subject:( mtDNA mutations )

Vanderbilt University

1. Song, Zhuo. Stochastic modeling of mitochondrial polymerase gamma replication and novel algorithms to enrich rare disease alleles and detect tumor somatic mutations in deep sequencing data.

Degree: PhD, Human Genetics, 2012, Vanderbilt University

URL: http://hdl.handle.net/1803/10702

► The activity of polymerase ã (pol ã) is complicated. To understand how its kinetics values affect the final function of the pol ã, I created… (more)

Subjects/Keywords: tumor somatic mutations; targeted sequencing; NRTI; polymerase gamma; mtDNA replication

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APA (6^th Edition):

Song, Z. (2012). Stochastic modeling of mitochondrial polymerase gamma replication and novel algorithms to enrich rare disease alleles and detect tumor somatic mutations in deep sequencing data. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/10702

Chicago Manual of Style (16^th Edition):

Song, Zhuo. “Stochastic modeling of mitochondrial polymerase gamma replication and novel algorithms to enrich rare disease alleles and detect tumor somatic mutations in deep sequencing data.” 2012. Doctoral Dissertation, Vanderbilt University. Accessed January 22, 2021. http://hdl.handle.net/1803/10702.

MLA Handbook (7^th Edition):

Song, Zhuo. “Stochastic modeling of mitochondrial polymerase gamma replication and novel algorithms to enrich rare disease alleles and detect tumor somatic mutations in deep sequencing data.” 2012. Web. 22 Jan 2021.

Vancouver:

Song Z. Stochastic modeling of mitochondrial polymerase gamma replication and novel algorithms to enrich rare disease alleles and detect tumor somatic mutations in deep sequencing data. [Internet] [Doctoral dissertation]. Vanderbilt University; 2012. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/1803/10702.

Council of Science Editors:

Song Z. Stochastic modeling of mitochondrial polymerase gamma replication and novel algorithms to enrich rare disease alleles and detect tumor somatic mutations in deep sequencing data. [Doctoral Dissertation]. Vanderbilt University; 2012. Available from: http://hdl.handle.net/1803/10702

2. Gutierrez Cortes, Nicolas. Expression métabolique des polymorphismes mitochondriaux : mutations pathogènes et haplogroupes : Metabolic expression of mitochondrial polymorphisms : pathological mutations and haplogroups.

Degree: Docteur es, Sciences, technologie, santé. Biologie cellulaire et physiopathologie, 2011, Université de Bordeaux Segalen

URL: http://www.theses.fr/2011BOR21877

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Les mitochondries, organelles intracellulaires des eucaryotes, fournissent par les oxydations phosphorylantes l'essentiel de l'énergie nécessaire aux différents travaux cellulaires sous la forme d'ATP grâce à… (more)

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Les mitochondries, organelles intracellulaires des eucaryotes, fournissent par les oxydations phosphorylantes l'essentiel de l'énergie nécessaire aux différents travaux cellulaires sous la forme d'ATP grâce à un couplage entre la chaîne respiratoire et l’ATPsynthase. Ces réactions du métabolisme énergétique sont assurées par des complexes enzymatiques constitués de sous-unités codées à la fois par l'ADN nucléaire et par l'ADN mitochondrial. Il a été montré que des défauts dans l'activité de ces complexes pouvaient être responsables de l’apparition de pathologies regroupées sous le nom de cytopathies d’origine mitochondriale. Un des problèmes fondamentaux qui se pose lors de l’étude des mécanismes conduisant aux pathologies mitochondriales est de comprendre l’influence de l’ADN mitochondrial sur le métabolisme de la mitochondrie. En effet, la mitochondrie possède son propre ADN, et les mutations de cet ADN sont classées selon leur impact sur le métabolisme mitochondrial : des mutations pathogènes, qui ont des répercussions négatives sur ce métabolisme, et des polymorphismes, qui sont considérés comme étant neutres.Pour étudier l’influence de l’ADNmt sur le métabolisme énergétique, j’ai utilisé deux modèles d’étude : des cybrids portant des mutations de l’ADNmt retrouvées chez des patients atteints de surdité non-syndromique, et des cybrids portant des polymorphismes caractéristiques de l’haplogroupe J.Les résultats obtenus nous indiquent clairement que la différence entre des mutations pathogènes et des polymorphismes n’est pas aussi importante que ce qui était jusqu’à alors supposé. En effet, elle dépend d’un ensemble de facteurs tels que (i) le fonds génétique nucléaire et mitochondrial, (ii) de facteurs environnementaux. Car sous l’influence de ces différents facteurs une mutation considérée comme pathogène peut devenir neutre, et un polymorphisme considéré comme neutre peut devenir pathogène.

Mitochondria, intracellular organelles of eukaryotic organisms, provide most of the necessary energy for cellular activity through oxidative phosphorylation, synthesizing ATP (energy source for the cell) by a coupling between the respiratory chain and the ATPsynthase. These energy metabolism reactions are carried out by enzymatic complexes constituted by sub-units coded by both nuclear and mitochondrial DNA. It has been shown that activity defects in these complexes could be responsible for a group of pathologies under the name of mitochondrial cytopathies.One of the fundamental issues of the study of the mechanisms that lead to mitochondrial cytopathies is the understanding of the influence that mitochondrial DNA has over mitochondrial metabolism. Indeed, mitochondria have their own DNA, and mutations in this DNA are classified according to their impact on mitochondrial metabolism: pathological mutations, which have negative consequences on mitochondrial metabolism, and polymorphisms, which are considered to be neutral.In order to study the influence of mtDNA on energy metabolism, I used two different models: cybrid cells…

Advisors/Committee Members: Rocher, Christophe (thesis director).

Subjects/Keywords: Mitochondrie; ADNmt; OXPHOS; Cytopathies d’origine mitochondriale; Mutations de l’ADNmt; Polymorphismes; Haplogroupes; Surdité; Mitochondria; MtDNA; OXPHOS; Mitochondrial cytopathies; MtDNA mutations; Polymorphisms; Polymorphisms, haplogroups; Deafness

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Gutierrez Cortes, N. (2011). Expression métabolique des polymorphismes mitochondriaux : mutations pathogènes et haplogroupes : Metabolic expression of mitochondrial polymorphisms : pathological mutations and haplogroups. (Doctoral Dissertation). Université de Bordeaux Segalen. Retrieved from http://www.theses.fr/2011BOR21877

Chicago Manual of Style (16^th Edition):

Gutierrez Cortes, Nicolas. “Expression métabolique des polymorphismes mitochondriaux : mutations pathogènes et haplogroupes : Metabolic expression of mitochondrial polymorphisms : pathological mutations and haplogroups.” 2011. Doctoral Dissertation, Université de Bordeaux Segalen. Accessed January 22, 2021. http://www.theses.fr/2011BOR21877.

MLA Handbook (7^th Edition):

Gutierrez Cortes, Nicolas. “Expression métabolique des polymorphismes mitochondriaux : mutations pathogènes et haplogroupes : Metabolic expression of mitochondrial polymorphisms : pathological mutations and haplogroups.” 2011. Web. 22 Jan 2021.

Vancouver:

Gutierrez Cortes N. Expression métabolique des polymorphismes mitochondriaux : mutations pathogènes et haplogroupes : Metabolic expression of mitochondrial polymorphisms : pathological mutations and haplogroups. [Internet] [Doctoral dissertation]. Université de Bordeaux Segalen; 2011. [cited 2021 Jan 22]. Available from: http://www.theses.fr/2011BOR21877.

Council of Science Editors:

Gutierrez Cortes N. Expression métabolique des polymorphismes mitochondriaux : mutations pathogènes et haplogroupes : Metabolic expression of mitochondrial polymorphisms : pathological mutations and haplogroups. [Doctoral Dissertation]. Université de Bordeaux Segalen; 2011. Available from: http://www.theses.fr/2011BOR21877

3. SURESH KUMAR POOVATHINGAL. SYSTEMS BIOLOGY OF AGING: MODELING & ANALYSIS OF MITOCHONDRIAL GENOME INTEGRITY.

Degree: 2011, National University of Singapore

URL: http://scholarbank.nus.edu.sg/handle/10635/29959

Subjects/Keywords: Computational Biology; Stochastic Drift; Aging; Mitochondrial DNA(mtDNA); mtDNA Mutations.

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APA (6^th Edition):

POOVATHINGAL, S. K. (2011). SYSTEMS BIOLOGY OF AGING: MODELING & ANALYSIS OF MITOCHONDRIAL GENOME INTEGRITY. (Thesis). National University of Singapore. Retrieved from http://scholarbank.nus.edu.sg/handle/10635/29959

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

POOVATHINGAL, SURESH KUMAR. “SYSTEMS BIOLOGY OF AGING: MODELING & ANALYSIS OF MITOCHONDRIAL GENOME INTEGRITY.” 2011. Thesis, National University of Singapore. Accessed January 22, 2021. http://scholarbank.nus.edu.sg/handle/10635/29959.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

POOVATHINGAL, SURESH KUMAR. “SYSTEMS BIOLOGY OF AGING: MODELING & ANALYSIS OF MITOCHONDRIAL GENOME INTEGRITY.” 2011. Web. 22 Jan 2021.

Vancouver:

POOVATHINGAL SK. SYSTEMS BIOLOGY OF AGING: MODELING & ANALYSIS OF MITOCHONDRIAL GENOME INTEGRITY. [Internet] [Thesis]. National University of Singapore; 2011. [cited 2021 Jan 22]. Available from: http://scholarbank.nus.edu.sg/handle/10635/29959.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

POOVATHINGAL SK. SYSTEMS BIOLOGY OF AGING: MODELING & ANALYSIS OF MITOCHONDRIAL GENOME INTEGRITY. [Thesis]. National University of Singapore; 2011. Available from: http://scholarbank.nus.edu.sg/handle/10635/29959

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Freie Universität Berlin

4. Lüth, Maria. Analysis of mitochondrial DNA mutations in patients with neuroectodermal tumors.

Degree: 2011, Freie Universität Berlin

URL: https://refubium.fu-berlin.de/handle/fub188/13747

► To detect somatic mitochondrial DNA mutations in neuroectodermal tumors, mutation analysis in patients with medulloblastoma, pilocytic astrocytoma and neurofibromatosis type 1-associated tumors was performed. MtDNA… (more)

▼ To detect somatic mitochondrial DNA mutations in neuroectodermal tumors, mutation analysis in patients with medulloblastoma, pilocytic astrocytoma and neurofibromatosis type 1-associated tumors was performed. MtDNA alterations in the entire mitochondrial genome were analyzed by temporal temperature gradient gelelectrophoresis followed by DNA sequencing. We have analyzed the entire mitochondrial genome in 15 cases of medulloblastoma and the corresponding cerebrospinal fluid (CSF) samples in 10 of the 15 cases. Six of the fifteen cases (40%) showed at least one mtDNA mutation in the tumors. A total of 18 somatic mtDNA mutations were detected with one of the tumors having 11 mutations of which 9 were novel. Three of the six cases with mtDNA mutation also showed mutation in the cell-free CSF collected at various times during therapy. Somatic mtDNA mutations in tumors were found in 7 of 19 individuals with cutaneous neurofibromas and in 9 of 18 patients with plexiform neurofibromas. A total of 34 somatic mtDNA mutations were found. All mutations were located in the displacement loop region of the mitochondrial genome. Several plexiform neurofibromas from individual patients had multiple homoplasmic mtDNA mutations. In cutaneous neurofibromas, the same mtDNA mutations were always present in tumors from different locations of the same individual. An increase in the proportion of the mutant mtDNA was always found in the neurofibromas when compared with nontumor tissues. The somatic mtDNA mutations were present in the Schwann cells of the analyzed multiple cutaneous neurofibromas of the same individual. The observed dominance of a single mtDNA mutation in multiple cutaneous neurofibromas of individual patients indicates a common tumor cell ancestry and suggests a replicative advantage rather than random segregation for cells carrying these mutated mitochondria. Advisors/Committee Members: [email protected] (contact), w (gender), PD Dr. med. P. Hernáiz-Driever (firstReferee), Prof. Dr. med. M. Hasselblatt (furtherReferee), Prof. Dr. med. F. Aksu (furtherReferee).

Subjects/Keywords: mtDNA; somatic mutations; neurofibromatosis type 1-associated tumors; pilocytic astrocytoma; medulloblastoma; 600 Technik, Medizin, angewandte Wissenschaften::610 Medizin und Gesundheit

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Lüth, M. (2011). Analysis of mitochondrial DNA mutations in patients with neuroectodermal tumors. (Thesis). Freie Universität Berlin. Retrieved from https://refubium.fu-berlin.de/handle/fub188/13747

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Lüth, Maria. “Analysis of mitochondrial DNA mutations in patients with neuroectodermal tumors.” 2011. Thesis, Freie Universität Berlin. Accessed January 22, 2021. https://refubium.fu-berlin.de/handle/fub188/13747.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Lüth, Maria. “Analysis of mitochondrial DNA mutations in patients with neuroectodermal tumors.” 2011. Web. 22 Jan 2021.

