DPS-Like Peroxide Resistance Protein: Structural and Functional Studies on a Versatile Nanocontainer

Oxidative stress is a constant threat to almost all organisms. It damages a number of biomolecules and leads to the disruption of many crucial cellular functions. It is caused by reactive oxygen species (ROS), such as hydrogen peroxide (H2O₂), superoxide (•O₂ -), and hydroxyl radical (•OH). The most harmful of these compounds is •OH, which is only formed in cells in the presence of redox-cycling transition metals, such as iron and copper. Bacteria have developed a number of mechanisms to cope with ROS. One of the most widespread means employed by bacteria is the DNA-binding proteins from starved cells (Dps). Dps proteins protect the cells by binding and oxidizing Fe2+, thus greatly reducing the production of •OH. The oxidized iron is stored inside the protein as an iron core. In addition, Dps proteins bind directly to DNA forming a protective coating that shields DNA from harmful agents. Moreover, Dps proteins have been found to elicit other protective functions in cells and to participate in bacterial virulence. Dps proteins are of special importance to Streptococci owing to the lack of catalase in this genus of bacteria.This study was focused on structural and functional characterization of streptococcal Dpslike peroxide resistance (Dpr) proteins. Initially, crystal structures of Streptococcus pyogenes Dpr were determined. The data confirmed the presence of a di-metal ferroxidase center (FOC) in Dpr proteins and revealed the presence of a novel N-terminal helix as well as a surface metal-binding site. The crystal structures of Streptococcus suis Dpr complexed with transition metals demonstrated the metal specificity of the FOC. Solution binding studies also indicated the presence of a di-metal FOC. These results suggested a possible role for Dpr in the detoxification of various metals. Iron was found to mineralize inside the protein as ferrihydrite based on X-ray absorption spectroscopy data. The iron core was found to exhibit clear superparamagnetic behaviour using magnetic and Mössbauer measurements. The results from this study are expected to further increase our understanding on the binding, oxidation, and mineralization of iron and other metals in Dpr proteins. In particular, the structural and magnetic properties of the iron core can form a basis for potential new applications in nanotechnology. From the streptococcal viewpoint, the results would help in understanding better the complicated picture of bacterial pathogenesis. Dpr proteins may also provide a novel target for drug design due to their tight involvement in bacterial virulence.

Development of simple and efficient synthetic strategies for production of fine chemicals of pharmaceutical relevance : metal-mediated allylation combined with applied catalysis

Den snart 200 år gamla vetenskapsgrenen organisk synteskemi har starkt bidragit till moderna samhällens välfärd. Ett av flaggskeppen för den organiska synteskemin är utvecklingen och produktionen av nya läkemedel och speciellt de aktiva substanserna däri. Därmed är det viktigt att utveckla nya syntesmetoder, som kan tillämpas vid framställningen av farmaceutiskt relevanta målstrukturer. I detta sammanhang är den ultimata målsättningen dock inte endast en lyckad syntes av målmolekylen, utan det är allt viktigare att utveckla syntesrutter som uppfyller kriterierna för den hållbara utvecklingen. Ett av de centralaste verktygen som en organisk kemist har till förfogande i detta sammanhang är katalys, eller mera specifikt möjligheten att tillämpa olika katalytiska reaktioner vid framställning av komplexa målstrukturer. De motsvarande industriella processerna karakteriseras av hög effektivitet och minimerad avfallsproduktion, vilket naturligtvis gynnar den kemiska industrin samtidigt som de negativa miljöeffekterna minskas avsevärt. I denna doktorsavhandling har nya syntesrutter för produktion av finkemikalier med farmaceutisk relevans utvecklats genom att kombinera förhållandevis enkla transformationer till nya reaktionssekvenser. Alla reaktionssekvenser som diskuteras i denna avhandling påbörjades med en metallförmedlad allylering av utvalda aldehyder eller aldiminer. De erhållna produkterna innehållende en kol-koldubbelbindning med en närliggande hydroxyl- eller aminogrupp modifierades sedan vidare genom att tillämpa välkända katalytiska reaktioner. Alla syntetiserade molekyler som presenteras i denna avhandling karakteriseras som finkemikalier med hög potential vid farmaceutiska tillämpningar. Utöver detta tillämpades en mängd olika katalytiska reaktioner framgångsrikt vid syntes av dessa molekyler, vilket i sin tur förstärker betydelsen för de katalytiska verktygen i organiska kemins verktygslåda.

