Lors de la phase haploïde de la spermatogenèse (spermiogenèse) des mammifères, un important remodelage de la chromatine est nécessaire à la compaction de l'ADN. Au cours de ce remodelage, les histones sont remplacées successivement par les protéines de transition, puis finalement par les protamines. Ce processus implique une succession encore peu connue de modifications post-traductionnelles des histones telles que l'acétylation et la méthylation.Lors de récents travaux, notre laboratoire a montré des évidences suggérant que l'hyperacétylation de l'histone H4 (H4h) semble impliquée dans ce remaniement de la chromatine et fournirait un contexte favorable à l'apparition de cassures de l'ADN. Puisque le contexte chromatinien d'une spermatide diffère de celui d'une cellule somatique, la mise au point de techniques pouvant établir la distribution de H4h dans cette cellule germinale haploïde serait un atout précieux pour établir l'association de cette modification post-traductionnelle à la formation des cassures. Ce mémoire présente ainsi une démarche bipartite visant la mise au point d'approches microscopiques de même que le développement d'une approche d'immunoprécipitation de la chromatine pouvant s'appliquer à la chromatine particulière des spermatides. Grâce à la mise au point de la technique d'immunoprécipitation de la chromatine combinée à l'utilisation de biopuces d'ADN (ChIP-on-chip), nous tentons d'établir la cartographie de H4Ac sur une portion du chromosome X utilisé en guise de sentinelle. Avec la cartographie simultanée de [gamma]-H2AX (H2AFX) en tant que marqueur des cassures bicaténaires de l'ADN, nous tentons de vérifier, au niveau moléculaire, l'hypothèse d'une relation entre l'hyperacétylation des histones et l'apparition des cassures dans les spermatides allongeantes. La compréhension de la formation des cassures est importante puisque la réparation de l'ADN, dans cette cellule haploïde, ne peut compter sur la recombinaison homologue; l'instabilité génétique associée à ce phénomène pourrait fournir l'étiologie d'anomalies génétiques idiopathiques associées au développement de l'embryon. A l'aide d'anticorps couplés à des billes d'or, la microscopie électronique nous permet d'obtenir les premiers résultats d'une double détection de l'histone H4 hyperacétylée et des cassures de l'ADN au sein des noyaux des cellules germinales de la spermatogenèse. Les travaux d'immunoprécipitation de la chromatine dévoilent une répartition hétérogène de l'hyperacétylation de l'histone H4 au niveau du chromosome X, suggérant que l'hyperacétylation du génome lors de la spermiogenèse est progressive. Nous démontrons aussi qu'il existe une interaction entre cette chromatine et le variant d'histone [gamma]-H2AX. Les différences entre les patrons de distribution des deux histones ne permettent pas d'établir si l'hyperacétylation de la chromatine serait à l'origine du dépôt de [gamma]-H2AX, par le biais des cassures double brin.

Thesis (MSc)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Habitat fragmentation through the loss and modification of natural ecosystems poses a serious threat to biodiversity globally. Mechanisms and ecological implications of fragmentation have been extensively studied, yet new and meaningful insights continue to be produced. The highly diverse and ecologically complex fynbos shrubland communities that occur in the Cape Floristic Region of South Africa are amongst the most threatened by habitat fragmentation by urban, agricultural and silvicultural land uses and to the spread of invasive alien plants. Fynbos vegetation communities are fire-adapted and exploit the post-fire regeneration niche. Natural stochasticity in the fire regime means that these communities are temporally unstable; a factor that allows for the coexistence of such extreme diversity. Few studies have attempted to assess the influence of habitat fragmentation on this stochasticity, or to investigate the response of biological communities to the conditions that result. It is unknown whether this temporal instability will lead to delayed extinctions in fragmented communities, thus generating extinction debt. South Outeniqua Sandstone Fynbos occurs as a unique landscape mosaic of both insular and extensive habitats, suited to study through an island biogeography framework. Vegetation community stability was assessed through the comparison of historic and recent data sets. The responses of local vegetation and avifaunal communities to habitat fragmentation were assessed and compared on the basis of their differing motility. The unique habitat configurations also allowed for the investigation of extinction debt in the local communities and provided an opportunity to assess the influence of the surrounding matrix on species persistence and on connectivity in the artificial fragments. Data were analysed through simple regression analyses, modified Chi-squared tests and through ordination analyses. Ultimately the value of the artificial habitat fragments for the conservation of biological communities was assessed. Stability was observed in the vegetation species-area relationship for the natural islands and the mainland sites over twenty-two years. Smaller islands were found to