Mikrosekundilise luminestsentsi elueaga orgaaniliste sondide iseloomustamine ja rakendamine proteiinkinaaside uurimiseks

Väitekirja elektrooniline versioon ei sisalda publikatsioone.Ensüümid on valgud, mis katalüüsivad biokeemilisi reaktsioone. Ensüümid osalevad signaaliülekande- ja ainevahetusradades, mõjutades seeläbi rakkude arengut ja kasvu ning rakkude reaktsioone keskkonnatingimustele. Ensüümide tavapärasest erinev kolmedimensionaalne struktuur, ensüümi lokalisatsioon ja ensüümi aktiivsus rakkudes võib põhjustada organismi haiguslikke seisundeid. Selleks, et muutusi ensüümide struktuuris, paiknemises ja ensüümide aktiivsuses rakkudes saaks detekteerida juba muutuste varajases arengujärgus, on vaja arendada tundlikke mõõtmismeetodeid. Käesolevas töös uuriti süvitsi ühte võimalikku lähenemist ensüümi-tundlike sondide arendamisele. Uurimistöös kasutati Tartu Ülikooli keemia instituudis välja arendatud fotoluminestsentssonde [ARC-Lum(Fluo) sonde], mille luminestsentsomadused muutuvad oluliselt seondumisel proteiinkinaasidele. Kui proteiinkinaasidele seondunud ARC-Lum(Fluo) sonde ergastada ultravioletse kiirgusega, siis emiteerivad need pikaealist fotoluminestsentskiirgust, mille eluiga jääb mikrosekundilisse suurusjärku. ARC-Lum(Fluo) sondide pikk luminestsentsi eluiga kompleksis proteiinkinaasiga võimaldab kasutada kompleksi detekteerimiseks aegviivitusega mõõtmistehnikaid, mis tagavad pikaealise luminestsentsi selge eristamise bioloogiliste proovide autofluorestsentsist, mille eluiga jääb tavapäraselt nanosekundilisse suurusjärku. Ühtlasi on tagatud mõõtmismeetodi hea signaal-müra suhe ning võimaldatud proteiinkinaaside detektsioon väga väikeses kontsentratsioonis. Käesolevas töös uuriti ARC-Lum(Fluo) sondide fotoluminestsentsi omadusi. Lisaks rakendati ARC-Lum(Fluo) sonde proteiinkinaaside seireks elusates rakkudes aegviivitusega luminestsentsmikroskoopia abil. Uurimistöö tulemusi saab kasutada sarnasel põhimõttel disainitud sondide arendamiseks teistele ensüümidele.Enzymes are proteins that catalyze biochemical reactions. Enzymes participate in signal transduction pathways and metabolic pathways and thereby affect the development and growth of cells and how cells react to environmental stimuli. The abnormal three-dimensional structure, localization and activity of an enzyme in cells may lead to diseases. The early detection of changes in the structure, localization profile and abundance in cells requires the application of sensitive measurement techniques. The current project was conducted to study one possible approach for the design of sensitive probes for enzymes. The probes that were applied for the study [ARC-Lum(Fluo) probes] have been developed in the Institute of Chemistry at the University of Tartu. ARC-Lum(Fluo) probes bind to a group of enzymes that are termed basophilic protein kinases (PKs). Upon binding to a PK ARC-Lum(Fluo) probes possess luminescence decay time in the microsecond range. The high brightness of the probes is achieved by intramolecular Förster resonant energy transfer (FRET) from a low-QY donor phosphor linked to short-lifetime acceptor with high QY. The long-lifetime donor induces slow acceptor decay, which is due to Förster resonant energy transfer (FRET) from the exited triplet state of the donor (3D*) to the singlet state of the acceptor (1A*). The energy is stored in 3D* and released gradually via FRET to the acceptor fluorescent dye, leading to 1A* of the latter and the following light emission from the dye. The long luminescence lifetime of the probes enables the application of time-gated measurement techniques, which effectively separate the microsecond-scale signal from the background fluorescence of biological samples that have mainly nanosecond-scale lifetime. The current study was performed to characterize the photoluminescence properties of ARC-Lum(Fluo) probes and to determine the applicability of the probes for mapping and monitoring the activity of PKs in live cells by time-gated luminescence microscopy. The obtained knowledge can be applied for further improvement of organic probes for analysis of different proteins in biological samples as we have shown to be possible for PKs

