In the pentose phosphate pathway, carbohydrates such as glucose and ribose are degraded with production of reductive power and energy. Another important function is to produce essential pentoses, such as ribose 5-phosphate, which later can be used in biosynthesis of nucleic acids and cofactors. This thesis presents structural and functional studies on three enzymes involved in ribose metabolism in Escherichia coli. Ribokinase is an enzyme that phosphorylates ribose in the presence of ATP and magnesium, as the first step of exogenous ribose metabolism. Two important aspects of ribokinase function, not previously known, have been elucidated. Ribokinase was shown to be activated by monovalent cations, specifically potassium. Structural analysis of the monovalent ion binding site indicates that the ion has a structural rather than catalytic role; a mode of activation involving a conformational change has been suggested. Product inhibition studies suggest that ATP is the first substrate to bind the enzyme. Independent Kd measurements with the ATP analogue AMP-PCP support this. The results presented here will have implications for several enzymes in the protein family to which ribokinase belongs, in particular the medically interesting enzyme adenosine kinase. Ribose 5-phosphate isomerases convert ribose 5-phosphate into ribulose 5-phosphate or vice versa. Structural studies on the two genetically distinct isomerases in E. coli have shown them to be fundamentally different in many aspects, including active site architecture. However, a kinetic study has demonstrated both enzymes to be efficient in terms of catalysis. Sequence searches of completed genomes show ribose 5-phosphate isomerase B to be the sole isomerase in many bacteria, although ribose 5-phosphate isomerase A is a nearly universal enzyme. All genomes contain at least one of the two enzymes. These results confirm that both enzymes must be independently capable of supporting ribose metabolism, a fact that had not previously been established.

Fluctuations in protein structure are vital to function. This contrasts the dominating structure-function paradigm, which connects the well-defined three-dimensional protein structure to its function. However, catalysis is observed in disordered enzymes, which lack a defined structure. Disordered proteins are involved in molecular recognition events as well. The aim of this Thesis is to describe the structural changes occuring in protein structure and to investigate the mechanism of molecular recognition. Protein architecture is classified in a hierarchical manner, that is, it is categorized into primary, secondary, and tertiary levels. One of the major questions in biology today is how proteins fold into a defined three-dimensional structure. Some protein folding models, like the framework model, suggest that the secondary structure, like α-helices, is formed before the tertiary structure. This Thesis raises two questions: First, are structural fluctuations that occur in the protein related to the folding of the protein structure? Second, is the hierarchic classification of the protein architecture useful to describe said structural fluctuations? Kinetic studies of protein folding show that important dynamical processes of the folding occur on the microsecond timescale, which is why time-resolved fluorescence spectroscopy was chosen as the principal method for studying structural fluctuations in the peptides. Time-resolved fluorescence spectroscopy offers a number of experimental advantages and is useful for characterizing typical structural elements of the peptides on the sub-microsecond timescale. By observing the fluorescence lifetime distribution of the fluorescent probe, which is a part of the hydrophobic core of a four-helix bundle, it is shown that the hydrophobic core changes hydration state, from a completely dehydrated to a partly hydrated hydrophobic core. These fluctuations are related to the tertiary structure of the four-helix bundle and constitute structural transitions between the completely folded four-helix bundle and the molten globule version. Equilibrium unfolding of the four-helix bundle, using chemical denaturants or increased temperature, shows that the tertiary structure unfolds before the secondary structure, via the molten globule state, which suggests a hierarchic folding mechanism of the four-helix bundle. Fluctuations of a 12 amino acid long helical segment, without tertiary structure, involve a conformational search of different helical organizations of the backbone. Binding and recognition of a helix-loop-helix to carbonic anhydrase occurs through a partly folded intermediate before the final tertiary and bimolecular structure is formed between the two biomolecules. This confirms the latest established theory of recognition that the binding and the folding processes are coupled for the binding molecules.

