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.

Blue and Uv-Emitting Upconversion Nanoparticles: Synthesis and (Bio) Analytical Applications.

Rare-earth based upconverting nanoparticles (UCNPs) have attracted much attention due to their unique luminescent properties. The ability to convert multiple photons of lower energy to ones with higher energy through an upconversion (UC) process offers a wide range of applications for UCNPs. The emission intensities and wavelengths of UCNPs are important performance characteristics, which determine the appropriate applications. However, insufficient intensities still limit the use of UCNPs; especially the efficient emission of blue and ultraviolet (UV) light via upconversion remains challenging, as these events require three or more near-infrared (NIR) photons. The aim of the study was to enhance the blue and UV upconversion emission intensities of Tm3+ doped NaYF4 nanoparticles and to demonstrate their utility in in vitro diagnostics. As the distance between the sensitizer and the activator significantly affect the energy transfer efficiency, different strategies were explored to change the local symmetry around the doped lanthanides. One important strategy is the intentional co-doping of active (participate in energy transfer) or passive (do not participate in energy transfer) impurities into the host matrix. The roles of doped passive impurities (K+ and Sc3+) in enhancing the blue and UV upconversions, as well as in influencing the intense UV upconversion emission through excess sensitization (active impurity) were studied. Additionally, the effects of both active and passive impurity doping on the morphological and optical performance of UCNPs were investigated. The applicability of UV emitting UCNPs as an internal light source for glucose sensing in a dry chemistry test strip was demonstrated. The measurements were in agreement with the traditional method based on reflectance measurements using an external UV light source. The use of UCNPs in the glucose test strip offers an alternative detection method with advantages such as control signals for minimizing errors and high penetration of the NIR excitation through the blood sample, which gives more freedom for designing the optical setup. In bioimaging, the excitation of the UCNPs in the transparent IR region of the tissue permits measurements, which are free of background fluorescence and have a high signal-to-background ratio. In addition, the narrow emission bandwidth of the UCNPs enables multiplexed detections. An array-in-well immunoassay was developed using two different UC emission colours. The differentiation between different viral infections and the classification of antibody responses were achieved based on both the position and colour of the signal. The study demonstrates the potential of spectral and spatial multiplexing in the imaging based array-in-well assays.

Fluorescence in situ hybridization of potato somatohaploids and their somatic hybrid donors using two Solanum brevidens specific sequences

Selostus: Perunan somaattisten hybridien ja niiden somatohaploidien fluoresenssi in situ -hybridisaatio Solanum brevidens -lajin spesifisten sekvenssien avulla

Painatuksen UV-stabiilisuuden optimointi fenolihartsatussa paperissa

Tässä diplomityössä tutkittiin painetun paperin ja siitä fenoliformaldehydihartsilla impregnoimalla valmistetun pinnoituskalvon UV-stabiilisuuden parantamis-mahdollisuuksia. Työn kirjallisuusosassa käsitellään painetun pinnoituskalvon valmistusprosessia ja painatuksen UV-valonkestoon vaikuttavia tekijöitä. Painovärin pigmentti, sen määrä ja käsittely, painovärin sideaine sekä fenoliformaldehydihartsi ja sen lisäaineet vaikuttavat pinnoitetun betonoimisvanerin säänkesto-ominaisuuksiin. Erilaisilla epäorgaanisilla valkoisilla pigmenteillä ja kidemuodoilla on erilainen UV-valonkesto ja taitekerroin. Päällystämällä titaanidioksidi esimerkiksi alumiini- tai zirkoniumoksideilla sen UV-valonkestoa voidaan parantaa merkittävästi. UV-hajoaminen voidaan havaita painetun pinnoitteen liituuntumisena. Liituuntumista voidaan pitää veden ja hapen välisenä reaktiona, jota titaanidioksidi ja UV-säteily katalysoivat. Sen takia myös muiden valkoisten epäorgaanisten pigmenttien ominaisuuksia ja käyttöä selvitettiin. Kokeissa käytettiin yhdeksää eri painoväriä, kahta eri paksuista paperia ja kahta eri tyyppistä hartsia. Painovärejä ohennettiin vedellä ja paperin painopuolta vaihdeltiin. Kaikissa painatuksissa käytettiin kolmea eri rasterointiasteen laattaa, jolloin painovärin määrää paperissa saatiin vähennettyä. Painetuista papereista mitattiin densiteetti, värimäärä, pisara-absorptio vedellä ja kontaktikulma hartsilla. Myös painovärin tunkeumaa selvitettiin paperin poikkileikeistä tehtyjen SEM-kuvien avulla. Painetut paperit impregnoitiin fenoliformaldehydihartsilla kalvoksi. Pinnoituskalvot puristettiin vanerin pinnalle laboratoriopuristimella. Koekappaleet altistettiin UV-valolle, sateelle ja pakkaselle sääkaapissa 400 h ajan, mikä vastaa noin 1,5 vuotta ulkona Suomen oloissa. Kappaleista mitattiin kiilto, värinmuutos ja liituuntuminen. Pinnoitteen liituuntumista tapahtui vähiten niissä koepisteissä, joissa painatus oli tehty 30 % rasteroidulla laatallaSäänkestävä TiO2 osoittautui hyväksi, mutta myös ZnO-pigmentillä saatiin hyviä tuloksia. ZnO-koepisteessä liituuntumisreaktio ei ole niin voimakkaasti katalysoitu kuin TiO2-koepisteissä. Paksun paperin painatuspuolella näytti olevan merkitystä säänkestoon. Huopapuolelle painettuna pinnoitteen liituuntuminen oli vähäisempää

