La chromatine sert de support à de multiples processus biologiques, cependant son organisation spatiale diffère fortement selon l'échelle considérée. L'expression des gènes est ainsi coordonnée par des éléments régulateurs dispersés dans le génome mais capables d'interagir entre eux. Chez les métazoaires, des expériences de capture de conformation de chromosome (3C) combinées au séquençage haut-débit (Hi-C) ont permis la découverte de domaines d'association topologique (TAD), à l'échelle de la mégabase. Puisque la résolution du Hi-C reste limitée, nous avons utilisé la 3C-qPCR pour explorer, dans des cellules souches embryonnaires murines, la dynamique chromatinienne à l'intérieur de ces domaines ainsi qu'à leurs bordures. Nous identifions ainsi une modulation des fréquences de contacts, sur quelques centaines de kilobases. Cette modulation est plus ou moins importante en fonction du contenu en gènes des domaines, mais elle semble néanmoins universelle. Des modèles dérivés de la physique des polymères permettent de décrire cette modulation sous la forme d'une hélice statistique, que la chromatine adopterait en moyenne et en l'absence d'interactions spécifiques, à l'intérieur des TAD. Cette hélice reflète certaines contraintes que la chromatine subit à l'échelle supranucléosomale. Elle est très affectée par les bordures, qui bloquent la modulation, mais elle l'est beaucoup moins par le contenu en histone de liaison H1. Par ailleurs, grâce à des résultats de Hi-C à haute résolution, nous montrons que la modulation observée chez les souris n'est pas retrouvée chez la drosophile, où les caractéristiques des TAD semblent avant tout liées au paysage épigénétique local. Pour ces deux organismes, la dynamique chromatinienne à l'intérieur des domaines est donc sous le contrôle de phénomènes différents / The chromatin hosts various biological processes. However, its organization differs considerably depending on the scale. For example, gene expression is coordinated by regulatory elements that are dispersed in the genome but that are able to interact within the tridimensional space of the nucleus. In the Metazoa, chromosome conformation capture (3C) assays combined with high-throughput sequencing (Hi-C) uncovered the existence of topologically associating domains (TADs), at the mégabase scale. Due to the limited resolution of Hi-C, we used the 3C-qPCR method to explore, in murine embryonic stem cells, the chromatin dynamics inside TADs as well as at their borders. We found that contact frequencies undergo a periodic modulation over large genomic distances (few hundred kilobases). This modulation is weaker in gene-deserts than in gene-containing domains but it seems nevertheless to be universal. Using models derived from polymer physics, we show that this modulation can be understood as a fundamental helix shape that chromatin tends to adopt statistically, when no strong locus-specific interaction takes place, within the TADs. This statistical helix reflects some constraints that the chromatin undergoes at the supranucleosomal scale. It is affected by TADs borders, which disrupt the modulation, but linker histone H1 depletion only leads to subtle changes in the helix characteristics. Furthermore, using high-resolution Hi-C data, we found that chromatin dynamics is unconstrained in Drosophila where it seems mainly linked to the local epigenetics landscape. Therefore, distinct genome organization principles govern chromatin dynamics within mouse and Drosophila topologically associating domains.

