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1
Mularoni, Loris. "Comparative genomics of amino acid tandem repeats." Doctoral thesis, Universitat Pompeu Fabra, 2009. http://hdl.handle.net/10803/7187.
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Tandem amino acid repeats, also known as homopolimeric tract or homopeptides, are very common features of eukaryotic genomes and are present in nearly one-fifth of human encoded proteins. These structures have attracted much interest in the early 1990s when a number of neurological diseases associated with repeat expansion mutations were discovered in humans. Despite their abundance in coding proteins, little is known about their functional consequences. Two scenarios have been proposed. In one, tandem amino acid repeat is considered a neutral structure generated by slippage event and eventually tolerated in protein as long as it does not disrupt the protein function. However, an increasing number of studies proposed that tandem amino acid repeats may be involved in important functional or structural roles. For instance, tandem amino acid repeats had been found to be especially abundant in transcription factors and developmental proteins, where they can potentially modulate protein-protein interaction, exert an effect on gene transcriptional activity, or act as spacer between different protein domains. In addition, several studies have linked changes in repeat size to modification in developmental processes. Despite the advancement made in the last decade, little is known about the selective forces that shape their evolution. The aim of this thesis has been to gain further insight onto the evolutionary dynamics of tandem amino acid repeats by studying the different types of mutations that occur in the amino acid component of the human proteome, by studying the relationship between variability and abundance of amino acid tandem with the evolutionary constraints operating on the proteins, and by studying their conservation and distribution across various vertebrate genomes in both coding and non-coding sequences. The integration of these approaches enabled us to outline an evolutionary model of these structures.
2
Kinnard, Krista. "Human Tandem Repeats in Breast Cancer Progression." Thesis, The University of Arizona, 2010. http://hdl.handle.net/10150/146036.
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A tandemly-repeated sequence of DNA located approximately 1kb upstream of HIC1 has been identified which appears to regulate the expression of this important tumor suppressor gene. Loss of HIC1 expression in tumors, either by deletion or hypermethylation, has previously been shown to correlate with a more severe prognosis in multiple cancers. Initial data show that larger alleles of this tandem repeat do not influence incidence of disease but do appear to correspond with a heritable predisposition to more aggressive cancers, represented by earlier onset and increased metastasis. This study hypothesizes that there may be a connection between these more aggressive types of cancer but also with the deleterious BRCA mutation.
3
Belele, Christiane. "Tandem Repeats are Sufficient for b1 Paramutation." Diss., The University of Arizona, 2006. http://hdl.handle.net/10150/194275.
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Paramutation is an allele interaction that causes a heritable change in the expression of one allele. At the b1 locus an interaction between B' and B-I alleles results in a change of B-I to B', symbolized by B'*. A combination of fine-structure mapping and transgenic approaches have demonstrated that the tandem repeats located ~100 kb upstream of the b1 transcription start site are sufficient for both paramutation and high expression.Plants carrying transgenes with tandem repeats in ectopic locations (repeat-transgene) were able to change B-I into B'*. The B'* state induced by the repeat-transgene was heritable and paramutagenic when segregated from the repeat-transgene. In addition, the repeat-transgene induced B-I silencing was prevented by the trans-acting mutation required for paramutation mop1-1, which was recently found to encode a RNA-dependent RNA polymerase (RdRP). Transgenes containing seven tandem repeats of only the 5' half of the sequence were able to paramutate B-I. Taken together, these results demonstrate that the paramutation sequences are contained in the 5' half of the repeats and they can paramutate B-I from non-allelic positions. Because paramutation induced by the repeat-transgenes and the endogenous B' allele are both heritable and depend on a functional RdRP, they likely involve a similar mechanism of RNA-mediated chromatin modification.Furthermore, we found that the tandem repeats are also sufficient for high expression of the b1 gene. When fused to a GUS reporter gene and introduced into maize, the tandem repeats enhanced GUS expression above the level observed for GUS transgenes that did not have the repeats. As observed with the endogenous B-I allele, the enhancer function of the repeats in the GUS transgenes is silenced by B' and the paramutagenic repeat-transgenes. After being with B' or the paramutagenic repeat-transgenes the repeats in the GUS constructs lost their ability to enhance gene expression.The identification of the tandem repeats as the sequences mediating paramutation suggest a new function for tandem repeats, mediating trans-interactions to establish heritable epigenetic states. Models are discussed for how alleles might communicate in trans to establish different epigenetic states and how the epigenetic state is maintained through mitosis and meiosis.
4
Jochens, Arne [Verfasser]. "Zur Evolution von Short Tandem Repeats / Arne Jochens." Kiel : Universitätsbibliothek Kiel, 2014. http://d-nb.info/1050388720/34.
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5
Redden, Matthew Wyatt. "Tandem repeats in the genome of Schizosaccharomyces pombe." Thesis, University of Exeter, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.410818.
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6
Chang, En Pu. "Aspects of human relationship identification using short tandem repeats." Thesis, University of Strathclyde, 2009. http://oleg.lib.strath.ac.uk:80/R/?func=dbin-jump-full&object_id=11250.
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7
Ledda, Alice. "Distribution and evolution of short sequence tandem repeats in eukariotic genomes." Doctoral thesis, Universitat Pompeu Fabra, 2011. http://hdl.handle.net/10803/31968.
Full textAbstract:
Els microsat el lits s on seq u encies d'ADN formades per repeticions en
t andem de motius curts. Les curtes seq u encies repetides en t andem s on
ubiq ues en els genomes dels eucariotes, tant en les regions codi cants com
en les regions no codi cants. Aquestes seq u encies tenen un nivell molt elevat
de polimor sme i de diverg encia interespec ca.
Hem investigat si les dades obtingudes mitjan cant la seq uenciaci o de nova
generaci o del Projecte Pilot dels 1000 Genomes s on utils per quanti car la
variabilitat dels microsat el lits en les poblacions humanes i per descobrir
nous loci hipot eticament implicats en malalties causades per l'expansi o de
repeticions de trinucle otids.
Hem analitzat la conservaci o ologen etica dels microsat el lits per entendre
el rol que juga la selecci o en l'evoluci o dels microsat el lits. El primer
estudi conclou que en els llinatges dels vertebrats, les repeticions en t andem
d'amino acids estan m es conservades que altres seq u encies similars localitzades
a les regions no codi cants. Aix o ens porta a concloure que l'evoluci o
ha mantingut les repeticions a les regions codi cants de les prote nes. En
una segona fase hem analitzat la conservaci o dels microsat el lits en diferents
regions gen omiques, comparant-les amb la conservaci o dels microsat el lits
a les regions interg eniques. Concloem que la selecci o no mant e nom es els
microsat el lits als exons, sin o que tamb e a altres regions gen omiques.Microsatellites are DNA sequences formed by tandem repetition of short motifs. Short sequence tandem repeats are ubiquitous in eukaryotic genomes both in coding and non-coding regions. They show a very high level of polymophism and interspeci c divergence. We investigated the use of next generation sequencing data, from the 1000 Genomes Pilot Prjects, to quantify microsatellite variability in the human population and discover putative new loci involved in trinucleotide repeat expansion diseases. We analysed microsatellites phylogenetic conservation to learn about the role of selection in shaping microsatellite evolution. The rst study con- cluded that in vertebrate lineages amino acid tandem repeats were more conserved than similar sequences located in non-coding regions. This lead us to the conclusion that evolution was preserving repeats in protein-coding regions. In a second stage we analzed the conservation of microsatellites in di erent genomic regions, comparing them with the of microsatellite in inter- genic region. We concluded that selection was not preserving microsatellites only in exons but also in other genomic regions. 1
8
葉本志 and Poon-chi Benedict Yip. "Uses of short tandem repeats in the diagnosis of genetic diseases." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1997. http://hub.hku.hk/bib/B31214848.
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9
Ahmed, Amany Mahmoud. "The application of short tandem repeats to paternity testing in Egypt." Thesis, University of Glasgow, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.340294.
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Yip, Poon-chi Benedict. "Uses of short tandem repeats in the diagnosis of genetic diseases /." Hong Kong : University of Hong Kong, 1997. http://sunzi.lib.hku.hk/hkuto/record.jsp?B18865458.
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11
SaidQasem, Osama. "Temporal and spatial explorations of Clostridium difficile variable number tandem repeats." Thesis, University of Aberdeen, 2014. http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?pid=211224.
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Clostridium difficile infection (CDI) has recently emerged as a major health problem. An understanding of the micro-epidemiology of the infection is decisive for the design and implementation of control polices. Presently, typing using PCR ribotyping (RT), Multi-locus Sequence Typing (MLST) and Multi-locus Variable Number Tandem Repeat Analysis (MLVA) can be used to investigate recent transmission events of C. difficile. In the case of MLVA, different criteria have been used to classify strains and this reflects inconsistencies in the contemporary knowledge of change in MLVA polymorphisms. In this study, temporal and spatial investigations were conducted to better understand the dynamics of change in C. difficile VNTR loci. The 164 isolates from the collection yielded 25 different STs, with ST161 and ST171 being newly described. The congruence of MLST to the other typing methods of RT and tcdC, strengthens the robustness of discrimination of these methods. Sub-typing using MLVA, however yielded 139 strains, and again there was congruence to the aforementioned methods. Clustering of MLVA strains into groups revealed Single and Multi-Isolate Strains linked together as single locus variants with groups coordinating with MLST types within ST1 and ST3. The lowest MLVA diversity was seen in the Period of Increased Incidence and was primarily responsible for high incidence rates. These groups of MLVA related isolates were used to characterise the instability of the repeat sequences of MLVA loci. 2 Locus differences were examined from the perspective of the genetic role of the locus, DNA polymerase amplification, the impact of different growth conditions on the fitness of the repeat sequences and of the frequency of repeat changes in the natural population. These studies have focused on the on the drivers of change of VNTR loci in general and will allow a more rational approach to using MLVA loci in epidemiological studies.
12
Melters, Daniel Patrick. "Comparative Analysis of Tandem Repeats from Eukaryotic Genomes| Insight in Centromere Evolution." Thesis, University of California, Davis, 2014. http://pqdtopen.proquest.com/#viewpdf?dispub=3602160.