A class of linear diamidines was synthesized for the evaluation as a treatment of Human African Trypanosomiasis. These fused heterocyclic compounds are thiazole[5,4-d]thiazoles and are of interest because the parent compound, 2,5-Bis(4-amidinophenyl)-thiazolo[5,4-d]thiazole HCl salt, which is also called DB 1929, has exhibited a low nanomolar IC50 value against Trypanosoma brucei rhodesiense and has shown selectivity for binding to the human telomere G-quadruplex over that of DNA duplex. A fluoro and a methoxy derivative have been synthesized and are currently undergoing testing for activity and binding affinity. In addition, fluorescence studies of selected diamidines were done to study the effect of structural variation on fluorescence. This data is useful since it can determine what types of moieties are needed to yield a compound that will fluoresce in the higher wavelengths (500 nm and above) of the visible spectrum, which would be advantageous in determining the uptake of the drug in the trypanosome within the endemic areas of Africa with a simple microscope.

Membrane proteins are vital for cellular homeostasis. They maintain the electrochemical gradients that are essential for signaling and control the fine balance of trace elements. In order to fulfill these tasks, they need to undergo controlled conformational transitions within the lipid bilayer of a cell membrane. It is well-recognized that membrane protein structure and function depends on the lipid membrane. However, much less is known about the role of water re-partitioning at the protein–lipid interface and particularly within a membrane protein during functional transitions. Intra-membrane protein hydration is expected to be particularly important for ion transport processes, where the hydration shell of a solvated ion needs to be rearranged and partially removed in order to bind the ion within the transporter before it is re-solvated upon exiting the membrane protein. These processes are spatially and temporally organized in metal-transporting ATPases of the PIB-subtype of P-type ATPases. Here, the functional role of water entry into the transmembrane region of the copper-transporting PIB-type ATPase CopA from Legionella pneumophila (LpCopA) has been investigated. The recombinant protein was affinity-purified and functionally reconstituted into nanodiscs prepared with the extended scaffolding protein MSP1E3D1. Nanodiscs provide a planar native-like lipid bilayer in a water-soluble nanoparticle with advantageous optical properties for spectroscopy. The small polarity-sensitive fluorophore 6-bromoacetyl-2-dimethylaminonaphthalene (BADAN) was used as a probe for the molecular environment of the conserved copper-binding cysteine-proline-cysteine (CPC) motif which is located close to a wide “entry platform” for Cu+ to the transmembrane (TM) channel. The systematic study of proteins with mutated metal-binding motifs using steady-state and time-resolved fluorescence spectroscopy indicates that strong gradients of hydration and protein flexibility can exist across the narrow range of the CPC motif. The data suggest that Cu+ passes a “hydrophobic gate” at the more cytoplasmic C384 provided by rather stable TM helix packing before entering a more flexible and readily hydratable site in the interior of LpCopA around C382 where the polarity is strongly regulated by protein–lipid interactions. This flexibility could also be partly mediated by rearrangements of an adjacent amphipathic protein stretch that runs parallel to the membrane surface as a part of the cytoplasmic entry site. Using tryptophan fluorescence, circular dichroism, and Fourier-transform infrared absorption spectroscopy of a synthetic peptide derived from this segment, its lipid-dependent structural variability could be revealed. Depending on lipid-mediated helix packing interactions, the CPC motif has the potential to support a strong dielectric gradient with about ten units difference in permittivity across the CPC distance. This property may be crucial in establishing the directionality of ion transport by a non-symmetric re-solvation potential in the ion release channel of LpCopA. The experimental elucidation of these molecular details emphasizes not only the importance of intra-membrane protein water which has been hypothesized particularly for PIB-type ATPases. Moreover it is shown here, that the lateral pressure of a cell membrane may provide a force that restores a low hydration state from a transiently formed state of high internal water content at the distal side of the CPC motif. ATP-driven conformational changes that induce intra-membrane protein hydration of a conformational intermediate of the Post-Albers cycle could thus be set back efficiently by lateral pressure of the cell membrane at a later step of the cycle.

