Aspects and Applications of Pulse Sequence Design for Solution-State Nuclear Magnetic Resonance Spectroscopy

NMR spectroscopy enables the study of biomolecules from peptides and carbohydrates to proteins at atomic resolution. The technique uniquely allows for structure determination of molecules in solution-state. It also gives insights into dynamics and intermolecular interactions important for determining biological function. Detailed molecular information is entangled in the nuclear spin states. The information can be extracted by pulse sequences designed to measure the desired molecular parameters. Advancement of pulse sequence methodology therefore plays a key role in the development of biomolecular NMR spectroscopy. A range of novel pulse sequences for solution-state NMR spectroscopy are presented in this thesis. The pulse sequences are described in relation to the molecular information they provide. The pulse sequence experiments represent several advances in NMR spectroscopy with particular emphasis on applications for proteins. Some of the novel methods are focusing on methyl-containing amino acids which are pivotal for structure determination. Methyl-specific assignment schemes are introduced for increasing the size range of 13C,15N labeled proteins amenable to structure determination without resolving to more elaborate labeling schemes. Furthermore, cost-effective means are presented for monitoring amide and methyl correlations simultaneously. Residual dipolar couplings can be applied for structure refinement as well as for studying dynamics. Accurate methods for measuring residual dipolar couplings in small proteins are devised along with special techniques applicable when proteins require high pH or high temperature solvent conditions. Finally, a new technique is demonstrated to diminish strong-coupling induced artifacts in HMBC, a routine experiment for establishing long-range correlations in unlabeled molecules. The presented experiments facilitate structural studies of biomolecules by NMR spectroscopy.

Hyperfine effects in the nuclear magnetic resonance of paramagnetic molecules

Paramagnetic, or open-shell, systems are often encountered in the context of metalloproteins, and they are also an essential part of molecular magnets. Nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for chemical structure elucidation, but for paramagnetic molecules it is substantially more complicated than in the diamagnetic case. Before the present work, the theory of NMR of paramagnetic molecules was limited to spin-1/2 systems and it did not include relativistic corrections to the hyperfine effects. It also was not systematically expandable. --- The theory was first expanded by including hyperfine contributions up to the fourth power in the fine structure constant α. It was then reformulated and its scope widened to allow any spin state in any spatial symmetry. This involved including zero-field splitting effects. In both stages the theory was implemented into a separate analysis program. The different levels of theory were tested by demonstrative density functional calculations on molecules selected to showcase the relative strength of new NMR shielding terms. The theory was also tested in a joint experimental and computational effort to confirm assignment of 11 B signals. The new terms were found to be significant and comparable with the terms in the earlier levels of theory. The leading-order magnetic-field dependence of shielding in paramagnetic systems was formulated. The theory is now systematically expandable, allowing for higher-order field dependence and relativistic contributions. The prevailing experimental view of pseudocontact shift was found to be significantly incomplete, as it only includes specific geometric dependence, which is not present in most of the new terms introduced here. The computational uncertainty in density functional calculations of the Fermi contact hyperfine constant and zero-field splitting tensor sets a limit for quantitative prediction of paramagnetic shielding for now.

Disabled Revolutionary War Veterans and the Construction of Disability in the Early United States, c. 1776-1840

This thesis addresses the following broad research question: what did it mean to be a disabled Revolutionary War veteran in the early United States during the period from 1776 to roughly 1840? The study approaches the question from two angles: a state-centred one and an experiential one. In both cases, the theoretical framework employed comes from disability studies. Consequently, disability is regarded as a sociocultural phenomenon rather than a medical condition. The state-centred dimension of the study explores the meaning of disability and disabled veterans to the early American state through an examination of the major military pension laws of the period. An analysis of this legislation, particularly the invalid pension acts of 1793 and 1806, indicates that the early United States represents a key period in the development of the modern disability category. The experiential approach, in contrast, shifts the focus of attention away from the state towards the lived experiences of disabled veterans. It seeks to address the issue of whether or not the disabilities of disabled veterans had any significant material impact on their everyday lives. It does this through a comparison of the situation of 153 disabled veterans with that of an equivalent number of nondisabled veterans. The former group received invalid pensions while the latter did not. In comparing the material conditions of disabled and nondisabled veterans, a wide range of primary sources from military records to memoirs and letters are used. The most important sources in this regard are the pension application papers submitted by veterans in the early nineteenth century. These provide us with a unique insight into the everyday lives of veterans. Looking at the issue of experience through the window of the pension files reveals that there was not much difference in the broad contours of disabled and nondisabled veteran life. This finding has implications for the theorisation of disability that are highlighted and discussed in the thesis. The main themes covered in this study are: the wartime experiences of injured American soldiers, the military pension establishment of the early United States and the legal construction of disability, and the post-war working and family lives of disabled veterans. Keywords: disability, early America, veterans, military pensions, disabled people, Revolutionary War, United States, disability theory.

