VIRVE-tukiaseman peittoalueen mallintaminen

Tekniikan kehityksen myötä reaalimaailman ilmiöitä voidaan mallintaa yhä tarkemmin. Tässä työssä tutkitaan VIRVE-radioverkon tukiaseman peittoalueen mallintamista. Työn tavoitteena oli mallintaa VIRVE-tukiaseman peittoalue mahdollisimman tarkasti. Tavoitteena oli myös löytää VIRVE-tukiasemaan peittoalueen kannalta nykyistä paremmat antenniratkaisut. Tutkimuksen teoreettisessa osuudessa selvitettiin tukiaseman peittoalueen mallintamiseen liittyviä tekijöitä, kuten radioaaltojen ominaisuuksia ja etenemismalleja sekä antennien teoriaa. Eri etenemismalleilla laskettuja tukiasemien peittoennusteita verrattiin empiirisesti toteutettuihin tukiasemien peittoalueiden mittaustuloksiin. Työn tuloksena löydettiin radioaaltojen etenemismalli, jolla mallinnettavien tukiasemien peittoalue-ennusteet vastasivat hyvin empiirisesti mitattuja tuloksia. Lisäksi löydettiin nykyistä paremmat antenniratkaisut VIRVE-tukiasemiin.

Switchable lanthanide fluorescence probes in homogenous molecular diagnostics

The number of molecular diagnostic assays has increased tremendously in recent years.Nucleic acid diagnostic assays have been developed, especially for the detection of human pathogenic microbes and genetic markers predisposing to certain diseases. Closed-tube methods are preferred because they are usually faster and easier to perform than heterogenous methods and in addition, target nucleic acids are commonly amplified leading to risk of contamination of the following reactions by the amplification product if the reactions are opened. The present study introduces a new closed-tube switchable complementation probes based PCR assay concept where two non-fluorescent probes form a fluorescent lanthanide chelate complex in the presence of the target DNA. In this dual-probe PCR assay method one oligonucleotide probe carries a non-fluorescent lanthanide chelate and another probe a light absorbing antenna ligand. The fluorescent lanthanide chelate complex is formed only when the non-fluorescent probes are hybridized to adjacent positions into the target DNA bringing the reporter moieties in close proximity. The complex is formed by self-assembled lanthanide chelate complementation where the antenna ligand is coordinated to the lanthanide ion captured in the chelate. The complementation probes based assays with time-resolved fluorescence measurement showed low background signal level and hence, relatively high nucleic acid detection sensitivity (low picomolar target concentration). Different lanthanide chelate structures were explored and a new cyclic seven dentate lanthanide chelate was found suitable for complementation probe method. It was also found to resist relatively high PCR reaction temperatures, which was essential for the PCR assay applications. A seven-dentate chelate with two unoccupied coordination sites must be used instead of a more stable eight- or nine-dentate chelate because the antenna ligand needs to be coordinated to the free coordination sites of the lanthanide ion. The previously used linear seven-dentate lanthanide chelate was found to be unstable in PCR conditions and hence, the new cyclic chelate was needed. The complementation probe PCR assay method showed high signal-to-background ratio up to 300 due to a low background fluorescence level and the results (threshold cycles) in real-time PCR were reached approximately 6 amplification cycles earlier compared to the commonly used FRET-based closed-tube PCR method. The suitability of the complementation probe method for different nucleic acid assay applications was studied. 1) A duplex complementation probe C. trachomatis PCR assay with a simple 10-minute urine sample preparation was developed to study suitability of the method for clinical diagnostics. The performance of the C. trachomatis assay was equal to the commercial C. trachomatis nucleic acid amplification assay containing more complex sample preparation based on DNA extraction. 2) A PCR assay for the detection of HLA-DQA1*05 allele, that is used to predict the risk of type 1 diabetes, was developed to study the performance of the method in genotyping. A simple blood sample preparation was used where the nucleic acids were released from dried blood sample punches using high temperature and alkaline reaction conditions. The complementation probe HLA-DQA1*05 PCR assay showed good genotyping performance correlating 100% with the routinely used heterogenous reference assay. 3) To study the suitability of the complementation probe method for direct measurement of the target organism, e.g., in the culture media, the complementation probes were applied to amplificationfree closed-tube bacteriophage quantification by measuring M13 bacteriophage ssDNA. A low picomolar bacteriophage concentration was detected in a rapid 20- minute assay. The assay provides a quick and reliable alternative to the commonly used and relatively unreliable UV-photometry and time-consuming culture based bacteriophage detection methods and indicates that the method could also be used for direct measurement of other micro-organisms. The complementation probe PCR method has a low background signal level leading to a high signal-to-background ratio and relatively sensitive nucleic acid detection. The method is compatible with simple sample preparation and it was shown to tolerate residues of urine, blood, bacteria and bacterial culture media. The common trend in nucleic acid diagnostics is to create easy-to-use assays suitable for rapid near patient analysis. The complementation probe PCR assays with a brief sample preparation should be relatively easy to automate and hence, would allow the development of highperformance nucleic acid amplification assays with a short overall assay time.