Vancouver:

Lüth M. Analysis of mitochondrial DNA mutations in patients with neuroectodermal tumors. [Internet] [Thesis]. Freie Universität Berlin; 2011. [cited 2021 Jan 22]. Available from: https://refubium.fu-berlin.de/handle/fub188/13747.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Lüth M. Analysis of mitochondrial DNA mutations in patients with neuroectodermal tumors. [Thesis]. Freie Universität Berlin; 2011. Available from: https://refubium.fu-berlin.de/handle/fub188/13747

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Tampere University

5. Rovio, Anja. DNA Polymerase Gamma Mutations in Male Infertility and Ageing .

Degree: Lääketieteellisen teknologian instituutti - Institute of Medical Technology, 2006, Tampere University

URL: https://trepo.tuni.fi/handle/10024/67615

► Mitokondrio on solun energiaa tuottava organelli, jolla on oma genomi, mitokondriaalinen DNA (mtDNA). Mitokondrion DNA:ta monistaa yksi ainoa polymeraasi, polymeraasi gamma (POLG). Kirjallisuudessa on kuvattu… (more)

▼ Mitokondrio on solun energiaa tuottava organelli, jolla on oma genomi, mitokondriaalinen DNA (mtDNA). Mitokondrion DNA:ta monistaa yksi ainoa polymeraasi, polymeraasi gamma (POLG). Kirjallisuudessa on kuvattu jo noin 50 POLG mutaatiota eli geenivirhettä, ja jo pitkään niiden on uskottu olevan yhteydessä paitsi moniin hermosto- ja lihasrappeuma sairauksiin, myös vanhenemiseen liittyvien oireiden syntyyn. Tämän tutkimuksen ensimmäisessä osassa analysoitiin POLG:ssä olevan CAG-toistoalueen pituusvaihteluja eri väestöryhmissä, yleisimmissä mitokondriaalisissa sairauksissa ja lapsettomilla miehillä. Kaikissa tutkituissa väestöryhmissä toistoalueen pituus oli hyvin vakaa, yleisimmän alleelin sisältäessä 10 CAG-jaksoa. Myös kaikilla kädellisten ryhmillä on oma lajityypillinen, yleinen CAG-pituutensa, joka pitenee tultaessa pienistä apinoista simpanssin kautta gorillaan ja ihmiseen. Toistojakson pituus ei tavallisimmissa mitokondriaalisissa sairauksissa poikennut kontrolliväestöstä. Sen sijaan havaittiin, että noin 10%:lla lapsettomista miehistä puuttuu tämä ns. yleinen alleeli, kun taas tunnetusti fertiileillä miehillä se ei puuttunut yhdeltäkään. Näillä miehillä oli alentunut siittiöiden määrä, liikkuvuus oli huonontunut ja myös rakenteessa oli normaalia enemmän virheitä. Lapsettomilla miehillä havaittiin myös useita muita POLG mutaatioita, sekä kohonnut mtDNA:n mutaatioiden määrä. Muiden ryhmien tekemissä tutkimuksissa on havaittu, että näitä pariskuntia voidaan auttaa saamaan lapsi ICSI-tekniikalla, jossa siittiö viedään neulalla munasolun sisään. POLG toistoalueen pituutta kannattaisikin käyttää yhtenä kriteerinä hoitokeinoja mietittäessä niissä tapauksissa, joissa mitään muuta syytä lapsettomuuteen ei tiedetä. Tutkimuksen toinen osa keskittyi mtDNA:n mutaatioiden osuuteen vanhenemisessa. Vanhoilla ihmisillä on havaittu olevan enemmän mtDNA mutaatioita kuin nuorilla. Tämän uskotaan johtavan lisääntyneeseen happiradikaalien muodostumiseen solussa ja edelleen lisäävän mtDNA:n mutaatioiden määrää. Teoriaa testattiin Tukholmassa tehdyllä koemallilla, jossa POLG-entsyymissä oleva mtDNA:n korjausaktiivisuus turmeltiin mutaatiolla, ja tämä vioitettu "mutaattori" geeni vietiin hiireen. Mutaattorihiiret syntyivät normaaleina, mutta alkoivat jo puolen vuoden iässä vanheta näkyvästi. Niillä oli mm. osteoporoosia, kyttyräselkä, hiustenlähtöä, anemiaa, selkeää painonpudotusta, sydänsairauden ja hermoston rappeutumisen merkkejä. Sekä koirailla että naarailla oli enneaikaista hedelmättömyyttä. Tampereella tehdyissä geneettisissä analyyseissä todettiin, että hiirten kaikkiin kudoksiin kertyi moninkertaisesti enemmän mtDNA:n mutaatioita kuin samanikäisiin verrokkihiiriin. Tämä ilmeni soluhengityksen vajavaisuutena ja vähentyneenä energiantuottona kudoksissa. Hiirillä ei kuitenkaan ilmennyt selkeästi lisääntynyttä happiradikaalien tuotantoa. Hiirten keskimääräinen elinikä oli lyhentynyt, noin 48 viikkoa, kun se vastaavilla verrokkeilla oli noin 2,5 vuotta. Mutaattorihiiri mallina osoittaa, että suuri mtDNA:n mutaatioiden määrä johtaa…

Subjects/Keywords: polymeraasi gamma ; miehen lapsettomuus ; vanheneminen ; POLG ; male infertility ; ageing ; mtDNA mutations

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Rovio, A. (2006). DNA Polymerase Gamma Mutations in Male Infertility and Ageing . (Doctoral Dissertation). Tampere University. Retrieved from https://trepo.tuni.fi/handle/10024/67615

Chicago Manual of Style (16^th Edition):

Rovio, Anja. “DNA Polymerase Gamma Mutations in Male Infertility and Ageing .” 2006. Doctoral Dissertation, Tampere University. Accessed January 22, 2021. https://trepo.tuni.fi/handle/10024/67615.

MLA Handbook (7^th Edition):

Rovio, Anja. “DNA Polymerase Gamma Mutations in Male Infertility and Ageing .” 2006. Web. 22 Jan 2021.

Vancouver:

Rovio A. DNA Polymerase Gamma Mutations in Male Infertility and Ageing . [Internet] [Doctoral dissertation]. Tampere University; 2006. [cited 2021 Jan 22]. Available from: https://trepo.tuni.fi/handle/10024/67615.

Council of Science Editors:

Rovio A. DNA Polymerase Gamma Mutations in Male Infertility and Ageing . [Doctoral Dissertation]. Tampere University; 2006. Available from: https://trepo.tuni.fi/handle/10024/67615

University of Edinburgh

6. Simmonte Owens, Matthew John. Polymer microarrays for biomedical applications.

Degree: PhD, 2017, University of Edinburgh

URL: http://hdl.handle.net/1842/28953

► 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… (more)

▼ 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…

Subjects/Keywords: polymers; polymer microarrays; mtDNA; mtDNA binding

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Simmonte Owens, M. J. (2017). Polymer microarrays for biomedical applications. (Doctoral Dissertation). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/28953

Chicago Manual of Style (16^th Edition):

Simmonte Owens, Matthew John. “Polymer microarrays for biomedical applications.” 2017. Doctoral Dissertation, University of Edinburgh. Accessed January 22, 2021. http://hdl.handle.net/1842/28953.

MLA Handbook (7^th Edition):

Simmonte Owens, Matthew John. “Polymer microarrays for biomedical applications.” 2017. Web. 22 Jan 2021.

Vancouver:

Simmonte Owens MJ. Polymer microarrays for biomedical applications. [Internet] [Doctoral dissertation]. University of Edinburgh; 2017. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/1842/28953.

Council of Science Editors:

Simmonte Owens MJ. Polymer microarrays for biomedical applications. [Doctoral Dissertation]. University of Edinburgh; 2017. Available from: http://hdl.handle.net/1842/28953

7. Dovydenko, Ilya. Mise au point d'aptamères aux capacités thérapeutiques basés sur les ARN importables dans les mitochondries humaines : Design of therapeutic RNA aptamers imported into mitochodria ot human cells.

Degree: Docteur es, Aspects moléculaires et cellulaires de la biologie, 2015, Université de Strasbourg

URL: http://www.theses.fr/2015STRAJ046

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Les défauts de génome mitochondrial provoquent des maladies neuromusculaires, pour lequel aucun traitement efficace n'a été mis au point. La plupart des mutations mitochondriales sont… (more)

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Les défauts de génome mitochondrial provoquent des maladies neuromusculaires, pour lequel aucun traitement efficace n'a été mis au point. La plupart des mutations mitochondriales sont hétéroplasmique, ce qui signifie que l'ADN mitochondrial (ADNmt) de type sauvage et muté coexistent dans la même cellule, et le changement de proportion entre deux types d'ADNmt pourrait rétablir les fonctions mitochondriales. Le but du projet était le développement du système pour cibler l'ARN thérapeutique dans les cellules humaines vivantes. Au cours de ma thèse j'ai synthétisé une série de nouveaux ARN anti-réplicatifs contenant modifications chimiques pour augmenter leur stabilité dans la cellule, et mis au point la nouvelle méthode de synthèse chimique des molécules d'ARN contenant cholestérol fixé par l'intermédiaire d'un pont biodégradable. Ces ARN étaient capable de pénétrer dans les cellules humains, d'être adressées dans les mitochondries et de diminuer la proportion d' ADNmt muté.

Defects in mitochondrial genome cause neuromuscular diseases, for which no efficient therapy has been developed. Since most mitochondrial mutations are heteroplasmic, wild type and mutated mitochondrial DNA (mtDNA) coexist in the same cell, and the shift in proportion between two mtDNA types could restore mitochondrial functions. The aim of the project was development of carrier-free system for targeting the therapeutic mitochondrially importable RNA into living human cells. During my PhD study, I have synthesized a set of new anti-replicative RNAs containing various chemical modifications, aiming to increase their stability in the cell, and developed a new method for the chemical synthesis of RNA molecules containing cholesterol attached through a biodegradable bridge. Cholesterol containing antireplicative RNAs were characterised by efficient cellular uptake, partial colocalisation with mitochondria and ability to decrease the proportion of mutant mtDNA.

Advisors/Committee Members: Entelis, Nina (thesis director), Venyaminova, Alia (thesis director).

Subjects/Keywords: ADN mitochondrial; ADNmt; ARN anti-réplicatif; Mutations mitochondriales hétéroplasmiques; Thérapie génique; Cell delivery; Antireplicative RNA; Cholesterol containing RNA conjugates; Mitochondrial drug delivery; Mitochondrial diseases; Modified oligonucleotides; MtDNA Heteroplasmy; RNA import; 571.6; 572.8

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APA (6^th Edition):

Dovydenko, I. (2015). Mise au point d'aptamères aux capacités thérapeutiques basés sur les ARN importables dans les mitochondries humaines : Design of therapeutic RNA aptamers imported into mitochodria ot human cells. (Doctoral Dissertation). Université de Strasbourg. Retrieved from http://www.theses.fr/2015STRAJ046

Chicago Manual of Style (16^th Edition):

Dovydenko, Ilya. “Mise au point d'aptamères aux capacités thérapeutiques basés sur les ARN importables dans les mitochondries humaines : Design of therapeutic RNA aptamers imported into mitochodria ot human cells.” 2015. Doctoral Dissertation, Université de Strasbourg. Accessed January 22, 2021. http://www.theses.fr/2015STRAJ046.

MLA Handbook (7^th Edition):

Dovydenko, Ilya. “Mise au point d'aptamères aux capacités thérapeutiques basés sur les ARN importables dans les mitochondries humaines : Design of therapeutic RNA aptamers imported into mitochodria ot human cells.” 2015. Web. 22 Jan 2021.

Vancouver:

Dovydenko I. Mise au point d'aptamères aux capacités thérapeutiques basés sur les ARN importables dans les mitochondries humaines : Design of therapeutic RNA aptamers imported into mitochodria ot human cells. [Internet] [Doctoral dissertation]. Université de Strasbourg; 2015. [cited 2021 Jan 22]. Available from: http://www.theses.fr/2015STRAJ046.

Council of Science Editors:

Dovydenko I. Mise au point d'aptamères aux capacités thérapeutiques basés sur les ARN importables dans les mitochondries humaines : Design of therapeutic RNA aptamers imported into mitochodria ot human cells. [Doctoral Dissertation]. Université de Strasbourg; 2015. Available from: http://www.theses.fr/2015STRAJ046

Virginia Tech

8. Rajasimha, Harsha Karur. Insights Into Mitochondrial Genetic and Morphologic Dynamics Gained by Stochastic Simulation.

Degree: PhD, Genetics, Bioinformatics, and Computational Biology, 2007, Virginia Tech

URL: http://hdl.handle.net/10919/29961

► MtDNA mutations in mammalian cells are implicated in cellular ageing and encephalomyopathies, although mechanisms involved are not completely understood. The mitochondrial genetic bottleneck has puzzled… (more)

▼ MtDNA mutations in mammalian cells are implicated in cellular ageing and encephalomyopathies, although mechanisms involved are not completely understood. The mitochondrial genetic bottleneck has puzzled biologists for a long time. Approximate models of genetic bottleneck proposed in the literature do not accurately model underlying biology. Recent studies indicate mitochondrial morphology changes during cellular aging in culture. In particular, the rates of mitochondrial fission and fusion are shown to be in tight balance, though this rate decreases with age. Some proteins involved in mitochondrial morphology maintenance are implicated in apoptosis. Hence, mitochondrial genetic and morphologic dynamics are critical to the life and death of cells. By working closely with experimental collaborators and by utilizing data derived from literature, we have developed stochastic simulation models of mitochondrial genetic and morphologic dynamics. Hypotheses from the mitochondrial genetic dynamics model include: (1) the decay of mtDNA heteroplasmy in blood is exponential and not linear as reported in literature. (2) Blood heteroplasmy measurements are a good proxy for the blood stem cell heteroplasmy. (3) By analyzing our simulation results in tandem with published longitudinal clinical data, we propose for the first time, a way to correct for the patient's age in the analysis of heteroplasmy data. (4) We develop a direct model of the genetic bottleneck process during mouse embryogenesis. (5) Partitioning of mtDNA into daughter cells during blastocyst formation and relaxed replication of mtDNA during the exponential growth phase of primordial germ cells leads to the variation in heteroplasmy inherited by offspring from the same mother. (6) We develop a “simulation control” for experimental studies on mtDNA heteroplasmy variation in cell cultures. Hypothesis from the mitochondrial morphologic dynamics model: (7) A cell adjusts the mitochondrial fusion rate to compensate for the fluctuations in the fission rate, but not vice versa. A deterministic model for this control is proposed. Contributions: extensible simulation models of mitochondrial genetic and morphologic dynamics to aide in the powerful analysis of published and new experimental data. Our results have direct relevance to cell biology and clinical diagnosis. The work also illustrates scientific success by tight integration of theory with practice. Advisors/Committee Members: Samuels, David C. (committeechair), Tyson, John J. (committee member), Vullikanti, Anil Kumar S. (committee member), Onufriev, Alexey V. (committee member), Bevan, David R. (committee member).

