Dissertations / Theses on the topic 'MtDNA'
To see the other types of publications on this topic, follow the link: MtDNA.
Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles
Consult the top 50 dissertations / theses for your research on the topic 'MtDNA.'
Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.
You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.
Browse dissertations / theses on a wide variety of disciplines and organise your bibliography correctly.
1
Llewellyn, Barbara Ellen. "Utilization of a MAGIChip for mtDNA typing." Thesis, University of Strathclyde, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.275159.
Full text
2
Simmonte, Owens Matthew John. "Polymer microarrays for biomedical applications." Thesis, University of Edinburgh, 2017. http://hdl.handle.net/1842/28953.
Full textAbstract:
Biocompatible polymers are used exhaustively within the biomedical arena, demonstrating a mechanical and chemical diversity that few other materials possess. As polymer technologies evolves to cater for new medical demands, even the most niche biomedical application becomes an achievable reality. However, the discovery of new polymers is hindered by the complexity and intricacy in which the biological milieu interacts with a new substrate, reducing the ability to predict the appropriateness of a certain polymer for a specific application. This drawback can be countered by the high-throughput evaluation of large numbers of chemically diverse polymer candidates. In this thesis, the use of polymer microarrays is invoked to address two separate medically-relevant issues: the control of inflammation, and the improvement of cancer screening. In addition, I provide details of how polymer microarray techniques and technology can be employed to expand the repertoire of biomaterials research. Mitochondrial DNA (mtDNA) is an alarm molecule that contributes to the cytokine storm observed during severe tissue injury. An application where control of this systemic inflammation is achieved through scavenging of mtDNA by a polymer was proposed. Primary screening highlighted that 166 out of the 380 polymers evaluated bound to blood cells, making them unsuitable for a blood-based application. The remaining 214 blood-compatible polymers were cross-examined for mtDNA binding. Through polymer microarray and subsequent scale-up of promising candidates, a poly(methoxyethyl methacrylate-co-di(ethylamino)ethyl acrylate-co-methoxyethyl acrylate) was found to have a remarkable ability to scavenge mtDNA. Removal of cell-free mtDNA using this polymer is proposed to remove a key trigger of systemic inflammation. Cervical cancer screening includes the cytological evaluation of patient material for developed or developing abnormalities. An application was sought that would enrich for cancerous/pre-cancerous cells and improve upon current standards for detection. Four cancerous cervical cell lines (HeLa, CaSki, SiHa, and C33a) and four precancerous cell lines (W12E, W12G, W12GPX, and W12GPXY) were interrogated to identify polymers with consistent binding that may improve routine cytological evaluation. A short-list of 24 polymers was assembled, and cells from liquid based cytology samples from healthy patient were spiked with DiI-labelled cancerous/precancerous cells and the short-listed polymers were re-evaluated for preferential binding. An enrichment of abnormal cervical cells was observed with three polymers, which could form the foundation for improved screening resources. Inkjet printing can be a useful tool in developing patterned substrates, such as polymer microarrays. A piezoelectric drop-on-demand printer was used to explore the methods in which these can be fabricated. A wettability assay using picolitre volumes was developed and used to characterise O2 plasma treatment of glass slides. Additionally, the printing of a cell-binding polymer using this approach enabled the decoration of cells with precise spatial resolution.
3
Yuncu, Eren. "Mitochondrial Dna (mtdna) Haplogroup Composition In Turkish Sheep Breeds." Master's thesis, METU, 2009. http://etd.lib.metu.edu.tr/upload/12610314/index.pdf.
Full textAbstract:
In the present study, haplogroup composition of five native Turkish sheep breeds, (Karayaka, Akkaraman, Gökç
eada, Dagliç
, Morkaraman) and two sheep breeds from neighboring countries (Herik from Iran, samples from Azerbaijan) were determined by single strand length polymorphism (SSCP) analysis of mitochondrial DNA (mtDNA) NADH dehydrogenase subunit 4 (ND4) region and restriction fragment length polymorphism (RFLP) analysis of mtDNA control (CR) region. Results of the SSCP and RFLP approaches were found to be 96,82% consistent. Most of the 3,18% inconsistency was due to unidentified band patterns of 9 individuals. SSCP method could identify haplogroups A, B and C, but not D and E. Similarly RFLP method could identify haplogroup A, B and possibly D, but not E and C. Data of the present study were compared with those of the previous studies to test the robustness of results under different samplings and were found to be homogenous with a previous study with similar sampling strategy. Neighbor joining tree, principal component analysis (PCA), Delaunay network analysis and analysis of molecular variance (AMOVA) were employed to analyze the haplogroup frequencies and breeds were separated in four groups according to the genetic barriers between breeds from different geographical locations. Strongest differentiation was present between two groups which were eastern breeds (Morkaraman, Herik-Iran and Azerbaijan) and western breeds (Gö
kç
eada, Akkaraman, Karayaka and Dagliç
). Additionally, Azerbaijan was proposed as the entrance point of the haplogroup A and the Iran was proposed as the entrance point of haplogroup C to Anatolia with the Spearman rank correlation test.
4
Blei, Daniel [Verfasser]. "Effects of Mitochondrial Nucleases on mtDNA Degradation / Daniel Blei." Bonn : Universitäts- und Landesbibliothek Bonn, 2019. http://d-nb.info/1177881683/34.
Full text
5
Pierson, Melanie Jane. "Deciphering the mtDNA record of prehistoric population movements in Oceania." Thesis, University of Canterbury. Biological Sciences, 2007. http://hdl.handle.net/10092/1487.
Full textAbstract:
This thesis uses mitochondrial DNA (mtDNA) phylogenies to explore patterns of past human mobility in Oceania. To extend the current knowledge of mtDNA variation in Oceania, 20 entire mt genomes were sequenced and analysed in a data set of more than 144 sequences from Australia, Oceania, Island Southeast Asia and Taiwan. The MinMax Squeeze method enabled this large data set to be analysed with an optimality criterion (Pierson et al. 2006). The analysis revealed two major groups of haplogroups in Oceania, distinguished by the relationships to others outside of the region: an 'ancient' set of types whose phylogenies and distributions suggest they are descended from the Pleistocene-era settlers of Near Oceania, and a second 'young' group whose presence in Oceanic populations may reflect more recent movements into Near Oceania. The detailed phylogenies of these haplogroups presented here will aid in future investigations of human mtDNA in Oceania, allowing samples to be screened by defining mutations to target haplogroups of interest. A large data set of global entire human mt DNA sequences was assembled from public data bases and tested for evidence of selection and recombination. These tests, and phylogenetic analyses of random subsets of the data set, found high levels of homoplasy in the sequences. Homoplasy in the control region of the mtDNA molecule was examined in particular, resulting in a relative scale of mutability at each position of the ~1kb sequence. Subsequent phylogenetic tests of weighting schemes derived from this analysis for the control hypervariable region I (HVR-I) did not show demonstrable improvements over the unweighted examples, but did highlight instances in which the HVR-I sequence failed to predict the more robust trees generated by the coding region. Finally, the HVR-I and diagnostic SNPs were sequenced in a set of 46 Polynesian samples from Auckland, and this data was analysed within a large set of HVR-I sequences (more than 4000) from Oceanic, Asian and the American populations available from public data bases. These analyses were informed by the whole mtDNA phylogenies generated earlier in the project, and add population level data to the emerging picture of prehistoric female mobility gained from entire mtDNA analyses.
6
Fan, Xiucheng. "Investigation of quantitative and qualitative MtDNA alteration in breast cancer /." [S.l.] : [s.n.], 2009. http://edoc.unibas.ch/diss/DissB_8811.
Full text
7
Gokcek, Cigdem. "Mitochondrial Dna (mtdna) Sequence Analyses Of Kangal Dogs In Turkey." Master's thesis, METU, 2005. http://etd.lib.metu.edu.tr/upload/12606579/index.pdf.
Full textAbstract:
Kangal dogs are the most popular dogs of Turkey due to their strength, intelligence, loyalty, endurance to extreme temperatures and their lack of predatory behavior towards livestock. In this study to provide genetic information about the distinctness of Kangal and Akbash dogs and hence to provide a basis to conserve them separately, 585 base pair of the mitochondrial DNA (mtDNA) control region sequence was analysed in 105 Kangal and 9 Akbash dog samples. All the results indicated that Kangal and Akbash dogs were different from each other. Comparison of the Turkish data with those from other dogs revealed that Kangal dogs harbour a rare haplogroup which is only seen in Scandinavian (36%), Portuguese (20%), Turkish (20%) dogs and only one Spanish dog, but not in Akbash, Middle Eastern, other European, Eastern Asian and Indian dogs. Furthermore, comparison of the Kangal and Akbash dogs with the dogs from different geographic regions indicated that Kangal dogs are genetically closer to Scandinavian and South West Asian dogs whereas Akbash dogs are more similar to European and East Asian dogs, based on the mtDNA control region sequences Today, the sizes of Kangal and especially Akbash populations are decreasing. An urgent program for their conservation is needed. In order to conserve them separately, it must be understood that these two dogs are genetically distinct. That is why, the main purpose of the present study is to provide genetic information about the distinctness of Kangal and Akbash dogs.
8
Pierre, Tracey Lynn. "mtDNA variation of Canadian Athapaskan populations : the Southern Athapaskan migration." Thesis, University of Cambridge, 2010. https://www.repository.cam.ac.uk/handle/1810/252182.
Full text
9
Rantanen, Anja. "Regulation of mitochondrial transcription and mtDNA copy number in mammals /." Stockholm, 2003. http://diss.kib.ki.se/2003/91-7349-526-3/.
Full text
10
Battersby, Brendan James. "Genetic basis for MTDNA segregation in a heteroplasmic mouse model." Thesis, McGill University, 2002. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=38462.
Full textAbstract:
Mammalian mitochondrial DNA (mtDNA) is a maternally inherited, multi-copy, small circular genome approximately 16 kb in size that codes for 13 polypeptides of the mitochondrial respiratory chain. Typically, mtDNA is present as only one genotype in a cell, a state known as homoplasmy. In rare circumstances, two or more mtDNA sequence variants can be present in a cell, a state known as heteroplasmy, and these sequence variants can segregate during mitosis and meiosis. In this thesis, I have investigated the basis for a novel tissue-specific segregation of mtDNA in a heteroplasmic mouse model that had been previously constructed from two inbred strains (NZB/BinJ and BALB/c mtDNA). In these mice, four tissues showed directional selection for an mtDNA genotype: in the liver and kidney for the NZB mtDNA genotype; and in the spleen and blood for the BALB mtDNA genotype. I investigated the mechanism responsible for selection of NZB mtDNA, focusing on the liver which showed the strongest effect. In this tissue, selection for the NZB mtDNA genotype is constant with time, independent of allele frequency and does not appear to be mediated through an advantage of respiratory chain function or replication rate of mtDNA. To identify the genetic basis for this mtDNA selection, I set up an intersubspecific intercross and used quantitative trait loci (QTL) mapping to map three QTL in F2 mice that are strong gene effects in the liver, kidney, and spleen. These QTLs, Smdq-1 (liver), Smdq-2 (kidney), and Smdq-3 (kidney & spleen) (s&barbelow;egregation of m&barbelow;itochondrial D&barbelow;NA Q&barbelow;TL-#) map to chromosome 5, 2, and 6 respectively. Smdq-1 was a dominant QTL in the liver that mapped to a 2 LOD support interval of approximately 1 cM and accounted for 34% of the variation in the trait. To reduce the interval size of Smdq-1 and confirm the map position, BALB chromosome 5 interval-specific congenic mice lines are being generated across a 20 cM interval. This is the fir
11
Pitayu, Laras. "Mitochondrial Disorders Linked to mtDNA instability : From Therapy to Mechanism." Thesis, Paris 11, 2015. http://www.theses.fr/2015PA112233.
