Type II aromatic polyketide biosynthetic tailoring enzymes: diversity and adaptation in Streptomyces secondary metabolism.

Members of the bacterial genus Streptomyces are well known for their ability to produce an exceptionally wide selection of diverse secondary metabolites. These include natural bioactive chemical compounds which have potential applications in medicine, agriculture and other fields of commerce. The outstanding biosynthetic capacity derives from the characteristic genetic flexibility of Streptomyces secondary metabolism pathways: i) Clustering of the biosynthetic genes in chromosome regions redundant for vital primary functions, and ii) the presence of numerous genetic elements within these regions which facilitate DNA rearrangement and transfer between non-progeny species. Decades of intensive genetic research on the organization and function of the biosynthetic routes has led to a variety of molecular biology applications, which can be used to expand the diversity of compounds synthesized. These include techniques which, for example, allow modification and artificial construction of novel pathways, and enable gene-level detection of silent secondary metabolite clusters. Over the years the research has expanded to cover molecular-level analysis of the enzymes responsible for the individual catalytic reactions. In vitro studies of the enzymes provide a detailed insight into their catalytic functions, mechanisms, substrate specificities, interactions and stereochemical determinants. These are factors that are essential for the thorough understanding and rational design of novel biosynthetic routes. The current study is a part of a more extensive research project (Antibiotic Biosynthetic Enzymes; www.sci.utu.fi/projects/biokemia/abe), which focuses on the post-PKS tailoring enzymes involved in various type II aromatic polyketide biosynthetic pathways in Streptomyces bacteria. The initiative here was to investigate specific catalytic steps in anthracycline and angucycline biosynthesis through in vitro biochemical enzyme characterization and structural enzymology. The objectives were to elucidate detailed mechanisms and enzyme-level interactions which cannot be resolved by in vivo genetic studies alone. The first part of the experimental work concerns the homologous polyketide cyclases SnoaL and AknH. These catalyze the closure of the last carbon ring of the tetracyclic carbon frame common to all anthracycline-type compounds. The second part of the study primarily deals with tailoring enzymes PgaE (and its homolog CabE) and PgaM, which are responsible for a cascade of sequential modification reactions in angucycline biosynthesis. The results complemented earlier in vivo findings and confirmed the enzyme functions in vitro. Importantly, we were able to identify the amino acid -level determinants that influence AknH and SnoaL stereoselectivity and to determine the complex biosynthetic steps of the angucycline oxygenation cascade of PgaE and PgaM. In addition, the findings revealed interesting cases of enzyme-level adaptation, as some of the catalytic mechanisms did not coincide with those described for characterised homologs or enzymes of known function. Specifically, SnoaL and AknH were shown to employ a novel acid-base mechanism for aldol condenzation, whereas the hydroxylation reaction catalysed by PgaM involved unexpected oxygen chemistry. Owing to a gene-level fusion of two ancestral reading frames, PgaM was also shown to adopt an unusual quaternary sturucture, a non-covalent fusion complex of two alternative forms of the protein. Furthermore, the work highlighted some common themes encountered in polyketide biosynthetic pathways such as enzyme substrate specificity and intermediate reactivity. These are discussed in the final chapters of the work.

Cuticular and Suberin Polymers of Edible Plants. Analysis by Gas Chromatographic-Mass Spectrometric and Solid State Spectroscopic Methods

