Maintaining genomic integrity is crucial for cell survival. In Escherichia coli, Rec-Amediated homologous recombination (HR) plays an essential role in the repair of DNA double-strand breaks (DSB) and the SOS response through a series of highly dynamic interactions with the chromosome. A greater understanding of the mechanism of homologous recombination requires quantitative analysis of genomic studies in live cells. The aim of this thesis was to investigate the dynamics of the RecA-DNA interactions in vivo following the induction of a site-specific DSB in the chromosome of E. coli. This DSB is caused by the cleavage of a DNA hairpin by the hairpin-specific endonuclease, SbcCD. The DNA hairpin is formed only on the lagging strand template of replication by a 246 bp-interrupted palindrome. As a result cleavage only occurs on one sister chromosome, leaving one unbroken chromosome to serve as a template for repair by HR. Here, this system has been used as a basis to develop a method that combines chromatin immunoprecipitation with quantitative PCR (ChIP-qPCR) and next-generation sequencing (ChIP-Seq) to quantify RecA protein binding during the active repair of a single chromosomal DSB. This study reports that DSB-dependent RecA binding is stimulated in response to the eight base DNA sequence Chi (5’-GCTGGTGG-3’). Increasing the number of Chi sites close to the DSB stimulates more RecA loading to DNA, with ChIP-Seq analysis also revealing a role for subsequent Chi sites in RecA binding during DSBR. If the Chi sites close to the DSB are removed then Chi-dependent RecA binding to DNA can be observed at distances greater than 100 kb from the DSB, suggesting that these subsequent Chi sites can be engaged in DSBR. Through collaboration, these in vivo data were combined with stochastic modeling to determine that, in vivo, Chi is recognised by the RecBCD complex with an efficiency of 20- 35%. The genomic analysis also revealed two unexpected aspects of RecA protein binding. First, ChIP-Seq analyses identified that following a DSB at lacZ there is RecA enrichment detected in the terminus region of the E. coli chromosome. This RecA binding is Chi-dependent, indicating a role for HR. Second, DSB-independent binding was observed at the RNA encoding genes dispersed throughout the chromosome. A temporal analysis of RecA dynamics was also performed. These analyses revealed that RecA binding to DNA near the DSB is extremely dynamic, cycling between periods of high RecA enrichment and periods of low RecA enrichment. This is the first in vivo study of DSB-dependent RecA-DNA distribution and dynamics in recombination proficient E. coli cells.

Models for electron transport and back reaction in dye-sensitized nanocrystalline solar cells were investigated by developing novel measurement techniques and the results were used to test two complementary models; diffusive electron transport within the TiO2 medium and the quasi-static approximation to deal with non steady-state conditions where trapping plays a role. These will be shown to be partly correct and the shortfalls highlighted and discussed. In the end it was found that more knowledge of the parameters governing the behaviour of electrons is required to further test and develop the models. The incorporation of a secondary sensing electrode allowed the internal quasi-Fermi level (QFL) within the TiO2 to be probed. The behaviour of the voltage measured by the secondary sensing electrode was in accordance with diffusive electron transport in the TiO2. This was confirmed by measuring the QFL along the current-voltage curve of the cell, and by the temperature dependence of the measured QFL. Discrepancies concerning the behaviour of the ideality of the open-circuit voltage (and hence the electron lifetime) between experiment and modelling are highlighted and discussed throughout. Assuming an Arrhenius relationship simple expressions for the temperature dependence of the open-circuit voltage were derived and experimentally tested. The trapped electron density was measured along the current-voltage curve. With the inclusion of the secondary sensing electrode and measuring the trap distribution, the way the trapped charge varied could be modelled and compared to experiment. This provided an important link between the free and trapped electron density profiles but again highlighted shortcomings of the applied models. The quasi-static approximation was tested against a full numerical solution (continuum model) to determine the phase space in which it is applicable. Knowing this, an almost ideally behaving cell was used to test the quasi-static approximation. Having shown that it was valid for the given cell, the quasi-static approximation was used to determine how the conduction band electron lifetime varied with temperature, resulting in an Arrhenius dependence of the back reaction rate of electrons. A strong temperature dependence of the electron lifetime, and hence a strong temperature dependence of the electron diffusion length was demonstrated.