Full textAbstract:
L’instabilité d’ADN mitochondrial (ADNmt) peut être quantitative avec la déplétion de l’ADNmt ou qualitative avec des délétions de l’ADNmt. Ces anomalies sont une des causes les plus commmunes des maladies mitochondriales. Un des gènes qui contrôle la stabilité et le maintien de l’ADNmt est POLG. Ce gène code pour la polymerase gamma mitochondriale. Chez l’homme, les mutations dans le gène POLG sont liées aux maladies mitochondriales telle que; l’insuffisance hépatique, le syndrome d’Alpers, le PEO ou Progressive External Ophtalmoplegia, la neuropathie sensorielle et l’ataxie. Des mutations dans le gène POLG sont aussi associées au syndrome de Parkinson. Aujourd’hui, il n’existe aucune thérapie pour ces maladies. Compte tenu de la conservation évolutive de la fonction mitochondriale de la levure à l’homme, nous avons utilisé deux organismes modèles, Saccharomyces cerevisiae et Caenorhabditis elegans, pour identifier des molecules chimiques capables de compenser l’instabilité de l’ADNmt liée à des mutations du gène POLG dans des fibroblastes d’un patient. Nous avons trouvé trois molécules candidates potentielles: MRS2, MRS3 et MRS4, à partir d’un criblage primaire chez la levure, en utilisant une chimiothèque d’environ 2000 molécules chimiques. MRS3 est la molécule candidate la plus efficace pour la stabilization d’ADNmt chez des mutants POLG de la levure, du champignon filamenteux, du nématode et sur des fibroblastes de patients. MRS3, ou clofilium tosylate (CLO), est un agent antiarrhytmique, médicament pour soigner les troubles du rythme cardiaque. Dans cette étude, nous avons aussi montré que deux autres antiarrhythmiques appartenant à la même classe que CLO avaient un effet positive chez un mutant POLG de C. elegans. En utilisant une approche de chemogénomique chez la levure, nous avons identifié Fis1, un acteur de la fission mitochondriale qui pourrait être impliqué dans la mode d’action de CLO. Fis1 est requise pour la viabilité cellulaire en concentration légèrement toxique de CLO et nécesaire pour la stabilization de l’ADNmt par CLO. L’ensemble de ces résultats ont montré que CLO pourrait être la première molécule chimique qui stimule la réplication de l’ADNmt et qui pourrait être développée pour le traitement des maladies liées à des mutations dans le gène POLG. Ces résultats ont aussi permis de mettre en évidence une nouvelle connexion entre replication de l’ADNmt et la fission mitochondrialeThe instability of mitochondrial DNA (mtDNA) in form of mtDNA depletion (quantitative instability) or large deletion (qualitative instability) is one of the most common cause of mitochondrial diseases.. One of the genes responsible for human mtDNA stability, POLG, is exploited in this study. POLG encodes the human mitochondrial polymerase gamma. In human, POLG mutations are a major cause of mitochondrial disorders including hepatic insufficiency; Alpers syndrome, progressive external ophthalmoplegia, sensory neuropathy and ataxia. They are also associated with Parkinsonism. Currently, there is no effective and disease-specific therapy for these diseases. Based on the conservation of mitochondrial function from yeast to human, we used Saccharomyces cerevisiae and Caenorhabditis elegans as first pass filters to identify chemical compounds that suppresses mtDNA instability in cultured fibroblasts of a POLG-deficient patient. We found three potential candidates, MRS2, MRS3 and MRS4, from a chemical screening of nearly 2000 compounds in yeast. MRS3 is the most efficacious in stabilizing mtDNA in yeast, filamentous fungi, worm and patient fibroblasts. This unsuspected compound, clofilium tosylate (CLO), belongs to a class of antiarrhythmic agents for cardiovascular disease. Two other antiarrhythmic agents (FDA-approved) sharing common pharmacological properties and chemical structure with CLO also show potential benefit for POLG deficiency in C. elegans. Using a chemogenomic approach in yeast, we also discovered that a mitochondrial fission actor Fis1 is implicated in the mechanism of action of CLO. Fis1 is important for cellular viability in a slightly toxic concentration of CLO and is required for the mtDNA stabilizing potency of CLO. Our findings provide evidence of the first mtDNA-stabilizing compound that may be an effective pharmacological alternative for the treatment of POLG-related diseases and uncover a new connection between the mitochondrial fission process and mtDNA replication
Ketidakstabilan DNA mitokondria (mtDNA) dalam bentuk pengurangan kopi mtDNA di dalam sel (ketidakstabilan kuantitatif), atau pun dalam bentuk delesi pada sekuens mtDNA (ketidakstabilan kualitatif) merupakan salah satu penyebab penyakit mitokondria. Salah satu gen yang bertanggung jawab dalam menjamin kestabilan mtDNA adalah POLG. Gen POLG mengkode protein polimerase gamma pada manusia, yang mereplikasi dan mereparasi mtDNA di dalam mitokondria. Mutasi pada gen POLG dapat menyebabkan penyakit kelainan mitokondria pada manusia, seperti gagal ginjal, sindrom Alpers, Progressive External Ophtalmoplegia, neuropati sensorial, ataxia dan bisa dikaitkan dalam beberapa gejala Parkinsonisme. Saat ini, belum ada terapi obat yang dapat mengatasi penyakit – penyakit tersebut. Berdasarkan kesamaan evolutif dari ragi hingga manusia, pada studi ini kami menggunakan Saccharomyces cerevisiae dan Caenorhabditis elegans untuk mengidentifikasi molekul obat yang berpotensi mengatasi ketidakstabilan mtDNA dari fibroblas pasien manusia yang memiliki mutasi gen POLG. Kami mengidentifikasi tiga kandidat potensial, yakni MRS2, MRS3 dan MRS4 dari penapisan kurang lebih 2000 molekul obat dengan menggunakan ragi. MRS3 adalah kandidat yang paling berkhasiat dan mampu mengatasi ketidakstabilan mtDNA pada ragi, Podospora, cacing dan fibroblas manusia. MRS3 adalah alias bagi clofilium tosylate (CLO), sebuah molekul antiaritmia untuk penyakit kardiovaskuler. Pada studi ini, kami juga menguji aktifitas dua molekul antiaritmia lain yang tergabung dalam kelas yang sama dengan CLO, dan menemukan bahwa kedua molekul ini juga berpotensi mengatasi defisit POLG pada cacing C. elegans. Dengan menggunakan metode kemogenomik pada ragi, kami juga mengidentifikasi sebuah aktor prosesus pembelahan mitokondria, Fis1, yang berpotensi terlibat dalam mekanisme seluler CLO. Fis1 dibutuhkan untuk: (1) kelangsungan hidup ragi pada konsentrasi toksik CLO dan (2) efek CLO dalam menstabilkan mtDNA pada ragi. Keseluruhan studi ini membuktikan potensi CLO sebagai molekul penstabil mtDNA yang pertama, yang dapat dikembangkan sebagai salah satu alternatif terapi obat untuk penyakit – penyakit mitokondria terkait mutasi POLG. Melalui studi ini, juga diungkap adanya hubungan antara kestabilan mtDNA dan prosesus pembelahan mitokondria
12
Campbell, Georgia Elizabeth. "Investigating the mechanism of clonal expansion of deleted mtDNA species." Thesis, University of Newcastle upon Tyne, 2014. http://hdl.handle.net/10443/2519.
Full textAbstract:
Mitochondrial DNA deletions are a primary cause of inherited and sporadic mitochondrial disease, whilst somatic mtDNA deletions contribute to the focal respiratory chain deficiency observed in post-mitotic cells associated with ageing and neurodegenerative disorders. As mtDNA deletions only cause cellular pathology at high levels of heteroplasmy, an mtDNA deletion formed within a cell must accumulate by a process known as clonal expansion to levels which result in biochemical dysfunction. The mechanism driving clonal expansion remains uncertain; this research aimed to investigate clonally expanded mtDNA deletions in sporadic and inherited mitochondrial myopathies in order to elucidate this mechanism. A number of different approaches were taken to assess the mechanism driving accumulation of mtDNA deletions. The effect of the mtDNA deletion size on clonal expansion was first investigated by assessing the longitudinal spread of mtDNA deletions in single muscle fibres isolated from patients presenting with mtDNA maintenance disorders; no relationship was found to exist between mtDNA deletion size and the area over which the mutation has accumulated. A longitudinal study was carried out using tissue acquired over a 13-year period from a single patient with a sporadic mtDNA deletion, to identify whether the mtDNA deletion heteroplasmy level continued to increase over time, as would be expected if the mutation displayed a selective advantage over wildtype mtDNA – however, both the genetic and biochemical defect were found to be stable over time in this patient. A subsequent study aimed to identify a correlation between mtDNA deletion size and heteroplasmy levels at the whole tissue level in a cohort of patients with sporadic single mtDNA deletions, but no evidence was found to suggest that larger mtDNA deletions accumulate to higher levels of heteroplasmy. Finally, single cytochrome c oxidase- deficient muscle fibres were investigated using single-molecule PCR to assess whether clonal expansion of multiple mtDNA deletions could be observed in single cells. Evidence of multiple clonally expanded mtDNA species was found in approximately 40% of all examined fibres, with no correlation between mtDNA deletion size and level of accumulation. Each of these four studies has highlighted accumulation by random genetic drift to be the most likely mechanism for clonal expansion of mtDNA deletions in human muscle; no evidence has been found to support the presence of a selective advantage for mtDNA deletion species over wildtype mtDNA.
13
Gomes, Christina Sibylle Marcial. "Mitochondrial DNA (mtDNA) characterization of human populations from East Timor." Doctoral thesis, Universidade de Aveiro, 2015. http://hdl.handle.net/10773/14139.
Full textAbstract:
Doutoramento em BiologiaEstudos anteriores do segmento hipervariável (HVS-1) do DNA mitocondrial (mtDNA) demonstraram que as ilhas no Sudeste Asiático tem uma história de migração complexa. No entanto, há uma falta de dados a respeito da região controle (RC) do mtDNA nem da sequência completa do genoma mitocondrial (mitogenoma) das populações de Timor-Leste. Neste sentido, no presente estudo analisaram-se sequências do mtDNA para descrever a composição estrutural materna da população do Timor-Leste e estudar a história da migração humana nesta região. Complementarmente, investigou-se também a relação entre a língua e a genética incluindo deste modo dados do Cromossoma Y (NRY). Na primeira fase deste estudo avaliou-se a aplicabilidade da tecnologia de sequenciação de nova geração (NGS) em chips semicondutores (Personal Genome Machine – PGM) e compararam-se os resultados com o método de Sanger (MS) para 42 amostras. Os resultados obtidos a partir do PGM indicaram alta concordância com o MS. Em relação à população de Timor-Leste, o DNA extraído de >300 amostras foi usado para gerar sequências da RC do mtDNA através do MS. Além disso, perfis inteiros do mitogenoma de 17 amostras foram gerados com a tecnologia NGS. Com base nas estimativas de idade e distribuição das linhagens do mtDNA P1 (e outras P e Q), foi possível detetar evidências de que: 1) A primeira migração para o sul de Sahul (Austrália atual) provavelmente ocorreu a >37000 anos atrás; 2) O Norte de Sahul (Nova Guiné de hoje) foi provavelmente povoado (mais cedo) a partir do mesmo grupo de fundadores; 3) Os aborígenes da Nova Guiné e da Austrália foram separados logo no início após a sua fixação nestas regiões, ocorrendo poucas trocas genéticas posteriores à sua separação; 4) Após um período de incubação, a migração reversa trouxe as linhagens P e Q da Nova Guiné para Timor-Leste; 5) A chegada das linhagens P e Q a Timor- Leste deve ter ocorrido a <28000 anos atrás. Na última parte deste estudo, as sequências do mtDNA e os dados do NRY de >550 amostras foram avaliadas e agrupadas de acordo com a linguística [Austronésia (AN) e não-Austronésia (NAN)] e com a origem (local de nascimento). Os dados genéticos e linguísticos de timorenses demonstraram dupla origem do Leste/Sudeste da Ásia e da Near Oceania, e uma elevada mistura genética (mais comum no sexo feminino do que no masculino) entre grupos linguísticos AN e NAN. Foi também apresentado neste estudo outro exemplo onde os dados genéticos e linguísticos não são coincidentes devido à mistura recíproca das mulheres e à mistura direcional dos homens. O presente estudo contribui com novos dados e amplia o nosso conhecimento a respeito da primeira migração e sobre a complexa história das migrações em Timor-Leste e nas regiões vizinhas.
Previous researches predominantly based on the first mitochondrial DNA (mtDNA) hypervariable segment (HVS-1) have shown that Island Southeast Asia has a complex migration history. However, there is a lack of studies on the entire mtDNA control region (CR) and complete mitogenome data from East Timor’s population. Here, we used sequence data obtained from mtDNA to describe the maternal structural composition of East Timor’s population to study its migration history, and extended our analyses to investigate the relation between languages and genetics including Y-chromosomal data (NRY). Initially in this study we evaluated a Next-generation sequencing (NGS) approach on the Personal Genome Machine (PGM) in comparison to Sangertype sequencing (STS) for 42 samples. Results obtained from the PGM indicated high concordance with gold standard STS. Concerning East Timor’s population, DNA extracts from >300 samples were used to generate entire CR mtDNA sequences by STS. In addition, whole mitogenome profiles of 17 samples were sequenced with NGS. Based on the age estimates and distribution of P1, and further mtDNA lineages we suggest: 1) The first migration into southern Sahul (today’s Australia) is estimated to be >37 kya; 2) Northern Sahul (today’s New Guinea) was probably populated (earlier) from the same group of founders; 3) The aborigines of Australia and New Guinea were separated early, with little later genetic exchange; 4) A westwards (back) migration from New Guinea brought the P and Q lineages into East Timor’s region after an incubation period; 5) We estimated the arrival of P and Q lineages to be <28 kya. In the last part of our investigation, mtDNA and NRY of >550 samples were evaluated and grouped according to linguistic [Austronesian (AN) and non- Austronesian (NAN) languages] and origin (birthplaces). Genetic and linguistic data of Timorese demonstrated dual origin of East/Southeast Asia (E/SE Asian) and Near Oceania (NO), and high genetic admixture (more via women than men) between AN and NAN linguistic groups. We provide another example where genetic and linguistic data are not conform due to reciprocal female and directional male admixture. This work shed light on the first migration and on the complex migration history into East Timor and surrounding regions.
14
Robinson, Jason M. "Functional Significance of mtDNA Cytosine Modification Tested by Genome Editing." VCU Scholars Compass, 2016. http://scholarscompass.vcu.edu/etd/4561.
Full textAbstract:
The field of epigenetics is gaining popularity and speed, due in part to its capability to answer lingering questions about the root cause of certain diseases. Epigenetics plays a crucial role in regulation of the cell and cell survival, particularly by cytosine methylation. It remains controversial if DNMT’s which facilitate methylation are present in mammalian mitochondria and what the functional significance they may have on modification of mitochondrial DNA. CRISPR-Cas9 technology enabled genome editing to remove the MTS (mitochondrial targeting sequence) from DNMT1 of HCT116 cells, purposefully minimizing effects on nuclear cytosine methylation, while exclusively impacting mitochondrial modification. Removal of the DNMT1 MTS did not completely prevent the localization of this enzyme to the mitochondria according to immunoblot analysis. As well, deletion of the MTS in DNMT1 revealed only a small decline in transcription; not until removal of DNMT3B did we see a two-fold decrease in transcription from mitochondrial protein coding genes. No significant decline in transcription occurred when a DNMT3B knockout also lost the MTS of DNMT1; this study is evidencing that DNMT3B is possibly the more significant methyltransferase in the mitochondria. Our aim from this study and future research is to clearly characterize which enzymes in the mitochondria are controlling cytosine modifications and to understand the mechanistic complexities that accompany cause and consequence of epigenetic modifications.
15
Araujo, Reno Roldi de. "Estudo em larga escala dos efeitos da idade sobre os parâmetros reprodutivos e viabilidade de oócitos equinos após injeção intracitoplasmática de espermatozóide (ICSI) usando sêmen sexado." Universidade de São Paulo, 2015. http://www.teses.usp.br/teses/disponiveis/10/10132/tde-04092015-162237/.