The operation of VEGA/CHARA : from the scientific idea to the final products

We describe the data flow in the operation of the VEGA/CHARA instrument. After a brief summary of the main characteristics and scientific objectives of the VEGA instrument, we explain the standard procedure from the scientific idea up to the execution of the observation. Then, we describe the different steps done after the observation, from the raw data to the archives and the final products. Many tools are used and we show how the Virtual Observatory principles have been implemented for the interoperability of these software and databases.Comment: 9 pages, 3 figure

University students reasons for committing academic dishonesty and knowledge about regulations

http://tartu.ester.ee/record=b2694217~S1*es

Lähi-kaugseire meetodite arendamine veekogude seisundi hindamiseks

Väitekirja elektrooniline versioon ei sisalda publikatsioone.Veekogude kvaliteedi hindamine on inimkonnale oluline olnud juba tuhandeid aastaid ja viimastel aastakümnetel on rohkem tähelepanu hakatud pöörama ka veekogude ökoloogilisele seisundile. Euroopas on veekogude kvaliteedi hindamise aluseks kaks dokumenti: Euroopa Liidu Vee Raamdirektiiv ja Euroopa Liidu Merestrateegia Raamdirektiiv. Mõlemad dokumendid sätestavad, et aastaks 2020 tuleb Euroopa Liidu veekogudes saavutada „hea“ seisund. Nende eesmärkide täitmiseks tuleb regulaarselt veekogude seisundit seirata. Kuivõrd kõikidelt veekogudelt veeproovide võtmine ja laboris analüüsimine ei ole võimalik (liigne raha ja tööjõukulu) ning lisaks ei anna sellised proovid ülevaadet veekogu seisundi parameetrite ruumilise jaotuse kohta tuleb appi võtta optilised instrumendid. Lisaks välitöödel kasutatavale optikale on Copernicus programmi raames järgnevatel aastakümnetel kättesaadav ka mitu erinevat satelliiditulemit. Nende tulemite kasutamiseks peab aga pidevalt nende täpsust hindama ja leidma täpsemaid arvutusmeetmeid, mis sobiksid konkreetsete parameetrite hindamiseks. Töö käigus tõestati, et vee optilised omadused, nagu neeldumine ja hajumine, varieeruvad Läänemere rannikuosas rohkem, kui on variatsioon ranniku ja mere keskosa vahel. Lisaks absoluutväärtuste erinevusele tuvastati ka spektraalse kuju muutusi eri piirkondade vahel. Tõestati, et elektromagnetkiirguse lähisinfrapuna piirkonda saab rakendada veekogude seires (tavaliselt eeldatakse, et selles spektripiirkonnas on veest tulev signaal null) ja eriti on see kasulik ohtralt lahustunud orgaanikat sisaldavate järvede seires. Testiti ja pakuti välja sobivaid kaugseire algoritme Läänemere vee kvaliteedi parameetrite hindamiseks. Analüüsiti erinevate spektromeetrite tulemuste varieeruvust ja leiti, et mõõtmisprotokolli korrektsel jälgimisel on erinevate sensorite tulemused küll erinevad, ent seire teostamiseks piisavalt sarnased. Lõpetuseks uuriti, millised on erinevate käsispektromeetrite potentsiaalsed rakendused.Knowing the quality of different waterbodies has been essential for human kind for thousands of years. There are two main European Union’s documents guiding the status assessment of water bodies: Water Framework Directive and Marine Strategy Framework Directive. Both of these documents state that all waterbodies in the European Union have to achieve “good” status by the year 2020. In order to fulfil this requirement, water bodies have to be monitored in regular bases. It is impossible to collect laboratory samples from every waterbody as it would be too expensive and would require many workers and still wouldn’t provide information about the spatial distribution of water quality parameters within each waterbody. Optical instruments can provide data fast and over larger areas and therefore have to be included in the monitoring programs. In addition to devices used at the in situ measurements are several satellite products that are available through Copernicus program for the coming decades. These products must, however, be constantly validated with in situ measurements. Additionally, new calculation methods have to be developed to improve the results precision. During this thesis, the variability of optical properties (like absorption and scattering) was assessed in the Baltic Sea. It was studied how much this variability influences the reflectance signal that reaches water remote sensing instruments. The performance of different set-ups and protocols of field spectrometers to collect reflectance data was assessed. The possibility to use near-infrared part of the spectrum in water remote sensing was investigated. In extreme absorbing lakes this is the only part of radiation providing us information about the water properties, but it proved to be useful also in other waterbodies. The performance of many remote sensing algorithms in retrieving water quality parameters in the Baltic Sea was tested. The possible applications for hand-held spectrometers were investigated