Τα φωτοβολταϊκά στοιχεία με ευαισθητοποίηση χρωστικής (Dye Sensitized Solar Cells, DSSCs) κίνησαν το ενδιαφέρον της επιστημονικής κοινότητας ύστερα από την πρωτότυπη δημοσίευση του 1991 των Grätzel και O' Regan. Προτάθηκαν ως μία φθηνή εναλλακτική λύση σε σύγκριση με τα συμβατικά ηλιακά στοιχεία από άμορφο πυρίτιο (amorphous silicon). Οι κύριοι παράγοντες που οδήγησαν την επιστημονική κοινότητα να στραφεί προς αυτή την κατεύθυνση ήταν η ευκολία σύνθεσης των χρωστικών με σχετικά απλές χημικές διαδικασίες και η λειτουργία των νέων αυτών φωτοβολταϊκών στοιχείων υπό συνθήκες διάχυτου φωτός. Γενικά, ένα τέτοιο φωτοβολταϊκό στοιχείο αποτελείται από μία φωτοάνοδο (photoanode), ένα πορώδες υπόστρωμα από ημιαγώγιμο οξείδιο μετάλλου (metal oxide semiconducting film), μία χρωστική που χρησιμοποιείται ως φωτοευαισθητοποιητής (sensitizer), έναν ηλεκτρολύτη (electrolyte) και ένα αντιηλεκτρόδιο (counter electrode), το οποίο, συνήθως, επικαλύπτεται με ένα λεπτό στρώμα από πλατίνα (Pt). Η κύρια διεργασία που λαμβάνει μέρος σε ένα DSSC, μετά από την απορρόφηση φωτός, είναι μία διεπιφανειακή μεταφορά φορτίου (interfacial electron transfer IET) από την ηλεκτρονιακά διεγερμένη στάθμη της χρωστικής προς τη ζώνη αγωγιμότητας του ημιαγωγού. Η χρονική της διάρκεια είναι της τάξεως των μερικών εκατοντάδων fs και κατατάσσεται στα υπερταχέα φαινόμενα. Ο όρος που έχει επικρατήσει, για τη διεργασία αυτή στα DSSCs, είναι έκχυση ηλεκτρονίων (electron injection) και χρησιμοποιείται στην παρούσα διπλωματική εργασία. Η τεχνική της φασματοσκοπίας φθορισμού χρονικής ανάλυσης με παλμούς διάρκειας μερικών δεκάδων fs, αποτελεί μία από τις πιο αξιόπιστες και άμεσες τεχνικές για την καλύτερη δυνατή καταγραφή υπερταχέων φαινομένων, όπως η έκχυση ηλεκτρονίων. Σκοπός της παρούσας διπλωματικής εργασίας είναι η μελέτη της έκχυσης ηλεκτρονίων με τη χρήση δύο νέων οργανικών χρωστικών, της μορφής D-π-A, ως φωτοευαισθητοποιητές σε DSSCs με την τεχνική αυτή.Στο πρώτο κεφάλαιο πραγματοποιείται μία γενική επισκόπηση των βασικών αρχών που διέπουν τα φωτοβολταϊκά στοιχεία με ευαισθητοποίηση χρωστικής. Αρχικά, γίνεται αναφορά στα μέρη που αποτελούν ένα τέτοιο φωτοβολταϊκό στοιχείο και ακολούθως στα υλικά και στις διεργασίες οι οποίες συμμετέχουν σε ένα ολοκληρωμένο DSSC.Στο δεύτερο κεφάλαιο επιχειρείται, στο πρώτο σκέλος, μία γενική ανασκόπηση της θεωρίας του Markus για τη μεταφορά των ηλεκτρονίων (Markus Theory). Έπειτα, πραγματοποιείται μία αναλυτική επισκόπηση της δυναμικής και κινηματικής των διεργασιών που συντελούνται στα DSSCs. Συνεχίζοντας στο τρίτο κεφάλαιο, παρουσιάζονται πληροφορίες σχετικές με τα υποστρώματα και τις χρωστικές που χρησιμοποιούνται στα DSSCs. Το κεφάλαιο επικεντρώνεται στην περιγραφή των υποστρωμάτων TiO2 και ΖnO, τα οποία αποτελούν τα κύρια υποστρώματα που χρησιμοποιούνται στα DSSCs. Στο δεύτερο σκέλος του κεφαλαίου, πραγματοποιείται αναφορά στις ιδιότητες που οφείλουν να πληρούν οι χρωστικές, για τη χρήση τους στα DSSCs, καθώς και εκτενής ανασκόπηση των χρωστικών, οι οποίες έχουν χρησιμοποιηθεί, μέχρι σήμερα, ως φωτοευαισθητοποιητές. Στο τέταρτο κεφάλαιο παρουσιάζονται οι μηχανισμοί που συμμετέχουν κατά την αποδιέγερση ενός οργανικού μορίου και οι χρονικές κλίμακες, που αυτοί εμφανίζονται (διάγραμμα Jablonski). Επίσης, γίνεται αναφορά στις πληροφορίες που εξάγονται από τα φάσματα σταθερής κατάστασης (steady state