<p>Ssu72 is a protein phosphatase that selectively targets phosphorylated serine residues at the 5th position (pS5) in the heptad repeats of the C-terminal domain (CTD) of RNA polymerase II, in order to regulate the CTD-mediated coupling between eukaryotic transcription and co-transcriptional events. The biological importance of Ssu72 is underscored by (1) the requirement of its activity for viability in yeast, and (2) the numerous phenotypes - affecting all three stages of the transcription cycle - that result from its mutation in yeast. Despite limited homology to the low molecular weight (LMW) subclass of protein tyrosine phosphatases (PTPs), several lines of evidence suggest that Ssu72 represents the founding member of a new class of enzymes, including its unique substrate specificity and an in vivo connection with the activity of proline isomerase Ess1.</p><p>The main focus of this thesis has been to structurally and kinetically characterize Ssu72, in order to define its relation to known enzyme families, to provide biochemical explanations for extant in vivo observations, and to allow future structure-guided investigations of its role in coordinating transcription with co-transcriptional events. To this end, we solved the structure of Ssu72 in complex with its pS5 CTD substrate, revealing an enzyme fold with unique structural features and a surprising substrate conformation with the pS5-P6 motif of the CTD adopting the cis configuration. Together with kinetic assays, the structure provides a new interpretation of the role of proline isomers in regulating the CTD phosphorylation state, with broad implications for CTD biology.</p><p>The second goal of this thesis has been to develop new methods for NMR studies of large proteins, which present unique challenges to conventional methods, including fast signal decay and severe signal degeneracy. The first of these new methods, the `just-in-time' HN(CA)CO, improves the sensitivity of a common backbone assignment experiment. The next two methods, the 4-D diagonal-suppressed TROSY-NOESY-TROSY and the 4-D time-shared NOESY, were designed for use with sparse sampling techniques that allow the acquisition of high-resolution, high-dimensionality datasets. These efforts culminate with global fold calculations for large proteins, including the 23 kDa Ssu72, with accurate and unambiguous automated assignment of NOE crosspeaks. We expect that the methods presented here will be particularly useful as the NMR community continues to push toward higher molecular weight targets.</p> / Dissertation

Le codage parcimonieux permet la reconstruction d'un signal à partir de quelques projections linéaires de celui-ci, sous l'hypothèse que le signal se décompose de manière parcimonieuse, c'est-à-dire avec peu de coefficients, sur un dictionnaire connu. Le codage est simple, et la complexité est déportée sur la reconstruction. Après une explication détaillée du fonctionnement du codage parcimonieux, une présentation de quelques résultats théoriques et quelques simulations pour cerner les performances envisageables, nous nous intéressons à trois problèmes : d'abord, l'étude de conception d'un système permettant le codage d'un signal par une matrice binaire, et des avantages apportés par une telle implémentation. Ensuite, nous nous intéressons à la détermination du dictionnaire de représentation parcimonieuse du signal par des méthodes d'apprentissage. Enfin, nous discutons la possibilité d'effectuer des opérations comme la classification sur le signal sans le reconstruire. / Compressed sensing allows to reconstruct a signal from a few linear projections, under the assumption that the signal can be sparsely represented, that is, with only a few coefficients, on a known dictionary. Coding is very simple and all the complexity is gathered on the reconstruction. After more detailed explanations of the principle of compressed sensing, some theoretic resultats from literature and a few simulations allowing to get an idea of expected performances, we focusson three problems: First, the study for the building of a system using compressed sensing with a binary matrix and the obtained benefits. Then, we have a look at the building of a dictionary for sparse representations of the signal. And lastly, we discuss the possibility of processing signal without reconstruction, with an example in classification.

<p>Standard MRI is used to image objects at rest. In addition to standard MRI images, which measure tissues at rest, Phase Contrast MRI can be used to quantify the motion of blood and tissue in the human body. The current method used in Phase Contrast MRI is time consuming. The development of new trajectories has minimized imaging time, but creates sub-sampling errors. The proposed method uses regularization of velocities and proton densities to eliminate errors arising from k-space under-sampling.</p> / Master of Applied Science (MASc)

We investigated age-related differences in neural activation associated with recognition of familiar melodies, a process that requires retrieval from musical semantic memory and leads to a feeling of familiarity. We used sparse sampling fMRI to determine the neural correlates of melody processing and familiarity by comparing activation when listening to melodies versus signal-correlated noise, and to familiar versus unfamiliar melodies, respectively. Overall, activity in the bilateral superior temporal gyrus correlated well with melody processing. Familiarity was associated with several frontal regions (bilateral inferior frontal gyrus, superior frontal gyrus, and precentral gyrus; left insular cortex), right superior temporal gyrus; left supramarginal gyrus and cingulate gyrus; bilateral putamen and thalamus; cerebellum and brainstem. No significant differences were found between younger and older adults for either melody processing or familiarity based activation. Assessment of familiarity-related group differences using less stringent criteria identified plausible areas; greater activation was seen bilaterally in the superior temporal gyrus in younger adults and in some left parietal regions in older adults. This study adds to the knowledge of musical semantic memory with results based on a large sample (N = 40) that includes older adults. Our findings for activation associated with melody processing and familiarity support some, but not all, previous results of related studies. We were unable to find conclusive evidence of age-related differences in neural correlates of musical semantic memory, while also being the first study (to the best of our knowledge) to search for these differences. / Thesis (Master, Neuroscience Studies) -- Queen's University, 2013-09-16 12:38:10.757

We investigated age-related differences in neural activation associated with recognition of familiar melodies, a process that requires retrieval from musical semantic memory and leads to a feeling of familiarity. We used sparse sampling fMRI to determine the neural correlates of melody processing and familiarity by comparing activation when listening to melodies versus signal-correlated noise, and to familiar versus unfamiliar melodies, respectively. Overall, activity in the bilateral superior temporal gyrus correlated well with melody processing. Familiarity was associated with several frontal regions (bilateral inferior frontal gyrus, superior frontal gyrus, and precentral gyrus; left insular cortex), right superior temporal gyrus; left supramarginal gyrus and cingulate gyrus; bilateral putamen and thalamus; cerebellum and brainstem. No significant differences were found between younger and older adults for either melody processing or familiarity based activation. Assessment of familiarity-related group differences using less stringent criteria identified plausible areas; greater activation was seen bilaterally in the superior temporal gyrus in younger adults and in some left parietal regions in older adults. This study adds to the knowledge of musical semantic memory with results based on a large sample (N = 40) that includes older adults. Our findings for activation associated with melody processing and familiarity support some, but not all, previous results of related studies. We were unable to find conclusive evidence of age-related differences in neural correlates of musical semantic memory, while also being the first study (to the best of our knowledge) to search for these differences. / Thesis (Master, Neuroscience Studies) -- Queen's University, 2013-09-16 12:38:10.757