published_or_final_version / Biochemistry / Doctoral / Doctor of Philosophy

This study determined whether variation in clone, weed control treatment, or stem dimensions, could have an impact upon outerwood stiffness in 17 year old Pinus radiata stems. An experiment located south west of the Dunsandel township in Canterbury, New Zealand, was used to collect measures of acoustic velocity (windward and downward sides) from each of the 278 trees. Diameter at breast height, tree height, and height to live crown were also recorded for each tree. Findings from this research were compared with previous research carried out when the trees were ages eight and eleven. Assuming a green density of 1,000 kg/m3, Young’s Modulus equation was used to convert acoustic velocity to wood stiffness, or, Modulus of Elasticity (MOE). The effect of wind direction upon mean wood stiffness was not significant (α = 0.05). Consequently, one measure of wood stiffness was calculated per tree. Mean stem slenderness and mean wood stiffness values were calculated by block, weed control treatment, and clone. Weed control treatments had a significant impact upon mean wood stiffness in comparison to the control treatment (0.03 m2 area of weed control). Significant differences did not exist between different levels of weed control, ie., 0.75 m2, 3.14 m2 and 9 m2 chemical spot spray area. Clonal variation and stem slenderness significantly affected mean wood stiffness measures. Stem slenderness appeared to be correlated with clonal variation (interaction between clone and slenderness was not significant), however, according to Dr. Euan Mason, this finding is not corroborated by findings from other research on the wood quality of clones in Canterbury (personal communication, September 16, 2013). An analysis of covariance (ANCOVA) determined that mean height to the live crown was not a significant predictor of wood stiffness. Comparison with earlier research showed no change in the ranking of wood stiffness values by clone or treatment.

Mitochondrial DNA encodes thirteen protein subunits in the oxidative phosphorylation system (OXPHOS) that is responsible for cellular energy production. Mitochondrial disorders have been identified to be associated with mtDNA mutations. However, the molecular mechanisms of specific mtDNA mutations are still being explored in order to establish causative links. This study tries to elucidate the mutational effects of mtDNA on OXPHOS complex activities and cell growths. Using mouse 3T3 fibroblasts as a cell model, single-cell clones with different growth rates were isolated. The entire mtDNA genome was sequenced for mutations. The enzymatic activities of OXPHOS complex I to V were analysed. Three growth patterns represented by five clones were identified. Three clones (clone #2, #3, and #6) had the shortest doubling times (11.5 - 14.9 hours). Clone #1 had a medium growth rate (19.2 hous); and clone #5 had a significantly slow growth rate (22 hours). MtDNA sequencing results revealed that clone #5 had several heteroplasmic mutations (one in 16S rRNA, two in tRNAser (UCN), three in tRNAasp, one in tRNAlys, one in COI, five in COII, and one in ATPase8) while the other four clones showed sequence homology. Enzymatic analyses showed that on average clone #5 had significantly low complex III, IV, and V activities (p < 0.05). Changes in biochemical properties and protein structure were analyzed to deduct possible mechanisms for reduced respiration. In conclusion, the slow growth rate is associated with reduced OXPHOS enzyme functions. It is most likely that the combination of COI and COII mutations resulted in the reduction of complex IV function. It is still unclear whether the ATPase8 mutation (T7869A) in the non-conserved region alone can have such a pronounced phenotypic effect. A reduction in complex III also cannot be explained since there were no mutations in the only mtDNA-encoded complex III gene, but it is possible that there are mutations in the nDNA-encoded complex III genes. Mutations in tRNA and rRNA genes may also be responsible for reduced protein syntheses and consequently reduced OXPHOS activities. It is unclear why complex I activity was not affected. Although the mutational effect of individual mtDNA mutation observed cannot be clearly identified, this study establishes a correlation between mtDNA mutation and cell energy production and growth.

Thèse diffusée initialement dans le cadre d'un projet pilote des Presses de l'Université de Montréal/Centre d'édition numérique UdeM (1997-2008) avec l'autorisation de l'auteur.

Xenopus leavis was a favorite model organism during the 20th. century, but nowadays it has been replaced by diploid Xenopus tropicalis, which has not only shorter generation time, but also smaller genom. One of the disadvantages of Xenopus tropicalis is the lack of full physical and linkage map. According to JGI genome database (assembly 4.1) there are unmapped regions on short arm of the chromosome 2 and 7 . Several BAC clones ( with a single or dual-end sequence) has been found to be located within this region, according to a recent assembly 7.1. However , it isn't clear whether 100bp length of BAC ends is enough to place entire BAC clone into the genom of Xenopus tropicalis. In order to prove correct inclusion of these BAC clones into JGI database, several BAC clones, which are supposed to be located on short arm of chromosome 2, were picked. Using fluorescence in situ hybridisation, the signal of these BAC clones was localised on the short arm of chromosome 1 instead of chromosome 2 and in most cases they had opposite orientation. It means that the 100bp lenght of BAC ends propably isn't sufficient to place entire BAC clone on chromosome. New working protocol of BAC DNA isolation and labeling was established.

