O dano muscular induzido pelo exercício (DMIE) e os diferentes elementos envolvidos em seu processo têm sido amplamente estudados. A doença periodontal (DP), por sua vez, tem sido indicada como um possível fator de risco para várias condições sistêmicas, como diabetes, doenças cardiovasculares, partos prematuros, obesidade, entre outros. Tais associações têm sido atribuídas à possibilidade de que a DP possa induzir um processo de inflamação sistêmica de baixa intensidade, caracterizado pela elevação de biomarcadores sanguíneos que também estão envolvidos no mecanismo de dano muscular induzido pelo exercício (DMIE). O objetivo do presente estudo é investigar se a doença periodontal pode atuar como um modificador do DMIE em homens saudáveis. Foram avaliados 40 indivíduos, com idade entre 25 e 45 anos, que buscaram atendimento na faculdade de odontologia da UFRGS ou eram praticantes de atividades físicas. Questionário estruturado para obtenção de dados demográficos e comportamentais e o IPAQ (International Physical Activity Questionnaire) foram aplicados. Dois periodontistas examinaram perda de inserção (PI), profundidade de sondagem, sangramento à sondagem e índices de placa e sangramento gengival no exame basal, juntamente com avaliações antropométricas. Os participantes então realizaram um protocolo de indução de dano muscular que incluiu cinco séries de 15 contrações excêntricas máximas dos quadríceps de uma perna, em um dinamômetro isocinético. Força muscular (contrações isométricas voluntárias máximas - CIVM), espessura e ecogenicidade muscular (ultrassonografia) e dor (escala visual analógica) foram avaliadas em diferentes momentos em relação ao protocolo. Modelos de regressão logística multivariados foram ajustados para idade, educação, índice de massa corporal, fumo, consumo de álcool, proteína C reativa e nível de atividade física. Nessa amostra, PI esteve associada a maiores reduções de força muscular após o protocolo, com um aumento de 1 mm na média de PI representando 7% a mais de redução na CIVM. Pode-se concluir, a partir dessa análise preliminar, que a doença periodontal pode ser considerada um modificador do processo de dano muscular, aumentando a deterioração da força muscular. / Exercise-induced muscle damage (EIMD) and the different elements involved in it´s process has been largely studied. Periodontal diseases (PD) has been pointed out as a possible risk fator for a number of systemic conditions, like diabetes, cardiovascular diseases, preterm birth, obesity, and others. Such associations has been atribbuted to the fact that PD can lead to a low-grade inflammatory process, characterized by elevated blood concentrations of biomarkers that are also involved in the EIMD mechanisms. The aim of this study is to assess whether PD can act as a EIMD modifier in healthy men. This study included 40 healthy males with 25-45 yrs that seek for treatment at Dentistry Faculty or are physical activiy practitioners. A structured questionnaire to obtain demographic and comportamental data and the IPAQ (International Physical Activity Questionnaire) were applied. Two periodontists assessed attachment loss (AL), probing depth (PD), bleeding on probing (BOP), plaque and bleeding index in the baseline exam, together with anthropometrical evaluation. The participants then performed a muscle damage protocol comprising five sets of 15 maximum eccentric contractions of the quadriceps muscles of one leg in a isokinetic dynamometer. Evaluations of muscle strength (maximal voluntary isometric contraction), muscle thickness and echo intensity (ultrasonography images) and soreness (visual analogue scale) were made at different periods in relation to the protocol. Multivariable logistic models were fitted adjusting for age, education, body mass index (BMI), smoking, alcohol consumption, C-reactive protein (CRP) and physical activiy level. In this sample, AL was associated with higher reductions of muscle force, with a 1- mm increment in AL mean significantly decreased CIVM by 7%. It can be concuded, based on this preliminar analysis, that PD may be considered as a modifier of EIMD, increasing muscle strenght deterioration.