Leung Ka-Kit. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2002. / Includes bibliographical references (leaves 129-131). / Abstracts in English and Chinese. / Abstract --- p.1 / Chapter CHAPTER 1. --- introduction --- p.14 / Chapter 1.1 --- Preamble --- p.14 / Chapter 1.2 --- Biological background --- p.14 / Chapter CHAPTER 2. --- previous related work --- p.18 / Chapter 2.1 --- Protein functionality analysis --- p.18 / Chapter 2.1.1 --- Analysis from primary structure --- p.18 / Chapter 2.1.2 --- Analysis from tertiary structure --- p.20 / Chapter 2.2 --- Secondary structure prediction --- p.21 / Chapter 2.3 --- Motivation - Challenges from protein complexity --- p.22 / Chapter CHAPTER 3. --- mathematical representations for protein properties and sequence alignment --- p.24 / Chapter 3.1 --- Secondary structure sequence model --- p.24 / Chapter 3.2 --- Substitution matrix --- p.26 / Chapter 3.3 --- Gap --- p.26 / Chapter 3.4 --- Similarity measurement --- p.27 / Chapter 3.5 --- Geometric Model for Protein --- p.28 / Chapter CHAPTER 4. --- overall system design --- p.30 / Chapter 4.1 --- System architecture and design --- p.30 / Chapter 4.2 --- System environment --- p.32 / Chapter 4.3 --- Experimental data --- p.32 / Chapter CHAPTER 5. --- adaptive dynamic programming (adp)- general global alignment consideration --- p.35 / Chapter 5.1 --- t-triangles cutting --- p.35 / Chapter 5.1.1 --- Theoretical time and memory requirements of ADP with z-triangles cutting --- p.43 / Chapter 5.1.1.1 --- Study of parameters affecting h in case 1 --- p.44 / Chapter 5.1.1.2 --- Study of parameters affecting h in case 2 --- p.45 / Chapter 5.1.2 --- Experimental results of ADP with z-triangles cutting --- p.46 / Chapter 5.2 --- Constructing the path matrix by expansion --- p.51 / Chapter 5.2.1 --- Time and memory requirements of EXPAND --- p.57 / Chapter 5.2.2 --- Experimental results and discussions --- p.58 / Chapter CHAPTER 6. --- adp - global alignment of sequences with consecutive repeated characters --- p.65 / Chapter 6.1 --- Estimation of similarity upper bound (Ba) --- p.65 / Chapter 6.1.1 --- Sequence composition (SC) consideration --- p.65 / Chapter 6.1.2 --- Implementation of SC --- p.67 / Chapter 6.1.3 --- Experimental results --- p.69 / Chapter 6.1.4 --- Overall trend of change of structures (OTCS) --- p.74 / Chapter 6.1.5 --- Uninformed search --- p.76 / Chapter 6.2 --- Short-cut --- p.80 / Chapter 6.2.1 --- Time and memory requirements --- p.86 / Chapter 6.2.2 --- Experimental results and discussions --- p.86 / Chapter CHAPTER 7. --- ga based topology discovery --- p.87 / Chapter 7.1 --- Chromosome encoding --- p.87 / Chapter 7.2 --- Non-sequential order penalty --- p.88 / Chapter 7.3 --- Fitness function --- p.88 / Chapter 7.4 --- Genetic operators --- p.88 / Chapter 7.4.1 --- Hop operator --- p.89 / Chapter 7.4.2 --- Inverse operator --- p.89 / Chapter 7.4.3 --- Shift operator --- p.90 / Chapter 7.4.4 --- Selection pressure --- p.90 / Chapter 7.5 --- Selection of progeny --- p.91 / Chapter 7.6 --- Implementation --- p.91 / Chapter 7.6.1 --- Size of population and generation --- p.91 / Chapter 7.6.2 --- Parallelization --- p.91 / Chapter 7.6.3 --- Crowding Handling --- p.92 / Chapter 7.6.4 --- Selection of progeny --- p.92 / Chapter 7.7 --- Results of alignment with GA exploration on topological order --- p.93 / Chapter CHAPTER 8. --- FILTERING OF FALSE POSITIVES --- p.103 / Chapter 8.1 --- Alignment Segments to Gap Ratio (ASGR) --- p.103 / Chapter 8.2 --- Tolerance --- p.104 / Chapter 8.3 --- Overall trend of change of structures (OTCS) --- p.104 / Chapter 8.4 --- Results and discussions --- p.105 / Chapter CHAPTER 9. --- SECONDARY STRUCTURE PREDICTION --- p.111 / Chapter 9.1 --- 3-STATE SECONDARY STRUCTURE PREDICTION IMPROVEMENT --- p.111 / Chapter 9.2 --- 8-state secondary structure prediction --- p.117 / Chapter 9.3 --- Iterative Subordinate Voting (IS V) --- p.117 / Chapter 9.4 --- ISV Results and discussion --- p.119 / Chapter CHAPTER 10. --- CONCLUSIONS --- p.123 / Chapter 10.1 --- Contributions --- p.123 / Chapter 10.2 --- Future Work --- p.126 / Chapter 10.2.1 --- Using database indexing --- p.126 / Chapter 10.2.2 --- 3-state secondary structure prediction improvement --- p.127 / appendix --- p.128 / Chapter ´Ø --- Interpretation on the dp一filter results --- p.128