Planet transit and stellar granulation detection with interferometry

Aims. We used realistic three-dimensional (3D) radiative hydrodynamical (RHD) simulations from the Stagger-grid and synthetic images computed with the radiative transfer code Optim3D to provide interferometric observables to extract the signature of stellar granulation and transiting planets. Methods. We computed intensity maps from RHD simulations for twelve interferometric instruments covering wavelengths ranging from optical to infrared. The stellar surface asymmetries in the brightness distribution mostly affect closure phases. We compared the closure phases of the system star with a transiting planet and the star alone and considered the impact of magnetic spots constructing a hypothetical starspots image. Results. All the simulations show departure from the axisymmetric case at all wavelengths. We presented two possible targets (Beta Com and Procyon) and found that departures up to 16 deg can be detected on the 3rd lobe and higher. In particular, MIRC is the most appropriate instrument because it combines good UV coverage and long baselines. Moreover, we explored the impact of convection on interferometric planet signature for three prototypes of planets. It is possible to disentangle the signature of the planet at particular wavelengths (either in the infrared or in the optical) by comparing the closure phases of the star at difference phases of the planetary transit. Conclusions. The detection and characterisation of planets must be based on a comprehensive knowledge of the host star; this includes the detailed study of the stellar surface convection with interferometric techniques. In this context, RHD simulations are crucial to reach this aim. We emphasize that interferometric observations should be pushed at high spatial frequencies by accumulating observations on closure phases at short and long baselines.Comment: accepted in Astronomy and Astrophysics, 13 pages. Some figures have reduced resolution to decrease the size of the output file. Please contact [email protected] to have the high resolution version of the pape

Water-rich basalts at mid-ocean-ridge cold spots

Although water is only present in trace amounts in the suboceanic upper mantle, it is thought to play a significant role in affecting mantle viscosity, melting and the generation of crust at mid-ocean ridges. The concentration of water in oceanic basalts has been observed to stay below 0.2wt%, except for water-rich basalts sampled near hotspots and generated by 'wet' mantle plumes. Here, however, we report unusually high water content in basaltic glasses from a cold region of the mid-ocean-ridge system in the equatorial Atlantic Ocean. These basalts are sodium-rich, having been generated by low degrees of melting of the mantle, and contain unusually high ratios of light versus heavy rare-earth elements, implying the presence of garnet in the melting region. We infer that water-rich basalts from such regions of thermal minima derive from low degrees of 'wet' melting greater than 60 km deep in the mantle, with minor dilution by melts produced by shallower 'dry' melting—a view supported by numerical modelling. We therefore conclude that oceanic basalts are water-rich not only near hotspots, but also at 'cold spots'

Eesti ja Soome põhikooli 9. klassi õpilaste suhtumine spikerdamisse

http://tartu.ester.ee/record=b2555960~S1*es

Post-Mesozoic Rapid Increase of Seawater Mg/Ca due to Enhanced Mantle-Seawater Interaction

The seawater Mg/Ca ratio increased significantly from , 80 Ma to present, as suggested by studies of carbonate veins in oceanic basalts and of fluid inclusions in halite. We show here that reactions of mantle-derived peridotites with seawater along slow spreading mid-ocean ridges contributed to the post-Cretaceous Mg/Ca increase. These reactions can release to modern seawater up to 20% of the yearly Mg river input. However, no significant peridotite-seawater interaction and Mg-release to the ocean occur in fast spreading, East Pacific Rise-type ridges. The Mesozoic Pangean superocean implies a hot fast spreading ridge system. This prevented peridotite-seawater interaction and Mg release to the Mesozoic ocean, but favored hydrothermal Mg capture and Ca release by the basaltic crust, resulting in a low seawater Mg/Ca ratio. Continent dispersal and development of slow spreading ridges allowed Mg release to the ocean by peridotite-seawater reactions, contributing to the increase of the Mg/Ca ratio of post-Mesozoic seawater