Siu Yau Lung, Philip. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2000. / Includes bibliographical references (leaves 99-119). / Abstracts in English and Chinese. / Abstract (English) --- p.i / Abstract (Chinese) --- p.iii / Acknowledgments --- p.iv / Declaration --- p.v / Scientific publication --- p.vi / Abbreviations --- p.vii / Genetic symbols --- p.ix / Table of contents --- p.x / List of tables --- p.xiv / List of figures --- p.xv / Chapter Chapter One --- Introduction / Chapter 1.1 --- Thesis outline --- p.1 / Chapter 1.2 --- Candida albicans --- p.2 / Chapter 1.3 --- Physical characterization of C. albicans --- p.3 / Chapter 1.3.1 --- Strain identification --- p.3 / Chapter 1.3.2 --- Dimorphism --- p.5 / Chapter 1.3.3 --- Genome of C. albicans --- p.10 / Chapter 1.3.4 --- Karyotype --- p.11 / Chapter 1.4 --- Candidiasis --- p.12 / Chapter 1.4.1 --- Superficial candidiasis --- p.15 / Chapter 1.4.2 --- Systemic candidiasis --- p.16 / Chapter 1.4.3 --- Virulence --- p.16 / Chapter 1.4.4 --- Multi-drug resistance --- p.17 / Chapter 1.5 --- Parasexual genetics --- p.20 / Chapter 1.5.1 --- Mutant isolation --- p.20 / Chapter 1.5.2 --- Spheroplasts complementation --- p.21 / Chapter 1.5.3 --- Mitotic complementation --- p.22 / Chapter 1.6 --- Natural heterozygosity in C. albicans --- p.22 / Chapter 1.7 --- Adenine biosynthesis --- p.26 / Chapter 1.7.1 --- de novo pathway --- p.26 / Chapter 1.7.2 --- Salvage pathway --- p.29 / Chapter 1.7.3 --- Importance of C. albicans ADE1 and ADE2 genes --- p.29 / Chapter 1.8 --- Aim of study --- p.30 / Chapter Chapter Two --- Construction of disrupted C. albicans ADE1 gene / Chapter 2.1 --- Introduction --- p.32 / Chapter 2.2 --- Materials and Methods --- p.34 / Chapter 2.2.1 --- Strains --- p.34 / Chapter 2.2.2 --- Construction of plasmid pGEMTE-ADEl --- p.34 / Chapter 2.2.2.1 --- Isolation of Candida genomic DNA --- p.34 / Chapter 2.2.2.2 --- Isolation of C. albicans ADE1 gene from CAM --- p.36 / Chapter 2.2.2.2.1 --- Amplification of C. albicans ADE1 gene --- p.36 / Chapter 2.2.2.2.2 --- Purification of PCR product --- p.37 / Chapter 2.2.2.3 --- Cloning of ADEl gene into pGEMT-Easy vector --- p.38 / Chapter 2.2.2.3.1 --- Cloning vector pGEMT-Easy --- p.38 / Chapter 2.2.2.3.2 --- Ligation --- p.38 / Chapter 2.2.2.4 --- Transformation of E. coli DH5a cells --- p.39 / Chapter 2.2.2.4.1 --- Preparation of competent E. coli DH5a cells --- p.39 / Chapter 2.2.2.4.2 --- Plasmid DNA transformation --- p.40 / Chapter 2.2.2.4.3 --- Isolation ofplasmid DNA from E. coli --- p.40 / Chapter 2.2.3 --- Construction of pGEMTE-ADElA-URA3 --- p.41 / Chapter 2.2.3.1 --- Isolation of C. albicans URA3 gene from plasmid pCUB-6 --- p.41 / Chapter 2.2.3.2 --- Preparation of cloning vector pGEMTE-ADE 1Δ --- p.42 / Chapter 2.2.3.2.1 --- PCR amplification of vector pGEMTE-ADElΔ --- p.42 / Chapter 2.2.3.2.2 --- Modification of PCR vector pGEMTE-ADElΔ --- p.44 / Chapter 2.2.3.2.3 --- Dephosphorylation --- p.45 / Chapter 2.2.3.3 --- Cloning and isolation of plasmid pGEMTE-ADE1Δ-URA3 --- p.46 / Chapter 2.3 --- Results and Discussion --- p.47 / Chapter Chapter Three --- Gene disruption of C. albicans CAI4 by electroporation / Chapter 3.1 --- Introduction --- p.51 / Chapter 3.2 --- Materials and Methods --- p.54 / Chapter 3.2.1 --- Strains --- p.54 / Chapter 3.2.2 --- Transforming DNA --- p.54 / Chapter 3.2.3 --- Purification of PCR product --- p.55 / Chapter 3.2.4 --- DNA transformation --- p.55 / Chapter 3.2.5 --- Transformation efficiency --- p.56 / Chapter 3.2.5.1 --- Pulse length --- p.56 / Chapter 3.2.5.2 --- Amount of DNA --- p.57 / Chapter 3.2.6 --- Southern analysis of transformants --- p.57 / Chapter 3.2.6.1 --- Isolation of Candida genomic DNA --- p.57 / Chapter 