You searched for subject:(Mutation).
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University of Georgia
1.
Gresham, Cory Sands.
The oocyte as a transmitter and mediator of genetic damage to offspring.
Degree: PhD, Toxicology, 2013, University of Georgia
URL: http://purl.galileo.usg.edu/uga_etd/gresham_cory_s_201312_phd 
► Although numerous chemical germ cell mutagens have been identified in research animals, no chemical mutagens have been positively identified in human germ cells. The paucity…
(more)
▼ Although numerous chemical germ cell mutagens have been identified in research animals, no chemical mutagens have been positively identified in human germ cells. The paucity of effective methods to investigate mutations in human germ cells intensifies the need for germ cell
mutation research in animal models. Furthermore, the vast majority of existing germline mutagenesis research has focused exclusively on male germ cells while very little is known about mutagenesis in female germ cells. The λ transgenic medaka (a small fish carrying the cII
mutation reporter gene) was used to investigate the various roles of the oocyte in the transmission and repair of
mutations from mutagen-treated parents to their offspring. To investigate the direct transmission of genetic damage to offspring via the oocyte, female transgenic medaka were exposed to the chemical mutagen, 1-ethyl-1-nitrosourea, and bred to wild-type males. Eighteen percent of the offspring (14/80) displayed an increased frequency of mutations in the cII gene (cII MF). This frequency of mutant offspring indicated that female germ cells were more sensitive to chemical mutagens than premeiotic male germ cells (18% vs. 4%, X2, p<0.01), which contradicted past research. Further experiments revealed 2% of offspring derived from treated oocytes showed increased cII MF in the unexposed, paternally derived cII gene. These untargeted mutations
occurred in regions of DNA never exposed to the mutagen, a hallmark of genomic instability. Untargeted experiments were repeated in transgenic mice to further investigate untargeted mutations, and revealed a similar response in both fish and mammalian animal models, thus indicating a conserved mechanism. The untargeted mutations occurred post-fertilization, under the direction of the early embryo. Finally, the role of the oocyte’s DNA repair enzymes in response to DNA damage in the early embryo was investigated. The frequency of affected offspring derived from oocytes lacking functional p53 was significantly higher than offspring derived from wild-type oocytes (36% vs. 11%, X2, p<0.01). These experiments demonstrated that female germ-cells may be equally sensitive to chemical mutagens as male germ cells. Additionally, mutations observed in the offspring were fixed after fertilization, where DNA damage responses likely depended on the cellular processes of the oocyte.
Advisors/Committee Members: Travis C. Glenn.
Subjects/Keywords: Mutation
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APA (6th Edition):
Gresham, C. S. (2013). The oocyte as a transmitter and mediator of genetic damage to offspring. (Doctoral Dissertation). University of Georgia. Retrieved from http://purl.galileo.usg.edu/uga_etd/gresham_cory_s_201312_phd
Chicago Manual of Style (16th Edition):
Gresham, Cory Sands. “The oocyte as a transmitter and mediator of genetic damage to offspring.” 2013. Doctoral Dissertation, University of Georgia. Accessed February 16, 2020.
http://purl.galileo.usg.edu/uga_etd/gresham_cory_s_201312_phd.
MLA Handbook (7th Edition):
Gresham, Cory Sands. “The oocyte as a transmitter and mediator of genetic damage to offspring.” 2013. Web. 16 Feb 2020.
Vancouver:
Gresham CS. The oocyte as a transmitter and mediator of genetic damage to offspring. [Internet] [Doctoral dissertation]. University of Georgia; 2013. [cited 2020 Feb 16].
Available from: http://purl.galileo.usg.edu/uga_etd/gresham_cory_s_201312_phd.
Council of Science Editors:
Gresham CS. The oocyte as a transmitter and mediator of genetic damage to offspring. [Doctoral Dissertation]. University of Georgia; 2013. Available from: http://purl.galileo.usg.edu/uga_etd/gresham_cory_s_201312_phd
University of Georgia
2.
de Souza Amado, Joaquim Eustaquio.
Characterization of Campylobacter jejuni response to the mutant prevention concentration hypothesis.
Degree: PhD, Veterinary Pathology, 2008, University of Georgia
URL: http://purl.galileo.usg.edu/uga_etd/de_souza_amado_joaquim_e_200812_phd
► In this age of antimicrobial resistance concerns, a new hypothesis has been proposed that could serve to increase the lifespan of our antimicrobial stock. It…
(more)
▼ In this age of antimicrobial resistance concerns, a new hypothesis has been proposed that could serve to increase the lifespan of our antimicrobial stock. It is termed the mutant prevention concentration (MPC) hypothesis, and it states that in every interaction between microbe and antibiotic there is a concentration that will prevent first step spontaneous mutants from appearing after approximately 10
10 CFUs of bacteria are exposed to the drug of choice. Additional research is needed before this hypothesis could be useful in practical determinations to help establish day-to-day treatment of bacterial infections both in humans and animals. There are many factors, beside the classical and known antimicrobial targets, that are involved in antimicrobial resistance acquisition and facilitation of such events.
Approximately 10
10 CFU of Campylobacter jejuni 81116 and three laboratory derived mutants carrying insertional deletions respectively at cmeB (efflux pump), cmeR (regulator of the efflux pump) and one presenting a Thr-86-Ile
mutation in the gyrA gene, were exposed to 2-fold increasing concentrations of nalidixic acid, norfloxacin, enrofloxacin and ciprofloxacin.
Mutation frequencies were recorded at each concentration along with the mutant prevention concentration (MPC), and minimum inhibitory concentrations (MICs) for isolated colonies selected over several trials. Susceptibility results (MICs) were also recorded for each isolate before exposure to each antimicrobial. Susceptibility measurements before exposure of the parent and its transformants to each fluoroquinolone showed a 2-fold decrease for the cmeB DNA sequence deleted transformant. Additionally, the absence of CmeB protein decreased the MPC consistently by 2-fold for every fluoroquinolone tested. This protein absence also translated into statistically significant
mutation frequency decrease. When CmeB protein was over-expressed in the cmeR sequence insertionally deleted transformant, there were no apparent impacts on MPC or on
mutation frequencies.
The data from these studies reveal how MPC could be used as a tool to predict the usefulness of an antimicrobial coupled with the MIC methodology. It also shows that MPC could be another tool for deciding which dose of an antimicrobial to use and which antimicrobial is the one of choice.
Advisors/Committee Members: Paula Fedorka-Cray.
Subjects/Keywords: mutation frequency
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APA (6th Edition):
de Souza Amado, J. E. (2008). Characterization of Campylobacter jejuni response to the mutant prevention concentration hypothesis. (Doctoral Dissertation). University of Georgia. Retrieved from http://purl.galileo.usg.edu/uga_etd/de_souza_amado_joaquim_e_200812_phd
Chicago Manual of Style (16th Edition):
de Souza Amado, Joaquim Eustaquio. “Characterization of Campylobacter jejuni response to the mutant prevention concentration hypothesis.” 2008. Doctoral Dissertation, University of Georgia. Accessed February 16, 2020.
http://purl.galileo.usg.edu/uga_etd/de_souza_amado_joaquim_e_200812_phd.
MLA Handbook (7th Edition):
de Souza Amado, Joaquim Eustaquio. “Characterization of Campylobacter jejuni response to the mutant prevention concentration hypothesis.” 2008. Web. 16 Feb 2020.
Vancouver:
de Souza Amado JE. Characterization of Campylobacter jejuni response to the mutant prevention concentration hypothesis. [Internet] [Doctoral dissertation]. University of Georgia; 2008. [cited 2020 Feb 16].
Available from: http://purl.galileo.usg.edu/uga_etd/de_souza_amado_joaquim_e_200812_phd.
Council of Science Editors:
de Souza Amado JE. Characterization of Campylobacter jejuni response to the mutant prevention concentration hypothesis. [Doctoral Dissertation]. University of Georgia; 2008. Available from: http://purl.galileo.usg.edu/uga_etd/de_souza_amado_joaquim_e_200812_phd
University of Utah
3.
Jeong, Hotcherl.
Pyridine transport and assimilation in salmonella enterica.
Degree: PhD, Biology;, 2002, University of Utah
URL: http://content.lib.utah.edu/cdm/singleitem/collection/etd2/id/1417/rec/945
► The goal of this work was to reveal how various pyridines are transported and assimilated in Salmonella enterica. In the first strategy, mutants were isolated…
(more)
▼ The goal of this work was to reveal how various pyridines are transported and assimilated in Salmonella enterica. In the first strategy, mutants were isolated that allow the use of nicotinamide mononucleotide (NMN) as a sole pyridine source when all known import routes are blocked. The major responsible mutations (pnuP*) affected a transmembrane-spanning protein, whose closest homolog is YegT, a putative nucleoside transporter. A minor class (pnuP*) affected the ydeA gene encoding a homolog of drug:H+ antiporters. It is suggested that PnuD and PnuP are both adapted transporters that have been altered to transport nicotinamide ribonucleoside (NmR). As seen for the PnuC transporter, assimilation of NMN using PnuD* or PnuP* depended on AphA and Nadl(T) functions. It is suggested that NMN is converted to NmR prior to import through PnuC, PnuD*, or PnuP*, and NmR is phosphorylated by Nadl(T) after entry. In the second strategy, mutants were isolated that improve quinolinic acid (Qa) assimilation. Mutants able to grow on a low concentration of Qa affected eight different loci. The affected genes were grouped into three categories based on their mode of action. Group I included four classes of mutations that recruited an adapted transporter: the pnuF* (yabN), pnuG* (opp), pnuH* (kefA), and pnul* mutations. It is suggested that wild-type PnuF and Opp may contribute to pyridine transport under some conditions. Group II comprised mutations in genes encoding enzymes involved in glycolysis: pgi, pfkA, and ptsG. It is proposed that these mutations enhance Qa assimilation by increasing the level of cAMP, which induces Qa transporter(s). Group III (pnuM) appeared to amplify the gabP gene encoding the GABA permease. This is the first report, in which the GABA transporter has been shown to transport Qa in any organism.
Subjects/Keywords: Mutation
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APA (6th Edition):
Jeong, H. (2002). Pyridine transport and assimilation in salmonella enterica. (Doctoral Dissertation). University of Utah. Retrieved from http://content.lib.utah.edu/cdm/singleitem/collection/etd2/id/1417/rec/945
Chicago Manual of Style (16th Edition):
Jeong, Hotcherl. “Pyridine transport and assimilation in salmonella enterica.” 2002. Doctoral Dissertation, University of Utah. Accessed February 16, 2020.
http://content.lib.utah.edu/cdm/singleitem/collection/etd2/id/1417/rec/945.
MLA Handbook (7th Edition):
Jeong, Hotcherl. “Pyridine transport and assimilation in salmonella enterica.” 2002. Web. 16 Feb 2020.
Vancouver:
Jeong H. Pyridine transport and assimilation in salmonella enterica. [Internet] [Doctoral dissertation]. University of Utah; 2002. [cited 2020 Feb 16].
Available from: http://content.lib.utah.edu/cdm/singleitem/collection/etd2/id/1417/rec/945.
Council of Science Editors:
Jeong H. Pyridine transport and assimilation in salmonella enterica. [Doctoral Dissertation]. University of Utah; 2002. Available from: http://content.lib.utah.edu/cdm/singleitem/collection/etd2/id/1417/rec/945
McGill University
4.
Slater, Mark.
Identification of Mutations at Codon 184 of Simian Immunodeficiency VirusReverse Transcriptase Which Confer Resistance to 3TC.
Degree: MS, Department of Microbiology and Immunology, 1999, McGill University
URL: http://digitool.library.mcgill.ca/thesisfile150598.pdf
► SNmac variants resistant to 3TC were generated by in vitro passage with drug selection. C8166 human T-cells were infected with SIVmac32H and passaged in tissue…
(more)
▼ SNmac variants resistant to 3TC were generated by in vitro passage with drug selection. C8166 human T-cells were infected with SIVmac32H and passaged in tissue culture with increasing 3TC selective pressure. At 8 weeks (2.5uM 3TC) viral variants were capable of growth at > 1 OOO-fold the normal inhibitory concentration of3TC, and at 24 weeks (750uM 3TC) were capable of growth at >4000-fold normal inhibitory concentration. RT-coding regions of3TC-resistant variants were then PCR-amplified, cloned, and sequenced. All 2.5 uM clones sequenced contained a M1841 (ATG->ATA) substitution, while all 750 uM clones contained a M184V (ATG->GTA) substitution. We introduced M1841 and M184V mutations into SIVmac239 by site-directed mutagenesis and analyzed the susceptibility of these mutants to several antiviral compounds. M1841 and M184V mutants displayed elevated 3TC resistance (IC50's >500uM for both, versus 1.8uM for wild type SN), thus substantiating the role of these mutations in SIV resistance to 3TC.
Cellules de la ligne humaine C8166 étaient infectes avec le VISmac32H et propages en culture de tissu avec de la pression sélective exercée par le 3TC. Après huit semaines (2.5uM 3TC) les variants étaient capable de croissance a > 1000 -fois la concentration inhibitoire normale de 3TC. Après vingt-quatre semaines (750uM 3TC), les variants étaient capable de croissance a>4000-fois la normale. Séquences RT des variants résistantes a3TC (2.5 et 750IlM) étaient amplifiées par PCR, clonées, puis séquencées. Tous les clones résistants (2.5IlM) séquences avait un mutation MI84I. Tous les clones résistants (750tlM) séquence avait un mutation MI84V (ATG~GTA). Nous avons introduit des mutations MI84I et Ml84V dans le VISmac239 par mutagenese dirigée. Les formes mutées ont démontrées un résistance élevée au 3TC (IC5o>500uM pour MI84I et MI84V, versus 1.8uM pour le type sauvage VIS). Ceci justifie le rôle qu'ont ces mutations auprès de la résistance qu'a le VIS au 3TC.
Advisors/Committee Members: ().
Subjects/Keywords: Mutation
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Université de Neuchâtel
5.
Lovis, Leonore.
Evaluation of acaricide resistance in the cattle tick,
'Rhipicephalus (Boophilus) microplus', using a new in vitro test
and molecular tools.
