Applications of gene sequence polymorphisms in evolutionary genetic studies of Atlantic salmon (Salmo salar) and other teleost fish species

Evolutionary genetics incorporates traditional population genetics and studies of the origins of genetic variation by mutation and recombination, and the molecular evolution of genomes. Among the primary forces that have potential to affect the genetic variation within and among populations, including those that may lead to adaptation and speciation, are genetic drift, gene flow, mutations and natural selection. The main challenges in knowing the genetic basis of evolutionary changes is to distinguish the adaptive selection forces that cause existent DNA sequence variants and also to identify the nucleotide differences responsible for the observed phenotypic variation. To understand the effects of various forces, interpretation of gene sequence variation has been the principal basis of many evolutionary genetic studies. The main aim of this thesis was to assess different forms of teleost gene sequence polymorphisms in evolutionary genetic studies of Atlantic salmon (Salmo salar) and other species. Firstly, the level of Darwinian adaptive evolution affected coding regions of the growth hormone (GH) gene during the teleost evolution was investigated based on the sequence data existing in public databases. Secondly, a target gene approach was used to identify within population variation in the growth hormone 1 (GH1) gene in salmon. Then, a new strategy for single nucleotide polymorphisms (SNPs) discovery in salmonid fishes was introduced, and, finally, the usefulness of a limited number of SNP markers as molecular tools in several applications of population genetics in Atlantic salmon was assessed. This thesis showed that the gene sequences in databases can be utilized to perform comparative studies of molecular evolution, and some putative evidence of the existence of Darwinian selection during the teleost GH evolution was presented. In addition, existent sequence data was exploited to investigate GH1 gene variation within Atlantic salmon populations throughout its range. Purifying selection is suggested to be the predominant evolutionary force controlling the genetic variation of this gene in salmon, and some support for gene flow between continents was also observed. The novel approach to SNP discovery in species with duplicated genome fragments introduced here proved to be an effective method, and this may have several applications in evolutionary genetics with different species - e.g. when developing gene-targeted markers to investigate quantitative genetic variation. The thesis also demonstrated that only a few SNPs performed highly similar signals in some of the population genetic analyses when compared with the microsatellite markers. This may have useful applications when estimating genetic diversity in genes having a potential role in ecological and conservation issues, or when using hard biological samples in genetic studies as SNPs can be applied with relatively highly degraded DNA.

Distribution of non-biting midges (Diptera, Chironomidae) in subarctic lakes of Finnish Lapland applications in lake classification and palaeolimnology

Climate change contributes directly or indirectly to changes in species distributions, and there is very high confidence that recent climate warming is already affecting ecosystems. The Arctic has already experienced the greatest regional warming in recent decades, and the trend is continuing. However, studies on the northern ecosystems are scarce compared to more southerly regions. Better understanding of the past and present environmental change is needed to be able to forecast the future. Multivariate methods were used to explore the distributional patterns of chironomids in 50 shallow (≤ 10m) lakes in relation to 24 variables determined in northern Fennoscandia at the ecotonal area from the boreal forest in the south to the orohemiarctic zone in the north. Highest taxon richness was noted at middle elevations around 400 m a.s.l. Significantly lower values were observed from cold lakes situated in the tundra zone. Lake water alkalinity had the strongest positive correlation with the taxon richness. Many taxa had preference for lakes either on tundra area or forested area. The variation in the chironomid abundance data was best correlated with sediment organic content (LOI), lake water total organic carbon content, pH and air temperature, with LOI being the strongest variable. Three major lake groups were separated on the basis of their chironomid assemblages: (i) small and shallow organic-rich lakes, (ii) large and base-rich lakes, and (iii) cold and clear oligotrophic tundra lakes. Environmental variables best discriminating the lake groups were LOI, taxon richness, and Mg. When repeated, this kind of an approach could be useful and efficient in monitoring the effects of global change on species ranges. Many species of fast spreading insects, including chironomids, show a remarkable ability to track environmental changes. Based on this ability, past environmental conditions have been reconstructed using their chitinous remains in the lake sediment profiles. In order to study the Holocene environmental history of subarctic aquatic systems, and quantitatively reconstruct the past temperatures at or near the treeline, long sediment cores covering the last 10000 years (the Holocene) were collected from three lakes. Lower temperature values than expected based on the presence of pine in the catchment during the mid-Holocene were reconstructed from a lake with great water volume and depth. The lake provided thermal refuge for profundal, cold adapted taxa during the warm period. In a shallow lake, the decrease in the reconstructed temperatures during the late Holocene may reflect the indirect response of the midges to climate change through, e.g., pH change. The results from three lakes indicated that the response of chironomids to climate have been more or less indirect. However, concurrent shifts in assemblages of chironomids and vegetation in two lakes during the Holocene time period indicated that the midges together with the terrestrial vegetation had responded to the same ultimate cause, which most likely was the Holocene climate change. This was also supported by the similarity in the long-term trends in faunal succession for the chironomid assemblages in several lakes in the area. In northern Finnish Lapland the distribution of chironomids were significantly correlated with physical and limnological factors that are most likely to change as a result of future climate change. The indirect and individualistic response of aquatic systems, as reconstructed using the chironomid assemblages, to the climate change in the past suggests that in the future, the lake ecosystems in the north do not respond in one predictable way to the global climate change. Lakes in the north may respond to global climate change in various ways that are dependent on the initial characters of the catchment area and the lake.

