High-Throughput Screening for Novel Prostate Cancer Drug Targets –Getting Personal

Prostate cancers form a heterogeneous group of diseases and there is a need for novel biomarkers, and for more efficient and targeted methods of treatment. In this thesis, the potential of microarray data, RNA interference (RNAi) and compound screens were utilized in order to identify novel biomarkers, drug targets and drugs for future personalized prostate cancer therapeutics. First, a bioinformatic mRNA expression analysis covering 9873 human tissue and cell samples, including 349 prostate cancer and 147 normal prostate samples, was used to distinguish in silico prevalidated putative prostate cancer biomarkers and drug targets. Second, RNAi based high-throughput (HT) functional profiling of 295 prostate and prostate cancer tissue specific genes was performed in cultured prostate cancer cells. Third, a HT compound screen approach using a library of 4910 drugs and drug-like molecules was exploited to identify potential drugs inhibiting prostate cancer cell growth. Nine candidate drug targets, with biomarker potential, and one cancer selective compound were validated in vitro and in vivo. In addition to androgen receptor (AR) signaling, endoplasmic reticulum (ER) function, arachidonic acid (AA) pathway, redox homeostasis and mitosis were identified as vital processes in prostate cancer cells. ERG oncogene positive cancer cells exhibited sensitivity to induction of oxidative and ER stress, whereas advanced and castrate-resistant prostate cancer (CRPC) could be potentially targeted through AR signaling and mitosis. In conclusion, this thesis illustrates the power of systems biological data analysis in the discovery of potential vulnerabilities present in prostate cancer cells, as well as novel options for personalized cancer management.

Regioselective modification of galactose-containing polysaccharides in aqueous media

Biorefining is defined as sustainable conversion of biomass into marketable products and energy. Forests cover almost one third of earth’s land area, and account for approximately 40% of the total annual biomass production. In forest biorefining, the wood components are, in addition to the traditional paper and board products, converted into chemicals and biofuels. The major components in wood are cellulose, hemicelluloses, and lignin. The main hemicellulose in softwoods, which are of interest especially for the Nordic forest industry, is O-acetyl galactoglucomannan (GGM). GGM can be isolated in industrial scale from the waste waters of the mechanical pulping process, but is not yet today industrially utilized. In order to attain desired properties of GGM for specific end-uses, chemical and enzymatic modifications can be performed. Regioselective modifications of GGM, and other galactose-containing polysaccharides were done by oxidations, and by combining oxidations with subsequent derivatizations of the formed carbonyl or carboxyl groups. Two different pathways were investigated: activation of the C-6 positions in different sugar units by TEMPO-mediated oxidation, and activation of C-6 position in only galactose-units by oxidation catalyzed by the enzyme galactose oxidase. The activated sites were further selectively derivatized; TEMPO-oxidized GGM by a carbodiimide-mediated reaction forming amides, and GO-oxidized GGM by indium-mediated allylation introducing double or triple bonds to the molecule. In order to better understand the reaction, and to develop a MALDI-TOF-MS method for characterization of regioselectively allylated GGM, α-D-galactopyranoside and raffinose were used as model compounds. All reactions were done in aqueous media. To investigate the applicability of the modified polysaccharides for, e.g., cellulose surface functionalization, their sorption onto pulp fibres was studied. Carboxylation affects the sorption tendency significantly; a higher degree of oxidation leads to lower sorption. By controlling the degree of oxidation of the polysaccharides and the ionic strength of the sorption media, high degrees of sorption of carboxylated polysaccharides onto cellulose could, however, be obtained. Anionic polysaccharides were used as templates during laccase-catalyzed polymerization of aniline, offering a green, chemo-enzymatic route for synthesis of conducting polyaniline (PANI) composite materials. Different polysaccharide templates, such as, native GGM, TEMPO-oxidized GGM, naturally anionic κ-carrageenan, and nanofibrillated cellulose produced by TEMPO-oxidation, were assessed. The conductivity of the synthesized polysaccharide/PANI biocomposites varies depending on the polysaccharide template; κ-CGN, the anionic polysaccharide with the lowest pKa value, produces the polysaccharide/PANI biocomposites with the highest conductivity. The presented derivatization, sorption, and polymerization procedures open new application windows for polysaccharides, such as spruce GGM. The modified polysaccharides and the conducting biocomposites produced provide potential applications in biosensors, electronic devices, and tissue engineering.

