From Unspecific Quenching to Specific Signaling: Functional GTPase Assays Utilizing Quenching Resonance Energy Transfer (QRET) Technology

The aim of the work presented in this study was to demonstrate the wide applicability of a single-label quenching resonance energy transfer (QRET) assay based on time-resolved lanthanide luminescence. QRET technology is proximity dependent method utilizing weak and unspecific interaction between soluble quencher molecule and lanthanide chelate. The interaction between quencher and chelate is lost when the ligand binds to its target molecule. The properties of QRET technology are especially useful in high throughput screening (HTS) assays. At the beginning of this study, only end-point type QRET technology was available. To enable efficient study of enzymatic reactions, the QRET technology was further developed to enable measurement of reaction kinetics. This was performed using proteindeoxyribonuclei acid (DNA) interaction as a first tool to monitor reaction kinetics. Later, the QRET was used to study nucleotide exchange reaction kinetics and mutation induced effects to the small GTPase activity. Small GTPases act as a molecular switch shifting between active GTP bound and inactive GDP bound conformation. The possibility of monitoring reaction kinetics using the QRET technology was evaluated using two homogeneous assays: a direct growth factor detection assay and a nucleotide exchange monitoring assay with small GTPases. To complete the list, a heterogeneous assay for monitoring GTP hydrolysis using small GTPases, was developed. All these small GTPase assays could be performed using nanomolar protein concentrations without GTPase pretreatment. The results from these studies demonstrated that QRET technology can be used to monitor reaction kinetics and further enable the possibility to use the same method for screening.

Monooxygenase Diversity and Oxygen Activation within Polyketide Antibiotic Biosynthesis

Molecular oxygen (O2) is a key component in cellular respiration and aerobic life. Through the redox potential of O2, the amount of free energy available to organisms that utilize it is greatly increased. Yet, due to the nature of the O2 electron configuration, it is non-reactive to most organic molecules in the ground state. For O2 to react with most organic compounds it must be activated. By activating O2, oxygenases can catalyze reactions involving oxygen incorporation into organic compounds. The oxygen activation mechanisms employed by many oxygenases to have been studied, and they often include transition metals and selected organic compounds. Despite the diversity of mechanisms for O2 activation explored in this thesis, all of the monooxygenases studied in the experimental part activate O2 through a transient carbanion intermediate. One of these enzymes is the small cofactorless monooxygenase SnoaB. Cofactorless monooxygenases are unusual oxygenases that require neither transition metals nor cofactors to activate oxygen. Based on our biochemical characterization and the crystal structure of this enzyme, the mechanism most likely employed by SnoaB relies on a carbanion intermediate to activate oxygen, which is consistent with the proposed substrate-assisted mechanism for this family of enzymes. From the studies conducted on the two-component system AlnT and AlnH, both the functions of the NADH-dependent flavin reductase, AlnH, and the reduced flavin dependent monooxygenase, AlnT, were confirmed. The unusual regiochemistry proposed for AlnT was also confirmed on the basis of the structure of a reaction product. The mechanism of AlnT, as with other flavin-dependent monooxygenases, is likely to involve a caged radical pair consisting of a superoxide anion and a neutral flavin radical formed from an initial carbanion intermediate. In the studies concerning the engineering of the S-adenosyl-L-methionine (SAM) dependent 4-O-methylase DnrK and the homologous atypical 10-hydroxylase RdmB, our data suggest that an initial decarboxylation of the substrate is catalyzed by both of these enzymes, which results in the generation of a carbanion intermediate. This intermediate is not essential for the 4-O-methylation reaction, but it is important for the 10-hydroxylation reaction, since it enables substrate-assisted activation of molecular oxygen involving a single electron transfer to O2 from a carbanion intermediate. The only role for SAM in the hydroxylation reaction is likely to be stabilization of the carbanion through the positive charge of the cofactor. Based on the DnrK variant crystal structure and the characterizations of several DnrK variants, the insertion of a single amino acid in DnrK (S297) is sufficient for gaining a hydroxylation function, which is likely caused by carbanion stabilization through active site solvent restriction. Despite large differences in the three-dimensional structures of the oxygenases and the potential for multiple oxygen activation mechanisms, all the enzymes in my studies rely on carbanion intermediates to activate oxygen from either flavins or their substrates. This thesis provides interesting examples of divergent evolution and the prevalence of carbanion intermediates within polyketide biosynthesis. This mechanism appears to be recurrent in aromatic polyketide biosynthesis and may reflect the acidic nature of these compounds, propensity towards hydrogen bonding and their ability to delocalize π-electrons.

