Soit Σ une surface compacte connexe orientée avec une seule composante du bord. Notons par M le groupe d'homéotopie de Σ. En considérant l'action de M sur le groupe fondamental de Σ, il est possible de définir différentes filtrations de M ainsi que des homomorphismes sur chaque terme de ces filtrations. Le but de cette thèse est double. En premier lieu, nous étudions deux filtrations de M : la " filtration de Johnson-Levine " introduite par Levine et la " filtration de Johnson alternative " introduite recemment par Habiro et Massuyeau. Les définitions de ces deux filtrations prennent en compte un corps en anses bordé par la surface. Nous nous référons à ces filtrations comme " filtrations de type Johnson " et les homomorphismes correspondants sont appelés " homomorphismes de type Johnson " par leur analogie avec la filtration de Johnson originale et les homomorphismes de Johnson usuels. Nous donnons une comparaison de la filtration de Johnson avec la filtration de Johnson-Levine au niveau du monoïde des cobordismes d'homologie de Σ. Nous donnons également une comparaison entre la filtration de Johnson alternative, la filtration Johnson-Levine et la filtration de Johnson au niveau du groupe d'homéotopie. Deuxièmement, nous étudions la relation entre les " homomorphismes de type Johnson" et l'extension fonctorielle de l'invariant perturbatif universel des variétés de dimension trois (l'invariant de Le-Murakami-Ohtsuki ou invariant LMO). Cette extension fonctorielle s'appelle le foncteur LMO et il prend ses valeurs dans une catégorie de diagrammes. Nous démontrons que les "homomorphismes de type Johnson " peuvent être lus dans la réduction arborée du foncteur LMO. En particulier, cela fournit une nouvelle grille de lecture de la réduction arborée du foncteur LMO. / Let Σ be a compact oriented surface with one boundary component and let M denote the mapping class group of Σ. By considering the action of M on the fundamental group of Σ it is possible to define different filtrations of M together with some homomorphisms on each term of the filtrations. The aim of this thesis is twofold. First, we study two filtrations of M : the « Johnson-Levine filtration » introduced by Levine and « the alternative Johsnon filtration » introduced recently by Habiro and Massuyeau. The definition of both filtrations involve a handlebody bounded by Σ. We refer to these filtrations as ≪ Johnson-type filtrations » and the corresponding homomorphisms have referred to as « Johnson-type homomorphisms » by their analogy with the original Johnson filtration and the usual Johnson homomorphisms. We provide a comparison of the Johnson filtration with the Johnson-Levine filtration at the level of the monoid of homology cobordisms of Σ. We also provide a comparison of the alternative Johnson filtration with the Johnson-Levine filtration and the Johnson filtration at the level of the mapping class group. Secondly, we study the relationship between the « Johnson-type homomorphisms » and the functorial extension of the universal perturbative invariant of 3-manifolds (the Le-Murakami-Ohtsuki invariant or LMO invariant). This functorial extension is calling the LMO functor and it takes values in a category of diagrams. We prove that the « Johnson-type homomorphisms » is in the tree reduction of the LMO functor. In particular, this provides a new reading grid of the tree reduction of the LMO functor.

The plant homeodomain (PHD) is a protein domain of ~45�100 residues characterised by a Cys4-His-Cys3 zinc-binding motif. When we commenced our study of the PHD in 2000, it was clear that the domain was commonly found in proteins involved in transcription. Sequence alignments indicate that while the cysteines, histidine and a few other key residues are strictly conserved, the rest of the domain varies greatly in terms of both amino acid composition and length. However, no structural information was available on the PHD and little was known about its function. We were therefore interested in determining the structure of a PHD in the hope that this might shed some light on its function and molecular mechanism of action. Our work began with the structure determination of a representative PHD, Mi2b-P2, and this work is presented in Chapter 3. Through comparison of this structure with the two other PHD structures that were determined during the course of our work, it became clear that PHDs adopt a well-defined globular fold with a superimposable core region. In addition, PHDs contain two loop regions (termed L1 and L3) that display increased flexibility and overlay less well between the three PHD structures available. These L1 and L3 regions correspond to variable regions identified earlier in PHD sequence alignments, indicating that L1 and L3 are probably not crucial for the PHD fold, but are instead likely to be responsible for imparting function(s) to the PHD. Indeed, numerous recent functional studies of PHDs from different proteins have since demonstrated their ability in binding a range of other proteins. In order to ascertain whether or not L1 and L3 were in fact dispensable for folding, we made extensive mutations (including both insertions and substitutions) in the loop regions of Mi2b-P2 and showed that the structure was maintained. We then went on to illustrate that a new function could be imparted to Mi2b-P2 by inserting a five-residue CtBP-binding motif into the L1 region and showed this chimera could fold and bind CtBP. Having established that the PHD could adopt a new binding function, we next sought to use combinatorial methods to introduce other novel functions into the PHD