Les matériaux en contact avec des fluides biologiques peuvent être colonisés par de nombreux microorganismes (bactéries, levures…) et des macromolécules telles que les protéines. Lorsqu’il s’agit de bactéries pathogènes, l’adhésion bactérienne devient un problème, en particulier dans les milieux agroalimentaire et biomédical, car elle se poursuit jusqu’à la formation de biofilms bactériens, des bio-structures plus résistantes à l’action des antibiotiques que les bactéries isolées. Malgré une littérature abondante sur les processus d’adhésion bactérienne, l’interface surface – bactérie est encore mal comprise principalement à cause du manque de caractérisation à l’échelle moléculaire. Dans ce travail, nous utilisons une technique d’optique non linéaire du second ordre, la spectroscopie vibrationnelle de Génération de Fréquence Somme (SFG) à large bande, pour sonder spécifiquement des interfaces ordonnées à l’échelle moléculaire. Le principe consiste à envoyer un faisceau picoseconde visible et un faisceau femtoseconde infrarouge (accordé aux longueurs d’onde des vibrations des molécules de la surface) sur le substrat en contact avec des biomolécules en milieu aqueux. L’optimisation de la déconvolution et la modélisation du spectre SFG expérimental, réalisées dans le cadre de travail, permettent d’obtenir quantitativement la conformation des molécules de la surface du substrat. Nous nous sommes intéressés à la colonisation d’une surface structurée en « brosse » composée de monocouches autoassemblées (SAM) hydrophobes d’OctaDécaneThiol (ODT) par des bactéries Lactococcus lactis. Afin de reproduire les conditions naturelles de la colonisation bactérienne, nous avons aussi étudié le rôle de la présence de protéines, en l’occurrence l’albumine de sérum bovin. L’étude par spectroscopie SFG couplée avec des mesures de microscopie confocale de fluorescence a permis de proposer un mécanisme de l’adhésion bactérienne sur la SAM d’ODT, qui dépend de la présence des protéines. Nous avons démontré que les bactéries seules en suspension avaient un impact sur la conformation du support pouvant conduire à une augmentation ou à une diminution de la colonisation bactérienne selon le caractère hydrophobe / hydrophile de la paroi bactérienne. La présence des protéines avant ou pendant la colonisation bactérienne conduit à de nouveaux changements structuraux de la SAM d’ODT et à une importante diminution de l’adhésion bactérienne et du biofilm résultant (indépendamment du caractère hydrophobe / hydrophile de la paroi bactérienne). Cette étude démontre d’une part la faisabilité et l’intérêt de la spectroscopie vibrationnelle SFG pour l’étude de l’adhésion bactérienne in situ, et d’autre part que l’effet des bactéries et des protéines sur la conformation des surfaces est à prendre en compte lors de l’ingénierie de nouveaux matériaux à effet antiadhésif et/ou bactéricide. / Materials exposed to a fluid can be contaminated by microorganisms and macromolecules such as proteins. In food industry or biomedicine, surface colonization by pathogenic bacteria is harmful because it leads to biofilm formation, a microbial consortium more resistant to antiobiotics than planktonic bacteria. Despite of an abundant literature on bacterial adhesion, bacteria-surface interactions still require more studies, in particular at the molecular level. In this work, Broad Band Sum Frequency Generation (BBSFG) spectroscopy was employed to investigate specifically well-ordered interfaces at the molecular level. BBSFG consists in overlapping in time and in space a picosecond visible beam and a femtosecond infrared beam onto the sample in contact with bacteria in water. The IR beam is tuned to the wavelength range of suitable vibrational transitions of adsorbed molecules. Optimisation of the deconvolution procedure of SFG spectra and modeling were performed to derive quantitatively the molecular conformational changes of the interface in response to bacterial adhesion. We have studied the colonization of a well-defined “brush” surface composed of hydrophobic OctaDecaneThiols (ODT) Self-Assembled Monolayer (SAM) by Lactococcus lactis bacteria. In order to mimic natural conditions of bacterial adhesion, where bacteria and proteins coexist, we have also studied the role of Bovin Serum Albumin (BSA) proteins. SFG data and fluorescence confocal microscopy measurements led us to propose a mechanism of bacterial adhesion onto the ODT SAM which depends on the presence of BSA. We have demonstrated that adhesion of bacteria in distilled water induces measurable effects on the ODT SAM conformation and on the bacterial adhesion strength, depending on the hydrophobic / hydrophilic character of the bacterial cell wall. Different behaviors of the ODT were observed when BSA proteins were present before or during bacterial colonization. In particular, BSA leads to a marked antimicrobial effect (independent of the hydrophobic / hydrophilic character of the bacterial surface). This study demonstrates the potential of BBSFG to study in situ bacterial adhesion. It also shows that the modification of surface properties by bacterial adhesion must be taken into account for the design of materials suitable to control or eradicate biofilm formation.

