L'étude des interactions ADN-protéines et de la structure de la chromatine dans les cellules vivantes est nécessaire à la compréhension des mécanismes de l'expression génique. La technique LMPCR ("ligation mediated polymerase chain reaction") permet l'étude in vivo de ces interactions par une analyse plus réelle des événements qui se déroulent au sein même des cellules, comparativement aux études in vitro. Par contre, la qualité des résultats peut-être grandement influencée par l'ADN polymérase utilisée et nécessite donc l'optimisation de plusieurs paramètres. De ce fait, nous avons identifié les conditions optimales d'utilisation de l'ADN polymérase Thermococcus litoralis exo- (Vent exo-) dans la technique LMPCR telle que la quantité de polymérase et d'ADN. Nous avons montré que l'efficacité de Vent exo- à l'extension d'amorces et à l'amplification était similaire à celle de Pyrococcus furiosus exo- (Pfu exo-) et supérieure à Thermus aquaticus (Taq). De plus, nous avons observé que la thermostabilité de Vent exo- lui permettait de soutenir un plus grand nombre de cycles d'amplification que Taq facilitant ainsi la résolution de séquences riches en GC. D'autre part, nous avons montré que l'activité terminale transférase de Vent exo- était inhibée dans la plupart de nos conditions expérimentales et qu'il était donc possible de l'utiliser efficacement pour la production d'extrémités franches lors de l'étape d'extension d'amorces. Finalement, l'ADN polymérase Vent exo- s'avère être une alternative efficace pour les étapes d'extension d'amorces et d'amplification PCR dans la technologie LMPCR.

Common amplicons were delineated throughout the NPC genome in a large panel of NPC cell lines, xenografts, and primary tumors by two high-density genomic arrays with ∼1 Mb and 35 kb resolution. Apart from the genetic changes reported in previous studies, a number of novel chromosomal aberrations were discovered, including gains at 7p11, 16p13.3, 19p13, 19q13-q43 and 20q13. Most distinctively, common amplicons at 11q13 and 12p13 were found in this cancer. Two smallest amplification regions with 5.4 Mb and 2.16 Mb were delineated at 11q13.1-q13.3 and 12p13.31 respectively. The high prevalence of these 2 amplified regions have led to the hypothesis that activation of the target oncogenes in these regions are critical events for NPC development. / Expression of candidate genes located within 11q13.3 was examined and consistent overexpression of CCND1 in cell lines and xenografts were identified in the 11q13.3. Frequent concordant gains and overexpression of CCND1 were further confirmed in primary tumors. Knockdown of CCND1 mRNA by siRNA technique was found to inhibit cell growth and lead to cell cycle arrest at G1. Alterations of protein expressions of other cell cycle components were also observed. Moreover, inactivation of p16 and overexpression of cyclin D1 were commonly occurred in NPC. These findings provided evidence that cyclin D1 may have cell cycle-independent functions, which is critical in NPC tumongenesis. / Frequent gains of 12p13.31 region were confirmed by fluorescence in situ hybridization (FISH) analysis. According to expression array and real-time RT-PCR results, LTbetaR, TNFRSF1A and FLJ10665 were the three genes showing concordant amplification and overexpression in NPC xenograft. The LTbetaR protein, which is a lymphotoxin beta receptor, was confirmed to be recurrently overexpressed in NPC primary tumors and its overexpression may be involved in the activation of NF-kappaB in NPC. The findings suggested that it is one of the candidate oncogenes of this cancer. / In summary, three candidate NPC-associated oncogenes locating at 3q26.32, 11q13.3 and 12p13.31 were identified by genome-wide mapping analysis. Molecular and functional characterizations of these genes have provided evidences that they play critical roles in NPC tumorigenesis. / In this study, detailed investigation was carried out on a candidate NPC-associated oncogene, PIK3CA at 38q26.32, an amplicon reported previously. Copy number gains and amplifications of this gene, but not mutation, were demonstrated to be common events in NPC. The findings hence implied the importance of PIK3CA in NPC tumorigenesis. / Nasopharyngeal carcinoma is a common cancer in Southern China. Despite multiple genetic changes have been reported previously, limited information of NPC-associated oncogene is available. Since amplification is one of the major mechanisms in oncogene activation, a comprehensive characterization of common amplicons in human cancers is expected to facilitate the identification of the oncogenes involved in tumorigenesis. The aims of the present study is to define and characterize the common amplicons in NPC genome and then to identify NPC-associated oncogenes. / Or Yan Yan. / "July 2006." / Adviser: Kwok Wai Lo. / Source: Dissertation Abstracts International, Volume: 68-09, Section: B, page: 5715. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2006. / Includes bibliographical references (p. 179-201). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstracts in English and Chinese. / School code: 1307.