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Centromeres are the chromosomal loci where microtubule spindles bind, via the kinetochore, during mitosis and meiosis. Paradoxically the centromere, as a functional unit, is essential to guarantee faithful chromosome segregation, whereas its underlying DNA sequences and associated kinetochore proteins are fast evolving. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. In spite of their importance, very little is known about the degree to which centromeric tandem repeats share common properties between different species across different phyla. We used bioinformatic methods to identify high-copy tandem repeats from species using publicly available genomic sequence and our own data. We found that despite an overall lack of sequence conservation, centromeric tandem repeats from diverse species showed similar modes of evolution. Furthermore, phylogenetic analysis of sequence homology showed little evidence of sequence conservation beyond approximately 50 million years of divergence. In addition, we performed a survey of fungi genomes for the presence of high-copy tandem repeats, but found little evidence to suggest that high-copy centromeric repeats are a common feature feature in fungi, with the possible exception of the Zygomycota. phylum. Finally, in most species the kinetochore assembles at a single locus, but in some cases the kinetochore forms along the entire length of the chromosomes forming holocentric chromosomes. Following a literature review we estimate that holocentricity is very common and has evolved at least thirteen times.
13
Willems, Thomas F. (Thomas Frederick). "Uncovering the variability, regulatory roles and mutation rates of short tandem repeats." Thesis, Massachusetts Institute of Technology, 2016. http://hdl.handle.net/1721.1/104465.
Full textAbstract:
Thesis: Ph. D., Massachusetts Institute of Technology, Computational and Systems Biology Program, 2016.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references (pages 163-186).
Over the past decade, the advent of next-generation DNA sequencing technologies has ushered in an exciting era of biological research. Through large-scale sequencing projects, scientists have begun to unveil the variability and function of millions of DNA mutations called single nucleotide polymorphisms. Despite this rapid growth in understanding, short tandem repeats (STRs), genomic elements consisting of a repeating pattern of 2-6 bases, have remained poorly understood. Mutating orders of magnitude more rapidly than most of the human genome, STRs have been identified as the causal variants in diseases such as Fragile X syndrome and Huntington's disease. However, in spite of their potentially profound biological consequences, STRs remain systematically understudied due to difficulties associated with obtaining accurate genotypes. To address this issue, we developed a series of bioinformatics approaches and applied them to population-scale whole-genome sequencing data sets. Using data from the 1000 Genomes Project, we performed the first genome-wide characterization of STR variability by analyzing over 700,000 loci in more than 1000 individuals. Next, we integrated these genotypes with expression data to assess the contribution of STRs to gene expression in humans, uncovering their substantial regulatory role. We then developed a state-of-the-art algorithm to genotype STRs, resulting in vastly improved accuracy and uncovering hundreds of replicable de novo mutations in a deeply sequenced trio. Lastly, we developed a novel approach to estimate mutation rates for STRs on the Y-chromosome (Y-STR), resulting in rates for hundreds of previously uncharacterized markers. Collectively, these analyses highlight the extreme variability of STRs and provide a framework for incorporating them into future studies.
by Thomas F. Willems.
Ph. D.
14
Matos, Sara Mulenas Sá de. "Identificação genética humana: estudos de novos marcadores genéticos do tipo STR e InDel." Master's thesis, Escola Superior de Saúde Egas Moniz, 2013. http://hdl.handle.net/10400.26/5125.
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Dissertação para a obtenção do grau de Mestre em Biologia Molecular em SaúdeOs marcadores genéticos do tipo Short Tandem Repeats (STR), são os atualmente recomendados para a obtenção de perfis genéticos, sendo que, muito recentemente foi apresentado como obrigatório para uso forense, um novo conjunto destes marcadores. Não obstante, existem também outros tipos de marcadores genéticos passíveis de utilização para definir perfis genéticos, designadamente marcadores do tipo Inserção/Deleção, ou InDel. Os novos marcadores STR e a grande maioria dos marcadores InDel ainda não estão suficientemente estudados e implementados nos laboratórios forenses, pelo que é necessário validar a reação, calcular frequências alélicas, parâmetros estatísticos populacionais e forenses. Estudámos os novos marcadores STR e um conjunto de marcadores do tipo InDel numa amostra com cerca de 120 indivíduos do sul de Portugal, intervenientes em perícias médico-legais a decorrer no Instituto Nacional de Medicina Legal e Ciências Forenses. No que concerne aos marcadores STR incluídos no kit PowerPlex®ESI17 (promega), os ensaios de validação demonstraram a sua elevada sensibilidade, precisão e capacidade de detetar misturas de DNA. No entanto, relativamente aos limiares analíticos não está de acordo com o descrito anteriormente. Os parâmetros estatísticos populacionais e forenses estão de acordo com o esperado e o cálculo das distâncias genéticas demonstrou existir diferenças genéticas entre as populações em estudo. Relativamente aos marcadores do tipo InDel incluídos no kit Investigator DIPPlex® (Qiagen), os ensaios de validação demonstraram que o kit tem uma elevada sensibilidade, limiares analíticos relativamente baixos, boa capacidade de detetar misturas e boa precisão. As frequências alélicas estão em equilíbrio Hardy-Weinberg, no entanto os valores de heterozigotia não são os esperados. Os parâmetros estatísticos forenses estão de acordo com o esperado e o cálculo das 4 distâncias genéticas demonstrou que existem diferenças genéticas significativas relativamente a outras populações. Concluímos que ambos os kits poderão ser utilizados para a prática forense apesar de, aparentemente, não preencherem todos os requisitos habitualmente avançados para os marcadores genéticos a utilizar na rotina forense. Deverão ser realizados mais estudos com maior número de indivíduos e de diferentes populações.
15
Teló, Enio Paulo. "Estimativa de mistura étnica avaliada por Mercadores Informativos de Ancestralidade (AIMs) e Microssatélites (STRs)." reponame:Repositório Institucional da FIOCRUZ, 2010. https://www.arca.fiocruz.br/handle/icict/4171.
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Submitted by Ana Maria Fiscina Sampaio (fiscina@bahia.fiocruz.br) on 2012-07-16T21:36:49Z
No. of bitstreams: 1
Enio Paulo Estimativa de mistura étnica avaliada por Marcadores Informativos de.pdf: 352598 bytes, checksum: 7d448dc54afe1ec271f59fc912275f41 (MD5)Made available in DSpace on 2012-07-16T21:36:49Z (GMT). No. of bitstreams: 1 Enio Paulo Estimativa de mistura étnica avaliada por Marcadores Informativos de.pdf: 352598 bytes, checksum: 7d448dc54afe1ec271f59fc912275f41 (MD5) Previous issue date: 2010
Fundação Oswaldo Cruz. Centro de Pesquisas Gonçalo Moniz. Salvador, Bahia, Brasil
A miscigenação entre os três principais grupos étnicos (ameríndios, europeus e africanos) originou a alta diversidade genética da população brasileira. Na Bahia a proporção de afrodescendentes é de 77,5%, sendo que em Salvador 79,8% se auto-denominam negros ou pardos. Poucos estudos descrevem a diversidade genética da população baiana e a contribuição de cada grupo étnico na sua formação. Diversos marcadores de DNA são atualmente utilizados para estimar mistura étnica em populações miscigenadas. Estes marcadores são denominados alelos específicos de população (PSAs) ou marcadores informativos de ancestralidade (AIMs) e apresentam alelos com grandes diferenciais de freqüência, superiores a 30%, entre populações geográfica ou etnicamente definidas. Os microssatélites (STRs) são variantes genéticos úteis no mapeamento genético de espécies, na identificação de pessoas, mapeamento genético e análise de populações. Alguns STRs apresentam alelos com freqüências marcantes em determinados grupos populacionais. Com objetivo de comparar a ancestralidade genomica avaliada com dois tipos de marcadores, foram estudados 8 microssatélites STRs autossômicos (TH01, vWA31, D18S51, FGA, TPOX, D7S820, D3S1358, D8S1179) e 9 AIMs (FY-Null, LPL, AT3-I/D, Sb19.3, APO, PV92, CYP3A4, CKMM, GC-1F e GC-1S), em 203 indivíduos miscigenados da Bahia. A genotipagem foi realizada por PCR (Polimerase Chain Reaction), para deleções, inserções e para os microssatélites e PCR quantitativo em tempo real para mutações pontuais. As contribuições africana, européia e ameríndia observadas foram respectivamente 33,5%, 58,6% e 7,9% para os STRs e 45,08%, 45,16% e 9,75% para os AIMs, comprovando a miscigenação da população. O Índice Kappa, mostrou que a concordância entre as estimativas de ancestralidade utilizando os dois tipos de marcadores (AIMs e STRs), foi muito baixa (kappa = 0,12). Foi observada associação entre sobrenome de conotação religiosa e ancestralidade africana
The mixing between the three main ethnic groups (Amerindians, Europeans and Africans) produced a high genetic diversity of the braziliam population. In Bahia, the proportion of African descent that call themselves black or brown is 77.5% and 79.8% in Salvador. Few studies describe the genetic diversity of the population of Bahia and the contribution of each ethnic group in its formation. Several DNA markers are currently used to estimate ethnic mix in admixed populations. These markers are called alleles specific population (PSAs) or ancestry informative markers (AIMs) and carry alleles with large differences in frequency above 30% between populations geographically or ethnically defined. Microsatellites (STRs) are useful genetic variants in the genetic mapping of species, identification of persons, genetic mapping and analysis of populations. Some STRs have alleles with frequencies marked in certain population groups. To compare the ancestry genomica evaluated with two types of markers were studied 8 microsatellite autosomal STRs (TH01, vWA31, D18S51, FGA, TPOX, D7S820, D3S1358, D8S1179) and 9 AIMs (FY-Null, LPL, AT3-I /D, Sb19.3, APO, PV92, CYP3A4, CK-MM, GC and GC-1F-1S) in 203 subjects with mixed Bahia. Genotyping was performed by PCR (Polymerase Chain Reaction), for deletions, insertions and for microsatellite and quantitative PCR in real time for mutations. The contributions of African, European and Amerindian observed were respectively 33.5%, 58.6% and 7.9% for the STRs and 45.08%, 45.16% and 9.75% for the AIMs, proving the mixing of population. The Kappa index showed that the correlation between the estimates of ancestry using both types of markers (AIMs and STRs), was very low (kappa = 0.12). Association was found between devotional surnames and African ancestry.
16
Richard, François D. "Développement et application de méthodes bioinformatiques pour l'analyse des protéines contenant des répétitions en tandem." Thesis, Montpellier, 2016. http://www.theses.fr/2016MONTT084.