Applications of coralline hydroxyapatite with bioabsorbable containment and reinforcement as bone graft substitute : An experimental study

The aim of the present experimental study was to find out if the applications of coralline hydroxyapatite (HA) can be improved by using bioabsorbable containment or binding substance with particulate HA in mandibular contour augmentation and by using bioabsorbable fibre-reinforced HA blocks in filling bone defects and in anterior lumbar interbody fusion. The use of a separate curved polyglycolide (PGA) containment alone or together with a fast resorbing polyglycolide/polylactide (PGA/PLA) binding substance were compared to the conventional non-contained method in ridge augmentation in sheep. The contained methods decreased HA migration, but the augmentations did not differ significantly. The use of the containment caused a risk for wound dehiscence and infection. Histologically there was a rapid connective tissue ingrowth into the HA graft and it was more abundant with the PGA containment compared to the non-contained augmentation and even additionally rich when the HA particles were bound with PGA/PLA copolymer. However, the bone ingrowth was best in the non-contained augmentation exceeding 10-12 % of the total graft area at 24 weeks. Negligible or no bone ingrowth was seen in the cases where the polymer composite was added to the HA particles and, related to that, foreign-body type cells were seen at the interface between the HA and host bone. The PGA and poly-dl/l-lactide (PDLLA) fibre-reinforced coralline HA blocks were studied in the metaphyseal and in the diaphyseal defects in rabbits. A rapid bone ingrowth was seen inside the both types of implants. Both PGA and PDLLA fibres induced an inflammatory fibrous reaction around themselves but it did not hinder the bone ingrowth. The bone ingrowth pattern was directed according to the loading conditions so that the load-carrying cortical ends of the implants as well as the implants sited in the diaphyseal defects were the most ossified. The fibre-reinforced coralline HA implants were further studied as stand-alone grafts in the lumbar anterior interbody implantation in pigs. The strength of the HA implants proved not to be adequate, the implants fractured in six weeks and the disc space was gradually lost similarly to that of the discectomized spaces. Histologically, small quantities of bone ingrowth was seen in some of the PGA and PDLLA reinforced coralline implants while no bone formation was identified in any of the PDLLA reinforced synthetic porous HA implants. While fragmented, the inner structure of the implants was lost, the bone ingrowth was minimal, and the disc was replaced by the fibrous connective tissue. When evaluated radiologically the grade of ossification was assessed as better than histologically, and, when related to the histologic findings, CT was more dependable than the plain films to show ossification of the implanted disc space. Local kyphosis was a frequent finding along with anterior bone bridging and ligament ossification as a consequence of instability of the implanted segment.