Suodatuskalvon puhdistaminen UV-valolla tai ultraäänellä aktivoidulla titaanidioksidilla

Kalvotekniikan suurin ongelma on edelleen kalvon likaantuminen, jonka tuloksena kalvon erotuskyky voi muuttua ja liuoksen vuo kalvon läpi pientyä huomattavasti. Kalvotekniikan teollisissa sovelluksissa kalvojen puhdistus on yksi tärkeimmistä pääkohdista, sillä se määrittää kalvon käyttöikää ja käyttötehokkuutta. Yleisimmin käytetyn kemiallisen pesun tuloksena muodostuu hävitettävä pesuliuos, joka sisältää sekä kemikaaleja, että kalvosta poistetun lian. Työssä on tutkittu kalvon puhdistusta ultravioletti-valo- tai ultraäänikäsittelyssä titaanidioksidin läsnäollessa. Menetelmien mahdollisina etuina ovat kalvosta poistetun lian hajotus harmittomiksi komponenteiksi ja mahdollisesti kalvon pienempi kuluminen pesussa. Työn kirjallisuusosassa on käsitelty orgaanisten ja epäorgaanisten aineiden hajottamista ultraviolettivalon tai ultraäänikäsittelyn avulla titaanidioksidin läsnäollessa sekä olosuhteiden vaikutusta menetelmien tehokkuuteen. Tämän lisäksi työssä on keskitytty polymeerikalvojen UV-valo- ja ultraäänikäsittelykestävyyteen. Kokeellisessa osassa on tutkittu UV-valo- ja ultraäänikäsittelyjen sopivuutta liatun PVDF-kalvon puhdistukseen titaanidioksidin läsnäollessa. Tavoitteena oli liatun kalvon permeabiliteetin palautus puhtaan kalvon tasolle käsittelyn avulla. Kalvon kestävyyttä on myös tutkittu. Tämän työn perusteella tutkittuja menetelmiä ei voida soveltaa tarkistettavan PVDF-kalvon puhdistukseen, ainakaan testeissä käytetyissä olosuhteissa, sillä kalvon ominaisuudet muuttuvat käsittelyissä.

Lanthanide Chelates as Donors in Fluorescence Resonance Energy Transfer: Exciting Prospects for Bioaffinity Assay Detection

Fluorescence resonance energy transfer (FRET) is a non-radiative energy transfer from a fluorescent donor molecule to an appropriate acceptor molecule and a commonly used technique to develop homogeneous assays. If the emission spectrum of the donor overlaps with the excitation spectrum of the acceptor, FRET might occur. As a consequence, the emission of the donor is decreased and the emission of the acceptor (if fluorescent) increased. Furthermore, the distance between the donor and the acceptor needs to be short enough, commonly 10-100 Å. Typically, the close proximity between the donor and the acceptor is achieved via bioaffinity interactions e.g. antibody binding antigen. Large variety of donors and acceptors exist. The selection of the donor/acceptor pair should be done not only based on the requirements of FRET but also the performance expectancies and the objectives of the application should be considered. In this study, the exceptional fluorescence properties of the lanthanide chelates were employed to develop two novel homogeneous immunoassays: a non-competitive hapten (estradiol) assay based on a single binder and a dual-parametric total and free PSA assay. In addition, the quenching efficiencies and energy transfer properties of various donor/acceptor pairs were studied. The applied donors were either europium(III) or terbium(III) chelates; whereas several organic dyes (both fluorescent and quenchers) acted as acceptors. First, it was shown that if the interaction between the donor/acceptor complexes is of high quality (e.g. biotin-streptavidin) the fluorescence of the europium(III) chelate could be quenched rather efficiently. Furthermore, the quenching based homogeneous non-competitive assay for estradiol had significantly better sensitivity (~67 times) than a corresponding homogeneous competitive assay using the same assay components. Second, if the acceptors were chosen to emit at the emission minima of the terbium(III) chelate, several acceptor emissions could be measured simultaneously without significant cross-talk from other acceptors. Based on these results, the appropriate acceptors were chosen for the dual-parameter assay. The developed homogeneous dual-parameter assay was able to measure both total and free PSA simultaneously using a simple mix and measure protocol. Correlation of this assay to a heterogeneous single parameter assay was excellent (above 0.99 for both) when spiked human plasma samples were used. However, due to the interference of the sample material, the obtained concentrations were slightly lower with the homogeneous than the heterogeneous assay, especially for the free PSA. To conclude, in this work two novel immunoassay principles were developed, which both are adaptable to other analytes. However, the hapten assay requires a rather good antibody with low dissociation rate and high affinity; whereas the dual-parameter assay principle is applicable whenever two immunometric complexes can form simultaneously, provided that the requirements of FRET are fulfilled.

