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Chromosomal rearrangements can lead to loss of heterozygosity (LOH) and oncogene activation, both of which represent possible causative events in cancer development. Such outcomes can result from the misrepair of DNA damage arising from a variety of events including DNA double-strand breaks (DSBs), collapsed replication forks, and dysfunctional telomeres. In response to a DSB, chromosomal stability is principally maintained through the two major DNA repair pathways; non- homologous DNA end-joining (NHEJ) and homologous recombination (HR). The objective of this thesis was to identify novel factors functioning in prevention of chromosomal instability in response to a DSB in Schizosaccharomyces pombe. To achieve this, a central aim was to identify the genes mutated in a number of radiation-sensitive mutants in fission yeast, previously isolated by the laboratory. These include the ‘loh’ mutants loh-2, loh-5, loh-6 and loh-7, which were found to harbour mutations in known DNA repair genes rad3, rad17, and rad57. Further, a pan-genomic screen for novel HR repair factors was carried out. The Bioneer Version 2 deletion-library, consisting of 3308 haploid deletion strains, was screened for strains displaying hypersensitivity to the DNA damaging agents MMS, bleomycin and camptothecin. This screen yielded 209 hits which were further characterised, utilising a set of non-essential Ch¹⁶ minichromosomes . The minichromosome Ch¹⁶-LMYAU harbours an HO endonuclease recognition sequence and a centromere-distal ade6-M216 heteroallele. Following break-induction, failed repair of the DSB leads to loss of the ade6 allele, indicated by pink sectoring on low adenine plates. 39 sectoring hits were identified and further characterised to quantify levels of gene conversion via HR in response to a DSB, utilising Ch¹⁶-RMYAH. As a result of this study, a group of novel genes functioning in HR repair were identified. Finally, one of these hits, putative RNA metabolism protein Nrl1, was subjected to further characterisation, associating this protein with DNA damage repair for the first time. The work presented here, documents the approaches taken to successfully identify novel DNA repair factors in fission yeast.

The human endometrium is a dynamic, multi-cellular tissue that lines the inside of the uterine cavity. During a woman’s reproductive lifespan the endometrium is subjected to cyclical episodes of proliferation, angiogenesis, differentiation/decidualisation, shedding (menstruation), repair and regeneration in response to fluctuating levels of oestrogen and progesterone secreted by the ovaries. The endometrium displays unparalleled, tightly regulated, tissue remodelling resulting in a healed, scar-free tissue following menses or parturition. Mechanisms responsible for initiation of menses have been well documented: following progesterone withdrawal there is an increase in inflammatory mediators, focal hypoxia and induction and activation of matrix-degrading enzymes. In contrast, the molecular and cellular changes responsible for rapid, regulated, tissue repair at a time when oestrogen and progesterone are low are poorly understood. Histological studies using human menstrual phase endometrium have revealed that tissue destruction and shedding occur in close proximity to re-epithelialisation/repair. It has been proposed that re-epithelialisation involves proliferation of glandular epithelial cells in the remaining basal compartment; there is also evidence for a contribution from the underlying stroma. A role for androgens in the regulation of apoptosis of endometrial stromal cells has been proposed but the impact of androgens on tissue repair has not been investigated. Studies using human xenografts and primates have been used to model some aspects of the impact of progesterone withdrawal but simultaneous shedding (menses) and repair have not been modelled in mice; the species of choice for translational biomedical research. In the course of the studies described in this thesis, the following aims have been addressed: 1. To establish a model of menses in the mouse which mimics menses in women, namely; simultaneous breakdown and repair, overt menstruation, immune cell influx, tissue necrosis and re-epithelialisation. 2. To use this model to determine if the stromal cell compartment contributes to endometrial repair. 3. To examine the impact of androgens on the regulation of menses (shedding) and repair. An informative mouse model of endometrial breakdown that was characterised by overt menses, as well as rapid repair, was developed. Immunohistological evidence for extensive tissue remodelling including active angiogenesis, transient hypoxia, epithelial cell-specific proliferation and re-epithelialisation were obtained by examining uterine tissues recovered during an “early window of breakdown and repair” (4 to 24 hours after progesterone withdrawal). Novel data included identification of stromal cells that expressed epithelial cell markers, close to the luminal surface following endometrial shedding, suggesting a role for mesenchymal to epithelial transition (MET) in re-epithelialisation of the endometrium. In support of this idea, array and qRTPCR analyses revealed dynamic changes in expression of mRNAs encoded by genes known to be involved in MET during the window of breakdown and repair. Roles for hypoxia and tissue-resident macrophages in breakdown and tissue remodelling were identified. Treatment of mice with dihydrotestosterone to mimic concentrations of androgens circulated in women at the time of menses had an impact on the timing and duration of endometrial breakdown. Array analysis revealed altered expression of genes implicated in MET and angiogenesis/inflammation highlighting a potential, previously unrecognised role for androgens in regulation of tissue turnover during menstruation. In summary, using a newly refined mouse model new insights were obtained, implicating androgens and stromal MET in restoration of endometrial tissue homeostasis during menstruation. These findings may inform development of new treatments for disorders associated with aberrant repair such as heavy menstrual bleeding and endometriosis.