Subjects/Keywords: heteroplasmy; fusion; fission; blood; inheritance; model; morphology; mtDNA; stem cells; segregation; oogenesis; ageing; mutations

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Rajasimha, H. K. (2007). Insights Into Mitochondrial Genetic and Morphologic Dynamics Gained by Stochastic Simulation. (Doctoral Dissertation). Virginia Tech. Retrieved from http://hdl.handle.net/10919/29961

Chicago Manual of Style (16^th Edition):

Rajasimha, Harsha Karur. “Insights Into Mitochondrial Genetic and Morphologic Dynamics Gained by Stochastic Simulation.” 2007. Doctoral Dissertation, Virginia Tech. Accessed January 22, 2021. http://hdl.handle.net/10919/29961.

MLA Handbook (7^th Edition):

Rajasimha, Harsha Karur. “Insights Into Mitochondrial Genetic and Morphologic Dynamics Gained by Stochastic Simulation.” 2007. Web. 22 Jan 2021.

Vancouver:

Rajasimha HK. Insights Into Mitochondrial Genetic and Morphologic Dynamics Gained by Stochastic Simulation. [Internet] [Doctoral dissertation]. Virginia Tech; 2007. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/10919/29961.

Council of Science Editors:

Rajasimha HK. Insights Into Mitochondrial Genetic and Morphologic Dynamics Gained by Stochastic Simulation. [Doctoral Dissertation]. Virginia Tech; 2007. Available from: http://hdl.handle.net/10919/29961

9. Magdoud, Hajer. Implication fonctionnelle de la protéine adaptatrice Lnk dans les cellules normales et pathologiques du lignage mégacaryocytaire : Functional application of the Lnk adaptor protein in normal and pathological megakaryopoiesis.

Degree: Docteur es, Biologie moléculaire et cellulaire, 2014, Paris 13

URL: http://www.theses.fr/2014PA132003

► L’adaptateur Lnk est un inhibiteur clé dans le système hématopoïétique. Son invalidation chez la souris entraîne l’hyperprolifération des lignages myéloïdes (mégacaryocytaire et érythoïde). Les cellules… (more)

▼ L’adaptateur Lnk est un inhibiteur clé dans le système hématopoïétique. Son invalidation chez la souris entraîne l’hyperprolifération des lignages myéloïdes (mégacaryocytaire et érythoïde). Les cellules Lnk présentent une hypersensibilité à certaines cytokines dont la Trombopoïétine (TPO) et l’Erythropoïétine (EPO) et la dérégulation de leurs voies de signalisation (JAK/STAT et MAPK). D’autre part, le phénotype Lnk s’assimile aux caractéristiques trouvées chez les patients atteints des syndromes myéloprolifératifs (SMPs), suggérant un rôle clé de Lnk dans ces maladies. L’identification récente des mutations de LNK dans ces hémopathies l’a confirmé. Ainsi, l’objectif de mon travail de thèse était de définir les mécanismes moléculaires par lesquels Lnk régule la mégacaryopoïèse en disséquant son interaction avec son partenaire, la kinase JAK2, dans la voie TPO/Mpl. En parallèle, nous avons visé à déterminer le rôle de Lnk dans la pathogénèse de SMPs. Afin d’étudier le rôle de Lnk dans les SMPs, nous avons effectué une analyse transcriptionnelle de Lnk dans les cellules CD34 et les plaquettes de patients exprimant JAK2WT ou JAK2V617F. Nos résultats ont montré uns surexpression de Lnk, dans les témoins sains. Cette surexpression est due à l’induction de l’expression de Lnk par la TPO, montrant une boucle de rétrorégulation par Lnk de la voieTPO/Mpl/JAK2. Par ailleurs l’analyse de l’interaction Lnk/JAK2 dans les plaquettes des patients atteints de SMPs a démontré que Lnk est capable de s’associer à JAK2 (JAK2WT et JAK2V617F) E outre cette liaison est indépendante de la stimulation par la TPO et abouti à une phosphorylation constitutive de Lnk.Notre analyse au niveau moléculaire de l’interaction Lnk/JALK2 a révélé, qu’en plus du domaine SH2 de Lnk, la région N-terminale et le domaine PH de Lnk ont un nouveau rôle important dans l’inhibition de la kinase JAK2. Nous avons également montré une association entre Lnk et les formes mutées dans les SMPs, JAK2V617F ou JAK2K539L avec une infimité plus élevée qu’avec JAK2WT, suggérant ainsi une régulation différentielle de ces formes par Lnk. L’analyse fonctionnelle de ces formes par Lnk. L’analyse fonctionnelle par des essais de prolifération cellulaire, a montré que Lnk, inhibe la croissance de cellules exprimant JAK2V617F et ceci de manière dos-dépendante. Nous avons ensuite entrepris l’étude des effets des mutations de LNK (LNKG152R et LNKE208Q) identifiées dans les SMPs. Nos résultats ont indiqué que seule la mutation LNKE208Q semble affecter la localisation membranaire de l’adaptateur. De plus nous avons montré que cette mutation de LNK altère son effet inhibiteur sur la croissance cellulaire dépendante de JAK2, contrairement à la mutation de LNKG152R ayant elle-même un effet modéré. Ces résultats montrent que ces mutations de LNK affectent différemment les réponses cellulaires dépendantes de JAK2 dans les SMPs. Ainsi, nos données suggèrent que la région N-terminale et le domaine PH de LNK sont importants pour moduler sa fonction inhibitrice sur JAK2. L’ensemble de nos travaux… Advisors/Committee Members: Velazquez, Laura (thesis director).

Subjects/Keywords: Mutations de Lnk; Lnk mutations

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APA (6^th Edition):

Magdoud, H. (2014). Implication fonctionnelle de la protéine adaptatrice Lnk dans les cellules normales et pathologiques du lignage mégacaryocytaire : Functional application of the Lnk adaptor protein in normal and pathological megakaryopoiesis. (Doctoral Dissertation). Paris 13. Retrieved from http://www.theses.fr/2014PA132003

Chicago Manual of Style (16^th Edition):

Magdoud, Hajer. “Implication fonctionnelle de la protéine adaptatrice Lnk dans les cellules normales et pathologiques du lignage mégacaryocytaire : Functional application of the Lnk adaptor protein in normal and pathological megakaryopoiesis.” 2014. Doctoral Dissertation, Paris 13. Accessed January 22, 2021. http://www.theses.fr/2014PA132003.

MLA Handbook (7^th Edition):

Magdoud, Hajer. “Implication fonctionnelle de la protéine adaptatrice Lnk dans les cellules normales et pathologiques du lignage mégacaryocytaire : Functional application of the Lnk adaptor protein in normal and pathological megakaryopoiesis.” 2014. Web. 22 Jan 2021.

Vancouver:

Magdoud H. Implication fonctionnelle de la protéine adaptatrice Lnk dans les cellules normales et pathologiques du lignage mégacaryocytaire : Functional application of the Lnk adaptor protein in normal and pathological megakaryopoiesis. [Internet] [Doctoral dissertation]. Paris 13; 2014. [cited 2021 Jan 22]. Available from: http://www.theses.fr/2014PA132003.

Council of Science Editors:

Magdoud H. Implication fonctionnelle de la protéine adaptatrice Lnk dans les cellules normales et pathologiques du lignage mégacaryocytaire : Functional application of the Lnk adaptor protein in normal and pathological megakaryopoiesis. [Doctoral Dissertation]. Paris 13; 2014. Available from: http://www.theses.fr/2014PA132003

Brigham Young University

10. Benavides, Edgar. Evolution in Neotropical Herpetofauna: Species Boundaries in High Andean Frogs and Evolutionary Genetics in the Lava Lizard Genus Microlophus (Squamata: tropiduridae): A History of Colonization and Dispersal.

Degree: PhD, 2006, Brigham Young University

URL: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=2299&context=etd

► In this collection of papers I have summarized my investigations into the field of evolutionary genetics and more specifically into patterns of biodiversity and… (more)

▼ In this collection of papers I have summarized my investigations into the field of evolutionary genetics and more specifically into patterns of biodiversity and evolutionary processes. The lizards (and frogs) studied here share common features in that they are largely present in unique environments, which are also regions that are biologically understudied. Most of these taxa show high degrees of endemism, interesting natural history characteristics, and each group manifests distinctive adaptations of general evolutionary interest. My work in the genus Telmatobius has been a progressive approach that began in my MS program, and it first focused on alpha taxonomy, morphological variation, and species boundaries. This work led to new studies initiated and completed at BYU involving further taxonomic revision (Formas et al., 2003; Chapter 1), and then revisiting and re-evaluating species boundaries established earlier (with allozyme markers) and this time with population level molecular (mitochondrial DNA) markers (Chapter 2). Our results indicate that the striking differences in size, coloration and general appearance in the various Lake Titicaca morphotypes are not genetically based. Further, there is evidence that these morphotypes have evolved very rapidly after demographic bottlenecks eroded present genetic variability. Telmatobius frogs of Lake Titicaca are listed by the International (IUCN) as critically endangered. We support this classification and further suggest studies to explore open questions like the possibility of adaptation along ecological resource gradients. Lizards of the genus Microlophus are interesting but for different reasons, and studies of this group constitutes the bulk of my dissertation work. The genus includes both Galapagos insular species, and continental taxa distributed in a linear gradient along > 4000 km of the western coast of South America. In studying Microlophus I first tackled the unresolved phylogenetic relationships within the genus (Chapter 3) and then pay attention to phylogeographic aspects of the most speciose lizard radiation in the Galapagos Archipelago (Chapter 4). Chapter 3 is a single manuscript provisionally accepted in the journal Systematic Biology. This paper introduces the lizard genus Microlophus (“lava lizards”) as a study system, and includes a large nuclear data set accompanied by an equally large mitochondrial data set (7877 characters in total). This paper explicitly differentiates among sequence alignments of gene regions that vary in tempo and class of mutational events. We show that this recognition is important and we suggest ways to appropriately deal with the alignment of multi-locus non-coding DNA data sets. A secondary finding in this study is that mtDNA and nDNA topologies are discordant with each other but that both are strongly supported, and that the nuclear topology is concordant with species distribution patterns along coastal South America. We hypothesize that in this particular region of the tree, the nuclear genome recovers a topology…

Subjects/Keywords: nuclear introns; alignment; length mutations; Microlophus; secondary contact; mitochondrial-nuclear conflict; phylogenetics; Galapagos; mtDNA; phylogeography; nested clade analysis; colonization routes; volcanism; lava lizards; Biology

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APA (6^th Edition):

Benavides, E. (2006). Evolution in Neotropical Herpetofauna: Species Boundaries in High Andean Frogs and Evolutionary Genetics in the Lava Lizard Genus Microlophus (Squamata: tropiduridae): A History of Colonization and Dispersal. (Doctoral Dissertation). Brigham Young University. Retrieved from https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=2299&context=etd

Chicago Manual of Style (16^th Edition):

Benavides, Edgar. “Evolution in Neotropical Herpetofauna: Species Boundaries in High Andean Frogs and Evolutionary Genetics in the Lava Lizard Genus Microlophus (Squamata: tropiduridae): A History of Colonization and Dispersal.” 2006. Doctoral Dissertation, Brigham Young University. Accessed January 22, 2021. https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=2299&context=etd.

MLA Handbook (7^th Edition):

Benavides, Edgar. “Evolution in Neotropical Herpetofauna: Species Boundaries in High Andean Frogs and Evolutionary Genetics in the Lava Lizard Genus Microlophus (Squamata: tropiduridae): A History of Colonization and Dispersal.” 2006. Web. 22 Jan 2021.

Vancouver:

Benavides E. Evolution in Neotropical Herpetofauna: Species Boundaries in High Andean Frogs and Evolutionary Genetics in the Lava Lizard Genus Microlophus (Squamata: tropiduridae): A History of Colonization and Dispersal. [Internet] [Doctoral dissertation]. Brigham Young University; 2006. [cited 2021 Jan 22]. Available from: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=2299&context=etd.

