Simulation and graph mining tools for improving gene mapping efficiency

Gene mapping is a systematic search for genes that affect observable characteristics of an organism. In this thesis we offer computational tools to improve the efficiency of (disease) gene-mapping efforts. In the first part of the thesis we propose an efficient simulation procedure for generating realistic genetical data from isolated populations. Simulated data is useful for evaluating hypothesised gene-mapping study designs and computational analysis tools. As an example of such evaluation, we demonstrate how a population-based study design can be a powerful alternative to traditional family-based designs in association-based gene-mapping projects. In the second part of the thesis we consider a prioritisation of a (typically large) set of putative disease-associated genes acquired from an initial gene-mapping analysis. Prioritisation is necessary to be able to focus on the most promising candidates. We show how to harness the current biomedical knowledge for the prioritisation task by integrating various publicly available biological databases into a weighted biological graph. We then demonstrate how to find and evaluate connections between entities, such as genes and diseases, from this unified schema by graph mining techniques. Finally, in the last part of the thesis, we define the concept of reliable subgraph and the corresponding subgraph extraction problem. Reliable subgraphs concisely describe strong and independent connections between two given vertices in a random graph, and hence they are especially useful for visualising such connections. We propose novel algorithms for extracting reliable subgraphs from large random graphs. The efficiency and scalability of the proposed graph mining methods are backed by extensive experiments on real data. While our application focus is in genetics, the concepts and algorithms can be applied to other domains as well. We demonstrate this generality by considering coauthor graphs in addition to biological graphs in the experiments.

Analisi contrastiva delle modalità di traduzione in finnico dei Tempi verbali e delle perifrasi aspettuali dell'italiano

Analisi contrastiva delle modalità di traduzione in finnico dei Tempi verbali e delle perifrasi aspettuali dell italiano (Italian Philology) The topic of this research is a contrastive study of tenses and aspect in Italian and in Finnish. The study aims to develop a research method for analyzing translations and comparable texts (non-translation) written in a target language. Thus, the analysis is based on empirical data consisting of translations of novels from Italian to Finnish and vice versa. In addition to this, for the section devoted to solutions adopted in Finnish for translating the Italian tenses Perfetto Semplice and Perfetto Composto, 39 Finnish native speakers were asked to answer questions concerning the choice of Perfekti and Imperfekti in Finnish. The responses given by the Finnish informants were compared to the choices made by translators in the target language, and in this way it was possible both to benefit from the motivation provided by native speakers to explain the selection of a tense (Imperfekti/Perfekti) in a specific context compared with the Italian formal equivalents (Perfetto Composto/Perfetto Semplice), and to define the specific features of the Finnish verb tenses. The research aims to develop a qualitative method for the analysis of formal equivalents and translational changes ( shifts ). Although, as the choice of Italian and Finnish progressive forms is optional and related to speaker preferences, besides the qualitative analysis, I also considered it necessary to operate a quantitative one in order to find out whether the two items share the same degree of correspondence in frequency of use. In this study I explain translation choices in light of cognitive grammar, suggesting that particular translation relationships derive from so-called construal operations. I use the concepts of cognitive linguistics not only to analyze the convergences and divergences of the two aspectual systems, but also to redefine some general procedures related to the phenomenon of translation. For the practical analysis of the corpus were for the most part employed theoretical categories developed in a framework proposed by Pier Marco Bertinetto. Following this approach, the notions of aspect (the morphologic or morphosyntactic, subjective level) and actionality (the lexical aspect or objective level, traditionally Aktionsart) are carefully distinguished. This also allowed me to test the applicability of these distinctions to two languages typologically different from each other. The data allowed both the analysis of the semantic and pragmatic features that determine tense and aspect choices in these two languages, and to discover the correspondences between the two language systems and the strategies that translators are forced to resort to in particular situations. The research provides not only a detailed and analytically argued inventory about possible solutions for translating Italian tenses and aspectual devices in Finnish that could be of pedagogical relevance, but also new contributions about the specific uses of time-aspectual devices in the two languages in question.

Les fleuves dans l'œuvre romanesque de Jean-Marie Gustave Le Clézio

Relying on Merleau-Ponty's phenomenology of perception and on Mircea Eliade's works on the Sacred and the Profane, this study explores the river as a perceptual space and as the sacred Center in a cosmic vision of the world in twelve of Jean-Marie Gustave Le Clézio's fictional works, from The Interrogation (1963) to Revolutions (2003). In the first chapter, after introducing the field of study, I discuss the relation between the radical subjectivity and the evasiveness of perceiving subjects in Le Clézio's fiction. Next are some thoughts on the relation between Merleau-Ponty's and Le Clézio's ideas. The second chapter studies the river as an experience in the text, first as a topographical space, then as a sound world. The investigations move on to its water as a visual and a tactile phenomenon. Then follows the human use of the river, the (absence of) baths, and the river as a traveling space. The chapter closes with the study of the metaphorical use of the word, occurring mainly in urban space and for phenomena in the sky. The third chapter is organized around the river as the Center of the world in a religious cosmogony, where the river represents the origin of the world and of the human race. The core analysis shows how the middle of the river is a symbolic space of a new beginning. As a sacred space, the river abolishes time as the object of contemplation and as relative immobility from the point of view of a person drifting downstream. The functions of a new beginning and of abolition of time are combined in the symbolic immersions in the water. Finally, the dissertation explores other symbolical spaces, such as the unknown destination of the drift, and the river as the Center of a utopia. The chapter closes with the existential agony as a result of the elimination of the Center in the urban environment. In the final chapter, the river is compared to other watercourses : the creek, the brook and the rapids. The river is more of a spatial entity, whereas the actual water is more important in the smaller watercourses. The river is more common than the other watercourses as a topographical element in the landscape, whereas the minor watercourses invite the characters to a closer contact with their element, in immersions and in drinking their water. Finally, the work situates the rivers in a broader context of different fictional spaces in Le Clézio's text.