Full textAbstract:
O objetivo do presente estudo foi comparar o efeito da idade de doadores de oócitos sobre os parâmetros reprodutivos, a taxa de recuperação e qualidade de oócitos após ICSI utilizando sêmen sexado. Éguas Pôneis de Polo (n = 79) e Puro-Sangue (n = 23) doadoras de oócitos (400-600kg e 3-29 anos) foram utilizados durante as estações reprodutivas de 2009/2010 e 2011 no hemisfério Sul (San Luis, Argentina) e norte (Kentucky, EUA), respectivamente. As éguas foram divididas em três categorias experimentais: Jovens (YM: 3-10 anos), Meia Idade (MA: 11-17a) e Idosas (OM≥18a). Um total de 326 oócitos recuperados in vivo a partir de folículos pré-ovulatórios (n=279) e folículos imaturos em crescimento (n=47). Desses, 224 oócitos foram recuperados, classificado e dirigido a um programa comercial ICSI com Pôneis de Polo (primeira estação). Durante a segunda estação, 57 oócitos foram recuperados a partir de folículos pré-ovulatórios e 47 oócitos de folículos em crescimento e congelados em nitrogênio líquido para ser usado posteriormente em outro estudo. Os pontos experimentais avaliados foram: intervalos (dias) entre a aspiração ou a ovulação (AS/OV) ao PGF, PGF ao GnRH (Dia 0=GnRH), AS/OV ao Dia 0, e AS/OV ao Dia+1; edema uterino (UE); tonus cervical (CT); diâmetro máximo do folículo dominante (MdF1) em D0 e D+1, e a taxa de crescimento folicular. O número total de aspirações, o número de folículos aspirados e oócitos por aspiração e/ou folículo, o grau de expansão das células do cúmulos, a presença e qualidade do corpo polar (PB), o volume ooplasma, o intervalo de GnRH a aspiração, a GnRH a ICSI, e a taxa de clivagem (CR) depois da ICSI também foram avaliados. Foram observadas diferenças significativas entre as três categorias experimentais (YM, MA e OM) para: intervalos (dias) entre PGF-GnRH, AS/OV-GnRH, AS/OV-Day 1, edema uterino no Dia 0, CT em Dia 1, MdF1 no D0 e D+1 e volume de ooplasma. A taxa de recuperação in vivo (RR) não foi afetada pela idade (média de 102%, 85% e 73,4% de oócitos recuperados por ciclo, por F1 e por folículo, respectivamente, P> 0,05). O CR não diferiu entre as por ciclo, por F1 e por folículo, respectivamente, P> 0,05). O CR não diferiu entre as categorias experimentais. Em conclusão, um efeito de envelhecimento pode ser observado em vários parâmetros reprodutivos em éguas. Os ovócitos no presente estudo tiveram um menor volume de ooplasma para OM comparados com YM, mas isso não foi eficaz em predizer a viabilidade dos oócitos ou o potencial para o desenvolvimento para a avaliação da taxa de clivagem após ICSI utilizando sêmen sexadoThe aim of the present study was to compare the effect of oocyte donors` age on reproductive parameters, recovery rate and quality of oocytes after ICSI using sexed semen. Polo Ponies (n=79) and Thoroughbred (n=23) oocyte donor mares (400-600kg and 3-29 years) were used during the 2009/2010 and 2011 reproductive seasons in the Southern (San Luis, Argentina) and in the Northern hemispheres (Kentucky, USA), respectively. Mares were divided into three experimental categories: Young Mares (YM: 3-10У), Middle Age Mares (MA: 11-17У) and Old Mares (OM18У). A total of 326 oocytes were recovered in vivo from pre-ovulatory follicles (n=279) and immature-growing follicles (n=47). From those, 224 oocytes were recovered, sorted and directed to a commercial ICSI program with Polo Ponies (first season). During the study`s second season, 57 oocytes were recovered from pre-ovulatory follicles and 47 oocytes from growing follicles and frozen in liquid nitrogen to be used in another study. The evaluated experimental end-points were: Intervals (days) between aspiration or ovulation (AS/OV) to PGF, PGF to GnRH (Day 0=GnRH), AS/OV to Day 0, and AS/OV to Day + 1; uterine edema (UE); cervical tone (CT); maximum diameter of dominant follicle (MdF1) on D0 and D+1, and follicular growth rate. Total number of aspirations, number of follicles aspirated and oocytes recovered per aspiration and/or follicle, the degree of cumulus cell expansion, the presence and quality of polar body (PB), the ooplasm volume, the interval from GnRH to aspiration, GnRH to ICSI, and the cleavage rate (CR) after ICSI were also evaluated. Significant differences between the three experimental categories (YM, MA and OM) were observed for: intervals (days) between PGF-GnRH, AS/OV-GnRH, AS/OV-Day +1, uterine edema on Day 0, CT on Day +1, MdF1 on D0 and D+1 and ooplasm volume. The in vivo recovery rate (RR) was not affected by age (average of 102%, 85% and 73.4% of oocyte recovered per cycle, per F1 and per follicle, respectively; P>0.05). The CR did not differ among experimental categories. In conclusion, an effect of aging could be observed in several reproductive parameters in mares. The oocytes in the present study had a smaller ooplasm volume for OM compared to YM, but this was not effective in predicting oocyte viability or the potential to development through evaluation of the cleavage rate after ICSI using sexed semen
16
Metspalu, Mait. "Through the course of prehistory in India : tracing the mtDNA trail /." Tartu, Estonia : Tartu University Press, 2005. http://dspace.utlib.ee/dspace/bitstream/10062/853/5/metspalu.pdf.
Full text
17
Farooq, Muhammad Ali. "Iron Citrate Toxicity Causes aco1Δ-induced mtDNA Loss in Saccharomyces cerevisiae." ScholarWorks@UNO, 2013. http://scholarworks.uno.edu/honors_theses/34.
Full textAbstract:
Aconitase is an enzyme of the Krebs cycle that catalyzes the isomerization of citrate to isocitrate. In addition to its enzymatic activity, Aco1 has been reported to bind to mitochondrial DNA (mtDNA) and mediate its maintenance in the budding yeast S. cerevisiae. In the absence of Aco1, cells rapidly lose mtDNA and become “petite” mutants. The purpose of this study is to uncover the mechanism behind mtDNA loss due to an aco1 deletion mutation. We found that an aco1 mutation activates the mitochondria-to-nucleus retrograde (RTG) signaling pathway, resulting in increased expression of citrate synthases (CIT) through the activation of two transcription factors Rtg1 and Rtg3. Increased activity of CIT leads to increased iron accumulation in cells, which is known to raise reactive oxygen species (ROS). By deleting RTG1, RTG3, genes encoding citrate synthases, orMRS3 and MRS4, encoding two irontransporters in the mitochondrial inner membranes, mtDNA loss can be prevented in aco1 deletion mutant cells. We further show that the loss of SOD1, encoding the cytoplasmic isoform of superoxide dismutase, but not SOD2, encoding the mitochondrial isoform of superoxide dismutase, prevents mtDNA loss in aco1 mutant cells. Altogether, our data suggest that mtDNA loss in aco1 mutant cells is caused by the activation of the RTG pathway and subsequent iron accumulation and toxicity in the mitochondria.
18
Sahyoun, Abdullah. "Computational investigations into the evolution of mitochondrial genomes." Doctoral thesis, Universitätsbibliothek Leipzig, 2015. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-161437.
Full textAbstract:
Mitochondria are organelles present in most eukaryotic cells. They generate most of the cells adenosine triphosphate (ATP) supply which make them essential for cell viability. It is assumed that they are derived from a proteobacterial ancestor as they retain their own, drastically small genome.
The importance in studying mitochondrial genome evolution came from the discovery of a large number of human diseases that are caused by mitochondrial dysfunction (e.g., Parkinson and Alzheimer). Many of these diseases are a result of a mutation in one of the mitochondrial genes or a defective mitochondrial DNA (mtDNA) maintenance, mostly caused by genetic defects in proteins involved in mtDNA replication. In order to explore
the diversity and understand the evolution of mitochondrial genomes (mitogenomes) in animals, multiple methods have been developed in this study to deal with two biological problems related to the mitochondrial genome evolution.
A new method for identifying the mitochondrial origins of replication is presented. This method deals with the problem of determining the origins of replication, which despite many previous efforts has remained non-trivial even in the small genomes of animal mitochondria. The replication mechanism is of central interest to understand the evolution of mitochondrial genomes since it allows the duplication of the genetic information.
The extensive work that has been done to study the replication of mitochondrial genomes has generated the assumption of the strand displacement model (SDM) also known as the standard model of replication that is known to leave the mitochondrial H-strand in a single stranded state exposing it to mutation and damage. Later on, other models of replication have been suggested such as the strand coupled bidirectional replication
model, its refinement which assumes the bidirectional mode but with a unidirectional start, and the \"RNA incorporation throughout the lagging strand\" (RITOLS) model proposed as a refinement of the strand displacement model. Based on the observation that the GC-skew is correlated with the distance from the replication origins in the light of the strand displacement model of replication, a new computational method to infer the position of both the heavy strand and the light strand origins from nucleotide skew
data has been developed. The method has been applied in a comprehensive survey of deuterostome mitochondria where conserved positions of the replication origins for the vast majority of vertebrates and cephalochordates have been inferred. Deviations from the consensus picture are presumably associated with genome rearrangements.
Additionally, two methods for the identification of tRNA remolding events throughout Metazoa have been developed. Remolding changes the identity of a tRNA by a duplication and a point mutation(s) of the anticodon. This new tRNA takes the identity of another tRNA which is then lost. This can lead to artifacts in the annotation of mitogenomes and thus in studies of mitogenomic evolution. In this work, novel methods are developed to detect tRNA remolding in large-scale data sets. The first method represents an extension of the similarity-based approach to determine remolding candidates with high confidence. This approach uses an extended set of criteria based on both sequence and structural similarities of the tRNAs in conjunction with statistical tests. The second method is a novel phylogeny-based likelihood method which evaluates specific topologies of gene phylogenies of the two tRNA families relevant to a putative remolding event. Both methods have been applied to survey tRNA remolding throughout animal evolution. At least three novel remolding events are identified in addition to the ones previously mentioned in the literature. A detailed analysis of these remoldings showed that many of them are derived ancestral events.
19
Kim, Boa. "EFFECTS OF LAMINAR SHEAR STRESS ON MITOCHONDRIAL DNA INTEGRITY IN ENDOTHELIAL CELLS." Diss., Temple University Libraries, 2014. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/266464.
Full textAbstract:
KinesiologyPh.D.
Purpose/hypothesis: Regular practice of exercise is the most effective non-pharmacological intervention that improves vascular health, which is thought to be mediated by a repeated exposure of vessel walls to increased hemodynamic shear stress (SS). Mitochondria have been shown to be essential cellular structures responsible for a wide variety of vascular functions, and its impairment is often associated with cardiovascular disease. However, researches on vascular mitochondrial adaptations to SS are in a very early stage and many questions remain unresolved. The objective of this study is to investigate the effect of exercise preconditioning on endothelial mitochondria in an angiotensin (Ang) II-induced hypertension model. It was hypothesized that exercise preconditioning prevents Ang II induced-hypertensive phenotypes by improving mitochondrial homeostasis in the endothelium. Methods: High-magnitude laminar SS (LSS) (20 dyne/cm2) was applied to human aortic endothelial cells (HAECs) using a cone-and-plate shear apparatus for 48 hours. Either LSS-preconditioned or static flow-situated HAECs were incubated with Ang II. In in vivo experiments, C57BL/6J mice were singly housed with or without a voluntary running wheel for 7 weeks. Ang II or saline was infused in a constant rate using an implantable osmotic pump for the last 2 weeks of the experimental period. Mitochondrial membrane potential (ÄØm) and mitoROS production were measured using fluorochrome molecular probe-based microscopic techniques, and mtDNA damage was assessed by a long amplicon quantitative PCR (LA-QPCR) method. Results: In HAECs, LSS preconditioning attenuated Ang II-induced mitochondrial dysfunction, which was evidenced by decreased mitoROS generation, increased ÄØm, and reduced mtDNA damage. Likewise, in aortic tissues, Ang II-induced mitochondrial phenotypic changes (i.e. mitoROS production, mtDNA damage and ÄØm reduction) were significantly reduced in exercise-preconditioned mice compared to sedentary controls. Moreover, Ang II-induced blood pressure elevation was completely blocked in exercise preconditioned animals. Conclusion: Taken together, high-magnitude LSS improves endothelial function by enhancing mtDNA integrity and mitochondrial function. These findings further support the idea that aerobic exercise is a prominent life-style modification strategy to prevent hypertension by targeting dysfunctional mitochondria in the vessel wall.
Temple University--Theses
20
Lunt, David H. "mtDNA differentiation across Europe in the meadow grasshopper Chorthippus parallelus (Orthoptera: acrididae)." Thesis, University of East Anglia, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.298311.
Full textAbstract:
This thesis examines the European phylogeography of the meadow grasshopper Chorthippus paralleJus. This common species has a very large range covering Europe, southern Scandinavia, Turkey and Russia, with two recognized subspecies. These are c.p.erythropus in Spain and c.p.paraJ1eJus in other regions. This species has been studied using mtDNA RFLPs and sequence data. The greatest levels of genetic subdivision were found to occur between southern Spain, southern Italy and the Balkans. No subdivision was detected between Balkan populations and those in central and northern Europe. These data were interpreted as indications that at least three refugia existed in Europe during the last glaciation. The historical locations of these refugia can be inferred to have been in southern Spain, southern Italy and the Balkans. Furthermore, postglacial expansion from the Balkan refugium is indicated as the origin of central and northern European populations of C.paralleJus. A phylogeny of common European Chorthippus species, and closely related genera, is presented from analysis of mtDNA sequence data. This analysis indicates that, although there are many similarities to the traditional morphological taxonomic arrangement, several revisions need to be considered and investigated further. These include the position of the monospecific genus Stauroderus outside of the Chorthippus clade and the division of these Chorthippus species into 3 subgenera. Finally, the evolutionary patterns of the cytochrome oxidase subunit I (COl) gene, which was used for the Chorthippus studies, are investigated for insects in general. The patterns of amino acid variability indicate regions of very different substitutional rates within this gene. These regions are discussed in terms of the known and assumed functional constraints on gene function. The variety of evolutionary rates in adjacent regions are considered further with regard to their utility in different levels of phylogenetic study, and conserved insect primers for the exploitation of these regions are presented.
21
Ricardo, Paulo Cseri. "Heteroplasmia em Bombus morio (Hymenoptera, Apidae) e impactos em estudos evolutivos." Universidade de São Paulo, 2017. http://www.teses.usp.br/teses/disponiveis/41/41131/tde-02042018-150706/.