Degree: 2012, Université de Neuchâtel
URL: http://doc.rero.ch/record/30407
► <i>Rhipicephalus (Boophilus) microplus</i> est une tique des bovins à un hôte qui se trouve dans les zones tropicales et subtropicales. Cet ectoparasite a un impact…
(more)
▼ <i>Rhipicephalus (Boophilus) microplus</i>
est une tique des bovins à un hôte qui se trouve dans les zones
tropicales et subtropicales. Cet ectoparasite a un impact
économique très important sur l’élevage bovin dans toutes les
régions où il se trouve. Au Brésil, par exemple, les pertes dues à
son impact direct et indirect ont été estimées à 2 milliards de
dollars US en 2000. Le contrôle des populations de tiques des
bovins repose essentiellement sur l’utilisation d’acaricides.
L’utilisation intensive de ce moyen de lutte a eu pour conséquence
le développement de résistances à la majorité des classes
d’acaricides disponibles sur le marché. Un suivi local de la
résistance aux acaricides est essentiel afin que les éleveurs
puissent recevoir des informations sur les composés auxquels les
populations de tiques présentes dans leur établissement sont
résistantes et être guidés dans le choix de composés de
remplacement à disposition. A une échelle globale, le suivi de la
résistance permet d’observer sa progression afin d’essayer de
ralentir son développement et d’allonger la durée d’utilisation des
composés. Les tests <i>in vitro</i> sont des
méthodes très utiles pour détecter la résistance des tiques. La FAO
recommande deux d’entre eux, l’un utilisant des larves, nommé
Larval Packet test (LPT), l’autre utilisant des adultes, appelé
Adult Immersion Test (AIT). Chaque test a ses avantages et ses
inconvénients : le LPT est un test laborieux qui prend beaucoup de
temps alors que le AIT nécessite une grande quantité de tiques. Ces
désavantages limitent le nombre de composés et de doses pouvant
être testés, limitant ainsi l’information obtenue. Pour surmonter
ces difficultés, nous avons développé un nouveau test, nommé Larval
Tarsal Test (LTT), qui permet de tester de nombreux composés en peu
de temps et avec un minimum de tiques. Dans ce test, des œufs de
tiques sont distribués dans des puits de plaques de microtritation
préalablement traités avec les acaricides voulant être testés. Les
œufs sont incubés jusqu’à l’éclosion des larves, qui sont ainsi
exposées aux composés. La résistance des souches de tiques est
alors évaluée en fonction de la mortalité des larves écloses. La
capacité du LTT à détecter la résistance a été comparée au LPT, un
des tests recommandés par la FAO. Pour cela, une souche de tiques
sensible ainsi qu’une souche résistante de référence ont été
exposées à neuf composés de cinq classes principales d’acaricides :
les organophosphorés (OP), les pyréthroïdes de synthèse (SP), les
amidines, les lactones macrocycliques (ML) et les phénylpyrazoles.
Le LTT a permis d’obtenir de bonnes courbes de dose-réponse, il
s’est montré aussi sensible que le LPT et, à mortalités
équivalentes, a nécessité des doses de composés nettement plus
basses que le LPT. Ayant démontré que le LTT est un test
adéquat, des populations de tiques provenant d’Argentine, d’Afrique
du Sud et d’Australie ont été envoyées en Suisse pour évaluer leur
résistance à l’aide du LTT. Ces tests ont confirmé l’intérêt du LTT
à être utilisé pour…
Advisors/Committee Members: Bruno (Dir.), Heinz (Codir.).
Subjects/Keywords: point mutation
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APA (6th Edition):
Lovis, L. (2012). Evaluation of acaricide resistance in the cattle tick,
'Rhipicephalus (Boophilus) microplus', using a new in vitro test
and molecular tools. (Thesis). Université de Neuchâtel. Retrieved from http://doc.rero.ch/record/30407
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Lovis, Leonore. “Evaluation of acaricide resistance in the cattle tick,
'Rhipicephalus (Boophilus) microplus', using a new in vitro test
and molecular tools.” 2012. Thesis, Université de Neuchâtel. Accessed February 16, 2020.
http://doc.rero.ch/record/30407.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Lovis, Leonore. “Evaluation of acaricide resistance in the cattle tick,
'Rhipicephalus (Boophilus) microplus', using a new in vitro test
and molecular tools.” 2012. Web. 16 Feb 2020.
Vancouver:
Lovis L. Evaluation of acaricide resistance in the cattle tick,
'Rhipicephalus (Boophilus) microplus', using a new in vitro test
and molecular tools. [Internet] [Thesis]. Université de Neuchâtel; 2012. [cited 2020 Feb 16].
Available from: http://doc.rero.ch/record/30407.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Lovis L. Evaluation of acaricide resistance in the cattle tick,
'Rhipicephalus (Boophilus) microplus', using a new in vitro test
and molecular tools. [Thesis]. Université de Neuchâtel; 2012. Available from: http://doc.rero.ch/record/30407
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Pennsylvania
6.
Singh, Tanya.
Hypermutability in Asexuals: Investigating the Effects of Deleterious Mutations.
Degree: 2016, University of Pennsylvania
URL: https://repository.upenn.edu/edissertations/2020
► Mutation is the ultimate source of the genetic variation—including genetic variation for mutation rate itself—that fuels evolution. Selection to increase the genomic mutation rate, driven…
(more)
▼ Mutation is the ultimate source of the genetic variation—including genetic variation for mutation rate itself—that fuels evolution. Selection to increase the genomic mutation rate, driven by selective sweeps of beneficial mutations, can be strong and rapid where genetic linkage is present, as evidenced by numerous observations in experimental microbial populations. Selection to decrease the mutation rate, in contrast, is expected to depend on avoidance of mutational load and act over a longer time scale. In keeping with this latter expectation, there have been relatively few experimental observations of the evolution of reduced genomic mutation rates. Here, I report the rapid evolution of reduced mutation rates in hypermutable E. coli populations propagated at extremely small effective size—a circumstance under which selection is generally minimized. I hypothesize that high deleterious mutation pressure can strengthen indirect selection favoring lower mutation rates in these populations, and find both phenotypic and genotypic evidence to support this hypothesis. Additionally, I use simulations to analyze the effect of high deleterious mutation pressure on nascent neutral lineages that arise in an expanding asexual population and find that the spread of these lineages can be impaired. I discuss these results in the light of fates of novel mutations and point to future work that will involve studying the fates of adaptive mutation under high deleterious mutation pressure.
Subjects/Keywords: Deleterious Mutation; Evolutionary Genetics; Mutation; Mutation Accumulation; Mutation Rate Evolution; Neutral Mutation; Biology; Microbiology
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APA ·
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APA (6th Edition):
Singh, T. (2016). Hypermutability in Asexuals: Investigating the Effects of Deleterious Mutations. (Thesis). University of Pennsylvania. Retrieved from https://repository.upenn.edu/edissertations/2020
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Singh, Tanya. “Hypermutability in Asexuals: Investigating the Effects of Deleterious Mutations.” 2016. Thesis, University of Pennsylvania. Accessed February 16, 2020.
https://repository.upenn.edu/edissertations/2020.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Singh, Tanya. “Hypermutability in Asexuals: Investigating the Effects of Deleterious Mutations.” 2016. Web. 16 Feb 2020.
Vancouver:
Singh T. Hypermutability in Asexuals: Investigating the Effects of Deleterious Mutations. [Internet] [Thesis]. University of Pennsylvania; 2016. [cited 2020 Feb 16].
Available from: https://repository.upenn.edu/edissertations/2020.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Singh T. Hypermutability in Asexuals: Investigating the Effects of Deleterious Mutations. [Thesis]. University of Pennsylvania; 2016. Available from: https://repository.upenn.edu/edissertations/2020
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Texas – Austin
7.
Wang, Kaiyuan.
MuAlloy : an automated mutation system for alloy.
Degree: MSin Engineering, Electrical and Computer Engineering, 2015, University of Texas – Austin
URL: http://hdl.handle.net/2152/31865
► Mutation is a powerful technique that researchers have studied for several decades in the context of imperative code. For example, mutation testing is commonly considered…
(more)
▼ Mutation is a powerful technique that researchers have studied for several decades in the context of imperative code. For example,
mutation testing is commonly considered a '"gold standard"' for test suite quality.
Mutation in the context of declarative languages is a less studied problem. This thesis introduces a foundation for
mutation-driven analyses for Alloy, a first-order, declarative language based on relations. Specifically, we introduce a family of
mutation operators for Alloy models and define algorithms for applying the operators on different parts of the models. We embody these operators and algorithms in our prototype tool MuAlloy that provides a GUI-based front-end for customizing the application of
mutation operators. To demonstrate the potential of our approach, we illustrate the use of MuAlloy in two application scenarios: (1)
mutation testing for Alloy (in the spirit of traditional
mutation testing for imperative languages); and (2) program repair for Alloy using
mutation.
Advisors/Committee Members: Khurshid, Sarfraz (advisor), Perry, Dewayne E. (committee member).
Subjects/Keywords: MuAlloy; Mutation; Alloy; Mutation testing; Repair
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APA ·
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APA (6th Edition):
Wang, K. (2015). MuAlloy : an automated mutation system for alloy. (Masters Thesis). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/31865
Chicago Manual of Style (16th Edition):
Wang, Kaiyuan. “MuAlloy : an automated mutation system for alloy.” 2015. Masters Thesis, University of Texas – Austin. Accessed February 16, 2020.
http://hdl.handle.net/2152/31865.
MLA Handbook (7th Edition):
Wang, Kaiyuan. “MuAlloy : an automated mutation system for alloy.” 2015. Web. 16 Feb 2020.
Vancouver:
Wang K. MuAlloy : an automated mutation system for alloy. [Internet] [Masters thesis]. University of Texas – Austin; 2015. [cited 2020 Feb 16].
Available from: http://hdl.handle.net/2152/31865.
Council of Science Editors:
Wang K. MuAlloy : an automated mutation system for alloy. [Masters Thesis]. University of Texas – Austin; 2015. Available from: http://hdl.handle.net/2152/31865
University of Minnesota
8.
Burns, Michael Bradley.
APOBEC3B-driven mutagenesis in breast and other human cancers.
Degree: PhD, Biochemistry, Molecular Bio, and Biophysics, 2013, University of Minnesota
URL: http://purl.umn.edu/159637
► Cancer is a disease that results from alteration of the cellular genome. The sources of these changes are multifarious, and in many cases unknown. This…
(more)
▼ Cancer is a disease that results from alteration of the cellular genome. The sources of these changes are multifarious, and in many cases unknown. This thesis focuses on the polynucleotide cytosine deaminase, APOBEC3B, as a newly discovered source of mutation in multiple human cancers. As a deaminase, APOBEC3B converts cytosines to uracils in single-stranded DNA. These uracil lesions are mutagenic as failure to properly repair them can result in a wide variety of mutation types.
The initial discovery of this mutational phenomenon was described mechanistically using a variety of biochemical, genetic, and cellular assays in breast cancer cell lines. Follow-up work using publicly available next generation sequencing and clinical data indicated that this effect is operating in a large proportion of breast cancers. Expanded bioinformatic analysis that assessed APOBEC3B's potential impact was expanded to include 18 other human cancer types in addition to breast. This work shows that APOBEC3B is likely a significant contributor to the genetic heterogeneity in breast, head & neck, bladder, cervical, and lung (adeno- and squamous cell) carcinomas as evidenced by differential levels of expression in cancer tissues, increased mutation load, mutation clusters (kataegis), and an APOBEC3B mutation signature in tumors expressing high levels of this enzyme. Taken together, this thesis is a body of work describing a previously unappreciated source of genetic heterogeneity in several human cancers.
Subjects/Keywords: APOBEC3B; Cancer; Mutation
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APA ·
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APA (6th Edition):
Burns, M. B. (2013). APOBEC3B-driven mutagenesis in breast and other human cancers. (Doctoral Dissertation). University of Minnesota. Retrieved from http://purl.umn.edu/159637
Chicago Manual of Style (16th Edition):
Burns, Michael Bradley. “APOBEC3B-driven mutagenesis in breast and other human cancers.” 2013. Doctoral Dissertation, University of Minnesota. Accessed February 16, 2020.
http://purl.umn.edu/159637.
MLA Handbook (7th Edition):
Burns, Michael Bradley. “APOBEC3B-driven mutagenesis in breast and other human cancers.” 2013. Web. 16 Feb 2020.
Vancouver:
Burns MB. APOBEC3B-driven mutagenesis in breast and other human cancers. [Internet] [Doctoral dissertation]. University of Minnesota; 2013. [cited 2020 Feb 16].
Available from: http://purl.umn.edu/159637.
Council of Science Editors:
Burns MB. APOBEC3B-driven mutagenesis in breast and other human cancers. [Doctoral Dissertation]. University of Minnesota; 2013. Available from: http://purl.umn.edu/159637
University of Houston
9.
Wang, Mu 1988-.
MUTAGENIC EFFECTS OF CHROMIUM (IV) ON HUMAN ENDOTHELIAL AND LUNG EPITHELIAL CELLS.
Degree: Chemistry, Department of, 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)
▼ 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 morphological, cell viability, gene expression, and cDNA sequencing assays. The cell morphology showed both HUVEC and BEAS-2B cells suffered significant but different degrees of damage and demonstrated features indicating carcinogenesis when these cell lines were exposed to Cr(IV)-DPO for different time durations. Results from viability and morphological assays indicated that genotoxic damages of Cr(IV)-DPO to HUVEC and BEAS-2B cells were both concentration and time dependent. With longer time exposure up to 72 hr or higher concentration up to 100 µM, these damages were more pronounced. To understand the specific nature of these damages, expressions of apoptotic and DNA repair genes by RT2-PCR arrays, and cDNA sequencing studies were carried out. Expressions of most apoptotic genes of HUVEC were altered; in particular, they were over-expressed due to the chronic Cr(IV)-DPO exposure (5 µM, 48 hr), indicating that Cr(IV) inhibited cellular proliferation in response to the oxidative damage. When BEAS-2B cells were treated with the same concentration of Cr(IV)-DPO, DNA repair genes displayed responses less actively as the exposure time increased. Gene sequencing experiments on Cr(IV)- treated BEAS-2B cells exhibited remarkable mutations with transverse mutations dominated the variants. These gene mutations were random and not confined to guanine bases as reported in the literature.
