1. The response of microbes to anthropogenically induced perturbations in the Gulf of Trieste (northern Adriatic Sea) : dissertationNeža Orel, Tinkara Tinta, 2025, doktorska disertacija Opis: Marine ecosystems are constantly influenced by anthropogenic pressures, including inputs of nutrients, pollutants, and allochthonous microorganisms. These inputs can disrupt the dynamics of marine microbiomes, which encompass the majority of biomass and highest diversity of all life forms, controlling most biogeochemical cycles in the ocean realm. Despite their importance for public safety and potential influence on marine ecosystems functioning, knowledge of the impact of these perturbations on coastal microbiome dynamics remains in its infancy. The research objectives of this dissertation were to: (1) characterize the composition of the coastal microbiome in anthropogenically impacted coastal ecosystem; (2) investigate the genetic potential of selected microorganisms for pathogenicity and ecological adaptations; and (3) explore the effects of wastewater on the dynamics and functioning of the coastal microbiome, as well as its implications for the biogeochemical state of the ecosystem.
To address the first aim, we conducted a year-round in situ survey of the pelagic microbiome within anthropogenically impacted coastal ecosystem, focusing on the seasonal and spatial dynamics of traditional and alternative faecal bacterial indicators. We used a culture-independent approach combined with 16S rRNA amplicon sequencing, which overcome limitations of culture-based methods. This analysis revealed that the microbiome was primarily structured by seasonal changes, regardless of proximity to pollution sources. The statistical tool and oceanographic model we applied indicated that riverine water serves as a key vector for introducing allochthonous microbes. This study underscores the importance of molecular approaches combined with statistical and oceanographic modelling for advancing environmental health assessments and detecting microbial indicators.
To address the second aim, we applied whole-genome sequencing to assess the pathogenic potential and genomic features of selected Vibrio isolates. During the analysis, we identified cross-contamination in one isolate, which presented an opportunity to evaluate the effectiveness of bioinformatics workflows for contaminant removal and genome recovery. We reconstructed high-quality genomes of one Vibrio isolate from both axenic and contaminated cultures. Genomic analyses revealed that this isolate belongs to a sub-lineage of Vibrio campbellii associated with diseases in marine organisms. Moreover, this genome harboured a novel Vibrio plasmid linked to bacterial defense mechanisms and horizontal gene transfer, potentially offering a competitive advantage to this putative pathogen. This study highlights the utility of WGS and advanced bioinformatics in overcoming challenges posed by non-axenic cultures and provides new insights into the genomic characteristics of V. campbellii.
To address the third aim, we conducted a short-term microcosm experiment simulating wastewater discharge into coastal seawater, testing two types of wastewaters: (a) unfiltered, containing nutrients, pollutants, and allochthonous microbes, and (b) pre-filtered, retaining only nutrients and pollutants. Our results showed that wastewater, significantly increased nutrient levels (dissolved organic carbon, ammonium, orthophosphate). Using a multi-omics approach with measurements of microbial metabolic activity, we found that nutrient enrichment significantly influenced bacterial metabolism. This was evidenced by enriched protein profiles and increased leucine aminopeptidase and olease activity, indicating bacterial degradation of complex proteins and lipids. At the same time, the phosphate input resulted in a decreased alkaline phosphatase activity, with important implications for phosphorus cycling. Overall, wastewater primarily induced functional shifts in coastal microbiomes, highlighting the resilience and functional redundancy of coastal microbial communities and hence the biogeochemical processes they operate. Ključne besede: coastal microbiome, anthropogenic impact, wastewater pollution, bacterial community dynamics, allochthonous microorganisms, potential pathogens, Vibrio campbellii, multi-omics, whole-genome assembly, dissertations Objavljeno v RUNG: 16.04.2025; Ogledov: 219; Prenosov: 2
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2. Integrating cultural heritage and urban subway infrastructures : spatial distribution, value assessment, and impacts of the Beijing metro line on cultural heritage regional developmentHaisheng Hu, 2025, doktorska disertacija Opis: This research examines the spatial patterns and economic significance of cultural heritage sites along Beijing’s metro lines, with an emphasis on how urban infrastructure influences heritage preservation. Using spatial analysis methods, including the nearest-neighbor index, geographic concentration index, and location entropy, the research identifies patterns in the distribution of cultural heritage sites - such as ancient architecture, industrial heritage, and tombs - particularly concentrated within Beijing’s second ring road.