Cutin and suberin are structural and protective polymers of plant surfaces. The epidermal cells of the aerial parts of plants are covered with an extracellular cuticular layer, which consists of polyester cutin, highly resistant cutan, cuticular waxes and polysaccharides which link the layer to the epidermal cells. A similar protective layer is formed by a polyaromatic-polyaliphatic biopolymer suberin, which is present particularly in the cell walls of the phellem layer of periderm of the underground parts of plants (e.g. roots and tubers) and the bark of trees. In addition, suberization is also a major factor in wound healing and wound periderm formation regardless of the plants’ tissue. Knowledge of the composition and functions of cuticular and suberin polymers is important for understanding the physiological properties for the plants and for nutritional quality when these plants are consumed as foods. The aims of the practical work were to assess the chemical composition of cuticular polymers of several northern berries and seeds and suberin of two varieties of potatoes. Cutin and suberin were studied as isolated polymers and further after depolymerization as soluble monomers and solid residues. Chemical and enzymatic depolymerization techniques were compared and a new chemical depolymerization method was developed. Gas chromatographic analysis with mass spectrometric detection (GC-MS) was used to assess the monomer compositions. Polymer investigations were conducted with solid state carbon-13 cross polarization magic angle spinning nuclear magnetic resonance spectroscopy (13C CP-MAS NMR), Fourier transform infrared spectroscopy (FTIR) and microscopic analysis. Furthermore, the development of suberin over one year of post-harvest storage was investigated and the cuticular layers from berries grown in the North and South of Finland were compared. The results show that the amounts of isolated cuticular layers and cutin monomers, as well as monomeric compositions vary greatly between the berries. The monomer composition of seeds was found to differ from the corresponding berry peel monomers. The berry cutin monomers were composed mostly of long-chain aliphatic ω-hydroxy acids, with various mid-chain functionalities (double-bonds, epoxy, hydroxy and keto groups). Substituted α,ω-diacids predominated over ω-hydroxy acids in potato suberin monomers and slight differences were found between the varieties. The newly-developed closed tube chemical method was found to be suitable for cutin and suberin analysis and preferred over the solvent-consuming and laborious reflux method. Enzymatic hydrolysis with cutinase was less effective than chemical methanolysis and showed specificity towards α,ω-diacid bonds. According to ₁₃C CP-MAS NMR and FTIR, the depolymerization residues contained significant amounts of aromatic structures, polysaccharides and possible cutan-type aliphatic moieties. Cultivation location seems to have effect on cuticular composition. The materials studied contained significant amounts of different types of biopolymers that could be utilized for several purposes with or without further processing. The importance of the so-called waste material from industrial processes of berries and potatoes as a source of either dietary fiber or specialty chemicals should be further investigated in detail. The evident impact of cuticular and suberin polymers, among other fiber components, on human health should be investigated in clinical trials. These by-product materials may be used as value-added fiber fractions in the food industry and as raw materials for specialty chemicals such as lubricants and emulsifiers, or as building blocks for novel polymers.

Biosynthesis of pyranonaphthoquinone polyketides:characterization of the alnumycin pathway

Alnumycin A is an aromatic pyranonaphthoquinone (PNQ) polyketide closely related to the model compound actinorhodin. While some PNQ polyketides are glycosylated, alnumycin A contains a unique sugar-like dioxane moiety. This unusual structural feature made alnumycin A an interesting research target, since no information was available about its biosynthesis. Thus, the main objective of the thesis work became to identify the steps and the enzymes responsible for the biosynthesis of the dioxane moiety. Cloning, sequencing and heterologous expression of the complete alnumycin gene cluster from Streptomyces sp. CM020 enabled the inactivation of several alnumycin biosynthetic genes and preliminary identification of the gene products responsible for pyran ring formation, quinone formation and dioxane biosynthesis. The individual deletions of the genes resulted in the production of several novel metabolites, which in many cases turned out to be pathway intermediates and could be used for stepwise enzymatic reconstruction of the complete dioxane biosynthetic pathway in vitro. Furthermore, the in vitro reactions with purified alnumycin biosynthetic enzymes resulted in the production of other novel compounds, both pathway intermediates and side products. Identification and molecular level studies of the enzymes AlnA and AlnB catalyzing the first step of dioxane biosynthesis – an unusual C-ribosylation step – led to a mechanistic proposal for the C-ribosylation of the polyketide aglycone. The next step on the dioxane biosynthetic pathway was found to be the oxidative conversion of the attached ribose into a highly unusual dioxolane unit by Aln6 belonging to an uncharacterized protein family, which unexpectedly occurred without any apparent cofactors. Finally, the last step of the pathway was found to be catalyzed by the NADPH-dependent reductase Aln4, which is able to catalyze the conversion of the formed dioxolane into a dioxane moiety. The work presented here and the knowledge gained of the enzymes involved in dioxane biosynthesis enables their use in the rational design of novel compounds containing C–C bound ribose, dioxolane and dioxane moieties.

