RAPID UPLC-ESI-MS/MS BASED ASSAY FOR DISCOVERY OF UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE (MurD) LIGASE INHIBITORSVjekoslava Car
, 2016, magistrsko delo
Opis: A rapid, selective, robust and sensitive analytical assay method, operating in a short time frame with acceptable levels of precision, linear range and the accuracy necessary for successful Mur ligases inhibitors discovery, was developed.
An LC-MS/MS analytical procedure was designed for the determination of a MurD ligase reaction product (UMAG). The special focus of this work was on UDP-N-acetylmuramyl-L-alanine:D-glutamate ligase (MurD) activity. The assay method is especially valuable as an orthogonal (secondary) assay for the primary high throughput fluorescent-based assay screening of potential Mur ligase inhibitors. The LC-MS/MS assay is fully compatible with the components from the primary fluorescent-based assay and enables the analysis of the same samples by both methodologies. The presented LC-MS/MS assay procedure is used for the evaluation of the false positive hits (molecules) from the primary, fluorescence based, high throughput screening assay experiments. This is important for the elimination of false positive hits from the prohibitively expensive and time-consuming investigation process.
Method development describes the evaluation and optimization of the various stages of sample preparation, chromatographic separation, MS/MS determination and quantification. An enzyme reaction is performed in a 96-well plate. The quenched reaction mixture samples were spiked with an internal standard (phenacetin). The permeate was injected onto the U(H)PLC-MS/MS triple quadrupole system after sample ultrafiltration. Chromatographic separation was achieved on the ACQUITY UPLCTM HSS T3 column (100 x 2.1 mm i.d., 1.8 µm particle size) using an ammonium format buffer at pH 2.8 and acetonitrile as eluent. Elution initiated with an isocratic-hold for 1.1 min, followed by a two-step linear gradient of up to 3 min, giving a total run time of 5 min including equilibration. The flow rate was kept at a constant 0.4 mL/min.
UMAG quantitative analysis was performed by positive electrospray ionization, followed by tandem mass spectrometry (ESI-MS/MS). The analytical assay quantifies UMAG in a linear range from 0.25 to 20 µM using 70 µL of samples. Validation results demonstrated that UMAG concentrations can be accurately and precisely determined in samples from the primary assay.
Evaluation of inhibitory activities of compounds measured by both the fluorescence and the LC-MS/MS method demonstrated that the values were in a very good agreement. This analytical method can be used to screen a compound library at a defined concentration of each compound to obtain the percentage of inhibition, or with a series of compound concentrations to obtain inhibition potency of a compound (IC50). The selected Lek compounds no. 1 and 2 from the virtual screening campaign were presented, tested and further investigated due to the expression of significant MurD ligase inhibitory action acquired by primary high throughput tests.
This assay has been developed for MurD, but during development, chromatographic and MS/MS conditions for UM and UMA were studied and defined as well. Therefore, this analytical assay method can easily be applied to other Mur ligases (i.e. MurC, MurE) enzyme activity monitoring in the process of bacteria cell wall peptidoglycan formation. This method enables the identification of many different Mur ligase inhibitors in a continued search for new Gram positive and Gram negative bacteria antibiotics.
