Friedreich ataxia (FRDA) is an autosomal recessive, neurodegenerative disease caused by the excessive pathological expansion of an unstable GAA trinucleotide repeat within intron 1 of the FXN gene. FRDA occurs due to a pathological GAA repeat ranging from 70-1200 repeats, whereas normal individuals have up to 40 repeats. The prevalence of FRDA in Caucasians is 1:50,000 and it is the most common inherited ataxia. The presence of this large GAA repeat leads to silencing of the FXN gene, resulting in severely diminished levels of the essential mitochondrial protein, frataxin. Frataxin is required throughout development. Therefore, decreased frataxin levels affect the onset and progression of FRDA due to mitochondrial iron accumulation and an increase in oxidative damage, leading to detrimental cellular defects. The pathology of FRDA predominantly affects the cerebellum. Various FRDA cellular and mouse models have been developed to represent the characteristics of this debilitating disease. Data has revealed a positive correlation to exist between an increase in the number of GAA repeats and the severity of the disease. The analysis of these models has shown the expansion of the GAA repeat to be unstable, resulting in both somatic and intergenerational instability. In recent times, a single nucleotide polymorphism (SNP), Asn/Ser46, in the Sirt6 protein of FRDA patients has been associated with a better outcome of the disease. Therefore, Sirt6 heterozygote knockout mice obtained from the Jackson Laboratory were bred with YG8sR FRDA mice, to observe the effects of Sirt6 status on expanded GAA repeat instability, compared to Sirt6 wild type YG8sR FRDA mice. Densitometry analysis showed decreased levels of somatic GAA repeat instability and an increase in FXN protein in 6-month old heterozygous Sirt6 KO mice. However, increased levels of GAA repeat instability and decreased levels of FXN protein was seen in 12-month heterozygous Sirt6 KO mice. The SNP and decreased Sirt6 function may be beneficial to begin with, but not in the long run. A major aim of scientific research is to pave way for the generation of effective therapy. Therefore, attention turned to therapy to increase frataxin protein levels in YG8sR transgenic mice. The effects of the Src kinase inhibitor dasatinib, which had previously been shown to increase frataxin in cell culture, were investigated in YG8sR mice. Dasatinib was administered over a 3-month period, during which time motor coordination ability and frataxin protein levels were investigated. No effect on motor coordination was seen over the course of the treatment. Although, there was a non-significant decrease in frataxin protein levels in the brain in comparison to the vehicle-treated mice. In addition, further analysis by immunohistochemistry showed a decrease of frataxin protein expression in the dorsal root ganglia (DRG). Furthermore, the mean body weight of the dasatinib-treated mice was shown to decrease over time in comparison to vehicle-treated mice. Overall, these studies do not support the use of dasatinib for FRDA therapy. Further studies investigated a new line of GAA repeat expansion-containing FRDA transgenic mice, designated 'YG8LR'. These mice contain approximately 410 GAA repeats, which is significantly more than the previous 'YG8sR' line of mice which contained approximately 220 GAA repeats. As result of this larger GAA repeat, a further decrease of frataxin mRNA and protein was detected in the cerebellum and heart of YG8LR mice compared to YG8sR mice. Further investigations were undertaken to study the epigenetic status and the effects of lowered frataxin protein on the phenotype of the YG8LR model. Increased levels of histone deacetylation and methylation, together with DNA methylation, were detected at the FXN transgenic locus. The YG8LR mice also showed somatic and intergenerational GAA repeat instability as previously detected in earlier FRDA mouse models. Immunohistochemistry analysis of DRG sections showed a decreased level of frataxin protein in YG8LR mice. However, there was an absence of vacuoles in the DRG of the YG8LR mice as previously seen in YG8sR mice, although this particular phenotype is not actually seen in FRDA patients. Motor coordination ability and locomotor activity were significantly decreased as assessed by accelerating rotarod, beam-walk and beam-breaker open-field locomotor analysis. YG8LR mice showed increased glucose intolerance and insulin hypersensitivity in comparison to YG8sR and Y47R mice, investigated by glucose and insulin tolerance tests. Moreover, the most common cause of death in FRDA patients is caused by cardiomyopathy, therefore heart weights were obtained from B6, Y47R, YG8sR and YG8LR mice and a slight increase in mean heart weight was observed in YG8LR mice compared to the other models. This could suggest the lower levels of frataxin leads to the pathology of the heart as seen in FRDA patients. These investigations may help to provide an insight into and confirm molecular mechanisms of the disease, as well as providing a great mouse model for testing future FRDA therapies.