Taxol (1) was first isolated from the bark of the Pacific yew about 35 years ago by Drs. Wall and Wani. Although its development as an anticancer agent was delayed by numerous reasons, including its scarcity and insolubility, the discovery of its tubulin-assembly activity and other factors motivated oncologists to overcome these problems. It has since become one of the most important current drugs for the treatment of several cancers, including breast and ovarian cancers. Like almost all anticancer drugs taxol does have some toxic side effects and many tumors also show significant resistance to therapy with taxol. Drug targeting studies aimed at improving its selectivity and efficacy is described. Two targeting methods, the estrogen receptor (ER) directed targeting and colloidal gold (cAu)directed targeting, were used in our research. In this dissertation, a series of estradiol-taxol conjugates (ETCs) were synthesized. They were active in four cytotoxicity assays and tubulin polymerization assay, but less active than taxol. One of them showed the desired selectivity for ER positive cancer cells. Recently, several studies have attempted to elucidate the bioactive binding conformation of taxol on microtubules. Three models have been proposed for this conformation. The T-taxol conformation was proposed by Dr. Snyder based on electron crystallographic density and molecular modeling. In this dessertation, a series of cyclopropyl-containing taxol analogs and macrocyclic taxol lactones were synthesized. The bioassay results showed they are less active than taxol. The molecular modeling studies suggested that the cyclopropyl-containing taxol analogs could not adopt the T-taxol conformation, which would result in the loss of bioactivities. It is an indirect evidence to support T-taxol conformation. As for macrocyclic taxol lactones, it is proposed that they would have a close contact between the ester moiety on the C-3' phenyl ring and Phe272 of the β-tubulin protein when they adopt T-taxol conformation. It will push the macrocyclics out of the binding pocket and lead to the lost of bioactivities. / Ph. D.

La protéine Tat (Trans-activator of transcription) est certainement l’une des cibles présentant le plus d’intérêts dans la lutte contre le VIH-1. En effet, synthétisée précocement, elle joue un rôle central dans le cycle viral et protège les cellules infectées. Secrétée dans le milieu extracellulaire, elle participe à l’immunodéficience en inhibant certaines fonctions ou en induisant l’apoptose des cellules du système immunitaire. Elle est également impliquée directement dans de nombreuses pathologies associées au VIH-1. Dans une première étude, nous avons voulu savoir si la trithérapie était capable d’inhiber la synthèse et la sécrétion de la protéine Tat. Nous avons proposé à des patients infectés, sous trithérapie, ayant une charge virale indétectable, de nous permettre de faire cinq prélèvements sanguins (un tous les trois mois pendant un an) afin de vérifier la présence d’anticorps anti-Tat. Nous avons pu constater que 86% des patients avaient des anticorps anti-Tat mais que ces anticorps pouvaient disparaître ou apparaître chez une majorité de patients, démontrant que la protéine Tat continue d’être sécrétée malgré les antiviraux. Une deuxième étude, sur des sérums de patients, a été effectuée afin de déterminer si la protéine Tat était structurée dans le sang des patients. Il existait une polémique, dans la littérature, sur le fait que la protéine Tat soit naturellement non structurée. Nous avons démontré que la protéine Tat est structurée dans le sérum de patients. De plus, l’activité biologique de la protéine Tat est étroitement liée à l’acquisition de sa conformation. Dans le cadre du développement clinique d’un vaccin anti-Tat dans le laboratoire, nous avons effectué des vaccinations sur des souris afin de déterminer la dose, l’adjuvant, la voie d’administration et le nombre de rappels à effectuer ainsi que la vérification de la tolérance et de la toxicité du vaccin. Des essais cliniques sont en préparation dans le cadre d’un protocole thérapeutique. Le laboratoire développe également une autre approche thérapeutique avec un anticorps monoclonal de souris capable de reconnaitre et de neutraliser les variants Tat représentatifs des cinq principaux sous-types du VIH-1. Cet anticorps qui sera humanisé, servirait à une future immunothérapie en combinaison à la trithérapie pour des patients en phase précoce ou tardive ou encore pour des nouveaux nés dont le système immunitaire est peu fonctionnel. / The