Si, CdTe and CdZnTe radiation detectors for imaging applications

The structure and operation of CdTe, CdZnTe and Si pixel detectors based on crystalline semiconductors, bump bonding and CMOS technology and developed mainly at Oy Simage Ltd. And Oy Ajat Ltd., Finland for X- and gamma ray imaging are presented. This detector technology evolved from the development of Si strip detectors at the Finnish Research Institute for High Energy Physics (SEFT) which later merged with other physics research units to form the Helsinki Institute of Physics (HIP). General issues of X-ray imaging such as the benefits of the method of direct conversion of X-rays to signal charge in comparison to the indirect method and the pros and cons of photon counting vs. charge integration are discussed. A novel design of Si and CdTe pixel detectors and the analysis of their imaging performance in terms of SNR, MTF, DQE and dynamic range are presented in detail. The analysis shows that directly converting crystalline semiconductor pixel detectors operated in the charge integration mode can be used in X-ray imaging very close to the theoretical performance limits in terms of efficiency and resolution. Examples of the application of the developed imaging technology to dental intra oral and panoramic and to real time X-ray imaging are given. A CdTe photon counting gamma imager is introduced. A physical model to calculate the photo peak efficiency of photon counting CdTe pixel detectors is developed and described in detail. Simulation results indicates that the charge sharing phenomenon due to diffusion of signal charge carriers limits the pixel size of photon counting detectors to about 250 μm. Radiation hardness issues related to gamma and X-ray imaging detectors are discussed.

Applications of Gauge/Gravity Duality to QCD and Heavy Ion Collisions

The description of quarks and gluons, using the theory of quantum chromodynamics (QCD), has been known for a long time. Nevertheless, many fundamental questions in QCD remain unanswered. This is mainly due to problems in solving the theory at low energies, where the theory is strongly interacting. AdS/CFT is a duality between a specific string theory and a conformal field theory. Duality provides new tools to solve the conformal field theory in the strong coupling regime. There is also some evidence that using the duality, one can get at least qualitative understanding of how QCD behaves at strong coupling. In this thesis, we try to address some issues related to QCD and heavy ion collisions, applying the duality in various ways.

Studies of electronic structure by x-ray Raman and emission spectroscopy: applications to MgB2 superconductors and high pressure physics

X-ray Raman scattering and x-ray emission spectroscopies were used to study the electronic properties and phase transitions in several condensed matter systems. The experimental work, carried out at the European Synchrotron Radiation Facility, was complemented by theoretical calculations of the x-ray spectra and of the electronic structure. The electronic structure of MgB2 at the Fermi level is dominated by the boron σ and π bands. The high density of states provided by these bands is the key feature of the electronic structure contributing to the high critical temperature of superconductivity in MgB2. The electronic structure of MgB2 can be modified by atomic substitutions, which introduce extra electrons or holes into the bands. X ray Raman scattering was used to probe the interesting σ and π band hole states in pure and aluminum substituted MgB2. A method for determining the final state density of electron states from experimental x-ray Raman scattering spectra was examined and applied to the experimental data on both pure MgB2 and on Mg(0.83)Al(0.17)B2. The extracted final state density of electron states for the pure and aluminum substituted samples revealed clear substitution induced changes in the σ and π bands. The experimental work was supported by theoretical calculations of the electronic structure and x-ray Raman spectra. X-ray emission at the metal Kβ line was applied to the studies of pressure and temperature induced spin state transitions in transition metal oxides. The experimental studies were complemented by cluster multiplet calculations of the electronic structure and emission spectra. In LaCoO3 evidence for the appearance of an intermediate spin state was found and the presence of a pressure induced spin transition was confirmed. Pressure induced changes in the electronic structure of transition metal monoxides were studied experimentally and were analyzed using the cluster multiplet approach. The effects of hybridization, bandwidth and crystal field splitting in stabilizing the high pressure spin state were discussed. Emission spectroscopy at the Kβ line was also applied to FeCO3 and a pressure induced iron spin state transition was discovered.