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A string is a sequence of symbols, usually called letters, drawn from some alphabet. It is one of the most fundamental and important structures in computing, bioinformatics and mathematics. Computer files, contents of a computer memory, network and satellite signals are all instances of strings. The genome of every living thing can be represented by a string drawn from the alphabet {a, c, g, t}. The algorithms processing strings have a wide range of applications such as information retrieval, search engines, data compression, cryptography and bioinformatics. In a DNA sequence the indeterminate symbol {a, c} is used when it is unclear whether a given nucleotide is a or c, We could then say that {a, c} matches another symbol {c, g} which in turn matches {g, t}, but {a, c} certainly does not match {g, t}. The processing of indeterminate strings is much more difficult because of this nontransitivity of matching. Thus a combinatorial understanding of indeterminate strings becomes essential to the development of efficient methods for their processing. With indeterminate strings, as with ordinary ones, the main task is the recognition/computation of patterns called regularities . We are particularly interested in regularities called repeats, whether tandem such as acgacg or nontandem (acgtacg). In this thesis we focus on newly-discovered regularities in strings, especially the enhanced cover array and the Lyndon array, with attention paid to extending the computations to indeterminate strings. Much of this work is necessarily abstract in nature, because the intention is to produce results that are applicable over a wide range of application areas. We will focus on finding algorithms to construct different data structures to represent strings such as cover arrays and Lyndon arrays. The idea of cover comes from strings which are not truly periodic but "almost" periodic in nature. For example abaababa is covered by aba but is not periodic. Similarly the Lyndon array describes the string in another unique way and is used in many fields of string algorithms. These data structures will help us in the field of string processing. As one application of these data structures we will work on "Reverse Engineering"; that is, given data structures derived from of a string, how can we get the string back. Since DNA, RNA and peptide sequences are effectively "strings" with unique properties, we will adapt our algorithms for regular or indeterminate strings to these sequences. Sequence analysis can be used to assign function to genes and proteins by observing the similarities between the compared sequences. Identifying unusual repetitive patterns will aid in the identification of intrinsic features of the sequence such as active sites, gene-structures and regulatory elements. As an application of periodic strings we investigate microsatellites which are short repetitive DNA patterns where repeated substrings are of length 2 to 5. Microsatellites are used in a wide range of studies due to their small size and repetitive nature, and they have played an important role in the identification of numerous important genetic loci. A deeper understanding of the evolutionary and mutational properties of microsatellites is needed, not only to understand how the genome is organized, but also to correctly interpret and use microsatellite data in population genetics studies. / Thesis / Doctor of Philosophy (PhD)

Gene-specific trinucleotide repeat expansions are the cause of an ever-growing number of disorders, including myotonic dystrophy type 1 (DM1) and spinocerebellar ataxia type 7 (SCA7). Both DM1, and SCA7 are characterized by large differences in repeat numbers between tissues that are differentially affected, indicating tissue-specific mechanisms of repeat instability. The mechanism(s) of both somatic as well as germline instability are complex and still poorly understood, with evidence supporting the contribution of cis-elements, trans factors, and DNA metabolic processes that are hypothesized to involve alternative structure formation within the DNA tract. This thesis involves investigations into the role of a particular cis-element (CTCF) on instability, as well as the detection of slipped-DNAs in patient tissues and the presence of rare mutations within those same tissues. Here I identify the first endogenous cis-element reported to show regulation of instability at a trinucleotide repeat disease locus, the DNA binding site for the insulator protein CCCTC- binding factor (CTCF) downstream of the SCA7 repeat. Using a mouse model with a mutation in the CTCF binding domain, I show that the loss of CTCF binding stimulates germline and somatic instability in a tissue-specific and age-dependent manner. The binding of CTCF likely protects the repeat tract from expansion by shielding it from other elements that may contribute to expansion. DNA metabolic processes such as replication, repair, and transcription likely play a role in repeat expansion at disease loci, with the general mechanism hypothesized to be the extrusion and aberrant repair of slipped-DNA structures during the unwinding process for each. While characterizing DM1 patient tissues in order to isolate slipped-DNA structures, I characterized two non-CTG repeat insertion mutations that had completely replaced the repeat tract in a small subset of cells in only two tissues in one patient. Given the hypermutable nature of expanded repeat tracts, it is possible that these types of mutations are more common than suspected. Finally, I report on the detection and isolation of slipped-DNA structures from the endogenous DM1 locus from patient tissues. The slip-outs appear as clusters along a length of DNA, rather than single isolated slip-outs, and more unstable tissues contain greater amounts of slipped-DNA compared to more stable tissues. This detection implies that slipped-DNA structures are not merely transient intermediates in the mutation and expansion process as has long been assumed, but remain within the DNA at detectable levels. The data reported herein both furthers our understanding of trinucleotide repeat instability, and additionally confirms the decades-long hypothesis that slipped-DNAs are in fact forming in patient tissues in a tissue-specific manner.