Three Sides of a Wall : Obstacles and Border States in Paul Auster's Novels

Tutkielmani käsittelee yhdysvaltalaisen kirjailijan Paul Austerin (s. 1947) romaanituotannossa esiintyviä esteitä ja rajatiloja. Erityisesti olen kiinnostunut siitä, miten Auster liittää nämä "marginaalitilat" amerikkalaiseen vapauden ja laajentumisen ideologiaan sekä kieleen ja kirjoittamiseen. Austerin romaaneissa esteiden ja rajatilojen käsittely voidaan jakaa kolmeen vaiheeseen. Ensimmäisessä vaiheessa henkilöt ovat vahvojen esteiden rajoittamia tai rakentavat niitä itse. Rajoittuneisuus ei kuitenkaan aina tunnu häiritsevän heitä - itse asiassa monet päähenkilöistä tuntevat itsensä onnellisiksi tai vähintäänkin tyytyväisiksi joutuessaan esteen takia pysähdyttämään vapaan liikkeensä. Toisessa vaiheessa henkilöt pyrkivät ylittämään tai rikkomaan esteen päästäkseen toiselle puolelle. Kuten amerikkalaiset esi-isänsä aikoinaan, he etsivät rajatonta, laajaa ja tyhjää tilaa - "suurta tuntematonta" valloitettavakseen. Tällaisen tilan kohdatessaan he joutuvat kuitenkin usein epävarmuuden valtaan. Kolmas vaihe on tutkielmani kannalta tärkein: välitila, josta käytän työssäni nimitystä "in-betweenity". Tähän vaiheeseen päästään kulkemalla ensin kahden muun vaiheen kautta. Juuri tietoisuus näistä kahdesta muusta vaiheesta synnyttää tämän kolmannen tilan, eräänlaisen rajatilan, jossa tajutaan sekä esteiden että esteettömyyden tärkeys. Tämä välitila on Austerille tyypillinen tila, joka kertoo paitsi amerikkalaisen unelman paradoksaalisuudesta myös (kaunokirjallisen) kielenkäytön prosessista. Monet Austerin kirjojen muurin rakentajista tai purkajista voidaan nähdä kirjailijahahmoina, joiden omituinen suhde esteisiin ja rajoihin kumpuaa juuri siitä rajatilasta, jonka asukkaita he kielentaiteilijoina väistämättä ovat. Tällaisen tilan/tilattomuuden kuvaaminen tekee Austerista oman postmodernin aikamme tärkeän kirjailijan - kirjailijan, joka sen sijaan, että pyrkisi eroon paradokseista, sijoittaa hahmonsa niiden sisään. Rajoihin ja esteisiin liittyvä problematiikka ei kuitenkaan ole pelkästään nykyajan ongelma vaan kysymys, joka ihmisen toisaalta rajoja kaipaavan toisaalta rajattomuutta kaipaavan luonteen vuoksi säilyy aina ajankohtaisena. Avainsanat: Paul Auster, este, muuri, raja, Yhdysvallat

Ranskan rooli ja asema läntisessä liittoutumassa neljännen ja viidennen tasavallan vaihtumakohdassa 1956-1958

