Genetic regulatory networks in avian B cells

Biology is turning into an information science. The science of systems biology seeks to understand the genetic networks that govern organism development and functions. In this study the chicken was used as a model organism in the study of B cell regulatory factors. These studies open new avenues for plasma cell research by connecting the down regulation of the B cell gene expression program directly to the initiation of plasma cell differentiation. The unique advantages of the DT40 avian B cell model system, specifically its high homologous recombination rate, were utilized to study gene regulation in Pax5 knock out cell lines and to gain new insights into the B cell to plasma cell transitions that underlie the secretion of antibodies as part of the adaptive immune response. The Pax5 transcription factor is central to the commitment, development and maintenance of the B cell phenotype. Mice lacking the Pax5 gene have an arrest in development at the pro-B lymphocyte stage while DT40 cells have been derived from cells at a more mature stage of development. The DT40 Pax5-/- cells exhibited gene expression similarities with primary chicken plasma cells. The expression of the plasma cell transcription factors Blimp-1 and XBP-1 were significantly upregulated while the expression of the germinal centre factor BCL6 was diminished in Pax5-/- cells, and this alteration was normalized by Pax5 re-introduction. The Pax5-deficient cells further manifested substantially elevated secretion of IgM into the supernatant, another characteristic of plasma cells. These results for the first time indicated that the downregulation of the Pax5 gene in B cells promotes plasma cell differentiation. Cross-species meta-analysis of chicken and mouse Pax5 gene knockout studies uncovers genes and pathways whose regulatory relationship to Pax5 has remained unchanged for over 300 million years. Restriction of the hematopoietic stem cell fate to produce T, B and NK cell lineages is dependent on the Ikaros and its molecular partners, the closely related Helios and Aiolos. Ikaros family members are zinc finger proteins which act as transcriptional repressors while helping to activate lymphoid genes. Helios in mice is expressed from the hematopoietic stem cell level onwards, although later in development its expression seems to predominate in the T cell lineage. This study establishes the emergence and sequence of the chicken Ikaros family members. Helios expression in the bursa of Fabricius, germinal centres and B cell lines suggested a role for Helios in the avian B-cell lineage, too. Phylogenetic studies of the Ikaros family connect the expansion of the Ikaros family, and thus possibly the emergence of the adaptive immune system, with the second round of genome duplications originally proposed by Ohno. Paralogs that have arisen as a result of genome-wide duplications are sometimes termed ohnologs – Ikaros family proteins appear to fit that definition. This study highlighted the opportunities afforded by the genome sequencing efforts and somatic cell reverse genetics approaches using the DT40 cell line. The DT40 cell line and the avian model system promise to remain a fruitful model for mechanistic insight in the post-genomic era as well.

Islet antigen-specific T cells and regulatory T cells in type 1 diabetes

T cells are the key players in the development of type 1 diabetes (T1D), mediating autoimmune reactions leading to the destruction of insulin producing beta cells in the islets. We aimed to analyze the role of different T-cell subtypes in the autoimmunity and pathogenesis of T1D. The frequency of islet antigen-specific (GAD65-, proinsulin-, and insulin-specific) CD4+ T cells was investigated in vitro in T1D patients, at-risk individuals (diabetes-associated autoantibody positive), and in controls, using MHC class II tetramers. An overall higher frequency of CD4+ T-cells recognizing the GAD65 555−567 peptide was detected in at-risk individuals. In addition, increased CD4+ T-cell responses to the same GAD65 epitope displaying a memory phenotype were observed in at-risk and diabetic children, which demonstrate a previous encounter with the antigen in vivo. Avidity and phenotypic differences were also observed among CD4+ T-cell clones induced by distinct doses of GAD65 autoantigen. T-cell clones generated at the lowest peptide dose displayed the highest avidity and expressed more frequently the TCR Vβ5.1 chain than low-avidity T cells. These findings raise attention to the antigen dose when investigating the diversity of antigen-specific T cells. Furthermore, an increased regulatory response during the preclinical phase of T1D was also found in genetically at-risk children. Higher frequencies of regulatory T (Treg) cells (CD4+CD25_high HLA-DR-/CD69-) and natural killer T (NKT) cells (CD161+Vbeta11+) were observed in children with multiple autoantibodies compared to autoantibody-negative controls. Taken together, these data showed increased frequency of islet-specific CD4+ T-cells, especially to the GAD65 555-567 epitope, and Treg and NKT cell upregulation in children at-risk for T1D, suggesting their importance in T1D pathogenesis