RNA-cleaving DNAzymes (RCDs) are a class of functional nucleic acids that can bind various targets ranging in size from small molecules to large proteins, which results in activation of cleavage activity. The activation of RCDs results in the cleavage of a ribonucleotide site in an otherwise all-DNA substrate, leading to two cleavage fragments. In this work, a previously identified DNAzyme that binds to a protein biomarker endogenous to Helicobacter pylori (J99) crude extracellular matrix was evaluated for coupling to an isothermal amplification method termed rolling circle amplification (RCA) as a way to improve the originally reported detection limit. Three RCD constructs were designed with the goal of generating a cleavage fragment that could act as a primer to initiate RCA. The first method used the original HP DNAzyme, which liberated a short cleavage fragment that could be used as a primer. However, the primer fragment was rapidly digested by the bacterial matrix, preventing RCA. A second method evaluated use of a circularized substrate and separate RCD to generate a primer, however this system was not capable of generating a cleavage fragment. A final method redesigned the original RCD to move the substrate region from the 3’ to the 5’ end of the RCD, causing the longer RCD-containing fragment to be the primer for RCA. In this case, target-triggered cleavage was observed and the resulting primer was sufficiently resistant to digestion to allow its use as a primer for RCA. Preliminary characterization of the rearranged RCD showed that it retained selectivity similar to the original RCD, but that the cleavage rate was slower. In addition, the RCA based reaction, while successful, did not produce improved detection sensitivity relative to unamplified assays. Methods to further improve RCA performance are discussed for future work. / Thesis / Master of Science (MSc)

No description available.

No description available.

Amplification techniques such as the Polymerase Chain Reaction (PCR) are held to be largely qualitative procedures and are widely used as such. Since the efficiency of amplification is less than perfect, small changes in efficiency can yield dramatic differences in the final amount of product generated. Despite this unpredictability the exquisite sensitivity of PCR makes the demanding goal of absolute quantification highly desirable. Consequently, the use of this technique for the quantification of nucleic acids has increased at an exponential rate. However, the ability of PCR to accurately quantify absolute levels of DNA is still not universally accepted. The overall aim of this investigation was to determine the critical factors affecting the quantification of DNA using PCR and to use these findings to develop an assay for the absolute quantification of DNA in a model system. The novel work presented here illustrates the need for careful examination of sequencesfo r GC-rich domains which could give rise to stable secondary structures and reduce the efficiency of amplification by serving as termination sites. To determine the accuracy of competitive PCR, CE and IP-RP-HPLC were employed to quantify PCR- products. These two techniques provided valuable information on the identification and elimination of sources of error which led to improvements in speed, accuracy and precision, as well as ease of quantification by PCR. They also yielded information on the process of heteroduplex formation whilst simultaneously revealing assay limitations. Consequently, the on-line fluorescence monitoring of PCR was used as an alternative method for the quantification of Legionella pneumophila. This technique was highly reproducible however, mispriming and the subsequent amplification of non-specific PCR products limited the level of detection. The Y-end labelling of degraded DNA with DIG prevented short DNA fragments from mispriming (and consequently extending) allowing the amplification of DNA targets. Therefore, to reduce mispriming and hence improve assay sensitivity, this approach was adapted for the first time to produce 5'-degenerate, 3'- DIG-terminated competitive primer analogues. These analogues, coupled with the use of the LightcyclerTm, allowed the detection and absolute quantification of a single cell of Legionella pneumophila. This is the first time that this level of sensitivity has been achieved using this type of assay. This technique should provide a very rapid and sensitive alternative for quantification comparedt o the other,m oree xpensivete chnologiesa vailablea t present.