3.2.6.2 --- Preparation of Candida genomic DNA for Southern analysis --- p.57 / Chapter 3.2.6.3 --- Southern hybridization --- p.58 / Chapter 3.2.6.4 --- Preparation of radioactive probe --- p.60 / Chapter 3.2.6.5 --- Radioactive labelling of the probe --- p.61 / Chapter 3.2.6.6 --- Hybridization of nylon membrane --- p.62 / Chapter 3.2.6.7 --- Stringency washes --- p.62 / Chapter 3.2.6.8 --- Auto-radiography --- p.62 / Chapter 3.3 --- Results and Discussion --- p.64 / Chapter Chapter Four --- UV mutagenesis of disrupted C. albicans / Chapter 4.1 --- Introduction --- p.73 / Chapter 4.2 --- Materials and Methods --- p.76 / Chapter 4.2.1 --- Strains --- p.76 / Chapter 4.2.2 --- Generation of recombinants by UV irradiation --- p.76 / Chapter 4.2.3 --- Analyses of twin-sectored colonies --- p.77 / Chapter 4.2.3.1 --- Replica analyses of twin-sectored colonies --- p.77 / Chapter 4.2.3.2 --- Southern analysis of segregants --- p.77 / Chapter 4.3 --- Results and Discussion --- p.78 / Chapter Chapter Five --- Concluding remarks and perspectives --- p.96 / Bibliography --- p.99

During meiosis, homologous chromosomes pair and undergo reciprocal genetic exchange, producing crossovers. This generates genetic diversity and is required for balanced homolog segregation. Despite the critical functions of crossovers, their frequency and distribution varies extensively within and between species. This crossover variation can be caused by trans-modifiers within populations, which encode diffusible molecules that influence crossover formation elsewhere in the genome. This project utilised natural accessions of Arabidopsis thaliana to identify trans-modifying loci underlying crossover variation within the species. I performed Quantitative Trait Loci (QTL) mapping using a fluorescence-based crossover reporter system to measure recombination frequency in a genomic interval on chromosome 3, termed 420. Mapping in a Col-420 × Bur-0 F2 population revealed four major recombination QTLs (rQTLs) that influence crossover frequency. A novel recessive rQTL on chromosome 1 that reduced crossovers within the interval was fine-mapped to a premature stop codon in TATA Binding Protein (TBP)-associated factor 4b (TAF4b) in Bur-0 (taf4b-1). TAF4b is a subunit of the TFIID complex, a multi-protein general transcription factor complex comprising TBP and numerous TAFs that forms a component of the pre-initiation complex that recruits RNA polymerase II to promoters. Transformation-based complementation experiments and the isolation of several independent taf4b alleles provided genetic proof that TAF4b is essential for wild-type levels of crossover within 420. Analysis of the prevalence of the taf4b-1 mutation in the global Arabidopsis accession collection demonstrated its specificity to three accessions in the British Isles. A combination of cytology, genetic analysis using additional fluorescent reporter lines, and sequencing in F2 recombinant populations demonstrated a genome-wide reduction in crossover frequency in taf4b-1. In addition, RNA sequencing identified numerous transcriptional changes in taf4b-1. Both up- and down-regulated gene sets displayed significant enrichment for genes that are predominantly expressed in meiocytes, and several gene ontology terms pertaining to protein modification and meiotic processes. These results further demonstrate the existence of genetic modifiers of crossover frequency in natural populations of A. thaliana, and the characterisation of a novel trans-modifier of recombination, TAF4b. This signifies a novel function for TAF4b in Arabidopsis, and further enhances our understanding of the molecular factors controlling the frequency and distribution of meiotic crossovers in plants.

