<p> Repair of double-strand breaks is critical for the preservation of genomic integrity and cellular viability. A predominant pathway implicated in the repair of such lesions is the evolutionarily conserved non-homologous end-joining (NHEJ) pathway. Among the major constituents of this pathway in Saccharomyces cerevisiae is Nej1, for which a clear biochemical function has not been determined. The results presented in this work demonstrate that Nej1 exhibits a DNA binding activity comparable to Lif1, with an apparent dissociation constant of 1.8 μM. Characterization of the DNA binding activity revealed that although short ~20 bp substrates can suffice, binding is enhanced with longer substrates (>300). This DNA binding activity supports the hypothesis that Nej1 plays a direct role in the repair of DNA double-strand breaks. Structure-function studies indicated that the C-terminus of Nej1 is not only required, but is sufficient, for mediating DNA interactions. Structural characterization revealed that Nej1 exists as a dimer, and that residues 1-244 are sufficient for dimer formation. Examining the ability of this truncated Nej1 (aa 1-244) to perform NHEJ, revealed a defect in end-joining as measured by an in vivo plasmid repair assay. Preliminary functional and structural studies on the Nej1-Lif1 complex suggest that the proteins stably co-purify and the complex binds DNA with a higher affinity than each independent component. The significance of these results is discussed with reference to current literature on Nej1 and other end-joining factors (mammalian and yeast), specifically the recently identified putative mammalian homologue of Nej1, XLF. Collectively, these results demonstrate that although there are several functional similarities, there also appear to be important differences in the structure-function relationships of Nej1 and XLF, and Nej1/XLF and Lif1/Xrcc4.</p> / Thesis / Master of Science (MSc)

The teratogenic effects of valproic acid (VPA) are well known, though its teratogenic mechanism remains unknown. VPA induces oxidative stress, which may lead to double strand breaks (DSBs) in DNA. Though the cell may repair this damage via homologous recombination (HR) and non-homologous end joining (NHEJ), repair is not always error-free; genomic instability may arise from gene deletions, amplifications, rearrangements, and loss of heterozygosity. Such alterations may underpin VPAʼs teratogenicity. The present study evaluated VPAʼs ability to induce NHEJ and HR and characterized the changes in expression of two proteins key to HR (RAD51) and NHEJ (XRCC4). Using pKZ1 transgenic mice (C57BL/6 genetic background), we sought to measure NHEJ events via X-gal staining. Although consistent staining was observed in adult male brain (positive control), no staining was observed in embryos 12 or 24 hours after in utero exposure to a teratogenic dose of VPA (500 mg/kg, maternal subcutaneous dose) on gestational day 9 (GD9). To determine whether the lack of staining observed in embryos was due to low/absent expression of key DSB-repair proteins, we measured mRNA/protein expression of RAD51 and XRCC4 in C57BL/6, GD9-exposed embryos and maternal brain. One hour after treatment, XRCC4 was increased at the protein level in brain and embryo. RAD51 was not increased in embryos and not detected in adult brain. These data suggest that embryos do possess the protein mediators of NHEJ and HR and that VPA-induced changes in expression of XRCC4 may influence the type of repair pursued, potentially affecting DSB repair fidelity (accuracy). Determination of fidelity of VPA-induced HR was attempted with the Chinese hamster ovary cell line (CHO33) using DNA sequencing; low template concentration and purity precluded successful sequencing of DNA from recombinant colonies and the assessment of fidelity. Overall, these data demonstrate that the lack of X-gal staining observed in pKZ1 embryos is not due to an underexpression of at least one key protein in the NHEJ pathway. Furthermore, a VPA-induced change in the the type of repair pathway pursued by the embryo may have teratological implications. / Thesis (Master, Pharmacology & Toxicology) -- Queen's University, 2012-10-15 11:06:30.613