Switchable Lanthanide Luminescence for Detection of Biomolecules

Binary probes are oligonucleotide probe pairs that hybridize adjacently to a complementary target nucleic acid. In order to detect this hybridization, the two probes can be modified with, for example, fluorescent molecules, chemically reactive groups or nucleic acid enzymes. The benefit of this kind of binary probe based approach is that the hybridization elicits a detectable signal which is distinguishable from background noise even though unbound probes are not removed by washing before measurement. In addition, the requirement of two simultaneous binding events increases specificity. Similarly to binary oligonucleotide probes, also certain enzymes and fluorescent proteins can be divided into two parts and used in separation-free assays. Split enzyme and fluorescent protein reporters have practical applications among others as tools to investigate protein-protein interactions within living cells. In this study, a novel label technology, switchable lanthanide luminescence, was introduced and used successfully in model assays for nucleic acid and protein detection. This label technology is based on a luminescent lanthanide chelate divided into two inherently non-luminescent moieties, an ion carrier chelate and a light harvesting antenna ligand. These form a highly luminescent complex when brought into close proximity; i.e., the label moieties switch from a dark state to a luminescent state. This kind of mixed lanthanide complex has the same beneficial photophysical properties as the more typical lanthanide chelates and cryptates - sharp emission peaks, long emission lifetime enabling time-resolved measurement, and large Stokes’ shift, which minimize the background signal. Furthermore, the switchable lanthanide luminescence technique enables a homogeneous assay set-up. Here, switchable lanthanide luminescence label technology was first applied to sensitive, homogeneous, single-target nucleic acid and protein assays with picomolar detection limits and high signal to background ratios. Thereafter, a homogeneous four-plex nucleic acid array-based assay was developed. Finally, the label technology was shown to be effective in discrimination of single nucleotide mismatched targets from fully matched targets and the luminescent complex formation was analyzed more thoroughly. In conclusion, this study demonstrates that the switchable lanthanide luminescencebased label technology can be used in various homogeneous bioanalytical assays.