Double-strand breaks (DSBs) are highly cytotoxic DNA lesions that are usually repaired by two major mechanisms: non-homologous end joining (NHEJ) and homologous recombination (HR). HR is initiated by 5'-3' resection, generating 3' single stranded DNA tails coated by Replication protein A (RPA), which can be used in later steps for homology search and repair. The 5'-3' resection step is a critical determinant of repair pathway choice that commits cells to HR instead of NHEJ, and it's also required for DNA damage checkpoint activation. Studies in the budding yeast Saccharomyces cerevisiae have shown that the conserved Mre11-Rad50-Xrs2 (MRX) complex, together with Sae2, initiates end resection while more extensive processing of 5' strands requires the 5'-3' exonuclease Exo1, or the combined activities of the Sgs1 helicase and Dna2 endonuclease. In this thesis we will discuss the function of RPA and Sae2 based on our experimental observations. RPA is an essential eukaryotic single-stranded DNA binding protein with a central role in DNA metabolism. It has been shown in vitro that RPA directly participates in end resection by stimulating the Sgs1 helicase and Dna2 endonuclease. To investigate the role of RPA for end resection in vivo, we used a heat-inducible degron allele (td-RFA1) that allows rapid conditional depletion of RPA in Saccharomyces cerevisiae. Complete loss of RPA resulted in a defect in both the Exo1 and Sgs1-Dna2 extensive resection mechanisms, while resection initiation by MRX-Sae2 was unaffected. Interestingly, Dna2 was unable to localize to DSBs in the absence of RPA, whereas Exo1 localization was unaffected indicating that the role of RPA in the resection pathways is distinct. The short single-stranded DNA tails formed in the absence of RPA were unstable, represented by 3' strand loss and formation of foldback hairpin structures. Thus, RPA is required to generate ssDNA, and also to protect ssDNA from degradation and inappropriate annealing that could lead to genome rearrangements. While Mre11 possesses 3'-5' dsDNA exonuclease and ssDNA endonuclease activities, Sae2 was reported to activate its endonuclease activity, which initiates end resection. We identified mre11-P110L and four more mutants from a screen that bypass Sae2 for camptothecin (CPT) and MMS resistance. None of them restored endonuclease activity, neither did they improve resection. Persistent Mre11 foci and hyper-checkpoint signaling caused by sae2Δ upon DNA damage was suppressed by mre11-P110L. These findings demonstrate that the DNA damage sensitivity of sae2Δ is not caused by defective resection, but by failure to remove MRX from ends and switch off checkpoint.

DNA is continuously subjected to various types of damage during normal cellular metabolism. Among these, a DNA double-strand break (DSB) is one of the most cytotoxic lesions, and can lead to genomic instability or cell death if misrepaired or left unrepaired. The Mre11-Rad50-Xrs2/Nbs1 (MRX/N) complex orchestrates the cellular response to DNA damage through its structural, enzymatic, and signaling roles. It senses DSBs and is essential for both of the two major repair mechanisms: non-homologous end joining (NHEJ) and homologous recombination (HR). In addition, the complex tethers DNA ends, activates Tel1/ATM kinase, resolves hairpin capped DNA ends and maintains telomere homeostasis. Although significant progress has been made in characterizing the complex, many questions regarding the precise mechanism of how this highly conserved, multifunctional complex manages its various activities in chromosome metabolism remain to be solved. The overarching focus of this thesis is to further expand our understanding of the molecular mechanism and regulation of the MRX complex. Specifically, the contributions of Xrs2, Tel1, and Mre11 3’-5’ dsDNA exonuclease in the multiple roles of the MRX complex are examined. Xrs2/Nbs1, the eukaryotic-specific component of the complex, is required for the nuclear transport of Mre11 and Rad50 and harbors several protein-interacting domains. In order to define the role of Xrs2 as a component of the MRX complex once inside the nucleus, we fused a nuclear localization signal (NLS) to the C terminus of Mre11 and assayed for complementation of xrs2Δ defects. We found that nuclear localization of Mre11 (Mre11-NLS) is able to bypass several functions of Xrs2, including DNA end resection, meiosis, hairpin resolution, and cellular resistance to clastogens. Using purified components, we showed that the MR complex has the equivalent activity to MRX in cleavage of protein-blocked DNA ends. Although Xrs2 physically interacts with Sae2, end resection in its absence remained Sae2 dependent in vivo and in vitro. MRE11-NLS was unable to rescue the xrs2Δ defects in Tel1 kinase signaling and NHEJ, consistent with the role of Xrs2 as a chaperone and adaptor protein coordinating interactions between the MR and other repair proteins. To further characterize the role of Xrs2 in Tel1 activation, we fused the Tel1 interaction domain of Xrs2 to Mre11-NLS (Mre11-NLS-TID). Mre11-NLS-TID was sufficient to restore telomere elongation and Tel1 signaling to Xrs2-deficient cells, indicating that Tel1 recruitment and activation are separate functions of the MRX complex. Unexpectedly, we found a role for Tel1 in stabilizing Mre11-DNA association independently of its kinase activity. This stabilization function becomes important for DNA damage resistance in the absence of Xrs2. Moreover, while nuclear-localized MR complex is sufficient for HR without Xrs2, MR is insufficient for DNA tethering, stalled replication fork stability, and suppression of chromosomal rearrangements. Enforcing Tel1 recruitment to the MR complex fully rescued these defects, highlighting the important roles for Xrs2 and Tel1 in stabilizing the MR complex to prevent replication fork collapse and genomic instability. Lastly, in order to decipher the functional significance of the Mre11 3’-5’ dsDNA exonuclease activity in DSB repair, mre11 mutant alleles reported to be proficient endonuclease and deficient exonuclease were analyzed in vivo and in vitro. Although we did not observe a clear separation of the nuclease activities in vitro, our genetic analysis of the mutant allele is consistent with the current two-stepped, bidirectional model of end resection.