Applications of dimensional reduction to electroweak and QCD matter

When heated to high temperatures, the behavior of matter changes dramatically. The standard model fields go through phase transitions, where the strongly interacting quarks and gluons are liberated from their confinement to hadrons, and the Higgs field condensate melts, restoring the electroweak symmetry. The theoretical framework for describing matter at these extreme conditions is thermal field theory, combining relativistic field theory and quantum statistical mechanics. For static observables the physics is simplified at very high temperatures, and an effective three-dimensional theory can be used instead of the full four-dimensional one via a method called dimensional reduction. In this thesis dimensional reduction is applied to two distinct problems, the pressure of electroweak theory and the screening masses of mesonic operators in quantum chromodynamics (QCD). The introductory part contains a brief review of finite-temperature field theory, dimensional reduction and the central results, while the details of the computations are contained in the original research papers. The electroweak pressure is shown to converge well to a value slightly below the ideal gas result, whereas the pressure of the full standard model is dominated by the QCD pressure with worse convergence properties. For the mesonic screening masses a small positive perturbative correction is found, and the interpretation of dimensional reduction on the fermionic sector is discussed.

Studies on Binary Time Series Models with Applications to Empirical Macroeconomics and Finance

This thesis studies binary time series models and their applications in empirical macroeconomics and finance. In addition to previously suggested models, new dynamic extensions are proposed to the static probit model commonly used in the previous literature. In particular, we are interested in probit models with an autoregressive model structure. In Chapter 2, the main objective is to compare the predictive performance of the static and dynamic probit models in forecasting the U.S. and German business cycle recession periods. Financial variables, such as interest rates and stock market returns, are used as predictive variables. The empirical results suggest that the recession periods are predictable and dynamic probit models, especially models with the autoregressive structure, outperform the static model. Chapter 3 proposes a Lagrange Multiplier (LM) test for the usefulness of the autoregressive structure of the probit model. The finite sample properties of the LM test are considered with simulation experiments. Results indicate that the two alternative LM test statistics have reasonable size and power in large samples. In small samples, a parametric bootstrap method is suggested to obtain approximately correct size. In Chapter 4, the predictive power of dynamic probit models in predicting the direction of stock market returns are examined. The novel idea is to use recession forecast (see Chapter 2) as a predictor of the stock return sign. The evidence suggests that the signs of the U.S. excess stock returns over the risk-free return are predictable both in and out of sample. The new "error correction" probit model yields the best forecasts and it also outperforms other predictive models, such as ARMAX models, in terms of statistical and economic goodness-of-fit measures. Chapter 5 generalizes the analysis of univariate models considered in Chapters 2 4 to the case of a bivariate model. A new bivariate autoregressive probit model is applied to predict the current state of the U.S. business cycle and growth rate cycle periods. Evidence of predictability of both cycle indicators is obtained and the bivariate model is found to outperform the univariate models in terms of predictive power.

E-learning in a rural context: Alternative media and contemporary applications

This report has been written as part of the E-ruralnet –project that addresses e-learning as a means for enhancing lifelong learning opportunities in rural areas, with emphasis on SMEs, micro-enterprises, self-employed and persons seeking employment. E-ruralnet is a European network project part-funded by the European Commission in the context of the Lifelong Learning Programme, Transversal projects-ICT. This report aims to address two issues identified as requiring attention in the previous Observatory study: firstly, access to e-learning for rural areas that have not adequate ICT infrastructure; and secondly new learning approaches introduced through new interactive ICT tools such as web 2.0., wikis, podcasts etc. The possibility of using alternative technology in addition to computers is examined (mobile telephones, DVDs) as well as new approaches to learning (simulation, serious games). The first part of the report examines existing literature on e-learning and what e-learning is all about. Institutional users, learners and instructors/teachers are all looked at separately. We then turn to the implementation of e-learning from the organizational point of view and focus on quality issues related to e-learning. The report includes a separate chapter or e-learning from the rural perspective since most of Europe is geographically speaking rural and the population in those areas is that which could most benefit from the possibilities introduced by the e-learning development. The section titled “Alternative media”, in accordance with the project terminology, looks at standalone technology that is of particular use to rural areas without proper internet connection. It also evaluates the use of new tools and media in e-learning and takes a look at m-learning. Finally, the use of games, serious games and simulations in learning is considered. Practical examples and cases are displayed in a box to facilitate pleasant reading.

