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1.
Study of expression systems for large-scale protein production in CHO cells
Juan Pedro Menvielle, 2013, doktorska disertacija

Objavljeno: 28.07.2017; Ogledov: 479; Prenosov: 5
.pdf Polno besedilo (3,44 MB)

2.
Molecular characterization of REEP1 function in Drosophila melanogaster
Chiara Appocher, 2013, doktorska disertacija

Objavljeno: 28.07.2017; Ogledov: 414; Prenosov: 5
.pdf Polno besedilo (6,32 MB)

3.
Meshless modeling of thermo-mechanics of low-frequency electromagnetic direct chill casting
Boštjan Mavrič, 2017, doktorska disertacija

Opis: The aim of this dissertation is to devise a meshless model describing the thermomechanical phenomena, which occur during DC casting of aluminium alloys under the influence of electromagnetic stirring. The thermoemchanical phenomena are important, because they can cause several type of defects, which can significantly deteriorate the quality of the resulting billet. The two most important of them are the hot tearing, which causes cracks to appear in the mushy zone, and the porosity, which demonstrates itself as micrometer sized voids in the microstructure of the billet. To calculate the stresses and strains, a computational model of the stationary state of the process, stated in axial symmetry, is formulated. It uses Eulerian formulation by fixing the computational domain to the mold of the casting device allowing the material to move through the computational domain. The stresses are calculated from the stress equilibrium equations. The small strain approximation is used to consider the three contributions to strain. The strain consists of the thermal strain, which is caused by the inhomogeneous thermal profile in the billet, the viscoplastic strain, which is caused by the irreversible deformation because of the large stresses occurring in the billet, and the elastic strain. The spatial discretization of the governing equations is performed by local radial basis function collocation method (LRBFCM) and the temporal discretization is achieved by the method of lines with implicit Euler formula. The method used for spatial discretization uses radial basis functions augmented by monomials to approximate the solution values on localized stencils. This approximation is used to construct the discretization coefficients of the differential operators present in the model. A flexible framework for formulation of multiphysics problems is developed to use the obtained discretization coefficients to construct the temporal discretization of the governing equations. The node arrangement, on which the spatial discretization is performed, was generated by a point-repel algorithm. The performance of the method is tested on several benchmark test cases. The accuracy of the discretization is estimated by comparing the analytic and the numerical solution to several stationary problems in thermomechancis. Of special interest is the performance of the method with respect to the choice of the shape parameter, which determines the spatial scale of the radial basis functions. Besides this, the dependence of the condition number of the interpolation matrix on the shape parameter is studied. The condition number is found fit to replace the condition number as the shape-determining free parameter of the method. The implementation of the solver of time dependent problems is tested on problem of thermoelasticity, which couples the thermal transport with the elastic waves. The results of the problem are compared with the finite element method, showing good agreement of the two methods. The results are also compared with the results obtained by meshless local Petrov-Galerkin method and the proposed local collocation method demonstrated significantly better solution quality in the studied case. The performance of the solver used to solve the system of nonlinear equations given by the viscoplastic constitutive equations is estimated on a quasi zero-dimensional problem. The results are found to match perfectly. Solution of a more complicated problem is obtained with the proposed method and the finite-element method, both methods giving practically the same solution, although some serious limitations of the chosen finite element solver are exposed during the selection of the problem parameters. Finally, the devised method is applied to the problem of DC casting of aluminium alloys. The thermomechanical model relies on a model of heat and mass transfer to obtain the input fields needed in the solver. The required fields are: temperature, pressure, liquid
Ključne besede: thermomechanics, viscoplasticity, aluminium alloys, direct-chill casting, electromagnetic stirring, hot tearing, porosity, meshless methods, local collocation method, radial basis functions, shape parameter
Objavljeno: 28.06.2017; Ogledov: 243; Prenosov: 6
.pdf Polno besedilo (21,30 MB)

4.
RE-CONCEPTUALIZATION OF THE CONSERVATION THEORY FOR THE MANAGEMENT OF ARCHAEOLOGICAL HERITAGE
Usman Ali, 2017, doktorska disertacija

