Contrasting tree-ring data with fire record in a pine-dominated landscape in the Komi Republic (Eastern European Russia) : recovering a common climate signal

Abstract

Biodiversity value of potential forest fertilisation stands, as assessed by red-listed and "signal" bryophytes and lichens

Abstract

The Development of Weak Signal Concept

Tämän hetken trendit kuten globalisoituminen, ympäristömme turbulenttisuus, elintason nousu, turvallisuuden tarpeen kasvu ja teknologian kehitysnopeus korostavatmuutosten ennakoinnin tarpeellisuutta. Pysyäkseen kilpailukykyisenä yritysten tulee kerätä, analysoida ja hyödyntää liiketoimintatietoa, jokatukee niiden toimintaa viranomaisten, kilpailijoiden ja asiakkaiden toimenpiteiden ennakoinnissa. Innovoinnin ja uusien konseptien kehittäminen, kilpailijoiden toiminnan arviointi, asiakkaiden tarpeet muun muassa vaativatennakoivaa arviointia. Heikot signaalit ovat keskeisessä osassa organisaatioiden valmistautumisessa tulevaisuuden tapahtumiin. Opinnäytetyön tarkoitus on luoda ja kehittää heikkojen signaalien ymmärrystä ja hallintaa sekäkehittää konseptuaalinen ja käytännöllinen lähestymistapa ennakoivan toiminnan edistämiselle. Heikkojen signaalien tyyppien luokittelu perustuu ominaisuuksiin ajan, voimakkuuden ja liiketoimintaan integroinnin suhteen. Erityyppiset heikot signaalit piirteineen luovat reunaehdot laatutekijöiden keräämiselle ja siitä edelleen laatujärjestelmän ja matemaattiseen malliin perustuvan työvälineen kehittämiselle. Heikkojen signaalien laatutekijät on kerätty yhteen kaikista heikkojen signaalien konseptin alueista. Analysoidut ja kohdistetut laatumuuttujat antavat mahdollisuuden kehittää esianalyysiä ja ICT - työvälineitä perustuen matemaattisen mallin käyttöön. Opinnäytetyön tavoitteiden saavuttamiseksi tehtiin ensin Business Intelligence -kirjallisuustutkimus. Hiekkojen signaalien prosessi ja systeemi perustuvat koottuun Business Intelligence - systeemiin. Keskeisinä kehitysalueina tarkasteltiin liiketoiminnan integraatiota ja systemaattisen menetelmän kehitysaluetta. Heikkojen signaalien menetelmien ja määritelmien kerääminen sekä integrointi määriteltyyn prosessiin luovat uuden konseptin perustan, johon tyypitys ja laatutekijät kytkeytyvät. Käytännöllisen toiminnan tarkastelun ja käyttöönoton mahdollistamiseksi toteutettiin Business Intelligence markkinatutkimus (n=156) sekä yhteenveto muihin saatavilla oleviin markkinatutkimuksiin. Syvähaastatteluilla (n=21) varmennettiin laadullisen tarkastelun oikeellisuus. Lisäksi analysoitiin neljä käytännön projektia, joiden yhteenvedot kytkettiin uuden konseptin kehittämiseen. Prosessi voidaan jakaa kahteen luokkaan: yritysten markkinasignaalit vuoden ennakoinnilla ja julkisen sektorin verkostoprojektit kehittäen ennakoinnin struktuurin luonnin 7-15 vuoden ennakoivalle toiminnalle. Tutkimus rajattiin koskemaan pääasiassa ulkoisen tiedon aluetta. IT työvälineet ja lopullisen laatusysteemin kehittäminen jätettiin tutkimuksen ulkopuolelle. Opinnäytetyön tavoitteena ollut heikkojen signaalien konseptin kehittäminen toteutti sille asetetut odotusarvot. Heikkojen signaalien systemaattista tarkastelua ja kehittämistyötä on mahdollista edistää Business Intelligence - systematiikan hyödyntämisellä. Business Intelligence - systematiikkaa käytetään isojen yritysten liiketoiminnan suunnittelun tukena.Organisaatioiden toiminnassa ei ole kuitenkaan yleisesti hyödynnetty laadulliseen analyysiin tukeutuvaa ennakoinnin weak signals - toimintaa. Ulkoisenja sisäisen tiedon integroinnin ja systematiikan hyödyt PK -yritysten tukena vaativat merkittävää panostusta julkishallinnon rahoituksen ja kehitystoiminnan tukimuotoina. Ennakointi onkin tuottanut lukuisia julkishallinnon raportteja, mutta ei käytännön toteutuksia. Toisaalta analysoitujen case-tapausten tuloksena voidaan nähdä, ettei organisaatioissa välttämättä tarvita omaa projektipäällikköä liiketoiminnan tuen kehittämiseksi. Business vastuun ottamiseksi ja asiaan sitoutumiseen on kuitenkin löydyttävä oikea henkilö