Feasibility study of metal to polymer hybrid joining

The increasing demand for lightweight components has led to a huge exploitation of non-metallic materials such as polymers, fibers and elastomers in industrial and manufacturing processes. Recent trends towards cost effectiveness, weight reduction and production flexibility in industrial production and manufacturing processes has led to a growing interest in hybrid components where two or more dissimilar materials coexist to achieving specifically optimized characteristics. The importance of this research is to serve as a bridge to understanding the theories behind various joining techniques and the adaptation of the process for metal to polymer hybrid joints. Moreso, it helps companies to select the most productive and yet economical joining process for realization of lightweight metal to polymer hybrid components. This thesis is a literature review analyzing various materials that has been published on various joining methods for metal to polymer hybrid joints on the feasibility and eventual realization of the joint between these dissimilar materials. This study is aimed at theoretically evaluating the feasibility of joining processes between metal and plastic components by exploiting exhaustively joining and welding sources.

Sorption of metal ions to wood, pulp and bark materials

Ett huvudmål med denna avhandling var att erhålla ny information om växelverkan mellan metalljoner i vattenfas och träbaserade material såsom olika pappersmassor, ved och bark. Material av gran, tall och björk har studerats. En ny känslig kolonnkromatografisk metod utvecklades för bestämning av affinitetsordningar för 17 olika metalljoner. Av dessa bands trevärt järn och de mycket toxiska tungmetallerna bly, koppar och kadmium starkast till de studerade materialen. Växelverkan i dessa tvåfas system sker som jonbyte, huvudsakligen via komplexbildning av metalljoner till funktionella grupper i den fasta fasen. Vattenfasens pH är den viktigaste parametern som bestämmer totala halten av metalljoner som binds till materialen. Resultatet i denna avhandling kan delvis betraktas som grundforskning. En ny kunskap om metalljoners förekomst och kemiska reaktioner i dessa system är även av stor ekonomisk och ekologisk, betydelse, när man strävar till allt mera slutna system i moderna massafabriker. Avhandlingen visar också att trädbark har stor potential för biosorption av tungmetaller t.ex. från avfallsvatten. Trädbark har nästan lika stor bindningskapacitet som dyra syntetiska jonbytare.

Element speciation and behaviour in metal-rich Boreal river and estuarine systems using ultrafiltration and chemical modelling