Council of Science Editors:

Benavides E. Evolution in Neotropical Herpetofauna: Species Boundaries in High Andean Frogs and Evolutionary Genetics in the Lava Lizard Genus Microlophus (Squamata: tropiduridae): A History of Colonization and Dispersal. [Doctoral Dissertation]. Brigham Young University; 2006. Available from: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=2299&context=etd

University of Alberta

11. Bahitham, Wesam Ahmad. Novel Alterations of Morphology and Genome of Mitochondria of Cholangiocellular Carcinoma.

Degree: MS, Medical Sciences- Laboratory Medicine and Pathology, 2013, University of Alberta

URL: https://era.library.ualberta.ca/files/mc87pq769

► Cholangiocellular carcinoma (CCA) is the second most common hepatic malignancy, but its carcinogenesis is poorly understood. Somatic mitochondrial DNA (mtDNA) mutations have been demonstrated in… (more)

Subjects/Keywords: mtDNA; Cholangiocarcinoma; Mitochondrial dysfunction; MitoChip

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APA (6^th Edition):

Bahitham, W. A. (2013). Novel Alterations of Morphology and Genome of Mitochondria of Cholangiocellular Carcinoma. (Masters Thesis). University of Alberta. Retrieved from https://era.library.ualberta.ca/files/mc87pq769

Chicago Manual of Style (16^th Edition):

Bahitham, Wesam Ahmad. “Novel Alterations of Morphology and Genome of Mitochondria of Cholangiocellular Carcinoma.” 2013. Masters Thesis, University of Alberta. Accessed January 22, 2021. https://era.library.ualberta.ca/files/mc87pq769.

MLA Handbook (7^th Edition):

Bahitham, Wesam Ahmad. “Novel Alterations of Morphology and Genome of Mitochondria of Cholangiocellular Carcinoma.” 2013. Web. 22 Jan 2021.

Vancouver:

Bahitham WA. Novel Alterations of Morphology and Genome of Mitochondria of Cholangiocellular Carcinoma. [Internet] [Masters thesis]. University of Alberta; 2013. [cited 2021 Jan 22]. Available from: https://era.library.ualberta.ca/files/mc87pq769.

Council of Science Editors:

Bahitham WA. Novel Alterations of Morphology and Genome of Mitochondria of Cholangiocellular Carcinoma. [Masters Thesis]. University of Alberta; 2013. Available from: https://era.library.ualberta.ca/files/mc87pq769

Vanderbilt University

12. Gandhi, Vishal V. Investigating mitochondrial deoxyribonucleotide metabolism and its role in a family of genetic diseases.

Degree: PhD, Human Genetics, 2011, Vanderbilt University

URL: http://hdl.handle.net/1803/14867

► Abnormal regulation of mitochondrial deoxyribonucleoside triphosphate pools can lead to mitochondrial DNA depletion syndromes, a set of genetic diseases associated with depletion of mitochondrial DNA.… (more)

▼ Abnormal regulation of mitochondrial deoxyribonucleoside triphosphate pools can lead to mitochondrial DNA depletion syndromes, a set of genetic diseases associated with depletion of mitochondrial DNA. Besides mitochondrial DNA depletion syndromes, improper maintenance of mitochondrial deoxyribonucleoside triphosphate pools and mitochondrial DNA have also been implicated in a host of other human pathologies. The unifying objective of this dissertation was to enhance our knowledge of the regulation of mitochondrial deoxyribonucleoside triphosphate pools. The first step was to investigate the characteristics of mitochondrial and cytoplasmic deoxyribonucleoside triphosphate levels. I calculated mitochondrial and cytoplasmic deoxyribonucleoside triphosphate concentrations from previously published data. Cytoplasmic and mitochondrial deoxyribonucleoside triphosphates are strongly correlated in normal cells but not in transformed cells. Following up this discovery with analysis of gene expression, I discovered that, consistent with the trends in deoxyribonucleoside triphosphate concentrations in cells, genes coding for enzymes that maintain cytoplasmic and mitochondrial deoxyribonucleoside triphosphates have correlated expression across normal tissues but not across transformed tissues. To further understand the influence of cytoplasmic deoxyribonucleoside triphosphates on mitochondrial deoxyribonucleoside triphosphates, I simulated the metabolism of mitochondrial deoxyribonucleosides with a computational model. Cytoplasmic deoxyribonucleotides have a substantial and indispensable contribution to mitochondrial deoxyribonucleoside triphosphates in most circumstances. My results further show that import from the cytoplasm would need to occur at either deoxyribonucleoside diphosphate or triphosphate levels. Advisors/Committee Members: Emmanuele DiBenedetto (committee member), David Samuels (committee member), Scott Williams (committee member), Todd Hulgan (committee member), Tricia Thornton-Wells (Committee Chair).

Subjects/Keywords: depletion; dNTP; mitochondria; nucleotide; mtDNA

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APA (6^th Edition):

Gandhi, V. V. (2011). Investigating mitochondrial deoxyribonucleotide metabolism and its role in a family of genetic diseases. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/14867

Chicago Manual of Style (16^th Edition):

Gandhi, Vishal V. “Investigating mitochondrial deoxyribonucleotide metabolism and its role in a family of genetic diseases.” 2011. Doctoral Dissertation, Vanderbilt University. Accessed January 22, 2021. http://hdl.handle.net/1803/14867.

MLA Handbook (7^th Edition):

Gandhi, Vishal V. “Investigating mitochondrial deoxyribonucleotide metabolism and its role in a family of genetic diseases.” 2011. Web. 22 Jan 2021.

Vancouver:

Gandhi VV. Investigating mitochondrial deoxyribonucleotide metabolism and its role in a family of genetic diseases. [Internet] [Doctoral dissertation]. Vanderbilt University; 2011. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/1803/14867.

Council of Science Editors:

Gandhi VV. Investigating mitochondrial deoxyribonucleotide metabolism and its role in a family of genetic diseases. [Doctoral Dissertation]. Vanderbilt University; 2011. Available from: http://hdl.handle.net/1803/14867

McMaster University

13. Hale, Richard Lawrence. An Analysis of the Population Genetic Structure and Species History of Drosophila Melanogaster and Drosophila Simulans Using Restriction Fragment Length Polymorphisms of Mitochondrial DNA.

Degree: PhD, 1989, McMaster University

URL: http://hdl.handle.net/11375/6588

► Animal mitochondrial DNA (mtDNA) has several features that give it great utility in the study of geographic structure of natural populations. Its small size… (more)

▼ Animal mitochondrial DNA (mtDNA) has several features that give it great utility in the study of geographic structure of natural populations. Its small size and covalently closed circular conformation make it easy to purify. Strict maternal inheritance and homoplasmy makes the effective copy number of mtDNA as little as 1/4 that of nuclear loci; this renders populational complements of mtDNA less susceptible to the homogenizing effects of gene flow due to migration, and more susceptible to founder effects due to fluctuations in effective population size. The absence of recombination allows for comparatively simple reconstruction of genealogies of mtDNA variants. A comparatively high rate of base substitution assures that most species will have enough mtDNA variants to make population genetic inferences meaningful. Finally, sequence variants of mtDNA harboured in natural populations are presumed to be selectively neutral (i.e. has no effect on organismal fitness). This means that the distribution of mtDNA variants in populations will be due entirely to the stochastic and deterministic effects of species history, and not to natural selection. As a result, mtDNA can be used to infer species history directly and, after allowing for differences in modes of transmission, to infer the action of natural selection on other genetically determined factors like allozymes. The research of this dissertation was to survey world-wide natural populations of Drosophila melanogaster and its sibling species D. simulans for restriction fragment length polymorphisms of mtDNA. These cosmopolitan species have been widely studied for variation of allozymes and many other genetically determined factors (e.g. chromosomal inversions, morphometric characters). A total of 144 isofemale lines of D. melanogaster were analyzed from 18 geographic populations. Considerable size variation was observed in this sample. Most size variation occurs in the major non-coding region (A+T-rich region), yielding a total size range of 18.2 kbp to 19.9 kbp. The occurrence of several size variants among all haplotypes indicates that the rate of size mutation is quite high. Further, the frequency distribution of size variants suggests that there is selection against larger sized mtDNA molecules; a replication advantage to smaller sized molecules is a likely explanation. Finally, there is evidence for 'small-scale' size variation (i.e. a total range of 20 bp) in the coding region of mtDNA. However, it could not be determined if the observed mobility variation of the fragments in question was actually due to addition/deletion of DNA or due to conformational effects of particular base substitutions. Using 10 restriction enzymes, 23 restriction haplotypes were observed in D. melanogaster mtDNA. The phylogeographic distribution of these haplotypes allowed populations to be roughly divided into three longitudinal regions. Euro-African populations showed high intra- and inter-populational diversity and were inferred to be the oldest. Far East… Advisors/Committee Members: Singh, Rama S., Biology.

Subjects/Keywords: Biology; mtDNA

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APA (6^th Edition):

Hale, R. L. (1989). An Analysis of the Population Genetic Structure and Species History of Drosophila Melanogaster and Drosophila Simulans Using Restriction Fragment Length Polymorphisms of Mitochondrial DNA. (Doctoral Dissertation). McMaster University. Retrieved from http://hdl.handle.net/11375/6588

Chicago Manual of Style (16^th Edition):

Hale, Richard Lawrence. “An Analysis of the Population Genetic Structure and Species History of Drosophila Melanogaster and Drosophila Simulans Using Restriction Fragment Length Polymorphisms of Mitochondrial DNA.” 1989. Doctoral Dissertation, McMaster University. Accessed January 22, 2021. http://hdl.handle.net/11375/6588.

MLA Handbook (7^th Edition):

Hale, Richard Lawrence. “An Analysis of the Population Genetic Structure and Species History of Drosophila Melanogaster and Drosophila Simulans Using Restriction Fragment Length Polymorphisms of Mitochondrial DNA.” 1989. Web. 22 Jan 2021.

Vancouver:

Hale RL. An Analysis of the Population Genetic Structure and Species History of Drosophila Melanogaster and Drosophila Simulans Using Restriction Fragment Length Polymorphisms of Mitochondrial DNA. [Internet] [Doctoral dissertation]. McMaster University; 1989. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/11375/6588.

Council of Science Editors:

Hale RL. An Analysis of the Population Genetic Structure and Species History of Drosophila Melanogaster and Drosophila Simulans Using Restriction Fragment Length Polymorphisms of Mitochondrial DNA. [Doctoral Dissertation]. McMaster University; 1989. Available from: http://hdl.handle.net/11375/6588

14. ARAÚJO, Guilhermy Victor Sousa de. Significado clínico do número relativo de cópias de DNA mitocondrial (mtDNA) em neoplasias hematológicas de origem mieloide .

Degree: 2018, Universidade Federal de Pernambuco

URL: https://repositorio.ufpe.br/handle/123456789/32688

► Variações no conteúdo de DNA mitocondrial (mtDNA) vêm sendo amplamente associados com um pior prognóstico e progressão da doença em vários tipos de tumores humanos.… (more)

Subjects/Keywords: mtDNA; Neoplasias mieloides; Prognóstico

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APA (6^th Edition):

ARAÚJO, G. V. S. d. (2018). Significado clínico do número relativo de cópias de DNA mitocondrial (mtDNA) em neoplasias hematológicas de origem mieloide . (Masters Thesis). Universidade Federal de Pernambuco. Retrieved from https://repositorio.ufpe.br/handle/123456789/32688

Chicago Manual of Style (16^th Edition):

ARAÚJO, Guilhermy Victor Sousa de. “Significado clínico do número relativo de cópias de DNA mitocondrial (mtDNA) em neoplasias hematológicas de origem mieloide .” 2018. Masters Thesis, Universidade Federal de Pernambuco. Accessed January 22, 2021. https://repositorio.ufpe.br/handle/123456789/32688.

MLA Handbook (7^th Edition):

ARAÚJO, Guilhermy Victor Sousa de. “Significado clínico do número relativo de cópias de DNA mitocondrial (mtDNA) em neoplasias hematológicas de origem mieloide .” 2018. Web. 22 Jan 2021.

Vancouver:

ARAÚJO GVSd. Significado clínico do número relativo de cópias de DNA mitocondrial (mtDNA) em neoplasias hematológicas de origem mieloide . [Internet] [Masters thesis]. Universidade Federal de Pernambuco; 2018. [cited 2021 Jan 22]. Available from: https://repositorio.ufpe.br/handle/123456789/32688.

Council of Science Editors:

ARAÚJO GVSd. Significado clínico do número relativo de cópias de DNA mitocondrial (mtDNA) em neoplasias hematológicas de origem mieloide . [Masters Thesis]. Universidade Federal de Pernambuco; 2018. Available from: https://repositorio.ufpe.br/handle/123456789/32688

15. Cain, Gregory Omar. Historical Genetic Analysis Of Horned Lark (Eremophila Alpestris) Specimens From The Prairie Pothole Region.