Life on Earth relies on a set of instructions encoded within an organism’s genome that is passed along from one generation to the next. Inherent to this mechanism of propagation is the need to copy the genetic material before passing it along to the progeny. Errors in this process coupled with stochastic damage will inevitably lead to changes in these instructions and may result in a reduction of fitness or even death of an individual. Yet, these same changes are also responsible for the adaptation mandated by our dynamic environment. Thus, there exists a delicate balance between maintenance and alteration of genetic material that is embodied to a large part at the various intersections of DNA replication, recombination and repair. Homologous recombination (HR) has been well studied and found to play vital roles in many cellular processes from the repair of the harrowing double-stranded break, the restart of a stalled or collapsed replication fork, as well as proper chromosome segregation during meiosis, all with the goal of striking this delicate balance. And yet, while HR is incumbent for the fitness of an organism, if left unchecked this same process can become detrimental by preventing better suited DNA repair pathways, permanently arresting cell cycle progression and creating some of the very problems it was meant to address such as aneuploidy or cancer. Despite a wealth of knowledge, the precise regulatory mechanisms remain an active area of research as they provide likely targets to combat these persistent diseases. Motor proteins that translocate along DNA have been particularly compelling and elusive due to their transitory nature, as well as the inevitability of collisions with bound protein(s) or nucleic acid structures that are likely regulated intermediates in the process. The yeast Srs2 helicase/translocase has long been regarded as the prototypical “anti-recombinase” as it has been shown to dismantle the Rad51 presynaptic filament, but also displays contradictory pro-recombinase functions. In vivo studies of Srs2 have been hampered by its involvement in multiple bioprocesses beyond recombination, while bulk in vitro approaches often produce conflicting results. Recent single molecule imaging of these players has shed light onto their involvement in the regulation of the various stages of the canonical pathway of HR. The Greene laboratory has developed ssDNA curtains to study the pre-synaptic filament and shown that Rad51-ssDNA filaments can create bonafide D-loop intermediates that would be incapable of repair and thus represent a toxic intermediate. These structures persist far longer than the entire process of DSBR in vivo and led us to hypothesize that motor proteins would be a key regulatory element to dismantle improperly paired intermediates for redistribution of the bound proteins and reengagement of the homology search process. Here I extend the use of ssDNA curtains to study Srs2 as it assembles into multimeric complexes to perform long-range disruption of various pre- and post-synaptic filament assemblies that include replication protein A (RPA), Rad51, Rad52, and D-loops. For the first time, direct observation of Srs2 translocating over RPA filaments is provided and shows these proteins are efficiently removed by Srs2. By including Rad52 on the RPA filament, I offer a refined model of the contradictory pro- and anti-recombinase activities of Srs2 through its antagonism of the single-strand annealing pathway in favor of HR. Additionally, Srs2 was found to initiate Rad51 disruption at breaks in the continuity of the filament marked by the persistence of replication protein A (RPA), Rad52, or the presence of an improper D-loop intermediate, the latter of which is efficiently disrupted before continuing translocation. In contrast to the prevailing model, we demonstrate that direct interaction between Srs2 and Rad51 is not necessary for long-range Rad51 clearance. These findings offer insights into the dynamic regulation of crucial HR intermediates by Srs2 and demonstrate that sub-nuclear concentrations of these proteins may be a likely driver for their activities.