The bioavailability of metals and their potential for environmental pollution depends not simply on total concentrations, but is to a great extent determined by their chemical form. Consequently, knowledge of aqueous metal species is essential in investigating potential metal toxicity and mobility. The overall aim of this thesis is, thus, to determine the species of major and trace elements and the size distribution among the different forms (e.g. ions, molecules and mineral particles) in selected metal-enriched Boreal river and estuarine systems by utilising filtration techniques and geochemical modelling. On the basis of the spatial physicochemical patterns found, the fractionation and complexation processes of elements (mainly related to input of humic matter and pH-change) were examined. Dissolved (<1 kDa), colloidal (1 kDa-0.45 μm) and particulate (>0.45 μm) size fractions of sulfate, organic carbon (OC) and 44 metals/metalloids were investigated in the extremely acidic Vörå River system and its estuary in W Finland, and in four river systems in SW Finland (Sirppujoki, Laajoki, Mynäjoki and Paimionjoki), largely affected by soil erosion and acid sulfate (AS) soils. In addition, geochemical modelling was used to predict the formation of free ions and complexes in these investigated waters. One of the most important findings of this study is that the very large amounts of metals known to be released from AS soils (including Al, Ca, Cd, Co, Cu, Mg, Mn, Na, Ni, Si, U and the lanthanoids) occur and can prevail mainly in toxic forms throughout acidic river systems; as free ions and/or sulfate-complexes. This has serious effects on the biota and especially dissolved Al is expected to have acute effects on fish and other organisms, but also other potentially toxic dissolved elements (e.g. Cd, Cu, Mn and Ni) can have fatal effects on the biota in these environments. In upstream areas that are generally relatively forested (higher pH and contents of OC) fewer bioavailable elements (including Al, Cu, Ni and U) may be found due to complexation with the more abundantly occurring colloidal OC. In the rivers in SW Finland total metal concentrations were relatively high, but most of the elements occurred largely in a colloidal or particulate form and even elements expected to be very soluble (Ca, K, Mg, Na and Sr) occurred to a large extent in colloidal form. According to geochemical modelling, these patterns may only to a limited extent be explained by in-stream metal complexation/adsorption. Instead there were strong indications that the high metal concentrations and dominant solid fractions were largely caused by erosion of metal bearing phyllosilicates. A strong influence of AS soils, known to exist in the catchment, could be clearly distinguished in the Sirppujoki River as it had very high concentrations of a metal sequence typical of AS soils in a dissolved form (Ba, Br, Ca, Cd, Co, K, Mg, Mn, Na, Ni, Rb and Sr). In the Paimionjoki River, metal concentrations (including Ba, Cs, Fe, Hf, Pb, Rb, Si, Th, Ti, Tl and V; not typical of AS soils in the area) were high, but it was found that the main cause of this was erosion of metal bearing phyllosilicates and thus these metals occurred dominantly in less toxic colloidal and particulate fractions. In the two nearby rivers (Laajoki and Mynäjoki) there was influence of AS soils, but it was largely masked by eroded phyllosilicates. Consequently, rivers draining clay plains sensitive to erosion, like those in SW Finland, have generally high background metal concentrations due to erosion. Thus, relying on only semi-dissolved (<0.45 μm) concentrations obtained in routine monitoring, or geochemical modelling based on such data, can lead to a great overestimation of the water toxicity in this environment. The potentially toxic elements that are of concern in AS soil areas will ultimately be precipitated in the recipient estuary or sea, where the acidic metalrich river water will gradually be diluted/neutralised with brackish seawater. Along such a rising pH gradient Al, Cu and U will precipitate first together with organic matter closest to the river mouth. Manganese is relatively persistent in solution and, thus, precipitates further down the estuary as Mn oxides together with elements such as Ba, Cd, Co, Cu and Ni. Iron oxides, on the contrary, are not important scavengers of metals in the estuary, they are predicted to be associated only with As and PO4.

Russian metals for arctic offshore structures

With an increasingly growing demand for natural resources, the Arctic region has become an attractive area, holding about 15% of world oil. Ice shrinkage caused by global warming encourages the development of offshore and ship-building sectors. Russia, as one of the leading oil and gas production countries is participating actively in cold resistant materials research, since half of its territory belongs to the Arctic environment, which held considerable stores of oil. Nowadays most Russian offshore platforms are located in the Sakhalin Island area, which geographically does not belong to the Arctic, but has com-parable environmental conditions. Russia recently has manufactured several offshore platforms. It became clear that further development of the Arctic off-shore structures with necessary reliability is highly depending on the materials employed. This work pursues the following objectives:  to provide a comprehensive review on Russian metals used for Arctic offshore structures on the base of standards, books, journal articles and companies reports  to overview various Arctic offshore structures and its structural characteristics  briefly discuss materials testing methods for low temperatures Master`s thesis focuses on specifications and description of Russian metals which are already in use and can be used for Arctic offshore structures. Work overviews several groups of steel, such as low carbon, low alloy, chromium containing steels, stainless steels, aluminium and nanostructured steels. Materials under discussion are grouped based on the standards, for instance the work covers shipbuilding and structural steels at the different sections. This paper provides an overview of important Russian Arctic offshore projects built for use in Russia and ordered by foreign countries. Future trends in development of the Arctic materials are discussed. Based on the information provided in this Master`s thesis it is possible to learn about Russian metals used for ships and offshore platforms operated in the Arctic region. Paper can be used as the comprehensive review of current materials, such as various steels, aluminium and nanomaterials.

