The interplay of JNK and SCG10 during cortical development and in excitotoxic responses in brain

Initially identified as stress activated protein kinases (SAPKs), the c-Jun Nterminal kinases (JNKs) are currently accepted as potent regulators of various physiologically important cellular events. Named after their competence to phosphorylate transcription factor c-Jun in response to UVtreatment, JNKs play a key role in cell proliferation, cell death or cell migration. Interestingly, these functions are crucial for proper brain formation. The family consists of three JNK isoforms, JNK1, JNK2 and JNK3. Unlike brain specific JNK3 isoform, JNK1 and JNK2 are ubiquitously expressed. It is estimated that ten splice variants exist. However, the detailed cellular functions of these remain undetermined. In addition, physiological conditions keep the activities of JNK2 and JNK3 low in comparison with JNK1, whereas cellular stress raises the activity of these isoforms dramatically. Importantly, JNK1 activity is constitutively high in neurons, yet it does not stimulate cell death. This suggests a valuable role for JNK1 in brain development, but also as an important mediator of cell wellbeing. The aim of this thesis was to characterize the functional relationship between JNK1 and SCG10. We found that SCG10 is a bona fide target for JNK. By employing differential centrifugation we showed that SCG10 co-localized with active JNK, MKK7 and JIP1 in a fraction containing endosomes and Golgi vesicles. Investigation of JNK knockout tissues using phosphospecific antibodies recognizing JNK-specific phosphorylation sites on SCG10 (Ser 62/Ser 73) showed that phosphorylation of endogenous SCG10 was dramatically decreased in Jnk1-/- brains. Moreover, we found that JNK and SCG10 co-express during early embryonic days in brain regions that undergo extensive neuronal migration. Our study revealed that selective inhibition of JNK in the cytoplasm significantly increased both the frequency of exit from the multipolar stage and radial migration rate. However, as a consequence, it led to ill-defined cellular organization. Furthermore, we found that multipolar exit and radial migration in Jnk1 deficient mice can be connected to changes in phosphorylation state of SCG10. Also, the expression of a pseudo-phosphorylated mutant form of SCG10, mimicking the JNK1- phopshorylated form, brings migration rate back to normal in Jnk1 knockout mouse embryos. Furthermore, we investigated the role of SCG10 and JNK in regulation of Golgi apparatus (GA) biogenesis and whether pathological JNK action could be discernible by its deregulation. We found that SCG10 maintains GA integrity as with the absence of SCG10 neurons present more compact fragmented GA structure, as shown by the knockdown approach. Interestingly, neurons isolated from Jnk1-/- mice show similar characteristics. Block of ER to GA is believed to be involved in development of Parkinson's disease. Hence, by using a pharmacological approach (Brefeldin A treatment), we showed that GA recovery is delayed upon removal of the drug in Jnk1-/- neurons to an extent similar to the shRNA SCG10-treated cells. Finally, we investigated the role of the JNK1-SCG10 duo in the maintenance of GA biogenesis following excitotoxic insult. Although the GA underwent fragmentation in response to NMDA treatment, we observed a substantial delay in GA disintegration in neurons lacking either JNK1 or SCG10.

Molecular Mechanisms and Interactions in Regulation of Photosynthetic Reactions

In photosynthesis, light energy is converted to chemical energy, which is consumed for carbon assimilation in the Calvin-Benson-Bassham (CBB) cycle. Intensive research has significantly advanced the understanding of how photosynthesis can survive in the ever-changing light conditions. However, precise details concerning the dynamic regulation of photosynthetic processes have remained elusive. The aim of my thesis was to specify some molecular mechanisms and interactions behind the regulation of photosynthetic reactions under environmental fluctuations. A genetic approach was employed, whereby Arabidopsis thaliana mutants deficient in specific photosynthetic protein components were subjected to adverse light conditions and assessed for functional deficiencies in the photosynthetic machinery. I examined three interconnected mechanisms: (i) auxiliary functions of PsbO1 and PsbO2 isoforms in the oxygen evolving complex of photosystem II (PSII), (ii) the regulatory function of PGR5 in photosynthetic electron transfer and (iii) the involvement of the Calcium Sensing Receptor CaS in photosynthetic performance. Analysis of photosynthetic properties in psbo1 and psbo2 mutants demonstrated that PSII is sensitive to light induced damage when PsbO2, rather than PsbO1, is present in the oxygen evolving complex. PsbO1 stabilizes PSII more efficiently compared to PsbO2 under light stress. However, PsbO2 shows a higher GTPase activity compared to PsbO1, and plants may partially compensate the lack of PsbO1 by increasing the rate of the PSII repair cycle. PGR5 proved vital in the protection of photosystem I (PSI) under fluctuating light conditions. Biophysical characterization of photosynthetic electron transfer reactions revealed that PGR5 regulates linear electron transfer by controlling proton motive force, which is crucial for the induction of the photoprotective non-photochemical quenching and the control of electron flow from PSII to PSI. I conclude that PGR5 controls linear electron transfer to protect PSI against light induced oxidative damage. I also found that PGR5 physically interacts with CaS, which is not needed for photoprotection of PSII or PSI in higher plants. Rather, transcript profiling and quantitative proteomic analysis suggested that CaS is functionally connected with the CBB cycle. This conclusion was supported by lowered amounts of specific calciumregulated CBB enzymes in cas mutant chloroplasts and by slow electron flow to PSI electron acceptors when leaves were reilluminated after an extended dark period. I propose that CaS is required for calcium regulation of the CBB cycle during periods of darkness. Moreover, CaS may also have a regulatory role in the activation of chloroplast ATPase. Through their diverse interactions, components of the photosynthetic machinery ensure optimization of light-driven electron transport and efficient basic production, while minimizing the harm caused by light induced photodamage.