Within the life of an organism, its deoxyribonucleic acid (DNA) is constantly bombarded with damaging agents from exogenous and endogenous sources. One of the most deleterious types of damage is the double-stranded break (DSB) in which a continuous strand of DNA is broken in two. As a result, the information stored in their connection is lost. If improperly repaired, a cell will either not survive or transform into a neoplasm. Homologous recombination (HR) is a mechanism by which the cell processes these broken ends and uses proteins called recombinases to search for an undamaged homologous DNA template for repairing the break, the homology search. Generally for eukaryotes, the recombinase, Rad51, performs the homology search. Without it, cells cannot repair spontaneous DSBs by recombination and instead, must use alternative, less efficacious pathways. This type of reparative homologous recombination generally occurs during mitosis and is thus called mitotic recombination. In addition to its role in repair, HR is employed by eukaryotes during the first stage of meiosis to create crossover events, or chiasmata, between DNA homologs. The formation of these chiasmata is necessary for proper segregation of the chromosomes, preventing aneuploidy in the haploid cells destined for sexual reproduction. These crossover events have an added evolutionary benefit of mixing genes between the parental chromosomes, creating allelic diversity in the haploid cells. Eukaryotes have evolved a subset of meioticallyexpressed proteins to mediate this process. Dmc1 is a meiosis-specific, second recombinase that eukaryotes require to properly form these crossover events between homologs. It is not entirely understood why most eukaryotes require a second recombinase specifically designed for meiotic HR. A potential reason for this second recombinase may lie in the preferred templates for recombination that Rad51 and Dmc1 seek. Rad51 is employed mitotically to repair spontaneous DSBs and thus searches for the perfect undamaged copy, the sister chromatid, to prevent the loss of genetic information. Conversely, Dmc1 is employ meiotically to purposely form crossover events between homologs, which carry single-nucleotide polymorphisms (SNPs) between parental chromosomes. Thus, Dmc1 must be able to anneal DNA strands that aren’t perfectly the same. This work uses the single-molecule technique of DNA curtains to understand the factors that effect Rad51 and Dmc1 homologous DNA-capture stability. The first part of Chapter 1 is a historical exploration of homologous recombination research and a review of the current understanding of the pathway. The second part of Chapter 1 discusses human diseases that are associated with the failure to properly repair double-strand breaks. Chapter 2 will explain the single-molecule DNA curtain technique used throughout this work. Chapter 3 will show that Dmc1 is more tolerant of mismatches in captured DNA than Rad51. Chapter 4 will test the limits of Dmc1’s tolerance to imperfect DNA and attempts understand how it accomplishes this tolerance. Chapter 5 will demonstrate that this tolerance of mismatches is mediated by a specific structural element in recombinases, loop L1, and a chimeric Rad51 with a Dmc1-like L1 can tolerate mismatches in vitro and in vivo. Chapter 6 will explore how recombinase mediators such as BARD1 and BRCA1 enhance RAD51’s ability to capture DNA during the homology search.

Meiosis is the unique process in which diploid cells undergo two consecutive divisions to produce haploid daughter cells. It is indispensable for sexual reproduction in all eukaryotic organisms and maintains proper chromosome number through generations. An integral step in the meiotic program is genetic recombination; recombination is required for a successful reductional division. In the yeast Saccharomyces cerevisiae, recombination is initiated by DNA double strand breaks (DSBs) that are created by ten recombination initiation proteins. Similar phenotypes are observed when any of these genes is mutated. This has made the mechanism by which these proteins function to initiate recombination difficult to unravel. One hypothesis is that these proteins form a functional complex for activity, in which all (or most) of them physically interact. The work described in Chapter 2 contributes to understanding the putative DSB-producing recombination initiation complex, suggesting there is substantial flexibility among initiation protein interactions. The results are also consistent with the view that the proteins assemble on the DNA. Studies in Chapter 3 examined the recombination initiation protein interactions during DSB formation in more detail using a novel experimental approach. While the initial experiments using this approach produced unexpected results, the assay is a promising tool for the future. In addition to creating DSBs, a subset of the initiation proteins perform a second function during early meiosis; they create a recombination initiation signal (RIS) to delay the onset of the reductional division in wild-type cells. Although the signal and the downstream target are well-defined, less is known about how the RIS is transduced to the downstream target. The work in Chapter 4 contributes to defining this transduction, and therefore enhances our understanding of the relationship between the recombination initiation proteins and the reductional division.