Veden desinfiointi UV-LED-valolla

Veden riittämätön puhdistus aiheuttaa riskin veden käyttäjille. Miljoonia kuolemia vuosittain aiheuttavien vesiteitse leviävien sairauksien ehkäisemiseksi vaaditaan tehokkaita juomaveden desinfiointimenetelmiä. Kuivuuden ja väestönkasvun myötä veden tarve on lisääntynyt ja vedenkulutus tulee yhä kasvamaan. Tästä syystä mahdollisuus kierrättää vettä hyödyntäen sitä esimerkiksi kasteluun on saanut yhä enemmän huomiota. Kierrätettävä vesi on kuitenkin käsiteltävä huolellisesti sen sisältämän mikrobiologisen kontaminaatioriskin vuoksi. Ultraviolettisäteily luokitellaan fysikaaliseksi desinfiointimenetelmäksi. Sen tehokkuus perustuu mikro-organismien absorboimaan UV-säteilyyn, jonka aiheuttamien DNA:ssa tai RNA:ssa tapahtuvien muutoksien seurauksena mikro-organismi inaktivoituu ja estyy lisääntymästä. UV-desinfioinnissa on tyypillisesti käytetty elohopeahöyrylamppuja. Vaihtoehtoinen UV-säteilyn lähde ovat LEDit eli valoa emittoivat diodit. Matalapaine-elohopeahöyrylamppujen emittoima säteily on aallonpituudella 254 nm ja keskipaine-elohopeahöyrylamppujen emittoima säteily on laajakaistaista säteilyä. Energiatehokkuuden lisäksi LEDien etuna on, että niillä voidaan tuottaa kapeakaista säteilyä aallonpituudella, joka parhaiten absorboituu DNA:han. Tämän diplomityön tarkoituksena oli tutkia, onko UVC-alueen aallonpituuksien yhdistelmillä synergistisiä etuja LEDien desinfiointitehokkuuteen, kun desinfioidaan virtaavaa vettä useilla säteilyannoksilla ja indikaattorimikrobina käytetään kolibakteeria. Tavoitteena oli myös tutkia tällä hetkellä saatavissa olevien LEDien desinfiointitehokkuutta energiatehokkuuden näkökulmasta. Yksittäisistä aallonpituuksista desinfiointitehokkuudeltaan parhaimmaksi osoittautui 260 nm, aallonpituuksien yhdistelmistä tehokkain oli 265 nm:n ja 260 nm:n yhdistelmä. Muilla aallonpituuksien yhdistelmillä ei saavutettu odotettua parempaa desinfiointitehokkuutta. Optiselta teholtaan parhaimmat LEDit, 265 nm, 270 nm ja 275 nm olivat kokeiden perusteella myös energiatehokkuuden kannalta tarkasteltuina parhaimmat sekä yksittäin että yhdistelminä. UVC-aallonpituuksia emittoivien LEDien optisen tehokkuuden paraneminen on edellytys LEDien hyödyntämiselle desinfioinnissa.

Modeling of fractal antennas

In this Master Thesis the characteristics of the chosen fractal microstrip antennas are investigated. For modeling has been used the structure of the square Serpinsky fractal curves. During the elaboration of this Master thesis the following steps were undertaken: 1) calculation and simulation of square microstrip antennа, 2) optimizing for obtaining the required characteristics on the frequency 2.5 GHz, 3) simulation and calculation of the second and third iteration of the Serpinsky fractal curves, 4) radiation patterns and intensity distribution of these antennas. In this Master’s Thesis the search for the optimal position of the port and fractal elements was conducted. These structures can be used in perspective for creation of antennas working at the same time in different frequency range.

Radar cross-section measurement using the Doppler effect

In this Master Thesis we discuss issues related to the measurement of the effective scattering surface, based on the Doppler Effect. Modeling of the detected signal was made. Narrowband signal filtering using low-frequency amplifier was observed. Parameters of the proposed horn antennas were studied; radar cross section charts for three different objects were received.

Determinants of Bone Strength and Predictors of Hip Fracture among Finnish Adults. Results from the Health 2000 Survey and the Mini-Finland Health Survey

The objective of this thesis was to identify the determinants of bone strength and predictors of hip fracture in representative samples of Finnish adults. A secondary objective was to construct a simple multifactorial model for hip fracture prediction over a 10-year follow-up period. The study was based on the Health 2000 Survey conducted during 2000 to 2001 (men and women aged 30 years or over, n=6 035) and the Mini-Finland Health Survey conducted during 1978 to 1980 (women aged 45 years or over, n=2 039). Study subjects participated in health interviews and comprehensive health examination. In the Health 2000 Survey, bone strength was assessed by means of calcaneal quantitative ultrasound (QUS). The follow-up information about hip fractures was drawn from the National Hospital Discharge Register. In this study, age, weight, height, serum 25-hydroxyvitamin D (S-25(OH)D), physical activity, smoking and alcohol consumption as well as menopause and eventual HRT in women were found to be associated with calcaneal broadband ultrasound attenuation (BUA) and speed of sound (SOS). Parity was associated with a decreased risk of hip fracture in postmenopausal women. Age, height, weight or waist circumference, quantitative ultrasound index (QUI), S-25(OH)D and fall-related factors, such as maximal walking speed, Parkinson’s disease, and the number of prescribed CNS active medication were significant independent predictors of hip fracture. At the population level, the incremental value of QUS appeared to be minor in hip fracture prediction when the fall-related risk factors were taken into account. A simple multifactorial model for hip fracture prediction presented in this study was based on readily available factors (age, gender, height, waist circumference, and fallrelated factors). Prospective studies are needed to test this model in patient-based study populations.