Full textAbstract:
De nos jours, l’augmentation du volume des données de séquençage est bien plus forte que celle de notre capacité à analyser ces données. En lien avec ce déluge de données et le besoin urgent de nouveaux outils bioinformatiques pour les analyser, notre travail consiste à développer de nouveaux algorithmes pour mieux comprendre les relations entre séquence, structure, et fonction des protéines. Les protéines contiennent de larges portions de séquences périodiques, qui forment des motifs d’acides aminés répétés les uns à la suite des autres que l’on appelle des répétitions en tandem. Elles se retrouvent dans 14% des protéines. De nombreuses études ont montré leur importance fonctionnelle ainsi que leur implication dans de nombreuses maladies humaines, notamment le cancer. Ici, nous montrons l’importance d’adopter une approche incluant plusieurs outils de détection de répétition en tandem afin de s’assurer d’obtenir le jeu de données le plus complet. Nous avons ainsi réalisé un pipeline approprié, et développé deux outils spécifiques : un filtre, pour gagner en rapidité, et un score, pour sélectionner les répétitions les plus pertinentes dans les régions structurées des protéines. Enfin, nous avons utilisé ce pipeline sur une sélection de 94 protéomes. Cette analyse a permis de mettre à jour le précédent recensement des répétitions, montrant que 64% des protéines contenaient des répétitions en tandem. Elle a également permis de mieux comprendre les répétions en tandem dans leurs caractéristiques, leurs compositions et leurs implications dans les maladies humainesToday, the growth of protein sequencing data significantly exceeds the growth of capacities to analyze these data. In line with this data deluge and urgent needs in new bioinformatics tools our work deals with the development of new algorithms to better understand the sequence-structure-function relationship. Proteins contain a large portion of periodic sequences representing arrays of repeats that are directly adjacent to each other, so called tandem repeats (TRs). TRs occur at least in 14% of all proteins. Highly divergent, they range from a single amino acid repetition to domains of 100 or more repeated residues. Numerous studies demonstrated the fundamental functional importance of such TRs and their involvement in human diseases, especially cancers. Here we show the importance of integrating several TR detectors to get the most complete set of TRs in proteomes. We designed an appropriate pipeline and developed a filter to speed the process as well as a new scoring module to select relevant structured TRs. In addition, we undertook a large scale analysis of TRs in 94 proteomes. This large scale analysis allowed us to update previous census of TR showing that TRs occurs in 64% of all proteins and leads to a better understanding of TR in terms of their characteristics, composition and implication in human disease
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Tonkin, Emma Tamsin. "Towards the identification of genetic factors influencing the stability of short tandem repeats." Thesis, University of Aberdeen, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.312457.
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This work has identified three distinct approaches that can be used to identify genetic factors involved in the STR instability process. We propose that Schizosaccharomyces pombe, a yeast now recognised as being a good model for the study of many cellular processes in higher eukaryotes, is also suitable for the study of STR instability. We have demonstrated that in S. pombe a plasmid based (CAG/CTG)n sequence containing between 25-74 repeat units is stable over approximately 55 mitotic divisions. A frame-dependent reporter gene construct, based on colour, has also been created containing the dinucleotide repeat (CA/GT)12. By following the change in repeat length or colony colour (for the two constructs respectively) in strains containing both known or randomly created genomic disruptions/mutations it will be possible to identify factors that directly impact upon repeat length. One factor that we have considered as a potential candidate is the product of the S. cerivisiae postreplication repair gene RAD5. An increase in the stability of the dinucleotide repeat (CA/GT)n has been demonstrated in strains deleted for this gene (Johnson et al., 1992). Discussed are the attempts that have been made to clone the S. pombe homologue in order to determine whether this function is maintained between species. Also identified, through the technique of Southwestern blotting, are a number of proteins that bind both single stranded [(CAG)10, (CTG)10, (CCG)10, and (CGG)10] and double stranded [(CAG/CTG)10 and (CCG/CGG)10] trinucleotide repeats. The interactions, with the (CCG)10, oligonucleotide, of a group of proteins ranging in size from 18-45 kDa have been demonstrated to be specific. Further identification of these proteins and their function(s) in binding this particular sequence may identify a role in (CCG/CGG)n instability and may in turn suggest other proteins or pathways to be investigated in the future. This work demonstrates that a number of methods are available for the study of STR instability. A combined approach based on the identification of i) novel sequences using reporter gene constructs; ii) proteins that interact with repetitive DNA and iii) candidate sequences, pathways and mechanisms elucidated in other organisms, will in the future, enable short tandem repeat instability to be more fully understood.
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Manca, Maurizio. "Role of Variable Number Tandem Repeats (VNTRs) on gene expression in the CNS." Thesis, University of Liverpool, 2016. http://livrepository.liverpool.ac.uk/3007520/.
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It is now known that at least 80% of the human genome is composed of non-coding DNA which has a biochemical activity and is involved in a wide range of activities and mechanisms. Among these, epigenetic modifications, cis-trans gene expression regulation, transcription factor binding sequences, are the most studied. Non-coding DNA is often characterised by a polymorphic and repetitive nature and it is composed of a high density of GC nucleotides. These polymorphic and repetitive regions within the population may represent either protective elements or risk factors, based on population studies in various diseases, for several conditions and at the same time have the power to shape our behaviours or wellbeing. The compositions of transcription factor binding sites (BSs) and epigenetic factors at these regions act in concert with external and environmental factors to modify gene function and gene expression. This combined effect of environmental and genetic factors capable of influence people's wellbeing or disease risk is known as Gene - Environment Interaction (GxE) and it is a key feature that allows us to adapt to our surrounding. The data presented in this thesis will try to address some of the well characterised polymorphic variants associated with Central Nervous System (CNS) conditions, such as the Monoamine oxidase A (MAOA) gene, and I will show how they can modify gene expression in response to environmental stimuli. We also report two regulatory regions in the CACNA1C (Calcium Voltage-Gated Channel Subunit Alpha1 C) gene, strongly associated to schizophrenia by GWAS (Genome-Wide Association Study) investigations. Finally I will also report a novel polymorphic microsatellite in the promoter region of the gene that has been defined 'the master regulator' of transcription, the RE1-Silencing Transcription factor (REST) gene, that strongly suggests an association with Alzheimer's disease. Therefore I demonstrate a similarity in mechanisms and in the activity of these repeat elements in the promoter regions of three key genes for CNS behaviour and illustrate the potential power of these elements as transcriptional regulatory DNA regions.
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Gymrek, Melissa A. "Characterizing variation at short tandem repeats and their role in human genome regulation." Thesis, Massachusetts Institute of Technology, 2016. http://hdl.handle.net/1721.1/103501.
Full textAbstract:
Thesis: Ph. D., Harvard-MIT Program in Health Sciences and Technology, 2016.Cataloged from PDF version of thesis.
Includes bibliographical references (pages 225-251).
A central goal in genomics is to understand the genetic variants that underlie molecular changes and lead to disease. Recent studies have identified thousands of genetic loci associated with human phenotypes. These have primarily analyzed point mutations, ignoring more complex types of variation. Here we focus on Short Tandem Repeats (STRs) as a model for complex variation. STRs are comprised of repeating motifs of 1-6bp that span over 1% of the human genome. The level of STR variation and its effect on phenotypes remains mostly uncharted, mainly due to the difficulty in accurately genotyping STRs on a large scale. To overcome bioinformatic challenges in STR genotyping, we developed lobSTR, an algorithm for profiling STRs from high throughput sequencing data. lobSTR employs a unique mapping strategy to rapidly align repetitive reads, and uses statistical learning techniques to account for STR-specific noise patterns. We applied lobSTR to generate the largest and highest quality STR catalog to date. This provided the first characterization of more than a million loci and gave novel insights into population-wide trends of STR variation. We used our catalog to conduct a genome-wide analysis of the contribution of STRs to gene expression in humans. This revealed that STRs explain 10-15% of the cis heritability of expression mediated by common variants and potentially play a role in various clinically relevant conditions. Overall these studies highlight the contribution of STRs to the genetic architecture of quantitative traits. We anticipate that integrating repetitive elements, specifically STRs, into genome-wide analyses will lead to the discovery of new genetic variants relevant to human conditions.
by Melissa A. Gymrek.
Ph. D.
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Patch, Ann-Marie. "A comparative analysis of tandem repeats in the fission yeast and budding yeast genomes." Thesis, University of Exeter, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.425493.
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Merkel, Angelika. "Microsatellite Evolution in The Yeast Genome - A Genomic Approach." Thesis, University of Canterbury. School of Biological Sciences, 2008. http://hdl.handle.net/10092/3327.
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Microsatellites are short (1-6bp long) highly polymorphic tandem repeats, found in all genomes analyzed so far. Popular genetic markers for many applications including population genetics, pedigree analysis, genetic mapping and linkage analysis, some microsatellites also can cause a variety of human neurodegenerative diseases and may act as agents of adaptive evolution through the regulation of gene expression. As a consequence of these diverse uses and functions, the mutational and evolutionary dynamics of microsatellite sequences have gained much attention in recent years. Mostly, the focus of studies investigating microsatellite evolution has been to develop more refined evolutionary models for estimating parameters such as genetic distance or linkage disequilibrium. However, there is an incentive in using our understanding of the evolutionary processes that affect these sequences to examine the functional implications of microsatellite evolution. What has emerged from nearly two decades of study are highly complex mutational dynamics, with mutation rates varying across species, loci and alleles, and a multitude of potential influences on these rates, most of which are not yet fully understood. The increasing availability of whole genome sequences has immensely extended the scope for studying microsatellite evolution. For example, where once it was common to examine single loci, it is now possible to examine microsatellites using genome wide approaches. In the first part of my dissertation I discuss approaches and issues associated with detecting microsatellites in genomic data. In Chapter 2 I undertook a meta-analysis of studies investigating the distribution of microsatellites in yeast and showed that studies comparing the distribution of microsatellites in genomic data can be fraught due to the application of different definitions for microsatellites by different investigators. In particular, I found that variation in how investigators choose the repeat unit size of a microsatellite, handle imperfections in the array and especially the choice of minimum array length used, leads to a large divergence in results and can distort the conclusions drawn from such studies, particularly where inter-specific comparisons are being made. In a review of the currently available suite of bioinformatics tools (Chapter 3), I further showed that this bias extends beyond a solely theoretical controversy into a methodological issue because most software tools not only incorporate different definitions for the key parameters used to define microsatellites, but also employ different strategies to search and filter for microsatellites in genomic data. In this chapter I provide an overview of the available tools and a practical guide to help other researchers choose the appropriate tool for their research purpose. In the second part of my thesis, I use the analytical framework developed from the previous chapters to explore the biological significance of microsatellites exploiting the well annotated genome of the model organism Saccharomyces cerevisiae (baker’s yeast). Several studies in different organisms have indicated spatial associations between microsatellites and individual genomic features, such as transposable elements, recombinational hotspots, GC-content or local substitution rate. In Chapter 4, I summarized these studies and tested some of the underlying hypotheses on microsatellite distribution in the yeast genome using Generalized Linear Models (GLM) and wavelet transformation. I found that microsatellite type and distribution within the genome is strongly governed by local sequence composition and negative selection in coding regions, and that microsatellite frequency is inversely correlated with SNP density reflecting the stabilizing effect point mutations have on microsatellites. Microsatellites may also be markers for recent genome modifications, due to their depletion in regions nearby LTR transposons, and elements of potential structural importance, since I found associations with features such as meiotic double strand breaks, regulatory sites and nucleosomes. Microsatellites are subject to local genomic influences, particularly on small (1-2kb) scales. Although, these local scale influences might not be as dominant as other factors on a genome-wide scale they are certainly of importance with respect to individual loci. Analysis of locus conservation across 40 related yeast strains (Chapter 5) showed no bias in the type of microsatellites conserved, only a negative influence of coding sequences, which supports again the idea that microsatellites evolve neutrally. Polymorphism was rare, and despite a positive correlation with array length, there was no relationship with either genomic fraction or repeat size. However, the analysis also revealed a non-random distribution of microsatellites in genes of functionally distinct groups. For example, conserved microsatellites (similar to general microsatellites in yeast) are mostly found in genes associated with the regulation of biological and cellular processes. Polymorphic loci show further an association with the organization and biogenesis of cellular components, morphogenesis, development of anatomical structures and pheromone response, which, is absent for monomorphic loci. Whether this distribution is an indication of functionality or simply neutral mutation (e.g. genetic hitch-hiking) is debatable since most conserved microsatellites, particularly variable loci, are located within genes that show low selective constraints. Overall, microsatellites appear as neutrally evolving sequences, but owing to the sheer number of loci within a single genome, individual loci may well acquire some functionality. More work is definitely needed in this area, particularly experimental studies, such as reporter-gene expression assays, to confirm phenotypic effects.