Bridging East and West : The Establishment of the International Institute for Applied Systems Analysis (IIASA) in the United States Foreign Policy of Bridge Building, 1964-1972.

The dissertation examines the foreign policies of the United States through the prism of science and technology. In the focal point of scrutiny is the policy establishing the International Institute for Applied Systems Analysis (IIASA) and the development of the multilateral part of bridge building in American foreign policy during the 1960s and early 1970s. After a long and arduous negotiation process, the institute was finally established by twelve national member organizations from the following countries: Bulgaria, Canada, Czechoslovakia, Federal Republic of Germany (FRG), France, German Democratic Republic (GDR), Great Britain, Italy, Japan, Poland, Soviet Union and United States; a few years later Sweden, Finland and the Netherlands also joined. It is said that the goal of the institute was to bring together researchers from East and West to solve pertinent problems caused by the modernization process experienced in industrialized world. It originates from President Lyndon B. Johnson s bridge building policies that were launched in 1964, and was set in a well-contested and crowded domain of other international organizations of environmental and social planning. Since the distinct need for yet another organization was not evident, the process of negotiations in this multinational environment enlightens the foreign policy ambitions of the United States on the road to the Cold War détente. The study places this project within its political era, and juxtaposes it with other international organizations, especially that of the OECD, ECE and NATO. Conventionally, Lyndon Johnson s bridge building policies have been seen as a means to normalize its international relations bilaterally with different East European countries, and the multilateral dimension of the policy has been ignored. This is why IIASA s establishment process in this multilateral environment brings forth new information on US foreign policy goals, the means to achieve these goals, as well as its relations to other advanced industrialized societies before the time of détente, during the 1960s and early 1970s. Furthermore, the substance of the institute applied systems analysis illuminates the differences between European and American methodological thinking in social planning. Systems analysis is closely associated with (American) science and technology policies of the 1960s, especially in its military administrative applications, thus analysis within the foreign policy environment of the United States proved particularly fruitful. In the 1960s the institutional structures of European continent with faltering, and the growing tendencies of integration were in flux. One example of this was the long, drawn-out process of British membership in the EEC, another is de Gaulle s withdrawal from NATO s military-political cooperation. On the other hand, however, economic cooperation in Europe between East and West, and especially with the Soviet Union was expanding rapidly. This American initiative to form a new institutional actor has to be seen in that structural context, showing that bridge building was needed not only to the East, but also to the West. The narrative amounts to an analysis of how the United States managed both cooperation and conflict in its hegemonic aspirations in the emerging modern world, and how it used its special relationship with the United Kingdom to achieve its goals. The research is based on the archives of the United States, Great Britain, Sweden, Finland, and IIASA. The primary sources have been complemented with both contemporary and present day research literature, periodicals, and interviews.

Substance misuse problems during pregnancy with special emphasis on buprenorphine

Maternal drug abuse during pregnancy endangers the future health and wellbeing of the infant and growing child. On the other hand, via maternal abstinence, these problems would never occur; so the problems would be totally preventable. Buprenorphine is widely used in opioid maintenance treatment as a substitute medication. In Finland, during 2000 s buprenorphine misuse has steadily increased. In 2009 almost one third of clientele of substance treatment units were in treatment because of buprenorphine dependence. At Helsinki Women s Clinic the first child with prenatal buprenorphine exposure was born in 2001. During 1992-2001 in the three capital area maternity hospitals (Women s clinic, Maternity hospital, Jorvi hospital) 524 women were followed at special antenatal clinics due to substance abuse problems. Three control women were drawn from birth register to each case woman and matched for parity and same place and date of the index birth. According to register data mortality rate was 38-fold higher among cases than controls within 6-15 years after index birth. Especially, the risk for violent or accidental death was increased. The women with substance misuse problems had also elevated risk for viral hepatitis and psychiatric morbidity. They were more often reimbursed for psychopharmaceuticals. Disability pensions and rehabilitation allowances were more often granted to cases than controls. In total 626 children were born from these pregnancies. According to register data 38% of these children were placed in out-of-home care as part of child protection services by the age of two years, and half of them by the age of 12 years, the median follow-up time was 5.8 years. The risk for out-of-home care was associated with factors identifiable during the pre- and perinatal period. In 2002-2005 67 pregnant women with buprenorphine dependence were followed up at the Helsinki University Hospital, Department of Obstetrics and Gynecology. Their pregnancies were uneventful. The prematurity rate was similar and there were no more major anomalies compared to the national statistics. The neonates were lighter compared to the national statistics. They were also born in good condition, with no perinatal hypoxia as defined by standard clinical parameters or certain biochemical markers in the cord blood: erythropoietin, S100 and cardiac troponin-t. Almost 80% of newborns developed neonatal abstinence syndrome (NAS) and two third of them needed morphine medication for it. Maternal smoking over ten cigarettes per day aggravated and benzodiazepine use attenuated NAS. An infant s highest urinary norbuprenorphine concentration during their first 3 days of life correlated with the duration of morphine treatment. The average length of infant s hospital stay was 25 days.