De nombreuses études montrent un rôle important de l'architecture du noyau sur la stabilité du génome. Les lamines sont les constituants majeurs de l’enveloppe nucléaire et sont impliquées dans de nombreux processus, notamment, la régulation génique, la réplication et le maintien de la structure du noyau. Il en existe 2 types, les lamines A/C et les lamines B. Certaines mutations des lamines A/C sont à l’origine de syndromes progéroïdes, classés jusqu’à présents en deux catégories : ceux associés à une dérégulation des lamines (laminopathies) et ceux associés à un défaut de réparation de l’ADN, dont l’Ataxie Télangiectasie (A-T). Il est proposé que le vieillissement prématuré observé dans les laminopathies est dû à un défaut de réparation de l’ADN, qui serait alors la voie commune d’induction de sénescence des syndromes progéroïdes. Ceci est appuyé par le fait que de plus en plus de données associent les mutations des lamines A/C à des défauts de réparation de l’ADN. La mise en évidence, par notre laboratoire d’une accumulation de lamine B1 dans A-T et dans deux autres syndromes progéroïdes, pose la question de l’impact de la surexpression de la lamine B1 sur la réparation de l’ADN, d’autant plus que de plus en plus de données associent une augmentation de la lamine B1 à de nombreux cancers, bien que le mécanisme moléculaire ne soit pas connu. Au cours de ma thèse, j’ai donc pu montrer, notamment à l’aide de substrats intra-Chromosomiques, qu’une surexpression de lamine B1 entraînait un défaut de réparation des cassures double-Brin par NHEJ associé à un défaut de recrutement de 53BP1 à la cassure. La mise en évidence d’une interaction entre 53BP1 et la lamine B1, rompue après dommages permet de suggérer un nouveau rôle de la lamine B1 comme réservoir de 53BP1, régulant son recrutement aux cassures. De plus, d’autres résultats suggèrent que la lamine B1 agirait également au niveau de la signalisation du dommage en altérant l’activation d’ATM par un mécanisme qu’il reste à caractériser. L’ensemble de ces résultats montrent un nouveau rôle très important de la lamine B1 dans la signalisation des dommages et la régulation du recrutement des protéines de réparation, ouvrant la voie à une meilleure compréhension de l’implication de la lamine B1 dans la sénescence et le cancer. / Many studies show an important role of nuclear shape on genome stability. Lamins are the major components of the nuclear envelope and are implicated in numerous processes like gene regulation, DNA replication and the maintenance of nuclear structure. There are 2 types of lamins : lamin A/C and lamin B. Some mutations of lamin A/C cause progeroid syndromes, which are classified untill now in two categories : those due to lamins deregulation and those due to DNA repair defects, including Ataxia Telangiectasia (A-T). Accelerated aging observed in laminopathies is proposed to be due to a DNA repair defect, which would be the common pathway leading to senescence in progeroid syndromes. This is supported by many data linking lamin A mutations to DNA repair defects. Our laboratory reported that lamin B1 accumulates in A-T and Fanconi and another study showed also an accumulation in Werner syndrome, which is another progeroïd syndrome. This discovery raises a question about the impact of lamin B1 overexpression on DNA repair, especially as more and more data show an increase of lamin B1 in several cancers, although the molecular mechanism is still unclear. During my thesis, I showed, in particular with intrachromosomal substrates, that lamin B1 overexpression leads to an NHEJ double-Strand break (DSB) repair defect associated with a defect of 53BP1 recruitment to the break. The discovery of an interaction between 53BP1 and lamin B1, which is broken after damage, suggests a new role of lamin B1 as a « reservoir » of 53BP1, regulating its recruitment to the break. In addition, we obtained results suggesting that lamin B1 could also act in the DSB signalisation pathway by affecting ATM activation through a mechanism that we still have to characterize.All together, these datas show a new important role of lamin B1 in DSB signalisation and in the regulation of the recruitment of repair proteins, paving the way to a better understanding of the implication of lamin B1 in senescence and cancer.

