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1.
Structural and functional determinants of TDP-43 aggregation
Sanja Škaro, 2019, doktorska disertacija

Opis: TDP-43 (TAR DNA-binding protein) is an hnRNP that was identified as the main component of the brain inclusions characteristically found in patients suffering of Amyotrophic Lateral Sclerosis and Frontotemporal Lobar Degeneration. As an hnRNP protein, TDP-43 fulfills diverse roles in mRNA metabolism, localization and transport. Structurally, TDP-43 is composed of a well conserved N terminal domain (NTD), two RRM domains of which RRM1 is necessary for recognizing and binding to its target, UG rich RNA sequences, and the C-terminal domain (CTD) which is a Glycine rich domain. The CTD also contains a Q/N rich region that plays a key role in protein aggregation and interaction with another hnRNP proteins and polyglutamine repeats. This thesis focus on the structural determinants involved in the different TDP-43 interactions with itself and with other hnRNPs. Both the carboxyl and amino terminal domains are involved in these interactions. We have mapped the regions more relevant for the function of TDP-43 and for the aggregation process characteristic of the pathological pathway leading to neurodegeneration. We have started to further study the N-terminal domain. Previous results in our laboratory using a cellular aggregation model have shown that the N-terminal domain is also necessary for sequestering the endogenous TDP-43 into the aggregates. In particular, the intact NTD, specifically residues 1 to 77, have been shown to be needed to efficiently recruit TDP-43 monomers into these aggregates. We have extended our knowledge of NTD structure and function, by assessing the behavior of a series of proteins in which key structural features (α-helix and β-sheets) were modified and TDP-43 splicing function together with structure via NMR were analyzed. It was found that by disrupting protein secondary structure in the NTD (mutation in α-helix NTD-31V/R-32T/R) the capacity of the aggregates to sequester enough TDP-43 to induce loss of function was lost.In fact, this protein is also unable to recovery TDP-43 functionality when it is disrupted due to sequestration of the endogenous TDP-43 in add back experiments. Disturbing protein stability through substitution of residues in α-helix also affects its ability to form an active conformation. On the other hand, synthesis of hybrid peptides containing certain NTD and CTD segments was performed in order to see if they are capable to bind to the TDP-43 aggregates. However, it has been shown that these synthetic peptides have a greater ability to induce TDP-43 aggregation than to bind to them, probably due to specific functional characteristics of NTD and CTD segments used for their synthesis.The main focus of the thesis was on the C-terminal domain sequences involved in protein-protein interaction, misfolding and aggregation.A comparison of human, mouse, zebrafish, Annelida, flatworms and Drosophila showed a very strong conservation of the NTD and RRMs, but the C terminal regions of human and other TDP-43 orthologues are very different.I have studied Human and Drosophila melanogaster orthologues, because Drosophila orthologue contains different paralogs of TDP-43.Through a series of deletions and mutations it was shown that the shorter paralog of Drosophila TDP-43 (TBPH-RA) is more active than the longer one (TBPH-RC), and that this is due to a combination of two factors: 1. TBPH-RC by itself aggregates more than TBPH-RA, 2. The functionality of TBPH-RC is downregulated by intramolecular interactions in the C terminal domain. Apparently there is a cation-π interaction involving Tryptophan and Arginine in TBPH-RC that has a high relevance to the protein function and is lacking in the TBPH-RA.Overall this data has identified structural features essential for the proper function of TDP-43.In addition, we have also identified sequences that are critical in the pathological aggregation process of TDP-43 that lead to the characteristic brain inclusions in ALS and FTLD and to the loss of functionality
Ključne besede: TDP-43 structural determinants, hybrid peptides, protein-protein interactions, intramolecular interaction, cation-π interaction, Drosophila orthologues.
Objavljeno: 22.07.2019; Ogledov: 145; Prenosov: 2
.pdf Polno besedilo (6,84 MB)

2.
Regional biodiversity and seasonal dynamics of the bacterial communities in karstic springs of Slovenia
Maja Opalički Slabe, 2019, doktorska disertacija

