Group I Introns and Homing Endonucleases in T-even-like Bacteriophages

Homing endonucleases are rare-cutting enzymes that cleave DNA at a site near their own location, preferentially in alleles lacking the homing endonuclease gene (HEG). By cleaving HEG-less alleles the homing endonuclease can mediate the transfer of its own gene to the cleaved site via a process called homing, involving double strand break repair. Via homing, HEGs are efficiently transferred into new genomes when horizontal exchange of DNA occurs between organisms. Group I introns are intervening sequences that can catalyse their own excision from the unprocessed transcript without the need of any proteins. They are widespread, occurring both in eukaryotes and prokaryotes and in their viruses. Many group I introns encode a HEG within them that confers mobility also to the intron and mediates the combined transfer of the intron/HEG to intronless alleles via homing. Bacteriophage T4 contains three such group I introns and at least 12 freestanding HEGs in its genome. The majority of phages besides T4 do not contain any introns, and freestanding HEGs are also scarcely represented among other phages. In the first paper we looked into why group I introns are so rare in phages related to T4 in spite of the fact that they can spread between phages via homing. We have identified the first phage besides T4 that contains all three T-even introns and also shown that homing of at least one of the introns has occurred recently between some of the phages in Nature. We also show that intron homing can be highly efficient between related phages if two phages infect the same bacterium but that there also exists counteracting mechanisms that can restrict the spread of introns between phages. In the second paper we have looked at how the presence of introns can affect gene expression in the phage. We find that the efficiency of splicing can be affected by variation of translation of the upstream exon for all three introns in T4. Furthermore, we find that splicing is also compromised upon infection of stationary-phase bacteria. This is the first time that the efficiency of self-splicing of group I introns has been coupled to environmental conditions and the potential effect of this on phage viability is discussed. In the third paper we have characterised two novel freestanding homing endonucleases that in some T-even-like phages replace two of the putative HEGs in T4. We also present a new theory on why it is a selective advantage for freestanding, phage homing endonucleases to cleave both HEG-containing and HEG-less genomes.

Deictic Demonstratives in Japanese, Finnish and Swedish : First and Third Language Perspectives

The goal of this thesis is twofold. Firstly, it investigates the actual, native use of spatial-deictic demonstratives in Japanese, Finnish and Swedish. Secondly, it investigates and elucidates the interlanguage of Finnish-speaking and Swedish-speaking learners of Japanese regarding their use of Japanese spatial-deictic demonstratives in the light of respective native use and, in comparison to the descriptions of demonstratives in the teaching materials used. Thus, the present study deals with analyses of two sets of empirical data: data produced by native-speaking informants (L1 data) and data produced by language learners (L2 data). These were elicited by Discourse Completion Tasks (DCTs) designed, collected and analyzed using both quantitative and qualitative methods by the author. The results showed that the actual use of demonstratives by the native informants was not always in accordance with the way described in grammars. The typological similarities between Japanese and Finnish were in this study not reflected in the native use of demonstratives, and some uses were not solely based on the spatial relations between the referent, the speaker and the addressee, but rather on social-interactional factors. The main findings regarding the learner data revealed some differences in the usage rate of the demonstratives between the two Finnish-speaking groups and the one Swedish-speaking learner group studied. There were, however, no particular differences found between them regarding the type of demonstrative used. It is suggested that these differences are first and foremost connected both with the teaching materials used and the more or less heterogeneous linguistic environment in which the learners reside, and only thereafter with the typological similarities or differences between their respective native languages, Finnish and Swedish, and the target language, Japanese. It is further argued that the learners’ use of the different Japanese demonstratives, that is the type of demonstrative used, could be explained in terms of familiarity with the grammar. That is, when the situations used in the DCTs were exemplified in teaching materials and were familiar to them, the learners seemed to use Japanese demonstratives as they are described in the teaching materials and as the native Japanese speakers use them. When the situations used in the DCTs were not exemplified in the teaching materials, the learners seem to rely more on their native language. The results, thus, suggest that the learners’ interlanguage is influenced by the grammar of the target language known to the learners, but also by the number of languages (or varieties) that the learners have contact with at the time of learning. The results of the present study have implications for the teaching of Japanese in at least two ways. Firstly, the importance of grammar instruction must be emphasized since its effect on the learners’ language is apparent. Secondly, the contents of teaching materials should be revised on the basis of the native speakers’ actual use of the grammar.