Opis: ver the last few decades, the concept of “authenticity” has commonly been used as a criterion for heritage conservation and management in various regions around the world. In 1994, ICOMOS adopted the Nara document on Authenticity as an international recommendation to draw the attention of policy and decision makers on the values of cultural heritage, stressing on interdisciplinary of approaches. Interdisciplinary research of heritage studies includes analysis and evaluation methods to redefine the theories and methodologies of heritage preservation and management in different contexts. But, when dealing with Archaeological Heritage Management, various difficulties emerge in the adoption of prescribed criteria for heritage conservation and management. The aim of this research is to examine and evaluate the compatibility and potential adaptation of these significant criteria from the Heritage International practice (I.e. UNESCO), including the spheres of law and philosophy, in the Management of Archaeological Heritage. Consequently, this dissertation is articulating according to the following concepts: 1. UNESCO already prescribed parameters and criteria of conservation and management of cultural heritage, but their full applicability on Archaeological Heritage Management should be verified; 2. The level of similarities and differences between Cultural and Archaeological Heritage in the conservation and management process should be discussed to highlight potential new research channels; 3. Is the adoption of the concept of Authenticity as a criterion, prescribed in UNESCO Operational Guideline, compatible enough to be applied to the Management of Archaeological Heritage or not? 4. Archaeological practice as a source of information provides various data and parameters. Are these attributions determining the management? This dissertation concludes that thematic divisions of heritage studies foster and formulate various models and concepts (implicitly and explicitly), which determine many substantial criteria and integrated factors for the sustainability of archaeological heritage. These criteria and factors give 7 importance to the common theoretical and methodological research in archaeological heritage conservation theory and practice.
Ključne besede: World Heritage Studies, Archaeological Heritage Management, Authenticity, Heritage Conservation, Archaeological Theories, Heritage International Doctrine.
Objavljeno: 22.06.2017; Ogledov: 233; Prenosov: 16
.pdf Polno besedilo (2,37 MB)

5.
Synthesis and characterization of metal/semiconductor nanocomposites for photocatalysis
Tina Mavrič, doktorska disertacija

Opis: The doctoral dissertation focused on improving photocatalytic activity of nanopowdered ZnO by constructing I) Metal-Semiconductor and II) Semiconductor-Semiconductor heterostructures. Both heterostructure types have been reported to have a beneficial effect on photocatalytic efficiency. For the first part (I) Ag/ZnO nanocomposite was synthesized. Here we investigated an influence of polyvinylpyrrolidone (PVP) addition during the synthesis on the particle properties and their photoactivity. The second part (II) describes procedure development of ZnO based semiconductor-semiconductor composite that resulted in synthesis of highly efficient ZnO/CuWO4 composite. Ag/ZnO nanocomposite was synthesized from precursors in ethylene glycol (EG) in a hydrothermal reactor at 180 °C for 3h. No further thermal treatment was required after the synthesis since all samples showed good crystallinity. Silver precursor loading was 2.7 wt%, because this amount has shown the best photoactivity in preliminary sample testings. Two separate batches of Ag/ZnO nanopowders were prepared, one with addition of PVP, one without (labelled Ag/ZnO and Ag/ZnO*, respectively). All powders were in nanometer range, TEM images showed a major difference between the samples with and without PVP. While Ag nanoparticles were deposited uniformly over ZnO, Ag/ZnO* exhibited a substantial agglomeration of Ag. The photocatalytic efficiency was assessed under UV-Vis light. Ag/ZnO reached complete decolourization of 10–5 M methyl orange (MO) already in 80 min after the beginning of irradiation. The calculated degradation rate constant (k) for the Ag/ZnO was almost 2-times larger than for TiO2 P25 and 4-times larger than for ZnO. Ag/ZnO* also showed higher activity than pure ZnO*, but was inferior to Ag/ZnO (1.6-times of Ag/ZnO*). A reusability test performed on Ag/ZnO showed an excellent photoactivity of reused powders; second and third cycle exhibited higher photoactivity than the first cycle. The supreme photocatalytic activity of Ag/ZnO was also confirmed by degradation of terephthalic acid. To develop an efficient semiconductor-semiconductor heterostructure we have synthesized a combination of several materials with ZnO. We performed preliminary photocatalytic tests in order to assess the functionality of these heterostructures. The tested systems were the following: ZnO/MWCNT, ZnO/GO, ZnO/SiC, ZnO/Co3O4, ZnO/AgVO3. The synthesis of heterostructures was done via hydrothermal synthesis. The commercial or synthesized powers were dispersed together with the ZnO precursor in EG medium (180 °C/3h). The aim was to obtain higher photoactivity than that of pure ZnO. None of these systems was able to outperform pure ZnO. ZnO/CuWO4 system has, however, significantly improved ZnO photoactivity. Several synthesis routes were investigated, including the influence of different structure directing agents (PVP, CTAB, starch). The best performing system was obtained by separate hydrothermal synthesis of ZnO and CuWO4 in water with PVP. XRD analysis confirmed that to obtain the crystalline CuWO4 thermal treatment (500 °C) is needed. The heterostructure was also synthesized in ethanolic solution. ZnO particles were in a nanometer range, CuWO4 were larger and ranged from 200 to 400 nm. CuWO4 has successfully decreased the charge recombination in ZnO, which was confirmed by transient absorption spectroscopy studies. The photocatalytic activity was assessed for both MO and TPA (10–4 M) degradation. The ZnO/CuWO4 composite has completely decolourized the dye in 60 min of UV-Vis irradiation. k for ZnO/CuWO4 was ~2.5-times larger than that of ZnO. A 3-cycle reusability test with MO showed a small decrease in efficiency in the last cycle. TPA degradation has revealed lower efficiency for ZnO/CuWO4 in air but high efficiency in O2 and N2 atmosphere, where it reached 90% and 55% degradation rate, respectively.
Ključne besede: photocatalysis, zinc oxide, heterostructures, powders, Ag/ZnO composites, ZnO/CuWO4 composites
Objavljeno: 31.05.2017; Ogledov: 440; Prenosov: 60
.pdf Polno besedilo (4,11 MB)