spectra) και χρονικής ανάλυσης (time-resolved spectra), καθώς και η μεταξύ τους σύγκριση. Στο πέμπτο κεφάλαιο πραγματοποιείται μία αναλυτική περιγραφή της πειραματικής διάταξης, η οποία χρησιμοποιήθηκε για την εξαγωγή των πειραματικών δεδομένων. Τέλος, στα τελευταία δύο κεφάλαια (πέμπτο και έκτο) περιγράφεται, στο πρώτο, ο φωτοφυσικός χαρακτηρισμός των δύο νέων οργανικών χρωστικών, ΜΖ-173 και ΜΖ-175, της δομής D-π-Α, σε διάλυμα THF και σε στερεό υπόστρωμα TiO2 αντίστοιχα, το οποίο χρησιμοποιήθηκε ως το υπόστρωμα προσρόφησης των χρωστικών. Ακολούθως, μελετήθηκε η δυναμική και η απόδοση της έκχυσης των ηλεκτρονίων από τις χρωστικές αυτές προς το ημιαγώγιμο υπόστρωμα TiO2, με χρήση της τεχνικής της φασματοσκοπίας χρονικής ανάλυσης φθορισμού με παλμούς διάρκειας μερικών δεκάδων fs (femtosecond time resolved fluorescence spectroscopy). Ως δείγμα αναφοράς, για την εύρεση της απόδοσης της έκχυσης των ηλεκτρονίων στη ζώνη αγωγιμότητας του ημιαγωγού, χρησιμοποιήθηκε νανοκρυσταλλικό υπόστρωμα Al2O3. Τέλος, πραγματοποιήθηκε η μελέτη της δυναμικής της έκχυσης των ηλεκτρονίων με τη χρήση του μορίου CDCA, ως συνπροσροφητή στην επιφάνεια των υποστρωμάτων TiO2 και Al2O3, μαζί με χρωστική ΜΖ-173, σε διάφορες συγκεντρώσεις. Αυτή η μελέτη έγινε με σκοπό τη μείωση της συσσωμάτωσης των μορίων της χρωστικής, αφού το μόριο CDCA έχει την ιδιότητα, λόγω της δομής του, να κρατά σε απόσταση τα μόρια της χρωστικής. / Dye-sensitized solar cells (DSSCs) have attracted great scientific interest after the first demonstration of Grätzel and O’Regan in 1991. They were proposed as low cost alternatives to the conventional amorphous silicon solar cells. The key factors which led the scientific community to this direction are the simplicity of their fabrication procedures with mild chemical processes and their operation under ambient conditions of diffused light. Generally, a DSSC consists of a photoanode, a nanostructured metal oxide semiconducting film, a dye sensitizer, an electrolyte and a counter electrode which is usually coated with Pt. The fundamental process that takes place in a DSSC, after the absorption of a photon by the dye, is an interfacial electron transfer (IET) from the dye’s electronically excited state to the semiconductor’s conduction band (CB), taking place within a few hundred femtoseconds. The term which is generally used for this process in DSSCs is electron injection. Ultrafast fluorescence upconversion spectroscopy is one of the most precise and direct techniques for the study and interpretation of such phenomena. The main subject of this master thesis is the presentation of two novel synthesized organic dyes with D-π-A structure and their study as photosensitizers for DSSCs. It is focused on the photophycical properties of these two dyes in solution and on titanium dioxide (TiO2) substrate, which is used as the metal oxide semiconducting film, and especially on the dynamics of electron injection process from the dye’s excited state to the conduction band of the TiO2 with the aforementioned technique. Finally, the electron injection dynamics of one of dyes with coadsorption of co-adsorbers also investigated. This type of molecules can decrease the amount of aggregates penetrating among the dye molecules but on the same time they cause a decrease of the total amount of the adsorbed dye molecules.

