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

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.

Investigation of interaction between native and impurity defects in ZnSe

Zinc selenide is a prospective material for optoelectronics. The fabrication of ZnSe­based light-emitting diodes is hindered by complexity of p-type doping of the component materials. The interaction between native and impurity defects, the tendency of doping impurity to form associative centres with native defects and the tendency to self-compensation are the main factors impeding effective control of the value and type of conductivity. The thesis is devoted to the study of the processes of interaction between native and impurity defects in zinc selenide. It is established that the Au impurity has the most prominent amphoteric properties in ZnSe among Cu, Ag and Au impurities, as it forms a great number of both Au; donors and Auz„ acceptors. Electrical measurements show that Ag and Au ions introduced into vacant sites of the Zn sublattice form simple single-charged Agz„+ and Auzn+ states with d1° electron configuration, while Cu ions can form both single-charged Cuz„ (d1) and double-charged Cuzr`+ (d`o) centres. Amphoteric properties of Ag and Au transition metals stimulated by time are found for the first time from both electrical and luminescent measurements. A model that explains the changes in electrical and luminescent parameters by displacement of Ag ions into interstitial sites due to lattice deformation forces is proposed. Formation of an Ag;-donor impurity band in ZnSe samples doped with Ag and stored at room temperature is also studied. Thus, the properties of the doped samples are modified due to large lattice relaxation during aging. This fact should be taken into account in optoelectronic applications of doped ZnSe and related compounds.

Sisäisten donorien vaikutus Polypropeeni Ziegler-Natta katalyytissä

Tässä työssä tutkittiin erilaisten sisäisten donorien vaikutusta polypropeenin ominaisuuksiin käytettäessä Ziegler-Natta-katalyyttiä, joka valmistettiin Borealiksen aiemmin kehittämällä kaksifaasimenetelmällä. Tällä uudella menetelmällä katalyytti voidaan valmistaa ilman lisättyä sisäistä donoria ja kantajaa. Katalyyttihiukkaset saadaan kaksifaasisysteemin ansiosta muodoltaan pyöreiksi. Työn kokeellisessa osassa valmistettiin erilaisia Mg-komplekseja, jossa sisäinen donori muodostuu in-situ alkoholin ja karboksyylihappokloridin reagoidessa keskenään. Katalyyttisynteesissä Mg-kompleksi reagoi TiCl4:n kanssa. Saatujen katalyyttien ominaisuuksia testattiin polymeroimalla niillä propeenia 70 °C:ssa tunnin ajan. Polymeerien ominaisuuksia tutkittiin useiden eri karakterisointimenetelmien avulla. Lisäksi tutkittiin mahdollisuutta valmistaa katalyytti, joka ei sisältäisi ftalaattia. Työssä havaittiin, että katalyytin valmistusmenetelmä on käyttökelpoinen myös muilla sisäisillä donoreilla kuin referenssinä käytetyllä DOP:lla. Kaksiliuosfaasi-systeemi saatiin aikaan myös kahdella muulla työssä tutkitulla sisäisellä donorilla. Lisäksi faasitasapainokokeissa kahden liuosfaasin systeemi saatiin aikaan sisäisellä donorilla, joka ei sisältänyt ftalaattia. Kyseisellä katalyytillä havaittiin olevan muista katalyyteistä poikkeavia ominaisuuksia. Esimerkiksi se antoi matalamman isotaktisuuden kuin referenssikatalyytti ja se saattaisikin soveltua matalan isotaktisuuden pehmeille tuotteille. Työssä kokeiltiin yhdellä uudella katalyytillä myös eteenin polymerointia, sillä katalyytin donoripitoisuus oli hyvin matala. Katalyytin aktiivisuus eteenipolymeroinnissa oli varsin hyvä.