DNA sequence information is constantly threatened by damage. In the clinic, intentional DNA damage is often used to treat cancer. Cisplatin, a first-line chemotherapy used to treat millions of patients, functions specifically by generating physical links within DNA strands, blocking DNA replication, and killing dividing cells. To maintain genome integrity, organisms have evolved the capacity to repair, respond, or otherwise resist change to the DNA sequence through a network of genetically encoded DNA damage tolerance pathways. In chapter 1, I present advances in experimental design and current progress for a systems genetics approach, using Saccharomyces cerevisiae, to reveal relationships between cisplatin tolerance pathways. Additionally, recent efforts to sequence thousands of cancer genomes have revealed recurrent genetic changes that cause overexpression of specific cisplatin tolerance genes. In chapter 2, I present a submitted manuscript that models overexpression of an essential cisplatin tolerance gene. This study uses a systems genetics approach to reveal the genetic pathways that are essential for tolerating this perturbation, which ultimately led to mechanistic insights for this gene. Convenient genome engineering in Saccharomyces has made this organism an ideal model to develop systems genetics concepts and approaches. In chapter 3, I present a published manuscript that demonstrates a new approach to disrupting genes by making site-specific nonsense mutations. Importantly, this approach does not require cytotoxic double-strand DNA breaks and is applicable to many model organisms for disrupting almost any gene, which may advance systems genetics into new model organisms. Systems genetics provides a framework for determining how DNA damage tolerance pathways act together to maintain cellular fitness and genome integrity. Such insights may one day help clinicians predict which cancers will respond to treatment, potentially sparing patients from unnecessary chemotherapy.

Severing the DNA double helix is a requisite step in the exchange of genetic material between homologous chromosomes in meiosis and between immunoglobulin domains during the generation of immune-receptor diversity. While these DNA transactions are essential for human fertility and the development of the immune system, misrepaired or unrepaired DNA double-strand breaks (DSBs) can lead to chromosome rearrangements or cell death. Indeed, ionizing radiation which generates DSBs in tumors is a cornerstone of cancer therapy. However, tumor cells can tolerate otherwise lethal levels of DNA damage by exploiting DNA repair pathways. Thus, discovering new strategies to selectively inhibit the repair of DSBs remains a major goal in the development of more effective cancer therapies. DSB repair may occur by multiple pathways, and the decision to use one pathway over another is influenced by cell cycle stage, the chromatin state, and the complexity of the inciting lesion. Mammalian cells primarily resolve DSBs by ligating the free ends together during a process termed “non-homologous end joining” (NHEJ). However, chemically modified or damaged DSB ends cannot be directly ligated by the NHEJ machinery. If NHEJ fails, DSBs may be nucleolytically cleaved to generate 3’ single-stranded DNA overhangs via a process called end resection. The resected DNA strands are poor substrates for NHEJ and instead search for homology in the genome to resynthesize the sequence surrounding the break site. This process is termed “homology-directed repair” (HDR). HDR is tightly coupled to cell cycle phase to ensure that resection occurs during late S and G2 when the ideal template, the sister chromatid, may be utilized. Following DNA damage, repair factors accumulate at DSB sites and form microscopically-detectable DNA repair foci. The dynamics of these foci may be observed by time-lapse microscopy making it possible to observe the behavior of breaks undergoing HDR and NHEJ. Interestingly, in yeast and mammalian cells, DNA motion is increased following DSB generation. DNA movements can lead to the clustering of DSBs into a common repair focus. DSB movements are intricately related to repair by HDR and require factors critical for resection initiation and downstream recombination. In contrast, DSBs undergoing NHEJ are relatively immobile. These observations suggest that the commitment of DSB repair to HDR regulates DSB movement and clustering; however, how DSB clustering might promote repair and whether active mechanisms drive this process remain relatively obscure. Recent studies have proposed roles for cytoskeletal proteins in genome organization and chromosomal dynamics. The Arp2/3 complex generates propulsive forces by nucleating a highly branched network of actin filaments. Genotoxic agents trigger actin polymerization in the nucleus. However, how DSB repair