Opis: Information on groundwater’s natural bacterial communities is important for evaluating pristine groundwater’s quality, as environmental changes potentially lead to alterations in bacterial community structures. In four seasons, 15 hypothetically pristine springs across five karst eco-regions in Slovenia (Central Europe) were analysed during their low discharge, and their basic physical and chemical parameters were recorded. The diversity of bacterial community structures was assessed with a terminal restriction fragment length polymorphism fingerprinting method. Total cell counts as bacterial abundance and electron transport system activity as bacterial respiratory activity were used for quantitative evaluation of bacterial communities. To detect anthropogenic pollution, spring water was tested by the cultivation of coliform bacteria and Escherichia coli (E. coli). Results indicate distinct regional differences in environmental parameters, bacterial respiratory activity, presence of coliforms and E. coli, bacterial abundances, and qualitative bacterial community structures, but there were no regional differences in the numbers of operational taxonomic units and biodiversity indices (Shannon-Wiener’s and Simpson’s diversity index, Buzas and Gibson’s evenness). The analysis of seasonal environmental parameters showed significant differences in dissolved organic carbon and pH, and also significant changes in bacterial respiratory activity and abundances, as well as differences in bacterial community structures, the numbers of operational taxonomic units, and biodiversity indices. No seasonal variations were shown for coliforms and E. coli. Despite seasonal oscillations, regional differences prevailed among five karst eco-regions and indicate a significant influence on the qualitative and quantitative aspects of groundwater bacterial community structures. The study confirmed both regional and seasonal differences in groundwater bacterial community structures, which should be included in further sustainable management plans of the aquifers.
Ključne besede: karst springs, bacterial community structure (BCS), terminal restriction fragment length polymorphism (T-RFLP), total cell counts (TCC), electron transport system activity (ETSA)
Objavljeno: 26.06.2019; Ogledov: 153; Prenosov: 6
.pdf Polno besedilo (3,76 MB)

3.
Evaluation of policy and technical factors for the protection of karst aquifers
Katarina Kosič Ficco, 2019, doktorska disertacija

Opis: Karst aquifer protection remains inchoate. National and international legally-binding mechanisms rarely consider implementation of karst-specific measures for their evaluation and protection. Although developing suitable protection measures for karst aquifers is challenging because their variable character hampers implementation of generalized methods, it is not impossible. As presented in this dissertation, consideration of scientific aspects and inclusion of karst-specific evaluation methods is of great importance. However, the additional inclusion of socio-political aspects is also crucial for advances in karst aquifer protection. Analyses of current European Union and United States of America policies performed in this study have shown that they can provide valuable input regarding the topic. It is also clear that accounting for the interests of affected entities, such as policy-makers, stakeholders and the public, is critical. Satisfying their needs, and assuring their understanding of karst aquifers, can ease and improve implementations of adopted measures. By recognizing these aspects, an interdisciplinary framework for karst aquifer protection was developed, and is presented in this study. The so-called K-framework, developed as a checklist, assures implementation of necessary steps for comprehensive karst aquifer evaluation and management. It further defines how each entity can contribute to the process by providing their knowledge, and allocates responsibilities of each sphere. An important attribute of the proposed framework is that it can be used on varying karst terrains and for various impacts that might threaten karst aquifers. Additionally, it is cost- and time-efficient, while still considering important aspects of karst and insuring the inclusion of important affected parties.
Ključne besede: aquifer, groundwater, karst, protection, environmental legislation, confined animal feeding operation, vulnerability mapping
Objavljeno: 17.06.2019; Ogledov: 225; Prenosov: 10
.pdf Polno besedilo (11,63 MB)

4.
OXYGEN-EXCESS RELATED DEFECTS IN SiO2-BASED MATERIALS: COUPLING THEORY AND EXPERIMENTS
Blaž Winkler, doktorska disertacija