Meiotic recombination promotes genetic variation by reciprocal exchange of genetic material producing novel allelic combinations that influence important agronomic traits in crop plants. Therefore, harnessing meiotic recombination has the potential to accelerate crop improvement via classical breeding. Numerous genes involved in crossover formation have been identified in model systems. For example, SPO11 mediates generation of meiotic DNA double-strand breaks (DSBs) across all eukaryotes, which may be repaired as crossovers. However, downstream regulators of recombination remain to be identified, including those with species-specific roles. To isolate crossover frequency modifiers I performed a high-throughput forward genetic screen using EMS mutagenesis of Arabidopsis carrying a fluorescent crossover reporter line called 420. The primary screen isolated nine mutants from ~3,000 scored individuals that showed significantly higher (high crossover rate, hcr) or lower (low crossover rate, lcr) crossover frequency, including a new fancm allele. Four mutants (hcr1, hcr2, hcr3 and lcr1) were mapped by sequencing and candidate genes identified. The hcr1 mutation was confirmed as being located within the PROTEIN PHOSPHATASE X-1 (PPX-1) gene, using isolation of an independent allele and complementation studies. Similarly, the lcr1 mutation was confirmed to be within the gene TBP-ASSOCIATED FACTOR 4B (TAF4B). Using immunocytological staining I observed that hcr1 did not show changes in DSB-associated foci (RAD51), but it did show a significant increase in crossover-associated MLH1 foci. The hcr1 mutation increases crossovers mainly in the sub-telomeric chromosome regions, which remain sensitive to crossover interference. Also the genetic interaction between the hcr1 and fancm mutations is additive. These results support a model where PPX- 1 acts to limit recombination via the Class I interfering CO pathway, downstream of DSB formation. In summary, this genetic screen has led to discovery of novel genes that regulate meiotic recombination and their functional characterization may find utility in crop breeding programs.

Deoxyribonucleic acid (DNA), like the hard drive in a computer, stores all the essential information for cell function and survival in nearly every single cell in our body. Four different bases are the building blocks of DNA that encode all the messages. As each cell divides, it must pass down its entire genomic DNA to both of its daughter cells. Given the vast amount of data that exists, many errors occur naturally every day and threaten the integrity of this biological hard drive. Normal cells are equipped with many repair tools to quickly and effectively respond to the lesions. When some of these errors disrupt the tightly regulated cell division, cells could undergo changes like an increase in the rate of division that eventually lead to cancer. One type of DNA damage that has a high propensity to cause genetic instability is the double-stranded break (DSB). Therefore, mechanisms that repair DSB are an important area of study in the fight against cancer and cancer causing syndromes. One of these repair pathways is homologous recombination (HR), which uses homologous sequences from either a sister chromatid or a homologue to fill in the information lost during a DSB. This homology pairing reaction requires a class of ATP-dependent proteins known as recombinases, with RAD51 being the one for humans. During HR, the early stages before pairing involve resection of the newly generated DSB ends to generate single-stranded DNA (ssDNA) overhangs, which are protected from degradation by replication protein A (RPA). RAD51 needs to displace the RPA from ssDNA and form a filament (the presynaptic complex) in order to initiate homology search. This process can be sped up by recombination mediators, which act to help RAD51 overcome the strong affinity of RPA for ssDNA that inhibits RAD51 binding and filament formation. Although Rad52 is the most important mediator in budding yeast, human RAD52 does not appear to have mediator function despite a high level of structural conservation. However, human RAD52 mediates ssDNA annealing and its deficiency is synthetic lethal with several important recombination proteins. Here, I use the single-molecule imaging technique of DNA curtains to visualize in real-time the competition and cooperativity between RPA, RAD52, and RAD51 on ssDNA through fluorescent labeling of RPA and RAD52. Using ssDNA curtains, I examine the conservation of facilitated dissociation from budding yeast to humans and show it does not require species-specific contacts. I also monitor the interactions of RAD52 with the RPA-ssDNA and find another point of conservation in the ability of RAD52 to upregulate the stability of RPA on ssDNA concerning facilitated dissociation. These RAD52-RPA-ssDNA complexes are long-lived; however, they are effectively displaced by RAD51 during filament assembly and do not re-bind appreciably to the RAD51 filament. Although RAD51 can still assemble on RAD52-RPA-ssDNA, I observe a significant inhibition on its nucleation (the first step in filament formation), but not elongation, by the presence of free RPA in solution. As DNA curtains allow efficient exchange of buffers in the micro-fluidic chambers while keeping ssDNA molecules tethered, I am able to follow individual DNA molecules overtime as they undergo different binding and filament assembly and disassembly reactions.