Nanoparticle Labels in Bioaffinity Assays

Nanoparticles offer adjustable and expandable reactive surface area compared to the more traditional solid phase forms utilized in bioaffinity assays due to the high surface to-volume ratio. The versatility of nanoparticles is further improved by the ability to incorporate various molecular complexes such as luminophores into the core. Nanoparticle labels composed of polystyrene, silica, inorganic crystals doped with high number of luminophores, preferably lanthanide(III) complexes, are employed in bioaffinity assays. Other label species such as semiconductor crystals (quantum dots) or colloidal gold clusters are also utilized. The surface derivatization of such particles with biomolecules is crucial for the applicability to bioaffinity assays. The effectiveness of a coating is reliant on the biomolecule and particle surface characteristics and the selected coupling technique. The most critical aspects of the particle labels in bioaffinity assays are their size-dependent features. For polystyrene, silica and inorganic phosphor particles, these include the kinetics, specific activity and colloidal stability. For quantum dots and gold colloids, the spectral properties are also dependent on particle size. This study reports the utilization of europium(III)-chelate-embedded nanoparticle labels in the development of bioaffinity assays. The experimental covers both the heterogeneous and homogeneous assay formats elucidating the wide applicability of the nanoparticles. It was revealed that the employment of europium(III) nanoparticles in heterogeneous assays for viral antigens, adenovirus hexon and hepatitis B surface antigen (HBsAg), resulted in sensitivity improvement of 10-1000 fold compared to the reference methods. This improvement was attributed to the extreme specific activity and enhanced monovalent affinity of the nanoparticles conjugates. The applicability of europium(III)-chelate-doped nanoparticles to homogeneous assay formats were proved in two completely different experimental settings; assays based on immunological recognition or proteolytic activity. It was shown that in addition to small molecule acceptors, particulate acceptors may also be employed due to the high specific activity of the particles promoting proximity-induced reabsorptive energy transfer in addition to non-radiative energy transfer. The principle of proteolytic activity assay relied on a novel dual-step FRET concept, wherein the streptavidin-derivatized europium(III)-chelate-doped nanoparticles were used as donors for peptide substrates modified with biotin and terminal europium emission compliant primary acceptor and a secondary quencher acceptor. The recorded sensitized emission was proportional to the enzyme activity, and the assay response to various inhibitor doses was in agreement with those found in literature showing the feasibility of the technique. Experiments regarding the impact of donor particle size on the extent of direct donor fluorescence and reabsorptive excitation interference in a FRET-based application was conducted with differently sized europium(III)-chelate-doped nanoparticles. It was shown that the size effect was minimal

Upconverting Phosphor Technology: Exceptional Photoluminescent Properties Light Up Homogeneous Bioanalytical Assays

The aim of the present study was to demonstrate the wide applicability of the novel photoluminescent labels called upconverting phosphors (UCPs) in proximity-based bioanalytical assays. The exceptional features of the lanthanide-doped inorganic UCP compounds stem from their capability for photon upconversion resulting in anti-Stokes photoluminescence at visible wavelengths under near-infrared (NIR) excitation. Major limitations related to conventional photoluminescent labels are avoided, rendering the UCPs a competitive next-generation label technology. First, the background luminescence is minimized due to total elimination of autofluorescence. Consequently, improvements in detectability are expected. Second, at the long wavelengths (>600 nm) used for exciting and detecting the UCPs, the transmittance of sample matrixes is significantly greater in comparison with shorter wavelengths. Colored samples are no longer an obstacle to the luminescence measurement, and more flexibility is allowed even in homogeneous assay concepts, where the sample matrix remains present during the entire analysis procedure, including label detection. To transform a UCP particle into a biocompatible label suitable for bioanalytical assays, it must be colloidal in an aqueous environment and covered with biomolecules capable of recognizing the analyte molecule. At the beginning of this study, only UCP bulk material was available, and it was necessary to process the material to submicrometer-sized particles prior to use. Later, the ground UCPs, with irregular shape, wide size-distribution and heterogeneous luminescence properties, were substituted by a smaller-sized spherical UCP material. The surface functionalization of the UCPs was realized by producing a thin hydrophilic coating. Polymer adsorption on the UCP surface is a simple way to introduce functional groups for bioconjugation purposes, but possible stability issues encouraged us to optimize an optional silica-encapsulation method which produces a coating that is not detached in storage or assay conditions. An extremely thin monolayer around the UCPs was pursued due to their intended use as short-distance energy donors, and much attention was paid to controlling the thickness of the coating. The performance of the UCP technology was evaluated in three different homogeneous resonance energy transfer-based bioanalytical assays: a competitive ligand binding assay, a hybridization assay for nucleic acid detection and an enzyme activity assay. To complete the list, a competitive immunoassay has been published previously. Our systematic investigation showed that a nonradiative energy transfer mechanism is indeed involved, when a UCP and an acceptor fluorophore are brought into close proximity in aqueous suspension. This process is the basis for the above-mentioned homogeneous assays, in which the distance between the fluorescent species depends on a specific biomolecular binding event. According to the studies, the submicrometer-sized UCP labels allow versatile proximity-based bioanalysis with low detection limits (a low-nanomolar concentration for biotin, 0.01 U for benzonase enzyme, 0.35 nM for target DNA sequence).

