Transposable elements: structure and dynamic of the autonomous retrotransposon R2 in Arthropoda with non-canonical reproduction

Eukaryotic ribosomal DNA constitutes a multi gene family organized in a cluster called nucleolar organizer region (NOR); this region is composed usually by hundreds to thousands of tandemly repeated units. Ribosomal genes, being repeated sequences, evolve following the typical pattern of concerted evolution. The autonomous retroelement R2 inserts in the ribosomal gene 28S, leading to defective 28S rDNA genes. R2 element, being a retrotransposon, performs its activity in the genome multiplying its copy number through a “copy and paste” mechanism called target primed reverse transcription. It consists in the retrotranscription of the element’s mRNA into DNA, then the DNA is integrated in the target site. Since the retrotranscription can be interrupted, but the integration will be carried out anyway, truncated copies of the element will also be present in the genome. The study of these truncated variants is a tool to examine the activity of the element. R2 phylogeny appears, in general, not consistent with that of its hosts, except some cases (e.g. Drosophila spp. and Reticulitermes spp.); moreover R2 is absent in some species (Fugu rubripes, human, mouse, etc.), while other species have more R2 lineages in their genome (the turtle Mauremys reevesii, the Japanese beetle Popilia japonica, etc). R2 elements here presented are isolated in 4 species of notostracan branchiopods and in two species of stick insects, whose reproductive strategies range from strict gonochorism to unisexuality. From sequencing data emerges that in Triops cancriformis (Spanish gonochoric population), in Lepidurus arcticus (two putatively unisexual populations from Iceland) and in Bacillus rossius (gonochoric population from Capalbio) the R2 elements are complete and encode functional proteins, reflecting the general features of this family of transposable elements. On the other hand, R2 from Italian and Austrian populations of T. cancriformis (respectively unisexual and hermaphroditic), Lepidurus lubbocki (two elements within the same Italian population, gonochoric but with unfunctional males) and Bacillus grandii grandii (gonochoric population from Ponte Manghisi) have sequences that encode incomplete or non-functional proteins in which it is possible to recognize only part of the characteristic domains. In Lepidurus couesii (Italian gonochoric populations) different elements were found as in L. lubbocki, and the sequencing is still in progress. Two hypothesis are given to explain the inconsistency of R2/host phylogeny: vertical inheritance of the element followed by extinction/diversification or horizontal transmission. My data support previous study that state the vertical transmission as the most likely explanation; nevertheless horizontal transfer events can’t be excluded. I also studied the element’s activity in Spanish populations of T. cancriformis, in L. lubbocki, in L. arcticus and in gonochoric and parthenogenetic populations of B. rossius. In gonochoric populations of T. cancriformis and B. rossius I found that each individual has its own private set of truncated variants. The situation is the opposite for the remaining hermaphroditic/parthenogenetic species and populations, all individuals sharing – in the so far analyzed samples - the majority of variants. This situation is very interesting, because it isn’t concordant with the Muller’s ratchet theory that hypothesizes the parthenogenetic populations being either devoided of transposable elements or TEs overloaded. My data suggest a possible epigenetic mechanism that can block the retrotransposon activity, and in this way deleterious mutations don’t accumulate.

A corpus-assisted approach to apology-like expressions in Japanese computer-mediated discourse

This thesis provides a corpus-assisted pragmatic investigation of three Japanese expressions commonly signalled as apologetic, namely gomen, su(m)imasen and mōshiwake arimasen, which can be roughly translated in English with ‘(I’m) sorry’. The analysis is based on a web corpus of 306,670 tokens collected from the Q&A website Yahoo! Chiebukuro, which is examined combining quantitative (statistical) and qualitative (traditional close reading) methods. By adopting a form-to-function approach, the aim of the study is to shed light on three main topics of interest: the pragmatic functions of apology-like expressions, the discursive strategies they co-occur with, and the behaviours that warrant them. The overall findings reveal that apology-like expressions are multifunctional devices whose meanings extend well beyond ‘apology’ alone. These meanings are affected by a number of discursive strategies that can either increase or decrease the perceived (im)politeness level of the speech act to serve interactants’ face needs and communicative goals. The study also identifies a variety of behaviours that people frame as violations, not necessarily because they are actually face-threatening to the receiver, but because doing so is functional to the projection of the apologiser as a moral persona. An additional finding that emerged from the analysis is the pervasiveness of reflexive usages of apology-like expressions, which are often employed metadiscursively to convey, negotiate and challenge opinions on how language should be used. To conclude, the study provides a unique insight into the use of three expressions whose pragmatic meanings are more varied than anticipated. The findings reflect the use of (im)politeness in an online and non-Western context and, hopefully, represent a step towards a more inclusive notion of ‘apologies’ and related speech acts.