scaffold. Phage display was selected for this purpose, because it is a well-established technique and has been used successfully to engineer zinc-binding domains by other researchers. However, in order to establish this technique in our laboratory, we first chose a control system in which two partner proteins were already known to interact in vitro. We chose the protein complex formed between the transcriptional regulators LMO2 and ldb1 as a test case. We have examined this interaction in detail in our laboratory, and determined its three-dimensional structure. Furthermore, inappropriate formation of this complex is implicated in the onset of T-cell acute lymphoblastic leukemia. We therefore sought to use phage display to engineer ldb1 mimics that could potentially compete against wild-type ldb1 for LMO2, and this work is described in Chapter 4. Using a phage library containing ~3 x 10 7 variants of the LMO2-binding region of ldb1, we isolated mutants that were able to interact with LMO2 with higher affinity and specificity than wild-type ldb1. These ldb1 mutants represent a first step towards finding potential therapeutics for treating LMO-associated diseases. Having established phage display in our laboratory, we went on to search for PHD mutants that could bind selected target proteins. This work is described in Chapter 5. We created three PHD libraries with eight randomized residues in each of L1, L3 or in both loops of the PHD. These PHD libraries were then screened against four target proteins. After four rounds of selection, we were able to isolate a PHD mutant (dubbed L13-FH6) that could bind our test protein Fli-ets. This result demonstrates that a novel function can be imparted to the PHD using combinatorial methods and opens the way for further work in applying the PHD scaffold to other protein design work. In summary, the work detailed in Chapters 3 and 5 demonstrates that the PHD possesses many of the properties that are desirable for a protein scaffold for molecular recognition, including small size, stability, and a well-characterised structure. Moreover, the PHD motif possesses two loops (L1 and L3) of substantial size that can be remodeled for target binding. This may lead to an enhancement of binding affinities and specificities over other small scaffolds that have only one variable loop. In light of the fact that PHDs are mainly found in nuclear proteins, it is reasonable to expect that engineered PHDs could be expressed and function in an intracellular environment, unlike many other scaffolds that can only function in an oxidizing environment. Therefore, our results together with other currently available genomic and functional information indicate PHD is an excellent candidate for a scaffold that could be used to modify cellular processes. Appendices 1 and 2 describe completed bodies of work on unrelated projects that I have carried out during the course of my PhD candidature. The first comprises the invention and application of DNA sequences that contain all N-base sequences in the minimum possible length. This work is presented as a reprint of our recently published paper in Nucleic Acids Research. The second Appendix describes our structural analysis of an antifreeze protein from the shorthorn sculpin, a fish that lives in the Arctic and Antarctic oceans. This work is presented as a manuscript that is currently under review at the Journal of the American Chemical Society.

The plant homeodomain (PHD) is a protein domain of ~45�100 residues characterised by a Cys4-His-Cys3 zinc-binding motif. When we commenced our study of the PHD in 2000, it was clear that the domain was commonly found in proteins involved in transcription. Sequence alignments indicate that while the cysteines, histidine and a few other key residues are strictly conserved, the rest of the domain varies greatly in terms of both amino acid composition and length. However, no structural information was available on the PHD and little was known about its function. We were therefore interested in determining the structure of a PHD in the hope that this might shed some light on its function and molecular mechanism of action. Our work began with the structure determination of a representative PHD, Mi2b-P2, and this work is presented in Chapter 3. Through comparison of this structure with the two other PHD structures that were determined during the course of our work, it became clear that PHDs adopt a well-defined globular fold with a superimposable core region. In addition, PHDs contain two loop regions (termed L1 and L3) that display increased flexibility and overlay less well between the three PHD structures available. These L1 and L3 regions correspond to variable regions identified earlier in PHD sequence alignments, indicating that L1 and L3 are probably not crucial for the PHD fold, but are instead likely to be responsible for imparting function(s) to the PHD. Indeed, numerous recent functional studies of PHDs from different proteins have since demonstrated their ability in binding a range of other proteins. In order to ascertain whether or not L1 and L3 were in fact dispensable for folding, we made extensive mutations (including both insertions and substitutions) in the loop regions of Mi2b-P2 and showed that the structure was maintained. We then went on to illustrate that a new function could be imparted to Mi2b-P2 by inserting a five-residue CtBP-binding motif into the L1 region and showed this chimera could fold and bind CtBP. Having established that the PHD could adopt a new binding function, we next sought to use combinatorial methods to introduce other novel