receive fewer fires than large islands and the mainland. This consistently over-extended fire-return interval reduces the stochasticity of the local fire regime causing stable yet depauperate vegetation communities to result. Vegetation communities in the artificial fragments were found to hold area-related extinction debt, possibly due to the relatively long-term demographic turnover that typically occurs in fynbos. Avifaunal communities varied in their response to fragmentation relative to the vegetation. Birds – being motile – were found to be unaffected by isolation distance or surrounding matrix type – their response due more to changes experienced in the vegetation community than to geographic constraints. Fynbos-typical birds responded to the post-fire age of vegetation. Frugivorous birds and the matrix-habitat edge were identified as sources of alien and non-fynbos plant species that colonise the artificial fragments, potentially reducing the quality of these habitats for avifauna. Fragmented communities of South Outeniqua Sandstone Fynbos have the potential to function as biological reserves. This potential can be realised through the implementation of a fire regime that acknowledges the stochasticity required by the vegetation, the frequency required by the vegetation and the avifauna, and the practicality required by surrounding anthropogenic land-uses. / AFRIKAANSE OPSOMMING: Habitat-fragmentering, deur die verlies en verandering van natuurlike ekosisteme, hou 'n ernstige bedreiging in vir biodiversiteit wêreldwyd. Meganismes en ekologiese implikasies van die fragmentering is al breedvoerig bestudeer, maar nuwe en betekenisvolle insigte word voortaan vervaardig. Die hoogs diverse en ekologies komplekse fynbos-struikveld gemeenskappe wat in die Kaapse Floristiese Streek van Suid-Afrika voorkom, word meeste bedreig deur habitat-fragmentering deur verstedeliking, landbou en houtteeltkundige grondgebruike en die verspreiding van indringerplante. Fynbos gemeenskappe is aangepas tot vuur en die uitbuiting van post- vuur herlewing nis. Natuurlike stogastisiteit in die vuur-bedeling beteken dat hierdie gemeenskappe tydelik onstabiel word, 'n faktor wat die mede-bestaan van uiterste diversiteit moontlik maak. Min studies het al die invloed van habitat-fragmentering op hierdie stogastisiteit ondersoek, of die reaksie van biologiese-gemeenskappe tot die voortspruitende omstandighede. Dit is onbekend of die tydelike onstabiliteit sal lei tot vertraagde uitsterwing in gefragmenteerde gemeenskappe, dus genereer uitsterwings-skuld. Suid Outeniqua Sandsteen Fynbos kom as 'n unieke landskap mosaïek van beide die eilande en uitgebreide habitatte voor, geskik om deur 'n eiland biogeografie raamwerk bestudeer te word. Plant-gemeenskappe se stabiliteit is bestudeer deur die vergelyking van historiese en onlangse data stelle. Die reaksies van die plaaslike plantegroei en voëllewe gemeenskappe tot hul habitat is bestudeer en vergelyk op grond van hul verskillende beweeglikheid. Die unieke habitat konfigurasies het ook toegelaat vir die ondersoek van uitsterwings-skuld in die plaaslike gemeenskappe en 'n geleentheid gebied om die invloed van die omliggende habitat-matriks op spesies volharding en op konneksie in die kunsmatige fragmente te bepaal. Die data is ontleed deur middel van eenvoudige regressie analises, aangepasde Chi -kwadraat toetse en deur koördinerings ontledings. Ten einde die waarde van die kunsmatige habitat fragmente vir die bewaring van biologiese gemeenskappe te bepaal. Stabiliteit in die plantspesies-area verhouding vir die natuurlike eilande en die vasteland van webwerwe oor twee en twintig jaar was waargeneem. Kleiner eilande het minder brande aangeneem as groot eilande en die vasteland. Hierdie herhaalde oor-uitbrei over-extended vuur-interval het die stogastisiteit verminder van die plaaslike vuur-bedeling wat stabiele tog spesie-arme plantegroei gemeenskappe veroorsaak het. Plantegroei gemeenskappe in die kunsmatige fragmente is bevind om spesie- area -verhouding uitsterwings-skuld te bevat, moontlik as gevolg van die relatiewe lang termyn demografiese omset wat tipies voorkom in fynbos. Voëllewe gemeenskappe het gewissel in hul reaksie tot die fragmentering relatief tot die plantegroei. Voëls – weens hul beweeglikheid – blyk om nie beinvloed te word deur isolasie afstand of omliggende habitat-matriks tipe nie - hul reaksie blyk meer asgevolg van veranderinge wat ervaar word in die plantegroei gemeenskap as geografiese beperkinge. Fynbos-tipiese voëls reageer op die post- vuur ouderdom van plantegroei. Vrugte-etende voëls en die habitat-matriks rand is geïdentifiseer as bronne van uitheemse en nie-fynbos plantspesies wat die kunsmatige fragmente koloniseer, wat potensieel die kwaliteit van hierdie habitatte vir voëls verminder. Gefragmenteerde gemeenskappe van Suid Outeniqua Sandsteen Fynbos het die potensiaal om as biologiese reserwes te funksioneer. Hierdie potensiaal kan verwesenlik word deur die implementering van 'n vuur-bedeling wat erkenning verleen aan die stogastiesiteit vereis deur die plantegroei, die frekwensie wat deur die plantegroei en die voëllewe vereis word , en die praktiese vereistes van die omliggende menslike grondgebruike.