The study discusses the position of France as the United States’ ally in NATO in 1956-1958. The concrete position of France and the role that it was envisioned to have are being treated from the point of view of three participants of the Cold War: France, the United States and the Soviet Union. How did these different parties perceive the question and did these views change when the French Fourth Republic turned into the Fifth in 1958? The study is based on published French and American documents of Foreign Affairs. Because of problems with accessibility to the Soviet archival sources, the study uses reports on France-NATO relations of Pravda newspaper, the official organ of the Communist Party of the USSR, to provide information about how the Soviet side saw the question. Due to the nature and use of source material, and the chronological structure of the work, the study belongs methodologically to the research field of History of International Relations. As distinct from political scientists’ field of research, more prone to theorize, the study is characteristically a historical research, a work based on qualitative method and original sources that aims at creating a coherent narrative of the views expressed during the period covered by the study. France’s road to a full membership of NATO is being treated on the basis of research literature, after which discussions about France’s position in the Western Alliance are being chronologically traced for the period of last years of the Fourth Republic and the immediate months of coming back to power of Charles de Gaulle. Right from the spring of 1956 there can be seen aspirations of France, on one hand, to maintain her freedom of action inside the Western Alliance and, on the other, to widen the dialogue between the allies. The decision on France’s own nuclear deterrent was made already during the Fourth Republic, when it was thought to become part of NATO’s common defence. This was to change with de Gaulle. The USA felt that France still fancied herself as a great power and that she could not participate in full in NATO’s common defence because of her colonies. The Soviet Union saw the concrete position of France in the Alliance as in complete dependence on the USA, but her desired role was expressed largely in “Gaullist” terms. The expressions used by the General and the Soviet propaganda were close to each other, but the Soviet Union could not support de Gaulle without endangering the position of the French Communist Party. Between the Fourth and Fifth Republics no great rupture in content took place concerning the views of France’s role and position in the Western Alliance. The questions posed by de Gaulle had been expressed during the whole period of Fourth Republic’s existence. Instead, along with the General the weight and rhetoric of these questions saw a great change. Already in the early phase the Americans saw it possible that with de Gaulle, France would try to change her role. The rupture took place in the form of expression, rather than in its content.

Assessing organizational culture in complex sociotechnical systems : Methodological evidence from studies in nuclear power plant maintenance organizations

Failures in industrial organizations dealing with hazardous technologies can have widespread consequences for the safety of the workers and the general population. Psychology can have a major role in contributing to the safe and reliable operation of these technologies. Most current models of safety management in complex sociotechnical systems such as nuclear power plant maintenance are either non-contextual or based on an overly-rational image of an organization. Thus, they fail to grasp either the actual requirements of the work or the socially-constructed nature of the work in question. The general aim of the present study is to develop and test a methodology for contextual assessment of organizational culture in complex sociotechnical systems. This is done by demonstrating the findings that the application of the emerging methodology produces in the domain of maintenance of a nuclear power plant (NPP). The concepts of organizational culture and organizational core task (OCT) are operationalized and tested in the case studies. We argue that when the complexity of the work, technology and social environment is increased, the significance of the most implicit features of organizational culture as a means of coordinating the work and achieving safety and effectiveness of the activities also increases. For this reason a cultural perspective could provide additional insight into the problem of safety management. The present study aims to determine; (1) the elements of the organizational culture in complex sociotechnical systems; (2) the demands the maintenance task sets for the organizational culture; (3) how the current organizational culture at the case organizations supports the perception and fulfilment of the demands of the maintenance work; (4) the similarities and differences between the maintenance cultures at the case organizations, and (5) the necessary assessment of the organizational culture in complex sociotechnical systems. Three in-depth case studies were carried out at the maintenance units of three Nordic NPPs. The case studies employed an iterative and multimethod research strategy. The following methods were used: interviews, CULTURE-survey, seminars, document analysis and group work. Both cultural analysis and task modelling were carried out. The results indicate that organizational culture in complex sociotechnical systems can be characterised according to three qualitatively different elements: structure, internal integration and conceptions. All three of these elements of culture as well as their interrelations have to be considered in organizational assessments or important aspects of the organizational dynamics will be overlooked. On the basis of OCT modelling, the maintenance core task was defined as balancing between three critical demands: anticipating the condition of the plant and conducting preventive maintenance accordingly, reacting to unexpected technical faults and monitoring and reflecting on the effects of maintenance actions and the condition of the plant. The results indicate that safety was highly valued at all three plants, and in that sense they all had strong safety cultures. In other respects the cultural features were quite different, and thus the culturally-accepted means of maintaining high safety also differed. The handicraft nature of maintenance work was emphasised as a source of identity at the NPPs. Overall, the importance of safety was taken for granted, but the cultural norms concerning the appropriate means to guarantee it were little reflected. A sense of control, personal responsibility and organizational changes emerged as challenging issues at all the plants. The study shows that in complex sociotechnical systems it is both necessary and possible to analyse the safety and effectiveness of the organizational culture. Safety in complex sociotechnical systems cannot be understood or managed without understanding the demands of the organizational core task and managing the dynamics between the three elements of the organizational culture.