GPS-signal Source Based on Direct Digital Synthesis

This thesis presents the design and implementation of a GPS-signal source suitable for receiver measurements. The developed signal source is based on direct digital synthesis which generates the intermediate frequency. The intermediate frequency is transfered to the final frequency with the aid of an Inphase/Quadrature modulator. The modulating GPS-data was generated with MATLAB. The signal source was duplicated to form a multi channel source. It was shown that, GPS-signals ment for civil navigation are easy to generate in the laboratory. The hardware does not need to be technically advanced if navigation with high level of accuracy is not needed. It was also shown that, the Inphase/Quadrature modulator can function as a single side band upconverter even with a high intermediate frequency. This concept reduces the demands required for output filtering.

Imaging techniques applied for detection of secretion, transgene delivery and G proteincoupled receptors in reproductive and endocrine cells in vivo and in vitro

Post-testicular sperm maturation occurs in the epididymis. The ion concentration and proteins secreted into the epididymal lumen, together with testicular factors, are believed to be responsible for the maturation of spermatozoa. Disruption of the maturation of spermatozoa in the epididymis provides a promising strategy for generating a male contraceptive. However, little is known about the proteins involved. For drug development, it is also essential to have tools to study the function of these proteins in vitro. One approach for screening novel targets is to study the secretory products of the epididymis or the G protein-coupled receptors (GPCRs) that are involved in the maturation process of the spermatozoa. The modified Ca2+ imaging technique to monitor release from PC12 pheochromocytoma cells can also be applied to monitor secretory products involved in the maturational processes of spermatozoa. PC12 pheochromocytoma cells were chosen for evaluation of this technique as they release catecholamines from their cell body, thus behaving like endocrine secretory cells. The results of the study demonstrate that depolarisation of nerve growth factor -differentiated PC12 cells releases factors which activate nearby randomly distributed HEL erythroleukemia cells. Thus, during the release process, the ligands reach concentrations high enough to activate receptors even in cells some distance from the release site. This suggests that communication between randomly dispersed cells is possible even if the actual quantities of transmitter released are extremely small. The development of a novel method to analyse GPCR-dependent Ca2+ signalling in living slices of mouse caput epididymis is an additional tool for screening for drug targets. By this technique it was possible to analyse functional GPCRs in the epithelial cells of the ductus epididymis. The results revealed that, both P2X- and P2Y-type purinergic receptors are responsible for the rapid and transient Ca2+ signal detected in the epithelial cells of caput epididymides. Immunohistochemical and reverse transcriptase-polymerase chain reaction (RTPCR) analyses showed the expression of at least P2X1, P2X2, P2X4 and P2X7, and P2Y1 and P2Y2 receptors in the epididymis. Searching for epididymis-specific promoters for transgene delivery into the epididymis is of key importance for the development of specific models for drug development. We used EGFP as the reporter gene to identify proper promoters to deliver transgenes into the epithelial cells of the mouse epididymis in vivo. Our results revealed that the 5.0 kb murine Glutathione peroxidase 5 (GPX5) promoter can be used to target transgene expression into the epididymis while the 3.8 kb Cysteine-rich secretory protein-1 (CRISP-1) promoter can be used to target transgene expression into the testis. Although the visualisation of EGFP in living cells in culture usually poses few problems, the detection of EGFP in tissue sections can be more difficult because soluble EGFP molecules can be lost if the cell membrane is damaged by freezing, sectioning, or permeabilisation. Furthermore, the fluorescence of EGFP is dependent on its conformation. Therefore, fixation protocols that immobilise EGFP may also destroy its usefulness as a fluorescent reporter. We therefore developed a novel tissue preparation and preservation techniques for EGFP. In addition, fluorescence spectrophotometry with epididymal epithelial cells in suspension revealed the expression of functional purinergic, adrenergic, cholinergic and bradykinin receptors in these cell lines (mE-Cap27 and mE-Cap28). In conclusion, we developed new tools for studying the role of the epididymis in sperm maturation. We developed a new technique to analyse GPCR dependent Ca2+ signalling in living slices of mouse caput epididymis. In addition, we improved the method of detecting reporter gene expression. Furthermore, we characterised two epididymis-specific gene promoters, analysed the expression of GPCRs in epididymal epithelial cells and developed a novel technique for measurement of secretion from cells.