Opis: This work is primarily focused on application of standard first-principle computational approaches to model oxygen excess related point defects in amorphous silica. Atomic models with their respective electronic and optical properties are explored together with some conversion mechanisms between defect models. The first chapter overviews extensive literature about the already known properties of oxygen related defects. Second chapter briefly introduces main methods that have been used in this research, in particular Density Functional Theory (DFT) as energy and force engine with short description of minimal energy path (MEP) algorithm used for modeling chemical/migration reactions, GW approximation for charged electronic excitations (band structure) and Bethe-Salpeter Equation (BSE) for neutral excitations (optical absorption and excitonic structure including electron hole interaction). The third chapter is devoted to the presentation of results. Thanks to the calculation of optical properties of peroxy bridge (POL), a correlation has been found between structural disorder, specifically dihedral angle dispersion, and low coupling with light, which has been identified as main reason why no clear absorption bands have been assigned to the POL. Structure and stability of some other defects, like interstitial ozone molecule (ozonyl) and dioxasilirane (silicon analogy of dioxirane), have been studied. These defects are usually not considered as most important species, however their calculated formation energies are lower compared to some known defects, which indicates they might be present in silica. From a detailed study on possible reaction mechanisms, it has been found that ozonyl might be one of the most important intermediate steps for oxygen exchange reactions. Results also show that dioxasilirane can be spontaneously created during the interaction of oxygen with lone pair defects. By exploring different reactions between oxygen and pre-existing oxygen deficiency centers (ODCs), calculations predict two kinds of passivation behaviors: single-barrier reversible mechanisms with the formation of dioxasilirane-like groups, for which the network keeps the memory of the precursory lone pair defects, and single or multiple-barrier mechanisms, for which the network loses its memory, either because of the high reverse barrier or because of a reconstruction. Final part of this research has been devoted to experimental characterization of the response and tolerance of optical fibers loaded with oxygen under irradiation. These include experiments on commercial fiber along with canonical samples (Optical fibers developed with the intention of studying correlations between different fabrication parameters, dopant/impurity concentration and doping concentrations). Studied fibers also include rare-earth doped fibers.
Ključne besede: Silica, DFT, GW-approximation, Bethe-Salpeter equation, NEB, defect, oxygen, oxygen excess centers, oxygen deficiency centers, optical absorption, optical fibers, radiation induced attenuation.
Objavljeno: 07.05.2019; Ogledov: 254; Prenosov: 17
.pdf Polno besedilo (13,18 MB)

5.
Modelling of Macrosegregation of a Low-Frequency Electromagnetic Direct Chill Casting by a Meshless Method
Vanja Hatić, 2019, doktorska disertacija

Opis: The main aim of the dissertation is to develop a meshless model that describes the solidification and macrosegregation phenomena during the direct chill casting (DCC) of aluminium alloys under the influence of a low-frequency electromagnetic field. Macrosegregation is an undesired consequence of alloy solidification. It represents one of the major casting defects and substantially reduces the quality of the finished product. On the other hand, low-frequency electromagnetic casting (LFEC) is a process that promises to increase greatly the product quality, including the reduction of macrosegregation. The modelling of both processes is of tremendous importance to the metallurgical industry, due to the high costs of experiments during production. The volume-averaging formulation is used for the modelling of the solid-liquid interaction. The conservation equations for mass, energy, momentum, and species are used to model the solidification of aluminium-alloy billets in axysimmetry. The electromagnetic-induction equation is coupled with the melt flow. It is used to calculate the magnetic vector potential and the Lorentz force. The Lorentz force is time-averaged and included in the momentum-conservation equation, which intensifies the melt flow. The effect of Joule heating is neglected in the energy conservation due to its insignificant contribution. The semi-continuous casting process is modelled with the Eulerian approach. This implies that the global computational domain is fixed in space. The inflow of the liquid melt is assumed at the top boundary and the outflow of the solid metal is assumed at the bottom. It is assumed that the whole mushy area is a rigid porous media, which is modelled with the Darcy law. The Kozeny-Carman relation is used for the permeability definition. The incompressible mass conservation is ensured by the pressure correction, which is performed with the fractional step method. The conservation equations and the induction equation are posed in the cylindrical coordinate system. A linearised eutectic binary phase diagram is used to predict the solute redistribution in the solid and liquid phases. The micro model uses the lever rule to determine the temperature and the liquid fraction field from the transport equations. The partial differential equations are solved with the meshless-diffuse-approximate method (DAM). The DAM uses weighted least squares to determine a locally smooth approximation from a discrete set of data. The second-order polynomials are used as the trial functions, while the Gaussian function is used as the weight function. The method is localised by defining a smooth approximation for each computational node separately. This is performed by associating each node with a unique local neighbourhood, which is used for the minimisation. There are 14 nodes included in the local subdomains for the DCC and LFEC simulations. The stability of the advective term is achieved with a shift of the Gaussian weight in the upwind direction. This approach is called the adaptive upwind weight function and is used in the DAM for the first time. The Explicit-Euler scheme is used for temporal discretisation. The use of a meshless method and the automatic node-arrangement generation makes it possible to investigate the complicated flow structures, which are formed in geometrically complex inflow conditions in a straightforward way. A realistic inflow geometry and mould can therefore be included in the model. The number of computational nodes is increased in the mushy zone and decreased in the solid phase, due to the optimisation of the computational time and memory. The computational node arrangement is automatically adapted with time, as the position of the mushy zone is changed in shape and position.
Ključne besede: low-frequency electromagnetic casting, direct chill casting, macrosegregation, electromagnetic stirring, aluminium alloys, meshless methods, diffuse-approximate method, multiphysics model, solidification
Objavljeno: 25.04.2019; Ogledov: 220; Prenosov: 11
.pdf Polno besedilo (28,80 MB)