In broad terms, this thesis is concerned with the measurement and interpretation of carrier lifetimes in multicrystalline silicon. An understanding of these lifetimes in turn leads to a clearer picture of the limiting mechanisms in solar cells made with this promising material, and points to possible paths for improvement. The work falls into three broad categories: gettering, trapping and recombination. A further section discusses a powerful new technique for characterising impurities in semiconductors in general, and provides an example of its application. Gettering of recombination centres in multicrystalline silicon wafers improves the bulk lifetime, often considerably. Although not employed deliberately in most commercial cell processes, gettering nevertheless occurs to some extent during emitter formation, and so may have an important impact on cell performance. However, the response of different wafers to gettering is quite variable, and in some cases is non-existent. Work in this thesis shows that the response to gettering is best when the dislocation density is low and the density of mobile impurities is high. For Eurosolare material these conditions prevail at the bottom and to a lesser extent in the middle of an ingot. However, these conclusions can not always be applied to multicrystalline silicon produced by other manufacturers. Low resistivity multicrystalline silicon suffers from a concurrent thermally induced degradation of the lifetime. This had previously been attributed to the dissolution of precipitated metals, although we note that the crystallographic quality also appears to deteriorate. The thermal degradation effect results in an optimum gettering time for low resistivity material. Edge-defined Film-fed Growth (EFG) ribbon silicon was also found to respond to gettering, and even more so to bulk hydrogenation. Evidence for Cu contamination in the as-grown EFG wafers is presented. Multicrystalline silicon is often plagued by trapping effects, which can make lifetime measurement in the injection-level range of interest very difficult, and sometimes impossible. An old model based on centres that trap and release minority carriers, but do not interact with majority carriers, was found to provide a good explanation for these effects. These trapping states were linked with the presence of dislocations and also with boron-impurity complexes. Their annealing behaviour and lack of impact on device parameters can be explained in terms of the models developed. The trapping model allowed a recently proposed method for correcting trap-affected data to be tested using typical values of the trapping parameters. The correction method was found to extend the range of useable data to approximately an order of magnitude lower in terms of carrier density than would be available otherwise, an improvement that could prove useful in many practical cases. High efficiency PERL and PERC cells made on gettered multicrystalline silicon resulted in devices with open circuit voltages in the 640mV range that were almost entirely limited by bulk recombination. Furthermore, the injection-level dependence of the bulk lifetime resulted in decreased fill factors. Modelling showed that these effects are even more pronounced for cells dominated by interstitial iron recombination centres. Analysis of a commercial multicrystalline cell fabrication process revealed that recombination in the emitter created the most stringent limit on the open circuit voltage, followed by the bulk and the rear surface. The fill factors of these commercial cells were mostly affected by series resistance, although some reduction due to injection-level dependent lifetimes seems likely also. Secondary Ion Mass Spectroscopy on gettered layers of multicrystalline silicon revealed the presence of Cr and Fe in considerable quantities. Further evidence strongly implied that they resided almost exclusively as precipitates. More generally, injection-level dependent lifetime measurements offer the prospect of powerful contamination-monitoring tools, provided that the impurities are well characterised in terms of their energy levels and capture cross-sections. Conversely, lifetime measurements can assist with this process of characterising impurities, since they are extremely sensitive to their presence. This possibility is explored in this thesis, and a new technique, dubbed Injection-level Dependent Lifetime Spectroscopy (IDLS) is developed. To test its potential, the method was applied to the well-known case of FeB pairs in boron-doped silicon. The results indicate that the technique can offer much greater accuracy than more conventional DLTS methods, and may find applications in microelectronics as well as photovoltaics.