Oxygen Photoreduction in Cyanobacteria

Cyanobacteria are well-known for their role in the global production of O2 via photosynthetic water oxidation. However, with the use of light energy, cyanobacteria can also reduce O2. In my thesis work, I have investigated the impact of O2 photoreduction on protection of the photosynthetic apparatus as well as the N2-fixing machinery. Photosynthetic light reactions produce intermediate radicals and reduced electron carriers, which can easily react with O2 to generate various reactive oxygen species. To avoid prolonged reduction of photosynthetic components, cyanobacteria use “electron valves” that dissipate excess electrons from the photosynthetic electron transfer chain in a harmless way. In Synechocystis sp. PCC 6803, flavodiiron proteins Flv1 and Flv3 comprise a powerful electron sink redirecting electrons from the acceptor side of Photosystem I to O2 and reducing it directly to water. In this work, I demonstrate that upon Ci-depletion Flv1/3 can dissipate up to 60% of the electrons delivered from Photosystem II. O2 photoreduction by Flv1/3 was shown to be vital for cyanobacteria in natural aquatic environments and deletion of Flv1/3 was lethal for both Synechocystis sp. PCC 6803 and Anabaena sp. PCC 7120 under fluctuating light conditions. The lethal phenotype observed in the absence of Flv1/3 results from oxidative damage to Photosystem I, which appeared to be a primary target of reactive oxygen species produced upon sudden increases in light intensity. Importantly, cyanobacteria also possess other O2 photoreduction pathways which can protect the photosynthetic apparatus. This study demonstrates that respiratory terminal oxidases are also capable of initiating O2 photoreduction in mutant cells lacking the Flv1/3 proteins and grown under fluctuating light. Photoreduction of O2 by Rubisco was also shown in Ci-depleted cells of the mutants lacking Flv1/3, and thus provided the first evidence for active photorespiratory gas-exchange in cyanobacteria. Nevertheless, and despite the existence of other O2 photoreduction pathways, the Flv1/3 route appears to be the most robust and rapid system of photoprotection. Several groups of cyanobacteria are capable of N2 fixation. Filamentous heterocystous N2- fixing species, such as Anabaena sp. PCC 7120, are able to differentiate specialised cells called heterocysts for this purpose. In contrast to vegetative cells which perform oxygenic photosynthesis, heterocysts maintain a microoxic environment for the proper function of the nitrogenase enzyme, which is extremely sensitive to O2. The genome of Anabaena sp. PCC 7120 harbors two copies of genes encoding Flv1 and Flv3 proteins, designated as “A” and “B” forms. In this thesis work, I demonstrate that Flv1A and Flv3A are expressed only in the vegetative cells of filaments, whilst Flv1B and Flv3B are localized exclusively in heterocysts. I further revealed that the Flv3B protein is most responsible for the photoreduction of O2 in heterocysts, and that this reaction plays an important role in protection of the N2-fixing machinery and thus, the provision of filaments with fixed nitrogen. The function of the Flv1B protein remains to be elucidated; however the involvement of this protein in electron transfer reactions is feasible. Evidence provided in this thesis indicates the presence of a great diversity of O2 photoreduction reactions in cyanobacterial cells. These reactions appear to be crucial for the photoprotection of both photosynthesis and N2 fixation processes in an oxygenic environment.