Les toxines formeuses de pore (PFTs) sont des protéines exogènes responsables d’un grand nombre de maladies infectieuses qui perméabilisent les membranes cellulaires de leur hôte. La formation des pores ou l’introduction d’une enzyme dans le cytoplasme peut entrainer l’apparition de symptômes de maladies connues (l’anthrax, le botulisme) et, dans le pire des cas, la mort. Les mécanismes d’infection et de destruction des cellules infectées sont bien caractérisés. Toutefois, l’aspect dynamique des changements de conformation durant le processus de perméabilisation reste à découvrir pour la majorité des toxines formeuses de pore. Le but de cette thèse est d’étudier les mécanismes d’oligomérisation des PFTs, ainsi que la formation des pores à la membrane lipidique grâce à la spectroscopie de fluorescence. Nous avons choisi la toxine Cry1Aa, un bio pesticide produit par le bacille de Thuringe et qui a été rigoureusement caractérisé, en tant que modèle d’étude. La topologie de la Cry1Aa à l’état actif et inactif a pu être résolue grâce à l’utilisation d’une technique de spectroscopie de fluorescence, le FRET ou transfert d’énergie par résonance entre un fluorophore greffé au domaine formeur de pore (D1) et un accepteur non fluorescent (le DPA ou dipicrylamine) localisé dans la membrane et qui bouge selon le potentiel membranaire. Le courant électrique, ainsi que la fluorescence provenant de la bicouche lipidique membranaire horizontale ont été enregistrés simultanément. De cette manière, nous avons pu localiser toutes les boucles reliant les hélices de D1 avant et après la formation des pores. Dans la forme inactive de la toxine, toutes ces boucles se trouvent du côté interne de la bicouche lipidique, mais dans sa forme active l’épingle α3-α4 traverse du côté externe, alors que toutes les autres hélices demeurent du côté interne. Ces résultats suggèrent que α3-α4 forment le pore. Nous avons découvert que la toxine change significativement de conformation une fois qu’elle se trouve dans la bicouche lipidique, et que la Cry1Aa attaque la membrane lipidique de l’extérieur, mais en formant le pore de l’intérieur. Dans le but de caractériser la distribution de toxines à chaque extrémité de la bicouche, nous avons utilisé une technique de double FRET avec deux accepteurs ayant des vitesses de translocation différentes (le DPA et l’oxonol) dans la membrane lipidique. De cette manière, nous avons déterminé que la toxine était présente des deux côtés de la bicouche lipidique durant le processus de perméabilisation. La dynamique d’oligomérisation de la toxine dans une bicouche lipidique sans récepteurs a été étudiée avec une technique permettant le compte des sauts de fluorescence après le photoblanchiment des fluorophore liés aux sous unités composant un oligomère présent dans la bicouche lipidique supportée. Nous avons confirmé de cette manière que la protéine formait ultimement des tétramères, et que cet état résultait de la diffusion des monomères de toxine dans la bicouche et de leur assemblage subséquent. Enfin nous avons voulu étudier le « gating » de la colicine Ia, provenant de la bactérie E.Coli, dans le but d’observer les mouvements que font deux positions supposées traverser la bicouche lipidique selon le voltage imposé aux bornes de la bicouche. Nos résultats préliminaires nous permettent d’observer un mouvement partiel (et non total) de ces positions, tel que le suggèrent les études de conductances du canal. / Pore forming toxins (PFTs) are exogenous often pathogenic proteins that permeabilize the host membrane. Permeabilization or subsequent introduction of an enzyme leads to health disorders and sometimes death. Although the fundamental infection and destruction mechanisms are known, the underlying molecular basis and their link to the structural information remains undetermined for many pore forming toxins. The purpose of this thesis was to study the mechanisms of oligomerization on the membrane and pore formation of PFTs using fluorescence spectroscopy in planar lipid bilayer. We chose Cry1Aa as the most intensively studied member of Bacillus thuringiensis’s toxins. In order to probe the topology both in inactive and active congformation, we used Förster resonance energy transfer (FRET) between a fluorophore site-directedly attached to different positions in the pore forming domain (D1) of Cry1Aa toxin and an acceptor compound dipicrylamine (DPA) in the membrane, which moves in response to the membrane potential. Electrical current and fluorescence emission from planar lipid bilayers in a horizontal configuration were simultaneously recorded. We probed