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Zhao, Zhixin. "Genome-wide analysis of transcriptome dynamics in plants and algae." Miami University / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=miami1385672751.
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Tinah, Enass Nabeel. "A population study of Middle Eastern populations using DYS458 microvariants and Cohen Modal Short Tandem Repeats /." Diss., CLICK HERE for online access, 2008. http://contentdm.lib.byu.edu/ETD/image/etd2735.pdf.
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ANDRADE, Edilene Santos de. "Taxas de mutação de 14STRs autossômicas na população de Pernambuco." Universidade Federal de Pernambuco, 2008. https://repositorio.ufpe.br/handle/123456789/6286.
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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
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Jorda, Julien. "Analyse systématique des motifs répétés en tandem dans les séquences protéiques." Thesis, Montpellier 2, 2010. http://www.theses.fr/2010MON20090/document.
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Au cours des dernières décennies, les avancées techniques dans la biologie moléculaire telles que les projets de séquençage de génome ont eu pour conséquence un accroissement du volume des banques de données biologiques. Parmi ces données, des séquences présentent des motifs similaires entre eux, répétés de façon juxtaposée, appelés répétitions en tandem. L'objectif de cette thèse est de comprendre l'existence de ces répétitions dans les séquences protéiques via une analyse à grande échelleOver the last decades, technical advances in molecular biology such as the genome sequencing projects led to a huge increase of data in the biological databanks. Among them, there are particular motifs which are adjacently repeated and similar between them, called tandem repeats. The purpose of this thesis is to understand the existence of these repeats in protein sequences through a large-scale analysis
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Teo, Chee How. "LTR retrotransposons and tandem repeats in Musa genomes and their contribution to Musa diversity and genome evolution." Thesis, University of Leicester, 2007. http://hdl.handle.net/2381/29742.
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Musa is a large genus that includes many important staple crops particular in Asia and Africa. Pseudoviridae, LARD-like and three different groups of Metaviridae elements were identified based on their RT sequence heterogeneity. Additionally, full length elements were identified in published BAC sequences. Most of the LTR-retrotransposons were degenerated and disrupted at different positions, by other types of repetitive DNAs (retrotransposons and tandem repeats). Metaviridae elements are generally present in higher copy numbers than Pseudoviridae elements, and the A genome contains more retrotransposons than the B genome, possibly explaining the larger genome size of the A genome. However, genome specific LTR-retrotransposons were not detected. Retrotransposons were clustered in the centromeric regions, Pseudoviridae elements showing a more dispersed pattern while LARD-like and some of the Metaviridae elements were also found at the Nucleolar Organizing Region (NOR). Two genome-specific repeats, organised in long arrays are located at the NOR loci of seven Musa taxa and additionally at some to all centromeres of selected taxa. Different degrees of methylation of LTR retrotransposons and tandem repeat DNA, the latter generally being under-methylated were observed. The transcribed copies of the 45SrDNA sequences at the NOR are interspersed by MuTR repeats and weakly methylated, while the distal part of the NOR region and the chromosomal satellite beyond contains MuTR, Metavirdae and LARD-like sequences that are heavily methylated. The close chromosomal proximity and insertion within each other postulates a possible link in the evolution of LTR-retrotransposons, tandem repeats and 5S rRNA genes, but also a role of retrotransposon sequences in gene regulation RNA transcripts of both metaviridae and MuTR repeats indicates their activity, but also that they might be involved in siRNA silencing mechanisms.
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Cattani, Amanda Malvessi. "Elementos repetitivos na regulação da transcrição de Mycoplasma hyopneumoniae." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2016. http://hdl.handle.net/10183/143890.
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Mycoplasma hyopneumoniae é uma bactéria de tamanho diminuto, caracterizada por um genoma pequeno, com baixo conteúdo GC. Está associada com doenças respiratórias de suínos, resultando em prejuízos produtivos e econômicos na indústria animal. A presença de sequências de DNA repetitivas, que ocorrem em grandes quantidades em células eucarióticas, vem sendo cada vez mais identificadas em genomas de procariotos, sendo também associadas a um potencial papel regulador. Uma vez que a regulação da transcrição nesses organismos ainda é pouco entendida, o objetivo do presente estudo foi realizar uma busca in silico por elementos repetitivos nas regiões intergênicas do genoma de M. hyopneumoniae linhagem 7448. Dois tipos de repetições foram selecionados para a busca inicial: tandem e palindromes. Regiões intergênicas de até 500 pb a montante do sítio de início da tradução de todas as CDSs do genoma de M. hyopneumoniae linhagem 7448 foram utilizadas para a predição. Para cada tipo de elemento dois programas computacionais independentes foram utilizados. As predições in silico resultaram em 144 repetições em tandem e 1.171 palindromes. O DNA repetitivo se encontra distribuído a montante de 86% das unidades transcricionais de M. hyopneumoniae linhagem 7448. Análises comparativas entre genomas de micoplasmas demonstraram diferentes níveis de conservação dos elementos repetitivos entre linhagens patogênicas e não-patogênicas. Linhagens patogênicas revelaram uma conservação de 59%, enquanto que a não patogênica, somente de 46%. Através de ensaios de amplificação quantitativa de DNA, foi observado diferentes níveis de expressão em genes codificantes para importantes proteínas, como glicina hidroximetiltransferase, lipoproteína, adesinas e proteína ligadora de GTP. Os genes codificantes para essas proteínas divergiam no número de repetições palindromes e tandens na sua respectiva região intergênica. Além disso, repetições encontradas em 206 genes já descritos como regulados em diferentes condições em M. hyopneumoniae linhagem 232 mostraram aproximadamente 80% de conservação em relação à linhagem M. hyopneumoniae linhagem 7448. Todos esses resultados sugerem um potencial papel regulador das repetições de DNA em tandem e palindromes em Mycoplasma.Mycoplasma hyopneumoniae is a diminutive bacterium, characterized by a small genome with a low GC content. It is commonly associated with swine respiratory diseases, resulting in productivity and economic losses in the animal industry. Repetitive DNA, which occurs in large quantities in eukaryotic cells, has been increasingly identified in prokaryotic genomes, and has been associated with a potential regulatory function. Once transcription regulation in these organisms is still poorly understood, the aim of the current study was to perform an in silico search of repeat elements in the genomic intergenic regions of M. hyopneumoniae strain 7448. Two types of repeats were selected for initial search: Tandem and Palindromic. Intergenic regions up to 500 bp upstream from start codon of M. hyopneumoniae strain 7448 CDSs were used as input for the software’s prediction. For each type of repeat sequence, two independent software packages were used. Computational analysis results in 144 tandem repeats and 1,171 palindrome elements. The repeats were distributed in the upstream region of 86% of transcriptional units of M. hyopneumoniae strain 7448. Comparative analysis between distinct mycoplasmas, demonstrate different indices of repeat conservation among pathogenic and non-pathogenic strains. Pathogenic strains revealed 59% conservation, while non-pathogenic only 46%. Through assays of quantitative amplification of DNA, different levels of expression in genes coding important proteins have been demonstrated, as glycine hydroxymethyltransferase, lipoprotein, adhesins and GTP-binding protein. These protein coding genes differ in number of palindromes or tandem repeats in respective upstream regions. In addition, repeats found in 206 genes already described to be regulated in different grow conditions in M. hyopneumoniae strain 232 showed almost 80% of conservation in relation to M. hyopneumoniae strain 7448. All these findings, suggests a potential regulatory role of tandem and palindrome DNA repeats.
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Sagit, Rauan. "Variation in length of proteins by repeats and disorder regions." Doctoral thesis, Stockholms universitet, Institutionen för biokemi och biofysik, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-88553.
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Protein-coding genes evolve together with their genome and acquire changes, some of which affect the length of their protein products. This explains why equivalent proteins from different species can exhibit length differences. Variation in length of proteins during evolution arguably presents a large number of possibilities for improvement and innovation of protein structure and function. In order to contribute to an increased understanding of this process, we have studied variation caused by tandem domain duplications and insertions or deletions of intrinsically disordered residues. The study of two proteins, Nebulin and Filamin, together with a broader study of long repeat proteins (>10 domain repeats), began by confirming that tandem domains evolve by internal duplications. Next, we show that vertebrate Nebulins evolved by duplications of a seven-domain unit, yet the most recent duplications utilized different gene parts as duplication units. However, Filamin exhibits a checkered duplication pattern, indicating that duplications were followed by similarity erosions that were hindered at particular domains due to the presence of equivalent binding motifs. For long repeat proteins, we found that human segmental duplications are over-represented in long repeat genes. Additionally, domains that have formed long repeats achieved this primarily by duplications of two or more domains at a time. The study of homologous protein pairs from the well-characterized eukaryotes nematode, fruit fly and several fungi, demonstrated a link between variation in length and variation in the number of intrinsically disordered residues. Next, insertions and deletions (indels) estimated from HMM-HMM pairwise alignments showed that disordered residues are clearly more frequent among indel than non-indel residues. Additionally, a study of raw length differences showed that more than half of the variation in fungi proteins is composed of disordered residues. Finally, a model of indels and their immediate surroundings suggested that disordered indels occur in already disordered regions rather than in ordered regions.At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: In press. Paper 4: Manuscript.
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Kam, Janice Lik Ming. "MUC1 synthetic peptide inhibition of ICAM-1 and MUC1 binding is dependent on the number of tandem repeats." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/tape17/PQDD_0026/MQ34381.pdf.