Treatment of illicit opioid and γ-hydroxybutyrate overdose by Helsinki emergency medical services

Aims: To examine the characteristics, incidence, treatment and outcome of presumed opioid, γ-hydroxybutyrate (GHB) and γ-butyrolactone (GBL) overdoses involving users of illicit drugs in Helsinki. GHB/GBL were included in this study, despite not being opioids, due to the relative ease with which they can cause potentially fatal respiratory depression. The incidence and time interval of recurrent opioid toxicity after prehospital administration of naloxone, an opioid antagonist, was studied in presumed heroin overdose patients. Naloxone has been reported to have many adverse effects and the effects of naloxone administered during an opioid overdose on the cardiovascular system and catecholamine levels in piglets were studied. Materials and methods: Patients included in these published retrospective studies were from the following time periods: Study I: 1995-2002, II: 1997-2000, III: 1995-2000, V: 2006-2007. Presumed opioid overdose patients were examined in studies I, II and III. GHB/GBL overdoses among injecting drug users was examined in study V. Recurrent opioid toxicity after prehospital naloxone administration in heroin overdose patients was examined in study III. The effects of naloxone (80 μg/kg i.v.) on the cardiovascular system and catecholamine levels administered during morphine overdose (8mg/kg i.v.) and under propofol anesthesia with spontaneous breathing were studied in eight piglets (IV). In this thesis, previously unpublished data on the incidence of opioid overdose between 2001-2007 and comparison of the characteristics of buprenorphine and heroin overdose patients encountered in 1995-2005 are also included. Results: Helsinki Emergency Medical Service (EMS) ambulances were dispatched annually to 34,153- 45,118 calls from 1995 to 2007. Of them, 7-8% were coded as intoxications or overdoses. During this time, 436 patients were treated by the EMS for presumed opioid overdose. The peak incidence of opioid overdoses was in the year 2000 (113 cases), after which they declined to 6-26 cases annually. The annual incidence of buprenorphine related overdoses increased from 4 (4% of opioid overdoses) in the year 2000 to 8 (30% of opioid overdoses) in 2007. The annual number of GHB related overdose patients treated by Helsinki EMS increased from 21 to 73 between 2004-2007. There appeared to be a peak in the incidence of both GHB/GBL and opioid related overdoses on Saturdays. Characteristics of opioid overdose patients The median age of opioid overdose patients was 28 years (22;33, 25- and 75-percentiles), and 84% were male. Buprenorphine overdose patients had more polydrug, such as alcohol and/or benzodiazepines, use in comparison with heroin overdose patients, 70% versus 33%, respectively. Severe respiratory depression was reported less often with buprenorphine overdoses compared to heroin overdoses, in 67.0% versus 85.4%, respectively. Outcome of heroin overdose patients with cardiac arrest Ninety four patients suffered cardiac arrest due to acute drug poisoning/overdose and were thus considered for resuscitation. Resuscitation was attempted in 72 cases. Cardiac arrest was caused by heroin overdose for 19 patients of which three (16%) were discharged alive. Other agents also induced cardiac arrest in 53 patients, of which six (11%) were discharged alive. The arrest was either EMS witnessed or occurring after the emergency call for all survivors of heroin induced cardiac arrest. Characteristics of GHB/GBL overdose patients The records of 100 GHB/GBL related overdose patients from 2006-2007 were retrieved. The median age of GHB/GBL overdose patients encountered on weekend nights was 24 years (22;27, 25- and 75-percentiles) and 49% were male. Polydrug use was reported in 62-80% of the cases. Thirty nine patients were encountered on Friday-Saturday or Saturday-Sunday night between 11 pm-6 am. The remaining sixty one patients were outside this time frame. There was a statistically significant difference between these two groups in history of chronic injecting drug use (33% vs. 59%, respectively, p=0.012). Recurrent heroin toxicity after prehospital naloxone administration Study III included 145 presumed heroin overdose patients. After prehospital care, 84 patients refused further care and were not transported to an Emergency Department (ED). Seventy one (85%) of them were administered naloxone by the EMS. During a 12-h follow up period, none of these patients developed severe recurrent opioid toxicity. The remaining 61 patients were transported to an ED. Prior to transportation, 52 (85%) patients were administered naloxone by the EMS. Fifteen of them were administered naloxone also in the ED and recurrent opioid toxicity was evident either on arrival at the ED or shortly thereafter. Prehospital naloxone was administered either intravenously, intramuscularly (i.m.) or subcutaneously (s.c.). There was a tendency for more frequent recurrent heroin toxicity among the patients with only intravenous administration of prehospital naloxone (13/36) compared with the patients with intramuscular or subcutaneous prehospital naloxone (2/16), p=0.106. The effects of naloxone on the cardiovascular system and catecholamine levels in piglets The administration of morphine to piglets resulted in an obvious respiratory depression, which was reversed by naloxone. Two severely hypoxemic piglets developed cardiac arrest after naloxone administration. In the other six animals, the administration of naloxone did not provoke arrhythmias, cardiac ischemia or visible evidence of pulmonary edema. There was a statistically significant (p=0.012) increase in norepinephrine levels after morphine administration and before naloxone administration: from 1.9 (1.3-2.3) ng/ml at baseline, to 31.7 (8.3-83.0) ng/ml (median, 25 and 75 percentiles parentheses) after morphine administration. After the administration of naloxone, the catecholamine levels continued to increase in only one of the animals. Conclusions: The incidence of buprenorphine related overdoses increased during the study period, but was still lower in comparison to those involving heroin. Injecting drug users have also started to use GHB/GBL. While recreational drug users use GHB/GBL during weekend nights, a GHB/GBL overdose patient encounter during weekdays has a more probable history of injecting drug use. Patients with cardiac arrest after heroin overdose have a poor prognosis. It appears to be safe to leave heroin overdose patients on scene after prehospital treatment with naloxone. Although no statistically significant difference was observed, it seems prudent to administer part of the total naloxone dose s.c. or i.m. to reduce the risk of recurrent respiratory depression. If transported to an ED, an observation period of one to two hours after the last naloxone dose seems adequate. The treating physician must be vigilant, however, due to the high prevalence of polydrug use and high morbidity after non fatal heroin overdose. Furthermore, care should be taken regarding possible chronic disorders and drug rehabilitation should be addressed. In the experimental animal study, two animals developed cardiac arrest after receiving naloxone while in hypoxemia and bradycardia. Further studies are required to assess the effect of naloxone during opioid-induced hypercapnia and hypoxemia in animals addicted to opioids.