Advisors/Committee Members: Bose, Rathindra N. (advisor), Gilbertson, Scott R. (committee member), Thummel, Randolph P. (committee member), Wang, Yuhong (committee member).
Subjects/Keywords: Mutation; chromium(IV)
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APA (6th Edition):
Wang, M. 1. (2014). MUTAGENIC EFFECTS OF CHROMIUM (IV) ON HUMAN ENDOTHELIAL AND LUNG EPITHELIAL CELLS. (Thesis). University of Houston. Retrieved from http://hdl.handle.net/10657/1430
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Wang, Mu 1988-. “MUTAGENIC EFFECTS OF CHROMIUM (IV) ON HUMAN ENDOTHELIAL AND LUNG EPITHELIAL CELLS.” 2014. Thesis, University of Houston. Accessed February 16, 2020.
http://hdl.handle.net/10657/1430.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Wang, Mu 1988-. “MUTAGENIC EFFECTS OF CHROMIUM (IV) ON HUMAN ENDOTHELIAL AND LUNG EPITHELIAL CELLS.” 2014. Web. 16 Feb 2020.
Vancouver:
Wang M1. MUTAGENIC EFFECTS OF CHROMIUM (IV) ON HUMAN ENDOTHELIAL AND LUNG EPITHELIAL CELLS. [Internet] [Thesis]. University of Houston; 2014. [cited 2020 Feb 16].
Available from: http://hdl.handle.net/10657/1430.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Wang M1. MUTAGENIC EFFECTS OF CHROMIUM (IV) ON HUMAN ENDOTHELIAL AND LUNG EPITHELIAL CELLS. [Thesis]. University of Houston; 2014. Available from: http://hdl.handle.net/10657/1430
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Bradford
10.
Al-Shammari, Mohamad Hilal.
Integrated data analytics of germline mutation classes in human cancers : an integrated bioinformatics analysis to investigate associations between germline mutation classes and human cancers.
Degree: PhD, 2013, University of Bradford
URL: http://hdl.handle.net/10454/6318
► Biological and environmental factors contribute collectively to the development of human cancers. The primary focus of this research project was to investigate the impact of…
(more)
▼ Biological and environmental factors contribute collectively to the development of human cancers. The primary focus of this research project was to investigate the impact of germline gene mutations, as a significant biological factor, on 29 major primary human cancers. For this I obtained data from multiple databases, including the Genetic Association Database (GAD), Sanger database (COSMIC), HGMD database, OMIM data and PubMed literature. Using the Extraction Transform and Load (ETL) process, 424 genes were obtained with 8,879 cancer mutation records. By integrating these gene mutation records a Human Cancer Map (HCM) was constructed, from which several sub-maps were derived based on particular mutation classes. Furthermore, a Protein-Protein Interaction Map (PPIM) was constructed based on the encoded proteins of the 424 gene set. Several key questions were addressed using the HCM and its sub-maps including the following: (i) Are individual groups of primary cancers associated with specific subset of genes (within the 424 full set)? (ii) Are groups of primary cancers associated with particular mutation classes? (iii) If both questions prove to be true, are groups of cancers associated with particular mutation class of target genes? This project also explored whether a corresponding Protein-Protein Interaction Map, derived from the Missense/Non-sense Mutation portion of the HCM gene set, would provide further information on gene associations between primary cancers in terms of the consequent identical amino acid changes involved. Results showed that: (1) closely-connected human cancers in the HCM exhibited a strong association with a particular mutation class; (2) Missense /Nonsense and Regulatory mutations played a central role in connecting cancers (i.e. via primary nodes) and so significantly influenced the construction of the HCM; (3) Genes with Missense/Nonsense and Regulatory mutations tended to be involved in cancer-associated pathways; (4) Using the kappa test to measure the extent of agreement between two connected primary cancers in the sub-HCMs, BRCA1, BRCA2, PALB2, MSH2, MSH6, MLH1, CDKN2A, and TP53 showed highest agreement for 5 of 10 mutation classes; (5) From the PIPM, it was evident that BRCA1, MSH6, BARD1, TP53, MSH2 and CHEK2 proteins best connected Breast, Ovarian, Prostate and Bowel primary cancers, and so the latter could represent 'driver proteins' for these cancers. In summary, this project has approached the analysis of gene involvement in human primary cancers from the starting position of the mutation class that harbours the specific gene mutation. Together with their downstream resultant alterations in the associated proteins, this analysis can provide insights into the relatedness of primary human cancers and their potential gene hierarchies. These data may therefore help us to understand more fully the etiology, diagnosis and potentially personalized treatments for cancer.
Subjects/Keywords: 616.99; Cancer; Mutation; Chromosomes; Pathways
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APA (6th Edition):
Al-Shammari, M. H. (2013). Integrated data analytics of germline mutation classes in human cancers : an integrated bioinformatics analysis to investigate associations between germline mutation classes and human cancers. (Doctoral Dissertation). University of Bradford. Retrieved from http://hdl.handle.net/10454/6318
Chicago Manual of Style (16th Edition):
Al-Shammari, Mohamad Hilal. “Integrated data analytics of germline mutation classes in human cancers : an integrated bioinformatics analysis to investigate associations between germline mutation classes and human cancers.” 2013. Doctoral Dissertation, University of Bradford. Accessed February 16, 2020.
http://hdl.handle.net/10454/6318.
MLA Handbook (7th Edition):
Al-Shammari, Mohamad Hilal. “Integrated data analytics of germline mutation classes in human cancers : an integrated bioinformatics analysis to investigate associations between germline mutation classes and human cancers.” 2013. Web. 16 Feb 2020.
Vancouver:
Al-Shammari MH. Integrated data analytics of germline mutation classes in human cancers : an integrated bioinformatics analysis to investigate associations between germline mutation classes and human cancers. [Internet] [Doctoral dissertation]. University of Bradford; 2013. [cited 2020 Feb 16].
Available from: http://hdl.handle.net/10454/6318.
Council of Science Editors:
Al-Shammari MH. Integrated data analytics of germline mutation classes in human cancers : an integrated bioinformatics analysis to investigate associations between germline mutation classes and human cancers. [Doctoral Dissertation]. University of Bradford; 2013. Available from: http://hdl.handle.net/10454/6318
Dalhousie University
11.
Kozela, Christopher Paul.
ENVIRONMENT-DEPENDENT CAUSES AND CONSEQUENCES OF MUTATION IN
SACCHAROMYCES CEREVISIAE.
Degree: PhD, Department of Biology, 2012, Dalhousie University
URL: http://hdl.handle.net/10222/14821
► Environmental effects on mutation have been documented for many years but have concentrated on agents that directly interact with DNA. Mutation research in its early…
(more)
▼ Environmental effects on
mutation have been documented
for many years but have concentrated on agents that directly
interact with DNA.
Mutation research in its early history
investigated a variety of more mundane environmental factors at
levels that inhibited biological function and attempted to
characterize their mutagenicity. This thesis revisits these old
questions armed with more modern methods. It consists of one review
chapter and three experimental chapters. The review chapter
proposes that biological organization itself acts to direct
mutation pressure, and that many mutations are context dependent
within this organization. Experimentally, I performed an
approximately 1,500-generation
mutation accumulation (MA)
experiment using the budding yeast Saccharomyces cerevisiae as an
evolutionary genetic model. This thesis investigates the rates and
distribution of effects of new mutations on fitness when they
accumulate under a moderate salt stress. The first experimental
section describes the production of the MA lines, measures the
diploid fitness traits mitotic growth rate and sporulation, and
uses changes in fitness among replicate lines to infer
mutation
parameters affecting these traits.
Mutation rate estimates for
these traits were roughly doubled in the salt stress treatment. The
proportion of beneficial mutations was high for mutations affecting
sporulation in both MA treatments but zero for growth rate.
Measurements of haploid viability and haploid growth rate on
strains derived from the diploid MA lines were used to infer
mutation parameters.
Mutation rates affecting haploid growth were
ten-fold higher in our salt-line derivatives than those derived
from the non-stress treatment. Variance component analysis
identified a large fraction of genetic variation arising from
differences among haploids within the same tetrad. This component
was significantly larger in the salt MA treatment than the
non-stress treatment. MA lines were subjected to a novel weak-acid
stress.
Mutation rate estimates were 38-fold higher in the salt MA
treatment when lines were tested under acid stress.
Cross-environmental genetic correlation for growth in acid stress
versus standard media was significantly different between the two
MA treatments suggesting that both MA environment and test
environment are important factors when considering mutational
effects on fitness.
Advisors/Committee Members: David Hall (external-examiner), Hal Whitehead (graduate-coordinator), Robert Latta (thesis-reader), Robert Lee (thesis-reader), Mark O. Johnston (thesis-supervisor), Not Applicable (ethics-approval), Not Applicable (manuscripts), Not Applicable (copyright-release).
Subjects/Keywords: Evolutionary Genetics; Mutation; Environmental Stress
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APA ·
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CSE |
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Manager
APA (6th Edition):
Kozela, C. P. (2012). ENVIRONMENT-DEPENDENT CAUSES AND CONSEQUENCES OF MUTATION IN
SACCHAROMYCES CEREVISIAE. (Doctoral Dissertation). Dalhousie University. Retrieved from http://hdl.handle.net/10222/14821
Chicago Manual of Style (16th Edition):
Kozela, Christopher Paul. “ENVIRONMENT-DEPENDENT CAUSES AND CONSEQUENCES OF MUTATION IN
SACCHAROMYCES CEREVISIAE.” 2012. Doctoral Dissertation, Dalhousie University. Accessed February 16, 2020.
http://hdl.handle.net/10222/14821.
MLA Handbook (7th Edition):
Kozela, Christopher Paul. “ENVIRONMENT-DEPENDENT CAUSES AND CONSEQUENCES OF MUTATION IN
SACCHAROMYCES CEREVISIAE.” 2012. Web. 16 Feb 2020.
Vancouver:
Kozela CP. ENVIRONMENT-DEPENDENT CAUSES AND CONSEQUENCES OF MUTATION IN
SACCHAROMYCES CEREVISIAE. [Internet] [Doctoral dissertation]. Dalhousie University; 2012. [cited 2020 Feb 16].
Available from: http://hdl.handle.net/10222/14821.
Council of Science Editors:
Kozela CP. ENVIRONMENT-DEPENDENT CAUSES AND CONSEQUENCES OF MUTATION IN
SACCHAROMYCES CEREVISIAE. [Doctoral Dissertation]. Dalhousie University; 2012. Available from: http://hdl.handle.net/10222/14821
Texas A&M University
12.
Cutts, George Sherrod.
Genetic Analysis, Inheritance and Stability of Mutation-based Herbicide Tolerance in Cotton (Gossypium hirsutum L.).
Degree: 2013, Texas A&M University
URL: http://hdl.handle.net/1969.1/151805
► The evolution of herbicide-resistant weed species in cotton production has created a need for new herbicide technology tools. Herbicide technologies not classified as genetically modified…
(more)
▼ The evolution of herbicide-resistant weed species in cotton production has created a need for new herbicide technology tools. Herbicide technologies not classified as genetically modified by recombinant DNA can provide tools with less associated registration and development costs and regulatory and market barriers. Research herein aims to advance herbicide crop tolerance through improvement and genetic analysis of
mutation derived herbicide tolerance in cotton. Germplasm exhibiting elevated tolerance to the imidazolinone class of herbicides has been previously identified after mutagenesis with ethyl methanesulfonate (EMS). However, the physiological basis, genetic behavior, and potential for herbicide tolerance improvement are not fully understood and studies were designed to elucidate these factors.
Three lines (EM4-3-1-1, EM4-3-1-2, and SCM3-4-3-1) show high levels of imazamox tolerance. Data indicate that yield for all EMS treated lines was equal to or greater than their respective non-EMS treated cultivar. EMS treatment had no adverse effects on other cotton fiber properties. In 2012, levels of imazamox herbicide injury were seen at 14 days after application (DAA) ranging from 25-34 per cent. A greater level of injury was observed in 2013 ranging from 30-37% 7 DAA, and from 60-68% 14 DAA. Injury was transient throughout both growing seasons. Acetolactate synthase (ALS) gene sequencing characterized a
mutation at Ala122 that is classified as conferring tolerance to imidazolinone herbicides, but was inconsistent in lines evaluated. Sequencing also revealed lines that have a truncated form of the protein in this region that may inhibit imidazolinone binding to the ALS protein. Chi-square analysis indicated this trait behaves in a simple, dominant fashion. Data from parent-offspring regression analysis indicated moderate correlation between parents and F2 progeny (53%). Correlation is relatively high between F2 and F3 progeny (84%) and demonstrates a strong relationship between these generations. Gain from selection indicates a 13.6% improvement in herbicide tolerance, lending to low progress from selection. These studies have shown that non-transgenic breeding methods can confer and improve imidazolinone herbicide tolerance in cotton, though levels of imidazolinone herbicide injury remained commercially unacceptable.
Advisors/Committee Members: Smith, C Wayne (advisor), Dever, Jane K (advisor), Dotray, Peter A (committee member), Hague, Steve S (committee member), Robinson, John RC (committee member).
Subjects/Keywords: Cotton; Herbicide tolerance; Mutation; Inheritance
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APA ·
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APA (6th Edition):
Cutts, G. S. (2013). Genetic Analysis, Inheritance and Stability of Mutation-based Herbicide Tolerance in Cotton (Gossypium hirsutum L.). (Thesis). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/151805
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Cutts, George Sherrod. “Genetic Analysis, Inheritance and Stability of Mutation-based Herbicide Tolerance in Cotton (Gossypium hirsutum L.).” 2013. Thesis, Texas A&M University. Accessed February 16, 2020.
http://hdl.handle.net/1969.1/151805.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Cutts, George Sherrod. “Genetic Analysis, Inheritance and Stability of Mutation-based Herbicide Tolerance in Cotton (Gossypium hirsutum L.).” 2013. Web. 16 Feb 2020.
Vancouver:
Cutts GS. Genetic Analysis, Inheritance and Stability of Mutation-based Herbicide Tolerance in Cotton (Gossypium hirsutum L.). [Internet] [Thesis]. Texas A&M University; 2013. [cited 2020 Feb 16].