Degree: MS, Biology, 2013, University of North Dakota

URL: https://commons.und.edu/theses/1511

► The Horned Lark (Eremphila alpestris) is a generalist bird species with a global distribution. A previous phylogeographic study of this species from western North… (more)

▼ The Horned Lark (Eremphila alpestris) is a generalist bird species with a global distribution. A previous phylogeographic study of this species from western North America has been completed and identified three distinct mitochondrial DNA clades. This study aims to genetically characterize Horned Larks from the North Dakota region using the mtDNA NADH dehydrogenase subunit 2 (ND2) gene. Horned Larks were sampled from museum collections, with ages ranging from 13 - 120 years old. 5mm x 1mm feather cuttings were removed using a non-invasive feather sampling method from each specimen for genetic analysis. This sampling method was verified on 15 total museum specimens of Horned Larks, Red-winged Blackbirds (Agelaius phoeniceus) and Franklin's Gulls (Leucophaeus pipixcan) from the University of North Dakota Vertebrate Museum Collection. Sampling methodology was investigated by using three mechanisms of DNA isolation: EDTA with proteinase K followed by column-based purification, chelating resin with dithiothreitol, and a Direct PCR method without DNA purification. Three fragments of mitochondrial DNA loci were amplified including control region, cytochrome c oxidase I and NADH dehydrogenase subunit 2. Correct sequencing results indicated that this method is viable for amplification of museum DNA, while at the same time limiting physical damage to the museum specimen. Arsenic found in low concentrations from arsenic test strips, was not a factor seriously hindering the success of PCR. Phylogenetic reconstruction of historic Horned Lark genetic information using Bayesian Inference and Maximum Likelihood algorithms revealed the existence of a Nearctic South clade, and reclassifies the previously established Pacific Northwest clade as a broader Nearctic North clade. The use of sequences with uneven preservation from museum specimens had no effect on overall tree topology. Horned Larks from the North Dakota region population had higher nucleotide diversity than other populations, and were all part of the Nearctic Northern clade. Five new haplotypes and three new SNPs were identified from museum specimens in this study. Advisors/Committee Members: Igor V. Ovchinnikov.

Subjects/Keywords: Horned Lark; mtDNA; Museum specimens

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APA (6^th Edition):

Cain, G. O. (2013). Historical Genetic Analysis Of Horned Lark (Eremophila Alpestris) Specimens From The Prairie Pothole Region. (Masters Thesis). University of North Dakota. Retrieved from https://commons.und.edu/theses/1511

Chicago Manual of Style (16^th Edition):

Cain, Gregory Omar. “Historical Genetic Analysis Of Horned Lark (Eremophila Alpestris) Specimens From The Prairie Pothole Region.” 2013. Masters Thesis, University of North Dakota. Accessed January 22, 2021. https://commons.und.edu/theses/1511.

MLA Handbook (7^th Edition):

Cain, Gregory Omar. “Historical Genetic Analysis Of Horned Lark (Eremophila Alpestris) Specimens From The Prairie Pothole Region.” 2013. Web. 22 Jan 2021.

Vancouver:

Cain GO. Historical Genetic Analysis Of Horned Lark (Eremophila Alpestris) Specimens From The Prairie Pothole Region. [Internet] [Masters thesis]. University of North Dakota; 2013. [cited 2021 Jan 22]. Available from: https://commons.und.edu/theses/1511.

Council of Science Editors:

Cain GO. Historical Genetic Analysis Of Horned Lark (Eremophila Alpestris) Specimens From The Prairie Pothole Region. [Masters Thesis]. University of North Dakota; 2013. Available from: https://commons.und.edu/theses/1511

University of Manitoba

16. Imperial, Robin John Lester. Identification of critical residues in the carboxyl-terminal extension of the mitochondrial DNA polymerase in Saccharomyces cerevisiae.

Degree: Microbiology, 2011, University of Manitoba

URL: http://hdl.handle.net/1993/4798

► Mip1p is the highly processive monomeric mitochondrial DNA polymerase in Saccharomyces cerevisiae. Despite differences in enzyme structure, substrate topology, and possible nucleoid interactions, Mip1p continues… (more)

Subjects/Keywords: mtDNA; polymerase; polg; cte

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APA (6^th Edition):

Imperial, R. J. L. (2011). Identification of critical residues in the carboxyl-terminal extension of the mitochondrial DNA polymerase in Saccharomyces cerevisiae. (Masters Thesis). University of Manitoba. Retrieved from http://hdl.handle.net/1993/4798

Chicago Manual of Style (16^th Edition):

Imperial, Robin John Lester. “Identification of critical residues in the carboxyl-terminal extension of the mitochondrial DNA polymerase in Saccharomyces cerevisiae.” 2011. Masters Thesis, University of Manitoba. Accessed January 22, 2021. http://hdl.handle.net/1993/4798.

MLA Handbook (7^th Edition):

Imperial, Robin John Lester. “Identification of critical residues in the carboxyl-terminal extension of the mitochondrial DNA polymerase in Saccharomyces cerevisiae.” 2011. Web. 22 Jan 2021.

Vancouver:

Imperial RJL. Identification of critical residues in the carboxyl-terminal extension of the mitochondrial DNA polymerase in Saccharomyces cerevisiae. [Internet] [Masters thesis]. University of Manitoba; 2011. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/1993/4798.

Council of Science Editors:

Imperial RJL. Identification of critical residues in the carboxyl-terminal extension of the mitochondrial DNA polymerase in Saccharomyces cerevisiae. [Masters Thesis]. University of Manitoba; 2011. Available from: http://hdl.handle.net/1993/4798

University of Gothenburg / Göteborgs Universitet

17. Posse, Viktor. Molecular insights into mitochondrial transcription and its role in DNA replication.

Degree: 2016, University of Gothenburg / Göteborgs Universitet

URL: http://hdl.handle.net/2077/50132

► The mitochondrion is an organelle of the eukaryotic cell responsible for the production of most of the cellular energy-carrying molecule adenosine triphosphate (ATP), through the… (more)

▼ The mitochondrion is an organelle of the eukaryotic cell responsible for the production of most of the cellular energy-carrying molecule adenosine triphosphate (ATP), through the process of oxidative phosphorylation. The mitochondrion contains its own genome, a small circular DNA molecule (mtDNA), encoding essential subunits of the oxidative phosphorylation system. Initiation of mitochondrial transcription involves three proteins, the mitochondrial RNA polymerase, POLRMT, and its two transcription factors, TFAM and TFB2M. Even though the process of transcription has been reconstituted in vitro, a full molecular understanding is still missing. Initiation of mitochondrial DNA replication is believed to be primed by transcription prematurely terminated at a sequence known as CSBII. The mechanisms of replication initiation have however not been fully defined. In this thesis we have studied transcription and replication of mtDNA. In the first part of this thesis we demonstrate that the transcription initiation machinery is recruited in discrete steps. Furthermore, we find that a large domain of POLRMT known as the N-terminal extension is dispensable for transcription initiation, and instead functions in suppressing initiation events from non-promoter DNA. Additionally we demonstrate that TFB2M is the last factor that is recruited to the initiation complex and that it induces melting of the mitochondrial promoters. In this thesis we also demonstrate that POLRMT is a non-processive polymerase that needs the presence of the elongation factor TEFM for processive transcription. TEFM increases the affinity of POLRMT for an elongation-like RNA-DNA template and decreases the probability of premature transcription termination. Our data also suggest that TEFM might be of importance for mitochondrial replication initiation, since it affects termination at CSBII. In the last part of this thesis we study the RNA-DNA hybrids (R-loops) that can be formed by the CSBII terminated transcript. We characterize these R-loops and demonstrate that they can be processed by RNaseH1 to form replicative primers that can be used by the mitochondrial replication machinery.

Subjects/Keywords: mitochondrion; mtDNA; transcription; DNA replication

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APA (6^th Edition):

Posse, V. (2016). Molecular insights into mitochondrial transcription and its role in DNA replication. (Thesis). University of Gothenburg / Göteborgs Universitet. Retrieved from http://hdl.handle.net/2077/50132

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Posse, Viktor. “Molecular insights into mitochondrial transcription and its role in DNA replication.” 2016. Thesis, University of Gothenburg / Göteborgs Universitet. Accessed January 22, 2021. http://hdl.handle.net/2077/50132.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Posse, Viktor. “Molecular insights into mitochondrial transcription and its role in DNA replication.” 2016. Web. 22 Jan 2021.

Vancouver:

Posse V. Molecular insights into mitochondrial transcription and its role in DNA replication. [Internet] [Thesis]. University of Gothenburg / Göteborgs Universitet; 2016. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/2077/50132.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Posse V. Molecular insights into mitochondrial transcription and its role in DNA replication. [Thesis]. University of Gothenburg / Göteborgs Universitet; 2016. Available from: http://hdl.handle.net/2077/50132

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Tampere University

18. Rajala, Nina. Probing the Mammalian Mitochondrial Nucleoid .

Degree: 2015, Tampere University

URL: https://trepo.tuni.fi/handle/10024/96996

► Mitokondrioiden tärkein tehtävä on energian tuottaminen. Mitokondriot ovat solujen hengityskeskuksia, joissa 90 % tarvitsemastamme energiasta tuotetaan oksidatiivisen fosforylaation kautta elektroninsiirtoketjua apuna käyttäen. Kun mitokondriot eivät… (more)

▼ Mitokondrioiden tärkein tehtävä on energian tuottaminen. Mitokondriot ovat solujen hengityskeskuksia, joissa 90 % tarvitsemastamme energiasta tuotetaan oksidatiivisen fosforylaation kautta elektroninsiirtoketjua apuna käyttäen. Kun mitokondriot eivät toimi kunnolla, tuloksena voi olla energiakriisi, erityisesti lihaksissa, aivoissa ja sydämessä. Lisäksi mitokondrioilla on muita tehtäviä solun perustoiminnoissa, kuten ionitasapainon säilyttämisessä, aminohappojen synteesissä ja solun apoptoosissa eli ohjelmoidussa solukuolemassa. Mitokondrioilla on oma DNA (mtDNA), joka koodaa 13:a hengitysketjussa olevaa polypeptidiä. Loput hengitysketjun polypeptideistä koodataan tuman DNA:sta. Lisäksi mtDNA sisältää mitokondrion proteiinisynteesissä tarvittavat siirtäjä- ja ribosomaaliset RNA:t. Tuman DNA:sta koodataan myös kaikki mtDNA:n ylläpidossa tarvittavat proteiinit, jotka tuotetaan sytoplasmassa ja kuljetetaan mitokondrioihin. Mutaatiot mtDNA:n ylläpitoon osallistuvissa proteiineissa voivat vaikuttaa mitokondrion toimivuuteen. Esimerkiksi mitokondrion helikaasiproteiinissa, Twinklessä, esiintyvien mutaatioiden on osoitettu johtavan mtDNA-deleetioihin tai kopioluvun vähenemään, jotka johtavat neuromuskulaarisiin sairauksiin, kuten adPEO (etenevä silmälihas heikkous). Väitöskirjatyössäni olen selvittänyt Twinklen rakennetta. Havaintoni vahvistivat Twinklen esiintyvän heksameerisina ja heptameerisina rakenteina. Twinkle kuuluu SF4 heksameeriseen DnaB helikaasi -perheeseen ja se on lähisukulainen bakteriofagi T7 g4 -helikaasille. T7 gp4 -helikaasin linkkeri–alue osallistuu proteiinin oligomerisaatioon. Tutkimuksessani olen osoittanut, että toisin kuin T7 gp4 proteiinilla, linkkeri-alueen lisäksi Twinklen aminoterminaalinen osa toimii oligomerisaatiossa. Monet Twinklen mutaatiot esiintyvät tässä osassa proteiinia ja tiedot Twinklen rakenteesta auttavat meitä ymmärtämään, miten tietyt mutaatiot johtavat Twinklen toimintahäiriöihin. MtDNA on pakattu nukleoideiksi kutsuttuihin mtDNA-proteiinikomplekseihin, joiden rakentumista ei ole täysin ymmärretty. Vaikka nukleoidien koostumusta ei tunneta hyvin, tiedetään, että mtDNA:n monistamiseen käytetty koneisto on osa nukleoidien rakennetta. Tähän koneistoon kuuluu esimerkiksi Twinkle-helikaasi. Vaikka nukleoidien kiinnittymisestä mitokondrion sisäkalvolle on tiedetty jo 1960-luvulta lähtien, kiinnittymisen mekanismi on ollut epäselvä. Väitöskirjatutkimukseni on osoittanut, että nukleoidit kiinnittyvät mitokondrion sisäkalvolle Twinkle-helikaasin välityksellä. Tämä kiinnittyminen on dynaaminen siten, että vain aktiivisesti replikoituvat nukleoidit kiinnittyvät Twinkle-helikaasiin. Tutkimukseni on myös osoittanut että kaikki nukleoidit eivät ole pysyvästi kiinnittyneet mitokondrion sisäkalvolle, toisin kun on edellisten tutkimusten perusteella ajateltu. Monet tutkijat ovat olleet kiinnostuneita selvittämään nukleoidien koostumusta ja rakennetta, mutta tähänastinen nukleoiditutkimus on keskittynyt suurimmaksi osaksi ei-kvantitatiiviseen tutkimukseen. Olen kehittänyt uudenlaisen…

Subjects/Keywords: Mitokondria ; nukleoidi ; Twinkle ; mtDNA ; Nucleoid

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Rajala, N. (2015). Probing the Mammalian Mitochondrial Nucleoid . (Doctoral Dissertation). Tampere University. Retrieved from https://trepo.tuni.fi/handle/10024/96996

Chicago Manual of Style (16^th Edition):

Rajala, Nina. “Probing the Mammalian Mitochondrial Nucleoid .” 2015. Doctoral Dissertation, Tampere University. Accessed January 22, 2021. https://trepo.tuni.fi/handle/10024/96996.

MLA Handbook (7^th Edition):

Rajala, Nina. “Probing the Mammalian Mitochondrial Nucleoid .” 2015. Web. 22 Jan 2021.

Vancouver:

Rajala N. Probing the Mammalian Mitochondrial Nucleoid . [Internet] [Doctoral dissertation]. Tampere University; 2015. [cited 2021 Jan 22]. Available from: https://trepo.tuni.fi/handle/10024/96996.