The Feminist Transformation of Bioethics : An Analysis of Theoretical Perspectives and Practical Applications in Feminist Bioethics

The purpose of this study is to examine how transformation is defining feminist bioethics and to determine the nature of this transformation. Behind the quest for transformation is core feminism and its political implications, namely, that women and other marginalized groups have been given unequal consideration in society and the sciences and that this situation is unacceptable and should be remedied. The goal of the dissertation is to determine how feminist bioethicists integrate the transformation into their respective fields and how they apply the potential of feminism to bioethical theories and practice. On a theoretical level, feminist bioethicists wish to reveal how current ways of knowing are based on inequality. Feminists pay special attention especially to communal and political contexts and to the power relations endorsed by each community. In addition, feminist bioethicists endorse relational ethics, a relational account of the self in which the interconnectedness of persons is important. On the conceptual level, feminist bioethicists work with beliefs, concepts, and practices that give us our world. As an example, I examine how feminist bioethicists have criticized and redefined the concept of autonomy. Feminist bioethicists emphasize relational autonomy, which is based on the conviction that social relationships shape moral identities and values. On the practical level, I discuss stem cell research as a test case for feminist bioethics and its ability to employ its methodologies. Analyzing these perspectives allowed me first, to compare non-feminist and feminist accounts of stem cell ethics and, second, to analyze feminist perspectives on the novel biotechnology. Along with offering a critical evaluation of the stem cell debate, the study shows that sustainable stem cell policies should be grounded on empirical knowledge about how donors perceive stem cell research and the donation process. The study indicates that feminist bioethics should develop the use of empirical bioethics, which takes the nature of ethics seriously: ethical decisions are provisional and open for further consideration. In addition, the study shows that there is another area of development in feminist bioethics: the understanding of (moral) agency. I argue that agency should be understood to mean that actions create desires.

Developing Peer-To-Peer Web Applications

As the virtual world grows more complex, finding a standard way for storing data becomes increasingly important. Ideally, each data item would be brought into the computer system only once. References for data items need to be cryptographically verifiable, so the data can maintain its identity while being passed around. This way there will be only one copy of the users family photo album, while the user can use multiple tools to show or manipulate the album. Copies of users data could be stored on some of his family members computer, some of his computers, but also at some online services which he uses. When all actors operate over one replicated copy of the data, the system automatically avoids a single point of failure. Thus the data will not disappear with one computer breaking, or one service provider going out of business. One shared copy also makes it possible to delete a piece of data from all systems at once, on users request. In our research we tried to find a model that would make data manageable to users, and make it possible to have the same data stored at various locations. We studied three systems, Persona, Freenet, and GNUnet, that suggest different models for protecting user data. The main application areas of the systems studied include securing online social networks, providing anonymous web, and preventing censorship in file-sharing. Each of the systems studied store user data on machines belonging to third parties. The systems differ in measures they take to protect their users from data loss, forged information, censorship, and being monitored. All of the systems use cryptography to secure names used for the content, and to protect the data from outsiders. Based on the gained knowledge, we built a prototype platform called Peerscape, which stores user data in a synchronized, protected database. Data items themselves are protected with cryptography against forgery, but not encrypted as the focus has been disseminating the data directly among family and friends instead of letting third parties store the information. We turned the synchronizing database into peer-to-peer web by revealing its contents through an integrated http server. The REST-like http API supports development of applications in javascript. To evaluate the platform’s suitability for application development we wrote some simple applications, including a public chat room, bittorrent site, and a flower growing game. During our early tests we came to the conclusion that using the platform for simple applications works well. As web standards develop further, writing applications for the platform should become easier. Any system this complex will have its problems, and we are not expecting our platform to replace the existing web, but are fairly impressed with the results and consider our work important from the perspective of managing user data.