Ključne besede: Mur ligases, UDP-N-acetylmuramyl-L-alanine:D-glutamate (MurD) inhibitors, UNAM-Ala-Glu, LC-MS/MS, liquid chromatography, tandem mass spectrometry, antibiotics, drug discovery
Objavljeno: 23.09.2016; Ogledov: 2679; Prenosov: 153
Polno besedilo (2,62 MB)
FLOODPLAIN FORESTS OF SOČA RIVER BETWEEN KOBARID AND CONFLUENCE WITH RIVER TOLMINKA: CURRENT SITUATION AND DEVELOPMENTJanez Pagon
, 2016, magistrsko delo
Opis: In its upper course the Soča River is one of the best preserved Alpine rivers. Despite that, there have been few studies of its riverine forests, which are an integral part of the river. The research in this thesis encompasses part of the river basin between the towns of Kobarid and the confluence with the Tolminka River. It was found that the riverine forests in the study area are not a homogeneous habitat. Rather, they consist of numerous phytosociological communities with a syn-dynamic connection. The majority of riverine forests in the study area is younger than 50 years old and were established either by the overgrowing of agricultural land or from degraded forests. Accordingly, the forest structure is characterised mainly by uneven-aged stands or younger structural stages, which are frequently returned to their earlier stages due to human impacts. The majority of these forests have low quality prospects. Based on their vegetation and stand characteristics, the riverine forests under study were classified into six stand types. A comparison of the functions and characteristics of particular forest types revealed similarities between the stand types of initial willow, white willow and grey alder. Forests in this cluster are under the influence of soil water and high floodwaters. Their most pronounced function is ecological. In their growing stock, there is a large share of deciduous softwood. Forests in this cluster cover 62% of all riverine forests in the study area. Silvicultural measures are rare in these forests and are less important for the existence of the stands than environmental features like a high level of soil water and minimised human impact on their habitat and the river course. An important characteristic of the second cluster, which consists of pioneer forest on higher-lying river terraces and the riparian corridor stand type is a lack of contact with soil water. In the tree layer of the growing stock in this cluster, species appearing on drier riverine-forest sites prevail (European ash, small-leaved lime, European hornbeam, sessile oak). These forest stands have a greater timber industry potential; therefore, modest measures and limited human impact (especially that which leads to a change in land use like forest grazing and clearing) are recommended. The stands in this cluster cover 30% of the analysed riverine forest area. The third cluster of riverine forests consists of anthropogenic riverine forest stands where the human impact is so significant that they mainly perform a social function. The stand type of this cluster represents 8% of the riverine forests in the study area, and it is suggested that they should be managed as parkland and not as forest areas. Directing visitors to these areas would unburden other, more preserved stand types from the pressures created by human activities (tourism, recreation, construction work). Growth and increment analyses of the most common tree species in the riverine forests in the study area show that mainly olive and white willow, followed by grey alder, have substantial current height (both willow types up to 1.14 m/year), diametric (willow up to 1.4 cm/year) and volumetric increments. However, their rapid growth makes these subjects prone to rapid ageing. The region of northern Primorska was inhabited early in history. Accordingly, there was great pressure imposed on riverine forests already in the past. The analysis of old maps revealed that up to the beginning of the 20th century, the riverine forest area within the scope of analysis was under 50 ha. Within the process of the overgrowing of agricultural land in Slovenia, a process that is currently still underway, the aforementioned riverine forest area increased to 229.16 ha. This thesis shows that the study area is not an unspoiled wilderness. On contrary, just as in the past, it is a crossroads of numerous and frequently conflicting interests. The riverine forest situation on the Soča River in the area b
Ključne besede: the Soča river, riverine forests, successional stage, forest stand
Objavljeno: 20.09.2016; Ogledov: 2131; Prenosov: 30
Polno besedilo (8,00 MB)
Time restrictions in forest operations planningBoštjan Kepic
, 2016, magistrsko delo
Opis: This master’s thesis deals with annual harvest operations (AHO) planning with consideration of time restrictions. We developed five models of binary integer linear programming (BILP) that schedule working groups to harvest unit areas (HUAs) according to the lowest cost possible. Total AHO costs include felling and skidding costs, transportation costs, and machine relocation costs. The first model is based on the presumption that harvesting can be planned and executed freely throughout the year. In other four, scheduling was subject to time restrictions in HUAs and differed according to the extent of time restrictions. The second model takes into account time restrictions due to unfavourable natural conditions, the third model due to disturbance-free areas of animal species, the fourth and fifth model concurrently include the impact of time restrictions due to natural conditions and disturbance-free areas. The annual workplace time in Model 2 is reduced by 14.2 %, in Model 3 by 16.9 %, in Model 4 by 29.3 % and in Model 5 by 42.3 %. The model tool used to test all the models was designed in Microsoft Excel. All five models were tested with OpenSolver 2.7.1 software. Increasing the extent of time restrictions in forest operations reduces the utilization of the annual workplace time. In testing the second model, we demonstrated that with proper organisation of an AHO plan the planner can influence the working days fallout. In the other three models, we were able to ensure the implementation of AHO plan by introducing extra working groups. Further, we confirmed that time restrictions affect the scheduling of the working groups and the sequencing of tasks. The increases in total AHO costs were explained as an increase in working groups’ costs due to lower utilization rate, an increase in depreciation costs of machines and costs due to unrealized allowable annual cut and timber sales planned for the current year. We tested each model on two examples.