protein Tat (Trans-activator of transcription) is definitely one of the most interesting targets in the fight against HIV-1. Synthesized early, it plays a central role in the viral life cycle and protects infected cells. Secreted into the extracellular medium, it participates in the immunodeficiency by inhibiting some functions or inducing apoptosis of immune cells. It is also directly involved in many diseases associated with HIV-1. In a first study, we examined whether HAART was able to inhibit the synthesis and secretion of the Tat protein. We proposed to HIV-1 infected patients under HAART, with undetectable viral load, to allow us to do five blood samplings (one every three months for one year) to verify the presence of antibodies against Tat. We found that 86% of patients had antibodies against Tat but these antibodies could disappear or appear in a majority of patients showing that Tat protein continues to be secreted in spite of antiviral treatment. A second study of patient sera was carried out to determine if Tat was structured in the blood of patients. There was a controversy in the literature about the fact that Tat could be naturally unstructured. We showed that Tat is structured in the serum of patients. In addition, the biological activity of Tat is closely related to the acquisition of its conformation. As part of a clinical development of a Tat vaccine in the laboratory, we carried out vaccinations in mice to determine the dose, the adjuvant, the route of administration, the number of boosts, tolerance and toxicity of the vaccine. Clinical trials are planed with a therapeutic protocol. The laboratory is also developing another therapeutic approach with a mouse monoclonal antibody able to recognize and neutralize Tat variants representative of the five major subtypes of HIV-1. This antibody will be humanized and could be used for future immunotherapy, in combination with HAART for patients in early or late stage of the pathology or to newborn babies who have a weak immune system.

"An apparatus for the delivery of radiation to the tip-sample interface of an Atomic Force Microscope (AFM) is demonstrated. The Pulsed Light Delivery System (PLDS) was fabricated to probe photoinduced conformational changes of molecules using an AFM. The PLDS is 67 mm long, 59 mm wide, and 21 mm high, leaving clearance to mount the PLDS and a microscope slide coated with a thin film of photoactive molecules beneath the cantilever tip of a stand-alone AFM. The PLDS is coupled into a fiber pigtailed Nd:Yag frequency doubled laser, operating at a wavelength of 532 nm. The radiation delivered to a sample through the PLDS can be configured for continuous or pulsed mode. The maximum continuous wave (CW) power delivered was 0.903 mW and the minimum pulse width was 12.3 ms (maximal 401 ms), corresponding to a minimal energy of 0.150 nJ (maximal 362 nJ), and had a cycle duration of 10.0 ms. The PLDS consists of micro-optical components 3.0 mm and smaller in diameter. The optical design was inspired by the three-beam pick-up method used in CD players, which could provide a method to focus the pulse of light onto the sample layer. In addition, the system can be easily modified for different operational parameters (pulse width, wavelength, and power). As proof that the prototype design works, we observed a photoinduced ‘bimetallic’ bending of the cantilever, as evidenced by observing no photoinduced bending when a reflective-coated cantilever was replaced by an uncoated cantilever. Using the apparatus will allow investigation of many different types of molecules exhibiting photoinduced isomerization."

La détermination de la conformation d’une petite molécule liée à sa cible biologique nous permet de concevoir des drogues de propriété biologique améliorée. Cette détermination peut être difficile dû aux limitations techniques, comme indiqué par le débat sur la conformation de microtubule-lié d’une drogue anticancéreuse – paclitaxel. Les études utilisant la cristallographie des rayons X et la RMN du liquide ne peut pas fournir les informations détaillées sur la conformation espérée. La RMN du solide est un choix raisonnable en mesurant précisément des distances interatomiques de la molécule, et le marquage sélectif au tritium permet de mesurer une distance longue jusqu’à 14,4 Å avec une précision haute grâce au rapport gyromagnetique élevé de ce noyau. Aucune modification structurale n’a été rendue par le marquage au tritium. Ainsi notre sujet ayant pour l’objectif de déterminer la conformation bioactive du paclitaxel comporte la synthèse des 6 isotopomères de paclitaxel ditritiés sur les sites particuliers, suivie par la préparation des complexes de microtubule-paclitaxel marqué. L’analyse de RMN du tritium à l’état solide fournira les distances clés pour la détermination. 