Frequency-Domain and Wide-Pulse Time-Domain Measurements of Lanthanide Luminescence and Lanthanide-Based Resonance Energy Transfer

Resonance energy transfer (RET) is a non-radiative transfer of the excitation energy from the initially excited luminescent donor to an acceptor. The requirements for the resonance energy transfer are: i) the spectral overlap between the donor emission spectrum and the acceptor absorption spectrum, ii) the close proximity of the donor and the acceptor, and iii) the suitable relative orientations of the donor emission and the acceptor absorption transition dipoles. As a result of the RET process the donor luminescence intensity and the donor lifetime are decreased. If the acceptor is luminescent, a sensitized acceptor emission appears. The rate of RET depends strongly on the donor–acceptor distance (r) and is inversely proportional to r6. The distance dependence of RET is utilized in binding assays. The proximity requirement and the selective detection of the RET-modified emission signal allow homogeneous separation free assays. The term lanthanide-based RET is used when luminescent lanthanide compounds are used as donors. The long luminescence lifetimes, the large Stokes’ shifts and the intense, sharply-spiked emission spectra of the lanthanide donors offer advantages over the conventional organic donor molecules. Both the organic lanthanide chelates and the inorganic up-converting phosphor (UCP) particles have been used as donor labels in the RET based binding assays. In the present work lanthanide luminescence and lanthanide-based resonance energy transfer phenomena were studied. Luminescence lifetime measurements had an essential role in the research. Modular frequency-domain and time-domain luminometers were assembled and used successfully in the lifetime measurements. The frequency-domain luminometer operated in the low frequency domain ( 100 kHz) and utilized a novel dual-phase lock-in detection of the luminescence. One of the studied phenomena was the recently discovered non-overlapping fluorescence resonance energy transfer (nFRET). The studied properties were the distance and temperature dependences of nFRET. The distance dependence was found to deviate from the Förster theory and a clear temperature dependence was observed whereas conventional RET was completely independent of the temperature. Based on the experimental results two thermally activated mechanisms were proposed for the nFRET process. The work with the UCP particles involved the measurement of the luminescence properties of the UCP particles synthesized in our laboratory. The goal of the UCP particle research is to develop UCP donor labels for binding assays. In the present work the effect of the dopant concentrations and the core–shell structure on the total up-conversion luminescence intensity, the red–green emission ratio, and the luminescence lifetime was studied. Also the non-radiative nature of the energy transfer from the UCP particle donors to organic acceptors was demonstrated for the first time in aqueous environment and with a controlled donor–acceptor distance.

Luminescent Lanthanide Reporters: New Concepts for Use in Bioanalytical Applications

Lanthanides represent the chemical elements from lanthanum to lutetium. They intrinsically exhibit some very exciting photophysical properties, which can be further enhanced by incorporating the lanthanide ion into organic or inorganic sensitizing structures. A very popular approach is to conjugate the lanthanide ion to an organic chromophore structure forming lanthanide chelates. Another approach, which has quickly gained interest, is to incorporate the lanthanide ions into nanoparticle structures, thus attaining improved specific activity and binding capacity. The lanthanide-based reporters usually express strong luminescence emission, multiple narrow emission lines covering a wide wavelength range, and exceptionally long excited state lifetimes enabling timeresolved detection. Because of these properties, the lanthanide-based reporters have found widespread applications in various fields of life. This study focuses on the field of bioanalytical applications. The aim of the study was to demonstrate the utility of different lanthanide-based reporters in homogeneous Förster resonance energy transfer (FRET)-based bioaffinity assays. Several different model assays were constructed. One was a competitive bioaffinity assay that utilized energy transfer from lanthanide chelate donors to fluorescent protein acceptors. In addition to the conventional FRET phenomenon, a recently discovered non-overlapping FRET (nFRET) phenomenon was demonstrated for the first time for fluorescent proteins. The lack of spectral overlap in the nFRET mechanism provides sensitivity and versatility to energy transfer-based assays. The distance and temperature dependence of these phenomena were further studied in a DNA-hybridization assay. The distance dependence of nFRET deviated from that of FRET, and unlike FRET, nFRET demonstrated clear temperature dependence. Based on these results, a possible excitation mechanism operating in nFRET was proposed. In the study, two enzyme activity assays for caspase-3 were also constructed. One of these was a fluorescence quenching-based enzyme activity assay that utilized novel inorganic particulate reporters called upconverting phosphors (UCPs) as donors. The use of UCPs enabled the construction of a simple, rather inexpensive, and easily automated assay format that had a high throughput rate. The other enzyme activity assay took advantage of another novel reporter class, the lanthanidebinding peptides (LBPs). In this assay, energy was transferred from a LBP to a green fluorescent protein (GFP). Using the LBPs it was possible to avoid the rather laborious, often poorly repeatable, and randomly positioned chemical labeling. In most of the constructed assays, time-resolved detection was used to eliminate the interfering background signal caused by autofluorescence. The improved signal-to-background ratios resulted in increased assay sensitivity, often unobtainable in homogeneous assay formats using conventional organic fluorophores. The anti-Stokes luminescence of the UCPs, however, enabled the elimination of autofluorescence even without time-gating, thus simplifying the instrument setup. Together, the studied reporters and assay formats pave the way for increasingly sensitive, simple, and easily automated bioanalytical applications.