Mitotic regulation by Polo-like kinase 1 and the Chromosomal Passenger Complex

During mitosis, the duplicated genome must be accurately divided between two daughter cells. Polo-like kinase 1 (Plk1) and Aurora B kinase, together with its binding partners Incenp, Survivin and Borealin (chromosomal passenger complex, CPC), have key roles in coordinating mitotic events. The accuracy of cell division is safeguarded by a signaling cascade termed the mitotic spindle checkpoint (SC), which ensures that chromosomes are not physically separated before correct bipolar attachments have been formed between kinetochores and spindle microtubules (MT). An inhibitory “wait anaphase” signal, which delays chromosome separation (anaphase onset), is created at individual kinetochores and broadcasted throughout the cell in response to lack of kinetochore-microtubule (kMT) attachment or proper interkinetochore tension. It is believed that the fast turnover of SC molecules at kinetochores contributes to the cell’s ability to produce this signal and enables rapid responses to changing cellular conditions. Kinetochores that lack MT attachment and tension express a certain phosphoepitope called the 3F3/2 phosphoepitope, which has been linked to SC signaling. In the experimental part, we investigated the regulation of the 3F3/2 phosphoepitope, analyzed whether CPC molecules turn over at centromeres, and dissected the mitotic roles of the CPC using a microinjection technique that allowed precise temporal control over its function. We found that the kinetochore 3F3/2 phosphoepitope is created by Plk1, and that CPC proteins exhibit constant exchange at centromeres. Moreover, we found that CPC function is necessary in the regulation of chromatid movements and spindle morphology in anaphase. In summary, we identified new functions of key mitotic regulators Plk1 and CPC, and provided insighs into the coordination of mitotic events.

Highly functional binding surface for miniaturised solid-phase immunoassays. - A spot story -

Several bioaffinity assays are based on the detection of an analyte which is bound on a solid substrate via biochemical interaction. These so called solid phase assays are based on the adhesion of the primary binding partner on a solid surface, which then binds the analyte to be detected. In this thesis work a novel solid phase based assay technology, known as spot technology, was developed. The spot technology is based on combination of high-capacity solid phases, concentrated in a spot format, utilising modified streptavidin molecules and recombinant antibody fragments. The reduction of the solid phase binding surface to a size of a spot enabled denser binding of the target molecules, providing improved signal intensities and signal-to-background ratio when applied in different solid phase immunoassays. Streptavidin-biotin interactions are commonly utilised in numerous different bioaffinity assays and the ultimate nature of streptavidin to bind biotin is among the strongest non-covalent interaction reported between two biomolecules. In this study native core streptavidin was chemically modified to provide polymerised streptavidin molecules with altered adsorption properties. These streptavidin conjugates, when coated onto polystyrene surface, provided enhanced biotin binding capacity and surface stability when compared to a reference coating constructed with native streptavidin. Furthermore, the combination of chemically modified streptavidin, sitespecifically biotinylated antibody fragments and the spot coating technology provided highly dense solid phase coating with improved binding properties. The performance of the spot assay technology was further demonstrated in different immunoassay configurations. Human thyroid stimulating hormone (TSH) and human cardiac troponin I (cTnI) were used as model analytes to show the applicability of the highly sensitive spot-based solid-phase immunoassay for detection of very low levels of analytes. It was demonstrated that the spot technology provided an assay concept with enhanced sensitivity and short turn-around times, characteristics that are highly suitable for point-of-care applications.