Historically, New Zealand was almost completely forested below the alpine treeline, but 1000 years of Polynesian and European colonisation has resulted in the destruction of nearly three-quarters of the original forest cover. I assessed historical patterns of deforestation and forest fragmentation in relation to all major topographical, climatic and anthropogenic variables that may drive forest loss. Much of the deforestation occurred in regions with drier climates, reflecting the fact that human population density has always been highest in areas with moderately dry climates and that dry forests burned much more readily and extensively. The large remaining tracts of forest are mainly restricted to high elevations, while the lowland forests have been fragmented into small, isolated remnants. Fragmentation of the surviving forests increases their susceptibility to edge effects and invasion by adventive species, indelibly altering the ecological communities they support. Although a large proportion of the remaining forest is owned or managed by the Department of Conservation, the distribution of that protection is greatly skewed towards areas of low economic value and is not representative of the relative conservation value of landscapes that differ in their environments and degree of forest cover. Forest cover in the majority of New Zealand landscapes has been reduced below the level of an expected extinction threshold of 30 % forest cover in the landscape, and ongoing deforestation threatens to force more landscapes below the critical threshold. Deforestation is still occurring across the country, and it is concerning that current deforestation rates in some areas are far greater than those observed in tropical, developing nations. I showed that the remaining forest fragments in New Zealand have complex, irregular shapes, and find ubiquitous evidence that core habitats within individual fragments are spatially discontinuous, comprising multiple, disjunct cores of small average area. Because population density of forest-interior species typically decreases with decreasing habitat area, multiple, disjunct cores support a lower total population size than a single, discrete core of the same total area. I found in a spatially explicit, landscape-level analysis of habitat fragmentation in New Zealand that simple core-area models consistently overestimate the carrying capacity of habitat fragments. Habitat fragmentation and habitat destruction are widely recognised as two of the leading threats to the continued maintenance of global biodiversity. The effects of habitat fragmentation on biodiversity fall into five categories that describe the spatial and landscape attributes of fragmented ecosystems; (1) fragment area, (2) edge effects, (3) fragment shape, (4) fragment isolation, and (5) matrix structure. Each attribute affects species individually according to their particular biological requirements and life history strategies, leading to complex, and often conflicting, sets of results in the empirical literature. Furthermore, it is now apparent that the effects of fragmentation can take many decades to become apparent and that the spatial arrangement of habitat fragments can interact with other ecological processes to magnify the detrimental impacts of fragmentation on species. I synthesised the published effects of habitat fragmentation on the morphology, distribution and abundance of invertebrate populations, species and communities, and present examples of time lags and synergies from the fragmentation literature. I explicitly considered the underlying mechanisms determining the responses ofindividuals to fragmentation and discussed the role of species traits in determining species vulnerability to changes in the spatial attributes of fragmented landscapes. I sampled 35,461 beetles from a fragmented forest and matrix system in New Zealand over very large gradients of fragment area (10-2 to 106 ha) and edge distances (up to 1,024 m from the forest edge into both the forest and the adjacent matrix interiors). The beetle fauna was very diverse, with 893 species identified in 65 families, representing nearly 20 % of the known species in New Zealand. Beetle communities were strongly structured by forest fragmentation, but in species-specific ways. Distance to edge was consistently shown to have the largest effect on community composition, but, surprisingly, an interaction between area and distance to edge had a stronger impact on community structure than fragment area alone. I developed a new method to partition the variance in community composition that was explained by putative area and edge effects. The method uses backwards stepwise regression to determine significant predictors of gradients in beetle species composition that were identified by canonical ordination. I found that edge effects were driven partially by small-scale alterations to microhabitat and microclimate and partially by changes in landscape composition that varied with distance to edge. In contrast, fragment area effects were driven primarily by edge effects, the strength of which varied significantly with fragment area. I took a novel approach to characterising the responses of 185 common species to habitat edges by modelling species abundances across edges with a general logistic model that described sigmoid trends in abundance for forest specialist and matrix specialist species, as well as unimodal trends in abundance for edge specialist species. I used the second derivatives of the logistic and unimodal models to statistically determine the width of species response zones to edge effects. Beetle species responses to forest edges occurred over far greater scales than previously suspected, with edge response zones for some species extending for more than 1 km. Average edge response zones were 194 m wide and, for many species, began in the forest but extended into the adjacent matrix. Species were categorised according to their responses to fragment area and distance to edge. Closely related species were expected to be placed in similar response categories because they are predicted to share suites of traits that determine their susceptibility or resilience to fragmentation by virtue of common ancestry. Despite many species exhibiting responses that could be grouped into categories, individual species responses to fragmentation were largely idiosyncratic with even closely related species exhibiting strongly contrasting responses to fragmentation.