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Silva, Guilherme do Valle. "Análise de marcadores forenses (STRs e SNPs) rotineiramente empregados na identificação humana utilizando sequenciamento de nova geração." Universidade de São Paulo, 2018. http://www.teses.usp.br/teses/disponiveis/59/59138/tde-23112018-095204/.
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A genética forense vem se desenvolvendo cada vez mais, com novas tecnologias e implementação de novos conjuntos de marcadores de DNA com maiores níveis de informatividade. Os marcadores genéticos são amplamente usados na identificação humana, pois permitem distinguir indivíduos com alta acurácia. Duas classes de marcadores muito utilizadas atualmente são os STRs (Short Tandem Repeats) e os SNPs (Single Nucleotide Polymorphisms). Os STRs são altamente informativos e, portanto, úteis para a prática forense. Kits mais novos como GlobalFiler (Thermo Fisher Scientific) e PowerPlex Fusion System (Promega) apresentam a análise de mais de 20 loci STRs de uma só vez. Já os SNPs, por possuírem sua informatividade mais reduzida (necessita de mais loci analisados), são menos utilizados, porém apresentam vantagem em amostras degradadas de DNA; assim, conjuntos de identificação como o 52-plex desenvolvido pelo consórcio SNPforID e o conjunto IISNPs, vêm sendo estudados em várias populações do mundo. Com o desenvolvimento de técnicas de sequenciamento de nova geração (NGS Next Generation Sequencing) para análise de DNA, a obtenção de perfis de DNA se tornou mais acurada. Algumas plataformas permitem gerar perfis de até 96 indivíduos simultaneamente. Este estudo tem por objetivo principal analisar 171 marcadores genéticos (Amelogenina, Y-INDEL, 30 STRSs e 139 SNPs) em 340 indivíduos miscigenados da região da cidade de Ribeirão Preto (SP) utilizando a plataforma de sequenciamento de nova geração MiSeq Personal Sequencer (Illumina Inc.), bem como calcular as frequências alélicas e genotípicas, verificar a aderência ao equilíbrio de HardyWeinberg e estimar parâmetros forenses para os diferentes conjuntos de marcadores. Análises de ancestralidade foram realizadas para os conjuntos de SNPs. Para o preparo das bibliotecas de amostras a serem sequenciadas, foi utilizado o kit HaloPlex (Agilent Technologies, Inc), onde foram incluídos os marcadores dos kits GlobalFiler e PowerPlex Fusion System, e os SNPs existentes no conjunto do consórcio SNPforID (52-plex) e IISNPs (92 SNPs). De todos os marcadores incluídos no ensaio, apenas um SNP (rs763869) presente no conjunto SNPforID não pôde ser analisado devido a questões técnicas. Dos 139 SNPs analisados apenas seis apresentaram desvios significativos em relação ao equilíbrio de Hardy-Weinberg,número este esperado devido ao acaso. Os conjuntos de SNPs apresentam elevada informatividade com Probabilidade de Match de 6,48 x 10-21 (52-plex) a 4,91 x 10-38 (IISNP), e Poder de Exclusão de 0,9997 (52-plex) e 0,99999997 (IISNP). De modo geral, as inferências de ancestralidade obtida utilizando estes conjuntos, indicaram elevada contribuição europeia (superior a 70%) e baixa contribuição ameríndia (inferior a 10%) na população, enquanto que as análises de mistura individual se mostraram consistentes, com a maioria dos indivíduos apresentando elevada ancestralidade europeia. Os resultados dos marcadores relativos ao sexo (Amelogenina, Y-INDEL e DYS391) foram consistentes com o sexo dos doadores das amostras. As frequências alélicas e parâmetros forenses foram calculados para os STRs, revelando uma alta informatividade. A Probabilidade de Match combinada e o Poder de Exclusão combinado foram de 1,19 x 10-36 e 0,999999999997 respectivamente. Dos 29 STRs autossômicos presentes, seis apresentaram desvios ao equilíbrio de Hardy-Weinberg, refletindo possíveis falhas no sequenciamento e genotipagem destes marcadoresThe field of forensic genetics has developed increasingly with the implementation of new sets of DNA markers with higher levels of informativeness. The genetic markers are widely used in human identification as they allow distinguishing individuals with high accuracy. Two of the most commonly used markers are the Short Tandem Repeats (STRs) and the Single Nucleotide Polymorphisms (SNPs). Newer kits such as GlobalFiler (Thermo Fisher Scientific) and PowerPlex Fusion System (Promega) can analyze more than 20 STRs loci at once. When comparing with STRs, the SNPs are less informative and many more loci are needed to reach the same informativeness of STR kits. However, they are advantageous when using degraded DNA samples. The identification sets such as the 52-plex developed by the SNPforID Consortium and the IISNPs have been analyzed in many worldwide populations. With the development of next generation sequencing techniques (NGS Next Generation Sequencing), obtaining DNA profiles has become more accurate and some platforms allow generating profiles of up to 96 individuals simultaneously. The main goal of this study is to analyze 171 markers (Amelogenin, Y-INDEL, 30 STRs and 139 SNPs) in 340 admixed individuals from Ribeirão Preto, SP, using the NGS platform MiSeq Personal Sequencer (Illumina Inc.). This will allow the calculation of allele and genotype frequencies, the verification of adherence to Hardy-Weinbergs equilibrium and the estimation of forensic parameters for each set of marker. Ancestry analysis was performed for the sets of SNPs. The HaloPlex kit (Agilent Technologies, Inc) was used for library preparation including the STRs from the kits GlobalFiler and PowerPlex Fusion System and the SNPs from the SNPforID consortium (52-plex) and IISNPs (92 SNPs) identification sets. A single SNP (rs763869) from the SNPforID set was not analyzed due to technical issues. Only six of the 139 analyzed SNPs presented significant deviation from the Hardy-Weinberg equilibrium expectations, which is expected by chance alone. The SNPs sets exhibited high informativeness, with matchprobability ranging from 6.48 x 10-21 (52-plex) to 4.91 x 10-38 (IISNPs) and exclusion power of 0.9997 (52-plex) and 0.99999997 (IISNPs). In general, ancestry estimates obtained using these sets indicated a high European contribution (higher than 70%) and low Amerindian contribution (less than 10%) in the population sample, while the individual admixture analyses exhibited were highly consistent, with the majority of individuals presenting high European ancestry. The results of the sex markers (Amelogenin, Y-INDEL and DYS391) were in agreement with the reported sexes from sample donors. The allele frequencies and forensic parameters calculated for the STRs revealed high informativeness. The combined match probability and the combined exclusion power were 1.19 x 10-36 and 0.999999999997 respectively. Six of the 29 autosomal STRs presented significant deviations from the HardyWeinberg equilibrium expectations, reflecting possible failures in sequencing and genotyping of these markers
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Trujillo, Joshua T., Mark A. Beilstein, and Rebecca A. Mosher. "The Argonaute-binding platform of NRPE1 evolves through modulation of intrinsically disordered repeats." WILEY-BLACKWELL, 2016. http://hdl.handle.net/10150/622374.
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• Argonaute proteins are important effectors in RNA silencing pathways, but they must interact with other machinery to trigger silencing. Ago hooks have emerged as a conserved motif responsible for interaction with Argonaute proteins, but little is know about the sequence surrounding Ago hooks that must restrict or enable interaction with specific Argonautes.
• Here we investigated the evolutionary dynamics of an Argonaute-binding platform in NRPE1, the largest subunit of RNA Polymerase V. We compared NRPE1 sequences from more than 50 species, including dense sampling of two plant lineages.
• This study demonstrates that the Argonaute-binding platform of NRPE1 retains Ago-hooks, intrinsic disorder, and repetitive character while being highly labile at the sequence level. We reveal that loss of sequence conservation is due to relaxed selection and frequent expansions and contractions of tandem repeat arrays. These factors allow a complete restructuring of the Ago-binding platform over 50-60 million years. This evolutionary pattern is also detected in a second Ago-binding platform, suggesting it is a general mechanism.
• The presence of labile repeat arrays in all analyzed NRPE1 Ago-binding platforms indicates that selection maintains repetitive character, potentially to retain the ability to rapidly restructure the Ago-binding platform.
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Shea, Jessica Anna-Marie. "Streptavidin-biotin binding of DNA amplicons: methods for the typing and re-typing of forensically relevant short tandem repeats." Thesis, Boston University, 2012. https://hdl.handle.net/2144/12621.
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Thesis (M.S.)--Boston UniversitySubmission of evidentiary samples to DNA units for exhaustive testing is becoming commonplace. For these samples, only one attempt at amplification is possible. However, more than one amplification may be necessary if the condition of the DNA causes poor amplification, more than one type of STR kit testing is required, or if there is an instrument malfunction during amplification. Current research into the re-amplification of already amplified samples focuses on placing the PCR product back into the thermal cycler with new reagents for additional cycles. These methods typically result in outcomes which are unsatisfactory for forensic purposes. As a result, there is a need for a forensic method capable of recovering the original template DNA for purposes of re-amplification. This study outlines the development of a novel method to recover the original template DNA in a condition that allows for re-amplification using new STR loci. A dynamic model was designed to assist in the experimental optimization. Amplification was performed using biotinylated primers and the post PCR 'work product' was subsequently cleaned using streptavidin coated magnetic beads to remove the STR amplicons. Centrifugal filtration followed in order to remove any remaining primers and salts that may interfere with re-amplification. Re-amplification was then performed with non-biotinylated primers. Re-amplification of the template DNA using a new STR locus was successful, making the amplification of limited DNA samples non-destructive and the notion of 'exhaustive DNA typing' obsolete.
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Tsiana, Kebareng Jacobeth. "Y-STR profiling of four South African populations using the University of the Western Cape 10 locus set." University of the Western Cape, 2015. http://hdl.handle.net/11394/5116.