functions into the PHD scaffold. Phage display was selected for this purpose, because it is a well-established technique and has been used successfully to engineer zinc-binding domains by other researchers. However, in order to establish this technique in our laboratory, we first chose a control system in which two partner proteins were already known to interact in vitro. We chose the protein complex formed between the transcriptional regulators LMO2 and ldb1 as a test case. We have examined this interaction in detail in our laboratory, and determined its three-dimensional structure. Furthermore, inappropriate formation of this complex is implicated in the onset of T-cell acute lymphoblastic leukemia. We therefore sought to use phage display to engineer ldb1 mimics that could potentially compete against wild-type ldb1 for LMO2, and this work is described in Chapter 4. Using a phage library containing ~3 x 10 7 variants of the LMO2-binding region of ldb1, we isolated mutants that were able to interact with LMO2 with higher affinity and specificity than wild-type ldb1. These ldb1 mutants represent a first step towards finding potential therapeutics for treating LMO-associated diseases. Having established phage display in our laboratory, we went on to search for PHD mutants that could bind selected target proteins. This work is described in Chapter 5. We created three PHD libraries with eight randomized residues in each of L1, L3 or in both loops of the PHD. These PHD libraries were then screened against four target proteins. After four rounds of selection, we were able to isolate a PHD mutant (dubbed L13-FH6) that could bind our test protein Fli-ets. This result demonstrates that a novel function can be imparted to the PHD using combinatorial methods and opens the way for further work in applying the PHD scaffold to other protein design work. In summary, the work detailed in Chapters 3 and 5 demonstrates that the PHD possesses many of the properties that are desirable for a protein scaffold for molecular recognition, including small size, stability, and a well-characterised structure. Moreover, the PHD motif possesses two loops (L1 and L3) of substantial size that can be remodeled for target binding. This may lead to an enhancement of binding affinities and specificities over other small scaffolds that have only one variable loop. In light of the fact that PHDs are mainly found in nuclear proteins, it is reasonable to expect that engineered PHDs could be expressed and function in an intracellular environment, unlike many other scaffolds that can only function in an oxidizing environment. Therefore, our results together with other currently available genomic and functional information indicate PHD is an excellent candidate for a scaffold that could be used to modify cellular processes. Appendices 1 and 2 describe completed bodies of work on unrelated projects that I have carried out during the course of my PhD candidature. The first comprises the invention and application of DNA sequences that contain all N-base sequences in the minimum possible length. This work is presented as a reprint of our recently published paper in Nucleic Acids Research. The second Appendix describes our structural analysis of an antifreeze protein from the shorthorn sculpin, a fish that lives in the Arctic and Antarctic oceans. This work is presented as a manuscript that is currently under review at the Journal of the American Chemical Society.

Les batteries lithium-ion (Li-ion) sont privilégiées dans de nombreuses applications comme solution de stockage de l’énergie. Le composé Li4Ti5O12 (LTO) est une alternative au graphite qui demeure majoritairement utilisé comme matériau d’électrode négative dans les batteries Li-ion. Pour de potentielles applications à haute température, il est nécessaire d’étudier les couches interfaciales qui se forment dans ces conditions en surface des électrodes LTO. En effet, la formation de telles couches est un phénomène commun aux batteries Li-ion, dont la maîtrise revêt un rôle fondamental pour l’obtention de bonnes performances électrochimiques. La surface des électrodes LTO a pour cela été principalement caractérisée par Spectroscopie Photoélectronique à rayonnement X (XPS) et des analyses complémentaires ont aussi été ponctuellement menées en microscopie Auger à balayage (Scanning Auger Microscopy : SAM) pour l’acquisition de cartographies élémentaires et en spectrométrie de masse d’ions secondaires à temps de vol (Time-of-Flight Secondary Ions Spectrometry : ToF-SIMS) pour établir des profils de concentration élémentaires et moléculaires en profondeur. Ces résultats ont été systématiquement confrontés aux données électrochimiques. L’influence de différents paramètres sur les propriétés de la couche interfaciale formée en cyclage face au lithium a été évaluée. Une comparaison des couches interfaciales formées au premier cycle à température ambiante, 60 °C et 85 °C a ainsi montré qu’une température de cyclage plus élevée favorise la formation d’une couche interfaciale plus épaisse. L’utilisation d’un électrolyte contenant l’additif VC accélère la formation d’une SEI plus épaisse dès le premier cycle, moins sujette au phénomène de dissolution au cours de la délithiation et susceptible d'améliorer la rétention de capacité en longs cyclages. La substitution du sel de lithium LiPF6 par le sel LiTFSI entraîne la formation d’une couche plus fine, ce qui est principalement dû à une quantité de LiF déposée plus faible. De manière similaire, la substitution des solvants EC:DMC par les solvants PC:EMC, induit la formation d’une couche plus fine, du