Available from: http://hdl.handle.net/1969.1/151805.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Cutts GS. Genetic Analysis, Inheritance and Stability of Mutation-based Herbicide Tolerance in Cotton (Gossypium hirsutum L.). [Thesis]. Texas A&M University; 2013. Available from: http://hdl.handle.net/1969.1/151805
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
13.
安達, 裕行.
日本人重症先天性甲状腺機能低下症患者における新規遺伝子異変の同定 : Identification of novel genetic mutations in Japanese patients with severe congenital hypothyroidism.
Degree: 博士（医学）, 2017, Akita University / 秋田大学
URL: http://hdl.handle.net/10295/2513
► Objective: The prevalence of genetic mutations in congenital hypothyroidism (CH) remains undetermined. The objective of this study was to determine the prevalence of mutations in…
(more)
▼ Objective: The prevalence of genetic mutations in congenital hypothyroidism (CH) remains undetermined. The objective of this study was to determine the prevalence of mutations in DUOX2, TSHR, TG, PAX8, and TPO among severe permanent primary CH. Methods: Between April 1999 and March 2011, 114,733 newborns were screened for CH in Akita Prefecture, Japan. Among them, 330 were suspected of having CH and were referred to pediatricians. We recruited 40 patients who were referred to our institute. Among them, we identified 9 permanent primary CH patients who were severel y affected with an initial TSH .20 mU/l upon newborn screening and performed direct sequencing of the 5 candidate genes. Results: 3 of 9 patients (33%) had mutations in PAX8, TPO, and TSHR. Among the severely affected subjects, 60% had thyroid dysgenesis (TD), while for patients with initial TSH upon screening <20 mU/l only 12% had TD. Conclusions: Despite the high frequency of TD, the detection rate of mutations among severe permanent primary CH was higher than expected. This study suggests that the genetic analysis of 5 genes, namely, DUOX2, TSHR, TG, PAX8, and TPO, is useful for the diagnosis of CH, and that the actual prevalence of genetic mutations among CH might be higher than as previously estimated.
Subjects/Keywords: congenital hypothyroidism; genes; mutation; prevalence
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APA (6th Edition):
安達, . (2017). 日本人重症先天性甲状腺機能低下症患者における新規遺伝子異変の同定 : Identification of novel genetic mutations in Japanese patients with severe congenital hypothyroidism. (Thesis). Akita University / 秋田大学. Retrieved from http://hdl.handle.net/10295/2513
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
安達, 裕行. “日本人重症先天性甲状腺機能低下症患者における新規遺伝子異変の同定 : Identification of novel genetic mutations in Japanese patients with severe congenital hypothyroidism.” 2017. Thesis, Akita University / 秋田大学. Accessed February 16, 2020.
http://hdl.handle.net/10295/2513.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
安達, 裕行. “日本人重症先天性甲状腺機能低下症患者における新規遺伝子異変の同定 : Identification of novel genetic mutations in Japanese patients with severe congenital hypothyroidism.” 2017. Web. 16 Feb 2020.
Vancouver:
安達 . 日本人重症先天性甲状腺機能低下症患者における新規遺伝子異変の同定 : Identification of novel genetic mutations in Japanese patients with severe congenital hypothyroidism. [Internet] [Thesis]. Akita University / 秋田大学; 2017. [cited 2020 Feb 16].
Available from: http://hdl.handle.net/10295/2513.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
安達 . 日本人重症先天性甲状腺機能低下症患者における新規遺伝子異変の同定 : Identification of novel genetic mutations in Japanese patients with severe congenital hypothyroidism. [Thesis]. Akita University / 秋田大学; 2017. Available from: http://hdl.handle.net/10295/2513
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Hong Kong
14.
張柏恆; Cheung, Pak-hang, Peter.
Expermental [i.e. Experimental] analysis of the mutation
rate of influenza A viruses.
Degree: PhD, 2012, University of Hong Kong
URL: Cheung,
P.
P.
[張柏恆].
(2012).
Expermental
[i.e.
Experimental]
analysis
of
the
mutation
rate
of
influenza
A
viruses.
(Thesis).
University
of
Hong
Kong,
Pokfulam,
Hong
Kong
SAR.
Retrieved
from
http://dx.doi.org/10.5353/th_b5016252
;
http://dx.doi.org/10.5353/th_b5016252
;
http://hdl.handle.net/10722/224807
► As with other ribonucleic acid (RNA) viruses, influenza A virus (IAV), with its error-prone RNA-dependent RNA polymerase (RdRP), is able to generate complex populations of…
(more)
▼ As with other ribonucleic acid (RNA) viruses,
influenza A virus (IAV), with its error-prone RNA-dependent RNA
polymerase (RdRP), is able to generate complex populations of
genetically variant viruses referred to as quasispecies.
Mutation-driven quasispecies diversity is the main mechanism for
the acquisition of resistance to antivirals, immune escape, and
host adaptations, which can impact pathogenesis and
transmissibility. Current efforts in studying influenza
mutation
have been restricted to characterizing the functional roles of
individual amino acids linked to influenza pathogenesis. A hitherto
unexplored area of influenza research has been the role of
quasispecies in the biology of influenza because there is limited
methodology to accurately quantify influenza
mutation rates and an
absence of an unequivocal model to study influenza quasispecies
dynamics.
An accurate in vitro system was developed to assess the
mutational frequencies and spectra of the RdRP of two IAV strains
with different pathogenicity in mammals: human seasonal H3N2
A/Wuhan/359/95 (Wuhan) and highly pathogenic H5N1 A/Vietnam/1203/04
(VN1203). The intrinsic RdRP mutational frequencies and spectra of
the two polymerase complexes were compared and validated using the
spectra derived from live recombinant viruses. High-quality
mutational spectra were generated to make possible the use of
statistical and bioinformatics analysis. Statistically correlated
mutational spectra and comparable mutational frequencies were
observed, the first highly mutable motif of “AAAG” and “AAG” was
discovered in both H5N1 and H3N2 RdRPs, as well as in viral
progenies, which were recombinant A/Puerto Rico/8/34(PR8) viruses
that differed in the RdRPs of the H3N2 and H5N1 strains.
Non-segmented, positive-sense, single-stranded RNA viruses of the
Piconaviridae family and the Togaviridae family with altered RdRP
fidelity were selected in the presence of mutagens. To study the
biological significance of the influenza
mutation rate, ribavirin
was demonstrated to mutagenize the IAV genome and was used to
select mutagen-resistant variants of IAV that possess RdRP with
altered fidelity. Through serial passages of A/Wuhan/359/95 virus
in the presence of ribavirin in vitro, a
mutation defective,
high-fidelity (reduced
mutation rate) IAV that exhibits decreased
sensitivity to mutagens including ribavirin and manganese in vitro
was generated and characterized. Using plaque reduction assay and
mini-genome assay, the PB1-V43I
mutation was identified to confer
to decreased sensitivity to ribavirin and increased RdRP fidelity.
Applying plasmid-based reverse genetics, the PB1-V43I
mutation in
the H3N2 and H5N1 viruses was shown to decrease
mutation frequency
by 1.0-3.1 folds. These
mutation-defective viruses have decreased
ability to generate monoclonal antibody escape mutants. Compared
with wild-type, the
mutation-defective H5N1 virus was shown to
replicate to comparable titers in the lung of infected mice but is
less lethal and has lower viral titers in the brain (not
statistically…
Advisors/Committee Members: Peiris, JSM, Yen, H.
Subjects/Keywords: Influenza A virus; Microbial mutation
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Manager
APA (6th Edition):
張柏恆; Cheung, Pak-hang, P. (2012). Expermental [i.e. Experimental] analysis of the mutation
rate of influenza A viruses. (Doctoral Dissertation). University of Hong Kong. Retrieved from Cheung, P. P. [張柏恆]. (2012). Expermental [i.e. Experimental] analysis of the mutation rate of influenza A viruses. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b5016252 ; http://dx.doi.org/10.5353/th_b5016252 ; http://hdl.handle.net/10722/224807
Chicago Manual of Style (16th Edition):
張柏恆; Cheung, Pak-hang, Peter. “Expermental [i.e. Experimental] analysis of the mutation
rate of influenza A viruses.” 2012. Doctoral Dissertation, University of Hong Kong. Accessed February 16, 2020.
Cheung, P. P. [張柏恆]. (2012). Expermental [i.e. Experimental] analysis of the mutation rate of influenza A viruses. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b5016252 ; http://dx.doi.org/10.5353/th_b5016252 ; http://hdl.handle.net/10722/224807.
MLA Handbook (7th Edition):
張柏恆; Cheung, Pak-hang, Peter. “Expermental [i.e. Experimental] analysis of the mutation
rate of influenza A viruses.” 2012. Web. 16 Feb 2020.
Vancouver:
張柏恆; Cheung, Pak-hang P. Expermental [i.e. Experimental] analysis of the mutation
rate of influenza A viruses. [Internet] [Doctoral dissertation]. University of Hong Kong; 2012. [cited 2020 Feb 16].
Available from: Cheung, P. P. [張柏恆]. (2012). Expermental [i.e. Experimental] analysis of the mutation rate of influenza A viruses. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b5016252 ; http://dx.doi.org/10.5353/th_b5016252 ; http://hdl.handle.net/10722/224807.
Council of Science Editors:
張柏恆; Cheung, Pak-hang P. Expermental [i.e. Experimental] analysis of the mutation
rate of influenza A viruses. [Doctoral Dissertation]. University of Hong Kong; 2012. Available from: Cheung, P. P. [張柏恆]. (2012). Expermental [i.e. Experimental] analysis of the mutation rate of influenza A viruses. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_b5016252 ; http://dx.doi.org/10.5353/th_b5016252 ; http://hdl.handle.net/10722/224807
University of Illinois – Urbana-Champaign
15.
Hariri, Farah.
Exploring design decisions for mutation testing.
Degree: PhD, Computer Science, 2018, University of Illinois – Urbana-Champaign
URL: http://hdl.handle.net/2142/101008
► Software testing is by far the most popular technique used in industry for quality assurance. One key challenge of software testing is how to evaluate…
(more)
▼ Software testing is by far the most popular technique used in industry for quality assurance. One key challenge of software testing is how to evaluate the quality of test suites in terms of their bug-finding capability. A test suite with a large number of tests, or that achieves a high statement or branch coverage, does not necessarily have a high bug-finding capability.
Mutation testing is widely used in research to evaluate the quality of test suites, and it is often considered the most powerful approach for this purpose.
Mutation testing proceeds in two steps. The first step is mutant generation. A mutant is a modified version of the original program obtained by applying a
mutation operator. A
mutation operator is a program transformation that introduces a small syntactic change to the original program. The second step of
mutation testing is to run the test suite and determine which mutants are killed, i.e., which mutants lead to tests having a different output when run on them compared against running on the original program.
Mutation testing produces a measure of quality of the test suite called
mutation score. The
mutation score of a given test suite is the percentage of mutants killed by that test suite out of the total number of generated mutants.
In this dissertation, we explore three design decisions related to
mutation testing and provide recommendations to researchers in those regards. First, we look into
mutation operators. To provide insights about how to improve the test suites,
mutation testing requires both high quality and diverse
mutation operators that lead to different program behaviors. We propose the use of approximate transformations as
mutation operators. Approximate transformations were introduced in the emerging area of approximate computing for changing program semantics to trade the accuracy of results for improved energy efficiency or performance. We compared three approximate transformations with a set of conventional
mutation operators from the literature, on nine open-source Java subjects. The results showed that approximate transformations change program behavior differently from conventional
mutation operators. Our analysis uncovered code patterns in which approximate mutants survived (i.e., were not killed) and showed the practical value of approximate transformations both for understanding code amenable to approximations and for discovering bad tests. We submitted 11 pull requests to fix bad tests. Seven have already been integrated by the developers.
Second, we explore the effect of compiler optimizations on
mutation testing. Multiple
mutation testing tools were developed that perform
mutation at different levels. More recently
mutation testing has been performed at the level of compiler intermediate representation (IR), e.g., for the LLVM IR and Java bytecode/IR. Compiler optimizations are automatic program transformations applied at the IR level with the goal of improving a measure of program performance, while preserving program semantics. Applying mutations at the IR level…
Advisors/Committee Members: Marinov, Darko (advisor), Marinov, Darko (Committee Chair), Misailovic, Sasa (committee member), Xie, Tao (committee member), Khurshid, Sarfraz (committee member).
Subjects/Keywords: software testing; mutation testing
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APA (6th Edition):
Hariri, F. (2018). Exploring design decisions for mutation testing. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/101008
Chicago Manual of Style (16th Edition):
Hariri, Farah. “Exploring design decisions for mutation testing.” 2018. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed February 16, 2020.
http://hdl.handle.net/2142/101008.
MLA Handbook (7th Edition):
Hariri, Farah. “Exploring design decisions for mutation testing.” 2018. Web. 16 Feb 2020.
Vancouver:
Hariri F. Exploring design decisions for mutation testing. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2018. [cited 2020 Feb 16].
Available from: http://hdl.handle.net/2142/101008.
Council of Science Editors:
Hariri F. Exploring design decisions for mutation testing. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2018. Available from: http://hdl.handle.net/2142/101008
North Carolina State University
16.
Keebler, Jonathan Edward Myers.
Spontaneous Mutation Discovery via High-Throughput Sequencing of Pedigrees.
Degree: PhD, Bioinformatics, 2010, North Carolina State University
URL: http://www.lib.ncsu.edu/resolver/1840.16/6168
► Recent technological advances have made high-throughput DNA sequencing a routine laboratory experiment. This progression in technology has been made possible by the parallel production of…
(more)
▼ Recent technological advances have made high-throughput DNA sequencing a routine laboratory experiment. This progression in technology has been made possible by the parallel production of millions of short fragments of sequence. The responsibility of garnering biological information from these DNA fragments has shifted from the wet-lab to the bioinformatician. As sequencing technology is applied to a growing number of individual human genomes, entire families are now being sequenced. Information contained within the pedigree of a sequenced family can be leveraged when inferring the donors’ genotypes, a task that is not necessarily trivial using high-throughput sequencing reads. A violation of Mendelian inheritance laws observed amid the resequenced genomes of family members can indicate the presence of a de novo
mutation. A method for locating de novo mutations by probabilistically inferring genotypes across a pedigree using high-throughput sequencing is presented and applied to two resequenced nuclear families: one as a collaborative effort within The 1,000 Genomes Project, and the second in an attempt to discover candidate driver and passenger mutations within the genome of an Acute Lymphoblastic Leukemia. The
mutation findings within these projects are presented, and the approach is examined in detail, highlighting areas where method improvements may be made. Considering the challenges experienced in these studies within the larger context of the nascent field of Personal Genomics, an honest assessment is presented of developments that must be made before the application of whole-genome sequencing on the scale of an individual human can unequivocally be used to predict, diagnose, or treat human disease.