Nonlinear acoustic media for implementations of parametric generation of low frequencies has so far been restricted to small values of the parameter B/A, typically between 3 and 13. Parametric amplification, defined as the generation of a low difference frequency signal resulting from the nonlinear interactions of two higher frequency fundamentals is enhanced by medium with a large coefficient of nonlinearity and low sound speed. The acoustic properties of a highly nonlinear medium were estimated and introduced in a numerical model, to evaluate the parametric amplification induced by a thin layer of such material in contact with a spherical transducer. The numerical model predicted a significant enhancement of the sound pressure level for the difference frequency component relative to that obtained when the transducer is driven linearly at the difference frequency. A source was then constructed to compare the theoretical predictions with experimental values and an enhancement of 17dB compared to the linear operation of the transducer was measured. The difference between the parametric amplification achieved with the nonlinear medium and the parametric amplification that would be obtained in water is 73dB.

Trap-jaw ants are characterized by high-speed mandibles used for prey capture and defense. Power-amplified mandibles have independently evolved at least four times among ants, with each lineage using different structures as a latch, spring and trigger. We examined two species from the genus Myrmoteras (subfamily Formicinae), whose morphology is unique among trap-jaw ant lineages, and describe the performance characteristics, spring-loading mechanism and neuronal control of Myrmoteras strikes. Like other trap-jaw ants, Myrmoteras latch their jaws open while the large closer muscle loads potential energy in a spring. The latch differs from other lineages and is likely formed by the co-contraction of the mandible opener and closer muscles. The cuticle of the posterior margin of the head serves as a spring, and is deformed by approximately 6% prior to a strike. The mandibles are likely unlatched by a subgroup of closer muscle fibers with particularly short sarcomeres. These fast fibers are controlled by two large motor neurons whose dendrites overlap with terminals of large sensory neurons originating from labral trigger hairs. Upon stimulation of the trigger hairs, the mandibles shut in as little as 0.5 ms and at peak velocities that are comparable with other trap-jaw ants, but with much slower acceleration. The estimated power output of the mandible strike (21 kW kg(-1)) confirms that Myrmoteras jaws are indeed power amplified. However, the power output of Myrmoteras mandibles is significantly lower than distantly related trap-jaw ants using different spring-loading mechanisms, indicating a relationship between power-amplification mechanism and performance.

Multivalent aptamer refers to a technique that joins two or more identical or different types of aptamer monomers together, with or without the presence of structural or other functional elements. As a rapid and easy method for fabricating the multivalent aptamer constructs, rolling circle amplification (RCA) has attracted great attention in recent decades. The incorporation of properly designed structural elements, such as intra-molecular spacers, have been shown to greatly enhance the efficiency of the multivalent aptamer system [1]. The objective of this current study is to systemically investigate the effect of different lengths of poly thymine spacer designs (polyT, from no spacer/NT, 5T, 10T, and 15T) on the capturing performance of RCA-generated multivalent system. To achieve this, we designed four circular probe templates by inserting zero, five, ten, and fifteen adenine bases (polyA). These polyA domains in the circular probe template are complementary to polyT with respective lengths in between the adjacent aptamers on the resultant RCA products (RCAPs). We found that the resultant RCAPs with length shorter than 10T showed a lack or low ability to capture target cells E.Coli O157:H7. When spacer lengths reach or exceed 10T, the capturing performance of the respective multivalent aptamer chain is significantly enhanced. This phenomenon can be explained by larger hydrodynamic sizes and less nonspecific secondary structures observed in RCAP with spacer length no less than 10T. Moreover, we found that there is also a trade-off that the number of polyA bases added into the circular probe template can significantly impair the efficiency of RCA reaction in respective to cyclization yield and amplification rate. The results of this research explain with details how the design of spacer affects RCA reaction efficiency and RCAPs’ capturing performance, which provides ideas in designing an efficient RCA-generated multivalent system.