Role and regulatory mechanisms of heat shock factor 2

Protein homeostasis is essential for cells to prosper and survive. Various forms of stress, such as elevated temperatures, oxidative stress, heavy metals or bacterial infections cause protein damage, which might lead to improper folding and formation of toxic protein aggregates. Protein aggregation is associated with serious pathological conditions such as Alzheimer’s and Huntington’s disease. The heat shock response is a defense mechanism that protects the cell against protein-damaging stress. Its ancient origin and high conservation among eukaryotes suggest that the response is crucial for survival. The main regulator of the heat shock response is the transcription factor heat shock factor 1 (HSF1), which induces transcription of genes encoding protective molecular chaperones. In vertebrates, a family of four HSFs exists (HSF1-4), with versatile functions not only in coping with acute stress, but also in development, longevity and cancer. Thus, knowledge of the HSFs will aid in our understanding on how cells survive suboptimal circumstances, but will also provide insights into normal physiological processes as well as diseaseassociated conditions. In this study, the function and regulation of HSF2 have been investigated. Earlier gene inactivation experiments in mice have revealed roles for HSF2 in development, particularly in corticogenesis and spermatogenesis. Here, we demonstrate that HSF2 holds a role also in the heat shock response and influences stress-induced expression of heat shock proteins. Intriguingly, DNA-binding activity of HSF2 upon stress was dependent on the presence of intact HSF1, suggesting functional interplay between HSF1 and HSF2. The underlying mechanism for this phenomenon could be configuration of heterotrimers between the two factors, a possibility that was experimentally verified. By changing the levels of HSF2, the expression of HSF1-HSF2 heterotrimer target genes was altered, implementing HSF2 as a modulator of HSF-mediated transcription. The results further indicate that HSF2 activity is dependent on its concentration, which led us to ask the question of how accurate HSF2 levels are achieved. Using mouse spermatogenesis as a model system, HSF2 was found to be under direct control of miR-18, a miRNA belonging to the miR-17~92 cluster/Oncomir-1 and whose physiological function had remained unclear. Investigations on spermatogenesis are severely hampered by the lack of cell systems that would mimic the complex differentiation processes that constitute male germ cell development. Therefore, to verify that HSF2 is regulated by miR-18 in spermatogenesis, a novel method named T-GIST (Transfection of Germ cells in Intact Seminiferous Tubules) was developed. Employing this method, the functional consequences of miR-18-mediated regulation in vivo were demonstrated; inhibition of miR- 18 led to increased expression of HSF2 and altered the expression of HSF2 target genes Ssty2 and Speer4a. Consequently, the results link miR-18 to HSF2-mediated processes such as germ cell maturation and quality control and provide miR-18 with a physiological role in gene expression during spermatogenesis.Taken together, this study presents compelling evidence that HSF2 is a transcriptional regulator in the heat shock response and establishes the concept of physical interplay between HSF2 and HSF1 and functional consequences thereof. This is also the first study describing miRNA-mediated regulation of an HSF.

Biomarkers - regulatory and toxicological perspectives

Referaatti kongressiesitelmästä.