L'hétérochromatine, de nature compacte et répétitive, limite l’accès à l'ADN et fait de la réparation des DSBs un processus difficile que les cellules doivent surmonter afin de maintenir leur intégrité génomique. Pour y étudier la réparation des DSBs, nous avons conçu un système CRISPR / Cas9 dans lequel les DSB peuvent être efficacement et spécifiquement induites dans l'hétérochromatine de fibroblastes de souris NIH3T3. En développant un système CRISPR / Cas9 hautement spécifique et robuste pour cibler l'hétérochromatine péricentrique, nous avons montré que les DSB en G1 sont positionnellement stables et réparés par NHEJ. En S / G2, ils se déplacent vers la périphérie de ce domaine pour être réparés par HR. Ce processus de relocalisation dépend de la résection et de l'exclusion de RAD51 du domaine central de l'hétérochromatine. Si ces cassures ne se relocalisent pas, elles sont réparées dans le cœur du domaine de l'hétérochromatine par NHEJ ou SSA. D'autre part, les DSBs dans l'hétérochromatine centromérique activent NHEJ et HR tout au long du cycle cellulaire. Nos résultats révèlent le choix de la voie de réparation différentielle entre l'hétérochromatine centromérique et péricentrique, ce qui régule également la position des DSBs. / Heterochromatin is the tightly packed form of repetitive DNA, essential for cell viability. Its highly compacted and repetitive nature renders DSB repair a challenging process that cells need to overcome in order to maintain their genome integrity. Developing a highly specific and robust CRISPR/Cas9 system to target pericentric heterochromatin, we showed that DSBs in G1 are positionally stable and repaired by NHEJ. In S/G2, they relocate to the periphery of this domain to be repaired by HR. This relocation process is dependent of resection and RAD51 exclusion from the core domain of heterochromatin. If these breaks fail to relocate, they are repaired within heterochromatin by NHEJ or SSA. On the other hand, DSBs in centromeric heterochromatin activate both NHEJ and HR throughout the cell cycle. Our results reveal the differential repair pathway choice between centromeric and pericentric heterochromatin that also regulates the DSB position.

L'hétérochromatine est une caractéristique conservée des chromosomes eucaryotes, avec des rôles centraux dans la régulation de l'expression des gènes et le maintien de la stabilité du génome. Comment la réparation de l'ADN est régulée par l'hétérochromatine reste mal compris. Chez Saccharomyces cerevisiae, le complexe SIR (Silent Information Regulator) assemble une fibre de chromatine compacte. La chromatine SIR limite la résection aux cassures double-brin (DSB) protégeant les extrémités chromosomiques endommagées contre la perte d'informations génétiques. Toutefois, lesquels des trois complexes de résection redondants, MRX-Sae2, Exo1 et Sgs1-Dna2 sont inhibés et par quel(s) mécanisme(s) reste à decouvrir. Nous montrons que Sir3, le facteur de fixation des histones de l’hétérochromatine de Saccharomyces cerevisiae, interagit physiquement avec Sae2 et inhibe toutes ses fonctions. Cette interaction limite notamment la résection médiée par Sae2, stabilise MRX à la DSB et augmente le Non-Homologous End Joining (NHEJ). De plus, la chromatine répressive SIR inhibe partiellement les deux voies de résection extensive médiées par Exo1 et Sgs1-Dna2 par des mécanismes distincts. L'inhibition par les SIR de la résection extensive et de Sae2 favorise la NHEJ et limite le Break-Induced Replication (BIR), prévenant ainsi de la perte d'hétérozygotie au niveau des subtélomères. / Heterochromatin is a conserved feature of eukaryotic chromosomes, with central roles in regulation of gene expression and maintenance of genome stability. How DNA repair occurs in heterochromatin remains poorly described. In Saccharomyces cerevisiae, the Silent Information Regulator (SIR) complex assembles a compact chromatin fibre. SIR-mediated repressive chromatin limits Double Strand Break (DSB) resection protecting damaged chromosome ends against the loss of genetic information. However, which of the three redundant resection complexes, MRX-Sae2, Exo1 and Sgs1-Dna2 are inhibited and by which mechanism remains to be deciphered. We show that Sir3, the histone-binding factor of yeast heterochromatin, physically interacts with Sae2-mediated resection and inhibits all its functions. Notably, this interaction limits Sae2-mediated resection, delays MRX removal from DSB ends and promotes Non-Homologous End Joining (NHEJ). In addition, SIR-mediated repressive chromatin partially inhibits the two long range resection pathways mediated by Exo1 and Sgs1-Dna2 by distinct mechanisms. Altogether SIR mediated inhibition of extensive resection and of Sae2 promotes NHEJ and limits Break-Induced Replication (BIR) preventing loss of heterozygosity at subtelomeres.

