Finlands fiskar målade efter naturen = The fishes of Finland, drawn and coloured from life. Häft. 1-12

Gustaf (Gösta) Sundman (1854-1914) tuli tunnetuksi korkeatasoisten luonnontieteellisten kuvateosten kuvittajana. Finlands fiskar –teos ilmestyi kahtenatoista vihkona 1883-1893, upeat, metallihohtoiset kalojen kuvat irrallisina tauluina. Kalateokset tekstit ovat eläintieteen professori O. M. Reuterin ja eläintieteellisen museon amanuenssin A. J. Melan laatimia.

Conservation Genetics of Exploited Finnish Salmonid Fishes

Genetic diversity is one of the levels of biodiversity that the World Conservation Union (IUCN) has recognized as being important to preserve. This is because genetic diversity is fundamental to the future evolution and to the adaptive flexibility of a species to respond to the inherently dynamic nature of the natural world. Therefore, the key to maintaining biodiversity and healthy ecosystems is to identify, monitor and maintain locally-adapted populations, along with their unique gene pools, upon which future adaptation depends. Thus, conservation genetics deals with the genetic factors that affect extinction risk and the genetic management regimes required to minimize the risk. The conservation of exploited species, such as salmonid fishes, is particularly challenging due to the conflicts between different interest groups. In this thesis, I conduct a series of conservation genetic studies on primarily Finnish populations of two salmonid fish species (European grayling, Thymallus thymallus, and lake-run brown trout, Salmo trutta) which are popular recreational game fishes in Finland. The general aim of these studies was to apply and develop population genetic approaches to assist conservation and sustainable harvest of these populations. The approaches applied included: i) the characterization of population genetic structure at national and local scales; ii) the identification of management units and the prioritization of populations for conservation based on evolutionary forces shaping indigenous gene pools; iii) the detection of population declines and the testing of the assumptions underlying these tests; and iv) the evaluation of the contribution of natural populations to a mixed stock fishery. Based on microsatellite analyses, clear genetic structuring of exploited Finnish grayling and brown trout populations was detected at both national and local scales. Finnish grayling were clustered into three genetically distinct groups, corresponding to northern, Baltic and south-eastern geographic areas of Finland. The genetic differentiation among and within population groups of grayling ranged from moderate to high levels. Such strong genetic structuring combined with low genetic diversity strongly indicates that genetic drift plays a major role in the evolution of grayling populations. Further analyses of European grayling covering the majority of the species’ distribution range indicated a strong global footprint of population decline. Using a coalescent approach the beginning of population reduction was dated back to 1 000-10 000 years ago (ca. 200-2 000 generations). Forward simulations demonstrated that the bottleneck footprints measured using the M ratio can persist within small populations much longer than previously anticipated in the face of low levels of gene flow. In contrast to the M ratio, two alternative methods for genetic bottleneck detection identified recent bottlenecks in six grayling populations that warrant future monitoring. Consistent with the predominant role of random genetic drift, the effective population size (N_e) estimates of all grayling populations were very low with the majority of N_e estimates below 50. Taken together, highly structured local populations, limited gene flow and the small N_e of grayling populations indicates that grayling populations are vulnerable to overexploitation and, hence, monitoring and careful management using the precautionary principles is required not only in Finland but throughout Europe. Population genetic analyses of lake-run brown trout populations in the Inari basin (northernmost Finland) revealed hierarchical population structure where individual populations were clustered into three population groups largely corresponding to different geographic regions of the basin. Similar to my earlier work with European grayling, the genetic differentiation among and within population groups of lake-run brown trout was relatively high. Such strong differentiation indicated that the power to determine the relative contribution of populations in mixed fisheries should be relatively high. Consistent with these expectations, high accuracy and precision in mixed stock analysis (MSA) simulations were observed. Application of MSA to indigenous fish caught in the Inari basin identified altogether twelve populations that contributed significantly to mixed stock fisheries with the Ivalojoki river system being the major contributor (70%) to the total catch. When the contribution of wild trout populations to the fisheries was evaluated regionally, geographically nearby populations were the main contributors to the local catches. MSA also revealed a clear separation between the lower and upper reaches of Ivalojoki river system – in contrast to lower reaches of the Ivalojoki river that contributed considerably to the catch, populations from the upper reaches of the Ivalojoki river system (>140 km from the river mouth) did not contribute significantly to the fishery. This could be related to the available habitat size but also associated with a resident type life history and increased cost of migration. The studies in my thesis highlight the importance of dense sampling and wide population coverage at the scale being studied and also demonstrate the importance of critical evaluation of the underlying assumptions of the population genetic models and methods used. These results have important implications for conservation and sustainable fisheries management of Finnish populations of European grayling and brown trout in the Inari basin.