Licensing Model Development for Small Modular Reactors (SMRs) - Focusing on the Finnish Regulatory Framework

Recently, Small Modular Reactors (SMRs) have attracted increased public discussion. While large nuclear power plant new build projects are facing challenges, the focus of attention is turning to small modular reactors. One particular project challenge arises in the area of nuclear licensing, which plays a significant role in new build projects affecting their quality as well as costs and schedules. This dissertation - positioned in the field of nuclear engineering but also with a significant section in the field of systems engineering - examines the nuclear licensing processes and their suitability for the characteristics of SMRs. The study investigates the licensing processes in selected countries, as well as other safety critical industry fields. Viewing the licensing processes and their separate licensing steps in terms of SMRs, the study adopts two different analysis theories for review and comparison. The primary data consists of a literature review, semi-structured interviews, and questionnaire responses concerning licensing processes and practices. The result of the study is a recommendation for a new, optimized licensing process for SMRs. The most important SMR-specific feature, in terms of licensing, is the modularity of the design. Here the modularity indicates multi-module SMR designs, which creates new challenges in the licensing process. As this study focuses on Finland, the main features of the new licensing process are adapted to the current Finnish licensing process, aiming to achieve the main benefits with minimal modifications to the current process. The application of the new licensing process is developed using Systems Engineering, Requirements Management, and Project Management practices and tools. Nuclear licensing includes a large amount of data and documentation which needs to be managed in a suitable manner throughout the new build project and then during the whole life cycle of the nuclear power plant. To enable a smooth licensing process and therefore ensure the success of the new build nuclear power plant project, management processes and practices play a significant role. This study contributes to the theoretical understanding of how licensing processes are structured and how they are put into action in practice. The findings clarify the suitability of different licensing processes and their selected licensing steps for SMR licensing. The results combine the most suitable licensing steps into a new licensing process for SMRs. The results are also extended to the concept of licensing management practices and tools.

Maritime safety in the Gulf of Finland. Evaluation of the regulatory system

Growing traffic is believed to increase the risk of an accident in the Gulf of Finland. As the consequences of a large oil accident would be devastating in the vulnerable sea area, accident prevention is performed at the international, regional and national levels. Activities of shipping companies are governed with maritime safety policy instruments, which can be categorised into regulatory, economic and information instruments. The maritime regulatory system has been criticised for being inefficient because it has not been able to eliminate the violations that enable accidents. This report aims to discover how maritime governance systems or maritime safety policy instruments could be made more efficient in the future, in order to improve the maritime safety level. The results of the research are based on a literature review and nine expert interviews, with participants from shipping companies, interest groups and authorities. Based on the literature and the interviews, a suggestion can be made that in the future, instead of implementing new policy instruments, maritime safety risks should be eliminated by making the existing system more efficient and by influencing shipping companies’ safety culture and seafarers’ safety related attitudes. Based on this research, it can be stated that the development of maritime safety policy instruments should concentrate on harmonisation, automation and increasing national and cross-border cooperation. These three tasks could be primarily accomplished by developing the existing technology. Human error plays a role in a significant number of maritime accidents. Because of this, improving companies’ safety culture and voluntary activities that go beyond laws are acknowledged as potential ways of improving maritime safety. In the future, maritime regulatory system should be developed into a direction where the private sector has better possibilities to take part in decision-making.

Accounting for competition, governance and accountability during institutional change in not-for-profit and public sector organisations