all loops between the seven α helices of D1. All of them were located on the inner leaflet of the bilayer prior to pore formation. In the active form, the α3-α4 hairpin were found to translocate back to the outer leaflet of the bilayer, whereas all other positions remained in the inner leaflet, suggesting that α3-α4 are the pore lining helices. The toxins undergo significant conformational changes once they enter the host membrane, and we found Cry1Aa to attack from the exterior but translocate to the interior. To estimate the distribution of the toxins on either side of the membrane, we used the double-FRET technique. Here, two different acceptors (DPA and oxonol) with different dynamics (time constants) allowed us to determine that approximately equal amounts of the toxin were present on either leaflet during the permeabilization process. We also studied the oligomerization mechanism of Cry1Aa toxins inserted into supported lipid bilayers using a single subunit counting technique based on the step-wise photodestruction (bleaching) of the attached fluorophores. This system allowed determining the number of subunits composing each oligomer. We found that oligomerization is a highly dynamic process which occurs after insertion into the bilayer by lateral diffusion. The final (likely the pore forming) entity of the toxin is tetrameric. Finally, we used the same FRET approach to investigate the gating process of two positions of the pore forming domain of colicin Ia, an antibiotic toxin produced by E. coli. These positions were suspected to translocate reversibly from the outer to the inner leaflet during the gating process. In preliminary results, we found that these positions are moving between the two leaflets of the bilayer during pore formation.

This thesis is an investigation of novel mono-ADP-ribosylating toxins. In the current data-rich era, making the leap from sequence data to knowledge is a task that requires an elegant bioinformatics toolset to pinpoint questions. A strategy to expand important protein-family knowledge is required, particularly in cases in which primary sequence identity is low but structural conservation is high. For example, the mono-ADP-ribosylating toxins fit these criteria and several approaches have been used to accelerate the discovery of new family members. A newly developed tactic for detecting remote members of this family -- in which fold recognition dominates -- reduces reliance on sequence similarity and advances us toward a true structure-based protein-family expansion methodology. Chelt, a cholera-like toxin from Vibrio cholerae, and Certhrax, an anthrax-like toxin from Bacillus cereus, are among six new bacterial protein toxins identified and characterized using in silico and cell-based techniques. Medically relevant toxins from Mycobacterium avium and Enterococcus faecalis were also uncovered. Agriculturally relevant toxins were found in Photorhabdus luminescens and Vibrio splendidus. Computer software was used to build models and analyze each new toxin to understand features including: structure, secretion, cell entry, activation, NAD+ substrate binding, intracellular target binding and the reaction mechanism. Yeast-based activity tests have since confirmed activity. Vibrio cholerae produces cholix – a potent protein toxin of particular interest that has diphthamide-specific ADP-ribosyltransferase activity against eukaryotic elongation factor 2. Here we present a 2.1Å apo X-ray structure as well as a 1.8Å X-ray structure of cholix in complex with its natural substrate, nicotinamide adenine dinucleotide (NAD+). Hallmark catalytic residues were substituted and analyzed both for NAD+ binding and ADP-ribosyltransferase activity using a fluorescence-based assay. These new toxins serve as a reference for ongoing inhibitor development for this important class of virulence factors. In addition to using toxins as targets for antivirulence compounds, they can be used to make vaccines and new cancer therapies. / Natural Sciences and Engineering Research Council (CGS-D), Canadian Institutes of Health Research, Cystic Fibrosis Canada, Human Frontier Science Program, Ontario government (OGSST), University of Guelph (Graduate Research Scholarship)