Ključne besede: time restrictions, binary integer programming, forestry, annual harvest operations planning, harvesting, scheduling working teams
Objavljeno: 20.09.2016; Ogledov: 2241; Prenosov: 132
Polno besedilo (4,11 MB)
Birokratski stil v srbskem in slovenskem časopisju v času socializmaJelena Budimirović
, 2016, magistrsko delo
Opis: Glavni namen birokratskega stila ni komunikativen, temveč ritualno-ideološki. Takšen stil služi kot sredstvo jezikovne manipulacije in birokratom zagotavlja monopol pri političnem odločanju. Birokratski stil je v srbščini razcvet doživel v socializmu, v slovenščini pa se je razvijal pod vplivom srbščine. V tej nalogi analiziramo jezik srbskega časopisa Borba, oziroma slovenskih časopisov Ljudska pravica in Delo v času socializma, in sicer skozi dve obdobji – obdobje začetka socialističnega sistema v Jugoslaviji (1944–1947) ter poznejše obdobje, v katerem je imel socializem v Jugoslaviji za seboj že več desetletij (1974–1979). Za jezik prvega obdobja so značilni enostavnost, ideološkost in čustvenost. Za stil drugega obdobja je opazna izjemno močna birokratiziranost novinarskega stila, in smo ga zato analizirali glede na klasifikacijo značilnosti birokratskega stila: nominalnost, splošnost, nedoločenost, eksplicitnost, evfemizmi, presežek besed, kvaziznanstvenost in uporaba besed tujega izvora. Analiza opisuje slovnična in leksična sredstva birokratizacije in razlaga njihove učinke v sociolingvističnem kontekstu.
Ključne besede: birokratski stil, socializem, Borba, Ljudska pravica, Delo, manipulacija
Objavljeno: 19.09.2016; Ogledov: 1872; Prenosov: 26
Polno besedilo (7,29 MB)
STREET CHILDREN IN NIŠ (SERBIA): THE CASE OF DROP IN CENTRE FOR THE MOST AT RISK ADOLESCENTS (MARA)Miodrag Đorđević
, 2016, magistrsko delo
Opis: In 2009, a Drop in centre for street children - MARA was established in Niš,
Serbia. The purpose of the project was to provide health protection of adolescents,
who lived in structural disadvantages, was exposed to the risk of HIV, and who have
not been addressed by the institutional social care system.
Once on the streets, children have difficulty meeting their basic needs such as
obtaining food, clothes or shelter. Therefore, they employ a range of survival
strategies. Begging, car washing, collecting secondary resources, borrowing money,
and dealing drugs are common ways how to provide subsistence. Perhaps the most
dangerous survival strategy pertains to exchanging sex services for food or money.
Drug and alcohol use are common practices among street children.
The main goal of this thesis was to obtain new knowledge about these young
people in order to achieve a better understanding of their behaviours in the
framework of social marginalization, their coping strategies and their own
contributions to social exclusion. To provide better social, health and educational
services for street children in Niš a qualitative approach is necessary to understand
their survival strategies and their several needs as the persons at risk in certain social
The main approach was ethnography encompassing participant observation
during the fieldwork in Drop in centre in Niš. Following methods were employed:
Review of the scientific literature on the issue and analytical reading; Review and analysis of existing documents and
archive materials: UN/NGO/Government documents, and the documentation on the
projects from Drop in centre; Participant observation in the group of MARA; Semistructured
interviews with MARA; An ethnographic diary and ethnographic
fieldnotes of fieldwork in the Drop in centre in Niš.