Code clone Discovery Based on Functional Behavior by Ronald M Krawitz 2012 Legacy programs are used for many years and experience many cycles of use-maintenance-use-maintenance-use-etc. Source code or source code functionality is frequently replicated within these programs when it is written, as well as when it is maintained. Over time many different developers with greater or lesser understanding of the source code maintain the source code. Maintenance developers, when they have limited time or lack understanding of the program, frequently resort to short cuts that include cutting and pasting existing code and re-implementing functionality instead of refactoring. This means a specific functionality is often repeated several times, sometimes using different source code. Blocks of replicated source code or source code functionality are called code clones. Removing code clones improves extensibility, maintainability, and reusability of a program in addition to making the program more easily understood. It is generally accepted that four types of code clones exist. Type-1 and Type-2 code clones are comparatively straightforward to locate and tools exist to locate them. However, Type-3 and Type-4 code clones are very difficult to locate with only a few specialized tools capable of locating them with a lower level of precision. This dissertation presents a new methodology that discovered code clones by studying the functional behavior of blocks of code. Code Clone Discovery based on Functional Behavior (FCD) located code clone by comparing how the blocks of code reacted to various inputs. FCD stimulated the code blocks with the same input patterns and compared the resulting outputs. When a significant portion of the outputs matched, those blocks were declared to be a code clone candidate. Manual analysis confirmed that those blocks of code were code clones. Since FCD discovered code clones based on their black-box behavior, the actual source code syntax was irrelevant and manual inspection further confirmed FCD located code clones that included Type-3 and Type-4 code clones which are frequently excluded from code clone detection tools. FCD recognized the code clones regardless of whether or not they use identical code, similar code, or totally dissimilar code. This new technique allows for an improvement in software quality and has the potential to significantly reduce the cost of software over its lifetime.

Software is often large, complicated and expensive to build and maintain. Redundant code can make these applications even more costly and difficult to maintain. Duplicated code is often introduced into these systems for a variety of reasons. Some of which include developer churn, deficient developer application comprehension and lack of adherence to proper development practices. Code redundancy has several adverse effects on a software application including an increased size of the codebase and inconsistent developer changes due to elevated program comprehension needs. A code clone is defined as multiple code fragments that produce similar results when given the same input. There are generally four types of clones that are recognized. They range from simple type-1 and 2 clones, to the more complicated type-3 and 4 clones. Numerous clone detection mechanisms are able to identify the simpler types of code clone candidates, but far fewer claim the ability to find the more difficult type-3 clones. Before CCCD, MeCC and FCD were the only clone detection techniques capable of finding type-4 clones. A drawback of MeCC is the excessive time required to detect clones and the likely exploration of an unreasonably large number of possible paths. FCD requires extensive amounts of random data and a significant period of time in order to discover clones. This dissertation presents a new process for discovering code clones known as Concolic Code Clone Discovery (CCCD). This technique discovers code clone candidates based on the functionality of the application, not its syntactical nature. This means that things like naming conventions and comments in the source code have no effect on the proposed clone detection process. CCCD finds clones by first performing concolic analysis on the targeted source code. Concolic analysis combines concrete and symbolic execution in order to traverse all possible paths of the targeted program. These paths are represented by the generated concolic output. A diff tool is then used to determine if the concolic output for a method is identical to the output produced for another method. Duplicated output is indicative of a code clone. CCCD was validated against several open source applications along with clones of all four types as defined by previous research. The results demonstrate that CCCD was able to detect all types of clone candidates with a high level of accuracy. In the future, CCCD will be used to examine how software developers work with type-3 and type-4 clones. CCCD will also be applied to various areas of security research, including intrusion detection mechanisms.

Submitted by MURILO RAPHAEL DE MELO null (engenhariasp@piraflora.com.br) on 2017-03-29T19:30:16Z No. of bitstreams: 1 Dissertação Modelo novo Final.pdf: 1070767 bytes, checksum: 9448e5eb4a8f905c67d161d2933a9827 (MD5) / Approved for entry into archive by LUIZA DE MENEZES ROMANETTO (luizamenezes@reitoria.unesp.br) on 2017-03-30T18:20:46Z (GMT) No. of bitstreams: 1 melo_mr_me_bot.pdf: 1070767 bytes, checksum: 9448e5eb4a8f905c67d161d2933a9827 (MD5) / Made available in DSpace on 2017-03-30T18:20:46Z (GMT). No. of bitstreams: 1 melo_mr_me_bot.pdf: 1070767 bytes, checksum: 9448e5eb4a8f905c67d161d2933a9827 (MD5) Previous issue date: 2017-02-03 / Um dos fatores que mais contribuem para queda da produtividade em mudas de Eucalyptus spp. são as doenças. Nos últimos anos tem se observado o aumento gradativo de doenças de origem bacteriana, principalmente de ocorrência foliar. A mancha foliar bacteriana ocorrem em mudas de eucalipto em todas as fases de produção do viveiro, podendo facilmente ser levada a campo, prejudicando o desenvolvimento inicial da muda. No presente estudo foi avaliado o efeito da severidade de bacteriose e da desfolha no crescimento pós-plantio de mudas de Eucalipto. As plantas avaliadas apresentaram um retardo no desenvolvimento devido a doença e a desfolha, no entanto, mantendo a adubação, após a recuperação, as mudas tiveram seu crescimento normalizado. / Diseases are one of the factors that most contribute to decrease the Eucalyptus spp. productivity. Now a day observe the gradual increase of bacterial origin diseases, mainly of foliar occurrence. The bacterial leaf spot occurs in eucalyptus seedlings at all stages of nursery production, and it can easily take to the field, damaging the initial development of the seedlings. In this study was evaluated the effect of bacterial leaf spot severity and defoliation on post-planting growth of Eucalyptus seedlings. The evaluated plants presented a delay in the development due to disease and defoliation; however, maintaining the fertilization, after the recovery, the seedlings had their growth normalized.

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