Molecular Characterization of Viruses Causing the Cassava Brown Streak Disease Epidemic in Eastern Africa

Cassava brown streak disease (CBSD) was described for the first time in Tanganyika (now Tanzania) about seven decades ago. Tanganyika (now Tanzania) about seven decades ago. It was endemic in the lowland areas of East Africa and inland parts of Malawi and caused by Cassava brown streak virus (CBSV; genus Ipomovirus; Potyviridae). However, in 1990s CBSD was observed at high altitude areas in Uganda. The causes for spread to new locations were not known.The present work was thus initiated to generate information on genetic variability, clarify the taxonomy of the virus or viruses associated with CBSD in Eastern Africa as well as to understand the evolutionary forces acting on their genes. It also sought to develop a molecular based diagnostic tool for detection of CBSD-associated virus isolates. Comparison of the CP-encoding sequences of CBSD-associated virus isolates collected from Uganda and north-western Tanzania in 2007 and the partial sequences available in Genbank revealed occurrence of two genetically distinct groups of isolates. Two isolates were selected to represent the two groups. The complete genomes of isolates MLB3 (TZ:Mlb3:07) and Kor6 (TZ:Kor6:08) obtained from North-Western (Kagera) and North-Eastern (Tanga) Tanzania, respectively, were sequenced. The genomes were 9069 and 8995 nucleotides (nt), respectively. They translated into polyproteins that were predicted to yield ten mature proteins after cleavage. Nine proteins were typical in the family Potyviridae, namely P1, P3, 6K1, CI, 6K2, VPg, NIa-Pro, NIb and CP, but the viruses did not contain HC-Pro. Interestingly, genomes of both isolates contained a Maf/HAM1-like sequence (HAM1h; 678 nucleotides, 25 kDa) recombined between the NIb and CP domains in the 3’-proximal part of the genomes. HAM1h was also identified in Euphorbia ringspot virus (EuRSV) whose sequence was in GenBank. The HAM1 gene is widely spread in both prokaryotes and eukaryotes. In yeast (Saccharomyces cerevisiae) it is known to be a nucleoside triphosphate (NTP) pyrophosphatase. Novel information was obtained on the structural variation at the N-termini of polyproteins of viruses in the genus Ipomovirus. Cucumber vein yellowing virus (CVYV) and Squash vein yellowing virus (SqVYV) contain a duplicated P1 (P1a and P1b) but lack the HC-Pro. On the other hand, Sweet potato mild mottle virus (SPMMV), has a single but large P1 and has HC-Pro. Both virus isolates (TZ:Mlb3:07 & TZ:Kor6:08) characterized in this study contained a single P1 and lacked the HC-Pro which indicates unique evolution in the family Potyviridae. Comparison of 12 complete genomes of CBSD-associated viruses which included two genomes characterized in this study, revealed genetic identity of 69.0–70.3% (nt) and amino acid (aa) identities of 73.6–74.4% at polyprotein level. Comparison was also made among 68 complete CP sequences, which indicated 69.0-70.3 and 73.6-74.4 % identity at nt and aa levels, respectively. The genetic variation was large enough for dermacation of CBSD-associated virus isolates into two distinct species. The name CBSV was retained for isolates that were related to CBSV isolates available in database whereas the new virus described for the first time in this study was named Ugandan cassava brown streak virus (UCBSV) by the International Committee on Virus Taxonomy (ICTV). The isolates TZ:Mlb3:07 and TZ:Kor6:08 belong to UCBSV and CBSV, respectively. The isolates of CBSV and UCBSV were 79.3-95.5% and 86.3-99.3 % identitical at nt level, respectively, suggesting more variation amongst CBSV isolates. The main sources of variation in plant viruses are mutations and recombination. Signals for recombination events were detected in 50% of isolates of each virus. Recombination events were detected in coding and non-coding (3’-UTR) sequences except in the 5’UTR and P3. There was no evidence for recombination between isolates of CBSV and UCBSV. The non-synonomous (dN) to synonomous (dS) nucleotide substitution ratio (ω) for the HAM1h and CP domains of both viruses were ≤ 0.184 suggesting that most sites of these proteins were evolving under strong purifying selection. However, there were individual amino acid sites that were submitted to adaptive evolution. For instance, adaptive evolution was detected in the HAM1h of UCBSV (n=15) where 12 aa sites were under positive selection (P< 0.05) but not in CBSV (n=12). The CP of CBSV (n=23) contained 12 aa sites (p<0.01) while only 5 aa sites in the CP gene of UCBSV were predicted to be submitted to positive selection pressure (p<0.01). The advantages offered by the aa sites under positive selection could not be established but occurrence of such sites in the terminal ends of UCBSV-HAMIh, for example, was interpreted as a requirement for proteolysis during polyprotein processing. Two different primer pairs that simultaneously detect UCBSV and CBSV isolates were developed in this study. They were used successfully to study distribution of CBSV, UCBSV and their mixed infections in Tanzania and Uganda. It was established that the two viruses co-infect cassava and that incidences of co-infection could be as high as 50% around Lake Victoria on the Tanzanian side. Furthermore, it was revealed for the first time that both UCBSV and CBSV were widely distributed in Eastern Africa. The primer pair was also used to confirm infection in a close relative of cassava, Manihot glaziovii (Müller Arg.) with CBSV. DNA barcoding of M. glaziovii was done by sequencing the matK gene. Two out of seven M. glaziovii from the coastal areas of Korogwe and Kibaha in north eastern Tanzania were shown to be infected by CBSV but not UCBSV isolates. Detection in M. glaziovii has an implication in control and management of CBSD as it is likely to serve as virus reservoir. This study has contributed to the understanding of evolution of CBSV and UCBSV, which cause CBSD epidemic in Eastern Africa. The detection tools developed in this work will be useful in plant breeding, verification of the phytosanitary status of materials in regional and international movement of germplasm, and in all diagnostic activities related to management of CBSD. Whereas there are still many issues to be resolved such as the function and biological significance of HAM1h and its origin, this work has laid a foundation upon which the studies on these aspects can be based.