This thesis was focused on the following research questions: What is the
relationship between social stereotypes about MARA and MARA’s behaviour? Are
the stereotypes affecting MARA’s identities, behaviour and appearance or vice
versa? How do MARA act within their several environments? How MARA relate to
each other? How “street groups” influence MARA’s risky behaviour? What are
interactions within these groups? What are the commonly shared values among the
members of the groups? My research will explore more in detail common values in
the groups of drug users and sex workers. How MARA understand the risk of drug
use and commercial sex? What is the social context of risk perception? Do they have
any ideas how to prevent the risk? Did they have any concepts about the risk? And
how their concept coincides with the mainstream, project concepts?
Discussing all above research questions, the main expected result refers to
obtaining new knowledge in order to find better solution to their problems compared
to existing practices and understandings by several actors. Therefore,
this work will fight against poorly informed images and understandings of
adolescent Roma and street children, which are as a rule seen and understood within
ideological, commonsensical, racial and stereotypical considerations.
Roma studies have little academic research on at risk adolescent children,
especially in the Western Balkans.
The originality of this study is related to the unique material collected in the
ethnography through participant observation and fieldwork with appropriate
techniques of data collection with adolescent street children in Niš. The study was
carried out on the territory of former Socialist Yugoslavia, in Central Serbia, Niš. No
similar studies on structural inequality, marginality and Roma has been conducted in
Finally,concepts of structural inequality, marginality, street children, which
have been coined and developed by several authors in the contexof the Western
capitalist system, will be now reflected in the context of transition and postsocialist
radical social changes.
Ključne besede: Roma, marginality, childhood, street children, risky behaviour, stereotypes
Objavljeno: 16.09.2016; Ogledov: 1792; Prenosov: 133
Polno besedilo (657,26 KB)
PREPARATION AND CHARACTERIZATION OF HIGHLY PHOTOACTIVE COATINGS ON GLASS SUPPORTS FOR DEGRADATION OF PHARMACEUTICAL SUBSTANCE PARACETAMOL IN WATERLidija Sinovčić
, 2016, magistrsko delo
Opis: Pharmaceuticals in aquatic environment are considered as emerging environmental contaminants due to their constant presence, evironmental resistance and toxic effect they could have on aquatic organisms. Studies for Slovenia have shown the presence of pharmaceutical substances in waters to be comparable with published results of pharmaceutical water pollution in Europe. As conventional methods do not reach efficient pharmaceutical removal from water sources, more powerful and effective methods like heterogeneous photocatalysis using TiO2/UV have been implemented. Titanium dioxide coatings in silicate binder were prepared by the sol-gel process and deposited on a glass support with dip-coating technique. The films showed good quality and possibility of multiple use. The characterization of the films was performed with scanning electron microscope (SEM), x-ray diffraction (XRD) and hardness test (Elcometer 501 Pencil Hardness Tester). Effectiveness and quality of prepared TiO2 coatings for photodegradation of pharmaceutical compound paracetamol (PCT) were assessed during photocatalytic treatment and compared to photolysis, a process without presence of a catalyst. Photolysis caused substantial changes in paracetamol concentration between 120 and 180 minutes of irradiation where 92% of degradation was achieved, but with no changes in mineralization. Photocatalytic treatment was much faster and effective where 95% of paracetamol degraded within 90 minutes of UV irradiation and after prolonged irradiation time from 120 to 240 minutes also mineralization of paracetamol solution increased from 59% to 83%. Accordingly, toxicity decreased, but it was still not lower than in the starting PCT solution as it was shown by acute toxicity test on Daphnia magna aquatic organisms. The master thesis represents a step forward in studying photocatalytic removal of paracetamol from water, because to my knowledge all the published investigations on this pharmaceutical up to now include photocatalyst mostly in powder and not in immobilized form, which is more advantageous from application point of view.
Ključne besede: Pharmaceuticals, paracetamol, titanium dioxide, photocatalytic degradation, Daphnia magna.