How (not) to interview children : interviews with young children in sexual abuse investigations in Finland

The present thesis had two main objectives: The first was to assess how child sexual abuse (CSA) interviews in Finland are conducted through analysing the interviewing techniques applied and the language used by the interviewers, as well as to suggest ways to improve interviews if they were found to have deficiencies. The second main aim was to contribute to the growing research corpus concerning CSA interviews, in particular, by addressing how interviewers follow up information provided by the child, by analysing whether child health care professionals would use childadapted language, and by studying the kind of modifications in the verbal behaviour of interviewers and children that were associated with a) repeated interviews, b) a support person’s presence at the interview, and c) the use of anatomically detailed dolls. Two complementary samples of CSA interviews were analysed. The first one was composed of child interviews with 3-12-year-old children (N = 27) that had been considered problematic by lawyers or other involved professionals (Studies I and IV). The second sample consisted of unselected interviews (N = 43) with children aged 3 to 8 years conducted in a number of hospitals in different parts of the country (Studies II and III). Study I: The verbal interaction between interviewer and child was analysed in a sample of interviews that had been considered to be problematic by involved professionals. Results showed that interviewers used inappropriate questioning techniques, relying on option-posing, specific suggestive and unspecific suggestive questions to a significant extent, these comprising around 50% of all interviewer utterances. The proportion of invitations, which the research community recommends interviewers to rely on, was strikingly low. Invitations and directive utterances were associated with an increase in informative responses by the child in terms of response type, number of new details reported, as well as length of response. The opposite was true for option-posing and suggestive utterances. Longer questions by the interviewer (in number of words) often rendered no reply from the child, whereas shorter questions were followed by descriptive answers. Even after the child had provided an informative answer, interviewers failed to follow up the information in an adequate way and instead continued to rely on focused and leading questions. Study II: Due to the possible bias of the sample analysed in Study I, the most important analyses were rerun with the unselected sample and reported separately. Results were quite similar between the two studies, indicating that the problems observed in Study I, with interviewers relying on option-posing and suggestive questions to a significant extent, are likely to be general and not specific for those interviews. Even if suggestive questions were slightly less and invitations slightly more common in this sample than in the previous study, almost half of the interviewer questions were still optionposing or suggestive, and also in this sample, interviewers failed to follow up information by the child in a facilitating manner. Differentiating between judicial and contextual details showed that while facilitators, invitations, and directive utterances elicited more contextual than judicial details, the opposite was true for specific suggestive utterances. These results might be explained by the reluctance of children to describe sexual details related to the abuse events. Alternatively, they may also be due to children describing incorrect sexual details as a result of suggestive interviewing techniques. Study III: This study examined features of the language used by the interviewers. Interviewer utterances included multiple questions, long statements, complicated grammar and concepts, as well as unclear references to persons and situations. More than a fifth of the interviewer utterances were coded as belonging to at least one of these categories. The results suggest that even professionals who are experienced in interacting with children may have difficulties in using a child-sensitive language, adding to the pool of studies showing similar problems to occur in legal hearings with children conducted by lawyers. As children rarely comment on, or even recognise, their lack of comprehension, the use of a language that is too complex can have detrimental consequences for the outcomes of investigative interviews. Interviewers used different approaches to introduce the topic of abuse. While 15% of the children spontaneously addressed the topic of abuse, probably indicating that they felt confident with the interviewer and the situation, in almost 50% of the cases, the interviewer introduced the topic of abuse in a way that can be considered leading. Interviews were characterised by a lack of structure, apparent in frequent rapid switches of topic by the interviewer. This manner was associated with a decrease in the number of new details provided by the children. Study IV: This study analysed possible changes in the interview dynamics associated with repeated interviewing, the presence of a support person (related to the child), and the use of anatomically detailed (AD) dolls. Repeated interviewing, in combination with suggestive questions, has previously been found to seriously contaminate children’s accounts. In the present material, interviewers used significantly more suggestive utterances in the repeated condition, thus endangering the reliability of the children’s reports. Few studies have investigated the effects of a support person’s presence at the interview. The results of the present study showed that interviewers talked more and children provided less information when a support person was present. Supporting some earlier findings regarding the use of AD dolls, the present results showed that using AD dolls was associated with longer interviewer utterances and shorter, less responsive, and less detailed child responses. Interviewers used up to five times more unspecific suggestive utterances when dolls were used, for instance through repeatedly asking the child to show “what really happened” with the dolls. Conclusion: The results indicate that CSA interviews in Finland are not conducted in a manner that follows best practice as defined by the research community and as stated in a number of guidelines. When comparing these questioning strategies with the recommendations, which have been predominant in the field for more than ten years now, it can be concluded that the interviews analysed were conducted in a manner that undermines the possibility to elicit an uncontaminated and accurate narrative from the children. A particularly worrying finding was the fact that interviewers did not follow up relevant information by the children in an adequate way. A number of clinical implications can be drawn from the results, particularly concerning the need for improvement in the quality of CSA interviews. There is convincing research regarding how to improve CSA interviews, notably through training forensic child interviewers to use a structured interviewing protocol, and providing them with continuous supervision and feedback. Allocating appropriate resources to improve the quality of forensic child interviews is a matter of protecting the rights of all persons involved in CSA investigations, in particular those of the children.