Includes bibliographies. / {59} leaves : ill. ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / The Polycomblike gene of Drosophila melanogaster is required for the correct spatial expression of the homeotic genes of Antenapaedia and Bithorax Complexes. This thesis describes the isolation and molecular characterization of the Polycomblike gene. / Thesis (Ph.D.)--University of Adelaide, Dept. of Biochemistry, 1995

Graduation date: 1994

<p>Topoisomerase III&alpha; (Top3&alpha;) is an essential component of the double Holliday junction (dHJ) dissolvasome complex in metazoans. Previous work has shown that Top3&alpha; and Bloom's helicase (Blm) are able to convergently migrate the dHJ to create solely non-crossover products, thus preserving genomic integrity. However, many questions remain about the details of this process. Using a combination of biochemical and genetic tools, including dHJ substrate assays, gel electrophoresis, EMSA, pulldowns, fly crosses, and electron microscopy, this work expands our knowledge of the dissolution reaction. Tail mutants of Top3&alpha; were created and tested in a series of <italic>in vitro</italic> assays. Through these experiments, I discovered that the C-terminus of Top3&alpha; is important for binding Blm, interacting with DNA, conveying RPA stimulation, and <italic>in vivo</italic> functionality. I also observed that dissolution is an extremely processive reaction, with no accumulation of intermediates prior to product formation. When a non-specific topoisomerase was used (Top1, a type IB), accumulation of an intermediate was evident; however, contrary to predicted models, direct observation revealed that this intermediate is not a hemicatenane structure and still requires branch migration. Modifications were also made to the dHJ substrate creation method so that multiple types of HJ substrates could be produced efficiently.</p> / Dissertation

p53 promotes maintenance of genetic information either by causing apoptosis of damaged cells, or by altering the cell cycle and repair pathways such that damage can be accurately repaired. The nematode Caenorhabditis elegans possesses only one p53 family member, CEP-1, that controls apoptosis and the cell cycle in response to genotoxic stress. Mutation in the meiotic gene him-5 increases nondisjunction of the X chromosome, resulting in increased frequencies of XO male and XXX Dpy progeny, and it affects the frequency of meiotic recombination on X. him-5 is allelic to the ORF D1086.4, which encodes a putative basic protein with no clear homologues or domain structure. The modest embryonic lethality (Emb) of him-5 mutants is dramatically increased by mutation of cep-1 but no change is seen in the proportion of XO male or XXX Dpy progeny. The synergistic effects of cep-1 and him-5 mutation are independent of CEP-1's DNA damage regulators and other meiotic mutants, and they do not involve deregulated apoptosis. cep-1; him-5 double mutants have abnormal chromatin morphology in diakinesis-arrested oocytes reminiscent of that seen in double strand break (DSB) repair mutants. This phenotype depends on the presence of SPO-11-induced meiotic DSBs, suggesting CEP-1 and HIM-5 function together to promote accurate recombination during meiosis. In support of this hypothesis, cep-1; him-5 show a significant reduction in crossover frequency between autosomal markers compared to wild-type or either single mutant alone, suggesting they function together to promote meiotic crossing over. The X chromosome nondisjunction in both him-5 and cep-1; him-5 is a result of failure of DSB formation and subsequent chiasma formation on the X. However, the embryonic lethality phenotype of him-5 and cep-1; him-5 is caused by a defect either downstream or in parallel to meiotic DSB formation. The diakinesis chromatin phenotype of cep-1; him-5 suggests this defect may be in meiotic DSB repair. This is confirmed by the fact that cep-1; him-5 animals show more persistent meiotic DSB-associated RAD-51 foci staining compared to wild-type, suggesting CEP-1 and HIM-5 may function in efficient resolution of SPO-11-induced DSBs during meiosis. A role for CEP-1 in promoting accurate repair of DSBs during meiosis may be related to p53's function in promoting faithful meiotic recombination in mammalian cells. HIM-5's role in DSB formation and repair suggests another mechanistic link between these recombination steps. Meiotic recombination is vital for genome stability, and characterization of the role of CEP-1 and HIM-5 will increase our understanding of the p53 family and genetic redundancy at multiple steps in this process.