. Băncilă, Teo Delić, Cene Fišer, Nataša Mori, Žiga Ogorelec, Maja Zagmajster, 2024, original scientific article Abstract: Subterranean ecosystems (comprising terrestrial, semi-aquatic, and aquatic components) are increasingly threatened by human activities; however, the current network of surface-protected areas is inadequate to safeguard subterranean biodiversity. Establishing protected areas for subterranean ecosystems is challenging. First, there are technical obstacles in mapping three-dimensional ecosystems with uncertain boundaries. Second, the rarity and endemism of subterranean organisms, combined with a scarcity of taxonomists, delays the accumulation of essential biodiversity knowledge. Third, establishing agreements to preserve subterranean ecosystems requires collaboration among multiple actors with often competing interests. This perspective addresses the challenges of preserving subterranean biodiversity through protected areas. Even in the face of uncertainties, we suggest it is both timely and critical to assess general criteria for subterranean biodiversity protection and implement them based on precautionary principles. To this end, we examine the current status of European protected areas and discuss solutions to improve their coverage of subterranean ecosystems.
Keywords: ecology, subterranean ecosystems, biodiversity, protected areas, environmental assessment, environmental indicators, environmental protection
Published in DiRROS: 04.03.2025; Views: 78; Downloads: 30
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84. Nacionalna infrastruktura odprte znanosti in zakonodajni okvirPeter Čerče, 2024, other monographs and other completed works Keywords: Nacionalni portal odprte znanosti, odprta znanost, institucionalni repozitoriji, projekt Spoznaj, načela odprte znanosti, zakonodaja, odprtodostopne založniške platforme, odprtodostopne revije, znanost, odprti podatki
Published in DiRROS: 04.03.2025; Views: 81; Downloads: 26
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85. Characterization of Aureobasidium pullulans isolates selected as biocontrol agents against fruit decay pathogensJanja Zajc Žunič, Anja Černoša, Alessandra Di Francesco, Raffaello Castoria, Filippo De Curtis, Giuseppe Lima, Hanene Badri, Haissam Jijakli, Antonio Ippolito, Cene Gostinčar, Polona Zalar, Nina Gunde-Cimerman, Wojciech J. Janisiewicz, 2020, original scientific article Abstract: The "yeast-like" fungus, Aureobasidium pullulans, isolated from fruit and leaves exhibits strong biocontrol activity against postharvest decays on various fruit. Some strains were even developed into commercial products. We obtained 20 of these strains and investigated their characteristics related to biocontrol. Phylogenetic analyses based on internal transcribed spacer (ITS) and the D1/D2 domains of rRNA 28S gene regions confirmed that all the strains are most closely related to A. pullulans species. All strains grew at 0°C, which is very important to control decay at low storage temperature, and none grew at 37°C, which eliminates concern for human safety. Eighteen strains survived 2 hrs exposures to 50°C and two strains even survived for 24 hrs. Salt-tolerance varied; however, all strains grew on medium with 14% NaCl and 14 even with 18% NaCl. Such tolerances to high temperature and elevated salinity enable compatibility with postharvest practices. Substantial differences were observed in enzymatic activity, especially with respect to production of chitinases, xylanase, or urease. Siderophore production was detected and the ability to form biofilm varied widely between the strains. Knowledge of common characteristics of these strains may be very useful in future selection of the best antagonists within this species.
Keywords: biological control, postharvest disease management, antagonism, physiological variability, stress tolerance
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86. One-step RT-droplet digital PCR : a breakthrough in the quantification of waterborne RNA virusesNejc Rački, Dany Morisset, Ion Gutiérrez-Aguirre, Maja Ravnikar, 2014, original scientific article Abstract: 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.
Keywords: waterborne virus, quantification, droplet digital PCR, real-time PCR, digital PCR
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87. Quantitative analysis of food and feed samples with droplet digital PCRDany Morisset, Dejan Štebih, Mojca Milavec, Kristina Gruden, Jana Žel, 2013, original scientific article Abstract: In this study, the applicability of droplet digital PCR (ddPCR) for routine analysis in food and feed samples was demonstrated with the quantification of genetically modified organisms (GMOs). Real-time quantitative polymerase chain reaction (qPCR) is currently used for quantitative molecular analysis of the presence of GMOs in products. However, its use is limited for detecting and quantifying very small numbers of DNA targets, as in some complex food and feed matrices. Using ddPCR duplex assay, we have measured the absolute numbers of MON810 transgene and hmg maize reference gene copies in DNA samples. Key performance parameters of the assay were determined. The ddPCR system is shown to offer precise absolute and relative quantification of targets, without the need for calibration curves. The sensitivity (five target DNA copies) of the ddPCR assay compares well with those of individual qPCR assays and of the chamber digital PCR (cdPCR) approach. It offers a dynamic range over four orders of magnitude, greater than that of cdPCR. Moreover, when compared to qPCR, the ddPCR assay showed better repeatability at low target concentrations and a greater tolerance to inhibitors. Finally, ddPCR throughput and cost are advantageous relative to those of qPCR for routine GMO quantification. It is thus concluded that ddPCR technology can be applied for routine quantification of GMOs, or any other domain where quantitative analysis of food and feed samples is needed.