6.
MINERALOGY AND GEOMICROBIOLOGY IN ACTIVE VOLCANIC CAVE ENVIRONMENTS IN CENTRAL AMERICA
Andres Ulloa Carmiol, 2019, doktorska disertacija

Opis: Recently, the study of mineralogical and geomicrobiological interactions in volcanic caves is gaining relevance, because there are many factors to consider them as Mars analogues for astrobiology and planetary sciences. In addition, sulfuric acid caves have also shown to be an important field of study for the understanding of chemolithoautotrophic metabolic pathways, especially in regard to the biogeochemical cycle of sulfur compounds. Hitherto, sulfur-rich volcanic caves found in Central America were almost unknown to the scientific community. This work presents the mineralogical and microbiological diversity and the potential geomicrobiological links found in active volcanic settings, such as Cueva los Minerales (CMI) and Cueva los Mucolitos (CMU) at Irazú volcano (Costa Rica), and Cueva Hoyo de Koppen (CHK) at El Hoyo volcano (Nicaragua). The volcanic caves at Irazú volcano (Costa Rica) are located in the northwest (NW) foothills of the main crater. These caves became accessible after the partial collapse of the NW sector of the Irazú volcano in 1994, offering the opportunity to investigate in situ active minerogenetic processes. Detailed mineralogical and geochemical analyses were performed to study the speleothems at CMI and CMU. Mineralogical analyses included X-ray diffraction (XRD) and Raman spectroscopy, while geochemical characterization was done using Energy Dispersive X-ray spectroscopy (EDX) coupled to Scanning Electron Microscopy (SEM). In noveladdition, measurements of cave environmental parameters, cave drip water, and a compilation of geochemical analyses of the Irazú volcanic lake (located ca. 150 m above the cave level) and fumarole analyses, were conducted between 1991 and 2014. Forty-eight different mineral phases were identified, mostly rare hydrated sulfates of the alunite, halotrichite, copiapite, kieserite and rozenite groups; thirteen of which are described here, as cave minerals, for the first time, i.e. aplowite, bieberite, boyleite, dietrichite, ferricopiapite, ferrinatrite, lausenite, lishizhenite, magnesiocopiapite, marinellite, pentahydrite, szomolnokite, and wupatkiite. The presence of other novel cave minerals, such as tolbachite, mercallite, rhomboclase, cyanochroite, and retgersite, is likely, but this was not possible to confirm by the various mineralogical techniques employed in this study. It was determined that uplifting of sulfurous gases, water percolation from the Irazú volcanic lake, and hydrothermal interactions with the volcanic host rock are responsible for such extreme mineralogical diversity. Moreover, acidic (pH < 2) viscous biofilms, known as snottites, were observed hanging from both, walls and ceiling, of the caves at Irazú volcano, in close relation with the presence of sulfate minerals. Knowledge about snottites in volcanic caves is scarce, being biofilms present in carbonated rocks the most studied, e.g. at Frasassi and Acquasanta caves (Italy), and Cueva de Villa Luz and Luna Azufre (Mexico). 16S rRNA techniques (with primers for target Bacteria and Archaea), together with bioinformatics analyses, were used to investigate the snottites from CMU and CMI. The results indicated that both prokaryotic groups in the snottites offer a vast metabolic potential to execute various reactions, including redox reactions. The phylogenetic findings revealed that approximately 65% of the identified taxa corresponded to species related to sulfur-oxidizing metabolic pathways (e.g., Leptospirillum, Mycobacterium, Acidithiobacillus and Acidiphilium), while just 0.04% corresponded to sulfur-reducing species (Desulfosporosinus). Since sulfur-oxidizing microorganisms appeared to be dominant in the acidic snottites, induced-gypsum precipitation by changes in micro environmental conditions, is strongly suggested as the path for biomineralization at the studied caves. 34S isotope signature of sulfur minerals presented negative values (from -16.2 to -3.4 ‰), comparable with data obtained...
Ključne besede: Volcanic caves, Costa Rica, Irazú, Cueva los Mucolitos, Cueva los Minerales, Nicaragua, Hoyo, Cueva Hoyo de Koppen, mineralogy, sulfur isotopes, hydrated sulfates, active volcano, microbiology, snottites, geomicrobiology, astrobiology, Mars analogue.
Objavljeno: 15.04.2019; Ogledov: 240; Prenosov: 14
.pdf Polno besedilo (16,65 MB)