Council of Science Editors:

Rajala N. Probing the Mammalian Mitochondrial Nucleoid . [Doctoral Dissertation]. Tampere University; 2015. Available from: https://trepo.tuni.fi/handle/10024/96996

University of Otago

19. Antolik, Caroline. An investigation of mtDNA heteroplasmy in New Zealand chinook salmon (Oncorhynchus tshawytscha) and its effects on mitochondrial-based population studies .

Degree: 2013, University of Otago

URL: http://hdl.handle.net/10523/3792

► Mitochondrial DNA (mtDNA) is commonly used in population and evolutionary genetics due to its unique characteristics, such as maternal inheritance and a lack of recombination.… (more)

▼ Mitochondrial DNA (mtDNA) is commonly used in population and evolutionary genetics due to its unique characteristics, such as maternal inheritance and a lack of recombination. Increasing reports of paternal inheritance and heteroplasmy indicate that inheritance of this molecule may be more complex than originally assumed. As mtDNA is used in a wide range of studies, further work is needed to better understand its characteristics and inheritance. Here, the chinook salmon (Oncorhynchus tshawytscha) was used to investigate mtDNA heteroplasmy and its effect on the mitochondrial genome and population studies. Two heteroplasmic sites had been previously found in the ND1 gene of this population, and the entire genome of five individuals from the New Zealand population was searched for additional heteropaslmic sites. A detailed protocol using a combination of long-range (LR) and standard PCR with Sanger sequencing was developed to search for and confirm heteroplasmic sites in the mitochondrial genome. This process resulted in the discovery of two additional heteroplasmic sites in the COII gene of the New Zealand chinook salmon population. The sequences obtained during the search for heteroplasmy in the chinook salmon mitochondrial genome were used to undertake a more detailed study of selection in the mtDNA coding regions and examine the population structure of the New Zealand population and its source from the Sacramento River in California. Evidence of selection was found in several genes coding for subunits of complexes I, IV, and V (NADH dehydrogenase, cytochrome c oxidase, and ATP synthase, respectively) of the oxidative phosphorylation (OXPHOS) pathway in mitochondria. Analysis of the New Zealand and California populations using the ND1 and COII genes showed evidence of similar structuring in the two populations, with higher genetic diversity in the ND1 region for both New Zealand and California chinook salmon. The heteroplasmic sites seen in the New Zealand population were not found in any individuals from California, supporting other studies of this species that suggest it went through a bottleneck upon transplantation to New Zealand from California. Advisors/Committee Members: Gemmell, Neil (advisor).

Subjects/Keywords: mtDNA; chinook salmon; heteroplasmy; selection; Oncorhynchus tshawytscha; population genetics; mtDNA inheritance

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APA (6^th Edition):

Antolik, C. (2013). An investigation of mtDNA heteroplasmy in New Zealand chinook salmon (Oncorhynchus tshawytscha) and its effects on mitochondrial-based population studies . (Masters Thesis). University of Otago. Retrieved from http://hdl.handle.net/10523/3792

Chicago Manual of Style (16^th Edition):

Antolik, Caroline. “An investigation of mtDNA heteroplasmy in New Zealand chinook salmon (Oncorhynchus tshawytscha) and its effects on mitochondrial-based population studies .” 2013. Masters Thesis, University of Otago. Accessed January 22, 2021. http://hdl.handle.net/10523/3792.

MLA Handbook (7^th Edition):

Antolik, Caroline. “An investigation of mtDNA heteroplasmy in New Zealand chinook salmon (Oncorhynchus tshawytscha) and its effects on mitochondrial-based population studies .” 2013. Web. 22 Jan 2021.

Vancouver:

Antolik C. An investigation of mtDNA heteroplasmy in New Zealand chinook salmon (Oncorhynchus tshawytscha) and its effects on mitochondrial-based population studies . [Internet] [Masters thesis]. University of Otago; 2013. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/10523/3792.

Council of Science Editors:

Antolik C. An investigation of mtDNA heteroplasmy in New Zealand chinook salmon (Oncorhynchus tshawytscha) and its effects on mitochondrial-based population studies . [Masters Thesis]. University of Otago; 2013. Available from: http://hdl.handle.net/10523/3792

20. Karkanis, Dimitrios. Mutations économiques et démographiques en Chine : croissance ou développement ? : Economic and Demographic Mutations in China : Growth or Development?.

Degree: Docteur es, Sciences économiques et démographiques, 2016, Université Toulouse I – Capitole

URL: http://www.theses.fr/2016TOU10017

►

Le processus de croissance économique de la Chine ces dernières décennies, tiré principalement par la dynamique du secteur des exportations, est accompagné par une croissance… (more)

▼

Le processus de croissance économique de la Chine ces dernières décennies, tiré principalement par la dynamique du secteur des exportations, est accompagné par une croissance démographique rapide. Cette croissance contribue à la création d’une base considérable de consommateurs potentiels et à la constitution d’un grand réservoir en ressources humaines. Faisant partie du groupe des pays dits « émergents », le cas de la Chine présente un intérêt particulier dans le but d’examiner dans quelle mesure la croissance économique se traduit par un processus simultané de développement, cette dernière notion étant étroitement liée à l’amélioration de la vie humaine. La thèse est structurée en trois parties principales. La première partie concerne l’analyse des mutations économiques et démographiques en Chine pendant les dernières décennies, notamment depuis la montée au pouvoir du Deng Xiao Ping en 1978. L’analyse opérée établit d’abord une distinction entre les processus de globalisation et de libéralisation économique, ce, simultanément avec l’évaluation des évolutions de population liées au processus de transition démographique. Dans cette même partie est proposée par la suite une analyse des changements institutionnels liés aux politiques appliquées dans un contexte économique et démographique fortement évolutif. Dans la deuxième partie, la construction d’une base de « diagnostic » concernant certains risques et opportunités liés aux défis du développement de la Chine dans la période actuelle permet de déboucher sur la formulation des principales hypothèses de la recherche. La troisième partie évalue les hypothèses de travail identifiées et tente de construire la distinction proposée entre croissance et développement. Au-delà de la construction et de l’évaluation des hypothèses, la posture épistémologique corollaire de la thèse consiste à appréhender en ouverture disciplinaire le phénomène de co-évolution entre les variables économiques et démographiques dans le cas chinois. Les questions posées autour de la notion du développement imposent, en effet, une approche bidisciplinaire, à la fois économique et démographique.

The process of economic growth in China during the last decades, mainly driven by the dynamics of the export sector, is accompanied by a simultaneous and rapid population growth. This growth contributes, in turn, to the creation of a vast amount of potential consumers, as well of a large human resources reservoir, at a national level. Being part of the group of countries well known as “emerging”, the case of China is of special interest, in order to examine if and how economic growth can result in a simultaneous development process, the latter concept being closely related to the improvement of human life.This PhD thesis is structured mainly in three parts. The first part concerns the analysis of economic and demographic changes in China over the last decades, especially since the rise to the country’s leadership of Deng Xiaoping in the year 1978. The analysis carried out first distinguishes the processes…

Advisors/Committee Members: Colletis, Gabriel (thesis director), Kotzamanis, Byron (thesis director).

Subjects/Keywords: Mutations démographiques - Chine; Mutations économiques - Chine

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Karkanis, D. (2016). Mutations économiques et démographiques en Chine : croissance ou développement ? : Economic and Demographic Mutations in China : Growth or Development?. (Doctoral Dissertation). Université Toulouse I – Capitole. Retrieved from http://www.theses.fr/2016TOU10017

Chicago Manual of Style (16^th Edition):

Karkanis, Dimitrios. “Mutations économiques et démographiques en Chine : croissance ou développement ? : Economic and Demographic Mutations in China : Growth or Development?.” 2016. Doctoral Dissertation, Université Toulouse I – Capitole. Accessed January 22, 2021. http://www.theses.fr/2016TOU10017.

MLA Handbook (7^th Edition):

Karkanis, Dimitrios. “Mutations économiques et démographiques en Chine : croissance ou développement ? : Economic and Demographic Mutations in China : Growth or Development?.” 2016. Web. 22 Jan 2021.

Vancouver:

Karkanis D. Mutations économiques et démographiques en Chine : croissance ou développement ? : Economic and Demographic Mutations in China : Growth or Development?. [Internet] [Doctoral dissertation]. Université Toulouse I – Capitole; 2016. [cited 2021 Jan 22]. Available from: http://www.theses.fr/2016TOU10017.

Council of Science Editors:

Karkanis D. Mutations économiques et démographiques en Chine : croissance ou développement ? : Economic and Demographic Mutations in China : Growth or Development?. [Doctoral Dissertation]. Université Toulouse I – Capitole; 2016. Available from: http://www.theses.fr/2016TOU10017

University of Saskatchewan

21. MacAusland-Berg, Josh 1993-. FRK cancer-related mutations: Effect on enzymatic activity and cellular processes.

Degree: 2019, University of Saskatchewan

URL: http://hdl.handle.net/10388/12357

► Cancer-associated FRK mutations have not been thoroughly studied however, a previous study analyzed six cancer related mutations of BRK L16F, R131L, V253M, N317S, L343F, P450L;… (more)

▼ Cancer-associated FRK mutations have not been thoroughly studied however, a previous study analyzed six cancer related mutations of BRK L16F, R131L, V253M, N317S, L343F, P450L; and it was found that there are similar residues in FRK. We identified R64P, K87N, S145R, K265R, N359I, del V378-F379 (VF) found in breast cancer, large intestine cancer, ovarian cancer, and liver cancer. This study analyzes the effect of the mutation of these similar residues in the BRK study, as well as uncharacterized cancer related mutations of FRK. Mutating two of the similar residues maintained the same effects in BRK and FRK whereas the remaining mutants in FRK had no effect on activity. The uncharacterized cancer related mutations of FRK produced interesting results where the mutations in kinase domain (K265R, N359I, del VF) reduced, inactivated and increased kinase activity respectively. Proliferation, migration and invasion assays were also performed with the R64P, K265R, N358I and VF mutations. The proliferation data revealed that the cell line expressing wild type FRK reduced cell growth which is consistent with past findings. The other mutations also resulted in reduced cell growth in MDA-MB-231 breast cancer cells but were not significantly different to wild type FRK. The invasion assay results show that the wild type FRK significantly reduced invasion compared to the MDA-MB-231 cells compared to parental controls. Differing from the proliferation assay, the mutations R64P, K265R, N359I, and VF showed no reduction in cell invasiveness compared to the parental. The mutations expressed transiently in HEK293 were found to only impact STAT3 phosphorylation where all FRK constructs induced STAT3 phosphorylation except for N359I. Binding experiments were performed using rotational anisotropy and four peptides derived from FRK C terminus (ETDSS(pY)SDANN), SH2 consensus binding sequence (HF(pY)ENI), PTEN (PNVEEPSNPEASSS), and BRCA1 (DTYLIPQIPHSHY). The wild type SH2 domain was able of binding to both peptides from the FRK C terminus and the SH2 consensus binding sequence with a Kd of 2.5 M and 0.4 M respectively. The S145R SH2 domain was also capable of interacting with both peptides with a Kd of 1.4 M with the FRK C terminus and 0.8 M with the SH2 consensus binding sequence. Unfortunately, the SH3 domain was unable to bind to the sequences selected. Advisors/Committee Members: Lukong, Erique, Bonham, Keith, Luo, Yu, Uppalapati, Maruti.

Subjects/Keywords: Cancer associated mutations

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APA (6^th Edition):

MacAusland-Berg, J. 1. (2019). FRK cancer-related mutations: Effect on enzymatic activity and cellular processes. (Thesis). University of Saskatchewan. Retrieved from http://hdl.handle.net/10388/12357

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

MacAusland-Berg, Josh 1993-. “FRK cancer-related mutations: Effect on enzymatic activity and cellular processes.” 2019. Thesis, University of Saskatchewan. Accessed January 22, 2021. http://hdl.handle.net/10388/12357.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

MacAusland-Berg, Josh 1993-. “FRK cancer-related mutations: Effect on enzymatic activity and cellular processes.” 2019. Web. 22 Jan 2021.

Vancouver:

MacAusland-Berg J1. FRK cancer-related mutations: Effect on enzymatic activity and cellular processes. [Internet] [Thesis]. University of Saskatchewan; 2019. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/10388/12357.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

MacAusland-Berg J1. FRK cancer-related mutations: Effect on enzymatic activity and cellular processes. [Thesis]. University of Saskatchewan; 2019. Available from: http://hdl.handle.net/10388/12357

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Queens University

22. Chan, Marina. Studies of the Misprocessing Mutations R1202D and E1204K in the Drug and Organic Anion Transporter, MRP1 (ABCC1) in Cultured HEK cells .