Lignin oxidation by PCD technology

The purpose of this study is to investigate whether commercial Kraft lignin can be treated with pulsed corona discharge apparatus so that it becomes active. Active lignin refers to the kind of lignin that can be precipitated on the surface of a fiber by lowering the pH. A secondary agenda here is to remove the pungent smell of kraft lignin, which is caused by organically bound sulfur. It is expected that the study will identify mild processing conditions and parameters for achievement of the desired outcome. In the literature review, the properties of lignin are explained, as is their impact on any further processing. In addition, a number of processes are described for the oxidation of lignin in a variety of applications. In the experimental part of the study, test runs were conducted to determine the effects of oxygen supply and pulse frequency on oxidation results, where the purpose is to produce reactive lignin and to find a process that is feasible at an industrial scale. Based on the reported experiments, lignin could not be made active or precipitated to the surface of the fiber. Actual changes in the structure of lignin were not observed, but the pungent smell of lignin was removed. The exact reason for this change could not be established because sulfur NMR analysis did not work for the lignin samples.

Extreme Observables and Optimal Measurements in Quantum Theory

Optimization of quantum measurement processes has a pivotal role in carrying out better, more accurate or less disrupting, measurements and experiments on a quantum system. Especially, convex optimization, i.e., identifying the extreme points of the convex sets and subsets of quantum measuring devices plays an important part in quantum optimization since the typical figures of merit for measuring processes are affine functionals. In this thesis, we discuss results determining the extreme quantum devices and their relevance, e.g., in quantum-compatibility-related questions. Especially, we see that a compatible device pair where one device is extreme can be joined into a single apparatus essentially in a unique way. Moreover, we show that the question whether a pair of quantum observables can be measured jointly can often be formulated in a weaker form when some of the observables involved are extreme. Another major line of research treated in this thesis deals with convex analysis of special restricted quantum device sets, covariance structures or, in particular, generalized imprimitivity systems. Some results on the structure ofcovariant observables and instruments are listed as well as results identifying the extreme points of covariance structures in quantum theory. As a special case study, not published anywhere before, we study the structure of Euclidean-covariant localization observables for spin-0-particles. We also discuss the general form of Weyl-covariant phase-space instruments. Finally, certain optimality measures originating from convex geometry are introduced for quantum devices, namely, boundariness measuring how ‘close’ to the algebraic boundary of the device set a quantum apparatus is and the robustness of incompatibility quantifying the level of incompatibility for a quantum device pair by measuring the highest amount of noise the pair tolerates without becoming compatible. Boundariness is further associated to minimum-error discrimination of quantum devices, and robustness of incompatibility is shown to behave monotonically under certain compatibility-non-decreasing operations. Moreover, the value of robustness of incompatibility is given for a few special device pairs.

New threats - old routines : bureaucratic adaptability in the security policy environment

Within the framework of state security policy, the focus of this dissertation are the relations between how new security threats are perceived and the policy planning and bureaucratic implementation that are designed to address them. In addition, this thesis explores and studies some of the inertias that might exist in the core of the state apparatus as it addresses new threats and how these could be better managed. The dissertation is built on five thematic and interrelated articles highlighting different aspects of when new significant national security threats are detected by different governments until the threats on the policy planning side translate into protective measures within the society. The timeline differs widely between different countries and some key aspects of this process are also studied. One focus concerns mechanisms for adaptability within the Intelligence Community, another on the policy planning process within the Cabinet Offices/National Security Councils and the third focus is on the planning process and how policy is implemented within the bureaucracy. The issue of policy transfer is also analysed, revealing that there is some imitation of innovation within governmental structures and policies, for example within the field of cyber defence. The main findings of the dissertation are that this context has built-in inertias and bureaucratic seams found in most government bureaucratic machineries. As much of the information and planning measures imply security classification of the transparency and internal debate on these issues, alternative assessments become limited. To remedy this situation, the thesis recommends ways to improve the decision-making system in order to streamline the processes involved in making these decisions. Another special focus of the thesis concerns the role of the public policy think tanks in the United States as an instrument of change in the country’s national security decision-making environment, which is viewed from the perspective as being a possible source of new ideas and innovation. The findings in this part are based on unique interviews data on how think tanks become successful and influence the policy debate in a country such as the United States. It appears clearly that in countries such as the United States think tanks smooth the decision making processes, and that this model with some adaptations also might be transferrable to other democratic countries.