Molecular diagnostics of rare inherited SYNDROMES with a view on diagnostic test development

CHARGE syndrome, Sotos syndrome and 3p deletion syndrome are examples of rare inherited syndromes that have been recognized for decades but for which the molecular diagnostics only have been made possible by recent advances in genomic research. Despite these advances, development of diagnostic tests for rare syndromes has been hindered by diagnostic laboratories having limited funds for test development, and their prioritization of tests for which a (relatively) high demand can be expected. In this study, the molecular diagnostic tests for CHARGE syndrome and Sotos syndrome were developed, resulting in their successful translation into routine diagnostic testing in the laboratory of Medical Genetics (UTUlab). In the CHARGE syndrome group, mutation was identified in 40.5% of the patients and in the Sotos syndrome group, in 34%, reflecting the use of the tests in routine diagnostics in differential diagnostics. In CHARGE syndrome, the low prevalence of structural aberrations was also confirmed. In 3p deletion syndrome, it was shown that small terminal deletions are not causative for the syndrome, and that testing with arraybased analysis provides a reliable estimate of the deletion size but benign copy number variants complicate result interpretation. During the development of the tests, it was discovered that finding an optimal molecular diagnostic strategy for a given syndrome is always a compromise between the sensitivity, specificity and feasibility of applying a new method. In addition, the clinical utility of the test should be considered prior to test development: sometimes a test performing well in a laboratory has limited utility for the patient, whereas a test performing poorly in the laboratory may have a great impact on the patient and their family. At present, the development of next generation sequencing methods is changing the concept of molecular diagnostics of rare diseases from single tests towards whole-genome analysis.

An EDTA-β-cyclodextrin adsorbent for the adsorption of rare earth elements and its application in preconcentration of ultratrace rare earth elements from seawater

The objectives of this work were synthesizing an EDTA-β-CD adsorbent and investigating its adsorption potential and applications in preconcentration of REEs from aqueous phase. The adsorption capacity of EDTA-β-CD was investigated. The adsorption studies were performed by batch techniques both in one- and multi-component systems. The effects of pH, contact time and initial concentration were evaluated. The analytical detection methods and characterization methods were presented. EDTA-β-CD adsorbent was synthesized successfully with high EDTA coverage. The maximum REEs uptake was 0.310 mmol g-1 for La(III), 0.337 mmol g-1 for Ce(III) and 0.353 mmol g-1 for Eu(III), respectively. The kinetics of REEs onto EDTA-β-CD fitted well to pseudo-second-order model and the adsorption rate was affected by intra-particle diffusion. The experimental data of one component studies fitted to Langmuir isotherm model indicating the homogeneous surface of the adsorbent. The extended Sips model was applicable for the isotherm studies in three-component system. The electrostatic interaction, chelation and complexation were all involved in the adsorption mechanism. The preconcentration of RE ions and regeneration of EDTA-β-CD were successful. Overall, EDTA-β-CD is an effective adsorbent in adsorption and preconcentration of REEs.

Emission, kinetic and magnetic phenomena in rare-earth and transition metal doped ZnSe single crystals

In this work emission, optical, electrical and magnetic properties of the d- and f- elements doped zinc selenide crystals were investigated within a wide temperature range. Doping was performed in various technological processes: during the growth by chemical vapor transport method; by thermal diffusion from the Bi or Zn melt. Concentration of the doping impurity in the crystals was controlled by amount of the dopant in the source material or by its concentration in the doping media. Special interest in the work was paid to the influence of the different concentrations of Cr and Yb impurities on ZnSe crystals’ properties, correlations between observed effects and similarities with the Ni, Mn and Gd dopants are analysed. Possibility of formation of the excitons bound to the doping d-ions was shown. In contrast to this, it was observed that f-elements do not bound excitons, but prevent formation of excitons bound to some uncontrolled impurities. A mechanism of Cr doping impurity interaction with background impurities and zinc selenide structural defects was proposed based on experimental data. An assumption about resonant energy transfer between double charged chromium ions and complexes based on crystals’ vacancy defects was made. A correlation between emission and magnetic properties of the d- ions doped samples was established. Based on this correlation a mechanism explaining the concentration quench of the emission was proposed. It was found that f-ions bind electrically active shallow and deep donor and acceptor states of background impurity to electrically neutral complexes. This may be observed as “purification” of ZnSe crystals by doping with the rare-earth elements, resulting i tendency of the properties of f-ion doped crystals to the properties of intrinsic crystals, but with smaller concentration of uncontrolled native and impurity defects. A possible interpretation of this effect was proposed. It was shown that selenium substituting impurities decrease efficiency of the Yb doping. Based on this experimental results an attempt to determine ytterbium ion surroundings in the crystal lattice was made. It was shown that co-doping of zinc selenide crystals with the d- and f- ions leads to the combination of the impurities influence on the material’s properties. On the basis of obtained data an interaction mechanism of the d- and f-elements co-dopants was proposed. Guided by the model of the ytterbium ion incorporation in the selenide sublattice of the ZnSe crystals, an assumption about stabilization of single charged chromium ions in the zinc sublattice crystal nodes, by means of formation of the local charge compensating clusters, was made.

