Käytännön ohjelmointi -kurssin kehittäminen

Tämän tutkimuksen tavoitteena on selvittää opintojensa alussa olevien yliopisto-opiskelijoiden vaikeimpina pitämät käytännön ohjelmoinnin aihealueet sekä koostaa luentomoniste käytettäväksi seuraavalla alkavalla Käytännön ohjelmointi -kurssilla. Tutkimusmetodina käytettiin konstruktiivista tutkimusmetodia, jossa tavoitteen spesifioinnin jälkeen implementoitiin luentomoniste koostamalla määriteltyjen aihekokonaisuuksien lähdemateriaalia yhtenäiseksi, luettavaksi kokonaisuudeksi. Yliopistoissa ei yleisesti opeteta ohjelmistojen testausta ennen syventäviä ohjelmistotekniikan kursseja, mikä on kuitenkin puute työelämän kannalta. Tässä työssä esitetään perusteluja käytännönläheisten aihekokonaisuuksien painottamiselle ohjelmointikursseilla jo yliopisto-opintojen alkuvaiheessa. Työssä käsitellään Käytännön ohjelmointi -kurssin kurssipalautetta, missä havaittiin opiskelijoiden pitävän kurssin hankalimpina aihealueina linkitettyä listaa, osoittimia, dynaamista muistinhallintaa, tietorakenteita ja versionhallintaa. Työn avulla on pyritty kehittämään käytännön ohjelmoinnin yliopisto-opetusta Lappeenrannan teknillisessä yliopistossa luentomateriaalin avulla, jossa on muun muassa teoriaa, keskeisiä opiskelijoiden tarvitsemia komentoja, www-linkkejä sekä ohjelmoinnin tyyliopas.

Evolution of Bordetella pertussis post vaccination

Evolution of Bordetella pertussis post vaccination Whooping cough or pertussis is caused by the gram-negative bacterium Bordetella pertussis. It is a highly contiguous disease in the human respiratory tract. Characteristic of pertussis is a paroxysmal cough with whooping sound during gasps of breath after coughing episodes. It is potentially fatal to unvaccinated infants. The best approach to fight pertussis is to vaccinate. Vaccinations against pertussis have been available from the 1940s. Traditionally vaccines were whole-cell pertussis (wP) preparations as part of the combined diphtheria-tetanus-pertussis (DTP) vaccines. More recently acellular pertussis (aP) vaccines have replaced the wP vaccines in many countries. The aP vaccines are less reactogenic and can also be administered to school children and adults. There are several publications reporting variation in the i>B. pertussis virulence factors that are also aP vaccine antigens. This has occurred in the genes coding for pertussis toxin and pertactin about 15 to 30 years after the introduction of pertussis vaccines to immunisation programs. Resurgence of pertussis has also been reported in many countries with high vaccination coverage. In this study the evolution of B. pertussis was investigated in Finland, the United Kingdom, Poland, Serbia, China, Senegal and Kenya. These represent countries with a long history of high vaccination coverage with stable vaccines or changes in the vaccine formulation; countries which established high vaccination coverage late; and countries where vaccinations against pertussis were started late. With bacterial cytotoxicity and cytokine measurements, comparative genomic hybridisation, pulsed-field gel electrophoresis (PFGE), genotyping and serotyping it was found that changes in the vaccine composition can postpone the emergence of antigenic variants. It seems that the change in PFGE profiles and the loss of genetic material in the genome of B. pertussis are similar in most countries and the vaccine-induced immunity is selecting non-vaccine type strains. However, the differences in the formulation of the vaccines, the vaccination programs and in the coverage of pertussis vaccination have affected the speed and timing of these changes.

Structure-related magnetic fabric studies : implications for deformed and undeformed Precambrian rocks

