Gene flow and hybridization are pervasive in nature, and can lead to different evolutionary outcomes. They can either accelerate divergence and promote speciation or reverse differentiation. The process of divergence and speciation are strongly influenced by both neutral and selective forces. Disentangling the interplay between these processes in natural systems is important for understanding the general importance of interspecific gene flow in generating novel biodiversity in plants. This thesis first examines the importance of introgressive hybridization in the evolution of the genus Pinus as a whole, and then focusing on specific pine species, investigates the role of geographical, environmental and demographical factors in driving divergence and adaptation. By examining the distribution of cytoplasmic DNA variation across the wide biogeographic range of the genus Pinus, I revealed historical introgression and mtDNA capture events in several groups of different pine species. This finding suggests that introgressive hybridization was common during past species’ range contractions and expansions and thus has played an important role in the evolution of the genus. To understand the cause and process of hybrid speciation, I focused on the significant case of hybrid speciation in Pinus densata. I established the hybridization, colonization and differentiation processes that defined the origin of this species. I found P. densata originated via multiple hybridization events in the late Miocene. The direction and intensity of introgression with two parental species varied among geographic regions of this species. During the colonization on Tibetan Plateau from the ancestral hybrid zone, consecutive bottlenecks and surfing of rare alleles caused a significant reduction in genetic diversity and strong population differentiation. Divergence within P. densata started from the late Pliocene onwards, induced by regional topographic changes and Pleistocene glaciations. To address the role of neutral and selective forces on genetic divergence, I examined the association of ecological and geographical distance with genetic distance in Pinus yunnanensis populations. I found both neutral and selective forces have contributed to population structure and differentiation in P. yunnanensis, but their relative contributions varied across the complex landscape. Finally, I evaluated genetic diversity in the Vietnamese endemic Pinus krempfii. I found extremely low genetic diversity in this species, which is explained by a small ancestral population, short-term population expansion and recent population decline and habitat fragmentation. These findings highlight the role of hybridization in generating novel genetic diversity and the different mechanisms driving divergence and adaptation in the genus Pinus.

In this thesis techniques are presented that aim to determine individual DNA signatures by controlled synthesis of nucleic acid multimers. Allele-specific extension reactions with an improved specificity were applied for several genomic purposes. Since DNA polymerases extend some mismatched 3’-end primers, an improved specificity is a concern. This has been possible by exploiting the faster extension of matched primers and applying the enzymes apyrase or Proteinase K. The findings were applied to methods for resequencing and viral and single nucleotide polymorphism (SNP) genotyping. P53 mutation is the most frequent event in human cancers. Here, a model system for resequencing of 15 bps in p53 based on apyrase-mediated allele-specific extension (AMASE) is described, investigated and evaluated (Paper I). A microarray format with fluorescence detection was used. On each array, four oligonucleotides were printed for each base to resequence. Target PCR products were hybridized and an AMASE-reaction performed in situ to distinguish which of the printed oligonucleotides matched the target. The results showed that without the inclusion of apyrase, the resulting sequence was unreadable. The results open the possibilities for developing large-scale resequencing tools. The presence of certain types of human papillomaviruses (HPV) transforms normal cells into cervical cancer cells. Thus, HPV type determination is clinically important. Also, multiple HPV infections are common but difficult to distinguish. Therefore, a genotyping platform based on competitive hybridization and AMASE is described, used on clinical sample material and evaluated by comparison to Sanger DNA sequencing (Papers II and III). A flexible tag-microarray was used for detection and the two levels of discrimination gave a high level of specificity. Easy identification of multiple infections was possible which provides new opportunities to investigate the importance of multiply infected samples. To achieve highly multiplexed allele-specific extension reactions, large numbers of primers will be employed and lead to spurious hybridizations. Papers IV to VI focus on an alternative approach to control oligomerization by using protease mediated allele-specific extension (PrASE). In order to maintain stringency at higher temperatures, Proteinase K, was used instead of apyrase, leading to DNA polymerase degradation and preventing unspecific extensions. An automated assay with tag-array detection for SNP genotyping was established. First PrASE was introduced and characterized (Paper IV), then used for genotyping of 10 SNPs in 442 samples (Paper V). A 99.8 % concordance to pyrosequencing was found. PrASE is a flexible tool for association studies and the results indicate an improved assay conversion rate as compared to plain allele-specific extension. The highly polymorphic melanocortin-1 receptor gene (MC1R) is involved in melanogenesis. Twenty-one MC1R variants were genotyped with PrASE since variants in the gene have been associated to an increased risk of developing melanoma. A pilot study was performed to establish the assay (Paper VI) and subsequently a larger study was executed to investigate allele frequencies in the Swedish population (Paper VII). The case and control groups consisted of 1001 and 721 samples respectively. A two to sevenfold increased risk of developing melanoma was observed for carriers of variants. / QC 20101028