Luminescence-based assay methods in drug discovery

The drug discovery process is facing new challenges in the evaluation process of the lead compounds as the number of new compounds synthesized is increasing. The potentiality of test compounds is most frequently assayed through the binding of the test compound to the target molecule or receptor, or measuring functional secondary effects caused by the test compound in the target model cells, tissues or organism. Modern homogeneous high-throughput-screening (HTS) assays for purified estrogen receptors (ER) utilize various luminescence based detection methods. Fluorescence polarization (FP) is a standard method for ER ligand binding assay. It was used to demonstrate the performance of two-photon excitation of fluorescence (TPFE) vs. the conventional one-photon excitation method. As result, the TPFE method showed improved dynamics and was found to be comparable with the conventional method. It also held potential for efficient miniaturization. Other luminescence based ER assays utilize energy transfer from a long-lifetime luminescent label e.g. lanthanide chelates (Eu, Tb) to a prompt luminescent label, the signal being read in a time-resolved mode. As an alternative to this method, a new single-label (Eu) time-resolved detection method was developed, based on the quenching of the label by a soluble quencher molecule when displaced from the receptor to the solution phase by an unlabeled competing ligand. The new method was paralleled with the standard FP method. It was shown to yield comparable results with the FP method and found to hold a significantly higher signal-tobackground ratio than FP. Cell-based functional assays for determining the extent of cell surface adhesion molecule (CAM) expression combined with microscopy analysis of the target molecules would provide improved information content, compared to an expression level assay alone. In this work, immune response was simulated by exposing endothelial cells to cytokine stimulation and the resulting increase in the level of adhesion molecule expression was analyzed on fixed cells by means of immunocytochemistry utilizing specific long-lifetime luminophore labeled antibodies against chosen adhesion molecules. Results showed that the method was capable of use in amulti-parametric assay for protein expression levels of several CAMs simultaneously, combined with analysis of the cellular localization of the chosen adhesion molecules through time-resolved luminescence microscopy inspection.

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.

System-wide approaches to uncover Th2 cell lineage commitment

T helper (Th) cells are vital regulators of the adaptive immune system. When activated by presentation of cognate antigen, Th cells demonstrate capacity to differentiate into functionally distinct effector cell subsets. The Th2 subset is required for protection against extracellular parasites, such as helminths, but is also closely linked to pathogenesis of asthma and allergies. The intracellular molecular signal transduction pathways regulating T helper cell subset differentiation are still incompletely known. Moreover, great majority of studies regarding Th2 differentiation have been conducted with mice models, while studies with human cells have been fewer in comparison. The goal of this thesis was to characterize molecular mechanisms promoting the development of Th2 phenotype, focusing specifically on human umbilical cord blood T cells as an experimental model. These primary cells, activated and differentiated to Th2 cells in vitro, were investigated by complementary system-wide approaches, targeting levels of mRNA, proteins, and lipid molecules. Specifically, the results indicated IL4-regulated recruitment of nuclear protein, and described novel components of the Th2-promoting STAT6 enhanceosome complex. Furthermore, the development of the activated effector cell phenotype was found to correlate with remodeling of the cellular lipidome. These findings will hopefully advance the understanding of human Th2 cell lineage commitment and development of Th2-associated disease states.