fait d’une quantité moins importante de LiF déposée. Par ailleurs, plus la surface spécifique de l’additif carboné entrant dans la composition des électrodes est élevée, plus la part de LiF parmi les espèces de la couche interfaciale formée est élevée, sans que cela n’influence son épaisseur. Puis, le comportement des interfaces électrode/électrolyte dans une batterie LiMn2O4/Li4Ti5O12 a finalement été étudié. Une couche interfaciale se forme en surface des deux électrodes. Néanmoins la couche formée sur l’électrode positive est plus fine que celle formée sur l’électrode négative. Leur composition est similaire, à l’exception du composé MnF2 uniquement détecté sur l’électrode négative et provenant d’un phénomène de dissolution du matériau LiMn2O4. Un prolongement de ce travail peut être envisagé concernant des électrodes à base de particules LTO avec différents coatings. De plus, une synergie systématique entre les trois techniques utilisées dans cette thèse pourra être encouragée. / Lithium-ion (Li-ion) batteries have been considered as the solution of choice for energy storage in numerous applications. Li4Ti5O12 (LTO) compound is an alternative to the widely used graphite, as a negative electrode material. For potential high temperature applications, the study of interfacial layers formed on top of LTO electrodes in such conditions is a necessary step. The formation of such surface layers is commonly observed in lithium-ion batteries and their properties are critical for maintaining good batteries performances. Therefore, LTO electrodes surfaces were mainly analyzed by X-ray Photoelectron Spectroscopy (XPS) and complementary measurements were performed by Scanning Auger Microscopy (SAM) for the acquisition of elemental mappings and by Time-of-Flight Secondary Ions Spectrometry (ToF-SIMS) for depth profile analysis. Surface analysis results were systematically linked to electrochemical data. The influence of several parameters was investigated for LTO electrodes cycled versus lithium. The comparison of surface layers formed during the first cycle at room temperature, 60 °C and 85 °C showed that higher cycling temperatures induce the formation of a thicker layer. The use of a VC-containing electrolyte accelerates the formation of a thicker layer since the first cycle, less prone to dissolution during delithiation and susceptible to enhance the capacity retention for long cycling. Substitution of LiPF6 lithium salt by LiTFSI leads to the formation of thinner layer, which is mainly due to a lower amount of deposited LiF. Similar results are obtained for the substitution of EC:DMC solvants by PC:EMC. Furthermore, the higher the specific surface of the electrode carbonaceous additive is, the higher the share of LiF in the interfacial layer composition is, even if its thickness remains similar. Finally, the behavior of electrode/electrolyte interfaces was studied in a LiMn2O4 /Li4Ti5O12 full cell. Interfacial layers are formed on the surface of both electrodes. Nevertheless, the layer on the positive electrode is thinner than the one on the negative electrode. Their composition are similar except for MnF2 compound, coming from LiMn2O4 dissolution at the positive electrode, which is only detected on the negative electrode. This work could be continued with the study of electrodes based on coated LTO particles. Moreover, a greater synergy between three characterization techniques used in this work could be promoted.

The production of adult blood initiates from the haematopoietic stem cell (HSC). This clinically important cell has the capacity to maintain all blood lineages throughout the lifetime of an organism. HSCs emerge de novo from the haemogenic endothelium in the ventral wall of the embryonic dorsal aorta, from where they go on to seed adult sites of haematopoiesis. We have shown that Lmo4a is required for the emergence of HSCs in the zebrafish, and go on to demonstrate that Lmo4a regulates expression of the critical transcription factor, gata2a. Strikingly, both over- and under-expression of gata2a in the dorsal aorta severely diminishes HSC production. The LIM-only domain protein Lmo4 has previously been shown to interact with the known haematopoietic regulator, Ldb1. Together with our collaborators, we have identified novel binding partners of Lmo4 in mouse erythroleukaemic cells. Our functional analysis shows that many of these partners are also necessary for HSC emergence, thus revealing several new potential regulators of HSC formation. Given that these proteins were identified in an in vitro model of definitive erythropoiesis, it is remarkable that they also appear to act together in vivo at the level of HSC formation, and our data suggests that a transcriptional complex containing Lmo4 and these partners may directly repress gata2a. The related protein Lmo2 is also known to bind Ldb1. Together with Scl, Lmo2 is a master regulator of the haemangioblast programme. We have been utilising this activity, together with recent structural studies, to identify functionally important residues in the Lmo2 molecule. As a cell’s transcriptional programme drives both normal and pathological development, and misexpression of both Lmo2 and Lmo4 is involved in a variety of oncogenic states, the work presented in this thesis is likely to inform efforts to develop therapeutically relevant reagents.

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第21545号 / 理博第4452号 / 新制||理||1639(附属図書館) / 京都大学大学院理学研究科数学・数理解析専攻 / (主査)教授 大槻 知忠, 教授 向井 茂, 教授 小野 薫 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

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