Temperature-Sensitive Src-Transformed Mdck Cells nn 3d Cultures as a Model of Malignant Transformation of Epithelial Cells

The equilibrium between cell proliferation, differentiation, and apoptosis is crucial for maintaining homeostasis in epithelial tissues. In order for the epithelium to function properly, individual cells must gain normal structural and functional polarity. The junctional proteins have an important role both in binding the cells together and in taking part in cell signaling. Cadherins form adherens junctions. Cadherins initiate the polarization process by first recognizing and binding the neighboring cells together, and then guiding the formation of tight junctions. Tight junctions form a barrier in dividing the plasma membranes to apical and basolateral membrane domains. In glandular tissues, single layered and polarized epithelium is folded into tubes or spheres, in which the basal side of the epithelial layer faces the outer basal membrane, and the apical side the lumen. In carcinogenesis, the differentiated architecture of an epithelial layer is disrupted. Filling of the luminal space is a hallmark of early epithelial tumors in tubular and glandular structures. In order for the transformed tumor cells to populate the lumen, enhanced proliferation as well as inhibition of apoptosis is required. Most advances in cancer biology have been achieved by using two-dimensional (2D) cell culture models, in which the cells are cultured on flat surfaces as monolayers. However, the 2D cultures are limited in their capacity to recapitulate the structural and functional features of tubular structures and to represent cell growth and differentiation in vivo. The development of three-dimensional (3D) cell culture methods enables the cells to grow and to be studied in a more natural environment. Despite the wide use of 2D cell culture models and the development of novel 3D culture methods, it is not clear how the change of the dimensionality of culture conditions alters the polarization and transformation process and the molecular mechanisms behind them. Src is a well-known oncogene. It is found in focal and adherens junctions of cultured cells. Active src disrupts cell-cell junctions and interferes with cell-matrix binding. It promotes cell motility and survival. Src transformation in 2D disrupts adherens junctions and the fibroblastic phenotype of the cells. In 3D, the adherens junctions are weakened, and in glandular structures, the lumen is filled with nonpolarized vital cells. Madin-Darby canine kidney (MDCK) cells are an epithelial cell type commonly used as a model for cell polarization. Its-src-transformed variants are useful model systems for analyzing the changes in cell morphology, and they play a role in src-induced malignant transformation. This study investigates src-transformed cells in 3D cell cultures as a model for malignant transformation. The following questions were posed. Firstly: What is the role of the composition and stiffness of the extracellular matrix (ECM) on the polarization and transformation of ts v-src MDCK cells in 3D cell cultures? Secondly: How do the culture conditions affect gene expression? What is the effect of v-src transformation in 2D and in 3D cell models? How does the shift from 2D to 3D affect cell polarity and gene expression? Thirdly: What is the role of survivin and its regulator phosphatase and tensin homolog protein (PTEN) in cell polarization and transformation, and in determining cell fate? How does their expression correlate with impaired mitochondrial function in transformed cells? In order to answer the above questions, novel methods of culturing and monitoring cells had to be created: novel 3D methods of culturing epithelial cells were engineered, enabling real time monitoring of a polarization and transformation process, and functional testing of 3D cell cultures. Novel 3D cell culture models and imaging techniques were created for the study. Attention was focused especially on confocal microscopy and live-cell imaging. Src-transformation disturbed the polarization of the epithelium by disrupting cell adhesion, and sensitized the cells to their environment. With active src, the morphology of the cell cluster depended on the composition and stiffness of the matrix. Gene expression studies revealed a broader impact of src transformation than mere continuous activity of src-kinase. In 2D cultures, src transformation altered the expression of immunological, actin cytoskeleton and extracellular matrix (ECM). In 3D, the genes regulating cell division, inhibition of apoptosis, cell metabolism, mitochondrial function, actin cytoskeleton and mechano-sensing proteins were altered. Surprisingly, changing the culture conditions from 2D to 3D affected also gene expression considerably. The microarray hit survivin, an inhibitor of apoptosis, played a crucial role in the survival and proliferation of src-transformed cells.

Tiedostumaton nykytaiteessa : Katse, ääni ja aika vuosituhannen taitteen suomalaisessa nykytaiteessa

Leevi Haapala explores moving image works, sculptures and installations from a psychoanalytic perspective in his study The Unconscious in Contemporary Art. The Gaze, Voice and Time in Finnish Contemporary Art at the Turn of the Millennium . The artists included in the study are Eija-Liisa Ahtila, Hans-Christian Berg, Markus Copper, Liisa Lounila and Salla Tykkä. The theoretical framework includes different psychoanalytic readings of the concepts of the gaze, voice and temporality. The installations are based on spatiality and temporality, and their detailed reading emphasizes the medium-specific features of the works as well as their fragmentary nature, heterogeneity and affectivity. The study is cross-disciplinary in that it connects perspectives from the visual culture, new art history and theory to the interpretation of contemporary art. The most important concepts from psychoanalysis, affect theory and trauma discourse used in the study include affect, object a (objet petit a) as articulated by Jacques Lacan, Sigmund Freud s uncanny (das Unheimliche) and trauma. Das Unheimliche has been translated as uncanny in art history under the influence of Rosalind Krauss. The object of the study, the unconscious in contemporary art, is approached through these concepts. The study focuses on Lacan s additions to the list of partial drives: the gaze and voice as scopic and invocative drives and their interpretations in the studies of the moving image. The texts by the American film theorist and art historian Kaja Silverman are in crucial role. The study locates contemporary art as part of trauma culture, which has a tendency to define individual and historical experiences through trauma. Some of the art works point towards trauma, which may appear as a theoretic or fictitious construction. The study presents a comprehensive collection of different kinds of trauma discourse in the field of art research through the texts of Hal Foster, Cathy Caruth, Ruth Leys and Shoshana Felman. The study connects trauma theory with the theoretical analysis of the interference and discontinuity of the moving image in the readings by Susan Buck-Morss, Mary Ann Doane and Peter Osborn among others. The analysis emphasizes different ways of seeing and multisensoriality in the reception of contemporary art. With their reflections and inverse projections, the surprising mechanisms of Hans-Christian Berg s sculptures are connected with Lacan s views on the early mirroring and imitation attempts of the individual s body image. Salla Tykkä s film trilogy Cave invites one to contemplate the Lacanian theory of the gaze in relation to the experiences of being seen. The three oceanic sculpture installations by Markus Copper are studied through the vocality they create, often through an aggressive way of acting, as well as from the point of view of the functioning of an invocative drive. The study compares the work of fiction and Freud s texts on paranoia and psychosis to Eija-Liisa Ahtila s manuscripts and moving image installations about the same topic. The cinematic time in Liisa Lounila s time-slice video installations is approached through the theoretical study of the unconscious temporal structure. The viewer of the moving image is inside the work in an in-between state: in a space produced by the contents of the work and its technology. The installations of the moving image enable us to inhabit different kinds of virtual bodies or spaces, which do not correspond with our everyday experiences. Nevertheless, the works of art often try to deconstruct the identification to what has been shown on screen. This way, the viewer s attention can be fixed on his own unconscious experiences in parallel with the work s deconstructed nature as representation. The study shows that contemporary art is a central cultural practice, which allows us to discuss the unconscious in a meaningful way. The study suggests that the agency that is discursively diffuse and consists of several different praxes should be called the unconscious. The emergence of the unconscious can happen in two areas: in contemporary art through different senses and discursive elements, and in the study of contemporary art, which, being a linguistic activity is sensitive to the movements of the unconscious. One of the missions of art research is to build different kinds of articulated constructs and to open an interpretative space for the nature of art as an event.