Purpose The aim of this thesis1 is to analyse theoretically how institutionalisation of competitive tendering2, governance and budgetary policies cannot be taken for granted to lead to accountability among institutional actors3. The nature of an institutionalised management accounting policy, its relevance as a source of power in organisational decision making, and in negotiating inter-organisational relationships, are also analysed. Practical motivation The practical motivation of the thesis is to show how practitioners and policy makers can institutionalise changes which improve the power of management accounting and control systems4 as a mechanism of accountability among institutional actors and in negotiating relationships with other organisations. Theoretical motivation and conceptual approach The theoretical motivation of the thesis is to extend the institutional framework of management accounting change proposed by Burns and Scapens (2000) by using the theories of critical realism, communicative action, negotiated order and the framework of circuits of power. The Burns and Scapens framework needs further theorisation to analyse the relationship between the institutionalisation of management accounting and accountability; and the relevance of management accounting information in negotiating in inter-organisational relationships. Methodology and field studies Field research took place in public and not-for-profit health care organisations and a municipality in Finland from 2008 to 2013. Data were gathered by document analysis, interviews, participation in meetings and observations. Findings The findings are explained in four different essays that show that institutionalisation of competitive tendering, governance and budgetary policies cannot be taken for granted to lead to accountability among institutional actors. The ways by which institutional actors think and act can be influenced by other institutional mechanisms, such as inter-organisational circuits of power and intraorganisational governance policies, independent of the institutional change process. The relevance of institutionalised management accounting policies in negotiating relationships between two or more organisations depends on processes and contexts through which institutional actors use management accounting information as a tool of communication, mutual understanding and power. Research limitations / implications The theoretical framework used can be applied validly in other studies. The empirical findings cannot be generalised directly to other organisations than the organisations analysed. Practical implications Competitive tendering and budgetary policies can be institutionalised to shape actions of institutional actors within an organisation. To lead to accountability, practitioners and policy makers should implement governance policies that increase the use of management accounting information in institutional actors’ thinking, actions and responsibility for their actions. To reach a negotiated order between organisations, institutionalised management accounting policies should be used as one of the tools of communication aiming to reach mutual agreement among institutional actors.

Novel genes and regulatory systems in epididymal differentiation and sperm maturation of the mouse.

Mammalian spermatozoa gain their fertilizing ability during maturation in the epididymis. Proteins and lipids secreted into the epididymal lumen remodel the sperm membrane, thereby providing the structure necessary for progressive motility and oocyte interaction. In the current study, genetically modified mouse models were utilized to determine the role of novel genes and regulatory systems in the postnatal development and function of the epididymis. Ablation of the mouse β-defensin, Defb41, altered the flagellar movements of sperm and reduced the ability of sperm to bind to the oocyte in vitro. The Defb41-deficient iCre knock-in mouse model was furthermore utilized to generate Dicer1 conditional knock-out (cKO) mice. DICER1 is required for production of mature microRNAs in the regulation of gene expression by RNA interference. Dicer1 cKO gave rise to dedifferentiation of the epididymal epithelium and an altered expression of genes involved in lipid synthesis. As a consequence, the cholesterol:polyunsaturated fatty acid ratio of the Dicer1 cKO sperm membrane was increased, which resulted in membrane instability and infertility. In conclusion, the results of the Defb41 study further support the important role of β-defensin family members in sperm maturation. The regulatory role of Dicer1 was also shown to be required for epididymal development. In addition, the study is the first to show a clear connection between lipid homeostasis in the epididymis and sperm membrane integrity. Taken together, the results give important new evidence on the regulatory system guiding epididymal development and function

Incentivising Innovation? The competition law approach to the new challenge clauses in the competition rules for technology licensing agreements of the EU