Full textAbstract:
A utilização de sequências do DNA mitocondrial (mtDNA) como marcadores moleculares na investigação da diversidade genética e evolução é muito difundida, auxiliando na realização de inferências em inúmeros trabalhos. Apesar de sua inegável importância, a utilização dessas sequências como marcadores moleculares suscita algumas questões. A heteroplasmia, por exemplo, é reconhecida como um desafio na utilização de sequências do mtDNA. Este estado ocorre quando um organismo apresenta diferentes haplótipos mitocondriais. Em um trabalho anterior, foram encontrados indícios que sugeriam a presença de heteroplasmia na espécie de abelha Bombus morio. O trabalho atual investigou de forma mais detalhada a presença de heteroplasmia nessa espécie, assim como fatores que podem influenciar na identificação desse estado. Os resultados obtidos confirmaram a existência de heteroplasmia nessa espécie, e identificaram que alguns haplótipos heteroplásmicos foram compartilhados entre indivíduos de localidades distintas. Esses haplótipos heteroplásmicos compartilhados sugerem a existência de heteroplasmia estável em B. morio, o que pode influenciar inferências evolutivas, e em especial, os estudos populacionais. Também foi detectada a presença de NUMTs, pseudogenes nucleares resultantes da transferência de sequências do mtDNA para o genoma nuclear. Esses NUMTs apresentaram grande divergência de sequência em relação aos haplótipos mitocondriais, o que poderia afetar análises filogenéticas e populacionais, além da identificação de espécies por meio do DNA barcoding. Ainda, erros de amplificação podem ser falsamente interpretados como variação intraindividual do DNA mitocondrial (mtDNA), superestimando o número de haplótipos, principalmente quando polimerases de baixa fidelidade são utilizadas. Por fim, os resultados observados neste trabalho sugerem que a utilização de sequências do mtDNA deve ser utilizada de forma cautelosa, e indícios de heteroplasmia, como a presença de picos duplos, não devem ser ignorados. Quando essas evidências são observadas investigações mais detalhadas devem ser aplicadas, a fim de aferir qual a sua origem, e, no caso da heteroplasmia ser confirmada, quais as possíveis consequências produzidas pela presença desse estadoThe mitochondrial DNA sequences (mtDNA) have been widely applied as molecular markers in the investigation of genetic diversity and evolution. Despite its undeniable importance, the use of these sequences as molecular markers may present some drawbacks. Heteroplasmy, for example, is recognized as a challenge. This state occurs when an individual has different mitochondrial haplotypes. In a previous work, evidences suggesting the presence of heteroplasmy in the bumblebee Bombus morio were verified. The present work investigated in more detail the presence of heteroplasmy in this species, as well as factors that may influence the identification of this state. The results confirmed the existence of heteroplasmy in this species, and identified that some heteroplasmic haplotypes were shared between individuals from different locations. These shared heteroplasmic haplotypes suggest the existence of stable heteroplasmy in B. morio, which may interfere in evolutionary inferences, especially in population studies. NUMTs, nuclear pseudogenes resulting from the transfer of mtDNA sequences to the nuclear genome, were also detected. These NUMTs showed great sequence divergence from mitochondrial haplotypes, which could affect phylogenetic and population analyzes, as well as species identification through DNA barcoding. In addition, it was observed that amplification errors might be misinterpreted as mtDNA intraindividual variation and overestimates the number of intraindividual haplotypes, especially when low fidelity polymerases are used. Finally, the results observed in this study suggest that the use of mtDNA sequences should be used carefully, and evidences of heteroplasmy, such as the presence of double peaks, should not be ignored. Additional investigations should be applied in case of heteroplasmy evidences to ascertain your source and the consequences of the presence of this state
22
Homeister, Anne. "Ancient DNA studies : of the Asiatic Eskimo site Ekven." Thesis, Stockholms universitet, Arkeologiska forskningslaboratoriet, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-86934.
Full textAbstract:
Den här uppsatsen behandlar gammal DNA från 32 människor från den prehistoriska byn Ekwen belägen in nordöst Asien. Proverna har blivit masskopierade med hjälp av PCR och sekvenserad med FLX pyrosekvensering. Autentiska sekvenser har blivit bedömt genom användningen av PhyloNet och c-statistik och senare anpassad och jämförd med en referens sekvens (CRS). Tydliga C-T, T-C och A-G skador har upptäckts vid nukleotidpositioner vilket visar sig vara utmärkande för just den här populationen.
23
Godoy, Felipe Augusto. "Estudo do papel da proteína p53 em reparo por excisão de bases em mitocôndrias de células de mamíferos." Universidade de São Paulo, 2018. http://www.teses.usp.br/teses/disponiveis/85/85131/tde-21062018-090338/.
Full textAbstract:
Todos os organismos vivos estão constantemente expostos a uma variedade de agentes que podem causar modificações químicas e/ou estruturais no DNA, afetando processos essenciais como replicação e transcrição. Ao longo da evolução várias estratégias de reparo do DNA foram desenvolvidas para remover essas modificações, prevenindo o efeito citotóxico ou mutagênico dessas lesões. Mutações no mtDNA são frequentemente observadas em inúmeras patologias, o que reflete em alterações metabólicas ou até mesmo atenuação da resposta apoptótica a terapias antineoplásicas. Para manter a integridade genômica mitocondrial, alguns mecanismos de reparo são recrutados à organela, principalmente a via de reparo por excisão de bases, BER. No núcleo, a proteína supressora de tumor p53 colabora para a manutenção da estabilidade do DNA, em parte pela estimulação direta da via BER. Em resposta a certos estímulos celulares, p53 transloca-se para a mitocôndria, onde pode desencadear uma resposta apoptótica. Entretanto, foi demonstrado anteriormente que p53 pode estimular a atividade catalítica da DNA polimerase mitocondrial, DNA polimerase gama (pol γ), que participa da replicação e do reparo do mtDNA. Sendo assim, nesse trabalho buscou-se compreender, molecularmente, essa interação entre p53 e pol γ durante a modulação de BER em mitocôndrias de células humanas, investigando se: i) p53 se associa fisicamente a pol γ; ii) a proteína TFAM modula o papel de p53 no reparo do DNA em mitocôndrias; e iii) a translocação de p53 para a mitocôndria é mediada por processos redox durante o reparo do mtDNA. Para isso, métodos bioquímicos e moleculares foram empregados nos estudos da interação entre essas proteínas. Em conjunto, os resultados sugerem o envolvimento da proteína p53 no reparo por excisão de bases em mitocôndrias de células humanas, e a dependência de sua interação com TFAM e pol γ para o sustento dessa via. Isso reforça a importância dessas proteínas para a manutenção da estabilidade genômica mitocondrial e, provavelmente, para a função mitocondrial.All living organisms are constantly exposed to a variety of agents that can cause chemical and/or structural changes in DNA, affecting essential processes like replication and transcription. Throughout the evolution several strategies of DNA repair have been developed to remove these modifications, preventing the cytotoxic or mutagenic effect of these lesions. Mutations in mtDNA are often observed in numerous pathologies, reflecting metabolic changes or even attenuation of the apoptotic response to antineoplastic therapies. To maintain mitochondrial genomic integrity, some repair mechanisms are recruited to the organelle, mainly the base excision repair route, BER. In the nucleus, p53 tumor suppressor protein contributes to the maintenance of DNA stability, in part by direct stimulation of the BER pathway. In response to certain cellular stimuli, p53 translocate to the mitochondria, where it can trigger an apoptotic response. However, it has been shown previously that p53 can stimulate the catalytic activity of mitochondrial DNA polymerase, gamma polymerase (pol γ), which participates in the replication and repair of mtDNA. Thus, in this work we sought to understand, molecularly, this interaction between p53 and pol γ during a modulation of BER in mitochondria human cells, investigating if: i) p53 is physically associated with pol γ; ii) the TFAM protein modulates the role of p53 in DNA repair in mitochondria; and iii) the translocation of p53 to mitochondria is mediated by redox processes in mtDNA repair. For this, biochemical and molecular methods were used in the studies of protein interaction. Taken together, the results suggest the involvement of p53 protein in repair by base excision in mitochondria of human cells, and dependence of its interaction with TFAM and pol γ to support this pathway. This reinforces the importance of these proteins for the maintenance of mitochondrial genomic stability and probably for mitochondrial function.
24
Meyer, Katharina [Verfasser]. "The Role of Apoptosis Inducing Factor in Modulating mtDNA Copy Number / Katharina Meyer." Bonn : Universitäts- und Landesbibliothek Bonn, 2015. http://d-nb.info/1077290179/34.
Full text
25
Herkenhoff, Marcos Edgar. "Variabilidade Genética da Região Controladora do mtDNA (Alça-D) de Galinhas Caipiras Brasileiras." Universidade do Estado de Santa Catarina, 2013. http://tede.udesc.br/handle/handle/894.
Full textAbstract:
Made available in DSpace on 2016-12-08T16:24:15Z (GMT). No. of bitstreams: 1
PGCA13MA117.pdf: 974615 bytes, checksum: 1adc6a24dc175e42ba61d10eb2f142ea (MD5)
Previous issue date: 2013-02-28The domestic chicken (Gallus gallus domesticus) was originated by the jungle red flow chicken (Gallus gallus) and the bankiva chicken (Gallus gallus bankiva). Since the domestication, around 7000 years ago in the Asian Southeast, the chicken came with the human migration, and then scattered to the entire world and arrived to Brazil around 1500 BC. In Brazil has came breeds from Europe and Asia, and they were let in freedom and they crossed at random breeding generating the chicken as know as Brazilian caipira chicken. With development of the national chicken producing the caipira s chickens were forgotten in countryside in third world countries, to be considered less productive. However, with the growing consumption of product considered healthier, this chicken was recovered. In additional, to be more rustic and disease resistance, because their high genetic variability, these chickens are considered an important source for alleles which can be use in the animal genetic improvement. The mitochondrial DNA (mtDNA) is characterized by had an exclusively maternal inheritance and the most used method amplify the mtDNA control region (D-loop), which has a high genetic variability. This study aimed to investigate the origin and composition of the maternal lines on these lineages. . We collected blood samples from 105 Brazilian blue-egg caipira s chickens. The fragments were amplified by PCR, sequenced, and analyzed by the MEGA 4.0 software. As result, 89,52% of the chicken belong to the clade A, 7,62% to C e 2,86% to E, which means that participated animals most from Asian and few from European origin, in the maternal lineages. The results indicate that these strains analyzed of Brazilian chickens, have a higher genetic variability so that observed in non-commercial poultry and conserve a strong founder effect
A galinha doméstica (Gallus gallus domesticus) é originária da galinha vermelha do mato (Gallus gallus) e galinha bankiva (Gallus gallus bankiva). Desde a sua domesticação, que ocorreu por volta de 7000 anos atrás no Sudeste asiático, a galinha acompanhou a migração humana, e assim se espalhou pelo mundo inteiro, chegando ao Brasil por volta do ano de 1500. No Brasil chegaram aves oriundas da Europa e da Ásia, e aqui foram deixadas em liberdade e cruzaram de forma aleatória gerando o que hoje se conhece como galinha caipira. Com o desenvolvimento da avicultura, estas aves foram esquecidas nos quintais de casa, por serem consideradas menos produtivas. No entanto, com o crescente aumento no consumo de produtos considerados naturais, esta ave voltou ao mercado. Por ser mais rústica e resistente a doenças, em virtude de sua variabilidade genética alta, estas aves também são consideradas uma importante fonte de alelos que podem ser utilizados no melhoramento animal. O DNA mitocondrial (mtDNA) caracteriza-se por ser de exclusiva herança materna, sendo o método mais utilizado consiste em amplificar a região controle (alça-D), que possui grande variabilidade genética. Desta forma, este trabalho tem como objetivo determinar a origem e composição das linhas maternas nestas linhagens. Foram coletadas amostras de sangue de 105 galinhas caipiras de ovos azuis oriundas do município de Dois Lajeados-RS. Os fragmentos foram amplificados pela PCR, sequenciados, e analisados pelo software MEGA 4.0. Como resultado, 89,52% das aves pertencem ao haplogrupo A, 7,62% ao C e 2,86% ao E. Para a composição desta ave foram utilizados em sua maioria aves de origem asiática e um pouco de origem europeia, em sua linhagem materna. Os resultados obtidos indicam que estas aves analisadas, apresentam uma variabilidade genética semelhante a aves não comerciais e conservam ainda um efeito fundador muito forte
26
Burton, Elliot N. "Functional Consequences of mtDNA Methylation on Mitochondrial Transcription Factor Binding and Transcription Initiation." VCU Scholars Compass, 2016. http://scholarscompass.vcu.edu/etd/4185.
Full textAbstract:
The role of cytosine modifications on nuclear transcription has been well characterized, but the function of DNA methylation in the mitochondrial genome has not been determined. Previous studies conducted by the Taylor laboratory have shown overexpression of the mitochondrial isoform of DNMT1 leads to strand-specific changes in gene expression. Here, we show that increased mtDNMT1 expression leads to an increase in the polycistronic transcript encoding the ND1 and Cox1 sequences. In order to understand the mechanistic basis of these changes, we investigated the effects of CpG methylation in the heavy strand promoter on transcription initiation and TFAM binding. Methylation was found to increase transcription initiation from HSP1 and result in larger TFAM:DNA complexes forming at lower protein concentrations. Our data suggest a functional role for cytosine methylation in the mitochondria, which we propose may have an effect on oxidative phosphorylation and cellular function.
27
Schilf, Paul [Verfasser]. "Interplay of mtDNA, metabolism and microbiota in the pathogenesis of AIBD / Paul Schilf." Lübeck : Zentrale Hochschulbibliothek Lübeck, 2017. http://d-nb.info/1136441018/34.
Full text
28
Rodrigues, Marcos Alaniz. "Identificação baseada em mtDNA, recrutamento e dinâmica reprodutiva de Callinectes sapidus (RATHBUN, 1896)." reponame:Repositório Institucional da FURG, 2012. http://repositorio.furg.br/handle/1/4018.