2 isotopomères ont été synthétisés par tritier le paclitaxel dibromé et coupler la baccatine tritiée et la chaîne latérale tritiée, respectivement. La stratégie synthétique conçue permet de réaliser la synthèse avec un rendement généralement satisfaisant et une bonne stéréosélectivité. Différentes méthodes de tritiation ont été testées, dont un enrichissement isotopique supérieur à 92% a été obtenu. La synthèse des autres isotopomères ainsi que des complexes de microtubule-paclitaxel est en cours de réaliser dans notre laboratoire. / The determination of the conformation of small molecule bound to its biological target would facilitate people to design improved drugs. This determination can be difficult due to technical limitations, as exemplified by the long standing debate on the microtubule-binding conformation of a natural anticancer drug – paclitaxel. Previous studies using X-ray crystallography and solution-state NMR failed to furnish direct information on the expected conformation. Solid-state NMR may help in this task by providing precise interatomic distances, and the selective labeling on different sites with tritium atoms enables accurate measurement of long-range distances (up to 14.4 Å) owing to the high gyromagnetic ratio of this nucleus, without any structural modification of the molecule. So our project aiming at illustrating the bioactive conformation of paclitaxel consists the syntheses of 6 different paclitaxel isotopomers bearing a pair of tritiums at specified positions, flowing by the preparations of corresponding microtubule-labeled paclitaxel complexes. The solid-state tritium NMR analyses of these complexes would provide key distances for determining the expected conformation. Up to now, 2 paclitaxel isotopomers have been prepared from labelling the dibrominated paclitaxel precursor and from coupling the tritiated taxane rings and the tritiated side chains, respectively. The synthetic strategy allowed us to realize the syntheses in generally high yield and good stereoselectivity. Different tritiation methods have been used, from which an isotopic enrichment of higher than 92% was obtained. The syntheses of other 4 isotopomers, together with the microtubule complexes are currently underway in our lab.

Wong, Siu Lun. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2007. / Includes bibliographical references (leaves 129-141). / Abstracts in English and Chinese. / Abstract --- p.i / Abstract (Chinese version) --- p.iii / Acknowledgements --- p.iv / List of Abbreviations --- p.v / List of Tables --- p.vii / List of Figures --- p.viii / Chapter 1. --- INTRODUCTION / Chapter 1.1 --- Neurodegenerative disorders - a brief overview --- p.1 / Chapter 1.2 --- Polyglutamine diseases --- p.2 / Chapter 1.3 --- Microscopically visible polyglutamine protein aggregates and its relation to toxicity --- p.7 / Chapter 1.4 --- Polyglutamine protein conformers and their relation to toxicity --- p.10 / Chapter 1.5 --- Modeling polyglutamine diseases in Drosophila / Chapter 1.5.1 --- GAL4/UAS spatial transgene expression system in Drosophila --- p.14 / Chapter 1.5.2 --- Temporal control of GAL4/UAS transgene expression system in Drosophila --- p.16 / Chapter 1.5.3 --- Drosophila as a model to study human pathologies --- p.19 / Chapter 1.5.4 --- Drosophila as a model to study polyglutamine diseases --- p.21 / Chapter 1.6 --- Aims of study --- p.26 / Chapter 2. --- MATERIALS AND METHODS / Chapter 2.1 --- Drosophila culture and manipulation / Chapter 2.1.1 --- Drosophila culture --- p.27 / Chapter 2.1.2 --- Phenotypic examination of adult external eye degeneration --- p.27 / Chapter 2.1.3 --- Pseudopupil assay of adult retinal degeneration and observation of green fluorescent protein in adult eyes --- p.28 / Chapter 2.2 --- Semi-quantitative Reverse Transcription-Polymerase Chain Reaction / Chapter 2.2.1 --- RNA extraction from adult Drosophila heads --- p.30 / Chapter 2.2.2 --- DNase treatment of extracted RNA --- p.31 / Chapter 2.2.3 --- Reverse transcription-Polymerase Chain Reaction (RT-PCR) --- p.31 / Chapter 2.2.4 --- Agarose gel electrophoresis --- p.33 / Chapter 2.3 --- Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis (SDS-PAGE) / Chapter 2.3.1 --- Protein extraction from adult Drosophila heads --- p.33 / Chapter 2.3.2 --- Preparation