Glycosylation and Glycodiversification in Polyketide Antibiotics: Unraveling Biosynthetic Steps in Nogalamycin Formation

Soil-dwelling Streptomyces bacteria are known for their ability to produce biologically active compounds such as antimicrobial, immunosuppressant, antifungal and anticancer drugs. S. nogalater is the producer of nogalamycin, a potential anticancer drug exhibiting high cytotoxicity and activity against human topoisomerases I and II. Nogalamycin is an anthracycline polyketide comprising a four-ring aromatic backbone,a neutral deoxy sugar at C7, and an amino sugar attached via an O–C bond at C1 and a C–C bond between C2 and C5´´. This kind of attachment of the amino sugar is unusual thus making the structure of the compound highly interesting. The sugar is also associated with the biological activity of nogalamycin, as it facilitates binding to DNA. Furthermore, the sugar moieties of anthracyclines are often crucial for their biological activity. Together the interesting attachment of the amino sugar and the general reliance of polyketides on the sugar moieties for bioactivity have made the study of the biosynthesis of nogalamycin attractive. The sugar moieties are typically attached by glycosyltransferases, which use two substrates: the donor and the acceptor. The literature review of the thesis is focused on the glycosylation of polyketides and the possibilities to alter their glycosylation patterns. My own thesis work revolves around the biosynthesis of nogalamycin. We have elucidated the individual steps that lead to its rather unique structure. We reconstructed the whole biosynthetic pathway in the heterologous host S. albus using a cosmid and a plasmid. In the process, we were able to isolate new compounds when the cosmid, which contains the majority of the nogalamycin gene cluster, was expressed alone in the heterologous host. The new compounds included true intermediates of the pathway as well as metabolites, which were most likely altered by the endogenous enzymes of the host. The biological activity of the most interesting new products was tested against human topoisomerases I and II, and they were found to exhibit such activities. The heterologous expression system facilitated the generation of mutants with inactivated biosynthetic genes. In that process, we were able to identify the functions of the glycosyltransferases SnogE and SnogD, solve the structure of SnogD, discover a novel C1-hydroxylase system comprising SnoaW and SnoaL2, and establish that the two homologous non-heme α-ketoglutarate and Fe2+ dependent enzymes SnoK and SnoN catalyze atypical reactions on the pathway. We demonstrated that SnoK was responsible for the formation of the additional C–C bond, whereas SnoN is an epimerase. A combination of in vivo and in vitro techniques was utilized to unravel the details of these enzymes. Protein crystallography gave us an important means to understand the mechanisms. Furthermore, the solved structures serve as platforms for future rational design of the enzymes.

Practical applications of a systematic approach to the chemical abatement of pollutants in water and air