pathways might harness nuclear Arp2/3 machinery is unknown. Chapter 1 provides an overview of these pathways including the key steps of DSB repair, the regulation of actin nucleation, and the proteins involved in chromatin mobility. Chapter 1 provides context for the rest of the thesis in which I explore the contribution of nuclear actin polymerization to DSB repair. In Chapter 2, I detail our studies assessing the contribution of the Arp2/3 complex to DSB movement and clustering. Using Xenopus laevis cell-free extracts and mammalian cells, we show that actin nucleation machinery (WASP, Arp2/3, and actin) is recruited to damaged chromatin undergoing HDR. In this chapter, I also investigate how Arp2/3-driven DSB movements specifically promote the dynamics of HDR breaks, while Arp2/3 activity does not influence NHEJ breaks. Finally, I show that reduced DSB movement produces defects in DNA end processing and HDR efficiency, while the efficiency of end-joining is unaffected. I summarize all of these findings in Chapter 3 and discuss their implications for DNA repair, translocation formation, and clinical applications.

Polymers are among the most important of various oilfield chemicals and are used for a variety of applications in the oil and gas industry (OGI) including water and gas shutoff, drilling mud viscosity modification, filtration loss control (FLC), swellable packers, loss circulation material (LCM) pills, enhanced oil recovery (EOR), fracture treatment and cleanup, chemical placement, etc. The deposition and retention of polymer molecules in porous media and their interactions with rock and fluids present complex phenomena that can induce formation damage. Formation damage due to polymer retention can occur via mobility reduction in three possible mechanisms of polymer-induced formation damage: 1) pore-throat blocking, 2) wettability alteration (which can alter permeability), and 3) increase in reservoir fluid viscosity. Physical adsorption can also cause permanent permeability impairment (formation damage). This polymer-induced formation damage (causing a reduction in net oil recovery) continues to be a fundamental problem in the industry owing to the rather shallow understanding of the mechanics of polymer-brine-rock interactions and the polymer-aided formation damage mechanisms. Most models available for polymer risk assessments appear to be utilised for all scenarios with unsatisfying results. For example, only very little, if any, is known on how polymer type, particularly in the presence of brine type impact on formation damage. In order words, one of current industry challenges is finding effective polymers for high salinity environments. Also, the effect of polymer charge, as well as charges at the brine-rock interface are issues that require a deeper understanding in order to address the role polymer play in formation damage. Furthermore, no much recognition has been given to polymer rheological behaviour in complex porous media, etc. The OGI therefore still faces the challenge of the inability to correctly predict hydrolysed polyacrylamide (HPAM) viscosity under shear degradation; and consequently have not been able to meet the need of production predictions. The effect of the above mentioned factors, etc have not been fully integrated into the polymer formation damage modelling. In this PhD research work, theoretical, numerical, laboratory experiments and analytical methods were used to further investigate the mechanics of polymer-brine-rock interactions and establish the mechanisms for formation damage related to polymer application. Three different hydrolysed polyacrylamide (HPAM) products (SNF FP3630 S, 3330 S and FloComb C3525) were used in the experiments; while Xanthan gum was used in the simulation work. The following variables were considered: 1) polymer type, 2) effect of concentration, 3) effect of salinity/hardness, 4) effect of permeability and pore size distributions, 5) effect of inaccessible pore volume (IAPV) on retention, 6) effect of flow rate (where a special method was established to quantify the effect of flow rate on polymer retention). Laboratory rheological and adsorption experiments were designed and conducted. Experimental results indicate that higher concentration of calcium divalent ions in brine help promote polymer retention on rock surface. On the basis of the experimental results, empirical models were developed and validated to: 1) predict HPAM rheological behaviour over a wide range of shear rates, 2) predict salinity-dependent polymer-induced formation damage, 3) in addition, a modified screening model that can aid polymer selection for field application design is proposed. Overall, these models can therefore serve as useful tools, and be used for quick look-ahead prediction and evaluation of polymer related formation damage in oil and gas-bearing formations.