of SDS-polyacrylamide gel and electrophoresis --- p.34 / Chapter 2.3.3 --- Western blotting --- p.35 / Chapter 2.3.4 --- Immunodetection --- p.36 / Chapter 2.4 --- Immunoprecipitation --- p.38 / Chapter 2.5 --- Filter retardation assay --- p.39 / Chapter 2.6 --- Isolation and solubilization of SDS-insoluble protein --- p.40 / Chapter 2.7 --- Sucrose gradient sedimentation --- p.41 / Chapter 2.8 --- Preparation of Drosophila tissues for immunofluorescence analysis / Chapter 2.8.1 --- Dissection and immunostaining of Drosophila larval imaginal eye discs --- p.42 / Chapter 2.8.2 --- Cryosectioning and immunostaining of adult Drosophila heads --- p.44 / Chapter 2.9 --- Atomic force microscopy --- p.47 / Chapter 2.10 --- Reagents and buffers / Chapter 2.10.1 --- Reagents for Drosophila culture --- p.48 / Chapter 2.10.2 --- Reagents for RT-PCR --- p.52 / Chapter 2.10.3 --- Reagents for SDS-PAGE --- p.54 / Chapter 2.10.4 --- Reagents for immunoprecipitation --- p.57 / Chapter 2.10.5 --- Reagents for filter retardation assay --- p.57 / Chapter 2.10.6 --- Reagents for isolation and solubilization of SDS-insoluble protein --- p.58 / Chapter 2.10.7 --- Reagents for sucrose gradient sedimentation --- p.58 / Chapter 2.10.8 --- Reagents for immunofluorescence --- p.59 / Chapter 3. --- RESULTS / Chapter 3.1 --- Establishment of an inducible transgenic Drosophila model of polyglutamine diseases / Chapter 3.1.1 --- Introduction --- p.60 / Chapter 3.1.2 --- Results / Chapter 3.1.2.1 --- GAL80ts-mediated inducible expression of expanded polyglutamine protein in Drosophila / Chapter 3.1.2.1.1 --- GAL80ts controls GAL4/UAS-mediated polyQ protein expression --- p.61 / Chapter 3.1.2.1.2 --- Inducible expression of SDS-soluble expanded polyglutamine protein --- p.64 / Chapter 3.1.2.1.3 --- Inducible expression of expanded polyglutamine protein accumulates gradually in form of SDS-insoluble protein --- p.66 / Chapter 3.1.2.1.4 --- Inducible expression of expanded polyglutamine protein results in progressive accumulation of microscopically visible aggregates --- p.68 / Chapter 3.1.2.2 --- Inducible expression of expanded polyglutamine protein causes late-onset progressive neuronal degeneration in Drosophila / Chapter 3.1.2.2.1 --- Inducible expression of expanded polyglutamine protein leads to late-onset progressive deterioration of photoreceptor neurons --- p.68 / Chapter 3.1.2.2.2 --- Inducible expression of expanded polyglutamine protein neither causes external eye degenerative phenotype nor disrupts gross retinal morphology despite deterioration of photoreceptor neurons --- p.72 / Chapter 3.1.2.3 --- Co-expression of caspase inhibitor P35 suppresses polyglutamine-induced neuronal degeneration --- p.72 / Chapter 3.1.2.4 --- Co-expression of molecular chaperone Hsp70 suppresses polyglutamine-induced neuronal degeneration --- p.74 / Chapter 3.1.2.5 --- Inducible expression of expanded polyglutamine protein results in biphasic expression of molecular chaperone Hsp70 in Drosophila --- p.76 / Chapter 3.1.3 --- Discussion --- p.76 / Chapter 3.2 --- Involvement of microscopically visible polyglutamine aggregates in neurodegeneration / Chapter 3.2.1 --- Introduction --- p.83 / Chapter 3.2.2 --- Results / Chapter 3.2.2.1 --- Effect of Hsc70-K71S on microscopically visible polyglutamine aggregates and neuronal degeneration / Chapter 3.2.2.1.1 --- Co-expression of Hsc70-K71S reduces the level of microscopically visible polyglutamine aggregates --- p.83 / Chapter 3.2.2.1.2 --- Co-expression of Hsc70-K71S does not alter polyglutamine transgene expression --- p.84 / Chapter 3.2.2.1.3 --- Co-expression of Hsc70-K71S does not modify polyglutamine-induced neuronal degeneration --- p.87 / Chapter 3.2.2.2 --- Microscopically visible polyglutamine aggregates do not correlate with neuronal degeneration --- p.90 / Chapter 3.2.3 --- Discussion --- p.93 / Chapter 3.3 --- Detection of small SDS-insoluble expanded polyglutamine protein species and its association with neurodegeneration / Chapter 3.3.1 --- Introduction --- p.97 / Chapter 3.3.2 --- Results / Chapter 3.3.2.1 --- Accumulation of SDS-soluble expanded polyglutamine protein does not correlate with neuronal degeneration --- p.98 / Chapter 3.3.2.2 --- Identification of small SDS-insoluble expanded polyglutamine protein species / Chapter 3.3.2.2.1 --- Accumulation of total SDS-insoluble expanded polyglutamine protein positively correlates with progressive neuronal degeneration --- p.99 / Chapter 3.3.2.2.2 --- Accumulation of large SDS-insoluble expanded polyglutamine protein does not