High pressure near infrared study of the mutated light-harvesting complex LH2

The pressure sensitivities of the near infrared spectra of the light-harvesting (LH2) complex and a mutant complex with a simplified BChl-B850 binding pocket were compared. In the mutant an abrupt change in the spectral properties occurred at 250 MPa, which was not observed with the native sample. Increased disorder due to collapse of the chromophore pocket is suggested.

Prevalence of low trauma fractures in long-term kidney transplant patients with preserved renal function

We evaluated the prevalence of low bone mineral density (BMD) and osteoporotic fractures in kidney transplantation (KT) patients and determined risk factors associated with osteoporotic fractures. The study was conducted on 191 patients (94 men and 97 women) with first KT for 3 years or more presenting stable and preserved renal function (serum creatinine levels lower than 2.5 mg/dl). KT patients were on immunosuppressive therapy and the cumulative doses of these drugs were also evaluated. BMD was determined by dual-energy X-ray absorptiometry at multiple sites (spine, femur and total body). Quantitative ultrasound of the calcaneus (broadband ultrasound attenuation, speed of sound, and stiffness index, SI) was also performed. Twenty-four percent (46) of all patients had either vertebral (29/46) or appendicular (17/46) fractures. We found osteoporosis and osteopenia in 8.5-13.4 and 30.9-35.1% of KT patients, respectively. Women had more fractures than men. In women, prevalent fractures were associated with diabetes mellitus [OR = 11.5, 95% CI (2.4-55.7)], time since menopause [OR = 3.7, 95% CI (1.2-11.9)], femoral neck BMD [OR = 1.99, 95% CI (1.4-2.8)], cumulative dose of steroids [OR = 1.1, 95% CI (1.02-1.12)] and low SI [OR = 1.1, 95% CI (1.0-1.2)]. In men, fractures were associated with lower lumbar spine BMD [OR = 1.75, 95% CI (1.1-2.7)], lower SI [OR = 1.1, 95% CI (1.03-1.13)], duration of dialysis [OR = 1.3, 95% CI (1.13-2.7)], and lower body mass index [OR = 1.24, 95% CI (1.1-1.4). Our results demonstrate high prevalence of low BMD and osteoporotic fractures in patients receiving a successful kidney transplant and indicate the need for specific intervention to prevent osteoporosis in this population.

Modelling of faults in low-voltage cables

Power line modelling has become an interesting research area in recent years as a result of advances in the power line distribution network system. Extensive knowledge about the power line cable characteristics can be implemented in a software algorithm in a modern broadband power-line communication modem. In this study, a novel approach for modelling power line cables (AMCMK) based on the broadband impedance spectroscopy (BIS) and transmission line matrix (TLM) techniques is recommended in characterizing a healthy cable and the various faults associated with low-voltage cables for both open and short circuit situation. Models for different cable conditions are developed and tuned, which include six models for both healthy and faulty cables situations. The models are on the basis of impedance response analysis of the cable. The resulting spectra from the simulations are also cross-correlated to determine the degree of similarities between the healthy cable spectra and their respective faulty spectra.

Academic South and North ( September 2002)

The Academic South and Academic North buildings are located at the west end of campus. The 80 000 square-foot facilities include the Computer Commons, several multimedia lecture halls, office space, state-of-the-art labs, a food court, and student meeting space. The complex included some of the most modern technology, including broadband Internet video conferencing that enabled real-time visual contact between professors, students, and researchers from around the world.