Meiosis is a specialized division of germ cells in sexually reproducing organisms, which is a fundamental process with key implications for evolution and biodiversity. In two consecutive rounds of cell division, meiosis I and meiosis II, a normal, diploid set of chromosome is halved. From diploid mother cells haploid gametes are generated to create genetic individual cells. This genetic uniqueness is obtained during prophase of meiosis I by essential meiotic processes in meiotic recombination, as double strand break (DSB) formation and repair, formation of crossovers (CO) and holiday junctions (HJs). Checkpoint mechanisms ensure a smooth progress of these events. Despite extensive research key mechanisms are still not understood. Based on an analysis of Massive Parallel Sequencing (MPS) data I could identify 2 genes, Mcmdc2 and Prr19, with high implication in meiotic recombination. In the absence of Mcmdc2 both sexes are infertile and meiocytes arrest at a stage equivalent to mid-­‐pachytene in wt. Investigations of the synaptonemal complex (SC) formation revealed severe defects suggesting a role for MCMDC2 in homology search. Moreover, MCMDC2 does not seem to be essential for DSB repair, as DSB markers of early and mid recombination nodules, like DMC1 and RPA, are decreased in oocytes. Nevertheless, late recombination nodules, which are positive for MutL homolog 1 (MLH1), do not form in both sexes. The absence of the asynapsis surveillance checkpoint mechanism in Hormad2 deficient ovaries with Mcmdc2 mutant background allowed survival of oocytes. This points into the direction that Mcmdc2 knock­out oocytes get eliminated after prophase I due to failed homologous synapsis. Interestingly, MCMDC2 contains a conserved helicase domain, like the MCM protein family members MCM8 and MCM9. I therefore hyphothesize that Mcmdc2 promotes homolgy search.

Os rotavírus, membros da família Reoviridae, são uma importante causa de diarreia em mamíferos e aves. São partículas icosaédricas não envelopadas e seu genoma é formado por 11 segmentos de RNA fita dupla que codificam seis proteínas estruturais e seis proteínas não estruturais. O objetivo deste estudo foi caracterizar os genes codificadores das proteínas não estruturais (NSP1-5) e estruturais (VP1-4, VP6-7) dos rotavírus do grupo A em aves de criações comerciais (corte, postura, matrizeiros e avozeiros) localizadas em 12 estados brasileiros, seguido de análises de recombinação e pressão de seleção das amostras definidas. Um total de 226 amostras fecais foram triadas através de reações de RT-PCR tendo como alvo a amplificação da VP6 e NSP5. A frequência de ocorrência, baseada em cada uma destas provas, variou de 9,7% a 18,14%, respectivamente. Em seguida, 10 das amostras positivas foram processadas com primers específicos visando a amplificação dos demais genes, seguido do sequenciamento nucleotídico e filogenia baseada no método de maximum likelihood, tendo como modelos de substituição GTR (NSP1-3, VP1-3, VP4, VP6, VP7) e HKY (NSP4, NSP5) e 1.000 repetições de bootstrap. Foram definidas sequências parciais para os genes codificadores da VP1-4, VP6-7 e NSP1-4 e sequências completas para NSP5. As respectivas árvores demonstraram que as dez amostras definidas se agruparam em clados aviários previamente descritos. Duas constelações genotípicas foram caracterizadas: G19-P[31]-I11-R6-C6-M7-A16-N6-T8-E10-H8 e G19-P[31]-I4-R4-C4-M4-A16-N4-T4-E4-H4. Estes genotipos são tipicamente encontrados em aves, mas quando analisados em conjunto, esta é a primeira descrição destas constelações. Eventos de recombinação foram observados nos genes NSP2, VP1, VP3 e VP7. Pelo menos um códon com pressão de seleção positiva foi encontrado nos genes codificadores das proteínas NSP1, VP2 e VP3. Este estudo propicia um melhor entendimento acerca da epidemiologia e diversidade viral circulante nas criações aviárias brasileiras, servindo de base para o estabelecimento de medidas profiláticas mais eficazes. / Rotaviruses are members of the Reoviridae family and they are a common cause of acute diarrhea in several mammalian and avian species. They are non-enveloped icosahedral particles and its genome comprises 11 segments of double-stranded RNA, which encodes six structural proteins (VP1-4, VP6-7) and six nonstructural proteins (NSP1-6). The objective of this study was to characterize the RVA nonstructural and structural proteins coding genes (NSP1-NSP5, VP1-VP4, VP6 and VP7) from fecal samples from avian farms (broiler breeders, poultry, laying hens, and grandparents) raised in Brazilian commercial farms from 12 states, followed by recombination and selection pressure analysis from samples defined here. A total of 226 fecal samples were screened using a RT-PCR technique targeting the amplification of the VP6 and NSP5. The frequency of occurrence, using these techniques, ranging from 9.7% to 18,14%, respectively; and from these, ten samples were further processed with specific primers to amplify the remaining genes, followed by respective nucleotide sequencing of the amplicons and phylogeny based on method maximum likelihood, as substitutions models GTR (NSP1-3, VP1-3, VP4, VP6, VP7) and HKY (NSP4, NSP5) and 1.000 bootstrap repetitions. Partial nucleotide sequences of VP1-4, VP6-7, and NSP1-4, and complete from NSP5, were obtained in this study. The phylogenetic trees depicted that the ten Brazilian rotavirus strains segregated with previous avian RVA described elsewhere. Two avian genotype constellations have been characterized here: G19-P[31]-I11-R6-C6-M7-A16-N6-T8-E10-H8, and G19-P[31]-I4-R4-C4-M4-A16-N4-T4-E4-H4. These genotypes are typically found in avian species, although when analyzed together, this is the first report of such constellations. Recombination events were observed in NSP2, VP1, VP3, and VP7 coding genes. At least on positive selected site was observed in NSP1, VP2, and VP3 genes. This study provides a better understanding of rotavirus epidemiology, by the definition of genetic variability of circulating strains.