Machine vision methods for process measurements in pulping

The papermaking industry has been continuously developing intelligent solutions to characterize the raw materials it uses, to control the manufacturing process in a robust way, and to guarantee the desired quality of the end product. Based on the much improved imaging techniques and image-based analysis methods, it has become possible to look inside the manufacturing pipeline and propose more effective alternatives to human expertise. This study is focused on the development of image analyses methods for the pulping process of papermaking. Pulping starts with wood disintegration and forming the fiber suspension that is subsequently bleached, mixed with additives and chemicals, and finally dried and shipped to the papermaking mills. At each stage of the process it is important to analyze the properties of the raw material to guarantee the product quality. In order to evaluate properties of fibers, the main component of the pulp suspension, a framework for fiber characterization based on microscopic images is proposed in this thesis as the first contribution. The framework allows computation of fiber length and curl index correlating well with the ground truth values. The bubble detection method, the second contribution, was developed in order to estimate the gas volume at the delignification stage of the pulping process based on high-resolution in-line imaging. The gas volume was estimated accurately and the solution enabled just-in-time process termination whereas the accurate estimation of bubble size categories still remained challenging. As the third contribution of the study, optical flow computation was studied and the methods were successfully applied to pulp flow velocity estimation based on double-exposed images. Finally, a framework for classifying dirt particles in dried pulp sheets, including the semisynthetic ground truth generation, feature selection, and performance comparison of the state-of-the-art classification techniques, was proposed as the fourth contribution. The framework was successfully tested on the semisynthetic and real-world pulp sheet images. These four contributions assist in developing an integrated factory-level vision-based process control.

Täyteaineen ja tärkkelyksen annostelun optimointi paperikoneen lyhyeen kiertoon

Diplomityön tavoitteena oli selvittää tärkkelyksen ja täyteaineen annostelupaikkojen sekä – tapojen vaikutukset SC- heatset web offset -paperin ominaisuuksiin ja pintalujuuteen. Lisäksi selvitettiin, muuttuuko paperin pölyäminen annostelupaikkojen tai – tapojen vaikutuksesta. Diplomityön kirjallisuusosiossa käsiteltiin heatset web offset -painokoneen rakennetta ja sen toimintaa. Lisäksi käsiteltiin heatset web offset -painokoneella ilmenevät pölyongelmien tyypit ja, mitkä eri paperin tekijät vaikuttavat heatset web offset -painokoneen pölyämisongelmiin. Lisäksi kirjallisuusosiossa käsiteltiin yleisimmät pintalujuutta parantavat kemikaalit sekä näiden kemikaalien annostelupaikat paperikoneen lyhyeen kiertoon. Alkutason määrityksessä ja ensimmäisessä koeajossa havaittiin, että paperin huokoisuus ja huokosrakenne olivat tärkeimmät SC heatset web offset -paperin pintalujuuteen vaikuttavat tekijät. KCL:n HSWO–koepainokoneella painetuista rullista annostelutapa 4, jossa tärkkelystä ja täyteainetta annosteltiin perälaatikon syöttöpumpun imupuolelle perinteisesti, oli pintalujuudeltaan kestävin. Ahmatti-kokeissa havaittiin, että tärkkelyksen ja täyteaineen annostelu TrumpJet- laitteistolla lähempänä paperikoneen perälaatikkoa, annostelutapa 6, pienentää rullan sisäistä vetolujuushajontaa. Ahmatti -pilotkokeissa havaittiin myös, että paperin lujuusominaisuudet ja vetolujuushajonnat voitiin säilyttää entisellään, kun tärkkelystä ja täyteainetta annosteltiin perinteisesti perälaatikon syöttöpumpun imupuolelta. Toisesta koeajon koepainorullasta havaittiin KCL:n koepainatuksissa, että paperin pintalujuus heikentyy annosteltaessa tärkkelystä 8 kg/t verrattuna 10 kg/t tärkkelysannosteluun. Näiden tapojen ero ei ole merkittävä.