The present dissertation is devoted to the systematic approach to the development of organic toxic and refractory pollutants abatement by chemical decomposition methods in aqueous and gaseous phases. The systematic approach outlines the basic scenario of chemical decomposition process applications with a step-by-step approximation to the most effective result with a predictable outcome for the full-scale application, confirmed by successful experience. The strategy includes the following steps: chemistry studies, reaction kinetic studies in interaction with the mass transfer processes under conditions of different control parameters, contact equipment design and studies, mathematical description of the process for its modelling and simulation, processes integration into treatment technology and its optimisation, and the treatment plant design. The main idea of the systematic approach for oxidation process introduction consists of a search for the most effective combination between the chemical reaction and the treatment device, in which the reaction is supposed to take place. Under this strategy,a knowledge of the reaction pathways, its products, stoichiometry and kinetics is fundamental and, unfortunately, often unavailable from the preliminary knowledge. Therefore, research made in chemistry on novel treatment methods, comprisesnowadays a substantial part of the efforts. Chemical decomposition methods in the aqueous phase include oxidation by ozonation, ozone-associated methods (O3/H2O2, O3/UV, O3/TiO2), Fenton reagent (H2O2/Fe2+/3+) and photocatalytic oxidation (PCO). In the gaseous phase, PCO and catalytic hydrolysis over zero valent ironsare developed. The experimental studies within the described methodology involve aqueous phase oxidation of natural organic matter (NOM) of potable water, phenolic and aromatic amino compounds, ethylene glycol and its derivatives as de-icing agents, and oxygenated motor fuel additives ¿ methyl tert-butyl ether (MTBE) ¿ in leachates and polluted groundwater. Gas-phase chemical decomposition includes PCO of volatile organic compounds and dechlorination of chlorinated methane derivatives. The results of the research summarised here are presented in fifteenattachments (publications and papers submitted for publication and under preparation).

Suodatuskalvojen toimivuuden arviointi paperiteollisuuden sovelluksissa

Työn tavoitteena oli etsiä vaihtoehtoja paperiteollisuuden kiertovesien ja pastapitoisten jätevesien suodatusprosesseissa tällä hetkellä käytössä oleville kalvoille. Työssä pyrittiin myös määrittämään tekijöitä, joiden avulla voitaisiin ennustaa polymeerikalvon käyttäytymistä erilaisissa paperiteollisuuden kalvosovelluksissa. Työn kirjallisessa osassa tarkasteltiin polymeerikalvojen ominaisuuksia, jotka vaikuttavat kalvojen käyttäytymiseen suodatusprosesseissa. Työssä esiteltiin myös tavallisimmat kalvomateriaalit ja polymeerikalvojen valmistustavat sekä paperiteollisuuden kalvosovelluksia. Paperiteollisuuden kalvosuodatussovellukset eroavat toisistaan huomattavasti toimintaolosuhteiltaan ja käyttötarkoituksiltaan. Tästä johtuen on hankalaa löytää yhteisiä tekijöitä, joiden perusteella voitaisiin ennustaa kalvon käyttäytymistä eri sovelluksissa. Kalvon hydrofiilisyyden todettiin kuitenkin vaikuttavan positiivisesti suodatustapahtumaan useissa sovelluksissa. Kokeellisessa osassa verrattiin erilaisten polymeerikalvojen ja referenssikalvojen toimintaa happaman kirkkaan suodoksen ja pastapitoisen veden suodatuksessa. Kirkkaan suodoksen suodatuskokeet tehtiin UPM-Kymmene Oy:n Kaukaan tehtailla. Pastapitoista jätevettä mallinnettiin syöttöpanoksilla, jotka tehtiin laimentamalla CTC:n valmistamaa LWC-pastaa. Suodatukset tehtiin CR 200/1- ja CR 550/10 -suodattimilla. Kirkkaan suodoksen suodatuksissa käytettiin referenssikalvona regeneroidusta selluloosasta ja pastapitoisen veden suodatuksessa aromaattisesta polyamidista valmistettua kalvoa. Kirkkaan suodoksen koesuodatusten perusteella todettiin, ettei minkään vertailtavan ultrasuodatuskalvon suodatuskapasiteetti ollut yhtä korkea kuin referenssikalvon. Referenssikalvon toiminta suodatuksessa oli myös vakaata syötön laadun muutoksista huolimatta. Todennäköisesti referenssikalvon erittäin hydrofiilinen luonne tekee siitä vertailtavia kalvoja sopivamman kirkkaan suodoksen suodatukseen. Pastapitoisen veden suodatustulosten perusteella referenssikalvolle löytyi useita potentiaalisia korvaajia. Näistä parhaan kalvon valitseminen edellyttää kuitenkin jatkotutkimuksia. SEM-analyysituloksista huomattiin, että tietyntyyppinen kalvorakenne parantaa kalvon toimintaa pastapitoisen veden suodatuksessa.