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>Magister Scientiae - MScIn this study the 10 Y-specific loci of the University of the Western Cape (DYS710, DYS518 385a/b, DYS644, DYS612, DYS626, DYS504, DYS447, DYS447, and DYS481) were analysed in 492 individuals from South African population groups. Four different populations namely; Zulu, Coloured, Afrikaner and Asian Indian were sampled. A total of 488 haplotypes were observed, 412 of which were unique. Haplotype diversity was 0.9981. Gene Diversity values ranged from 0.8075 for DYS447 to 0.9209 for DYS710. The discriminatory capacity was 0.9106 which is high. The study showed that the University of the Western Cape 10 locus is a powerful discrimination tool for routine forensic applications and could be used in genealogical investigations as compared to other commercial kits when used on the South African populations (Zulu, Coloured, Afrikaner and Asian Indian) considering its high discriminatory capacity. This data will be used for the establishment of a Y-STR DNA databases for South African population which would aid law enforcement authorities in the investigation and resolution of crimes AMOVA computed using haplotype frequencies showed that when male haplotypes from the four different populations were compared, 0.22 % of the total genetic variation was due to the variability among populations and 99.78 % of the total variation is found within populations. However AMOVA computed using distance matrix showed that 5.97 % of the total variation was due to variability among populations and 94.07 % of the total variation is found within populations. Genetic substructure was found among the four studied South African population groups. All the six population pairwise comparisons using AMOVA were significant .Therefore Y-STRs are very useful in comparing closely related populations. It should be noted that their utility for evolutionary purposes, they need to be combined more stable Y-DNA markers such as single nucleotide polymorphisms (SNPs). Factorial Correspondence Analysis (FCA) showed that the Coloured population has large genetic contribution from Afrikaner population and lesser contribution from the Zulu and Asian Indian population groups.
National Research Foundation (NFR)
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Do, Viet Phuong. "Développement et applications de méthodes bioinformatiques pour l'identification des répétitions en tandem dans les structures des protéines." Thesis, Montpellier, 2016. http://www.theses.fr/2016MONTT072.
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Les structures protéiques peuvent être divisées en répétitives et apériodiques, les structures apériodiques correspondant pour la plupart à des protéines globulaires. Les protéines répétitives (PRs) contiennent des unités de répétitions adjacentes, appelées séquences répétées en tandem (TRs). Les PRs sont abondantes et ont une importance fonctionnelle fondamentale. De plus de nombreuses études ont démontré l'implication des TRs dans les pathologies humaines. Ainsi, la découverte des PRs et la compréhension de leur relation séquence-structure-fonction, offrent des perspectives de recherche prometteuses.Le développement d’initiatives en génomique structurale, combiné à une meilleure adaptation des techniques de cristallographie et de RMN à l’étude des protéines non globulaires, a permis d’élucider la structure d’un nombre croissant de PRs, d’où la nécessité de mettre en place un système de classification. Les structures répétitives ont été réparties en cinq classes, principalement fondées sur la longueur des TRs: Classe I - agrégats cristallins; Classe II - structures fibreuses; Classe III - structures allongées, dont la stabilité dépend des interactions qui s’établissent entre les motifs répétés. Classe IV - structures répétitives fermées ; Classe V - structures en collier de perles. Les efforts de ces dernières années ont abouti au développement d’outils bioinformatiques utiles à la détection et l'analyse d'éléments répétitifs présents au sein des structures protéiques (3D TRs). En fonction des caractéristiques des répétitions, certaines méthodes fonctionnent mieux que d'autres, mais, jusqu’à présent, aucune ne permettait de couvrir toute la gamme des répétitions. Ce constat nous a incités à développer une nouvelle méthode, appelée détecteur de protéines en tandem (TAPO). TAPO exploite les périodicités des coordonnées atomiques ainsi que d'autres types de représentation structurale, comprenant les chaînes générées par un alphabet conformationnel, les cartes de contact entre résidus, et les arrangements en vecteurs d'éléments de structure secondaire. Actuellement, sept scores, issus des caractéristiques analysées par TAPO, sont combinés à l’aide d’une Machine à Vecteur Support pour produire un score final permettant de différencier les protéines renfermant ou non des 3D TRs. En atteignant 94% de sensibilité et 97% de spécificité pour la référence actuelle, TAPO présente des performances améliorées par rapport aux autres méthodes de pointe. Le développement de TAPO offre de nouvelles opportunités pour l’analyse à grande échelle des protéines renfermant des 3D TRs. Ainsi, notre analyse de la base de données PDB, à l’aide de TAPO, a montré que 19% des protéines contiennent des 3D TRs. L'analyse à grande échelle des structures 3D TRs dans PDB nous a également permis de découvrir plusieurs nouveaux types de structures répétitives, absents de la classification existante et dont certains sont décrits ici.Nous avons entrepris une analyse complète des 3D TRs constitutifs du Rossmann Fold (RF). Notre intérêt pour les RFs a été suscité par le fait que de nombreuses protéines RFs représentent un cas ambigüe vis à vis des structures répétitives et non répétitives. A priori, les unités hélice α - feuillet β des RFs devraient avoir une forte tendance à s’empiler et donc, à former des structures répétitives. Afin de déterminer la fréquence à laquelle les RFs forment de longues unités de répétition empilées, nous avons sélectionné, à l’aide de TAPO, des structures contenant des RFs et les avons classées. Notre analyse montre que les RFs typiques ne peuvent pas être clairement définis comme des structures répétitives mais plutôt comme des unités de structures globulaires, comptant au plus trois répétitions α-β. Des éléments de discussion seront proposés pour tenter d’expliquer cette observation surprenanteIn general, protein structures can be divided into: repetitive and aperiodic structures. Most of the aperiodic structures are globular proteins. The repetitive proteins contain arrays of repeats that are adjacent to each other, called Tandem Repeats (TRs). Proteins containing TRs are abundant and have fundamental functional importance. Numerous studies demonstrated the involvement of such TR-containing proteins in human diseases. Furthermore, genetic instability of these regions can lead to emerging infection threats. Additionally, TR-containing structures have generated significant interest with respect to protein design as they can make excellent scaffolds for specific recognition of target molecules. Therefore, the discovery of these domains, understanding of their sequence–structure–function relationship promises to be a fertile direction for research.The growth of structural genomics initiatives, in combination with improvements in crystallographic and NMR techniques aimed at non-globular proteins, has resulted in an increase in structurally elucidated TR proteins. This has necessitated the development of classification schemes. Structural repeats were broadly divided into five classes mainly based on repeat length; Class I – crystalline aggregates; Class II – fibrous structures such as collagen; Class III – elongated structures where the repetitive units require each other for structural stability such as solenoid proteins; Class IV – closed repetitive structures, such as TIM-barrels and Class V – bead on a string structures such as tandems of Ig-fold domains. Despite this progress, the majority of bioinformatics approaches have focused on non-repetitive globular proteins.In recent years, efforts have been made to develop bioinformatics tools for the detection and analysis of repetitive elements in protein structures (3D TRs). Depending on the size and character of the repeats, some methods perform better than others, but currently no best approach exists to cover the whole range of repeats. This served as a motivation for the development of our method called the TAndem PrOtein detector (TAPO). TAPO exploits, periodicities of atomic coordinates and other types of structural representation, including strings generated by conformational alphabets, residue contact maps, and arrangements of vectors of secondary structure elements. Currently, seven feature based scores produced by TAPO are combined using a Support Vector Machine, producing a score to enable the differentiation between proteins with and without 3D TRs. TAPO shows an improved performance over other cutting edge methods, achieving 94% sensitivity and 97% specificity on the current benchmark. The development of TAPO provided new opportunities for large scale analysis of proteins with 3D TRs. In accordance with our analysis of PDB using TAPO, 19% of proteins contain 3D TRs. The large scale analysis of the 3D TR structures in PDB also allows us to discover several new types of TR structures that were absent in the existing classification. Some of them are described in the thesis manuscript. This suggests that TAPO can be used to regularly update the collection and classification of existing repetitive structures. In particular, a comprehensive analysis of 3D TRs related to Rossmann Fold (RF) was undertaken. Our special interest in RFs was based on the observation that many proteins with RFs represent borderline cases between repetitive and non-repetitive structures. In principle, α-helix-β-strand units of RFs should have a strong potential to stack one over the other, forming repetitive structures. To probe the question of how frequently RFs form long arrays of stacked repeats, we selected by using TAPO known RF-containing structures and classified them. Our analysis shows that typical RFs cannot be clearly defined as repetitive, rather they are part of globular structures with up to 3 αβ-repeats. We provide some explanations for this surprising observation
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Krummacher, Claudia [Verfasser], and Stefan [Akademischer Betreuer] Pollak. "Merkmalsverteilung der Y-chromosomalen Short Tandem Repeats (Y-STR) DYS437, DYS438, DYS439 in einer südwestdeutschen Population : : Nutzen für die forensische DNA-Analyse." Freiburg : Universität, 2014. http://d-nb.info/1123479151/34.
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Maybruck, Julie Lauren. "The identification and characterization of new y-chromosome short tandem repeat LOCI and a closer look at the YpXq 3-4mb homology block." Connect to this title online, 2004. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1085600591.
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Thesis (Ph. D.)--Ohio State University, 2004.Title from first page of PDF file. Document formatted into pages; contains xi, 133 p.; also includes graphics Includes bibliographical references (p. 127-133). Available online via OhioLINK's ETD Center
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Heynes, Kirstie. "A dual analysis of the South African Griqua population using ancestry informative mitochondrial DNA and discriminatory short tandem repeats on the Y chromosome." University of the Western Cape, 2015. http://hdl.handle.net/11394/5056.
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>Magister Scientiae - MScThe primary objective of this Masters project was to investigate the maternal ancient substructure of the Griqua population in South Africa. Genetic ancestry was determined by investigating ancestry informative single nucleotide polymorphisms. These are located in the control region of the mitochondrial genome. The auxiliary aim was to test the validity of the UWC 10plex system in relation to a sample group of Griqua males. This short tandem repeat multiplex targets specific mutations confined to paternal lineages. The Khoi Khoi or Hottentots were the first inhabitants in the Cape. Indigenous Khoi Khoi female slaves had offspring with the European settlers in the 1800s which resulted in the Griqua population group. The incorporated European paternal ancestry is what set the Griqua apart from the native population groups at that time. Colonisation events from the mid-17th to 19th Century and the apartheid regime resulted in land dispossession of the native population and an extensively mixed gene pool in South Africa. One hundred and seventy six (N=176) male and female Griqua people were collectively sampled in Kokstad (2012), Vredendal (2012 and 2013) and at the Griqua National Conference in Ratelgat (2013). All 176 samples were analysed using mtDNA control region Sanger sequencing. The sample group (N=176) was separated based on birthplace (Origin sample group and post-colonial sample group). The origin sample group consists of individuals whose ancestors were not part of the Griqua Trek to Northern regions of South Africa and were less likely to be exposed to colonial influences. Mutations within the hypervariable segments of the mtDNA control region were used to infer haplogroups with geographic-specific population data. In this way one can plot the extent of ancient Khoisan (L0d) and Bantu influences (L1-L5) as well as the influence of East (M, A, B, E) and West (N, R, J, H) Eurasian haplogroups in the maternal ancestry of the Griqua population group. The origin sample group showed 91% African ancestry (76.8% L0d) while the post-colonial group had 78% African ancestry (60% L0d). The origin sample group had 2% East Eurasian and 7% West Eurasian ancestry, while the post-colonial group contained 20% Eurasian ancestry. There is greater admixture in the post-colonial group which can be attributed to the integration of surrounding populations during settlement periods in parts of the Northern Cape and KwaZulu-Natal. The UWC 10plex STR kit was tested to see if it could discriminate between male individuals of this admixed sample group (N=91 males). The markers for this multiplex were selected according to their ability to differentiate between individuals of African descent. It proved to be a viable Y chromosome short tandem repeat testing tool, displaying a statistically significant discrimination capacity value of 0.966 and only having 3 shared haplotypes in the sample group of 91 Griqua males.