6.
NOVEL METHODS FOR DETECTION AND REMOVAL OF POLLUTANTS FROM WATERS
Franja Prosenc, 2017, doktorska disertacija

Opis: Water security and quality are a global issue of concern, which have recently become alarming due to the growth of the human population, industrialisation and expanded agricultural activities. Biologically active compounds, such as pharmaceuticals and personal care products can have major adverse effects on aquatic organisms, and are therefore one of the biggest threats in water quality. Another major concern is the spread of waterborne pathogens, including multidrug resistant (MDR) bacteria, which can cause serious illnesses in humans. In order to maintain water abundance and quality, it is necessary that adequate wastewater treatment and analytical techniques allowing for sensitive and fast-response detection of water hazards are in place. Conventional (waste)water treatment technologies often fail to adequately remove all of the water hazards detailed above. Moreover, conventional analytical techniques currently used in water quality control are, although highly selective and sensitive, time-extensive, with throughput of merely 2 to 3 samples per hour, excluding the time for sample preparation. With respect to these drawbacks, research was proposed to explore new approaches for degradation of recalcitrant compounds, inactivation of microorganisms, and fast screening methods, which are listed in the second chapter of this dissertation as research objectives. In the third chapter, an extensive theoretical background on the hazards found in aquatic environment, namely pharmaceuticals and waterborne pathogens, is given. Pharmaceuticals enter the environment through several routes (disposal of unused medication via the toilet, pharmaceuticals passing through the human body unchanged/slightly transformed, animal excretions of pharmaceutically active compounds, insufficient wastewater treatment, etc.); therefore, traces of pharmaceuticals have repeatedly been reported in surface waters, groundwater, wastewater effluents, and even drinking water. Iodinated contrast agents (ICAs), as the compounds of interest in this project are further described. ICAs are eliminated from the human body practically unchanged; therefore a large proportion of them end up in municipal and hospital wastewater, where they can be present in concentrations of up to 2.4 g/L. Their ecotoxicity, degradation attempts, as well as detection monitoring in the environment are reviewed within the chapter. Additionally, waterborne pathogens, which account for 2.2 million deaths per year, are reviewed in this chapter, with emphasis on multidrug-resistant (MDR) bacteria. Although MDR infections are mostly prevalent in hospital environments, the presence of MDR bacteria in the environment is not a rarity. A high percentage of bacterial isolates in waters have been shown to be of an MDR phenotype. The theoretical background in analytical methods in water quality monitoring is also given in this chapter. Vanguard and rearguard techniques are explained, the first offering simple, cheap, and rapid sample screening, but sacrificing sensitivity and selectivity, whereas the second providing the highest quality information, excellent sensitivity and selectivity, but in expense of complicated and timely sample handling and high-cost instruments. By combining the two techniques the benefits of both can be exploited in a single system. The basic principles of thermal lens spectrometry (TLS) and its miniaturised version - the thermal lens microscopy (TLM) as fast screening methods providing high sensitivity are further explained, and their practical applications are reviewed. Furthermore, composite materials have recently been finding applications in water treatment technologies, as filter materials, adsorptives for pollutants, catalysts for degradation reactions, and disinfectants. The applications of three main types of composites: synthetic composites, biocomposites, and nanocomposites, are also reviewed within this chapter. The core of this dissertation is presented in the fourth and the fifth chapter, which examine two separate approaches for water treatment, as well as analytical methods for fast screening purposes. The fourth chapter is investigating options for degradation