Design and production of protein nanostructures for biomolecular detection

Particulate nanostructures are increasingly used for analytical purposes. Such particles are often generated by chemical synthesis from non-renewable raw materials. Generation of uniform nanoscale particles is challenging and particle surfaces must be modified to make the particles biocompatible and water-soluble. Usually nanoparticles are functionalized with binding molecules (e.g., antibodies or their fragments) and a label substance (if needed). Overall, producing nanoparticles for use in bioaffinity assays is a multistep process requiring several manufacturing and purification steps. This study describes a biological method of generating functionalized protein-based nanoparticles with specific binding activity on the particle surface and label activity inside the particles. Traditional chemical bioconjugation of the particle and specific binding molecules is replaced with genetic fusion of the binding molecule gene and particle backbone gene. The entity of the particle shell and binding moieties are synthesized from generic raw materials by bacteria, and fermentation is combined with a simple purification method based on inclusion bodies. The label activity is introduced during the purification. The process results in particles that are ready-to-use as reagents in bioaffinity. Apoferritin was used as particle body and the system was demonstrated using three different binding moieties: a small protein, a peptide and a single chain Fv antibody fragment that represents a complex protein including disulfide bridge.If needed, Eu3+ was used as label substance. The results showed that production system resulted in pure protein preparations, and the particles were of homogeneous size when visualized with transmission electron microscopy. Passively introduced label was stably associated with the particles, and binding molecules genetically fused to the particle specifically bound target molecules. Functionality of the particles in bioaffinity assays were successfully demonstrated with two types of assays; as labels and in particle-enhanced agglutination assay. This biological production procedure features many advantages that make the process especially suited for applications that have frequent and recurring requirements for homogeneous functional particles. The production process of ready, functional and watersoluble particles follows principles of “green chemistry”, is upscalable, fast and cost-effective.

Altistuminen PAH-yhdisteille kreosoottikyllästetyn puun käsittelyssä

Tässä työssä selvitettiin altistutaanko kreosoottikyllästetyn puun käsittelyssä polysyklisille aromaattisille hiilivedyille ja mistä työsuojelullisista syistä altistumista tapahtuu. Lisäksi työssä selvitettiin mitä altistuminen tarkoittaa työnantajan kannalta. Altistumista tarkasteltiin työturvallisuuden näkökulmasta. Lähtöaineisto koostui maastossa toteutetuista tutkimuksista. Aineisto kerättiin kesällä 2009 kolmesta Itä-Suomessa sijaitsevasta kohteesta, joissa käsiteltiin kreosootilla kyllästettyä puuta. Altistumisen todentamiseksi tutkimukseen osallistuneilta työntekijöiltä pyydettiin virtsanäytteet, joista analysoitiin yhden yleisimmän PAH-altistumista indikoivan merkkiaineen, virtsan 1-pyrenolin pitoisuuksia työntekijöillä. Altistumisen syiden selvittämiseksi työntekijöitä haastateltiin ja havainnoitiin. Tulosten perusteella työntekijät altistuvat PAH-yhdisteille työssään. PAH-altistumisen merkkiaineena olleelle virtsan 1-pyrenolille ei toimenpiderajaa tällä hetkellä ole, mutta se on Työterveyslaitoksella suunnitteilla. Lainsäädäntö velvoittaa erinäisin toimenpitein työnantajaa minimoimaan työntekijöiden altistumisen syöpäsairauden vaaraa aiheuttaville aineille, kuten PAH-yhdisteille. Tulosten perusteella työsuojelutoimenpiteitä on syytä tehostaa altistumisen minimoimiseksi ja etenkin ihon suojaamiseen on syytä kiinnittää erityistä huomiota.