Transcriptional regulation by the orphan nuclear receptor ERRgamma

The nuclear receptor (NR) superfamily is comprised of receptors for small lipopfilic ligands such as steroid hormones, thyroid hormone, retinoids, and vitamin D. NRs are ligand-inducible transcription factors capable of both activating and repressing their target gene expression. They control a wide range of biological functions connected to growth, development, and homeostasis. In addition to the ligand-regulated receptors, the family includes a large group of receptors whose physiological ligands are unknown. These receptors are referred to as orphan NRs. Estrogen-related receptor gamma (ERRgamma) belongs to the ERR subfamily of orphan NRs together with the related ERRalpha and ERRbeta. ERRs share amino acid sequence homology with the classical estrogen receptors (ERs) but they are unable to bind natural estrogenic ligands. ERRgamma is expressed in several embryonic and adult tissues but its biological role is still largely unknown. ERRgamma activates reporter gene expression in transfected cells independently of added hormones implying that ERRgamma harbors constitutive activity. However, the intrinsic activity of ERRgamma can be inhibited by synthetic compounds such as the selective estrogen receptor modulator 4-hydroxytamoxifen (4-OHT). Ligands of NRs can act as agonists that activate transcription, as antagonists that prevent activation of transcription, or as inverse agonists that antagonize the constitutive transcriptional activity of receptor. Most of the synthetic ERRgamma ligands act as inverse agonists but recently, a synthetic ERRgamma agonist GSK4716 was identified. This demonstrates that it is possible to design and identify agonists for ERRgamma. Prior to this thesis work, the structural and functional characteristics of ERRgamma were largely unknown. The aim of this study was to define the functional requirements for ERRgamma-mediated transcriptional regulation and to examine the cross-talk between ERRgamma and other NRs. Due to the fact that natural physiological ligands of ERRgamma are unknown, another aim of this study was to seek new natural compounds that may affect transcriptional activity of ERRgamma. Plant-derived phytoestrogens have previously been shown to act as ligands for ERs and ERRalpha, and therefore the effects of these compounds were also studied on ERRgamma-mediated transcriptional regulation. This work demonstrated that ERRgamma-mediated transcriptional regulation was dependent on DNA-binding, dimerization and activation function-2. Heterodimerization with ERRalpha inhibited the transcriptional activity of ERRgamma. In addition to 4-OHT, another anti-estrogen, 4-hydroxytoremifene (4-OHtor), was identified as an inverse agonist of ERRgamma. Interestingly, ERRgamma activated transcription in the presence of 4-OHT and 4-OHtor on activator protein-1 binding sites. ERRgamma was found to interact with another orphan NR Nurr1 by repressing the ability of Nurr1 to activate transcription of the osteopontin gene. Transcriptional activity of ERRgamma was shown to be stimulated by the phytoestrogen equol. Structural model analysis and mutational experiments indicated that equol was able to bind to the ligand binding domain of ERRgamma. The growth inhibitory effect of ERRgamma on prostate cancer cells was found to be enhanced by equol. In summary, this study demonstrates that despite the absence of an endogenous physiological ligand, the activity of ERRgamma can be modulated in other ways such as dimerization with related receptors or by cross-talk with other transcription factors as well as by binding some synthetic or natural compounds.

