1. Tailoring the crystalline and amorphous phase ratios of TiO2 through the use of organic additives during hydrothermal synthesisNejc Rozman, Andrijana Sever Škapin, David Maria Tobaldi, Goran Dražić, Peter Nadrah, 2024, original scientific article Abstract: The photocatalytic properties of TiO2 are primarily determined by its crystallinity and crystalline phase ratios. To improve the photocatalytic properties of TiO2, greater control over the formation of crystalline and amorphous phases during synthesis is therefore required. In this study, we demonstrate how the addition of minute amounts of three organic compounds (isopropanol, acetone and acetic acid) during hydrothermal treatment affects the amorphous and crystalline phase ratios: the addition of isopropanol or acetone accelerates the phase transition from anatase and brookite to rutile, whereas the addition of acetic acid inhibits the transformation of anatase to rutile, increasing the content of amorphous phase compared to samples where no organic compound was added. We show that the combination of the organic compound added, along with the duration of the hydrothermal treatment, can be used to tailor the phase composition of TiO2, so as to obtain either: i) TiO2 with a high content of both rutile and amorphous phase, ii) TiO2 with a high rutile content and iii) TiO2 with different ratios of all four phases, when the duration of synthesis is short (2–4 h). The materials synthesized exhibited high photocatalytic activity (in most cases higher than P25), which is attributed to the beneficial phase composition and high specific surface area.
Keywords: sol-gel processes, X-ray methods, chemical properties, TiO2, photocatalysis
Published in DiRROS: 14.08.2024; Views: 43; Downloads: 87
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2. Groundwater is a hidden global keystone ecosystemMattia Saccò, Stefano Mammola, Florian Altermatt, Roman Alther, Rossano Bolpagni, Anton Brancelj, David Brankovits, Cene Fišer, Vasilis Gerovasileiou, Špela Borko, Maja Zagmajster, 2024, review article Abstract: Groundwater is a vital ecosystem of the global water cycle, hosting unique biodiversity and providing essential services to societies. Despite being the largest unfrozen freshwater resource, in a period of depletion by extraction and pollution, groundwater environments have been repeatedly overlooked in global biodiversity conservation agendas. Disregarding the importance of groundwater as an ecosystem ignores its critical role in preserving surface biomes. To foster timely global conservation of groundwater, we propose elevating the concept of keystone species into the realm of ecosystems, claiming groundwater as a keystone ecosystem that influences the integrity of many dependent ecosystems. Our global analysis shows that over half of land surface areas (52.6%) has a medium-to-high interaction with groundwater, reaching up to 74.9% when deserts and high mountains are excluded. We postulate that the intrinsic transboundary features of groundwater are critical for shifting perspectives towards more holistic approaches in aquatic ecology and beyond. Furthermore, we propose eight key themes to develop a science-policy integrated groundwater conservation agenda. Given ecosystems above and below the ground intersect at many levels, considering groundwater as an essential component of planetary health is pivotal to reduce biodiversity loss and buffer against climate change.
Keywords: groundwater, keystone ecosystem, surface-subterranean connectivity
Published in DiRROS: 07.08.2024; Views: 108; Downloads: 109
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3. In-depth comparison of adeno-associated virus containing fractions after CsCl ultracentrifugation gradient separationMojca Janc, Kaja Zevnik, Ana Dolinar, Tjaša Jakomin, Maja Štalekar, Katarina Bačnik, Denis Kutnjak, Magda Tušek-Žnidarič, Lorena Zentilin, Dmitri G. Fedorov, David Dobnik, 2024, original scientific article Abstract: Recombinant adeno-associated viruses (rAAVs) play a pivotal role in the treatment of genetic diseases. However, current production and purification processes yield AAV-based preparations that often contain unwanted empty, partially filled or damaged viral particles and impurities, including residual host cell DNA and proteins, plasmid DNA, and viral aggregates. To precisely understand the composition of AAV preparations, we systematically compared four different single-stranded AAV (ssAAV) and self-complementary (scAAV) fractions extracted from the CsCl ultracentrifugation gradient using established methods (transduction efficiency, analytical ultracentrifugation (AUC), quantitative and digital droplet PCR (qPCR and ddPCR), transmission electron microscopy (TEM) and enzyme-linked immunosorbent assay (ELISA)) alongside newer techniques (multiplex ddPCR, multi-angle light-scattering coupled to size-exclusion chromatography (SEC-MALS), multi-angle dynamic light scattering (MADLS), and high-throughput sequencing (HTS)). Suboptimal particle separation within the fractions resulted in unexpectedly similar infectivity levels. No single technique could simultaneously provide comprehensive insights in the presence of both bioactive particles and contaminants. Notably, multiplex ddPCR revealed distinct vector genome fragmentation patterns, differing between ssAAV and scAAV. This highlights the urgent need for innovative analytical and production approaches to optimize AAV vector production and enhance therapeutic outcomes.