Krigaren och transvestiten : gestaltningar av mörker och maskuliniteter i finländsk black metal

Avhandlingen undersöker gestaltningar av mörker och maskuliniteter i den finländska black metal-scenen. Normativa hegemoniska och normbrytande subversiva gestaltningar av maskuliniteter bland de mest aktiva anhängarna av den finländska black metal-scenen undersöks som uttryck för återkommande, kulturella mönster. Mönstren analyseras med hjälp av teorier om hegemonisk maskulinitet, heteronormativitet, genusperformativitet, subversivitet och protestmaskulinitet. Queerteori och (kritisk) mansforskning som har sina ursprung i feministisk forskning utgör avhandlingens teoretiska underlag. Begreppen stil och ideologi aktualiseras i en diskussion kring hur mörker, ett begrepp som är av centralt värde inom den finländska black metal-scenen, kan förstås och uttryckas av scenmedlemmarna. Mörkret, som ofta ideologimässigt består av antikristliga element, inom den finländska scenen i regel förknippade med satanism, uttrycks genom låttexter, det visuella och det musikaliska, vilka tillsammans utgör black metal-stilen.

Electrochemical Treatment of Wastewaters

Electrocoagulation is a process in which wastewater is treated under electrical current. Coagulant is formed during the process through the metal anode dissolution to respective ions which react with hydroxyl ions released in cathode. These metal hydroxides form complexes with pollutant ions. Pollutants are removed among metal hydroxide precipitates. This study was concentrated on describing chemistry and device structures in which electrochemical treatment operations are based on. Studied pollutants were nitrogen compounds, sulphate, trivalent and pentavalent arsenic, heavy metals, phosphate, fluoride, chloride, and bromide. In experimental part, removal of ammonium, nitrate, and sulphate during electrochemical treatment was studied separately. Main objective of this study was to find suitable metal plate material for ammonium, nitrate, and sulphate removal, respectively. Also other parameters such as pH of solution, concentration of pollutant and sodium chloride, and current density were optimized. According to this study the most suitable material for ammonium and sulphate removal by electrochemical treatment was stainless steel. Respectively, iron was the optimum material for nitrate removal. Rise in the pH of solution at the final stage of electrochemical treatment of ammonium, nitrate, and sulphate was detected. Conductivities of solutions decreased during ammonium removal in electrochemical processes. When nitrate and sulphate were removed electrochemically conductivities of solutions increased. Concentrations of residual metals in electrochemically treated solutions were not significant. Based on this study electrochemical treatment processes are recommended to be used in treatment of industrial wastewaters. Treatment conditions should be optimized for each wastewater matrix.

The effects of welding heat input on the usability of high strength steels in welded structures

High strength steel (HSS) has been in use in workshops since the 1980s. At that time, the significance of the term HSS differed from the modern conception as the maximum yield strength of HSSs has increased nearly every year. There are three different ways to make HSS. The first and oldest method is QT (quenched and tempered) followed by the TMCP (thermomechanical controlled process) and DQ (direct quenching) methods. This thesis consists of two parts, the first of which part introduces the research topic and discusses welded HSS structures by characterizing the most important variables. In the second part of the thesis, the usability of welded HSS structures is examined through a set of laboratory tests. The results of this study explain the differences in the usability of the welded HSSs made by the three different methods. The results additionally indicate that usage of different HSSs in the welded structures presumes that manufacturers know what kind of HSS they are welding. As manufacturers use greater strength HSSs in welded structures, the demands for welding rise as well. Therefore, during the manufacturing process, factors such as heat input, cooling time, weld quality, and more must be under careful observation.