Gene-specific trinucleotide repeat expansions are the cause of an ever-growing number of disorders, including myotonic dystrophy type 1 (DM1) and spinocerebellar ataxia type 7 (SCA7). Both DM1, and SCA7 are characterized by large differences in repeat numbers between tissues that are differentially affected, indicating tissue-specific mechanisms of repeat instability. The mechanism(s) of both somatic as well as germline instability are complex and still poorly understood, with evidence supporting the contribution of cis-elements, trans factors, and DNA metabolic processes that are hypothesized to involve alternative structure formation within the DNA tract. This thesis involves investigations into the role of a particular cis-element (CTCF) on instability, as well as the detection of slipped-DNAs in patient tissues and the presence of rare mutations within those same tissues. Here I identify the first endogenous cis-element reported to show regulation of instability at a trinucleotide repeat disease locus, the DNA binding site for the insulator protein CCCTC- binding factor (CTCF) downstream of the SCA7 repeat. Using a mouse model with a mutation in the CTCF binding domain, I show that the loss of CTCF binding stimulates germline and somatic instability in a tissue-specific and age-dependent manner. The binding of CTCF likely protects the repeat tract from expansion by shielding it from other elements that may contribute to expansion. DNA metabolic processes such as replication, repair, and transcription likely play a role in repeat expansion at disease loci, with the general mechanism hypothesized to be the extrusion and aberrant repair of slipped-DNA structures during the unwinding process for each. While characterizing DM1 patient tissues in order to isolate slipped-DNA structures, I characterized two non-CTG repeat insertion mutations that had completely replaced the repeat tract in a small subset of cells in only two tissues in one patient. Given the hypermutable nature of expanded repeat tracts, it is possible that these types of mutations are more common than suspected. Finally, I report on the detection and isolation of slipped-DNA structures from the endogenous DM1 locus from patient tissues. The slip-outs appear as clusters along a length of DNA, rather than single isolated slip-outs, and more unstable tissues contain greater amounts of slipped-DNA compared to more stable tissues. This detection implies that slipped-DNA structures are not merely transient intermediates in the mutation and expansion process as has long been assumed, but remain within the DNA at detectable levels. The data reported herein both furthers our understanding of trinucleotide repeat instability, and additionally confirms the decades-long hypothesis that slipped-DNAs are in fact forming in patient tissues in a tissue-specific manner.