Neste trabalho, investigamos a influência da estrutura de energia das minibandas dos estados eletrônicos ocupados no tempo de recombinação em poços quânticos múltiplos (MQW) fracamente acoplados de GaAs / AlGaAs. Um dos melhores métodos para estudar o efeito da estrutura energética consiste em medir o tempo de recombinação eletrônica em função de parâmetros expostas à influência externa que afeta a estrutura energética, por isso, aplicamos um campo magnético externo. O espectro da emissão de fotoluminescência foi composta pelas contribuições das minibandas da banda de condução, Γ – Γ e Γ – XZ. Observou-se um aumento notável do tempo de recombinação quando o campo magnético causou a despopulação da minibanda de maior energia, Γ – XZ. O efeito observado é atribuído à variação induzida pelo campo magnético na densidade dos estados eletrônicos. / In the present work, we investigate the influence of the miniband energy structure of the populated electron states on the recombination time in GaAs/AlGaAs weakly coupled multiple quantum wells (MQW). The best method to study the effect of the energy structure is to measure the recombination time in the same sample subject to external influence which affects the energy structure, therefore, we apply an external magnetic field. The photoluminescence emission was composed of the contributions from the Γ – Γ and Γ – XZ conduction band minibands. Remarkable enhancement of the recombination time was observed when the magnetic field caused depopulation of the higher energy Γ – XZ miniband. The observed effect is attributed to the magnetic field induced variation of the electron density of states.

SbcCD has been shown to cleave a DNA hairpin formed by a palindromic DNA sequence on the lagging strand template of the E. coli chromosome. This activity was exploited to create a unique system for inducing a single site-specific DNA double-strand break (DSB) once per replication cycle. First, this work shows that the SOS response induced by this DSB is only essential for viability following multiple cycles of cleavage and repair. Next, the SOS-inducible inhibitor of cell division SfiA is shown to be dispensable for survival, despite demonstrating that cleavage of the palindrome causes both an increase in cell size and a delay in nucleoid segregation. A model of the E. coli cell cycle is presented to reconcile the observation that growth under chronic DSB induced conditions has no effect on generation time despite causing an increase in cell size. This system of DSB induction was then coupled with fluorescence markers on both sides of the palindrome to visualise the consequence of the DSB in vivo. Cleavage of the DNA hairpin by SbcCD in a recAmutant was used to selectively degrade the chromosome that replicated the palindrome on the lagging strand of replication, allowing two genetically identical sister chromosomes to be distinguished. This approach was used to show that chromosome segregation in E. coli is not random, but results in the segregation of lagging strand replicated DNA to mid-cell and leading strand replicated DNA to cell poles. Finally, this system for visualising the site of an inducible DSB was optimised for use in various other mutant backgrounds to allow the events of DSB repair to be dissected. This work provides a solid basis for further investigation into the relationship between replication, recombination and chromosome segregation in the model organism E. coli.