Integrins in Tumorigenesis and Cancer Cell Invasion

The integrin family of transmembrane receptors are important for cell-matrix adhesion and signal transmission to the interior of the cell. Integrins are essential for many physiological processes and defective integrin function can consequently result in a multitude of diseases, including cancer. Integrin traffic is needed for completion of cytokinesis and cell division failure has been proposed to be an early event in the formation of chromosomally aberrant and transformed cells. Impaired integrin traffic and changes in integrin expression are known to promote invasion of malignant cells. However, the direct roles of impaired integrin traffic in tumorigenesis and increased integrin expression in oncogene driven invasion have not been examined. In this study we have investigated both of these aspects. We found that cells with reduced integrin endocytosis become binucleate and subsequently aneuploid. These aneuploid cells display characteristics of transformed cells; they are anchorage-independent, resistant to apoptosis and invasive in vitro. Importantly, subcutaneous injection of the aneuploid cells into athymic nude mice produced highly malignant tumors. Through gene expression profiling and analysis of integrin-triggered signaling pathways we have identified several molecules involved in the malignancy of these cells, including Src kinase and the transcription factor Twist2. Thus, even though chromosomal aberrations are associated with reduced cell fitness, we show that aneuploidy can facilitate tumor evolution and selection of transformed cells. Invasion and metastasis are the primary reason for deaths caused by cancer and the molecular pathways responsible for invasion are therefore attractive targets in cancer therapy. In addition to integrins, another major family of adhesion receptors are the proteoglycans syndecans. Integrins and syndecans are known to signal in a synergistic manner in controlling cell adhesion on 2D matrixes. Here we explored the role of syndecans as α2β1 integrin co-receptors in 3D collagen. We show that in breast cancer cells harbouring mutant K-Ras, increased levels of integrins, their co-receptors syndecans and matrix cleaving proteases are necessary for the invasive phenotype of these cells. Together, these findings increase our knowledge of the complicated changes that occur during tumorigenesis and the pathways that control the ability of cancer cells to invade and metastasize.

Cellular responses to stress and kinase signaling activation : apoptosis and differentiation

Stressignaler avkänns många gånger av membranbundna proteiner som översätter signalerna till kemisk modifiering av molekyler, ofta proteinkinaser Dessa kinaser överför de avkodade budskapen till specifika transkriptionsfaktorer genom en kaskad av sekventiella fosforyleringshändelser, transkriptionsfaktorerna aktiverar i sin tur de gener som behövs för att reagera på stressen. En av de mest kända måltavlorna för stressignaler är transkriptionsfaktor AP-1 familjemedlemen c-Jun. I denna studie har jag identifierat den nukleolära proteinet AATF som en ny regulator av c-Jun-medierad transkriptionsaktivitet. Jag visar att stresstimuli inducerar omlokalisering av AATF vilket i sin tur leder till aktivering av c-Jun. Den AATF-medierad ökningen av c-Jun-aktiviteten leder till en betydande ökning av programmerad celldöd. Parallellt har jag vidarekarakteriserat Cdk5/p35 signaleringskomplexet som tidigare har identifierats i vårt laboratorium som en viktig faktor för myoblastdifferentiering. Jag identifierade den atypiska PKCξ som en uppströms regulator av Cdk5/p35-komplexet och visar att klyvning och aktivering av Cdk5 regulatorn p35 är av fysiologisk betydelse för differentieringsprocessen och beroende av PKCξ aktivitet. Jag visar att vid induktion av differentiering fosforylerar PKCξ p35 vilket leder till calpain-medierad klyvning av p35 och därmed ökning av Cdk5-aktiviteten. Denna avhandling ökar förståelsen för de regulatoriska mekanismer som styr c-Jun-transkriptionsaktiviteten och c-Jun beroende apoptos genom att identifiera AATF som en viktig faktor. Dessutom ger detta arbete nya insikter om funktionen av Cdk5/p35-komplexet under myoblastdifferentiering och identifierar PKCξ som en uppströms regulator av Cdk5 aktivitet och myoblast differentiering.