Elämän ja entisyyden maisemat : Kolgujev nenetsien arjessa, muistelussa ja kerronnassa

The dissertation discusses the conceptions of place and landscape amongst Nenets living on the island of Kolguyev or being of Kolguyev descent. The conceptions are examined through the everyday life of the community, oral recollections and narration that unfold meanings related to the island. The research material has been collected in ethnographic fieldwork in 2000 2005. The duration of individual fieldworks varies from two weeks to three months and their total duration is nearly six months. The fieldwork has been conducted both on the island and in the city of Nar yan-Mar. The main methods have been participant observation and recorded and unrecorded informal interviews. In addition to the field work data, archive materials, travel accounts, and other historical texts by outsiders about Kolguyev or the Nenets living in the European side of Russia have been used as a research material. The analysis is based on the idea of the place as a meeting point of the physical features, experiences in them and collective narration about them. The concept sense of place is used to describe the interaction of these three. Lived space manifests individual s or collective sense of place. The places form different kinds of networks of meanings which are called landscapes. Hot spots are places where different meanings accumulate. Furthermore, the material is analysed using the concepts of Tale World and Story Realm by Katherine Young. The Tale World is a realm created during the Story Realm, i.e. the event of narrations. The Tale Worlds are true as such but become evaluated in the Story Realm. The Tale Worlds are seen to arise both from the physical features of a place and from oral tradition, but at the same time these worlds give meanings to the place. The Tale Worlds are one of the central ingredients for the sense of place. One of the most central hot spots in Kolguyev is the arok harbour, where most of the themes of the pre-Soviet Tale Worlds are placed: trade and interaction with the Russians, rituals of the popular religion and arrival of the first Nenets to the island. arok is also part of the landscape of the coast where the meetings of Nenets and the other(s) are generally connected. Furthermore, arok is connected to the network of amans graves but also more generally to the landscape of collective sacred and sacrificial places. Another hot spot is the population centre of Bugrino which unfolds through the evaluations of the Tale Worlds. It also is the centre of the everyday life of the community studied. The Tale Worlds of the radiant past fastens on the population centre which is described through the negative models within the genre of litany. Sacred places, that represent the possibility to meet the Otherworld or mark places were encounters with the Otherworld have taken place, generate many kinds of landscapes in the island. They fasten on the graves of the amans, sirtya tradition, and to collective sacred places with their associations. The networks are not closed systems but are given meanings and new associations continuously in narration and recollection. They form multi-level and significant landscapes which reflect the fastening of the Kolguyev Nenets in the tundra of the island. In the research material the holy places and the popular religiousness are emphasised which is one of the most significant research results. It can be seen to reflect collective resistance and the questioning of the atheistic propaganda of the Soviet years. The narration and the recollection often refer also to the discourse of the anti-religious propaganda or use its strategies. The centrality of the holy places is also based on the tenacity of the religious Tale Worlds and sense of place and to the collective significance of the religion in general.