The study highlights the connectivity provided by key metro lines, including Lines 1, 2, 4, 5, 7, and 8, which link cultural sites in a point distribution pattern. On these premises, the research established a hierarchical framework to evaluate cultural heritage based on proximity to metro stations, with historical and artistic values being the most significant factors.
The findings suggest that heritage sites within one kilometre of metro stations exert more significant influence on their surrounding areas and emphasize the importance of integrating metro infrastructure with cultural heritage preservation. This study contributes to understanding the spatial dynamics of cultural heritage in urban environments, offering a framework for assessing the impact of heritage within contemporary infrastructure systems.
Practically, the study offers insights for urban planners, metro authorities, and cultural preservation bodies, proposing thematic routes along metro lines—such as Line 1 representing a fusion of Chinese and Western cultures and Line 5 emphasizing religious culture—to enhance cultural tourism. It also emphasizes the need for coordinated efforts between stakeholders to balance heritage conservation and urban development for sustainable growth. Ključne besede: dissertations, linear cultural heritage, national cultural heritage, Beijing, spatial distribution, economic assessment Objavljeno v RUNG: 31.03.2025; Ogledov: 349; Prenosov: 9
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3. Modelling-assisted optimisation of hemicellulose-derived monosaccharide valorization : dissertationAna Jakob, 2025, doktorska disertacija Opis: Hemicellulose, one of the key components of lignocellulosic biomass, and its sugar monomers offer significant potential as a substrate for producing value-added platform chemicals. With both pentoses (xylose and arabinose) and hexoses (glucose, galactose, and mannose), the conversion of hemicellulose can yield various products including furfural, hydroxymethylfurfural (HMF), and levulinic acid. This doctoral thesis investigates the dehydration of various hemicellulose-derived monosaccharides, utilizing catalyst-free systems, as well as homogeneous and heterogeneous catalysts, in both aqueous and organic solvents. Monosaccharide conversion was evaluated in a catalyst-free aqueous solution at temperatures ranging between 130 – 190 °C. Conducting dehydration reactions under simple, hydrothermal conditions highlighted the differences in the reactivity of individual monosaccharides. Experimental data from extensive activity testing enabled the development of accurate kinetic models. Aiming at the optimization of reaction parameters relevant to the post-Organosolv production of furanics and levulinic acid, sulfuric and formic acid were introduced into the reaction system as homogeneous acid catalysts. Reaction kinetics of acid catalysed conversion using sulfuric and formic acid indicated a significant reduction in the activation energy of ketose dehydration. In addition, the addition of both acids enhanced the dehydration rates and promoted the conversion of HMF towards levulinic acid due to its low activation energies 86 – 91 kJ mol−1 and high reaction rate constants. The established kinetic model for individual saccharides was proven to be robust and able to accurately predict optimal reaction conditions for two distinct industrially relevant hemicellulose streams. In pursuit of a more sustainable and recyclable catalyst, various zeolites, specifically H-BEA, were tested. Although H-BEA exhibited excellent catalytic activity, its selectivity towards furanics remained limited in aqueous media. The low activation energy for HMF rehydration facilitated the formation of levulinic acid even at a moderate reaction temperature of 165 °C. Notably, the addition of THF as an organic solvent in combination with H-BEA, drastically improved the product selectivity towards furanics, particularly furfural. In addition to H-BEA zeolite, various types of zeolites with different Si/Al ratios were studied. Catalyst characterization revealed a strong correlation between catalytic activity and acidity. The addition of THF resulted in 90 mol % of furfural after only 30 min, demonstrating an exponential increase in dehydration rates and a decrease in activation energies. This zeolite-THF system was therefore applied for tandem reactions involving both xylose dehydration and furfural hydrogenation. The addition of metallic active sites via a Ni/H-BEA catalyst, and a hydrogen atmosphere, resulted in the catalytic hydrogenation of xylose to tetrahydrofurfuryl alcohol. Adjusting reaction