7.
Mass composition of ultra-high energy cosmic rays at the Pierre Auger Observatory
Gašper Kukec Mezek, 2019, doktorska disertacija

Opis: Cosmic rays with energies above 10^18 eV, usually referred to as ultra-high energy cosmic rays (UHECR), have been a mystery from the moment they have been discovered. Although we have now more information on their extragalactic origin, their direct sources still remain hidden due to deviations caused by galactic magnetic fields. Another mystery, apart from their production sites, is their nature. Their mass composition, still uncertain at these energies, would give us a better understanding on their production, acceleration, propagation and capacity to produce extensive air showers in the Earth's atmosphere. Mass composition studies of UHECR try to determine their nature from the difference in development of their extensive air showers. In this work, observational parameters from the hybrid detection system of the Pierre Auger Observatory are used in a multivariate analysis to obtain the mass composition of UHECR. The multivariate analysis (MVA) approach combines a number of mass composition sensitive variables and tries to improve the separation between different UHECR particle masses. Simulated distributions of different primary particles are fitted to measured observable distributions in order to determine individual elemental fractions of the composition. When including observables from the surface detector, we find a discrepancy in the estimated mass composition between a mixed simulation sample and the Pierre Auger data. Our analysis results from the Pierre Auger data are to a great degree independent on hadronic interaction models. Although they differ at higher primary masses, the different models are more consistent, when combining fractions of oxygen and iron. Compared to previously published results, the systematic uncertainty from hadronic interaction models is roughly four times smaller. Our analysis reports a predominantly heavy composition of UHECR, with more than a 50% fraction of oxygen and iron at low energies. The composition is then becoming heavier with increasing energy, with a fraction of oxygen and iron above 80% at the highest energies.
Ključne besede: astroparticle physics, ultra-high energy cosmic rays, extensive air showers, mass composition, Pierre Auger Observatory, machine learning, multivariate analysis
Objavljeno: 03.04.2019; Ogledov: 285; Prenosov: 20
.pdf Polno besedilo (17,53 MB)

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Urban Conservation System in China and Its Improvement by Using Historic Urban Landscape Approach
Chen Shujie, 2018, doktorska disertacija

Opis: In the last few decades, the Modern Conservation Movement has developed from European-limited practices into a global movement with universal common views and practical measures for managing heritage resources in different cultural contexts. As an innovative idea of this movement, the Historic Urban Landscape approach aims to protect and manage historic urban environments with respect to both the fundamental principles in the international doctrines and the local social/cultural/historical contexts. It recommends local authorities to use the HUL toolkit to identify, conserve and manage the overall landscape of their historic cities. In the case of China, who is an old civilization, a modern nation and a socialist country at the same time, the conservation practice needs to follow the basic and common conservation principles in the international doctrines, and meanwhile, it shall make its initiatives based on the actual social, cultural and political situations. The establishment of Historically and Culturally Famous City (HCF City in short) system is a positive attempt for such a purpose. The system manages various urban elements relating to the city’s historical and cultural features under a comprehensive notion of HCF City. However, the system is not prefect because it depends excessively on the top-down management of local governments, and also because it overlooks the spatial and spiritual relationships among the protected elements... The thesis provides a big picture of architectural and urban conservation practices in China. It introduces the forming process and the characteristics of historic urban fabric, as well as the history of urban conservation. Then, it takes a deep look at the existing HCF City system, including its basic ideas, structures and mechanism. It analyses the system’s initiatives and deficiencies. Finally, it provides feasible advices to improve the current system by using the HUL toolkit.
Ključne besede: Urban, History, Heritage, Conservation, Management International Principles, Modern Conservation Movement, Globalization, Localization Historic Urban Area, Historically and Culturally Famous Cities, Conservation System, Historic Urban Landscape Chinese Architecture, Chinese Urban Planning, Conservation History, Policy
Objavljeno: 11.02.2019; Ogledov: 340; Prenosov: 4
.pdf Polno besedilo (217,96 MB)

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