Full textAbstract:
Tese(doutorado) - Universidade Federal do Rio Grande, Programa de Pós–Graduação em Oceanografia Biológica, Instituto de Oceanografia, 2012.Submitted by Cristiane Gomides (cristiane_gomides@hotmail.com) on 2013-10-14T11:56:12Z No. of bitstreams: 1 Marcos.pdf: 15391646 bytes, checksum: 62f314b1feb734ad7e5f0c0ecef26f90 (MD5)
Approved for entry into archive by Sabrina Andrade (sabrinabeatriz@ibest.com.br) on 2013-10-17T02:56:08Z (GMT) No. of bitstreams: 1 Marcos.pdf: 15391646 bytes, checksum: 62f314b1feb734ad7e5f0c0ecef26f90 (MD5)
Made available in DSpace on 2013-10-17T02:56:08Z (GMT). No. of bitstreams: 1 Marcos.pdf: 15391646 bytes, checksum: 62f314b1feb734ad7e5f0c0ecef26f90 (MD5) Previous issue date: 2012
O siri-azul Callinectes sapidus é um importante recurso explorado ao longo de toda a área de ocorrência, tanto pela pescaria industrial, quanto pela pesca artesanal. As hipóteses testadas neste trabalho foram: Existem diferenças genéticas entre os siris que habitam as duas porções de distribuição ao longo do Continente Americano. Também a hipótese de que o recrutamento de juvenis responde de maneira positiva às variáveis ambientais, e o assentamento ocorre nas áreas internas dos estuários. Por fim foram testadas as hipóteses de que a reprodução poderia ocorrer de forma contínua, e de que o número de ovos produzido por fêmea varia com o tamanho destas. Nesta tese foram identificadas duas populações de Callinectes sapidus no Atlântico Ocidental através do uso de DNA mitocondrial, além de realizados estudos sobre aspectos reprodutivos e da estrutura populacional de C. sapidus no litoral sudeste/sul do Brasil. Para os estudos genéticos foram feitas coletas em locais de ocorrência da espécie ao longo da Costa Atlântica das Américas do Norte e do Sul. As coletas para os estudos de recrutamento e reprodução foram mensais nos estuários de Tramandaí e da Lagoa dos Patos no período entre maio de 2008 e maio de 2010. A identificação de populações foi realizada com base no sequenciamento de 650pb da região da Citocromo Oxidase do DNA mitocondrial, a partir coletas em toda a área de ocorrência da espécie no Brasil e nos Estados Unidos. A diversidade nucleotídica (π) variou de 0,002 a 0,006 e os menores valores foram encontrados nos extremos de distribuição em cada um dos grupos de populações (EUA e BR). A diversidade haplotípica variou de 0,57 a 1,00 e não seguiu o mesmo padrão de menores valores perto dos limites de distribuição. As distâncias calculadas (Fst) mostraram que podem ser separadas duas subpopulações ao longo da área de distribuição, uma compreendendo indivíduos dos Estados Unidos, e outra compreendendo os indivíduos do Brasil. Com relação ao recrutamento de juvenis de C. sapidus nos estuários da Lagoa dos Patos e Tramandaí, o padrão de resposta às variáveis ambientais foi semelhante para ambos os estuários, onde a temperatura parece ser determinante para o assentamento dos juvenis, e estes parecem se concentrar mais nos pontos com maior concentração de matéria orgânica, e significativamente mais nas margens do que nas áreas mais profundas. Em ambos os estuários, foram encontrados dois picos de recrutamento, com o primeiro ocorrendo no início do outono, e o segundo durante o inverno. Estes picos podem estar relacionados a condições ambientais favoráveis. As áreas internas do estuário são determinantes para o correto assentamento dos recrutas de siri-azul em ambos os estuários. Com relação à descrição do processo reprodutivo, através da determinação de parâmetros reprodutivos da espécie para o estuário da Lagoa dos Patos, conclui-se que a espécie apresenta reprodução anual, com machos maturando com tamanho menor do que as fêmeas. Na temporada reprodutiva de 2008 nota-se um equilíbrio entre o número de machos e fêmeas, o que não se repetiu na temporada de 2009, talvez pelo alto volume de chuvas registrado durante o período, que pode ter ocasionado a migração de fêmeas para áreas mais externas à saída do estuário. Callinectes sapidus é sensível a alterações ambientais, e longos períodos de chuva combinados com outros fatores ambientais como baixas salinidades podem comprometer futuras proles. Ainda com relação à variação na fecundidade e a abundância de fêmeas do siri-azul no estuário da Lagoa dos Patos, e a abundância das fêmeas ovígeras coletadas na área de desova relacionada com parâmetros ambientais, foi encontrada uma correlação positiva entre a fecundidade e a largura de carapaça. A abundância apresentou relação com a temperatura da água. A fecundidade da espécie para o estuário da Lagoa dos Patos parece ficar dentro dos limites encontrados em outros estuários de ocorrência, sugerindo que exista um padrão em seu potencial reprodutivo. A espécie apresenta um período de desova bem marcado durante o período que compreende o final da primavera e todo o verão. Futuros estudos em Callinectes sapidus deverão incluir ferramentas moleculares que possam definir a estrutura da população ao longo do gradiente brasileiro de distribuição, como microsatélites. A preferência dos juvenis pelas áreas internas de margem dos estuários torna evidente a preocupação com a proteção destas áreas, a fim de garantir a sustentabilidade do recurso. A proteção do estoque desovante deve ser continuada para todas as classes de tamanho, visto que todas contribuem para as futuras proles.
The blue crab Callinectes sapidus is an important resource, explored along its occurrence area, by the industrial fisheries, and by the artisanal fleet. The hypotheses tested in this work were: There are genetic differences between crabs that inhabit the two portions of distribution throughout the Americas. Also the hypothesis that recruitment of juveniles responds positively to environmental variables, and that settlement occurs in the internal areas of estuaries. Lastly we tested the hypothesis that reproduction could occur continuously, and that the number of eggs produced per female varies with the size of these. The aim of this work is to identify the population structure of Callinectes sapidus on the Western Atlantic with mtDNA, and study reproductive and population structure aspects of C. sapidus on the southeast/south of Brazil. Samplings were conducted monthly from May of 2008 to May of 2010. The genetic identification was analyzed based on the sequencing of 650 bp of the Cytochrome oxidase mtDNA region, from samplings along all the occurrence area of the species in Brazil and in the United States. Nucleotide diversity (π) ranged from 0.002 to 0.006 and smaller values were found on the extremes of distribution on each of the population groups (U.S. and Brazil). Haplotype diversity varied from 0.57 to 1.00 and did not follow the same pattern of smaller values close to the limits of distribution. The calculated distances (Fst) allow us to infer that can be separated two subpopulations along the distribution area, with the first with individuals from the United States, and the second one with the Brazilian crabs. Regarding the studies on recruitment of C. sapidus on the Patos Lagoon estuary and the Tramandaí river estuary the response pattern to the environmental conditions was similar to both estuaries, where the water temperature seems to be determinant to the settlement of juveniles, and there is a preference of juveniles for areas with more organic matter, and significantly more on the margins than in deeper areas. On both estuaries, two recruitment peaks were found, with the first at the beginning of autumn, and the second during winter. These peaks may be related to favorable environmental conditions. The internal areas of the estuary are determinant for the correct settlement of the blue crab cohorts on both estuaries. We also described the reproductive process through the determination of the reproductive period, of the species for the Patos Lagoon estuary, and concluded that C. sapidus presents annual reproduction, with males reaching sexual maturity with smaller size than females. On the 2008 reproductive season there is a balance between number of males and females, but it didn’t repeated for the 2009 season, perhaps because the high rainfall volume registered during the period. The species is sensitive to environmental conditions, and long periods of rainfall mixed with other factors like low salinities can compromise future breeds. We also studied the variation in fecundity and female abundance of the blue crab on the Patos Lagoon estuary. A positive correlation between number of eggs and carapace width was found. The abundance showed positive correlation with water temperature. Fecundity of the species in the Patos Lagoon estuary falls within the limits found in other estuaries, suggesting a pattern in the reproductive potential of C. sapidus. The species has a spawning season well known to occur during the late spring and summer, and as such it is necessary to protect the entire stock of spawning females, as these individuals allow for recruitment of juveniles during the next breeding season. Future studies in C. sapidus must include most accurate molecular tools, to define the population structure along the distribution gradient in Brazil. The preference for juveniles for the margin of the internal areas of the estuaries makes evident the concern with the protection of these areas, in a way of assure the sustainability of the resource. All size classes of the spawning stock should be protected, because they all contribute to future breeds.
29
Wolff, Jonci Nikolai. "Investigating Patterns of Mitochondrial DNA Inheritance Using New Zealand Chinook Salmon (Oncorhynchus tshawytscha) as a Model Organism." Thesis, University of Canterbury. Biological Sciences, 2008. http://hdl.handle.net/10092/1583.
Full textAbstract:
The laws for the inheritance of animal mitochondrial DNA differ from those revealed for nuclear DNA. In contrast to nuclear genes, animal mitochondrial DNA (mtDNA) is predominantly inherited through the maternal line and is typically assumed to be nonrecombining. The absence of both paternal transmission (hereafter: paternal leakage) and heterologous recombination of mtDNA are assumed to be key characteristics of mitochondrial DNA inheritance, which has enabled evolutionary models to be much simpler than those needed for the interpretation of nuclear DNA. However, recent revelations of paternal leakage in the animal kingdom challenge our current knowledge about mtDNA inheritance and the utility of mtDNA as a molecular marker. The occurrence of paternal leakage potentially introduces new haplotypes into populations and therefore impacts on the interpretation of mtDNA analysis. To date, it is unclear whether the documented cases of paternal leakage are exceptions to the general rule or if these events occur more frequently than so far believed. If this event occurred at a measurable frequency, it is vital to implement such data into models of mtDNA evolution to improve the accuracy at which evolutionary relationships and times of divergence are estimated. In this thesis, I aimed to provide an insight into the broader patterns of mtDNA inheritance using chinook salmon as a model organism. I first sought to delimit the frequency of paternal leakage in chinook salmon and further investigated two major mechanisms which are believed to limit paternal leakage: The many-fold dilution of paternal mtDNA by maternal mtDNA upon fertilization and the genetic bottleneck mtDNA is believed to be exposed to during early developmental stages. A screen of roughly 10.000 offspring did not reveal the presence of paternal mtDNA within these samples delimiting the maximum frequency of paternal leakage in this system to 0.18% (power of 0.95) and 0.27% (power of 0.99), suggesting that the occurrence of paternal leakage is most likely an exception to the general rule. To infer the dilution of paternal mtDNA upon fertilization, I employed real-time PCR and determined the mtDNA content of salmon spermatozoa and oocytes to be 5.73 ± 2.28 and 3.15x109 ± 9.98x108 molecules per gamete, respectively. Accordingly, the estimated ratio of paternal to maternal mtDNA in zygotes is 1:7.35x108 ± 4.67x108. This estimate is 3 to 5 orders of magnitude smaller than the ratio revealed for mammals. Consequently, and if the dilution acts as an efficient barrier against the transmission of paternal mtDNA, paternal inheritance of mtDNA per offspring will be much less likely in this system than in mammals. To estimate at what probability the diminutive contribution of paternal mtDNA in zygotes is potentially inherited to offspring, I determined the size of the bottleneck acting on mtDNA during both embryogenesis and oogensis by examining the transmission of mtDNA variants to offspring and oocytes within a pedigree of heteroplasmic individuals. The number of segregating units (mtDNAs) between a mother’s somatic tissue and oocytes was estimated to be 109.3 (median = 109.3; 62.4 < NeOog < 189.6; 95% confidence interval) and from a mother’s soma to offspring’s soma 105.4 (median = 105.4; 70.3 < NeEmb < 153.1; 95% confidence interval). Detected variances in allele frequency among oocytes were not significantly different from those in offspring, strongly suggesting that segregation of mtDNA occurs during oogenesis with its completion before oocyte maturation. However, considering a ratio of roughly 1:7.35x108 for paternal to maternal mtDNA in zygotes and that approximately 109.3 (NeOog) of the mitochondrial genomes present in zygotes are ultimately inherited to offspring, the probability for paternal mtDNA to be transmitted to offspring is in round terms 1.0x10-11/paternal mtDNA molecule. In summary, the results presented in this thesis document the presence of efficient barriers to prohibit the inheritance of minor allele contributions, such as paternal mtDNA, to offspring. These results strongly suggest that paternal leakage is an exception to the general rule. Furthermore, in comparison to studies undertaken in mammals, my results indicate that mechanisms in place to prevent paternal leakage may be unequally efficient among different animal taxa, reflecting differences in life traits, such as gamete morphology, gamete investment and reproductive strategies. Nonetheless, by the means of the dilution effect in zygotes and the genetic bottleneck during oogenesis, the occurrence of paternal leakage might be simply a quantitative phenomenon and cannot be excluded per se. The increasing number of documented cases of paternal leakage clarifies that its occurrence must be considered when applying mtDNA as a genetic marker. Furthermore, for species in which mtDNA inheritance can be confirmed to be purely random, theoretical frequencies of paternal leakage can be inferred and potentially implemented into models of mtDNA evolution.
30
Bidooki, Seyed Kazem. "Investigation of abnormal DNA in human disease." Thesis, University of Newcastle Upon Tyne, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.362474.
Full text
31
BARBOSA, Adriana Braga de Goes. "Determinação do polimorfismo das seqüências de DNA mitocondrial humano na população de Alagoas, Brasil." Universidade Federal de Pernambuco, 2006. https://repositorio.ufpe.br/handle/123456789/6596.
Full textAbstract:
Made available in DSpace on 2014-06-12T18:06:18Z (GMT). No. of bitstreams: 2
arquivo6292_1.pdf: 2278888 bytes, checksum: 0ebd2a7a155939e0bf1c1540b30d92da (MD5)
license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5)
Previous issue date: 2006A análise das seqüências de DNA mitocondrial humano (mtDNA) tem sido uma ferramenta muito útil na genética forense devido às características especiais do mtDNA como herança materna, ausência de recombinação e alto número de cópias por célula. O objetivo deste trabalho foi determinar o polimorfismo das regiões hipervariáveis 1 e 2 do mtDNA humano na população de Alagoas, Brasil. Para isso, foram seqüenciados 167 mtDNAs de indivíduos não relacionados desta população para análise dos dois segmentos hipervariáveis, HV1 e HV2, da região controle. A heteroplasmia de comprimento, nas regiões de trechos de citosina repetidas em HV1/HV2, foi observada em 22% (37/167) e 11% (19/167) da amostra, respectivamente. Dos 123 segmentos de HV1 e HV2 restantes, um total de 110 haplótipos diferentes foram encontrados, sendo determinados por 128 posições variáveis. O haplótipo mais freqüente (16111, 16223, 16290, 16319, 16362, 73, 146, 153, 235, 263, 309.1C, 315.1C - haplogrupo A) foi econtrado em cinco indivíduos, seguido por um haplótipo compartilhado por três indivíduos e um haplótipo compartilhado por duas pessoas em sete ocorrências diferentes (frequência de 1,6%). A diversidade genética foi estimada em 0,997 e a probabilidade de dois indivíduos ao acaso possuírem mtDNAs idênticos foi de 0,011. Baseado nos resultados dos perfis de mtDNA, 45% das sequências puderam ser classificadas como haplogrupos africanos, 27% como nativo-americanos e 25% como europeus. Cerca de 3% dos haplótipos não puderam ser classificados em nenhum haplogrupo. A diversidade genética das regiões HV1 e HV2 indica a importância desses locos para a identificação humana na população de Alagoas
32
Missarova, Alsu 1990. "mtDNA dynamics are a driving force of cell-to-cell heterogeneity in Saccharomyces cerevisiae." Doctoral thesis, Universitat Pompeu Fabra, 2018. http://hdl.handle.net/10803/663194.