temperatures allowed the production of secondary hydrogenated (2-methylfuran and 2-methyltetrahydrofuran) and dehydration products (tetrahydropyran), while the addition of water as a co-solvent with THF resulted in the complete inhibition of dehydration reactions and the selective formation of xylitol. Through a systematic study of reaction conditions and the development of comprehensive kinetic models, this work provides an in-depth investigation of monosaccharide dehydration. This doctoral thesis represents a comprehensive study to systematically investigate both catalytic and non-catalytic dehydration of five relevant monosaccharides, providing a methodical kinetic modelling approach that addresses the challenges associated with the complexity related to hemicellulose conversion. Ključne besede: hemicellulose, monosaccharides, kinetic modelling, furanics, catalysis, dissertations Objavljeno v RUNG: 19.02.2025; Ogledov: 695; Prenosov: 14
Celotno besedilo (11,80 MB) |
4. Development of molecular methods for the comprehensive evaluation of stress conditions affecting forest trees : dissertationClaudia D'Ercole, 2025, doktorska disertacija Ključne besede: protein complexes, adhirons, nanobodies, plant stress, immunoreagents, protoplasts, ascorbate peroxidase, dissertations Objavljeno v RUNG: 04.02.2025; Ogledov: 670; Prenosov: 9
Celotno besedilo (4,89 MB) |
5. Modeling of solvent role in protein folding experiments : dissertationKnarik Yeritsyan, 2025, doktorska disertacija Opis: The Zimm-Bragg (ZB) model serves as a fundamental framework for elucidating conformational transitions in biopolymers, offering simplicity and efficacy in processing experimental data. This study provides a comprehensive review of the Zimm-Bragg model and its Hamiltonian formulation, with particular emphasis on incorporating water interactions and chain size effects into the computational framework. We propose a modified ZB model that accounts for water-polypeptide interactions, demonstrating its ability to describe phenomena such as cold denaturation and helix-coil transitions. In the realm of NanoBioTechnologies, the manipulation of short polypeptide chains is commonplace. Experimental investigation of these chains in vitro often relies on techniques like Circular Dichroism (CD) and timeresolved infrared spectroscopy. Determining interaction parameters necessitates processing the temperature dependence of the normalized degree of helicity through model fitting. Leveraging recent advancements in the Hamiltonian formulation of the Zimm and Bragg model, we explicitly incorporate chain length and solvent effects into the theoretical description. The resulting expression for helicity degree adeptly fits experimental data, yielding hydrogen bonding energies and nucleation parameter values consistent with field standards. Differential Scanning Calorimetry (DSC) stands as a potent tool for measuring the specific heat profile of materials, including proteins. However, relating the measured profile to microscopic properties requires a suitable model for fitting. We propose a novel algorithm for processing DSC experimental data based on the ZB theory of protein folding in water. This approach complements the classical two-state paradigm and provides insights into protein-water and intraprotein hydrogen bonding energies. An analytical expression for heat capacity, considering water interaction, is derived and successfully applied to fit numerous DSC experimental datasets reported in the literature. Additionally, we compare this approach with the classical two-state model, demonstrating its efficacy in fitting DSC data. Furthermore, we have developed and launched a free online tool for processing CD and DSC experimental data related to protein folding, aiming to support scientific research. Ključne besede: Zimm-Bragg model, conformational transitions, helix-coil transitions, cold denaturation, circular dichroism, differential scanning calorimetry, protein folding, water-protein interaction, hydrogen bonding energy, degree of helicity, short polypeptide chains, protein heat capacity, protein data analysis, dissertations Objavljeno v RUNG: 27.01.2025; Ogledov: 726; Prenosov: 13
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7. Catalytic hydro(deoxy)genation of furfural and modelling of its reaction kinetics : dissertationRok Šivec, 2024, doktorska disertacija Opis: In recent decades, there has been a growing interest in producing biofuels and biochemicals from renewable sources. Furfural stands as one of the ligno(hemi)cellulosic biomass derived platform chemical, which can be transformed into numerous value-added products.