Terpenoid transformations over gold catalysts

Nowadays biomass transformation has a great potential for the synthesis of value-added compounds with a wide range of applications. Terpenoids, extracted from biomass, are inexpensive and renewable raw materials which often have a biological activity and are widely used as important organic platform molecules in the development of new medicines as well as in the synthesis of fine chemicals and intermediates. At the same time, special attention is devoted to the application of gold catalysts to fine chemical synthesis due to their outstanding activity and/or selectivity for transformations of complex organic compounds. Conversion of renewable terpenoids in the presence of gold nanoparticles is one of the new and promising directions in the transformation of biomass to valuable chemicals. In the doctoral thesis, different kinds of natural terpenoids, such as α-pinene, myrtenol and carvone were selected as starting materials. Gold catalysts were utilized for the promising routes of these compounds transformation. Investigation of selective α-pinene isomerization to camphene, which is an important step in an industrial process towards the synthesis of camphor as well as other valuable substrates for the pharmaceutical industry, was performed. A high activity of heterogeneous gold catalysts in the Wagner-Meerwein rearrangement was demonstrated for the first time. Gold on alumina carrier was found to reach the α-pinene isomerization conversion up to 99.9% and the selectivity of 60-80%, thus making this catalyst very promising from an industrial viewpoint. A detailed investigation of kinetic regularities including catalyst deactivation during the reaction was performed. The one-pot terpene alcohol amination, which is a promising approach to the synthesis of valuable complex amines having specific physiological properties, was investigated. The general regularities of the one-pot natural myrtenol amination in the presence of gold catalysts as well as a correlation between catalytic activity, catalyst redox treatment and the support nature were obtained. Catalytic activity and product distribution were shown to be strongly dependent on the support properties, namely acidity and basicity. The gold-zirconia (Au/ZrO2) catalyst pretreated under oxidizing atmosphere was observed to be rather active, resulting in the total conversion of myrtenol and the selectivity to the corresponding amine of about 53%. The reaction kinetics was modelled based on the mechanistic considerations with the catalyst deactivation step incorporated in the mechanism. Carvone hydrogenation over a gold catalyst was studied with the general idea of investigating both the activity of gold catalysts in competitive hydrogenation of different functional groups and developing an approach to the synthesis of valuable carvone derivatives. Gold was found to promote stereo- and chemoselective carvone hydrogenation to dihydrocarvone with a predominant formation of the trans-isomer, which generally is a novel synthetic method for an industrially valuable dihydrocarvone. The solvent effect on the catalytic activity as well as on the ratio between trans- and cis-dihydrocarvone was evaluated.

Behavior of black liquor nitrogen in combustion : formation of cyanate

The Kraft pulping process is the dominant chemical pulping process in the world. Roughly 195 million metric tons of black liquor are produced annually as a by-product from the Kraft pulping process. Black liquor consists of spent cooking chemicals and dissolved organics from the wood and can contain up to 0.15 wt% nitrogen on dry solids basis. The cooking chemicals from black liquor are recovered in a chemical recovery cycle. Water is evaporated in the first stage of the chemical recovery cycle, so the black liquor has a dry solids content of 65-85% prior to combustion. During combustion of black liquor, a portion of the black liquor nitrogen is volatilized, finally forming N2 or NO. The rest of the nitrogen remains in the char as char nitrogen. During char conversion, fixed carbon is burned off leaving the pulping chemicals as smelt, and the char nitrogen forms mostly smelt nitrogen (cyanate, OCN-). Smelt exits the recovery boiler and is dissolved in water. The cyanate from smelt decomposes in the presence of water, forming NH3, which causes nitrogen emissions from the rest of the chemical recovery cycle. This thesis had two focuses: firstly, to determine how the nitrogen chemistry in the recovery boiler is affected by modification of black liquor; and secondly, to find out what causes cyanate formation during thermal conversion, and which parameters affect cyanate formation and decomposition during thermal conversion of black liquor. The fate of added biosludge nitrogen in chemical recovery was determined in Paper I. The added biosludge increased the nitrogen content of black liquor. At the pulp mill, the added biosludge did not increase the NO formation in the recovery boiler, but instead increased the amount of cyanate in green liquor. The increased cyanate caused more NH3 formation, which increased the NCG boiler’s NO emissions. Laboratory-scale experiments showed an increase in both NO and cyanate formation after biosludge addition. Black liquor can be modified, for example by addition of a solid biomass to increase the energy density of black liquor, or by separation of lignin from black liquor by precipitation. The precipitated lignin can be utilized in the production of green chemicals or as a fuel. In Papers II and III, laboratory-scale experiments were conducted to determine the impact of black liquor modification on NO and cyanate formation. Removal of lignin from black liquor reduced the nitrogen content of the black liquor. In most cases NO and cyanate formation decreased with increasing lignin removal; the exception was NO formation from lignin lean soda liquors. The addition of biomass to black liquor resulted in a higher nitrogen content fuel mixture, due to the higher nitrogen content of biomass compared to black liquor. More NO and cyanate were formed from the fuel mixtures than from pure black liquor. The increased amount of formed cyanate led to the hypothesis that black liquor is catalytically active and converts a portion of the nitrogen in the mixed fuel to cyanate. The mechanism behind cyanate formation during thermal conversion of black liquor was not clear before this thesis. Paper IV studies the cyanate formation of alkali metal loaded fuels during gasification in a CO2 atmosphere. The salts K2CO3, Na2CO3, and K2SO4 all promoted char nitrogen to cyanate conversion during gasification, while KCl and CaCO3 did not. It is now assumed that cyanate is formed when alkali metal carbonate or an active intermediate of alkali metal carbonate (e.g. -CO2K) reacts with the char nitrogen forming cyanate. By testing different fuels (bark, peat, and coal), each of which had a different form of organic nitrogen, it was concluded that the form of organic nitrogen in char also has an impact on cyanate formation. Cyanate can be formed during pyrolysis of black liquor, but at temperatures 900°C or above, the formed cyanate will decompose. Cyanate formation in gasifying conditions with different levels of CO2 in the atmosphere was also studied. Most of the char nitrogen was converted to cyanate during gasification at 800-900°C in 13-50% CO2 in N2, and only 5% of the initial fuel nitrogen was converted to NO during char conversion. The formed smelt cyanate was stable at 800°C 13% CO2, while it decomposed at 900°C 13% CO2. The cyanate decomposition was faster at higher temperatures and in oxygen-containing atmospheres than in an inert atmosphere. The presence of CO2 in oxygencontaining atmospheres slowed down the decomposition of cyanate. This work will provide new information on how modification of black liquor affects the nitrogen chemistry during thermal conversion of black liquor and what causes cyanate formation during thermal conversion of black liquor. The formation and decomposition of cyanate was studied in order to provide new data, which would be useful in modeling of nitrogen chemistry in the recovery boiler.