Carriage of herpes simplex virus and human papillomavirus in oral mucosa is rare in young women: a long-term prospective follow-up

Herpes simplex -virus 1 (HSV-1) ja ihmisen papilloomavirus (HPV) infektoivat suun epiteelisoluja. Useimmissa tapauksissa näiden virusten infektio on kliinisesti oireeton. Suun limakalvojen oireeton HPV-infektio on aikuisilla yleinen, ja valtaosa näistä infektioista ovat ohimeneviä ja vain pieni osa johtaa krooniseen HPV-infektioon. Krooninen HPV-infektio lisää riskiä epiteelisolujen transformoitumiseen kohti syöpäsolua. HPV infektio ei ole yksinään riittävä aiheuttamaan syöpäsolun, vaan siihen tarvitaan myös muita riskitekijöitä.. Muut infektiot, kuten esimerkiksi HSV-1-infektio saattaa olla yksi näistä riskitekijöistä. Tämän syventävän opinnäytetyön tutkimuksen tavoitteena oli selvittää HSV-1-infektion esiintymistä naisten suun limakalvonäytteissä kuuden vuoden seurannassa. Toinen tavoitteemme oli selvittää HSV-1 ja HPV -yhteisinfektion esiintymistä suun epiteelisoluissa, erityisesti naisilla joilla havaittiin suun krooninen HPV-infektio. Tämä tutkimus on osa kuusivuotista seurantatutkimusta (Finnish Family HPV -tutkimus), joka suunniteltiin selvittämään HPV-infektioiden dynamiikkaa ja riskitekijöitä 329 suomalaisperheessä. Suun limakalvoilta otettiin harjausnäyte ennen synnytystä ja kuusi kertaa synnytyksen jälkeen kuuden vuoden aikana. Näytteistä eristettyä DNA:ta oli saatavilla riittävästi HSV-1-analyysiä varten yhteensä 304 naiselta (keski-ikä 25.6 vuotta). Kaikkiaan tutkittavia näytteitä oli 1,873, joista HSV-1:n esiintyminen tutkittiin käyttäen kvantitatiivista PCR:ää. Lisäksi epävarmat PCR-tulokset varmistettiin PCR-tuotteen Southern Blot hybridisaatiolla. HSV-1 tuloksia verrattiin aikaisemmin saatuihin HPV-tuloksiin. Suun limakalvonäytteistä 2.2% oli HSV-1-positiivisia ja 19.6% oli HPV-positiivisia. Yhteensä 11.8%:lla äideistä suunäyte oli HSV-1-DNA -positiivinen ainakin kerran seurannan aikana. HSV-1 ja HPV -yhteisinfektio löydettiin vain neljältä äidiltä. Suurin osa äideistä, jotka olivat HSV-1-positiivisia ennen syntymää, pysyivät HSV-1-positiivisina myös synnytyksen jälkeen. Kolmella naisella todettiin persistentti HPV-16 infektio ja kahdella heistä oli samanaikainen HSV-1 infektio. Tuloksemme osoittaa, että HSV-1:n ja HPV:n esiintyminen yhtä aikaa nuorten naisten suun limakalvolla on harvinaista. On suositeltavaa, että yhteisinfektion omaavia äitejä seurataan myös tulevaisuudessa, sillä HSV-1-infektio saattaa olla yksi riskitekijä suun limakalvon malignissa muutoksessa kroonisen HPV-infektion yhteydessä.