Photoinhibition of Photosystem II. Kinetics, Photoprotection and Mechanism

Photosystem II (PSII) is susceptible to light-induced damage defined as photoinhibition. In natural conditions, plants are capable of repairing the photoinhibited PSII by on-going degradation and re-synthesis of the D1 reaction centre protein of PSII. Photoinhibition is induced by both visible and ultraviolet light and photoinhibition occurs under all light intensities with the same efficiency per photon. In my thesis work, I studied the reaction kinetics and mechanism of photoinhibition of PSII, as well as photoprotection in leaves of higher plants. Action spectroscopy was used to identify photoreceptors of photoinhibition. I found that the action spectrum of photoinhibition in vivo shows resemblance to the absorption spectra of manganese model compounds of the oxygen evolving complex (OEC) suggesting a role for manganese as a photoreceptor of photoinhibition under UV and visible light. In order to study the protective effect of non-photochemical quenching, the action spectrum was measured from leaves of wild type Arabidopsis thaliana and two mutants impaired in nonphotochemical quenching of chlorophyll a excitations. The findings of action spectroscopy and simulations of chlorophyll-based photoinhibition mechanisms suggested that quenching of antenna excitations protects less efficiently than would be expected if antenna chlorophylls were the only photoreceptors of photoinhibition. The reaction kinetics of prolonged photoinhibition was studied in leaves of Cucurbita maxima and Capsicum annuum. The results indicated that photoinhibitory decrease in both the oxygen evolution activity and ratio of variable to maximum fluorescence follows firstorder kinetics in vivo. The persistence of first-order kinetics suggests that already photoinhibited reaction centres do not protect against photoinhibition and that the mechanism of photoinhibition does not have a reversible intermediate. When Cucurbita maxima leaves were photoinhibited with saturating single-turnover flashes and continuous light, the light response curve of photoinhibition was found to be essentially a straight line with both types of illumination, suggesting that similar photoinhibition mechanisms might function during illumination with continuous light and during illumination with short flashes.

Puulevystä valmistettujen kalusteosien pintakäsittelyn kehittäminen UV-telalinjalla

Diplomityö tehtiin Kidex Oy:lle, joka on Kiteellä sijaitseva Martela-konsernin tytäryhtiö. Kidex Oy toimii sopimusvalmistajana Martelalle sekä muille valituille levykalusteasiakkaille, ja tuotteet ovat pääasiassa toimisto- ja keittiökalusteita. Kevättalvella 2008 yritykseen siirrettiin Nummelasta pintakäsittelyosasto, jolla on tehty petsaus- ja lakkaustöitä. Näiden lisäksi tehtaalla on pohdittu mahdollisuuksia maalaustöihin, jotta UV-telalinjan kapasiteetti saataisiin paremmin käyttöön Työssä selvitettiin, mitä muutoksia UV-kovettuvilla aineilla maalaaminen vaatii linjaan ja luotiin edellytykset maalaustoiminnan aloittamiselle. Muutokset pyrittiin pitämään niin vähäisinä kuin mahdollista. Lisäksi määritettiin maalattavien tuotteiden laadun kriteerit ja todennusmenetelmät, jotka voidaan viestiä asiakkaille väärinkäsitysten välttämiseksi. Laadun todentamista varten valmistettiin sarja koekappaleita, joista mitattiin asiakkaan kannalta tärkeimmät maalikalvon ominaisuudet. Työssä tarkasteltiin myös pintakäsittelylaitoksia koskevaa VOC-asetusta ja verrattiin liuottimien kulutusta asetuksen määrittämiin rajoihin. Puulevystä valmistettujen kalusteosien pintakäsittely UV-telalinjalla eroaa oleellisesti perinteisistä menetelmistä esimerkiksi tuotantonopeuden osalta, joka johtuu pääasiassa pinnoitekalvon hetkessä tapahtuvasta kovettumisesta UV-valon vaikutuksesta. UV-aineet ovat käytännössä täysin kiinteistä aineista koostuvia, eivätkä näin sisällä vaarallisia haihtuvia liuottimia. UV-kovettuvilla tuotteilla maalaaminen on viime vuosina runsaasti tutkittu alue, joka eroaa tietyiltä osin myös pintakäsittelystä UV-kirkaslakoilla. Pigmentoitujen kalvojen kovettuminen vaatii erilaista UV-säteilyä ja levitysmäärien seuranta on huomattavasti tarkempaa.