The mechanism of the regulation of energy distribution between photosystems 1 and 2 in the cyanobacterium Synechococcus sp. strain PCC 7002 /

Cyanobacteria are able to regulate the distribution of absorbed light energy between photo systems 1 and 2 in response to light conditions. The mechanism of this regulation (the state transition) was investigated in the marine cyanobacterium Synechococcus sp. strain PCC 7002. Three cell types were used: the wild type, psaL mutant (deletion of a photo system 1 subunit thought to be involved in photo system 1 trimerization) and the apcD mutant (a deletion of a phycobilisome subunit thought to be responsible for energy transfer to photo system 1). Evidence from 77K fluorescence emission spectroscopy, room temperature fluorescence and absorption cross-section measurements were used to determine a model of energy distribution from the phycobilisome and chlorophyll antennas in state 1 and state 2. The data confirm that in state 1 the phycobilisome is primarily attached to PS2. In state 2, a portion of the phycobilisome absorbed light energy is redistributed to photo system 1. This energy is directly transferred to photo system 1 by one of the phycobilisome terminal emitters, the product of the apcD gene, rather than via the photo system 2 chlorophyll antenna by spillover (energy transfer between the photo system 2 and photo system 1 chlorophyll antenna). The data also show that energy absorbed by the photo system 2 chlorophyll antenna is redistributed to photo system 1 in state 2. This could occur in one of two ways; by spillover or in a way analogous to higher plants where a segment of the chlorophyll antenna is dissociated from photo system 2 and becomes part of the photo system 1 antenna. The presence of energy transfer between neighbouring photo system 2 antennae was determined at both the phycobilisome and chlorophyll level, in states 1 and 2. Increases in antenna absorption cross-section with increasing reaction center closure showed that there is energy transfer (connectivity) between photosystem 2 antennas. No significant difference was shown in the amount of connectivity under these four conditions.

Synechococcus sp. PCC 7002 CpcB lyase null mutations alter phycocyanin chromophore function and, consequently, affect the redistribution of excitation energy via the light state transition /

Phycobilisomes are the major light harvesting complexes for cyanobacteria and phycocyanin is the primary phycobiliprotein of the phycobilisome rod. The phycocyanobilin lyases responsible for chromophorylating the phycocyanin p subunit (CpcB) have been recently identified in the cyanobacterium Synechococcus sp. PCC 7002. Surprisingly, mutants missing the CpcB lyases were nevertheless capable of producing pigmented phycocyanin. 10K absorbance measurements revealed that the energy states of the p phycocyanin chromophores were only subtly shifted; however, 77K steady state fluorescence emission spectroscopy showed excitation energy transfer involving the targeted chromophores to be highly disrupted. Such evidence suggests that phycobilin orientation within the binding domain is specifically modified. We hypothesized that alternate, less specific lyases are able to act on the p binding sites. A phycocyanin linker-polypeptide deficient mutant was similarly characterized. The light state transition, a short term adaptation of the photosynthetic light harvesting apparatus resulting in the redistribution of excitation energy among the photo systems, was shown to be dominated by the reallocation of phycocyanin-absorbed excitation energy. Treatment with a high M phosphate buffer effectively prevented the redistribution of both chlorophyll a- and phycobilisome- absorbed excitation energy, suggesting that the two effects are not strictly independent. The mutant strains required a larger redistribution of excitation energy between light states, perhaps to compensate for their loss in phycobilisome antenna function.

Heterogeneity of photosystem II as it occurs in domain specific regions of the thylakoid membrane of spinach (spinacia oleracia L.)

Thylakoid membrane fractions were prepared from specific regions of thylakoid membranes of spinach (Spinacia oleracea). These fractions, which include grana (83), stroma (T3), grana core (8S), margins (Ma) and purified stroma (Y100) were prepared using a non-detergent method including a mild sonication and aqueous two-phase partitioning. The significance of PSlla and PSII~ centres have been described extensively in the literature. Previous work has characterized two types of PSII centres which are proposed to exist in different regions of the thylakoid membrane. a-centres are suggested to aggregate in stacked regions of grana whereas ~-centres are located in unstacked regions of stroma lamellae. The goal of this study is to characterize photosystem II from the isolated membrane vesicles representing different regions of the higher plant thylakoid membrane. The low temperature absorption spectra have been deconvoluted via Gaussian decomposition to estimate the relative sub-components that contribute to each fractions signature absorption spectrum. The relative sizes of the functional PSII antenna and the fluorescence induction kinetics were measured and used to determine the relative contributions of PSlla and PSII~ to each fraction. Picosecond chlorophyll fluorescence decay kinetics were collected for each fraction to characterize and gain insight into excitation energy transfer and primary electron transport in PSlla and PSII~ centres. The results presented here clearly illustrate the widely held notions of PSII/PS·I and PSlIa/PSII~ spatial separation. This study suggests that chlorophyll fluorescence decay lifetimes of PSII~ centres are shorter than those of PSlIa centres and, at FM, the longer lived of the two PSII components renders a larger yield in PSlIa-rich fractions, but smaller in PSIlr3-rich fractions.