Advisors/Committee Members: Alison Motsinger, Committee Member (advisor), Jeffrey Thorne, Committee Member (advisor), Ignzaio Carbone, Committee Member (advisor), Eric Stone, Committee Chair (advisor), Philip Awadalla, Committee Member (advisor).
Subjects/Keywords: Spontaneous Mutation; 1000 Genomes Project; de novo mutation; high throughput sequencing; next generation sequencing; human mutation rate; human germline mutation rate
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APA (6th Edition):
Keebler, J. E. M. (2010). Spontaneous Mutation Discovery via High-Throughput Sequencing of Pedigrees. (Doctoral Dissertation). North Carolina State University. Retrieved from http://www.lib.ncsu.edu/resolver/1840.16/6168
Chicago Manual of Style (16th Edition):
Keebler, Jonathan Edward Myers. “Spontaneous Mutation Discovery via High-Throughput Sequencing of Pedigrees.” 2010. Doctoral Dissertation, North Carolina State University. Accessed February 16, 2020.
http://www.lib.ncsu.edu/resolver/1840.16/6168.
MLA Handbook (7th Edition):
Keebler, Jonathan Edward Myers. “Spontaneous Mutation Discovery via High-Throughput Sequencing of Pedigrees.” 2010. Web. 16 Feb 2020.
Vancouver:
Keebler JEM. Spontaneous Mutation Discovery via High-Throughput Sequencing of Pedigrees. [Internet] [Doctoral dissertation]. North Carolina State University; 2010. [cited 2020 Feb 16].
Available from: http://www.lib.ncsu.edu/resolver/1840.16/6168.
Council of Science Editors:
Keebler JEM. Spontaneous Mutation Discovery via High-Throughput Sequencing of Pedigrees. [Doctoral Dissertation]. North Carolina State University; 2010. Available from: http://www.lib.ncsu.edu/resolver/1840.16/6168
17.
Stuart, Gregory Roy.
Influences of ageing and diet on mutational frequency and specificity in Big Blue® lacI transgenic rodents.
Degree: Department of Biology, 2018, University of Victoria
URL: https://dspace.library.uvic.ca//handle/1828/8991
► Big Blue® lacI transgenic mice and rats carry the E. coli lacI gene integrated as a tandem array of approximately 40 copies integrated at a…
(more)
▼ Big Blue® lacI transgenic mice and rats carry the E. coli lacI gene integrated as a tandem array of approximately 40 copies integrated at a single site in chromosome 4. This mutationally well-characterized gene is highly sensitive to base substitution mutations and is readily recovered from virtually any tissue of the transgenic host, facilitating the in vivo study of
mutation. The Big Blue® assay was used to investigate spontaneous and induced
mutation, with an emphasis on dietary influences on mutational frequency and specificity. The effects of ageing and dietary restriction on spontaneous
mutation in the lacI transgene were determined in mice, permitting evaluation of several well established theories of ageing.
Mutation frequencies were found to increase with age in tissues that proliferate (bladder and liver, but not brain), validating a principle tenet of the somatic ageing theory. However, the unexpected lack of a change in mutational specificity in ageing mice suggests that theories of ageing based on oxidative damage, or a reduction in DNA repair efficiency, may not be seminal to the ageing process, at least until more advanced age. Similarly, dietary restriction, which is known to extend lifespan in rodents and was predicted to decrease oxidative DNA-damage, had no appreciable effect on either the frequency or the specificity of spontaneous
mutation in liver of younger (6 month old) and older (12 month old) mice.
Dietary influences on induced
mutation were examined following treatment with aflatoxin B₁ (AFB₁) and 2-amino-1-methyl-6-phenylimidazo[4,5- b]pyridine (PhIP) powerful animal carcinogens which demonstrate tissue, species and sex-linked differences in rats and mice. As expected, AFB₁ was found to be potently mutagenic in rat but not mouse liver, in agreement with rodent carcinogenicity studies that found F344 rats to be highly susceptible to AFB₁-induced hepatocarcinogenesis, while C57BL/6 mice are highly resistant. PhIP was found to be potently and equally mutagenic in colon of both male and female rats. The result in female colon was surprising since PhIP predominantly induces colon cancer in male rats but mammary tumors in female rats. Therefore, the progression of PhIP-induced colon cancer in the rat colon is likely due to factors acting at a later stage in the tumorigenic process, following the damage and
mutation of DNA. Rat prostate tissue, another tumor target tissue in PhIP-treated rats, was also found to be highly susceptible to PhIP-induced mutagenesis. Lastly, the PhIP studies were extended to an additional transgene target located in the shuttle vector construct from Big Blue® rodents, the bacteriophage λ-derived cII gene. These studies validated the use of the λ cII gene as an alternative mutational target for use in the Big Blue® assay, while the analyses of
mutation in the lacI and the λcII transgenes serves as a paradigm for mutational studies which compare mutational responses in different genes. Collectively, these studies demonstrate the utility of the lacI (λ cII) transgenic…
Advisors/Committee Members: Glickman, Barry W. (supervisor).
Subjects/Keywords: Aging; Diet; Mutation (Biology)
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APA ·
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APA (6th Edition):
Stuart, G. R. (2018). Influences of ageing and diet on mutational frequency and specificity in Big Blue® lacI transgenic rodents. (Thesis). University of Victoria. Retrieved from https://dspace.library.uvic.ca//handle/1828/8991
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Stuart, Gregory Roy. “Influences of ageing and diet on mutational frequency and specificity in Big Blue® lacI transgenic rodents.” 2018. Thesis, University of Victoria. Accessed February 16, 2020.
https://dspace.library.uvic.ca//handle/1828/8991.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Stuart, Gregory Roy. “Influences of ageing and diet on mutational frequency and specificity in Big Blue® lacI transgenic rodents.” 2018. Web. 16 Feb 2020.
Vancouver:
Stuart GR. Influences of ageing and diet on mutational frequency and specificity in Big Blue® lacI transgenic rodents. [Internet] [Thesis]. University of Victoria; 2018. [cited 2020 Feb 16].
Available from: https://dspace.library.uvic.ca//handle/1828/8991.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Stuart GR. Influences of ageing and diet on mutational frequency and specificity in Big Blue® lacI transgenic rodents. [Thesis]. University of Victoria; 2018. Available from: https://dspace.library.uvic.ca//handle/1828/8991
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
18.
Curry, John Duncan.
Mutation monitoring in human populations.
Degree: Department of Biology, 2017, University of Victoria
URL: https://dspace.library.uvic.ca//handle/1828/8811
► Currently, the most widely used in vivo mutation monitoring system in humans is the hypoxanthine-guanine phosphoribosyltransferase (hprt) T-cell clonal assay. This dissertation examines the current…
(more)
▼ Currently, the most widely used in vivo
mutation monitoring system in humans is the hypoxanthine-guanine phosphoribosyltransferase (hprt) T-cell clonal assay. This dissertation examines the current state of the hprt monitoring system and the usefulness of hprt mutational spectra in revealing environmental exposures. The nature of spontaneous mutational spectra recovered through the implementation of this system is detailed. An examination of hprt
mutation frequencies obtained from a set of monozygotic twins revealed a striking influence of genetic factors. As age increases, the influence of genetic factors controlling
mutation frequency appears to be modified by environmental factors. Mutational spectra obtained from Russian individuals living in Moscow were distinct from the spectrum of
mutation observed in age-matched Western controls. Analysis of the relationship between
mutation frequency and
subject age clearly demonstrated the lack of any relationship for subjects after the age of 55. This finding contradicts many previously published reports on the relationship between
mutation frequency and age. Finally, the influence of tobacco smoking on mutational frequency is clear, however, no change in the mutational spectrum of smokers was revealed. Changes in mutational spectrum are analyzed in the context of the T-cell biology and reveal that the dynamics of this tissue are likely responsible for the observations made in this dissertation. Although the hprt gene is a highly robust and suitable target for the analysis of
mutation, the target has not yet been saturated, and new single base-pair substitutions are still being characterized. The data clearly suggest that the T-cell clonal assay in its current state may not be a suitable mutational monitoring system for human populations. This dissertation concludes that new mutational assays need to be developed for monitoring mutations in human populations.
Advisors/Committee Members: Glickman, Barry W. (supervisor).
Subjects/Keywords: Mutation (Biology); Human population genetics
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APA (6th Edition):
Curry, J. D. (2017). Mutation monitoring in human populations. (Thesis). University of Victoria. Retrieved from https://dspace.library.uvic.ca//handle/1828/8811
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Curry, John Duncan. “Mutation monitoring in human populations.” 2017. Thesis, University of Victoria. Accessed February 16, 2020.
https://dspace.library.uvic.ca//handle/1828/8811.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Curry, John Duncan. “Mutation monitoring in human populations.” 2017. Web. 16 Feb 2020.
Vancouver:
Curry JD. Mutation monitoring in human populations. [Internet] [Thesis]. University of Victoria; 2017. [cited 2020 Feb 16].
Available from: https://dspace.library.uvic.ca//handle/1828/8811.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Curry JD. Mutation monitoring in human populations. [Thesis]. University of Victoria; 2017. Available from: https://dspace.library.uvic.ca//handle/1828/8811
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Victoria
19.
Kotturi, Gopaul.
Correlating and measuring DNA damage and mutations.
Degree: Department of Biology, 2018, University of Victoria
URL: https://dspace.library.uvic.ca//handle/1828/9086
► Mutations are generally thought to be targeted events. The distribution of mutations is based upon the initial original deposition of DNA damage and the fidelity…
(more)
▼ Mutations are generally thought to be targeted events. The distribution of mutations is based upon the initial original deposition of DNA damage and the fidelity and efficiency of repair of this damage. These factors are dependent on the primary site of
DNA modification and the surrounding nucleotides (i.e.,
mutation is “context sensitive"). To better understand mutagenesis, I measured DNA damage and/or
mutation at the DNA sequence level, then considered the impact of
mutation location and the surrounding nucleotide environment. The selected mutagens, ultraviolet light (UV) and benzo(a)pyrene [B(a)P], were chosen because they produce well-characterized lesions and are environmentally relevant.
UVC (254nm) light-induced DNA damage is well documented. UVC produces a characteristic spectrum of mutations. The predominant UV-induced mutations are C → T transitions occurring at TC or CC sites, as well as CC → TT tandem transitions. The latter class of
mutation is considered the hallmark of UV mutagenesis. Quantitatively speaking, the primary types of UV-induced DNA lesions are cyclobutane pyrimidine dimers (CPDs) and the 6-4 pyrimidine/pyrimidone (64PyPy). These are also the suspected predominant pre-mutagenic lesions. Each lesion was independently measured at the DNA sequence level in a defined region of DNA. The pattern of UVC-induced DNA damage revealed a complex induction pattern. The flanking DNA nucleotides partially influenced the pattern of damage deposition. Sites where C → T transitions and CC → TT transitions were recovered at high frequencies were also frequently damaged. Thus, at these sites,
mutation fixation was potentially more influenced by initial DNA damage than the rate of DNA repair.
Two other components of the UV spectrum [UVB (290-320 nm) and UVA (320-400 nm)] are more environmentally relevant than UVC since UVB and UVA reach the surface of the earth.The results of UVC experiments were used as a guide to interpret the results obtained using UVB since direct light absorption by DNA has been shown to be one of the main biological effect at both wavelengths. The model that was chosen for the studies was an in vivo transgenic rodent mutagenesis assay. The research presented in the thesis represents one of the first studies to characterize UV-induced
mutation at the DNA sequence level in rodent skin. The backs of female C57B1/6 lacl transgenic mice were shaved and exposed to either UVB or UVA light. UVB was found to be significantly more mutagenic than UVA. The UVB-induced
mutation spectrum was characterized by C → T transitions at dipyrimidine sites, implicating CPD and/or 64PyPy lesions as premutational DNA lesions. The majority of UVA-induced mutations was C → T transitions at dipyrimidines sites and hence, as with UVB-induced
mutation, attributed to CPDs and 64PyPy. In the UVA-dose response experiments, the induced mutant frequency was lower than expected at higher doses. A statistically significant increase in putative clonal expansion suggested that skin cells might have undergone cell…
Advisors/Committee Members: Glickman, Barry W. (supervisor).
Subjects/Keywords: DNA damage; Mutation (Biology)
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APA ·
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APA (6th Edition):
Kotturi, G. (2018). Correlating and measuring DNA damage and mutations. (Thesis). University of Victoria. Retrieved from https://dspace.library.uvic.ca//handle/1828/9086
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Kotturi, Gopaul. “Correlating and measuring DNA damage and mutations.” 2018. Thesis, University of Victoria. Accessed February 16, 2020.
https://dspace.library.uvic.ca//handle/1828/9086.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Kotturi, Gopaul. “Correlating and measuring DNA damage and mutations.” 2018. Web. 16 Feb 2020.
Vancouver:
Kotturi G. Correlating and measuring DNA damage and mutations. [Internet] [Thesis]. University of Victoria; 2018. [cited 2020 Feb 16].
Available from: https://dspace.library.uvic.ca//handle/1828/9086.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Kotturi G. Correlating and measuring DNA damage and mutations. [Thesis]. University of Victoria; 2018. Available from: https://dspace.library.uvic.ca//handle/1828/9086
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Portland State University
20.
Christy, Stephen Fuller.
Adaptive Evolution under Favorable and Unfavorable Population Genetic Conditions in <i>Caenorhabditis elegans</i> Nematodes.