A vast array of high value parts in land- and air-based turbomachinery are subjected to non-isothermal cycling in the presence of mechanical loading. Crack initiation, growth and eventual failure more significantly reduce life in these components compared to isothermal conditions. More accurate simulation of the stress and strain evolution at critical locations of components, as well as test specimens, can lead to a more accurate prediction of remaining life to a structural integrity specialists. The focus of this thesis is to characterize the effects of thermomechanical fatigue (TMF) on generic turbomachinery alloy. An expression that can be used to estimate the maximum and minimum stress under a variety of loading conditions is formulated. Analytical expressions developed here are modifications of classic mechanics of materials methods (e.g. Neuber's Rule and Ramberg-Osgood). The novel models are developed from a collection of data based on parametric finite element analysis to encompass the complex load history present in turbine service conditions. Relevance of the observations and formulated solutions are also explored for the case of a tensile specimen containing a v-shaped notch. Accurate estimations of non-isothermal fatigue presented here endeavor to improve component lifing and decrease maintenance costs.

One of the major outcomes of a genome sequencing project is the availability of amino acid sequences of all the proteins encoded in the genome of the organism concerned. However, most commonly, for a substantial proportion of the proteins encoded in the genome no information in function is available either from experimental studies or by inference on the basis of homology with a protein of known function. Even if the general function of a protein is known, the region of the protein corresponding to the function might be a domain and there may be additional regions of considerable length in the protein with no known function. In such cases the information on function is incomplete. Lack of understanding of the repertoire of functions of proteins encoded in the genome limits the utility of the genomic data. While there are many experimental approaches available for deciphering functions of proteins at the genomic scale, bioinformatics approaches form a good early step in obtaining clues about functions of proteins at the genomic scale (Koonin et al, 1998). One of the common bioinformatics approaches is recognition of function by homology (Bork et al, 1994). If the evolutionary relationship between two proteins, one with known function and the other with unknown function, could be established it raises the possibility of common function and 3-D structure for these proteins(Bork and Gibson, 1996). While this approach is effective its utility is limited by the ability of the bioinformatics approach to identify related proteins when their evolutionary divergence is high leading to low amino acid sequence similarity which is typical of two unrelated proteins (Bork and Koonin, 1998). Use of 3-D structural information, obtained by predictive methods such as fold recognition, has offered approaches towards increasing the sensitivity of remote homology detection 9e.g., Kelley et al, 2000; Shi et al, 2001; Gough et al, 2001). The work embodied in this thesis has the general objective of analysis of evolution of structural features and functions of families of proteins and design of new bioinformatics approaches for recognizing distantly related proteins and their applications. After an introductory chapter, a few chapters report analysis of functional and structural features of homologous protein domains. Further chapters report development and assessment of new remote homology detection approaches and applications to the proteins encoded in two protozoan organisms. A further chapter is presented on the analysis of proteins involved in methylglyoxal detoxification pathways in kinetoplastid organisms. Chapter I of the thesis presents a brief introduction, based on the information available in the literature, to protein structures, classification, methods for structure comparison, popular methods for remote homology detection and homology-based methods for function annotation. Chapter 2 describes the steps involved in the update and improvements made in this database. In addition to the update, the domain structural families are integrated with the homologous sequences from the sequence databases. Thus, every family in PALI is enriched with a substantial volume of sequence information from proteins with no known structural information. Chapter 3 reports investigations on the inter-relationships