The Significance of Hydrogen Bonding Interactions in the Cleavage of RNA

RNA is essential for all living organisms. It has important roles in protein synthesis, controlling gene expression as well as catalyzing biological reactions. Chemically RNA is a very stable molecule, although in biological systems many agents catalyze the cleavage of RNA, such as naturally occurring enzymes and ribozymes. Much effort has been put in the last decades in developing highly active artificial ribonucleases since such molecules could have potential in the therapeutic field and provide tools for molecular biology. Several potential catalysts have emerged, but usually detailed cleavage mechanism remains unresolved. This thesis is aimed at clarifying mechanistic details of the cleavage and isomerization of RNA by using simpler nucleoside models of RNA. The topics in the experimental part cover three different studies, one concerning the mechanism of catalysis by large ribozymes, one dealing with the reactivity of modified and unmodified RNA oligonucleotides and one showing an efficient catalysis of the cleavage and isomerization of an RNA phosphodiester bond by a dinuclear metal ion complex. A review of the literature concerning stabilization of the phosphorane intermediate of the hydrolysis and isomerization of RNA phosphodiester bond is first presented. The results obtained in the experimental work followed by mechanistic interpretations are introduced in the second part of the thesis. Especially the significance of hydrogen bonding interactions is discussed.

Monikansalliset yritykset Venäjällä

Tämä kandidaatintyö käsittelee monikansallisten yritysten mahdollisuuksia sekä vaikutuksia Venäjällä. Työ koostuu neljästä kokonaisuudesta, joista ensimmäinen käsittelee teorioita keskittyen OLI-paradigman ja suoran ulkomaisen investoinnin käsitteisiin. Seuraavat kolme osiota tutkivat tutkimuskysymyksiä, joista ensimmäisessä selvitetään monikansallisten yritysten vaikutusta Venäjän talouteen lähinnä suorien ulkomaisten investointien näkökulmasta. Kaksi viimeistä kappaletta käsittelevät, kuinka yritykset pääsevät Venäjälle ja millaisia etuja ja uhkia siellä toimimisesta on monikansallisille yrityksille. Näissä osioissa käsitellään erilaisia tapoja, joita yritykset käyttävät päästäkseen Venäjän markkinoille sekä millaisia seikkoja niiden täytyy huomioida tehdessään investointipäätöksen.

The Structural Basis for inorganic Pyrophosphatase Catalysis and Regulation

Inorganic pyrophosphatases (PPases) are essential enzymes for every living cell. PPases provide the necessary thermodynamic pull for many biosynthetic reactions by hydrolyzing pyrophosphate. There are two types of PPases: integral membrane-bound and soluble enzymes. The latter type is divided into two non-homologous protein families, I and II. Family I PPases are present in all kingdoms of life, whereas family II PPases are only found in prokaryotes, including archae. Family I PPases, particularly that from Saccharomyces cerevisiae, are among the most extensively characterized phosphoryl transfer enzymes. In the present study, we have solved the structures of wild-type and seven active site variants of S. cerevisiae PPase bound to its natural metal cofactor, magnesium ion. These structures have facilitated derivation of the complete enzyme reaction scheme for PPase, fulfilling structures of all the reaction intermediates. The main focus in this study was on a novel subfamily of family II PPases (CBSPPase) containing a large insert formed by two CBS domains and a DRTGG domain within the catalytic domain. The CBS domain (named after cystathionine beta-synthase in which it was initially identified) usually occurs as tandem pairs with two or four copies in many proteins in all kingdoms of life. The structure formed by a pair of CBS domains is also known as a Bateman domain. CBS domains function as regulatory units, with adenylate ligands as the main effectors. The DRTGG domain (designated based on its most conserved residues) occurs less frequently and only in prokaryotes. Often, the domain co-exists with CBS domains, but its function remains unknown. The key objective of the current study was to explore the structural rearrangements in the CBS domains induced by regulatory adenylate ligands and their functional consequences. Two CBS-PPases were investigated, one from Clostridium perfringens (cpCBS-PPase) containing both CBS and DRTGG domains in its regulatory region and the other from Moorella thermoacetica (mt CBS-PPase) lacking the DRTGG domain. We additionally constructed a separate regulatory region of cpCBS-PPase (cpCBS). Both full-length enzymes and cpCBS formed homodimers. Two structures of the regulatory region of cpCBS-PPase complexed with the inhibitor, AMP, and activator, diadenosine tetraphosphate, were solved. The structures were significantly different, providing information on the structural pathway from bound adenylates to the interface between the regulatory and catalytic parts. To our knowledge, these are the first reported structures of a regulated CBS enzyme, which reveal large conformational changes upon regulator binding. The activator-bound structure was more open, consistent with the different thermostabilities of the activator- and inhibitor-bound forms of cpCBS-PPase. The results of the functional studies on wild-type and variant CBS-PPases provide support for inferences made on the basis of structural analyses. Moreover, these findings indicate that CBS-PPase activity is highly sensitive to adenine nucleotide distribution between AMP, ADP and ATP, and hence to the energy level of the cell. CBS-PPase activity is markedly inhibited at low energy levels, allowing PPi energy to be used for cell survival instead of being converted into heat.