The objective of this research was to develop fluorescence-based tools that are suitable for performing rapid, accurate and direct characterization of natural organic matter (NOM) and colloidal/particulate substances present in natural water. Most available characterization methods are neither suitable for characterizing all the major NOM fractions such as protein-, humic acid-, fulvic acid- and polysaccharide-like substances as well as colloidal/particulate matter present in natural water nor are they suitable for rapid analyses. The individual and combined contributions of these NOM fractions and colloidal/particulate matter present in natural water contribute to membrane fouling, disinfection by-products formation and undesirable biological growth in drinking water treatment processes and distribution systems. The novel techniques developed in this research therefore, provide an avenue for improved understanding of these negative effects and proactive implementation of control and/or optimization strategies. The fluorescence excitation-emission matrix (EEM) method was used for characterization of NOM and colloidal/particulate matter present in water. Unlike most NOM and colloidal/particulate matter characterization techniques, this method can provide fast and consistent analyses with high instrumental sensitivity. The feasibility of using this method for monitoring NOM at very low concentration levels was also demonstrated with an emphasis on optimizing the instrument parameters necessary to obtain reproducible fluorescence signals. Partial least squares regression (PLS) was used to develop calibration models by correlating the fluorescence EEM intensities of water samples that contained surrogate NOM fractions with their corresponding dissolved organic carbon (DOC) concentrations. These fluorescence-based calibration models were found to be suitable for identifying/monitoring the extent of the relative changes that occur in different NOM fractions and the interactions between polysaccharide- and protein-like NOM in water treatment processes and distribution systems. Principal component analysis (PCA) of fluorescence EEMs was identified as a viable tool for monitoring the performance of biological filtration as a pre-treatment step, as well as ultrafiltration (UF) and nanofiltration (NF) membrane systems. The principal components (PCs) extracted in this approach were related to the major membrane foulant groups such as humic substances (HS), protein-like and colloidal/particulate matter in natural water. The PC score plots generated using the fluorescence EEMs obtained after just one hour of UF or NF operation could be related to high fouling events likely caused by elevated levels of colloidal/particulate-like material in the biofilter effluents. This fluorescence EEM-based PCA approach was sensitive enough to be used at low organic carbon levels present in NF permeate and has potential as an early detection method to identify high fouling events, allowing appropriate operational countermeasures to be taken. This fluorescence EEM-based PCA approach was also used to extract information relevant to reversible and irreversible membrane fouling behaviour in a bench-scale flat sheet cross flow UF process consisting of cycles of permeation and back-washing. PC score-based analysis revealed that colloidal/particulate matter mostly contributed to reversible fouling, while HS and protein-like matter were largely responsible for irreversible fouling. This method therefore has potential for monitoring modes of membrane fouling in drinking water treatment applications. The above approach was further improved by utilizing the evolution of the PC scores over the filtration time and relating these to membrane fouling by the use of PC scores??? balanced-based differential equations. Using these equations the proposed fluorescence-based modeling approach was capable of forecasting UF fouling behaviours with good accuracy based solely on fluorescence data obtained at time = 15 min from the initiation of the filtration process. In addition, this approach was tested experimentally as a basis for optimization by modifying the UF back-washing times with the objective of minimizing energy consumption and maximizing water production. Preliminary optimization results demonstrated the potential of this approach to reduce power consumption by significant percentages. This approach was also useful for identifying the fouling components of the NOM that were contributing to reversible and irreversible membrane fouling. Grand River water (Southwestern Ontario, Canada) was used as the natural water source for developing the techniques presented in this thesis. Future research focusing on testing these methods for monitoring of membrane fouling and treatment processes in large-scale drinking water treatment facilities that experience different sources of raw water would be useful for identifying the limitation of these techniques and areas for improvements.