Degree: Pharmacology and Toxicology, 2013, Queens University

URL: http://hdl.handle.net/1974/8470

► Multidrug resistance protein 1 (MRP1) is a drug and organic anion transporter of the ATP-binding cassette superfamily. Previous studies showed that opposite charge substitutions of… (more)

▼ Multidrug resistance protein 1 (MRP1) is a drug and organic anion transporter of the ATP-binding cassette superfamily. Previous studies showed that opposite charge substitutions of Arg1202 or Glu1204 in transmembrane helix (TM) 16 cause a >80% reduction in MRP1 levels when expressed in human embryonic kidney (HEK) cells. These substitutions disrupt the folding and/or assembly of MRP1 which targets it for degradation. Attempts were made to enhance levels of the R1202D and E1204K misprocessing mutants by incubating transfected HEK cells at 30 ºC or 27 ºC. At both temperatures, cells expressed both fully glycosylated and underglycosylated mutants at levels 60–70% lower than wild-type MRP1in cells grown at 37 ºC. The subcellular localization patterns of the two mutants were similar to wild-type MRP1 at all three temperatures, with most of the transporter at the plasma membrane at 37 ºC, and in the endoplasmic reticulum at 30 ºC or 27 ºC. Thus, although poorly expressed, the R1202D and E1204K mutants retained the ability to traffic to the plasma membrane. Attempts were also made to enhance R1202D and E1204K levels by exposing transfected HEK cells to chemical chaperones. Dimethyl sulfoxide and glycerol increased E1204K levels by 20-30% but decreased or had no effect on R1202D and wild-type MRP1. 4-Phenylbutyric acid had little or no effect on either wild-type or mutant MRP1. Thus both mutants were relatively resistant to rescue by chemical chaperones. Finally, a “second-site rescue mutation” approach was taken, guided by an atomic homology model of MRP1. Mutations of Tyr1133 alone decreased MRP1 levels, like R1202D; however, although substituting TM15-Tyr1133 with Phe, His and Ala in R1202D was predicted to re-establish TM15-TM16 bonding interactions, levels of this mutant did not increase. E1204K levels were also not improved by substituting TM17-Val1248 with Asp or Glu although these substitutions were predicted to re-establish TM16-TM17 bonds disrupted in E1204K. These results suggest that the bonding interactions of Arg1202 and Glu1204 with other amino acids predicted by the MRP1 homology model used in this study are insufficient to predict the critical helix-helix interactions necessary for stable MRP1 expression in mammalian cells.

Subjects/Keywords: Misprocessing Mutations ; MRP1

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APA (6^th Edition):

Chan, M. (2013). Studies of the Misprocessing Mutations R1202D and E1204K in the Drug and Organic Anion Transporter, MRP1 (ABCC1) in Cultured HEK cells . (Thesis). Queens University. Retrieved from http://hdl.handle.net/1974/8470

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Chan, Marina. “Studies of the Misprocessing Mutations R1202D and E1204K in the Drug and Organic Anion Transporter, MRP1 (ABCC1) in Cultured HEK cells .” 2013. Thesis, Queens University. Accessed January 22, 2021. http://hdl.handle.net/1974/8470.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Chan, Marina. “Studies of the Misprocessing Mutations R1202D and E1204K in the Drug and Organic Anion Transporter, MRP1 (ABCC1) in Cultured HEK cells .” 2013. Web. 22 Jan 2021.

Vancouver:

Chan M. Studies of the Misprocessing Mutations R1202D and E1204K in the Drug and Organic Anion Transporter, MRP1 (ABCC1) in Cultured HEK cells . [Internet] [Thesis]. Queens University; 2013. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/1974/8470.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Chan M. Studies of the Misprocessing Mutations R1202D and E1204K in the Drug and Organic Anion Transporter, MRP1 (ABCC1) in Cultured HEK cells . [Thesis]. Queens University; 2013. Available from: http://hdl.handle.net/1974/8470

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

23. Birgy, André. Paysage adaptatif des bêta-lactamases TEM-1 et CTX-M-15 : Adaptative landscape of beta-lactamases TEM-1 and CTX-M-15.

Degree: Docteur es, Sciences de la vie et de la santé. Microbiologie, 2017, Sorbonne Paris Cité

URL: http://www.theses.fr/2017USPCC261

►

De part leur importance médicale, leur capacité à évoluer et leur facilité de manipulations, les bêta-lactamases TEM-1 et plus récemment CTX-M-15, se sont imposées comme… (more)

▼

De part leur importance médicale, leur capacité à évoluer et leur facilité de manipulations, les bêta-lactamases TEM-1 et plus récemment CTX-M-15, se sont imposées comme des modèles de biochimie mais aussi des modèles pour une étude évolutive des protéines. La caractérisation de la distribution de l'effet des mutations dans une protéine permet d'avancer dans la compréhension des mécanismes moléculaires et des contraintes influant sur l'évolution des gènes de résistance aux antibiotiques et de façon plus globale sur les protéines.Par une approche de mutagénèse exhaustive suivie d’une évolution expérimentale sous sélection antibiotique couplée à du séquençage à haut débit, nous avons pu déterminer et décrire la distribution des effets des mutations dans la protéine TEM-1. Trois catégories de mutants ont été identifiées comme ayant des comportements différents en termes de cinétique de mort face à l'antibiotique. Des études phénotypiques ont permis de proposer un scénario impliquant une saturation progressive des principales protéines liant la pénicilline en fonction de l’activité hydrolytique du mutant de bêta-lactamase. Enfin, un modèle biochimique qualitatif compatible avec cette cinétique est proposé. La comparaison des effets des mutations entre TEM-1 et CTX-M-15, deux bêta-lactamases de la famille des sérines protéases de classe A et homologue à 30%, permet d’étudier la notion de contexte-dépendance des mutations. Notamment, à travers le résidu 251 qui est différent entre ces 2 protéines et intolérant aux mutations, nous replaçons cette problématique dans une perspective évolutive globale. Cela nous permet d’étudier les incompatibilités mutationnelles au sein des protéines et les possibilités de compensation des sites destabilisés. Nous observons une compensation à la fois globale, au travers de l’effet sur la stabilité, mais aussi locale avec une épistasie forte entre le résidu 251 et le site compensateur. Enfin, afin d’étudier de façon exhaustive les intéractions épistatiques dans les protéines, nous nous sommes focalisés sur une hélice alpha de la protéine TEM-1. L’étude de près de 73% des 22000 combinaisons mutationnelles possibles a permis de souligner l’importance de la stabilité thermodynamique, celle-ci expliquant une grande part des effets des mutations. Cependant, un contingent d’interactions ne semble pas expliquable par ce modèle ce qui montre l’importance des interactions locales au sein des hélices. Le couplage de ces approches évolutives quantitatives et mécanistiques permettent à la fois d’avancer dans la compréhension des contraintes qui sous-tendent l’évolution des protéines mais aussi de plonger au cœur de la résistance aux antibiotiques et de ses mécanismes moléculaires.

Beta-lactamases TEM-1 and more recently CTX-M-15 are antibiotic resistance enzymes that combine a medical importance, a fast evolution in the wild and are easy amenable to manipulation in the laboratory. As such, they have become models of biochemistry and also models for the study of protein evolution. The characterization…

Advisors/Committee Members: Tenaillon, Olivier (thesis director), Jacquier, Hervé (thesis director).

Subjects/Keywords: Mutations compensatrices; Distribution de l'effet des mutations; Compensatory mutations; Distribution of the effect of mutations

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Birgy, A. (2017). Paysage adaptatif des bêta-lactamases TEM-1 et CTX-M-15 : Adaptative landscape of beta-lactamases TEM-1 and CTX-M-15. (Doctoral Dissertation). Sorbonne Paris Cité. Retrieved from http://www.theses.fr/2017USPCC261

Chicago Manual of Style (16^th Edition):

Birgy, André. “Paysage adaptatif des bêta-lactamases TEM-1 et CTX-M-15 : Adaptative landscape of beta-lactamases TEM-1 and CTX-M-15.” 2017. Doctoral Dissertation, Sorbonne Paris Cité. Accessed January 22, 2021. http://www.theses.fr/2017USPCC261.

MLA Handbook (7^th Edition):

Birgy, André. “Paysage adaptatif des bêta-lactamases TEM-1 et CTX-M-15 : Adaptative landscape of beta-lactamases TEM-1 and CTX-M-15.” 2017. Web. 22 Jan 2021.

Vancouver:

Birgy A. Paysage adaptatif des bêta-lactamases TEM-1 et CTX-M-15 : Adaptative landscape of beta-lactamases TEM-1 and CTX-M-15. [Internet] [Doctoral dissertation]. Sorbonne Paris Cité; 2017. [cited 2021 Jan 22]. Available from: http://www.theses.fr/2017USPCC261.

Council of Science Editors:

Birgy A. Paysage adaptatif des bêta-lactamases TEM-1 et CTX-M-15 : Adaptative landscape of beta-lactamases TEM-1 and CTX-M-15. [Doctoral Dissertation]. Sorbonne Paris Cité; 2017. Available from: http://www.theses.fr/2017USPCC261

University of Houston

24. Wang, Mu 1988-. MUTAGENIC EFFECTS OF CHROMIUM (IV) ON HUMAN ENDOTHELIAL AND LUNG EPITHELIAL CELLS.

Degree: MS, Chemistry, 2014, University of Houston

URL: http://hdl.handle.net/10657/1430

► Effects of a chromium (IV) compound,diperoxoaquoethylenediaminechromium (IV) monohydrate (Cr(IV)-DPO), on human umbilical vein endothelial cells (HUVEC) and human bronchial epithelial cells (BEAS-2B) were investigated through… (more)

Subjects/Keywords: Mutations; Chromium(IV)

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APA (6^th Edition):

Wang, M. 1. (2014). MUTAGENIC EFFECTS OF CHROMIUM (IV) ON HUMAN ENDOTHELIAL AND LUNG EPITHELIAL CELLS. (Masters Thesis). University of Houston. Retrieved from http://hdl.handle.net/10657/1430

Chicago Manual of Style (16^th Edition):

Wang, Mu 1988-. “MUTAGENIC EFFECTS OF CHROMIUM (IV) ON HUMAN ENDOTHELIAL AND LUNG EPITHELIAL CELLS.” 2014. Masters Thesis, University of Houston. Accessed January 22, 2021. http://hdl.handle.net/10657/1430.

MLA Handbook (7^th Edition):

Wang, Mu 1988-. “MUTAGENIC EFFECTS OF CHROMIUM (IV) ON HUMAN ENDOTHELIAL AND LUNG EPITHELIAL CELLS.” 2014. Web. 22 Jan 2021.

Vancouver:

Wang M1. MUTAGENIC EFFECTS OF CHROMIUM (IV) ON HUMAN ENDOTHELIAL AND LUNG EPITHELIAL CELLS. [Internet] [Masters thesis]. University of Houston; 2014. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/10657/1430.

Council of Science Editors:

Wang M1. MUTAGENIC EFFECTS OF CHROMIUM (IV) ON HUMAN ENDOTHELIAL AND LUNG EPITHELIAL CELLS. [Masters Thesis]. University of Houston; 2014. Available from: http://hdl.handle.net/10657/1430

25. Wells, Owen Spencer. Cellular and biochemical analyses of TDP1 mediated chromosomal break repair.

Degree: PhD, 2014, University of Sussex

URL: http://sro.sussex.ac.uk/id/eprint/49564/ ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.618903

► Tyrosyl DNA phosphodiesterase 1 (TDP1) is an end- rocessing enzyme involved in the repair of abortive topoisomerase I (Top1) complexes. Although not essential for survival,… (more)

Subjects/Keywords: 570; QH0460 Mutations

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APA (6^th Edition):

Wells, O. S. (2014). Cellular and biochemical analyses of TDP1 mediated chromosomal break repair. (Doctoral Dissertation). University of Sussex. Retrieved from http://sro.sussex.ac.uk/id/eprint/49564/ ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.618903

Chicago Manual of Style (16^th Edition):

Wells, Owen Spencer. “Cellular and biochemical analyses of TDP1 mediated chromosomal break repair.” 2014. Doctoral Dissertation, University of Sussex. Accessed January 22, 2021. http://sro.sussex.ac.uk/id/eprint/49564/ ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.618903.

MLA Handbook (7^th Edition):

Wells, Owen Spencer. “Cellular and biochemical analyses of TDP1 mediated chromosomal break repair.” 2014. Web. 22 Jan 2021.

Vancouver:

Wells OS. Cellular and biochemical analyses of TDP1 mediated chromosomal break repair. [Internet] [Doctoral dissertation]. University of Sussex; 2014. [cited 2021 Jan 22]. Available from: http://sro.sussex.ac.uk/id/eprint/49564/ ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.618903.

Council of Science Editors:

Wells OS. Cellular and biochemical analyses of TDP1 mediated chromosomal break repair. [Doctoral Dissertation]. University of Sussex; 2014. Available from: http://sro.sussex.ac.uk/id/eprint/49564/ ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.618903

University of New South Wales

26. Perera, Dilmi. Investigating the role of non-coding mutations in cancer.

Degree: Prince of Wales Clinical School, 2017, University of New South Wales

URL: http://handle.unsw.edu.au/1959.4/57601 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:44168/SOURCE02?view=true

► Whole genomes are being sequenced at an accelerated pace but research into cancer causing mutations has focused primarily on protein-coding mutations owing to difficulties associated… (more)

▼ Whole genomes are being sequenced at an accelerated pace but research into cancer causing mutations has focused primarily on protein-coding mutations owing to difficulties associated with identifying and interpreting causality of noncoding mutations. Nevertheless, projects such as ENCODE and the Epigenome Atlas have led to the generation of genome-wide datasets that have contributed to our understanding of the noncoding parts of the human genome. The integration of these datasets has the potential to shed light on the functions of noncoding sequences, gene regulatory modules and epistatic interactions underlying disease associations. Moreover, through technological advances it is now feasible to routinely sequence whole genomes of cancer samples which has enable large international consortiums such as TCGA and ICGC to create public datasets consisting of mutations from whole genome sequencing of 1000s of tumour samples. The integrative analyses of datasets from these resources have provided new opportunities to interrogate non-coding cancer mutations. In order to elucidate the role of cis-regulatory mutations in cancer, I developed an annotation method and web tool to study the effect of cis-regulatory mutations in cancer and to identify potential causal mutations for further investigations. Applying this tool to whole breast cancer genome sequencing data, I discovered a point mutation in the enhancer of CDK6 that results in the overexpression of the gene. I then conducted a pan-cancer analysis of cis-regulatory mutations using somatic mutations from 1161 whole tumour genomes across 14 cancer types from publicly available data sources which revealed a previously unknown mechanism linking transcription initiation and NER as a major contributor of somatic point mutation hotspots at active gene promoters in cancer genomes. In the final chapter of the thesis, I examined cancer mutations in non-coding RNA and their effect on structure and function. Through this thesis, I have been able to significantly contribute to our understanding of non-coding or regulatory regions of the genome and the role of mutations in these regions in cancer and to develop computational methods and tools to assist experimentalists to further explore this field of science. Advisors/Committee Members: Wong, Jason, Prince of Wales Clinical School, Faculty of Medicine, UNSW, Pimanda, John, Prince of Wales Clinical School, Faculty of Medicine, UNSW.