NADPH-Dependent Thioredoxin System In Regulation of Chloroplast Functions

Photosynthesis, the process in which carbon dioxide is converted into sugars using the energy of sunlight, is vital for heterotrophic life on Earth. In plants, photosynthesis takes place in specific organelles called chloroplasts. During chloroplast biogenesis, light is a prerequisite for the development of functional photosynthetic structures. In addition to photosynthesis, a number of other metabolic processes such as nitrogen assimilation, the biosynthesis of fatty acids, amino acids, vitamins, and hormones are localized to plant chloroplasts. The biosynthetic pathways in chloroplasts are tightly regulated, and especially the reduction/oxidation (redox) signals play important roles in controlling many developmental and metabolic processes in chloroplasts. Thioredoxins are universal regulatory proteins that mediate redox signals in chloroplasts. They are able to modify the structure and function of their target proteins by reduction of disulfide bonds. Oxidized thioredoxins are restored via the action of thioredoxin reductases. Two thioredoxin reductase systems exist in plant chloroplasts, the NADPHdependent thioredoxin reductase C (NTRC) and ferredoxin-thioredoxin reductase (FTR). The ferredoxin-thioredoxin system that is linked to photosynthetic light reactions is involved in light-activation of chloroplast proteins. NADPH can be produced via both the photosynthetic electron transfer reactions in light, and in darkness via the pentose phosphate pathway. These different pathways of NADPH production enable the regulation of diverse metabolic pathways in chloroplasts by the NADPH-dependent thioredoxin system. In this thesis, the role of NADPH-dependent thioredoxin system in the redox-control of chloroplast development and metabolism was studied by characterization of Arabidopsis thaliana T-DNA insertion lines of NTRC gene (ntrc) and by identification of chloroplast proteins regulated by NTRC. The ntrc plants showed the strongest visible phenotypes when grown under short 8-h photoperiod. This indicates that i) chloroplast NADPH-dependent thioredoxin system is non-redundant to ferredoxinthioredoxin system and that ii) NTRC particularly controls the chloroplast processes that are easily imbalanced in daily light/dark rhythms with short day and long night. I identified four processes and the redox-regulated proteins therein that are potentially regulated by NTRC; i) chloroplast development, ii) starch biosynthesis, iii) aromatic amino acid biosynthesis and iv) detoxification of H₂O₂. Such regulation can be achieved directly by modulating the redox state of intramolecular or intermolecular disulfide bridges of enzymes, or by protecting enzymes from oxidation in conjunction with 2-cysteine peroxiredoxins. This thesis work also demonstrated that the enzymatic antioxidant systems in chloroplasts, ascorbate peroxidases, superoxide dismutase and NTRC-dependent 2-cysteine peroxiredoxins are tightly linked up to prevent the detrimental accumulation of reactive oxygen species in plants.

Consumer Attitudes on Aroma Printing

Olfactory packaging is an emerging technology which uses the aromatic capsules to release various scents. Normally, manufacturers add these aromatic capsules in the printing ink, the label or packaging material itself. When the aromatic capsules meet suitable release triggers, the scents will be released. The common release triggers are external forces, temperature changes, humidity changes and so on. The aim for this Masters of Science Thesis is to understand the aroma printing technology from literature and make market research for this kind of technology. The main target is to collect the current technology principle of aroma packaging and figure out how they are implemented on products with those. In addition, an investigation is made about consumers' attitudes from Chinese and Finnish market through the questionnaire, and the market potential is analyzed as well. The key points researched in this work are: the general attitudes on aroma printing technology, market potential and economic possibilities. This thesis specifies the main technologies used in aroma printing, the solutions of products with aroma packaging and the original results of the questionnaires. It also includes analysis of the acceptance of Chinese and Finnish consumers, what are their opinions of the aroma printing technology and the products packed by aroma printing technology. In addition, various factors which impact the market is discussed in the thesis. At last, some comparisons are made from the point of views of similarities and differences between Chinese and Finnish market.

