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31.
Poročilo o preskusu št.: LVG 2024-238 : vzorec št. 2024/00892
Ana Brglez, Tine Hauptman, Patricija Podkrajšek, 2024, expertise, arbitration decision

Keywords: varstvo gozdov, morfološke analize
Published in DiRROS: 17.01.2025; Views: 20; Downloads: 10
.pdf Full text (1,17 MB)

32.
Evolution of a hybrid zone of willows (Salix L.) in the Alps analysed by RAD-seq and morphometrics
Pia Marinček, 2022, master's thesis

Abstract: Natural hybridization of plants can result in many outcomes with several evolutionary consequences, such as hybrid speciation and introgression. Natural hybrid zones can arise as a result of fluctuating climate during the exchange of glacial and interglacial periods, where species retract and expand their territories, resulting in secondary contacts. On mountain ranges, such as the European Alps, hybrid zones of alpine species are frequently formed where different lineages meet. Willows are a large genus of woody plants with an immense capability of interspecific crossing. About 33 species of this genus inhabit the Alps, where intermediate phenotypes were frequently observed and proclaimed as hybrids, but rarely examined in detail. One of the reasons was a lack of informative molecular markers and suitable analytical tools to analyse this highly diverse and convergent genus. With the development of the RAD-seq technology, several questions regarding willow phylogeny and hybridization could be answered. In this study, a putative hybrid zone of two sister species, S. foetida and S. waldsteiniana, was investigated to study the genomic structure of populations within and outside their contact zone, to find evidence for hybrid speciation or introgression, and to analyse if morphological phenotypes are reflected by their genotypes. Individuals of the two species were sampled across their distribution range in the Alps and examined with the use of RADseq data and morphometric analyses. The results showed that a hybrid zone between the two species was established within the range of their contact zone. Patterns of genetic admixture in homoploid hybrids indicated introgression with asymmetric backcrossing to one of the parental species. Morphometric characteristics of hybrids supported the molecular data and showed intermediacy with a bias towards S. waldsteiniana. Only one potentially divergent hybrid lineage was observed, hinting to a possibility of localised hybrid speciation events.
Keywords: alpine plants, hybridization, morphometry, RAD sequencing, master thesis
Published in DiRROS: 17.01.2025; Views: 35; Downloads: 10
.pdf Full text (4,66 MB)

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First-year dynamics of the anaerobic microbiome and archaeome in infants’ oral and gastrointestinal systems
Charlotte Neumann, Rokhsareh Mohammadzadeh, Pei Yee Woh, Tanja Kobal, Manuela-Raluca Pausan, Polona Mertelj, 2024, original scientific article

Abstract: Recent research provides new insights into the early establishment of the infant gut microbiome, emphasizing the influence of breastfeeding on the development of gastrointestinal microbiomes. In our study, we longitudinally examined the taxonomic and functional dynamics of the oral and gastrointestinal tract (GIT) microbiomes of healthy infants ( n = 30) in their first year, focusing on the often-over-looked aspects, the development of archaeal and anaerobic microbiomes. Breastfed (BF) infants exhibit a more defined transitional phase in their oral microbiome compared to non-breastfed (NBF) infants, marked by a decrease in Streptococcus and the emergence of anaerobic genera such as Granulicatella . This phase, characterized by increased alpha-diversity and significant changes in beta-diversity, occurs earlier in NBF infants (months 1–3) than in BF infants (months 4–6), suggesting that breastfeeding supports later, more defined microbiome maturation. We demonstrated the presence of archaea in the infant oral cavity and GIT microbiome from early infancy, with Methanobrevibacter being the predominant genus. Still, transient patterns show that no stable archaeome is formed. The GIT microbiome exhibited gradual development, with BF infants showing increased diversity and complexity between the third and eighth months, marked by anaerobic microbial networks. NBF infants showed complex microbial co-occurrence patterns from the start. These strong differences between BF and NBF infants’ GIT microbiomes are less pronounced on functional levels than on taxonomic levels. Overall, the infant microbiome differentiates and stabilizes over the first year, with breastfeeding playing a crucial role in shaping anaerobic microbial networks and overall microbiome maturation.
Keywords: breastfeeding, infants, gut microbiome, GIT, oral microbiome, infant development, early life, metagenomics, anaerobes, archaea, strain tracking, source tracking
Published in DiRROS: 17.01.2025; Views: 37; Downloads: 21
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38.
Proficiency testing and cross-laboratory method comparison to support standardisation of diatom DNA metabarcoding for freshwater biomonitoring
Valentin Vasselon, Sinziana F. Rivera, Éva Ács, Tina Eleršek, Maša Jablonska, 2025, original scientific article