Keywords: droplet digital PCR, ddPCR, genetically modified organisms
Published in DiRROS: 04.03.2025; Views: 76; Downloads: 45
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88. 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, original scientific article Abstract: 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.
Published in DiRROS: 04.03.2025; Views: 74; Downloads: 39
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89. Reconstitution of the costunolide biosynthetic pathway in yeast and Nicotiana benthamianaQing Liu, Mohammad Majdi, Katarina Cankar, Miriam Goedbloed, Tatsiana Charnikhova, Francel W. A. Verstappen, Ric de Vos, Jules Beekwilder, Sander van der Krol, Harro Bouwmeester, 2011, original scientific article Abstract: The sesquiterpene costunolide has a broad range of biological activities and is the parent compound for many other biologically active sesquiterpenes such as parthenolide. Two enzymes of the pathway leading to costunolide have been previously characterized: germacrene A synthase (GAS) and germacrene A oxidase(GAO), which together catalyse the biosynthesis of germacra-1(10),4,11(13)-trien-12-oic acid. However, the gene responsible for the last step toward costunolide has not been characterized until now. Here weshow that chicory costunolide synthase (CiCOS), CYP71BL3, can catalyse the oxidation of germacra-1(10),4,11(13)-trien-12-oic acid to yield costunolide. Co-expression of feverfew GAS (TpGAS), chicory GAO (CiGAO), and chicory COS (CiCOS) in yeast resulted in the biosynthesis of costunolide. The catalytic activity of TpGAS, CiGAO and CiCOS was also verified in planta by transient expression in Nicotiana benthamiana. Mitochondrial targeting of TpGAS resultedin a significant increase in the production of germacrene A compared with the native cytosolic targeting. When the N. benthamiana leaves were co-infiltrated with TpGAS and CiGAO, germacrene A almost completely disappeared as a result of the presence of CiGAO. Transient expression of TpGAS, CiGAO and CiCOS in N. benthamiana leaves resulted in costunolide production of up to 60 ng.g-1 FW. In addition, two new compounds were formed that were identified as costunolide-glutathione and costunolide-cysteine conjugates.
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90. Erwinia amylovora novel plasmid pEI70 : complete sequence, biogeography, and role in aggressiveness in the fire blight phytopathogenPablo Llop, J. Cabrefiga, T. Smits, Tanja Dreo, Silvia Barbé, Joanna Pulawska, Alain Bultreys, Jochen Blom, Brion Duffy, Emilio Montesinos, María M. López, 2011, original scientific article Abstract: Comparative genomics of several strains of Erwinia amylovora, a plant pathogenic bacterium causal agent of fire blight disease, revealed that its diversity is primarily attributable to the flexible genome comprised of plasmids. We recently identified and sequenced in full a novel 65.8 kb plasmid, called pEI70. Annotation revealed a lack of known virulence-related genes, but found evidence for a unique integrative conjugative element related to that of other plant and human pathogens. Comparative analyses using BLASTN showed that pEI70 is almost entirely included in plasmid pEB102 from E. billingiae, an epiphytic Erwinia of pome fruits, with sequence identities superior to 98%. A duplex PCR assay was developed to survey the prevalence of plasmid pEI70 and also that of pEA29, which had previously been described in several E. amylovora strains. Plasmid pEI70 was found widely dispersed across Europe with frequencies of 5–92%, but it was absent in E. amylovora analyzed populations from outside of Europe. Restriction analysis and hybridization demonstrated that this plasmid was identical in at least 13 strains. Curing E. amylovora strains of pEI70 reduced their aggressiveness on pear, and introducing pEI70 into low-aggressiveness strains lacking this plasmid increased symptoms development in this host. Discovery of this novel plasmid offers new insights into the biogeography, evolution and virulence determinants in E. amylovora.
Keywords: plant diseases, bacteria, plamid
Published in DiRROS: 04.03.2025; Views: 78; Downloads: 39
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