Pentraxin 3 (PTX3) is an acute phase protein which regulates peripheral inflammationand it has been suggested to have neuroprotective properties. Inflammation iscommonly associated with poor outcome during diverse central nervous system (CNS)disorders, but the role of PTX3 in brain inflammation is completely unknown. Westudied the role of PTX3 in brain inflammation and repair after stroke, a CNS disorderwhich is the third cause of death worldwide. To induce ischaemic stroke, we used themiddle cerebral artery occlusion (MCAo) model and found that the pro-inflammatorycytokine interleukin (IL)-1 was the inducer of PTX3 expression in the brain. Theanalysis of markers of inflammation and repair up to 14 days after MCAo in wild typeand PTX3 knockout (KO) mice revealed that, in general, lack of PTX3 has a negativeeffect on recovery after MCAo. PTX3 KO mice had delayed oedema resolution,defective glial scar, impaired microglial proliferation and reduced angiogenesis andneurogenesis. Therefore, PTX3 emerges as a target for stroke recovery and possiblyother CNS inflammatory diseases. PTX3 was, however, not involved in remoteneurodegeneration in the substantia nigra (SN) (an area of the brain remote butconnected with the area affected by the stroke), but we observed that remoteinflammation preceded remote neuronal death in the SN. Therefore, prevention ofremote inflammation may help prevent remote neurodegeneration in the SN afterstroke. This could have long term implications in SN neurodegeneration, which is akey pathological feature of Parkinson´s disease.

The ability of organisms to sense and respond to challenges to their genome integrity is key to survival. In particular, the ability to detect and respond to double-stranded DNA breaks (DSBs) is of fundamental importance as not only are DSBs potentially lethal as they can trigger apoptosis, but there is also the potential for the loss of genetic information. The response to DSBs is well conserved across Eukaryotes and comprises two stages: detection of the break and subsequent remedial action. The remedial action involves cell cycle arrest, DNA repair, and, if repair cannot be effected, possible apoptosis. Whilst many of the key components, especially in the initial detection of the break, are conserved there are also differences between plants and animals in some of the main components and their roles. In this thesis I have proposed an overall framework for the cellular response to DSBs in plants and have proposed two candidate genes, TCP20 and SOG1, as novel plant specific activators in this response. Their suitability has been addressed by considering their activation and their downstream targets. I have shown that TCP20 is necessary for growth arrest observed in shoot apical meristems after exposure to genotoxic stress. I have also shown that activation of one of the key targets of TCP20, CYCB1;1 requires TCP20 and that a key TCP20 binding motif in the promoter of CYCB1;1 is necessary for the up-regulation of CYCB1;1 in response to genotoxic stress. This motif is over-represented in the promoters of many of the genes involved in DNA damage repair, suggesting that TCP20 plays a role in the co-ordination of the cellular response to DSBs.