Thesis (Ph.D.); Submitted to the University of California at Berkeley, Berkeley, CA (US); 1 Sep 2003. / Published through the Information Bridge: DOE Scientific and Technical Information. "LBNL--55023" Li, Liang-shi. USDOE Director. Office of Science. Office of Basic Energy Sciences (US) 09/01/2003. Report is also available in paper and microfiche from NTIS.

La protéine UHRF1 est impliquée dans le maintien et la transmission des modifications épigénétiques. Lors du processus de réplication, elle recrute la méthyltransférase de l’ADN Dnmt1 au niveau des sites CpG hémi-méthylés via son domaine SRA (SET and RING Associated), favorisant la duplication des profils de méthylation. La structure tridimensionnelle du complexe SRA/ADN révèle que la protéine induit un basculement de la méthylcytosine qui permet un ancrage spécifique de la protéine sur les sites hémim éthylés, facilitant le recrutement de la Dnmt1 au niveau de ces positions stratégiques. Dans ce contexte, notre projet vise à comprendre les mécanismes d’interaction du domaine SRA de UHRF1 avec l’ADN hémi-méthylé. Des oligonucléotides doubles brins ont été marqués à la 2-aminopurine, un analogue nucléosidique fluorescent sensible à l’environnement, à différentes positions au voisinage d’un unique site de reconnaissance CpG hémi-méthylé. Les mesures de spectroscopie de fluorescence à l’état stationnaire et résolues en temps de ces duplexes liés au domaine SRA nous ont permis de caractériser de manière site spécifique les changements conformationnels induits par la liaison du domaine SRA. En accord avec la structure tridimensionnelle du complexe SRA/ADN, nos données suggèrent que le domaine SRA est capable de basculer la méthylcytosine tout en préservant la structure des autres bases dans le duplexe. Le domaine SRA semble se lier selon le même mécanisme aux duplexes hémi-méthylés, bi-méthylés et non-méthylés. La protéine UHRF1 jouerait ainsi un rôle de “lecteur“ capable de scanner la séquence d’ADN à la recherche de sites hémi-méthylés. / The UHRF1 protein plays a key role in the maintenance and transmission of epigenetic modifications. Duringthe replication process, it recruits the DNA methyltransferase Dnmt1 to hemi-methylated CpG sites via itsSRA (SET and RING Associated) domain, promoting the duplication of the methylation profiles. Thetridimensional structure of the SRA/DNA complex revealed that the protein induces a base-flipping of themethylcytosine that enables a specific anchoring of the protein to hemi-methylated sites facilitating therecruitment of Dnmt1 to this strategic position. In this context, our project was aimed to further understand themechanism of interaction of the SRA domain with hemi-methylated DNA. To this end, oligonucleotideduplexes were labeled by 2-aminopurine, a fluorescent nucleoside analogue sensitive to environment, atvarious positions close to the single hemi-methylated CpG recognition site. Steady-state and time-resolvedfluorescence spectroscopy measurements of these duplexes bound to the SRA domain enabled us to sitespecificallycharacterize the conformational changes induced by the binding of this domain. In agreement withthe tridimensional structure of the SRA/DNA complex, our data suggest that the SRA domain is able to flip themethylcytosine while preserving the structure of the surrounding bases in the duplex. The SRA domain wasshown to bind with the same mechanism to hemi-methylated, fully-methylated and non-methylated duplexes.Our data suggest the UHRF1 protein plays a role of “reader” that scans the DNA sequence for hemimethylatedsites.