Degree: MS(M.S.) in Biology, Biology, 2017, Portland State University
URL: https://pdxscholar.library.pdx.edu/open_access_etds/3534
► Mutation is a fundamental process that drives evolutionary change; however, most new mutations are deleterious for organismal fitness and can readily propagate within populations…
(more)
▼ Mutation is a fundamental process that drives evolutionary change; however, most new mutations are deleterious for organismal fitness and can readily propagate within populations under a broad range of conditions. Mutational processes able to counteract deleterious
mutation accumulation include: 1) reversion
mutation back to wildtype, 2) acquisition of generally beneficial mutations, and 3) compensatory mutations that specifically mitigate the effects of previously-acquired deleterious mutations through epistasis. The potential for any of these
mutation types alters our expectations for the impact of deleterious
mutation in populations, but since the fitness effects of individual mutations are rarely characterized, the relative importance of beneficial and compensatory epistatic mutations is unknown. In this thesis, I characterized the nuclear mutations that arose in a previous
mutation accumulation (MA) experiment using
Caenorhabditis elegans nematodes, in which mutations were allowed to accumulate under extreme drift conditions in replicate, independently evolving lines initiated from a low-fitness mitochondrial electron transport chain (ETC) mutant,
gas-1. In contrast to the results of typical MA experiments,
gas-1 MA lines improved fitness slightly compared to their ancestor. Here, I find that the
gas-1 MA lines demonstrate little increase in among-line variance and that the
gas-1 MA nuclear mutations are more narrowly functionally defined than wildtype MA nuclear mutations. When combined with evidence for zygotic or post zygotic selection these data suggest that selection – both purifying and positive – can be an extremely powerful force even in conditions of extreme genetic drift. Furthermore, functional characterization of a four-
mutation set isolated from one of the
gas-1 MA lines on
gas-1 and wildtype backgrounds shows fitness improvements on both backgrounds. This beneficial four-
mutation set is associated with a decrease in steady-state endogenous ROS on the
gas-1 background while exhibiting no effect on wildtype. I also find that steady-state ATP levels associated with the beneficial four-
mutation set decreased compared to wildtype suggesting that fermentation may be metabolic strategy to cope with increase oxidative stress. These findings suggest that we can detect and characterize specific genetic changes that lead to a partial recovery of fitness and phenotype in a low-fitness ETC-deficient mutant strain of
C. elegans. I extended my thesis to include analyses of fitness and phenotype of 24 replicate lineages of the
gas-1 ETC mutant evolved in large population (
n = 1000) sizes for 60 generations – conditions optimal for selection and fitness recovery (RC). I find that two distinct
gas-1 RC fitness groups emerged: one group with significantly higher average fitness than the ancestor and containing two lines that exceeded wildtype fitness levels, and another group with more modest and…
Advisors/Committee Members: Suzanne Estes.
Subjects/Keywords: Caenorhabditis elegans; Mutation (Biology); Biology
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APA (6th Edition):
Christy, S. F. (2017). Adaptive Evolution under Favorable and Unfavorable Population Genetic Conditions in <i>Caenorhabditis elegans</i> Nematodes. (Masters Thesis). Portland State University. Retrieved from https://pdxscholar.library.pdx.edu/open_access_etds/3534
Chicago Manual of Style (16th Edition):
Christy, Stephen Fuller. “Adaptive Evolution under Favorable and Unfavorable Population Genetic Conditions in <i>Caenorhabditis elegans</i> Nematodes.” 2017. Masters Thesis, Portland State University. Accessed February 16, 2020.
https://pdxscholar.library.pdx.edu/open_access_etds/3534.
MLA Handbook (7th Edition):
Christy, Stephen Fuller. “Adaptive Evolution under Favorable and Unfavorable Population Genetic Conditions in <i>Caenorhabditis elegans</i> Nematodes.” 2017. Web. 16 Feb 2020.
Vancouver:
Christy SF. Adaptive Evolution under Favorable and Unfavorable Population Genetic Conditions in <i>Caenorhabditis elegans</i> Nematodes. [Internet] [Masters thesis]. Portland State University; 2017. [cited 2020 Feb 16].
Available from: https://pdxscholar.library.pdx.edu/open_access_etds/3534.
Council of Science Editors:
Christy SF. Adaptive Evolution under Favorable and Unfavorable Population Genetic Conditions in <i>Caenorhabditis elegans</i> Nematodes. [Masters Thesis]. Portland State University; 2017. Available from: https://pdxscholar.library.pdx.edu/open_access_etds/3534
Universitat de Valencia
21.
Combe, Marine.
Variability and host-dependency of RNA virus mutation rates
.
Degree: 2015, Universitat de Valencia
URL: http://hdl.handle.net/10550/46762
► Los virus de ARN pueden infectar todo tipo de organismos, desde los procariotas a los eucariotas superiores, y estos agentes infecciosos parecen particularmente propensos a…
(more)
▼ Los virus de ARN pueden infectar todo tipo de organismos, desde los procariotas a los eucariotas superiores, y estos agentes infecciosos parecen particularmente propensos a causar enfermedades emergentes tanto en humanos, animales, como en plantas. Su habilidad para escapar del sistema inmunitario, evadir estrategias antivirales o infectar a nuevas especies son aspecto más de su rápida evolución. Por lo tanto, comprender los procesos básicos del la evolución de los virus de ARN podría ayudar en el diseño de nuevas estrategias antivirales.
Una de las principales características de los virus de ARN es su tasa de mutación extremadamente alta. De hecho, la alta diversidad genética de las poblaciones virales da lugar a una nube de variantes que interactúan y contribuyen colectivamente, conocido también por el término de cuasiespecies, y que permite a las poblaciones virales adaptarse rápidamente a entornos dinámicos. Estudios anteriores han demostrado que la tasa de mutaciones espontáneas de los virus de ARN varía de 10-6 a 10-4 sustituciones por nucleótido por célula infectada (s/n/c) y puede variar considerablemente, incluso para el mismo virus, aunque se sabe poco sobre las causas de esta variabilidad. Consecuentemente, el conocimiento de la tasa de mutación y el espectro molecular de mutaciones espontáneas son importantes para entender la evolución de la composición genética de las poblaciones virales.
En los virus de ARN las tasas de mutación están determinadas por factores codificados por el virus, como la fidelidad de la polimerasa viral, la presencia/ausencia de mecanismos correctores, o el modo de replicación viral. Sin embargo, sólo unos pocos estudios se han centrado en las características celulares que podrían explicar la variabilidad en la producción de la diversidad genética viral, o si esta variabilidad pudiera ser distribuida heterogéneamente entre células únicas.
En este estudio, se propuso analizar algunos de los factores subyacentes a la variabilidad en las tasas de mutación de los virus de ARN. En primer lugar, se estudió el efecto del tipo de célula que se infecta, y la variación en función del huésped en el que el virus se replica. A continuación, nos centramos en la variabilidad que ocurre a nivel de una célula única, mediante la caracterización de la diversidad genética de los virus liberados a partir de células individuales. Por último, nos fijamos en el potencial efecto de factores celulares de tipo ADAR, mediante la determinación del tipo de mutaciones espontáneas que se acumulan en el genoma de un norovirus.
Se utilizó la prueba de fluctuación de Luria-Delbrück para comprobar la variabilidad en la tasa de mutación del virus de la estomatitis vesicular (VSV) entre diferentes células de mamíferos, así como entre diferentes condiciones de cultivo. Se encontró una tasa de mutación similar entre las células BHK-21, así como en células embrionarias de ratón (MEF), células MEF inmortalizadas mediante deleción del gen p53, células de cáncer de colon murino (CT26) y de neuroblastoma…
Advisors/Committee Members: Sanjuán Verdeguer, Rafael (advisor).
Subjects/Keywords: RNA viruses;
viral mutation rates
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APA (6th Edition):
Combe, M. (2015). Variability and host-dependency of RNA virus mutation rates
. (Doctoral Dissertation). Universitat de Valencia. Retrieved from http://hdl.handle.net/10550/46762
Chicago Manual of Style (16th Edition):
Combe, Marine. “Variability and host-dependency of RNA virus mutation rates
.” 2015. Doctoral Dissertation, Universitat de Valencia. Accessed February 16, 2020.
http://hdl.handle.net/10550/46762.
MLA Handbook (7th Edition):
Combe, Marine. “Variability and host-dependency of RNA virus mutation rates
.” 2015. Web. 16 Feb 2020.
Vancouver:
Combe M. Variability and host-dependency of RNA virus mutation rates
. [Internet] [Doctoral dissertation]. Universitat de Valencia; 2015. [cited 2020 Feb 16].
Available from: http://hdl.handle.net/10550/46762.
Council of Science Editors:
Combe M. Variability and host-dependency of RNA virus mutation rates
. [Doctoral Dissertation]. Universitat de Valencia; 2015. Available from: http://hdl.handle.net/10550/46762
Oregon State University
22.
Bollmann, Stephanie R.
Reversion reporters in Arabidopsis thaliana to detect all six base substitution pathways.
Degree: PhD, Genetics, 2008, Oregon State University
URL: http://hdl.handle.net/1957/8924
► Maintaining genome integrity is essential for an organism, as mutation accumulation can lead to cancer, reduced fitness, and heritable diseases in offspring. Therefore the study…
(more)
▼ Maintaining genome integrity is essential for an organism, as
mutation
accumulation can lead to cancer, reduced fitness, and heritable diseases in offspring.
Therefore the study of mutations, how they are induced, and how they are prevented is
vital. Biomonitor systems are useful for understanding the relevant biological effects
of a given mutagen, and depending on the system, can even provide information on
specific molecular changes induced by the mutagen. Plants are ideal biomonitors, as a
sedentary lifestyle allows measurement of mutagens in air, soil, and water, even at low
doses. We constructed
mutation reporters in Arabidopsis designed to restore β-
glucuronidase (GUS) activity through one of six base substitution reversions. All six
mutant constructs contained inactivating base substitutions in the same codon, which
minimized sequence context effects. An AcV5 epitope tag sequence was fused to the
3' end of GUS to allow detection of the inactive protein and selection of sublines
based on levels of GUS protein expression. Initial characterization of these reversion
reporters with or without UV-C treatment and exposure to heavy metal ions (Cd²⁺ and
Zn²⁺) supports the ability of the lines to measure different mutations. UV-C radiation
induced T to C and C to T reversions, as well as T to G and T to A to a lesser extent.
Heavy-metal-ion-
mutation induction was inconsistent, showing variable increases in G to T and G to C, and no induction of T to C reversion. Of key interest is the G to T
reporter line, as this is the first such reporter in higher eukaryotes. This line showed a
large increase in spontaneous
mutation as well as potential germinal mutations when
compared to the other reporter lines, most likely due to endogenous oxidative damage
(i.e. 8-oxoguanine). Further experiments to test the reporter lines with various
mutagens as well as ways to improve the ability of the reporters to detect
mutation are discussed.
Advisors/Committee Members: Hays, John B. (advisor), Buermeyer, Andrew (committee member).
Subjects/Keywords: mutation reporter; Arabidopsis thaliana – Genetics
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APA (6th Edition):
Bollmann, S. R. (2008). Reversion reporters in Arabidopsis thaliana to detect all six base substitution pathways. (Doctoral Dissertation). Oregon State University. Retrieved from http://hdl.handle.net/1957/8924
Chicago Manual of Style (16th Edition):
Bollmann, Stephanie R. “Reversion reporters in Arabidopsis thaliana to detect all six base substitution pathways.” 2008. Doctoral Dissertation, Oregon State University. Accessed February 16, 2020.
http://hdl.handle.net/1957/8924.
MLA Handbook (7th Edition):
Bollmann, Stephanie R. “Reversion reporters in Arabidopsis thaliana to detect all six base substitution pathways.” 2008. Web. 16 Feb 2020.
Vancouver:
Bollmann SR. Reversion reporters in Arabidopsis thaliana to detect all six base substitution pathways. [Internet] [Doctoral dissertation]. Oregon State University; 2008. [cited 2020 Feb 16].
Available from: http://hdl.handle.net/1957/8924.
Council of Science Editors:
Bollmann SR. Reversion reporters in Arabidopsis thaliana to detect all six base substitution pathways. [Doctoral Dissertation]. Oregon State University; 2008. Available from: http://hdl.handle.net/1957/8924
Oregon State University
23.
Xu, Tanjin.
Exploration of Regression Models for Cancer Noncoding Mutation Recurrence.
Degree: MS, Computer Science, 2016, Oregon State University
URL: http://hdl.handle.net/1957/59204
► An important impact of the genome technology revolution will be the elucidation of mechanisms of cancer pathogenesis, leading to improvements in the diagnosis of cancer…
(more)
▼ An important impact of the genome technology revolution will be the elucidation of mechanisms of cancer pathogenesis, leading to improvements in the diagnosis of cancer and the selection of cancer treatment. Integrated with current well-studied massive knowledge and findings about the role of protein-coding mutations in cancer, demystifying the functional role of human "junk" DNA (non-protein-coding DNA) mutations for cancer development and progression is one of the most popular and promising approaches these days to improve our understanding of the complicated cellular mechanisms in cancer. In light of one recent finding that non-protein-coding driver mutations tend to be highly recurrent, in this thesis we explore three different kinds of regression models for predicting non-protein-coding
mutation recurrence: generalized linear models, conventional machine learning approaches and deep neural network learning models. We compare the regression model results and find the most accurate model for non-protein-coding
mutation recurrence prediction so that we can prioritize somatic mutations based on their predicted recurrence and provide insights for further biological validation and eventually improved cancer therapy.
Advisors/Committee Members: Ramsey, Stephen (advisor), Fern, Xiaoli (committee member).
Subjects/Keywords: Cancer; Mutation (Biology) – Statistical methods
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APA (6th Edition):
Xu, T. (2016). Exploration of Regression Models for Cancer Noncoding Mutation Recurrence. (Masters Thesis). Oregon State University. Retrieved from http://hdl.handle.net/1957/59204
Chicago Manual of Style (16th Edition):
Xu, Tanjin. “Exploration of Regression Models for Cancer Noncoding Mutation Recurrence.” 2016. Masters Thesis, Oregon State University. Accessed February 16, 2020.
http://hdl.handle.net/1957/59204.
MLA Handbook (7th Edition):
Xu, Tanjin. “Exploration of Regression Models for Cancer Noncoding Mutation Recurrence.” 2016. Web. 16 Feb 2020.