Full textAbstract:
Isogenic cells exhibit a large degree of cell-to-cell heterogeneity in proliferation, with a subpopulation of cells growing at a substantially lower rate. We conducted a high throughput microscopy screen to determine the proliferation distributions for a collection of wild isolates and 1592 single gene deletions in S. cerevisiae. We found that mitochondrial impairment is a primary cause of slow growth within an isogenic population and that high mitochondrial membrane potential is predictive of reduced growth and respiratory deficiency. We showed that respiratory deficiency can be recovered and that temporary respiratory deficiency is a common trait present in many genetic backgrounds. We developed a mathematical model that predicts the dynamics of the respiratory capacity of single cells within a population as a function of mtDNA state. Finally, we showed that growth in the antifungal agent fluconazole enriches for temporarily respiratory deficient cells, suggesting that this phenotype may be a form of bet-hedging in which a slow growing drug-resistant respiratory deficient cell with low mtDNA content can produce progeny with fast growth and fully functioning mitochondria.Les cèl·lules isogèniques mostren un gran grau d' heterogenietat cel·lular en la seva taxa de proliferació, amb una subpoblació de cèl·lules creixent de manera substancialment lenta. Hem realitzat un assaig de microsopia d’alt rendiment (high-throughput) i hem determinat les distribucions de proliferació d'un conjunt de més de 1590 delecions de gens individuals i de soques wild type de Saccharomyces cerevisiae. Hem trobat que la disfunció mitocondrial és una causa primària del creixement lent dins d'una població isogènica i hem observat que un potencial alt de la membrana mitocondrial ens permet predir la reducció del creixement i la deficiència respiratòria. Hem mostrat que aquesta reducció es pot revertir en determinades circumstàncies i que la deficiència respiratòria temporal és un tret comú en moltes soques. També hem relacionat la dinàmica de la capacitat respiratòria d'una cèl·lula amb l’estat del seu ADN mitocondrial. Finalment, hem mostrat que el creixement en presència d'agents antifúngics augmenta el nombre de cèl·lules amb deficiència temporal respiratòria, suggerint que aquest fenotip pot ser una forma de protecció (subpoblació resistent als fàrmacs amb ADN mitocondrial intacte).
33
Gattamorta, Marco Aurélio. "Ecologia, prevalência e caracterização molecular de Chelonid fibropapilloma-associated herpesvirus (CFPHV) em Tartarugas-Verdes (Chelonia mydas) em áreas da costa brasileira." Universidade de São Paulo, 2016. http://www.teses.usp.br/teses/disponiveis/91/91131/tde-19042016-101411/.
Full textAbstract:
Os herpesvírus são normalmente adaptados a um único grupo de hospedeiros, e esta associação parasita-hospedeiro está ligada à sua seleção e coevolução. Estes agentes podem causar infecções latentes, onde normalmente o vírus não se replica. Durante o ciclo lítico, no entanto, outras células são infectadas e liberam partículas virais capazes de infectar outros indivíduos. O CFPHV (Chelonid fibropapilloma-associated herpesvirus) tem sido apontado como principal agente infeccioso ligado a fibropapilomatose em tartarugas-marinhas. A doença caracteriza-se por uma proliferação cutânea benigna mas que, dependendo da sua severidade, pode comprometer a sobrevivência do indivíduo afetado, sendo por isso apontada como importante ameaça a conservação de tartarugas-marinhas, particularmente de tartarugas verdes (Chelonia mydas), a principal espécie acometida pela doença. Alguns aspectos da biologia do CFPHV e sua relação com as tartarugas verdes foram estudados no presente trabalho. Primeiramente, a capacidade deste agente em se disseminar pelo ambiente e infectar outros indivíduos, e as possíveis vias envolvidas nesta dispersão. Em seguida, avaliou-se os possíveis tecidos em que o herpesvírus pode estabelecer a infecção latente. Por fim, determinou-se a prevalência de indivíduos de Chelonia mydas infectados pelo CFPHV em duas áreas de alimentação (Ubatuba-SP e Vitória-ES) e em uma áreas mista - de alimentação e reprodução (Fernando de Noronha-PE). No primeiro estudo, observou-se que a prevalência de CFPHV nas amostras de secreções de Chelonia mydas variou entre 0%, no Espírito Santo, a 25%, em São Paulo. Os haplótipos afetados foram CMA-3 e CMA-8, e a variante viral encontrada não havia sido detectada anteriormente no Brasil, mas possui elevada similaridade com vírus provenientes do Golfo da Guiné e de Porto Rico. Os resultados sugerem que estes vírus podem ser transmitidos por secreções e também circular entre diferentes regiões. No segundo estudo, detectou-se a presença de CFPHV no cérebro de 5 animais necropsiados e também na pele e em lesões fibropapilomatosas. Em um dos animais foi detectada a presença de uma única variante de CFPHV no cérebro, pele e tumores. Esta variante ainda não havia sido detectada no Brasil e apresentou 100% de identidade com a variante detectada nas secreções. Para avaliar a relação entre haplótipos e variantes virais, o terceiro estudo determinou a prevalência de CFPHV em pele e tumores de 136 indivíduos - 9,56% de indivíduos sadios apresentavam o agente em tecido epitelial e 45,58% dos animais foram positivos para CFPHV, quando considerados também animais com fibropapilomatose. Duas novas variantes de herpesvírus foram encontradas: Var. 7, em Ubatuba-SP e Vitória-ES e Var. 8, em Vitória-ES. Não houve associação entre uma variante viral e um haplótipo. Os resultados observados permitem apontar que o CFPHV pode estabelecer infecções latentes; o vírus pode \"migrar\" entre diferentes regiões, junto com seus hospedeiros; partículas virais podem ser liberadas por secreções; duas novas variantes foram identificadas. Altas taxas de substituição de nucleotídeos em CFPHV podem indicar o surgimento das variantes destas áreas, mas a alta similaridade entre as variantes detectadas e àquelas de Porto Rico e Golfo da Guiné sugerem também a entrada de novas variantes na costa brasileira.Herpesviruses are usually adapted to a single group of hosts, and this host-parasite association is linked to its selection and co-evolution. These agents can cause latent infections, where the virus usually does not replicate. During the lytic cycle, however, other cells are infected and release viral particles capable of infecting other individuals.The CFPHV (Chelonid fibropapilloma-associated herpesviru) has been indicated as the main infectious agent linked to fibropapillomatosis on sea turtles. The disease is characterized by a benign skin proliferation, but, depending on its severity, can compromise the survival of the affected individual, therefore considered an important threat to the conservation of sea turtles, especially green turtles (Chelonia mydas), the main species affected by the disease. Some aspects of the CFPHV biology and its relation to green turtles were studied in this work. Firstly, the ability of this agent to spread in the environment and infect other individuals, and the possible pathways involved in this dispersion. Then, potential tissues wherein the herpesvirus can establish latent infection were assessed. Finally, we determined the prevalence of Chelonia mydas individuals infected by CFPHV in two feeding areas (Ubatuba-SP and Vitória-ES) and in a mixed area of feeding and reproduction (Fernando de Noronha-PE). In the first study, it was observed that the prevalence of CFPHV in samples of Chelonia mydas secretions ranged from 0% in Espírito Santo, to 25% in São Paulo. Affected haplotypes were CM-A3 and CM-A8, and viral variant found had not been previously detected in Brazil, but it is significantly similar to viruses found in the Gulf of Guinea and Puerto Rico. The results suggest that these viruses can be transmitted by secretions and can also circulate among different regions. Considering the low maintenance of the agent within the environment, they are probably brought by individuals with the latent virus, being capable of releasing viral particles during the herpesvirus replication cycle. In the second study, the presence of CFPHV was detected inside the brain of 5 necropsied animals, besides the detection of the virus on the skin and fibropapillomatosis lesions. In one of the animals, it was possible to characterize the CFPHV and the presence of a single viral variant inside the brain, tumors and on the skin of the same animal was detected. This variant had not yet been detected in Brazil and showed 100% identity with the variant detected in secretions. These results indicate that the virus may establish a latent infection in nerve tissue. To evaluate the relationship between haplotypes and viral variants, the third study determined the prevalence of CFPHV on skin and tumors of 136 individuals - 9.56% of healthy individuals showed the agent in epithelial tissue and 45.58% of the animals were positive for CFPHV, when also considered animals with fibropapillomatosis. Two new variants of the herpesvirus were found, Var. 7 in Ubatuba-SP and Vitória-ES and Var. 8 only in Vitória-ES. C. mydas individuals of different haplotypes were infected, and there was no association between a viral variant and a haplotype. The observed results permitted to point that CFPHV can establish latent infections in Chelonia mydas; the virus can \"migrate\" among different regions, along with its hosts; viral particles can be released by secretion; viral variants previously detected were not found in these areas, but two new variants were detected. The high nucleotide substitution rates observed in CFPHV may indicate the emergence of these variants in these areas, but the high similarity among the detected variants and those identified in Puerto Rico and Gulf of Guinea also suggest the entry of new variants into the Brazilian coast.
34
Frabotta, Laurence John. "Insights into relationships among rodent lineages based on mitochondrial genome sequence data." Texas A&M University, 2005. http://hdl.handle.net/1969.1/3084.
Full textAbstract:
This dissertation has two major sections. In Chapter II, complete mitochondrial
(mt DNA) genome sequences were used to construct a hypothesis for affinities of most
major lineages of rodents that arose quickly in the Eocene and were well established by
the end of the Oligocene. Determining the relationships among extant members of such
old lineages can be difficult. Two traditional schemes on subordinal classification of
rodents have persisted for over a century, dividing rodents into either two or three
suborders, with relationships among families or superfamilies remaining problematic.
The mtDNA sequences for four new rodent taxa (Aplodontia, Cratogeomys, Erethizon,
and Hystrix), along with previously published Euarchontoglires taxa, were analyzed
under parsimony, likelihood, and Bayesian criteria. Likelihood and Bayesian analyses
of the protein-coding genes converged on a single topology that weakly supported rodent
monophyly and was significantly better than the parsimony trees. Analysis of the
tRNAs failed to recover a monophyletic Rodentia and did not reach convergence on a
stationary distribution after fifty million generations. Most relationships hypothesized in
the likelihood topology have support from previous data. Mt tRNAs have been largely ignored with respect to molecular evolution or
phylogenetic utility. In Chapter III, the mt tRNAs from 141 mammals were used to
refine secondary structure models and examine their molecular evolution. Both H- and
L-encoded tRNAs are AT-rich with different %G and GC-skew and a difference in skew
between H- and L-strand stems. Proportion of W-C pairs is higher in the H-strand and
GU/UG pairs are higher in the L-strand, suggesting increased mismatch compensation in
L-strand tRNAs. Among rodents, the number of variable stem base-pairs was nearly
75% of that observed across all mammals combined. Compensatory base changes were
present only at divergences of 4% or greater. Neither loop reduction nor an
accumulation of deleterious mutations, both suggestive of mutational meltdown
(Muller's ratchet), was observed. Mutations associated with human pathologies are
correlated only with the coding strand, with H-strand tRNAs being linked to
substantially more of these mutations.
35
Wang, Yean. "Molecular polymorphisms for phylogeny, pedigree and population structure studies." University of Sydney, 2007. http://hdl.handle.net/2123/1541.
Full textAbstract:
Doctor of PhilosophyA number of types of molecular polymorphisms can be used for studying genetic relationship and evolutionary history. Microsatellites are hypervariable and can be very useful tools to determine population structure, distinguish sibling species, as well as verifying parental relationships and pedigrees. However, while microsatellite polymorphisms are useful for solving relationships between populations within a species, relations among species or genera will probably be obscured due to a high degree of homoplasy —identity arising from evolutionary convergence not by descent. For long range evolutionary history, such as phylogeny from old world monkey to human, mtDNA markers may be better candidates. The aim of this thesis is to assess molecular polymorphisms of different types and their optimal use in different situations. Two widely separated taxa were used for testing –the green monkey Chlorocebus sabaeus, and the sibling dipteran flies Bactrocera tryoni and B. neohumeralis, known collectively as the Queensland fruit fly. In the present study a complete 16,550 bp mtDNA sequence of the green monkey Chlorocebus sabaeus is reported for the fist time and has been annotated (Chapter 2). Knowledge of the mtDNA genome contributes not only to identification of large scale single nucleotide polymorphisms (SNPs) (Chapter 4) or other mtDNA polymorphisms development, but also to primate phylogenetic and evolutionary study (Chapter 3). Microsatellites used for the green monkey paternity and pedigree studies were developed by cross-amplification using human primers (Chapter 5). For studies of population structure and species discrimination in Queensland fruit fly (Chapter 7), microsatellites were isolated from a genomic library of Bactrocera tryoni (Chapter 6) The total length of 16550 bp of complete mtDNA of the green monkey C. sabaeus, which has been sequenced and annotated here, adds a new node to the primate phylogenetic tree, and creates great opportunity for SNP marker development. The heteroplasmic region was cloned and five different sequences from a single individual were obtained; the implication of this are discussed. The phylogenetic tree reconstructed using the complete mtDNA sequence of C. sabaeus and other primates was used to solve controversial taxonomic status of C. sabaeus. Phylogenies of primate evolution using different genes from mtDNA are discussed. Primate evolutionary trees using different substitution types are compared and the phylogenetic trees constructed using transversions for the complete mtDNA were found close to preconceived expectations than those with transversions + transitions. The sequence of C. sabaeus 12SrRNA reported here agrees with the one published by ven der Kuyl et al. (1996), but additional SNPs were identified. SNPs for other regions of mtDNA were explored using dHPLC. Twenty two PCR segments for 96 individuals were tested by dHPLC. Fifty five SNPs were found and 10 haplogroups were established. Microsatellite markers were used to construct a genealogy for a colony of green monkeys (C. sabaeus) in the UCLA Vervet Monkey Research Colony. Sixteen microsatellites cross-amplified from human primers were used to conduct paternity analysis and pedigree construction. Seventy-eight out of 417 offspring were assigned paternity successfully. The low success rate is attributed to a certain proportion of mismatches between mothers and offspring; the fact that not all candidate fathers were sampled, the limitations of microsatellite polymorphisms; and weakness of the exclusion method for paternity assessment. Due to the low success rate, the pedigree is split into a few small ones. In a complicated pedigree composed of 75 animals and up to four generations with multiple links a power male mated with 8 females and contributed 10 offspring to the pedigree. Close inbreeding was avoided. Population structure within two species of Queensland fruit fly Bactrocera tryoni and Bactrocera neohumeralis (Tephritidae: Diptera) is examined using microsatellite polymorphisms. Queensland fruit flies B. tryoni and B. neohumeralis are sympatric sibling species that have similar morphological and ecological features. They even share polymorphism at the molecular level. Mating time difference is the main mechanism by which they maintain separate species. In the present study, 22 polymorphic and scorable microsatellites were isolated from B. tryoni and tested in the two species sampled from sympatric distribution areas. Pairwise genetic distance analysis showed explicit differentiation in allele frequencies between the two species, but very weak differences between conspecific populations. Gene flow is higher within B. tryoni than within B. neohumeralis, and gene exchange between the two species exists. An averaging linkage clustering tree constructed by UPGMA showed two major clusters distinguishing the two species, and it appears that population structure is highly correlated with geographic distance. The relationship between molecular markers, evolution, and selection are discussed using comparative studies within two large taxa: primate and insect. The degree of conservation and polymorphism in microsatellites varies between taxa, over evolutionary time.