Smoking patterns and lung function : A longitudinal twin study

In many countries, the prevalence of smoking and smokers average cigarette consumption have decreased, with occasional smoking and daily light smoking (1-4 cigarettes per day, CPD) becoming more common. Despite these changes in smoking patterns, the prevalence of chronic obstructive pulmonary disease (COPD), a disorder characterized by a progressive decline in lung function, continues to rise globally. Smoking is the most important factor causing COPD, however, not all smokers develop the disease. Genetic factors partly explain the inter-individual differences in lung function and susceptibility of some smokers to COPD. No earlier research on the genetic and environmental determinants of lung function or on the phenomenon of light smoking exists in the Finnish population. Further, the association between low-rate smoking patterns and COPD remains partly unknown. This thesis aimed to study the prevalence and consistency of light smoking longitudinally in the Finnish population, to assess the characteristics of light smokers, and to examine the risks of chronic bronchitis and COPD associated with changing smoking patterns over time. A further aim was to estimate longitudinally the proportions of genetic and environmental factors that explain the inter-individual variances in lung function. Data from the Older Finnish Twin Cohort, including same-sex twin pairs born in Finland before 1958, were used. Smoking patterns and chronic bronchitis symptoms were consistently assessed in surveys conducted in 1975, 1981, and 1990. National registry data on reimbursement eligibilities and medication purchases were used to define COPD. Lung function data were obtained from a subsample of the cohort, 217 female twin pairs, who attended spirometry in 2000 and 2003 as part of the Finnish Twin Study on Ageing. The genetic and environmental influences on lung function were estimated by using genetic modeling. This thesis found that light smokers are more often female, well-educated, and exhibit a healthier lifestyle than heavy smokers. At individual level, light smoking is rarely a constant pattern. Light smoking, reducing from heavier smoking to light smoking, and relapsing to light smoking after quitting, are among patterns associated with an increased risk of chronic bronchitis and COPD. Constant light smoking is associated with an increased use of inhaled anticholinergics, a medication for CODP. In addition to smoking, other environmental factors influence lung function in the older age. During a three-year follow-up, new environmental effects influencing spirometry values were observed, whereas the genes affecting lung function remained mostly the same. In conclusion, no safe level of daily smoking exists with regard to pulmonary diseases. Even daily light smoking in middle-age is associated with increased respiratory morbidity later in life. Smoking reduction does not decrease the risk of COPD, and should not be recommended as an alternative to quitting smoking. In elderly people, attention should also be drawn to other factors that can prevent poor lung function.

Cohésion modale et subordination : Le conditionnel et le jussif finnois au miroir de la valeur sémantique et discursive du subjonctif français

Modal cohesion and subordination. The Finnish conditional and jussive moods in comparison to the French subjunctive This study examines verb moods in subordinate clauses in French and Finnish. The first part of the analysis deals with the syntax and semantics of the French subjunctive, mood occurring mostly in subordinate positions. The second part investigates Finnish verb moods. Although subordinate positions in Finnish grammar have no special finite verb form, certain uses of Finnish verb moods have been compared to those of subjunctives and conjunctives in other languages. The present study focuses on the subordinate uses of the Finnish conditional and jussive (i.e. the third person singular and plural of the imperative mood). The third part of the analysis discusses the functions of subordinate moods in contexts beyond complex sentences. The data used for the analysis include 1834 complex sentences gathered from newspapers, online discussion groups and blog texts, as well as audio-recorded interviews and conversations. The data thus consist of both written and oral texts as well as standard and non-standard variants. The analysis shows that the French subjunctive codes theoretical modality. The subjunctive does not determine the temporal and modal meaning of the event, but displays the event as virtual. In a complex sentence, the main clause determines the temporal and modal space within which the event coded by the subjunctive clause is interpreted. The subjunctive explicitly indicates that the space constructed in the main clause extends its scope over the subordinate clause. The subjunctive can therefore serve as a means for creating modal cohesion in the discourse. The Finnish conditional shares the function of making explicit the modal link between the components of a complex construction with the French subjunctive, but the two moods differ in their semantics. The conditional codes future time and can therefore occur only in non-factual or counterfactual contexts, whereas the event expressed by French subjunctive clauses can also be interpreted as realized. Such is the case when, for instance, generic and habitual meaning is involved. The Finnish jussive mood is used in a relatively limited number of subordinate clause types, but in these contexts its modal meaning is strikingly close to that of the French subjunctive. The permissive meaning, typical of the jussive in main clause positions, is modified in complex sentences so that it entails inter-clausal relation, namely concession. Like the French subjunctive, the jussive codes theoretical modal meaning with no implication of the truth value of the proposition. Finally, the analysis shows that verb moods mark modal cohesion, not only on the syntagmatic level (namely in complexe sentences), but also on the paradigmatic axis of discourse in order to create semantic links over entire segments of talk. In this study, the subjunctive thus appears, not as an empty category without function, as it is sometimes described, but as an open form that conveys the temporal and modal meanings emerging from the context.

Mechanism-based inhibition of CYP2C8 by gemfibrozil in humans : characterisation of time and dose relationships

Drug-drug interactions may cause serious, even fatal clinical consequences. Therefore, it is important to examine the interaction potential of new chemical entities early in drug development. Mechanism-based inhibition is a pharmacokinetic interaction type, which causes irreversible loss of enzyme activity and can therefore lead to unusually profound and long-lasting consequences. The in vitro in vivo extrapolation (IVIVE) of drug-drug interactions caused by mechanism-based inhibition is challenging. Consequently, many of these interactions have remained unrecognised for many years. The concomitant use of the fibrate-class lipid-lowering agent gemfibrozil increases the concentrations of some drugs and their effects markedly. Even fatal cases of rhabdomyolysis occurred in patients administering gemfibrozil and cerivastatin concomitantly. One of the main mechanisms behind this effect is the mechanism-based inhibition of the cytochrome P450 (CYP) 2C8 enzyme by a glucuronide metabolite of gemfibrozil leading to increased cerivastatin concentrations. Although the clinical use of gemfibrozil has clearly decreased during recent years, gemfibrozil is still needed in some special cases. To enable safe use of gemfibrozil concomitantly with other drugs, information concerning the time and dose relationships of CYP2C8 inhibition by gemfibrozil should be known. This work was carried out as four in vivo clinical drug-drug interaction studies to examine the time and dose relationships of the mechanism-based inhibitory effect of gemfibrozil on CYP2C8. The oral antidiabetic drug repaglinide was used as a probe drug for measuring CYP2C8 activity in healthy volunteers. In this work, mechanism-based inhibition of the CYP2C8 enzyme by gemfibrozil was found to occur rapidly in humans. The inhibitory effect developed to its maximum already when repaglinide was given 1-3 h after gemfibrozil intake. In addition, the inhibition was shown to abate slowly. A full recovery of CYP2C8 activity, as measured by repaglinide metabolism, was achieved 96 h after cessation of gemfibrozil treatment. The dose-dependency of the mechanism-based inhibition of CYP2C8 by gemfibrozil was shown for the first time in this work. CYP2C8 activity was halved by a single 30 mg dose of gemfibrozil or by twice daily administration of less than 30 mg of gemfibrozil. Furthermore, CYP2C8 activity was decreased over 90% by a single dose of 900 mg gemfibrozil or twice daily dosing of approximately 100 mg gemfibrozil. In addition, with the application of physiological models to the data obtained in the dose-dependency studies, the major role of mechanism-based inhibition of CYP2C8 in the interaction between gemfibrozil and repaglinide was confirmed. The results of this work enhance the proper use of gemfibrozil and the safety of patients. The information related to time-dependency of CYP2C8 inhibition by gemfibrozil may also give new insights in order to improve the IVIVE of the drug-drug interactions of new chemical entities. The information obtained by this work may be utilised also in the design of clinical drug-drug interaction studies in the future.