Objavljeno: 14.09.2016; Ogledov: 2635; Prenosov: 155
Polno besedilo (2,50 MB)
Kontrabantka. Njene poti s koščkom svobode. Življenje in vloga žensk v Vipavskih brdih prve polovice 20. stoletja.Darja Gorup
, 2016, magistrsko delo
Opis: V magistrski nalogi so predstavljene trgovske poti Gaberk iz Vipavskih brd ter vpliv le-teh na spreminjajočo se družbeno vlogo ženske v družini in vasi. Zaradi specifičnih družbeno-gospodarskih razmer, v katerih so živele, je bilo njihovo življenje kmečke gospodinje vse prej kot vpeto med štiri stene. Igrale so več vlog: bile so matere, žene, vaščanke, trgovke oziroma brangerce, kontrabantke in migrantke. Brangerca je ženska, ki je na razne nelegalne ali pollegalne načine nosila jajca, maslo, sezonsko zelenjavo, maline, meso, žganje in druge pridelke v italijanska mesta, jih tam prodala ali menjala in prinesla domov nekaj denarja ali živil in gospodinjskih potrebščin. Ker je državna oblast brangerski način trgovanja omejevala s plačilom taks in dajatev, predvsem pa je bila obdavčena dobičkonosna trgovina z žganjem in tobakom, so ženske pričele s tihotapljenjem. Tako so iz legalnih brangerc postale kontrabantke oziroma tihotapke, trgovke, ki so skušale priti do svojih strank po skrivnih poteh, predvsem pa z domiselno skritim trgovskim blagom. V iskanju boljših pogojev za življenje so se Gaberke tudi izseljevale v bližnja italijanska mesta.
V uvodu je predstavljen koncept naloge, teze in metodološka izhodišča. Jedrni del vstavi zgodbe brangerc v različne zgodovinske okoliščine (prva svetovna vojna, vinska kriza po postavitvi rapalske meje ter končno postavitev državne meje med Jugoslavijo in Italijo). Na podlagi podatkov, pridobljenih z metodo ustne zgodovine ter ohranjenega arhivskega ter matičnega gradiva, je predstavljeno vsakdanje življenje žensk ter njihove vloge.
V sklepnemu poglavju so zgoščena spoznanja o vrednotenju ženskega dela in vlogah ženske znotraj družine ter vasi. Sklepnemu poglavju sledi seznam literature in virov ter povzetek v angleškem jeziku.
Ključne besede: brangerca, kontrabant, krožne selitve, izseljevanje, Trst, Vipavska brda, rapalska meja
Objavljeno: 14.09.2016; Ogledov: 1788; Prenosov: 134
Polno besedilo (906,06 KB)
About TimeUna Rebić
, 2016, magistrsko delo
Opis: The practical work of my master project about time was carried out as processbased
experiments in practice. As a result, the thesis is a combination of
theoretical research taken from several fields—examining the notion of time from
perspective of psychology, sociology, science and spirituality. Alongside mentioned
research the thesis pairs artistic practices associated with each field discussed—
considering most significant artist and his/her practice or project(s) in which they
explore time. The third layer of the thesis pairs each section with my own personal
practice through experiments carried out in the process—each exploring time from
a different perspective. Since the thesis is the final project of the study developed
within a certain time frame, the last chapter discusses how I approached this
project in regard to my artistic practice.
Ključne besede: time, perception, On Kawara, sociology, speed, Hamish Fulton, quantum
entanglement, arrow of time, Hiroshi Sugimoto, spirituality, consciousness, Marina
Objavljeno: 14.09.2016; Ogledov: 1339; Prenosov: 1
Polno besedilo (8,39 MB)
EVALUATION OF MARINE SEDIMENTS FROM THE PORT OF LUKA KOPER FROM THE ENVIRONMENTAL PERSPECTIVE AND IN TERMS OF THEIR USABILITY IN THE BRICK INDUSTRYPatrik Baksa
, 2016, magistrsko delo
Opis: The majority of the world’s goods are transported over water and dredging is essential for the development of harbors and ports. Therefore, the management of dredged material is a worldwide issue. Due to its chemical and petrographic, mineralogical and homogeneity composition, marine sediments are an appropriate raw material to use in the brick industry. Marine sediments can serve as raw material for the production of clay blocks, roofing and ceramic tiles.
Different analyses were carried out in order to determine if the dredged material from the Port of Koper is environmentally friendly and suitable to use in the brick industry. These analyses included: a chemical analysis, a mineralogical analysis, a particle size analysis and a chloride content (Cl-) analysis, and tests of firing in a gradient furnace. Furthermore, tests of mechanical properties, as well as tests of frost-resistance of the samples were carried out.