National Research Foundation (NRF)
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Carvalho, Tiago Loureiro de 1987. "Tandem repeat variation in human and great ape populations and its impact on gene expression divergence." Doctoral thesis, Universitat Pompeu Fabra, 2016. http://hdl.handle.net/10803/383060.
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Genetic variation in humans and the great apes has been amply explored using a wide variety of markers, among them tandem repeats (TRs). Because of the nature of TRs, highly variable in length due to its high mutation rate, they are an important source of genetic variation, and thus especially informative in fields such as population and conservation genetics. Particularly, they are still often used to illuminate natural populations complex evolutionary histories and structure.
TR variation is also associated with several pathological conditions, and hypothesized to have an important role in the evolution of gene regulation.
In this work a recently developed TR genotyping algorithm was applied on human and nonhuman great apes whole-genome sequencing data. The analysis of the TR variation indicate that this information is useful to describe fine scale population variation, and hints at a substantial contribution of TRs to gene expression divergence during great apes evolution.La variación genética en los seres humanos y grandes simios ha sido ampliamente explorada usando una gran variedad de marcadores, entre ellos repeticiones en tándem (RT). Debido a la naturaleza de las RT, muy variables en longitud debido a su alta tasa de mutación, estas constituyen una importante fuente de variación genética, y por lo tanto altamente informativas en áreas como la genética de poblaciones y de la conservación. En particular, a menudo aún se utilizan para elucidar las complejas historias evolutivas de las poblaciones naturales y su estructura genética. La variación de RT está también asociada con varias enfermedads, y se cree que desempeña un papel importante en la evolución de la regulación génica. En este trabajo un algoritmo desarrollado recientemente que genotipa RT a nivel de todo el genoma, se aplicó sobre datos de secuenciación de genomas humanos y de grandes simios. El análisis de la variació de RT sugiere que esta información es útil para describir la variación en poblaciones, y alude a una aportación sustancial de las RT a la divergencia de expresión génica durante la evolución de los grandes simios.
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Castro, Sarah Gurgel de. "Estudo de frequências alélicas de 15 STRs autossômicos na população paraibana." Universidade Federal da Paraíba, 2014. http://tede.biblioteca.ufpb.br:8080/handle/tede/3657.
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Human identification is based on analyzing DNA through present throughout the genome molecular markers. These markers are transmitted from parents to offspring by heredity. STR markers are currently the most commonly used genetic markers in Forensic Genetics due to their high polymorphism, high reproducibility, possibility of being amplified by PCR in multiple copies in a single reaction, and minute quantities of DNA (1ng). The DNA test that allows individualization of the people is essential tool to the solution of forensic human identification cases, sex crimes, crime scenes (including or excluding suspects), mass disasters, and its result is presented in statistical calculations that consider allele frequency of markers used. So it is important to know the allele frequencies presented in the regional population so that the results are the most reliable possible. In this study , 15 autossomal markers (loci) STR or microsatellite (CSF1PO, D13S317, D16S539, D18S51, D19S433, D21S11, D2S1338, D3S1358, D5S818, D7S820, D8S1179, FGA, TH01, and VWA TPOX) were studied in 766 unrelated individuals paraibanos, demonstrating a tri population - hybrid formed Africans (25.86 %), Amerindian (6.81 %) and Europeans (67.33 %). The most informative were D21S11 and FGA, and were less informative TPOX, D7S820 and D13S317. The results are important for a database with allele frequencies found in Paraiba population can serve as a useful basis for calculating forensic practice in the State of Paraíba.
A identificação humana está baseada na análise do DNA através de marcadores moleculares presente em todo o genoma. Estes marcadores são transmitidos de pais para filhos por hereditariedade. Atualmente os marcadores STR são os marcadores genéticos mais utilizados em Genética Forense devido ao seu elevado polimorfismo, alta reprodutibilidade, possibilidade de serem amplificados por PCR em inúmeras cópias numa só reação e em mínimas quantidades de DNA (1ng). O exame de DNA que permite a individualização das pessoas é ferramenta indispensável à solução de casos forenses de identificação humana, crimes sexuais, locais de crime (incluindo ou excluindo suspeitos), desastres em massa, e tem seu resultado apresentado em cálculos estatísticos que consideram a frequência alélica dos marcadores usados. Por isso é importante o conhecimento das frequências alélicas apresentadas na população regional de forma que os resultados sejam os mais fidedignos possíveis. Neste trabalho, 15 marcadores autossômicos (loci) STR ou microssatélites (CSF1PO, D13S317, D16S539, D18S51, D19S433, D21S11, D2S1338, D3S1358, D5S818, D7S820, D8S1179, FGA, TH01, TPOX e vWA) foram estudados em 766 indivíduos paraibanos não aparentados, demonstrando uma população tri - hibrida, formada de africanos (25,86%), ameríndios (6,81%) e europeus (67,33%). Os mais informativos foram D21S11 e FGA, e os menos informativos foram TPOX, D7S820 e D13S317. Os resultados são importantes para que um banco de dados com as frequências alélicas encontradas na população paraibana possa servir de base de cálculo útil para prática forense no Estado da Paraíba.
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Ng, Sau-wah, and 吳秀華. "Population genetics study on the variable number of Tandem repeats (VNTR) loci of a Han Chinese population in Hong Kong and itsapplication in human identity." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2000. http://hub.hku.hk/bib/B31224994.
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Weipert, Christine [Verfasser]. "Die Heterozygotie des Längenpolymorphismus "variable number of tandem repeats" des thrombozytären Glykoproteins Iba alpha als Risikofaktor für koronare Herzkrankheit und Myokardinfarkt in Niedrigrisikogruppen / Christine Weipert." Gießen : Universitätsbibliothek, 2014. http://d-nb.info/1068591617/34.
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Radtke, Andreas. "Molecular Methods for Typing of Streptococcus agalactiae with Special Emphasis on the Development and Validation of a Multi-Locus Variable Number of Tandem Repeats Assay (MLVA)." Doctoral thesis, Norges teknisk-naturvitenskapelige universitet, Institutt for laboratoriemedisin, barne- og kvinnesykdommer, 2012. http://urn.kb.se/resolve?urn=urn:nbn:no:ntnu:diva-17135.
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Molekylære metoder for typing av Streptococcus agalactiae med særlig vektlegging av utvikling og validering av et multi-locus variable number of tandem repeats assay (MLVA) Sammendraget: Streptococcus agalactiae eller gruppe B streptokokker (GBS) forårsaker livsfarlige infeksjoner hos nyfødte, gravide eller voksne med kroniske sykdommer. Den forårsaker også jurbetennelse i storfe. Typing av GBS gir innblikk i bakteriens epidemiologi og dens fylogenetiske slektskap. Ulike deler av bakteriene kan være mål for typingsmetoder. Eldre immunologiske metoder fokuserer ofte på overflateegenskaper som polysakkarid- eller proteinstrukturer. Nyere molekylære metoder benytter bakteriens genmateriale til typing. Studien undersøkte om molekylære metoder hadde potensiale til å gi en bedre oppløsning av en stammesamling. I detalj ble typingen av overflateproteiner med både immunologiske og molekylære metoder sammenlignet og en multi-locus variable number of tandem repeats assay (MLVA) ble utviklet og evaluert. Sistnevnte metode er basert på variabiliteten i repeterte områder i bakteriens genom. Sammenligning av sero- og genotyping av GBS overflateproteiner er kompleks på grunn av kryssreaksjoner mellom de ulike proteinene som er sammensatt fra "samme byggesett". Positive resultat for begge metoder ble funnet for 122 av 147 stammer. Av disse hadde 74 % overensstemmende resultater. Ikke overensstemmende resultater ble funnet for tre og delvis overensstemmede resultater for 29 stammer. Utvikling av en MLVA for GBS ble gjort gjennom analyse av publiserte, helgenomer for tre stammer som resulterte i testing av i alt 18 kandidatloci. Videre undersøkelser identifiserte fem loci som ble inkludert i studiens MLVA. En stammesamling av 126 stammer fra nyfødte ble delt inn i 70 grupper av MLVA metoden, noe som representerte en klart overlegen oppløsning sammenlignet med to referansemetoder. Videre ble metodens egnethet for typing av epidemiologisk relaterte stammer demonstrert ved å undersøke 187 stammer som hadde forårsaket jurbetennelse hos storfe. Stammene var samlet inn fra 34 gårder og det ble funnet 37 typer, stort sett en type per gård. På en gård som var representert med 48 stammer ble en forandring av et av MLVA områdene under innsamlingsperioden observert og kan gjenspeile stabiliteten av repeterte områder under in-vivo forhold. Oppsummert ble det vist at immunologiske og molekylære metoder viser overensstemmende eller delvis overensstemmende resultater i det store flertall av stammer. Molekylære metoder er overlegen i typingssammenheng siden det fører til mindre tvetydighet. MLVA metoden for GBS fungerte eksellent i studien og viste veldig god evne til å skille stammene i epidemiologisk relaterte grupper.
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Ng, Sau-wah. "Population genetics study on the variable number of Tandem repeats (VNTR) loci of a Han Chinese population in Hong Kong and its application in human identity." Hong Kong : University of Hong Kong, 2000. http://sunzi.lib.hku.hk/hkuto/record.jsp?B2292582X.
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Dušan, Vapa. "Varijabilnost mikrosatelitskih lokusa X hromozoma u populaciji Vojvodine." Phd thesis, Univerzitet u Novom Sadu, Medicinski fakultet u Novom Sadu, 2016. https://www.cris.uns.ac.rs/record.jsf?recordId=95598&source=NDLTD&language=en.