Survey of transportation of liquid bulk chemicals in the Baltic Sea

This study is made as a part of the Chembaltic (Risks of Maritime Transportation of Chemicals in Baltic Sea) project which gathers information on the chemicals transported in the Baltic Sea. The purpose of this study is to provide an overview of handling volumes of liquid bulk chemicals (including liquefied gases) in the Baltic Sea ports and to find out what the most transported liquid bulk chemicals in the Baltic Sea are. Oil and oil products are also viewed in this study but only in a general level. Oils and oil products may also include chemical-related substances (e.g. certain bio-fuels which belong to MARPOL annex II category) in some cargo statistics. Chemicals in packaged form are excluded from the study. Most of the facts about the transport volumes of chemicals presented in this study are based on secondary written sources of Scandinavian, Russian, Baltic and international origin. Furthermore, statistical sources, academic journals, periodicals, newspapers and in later years also different homepages on the Internet have been used as sources of information. Chemical handling volumes in Finnish ports were examined in more detail by using a nationwide vessel traffic system called PortNet. Many previous studies have shown that the Baltic Sea ports are annually handling more than 11 million tonnes of liquid chemicals transported in bulk. Based on this study, it appears that the number may be even higher. The liquid bulk chemicals account for approximately 4 % of the total amount of liquid bulk cargoes handled in the Baltic Sea ports. Most of the liquid bulk chemicals are handled in Finnish and Swedish ports and their proportion of all liquid chemicals handled in the Baltic Sea is altogether over 50 %. The most handled chemicals in the Baltic Sea ports are methanol, sodium hydroxide solution, ammonia, sulphuric and phosphoric acid, pentanes, aromatic free solvents, xylenes, methyl tert-butyl ether (MTBE) and ethanol and ethanol solutions. All of these chemicals are handled at least hundred thousand tonnes or some of them even over 1 million tonnes per year, but since chemical-specific data from all the Baltic Sea countries is not available, the exact tonnages could not be calculated in this study. In addition to these above-mentioned chemicals, there are also other high volume chemicals handled in the Baltic Sea ports (e.g. ethylene, propane and butane) but exact tonnes are missing. Furthermore, high amounts of liquid fertilisers, such as solution of urea and ammonium nitrate in water, are transported in the Baltic Sea. The results of the study can be considered indicative. Updated information about transported chemicals in the Baltic Sea is the first step in the risk assessment of the chemicals. The chemical-specific transportation data help to target hazard or e.g. grounding/collision risk evaluations to chemicals that are handled most or have significant environmental hazard potential. Data gathered in this study will be used as background information in later stages of the Chembaltic project when the risks of the chemicals transported in the Baltic Sea are assessed to highlight the chemicals that require special attention from an environmental point of view in potential marine accident situations in the Baltic Sea area.

Synthesis, characterization and chemical sensor application of conducting polymers