of iodinated X-ray agents (ICAs), namely diatrizoate, through biodegradation with extracellular enzymes of white rot fungus Dichomitus squalens, and chemical oxidation with manganese(III) acetate. Enzymatic degradation with laccase (Lac) and manganese peroxidase (MnP) at low enzymatic activities was unsuccessful, whereas at approximately 3-times higher activities the enzymes were capable of 60 % degradation in 12 days. Chemical oxidation of diatrizoate with manganese(III) acetate resulted in 85 % degradation in 12 days. Moreover, the suitability of microfluidic flow injection analysis coupled with thermal lens microscopy (μFIA-TLM) as a fast screening method for diatrizoate degradation was examined. The degradation was monitored through the release of iodide from the diatrizoate molecule. μFIA-TLM proved to be a preferable method over UV-Vis spectrophotometry, due to its higher sensitivity, sample throughput, and simple sample handling. Limit of detection (LOD) for μFIA-TLM method was estimated to be 0.14 µM in a 100 µm channel, which is 9 times lower than LOD obtained in UV-Vis measurements. In addition to μFIA-TLM and UV-VIS, high-pressure liquid chromatography (HPLC) was used to monitor the remaining parent compound in the reaction mix. In the fifth chapter, the second water treatment approach is described. This includes synthesis of biocomposite materials from cellulose (CEL) and keratin (KER), with metal (Ag0, AgCl, Au0) nanoparticles (NPs). Materials were characterised for presence, species, and size of NPs with X-ray diffraction (XRD) and with scanning electron microscopy (SEM). Nanoparticles were confirmed to be of expected species, with sizes as follows: 6.3 ± 0.5 nm for Au NPs, 12 ± 2 nm for Ag NPs, and 22 ± 1 nm for AgCl NPs. In order to evaluate antibacterial properties of the materials, contact tests with gram-negative (Escherichia coli and Pseudomonas aeruginosa) and gram-positive bacteria (Staphylococcus aureus, Methicillin-resistant S. aureus (MRSA), and Vancomycin-resistant Enterococcus faecalis (VRE)) were conducted. Direct-contact assay over 24 hours showed a dose and species-dependent antibacterial activity of [CEL:KER + Ag NPs] materials. The highest potency against the selected bacteria (up to 6-log of reduction) was observed for the material with 500 mg of Ag NPs. AgCl NPs appeared to be less potent than Ag NPs, whereas Au NPs exhibited antibacterial activity only against MRSA and VRE. In addition, antiviral properties of materials were investigated on selected bacteriophages (MS2, phiX174, and fr). However, biocomposite materials with 500 mg of Ag NPs and AgCl NPs, as well as, 240 mg of Au NPs did not exhibit any activity against selected bacteriophages. Biocompatibility with human fibroblasts was evaluated through a direct contact assay for 3 and 7 days of exposure. High concentrations of metal NPs turned out to be cytotoxic for human fibroblasts, whereas the amount of 69 mg of Ag NPs in [CEL:KER] was low enough not to affect the viability of the fibroblasts after 3 days of exposure. Composites with Ag NPs and AgCl NPs were also tested for leachability of NPs out of the materials. Both types of NPs were leaching out in two different forms, as silver ions, and as colloidal silver. Leaching of ionic silver from both materials stabilised after 3 days, whereas colloidal silver was still leaching out on the 7th day. The overall percentage of the total silver (ionic + colloidal) leached was only 0.04 % of silver incorporated in the material. In summary, this dissertation investigates alternative approaches for water treatment technologies, which could potentially serve as unit improvements of existing technologies, or as on-point pre-treatment technologies to facilitate further conventional water treatment techniques. It also demonstrates the suitability of μFIA-TLM for fast screening measurements in aquatic samples, offering high sample throughput, simple handling of the samples and superior sensitivity over the UV-Vis spectrophotometry.
Ključne besede: Antibacterial biocomposites, nanomaterials, water treatment technologies, multidrug-resistant bacteria, iodinated contrast agents, thermal lens microscopy, flow-injection analysis, microfluidics
Objavljeno: 26.04.2017; Ogledov: 577; Prenosov: 15
.pdf Polno besedilo (27,08 MB)