Tutkielman aiheena on EU:n kilpailuoikeudellinen lähestymistapa challenge-lausekkeisiin teknologinsiirtosopimuksia koskevassa ryhmäpoikkeusasetuksessa. Teknologian lisensoinnin katsotaan olevan tärkeä väline teknologian kehityksen levittämisessä ja innovaation edistämisessä. Joissakin tapauksissa lisenssisopimus voi sisältää kilpailua rajoittavia lausekkeita, joiden voidaan kuitenkin nähdä hyödyttävän kilpailua kokonaisuutta arvostellen. Tällaisia lausekkeita ovat niin sanotut ”no-challenge” – lauseke, eli sopimusehto, jonka nojalla lisenssinsaaja sitoutuu olemaan haastamatta lisensoidun immateriaalioikeuden pätevyyttä ja ”termination-on-challenge” – lauseke, joka antaa lisensoijalle haastettaessa oikeuden päättää lisenssisopimus. Tutkielmassa perehdytään challenge -lausekkeiden hyväksyttävyyden arviointiin Euroopan unionin kilpailuoikeuden näkökulmasta uuden 1.5.2014 voimaan tulleen ryhmäpoikkeusasetuksen valossa. Muissa kuin yksinoikeuksia luovissa teknologiansiirtosopimuksissa olevat termination-on-challenge – lausekkeita tulee uusimmassa ryhmäpoikkeusetuksessa aina perustua yritysten itse suorittamaan tapauskohtaiseen arviointiin. No-challenge – lausekkeet ovat jatkossakin aiemman käytännön mukaisesti ryhmäpoikkeuksen soveltamisalan ulkopuolella. Komission on perustellut challenge - lausekkeiden jättämistä asetuksen ulkopuolelle julkisella intressillä, joka on päästä eroon mitättömistä immateriaalioikeuksista. Komission on katsonut, että challenge – lausekkeiden kilpailua rajoittava ominaisuus on mitättömien immateriaalioikeuksien esiintyminen markkinoilla, mikä osaltaan vääristää kilpailua ja hidastaa toimijoiden markkinoille pääsyä. Toisaalta lausekkeiden voidaan sanoa edistävän kilpailua, sillä ne usein tarjoavat immateriaalioikeuden haltijalle riittävän oikeussuojan ja kannustimen lisensoida teknologia, mikä lisää kilpailua, keksijöiden kannustimia panostaa innovaatioihin sekä vähentää transaktiokustannuksia. Tutkielman keskeinen tulos on ennen kaikkea challenge-lausekkeiden kilpailuvaikutusten tunnistamisessa ja komission perusteluiden kriittisessä arvioinnissa. Komission linjauksen perustelut eivät saa riittävää tukea ottaen huomioon vaikutustenarvioinnin, EU:n tuomioistuinkäytännön sekä taloustieteellisen lähestymistavan. Tutkielman tulosten pohjalta ja tukeutuen eri oikeuslähteisiin, taloustieteellisiin argumentteihin ja oikeusvertailevaan tutkimukseen, on mahdollista tehdä johtopäätöksiä niistä seikoista ja argumenteista, joilla on merkitystä uuden politiikkalinjauksen kilpailuvaikutuksiin.

Omnibus accounts to Finnish investors? – An analysis of the costs and benefits that omnibus account structure brings to Finnish account operators and investors

The Finnish Securities Markets are being harmonized to enable better, more reliable and timely settlement of securities. Omnibus accounts are a common practice in the European securities markets. Finland forbids the use of omnibus accounts from its domestic investors. There is a possibility that the omnibus account usage is allowed for Finnish investors in the future. This study aims to build a comprehensive image to Finnish investors and account operators in determining the costs and benefits that the omnibus account structure would have for them. This study uses qualitative research methods. A literature review provides the framework for this study. Different kinds of research articles, regulatory documents, studies performed by European organisations, and Finnish news reportages are used to analyse the costs and benefits of omnibus accounts. The viewpoint is strictly of account operators and investors, and different effects on them are contemplated. The results of the analysis show that there are a number of costs and benefits that investors and account operators must take into consideration regarding omnibus accounts. The costs are related to development of IT-systems so that participants are able to adapt to the new structure and operate according to its needs. Decrease in the holdings’ transparency is a disadvantage of the structure and needs to be assessed precisely to avoid some problems it might bring. Benefits are mostly related to the increased competition in the securities markets as well as to the possible cost reductions of securities settlement. The costs and benefits were analysed according to the study plan of this thesis and as a result, the significance and impact of omnibus accounts to Finnish investors and account operators depends on the competition level and the decisions that all market participants make when determining if the account structure is beneficial for their operations.