Keywords: recombinant adeno-associated viruses (rAAVs), CsCl ultracentrifugation gradient, analytical methods, digital droplet PCR (ddPCR), transmission electron microscopy (TEM), analytical ultracentrifugation (AUC), size-exclusion chromatography coupled with multi-angle light scattering (SEC-MALS), Illumina sequencing, virology
Published in DiRROS: 07.08.2024; Views: 92; Downloads: 73
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4. Critical assessment of digital PCR for the detection and quantification of genetically modified organismsTigst Demeke, David Dobnik, 2018, review article Abstract: The number of genetically modified organisms (GMOs) on the market is steadily increasing. Because of regulation of cultivation and trade of GMOs in several countries, there is pressure for their accurate detection and quantification. Today, DNA-based approaches are more popular for this purpose than protein-based methods, and real-time quantitative PCR (qPCR) is still the gold standard in GMO analytics. However, digital PCR (dPCR) offers several advantages over qPCR, making this new technique appealing also for GMO analysis. This critical review focuses on the use of dPCR for the purpose of GMO quantification and addresses parameters which are important for achieving accurate and reliable results, such as the quality and purity of DNA and reaction optimization. Three critical factors are explored and discussed in more depth: correct classification of partitions as positive, correctly determined partition volume, and dilution factor. This review could serve as a guide for all laboratories implementing dPCR. Most of the parameters discussed are applicable to fields other than purely GMO testing.
Keywords: digital PCR, droplet digital PCR, chip-based digital PCR, genetically modified organisms, quantification
Published in DiRROS: 06.08.2024; Views: 91; Downloads: 63
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5. Cold plasma, a new hope in the field of virus inactivationArijana Filipić, Ion Gutiérrez-Aguirre, Gregor Primc, Miran Mozetič, David Dobnik, 2020, review article Abstract: Viruses can infect all cell-based organisms, from bacteria to humans, animals, and plants. They are responsible for numerous cases of hospitalization, many deaths, and widespread crop destruction, all of which result in an enormous medical, economical, and biological burden. Each of the currently used decontamination methods has important drawbacks. Cold plasma (CP) has entered this field as a novel, efficient, and clean solution for virus inactivation. We present recent developments in this promising field of CP-mediated virus inactivation, and describe the applications and mechanisms of the inactivation. This is particularly relevant because viral pandemics, such as COVID-19, highlight the need for alternative virus inactivation methods to replace, complement, or upgrade existing procedures.
Published in DiRROS: 06.08.2024; Views: 165; Downloads: 164
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6. Between source and sea : the role of wastewater treatment in reducing marine microplasticsShirra Freeman, Andy M. Booth, Isam Sabbah, Rachel Tiller, Jan Dierking, Katja Klun, Ana Rotter, Eric Ben David, Jamileh Javidpour, Dror Angel, 2020, review article Abstract: Wastewater treatment plants (WWTPs) are a focal point for the removal of microplastic (MP) particles before they are discharged into aquatic environments. WWTPs are capable of removing substantial quantities of larger MP particles but are inefficient in removing particles with any one dimension of less than 100 μm, with influents and effluents tending to have similar quantities of these smaller particles. As a single WWTP may release >100 billion MP particles annually, collectively WWTPs are significant contributors to the problem of MP pollution of global surface waters. Currently, there are no policies or regulations requiring the removal of MPs during wastewater treatment, but as concern about MP pollution grows, the potential for wastewater technologies to capture particles before they reach surface waters has begun to attract attention. There are promising technologies in various stages of development that may improve the removal of MP particles from wastewater. Better incentivization could speed up the research, development and adoption of innovative practices. This paper describes the current state of knowledge regarding MPs, wastewater and relevant policies that could influence the development and deployment of new technologies within WWTPs. We review existing technologies for capturing very small MP particles and examine new developments that may have the potential to overcome the shortcomings of existing methods. The types of collaborations needed to encourage and incentivize innovation within the wastewater sector are also discussed, specifically strong partnerships among scientific and engineering researchers, industry stakeholders, and policy decision makers.