36
James, Danielle Nicole. "Mitochondrial DNA Diversity and its Determinants in the Southwest Pacific." Diss., Temple University Libraries, 2008. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/5604.
Full textAbstract:
AnthropologyPh.D.
The purpose of this study is to examine mitochondrial DNA variation in the Southwest Pacific and determine what factors contribute to the degree and patterning of the observed variation. Population variation is known to be influenced by factors including demographic history, natural selection, climate, isolation, island area/complexity, and population age, as older populations are generally more diverse. The groups compared are from three regions in the Southwest Pacific; (a) northeast New Guinea, (b) Manus in northern Island Melanesia and (c) Easter Island in eastern Polynesia. MtDNA surveys have revealed highly significant differences in molecular variance across these populations. According to traditional biogeographical theory, the likely determinants of these differences are (a) length of time since initial settlement, (b) the comparative isolation of particular islands or regions since settlement, and (c) the size and complexity of settlement areas. Evidence from archaeology and linguistics provides the necessary framework for the study. Detailed archaeological surveys for several of the study regions provides evidence for settlement dates as well as evidence for isolation and/or frequent contact with other areas, usually in the form of trade and translocation of animals and artifacts. Linguistics, though not as informative as archaeology for settlement dates, provides detailed evidence for isolation and/or contact in the form of language isolates, language families, borrowing and linguistic divergence. The mtDNA haplogroups found in this study belong to several documented haplogroups, some of Melanesian origin, and some of Southeast Asian origin. The distribution of mtDNA variants and the pattern and degree of variation was examined using Analysis of Molecular Variance, standard diversity measures and partial Mantel matrix correlations. There were strong positive correlations between insular area, isolation and degree of variation. There were also measurable differences between inland and coastal populations on the larger islands where diversity in the isolated inland populations was greater than diversity in the coastal population. While there was some confounding of the variables, the results of our analysis indicate that insular area/complexity and isolation influence the pattern of variance more than length of settlement time.
Temple University--Theses
37
Wang, Yean. "Molecular polymorphisms for phylogeny, pedigree and population structure studies." Thesis, The University of Sydney, 2006. http://hdl.handle.net/2123/1541.
Full textAbstract:
A number of types of molecular polymorphisms can be used for studying genetic relationship and evolutionary history. Microsatellites are hypervariable and can be very useful tools to determine population structure, distinguish sibling species, as well as verifying parental relationships and pedigrees. However, while microsatellite polymorphisms are useful for solving relationships between populations within a species, relations among species or genera will probably be obscured due to a high degree of homoplasy —identity arising from evolutionary convergence not by descent. For long range evolutionary history, such as phylogeny from old world monkey to human, mtDNA markers may be better candidates. The aim of this thesis is to assess molecular polymorphisms of different types and their optimal use in different situations. Two widely separated taxa were used for testing –the green monkey Chlorocebus sabaeus, and the sibling dipteran flies Bactrocera tryoni and B. neohumeralis, known collectively as the Queensland fruit fly. In the present study a complete 16,550 bp mtDNA sequence of the green monkey Chlorocebus sabaeus is reported for the fist time and has been annotated (Chapter 2). Knowledge of the mtDNA genome contributes not only to identification of large scale single nucleotide polymorphisms (SNPs) (Chapter 4) or other mtDNA polymorphisms development, but also to primate phylogenetic and evolutionary study (Chapter 3). Microsatellites used for the green monkey paternity and pedigree studies were developed by cross-amplification using human primers (Chapter 5). For studies of population structure and species discrimination in Queensland fruit fly (Chapter 7), microsatellites were isolated from a genomic library of Bactrocera tryoni (Chapter 6) The total length of 16550 bp of complete mtDNA of the green monkey C. sabaeus, which has been sequenced and annotated here, adds a new node to the primate phylogenetic tree, and creates great opportunity for SNP marker development. The heteroplasmic region was cloned and five different sequences from a single individual were obtained; the implication of this are discussed. The phylogenetic tree reconstructed using the complete mtDNA sequence of C. sabaeus and other primates was used to solve controversial taxonomic status of C. sabaeus. Phylogenies of primate evolution using different genes from mtDNA are discussed. Primate evolutionary trees using different substitution types are compared and the phylogenetic trees constructed using transversions for the complete mtDNA were found close to preconceived expectations than those with transversions + transitions. The sequence of C. sabaeus 12SrRNA reported here agrees with the one published by ven der Kuyl et al. (1996), but additional SNPs were identified. SNPs for other regions of mtDNA were explored using dHPLC. Twenty two PCR segments for 96 individuals were tested by dHPLC. Fifty five SNPs were found and 10 haplogroups were established. Microsatellite markers were used to construct a genealogy for a colony of green monkeys (C. sabaeus) in the UCLA Vervet Monkey Research Colony. Sixteen microsatellites cross-amplified from human primers were used to conduct paternity analysis and pedigree construction. Seventy-eight out of 417 offspring were assigned paternity successfully. The low success rate is attributed to a certain proportion of mismatches between mothers and offspring; the fact that not all candidate fathers were sampled, the limitations of microsatellite polymorphisms; and weakness of the exclusion method for paternity assessment. Due to the low success rate, the pedigree is split into a few small ones. In a complicated pedigree composed of 75 animals and up to four generations with multiple links a power male mated with 8 females and contributed 10 offspring to the pedigree. Close inbreeding was avoided. Population structure within two species of Queensland fruit fly Bactrocera tryoni and Bactrocera neohumeralis (Tephritidae: Diptera) is examined using microsatellite polymorphisms. Queensland fruit flies B. tryoni and B. neohumeralis are sympatric sibling species that have similar morphological and ecological features. They even share polymorphism at the molecular level. Mating time difference is the main mechanism by which they maintain separate species. In the present study, 22 polymorphic and scorable microsatellites were isolated from B. tryoni and tested in the two species sampled from sympatric distribution areas. Pairwise genetic distance analysis showed explicit differentiation in allele frequencies between the two species, but very weak differences between conspecific populations. Gene flow is higher within B. tryoni than within B. neohumeralis, and gene exchange between the two species exists. An averaging linkage clustering tree constructed by UPGMA showed two major clusters distinguishing the two species, and it appears that population structure is highly correlated with geographic distance. The relationship between molecular markers, evolution, and selection are discussed using comparative studies within two large taxa: primate and insect. The degree of conservation and polymorphism in microsatellites varies between taxa, over evolutionary time.
38
Jiang, Xioben. "Gene Flow and Dispersal of the Caddisfly, Neothremma alicia, in the Rocky Mountains of Utah: A Multiscale Analysis." BYU ScholarsArchive, 2010. https://scholarsarchive.byu.edu/etd/2508.
Full textAbstract:
We determined genetic variance and gene flow across multiple scales (reaches, tributaries, and catchments) to examine the dispersal ability of the caddisfly, Neothremma alicia in streams along the Wasatch Range in the Rocky Mountains of Utah. Neothremma alicia is one of the most abundant caddisflies in this region. We generated DNA sequence data (mitochondrial COI) from 34 reaches, nested in 15 tributaries distributed across 3 adjacent catchments. We identified 47 haplotypes from a total of 486 individuals. The most abundant haplotype (H1) was found at all sites/reaches and comprised 44% of the total number of individuals sequenced. The remaining rare haplotypes (46) were recently derived from the dominant, H1 haplotype. All of the rare haplotypes were restricted to a single catchment with 81 % restricted to either a single tributary or to two adjacent tributaries. We found the largest FST values among tributaries and the smallest FST values between reaches within tributaries suggesting that dispersal and gene flow is largely confined to within tributaries. This result supports the observation that aerial adults commonly crawl and fly along the stream corridor, especially in deeply incised valleys of mountainous regions. Our analyses show that this population has experienced a bottleneck that may have reduced population genetic variance from many haplotypes to one single dominant haplotype, H1. The rare haplotypes may have diverged since the bottleneck from the H1 haplotype and thus, have not had time to disperse outside their catchment and in most cases outside their specific tributary. Our analyses indicated that the bottleneck took place between 1,000 and 10,000 years ago. Thus, it appears that most rare haplotypes have been unable to colonize outside of the tributary they originated in for around 1,000 years.
39
Dragana, Šnjegota. "Genetička struktura i filogeografski položaj vuka (Canis lupus L. 1758) Bosne i Hercegovine." Phd thesis, Univerzitet u Novom Sadu, Prirodno-matematički fakultet u Novom Sadu, 2019. https://www.cris.uns.ac.rs/record.jsf?recordId=110220&source=NDLTD&language=en.
Full textAbstract:
Ovom tezom je obuhvaćena analiza genetičke strukture i filogeografskog položaja vuka (Canis lupus L. 1758) na teritoriji Bosne i Hercegovine, na uzorku od ukupno 79 jedinki. Analize su sprovedene primjenom (i) 18 mikrosatelitskih lokusa nDNK pomoću kojih su detektovani: nivo genetičke varijabilnosti, populaciona struktura, prolazak populacije kroz genetičko usko grlo, te ukrštanje u srodstvu, i (ii) kontrolnog regiona (CR) regiona mtDNK pomoću kojih su sprovedene filogeografske analize. U radu je uočeno je grupisanje jedinki vuka Bosne i Hercegovine u dva genetička klastera što, s obzirom na slabu statističku podržanost, najvjerovatnije ukazuje na prisustvo strukture na većem nivou. Prethodno navedeno je detektovano analizama populacione strukture dijela dinarsko - balkanske populacije vuka,gdje je uočena distribucija vukova Bosne i Hercegovine i Srbije u odvojene genetičke klastere. Statistički značajni signali prolaska populacije vuka Bosne i Hercegovine kroz genetičko usko grlo u skorijoj prošlosti nisu detektovani. Sekvence kontrolnog regiona mtDNK vuka pokazale su se dovoljno informativnim za detekciju jedinstvenih haplotipova vuka Bosne i Hercegovine, za koje je uočena distribucija u dvije, prethodno u literaturi, detektovane haplogrupe bez jasnog alopatrijskog obrasca. Pored toga, analizama sekvenci dijela kontrolnog regiona mtDNK uzorka vuka Evrope, uočeno je da se demografska ekspanzija haplogrupe 2 desila mnogo ranije u prošlosti u odnosu na period ekspanzije haplogrupe 1, koji se poklapa sa periodom razdvajanja navedenih haplogrupa, prije oko 13000 godina, što ukazuje da je posljednji glacijalni maksimum imao uticaja u oblikovanju strukture genetičkih linija vuka u prošlosti. Rezultati dobijeni u ovom istraživanju su veoma informativni u cilju uspostavljanja pravilnog menadžmenta vrste i kreiranja plana zaštite vuka na nivou Bosne i Hercegovine, odnosno, na nivou dinarsko - balkanske populacije vuka iz koje se vrše rekolonizacije jedinki u susjedne populacije.In this thesis, the genetic structure and phylogeography of the wolf (Canis L. 1758) in the territory of Bosnia and Hercegovina were analysed, from a total sample of 79 individuals. Analyses were conducted by applying (i) 18 microsatellite loci of nuclear DNA, by which we estimated: the level of genetic variability, population structure, kinship, bottleneck and inbreeding, and (ii) control region of mtDNA by which we analysed phylogeography. Two genetic clusters were observed for the wolf population from Bosnia and Hercegovina, although with statistically low support, which may point to structuring at the higher level. Indeed, after analysing the population structure at the higher, Dinaric - Balkan level, the distribution of wolves from Bosnia and Hercegovina and Serbia was observed as falling into two distinct genetic clusters. Statistically significant signs of the recent bottleneck were not observed in the wolf population from Bosnia and Hercegovina. Analyses of control region mtDNA were conducted with the aim of detecting haplotypes in the Bosnia and Hercegovina population, as well as in the European samples. Distribution of haplotypes into two haplogroups, described in previous literature, was observed, without a clear alopatric phylogeny pattern. Furthermore, the analyses of the same molecular marker showed that demographic expansion of haplogroup 2 occurred significantly earlier when compared to the demographic explosion of haplogroup 1 . Results from this study are extremely important for the creation of a management plan for wolves from Bosnia and Hercegovina, and at the higher Dinaric - Balkan level.
40
Navarro, Sastre Aleix. "Bases bioquímiques i genètiques de les deplecions De mtDNA i de les alteracions de NFU1." Doctoral thesis, Universitat Autònoma de Barcelona, 2012. http://hdl.handle.net/10803/117464.