7.
8.
Novel methods for detection of bioactive substances and their effects in organisms and in the environment
Tatjana Radovanović, doktorska disertacija

Opis: Since the concentration of bioactive substances and infectious agents in organisms and in the environment are low highly sensitive techniques such as: chromatography technology coupled with mass spectrometry (GC/MS, LC/MS and LC–MS/MS) and transmission electron microscopy (TEM) are needed for their detection. These techniques are highly sensitive, but time consuming, requiring use of expensive apparatus and large quantities of reagents and organic solvents which are harmful for the environment. Because there is a growing need for analysis of a large number of environmental samples it is necessary to develop new, so called vanguard methods that enable rapid and reliable screening of large numbers of samples in the shortest possible time. Analysis with such “screening” methods are often less accurate or even semi-quantitative, but nevertheless allow reliable identification of nonproblematic samples and in practice they limit the use of demanding classical analytical methods to only a few percent of all the samples. Therefore, general objectives of the thesis were development of novel methods for sensitive, fast and cost effective detection of pharmaceuticals, viruses and viral particles in waters and biological fluids and for detection of their effects in organisms. Novel methods were based on the combination of TLS (Thermal Lens Spectrometry), microfluidics and immunological methods such as ELISA. TLS as highly sensitive technique (allowing detection of absorbances of less than 10-6) coupled with microfluidic technology allows detection of very low analyte concentration, shorter time for analysis, higher sample throughput and low consumption of reagents. In such combination microfluidic technology can simplify or speed up antigen-antibody or enzyme-substrate interactions in bioanalytical systems. Decisive advantage of microfluidic systems lies in the fact that small dimensions of such systems, composed of capillaries and micro-reactors with dimensions from about 10 to 100 µm, significantly reduce diffusion time, which is inversely proportional to second power of distance. However, highly sensitive detection techniques are needed in microfludic systems, because the amounts of analytes in detection volumes are generally small and optical interaction lengths are two to three orders of magnitude shorter than in conventional spectrometric techniques. By combining microscopic TLS (TLM) with microfluidic technique it is possible to reach very low limits of detection and at the same time shorten ELISA analysis time from 20 h to 20 minutes as was described before in the literature for detection of BNP (brain natriuretic peptide). TLM furthermore allows measurements of extremely small volumes (sub-microliter) as well as fast signal response (milliseconds). In this Dissertation specific goals were the development of new methods for detection of selected bioactive substances and infectious agents: -iodinated contrast agents -NGAL (neutrophil gelatinase associated lipocalin) as a new biomarker of contrast induced nephropathy (CIN) -antibodies against human papilloma viruses (HPV) viruses and HPV-16 pseudovirions. For the development of new method for detection of iodinated contrast agents chemical degradation of iodinated contrast agents was investigated as well, as a potential method for their removal from waste water. For the determination of NGAL, a commercially available ELISA kit was used as the basis for method development. In the initial experiments the final product of the reaction of substrate with enzyme HRP (horse radish peroxidase) was transferred from microtiter plate into a microfluidic system, which served just for the sample transport to TLM detector on microchip. With comparable speed analysis we achieved LOD of 1.4 pg/mL which is 7 times lower in comparison to commercial ELISA test (LOD=10 pg/mL). For further development of the method for detection of NGAL with µFIA-TLM magnetic nanobeads were used as a solid support for primary antibodies of ELISA assay. By applying appropriate magnetic field the antibodies were kept in microfluidic system, which also enabled binding of NGAL, secondary antibodies and reaction of substrate with HRP. Developed method for NGAL detection with LOD of 2.3 pg/mL compares favorably with LOD for commercial ELISA tests (10 pg/mL) in standard microtiter plates and significantly reduces the analysis time. TLM in combination with microchip for NGAL detection reduces the duration of individual incubation steps (from one hour to 5 minutes) and at the same time shortens total analysis time from four hours for commercial ELISA test to 35 minutes allowing higher sample throughput. Analysis of real blood samples was also performed and it has shown good agreement between NGAL concentrations measured by magnetic