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Kratki uzastopni ponovci predstavljaju klasu mikrosatelitskih segmenata DNK, rasprostranjenih širom genoma čoveka. Građeni su od uzastopno ponavljajućih sekvenci dužine 2-6 parova nukleotida. Zahvaljujući različitom broju ponavljanja repetitivne jedinice, većina mikrosatelitskih markera pokazuje visok stepen polimorfizma dužine, koji je moguće ispitati primenom tehnike lančane reakcije polimeraze. Pored utvrđivanja spornih srodničkih odnosa, analiza X hromozom mikrosatelitskih markera može se uspešno koristiti i u oblastima kriminalistike, humane identifikacije, populaciono-genetičkim i demografskim istraživanjima i dr. Cilj istraživanja je izrada populacione studije, iz koje će se izračunati broj i frekvencija alela, struktura i frekvencija haplotipova, utvrditi vrednosti relevantnih statističkih parametara, oceniti mogućnost primene analize X-STR markera u slučajevima iz oblasti medicinske kriminalistike, humane identifikacije i veštačenja spornih srodničkih odnosa u populaciji Vojvodine. Istraživanjem je obuhvaćeno 200 odraslih, međusobno nesrodnih osoba. Izolacija DNK materijala iz krvnih mrlja vršena je Chelex metodom, a amplifikacija dobijenih uzoraka DNK metodom PCR, uz korišćenje komercijalnog Mentype® Argus X-12 PCR Amplification Kit – a. Razdvajanje i detekcija dobijenih fragmenata izvršeno je kapilarnom elektroforezom GeneScan i Genotyper programom. Statististička obrada rezultata izvršena je pomoću Arlequin i GENEPOP programa. Za vizuelizaciju interpopulacionih genetičkih odnosa, upotrebljen je program POPTREE2 i koordinatna analiza (Principal Coordinate Analysis - PCoA). Dobijeni rezultati ukazuju da se analiza ispitivanih X-STR markera može uspešno primeniti u slučajevima iz oblasti medicinske kriminalistike, humane identifikacije i veštačenja spornih srodničkih odnosa u populaciji Vojvodine, kao i da mogu poslužiti kao osnova za dalja istraživanja u populacionogenetičkim, antropološkim, demografskim i drugim oblastima.Short tandem repeats (STR) represent a class of microsatellites, widely spread throughout the human genome, consisting of tandemly repeated sequences of 2-6 bp. Related to variation in the number of repeat unit displayed, most of microsatellites show a high degree of length polymorphism, investigated by the PCR techniques. The aim of this research is to create a population study, which will be used to calculate allele and haplotype frequencies, determine the value of relevant statistical parameters and assess the possibility of applying X-STR markers analysis in the fields of forensics, human identification and kinship testing. The study included 200 unrelated adults. DNA isolation was performed by Chelex method and DNA amplification by PCR, using commercial Mentype Argus X-12 PCR Amplification Kit. Separation and detection of fragments was obtained by capillary electrophoresis using Gene Scanand Genotyper program. Statistical analysis of the result was performed using Arlequin and GENEPOP program. For visualization of inter population genetic distances POPTREE2 program and coordinate analysis (PCoA) was used. The results show that the analysis of X-STR markers can be successfully applied in the field of forensics, human identification and kinship testing in the population of Vojvodina, as well as to serve as a basis for further research in population genetic, anthropological, demographic and other scientific areas.
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Onteniente, Lucie. "Etude du polymorphisme associé aux répétitions en tandem pour le typage de bactéries pathogènes : Pseudomonas aeruginosa et Staphylococcus aureus." Phd thesis, Université d'Evry-Val d'Essonne, 2004. http://tel.archives-ouvertes.fr/tel-00333101.
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Les répétitions en tandem sont constituées de successions de motifs d'ADN. Ces structures présentes dans tous les organismes, procaryotes comme eucaryotes, ont des applications dans de nombreux domaines. Depuis quelques années seulement, les répétitions en tandem sont étudiées chez les bactéries. Le polymorphisme associé à ces séquences peut être utilisé pour le génotypage de bactéries pathogènes, permettant une identification précise au niveau de la souche. Le polymorphisme des séquences répétées est de deux types : polymorphisme de longueur et mutations internes aux motifs. Les génomes des deux bactéries pathogènes responsables d'infections nosocomiales, Staphylococcus aureus et Pseudomonas aeruginosa, ont été étudiés dans le but d'identifier des séquences répétées polymorphes. Un ensemble de marqueurs polymorphes a été validé expérimentalement pour ces deux espèces permettant un typage dit MLVA (pour « Multiple Locus VNTR Analysis »). Le travail plus classique de typage par la taille de la répétition a été complété par un travail de séquençage de certains allèles. Les résultats obtenus montrent comment le typage « MLVA » complété si nécessaire par le séquençage d'allèles, pourraient constituer de nouvelles méthodes peu coûteuses participant au contrôle des infections bactériennes.
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Bosch, Fusté Elena. "Diversitat genòmica a les poblacions del Nord d'Àfrica." Doctoral thesis, Universitat Pompeu Fabra, 2000. http://hdl.handle.net/10803/7064.
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S'ha estudiat la variabilitat genètica de les poblacions del nord d'Àfrica a partir de l'anàlisi de diverses regions genòmiques per tal d'entendre les poblacions analitzades d'una banda, i comprendre la dinàmica del genoma per l'altra. Els resultats obtinguts ens han permès verificar diferents hipòtesis sobre la història de les poblacions d'aquesta regió com són l'efecte paral·lel i independent de l'onada de difusió del neolític des de l'Orient Mitjà al llarg d'ambdues ribes de la Mediterrànea; i l'efecte de l'arabització. S'ha pogut estimar també la contribució genètica masculina nord africana a la península ibèrica i detectat certa contribució genètica del pobles sub-saharians a les poblacions nordafricanes. Per altra banda, el tipatge de marcadors genètics que evolucionen a velocitats diferents al cromosoma Y ha permès mostrar que el background genètic predomina sobre el background poblacional en l'estructura de la variació genètica dels microsatèl·lits en la regió no recombinant del cromosoma Y humà.The genetic variability of the North African populations has been studied through the analysis of different genomic regions in order to understand both the analysed populations and the dynamics of the genome. The obtained results allow us to verify different hypotheses about the population history of this region including the parallel and independent effect of the Neolithic wave of advance from the Middle East and along both Mediterranean coasts; and the effect of Arabization phenomena. We also tried to estimate the North African male genetic contribution to the Iberian peninsula and detected Sub-Saharian genetic influences to the North African peoples. Moreover, the typing of genetic markers with different evolutionary rates on the Y chromosome allowed us to demonstrate that variation in microsatellites is deeply structured by genetic background on the non-recombining region of the human Y chromosome.
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Ge, Jianye. "Computational Algorithms and Evidence Interpretation in DNA Forensics based on Genomic Data." University of Cincinnati / OhioLINK, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1234916402.
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Benediktsson, Elís Ingi. "Detection and analysis of megasatellites in the human genome using in silico methods." Thesis, University of Skövde, School of Humanities and Informatics, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-961.
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Megasatellites are polymorphic tandem repetitive sequences with repeat-units longer than or equal to 1000 base pairs. The novel algorithm Megasatfinder predicts megasatellites in the human genome. A structured method of analysing the algorithm is developed and conducted. The analysis method consists of six test scenarios. Scripts are created, which execute the algorithm using various parameter settings. Three nucleotide sequences are applied; a real sequence extracted from the human genome and two random sequences, generated using different base probabilities. Usability and accuracy are investigated, providing the user with confidence in the algorithm and its output. The results indicate that Megasatfinder is an excellent tool for the detection of megasatellites and that the generated results are highly reliable. The results of the complete analysis suggest alterations in the default parameter settings, presented as user guidelines, and state that artificially generated sequences are not applicable as models for real DNA in computational simulations.
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Jenčo, Michal. "Bioinformatický nástroj pro anotaci transposonů." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2017. http://www.nusl.cz/ntk/nusl-363823.
Full textAbstract:
This thesis provides theoretical resources for the design of a new bioinformatics tool for transposon annotation with focus on their additional structural elements. There is a biological description of transposons, the mobile elements in DNA, their classification and structure. It further deals with the overview and classification of available transposon identification and annotation bioinformatics tools, description of function and implementation of a select few. Next we state the scheme of a new bioinformatics tool for LTR retrotransposon identification and annotation with a focus on extra ORFs and tandem repeats. The functionality of this new tool was tested on the A. thaliana genome. We identified 95 groups of conserved extra ORFs and 10 groups of conserved tandem repeats.
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Varela, Filipa Alexandra Pereira Rosa. "Tipificação de Mycoplasma mycoides subsp. mycoides SC e detecção da sua aderência a células epiteliais pulmonares." Master's thesis, Faculdade de Ciências e Tecnologia, 2010. http://hdl.handle.net/10362/5092.
Full textAbstract:
Dissertação apresentada para a obtenção do Grau de Mestre em Genética Molecular e Biomedicina, pela Universidade Nova de Lisboa, Faculdade de Ciências e TecnologiaA Peripneumonia Contagiosa Bovina (PPCB) é uma doença respiratória infecciosa, de grande relevo no âmbito da produção de gado bovino, causada pela bactéria Mycoplasma mycoides subsp. mycoides SC (MmmSC). Actualmente, a PPCB permanece endémica apenas em África, sendo aí responsável por perdas incontornáveis no sector pecuário. O último surto de PPCB detectado na Europa ocorreu em Portugal em 1999 mas, devido à sua natureza insidiosa, o risco de re-emergência é permanente. As estirpes de MmmSC associadas aos últimos surtos europeus de PPCB são tradicionalmente consideradas geneticamente muito homogéneas. No entanto, trabalhos recentes de tipificação molecular revelaram a existência de uma variabilidade genética intraspecífica superior ao que se esperava. A realização deste trabalho teve como base dois objectivos fundamentais: a tipificação de estirpes de MmmSC isoladas durante os últimos surtos de PPCB que ocorreram em Portugal entre 1993 e 1998, e a aplicação de um método alternativo e inovador para a detecção e quantificação de MmmSC, após a infecção de culturas celulares. Para a concretização do primeiro objectivo foi realizada uma análise da variabilidade polimórfica de três regiões VNTR (Variable Number of Tandem Repeats) existentes no genoma de estirpes de MmmSC. O locus VNTR4 comprovou ser o mais polimórfico, detectando-se quatro perfis distintos entre as estirpes portuguesas. O perfil VNTR4 do tipo “9” (numerado em função das repetições da sequência de consenso) revelou-se amplamente distribuído geograficamente e foi predominante entre os isolados. No entanto, observou-se uma segregação geográfica de perfis, dado que na região da Beira Litoral apenas foram encontradas estirpes com o perfil VNTR4 do tipo “8”. Estes resultados sugerem que podem ter ocorrido, pelo menos, dois eventos de re-emergência de PPCB em Portugal, entre 1993 e 1998. Para a realização do segundo objectivo deste trabalho foi optimizada uma técnica baseada na hibridação in situ com sondas de DNA fluorescentes (FISH) que permitiu visualizar micoplasmas aderidos a culturas celulares. Esta técnica, que nunca tinha sido usada previamente na detecção de MmmSC, comprovou ser adequada para futuras aplicações em estudos de citoaderência e para a detecção de micoplasmas em culturas celulares.