Full textAbstract:
Les deplecions de DNA mitocondrial (mtDNA) i les alteracions de NFU1 són dos grups
de malalties que afecten vies molt importants dins de la mitocòndria i que alteren el
metabolisme energètic.
Clínicament, els pacients afectes de depleció de mtDNA es caracteritzen per mostrar
un ampli ventall de símptomes, depenent del gen afectat. Els símptomes clínics són
molt greus i la majoria de vegades porten a la mort del pacient. Els pacients amb
mutacions en el gen NFU1, descrits per primera vegada en aquest treball, presenten
una clínica més homogènia, caracteritzada sobretot per presentar una encefalopatia
infantil fatal i/o hipertensió pulmonar i un fenotip bioquímic molt particular però ben
definit, caracteritzat principalment per presentar acidosi làctica, hiperglicinèmia i
deficiència de l’activitat piruvat deshidrogenasa.
L’objectiu principal d’aquesta tesis ha consistit en millorar i implementar metodologies
per a contribuir al diagnòstic, i millorar la comprensió de la fisiopatologia d’aquestes
deficiències.
Per a tal fita s’ha posat a punt una tècnica de PCR a temps real per estudiar el número
de còpies de mtDNA i poder relacionar-lo amb l’activitat citrat sintasa. A més, la
depleció s’ha pogut estudiar en biòpsies incloses en parafina, una important font de
material biològic arxivat mai utilitzat fins al moment.
D’aquesta forma s’han pogut estudiat 50 pacients amb sospita clínica de depleció de
mtDNA i cercar mutacions en els gens relacionats; DGUOK, MPV17, C10orf2, SUCLG1,
SUCLA2 i POLG. L’estudi molecular ens ha permès identificar 4 mutacions no descrites
prèviament, c.70+5G>A en el gen MPV17, c.1048G>A i c.1049G>T en el gen SUCLA2, i
c.531+4A>T en el gen SUCLG1. A més s’han identificat 7 mutacions prèviament
descrites en un total de 10 pacients (8 famílies). Quan va ser possible, es va quantificar
el ràtio mtDNA/nDNA i la activitat citrat sintasa en la mateixa mostra de teixit, proveint
noves dades per l’estudi de les MDS. La depleció relacionada amb la citrat sintasa,
(mtDNA/nDNA)/CS, ha donat resposta a certes discrepàncies observades entre els
resultats de depleció i els resultats de la cadena respiratòria mitocondrial en alguns
pacients.
Per altra banda, utilitzant el mapatge per homozigositat, es va identificar una mutació
de canvi de sentit en homozigositat en el gen NFU1 (c.622G>T, p.Gly208Cys), que
codifica per una proteïna altament conservada en totes les espècies i que està implicada en la biogènesis dels clústers de sulfur de ferro (Fe-S). Aquesta ha esta la
primera vegada que s’ha associat mutacions en aquest gen a patologia humana.
El fenotip bioquímic dels pacients suggeria una activitat deficient de l’enzima lipoic
àcid sintasa (LAS), una proteïna que necessita clústers de Fe-S com a cofactor. Es va
poder constatar una disminució del grau de lipoilació de les proteïnes dependents
d’àcid lipoic, el que suggeria una manca d’ activitat LAS. Utilitzant models cel·lulars
hem demostrat que la proteïna NFU1 és necessària com a donadora de sulfur per la
biosíntesi d’àcid lipoic i també ens ha permès conèixer la funció específica en la
biosíntesi dels clústers de Fe-S i en la maduració de proteïnes Fe-S, concretament LAS i
la succinat deshidrogenasa (SDH).
La descripció clínica, bioquímica y genètica d’aquesta malaltia és molt important pel
diagnòstic de nous pacients i obre les portes a la cerca d’altres gens implicats en la
biosíntesi de l’àcid lipoic, així com al disseny futur de noves estratègies terapèutiques.Mitochondrial DNA (mtDNA) depletion syndromes (MDS) and NFU1 defects are two groups of diseases affecting crucial mitochondrial pathways of energetic metabolism. Clinically, patients affected of mtDNA depletion displayed a wide range of symptoms, depending on the altered gene. The clinical symptoms are severe and in most cases lead to death of the patient. Patients with NFU1 mutations, described for the first time in this paper, present a more homogeneous clinical phenotype, characterized by fatal infantile encephalopathy and / or pulmonary hypertension. NFU1 patients also showed a peculiar, but well defined, biochemical phenotype, presenting with lactic acidosis, hyperglycinemia and deficiency of pyruvate dehydrogenase activity. The main objective of the present thesis is to improve and to implement new methods for the diagnosis and understanding of the pathophysiology of these deficiencies. To this goal, a real-time PCR technique has been developed to study the mtDNA copy number and its relationship to citrate synthase activity in MDS patients. In addition, mtDNA depletion has been studied in formalin-fixed paraffin-embedded tissues, an important source of biological material never used for this purpose. We studied 50 paediatric individuals suspected to have mtDNA depletion and the appropriate MDS genes have been screened according to their clinical and biochemical phenotypes. Mutational study of DGUOK, MPV17, SUCLA2, SUCLG1 and POLG allowed us to identify 4 novel mutations; c.70+5G>A in MPV17, c.1048G>A and c.1049G>T in SUCLA2 and c.531+4A>T in SUCLG1, and 7 already known mutations in 10 patients (8 families). When possible, we quantified mtDNA/nDNA and CS activity in the same tissue sample, providing an additional tool for the study of MDS. The ratio (mtDNA/nDNA)/CS has shed some light in the discrepant results between the mtDNA copy number and the enzymatic respiratory chain activities of some cases. Using homozigosity mapping, we identified a homozygous missense mutation in NFU1 gene (c.622G> T, p.Gly208Cys), which encodes a conserved protein suggested to participate in Fe-S cluster biogenesis. This is the first time that a clinical phenotype has been associated with mutations to NFU1. The biochemical phenotype suggested an impaired activity of the Fe-S enzyme lipoic acid synthase (LAS), a protein that requires Fe-S cluster as a cofactor. Direct measurement of protein-bound lipoic acid in individual tissues indeed showed marked decreases, which suggested a lack of LAS activity. Human cell models studies showed that NFU1 protein is required as sulfur donor for the biosynthesis of lipoic acid and it performs a specific function in mitochondrial Fe-S proteins maturation, particularly succinate dehydrogenase and LAS (SDH). Clinical, biochemical and genetic description of NFU1 disease is very important for the diagnosis of new patients and will allow us to find other genes involved in the biosynthesis of lipoic acid, and provided the basis for the future design of new therapeutic strategies.
41
Lee, Joon-Hee. "Factors affecting development of ovine nuclear transfer produced embryos : oocyte kinase activities and somatic mtDNA." Thesis, University of Nottingham, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.416287.
Full text
42
Silva, Marina Soares da. "Phylogeography of mtDNA haplogroup L2." Master's thesis, 2014. https://repositorio-aberto.up.pt/handle/10216/80081.
Full text
43
Silva, Marina Soares da. "Phylogeography of mtDNA haplogroup L2." Dissertação, 2014. https://repositorio-aberto.up.pt/handle/10216/80081.
Full text
44
Cheng, Ning, and 成寧. "Correlation between mtDNA complexity and mtDNA replication mode in developing cotyledon mitochondria during mung bean seed germination." Thesis, 2016. http://ndltd.ncl.edu.tw/handle/6c4p46.
Full textAbstract:
博士國立臺灣大學
植物科學研究所
105
The highly dynamic changes in mitochondrial DNA (mtDNA) conformation, structure and complexity correspond to the activity of mtDNA recombination dependent replication (RDR). This study aimed to elucidate the interrelationship between mtDNA replication and genesis of the multi-genomic, highly complex structure of plant mtDNA in mung bean cotyledons. The results suggest that short DNA fragments convert to longer linear and rosette structures early in the development of cotyledon mitochondria. Consequently, a large number of rosette structures appear, with simultaneous elevation of mtDNA synthesis. A fork-like structure near the rosette core appears during mtDNA replication. With in vivo prolonged-cold incubation or in vitro freeze-thaw treatment, the rosette structure is converted to a much longer linear DNA structure and the rosette core disappears. This large linear DNA with displacement loops, Holliday junctions and other structures attached may increase in size more than 30 times as compared to the original rosette entity. The rosette core may consist of condensed mtDNA and play an initial and central role in RDR. The satellite cores in the rosette structure may represent the re-initiation sites of mtDNA RDR in the same parental molecule. Consequently, highly complex and giant mitochondrial DNA molecules, representing RDR intermediates, are formed in vivo. The core-and-rosette structures represent replicating DNA and almost certainly use RDR.
45
Abreu, Diogo Manuel de Castro. "Impact of mtDNA mutations on chromatin remodeling." Master's thesis, 2020. https://hdl.handle.net/10216/130940.
Full text
46
Abreu, Diogo Manuel de Castro. "Impact of mtDNA mutations on chromatin remodeling." Dissertação, 2020. https://hdl.handle.net/10216/130940.
Full text
47
Romeo, Giuseppe, G. Rose, Serena Dato, and Benedictis Giovanna De. "MtDNA heteroplasmy in longevity: a puzzling story." Thesis, 2013. http://hdl.handle.net/10955/337.
Full text
48
Li, Shiue Li, and 李雪莉. "Potential Effect of Nuclear mtDNA Sequence on Detecting mtDNA Mutations by Traditional DHPLC and Surveyor Nuclease with DHPLC Detection." Thesis, 2012. http://ndltd.ncl.edu.tw/handle/34731692464314006549.
Full textAbstract:
碩士長庚大學
醫學生物技術暨檢驗學系
100
The co-amplification of ancient mtDNA-derived nuclear mtDNA sequences (Numts) in nuclear DNA (nDNA) with modern human mtDNA during PCR may potentially cause misinterpretation of mutation or heteroplasmy/homoplasmy status on mtDNA. In this study, we investigated this effect when conducting traditional denaturing HPLC (DHPLC) and Surveyor Nuclease method followed by fluorescence detection on DHPLC (SN-DHPLC), which is a more efficient method. First, we compared the sensitivity of these two methods by mixing two cloned plasmid DNA for a fragment of human mtDNA with single nucleotide polymorphism. SN-DHPLC exhibited slightly higher sensitivity than DHPLC. To further prove Numts effect, we isolated mtDNA without nDNA contamination and demonstrated that heteroduplex detected by DHPLC for total DNA was due to Numts when using our published primers known to amplify DNA of 143B-ρ° cells lacking mtDNA. Next, we conducted bioinformatic search to predict whether the 48 primer pairs of Meierhofer et al. and 17 primer pairs of Bannwarth et al. used for screening human mtDNA mutations by DHPLC or SN could amplify Numts in same chromosomes. Among them, 21 primer pairs selected were confirmed to amplify Numts by using DNA of 143B-ρ° cells. These amplicons were then examined for Numts effect during DHPLC or SN-DHPLC analysis by using pure mtDNA and total DNA of 143B cells and a cybrid line with different mtDNA background. Results showed that there was no interference from Numts for DHPLC analysis, whereas multiple fragments before SN digestion or heteroduplex after digestion found in total DNA but not in mtDNA in two amplicons were due to Numts effect during SN-DHPLC analysis. This is the first study to prove that mtDNA mutation detection could be interfered by Numts when using DHPLC and SN-DHPLC, or PCR-based methods, and provide a strategy to screen such effect by using pure mtDNA.
49
Tlačbabová, Klára. "Diverzita sekvencí mtDNA a genetická struktura východoafrického sahelu." Master's thesis, 2017. http://www.nusl.cz/ntk/nusl-367778.
Full textAbstract:
Eastern part of the African Sahel, connecting sub-Saharan Africa with North and East Africa, play an important role as a bidirectional corridor for vertically and horizontally migrations of populations. It is the strategic region to study human genetic diversity due to the presence of ethnically, linguistically, culturally and geographically diversity. This work is focused on the analysis of HVS-I and HVS-II segments of mtDNA. The work provides new information about genetic structure and migration activity of this region by analysis twelve populations belonging to three African linguistic families and different subsistent strategies. Analysis of mtDNA revealed the higher diversity of the populations of east Sudan and Horn of Africa, which is connected with the spreading of populations along the Nile River. It seems, that in this region linguistic factors have bigger impact on genetic diversity then the geografic ones. The opposite situation is observed in populations of Chad, where populations with similiar geografic location and different linguistic affilation revealed low genetic differentiation. The intra-population analysis shows the significant influence of genetic drift on the pastoralists living on the Red Sea Coast - Beja and Rashaida. In Beja is probably due to decrease of size of...
50
Lee, Jine-Wen, and 李靜雯. "Establishment of mtDNA-depletion cells and further utilization." Thesis, 2004. http://ndltd.ncl.edu.tw/handle/13112938194790800853.
Full textAbstract:
碩士臺北醫學大學
醫學研究所
92
The aim of this study was to construct mitochondrial DNA-depletion cell lines by RNA interference or adding ethidium bromide (100 ng/mL). The mtDNA-depletion cell lines can be further used to fuse with primary cultured cells from the patients. We expect to use the cybrid cells for the research to mimic mtDNA depletion and mutation. The study of RNAi to inhibit mtDNA was divided into two parts: stable and transient inhibition. The appearance of the treated cell lines showed longer and narrower than the control group (143B TK- wild-type) and the growth was also slower. The cell lines of the experiment group went on apoptosis through flow cytometry analysis. mtTFA gene expression and mtDNA copy numbers were determined by RT-PCR and real-time quantitative PCR. mtDNA copy number decreased about 60% at the 6th days and 80~90% at the 16th days after adding ethidium bromide. In vitro study, transient transfection with RNAi inhibited 60~70% of mtTFA expression at 36th hrs. The same outcome was also determined in mtDNA copy numbers showed 70~80% inhibition effect. In the stable transfection, the effect was obvious at two weeks after selecting the stable clones. The mtTFA gene expression decreased about 50% at selected time and 80-90% at 5~6 weeks later, and the mtDNA copy number decreased 100-1000 fold in the selected clones compared with wide-type. In the protein assay, western blot was used to quantify the proteins encoded by mtDNA for measuring the expression leves of mitochondrial respiratory chain complex during the process of forming mtDNA-depletion cell lines. In conclusion, we get several mtDNA-depletion cell lines by adding ethidium bromide or blocking mtTFA gene expression with RNAi.