correlate with neuronal degeneration --- p.99 / Chapter 3.3.2.2.3 --- Accumulation of small SDS-insoluble expanded polyglutamine protein correlates with neuronal degeneration --- p.104 / Chapter 3.3.3 --- Discussion --- p.107 / Chapter 3.4 --- Biophysical characterization of small SDS-insoluble expanded polyglutamine protein species / Chapter 3.4.1 --- Introduction --- p.109 / Chapter 3.4.2 --- Results / Chapter 3.4.2.1 --- Separation of expanded polyglutamine protein species by sucrose gradient sedimentation --- p.110 / Chapter 3.4.2.2 --- Morphological studies of small SDS-insoluble expanded polyglutamine protein species by atomic force microscopy --- p.112 / Chapter 3.4.3 --- Discussion --- p.118 / Chapter 4. --- GENERAL DISCUSSION --- p.124 / Chapter 5. --- CONCLUSION --- p.127 / Chapter 6. --- REFERENCES --- p.129

Cell adhesion plays an important role in inflammation and immunological responses. Adhesion molecules (e.g., selectins and integrins) are key modulators in mediating these cellular responses, such as leukocyte trafficking under shear stress. In this thesis, we use a bio-membrane force probe (BFP) to study force regulation on kinetics and conformations of selectin and LFA-1 integrin. A new BFP was built up, and a new assay, using thermal fluctuation of the BFP, was developed and used to monitoring selectins and their ligands association and dissociations. The new BFP was also used to investigate the force and force history dependence of selectin-ligand interactions. We found tri-phasic transition of force-dependent off-rates and force-history dependence of selectin/ligaind interactions. The BFP was also used to characterize force-dependent lifetimes of the LFA-1-ICAM-1 interaction. We found that LFA-1/ICAM-1 bonds behaved as catch bond and that LFA-1-ICAM-1's catch bonds were abolished blocking the downward movement of αA domain α7 helix. Finally, the BFP was applied to dynamically probe the global conformational changes of LFA-1 and to characterize force-regulated transitions among different conformational states on a living cell. We observed dynamic transitions of LFA-1 between extended and bent conformations on living cells. The observed average distance change of LFA-1's extensions was about 18nm, while that of the bending was only about 14nm. We also found that forces could facilitate extension but they slow down the bending of LFA-1. The observed transition time of extension was less than 0.1s, while that of contraction was longer than 0.2s. Our observations here are the first in-situ evidence to demonstrate how integrins dynamically transit different conformations and how force regulates these transitions.

The transcription in the eukaryotic cells involves epigenetic regulatory mechanisms that control local and higher-order chromatin remodelling. In the skin, keratinocyte-specific genes are organized into distinct loci including Epidermal Differentiation Complex (EDC) and Keratin type I/II loci. This thesis introduces bioinformatics approaches to analyze multi-level regulatory mechanisms that control skin development and keratinocyte-specific differentiation. Firstly, integration of gene expression data with analyses of linear genome organization showed dramatic downregulation of the genes that comprise large genomic domains in the sweat glands including EDC locus, compared to ii hair follicles, suggesting substantial differences in global genome rearrangement during development of these two distinct skin appendages. Secondly, comparative analysis of the genetic programmes regulated in keratinocytes by Lhx2 transcription factor and chromatin remodeler Satb1 revealed that significant number of their target genes is clustered in the genome. Furthermore, it was shown in this study that Satb1 target genes are lineage-specific. Thirdly, analysis of the topological interactomes of Loricrin and Keratin 5 in hair follicle steam cells revealed presence of the cis- and trans-interactions and lineage specific genes (Wnt, TGF-beta/activin, Notch, etc.). Expression levels of the genes that comprise interactomes show correlation with their histone modification status. This study demonstrates the crucial role for integration of transcription factormediated and epigenetic regulatory mechanisms in establishing a proper balance of gene expression in keratinocytes during development and differentiation into distinct cell lineages and provides an integrated bioinformatics platform for further analyses of the changes in global organization of keratinocyte-specific genomic loci in normal and diseased skin.