Obstacles such as DNA damage can block the progression of DNA replication forks. This is a major source of genome instability that can lead to cell transformation or death. The budding yeast MMS1 and MMS22 genes were identified in a screen for mutants that were hypersensitive to DNA alkylation that blocks replisome progression. I set out to investigate the cellular roles of these genes and found that cells lacking MMS1 or MMS22 are hypersensitive to a wide variety of genotoxins that stall or block replication forks, and are severely defective in their ability to recover from DNA alkylation damage. Homologous recombination (HR) is an important mechanism for the rescue of stalled or blocked replication forks and for the repair of double-strand breaks (DSBs). Strikingly, MMS1 and MMS22 are required for HR induced by replication stress but not by DSBs, and the underlying mechanisms were explored.I next identified the uncharacterized protein C6ORF167 (MMS22L) as a putative human Mms22 orthologue. MMS22L interacts with NF?BIL2/TONSL, the histone chaperone ASF1 and subunits of the MCM replicative helicase. MMS22L colocalizes with TONSL at perturbed replication forks and at sites of DNA damage. MMS22L and TONSL are important for the repair of collapsed replication forks as depletion of MMS22L or TONSL from human cells causes DNA damage during S–phase and hypersensitivity to agents that cause fork collapse. These defects are consistent with the observations that MMS22L and TONSL are required for the efficient loading of the RAD51 recombinase onto resected DNA ends and for efficient HR. These data indicate that MMS22L and TONSL are novel regulators of genome stability that enable efficient HR.

Barley (Hordeum vulgare) is an economically important crop species with a large diploid genome. Around a half of the barley genome and a fifth of the genes are constrained within a low-recombining pericentromeric (LR-PC) region. I explored the LR-PC gene component with a genomic investigation of gene expression, diversity and evolution. Chromatin environments were also explored in the LR and high recombining (HR) regions by surveying the genic and genomic distributions of nine histone modifications. Firstly, regions of HR and LR were identified and compared for gene evolution, expression and diversity. LR regions of the barley genome were found to be restrictive for gene evolution and diversity, but not gene expression. I employed a bioinformatics approach to identify ancient gene pairs in barley to determine the long-term effects of residency in those regions upon gene evolution. Gene pair loss in LR regions was found to be elevated relative to the HR regions. Applying the same method to rice and Brachypodium distachyon revealed the same situation, suggesting a universal process in the grasses for loss of gene pairs in LR regions. The chromosomal distributions of transposable elements (TEs) were also explored and examined for correlations with recombination rate. Secondly, I developed a chromatin immunoprecipitation followed by Next Generation Sequencing (ChIP-seq) protocol for the investigation of histone modifications in barley seedlings. A protocol was optimised for the fixation, extraction and sonication of barley chromatin. The protocol was applied using antibodies against 13 different histone modifications. Following DNA library construction and Illumina sequencing, a bioinformatics pipeline was devised to analyse the sequence data. NGS reads were mapped to a custom assembly of the barley cultivar Morex reference genome sequence before peak calling. Genomic and genic locations were determined for the covalently modified histones. Four modifications were discarded from further study on the basis of low peak numbers or unexpected chromosomal locations. The remaining nine modifications were classified into four groups based on chromosomal distributions. Groupings were closely mirrored by peak sharing relationships between the modifications except histone H3 lysine-27 tri-methylation (H3K27me3). In addition, chromatin states representing local chromatin environments were defined in the barley genome using the peak sharing data. Mapping the states onto the genome revealed a striking chromatin structure of the gene-rich chromosome arms. A telomere-proximal region bearing high levels of H3K27me3-containing states was found adjacent to an interior gene-rich region characterised by active chromatin states lacking H3K27me3. The LTR retroelement-rich interior was found to be associated with repressive chromatin states. The histone modification status of TE classes were also probed revealing unexpected differences relating to the genomic and genic distributions of these elements. Finally, a genome browser was created to host the information publicly.