Abstract: DNA metabarcoding of benthic diatoms has been successfully applied for biomonitoring at the national scale and can now be considered technically ready for routine application. However, protocols and methods still vary between and within countries, limiting their transferability and the comparability of results. In order to overcome this, routine use of DNA metabarcoding for diatom biomonitoring requires knowledge of the sources of variability introduced by the different steps of the procedure. Here, we examine how elements of routine procedures contribute to variability between European laboratories. A set of four experiments were performed focusing on DNA extraction and PCR amplification steps to evaluate their reproducibility between different laboratories and the variability introduced by different protocols currently applied by the scientific community. Under the guidance of a reference laboratory, 17 participants from 14 countries performed DNA extraction and PCR amplification in parallel, using the same fixed protocol and their own choice of protocol. Experiments were performed by each participant on a set of standardised DNA and biofilm samples (river, lake and mock community) to investigate potential systematic and random errors. Our results revealed the successful transferability of a protocol amongst labs and a highly similar and consistent ecological assessment outcome obtained regardless of the protocols used by each participant. We propose an “all for one but prove them all” strategy, suggesting that distinct protocols can be used within the scientific community, as long as their consistency is be proven by following minimum standard requirements.
Keywords: cross-laboratory experiment, DNA-based approach, ecological status assessment, intercalibration, standardisation, environmental science, biomonitoring, DNA metabarcoding, benthic diatoms
Published in DiRROS: 17.01.2025; Views: 35; Downloads: 18
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39.
A particle swarm optimisation-based decision-support tool for efficient sizing of hydrogen systems in hydropower plants
David Jure Jovan, Gregor Dolanc, Boštjan Pregelj, 2025, original scientific article

Abstract: The integration of hydrogen technologies with renewable energy sources, such as hydropower, enhances the potential of green hydrogen production while maintaining electricity generation. This paper presents a method for optimally sizing a hydrogen system within a hydropower plant, enabling the cogeneration of green hydrogen and electricity. A decision-support tool based on particle swarm optimisation is developed to balance technical and economic factors, including hydrogen demand, water reserves, electrolyser efficiency, installation costs, and energy-market prices. The approach is applied to a case-study hydropower plant, utilising excess hydropower and photovoltaic electricity to produce hydrogen. The tool successfully optimises multiple objectives, such as income maximisation and hydrogen production targets, demonstrating its potential for integrating hydrogen systems into renewable energy frameworks. This work highlights a viable pathway for advancing the adoption of hydrogen technologies in sustainable energy systems
Published in DiRROS: 16.01.2025; Views: 60; Downloads: 17
.pdf Full text (3,76 MB)

40.
Incorporation of recombinant proteins into extracellular vesicles by Lactococcus cremoris
Tina Vida Plavec, Kristina Žagar, Giulia Della Pelle, Špela Zupančič, Robert Vidmar, Aleš Berlec, 2025, original scientific article

Abstract: Extracellular vesicles (EVs) are nanosized lipid bilayer particles released by various cellular organisms that carry an array of bioactive molecules. EVs have diagnostic potential, as they play a role in intercellular interspecies communication, and could be applied in drug delivery. In contrast to mammalian cell-derived EVs, the study of EVs from bacteria, particularly Gram-positive bacteria, received less research attention. This study aimed to investigate the production of EVs by lactic acid bacterium Lactococcus cremoris NZ9000 and to examine the impact of recombinant protein expression on their formation and protein content. Four different recombinant proteins were expressed in L. cremoris NZ9000, in different forms of expression and combinations, and the produced EVs were isolated using the standard ultracentrifugation method. The presence of vesicular structures (50–200 nm) in the samples was confirmed by transmission electron microscopy and by flow cytometry using membrane-specific stain. Mass spectrometry analyses confirmed the presence of recombinant proteins in the EVs fraction, with amounts ranging from 13.17 to 100%, highlighting their significant incorporation into the vesicles, together with intrinsic L. cremoris NZ9000 proteins that were either more abundant in the cytoplasm (ribosomal proteins, metabolic enzymes) or present in the membrane. The presence of the most abundant lactococcal proteins in EVs fraction suggests that protein cargo-loading of EVs in L. cremoris NZ9000 is not regulated. However, our data suggests that L. cremoris NZ9000 genetically engineered to express recombinant proteins can produce EVs containing these proteins in scalable manner. As L. cremoris NZ9000 is considered safe bacterium, EVs from L. cremoris NZ9000 could have several advantages over EVs from other bacteria, implying possible biotechnological applications, e.g. in therapeutic protein delivery.
Keywords: Lactococcus cremoris, extracellular vesicles, recombinant proteins, delivery vehicle
Published in DiRROS: 16.01.2025; Views: 55; Downloads: 26
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