Orphan nuclear receptor subfamily NR4A their interplay with other nuclear receptors and functions in osteoblasts

Nurr1, NGFI-B and Nor1 (NR4A2, NR4A1 and NR4A3, respectively) belong to the NR4A subfamily of nuclear receptors. The NR4A receptors are orphan nuclear receptors which means that activating or repressing ligands for these receptors have not been found. NR4A expression is rapidly induced in response to various stimuli including growth factors and the parathyroid hormone (PTH). The studies concerning the NR4A receptors in the central nervous system have demonstrated that they have a major role in the development and function of the dopaminergic neurons of the midbrain and in regulating hypothalamus-pituitary-adrenal-axis. However, the peripheral functions of the NR4A family are largely unknown. Cultured mouse primary osteoblasts, a preosteoblastic cell line and several osteoblastic cell lines were used to investigate the role of NR4A receptors in osteoblasts. NR4A receptors were shown to directly bind to and activate the promoter of the osteopontin gene (OPN) in osteoblastic cells, thus regulating its expression. OPN is a major bone matrix protein expressed throughout the differentiation of preosteoblastic cells into osteoblasts. The activation of the OPN promoter was shown to be dependent on the activation function-1 located in the N-terminal part of Nurr1 and to occur in both monomeric and RXR heterodimeric forms of NR4A receptors. Furthermore, PTH was shown to upregulate OPN expression through the NR4A family. It was also demonstrated that the fibroblast growth factor-8b (FGF-8b) induces the expression of NR4A receptors in osteoblasts as immediate early genes. This induction involved phosphatidylinositol-3 kinase, protein kinase C, and mitogen activated protein kinase, which are all major pathways of FGF signalling. Nurr1 and NGFI-B were shown to induce the proliferation of preosteoblastic cells and to reduce their apoptosis. FGF-8b was shown to stimulate the proliferation of osteoblastic cells through the NR4A receptors. These results suggest that NR4A receptors have a role both in the differentiation of osteoblasts and in the proliferation and apoptosis of preosteoblast. The NR4A receptors were found to bind to the same response element on OPN as the members of the NR3B family of orphan receptors do. Mutual repression was observed between the NR4A receptors and the NR3B receptors. This repression was shown to be dependent on the DNA-binding domains of both receptor families, but to result neither from the competition of DNA binding nor from the competition for coactivators. As the repression was dependent on the relative expression levels of the NR4As and NR3Bs, it seems likely that the ratio of the receptors mediates their activity on their response elements. Rapid induction of the NR4As in response to various stimuli and differential expression of the NR3Bs can effectively control the gene activation by the NR4A receptors. NR4A receptors can bind DNA as monomers, and Nurr1 and NGFI-B can form permissive heterodimers with the retinoid X receptor (RXR). Permissive heterodimers can be activated with RXR agonists, unlike non-permissive heterodimers, which are formed by RXR and retinoic acid receptor or thyroid hormone receptor (RAR and TR, respectively). Non-permissive heterodimers can only be activated by the agonists of the heterodimerizing partner. The mechanisms behind differential response to RXR agonists have remained unresolved. As there are no activating or repressing ligands for the NR4A receptors, it would be important to find out, how they are regulated. Permissiviness of Nurr1/RXR heterodimers was linked to the N-terminal part of Nurr1 ligand-binding domain. This region has previously been shown to mediate the interaction between NRs and corepressors. Non-permissive RAR and TR, permissive Nurr1 and NGFI-B, and RXR were overexpressed with corepressors silencing mediator for retinoic acid and thyroid hormone receptors (SMRT), and with nuclear receptor corepressor in several cell lines. Nurr1 and NGFI-B were found to be repressed by SMRT. The interaction of RXR heterodimers with corepressors was weak in permissive heterodimers and much stronger in non-permissive heterodimers. Non-permissive heterodimers also released corepressors only in response to the agonist of the heterodimeric partner of RXR. In the permissive Nurr1/RXR heterodimer, however, SMRT was released following the treatment with RXR agonists. Corepressor release in response to ligands was found to differentiate permissive heterodimers from non-permissive ones. Corepressors were thus connected to the regulation of NR4A functions. In summary, the studies presented here linked the NR4A family of orphan nuclear receptors to the regulation of osteoblasts. Nurr1 and NGFI-B were found to control the proliferation and apoptosis of preosteoblasts. The studies also demonstrated that cross-talk with the NR3B receptors controls the activity of these orphan receptors. The results clarified the mechanism of permissiviness of RXR-heterodimers. New information was obtained on the regulation and functions of NR4A receptors, for which the ligands are unknown.