Rotuun, etnisyyteen, luokkaan ja sukupuoleen kytkeytyvät valtasuhteet ja niiden problematisointi Julia Alvarezin romaanissa How the García Girls Lost Their Accents

Pro gradu -tutkielmani käsittelee valtasuhteita rotuun, etnisyyteen, luokkaan ja sukupuoleen kytkeytyvinä historiallisina verkostoina ja niiden vaikutuksia ihmisten elämään. Tutkielman kohdetekstinä on dominikaanilaisamerikkalaisen kirjailijan Julia Alvarezin (s. 1950) esikoisromaani How the García Girls Lost Their Accents (1991). Alvarezin romaani on omaelämäkerrallinen, ja se perustuu osittain historiallisiin tositapahtumiin. Tutkimusotteeni on kontekstualisoiva; teos asetetaan osaksi laajempia historiallisia tapahtumia ja niiden muodostamia valtahierarkioita. Teos sijoittuu päähenkilöiden kotimaan, Dominikaanisen tasavallan, lisäksi Yhdysvaltoihin, jonne Garcían perheen isä, äiti ja neljä tytärtä pakenevat diktaattori Trujillon tyranniaa 1960-luvulla. Tutkimukseni teoreettinen viitekehys nojaa postkoloniaaliseen ja feministiseen kirjallisuudentutkimukseen, joiden pyrkimyksenä on hegemonisten rakenteiden purkaminen. Valtasuhteiden dekonstruktiivisen paljastamisen avulla tuotettuja ja väärinkerrottuja historioita ja ruumiita kirjoitetaan uudelleen. Pohdin Alvarezin esikoisromaanin valtasuhteita esimerkiksi Michel Foucault’n vallan teoriaa hyödyntäen, mutta liitän analyysiin myös feminististä teoriaa etenkin Judith Butlerin ajatusten avulla. Tarkastelen työssäni romaanin henkilöhahmojen elämää ja identiteettien muodostumista rotuun, etnisyyteen, luokkaan ja sukupuoleen kytkeytyvän problemaattisen valtajaon näkökulmasta, jolla on juuri Karibian alueella vahvat historialliset erityispiirteensä kolonialismin sekä sen jälkivaikutusten runtelemana alueena. Työssäni tutkitaan muun muassa kolonialismin ja siirtolaisuuden diskursseissa päähenkilöiden elämään vaikuttavia valtasuhteita, ja etenkin kulttuuristen ja seksuaalisten identiteettien muodostumista marginalisoiduilla raja-alueilla. Osoitan, kuinka teoksesta käyvät ilmi erilaisten mutkikkaiden rotuun, etnisyyteen, luokkaan ja sukupuoleen liittyvien valtasuhteiden vaikutukset etenkin naisten elämään ja identiteetteihin. Mielestäni Alvarez tuo kerronnallaan ilmi valtasuhteiden kontekstisidonnaisuutta ja samalla niiden mielivaltaista ja rakenteellista luonnetta. Valta ja vallitsevat kaksijakoiset valtajärjestykset ovat tuotettuja ja toimivat yleensä poliittisesti jonkin ryhmän hyväksi toisia ryhmiä sortaen. Keskeinen tutkimustulos on, että Alvarezin teoksessa usein implisiittisesti kuvatut, kauas historiaan kytköksissä olevat valtasuhteet vaikuttavat monin tavoin teoksen päähenkilöiden elämään ja identiteettien muodostumiseen.

Formal and informal mechanisms for knowledge protection and sharing

The most important knowledge in firms is mostly tacit and embedded in individuals within the organization. This background knowledge that firms possess is used for creation of new knowledge and innovations. As firms today greatly concentrate on their core competencies, they need external knowledge from various collaboration partners. Thus, collaborative relationship governance, as well as control (use of appropriability mechanisms) over background (the input from each firm in innovative activities) and foreground knowledge (the output of collaboration activities) is needed in order to successfully create and capture value from innovative activities without losing core knowledge and competitiveness. Even though research has concentrated on knowledge protection and knowledge sharing, studies that combine both of these views and examine the effects of sharing and protection on value creation and capture have been rather limited. Studies have mainly focused on the protection of the output of innovation while forgetting the protection of the input of innovation. On the other hand, as the research concentrating on the output of innovation tends to favor formal mechanisms, informal mechanisms have remained more unknown to researchers as well as managers. This research aims to combine the perspectives of knowledge sharing and knowledge protection and their relationship with value creation and value capture. The sharing and protection are viewed from two points of view: the use of appropriability mechanisms, as well as governance of the collaborative relationship. The study consists of two parts. The first part introduces the research topic and discusses the overall results. The second part comprises six complementary research publications. Both qualitative and quantitative research methods are used in the study. In terms of results, the findings enhance understanding of the combined use of formal and informal mechanisms for knowledge protection and sharing. Informal mechanisms appear to be emphasized in the protection of background knowledge, and thus are prerequisites for innovation, whereas formal mechanisms are relied on more for protecting the results of innovative activities. However, the simultaneous use of the formal and informal mechanisms that are relevant to the particular industry and innovation context is recommendedthroughout the collaborative innovation process. Further, the study adds to the current knowledge on HRM as an appropriability mechanism: on the firm level its uses include assessing and hedging against employee-related risks such as knowledge leaking and knowledge leaving. A further contribution is to the research on HRM protection and its interrelations with other appropriability mechanisms, its constituents, and its potential use in the area of knowledge protection.

Kirjallisuutta

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Venäjä, uusiutuva energia ja kansainvälinen yhteistyö

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Naisten ja lasten sota

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