Localization of the mechanism of pH-dependent non- photochemical fluorescence quenching in thylakoid membranes

Higher plants have evolved a well-conserved set of photoprotective mechanisms, collectively designated Non-Photochemical Quenching of chlorophyll fluorescence (qN), to deal with the inhibitory absorption of excess light energy by the photosystems. Their main contribution originates from safe thermal deactivation of excited states promoted by a highly-energized thylakoid membrane, detected via lumen acidification. The precise origins of this energy- or LlpH-dependent quenching (qE), arising from either decreased energy transfer efficiency in PSII antennae (~ Young & Frank, 1996; Gilmore & Yamamoto, 1992; Ruban et aI., 1992), from alternative electron transfer pathways in PSII reaction centres (~ Schreiber & Neubauer, 1990; Thompson &Brudvig, 1988; Klimov et aI., 1977), or from both (Wagner et aI., 1996; Walters & Horton, 1993), are a source of considerable controversy. In this study, the origins of qE were investigated in spinach thylakoids using a combination of fluorescence spectroscopic techniques: Pulse Amplitude Modulated (PAM) fluorimetry, pump-probe fluorimetry for the measurement of PSII absorption crosssections, and picosecond fluorescence decay curves fit to a kinetic model for PSII. Quenching by qE (,..,600/0 of maximal fluorescence, Fm) was light-induced in circulating samples and the resulting pH gradient maintained during a dark delay by the lumenacidifying capabilities of thylakoid membrane H+ ATPases. Results for qE were compared to those for the addition of a known antenna quencher, 5-hydroxy-1,4naphthoquinone (5-0H-NQ), titrated to achieve the same degree of Fm quenching as for qE. Quenching of the minimal fluorescence yield, F0' was clear (8 to 130/0) during formation of qE, indicative of classical antenna quenching (Butler, 1984), although the degree was significantly less than that achieved by addition of 5-0H-NQ. Although qE induction resulted in an overall increase in absorption cross-section, unlike the decrease expected for antenna quenchers like the quinone, a larger increase in crosssection was observed when qE induction was attempted in thylakoids with collapsed pH gradients (uncoupled by nigericin), in the absence of xanthophyll cycle operation (inhibited by DTT), or in the absence of quenching (LlpH not maintained in the dark due to omission of ATP). Fluorescence decay curves exhibited a similar disparity between qE-quenched and 5-0H-NQ-quenched thylakoids, although both sets showed accelerated kinetics in the fastest decay components at both F0 and Fm. In addition, the kinetics of dark-adapted thylakoids were nearly identical to those in qEquenched samples at F0' both accelerated in comparison with thylakoids in which the redox poise of the Oxygen-Evolving Complex was randomized by exposure to low levels of background light (which allowed appropriate comparison with F0 yields from quenched samples). When modelled with the Reversible Radical Pair model for PSII (Schatz et aI., 1988), quinone quenching could be sufficiently described by increasing only the rate constant for decay in the antenna (as in Vasil'ev et aI., 1998), whereas modelling of data from qE-quenched thylakoids required changes in both the antenna rate constant and in rate constants for the reaction centre. The clear differences between qE and 5-0H-NQ quenching demonstrated that qE could not have its origins in the antenna alone, but is rather accompanied by reaction centre quenching. Defined mechanisms of reaction centre quenching are discussed, also in relation to the observed post-quenching depression in Fm associated with photoinhibition.