On the basis of primary analyses and samples prepared in a lab, it was established that marine sediments from the Port of Koper without any additives are only conditionally suitable as a source material for producing brick products. In collaboration with Gorica brickworks (Goriške opekarne), a pilot production from a mixture of 60% component B from Gorica brickworks and 40% component A (marine sediments) from the Port of Koper was prepared. Different tests showed the mixture could be appropriate for brick production.
Ključne besede: marine sediments, recycling, clay bricks, chemical analysis, mechanical properties, brick production.
Objavljeno: 05.09.2016; Ogledov: 1771; Prenosov: 143
Polno besedilo (3,30 MB)
THE STUDY OF OPTIMAL TECHNOLOGICAL PROCEDURES OF INTERNAL PLUMBING SYSTEM DISINFECTION FACILITIES IN USE BY THE SENSITIVE HUMAN POPULATIONSJanez Škarja
, 2016, magistrsko delo
Opis: In a developed world, water is used in a variety of installations and devices for the improvement of life standard. It is important for these elements to be suitably managed and maintained, otherwise they can present a risk to people's health. Although potable water from a public plumbing system coming via the water supply into an internal plumbing system normally is compliant with the regulations, the quality of water in an internal plumbing system often changes – water gets contaminated. There are several types of microorganisms that can grow in water. They carry a great potential for the growth and proliferation of bacteria from the genus Legionella that cause Legionnaires' disease and Pontiac Fever. Even the fact that Legionella infection has for several years been mentioned in the accident insurance conditions of insurance companies in relation to receiving the insurance fee as compensation for bed day, shows the extent and foremost the seriousness of the disease (5–15% mortality rate).
The research part of the master thesis focused mainly on determining the presence of bacteria from the genus Legionella in the water of internal plumbing systems of healthcare facilities. During the entire research period of 8 years, 2,676 samples of cold and hot water were acquired from 23 healthcare facilities.
The main purpose of the research was to determine the efficiency or adequacy of applied approaches, i.e. physical disinfection with heat and chemical disinfection with chlorine, in eliminating or reducing the amount of Legionella present in the water of selected healthcare facilities. Another aim was to evaluate the impact of softening potable water with polyphosphates on the proliferation of certain microorganisms in water, and to determine the by-products of chemical disinfection.
Upon sampling, an organoleptic examination of water (appearance, odour), electrometric measurements of water temperature, and colorimetric measurements of free chlorine concentrations in water were performed. The data for the analysis of Legionella presence were acquired by water sampling and the isolation of bacteria found in the water. In order to acquire laboratory results of specific physical and chemical parameters, ion chromatography, gas chromatography, spectrophotometry, titration, and inductively coupled plasma – mass detector were used.
Although water samples from only two healthcare facilities showed no presence of Legionella, the number of water samples with the presence of Legionella decreased for at least 25% from the beginning to the end of period set. Also, after certain general sanitary and technical measures a noticeable improvement within healthcare facilities after 2008 could be observed. Regarding the initial part of the set period, a more favourable relationship between positive and negative samples, a lower number of samples with highest concentrations of present Legionella, and a higher number of samples with lower concentrations of present Legionella were determined. The research has shown that the existing system of ensuring health-compliant water is fairly efficient; however, the results could be improved additionally by investing more into the preparation and renovation of systems. Due to a limited number of samples, a direct impact of adding polyphosphates to potable water could not be linked to the occurrence of Legionella. None of the samples showed an increased concentration of by-products of potable water disinfection.
In its conclusion, the research has shown that the procedures after overheating and after chlorine disinfection result in a similar success. While filtration proved to be most efficient, from the perspective of Legionella infections the use of medical bathtubs can present a high risk to people's health, therefore such devices should be subject to more frequent maintenance and supervision.
Ključne besede: potable water, internal plumbing system, biofilm, health facilities, disinfection, Legionella
Objavljeno: 05.09.2016; Ogledov: 2108; Prenosov: 138
Polno besedilo (1,70 MB)