Determination of sugars and organic acids in pulp samples by capillary electrophoresis with UV detection

This MSc work was done in the project of BIOMECON financed by Tekes. The prime target of the research was, to develop methods for separation and determination of carbohydrates (sugars), sugar acids and alcohols, and some other organic acids in hydrolyzed pulp samples by capillary electrophoresis (CE) using UV detection. Aspen, spruce, and birch pulps are commonly used for production of papers in Finland. Feedstock components in pulp predominantly consist of carbohydrates, organic acids, lignin, extractives, and proteins. Here in this study, pulps have been hydrolyzed in analytical chemistry laboratories of UPM Company and Lappeenranta University in order to convert them into sugars, acids, alcohols, and organic acids. Foremost objective of this study was to quantify and identify the main and by-products in the pulp samples. For the method development and optimization, increased precision in capillary electrophoresis was accomplished by calculating calibration data of 16 analytes such as D-(-)-fructose, D(+)-xylose, D(+)-mannose, D(+)-cellobiose, D-(+)-glucose, D-(+)-raffinose, D(-)-mannitol, sorbitol, rhamnose, sucrose, xylitol, galactose, maltose, arabinose, ribose, and, α-lactose monohydratesugars and 16 organic acids such as D-glucuronic, oxalic, acetic, propionic, formic, glycolic, malonic, maleic, citric, L-glutamic, tartaric, succinic, adipic, ascorbic, galacturonic, and glyoxylic acid. In carbohydrate and polyalcohol analyses, the experiments with CE coupled to direct UV detection and positive separation polarity was performed in 36 mM disodium hydrogen phosphate electrolyte solution. For acid analyses, CE coupled indirect UV detection, using negative polarity, and electrolyte solution made of 2,3 pyridinedicarboxylic acid, Ca2+ salt, Mg2+ salts, and myristyltrimethylammonium hydroxide in water was used. Under optimized conditions, limits of detection, relative standard deviations and correlation coefficients of each compound were measured. The optimized conditions were used for the identification and quantification of carbohydrates and acids produced by hydrolyses of pulp. The concentrations of the analytes varied between 1 mg – 0.138 g in liter hydrolysate.

Uv. Lilla slafvinnan ("Ali Baba") : alkusoitto

Soitinnus: orkesteri.

Reaaliaikaisen esikäsittelyn kehittäminen hemiselluloosa-analytiikalle

Tämän työn tavoitteena oli kehittää esikäsittelymenetelmä, jolla voidaan reaaliaikaisesti vähentää hydrolysaatin ligniinipitoisuutta ja näin vähentää fluoresenssia hemiselluloosan analysoimisessa. Työn kirjallisuusosassa käsitellään hemiselluloosien rakennetta sekä niiden erottamista puusta, sekä käydään läpi hemiselluloosien käyttömahdollisuuksia ja niiden reaaliaikaiseen analysointiin soveltuvia tekniikoita. Kokeellisessa osassa tutkittiin ultrasuodatusta sekä adsorptiohartsikäsittelyä hydrolysaatin esikäsittelynä ennen Raman-analyysiä. Esikäsittelyn tavoitteena oli vähentää Raman-analyysia häiritsevää ligniinistä johtuvaa fluoresenssia. Suodatukset tehtiin Amicon-suodatuslaitteistolla käyttäen viittä eri suodatuskalvoa. Hartsikäsittelyissä käytettiin Amberliten XAD16 ja XAD7HP adsorbtiohartseja. Hartsisuhteina käytettiin 1/80, 1/40, 1/19 ja 1/13. Käytetyt ultrauodatuskalvot osoittautuivat suodatusnäytteistä tehtyjen HPLC-analyysien perusteella cut-off-luvultaan liian pieniksi, sillä hemiselluloosien ja ligniinin erotus ei onnistunut, vaan molemmat väkevöityivät konsentraattiin. Hartsikäsittelyillä saatiin ligniiniä poistettua aiheuttamatta hemiselluloosahäviöitä. Parhaimmillaan ligniinin poistumista kuvaava UV-absorbanssi pieneni hartsilla XAD16 37 % ja hartsilla XAD7 25 %. Vaikka ligniinipitoisuus aleni, näytteet fluoresoivat edelleen voimakkaasti Raman-mittauksessa. Tulosten perusteella näyttäisi siltä, että hartsikäsittelyä optimoimalla analyysiä häiritsevää fluoresenssia olisi edelleen mahdollista vähentää.