between sequence, structure and functions of closely-related homologous enzyme domain families. Chapter 4 describes the investigations on the unusual differences in the lengths of closely-related homologous protein domains, accommodation of additional lengths in protein 3-D structures and their functional implications. Chapter 5 reports the development and assessment of a new approach for remote homology detection using dynamic multiple profiles of homologous protein domain families. Chapter 6 describes development of another remote homology detection approach which are multiple, static profiles generated using the bonafide members of the family. A rigorous assessment of the approach and strategies for improving the detection of distant homologues using the multiple profile approach are discussed in this chapter. Chapter 7 describes results of searches made in the database of multiple family profiles (MulPSSM database) in order to recognize the functions of hypothetical proteins encoded in two parasitic protozoa. Chapter 8 describes the sequence and structural analyses of two glyoxalase pathway proteins from the kinetoplastid organism Leishmania donovani which causes Leishmaniases. An alternate enzyme, which would probably substitute the glyoxalase pathway enzymes in certain kinetoplastid organisms which lack the glyoxalase enzymes are also discussed. Chapter 9 summarises the important findings from the various analyses discussed in this thesis. Appendix describes an analysis on the correlation between a measure of hydrophobicity of amino acid residues aligned in a multiple sequence alignment and residue depth in 3-D structures of proteins.

The type 1 insulin-like growth factor receptor (IGF-1R) is a receptor tyrosine kinase that mediates diverse cellular functions including growth, differentiation, migration and apoptosis protection. IGF-1R signalling has been implicated in tumorigenesis in a variety of cancers, and IGF-1R inhibitory drugs are currently undergoing clinical evaluation. Previous work in our laboratory has shown IGF-1R over-expression in urological cancers at both the mRNA and protein level, thus making it a potential therapeutic target. The first aim of this project was to develop a protocol for IGF-1R immunohistochemistry, investigate the expression and cellular distribution of the IGF-1R receptor in clear cell renal cell carcinomas (ccRCC), and assess correlation with clinical parameters. In tissue microarray analysis, IGF-1R was detected in ~90% of 195 ccRCCs, with signal in the plasma membrane, cytoplasm and also in the nucleus. The presence of nuclear IGF-1R in up to 50% of ccRCCs and its association with adverse prognosis was a novel finding, and suggests that nuclear IGF-1R may influence ccRCC biology. Further investigations will clarify its role in the nucleus and its potential as a prognostic biomarker. The second aim was to investigate effects of IGF-1R inhibition on radiosensitivity and DNA repair, following previous work in our laboratory showing that IGF-1R depletion enhances chemo- and radio-sensitivity, delays double strand break (DSB) resolution, and may play a role in the homologous recombination (HR) pathway of DNA DSB repair. However, the repair defect seen in these early experiments was larger than could be entirely explained by a defect in HR. The current project used a small molecule IGF-1R tyrosine kinase inhibitor AZ12253801 (AstraZeneca), which blocked IGF-1 induced IGF-1R activation and inhibited cell survival. AZ12253801 enhanced the radiosensitivity of prostate cancer cells, which appeared to be independent of effects of IGF-1R inhibition on cell cycle distribution and apoptosis induction. IGF-1R inhibition delayed the resolution of γH2AX foci, supporting a potential role for the IGF-1R in DSB repair. This delay in focus resolution was apparent at early time-points (less than 4 hr), and was epistatic with DNA dependent protein kinase (DNAPK) inhibition in prostate cancer cells and DNAPK deficiency in glioblastoma cells. These results suggest a role for the IGF-1R in the non-homologous end-joining (NHEJ) pathway of DNA DSB repair. A cell-based reporter assay in HEK-293 cells confirmed that IGF-1R inhibition suppressed DSB repair by NHEJ, helping to explain the radiosensitization demonstrated upon IGF-1R inhibition. There was lack of support for a transcriptional effect, with no significant change observed in gene expression on microarray analysis. Although the mechanism of this effect remains unclear, the observed inhibition of NHEJ has implications for the use of IGF-1R inhibitors in combination with DNA damaging agents in cancer treatment.