The lexA protein in E. coli is a specific repressor of the recA gene. The lexA protein is cleaved by the recA protein in response to DNA damage. Cleavage derepresses the recA gene resulting in high level synthesis of recA protein and the expression of other DNA damage inducible functions (SOS functions). The lexA3 mutation makes the lexA protein resistant to cleavage and thus inhibits expression of DNA damage inducible functions. A mutant of E. coli has been isolated which exhibits many of the properties expected of a strain carrying an operator-constitutive mutation in the recA gene. The mutation partially suppresses the UV sensitivity of lexA3 strains, maps near the recA structural gene, allows constitutive synthesis of the recA protein and the recA message, and is cis-acting. Strains carrying the recAo('c) mutation were used to study the role of amplified levels of recA protein in the expression of certain SOS functions. The recAo('c) mutation did not suppress the UV inhibitory effect of the lexA3 mutation on the expression of UV induced cellular mutagenesis, and the reactivation and mutagenesis of UV irradiated phage (lamda). The expression of these functions in lexA('+) strains was not enhanced by the recAo('c) mutation. Constitutive recA synthesis did not result in lethal filamentous growth. These results are consistent with those reported elsewhere that the expression of SOS function is not dependent on high levels of recA protein and that the various "SOS genes" are repressed by the lexA protein as is the recA gene. Thus, recA protein is required in SOS expression for the inactivation of lexA protein and recA amplification is a consequence, not a cause of SOS expression. The DNA sequence of the recA operator region from a (lamda)precA transducing phage thought to carry the recAo('c) mutation isolated here, was determined. No difference was detected between the supposed mutant DNA and wild type controls. The significance of these results and the possibility that the recAo('c) mutation was not transferred to the phage are discussed.

The product of the Escherichia coli lexA gene has been identified, and the regulation of lexA gene expression in vivo has been examined. A series of specialized transducing phages carring lexA⁺ and 3 different amber lexA alleles was constructed by in vivo recombination between λlexA3 and host lexA alleles. These phages were characterized extensively to confirm that they carried the appropriate lexA allele. The lexA gene product was identified by comparison of the polypeptides encoded by λlexA3 and the amber lexA phages. A 24,000 dalton polypeptide, synthesized after infection of both amber-suppressor and non-suppressor hosts by λlexA3 was not synthesized following amber lexA phage infection of non-suppressor hosts. Synthesis of this polypeptide following amber lexA phage infection was restored by the presence of an amber suppressor mutation in the host. On the basis of these data, the 24,000 dalton polypeptide was identified as the lexA gene product. Regulation of lexA gene expression in vivo was examined by hybridization experiments to measure lexA mRNA levels. The basla level of lexA mRNA in wild type E. coli was found to be .006% of total mRNA. Treatment of the bacteria with 100 erglmm² ultraviolet irradiation (UV) led to an eight-fold increase in lexA mRNA levels within 10 minutes, the lexA mRNA remained elevated until 70 minutes after irradiation, then slowly declined. By comparison, the level of recA mRNA increased from .05% to .51% of total mRNA within 10 minutes following UV irradiation, then declined. Both lexA and recA genes were induced by nalidixic acid treatment; the induction was not as rapid as UV induction and different relative induction kinetics of the two genes were seen. The levels of lexA and recA mRNAS were measured in several mutant strains following UV-irradiation.

The Secretary of the Interior’s Standards for the Treatment of Historic Buildings promote repair rather than replacement of deteriorated features when possible. Though replacement and retrofitted elements may provide improved energy efficiency with a minor impact on appearance, there is currently no guide for objectively considering the potential benefits of such treatments for historic buildings. In an effort to provide decision-making tools to those seeking to balance both preservation and economic/ sustainability concerns, this thesis will present an approach to weighing treatment options specifically for windows, including modifications for energy efficiency that are not specifically endorsed by the Secretary of the Interior’s Standards. This thesis explores the critical decision processes involved in selecting to repair or replace deteriorated historic windows, and examines those of the Main Building Tower of the University of Texas as a case study. The steel windows of the Tower, which was completed in 1937, suffer from corrosion and are not performing optimally in terms of energy efficiency. An understanding of the history and significance of the building, the current condition and performance of the windows, balanced against project-specific goals and an evaluation of current treatment options for historic windows helped narrow the potential options for the Tower. Including a “decision tree” that assists users in selecting an appropriate treatment, this thesis maps the considerations necessary to arrive at an informed solution, which may be applied to other projects with varying existing conditions and project objectives. / text

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