nanobeads based µFIA-TLM with the concentrations measured by a commercial ELISA test. Such short analysis time of analysis and possible further optimizations are opening new possibilities for application of µFIA-TLM in medical diagnostics and clinical research. By using appropriate antibodies the method for developed NGAL detection could be easily adopted for detection of different pharmaceuticals or pollutants in environmental samples. We have also developed a magnetic nanobeads based ELISA assay for detection of anti-HPV-16 L1 antibodies in the sera of HPV-16 infected women. To ensure the selectivity, HPV-16 pseudovirions were used as an antigen for anti-HPV-16 L1 antibodies, which were detected with secondary HRP labeled antibodies. Initially the ELISA assay for antibodies against HPV pseudovirions was performed on a microtiter plate and an LOD of 3.8 ng/mL was achieved by measurement on a microtiter plate reader. When performing a µFIA-TLM measurement of the final ELISA solution the LOD was reduced to 0.9 ng/mL. Similar to the method for NGAL detection based on magnetic nanobeads, these were used as solid support for HPV pseudovirions and after carrying out all the incubation steps of the ELISA test in microfluidic chip the final product of the reaction of substrate with HRP was detected on TLM. With magnetic nanobeads based ELISA assay with µFIA-TLM for measurement of antibodies against PsVs of HPV-16 virus an LOD of 0.6 ng/mL was achieved, which is six times lower in comparison to classic ELISA on microtiter plate. Furthermore, the analysis time was reduced from ten hours to 30 minutes. The novel method was successfully validated by analysis of real sera samples from women who were previously diagnosed for infection with HPV-16 virus. For determination of iodinated MRI contrast agents we developed a new method based on the measurement of concentration of released iodide which allows indirectly semi-quantitative detection of concentration of iodinated contrast agents. For iodide release from parent molecule of contrast agent we applied a chemical reaction with Cu2+ ions in the presence of H2O2. Released iodide was first oxidized into iodine and then extracted into chloroform. Contrast agents degradation reaction showed 70 % of efficiency for removal of iomeprol, taking into account the 60 % overall efficiency of iodide oxidation and extraction. The extract was injected into microfluidic chip and iodine concentration was determined with TLM. Chloroform as organic solvent with low thermal conductivity and high temperature coefficient of refractive index is a good choice for TLM measurement due to high TLS enhancement factor, which theoretically provides 40 times higher sensitivity of TLM measurements as compared to water and a four time improvement in sensitivity for each milliwatts of excitation power, when compared to spectrophotometry. The developed µFIA-TLM method for indirect determination of contrast agents based on detection of iodine provides around 60 times lower LOD, with low reagent and sample consumption in comparison to spectrophotometry. The LOD of 18 ng/mL for iomeprol achieved with TLM is 16 times lower in comparison to LOD of 294 ng/mL for iomeprol determination with HPLC. In comparison to LOD of 133 ng/mL for iomeprol achieved with detection of released iodide by ion chromatography, µFIA-TLM enables around 7 times lower LOD. HPLC and HPLC/MS analysis showed that the parent compounds is completely removed after 120 min. of chemical degradation and that different degradation products are formed by cleavage of one or two iodine atoms. By this we have shown that the applied chemical degradation is efficient for removal of iomeprol and could be applied for treatment of waste waters after further optimization and reduction of reaction time. New analytical methods developed within this work provide limits of detection for the selected compounds which are significantly lower (up to 60 times) in comparison to conventional analytical techniques based on transmission mode measurements. At the same time the new methods allows shorter time of analysis and higher sample throughput for the purpose of fast screening methods. Magnetic nanobeads based µFIA-TLM ELISA assays developed within this work offer several advantages in comparison to commercial ELISA tests on microtiter plates such as: higher surface for antibody binding, lower reagent consumption, and shorter analysis time. Although the TLS technique didn’t reach appropriate stage of development and applicability for routine chemical analysis, improved methods for detection of NGAL and antibodies against HPV viruses could be applied for clinical studies and development of commercial tests for detection of viruses or other bioactive substances, which are needed for diagnostic purposes in hospitals.
Ključne besede: ELISA, NGAL, PsVs, kontrastna sredstva, TLM
Objavljeno: 02.02.2017; Ogledov: 527; Prenosov: 47
.pdf Polno besedilo (4,66 MB)