Modeling fracture in geomaterials is essential to the understanding of many physical phenomenon which may posses natural hazards e.g. landslides, faults and iceberg calving or man-made processes e.g. hydraulic fracture and excavations. Continuum Damage Mechanics (CDM) models the crack as a solid region with a degraded stiffness. This continuum definition of cracks in CDM allows more feasible coupling with other forms of material non-linearity and eliminates the need to track complicated crack geometry. Using CDM to analyze fracture for the modeling of fracture in geomaterials encounters several challenges e.g.: 1) the need to model the multiple physical processes occurring in geomaterials, typically: coupled fluid flow and solid deformation, 2) the need to consider non-local damage and transport in order to capture the underlying long range interactions and achieve mesh-independent finite element solutions and 3) the elevated computational cost associated with non-linear mixed finite element formulations. The research presented in this thesis aims at improving the CDM formulations for modeling fracture geomaterials. This research can be divided into three main parts. The first is the introduction of a novel non-local damage transport formulation for modeling fracture in poroelastic media. The mathematical basis of the formulation are derived from thermodynamic equilibrium that considers non-local processes and homogenization principles. The non-local damage transport model leads to two additional regularization equations, one for non-local damage and the other for non-local transport which is reduced to non-local permeability. We consider two options for the implementation of the derived non-local transport damage model. The first option is the four-field formulation which extends the (u/P) formulation widely used in poroelasticity to include the non-local damage and transport phenomena. The second option is the three-field formulation, which is based on the coupling of the regularization equations under the assumptions of similar damage and permeability length scales and similar driving local stress/strain for the evolution of the damage and permeability. The three-field formulation is computationally cheaper but it degrades the physical modeling capabilities of the model. For each of these formulations, a non-linear mixed-finite element solution is developed and the Jacobian matrix is derived analytically. The developed formulations are used in the analysis of hydraulic fracture and consolidation examples. In the second part, a novel approach for CDM modeling of hydraulic fracture of glaciers is pretended. The presence of water-filled crevasses is known to increase the penetration depth of crevasses and this has been hypothesized to play an important role controlling iceberg calving rate. Here, we develop a continuum damage-based poro-mechanics formulation that enables the simulation of water-filled basal and/or surface crevasse propagation. The formulation incorporates a scalar isotropic damage variable into a Maxwell-type viscoelastic constitutive model for glacial ice and the effect of the water pressure on fracture propagation using the concept of effective solid stress. We illustrate the model by simulating quasi-static hydro-fracture in idealized rectangular slabs of ice in contact with the ocean. Our results indicate that water-filled basal crevasses only propagate when the water pressure is sufficiently large and that the interaction between simultaneously propagating water-filled surface and basal crevasses can have a mutually positive influence leading to deeper crevasse propagation which can critically affect glacial stability. In the third part, we propose a coupled Boundary Element Method (BEM) and Finite Element Method (FEM) for modeling localized damage growth in structures. BEM offers the flexibility of modeling large domains efficiently while the nonlinear damage growth is accurately accounted by a local FEM mesh. An integral-type nonlocal continuum damage mechanics with adapting FEM mesh is used to model multiple damage zones and follow their propagation in the structure. Strong form coupling, BEM hosted, is achieved using Lagrange multipliers. Since the non-linearity is isolated in the FEM part of the system of equations, the system size is reduced using Schur complement approach, then, the solution is obtained by a monolithic Newton method that is used to solve both domains simultaneously. The method is applied to multiple fractures growth benchmark problems and shows good agreement with the literature.

It is incumbent upon cellular life to ensure the faithful transmission of genetic material from mother cell to daughter cell and from parent to progeny. However, cells are under constant threat of DNA damage from sources both endogenous and exogenous, such as the products of metabolism and genotoxic chemicals. Thus, cells have evolved multiple systems of repair to ensure genome integrity. The DNA double-strand break (DSB) is among the most lethal forms of DNA damage, and a critical pathway to resolve these lesions is homologous recombination (HR). During HR, information lost at the cut site of one locus is repaired when the damaged site locates a homologous sequence in the nucleus to use as template for repair. The process by which a cut chromosome finds its homolog is known as homology search, and, while the enzymatic steps of HR have been well studied in recent years, the coordination of cell biological events like HS in the context of the crowded nucleus has remained poorly understood. Recently, our laboratory and others have studied a phenomenon known as DNA damage-induced increased chromosomal mobility, in which chromosomal loci, both damaged and undamaged, explore larger areas of the nucleus after the formation of DSBs. The increase in the mobility of cut loci is known as local mobility, and the increase in mobility of undamaged loci in response to a break elsewhere in the nucleus is known as global mobility. Here, I report that the recombination machinery and the DNA damage checkpoint cooperate in order to regulate global mobility of chromosomes following DSB formation. The RecA-like recombinase Rad51 is required for global mobility, and exerts its effect at single-stranded DNA (ssDNA), but its canonical homology search and strand exchange functions are not required. I find that Rad51 is ultimately required to displace Rad52, which is revealed to be an inhibitor of mobility when bound to ssDNA in the absence of Rad51. Thus, recombination factors can serve as DNA damage sensors, and relay information to the checkpoint apparatus in order to govern the initiation of increased mobility after DSB formation. I have also studied how the baseline confinement of loci is established, and assessed the contributions of several genes involved in repair to increased mobility. These observations offer novel insight into previously unappreciated regulatory functions performed by the recombination machinery, and demonstrate how the progression of DNA repair pathways influences nuclear organization.