This thesis essentially presents the experimental investigation of the fundamental phenomena of electric fuse element disintegration and its causation and influence on the subsequent fragmentation of the fuse elements when subjected to excessive fault currents. The basis of the study involved experimental observation of disintegration of fuse elements and the analysis of the dynamic responses of current-carrying conductors, which precipitate disintegration. The experimental techniques employed utilised commercially available video cameras to capture images of element disruptions during disintegration of fuse elements subjected to low short-circuit and high overload currents. Specialist experimental image capturing techniques and hardware implementations were developed to enable investigation of element disintegration caused by high short-circuit fault currents. Disintegration phenomena of fuse elements for all fault cases were compared within different time domains, which included specialist techniques to investigate disintegration of elements in sand and against glass substrates. Disintegration phenomena of elements in unconfined media such as air and water also constituted the studies. The studies diverged, finally, into experimental observations of the temporal development of arc initiation and extinction phenomena of fault current limiting of HBC fuses using spectroscopic analysis of the arc light radiation. The range of studies covered have led to new understandings of fundamental current limiting behaviour of HBC and open type fuses which contribute, in a small way, to the knowledge base of the subject and hopefully will be an aid to improved designs and development of new types of electric fuse.

Tandem mass spectrometry is widely used in proteomic studies because of its ability to identify large numbers of peptides from complex mixtures. In a typical LC-MS/MS experiment, thousands of tandem mass spectra will be collected and peptide identification algorithms are of great importance to translate them into peptide sequences. Though these spectra contain both m/z and intensity values, most popular protein identification algorithms primarily use predicted fragment m/z values to assign peptide sequences to fragmentation spectra. The intensity information is often undervalued, because it is not as easy to predict and incorporate into algorithms. Nevertheless, the use of intensity to assist peptide identification is an attractive prospect and can potentially improve the confidence of matches and generate more identifications. In this dissertation, an unsupervised statistical method, K-means clustering, was used to study peptide fragmentation patterns for both CID and ETD data, and many unique fragmentation features were discovered. For instance, strong c(n-1) ions were observed in ETD, indicating that the fragmentation site in ETD is highly related to the amino acid residue location. Based on the fragmentation patterns observed through data mining, a peptide identification algorithm that makes use of these patterns was developed. The program is named SQID and it is the first algorithm in our bioinformatics project. Our testing results using multiple public datasets indicated an improvement in the number of identified peptides compared with popular proteomics algorithms such as Sequest or X!Tandem. SQID was further extended to improve cross-linked peptide identification (SQID-XLink) as well as blind modification identification (SQID-Mod), and both of them showed significant improvement compared with existing methods. In this dissertation the SQID algorithm was also successfully applied to a mosquito proteomics project. We are incorporating new features and new algorithms to our software, such as more fragmentation methods, more accurate spectra prediction and more user-friendly interface. We hope the SQID project can continually benefit researchers and help to improve the data analysis of proteomics community.

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Fragmentation processes describe phenomena of random splitting, with possibly infinite activity, according to certain rules that give rise to a close relation of these processes to branching processes and L´evy processes. In this thesis we study some asymptotic properties of fragmentation processes. More specifically, we prove certain strong laws of large numbers for self–similar fragmentations and we deal with the existence and uniqueness of solutions ofthe one–sided FKPP travelling wave equation for homogenous fragmentation processes. In addition to being concerned with standard fragmentation processes we also consider fragmentation processes with immigration, fragmentations stopped at a stopping line as well as killed fragmentation processes.

We report a novel fragmentation and functionalization method using a cyclic iminyl radical. Formation of this radical occurs by microwave heating under mild conditions and short reaction times. The reaction avoids the use of explosive or toxic radical initiators and propagating agents. This reaction is versatile, with the ability to install two functional groups that are ultimately derived from a ketone in the substrate precursor. A variety of radical traps capable of forming both carbon-carbon bonds and carbon-heteroatom bonds have been tested, and the products are obtained in good yields. We demonstrate the power of this reaction by functionalizing complex natural products.