The goal of this PhD was to systematically study hydrotreatment reactions of furfural under varying operating conditions and to gain insights into the reaction mechanism and kinetics. An extensive experimental and computational study of hydrogenation, hydrodeoxygenation, oligomerisation and etherification of furfural in a three-phase batch reactor was performed. The goals were divided into three consecutive objectives.
In the first part, hydrotreatment of furfural over Pd/C catalyst under various reaction conditions, including the solvent selection (solventless conditions, tetrahydrofuran, isopropanol), atmosphere (nitrogen, hydrogen), temperature (100–200 °C), pressure (25–75 bar) and stirring speed, was studied. A reaction pathway network and a micro-kinetic model were developed, incorporating thermodynamics (hydrogen solubility), mass transfer, adsorption, desorption, and surface reactions. These phenomena and their contribution to the surface coverages, TOF’s and global reaction rates were studied. The hydrogen presence on the catalyst surface was found to influence the main reaction pathway, leading to ring, aldehyde group or full hydrogenation.
In the second part, various monometallic catalysts (Pd/C, Pt/C, Re/C, Ru/C, Rh/C, Ni/C, Cu/C) were tested at 100 -200 °C with 60 bar of hydrogen and tetrahydrofuran as solvent. A generalized reaction pathway network was developed. H2 temperature-programmed reduction (H2-TPR) and CO temperature-programmed desorption (CO-TPD) were conducted, and a regression analysis of the results was subsequently performed by numerical modelling and optimisation. The obtained adsorption and desorption kinetic parameters for active metallic sites were further used in a generalized micro-kinetic model, applicable to all tested catalysts. Pd/C exhibited high activity and non-selective hydrogenation of furfural, while other catalysts showed selective aldehyde group hydrogenation followed by deoxygenation, consistent with density functional theory (DFT) calculations. Ru/C uniquely produced 2 methyltetrahydrofuran and ring-opening products at 200 °C. In silico optimization of reaction conditions for promising catalysts ((Pd/C, Pt/C, Re/C, Ni/C) aimed to maximize the yield of the target product.
In the third part, the influence of support on catalytic activity was studied. Hydrotreatment of furfural over Pd/Al2O3, Pd/SiO2, Ru/Al2O3, Ru/SiO2, Ni/Al2O3, and Ni/SiO2 was performed between 150 - 200 °C, using 60 bar of hydrogen and tetrahydrofuran as solvent. The strength and rate of adsorption and desorption to/from acidic, metallic and interface site structures were determined, using H2-TPR, CO-TPD and NH3-TPD and subsequent regression analysis of the results by numerical modelling and optimisation. The resulting parameters were sequentially used in the generalized micro-kinetic model to quantify the contribution of the active metal (Ni, Pd, or Ru), support (Al2O3 or SiO2), interphase sites and their relationship on catalyst activity and selectivity. Evaluation of morphological and structural characteristics, adsorption/desorption and intrinsic reaction kinetics has indicated that the coverage of acidic sites (on alumina or silica) facilitated yielding ring hydrogenation and inhibited deoxygenation, decarbonylation and cyclic compound opening. The rates for aromatics or aldehyde functional groups were, nonetheless, affected in a different order.
The used and developed methods and findings of this PhD offer useful guidelines for transforming furfural into high-value chemicals through catalytic hydrotreatment, with significant implications for future research and industrial applications. Ključne besede: lignocellulosic biomass, furfural, catalytic hydrogenation, micro-kinetic mass transfer model, reaction kinetics, first-principle methods, furfuryl alcohol, tetrahydrofurfuryl alcoholv, dissertations Objavljeno v RUNG: 08.11.2024; Ogledov: 1114; Prenosov: 23
Celotno besedilo (9,22 MB) |
8. Reaction mechanism and microkinetics of heterogeneously catalysed lignin depolymerisation and (de)functionalization : dissertationTina Ročnik, 2024, doktorska disertacija Opis: Lignin, a complex aromatic polymer derived from lignocellulosic biomass, is a renewable resource for the production of aromatic-like chemicals and materials. However, its complex nature, depolymerisation and valorisation remain a major challenge for the bio-based community within biorefinery concepts. For this reason, lignin model compounds have been used to understand and design lignin depolymerisation, but insufficient attention has been paid to linking knowledge between simpler systems and applying it to a more complex problem. The objectives of this thesis were formulated accordingly to address the aforementioned gap in the literature. The objectives included a systematic approach correlating studies of lignin model compounds with lignin. Hydrodeoxygenation, cleavage of the β-O-4 bond and depolymerisation were investigated to evaluate the process- and structure-dependent correlations, effects on product distribution and kinetic parameters.