9.
DEVELOPMENT OF AN ANIMAL MODEL TO STUDY THE ROLE OF THE PHOSPHATASE PTPN22 IN THE PATHOGENESIS OF CHRONIC LYMPHOCYTIC LEUKEMIA
Öznur Özlem Ibrahimoğlu, 2016, doktorska disertacija

Opis: A polymorphic variant of the phosphatase PTPN22 has recently emerged as a major risk factor for the development of multiple autoimmune diseases. The mechanism how this variant increases the susceptibility for autoimmune diseases is still unclear. A recent study by our lab showed that PTPN22 is markedly overexpressed in chronic lymphocytic leukemia (CLL), which is a common lymphoid malignancy characterized by the clonal outgrowth of autoreactive B lymphocytes. This study also showed that PTPN22 functions primarily as a negative regulator of B cell receptor (BCR) signaling, but can also positively affect the activity of certain downstream signaling pathways. To understand the role of PTPN22 in the pathogenesis of CLL, we investigated PTPN22 expression in leukemias that develop in the Eµ-TCL1 transgenic mouse model. We observed that PTPN22 is highly overexpressed in these leukemias. We also evaluated expression of PTPN22 in normal murine B cell subsets corresponding to different stages of B cell development and differentiation. We detected high PTPN22 expression in B1 B cells, which are the normal counterparts of CLL B cells, and lower levels in marginal zone B cells, whereas PTPN22 was not expressed or was expressed at extremely low levels in most of the other investigated B cell subsets.We generated knockout mice with targeted disruption of PTPN22. We showed that PTPN22 is not expressed by any B cell subset in PTPN22-/- mice, including B1 B cells. To investigate the impact of PTPN22 deficiency on B1 and marginal zone B cell development and function, we performed immunophenotyping analysis of bone marrow, spleen and peritoneal cavity B cells from a large series of PTPN22-/- and age-matched wild type mice. A small but appreciable reduction in the percentage of marginal zone B cells and an increase in the percentage of B1 B cells in older PTPN22-/- mice was observed. These changes were consistent with the increased levels of natural antibodies typically produced by B1 B cells and lower levels of antibodies typically produced by marginal zone B cells in PTPN22 deficient mice. Altogether, these data suggest that PTPN22 deficiency results in reduced marginal zone and increased B1 B cell immune responses. Importantly, this phenotype is remarkably similar to the phenotype of SHP1-/- mice, although considerably milder. Since SHP1 is the main negative regulator of proximal BCR signaling in B cells, these findings suggest that one important function of PTPN22 could be to provide additional fine-tuning of the intensity of the BCR signal in B1 and marginal zone B cells. In support of this possibility, a modest but consistent increase in anti-IgM-induced calcium mobilization was observed in B1 B cells from PTPN22-deficient compared to wild type mice.To see how PTPN22 deficiency will affect leukemia development and behavior, we crossed PTPN22 knockout mice with E-TCL1 transgenic mice. PTPN22 deficiency accelerated the expansion of the malignant B cells in this model and resulted in earlier leukemia development in comparison to wild type E-TCL1 transgenic mice. These data are consistent with other recent studies from our group showing that a greater capacity to activate downstream signaling pathways upon engagement of the BCR with external ligand is associated with more rapid disease progression in both human CLL and the E-TCL1 model. In conclusion, we show that PTPN22 is equally overexpressed in normal and leukemic B1 B cells derived from E-TCL1 transgenic mice, suggesting that PTPN22 overexpression is not due to the transforming event, at least in the case of murine CLL. The greater BCR signaling capacity of B1 B cells and the accelerated leukemia development in PTPN22-deficient mice further argues for an important role of BCR signals in determining the aggressiveness of CLL.
Ključne besede: PTPN22, BCR signalling, B1 B cells, marginal zone B cells, chronic lymphocytic leukemia (CLL), autoimmunity.
Objavljeno: 31.01.2017; Ogledov: 254; Prenosov: 25
.pdf Polno besedilo (2,95 MB)