Keywords: wastewater, microplastic, particle removal, innovation, policy, jellyfish mucus
Published in DiRROS: 06.08.2024; Views: 153; Downloads: 66
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7. Framing cutting-edge integrative deep-sea biodiversity monitoring via environmental DNA and optoacoustic augmented infrastructuresSergio Stefanni, Luca Mirimin, David Stanković, Damianos Chatzievangelou, Lucia Bongiorni, Simone Marini, Maria Vittoria Modica, Elisabetta Manea, Federico Bonofiglio, Joaquin del Rio Fernandez, Neven Cukrov, Ana Gavrilović, Fabio C. De Leo, Jacopo Aguzzi, 2022, review article Abstract: Deep-sea ecosystems are reservoirs of biodiversity that are largely unexplored, but their exploration and biodiscovery are becoming a reality thanks to biotechnological advances (e.g., omics technologies) and their integration in an expanding network of marine infrastructures for the exploration of the seas, such as cabled observatories. While still in its infancy, the application of environmental DNA (eDNA) metabarcoding approaches is revolutionizing marine biodiversity monitoring capability. Indeed, the analysis of eDNA in conjunction with the collection of multidisciplinary optoacoustic and environmental data, can provide a more comprehensive monitoring of deep-sea biodiversity. Here, we describe the potential for acquiring eDNA as a core component for the expanding ecological monitoring capabilities through cabled observatories and their docked Internet Operated Vehicles (IOVs), such as crawlers. Furthermore, we provide a critical overview of four areas of development: (i) Integrating eDNA with optoacoustic imaging; (ii) Development of eDNA repositories and cross-linking with other biodiversity databases; (iii) Artificial Intelligence for eDNA analyses and integration with imaging data; and (iv) Benefits of eDNA augmented observatories for the conservation and sustainable management of deep-sea biodiversity. Finally, we discuss the technical limitations and recommendations for future eDNA monitoring of the deep-sea. It is hoped that this review will frame the future direction of an exciting journey of biodiscovery in remote and yet vulnerable areas of our planet, with the overall aim to understand deep-sea biodiversity and hence manage and protect vital marine resources.
Published in DiRROS: 05.08.2024; Views: 111; Downloads: 134
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8. Involvement of potato (Solanum tuberosum L.) MKK6 in response to Potato virus YAna Lazar, Anna Coll Rius, David Dobnik, Špela Baebler, Apolonija Bedina Zavec, Jana Žel, Kristina Gruden, 2014, original scientific article Abstract: Mitogen-activated protein kinase (MAPK) cascades have crucial roles in the regulation of plant development and in plant responses to stress. Plant recognition of pathogen-associated molecular patterns or pathogen-derived effector proteins has been shown to trigger activation of several MAPKs. This then controls defence responses, including synthesis and/or signalling of defence hormones and activation of defence related genes. The MAPK cascade genes are highly complex and interconnected, and thus the precise signalling mechanisms in specific plant%pathogen interactions are still not known. Here we investigated the MAPK signalling network involved in immune responses of potato (Solanum tuberosum L.) to Potato virus Y, an important potato pathogen worldwide. Sequence analysis was performed to identify the complete MAPK kinase (MKK) family in potato, and to identify those regulated in the hypersensitive resistance response to Potato virus Y infection. Arabidopsis has 10 MKK family members, of which we identified five in potato and tomato (Solanum lycopersicum L.), and eight in Nicotiana benthamiana. Among these, StMKK6 is the most strongly regulated gene in response to Potato virus Y. The salicylic acid treatment revealed that StMKK6 is regulated by the hormone that is in agreement with the salicylic acid-regulated domains found in the StMKK6 promoter. The involvement of StMKK6 in potato defence response was confirmed by localisation studies, where StMKK6 accumulated strongly only in Potato-virus-Y-infected plants, and predominantly in the cell nucleus. Using a yeast two-hybrid method, we identified three StMKK6 targets downstream in the MAPK cascade: StMAPK4_2, StMAPK6 and StMAPK13. These data together provide further insight into the StMKK6 signalling module and its involvement in plant defence.
Keywords: plant diseases, potato, molecular biology
Published in DiRROS: 02.08.2024; Views: 111; Downloads: 124
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9. EditorialDavid Ožura, 2024, preface, editorial, afterword Keywords: medical journals, oncology, open access, editorial, bibliographic databases, citation index
Published in DiRROS: 26.07.2024; Views: 103; Downloads: 72
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10. Citiranje strokovne literature v medicini : vancouvrski način citiranjaDavid Ožura, 2024, professional article Abstract: Strokovno besedilo, ki temelji na znanstvenoraziskovalnem delu, se od drugih besedil loči z doslednim sklicevanjem na ustrezne vire. V pričujočem prispevku si bomo podrobneje ogledali vancouvrski način citiranja, saj se ta slog sklicevanja najpogo-steje uporablja v medicini in zdravstvenih vedah. Predstavljeni so najpogostejši primeri navajanja osnovnih bibliografskih podatkov prispevkov v strokovnih revijah, posamičnih pri-spevkov v zbornikih, navajanja monografij ter informacijskih virov na internetu. Podani so osnovni napotki za označevanje, reproduciranje in citiranje tabel in slik s primeri. Na kratko so predstavljena tudi sodobna orodja za urejanje referenc in citiranja z njihovimi funkcionalnostmi.
Keywords: citiranje literature, znanstvene revije, medicina, vancouvrski način citiranja, orodja za organizacijo referenc in citranja, navajanje in označevanje tabel in slik, onkologija
Published in DiRROS: 26.07.2024; Views: 133; Downloads: 133
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