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The unusually long Cytoplasmic tail (CT) of Human Immunodeficiency Virus Type-1 (HIV-1) glycoprotein-41 (gp41) is highly conserved and engineered large truncations often render the virus non-infectious in a cell-type dependent manner. While large CT truncations occur infrequently in natural isolates, little is known about the mechanisms involved in infectious virions harbouring a large CT truncation. This thesis characterises RFgp34, a replication competent laboratory HIV-1 isolate with an acquired 100 amino acid CT truncation, and how it diverged from wildtype RF. The CT truncation and two possible compensatory mutations in Matrix (E40K and F44I) were introduced into the HIV-1 isolate NL4-3. These mutants were tested for infectivity, syncytia formation and glycoprotein incorporation into virions, alternative co-receptor usage and sensitivity to the fusion inhibitor T-20. Compared with RFwt, RFgp34-infected cultures displayed delayed viral replication kinetics in all cell types. Similar sized (MT-4 cells, PBMC) or larger and more numerous syncytia (Hut78 cells) were detected in RFgp34-infected cultures. Similar (Hut78 cells) or decreased (MT-4 cells, PBMC) amounts of glycoprotein was incorporated into RFgp34 virions, compared with RFwt virions. The increased syncytia in RFgp34-infected Hut78 cultures and the reduced glycoprotein incorporation into RFgp34 virions from MT-4 cells and PBMCs may explain the delayed RFgp34 replication kinetics. The Matrix E40K and F44I mutations were not able to directly compensate for the CT truncation to restore infectivity in Hut78 and MT-4 cells, as secondary mutations or the reversion of the CT truncation to a full-length CT were observed. In PBMCs the Matrix mutations alone were able to partially restore infectivity, suggesting specific mutations may compensate for the CT truncation in different cell types. None of the viruses utilised alternative HIV-1 co-receptors, nor were more resistant to T-20 than wildtype HIV-1 suggesting that the CT does not directly play a role in these viral functions. This thesis suggests that the sequence of mutations acquired by RFgp34 to compensate for the CT truncation and restore infectivity in multiple cell types may have occurred in a specific order and the evolution of RFgp34 to out-compete RFwt occurred over many passages.

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The tail dependence coefficient (TDC) is a natural tool to describe extremal dependence. Estimation of the tail dependence coefficient can be performed via empirical process theory. In case of extremal independence, the limit degenerates and hence one cannot construct a test for extremal independence. In order to deal with this issue, we consider an analog of the covariance matrix, namely the extremogram matrix, whose entries depend only on extremal observations. We show that under the null hypothesis of extremal independence and for finite dimension d ≥ 2, the largest eigenvalue of the sample extremogram matrix converges to the maximum of d independent normal random variables. This allows us to conduct an hypothesis testing for extremal independence by means of the asymptotic distribution of the largest eigenvalue. Simulation studies are performed to further illustrate this approach.

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第22229号 / 理博第4543号 / 新制||理||1653(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 濱田 穣, 准教授 平﨑 鋭矢, 教授 髙井 正成 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

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Tomato serves as an important model organism for Solanaceae in both molecular and agronomic research. With whole genome sequencing in progress, there is a need to study functional genetics through mutant lines that exceed the practical limitations imposed by the popular research cultivar, Micro-Tom. This project utilized Agrobacterium transformation and the transposon tagging construct, Ac-DsATag-Bar_gosGFP, to produce activation tagged and knockout mutants in the processing tomato variety, M82. The construct contained hygromycin resistance (hyg), green fluorescent protein (GFP), and maize transposase (TPase) on the stable Ac element, along with a 35S enhancer tetramer and glufosinate herbicide resistance (BAR) on the mobile Ds element. An in vitro propagation strategy was used to produce a population of 25 T0 plants from a single transformed plant regenerated in tissue culture. A T1 population of 10,568 selfed and M82 backcross progeny was produced from the functional T0 line. This population was screened by spraying with 0.05% Liberty® herbicide, followed by a 100 mg/L hygromycin leaf painting procedure to select for Ds only (herbicide tolerant and hygromycin sensitive) individuals. The T-DNA genotype of Ds only plants was confirmed through multiplex PCR and the location of insertions within the genome was determined through TAIL-PCR. Resulting product sequences were blasted against the pre-publication tomato genome browser to determine insertion sites. A population of 309 independent transposants dispersed to all twelve chromosomes from the original insertion site on chromosome five has been developed. The transposon tagged lines are currently being immortalized in seed stocks. / Master of Science

Aviation industry has a crucial impact on society on the grounds that it offers wider social and economic benefits. The demand of transportation is increasing and it is expected that the worldwide fleet of aircraft and rotorcraft will increase accordingly. This growth will introduce an increased environmental impact which can be controlled with the introduction and the implementation of new and greener technologies which can provide both a reduced carbon foot-print and increased efficiency. Therefore, the simulation of new designs with tools that can capture the flow physics accurately is crucial, on the grounds that an accurate simulation could provide novel designs and new ways in order to design from scratch new vehicles as well as providing a better appreciation of the physics that are involved. This work has a central aim to propose a methodology which combines CFD simulations and the method of performance mapping. It focuses on the application of a ducted tail rotor which can offer significant performance benefits compared to a conventional tail rotor. The developed methodology was tested against the results of an in-house rotorcraft comprehensive code and provided a reasonable qualitative correlation. In principle, this methodology can work for all helicopter flight phases such as hover, climb, cruise, descend but due to the complexity of the investigations, together with the lack of experimental data that can be used to refine the CFD model, only the hover and forward flight were considered. Although CFD studies of a ducted tail rotor currently exist in the literature (though scarce), this work can be considered, to the best knowledge of the author as a first attempt in investigating the performance of the configuration, from low to high forward flight speed, by combining CFD and performance mapping.