Ip Toi Yan. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1999. / Includes bibliographical references (leaves 81-105). / Abstracts in English and Chinese. / CONTENTS --- p.i-iii / ACKNOWLEDGEMENT --- p.iv / ABSTRACT --- p.v-vi / Chapter Chapter One --- INTRODUCTION --- p.1-2 / Chapter Chapter Two --- LITERATURE REVIEW --- p.3-37 / Chapter 2.1 --- Epidemiology and Etiology of Cervical and Endometrial Cancers --- p.3-4 / Chapter 2.1.1 --- Epidemiology and Etiology of Cervical cancer --- p.4 / Chapter 2.1.1.1 --- Incidence and Mortality --- p.4-6 / Chapter 2.1.1.2 --- Etiology --- p.6-8 / Chapter 2.1.2 --- Epidemiology and Etiology of Endometrial Cancer --- p.9 / Chapter 2.1.2.1 --- Incidence and Mortality --- p.9-11 / Chapter 2.1.2.2 --- Rick Factors --- p.11-14 / Chapter 2.2 --- Pathology of Cervical and Endometrial Cancers --- p.14 / Chapter 2.2.1 --- Pathology of Cervical Cancer --- p.14-15 / Chapter 2.2.1.1 --- Macroscopic Appearance --- p.15 / Chapter 2.2.1.2 --- Histology --- p.15-18 / Chapter 2.2.2 --- Staging of Cervical Cancer --- p.19-21 / Chapter 2.2.3 --- Pathology of Endometrial Cancer --- p.21 / Chapter 2.2.3.1 --- Macroscopic Appearance --- p.22 / Chapter 2.2.3.2 --- Histology --- p.22-24 / Chapter 2.2.4 --- Staging of Endometrial Cancer --- p.24-25 / Chapter 2.2 --- Introduction to Microsatellite Instability (MI) --- p.25 / Chapter 2.3.1 --- DNA structure --- p.25-27 / Chapter 2.3.2 --- Microsatellite --- p.27-28 / Chapter 2.3.3 --- Mismatch Repair (MMR) --- p.28-29 / Chapter 2.3.4 --- Microsatellite Instability (MI) --- p.30-33 / Chapter 2.3.5 --- Microsatellite Instability in various cancers --- p.33-37 / Chapter Chapter Three --- MATERIALS AND METHODS --- p.38-50 / Chapter 3.1 --- Materials --- p.38 / Chapter 3.1.1 --- Patients and Specimens --- p.38-39 / Chapter 3.1.2 --- Chemicals and Reagents --- p.39 / Chapter 3.1.2.1 --- Chemicals --- p.39-40 / Chapter 3.1.2.2 --- Solution --- p.40-41 / Chapter 3.1.2.3 --- Microsatellite Markers --- p.42 / Chapter 3.1.3 --- Major Equipment --- p.43 / Chapter 3.2 --- Methodology --- p.43 / Chapter 3.2.1 --- DNA Extraction --- p.43-45 / Chapter 3.2.2 --- DNA Amplification --- p.45 / Chapter 3.2.2.1 --- End-labeling of Primer --- p.45 / Chapter 3.2.2.2 --- Polymerase Chain Reaction (PCR) --- p.46 / Chapter 3.2.3 --- Electrophoresis of PCR Products and Autoradiography --- p.46-49 / Chapter 3.2.4 --- Determination Of Microsatellite Instability (MI) --- p.49 / Chapter 3.3 --- Statistical Analyses --- p.50 / Chapter Chapter Four --- Result --- p.51-66 / Chapter 4.1 --- Microsatellite Instability in Cervical Cancer --- p.51 / Chapter 4.1.1 --- Prevalence of MI in Cervical Cancer --- p.51 -54 / Chapter 4.1.2 --- MI and Age in Cervical Cancer --- p.55 / Chapter 4.1.3 --- MI and Histological Type in Cervical Cancer --- p.55-56 / Chapter 4.1.4 --- MI and Histologic Grades in Cervical Cancer --- p.56-57 / Chapter 4.1.5 --- MI and Clinical stage in Cervical Cancer --- p.57-58 / Chapter 4.1.6 --- MI and Clinical Status in Cervical Cancer --- p.58-59 / Chapter 4.2 --- Microsatellite Instability in Endometrial Cancer --- p.59 / Chapter 4.2.1 --- Prevalence of MI in Endometrial Cancer --- p.59-62 / Chapter 4.2.2 --- MI and Age Groups in Endometrial Cancer --- p.63 / Chapter 4.2.3 --- MI and Histological Type in Endometrial Cancer --- p.63-64 / Chapter 4.2.4 --- MI and Histologic Grades in Endometrial Cancer --- p.64-65 / Chapter 4.2.5 --- MI and Clinical stage of Endometrial Cancer --- p.65 / Chapter 4.2.6 --- MI and Clinical Status in Endometrial Cancer --- p.66 / Chapter Chapter Five --- Discussion --- p.67-77 / Chapter 5.1 --- MI detection --- p.67-71 / Chapter 5.2 --- MI of Cervical Cancer --- p.71 -74 / Chapter 5.3 --- MI of Endometrial Cancer --- p.74-77 / Chapter Chapter Six --- Conclusions --- p.78-80 / Reference --- p.81-112 / Appendix --- p.113-114