Feasibility of ASH DEC‐ process in treating sewage sludge and manure ash in Finland

In Finland the thermal treatment of sewage sludge has been moderate in 21th century. The reason has been the high moisture content of sludge. During 2005-2008, 97-99% of sewage sludge was utilized in landscaping and agriculture. However agricultural use has been during 2005-2007 less than 3 %. The aim of national waste management plan is that by 2016 100% of sludge is used either as soil amendment or energy. The most popular utilization method for manure is spreading it on arable land. The dry manures such as poultry manure and horse manure could also be used in incineration. The ashes could be used as fertilizers and while it is not suitable as a starter fertilizer, it is suitable in maintaining P levels in the soil. One of the main drivers for more efficient nutrient management is the eutrophication in lakes and the Baltic See. ASH DEC process can be used in concentrating phosphorus rich ashes while separating the heavy metals that could be included. ASH DEC process uses thermochemical treatment to produce renewable phosphate for fertilizer production. The process includes mixing of ashes and chlorine donors and subsequent treatment in rotary kiln for 20 min in temperature of 900 – 1 050 oC. The heavy metals evaporate and P-rich product is obtained. The toxic substances are retained in air pollution control system in form of mixed metal hydroxides. The aim of conducting this study is to estimate the potential of ASH DEC process in treating phosphorus rich ashes in Finland. The masses considered in are sewage sludge, dry manure from horses, and poultry and liquid pig manure. To date the usual treatment method for sewage sludge in Finland is composting or anaerobic digestion. Part of the amount of produced sewage sludge (800 kt/a fresh mass and 160 kt/a TS) could also be incinerated and the residual ashes used in ASH DEC process. Incinerating only manure can be economically difficult to manage because the incineration of manure is in Finland considered as waste incineration. Getting a permit for waste incineration is difficult and also small scale waste incineration is too expensive. The manure could act as an additional feedstock in counties with high density of animal husbandry where the land area might not be enough for spreading of manure. Now when the manure acts as a supplementary feedstock beside sludge, the ash can’t be used directly as fertilizer. Then it could be used in ASH DEC process. The perquisite is that the manure producers could pay for the incineration, which might prove problematic.

Spotlight: A Blacklight Plugin for Showcasing Digital Collections

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Verenluovuttajien rekisteritiedon hyödyntäminen ja kontaktoinnin kehittäminen CRM-järjestelmän avulla

Diplomityön tavoitteena on kartoittaa Suomen Punaisen Ristin Veripalvelun verenluovutustoiminnan luovuttajahallinnan nyky- ja tavoitetilaa haastattelujen, havainnoinnin sekä dokumentaation perusteella. Kartoituksen ja kuiluanalyysin avulla voidaan arvioida Microsoftin asiakassuhteiden hallintaan tarkoitetun järjestelmän soveltuvuutta Veripalvelun käyttöön. Lisäksi arvioidaan strategisen CRM-viitekehyksen soveltamista Veripalvelun luovuttajasuhteiden hallintaan, joka tarjoaa kokonaisvaltaisen ja poikkifunktionaalisen näkemyksen kriittisiin prosesseihin ja aktiviteetteihin. Asiakassuhteiden hallinta pitää nähdä kokonaisvaltaisena, koko organisaatiota koskevana jatkuvan kehittämisen kohteena olevana toimintona joka tuo lisäarvoa sekä organisaatiolle itselleen että sen asiakkaille. Voittoa tavoittelemattoman organisaation toimintaympäristössä Veripalvelulla ei ole suoraa kilpailua, joka on otettava huomioon luovuttajasuhteiden hallinnassa. Tulevaisuuden tavoitteet kartoittamalla voi kohdeorganisaatio huomioida strategisesti tärkeä osa-alueet, jotka takaavat kilpailukyvyn ja mahdollistavat arvonluonnin asiakasprosesseissa.