Vancouver:
Xu T. Exploration of Regression Models for Cancer Noncoding Mutation Recurrence. [Internet] [Masters thesis]. Oregon State University; 2016. [cited 2020 Feb 16].
Available from: http://hdl.handle.net/1957/59204.
Council of Science Editors:
Xu T. Exploration of Regression Models for Cancer Noncoding Mutation Recurrence. [Masters Thesis]. Oregon State University; 2016. Available from: http://hdl.handle.net/1957/59204
24.
Daccache, Anthony.
Etude du mécanisme d’agrégation de la protéine Tau et son inhibition par des composés polyphénoliques : Study of the aggregation mechanism of tau protein and its inhibition by polyphenolic compounds.
Degree: Docteur es, Molécules et Matières Condensées. Biochimie et biologie moléculaire, 2011, Université Lille I – Sciences et Technologies
URL: http://www.theses.fr/2011LIL10116
► Les isoformes de Tau font parties d’une famille de protéines associées aux microtubules, principalement exprimées dans les neurones du système nerveux central. Ils favorisent l'assemblage…
(more)
▼ Les isoformes de Tau font parties d’une famille de protéines associées aux microtubules, principalement exprimées dans les neurones du système nerveux central. Ils favorisent l'assemblage de monomères tubuline en microtubules et leurs stabilités, jouant un rôle structurel clé dans les axones neuronaux. Dans la maladie d’Alzheimer et autres tauopathies, la protéine Tau agrège sous forme d’enchevêtrements fibrillaires impliqués dans les lésions intraneuronales et gliales. A l’heure actuelle, le processus d’agrégation présent au sein des tauopathies n’est pas complètement élucidé malgré un grand nombre d’études effectués in vitro. L’essentiel du travail présenté dans ma thèse est basé sur un modèle d’étude in vitro utilisant une protéine Tau recombinante présentant la mutation P301L. Ce mutant ainsi que d’autres fragments de Tau ont été utilisés pour mieux comprendre le mécanisme d’agrégation, comme par exemple le rôle des cystéines, ou de la région riche en proline. Nous avons montré par des mesures de diffusion de la lumière et fluorescence de la Thioflavine S qu’il existe un système d’agrégation indépendant des ponts disulfures intermoléculaires. Nous avons également étudié la capacité anti agrégative de plusieurs polyphénols naturels et endogènes. Notre attention s’est en particulier portée sur trois dérivés phénoliques obtenus à partir d'huile d'olive : l'hydroxytyrosol, l'oleuropéine, l'oleuropéine aglycone. Ce dernier a été trouvé plus actif que l’inhibiteur de référence de Tau, le bleu de méthylène. Des résultats similaires ont été obtenu avec des molécules issues de la dimérisation du DOPAL. L’activité inhibitrice de la fibrillisation de ces molécules peut même atteindre des valeurs submicromolaires.
Tau isoforms are part of the microtubule-associated proteins family, mainly expressed in neurons of the central nervous system. They promote the assembly of tubulin monomers into microtubules and their stabilities, playing a key structural role in neuronal axons. In Alzheimer's disease and other tauopathies, the tau protein aggregates as fibrillar tangles involved in intraneuronal and glial lesions. At present, the process of aggregation present in the tauopathies is not fully understood despite a large number of studies performed in vitro. Most of the work presented in my thesis is based on an in vitro model study using recombinant tau protein with the P301L mutation. This mutant and other fragments of Tau were used to better understand the mechanism of aggregation, such as the role of the cysteines or the proline-rich region. We have shown by measurements of light scattering and fluorescence of Thioflavin S there is a system of aggregation independent of intermolecular disulfide bonds. We also studied the ability of several anti-aggregative natural polyphenols and endogenous. Our attention was particularly focused on three phenolic derivatives obtained from olive oil: hydroxytyrosol, oleuropein, oleuropein aglycone. The latter was found more active than the reference inhibitor of Tau, methylene blue. Similar…
Advisors/Committee Members: Cotelle, Philippe (thesis director), Lippens, Guy (thesis director).
Subjects/Keywords: Mutation P301L; Hydroxytyrosol; 572.633
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Chicago ·
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to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Daccache, A. (2011). Etude du mécanisme d’agrégation de la protéine Tau et son inhibition par des composés polyphénoliques : Study of the aggregation mechanism of tau protein and its inhibition by polyphenolic compounds. (Doctoral Dissertation). Université Lille I – Sciences et Technologies. Retrieved from http://www.theses.fr/2011LIL10116
Chicago Manual of Style (16th Edition):
Daccache, Anthony. “Etude du mécanisme d’agrégation de la protéine Tau et son inhibition par des composés polyphénoliques : Study of the aggregation mechanism of tau protein and its inhibition by polyphenolic compounds.” 2011. Doctoral Dissertation, Université Lille I – Sciences et Technologies. Accessed February 16, 2020.
http://www.theses.fr/2011LIL10116.
MLA Handbook (7th Edition):
Daccache, Anthony. “Etude du mécanisme d’agrégation de la protéine Tau et son inhibition par des composés polyphénoliques : Study of the aggregation mechanism of tau protein and its inhibition by polyphenolic compounds.” 2011. Web. 16 Feb 2020.
Vancouver:
Daccache A. Etude du mécanisme d’agrégation de la protéine Tau et son inhibition par des composés polyphénoliques : Study of the aggregation mechanism of tau protein and its inhibition by polyphenolic compounds. [Internet] [Doctoral dissertation]. Université Lille I – Sciences et Technologies; 2011. [cited 2020 Feb 16].
Available from: http://www.theses.fr/2011LIL10116.
Council of Science Editors:
Daccache A. Etude du mécanisme d’agrégation de la protéine Tau et son inhibition par des composés polyphénoliques : Study of the aggregation mechanism of tau protein and its inhibition by polyphenolic compounds. [Doctoral Dissertation]. Université Lille I – Sciences et Technologies; 2011. Available from: http://www.theses.fr/2011LIL10116
University of Wisconsin – La Cross
25.
Mamerow, Michael.
The effects of genetic bottlenecks on mutation fixation and replicative capacity of the influenza A virus.
Degree: 2018, University of Wisconsin – La Cross
URL: http://digital.library.wisc.edu/1793/78856
► The influenza A virus is a common cause of respiratory illness in humans. Seasonal epidemics of influenza in the United States can result in up…
(more)
▼ The influenza A virus is a common cause of respiratory illness in humans. Seasonal
epidemics of influenza in the United States can result in up to 40 million cases, with
annual hospitalizations and deaths reaching as high as 400,000 and 70,000, respectively.
The influenza A virus continually causes annual epidemics, despite yearly vaccines, as a
result of its high
mutation rate, leading to genetically diverse viral populations within
hosts. Respiratory droplet-mediated transmission of the virus between individuals is
accompanied by a bottleneck event that decreases the diversity of the viral population
passed to new hosts. Using controlled artificial bottlenecks of different sizes during in
vitro serial passaging, the impact of these bottleneck events on patterns of
mutation
fixation and replicative capacity of the influenza A virus was determined. Growth curves
and genome sequencing were used after passaging to characterize differences in
replicative capacity and identify genomic changes within the population. Serial passaging
at a bottleneck size of one virus generated virus populations with lower replicative
capacity as compared to the original parental virus. This effect was associated with
fixation of numerous mutations spread throughout the genome. An increase in replicative
capacity was evident after repeated bottlenecks of 1000 viruses, demonstrating that
sufficiently loose bottlenecks do not compromise viral replication kinetics and even allow
for improvement. This increase in replicative capacity was associated with several
mutations, clustered primarily in the hemagglutinin genome segment.
Advisors/Committee Members: WIlker, Peter.
Subjects/Keywords: Microbiology; Avian Influenza Viruses; Mutation
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APA (6th Edition):
Mamerow, M. (2018). The effects of genetic bottlenecks on mutation fixation and replicative capacity of the influenza A virus. (Thesis). University of Wisconsin – La Cross. Retrieved from http://digital.library.wisc.edu/1793/78856
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Mamerow, Michael. “The effects of genetic bottlenecks on mutation fixation and replicative capacity of the influenza A virus.” 2018. Thesis, University of Wisconsin – La Cross. Accessed February 16, 2020.
http://digital.library.wisc.edu/1793/78856.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Mamerow, Michael. “The effects of genetic bottlenecks on mutation fixation and replicative capacity of the influenza A virus.” 2018. Web. 16 Feb 2020.
Vancouver:
Mamerow M. The effects of genetic bottlenecks on mutation fixation and replicative capacity of the influenza A virus. [Internet] [Thesis]. University of Wisconsin – La Cross; 2018. [cited 2020 Feb 16].
Available from: http://digital.library.wisc.edu/1793/78856.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Mamerow M. The effects of genetic bottlenecks on mutation fixation and replicative capacity of the influenza A virus. [Thesis]. University of Wisconsin – La Cross; 2018. Available from: http://digital.library.wisc.edu/1793/78856
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Otago
26.
Sharma, Utsav.
Genetic basis of the activation of the cryptic dct genes in Mesorhizobium loti
.
Degree: 2010, University of Otago
URL: http://hdl.handle.net/10523/387
► Previous studies showed that, although non-symbiotic mesorhizobia carry a copy of the dctABD genes responsible for C4-dicarboxylate transport, most strains isolated from soil were unable…
(more)
▼ Previous studies showed that, although non-symbiotic mesorhizobia carry a copy of the dctABD genes responsible for C4-dicarboxylate transport, most strains isolated from soil were unable to utilise succinate as a carbon source, indicating that the genes were cryptic. Following prolonged incubation on solid media containing succinate as a sole carbon source, two strains (CJ1 and N18) gave rise to succinate-utilising colonies at a frequency much greater than expected by random
mutation alone. Sequence analysis revealed that point mutations had occurred within the dctB or dctD genes in these strains. A cosmid clone pJW5 that conferred the mutator phenotype on other Dct- non-symbiotic strains was isolated from a CJ1 genomic DNA library. Two gene clusters similar to the toxin-antitoxin module hipAB, designated hipB1A1 and hipA2B2, found on pJW5 were implicated in the mutator phenotype. pJW5 was mutagenised with transposon Tn5 and two insertions both within hipB2 were the only insertions found that abolished the mutator phenotype. Furthermore, it was reported that subclones of pJW5 containing either or both hipAB loci conferred the mutator phenotype. These findings led to the hypothesis that the hipAB loci enable the cells to mutate to succinate utilisation by allowing them to undergo adaptive
mutation through a dormant state known as persistence (Weaver, 2003 and personal communication).
In this study subcloning was employed in an effort to confirm that hipAB act as a toxin-antitoxin module and further define the contribution of the hipAB loci to the mutator phenotype. Attempts to express hipA1 or hipA2 from an inducible promoter failed to show that HipA acted as a toxin. Further subcloning studies suggested that neither individual hip genes, hipB1A1, hipA2B2, or both hipAB clusters alone could promote
mutation to succinate metabolism, indicating that other gene(s) in addition to hipB2 present on pJW5 are required. Subsequent restriction digests of pJW5 demarcated a region to the left end of pJW5 as most likely being involved in the mutator phenotype.
The underlying mechanism of
mutation to succinate utilisation, although still ambiguous, seems to harbour some functions of stress-induced mutagenesis (adaptive
mutation) and cryptic activation of silent genes. Involvement of other genes in the phenotype was postulated and the Bacterial Transcription Repair Coupling Factor (TRCF or Mfd) gene was identified as a possible candidate. Mfd facilitates recruitment of repair proteins to DNA lesions present on the coding DNA strand of actively transcribed genes. An R7ANS mfd mutant was constructed and analysis of the mutant suggested that the mfd gene plays a role in the mutator phenotype as the onset of mutant colonies was delayed in the mutant and their numbers were reduced.
Advisors/Committee Members: Ronson, Clive (advisor).
Subjects/Keywords: Cryptic genes;
Mutation;
Bacteria;
Genetics
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APA (6th Edition):
Sharma, U. (2010). Genetic basis of the activation of the cryptic dct genes in Mesorhizobium loti
. (Masters Thesis). University of Otago. Retrieved from http://hdl.handle.net/10523/387
Chicago Manual of Style (16th Edition):
Sharma, Utsav. “Genetic basis of the activation of the cryptic dct genes in Mesorhizobium loti
.” 2010. Masters Thesis, University of Otago. Accessed February 16, 2020.
http://hdl.handle.net/10523/387.
MLA Handbook (7th Edition):
Sharma, Utsav. “Genetic basis of the activation of the cryptic dct genes in Mesorhizobium loti
.” 2010. Web. 16 Feb 2020.
Vancouver:
Sharma U. Genetic basis of the activation of the cryptic dct genes in Mesorhizobium loti
. [Internet] [Masters thesis]. University of Otago; 2010. [cited 2020 Feb 16].
Available from: http://hdl.handle.net/10523/387.
Council of Science Editors:
Sharma U. Genetic basis of the activation of the cryptic dct genes in Mesorhizobium loti
. [Masters Thesis]. University of Otago; 2010. Available from: http://hdl.handle.net/10523/387
University of Arizona
27.
Lynn, Melissa L.
D230N-Tm Induced Dilated Cardiomyopathy and the Role of Fetal cTnT Isoform Switching in Modulating Disease Severity
.