Puuperäiset polymeerit synteettisten sideaineiden korvaajina

Tämän kandidaatintyön aiheena oli löytää biojalostamon näkökulmasta käyttökelpoisia tuotantoreittejä puuperäisistä materiaaleista bioperäisiin kemikaaleihin, joilla olisi mahdollista korvata synteettisiä sideaineita. Tällä hetkellä suurin osa sideaineista ja päällystemateriaaleista tuotetaan uusiutumattomista luonnonvaroista, kuten maakaasusta ja öljystä. Lopputuotteiden kierrätettävyyden ja vihreyden ohella yksi metsäteollisuuden tulevaisuuden trendejä on pyrkiä irti öljy- ja maakaasuriippuvuudesta. Muutoksella voidaan säästää sekä ympäristöä, että rahaa. Biopohjaisilla drop-in kemikaaleilla ja muilla biopohjaisilla vaihtoehdoilla tämä on mahdollista Tässä työssä tutkittiin ja havainnollistettiin mahdollisin tuotantoreitein useiden tällä hetkellä käytössä olevien sideaineiden korvaamista biopohjaisilla versioilla. Työ tehtiin kirjallisuustutkielmana, eikä siihen kuulunut laboratoriokokeita. Työn ensimmäisessä osassa painopiste on biojalostamossa ja dispersiopäällystyksessä. Toisessa osassa esitellään tällä hetkellä käytettyjä sideaineita ja niiden mahdollisia biopohjaisia korvaajia tuotantoreitteineen. Työn toissijainen tarkoitus oli selvittää lyhyesti mitä muita puuperäisiä komponentteja voidaan käyttää suoraan paperin ja kartongin päällystämiseen. Viimeiseksi on esitelty vielä lyhyesti kaupallisesti käytössä olevia biomuoveja ja päällysteitä.

Intensification of hemicellulose hot-water extraction from spruce wood by parameter tuning