10.
Geomorphological characteristics of karst on contact between limestone and dolomite in Slovenia
Petra Gostinčar, 2016, doktorska disertacija

Opis: Contact karst is a type of karst formed where allogenic waters from the surface influence the karst geomorphic system. Contact karst may be considered in both a strict sense and in a wide sense. In a strict sense, contact karst is the karst phenomena and forms influenced by the contact between a karstifiable rock and a non-karstifiable rock. In a wide sense, contact karst may also be the karst phenomena and forms influenced by the contact between two different karstifiable rocks, for example limestone and dolomite. This thesis focuses on the geomorphological characteristics of contact karst on limestone-dolomite contacts in Slovenia. The purpose of the research was to determine which processes contribute to the development of contact karst on the contact between limestone and dolomite, to define their dynamics, and to identify which surface and underground landforms are developed. The spatial distribution of contacts between limestone and dolomite in Slovenia was determined in a GIS. Using existing lithological data as a data layer, the extent of carbonate rock cover in Slovenia was calculated. Carbonate rocks cover 47 % of Slovenia’s territory (27 % limestone, 14 % dolomite, and 6 % clastic carbonate or impure carbonate rocks). And, there are 1,353 limestone-dolomite contact lines in the country, totalling a length of 2,625 km. Study areas were selected based on GIS analysis of the limestone-dolomite contacts. A total of 17 areas in Slovenia were studied in detail. Fieldwork at the study areas consisted of the collection and analysis of rock, sediment, and water samples, allowing each study area to be geomorphologically mapped. General factors contributing to contact karst development on the lithological contact between limestone and dolomite were determined. The most important factor appears to be the characteristics of the inflow part, formed on the dolomite. Where dolomite functions as a karst rock, the water is dispersedly drained into the karst. In that case, the limestone-dolomite contact does not function as contact karst. Alternatively, where the dolomite functions as fluviokarst, a point recharge, or sinking stream, is formed. In that case, contact karst may be formed. The fluviokarstic character of the dolomite depends on its chemical and mechanical properties. The dolomite bedrock must be positioned at a higher elevation than the neighbouring limestone bedrock. To meet this requirement, dolomite beds, which in Slovenia are generally older than limestone and hence stratigraphically positioned below the limestone beds, need to be positioned above limestone by either folding that leads to inverse stratification, overthrusting, or by displacement along faults. Along faults, the dolomite is more prone to mechanical weathering due to tectonic crushing in addition to its chemical properties. Hence, contact karst is more likely to form at thrust contacts between thrust limestone and dolomite. Limestone-dolomite contact karst develops predominately at higher elevations due to increased precipitation (where allogenic inflow is higher) and greater frost action due to lower temperatures. Intense mechanical weathering of dolomite over limestone directly affects contact karst processes and significantly contributes to the spatial distribution of these types of surfaces. The location of the water table close to the surface is also a leading factor in limestone-dolomite contact karst formation due to enhanced border corrosion. Landforms typical of contact karst were identified in the study areas during geomorphological analyses. However, they are not as clearly recognizable as those on contact between carbonate and non-carbonate rocks. The reason for this is the fact that allogenic waters from dolomitic catchment areas are by far not as corrosive as those from non-carbonate catchment areas.
Ključne besede: carbonate rocks, dolomite, limestone, contact karst, allogenic water, karst geomorphology
Objavljeno: 19.12.2016; Ogledov: 711; Prenosov: 38
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