The catalytic reactions were carried out in batch reactor and the conditions were applied and intensified according to the knowledge gained during the experimental work. The liquid samples for monomer yield evaluation were analysed by GC-MS, while the structural characteristics of lignin and oligomeric fragments, e.g. molecular weight, functionality/reactivity and structural features, were examined by SEC, quantitative 31P and 2D-HSQC NMR. Kinetic modelling was performed to determine the kinetic parameters (e.g. kinetic constants and activation energies) describing defunctionalisation, β-O-4 bond cleavage and depolymerisation.
The study with monomeric lignin compounds contributed to the understanding of the key parameters leading to condensation during hydrotreatment. The unsaturated alkyl side-chain of eugenol and the reactive hydroxyl groups bound irreversibly and formed the carbonaceous species, while 4-propylphenol and 4-propylguaiacol provided important insights into the contribution of steric hindrances to a favourable reaction mechanism. An initial assessment of β-O-4 cleavage was performed with β-O-4-model compound, 2-phenoxy-1-phenylethanol, and linked to the lignin macromolecule by process- and structure-dependent correlations. Although the lignin model compound lacks the structural complexity of lignin, important insights into possible reaction processes were gained and accurate kinetic parameters were determined. Furthermore, lignin isolated in 50 vol% EtOH/H2O solutions was depolymerised and the optimal
reaction conditions were defined at a temperature of 275 °C and a pressure of 1.5 MPa with regard to the product distribution and the changes in the structural characteristics of the corresponding oligomeric fragments. Depolymerisation of lignins isolated in different EtOH/H2O solutions showed the importance of the structural features, especially ethoxylation degree and the content of β-O-4 or α-ethoxylated β-O-4 bonds. A higher ethoxylation degree of lignin reduced its potential to depolymerise and achieve the theoretical monomer yield. Therefore, the structural characteristics of lignin play the main role in designing and prediction of lignin depolymerisation.
The thesis represents a systematic approach of increasing the complexity of structures exposed to hydrodeoxygenation and depolymerisation. The approach contributed to incorporating the knowledge gained from less complex model compounds to real lignin samples by tailoring and designing lignin depolymerisation to exploit the potential of lignin for biorefinery concepts. Ključne besede: model compounds, hydrodeoxygenation, organosolv lignin, depolymerisation, structural characteristics, kinetic modelling, dissertations Objavljeno v RUNG: 08.11.2024; Ogledov: 1126; Prenosov: 15
Celotno besedilo (5,04 MB) |
9. Quantitative detection of Microcystis aeruginosa (cyanobacteria) in water using single domain antibodies (VHH) : dissertationGbenga Folorunsho Oginni, 2024, doktorska disertacija Opis: Microcystis aeruginosa accumulation in freshwater poses a significant threat to aquatic organisms and human health. The toxicity of Cyanobacteria metabolites urges for the development of methods for their rapid and efficient detection but what is still almost completely missing is the availability of reagents for the quantification of M. aeruginosa cells in water to monitor the fluctuations of its population. In this study, nanobodies against cell surface antigens of the toxic Cyanobacteria M. aeruginosa were recovered bywhole-cell panning of a naive phage display library. Six unique sequences were identified and three of them sub-cloned and purified as fusion immunoreagents together with either green fluorescent protein or Avi-Tag to be used for diagnostics. Theirspecificity and sensitivity were evaluated by immunofluorescence, by fluorescent and colorimetric cell ELISA and by thermal lens spectrometry (TLS). No cross-reactivity with unrelated microalgae was detected, and both ELISA and TLS methods provided a linear range of detection of several logs. The limit-of-detection of TLS was as low as 1 cell/ml. Ključne besede: cyanobacteria, nanobodies, phage display, thermal lens spectrometry, dissertations Objavljeno v RUNG: 10.09.2024; Ogledov: 1292; Prenosov: 21
Celotno besedilo (3,80 MB) |