The growing population on earth along with diminishing fossil deposits and the climate change debate calls out for a better utilization of renewable, bio-based materials. In a biorefinery perspective, the renewable biomass is converted into many different products such as fuels, chemicals, and materials, quite similar to the petroleum refinery industry. Since forests cover about one third of the land surface on earth, ligno-cellulosic biomass is the most abundant renewable resource available. The natural first step in a biorefinery is separation and isolation of the different compounds the biomass is comprised of. The major components in wood are cellulose, hemicellulose, and lignin, all of which can be made into various end-products. Today, focus normally lies on utilizing only one component, e.g., the cellulose in the Kraft pulping process. It would be highly desirable to utilize all the different compounds, both from an economical and environmental point of view. The separation process should therefore be optimized. Hemicelluloses can partly be extracted with hot-water prior to pulping. Depending in the severity of the extraction, the hemicelluloses are degraded to various degrees. In order to be able to choose from a variety of different end-products, the hemicelluloses should be as intact as possible after the extraction. The main focus of this work has been on preserving the hemicellulose molar mass throughout the extraction at a high yield by actively controlling the extraction pH at the high temperatures used. Since it has not been possible to measure pH during an extraction due to the high temperatures, the extraction pH has remained a “black box”. Therefore, a high-temperature in-line pH measuring system was developed, validated, and tested for hot-water wood extractions. One crucial step in the measurements is calibration, therefore extensive efforts was put on developing a reliable calibration procedure. Initial extractions with wood showed that the actual extraction pH was ~0.35 pH units higher than previously believed. The measuring system was also equipped with a controller connected to a pump. With this addition it was possible to control the extraction to any desired pH set point. When the pH dropped below the set point, the controller started pumping in alkali and by that the desired set point was maintained very accurately. Analyses of the extracted hemicelluloses showed that less hemicelluloses were extracted at higher pH but with a higher molar-mass. Monomer formation could, at a certain pH level, be completely inhibited. Increasing the temperature, but maintaining a specific pH set point, would speed up the extraction without degrading the molar-mass of the hemicelluloses and thereby intensifying the extraction. The diffusion of the dissolved hemicelluloses from the wood particle is a major part of the extraction process. Therefore, a particle size study ranging from 0.5 mm wood particles to industrial size wood chips was conducted to investigate the internal mass transfer of the hemicelluloses. Unsurprisingly, it showed that hemicelluloses were extracted faster from smaller wood particles than larger although it did not seem to have a substantial effect on the average molar mass of the extracted hemicelluloses. However, smaller particle sizes require more energy to manufacture and thus increases the economic cost. Since bark comprises 10 – 15 % of a tree, it is important to also consider it in a biorefinery concept. Spruce inner and outer bark was hot-water extracted separately to investigate the possibility to isolate the bark hemicelluloses. It was showed that the bark hemicelluloses comprised mostly of pectic material and differed considerably from the wood hemicelluloses. The bark hemicelluloses, or pectins, could be extracted at lower temperatures than the wood hemicelluloses. A chemical characterization, done separately on inner and outer bark, showed that inner bark contained over 10 % stilbene glucosides that could be extracted already at 100 °C with aqueous acetone.

Ohuiden päällystyskerrosten applikointi puukuitupohjaisille materiaaleille

Työn aiheena oli tutkia vaahdon soveltuvuutta ohuiden päällystyskerrosten applikointiin paperin tai kartongin pinnalle. Paperia ja kartonkia päällystetään teollisessa mittakaavassa eri menetelmillä, mutta niille kaikille yhteistä on päällystyspastan laimentaminen vedellä ennen applikointia ja laimennusveden haihduttaminen applikoinnin jälkeen päällysteen asettamiseksi. Laimennus on tärkeää pastan komponenttien tasaisen levittämisen vuoksi, mutta veden haihduttaminen kuluttaa valtavasti energiaa. Tekstiiliteollisuudessa on saavutettu merkittäviä säästöjä kuivausenergiassa korvaamalla laajalti vedellä laimentaminen vaahdottamisella. Diplomityön kirjallisessa osassa käytiin läpi vaahdon kemiallisia ja fysikaalisia ominaisuuksia sekä selvitettiin mitä kemikaaleja ja laitteita vaahdotukseen käytetään. Lisäksi luotiin katsaus vaahtoprosessien käyttöön tekstiiliteollisuudessa ja muilla aloilla. Kokeellinen osa koostui esikokeista, joissa selvitettiin pastan koostumuksen vaikutuksia vaahtoamiseen, ja pilot-mittakaavan koeajoista, joissa esikokeiden tuloksia hyödynnettiin. Esikokeissa huomiota kiinnitettiin varsinkin eri polyvinyylialkoholien (PVA) seosten erinomaiseen vaahtoavuuteen. Pilot-koeajoissa vaahtopäällystys vaikutti lupaavalta menetelmältä, joskaan täysin tyydyttävää päällystystulosta ei saavutettu. Suurimpana ongelmana esiintyi ilman pääseminen pohjapaperin ja päällysteen väliin ja siitä seuraava huono päällystejälki. Toisen ongelmakokonaisuuden muodostivat päällysteeseen jäävät reiät. Vaahtopäällystys vaikuttaa lupaavalta tekniikalta ohuiden päällystekerrosten applikointiin, mutta pastareseptejä tulee optimoida ja ratkaista päällysteen alle pääsevän ilman ongelma.