DNA mixtures are frequently encountered in forensic casework especially in cases of sexual assault. When evidence is recovered, the sample may have come from multiple contributors in different proportions. The first part of this study examines the fidelity of contributor proportions by using the residual to analyze known mixture samples. The coefficient of determination between the expected and observed proportions was also determined and used to assess the fidelity of mixture proportions. The second part of this study involved separating major and minor contributors in a mixture by characterizing the observed proportions. Results for the 2-person mixture show that as the mass of amplified DNA decreases, the number of allele dropouts increases. Furthermore, as mass decreases, the level of variation between the expected and observed proportions increases, as determined by the residuals and the coefficients of determination. In addition, as mixture proportions become more disparate the amount of variations between the expected and observed proportions are not as great as the mass. For the 3-person mixtures, as mass decreases, the residuals increase. Also, when the coefficient of determination of the 3-person mixtures were compared to those obtained with the 2-person mixtures, it was determined that the R2 were larger for the former. This was a result of higher total amplification masses. In mixture 1:2/2:1, major and minor proportions are not distinguishable In mixture 1:4/4:1, major and minor proportions can be distinguished at 1 ng. In mixture 1:9/9:1, proportions are distinguishable at 1, and 0.5 ng. Mixtures could not be distinguished at the 0.25 ng level, despite proportion and is the result of the increase in variation with decreasing mass.

Poon Kin-yan. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2001. / Includes bibliographical references (leaves 119-147). / Abstracts in English and Chinese. / ACKNOWLEDGMENT --- p.i / ABSTRACT --- p.iii / ABBREVIATIONS --- p.viii / TABLE OF CONTENTS --- p.x / Chapter CHAPTER I --- INTRODUCTION --- p.1 / Chapter 1.1 --- Cervical Intraepithelial Neoplasia (CIN) and Cervical Cancer --- p.1 / Chapter 1.1.1 --- Epidemiology --- p.3 / Chapter 1.1.1.1 --- Descriptive Epidemiology --- p.4 / Chapter 1.1.1.2 --- Risk Factors --- p.7 / Chapter 1.1.2 --- Pathology --- p.22 / Chapter 1.1.2.1 --- Macroscopic Appearance --- p.22 / Chapter 1.1.2.2 --- Symptoms and Diagnosis --- p.23 / Chapter 1.1.2.3 --- Staging Classification --- p.25 / Chapter 1.1.2.4 --- Histopathology --- p.29 / Chapter 1.2 --- Microsatellite Instability (MSI) --- p.35 / Chapter 1.2.1 --- Microsatellite --- p.35 / Chapter 1.2.2 --- Mismatch Repair --- p.37 / Chapter 1.2.3 --- Microsatellite Instability (MSI) --- p.38 / Chapter 1.2.4 --- MSI in Various Cancers --- p.42 / Chapter 1.2.5 --- The Role of MSI in Carcinogenesis --- p.49 / Chapter 1.2.6 --- MSI as a Diagnostic / Prognostic Tool --- p.50 / Chapter CHAPTER II --- AIMS OF THE STUDY --- p.53 / Chapter CHAPTER III --- MATERIALS AND METHODS --- p.56 / Chapter 3.1 --- Materials --- p.56 / Chapter 3.1.1 --- Patients and Specimens --- p.56 / Chapter 3.1.2 --- Microsatellite Markers --- p.57 / Chapter 3.2 --- Methods --- p.59 / Chapter 3.2.1 --- Preparation of OCT-embedded Specimen Sections --- p.59 / Chapter 3.2.2 --- Microdissection of Epithelial Cells and Neoplastic Cells from Specimen Sections --- p.60 / Chapter 3.2.3 --- DNA Extraction --- p.60 / Chapter 3.2.3.1 --- Normal Blood --- p.61 / Chapter 