The aim of this thesis research was to gain a better understanding of the emplacement of rapakivi granite intrusions, as well as the emplacement of gold-bearing hydrothermal fluids in structurally controlled mineralizations. Based on investigations of the magnetic fabric, the internal structures could be analysed and the intrusion mechanisms for rapakivi granite intrusions and respectively different deformation stages within gold-bearing shear and fault zones identified. Aeromagnetic images revealed circular structures within the rapakivi granite batholiths of Wiborg, Vehmaa and Åland. These circular structures represent intrusions that eventually build up these large batholiths. The rapakivi granite intrusions of Vehmaa, Ruotsinpyhtää within the Wiborg batholith and Saltvik intrusions within the Åland batholith all show bimodal magnetic susceptibilities with paramagnetic and ferromagnetic components. The distribution of the bimodality is related to different magma batches of the studied intrusions. The anisotropy of magnetic susceptibility (AMS) reveals internal structures that cannot be studied macroscopically or by microscope. The Ruotsinpyhtää and Vehmaa intrusions represent similar intrusion geometries, with gently to moderately outward dipping magnetic foliations. In the case of Vehmaa, the magnetic lineations are gently plunging and trend in the directions of the slightly elongated intrusion. The magnetic lineations represent magma flow. The shapes of the AMS ellipsoids are also more planar (oblate) in the central part of the intrusion, whereas they become more linear (prolate) near the margin. These AMS results, together with field observations, indicate that the main intrusion mechanism has involved the subsidence of older blocks with successive intrusion of fractionated magma during repeated cauldron subsidence. The Saltvik area within the Åland batholith consists of a number of smaller elliptical intrusions of different rapakivi types forming a multiple intrusive complex. The magnetic fabric shows a general westward dipping of the pyterlite and eastward dipping of the contiguous even-grained rapakivi granite, which indicates a central inflow of magma batches towards the east and west resulting from a laccolitic emplacement of magma batches, while the main mechanism for space creation was derived from subsidence. The magnetic fabric of structurally controlled gold potential shear and fault zones in Jokisivu, Satulinmäki and Koijärvi was investigated in order to describe the internal structures and define the deformation history and emplacement of hydrothermal fluids. A further aim of the research was to combine AMS studies with palaeomagnetic methods to constrain the timing for the shearing event relative to the precipitation of ferromagnetic minerals and gold. All of the studied formations are dominated by monoclinic pyrrhotite. The AMS directions generally follow the tectonic structures within the formations. However, internal variations in the AMS direction as well as the shapes of the AMS ellipsoids are observed within the shear zones. In Jokisivu and Satulinmäki in particular, the magnetic signatures of the shear zone core differ from the margins. Furthermore, the shape of the magnetic fabric in the shear zone core of Jokisivu is dominated by oblate shapes, whereas the margins exhibit prolate shapes. These variations indicate a later effect of the hydrothermal fluids on the general shear event. The palaeo-magnetic results reveal a deflection from the original Svecofennian age geomagnetic direction. These results, coupled with correlations between the orientation of the NRM vectors and the magnetic and rock fabrics, imply that the gold-rich hydrothermal fluids were emplaced pre/syntectonically during the late stages of the Svecofennian orogeny.

Characterisation of Cladonia rangiferina transcriptome and genome, and the effects of dehydration and rehydration on its gene expression

Lichens are symbiotic organisms, which consist of the fungal partner and the photosynthetic partner, which can be either an alga or a cyanobacterium. In some lichen species the symbiosis is tripartite, where the relationship includes both an alga and a cyanobacterium alongside the primary symbiont, fungus. The lichen symbiosis is an evolutionarily old adaptation to life on land and many extant fungal species have evolved from lichenised ancestors. Lichens inhabit a wide range of habitats and are capable of living in harsh environments and on nutrient poor substrates, such as bare rocks, often enduring frequent cycles of drying and wetting. Most lichen species are desiccation tolerant, and they can survive long periods of dehydration, but can rapidly resume photosynthesis upon rehydration. The molecular mechanisms behind lichen desiccation tolerance are still largely uncharacterised and little information is available for any lichen species at the genomic or transcriptomic level. The emergence of the high-throughput next generation sequencing (NGS) technologies and the subsequent decrease in the cost of sequencing new genomes and transcriptomes has enabled non-model organism research on the whole genome level. In this doctoral work the transcriptome and genome of the grey reindeer lichen, Cladonia rangiferina, were sequenced, de novo assembled and characterised using NGS and traditional expressed sequence tag (EST) technologies. RNA extraction methods were optimised to improve the yield and quality of RNA extracted from lichen tissue. The effects of rehydration and desiccation on C. rangiferina gene expression on whole transcriptome level were studied and the most differentially expressed genes were identified. The secondary metabolites present in C. rangiferina decreased the quality – integrity, optical characteristics and utility for sensitive molecular biological applications – of the extracted RNA requiring an optimised RNA extraction method for isolating sufficient quantities of high-quality RNA from lichen tissue in a time- and cost-efficient manner. The de novo assembly of the transcriptome of C. rangiferina was used to produce a set of contiguous unigene sequences that were used to investigate the biological functions and pathways active in a hydrated lichen thallus. The de novo assembly of the genome yielded an assembly containing mostly genes derived from the fungal partner. The assembly was of sufficient quality, in size similar to other lichen-forming fungal genomes and included most of the core eukaryotic genes. Differences in gene expression were detected in all studied stages of desiccation and rehydration, but the largest changes occurred during the early stages of rehydration. The most differentially expressed genes did not have any annotations, making them potentially lichen-specific genes, but several genes known to participate in environmental stress tolerance in other organisms were also identified as differentially expressed.