Data analysis tools and methods for DNA microarray and high-throughput sequencing data

The recent rapid development of biotechnological approaches has enabled the production of large whole genome level biological data sets. In order to handle thesedata sets, reliable and efficient automated tools and methods for data processingand result interpretation are required. Bioinformatics, as the field of studying andprocessing biological data, tries to answer this need by combining methods and approaches across computer science, statistics, mathematics and engineering to studyand process biological data. The need is also increasing for tools that can be used by the biological researchers themselves who may not have a strong statistical or computational background, which requires creating tools and pipelines with intuitive user interfaces, robust analysis workflows and strong emphasis on result reportingand visualization. Within this thesis, several data analysis tools and methods have been developed for analyzing high-throughput biological data sets. These approaches, coveringseveral aspects of high-throughput data analysis, are specifically aimed for gene expression and genotyping data although in principle they are suitable for analyzing other data types as well. Coherent handling of the data across the various data analysis steps is highly important in order to ensure robust and reliable results. Thus,robust data analysis workflows are also described, putting the developed tools andmethods into a wider context. The choice of the correct analysis method may also depend on the properties of the specific data setandthereforeguidelinesforchoosing an optimal method are given. The data analysis tools, methods and workflows developed within this thesis have been applied to several research studies, of which two representative examplesare included in the thesis. The first study focuses on spermatogenesis in murinetestis and the second one examines cell lineage specification in mouse embryonicstem cells.

Viologen based electroactive polymers and composites for durable electrochromic systems

Electrochromism, the phenomenon of reversible color change induced by a small electric charge, forms the basis for operation of several devices including mirrors, displays and smart windows. Although, the history of electrochromism dates back to the 19th century, only the last quarter of the 20th century has its considerable scientific and technological impact. The commercial applications of electrochromics (ECs) are rather limited, besides top selling EC anti-glare mirrors by Gentex Corporation and airplane windows by Boeing, which made a huge commercial success and exposed the potential of EC materials for future glass industry. It is evident from their patents that viologens (salts of 4,4ʹ-bipyridilium) were the major active EC component for most of these marketed devices, signifying the motivation of this thesis focusing on EC viologens. Among the family of electrochromes, viologens have been utilized in electrochromic devices (ECDs) for a while, due to its intensely colored radical cation formation induced by applying a small cathodic potential. Viologens can be synthesized as oligomer or in the polymeric form or as functionality to conjugated polymers. In this thesis, polyviologens (PVs) were synthesized starting from cyanopyridinium (CNP) based monomer precursors. Reductive coupling of cross-connected cyano groups yields viologen and polyviologen under successive electropolymerization using for example the cyclic voltammetry (CV) technique. For further development, a polyviologen-graphene composite system was fabricated, focusing at the stability of the PV electrochrome without sacrificing its excellent EC properties. High electrical conductivity, high surface area offered by graphene sheets together with its non-covalent interactions and synergism with PV significantly improved the electrochrome durability in the composite matrix. The work thereby continued in developing a CNP functionalized thiophene derivative and its copolymer for possible utilization of viologen in the copolymer blend. Furthermore, the viologen functionalized thiophene derivative was synthesized and electropolymerized in order to explore enhancement in the EC contrast and overall EC performance. The findings suggest that such electroactive viologen/polyviologen systems and their nanostructured composite films as well as viologen functionalized conjugated polymers, can be potentially applied as an active EC material in future ECDs aiming at durable device performances.

Lignoselluloosapohjaisten väkevähappohydrolysaattien kromatografinen fraktiointi

Väkevän hapon katalysoiman hydrolyysin avulla lignoselluloosasta on mahdollista valmistaa arvokkaita sokereita. Katalyyttinä toimiva happo voidaan käyttää uudelleen hydrolyysissä, jos se saadaan erotettua sokereista ilman neutralointia. Tämän kandidaatintyön tavoitteena oli selvittää, soveltuuko happoretardaatiotekniikka väkevähappohydrolysaatin fraktiointiin. Työssä verrattiin happoretardaatiotekniikkaa elektrolyyttiekskluusiotekniikkaan. Työn kirjallisuusosassa käsiteltiin happoretardaation ja elektrolyyttiekskluusion teoriaa. Lisäksi esiteltiin elektrolyyttiekskluusioon ja happoretardaatioon liittyviä tutkimuksia. Työn kokeellisessa osassa suoritettiin panoskromatografiakokeita käyttäen syöttöliuoksena rikkihappoa, etikkahappoa, glukoosia ja ksyloosia sisältävää synteettistä liuosta. Erotusmateriaaleina käytettiin neljää eri anionin- ja yhtä kationinvaihtohartsia. Kokeiden perusteella tutkittiin anioninvaihtohartsin tyypin ja kolonnin latauksen vaikutusta happoretardaatiotekniikalla saavutettavaan erotustulokseen sekä verrattiin elektrolyyttiekskluusiota happoretardaatioon. Työn tulosten perusteella rikkihappo laimeni happoretardaatiotekniikalla jopa 20-kertaisesti kromatografiakolonniin syötettyyn liuokseen verrattuna, riippumatta kolonnin latauksesta ja anioninvaihtohartsista. Rikkihapon laimenemisen vuoksi happoretardaatio ei soveltunut lignoselluloosapohjaisten väkevähappohydrolysaattien fraktiointiin. Elektrolyyttiekskluusiotekniikalla rikkihapon laimeneminen oli merkittävästi vähäisempää, minkä vuoksi elektrolyyttiekskluusion todettiin soveltuvan happoretardaatiota paremmin lignoselluloosapohjaisten väkevähappohydrolysaattien fraktiointiin.