Sedimentary zooplankton remains as indicators of lake ecological quality and trophic structure

To protect and restore lake ecosystems under threats posed by the increasing human population, information on their ecological quality is needed. Lake sediments provide a data rich archive that allows identification of various biological components present prior to anthropogenic alterations as well as a constant record of changes. By providing a longer dimension of time than any ongoing monitoring programme, palaeolimnological methods can help in understanding natural variability and long-term ecological changes in lakes. As zooplankton have a central role in the lake food web, their remains can potentially provide versatile information on past trophic structure. However, various taphonomic processes operating in the lakes still raise questions concerning how subfossil assemblages reflect living communities. This thesis work aimed at improving the use of sedimentary zooplankton remains in the reconstruction of past zooplankton communities and the trophic structure in lakes. To quantify interspecific differences in the accumulation of remains, the subfossils of nine pelagic zooplankton taxa in annually laminated sediments were compared with monitoring results for live zooplankton in Lake Vesijärvi. This lake has a known history of eutrophication and recovery, which resulted from reduced external loading and effective fishing of plankti-benthivorous fish. The response of zooplankton assemblages to these known changes was resolved using annually laminated sediments. The generality of the responses observed in Lake Vesijärvi were further tested with a set of 31 lakes in Southern Finland, relating subfossils in surface sediments to contemporary water quality and fish density, as well as to lake morphometry. The results demonstrated differential preservation and retention of cladoceran species in the sediment. Daphnia, Diaphanosoma and Ceriodaphnia were clearly underrepresented in the sediment samples in comparison to well-preserved Bosmina species, Chydorus, Limnosida and Leptodora. For well-preserved species, the annual net accumulation rate was similar to or above the expected values, reflecting effective sediment focusing and accumulation in the deepest part of the lake. The decreased fish density and improved water quality led to subtle changes in zooplankton community composition. The abundance of Diaphanosoma and Limnosida increased after the reduction in fish density, while Ceriodaphnia and rotifers decreased. The most sensitive indicator of fish density was the mean size of Daphnia ephippia and Bosmina (E.) crassicornis ephippia and carapaces. The concentration of plant-associated species increased, reflecting expanding littoral vegetation along with increasing transparency. Several of the patterns observed in Lake Vesijärvi could also be found within the set of 31 lakes. According to this thesis work, the most useful cladoceran-based indices for nutrient status and planktivorous fish density in Finnish lakes were the relative abundances of certain pelagic taxa, and the mean size of Bosmina spp. carapaces, especially those of Bosmina (E.) cf. coregoni. The abundance of plant-associated species reflected the potential area for aquatic plants. Lake morphometry and sediment organic content, however, explained a relatively high proportion of the variance in the species data, and more studies are needed to quantify lake-specific differences in the accumulation and preservation of remains. Commonly occurring multicollinearity between environmental variables obstructs the cladoceran-based reconstruction of single environmental variables. As taphonomic factors and several direct and indirect structuring forces in lake ecosystems simultaneously affect zooplankton, the subfossil assemblages should be studied in a holistic way before making final conclusions about the trophic structure and the change in lake ecological quality.

Rätt som argument : Leo Mechelin och finska frågan 1886-1912

Right as an Argument. Leo Mechelin and the Finnish Question 1886-1912 At the turn of the 20th century the Finnish Question rose up as a political and juridical issue at the international arena. The vaguely précised position of Finland in the Russian empire led to diverse conclusions concerning the correctness of the February manifesto of 1899. It was predominantly among a European elite of politicians, cultural workers and academics the issue rose some interest. Finns were active making propaganda for their cause, and they put an emphasis on the claim that the right was on the Finnish side. In the study Elisabeth Stubb compare the Finnish, Russian and European statements about the Finnish Question and analyse their use of right as an argument. The Finnish Question offers at the same time a case study of a national entity which possesses a political sphere of life but is not fully independent, and its possibilities to drive its interests in an international context. Leo Mechelin (1839-1914), the leader of the Finnish propaganda organization abroad, is used as a point of departure. The biographical stance is formed into a triangle, where Leo Mechelin, the idea of right and the Finnish Question abroad are the three cornerstones. The treatment of one cornerstone sheds a ligth on the two others. The metaphor of triangulation also worked as a method to reach "a third stance" in a scinetific and political issue that usually is polarised into two opposite alternatives. An adherence to a strict legal right could not in the end offer a complete, unquestionable and satisfactory solution to the Finnsih Question, it was dependent on "the right of state wisdom and sound insight". The Finnish propaganda abroad used almost completely alternative ways of making politics. The propaganda did not have a decisive effect on countries' official politics, but gained unofficial support, especially in the public opinion and in academic statements. Mechelin claimed that the political field was dependent on public opinion and scientific research. Together with the official politics these two fields formed a triangle that shared the task of balancing the political arena and preventing it from making unwise decisions of taking an unjust turn. The international sphere worked as a balancing part in the Finnish Question. Mechelin tried by claiming the status of state for Finland's part to secure the country a place at the official international arena. At the same time, and especially when the claim was not fully adopted, he emphasised, and in a European context worked for, that right would become the guiding light not only for international relations, but also for the policy making in the inner life of the state.