Pour un grand nombre d'applications, les sources laser impulsionnelles femtoseconde (fs) doivent fournir des puissances toujours plus importantes. En régime impulsionnel, on recherche d'une part une forte puissance crête par impulsion, et d'autre part une forte puissance moyenne, c'est à dire un taux de répétition élevé. Parmi les technologies existantes, les amplificateurs à fibre optique dopée ytterbium présentent de nombreux avantages pour l'obtention de fortes puissances moyennes, cependant le fort confinement des faisceaux dans la fibre sur de grandes longueurs d'interaction induit inévitablement des effets non-linéaires, et limite ainsi la puissance crête accessible. Nous avons étudié lors de cette thèse la combinaison cohérente d'impulsions fs appliquée aux systèmes fibrés.Ayant déjà fait ses preuves dans les régimes d'amplification continu et nanoseconde, la combinaison cohérente de faisceaux (dite combinaison spatiale) permet de diviser une seule et unique source en N voies indépendantes, disposées en parallèle et incluant chacune un amplificateur. Les faisceaux amplifiés sont ensuite recombinés en espace libre en un seul et unique faisceau, qui contient toute la puissance des N amplificateurs sans accumuler les effets non-linéaires. Cette architecture permet théoriquement de monter d'un facteur N le niveau de puissance crête issu des systèmes d'amplification fibrés. Au cours de cette thèse, nous avons démontré la compatibilité et l'efficacité de cette méthode en régime d'amplification fs avec deux amplificateurs, selon différents procédés. Les expériences démontrent d'excellentes efficacités de combinaison ainsi qu'une très bonne préservation des caractéristiques temporelles et spatiales initiales de la source. Les procédés de combinaison cohérente nécessitent cependant un accord de phase entre différents amplificateurs stable dans le temps, assuré en premier lieu par une boucle de rétroaction. Nous avons poursuivi notre étude en concevant une architecture totalement passive, permettant une implémentation plus simple d'un système de combinaison à deux faisceaux sans asservissement électronique. Enfin, une méthode passive de combinaison cohérente dans le domaine temporel est étudiée et caractérisée dans le domaine fs, et implémentée simultanément avec la méthode passive de combinaison spatiale proposée précédemment. Ces expériences démontrent la validité et la variété des concepts proposés, ainsi que leurs nombreuses perspectives pour les systèmes d'amplification fs fibrés. / Applications addressed by femtosecond (fs) laser sources are requiring increasing pulse energies and increasing average powers. Ytterbium-doped fiber amplifiers are excellent candidates to generate high average powers at high repetition rates, but present strong disadvantages in terms of peak power. Indeed, the tight confinement of the beam over long interaction length induces nonlinear effects at high peak-powers that affect the overall performances of fiber systems. This work describes coherent combining methods that can be used to scale the performances of femtosecond laser sources.Coherent beam combining has been widely used in CW regime and more recently in the nanosecond range. It consists in splitting a single seed into N beam replicas, amplified each by independent amplifiers in parallel. Their respective outputs are combined in free space into one single beam that carries the power of the N amplifiers without cumulating nonlinearities. This architecture allows scaling both peak and average powers of the amplification systems. We have studied and demonstrated the efficiency of active coherent beam combining in the fs regime with two fiber amplifiers, which are peak-power limited. The experiments show the preservation of the temporal/spectral/spatial properties of the combined pulses, with high combination efficiencies.Coherent beam combining methods require phase-matching between all the beams to combine. This is usually achieved by an active feedback loop on each amplifier along with a phase detection scheme. We demonstrate that a Sagnac interferometer can be used to ensure perfect and stable phase-matching over time, which considerably simplifies the setup. Finally, another passive combining method known as divided-pulse amplification, acting in the temporal domain, is studied and demonstrated in the fs regime. It is coupled with the passive spatial combining method described above to scale the number of pulse divisions. All these experiments show the compatibility of coherent combining concepts in the fs regime and provide new opportunities for fiber amplifier systems.