Knowledge, processes and relationships in organizational change: Understanding how to facilitate management of intellectual capital in diverse organization structures and cultures.

This study examined relationships of organizational dependencies, change management and developed intellectual knowledge resources, in different intellectual capital based development programs on ICT-sector. Study was carried out in a research context, where high degree of external organizational contingencies existed and lots of changes in several development programs had taken place in the last years. From a scientific perspective the main contribution was that evidence between relationships of organizational dependencies, change model portfolio and developed knowledge resources could be suggested. From managerial perspective the primary implication was that in situations where sustainable competitive advantage is pursued by means of increasing knowledge based productivity of labor, firms should seek to pursue organizational settings where external dependencies have minimal amount of effect.

From War Pigs to Unsung Heroes: The Criticism and Justification of War in Metal Lyrics

Tässä tutkimuksessa käsitellään heavy metal -kappaleiden sanoitusten sisältöä. Tutkimusmateriaaliin on valittu yksi teema, sota, jonka avulla avataan sanoitusten sisältöä ja merkitystä. Metallimusiikki alakulttuurina on tyylillisesti ja temaattisesti spesifi, ja sillä on omat musiikilliset tavoitteensa. Tässä tutkimuksessa tarkastellaan erityisesti sitä miten sotaa kritisoidaan tai perustellaan heavy rock -sanoituksissa. Tutkimusmateriaalini koostuu 29 englanninkielisen kappaleen sanoituksesta vuosilta 1970–2012. Edustettuina on useita ajanjaksoja sekä maita. Yhdistävänä tekijänä on englannin kielen lisäksi se, että kaikki sanoitukset käsittelevät modernia länsimaista sodankäyntiä. Tekstit valittiin sen perusteella, että niissä ilmeni positiivinen tai negatiivinen näkökulma sotaan. Tutkimus nojaa Theo van Leeuwenin legitimaatioteoriaan, joka puolestaan pohjautuu diskurssianalyysiin. Legitimaatioteoria käsittää neljä strategiaa, jotka voivat joko kritisoida tai perustella sosiaalisia käytänteitä. Ne ovat auktoriteetteihin vetoaminen, moraalinen arviointi, järkeistäminen ja mytopoeesi. Yksi tavoitteistani tutkimuksessani on selvittää legitimaatioteorian toimivuutta omassa materiaalissani. Käytän metodina lähilukua, joka mahdollistaa niiden sanojen ja ilmaisujen identifioimisen, jotka ovat näkökulmaltaan joko positiivisesti tai negatiivisesti sotaan suhtautuvia. Analyysini kannalta tärkeitä ovat sekä kieli- että kulttuurikonteksti, sillä ne määrittelevät sanojen merkityksen. Analyysin perusteella kävi ilmi, että esimerkit jakautuivat eri strategioiden välille hyvin epätasaisesti. Auktoriteetteihin vetoamisen strategiasta löytyi vain yksi esimerkki, kun taas moraalisen arvioinnin esimerkkejä oli neljätoista. Lisäksi kaikkia legitimaatioteorian alaryhmiä ei löytynyt materiaalista ollenkaan. Osalla alaryhmistä oli useita esiintymiä, mutta osalla vain yksi. Esimerkkien epätasaista jakautumista selittää mm. se, että tutkimuksen materiaalin kannalta kaikki alakategoriat eivät ole relevantteja. Jotta tutkimustuloksista saataisiin edustavampi, laajempi otanta olisi tarpeen. Legitimaatioteorian soveltuvuutta sanoituksien yhteydessä tulisi tutkia laajemmin.

Om mörker, maskuliniteter, humor och lek inom black metal : lectio

Lectio praecursoria, Åbo Akademi 25.1 2013.