10. Green synthesis of Zeolitic Imidazolate Frameworks and their evaluation for ▫$CO_2$▫ capture in humid conditions : dissertationAljaž Škrjanc, 2024, doktorska disertacija Opis: Emissions of green-house gasses have been in the forefront of scientific research in recent decades. One of the approaches towards reducing the amount of green gas CO2 in the atmosphere is its capture and storage with subsequent conversion where pure enough CO2 can be regenerated. While CO2 capture widely utilizes two mature technologies, amine absorption and cryogenic distillation, they both have significant downsides, in either cost or potential new danger to the environment. To that end an adsorption-based CO2 capture has seen quite a lot of interest in recently. Nanoporous materials have been extensively studied for this application, starting with zeolites, followed by aluminophosphates and also the new members of the porous materials group, the so called reticular porous materials. Metal-Organic Frameworks (MOFs), the first discovered reticular porous materials have shown very promising results for post combustion CO2 capture and recently also for in-door and direct air capture. MOFs are in general enough thermally stable for CO2 capture, their main weakness for wide applicability is sometimes lower selectivity for CO2 in real gas mixtures and lower stability in humid conditions.
Zeolitic imidazolate frameworks (ZIFs), a subgroup of MOFs, have in recent years been extensively studied for sorption applications, also CO2, due to their superior stability and kinetics for vapour/gas adsorption if compared to carboxylate-based MOFs. While extensively studied, an overview of articles shows that most research is limited to a limited set group of frameworks, with ZIF-8 being used in more than half of ZIF papers. While ZIF-8 has successfully been prepared in water and even in solvent-free conditions, the rest of the ZIFs synthesis still heavily rely on solvothermal synthesis with formamide based solvent systems and synthesis times upwards of 5 days. Even in the case of ZIF-8, while greener synthesis approaches are available, dimethylformamide (DMF) synthesis still prevails in the cases tested for CO2 capture, mainly due to the increased CO2 uptake resulting from the synergistic contribution of the remaining DMF solvent in the pores.
The goal of this thesis was to develop green synthesis approaches, both solvothermal and mechanochemical, for known ZIFs and then to extend the scope towards preparation of new ZIF materials. The goal for latter was to experimentally determine the optimal topology and functionality of ZIFs for CO2 adsorption in humid conditions. Model humid gas isotherms were developed and measured for a series of ZIFs with mostly SOD (sodalite) and RHO framework topologies and Zn and Ni as metal nodes. Finally, some novel bio-based binder materials were tested for the use with ZIFs.
The sorption tests revealed than the SOD topology ZIFs have high potential for CO2 sorption applications, as the adsorption is rapid and further combination of terminally functionalised imidazoles in those frameworks drastically increases the frameworks affinity for CO2 at lower pressures. With most common 4,5- functionalised imidazole having hydrophilic functional groups, the challenge of competitive water sorption still remains. On the other hand some hydrophobic 4,5-substituted sodalite ZIFs, both with 4,5-dichloroimidazole, show excellent CO2 sorption and even complete hydrophobicity. The results led us to hypothesize that further research on ZIFs- for CO2 capture has to shift form 2 substituted sodalite frameworks to 4,5 substituted frameworks with strongly dipolar hydrophobic groups. The hydrophilic polar groups currently in use lead to issues with competitive water adsorption, due to their potential to form hydrogen bonds with water. Furthermore, some new agar and alginate based shaping methods were tested, as both potential binders are not environmentally toxic and are already used on the industrial scale world-wide for other applications. Ključne besede: carbon capture, synthesis, metal-organic frameworks, zeolitic imidazolate frameworks, nanoporous materials, dissertations Objavljeno v RUNG: 10.09.2024; Ogledov: 1324; Prenosov: 33
Celotno besedilo (15,56 MB) |