3.2.3.2 --- Dissected Cells --- p.62 / Chapter 3.2.4 --- DNA Amplification --- p.64 / Chapter 3.2.4.1 --- End-labeling of Primers --- p.64 / Chapter 3.2.4.2 --- Polymerase Chain Reaction --- p.65 / Chapter 3.2.5 --- Denaturing Polyacrylamide Gel Electrophoresis --- p.66 / Chapter 3.2.6 --- Autoradiography --- p.67 / Chapter 3.2.7 --- Determination of MSI --- p.67 / Chapter 3.2.8 --- HPV Detection --- p.68 / Chapter 3.2.9 --- Statistical Analysis --- p.69 / Chapter CHAPTER IV --- RESULTS --- p.70 / Chapter 4.1 --- Incidence of MSI in Cervix --- p.70 / Chapter 4.1.1 --- Incidence of MSI in Normal Cervix --- p.70 / Chapter 4.1.2 --- Incidence of MSI in CIN --- p.70 / Chapter 4.1.3 --- Incidence of MSI in Cervical Carcinoma --- p.71 / Chapter 4.1.4 --- Correlation of MSI-positive with the Evolution of Cervical Neoplasm --- p.77 / Chapter 4.2 --- Correlation of MSI-positive with Clinicopathological Characteristics in Cervical Carcinoma --- p.77 / Chapter 4.2.1 --- MSI and Age --- p.80 / Chapter 4.2.2 --- MSI and Clinical Stage --- p.80 / Chapter 4.2.3 --- MSI and Histological Grade --- p.80 / Chapter 4.2.4 --- MSI and Clinical Status --- p.81 / Chapter 4.3 --- Comparison between Two Panels of Microsatellite Markers used in MSI Detection --- p.84 / Chapter 4.4 --- Human Papilloma Virus (HPV) Infection in Cervical Neoplasm --- p.89 / Chapter 4.4.1 --- HPV Infection and Typing in CIN and Cervical Carcinoma --- p.89 / Chapter 4.4.2 --- Correlation of MSI-positive with HPV Infection in Cervical Carcinoma --- p.94 / Chapter CHAPTER V --- DISCUSSION --- p.96 / Chapter 5.1 --- MSI Detection --- p.96 / Chapter 5.1.1 --- Techniques in MSI Assays --- p.98 / Chapter 5.1.2 --- Choice of Microsatellite Markers --- p.101 / Chapter 5.1.3 --- Diagnostic Criteria of MSI --- p.105 / Chapter 5.2 --- The Role of MSI in the Carcinogenesis of Cervical Neoplasm --- p.107 / Chapter 5.3 --- The Clinical Significant of MSI in Cervical Carcinoma --- p.111 / Chapter 5.4 --- The Interaction between HPV Infection and MSI in Cervical Carcinoma --- p.113 / Chapter CHAPTER VI --- CONCLUSION --- p.116 / REFERENCES --- p.119

No description available.

Made available in DSpace on 2014-06-12T18:03:38Z (GMT). No. of bitstreams: 2 arquivo3714_1.pdf: 874379 bytes, checksum: 1a27595bb5f2f12e52d96545dd1b301b (MD5) license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5) Previous issue date: 2008 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / A definição das taxas de mutação dos locos de microssatélites ou Short Tandem Repeats (STRs) usados em análises forenses são úteis para a correta interpretação dos resultados dos perfis genéticos e para a definição dos critérios de exclusão em testes de paternidade. Mutações da linhagem germinativa de 14 locos de STRs foram estudadas através das análises de 54.105 transferências alélicas genitorcriança a partir de 2.575 casos de testes de paternidade realizados durante 2000- 2007 na população de Pernambuco, Nordeste do Brasil. O parentesco, em cada um desses casos, foi altamente validado (probabilidade > 99.99%). Foram identificadas 43 mutações em 12 locos. As taxas de mutação específicas para cada loco variaram entre 2 x 10-4 e 2 x 10-3, e a taxa de mutação total foi estimada em 8 x 10-4. Eventos de mutação na linhagem germinativa masculina foram mais freqüentes do que na feminina. A maioria das mutações (95%) pode ser explicada pela perda ou ganho de uma unidade repetitiva e não houve evidência para seleção entre mutações de adição ou deleção. Nossos dados foram comparados aos dados referentes a populações americanas e européias e demonstraram que as taxas de mutação dos locos de STRs não diferem entre as diferentes populações