The nature of communication structures of university students in an international web-based computer-supported collaborative learning (CSCL) course

Communication, the flow of ideas and information between individuals in a social context, is the heart of educational experience. Constructivism and constructivist theories form the foundation for the collaborative learning processes of creating and sharing meaning in online educational contexts. The Learning and Collaboration in Technology-enhanced Contexts (LeCoTec) course comprised of 66 participants drawn from four European universities (Oulu, Turku, Ghent and Ramon Llull). These participants were split into 15 groups with the express aim of learning about computer-supported collaborative learning (CSCL). The Community of Inquiry model (social, cognitive and teaching presences) provided the content and tools for learning and researching the collaborative interactions in this environment. The sampled comments from the collaborative phase were collected and analyzed at chain-level and group-level, with the aim of identifying the various message types that sustained high learning outcomes. Furthermore, the Social Network Analysis helped to view the density of whole group interactions, as well as the popular and active members within the highly collaborating groups. It was observed that long chains occur in groups having high quality outcomes. These chains were also characterized by Social, Interactivity, Administrative and Content comment-types. In addition, high outcomes were realized from the high interactive cases and high-density groups. In low interactive groups, commenting patterned around the one or two central group members. In conclusion, future online environments should support high-order learning and develop greater metacognition and self-regulation. Moreover, such an environment, with a wide variety of problem solving tools, would enhance interactivity.

Research and development of III-V semiconductor surfaces for improved device interfaces

This thesis is devoted to understanding and improving technologically important III-V compound semiconductor (e.g. GaAs, InAs, and InSb) surfaces and interfaces for devices. The surfaces and interfaces of crystalline III-V materials have a crucial role in the operation of field-effect-transistors (FET) and highefficiency solar-cells, for instance. However, the surfaces are also the most defective part of the semiconductor material and it is essential to decrease the amount of harmful surface or interface defects for the next-generation III-V semiconductor device applications. Any improvement in the crystal ordering at the semiconductor surface reduces the amount of defects and increases the material homogeneity. This is becoming more and more important when the semiconductor device structures decrease to atomic-scale dimensions. Toward that target, the effects of different adsorbates (i.e., Sn, In, and O) on the III-V surface structures and properties have been investigated in this work. Furthermore, novel thin-films have been synthesized, which show beneficial properties regarding the passivation of the reactive III-V surfaces. The work comprises ultra-high-vacuum (UHV) environment for the controlled fabrication of atomically ordered III-V(100) surfaces. The surface sensitive experimental methods [low energy electron diffraction (LEED), scanning tunneling microscopy/spectroscopy (STM/STS), and synchrotron radiation photoelectron spectroscopy (SRPES)] and computational density-functionaltheory (DFT) calculations are utilized for elucidating the atomic and electronic properties of the crucial III-V surfaces. The basic research results are also transferred to actual device tests by fabricating metal-oxide-semiconductor capacitors and utilizing the interface sensitive measurement techniques [capacitance voltage (CV) profiling, and photoluminescence (PL) spectroscopy] for the characterization. This part of the thesis includes the instrumentation of home-made UHV-compatible atomic-layer-deposition (ALD) reactor for growing good quality insulator layers. The results of this thesis elucidate the atomic structures of technologically promising Sn- and In-stabilized III-V compound semiconductor surfaces. It is shown that the Sn adsorbate induces an atomic structure with (1×2)/(1×4) surface symmetry which is characterized by Sn-group III dimers. Furthermore, the stability of peculiar ζa structure is demonstrated for the GaAs(100)-In surface. The beneficial effects of these surface structures regarding the crucial III-V oxide interface are demonstrated. Namely, it is found that it is possible to passivate the III-V surface by a careful atomic-scale engineering of the III-V surface prior to the gate-dielectric deposition. The thin (1×2)/(1×4)-Sn layer is found to catalyze the removal of harmful amorphous III-V oxides. Also, novel crystalline III-V-oxide structures are synthesized and it is shown that these structures improve the device characteristics. The finding of crystalline oxide structures is exploited by solving the atomic structure of InSb(100)(1×2) and elucidating the electronic structure of oxidized InSb(100) for the first time.