Research on analogies in science education has focussed on student interpretation of teacher and textbook analogies, psychological aspects of learning with analogies and structured approaches for teaching with analogies. Few studies have investigated how analogies might be pivotal in students’ growing participation in chemical discourse. To study analogies in this way requires a sociocultural perspective on learning that focuses on ways in which language, signs, symbols and practices mediate participation in chemical discourse. This study reports research findings from a teacher-research study of two analogy-writing activities in a chemistry class. The study began with a theoretical model, Third Space, which informed analyses and interpretation of data. Third Space was operationalized into two sub-constructs called Dialogical Interactions and Hybrid Discourses. The aims of this study were to investigate sociocultural aspects of learning chemistry with analogies in order to identify classroom activities where students generate Dialogical Interactions and Hybrid Discourses, and to refine the operationalization of Third Space. These aims were addressed through three research questions. The research questions were studied through an instrumental case study design. The study was conducted in my Year 11 chemistry class at City State High School for the duration of one Semester. Data were generated through a range of data collection methods and analysed through discourse analysis using the Dialogical Interactions and Hybrid Discourse sub-constructs as coding categories. Results indicated that student interactions differed between analogical activities and mathematical problem-solving activities. Specifically, students drew on discourses other than school chemical discourse to construct analogies and their growing participation in chemical discourse was tracked using the Third Space model as an interpretive lens. Results of this study led to modification of the theoretical model adopted at the beginning of the study to a new model called Merged Discourse. Merged Discourse represents the mutual relationship that formed during analogical activities between the Analog Discourse and the Target Discourse. This model can be used for interpreting and analysing classroom discourse centred on analogical activities from sociocultural perspectives. That is, it can be used to code classroom discourse to reveal students’ growing participation with chemical (or scientific) discourse consistent with sociocultural perspectives on learning.

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2007. / Härtill 4 uppsatser.

Diss. (sammanfattning) Stockholm : Karol. inst., 2003. / Härtill 5 uppsatser.

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniv. / Härtill 4 uppsatser.

Diss. (sammanfattning) Umeå : Sveriges lantbruksuniv., 2002. / Härtill 6 uppsatser.

Lic. -avh. (sammanfattning) Stockholm : Karolinska institutet, 2007. / Härtill 3 uppsatser.

Thesis (Ph. D.)--University of Washington, 2005. / Vita. Includes bibliographical references (leaves 214-243).

Sistemas poliméricos para a liberação de fármacos associados à terapêutica periodontal convencional têm sido desenvolvidos e aplicados com algumas vantagens em comparação ao debridamento mecânico isolado. Um dispositivo de liberação lenta para uso em bolsas periodontais contendo metronidazol como princípio ativo, foi desenvolvido e testado quanto à sua eficácia no tratamento de pacientes com periodontite crônica. Dezesseis pacientes foram selecionados e aleatoriamente alocados aos seguintes tratamentos com 8 indivíduos por grupo: 1) raspagem e alisamento radicular (controle ativo) ou 2) raspagem e alisamento radicular + aplicação de gel contendo metronidazol a 15% (experimental). Os efeitos dos tratamentos foram avaliados pelo acompanhamento longitudinal de parâmetros clínicos (profundidade do sulco gengival à sondagem e nível clínico de inserção) e microbiológicos (análise da microbiota subgengival pela técnica da hibridização DNA-DNA Checkerboard). O monitoramento das concentrações de metronidazol no fluido gengival colhido dos pacientes que receberem o gel foi realizado pela cromatografia líquida de alta eficiência. Os resultados da análise das concentrações de metronidazol na bolsa periodontal demonstraram que o gel só pôde ser detectado em concentrações efetivas até uma hora depois da aplicação. Em relação à análise microbiológica, foi observada diferença significante entre os grupos, nos três tempos de avaliação (antes, 7 e 30 dias depois do tratamento). A análise intragrupos indicou redução significante na contagem bacteriana somente para o grupo tratado com o gel de metronidazol, após 7 dias do tratamento. Embora tenha sido detectada diferença entre os grupos nenhum deles foi capaz de eliminar ou reduzir com significância as espécies periodontopatogênicas. No que se refere aos parâmetros clínicos, ambas as terapias foram eficazes em promover a redução na profundidade à sondagem e o ganho no nível de inserção, sem benefício significante para o emprego do gel de metronidazol. / Polymeric systems for drug delivery have been developed and implemented with several advantages compared to conventional therapy. A slow-release device for use in periodontal pockets containing metronidazole as active principle, was developed and tested for its efficacy in treating patients with chronic periodontitis. Sixteen patients were randomly allocated to treatments with eight subjects per group: 1) scaling and root planing (active control) or 2) scaling and root planing + application of 15% metronidazole gel (experimental). Treatment effects were assessed by longitudinal clinical parameters (gingival sulcus depth probing and clinical attachment level) and microbiological (analysis of subgingival microbiota by the technique of checkerboard DNA-DNA hybridization). The monitoring of concentrations of metronidazole in the gingival fluid collected from the patients receiving the gel was performed by high performance liquid chromatography. The results of the analysis of concentrations of metronidazole in periodontal pockets showed that the gel could only be detected at effective concentrations until one hour after application. Regarding microbiological analysis there was significant difference between groups in the three evaluated times (before, 7 and 30 days after treatment). The intragroup analysis showed a significant decrease in bacterial count only for the group treated with metronidazole gel after 7 days of treatment. Although difference was detected between both groups, none of them was able to eliminate or significantly reduce the periodontopathogenic species. With regard to clinical parameters, both therapies were effective in promoting reduction in depth probing and gain in attachment level, without significant benefit to the use of metronidazole gel.