All human chromosomes end with protective structures called telomeres, which consist of thousands of double-stranded TTAGGG repeats and end in a 3’ guanine-rich overhang. These structures shorten normally during each round of replication, and extremely short telomeres along with telomere dysfunction are thought to contribute to the development of aging and cancer. Although many proteins have roles in telomere maintenance, WRN, which is a 3’ to 5’ helicase that is deficient in the premature aging disorder Werner’s syndrome, has been proposed to play multiple roles at telomeres. In this study, I focus on the effect of telomeric sequences and/or structures formed during DNA replication or recombination and how WRN functions at these sites. This study suggests that WRN may promote proper replication of telomeres by accurately aligning telomeric sequences during replication fork regression, potentially the first step in responding to a blockage, such as DNA damage. However, even in the presence of WRN, replication of telomeric sequences is difficult, possibly due to the ability of G-rich sequences to form secondary structures such as G-quadruplexes. I demonstrate that the translesion polymerase pol η, as well as a variety of other polymerases, is unable to synthesize past an intramolecular G-quadruplex formed from telomeric sequence on the template strand. Furthermore, in physiological salt concentrations, WRN favors binding and unwinding a structure that mimics a strand invasion intermediate over other similar structures especially when it possesses G-telomeric sequence. In addition, WRN promotes unwinding of these structures in a direction that would promote additional annealing and strand invasion, supporting a role for WRN in promoting telomeric recombination and formation of a T-loop, a proposed protective structure specific to telomeres. Overall, the data suggest that telomeres may pose problems in replication due to the G-rich, repeating nature of the structures, while WRN may aid in promoting proper replication at these and other replication blocks. Furthermore, WRN may play a role in promoting additional formation of T-loops and other telomeric recombination, thus supporting the relationship of WRN, telomere maintenance, and potentially development of certain aging characteristics.

We examine the evolution of globular star clusters, modelled as spherically symmetric stellar systems, using various techniques. Such clusters possess a central region of approximately uniform density which is referred to as the core. We concentrate our analysis on the evolution of the cluster after the core has undergone core collapse; a process where its radius decreases and its density increases. After this collapse, the system as a whole can expand in a self-similar fashion (homologous post-collapse evolution) which has long been thought to be due to gravitational interactions between different populations of single stars and binary stars in the core. We confirm this assumption by constructing a simple analytical model which combines much of the theoretical knowledge of previous research in the field. This model consists of two stellar populations, each defined by the mass of the individual stars, and a separate core. Our simple model is itself constructed from two simpler models – a twocomponent model without a core and a single mass model with a core – and takes into account the main gravitational interactions thought to drive the post-collapse evolution. To ensure that no important mechanisms have been neglected in our simple model, we will compare it with an N-body simulation. We compute our N-body models with NBODY6 (using a GPU version for large N). When we compare the N-body model with the simple model, we find qualitative agreement between them for most cases. Even though some mechanisms (e.g. escape of stars) are neglected in our simple model, we find that both models show homologous post-collapse evolution. We also review the homologous post-collapse Fokker-Planck model in the case of equal stellar masses derived by H´enon (1961) with the intention of extending this for the two-component case. We present our numerical solutions for H´enon’s model and find that our numerical solutions are in satisfactory agreement with the results shown in this paper. When we extend this work for a general two-component model (i.e. with no restriction on the number of heavier stars), we find that a homologous solution cannot be found with this approach. By contrast, we suggest that it would be possible to find a homologous two-component solution by extending the one-component solution published later by H´enon (1965), which differs from the earlier model by neglecting the external tidal field of the parent galaxy. Much of the work shown in this thesis would be relevant for such future study.