Polymeric materials that conduct electricity are highly interesting for fundamental studies and beneficial for modern applications in e.g. solar cells, organic field effect transistors (OFETs) as well as in chemical and bio‐sensing. Therefore, it is important to characterize this class of materials with a wide variety of methods. This work summarizes the use of electrochemistry also in combination with spectroscopic methods in synthesis and characterization of electrically conducting polymers and other π‐conjugated systems. The materials studied in this work are intended for organic electronic devices and chemical sensors. Additionally, an important part of the presented work, concerns rational approaches to the development of water‐based inks containing conducting particles. Electrochemical synthesis and electroactivity of conducting polymers can be greatly enhanced in room temperature ionic liquids (RTILs) in comparison to conventional electrolytes. Therefore, poly(para‐phyenylene) (PPP) was electrochemically synthesized in the two representative RTILs: bmimPF6 and bmiTf2N (imidazolium and pyrrolidinium‐based salts, respectively). It was found that the electrochemical synthesis of PPP was significantly enhanced in bmimPF6. Additionally, the results from doping studies of PPP films indicate improved electroactivity in bmimPF6 during oxidation (p‐doping) and in bmiTf2N in the case of reduction (n‐doping). These findings were supported by in situ infrared spectroscopy studies. Conducting poly(benzimidazobenzophenanthroline) (BBL) is a material which can provide relatively high field‐effect mobility of charge carriers in OFET devices. The main disadvantage of this n‐type semiconductor is its limited processability. Therefore in this work BBL was functionalized with poly(ethylene oxide) PEO, varying the length of side chains enabling water dispersions of the studied polymer. It was found that functionalization did not distract the electrochemical activity of the BBL backbone while the processability was improved significantly in comparison to conventional BBL. Another objective was to study highly processable poly(3,4‐ethylenedioxythiophene) poly(styrenesulfonate) (PEDOT:PSS) water‐based inks for controlled patterning scaled‐down to nearly a nanodomain with the intention to fabricate various chemical sensors. Developed PEDOT:PSS inks greatly improved printing of nanoarrays and with further modification with quaternary ammonium cations enabled fabrication of PEDOT:PSS‐based chemical sensors for lead (II) ions with enhanced adhesion and stability in aqueous environments. This opens new possibilities for development of PEDOT:PSS films that can be used in bio‐related applications. Polycyclic aromatic hydrocarbons (PAHs) are a broad group of π‐conjugated materials consisting of aromatic rings in the range from naphthalene to even hundred rings in one molecule. The research on this type of materials is intriguing, due to their interesting optical properties and resemblance of graphene. The objective was to use electrochemical synthesis to yield relatively large PAHs and fabricate electroactive films that could be used as template material in chemical sensors. Spectroscopic, electrochemical and electrical investigations evidence formation of highly stable films with fast redox response, consisting of molecules with 40 to 60 carbon atoms. Additionally, this approach in synthesis, starting from relatively small PAH molecules was successfully used in chemical sensor for lead (II).

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.

Phenolics of the Inner Bark of Silver Birch: Characterization and Intraspecific Variation

This thesis describes work related to the in-depth characterization of the phenolic compounds of silver birch (Betula pendula) inner bark. Phenolic compounds are the most ubiquitous class of plant secondary compounds. The unifying feature of this structurally diverse group is an aromatic ring containing at least one hydroxyl group. Due to the structural diversity, phenolics have various roles in the plant defense against biotic and abiotic stresses. In addition, they can confer several health-promoting properties to humans. Furthermore, the structural diversity of this class of compounds causes challenges for their analysis. The study species in the present work, silver birch, is economically the most important hard wood species in northern Europe. Its inner bark contains a high level of phenolic compounds and it has shown one of the strongest antioxidant activities among 92 Finnish plant materials. The literature review surveys the diversity and organ specific distribution of phenolic compounds in silver birch as well as the proposed ecological functions of phenolic compounds in nature. In addition, the basis for the characterization of phenolics by mass spectrometry (MS), nuclear magnetic resonance spectroscopy (NMR), and circular dichroism spectroscopy (CD) are reviewed. The objective of the experimental work was to extract, purify, characterize, and quantify the inner bark phenolic compounds. Overall 36 compounds were characterized by MS and ultraviolet spectroscopy (UV). 24 compounds were isolated and their structures confirmed by NMR and CD spectroscopy. Five novel natural compounds were identified. Special emphasis was placed on the establishment of a method for the characterization of proanthocyanidins (PAs). Hydrophilic interaction liquid chromatography (HILIC) was utilized because of its high resolution power and predictable elution order of oligomeric and polymeric PAs according to an increasing degree of polymerization. The combination of HILIC and high-resolution MS detection allowed the identification of procyanidin (PC) polymers up to the degree of polymerization of 22. In addition, a series of oligomeric and polymeric PC monoxylosides were observed for the first time in nature. Season and genotype influenced the quantities of the main inner bark phenolics, yet qualitative differences were not observed. However, manual wounding of the inner bark induced the production of ellagitannins (ETs) in the wounded tissues, i.e. callus. Since ETs were not detected in the intact inner bark, this finding may reflect the capacity of silver birch to exploit ellagitannins in its defense.

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.