Degree: 2017, University of Arizona
URL: http://hdl.handle.net/10150/625579
► In 1980, the World Health Organization task force first sought to define and classify cardiomyopathies. They defined cardiomyopathies as "heart muscle diseases of unknown cause"…
(more)
▼ In 1980, the World Health Organization task force first sought to define and classify cardiomyopathies. They defined cardiomyopathies as "heart muscle diseases of unknown cause" with three main classifications including: hypertrophic cardiomyopathy (HCM), dilated cardiomyopathy (DCM), and restrictive cardiomyopathy [1]. Over the next three decades it became patently obvious that this simple definition was not sufficient to describe the complex heterogeneity of diseases present in the patient population. More robust definitions were necessary for mechanistic links to be established and meaningful therapeutics to be developed. Since then the accepted definition of a cardiomyopathy has evolved and the classifications have greatly expanded. The most recent definition from the American Heart Association Council on Clinical Cardiology states: Cardiomyopathies are a heterogeneous group of diseases of the myocardium associated with mechanical and/or electrical dysfunction that usually (but not invariably) exhibit inappropriate ventricular hypertrophy or dilatation and are due to a variety of causes that frequently are genetic. Cardiomyopathies either are confined to the heart or are part of generalized systemic disorders, often leading to cardiovascular death or progressive heart failure–related disability [2]. This latest definition (2006) reflects the growing recognition of molecular genetics as a key factor in the development of cardiomyopathies and highlights the ever-growing complexity of disease classification. Today the genetic basis of HCM and DCM is widely recognized yet our understanding of the precise mechanisms underlying the disease remains unclear. To add to this disconnect, by the time patients become symptomatic, pathology has progressed past the initial phase, where meaningful treatment could occur, to advanced end-stage pathology. By this time often the only treatment options available become "blunt sword" therapeutics that are non-specific and used primarily for symptom management. In fact, over the last 3 decades there has been a marked decline in the innovation of cardiovascular pharmaceuticals owed partially to the vast complexity of disease presentation and progression [3]. In this dissertation, I will focus on a genetic sarcomeric DCM caused by a
mutation in alpha-tropomyosin (Tm). Using novel accurate mouse models as a tool we will define the mechanism by which it leads to disease, investigate how disease severity due to the
mutation is modified in an age-dependent manner, and examine what this mechanism could mean in the larger picture of cardiomyopathic disease progression. I hope to convince you that by using accurate models of this DCM at multiple levels of biological complexity to tease out the precise mechanisms of disease we can establish meaningful genotype-phenotype relationships that could lead to the development of specific novel therapeutics.
Advisors/Committee Members: Tardiff, Jil C (advisor), Tardiff, Jil C. (committeemember), Konhilas, John P. (committeemember), Granzier, Hendrikus (committeemember), Lynch, Ronald (committeemember), Harris, Samantha (committeemember).
Subjects/Keywords: cardiomyopathy;
mutation;
sarcomere;
tropomyosin
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Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Lynn, M. L. (2017). D230N-Tm Induced Dilated Cardiomyopathy and the Role of Fetal cTnT Isoform Switching in Modulating Disease Severity
. (Doctoral Dissertation). University of Arizona. Retrieved from http://hdl.handle.net/10150/625579
Chicago Manual of Style (16th Edition):
Lynn, Melissa L. “D230N-Tm Induced Dilated Cardiomyopathy and the Role of Fetal cTnT Isoform Switching in Modulating Disease Severity
.” 2017. Doctoral Dissertation, University of Arizona. Accessed February 16, 2020.
http://hdl.handle.net/10150/625579.
MLA Handbook (7th Edition):
Lynn, Melissa L. “D230N-Tm Induced Dilated Cardiomyopathy and the Role of Fetal cTnT Isoform Switching in Modulating Disease Severity
.” 2017. Web. 16 Feb 2020.
Vancouver:
Lynn ML. D230N-Tm Induced Dilated Cardiomyopathy and the Role of Fetal cTnT Isoform Switching in Modulating Disease Severity
. [Internet] [Doctoral dissertation]. University of Arizona; 2017. [cited 2020 Feb 16].
Available from: http://hdl.handle.net/10150/625579.
Council of Science Editors:
Lynn ML. D230N-Tm Induced Dilated Cardiomyopathy and the Role of Fetal cTnT Isoform Switching in Modulating Disease Severity
. [Doctoral Dissertation]. University of Arizona; 2017. Available from: http://hdl.handle.net/10150/625579
28.
仲里, 秀次.
Early-Stage Induction of SWI/SNF Mutations during Esophageal Squamous Cell Carcinogenesis : SIW/SNF遺伝子異常の食道扁平上皮がん発がんの早期における誘発.
Degree: 博士(医学), 2017, University of the Ryukyus / 琉球大学
URL: http://hdl.handle.net/20.500.12000/36588
► The SWI/SNF chromatin remodeling complex is frequently inactivated by somaticmutations of its various components in various types of cancers, and also by aberrant DNA methylation.…
(more)
▼ The SWI/SNF chromatin remodeling complex is frequently inactivated by somaticmutations of its various components in various types of cancers, and also by aberrant DNA methylation. However, its somatic mutations and aberrant methylation in esophageal squamous cell carcinomas (ESCCs) have not been fully analyzed. In this study, we aimed to clarify in ESCC, what components of the SWI/SNF complex have somatic mutations and aberrant methylation, and when somatic mutations of the SWI/SNF complex occur. Deep sequencing of components of the SWI/SNF complex using a bench-top next Generation sequencer revealed that eight of 92 ESCCs (8.7%) had 11 somatic mutations of 7 genes, ARID1A, ARID2, ATRX, PBRM1, SMARCA4, SMARCAL1, and SMARCC1. TheSMARCA4 mutations were located in the Forkhead (85Ser>Leu) and SNF2 familyN-terminal (882Glu>Lys) domains. The PBRM1 mutations were located in a bromodomain(80Asn>Ser) and an HMG-box domain (1,377Glu>Lys). For most mutations, their Mutant allele frequency was 31-77% (mean 61%) of the fraction of cancer cells in the same samples, indicating that most of the cancer cells in individual ESCC samples had the SWI/SNF mutations on one allele, when present. In addition, a BeadChip array Analysis revealed that a component of the SWI/SNF complex, ACTL6B, had aberrant methylation at its promoter CpG island in 18 of 52 ESCCs (34.6%). These results showed that genetic and epigenetic alterations of the SWI/SNF complex are present in ESCCs, and suggested that genetic alterations are induced at an early stage of esophageal squamous cell carcinogenesis.
Subjects/Keywords: Epigenetics; SWI/SNF; mutation; ESCC
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APA (6th Edition):
仲里, . (2017). Early-Stage Induction of SWI/SNF Mutations during Esophageal Squamous Cell Carcinogenesis : SIW/SNF遺伝子異常の食道扁平上皮がん発がんの早期における誘発. (Thesis). University of the Ryukyus / 琉球大学. Retrieved from http://hdl.handle.net/20.500.12000/36588
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
仲里, 秀次. “Early-Stage Induction of SWI/SNF Mutations during Esophageal Squamous Cell Carcinogenesis : SIW/SNF遺伝子異常の食道扁平上皮がん発がんの早期における誘発.” 2017. Thesis, University of the Ryukyus / 琉球大学. Accessed February 16, 2020.
http://hdl.handle.net/20.500.12000/36588.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
仲里, 秀次. “Early-Stage Induction of SWI/SNF Mutations during Esophageal Squamous Cell Carcinogenesis : SIW/SNF遺伝子異常の食道扁平上皮がん発がんの早期における誘発.” 2017. Web. 16 Feb 2020.
Vancouver:
仲里 . Early-Stage Induction of SWI/SNF Mutations during Esophageal Squamous Cell Carcinogenesis : SIW/SNF遺伝子異常の食道扁平上皮がん発がんの早期における誘発. [Internet] [Thesis]. University of the Ryukyus / 琉球大学; 2017. [cited 2020 Feb 16].
Available from: http://hdl.handle.net/20.500.12000/36588.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
仲里 . Early-Stage Induction of SWI/SNF Mutations during Esophageal Squamous Cell Carcinogenesis : SIW/SNF遺伝子異常の食道扁平上皮がん発がんの早期における誘発. [Thesis]. University of the Ryukyus / 琉球大学; 2017. Available from: http://hdl.handle.net/20.500.12000/36588
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Cornell University
29.
Guo, Yu.
Understanding Mechanisms Of Human Diseases Through Biological Networks
.
Degree: 2015, Cornell University
URL: http://hdl.handle.net/1813/41176
► In the past few decades, great progress has been made in uncovering the molecular bases of many human diseases. As we begin to appreciate the…
(more)
▼ In the past few decades, great progress has been made in uncovering the molecular bases of many human diseases. As we begin to appreciate the complex cellular architecture, the "one-gene/one-enzyme/one-function" concept is no longer apt to explain the complex genotype-phenotype relationships. In fact, the cell functions as an intricate network of interacting genes, gene products and metabolites. Perturbations in biological networks may underlie many disease phenotypes. My dissertation examines the mechanisms of human diseases and disease mutations in the context of biological networks. First, I investigated the regulatory effects of transcription factors (TFs) and microRNAs (miRNAs) on target gene expression, protein-protein interaction and disease association in an integrated gene regulation network. My results suggest that TFs and miRNAs occupy distinct niches in the overall regulatory network within the cell. While TFs tend to regulate intra-module clusters, miRNAs tend to regulate intermodule clusters. Next, to better understand different molecular mechanisms through which mutations lead to diseases, I examined the effects of disease-associated mutations with different inheritance modes and molecular types in a three-dimensional protein interactome network. I found that although recessive mutations on the interaction interface of two interacting proteins tend to cause the same disease, this widelyaccepted "guilt-by-association" principle does not apply to dominant mutations. Furthermore, my analyses suggest that a significant fraction of truncating mutations, which are often considered as "loss-of-function" mutations, can generate functional protein products. Then, I investigated the molecular phenotypes of human disease mutations that are native in the orthologous proteins of other species. As these mutations are potentially compensated in the other species through epistatic selection, they are named potentially epistatic mutations (PEMs). Here, we experimentally demonstrated that PEMs are less deleterious than regular disease mutations, and identified potential intra- and inter-protein compensatory mutations for the PEMs. Finally, I set up a variant prioritizing pipeline that incorporates various biological data such as known disease genes, biological pathways, protein-protein interactions and protein structures to identify predisposing mutations from the wholegenome and whole-exome sequences of Crohn disease and multiple myeloma patients. This analysis pipeline led to the identification of a novel, high-risk variant in Crohn disease.
Advisors/Committee Members: Grimson,Andrew William (committeeMember), Mezey,Jason G. (committeeMember).
Subjects/Keywords: Human disease mutation;
Systems biology
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APA ·
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Export
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Manager
APA (6th Edition):
Guo, Y. (2015). Understanding Mechanisms Of Human Diseases Through Biological Networks
. (Thesis). Cornell University. Retrieved from http://hdl.handle.net/1813/41176
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Guo, Yu. “Understanding Mechanisms Of Human Diseases Through Biological Networks
.” 2015. Thesis, Cornell University. Accessed February 16, 2020.
http://hdl.handle.net/1813/41176.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Guo, Yu. “Understanding Mechanisms Of Human Diseases Through Biological Networks
.” 2015. Web. 16 Feb 2020.
Vancouver:
Guo Y. Understanding Mechanisms Of Human Diseases Through Biological Networks
. [Internet] [Thesis]. Cornell University; 2015. [cited 2020 Feb 16].
Available from: http://hdl.handle.net/1813/41176.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Guo Y. Understanding Mechanisms Of Human Diseases Through Biological Networks
. [Thesis]. Cornell University; 2015. Available from: http://hdl.handle.net/1813/41176
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Central Connecticut State University
30.
Ramirez, Francisco.
Making a chromosomal assignment for the juvenile alopecia (jal) mutation in mice.
Degree: Department of Biomolecular Sciences, 2012, Central Connecticut State University
URL: http://content.library.ccsu.edu/u?/ccsutheses,2081
► The juvenile alopecia (jal) mutation in mice arose on the standard C3H/HeJ inbred background. This mutation controls a poorly-understood recessive disorder in which affected subjects…
(more)
▼ The juvenile alopecia (jal) mutation in mice arose on the standard C3H/HeJ inbred background. This mutation controls a poorly-understood recessive disorder in which affected subjects display patchy hair loss at an early age, often retaining only small patches of fur. The site disrupted by this mutation is unknown, although a previous research publication (McElwee et al. 1999) attributed the mutation to mouse Chromosome (Chr) 13 without providing any supporting data. Here I aimed to verify and refine this chromosomal assignment for jal, using a standard intraspecific backcross mapping approach. To genetically map jal, I created an F1 generation by crossing C57BL/6J female mice with C3H/HeJ males that are homozygous for jal. The heterozygous females were backcrossed to C3H-jal/jal males to make an N2 generation that included 103 members. These mice were classified for their fur phenotype and typed for previously-mapped, PCR-scorable DNA markers. Independent assortment of jal and a particular DNA marker indicated that jal is not located near that site. Since my early analysis using markers from Chr 13 showed that jal is not located on Chr 13, I also assessed numerous markers from throughout the mouse genome for possible linkage with jal. While most sites tested assorted independently with jal, I finally detected linkage at the centromeric tip of mouse Chr 2. Because this region of the C57BL/6J strain offers very few usable markers to support further map refinement, I recommend that a new backcross be conducted using a partner strain that carries numerous molecular differences compared with the C3H/HeJ strain in this region.
Thesis advisor: Thomas R. King.; "Submitted in Partial Fulfillment of the Requirements for the Degree of Master of Arts in Biomolecular Sciences."; M.S.,Central Connecticut State University,2012.;
Advisors/Committee Members: King, Thomas R..
Subjects/Keywords: Mutation (Biology); Gene mapping.
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APA ·
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APA (6th Edition):
Ramirez, F. (2012). Making a chromosomal assignment for the juvenile alopecia (jal) mutation in mice. (Thesis). Central Connecticut State University. Retrieved from http://content.library.ccsu.edu/u?/ccsutheses,2081
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Ramirez, Francisco. “Making a chromosomal assignment for the juvenile alopecia (jal) mutation in mice.” 2012. Thesis, Central Connecticut State University. Accessed February 16, 2020.
http://content.library.ccsu.edu/u?/ccsutheses,2081.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Ramirez, Francisco. “Making a chromosomal assignment for the juvenile alopecia (jal) mutation in mice.” 2012. Web. 16 Feb 2020.
Vancouver:
Ramirez F. Making a chromosomal assignment for the juvenile alopecia (jal) mutation in mice. [Internet] [Thesis]. Central Connecticut State University; 2012. [cited 2020 Feb 16].
Available from: http://content.library.ccsu.edu/u?/ccsutheses,2081.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Ramirez F. Making a chromosomal assignment for the juvenile alopecia (jal) mutation in mice. [Thesis]. Central Connecticut State University; 2012. Available from: http://content.library.ccsu.edu/u?/ccsutheses,2081
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
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Open Access Theses and Dissertations