Novel cancer-related regulatory targets for the signalling sphingolipids sphingosine-1-phosphate and sphingosylphosphorylcholine

The signalling sphingolipid sphingosine-1-phosphate (S1P) is necessary for development of the immune system and vasculature and on a cellular level regulates migration, proliferation and survival. Due to these traits S1P has an important role in cancer biology. It is considered a primarily cancer-promoting factor and the enzyme which produces it, sphingosine kinase (SphK), is often over-expressed in tumours. S1P is naturally present in the blood, lymph, tissue fluids and cell cytoplasm and functions through its cell surface receptors (S1P1-5) and as an intracellular second messenger. Sphingosylphosphorylcholine (SPC) is closely related to S1P and has similar regulatory functions but has not been extensively studied. Both S1P and SPC are able to evoke either stimulatory or inhibitory effects on cancer cells depending on the context. The aim of this thesis work was to study novel regulatory targets of S1P and SPC, which mediate the effects of S1P/SPC signalling on cancer cell behaviour. The investigated targets are the transcription factor hypoxia-inducible factor 1 (HIF-1), the intermediate filament protein vimentin and components of the Hippo signalling pathway. HIF-1 has a central role in cancer biology, as it regulates a multitude of cancer-related genes and is potently activated by intratumoural hypoxia through stabilization of the regulatory subunit HIF-1α. Tumours typically harbour high HIF-1α levels and HIF-1, in turn, facilitates tumour angiogenesis and metastasis and regulates cancer cell metabolism. We found S1P to induce follicular thyroid cancer cell migration in normal oxygen conditions by increasing HIF-1α synthesis and stability and subsequently HIF-1 activity. Vimentin is a central regulator of cell motility and is also commonly over-expressed in cancers. Vimentin filaments form a cytoskeletal network in mesenchymal cells as well as epithelial cancer cells which have gone through epithelial-mesenchymal transition (EMT). Vimentin is heavily involved in cancer cell invasion and gives tumours metastatic potential. We saw both S1P and SPC induce phosphorylation of vimentin monomers and reorganization of the vimentin filament network in breast and anaplastic thyroid cancer cells. We also found vimentin to mediate the anti-migratory effect of S1P/SPC on these cells. The Hippo pathway is a novel signalling cascade which controls cancer-related processes such as cellular proliferation and survival in response to various extracellular signals. The core of the pathway consists of the transcriptional regulators YAP and TAZ, which activate predominantly cancer-promoting genes, and the tumour suppressive kinases Lats1 and Lats2 which inhibit YAP/TAZ. Increased YAP expression and activity has been reported for a wide variety of cancers. We found SPC to regulate Hippo signalling in breast cancer cells in a two-fold manner through effects on phosphorylation status, activity and/or expression of YAP and Lats2. In conclusion, this thesis reveals new details of the signalling function of S1P and SPC and regulation of the central oncogenic factors HIF-1 and vimentin as well as the novel cancer-related pathway Hippo.

Parental and Successor Liability in EU Competition Law Infringements

Under EU competition law, parent companies may be held jointly and severally liable for the competition law infringements committed by their subsidiaries. The possibility of holding parent companies liable demonstrates a significant exception from the idea of separate legal entities. However, it is not the only deviation developed under EU competition law. In cases, where the legal entity responsible for the anti-competitive conduct has changed its form, liability can be attributed to the new operator, in particular, to its successor. The principles of legal certainty and legitimate expectations are issues that surround the doctrines of parental and successor liability. The aim of this thesis is to present a comprehensive comparative analysis of the parental and successor liability doctrines and to clarify the conditions under which it is possible to attribute liability for the infringements of EU competition law. The main purpose is therefore to demonstrate the problems related to the allocation of liability and to discuss whether these liability principles, established to assure the effective enforcement of the EU competition rules, are good solutions. The research methods used in this thesis are the legal dogmatic approach and the comparative law approach. The former enables the possibility of using the case law and legislation as a framework in which the difficulties concerning the application of parental and successor liability can be discussed while the latter ensures the comparison of the characteristics and judgments. The doctrines of parental and successor liability are both well established, but the application practice has caused several difficulties. These problems derive from, inter alia, the broadness and disjointed developed of the doctrines. There has been much recent case law dealing with these issues and having the potential to open up a considerable risk and to allocate strict liability for parent and successor companies.