Perfluorattuja yhdisteitä sisältävien jätevesien puhdistus- ja analyysimenetelmät

Perfluoratut alkyyliyhdisteet eli PFAS-yhdisteet ovat synteettisiä orgaanisia yhdisteitä, joissa on fluorattu hiiliketju. Hiilen ja fluorin väliset vahvat sidokset ovat muodostuneet ongelmaksi jätevedenpuhdistamoilla, sillä yhdisteet eivät hajoa puhdistamoilla käytössä olevilla vedenpuhdistusmenetelmillä. Yhdisteitä kertyy luontoon jätevesien mukana. Kandidaatintyössä on vertailtu yhdisteitä sisältävien vesien käsittelymenetelmiä parhaiten soveltuvan menetelmän löytämiseksi. Menetelmien kustannuksia tai soveltuvuutta vedenpuhdistamomittakaavan prosessiksi ei ole arvioitu. Lisäksi työssä on koottu yhdisteitä sisältävien jätevesien analysointiin sopivia analyysimenetelmiä. Soveltuvat puhdistus- ja analyysimenetelmät on esitelty uusien tieteellisten artikkelien pohjalta. Mahdollisia erotusmenetelmiä ovat membraanierotus ja sorptio. Membraaneista soveltuvimpia ovat nanosuodatus- ja käänteisosmoosimembraanit, joilla erottuvat jopa 0,0001 μm:n kokoiset partikkelit. PFAS-yhdisteet voidaan erottaa sorptiolla muun muassa aktiivihiileen. Yhdisteiden rakenne hajoaa nykyaikaisilla hapetusmenetelmillä ja polttamalla lietteen mukana. Hapettaminen permanganaatin avulla ei tuottanut hyvää tulosta, mutta fotokemiallisella hapetuksella ja alhaisen lämpötilan plasmatekniikalla (NTP) yhdisteiden rakenne hajosi lähes kokonaan. Fotokemiallinen hapetus onnistui erityisesti perfluorokarboksyylihapoilla, joiden rakenne hajosi jopa kolmessa tunnissa. Yleisimmin käytetty analyysimenetelmä on nestekromatografin ja massaspektrometrin yhdistelmä (LC-MS/MS) ja matriisivaikutus minimoidaan tyypillisesti kiinteäfaasiuutolla (SPE). Työssä esitellyistä käsittelymenetelmistä parhaiten soveltuva on NTP-menetelmä, koska sillä saatiin tutkimusten mukaan hajotettua yhdisteiden rakenne muita menetelmiä lyhyemmässä ajassa ja se soveltuu parhaiten kaikille PFAS-yhdisteille. NTP-menetelmässä ei tarvita katalyyttiä tai lisäkemikaaleja. Voimakkaana hapettimena toimivat epästabiilit hydroksyyliradikaalit, jotka syntyvät koronapurkauksen kautta. Koronapurkauksessa muodostuu myös otsonia ja lisäksi vapaa happi voi tehostaa hapettumista. Menetelmässä muodostuvien hajoamistuotteiden hallinta vaatii lisätutkimusta. Mahdollinen hallintakeino voisi olla esimerkiksi hapettumisessa vapautuvien fluoridi-ionien saostaminen. Muodostuvien hajoamistuotteiden toksisuutta voitaisiin tarkkailla biosensorilla.

Quest/ion of Identities in African American Feminist Postmodern Drama: A Study of Selected Plays by Suzan-Lori Parks

Innovative and unconventional, Pulitzer Prize-winning playwright Suzan-Lori Parks belongs to the continuum of African American playwrights who have contributed to the quest/ion – the quest for and question – of identities for African Americans. Her plays are sites in which the quest/ion of identities for African Americans is pursued, raised and enacted. She makes use of both page and stage to emphasize the exigency of reshaping African Americans’ identities through questioning the dominant ideologies and metanarratives, delegitimizing some of the prevailing stereotypes imposed on them, drawing out the complicity of the media in perpetuating racism, evoking slavery, lynching and their aftereffects, rehistoricizing African American history, catalyzing reflections on the various intersections of sex, race, class and gender orientations, and proffering alternative perspectives to help readers think more critically about issues facing African Americans. In my dissertation, I approach three plays by Parks – The Death of the Last Black Man in the Whole Entire World (1990), Venus (1996) and Fucking A (2000) – from the standpoints of postmodern drama and African American feminism with a focus on the terrains that reflect the quest/ion of identities for African Americans, especially African American women. I argue that postmodern drama and African American feminism provide the ground for Parks to promote the development of a political agenda in order to call into question a number of dominant ideologies and metanarratives with regard to African Americans and draw upon the roles of those metanarratives as a powerful apparatus of racial and sexual oppressions. I also explore how Parks engages with postmodern drama and African American feminism to incorporate her own mininarratives in the dominant discourses. I argue that Parks in these plays uses postmodern drama and African American feminism to encourage reflections on intersectionality in order to reveal the concerns of African Americans, particularly African American women. Her plays challenge the dominant order of hierarchy and patriarchy, while in some cases urging unity and solidarity between African American men and women by showing how unity and solidarity can help them confront race, class and gender oppressions. Furthermore, I discuss how the utilization of postmodern techniques and devices helps Parks to transform the conventional features of playwriting, to create incredulity toward the dominant systems of oppression and to incorporate her mininarratives within the context of dominant discourses.