Subjects/Keywords: Non-coding mutations

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Perera, D. (2017). Investigating the role of non-coding mutations in cancer. (Doctoral Dissertation). University of New South Wales. Retrieved from http://handle.unsw.edu.au/1959.4/57601 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:44168/SOURCE02?view=true

Chicago Manual of Style (16^th Edition):

Perera, Dilmi. “Investigating the role of non-coding mutations in cancer.” 2017. Doctoral Dissertation, University of New South Wales. Accessed January 22, 2021. http://handle.unsw.edu.au/1959.4/57601 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:44168/SOURCE02?view=true.

MLA Handbook (7^th Edition):

Perera, Dilmi. “Investigating the role of non-coding mutations in cancer.” 2017. Web. 22 Jan 2021.

Vancouver:

Perera D. Investigating the role of non-coding mutations in cancer. [Internet] [Doctoral dissertation]. University of New South Wales; 2017. [cited 2021 Jan 22]. Available from: http://handle.unsw.edu.au/1959.4/57601 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:44168/SOURCE02?view=true.

Council of Science Editors:

Perera D. Investigating the role of non-coding mutations in cancer. [Doctoral Dissertation]. University of New South Wales; 2017. Available from: http://handle.unsw.edu.au/1959.4/57601 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:44168/SOURCE02?view=true

Wright State University

27. Alsaran, Hadel Mohammed. Functional characterization of cancer-related mutations of ERK3.

Degree: MS, Biochemistry and Molecular Biology, 2016, Wright State University

URL: http://rave.ohiolink.edu/etdc/view?acc_num=wright1483791134536552

► Extracellular signal-regulated kinase 3 (ERK3) is an atypical member of the mitogen-activated protein kinase (MAPK) family. Recent studies have shown that ERK3 is highly upregulated… (more)

▼ Extracellular signal-regulated kinase 3 (ERK3) is an atypical member of the mitogen-activated protein kinase (MAPK) family. Recent studies have shown that ERK3 is highly upregulated in multiple cancers, such as lung cancer and colon cancer. Importantly, ERK3 promotes cancer cell migration and invasion by phosphorylating steroid receptor activator 3 (SRC-3), hence upregulating pro-invasive matrix metalloproteinase genes. While the link between ERK3 and cancers has been recognized, little is known about ERK3 mutations in cancer progression. In this study, we have investigated ERK3 mutations on arginine 64 (arginine 64 mutated to cysteine or histidine, R64C or R64H) and leucine 290 (leucine 290 mutated to proline or valine, L290P or L290V) that are found in cancers of lung, large intestine and skin (COSMIC database). Interestingly, both R64 and L290 residues are located in the kinase domain of ERK3 and are conserved in all ERK isoforms (ERKs1-4). In order to characterize these mutations, we generated expression vectors coating plasmids of ERK3 and each ERK3 constructs containing point mutation, and then overexpressed them in HeLa cells and lung cancer cell lines with or without stable knockdown of endogenous ERK3. Notably, we found that all of these cancer-related mutations lead to reduction of ERK3 phosphorylation at S189 within the activation loop. To study the functional impact of these ERK3 mutations on cancer cell invasiveness, we expressed each of these mutants or the wild type (WT) ERK3 in HeLa cells and lung cancer cell lines with or without stable knockdown of endogenous ERK3 and performed trans-well migration and invasion assays. Interestingly, we found that in comparison with WT ERK3, both L290P and L290V mutations significantly increased ERK3’s ability in promoting cell migration and invasion, whereas R64C and R64H mutations resulted in a decrease in cell migration. Given that all these cancer-related mutations led to reduction of ERK3 phosphorylation at S189, these results suggest that S189 phosphorylation within the activation loop is not associated with ERK3’s function in promoting cancer cell motility. To elucidate the underlying mechanism by which ERK3 L290 mutants increase cancer cell invasiveness, we examined the kinase activity of WT and mutant ERK3 in vitro by assessing the phosphorylation of SRC-3, a substrate for ERK3. We found that ERK3 L290P and L290V mutants have similar kinase activity to that of WT ERK3. ERK3 protein is known to shuttle between the nucleus and the cytoplasm, which may alter its function. Interestingly, by immunofluorescent staining, we found that both L290P and L290V mutations greatly increased the cytoplasmic localization of ERK3 proteins, whereas WT ERK3 is mostly nuclear. In conclusion, this study demonstrates that cancer-related L290P and L290V mutations lead to increased ability of ERK3 to promote cancer cell migration and invasion, possibly through their increased cytoplasmic localization. Advisors/Committee Members: Long, Weiwen (Advisor).

Subjects/Keywords: Biochemistry; ERK3; mutations

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Alsaran, H. M. (2016). Functional characterization of cancer-related mutations of ERK3. (Masters Thesis). Wright State University. Retrieved from http://rave.ohiolink.edu/etdc/view?acc_num=wright1483791134536552

Chicago Manual of Style (16^th Edition):

Alsaran, Hadel Mohammed. “Functional characterization of cancer-related mutations of ERK3.” 2016. Masters Thesis, Wright State University. Accessed January 22, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=wright1483791134536552.

MLA Handbook (7^th Edition):

Alsaran, Hadel Mohammed. “Functional characterization of cancer-related mutations of ERK3.” 2016. Web. 22 Jan 2021.

Vancouver:

Alsaran HM. Functional characterization of cancer-related mutations of ERK3. [Internet] [Masters thesis]. Wright State University; 2016. [cited 2021 Jan 22]. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=wright1483791134536552.

Council of Science Editors:

Alsaran HM. Functional characterization of cancer-related mutations of ERK3. [Masters Thesis]. Wright State University; 2016. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=wright1483791134536552

NSYSU

28. Huang, Min-Ying. Mitochondrial DNA Sequence Analyses of Acromitus flagellatus.

Degree: Master, Marine Biotechnology and Resources, 2014, NSYSU

URL: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0809114-132609

► Jellyfish are no-polypform of the Cnidaria. And also are typical free-swimming marine animals that has umbrella-liked bell and many tentacles.They can found in freshwater and… (more)

Subjects/Keywords: Acromitus flagellates; jellyfish; Phylogenetic analyses; linear mtDNA

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APA (6^th Edition):

Huang, M. (2014). Mitochondrial DNA Sequence Analyses of Acromitus flagellatus. (Thesis). NSYSU. Retrieved from http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0809114-132609

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Huang, Min-Ying. “Mitochondrial DNA Sequence Analyses of Acromitus flagellatus.” 2014. Thesis, NSYSU. Accessed January 22, 2021. http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0809114-132609.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Huang, Min-Ying. “Mitochondrial DNA Sequence Analyses of Acromitus flagellatus.” 2014. Web. 22 Jan 2021.

Vancouver:

Huang M. Mitochondrial DNA Sequence Analyses of Acromitus flagellatus. [Internet] [Thesis]. NSYSU; 2014. [cited 2021 Jan 22]. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0809114-132609.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Huang M. Mitochondrial DNA Sequence Analyses of Acromitus flagellatus. [Thesis]. NSYSU; 2014. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0809114-132609

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Oregon State University

29. Sremba, Angie. A whale's tale of mtDNA diversity and differentiation : the Antarctic blue whale.

Degree: MS, Fisheries Science, 2011, Oregon State University

URL: http://hdl.handle.net/1957/20064

► Twentieth century commercial whaling drastically reduced the abundance of great whale populations in the Southern Ocean. Exploitation began on the south Atlantic island of South… (more)

▼ Twentieth century commercial whaling drastically reduced the abundance of great whale populations in the Southern Ocean. Exploitation began on the south Atlantic island of South Georgia, where catch records account for over 175,000 whales killed. Modern whaling within the Southern Ocean depleted populations rapidly, and by 1966, hunting blue whales south of 40°S was prohibited by the International Whaling Commission (IWC). After 40 years of protection, this species has shown little recovery. A current abundance estimate of 2,280 (CV=0.036) individuals from sighting data (1991/92-2003/04) represents less than 1% the original abundance. With such an intensive demographic 'bottleneck,' it is likely that genetic diversity has been lost from some or all components of the Southern Ocean population. Here I describe historical and contemporary Antarctic blue whale mtDNA diversity and report the first circumpolar analyses of contemporary population structure. In Chapter 2, historical mtDNA diversity is described from whale bones collected from the first Southern Hemisphere whaling stations established in 1904 on the island of South Georgia. A total of 281 whale bones were representative of three prominent species hunted in South Georgian waters. Using ancient DNA methods and sequencing of the mtDNA control region, bone samples were first identified to species, identifying 153 humpback, 49 fin, 18 blue, 2 sei, 1 southern right whale and 1 elephant seal. Within each of the three prominent historic species populations, mtDNA haplotypes were described resulting in 64 humpback, 34 fin, and 16 blue whale haplotypes. Haplotype and nucleotide diversity within each of the three historic species populations ranged from 0.980-0.987 and 1.87-3.16%, respectively. In chapter 3, I update the previous estimate of contemporary Antarctic blue whale mtDNA diversity with biopsy samples of living whales collected during research cruises conducted with IWC oversight from 1990-2009 (n=218) for comparison to historical blue whale mtDNA diversity. After the removal of replicate samples based on 15 microsatellite loci, the dataset described 167 individuals. This dataset was combined with additional published Antarctic blue whale mtDNA control region sequences (LeDuc et al. 2007; n=20) to represent the most comprehensive dataset available for Antarctic blue whale mtDNA diversity (n=187). A high haplotype diversity was described within this contemoporary population (0.968). With this dataset, I report the first evidence of population structure within the IWC Southern Ocean management Areas I-VI through an analysis of genetic differentiation. The identification of recaptures within the dataset through microsatellite genotyping, allows for the first inference of movement of six individuals with the Southern Ocean since the end of the Discovery marking program 50 years ago. In the final chapter of this thesis, I explore the impact of the 20th century commercial whaling industry on the Antarctic blue whale population through a comparison of historical and… Advisors/Committee Members: Baker, C. Scott (advisor), Liston, Aaron (committee member).

Subjects/Keywords: mtDNA diversity; Blue whale – Antarctic Ocean – Genetics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Sremba, A. (2011). A whale's tale of mtDNA diversity and differentiation : the Antarctic blue whale. (Masters Thesis). Oregon State University. Retrieved from http://hdl.handle.net/1957/20064

Chicago Manual of Style (16^th Edition):

Sremba, Angie. “A whale's tale of mtDNA diversity and differentiation : the Antarctic blue whale.” 2011. Masters Thesis, Oregon State University. Accessed January 22, 2021. http://hdl.handle.net/1957/20064.

MLA Handbook (7^th Edition):

Sremba, Angie. “A whale's tale of mtDNA diversity and differentiation : the Antarctic blue whale.” 2011. Web. 22 Jan 2021.

Vancouver:

Sremba A. A whale's tale of mtDNA diversity and differentiation : the Antarctic blue whale. [Internet] [Masters thesis]. Oregon State University; 2011. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/1957/20064.

Council of Science Editors:

Sremba A. A whale's tale of mtDNA diversity and differentiation : the Antarctic blue whale. [Masters Thesis]. Oregon State University; 2011. Available from: http://hdl.handle.net/1957/20064

Rochester Institute of Technology

30. Mizuki, Psalm. mtPrimer3: PCR primer design for mtDNA.

Degree: Thomas H. Gosnell School of Life Sciences (COS), 2010, Rochester Institute of Technology

URL: https://scholarworks.rit.edu/theses/4107

► Due to their usefulness in tracking the evolution of man and the discovery that they cause many different diseases, the scientific community has become extremely… (more)

Subjects/Keywords: mtDNA; Primer design

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APA (6^th Edition):

Mizuki, P. (2010). mtPrimer3: PCR primer design for mtDNA. (Thesis). Rochester Institute of Technology. Retrieved from https://scholarworks.rit.edu/theses/4107

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Mizuki, Psalm. “mtPrimer3: PCR primer design for mtDNA.” 2010. Thesis, Rochester Institute of Technology. Accessed January 22, 2021. https://scholarworks.rit.edu/theses/4107.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Mizuki, Psalm. “mtPrimer3: PCR primer design for mtDNA.” 2010. Web. 22 Jan 2021.

Vancouver:

Mizuki P. mtPrimer3: PCR primer design for mtDNA. [Internet] [Thesis]. Rochester Institute of Technology; 2010. [cited 2021 Jan 22]. Available from: https://scholarworks.rit.edu/theses/4107.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Mizuki P. mtPrimer3: PCR primer design for mtDNA. [Thesis]. Rochester Institute of Technology; 2010. Available from: https://scholarworks.rit.edu/theses/4107

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Open Access Theses and Dissertations