subject:( DNA polymerase gamma )

University of Texas – Austin

1. Ziehr, Jessica Lea. Kinetics and specificity of human mitochondrial DNA polymerase gamma and HIV-1 reverse transcriptase.

Degree: PhD, Cell and Molecular Biology, 2014, University of Texas – Austin

URL: http://hdl.handle.net/2152/31296

► The human mitochondrial DNA (mtDNA) genome must be faithfully maintained by the mitochondrial DNA replication machinery. Deficiencies in mtDNA maintenance result in the accumulation of… (more)

▼ The human mitochondrial DNA (mtDNA) genome must be faithfully maintained by the mitochondrial DNA replication machinery. Deficiencies in mtDNA maintenance result in the accumulation of mutations and deletions, which have been associated with a number of neuromuscular degenerative disorders including, mtDNA depletion syndrome, Alpers syndrome, progressive external opthalmoplegia (PEO), and sensory ataxic neuropathy, dysarthria, and opthalmoparesis (SANDO). The mtDNA replication machinery is comprised of a nuclearly-encoded DNA polymerase gamma (Pol γ), single-stranded DNA binding protein (mtSSB), and a hexameric mtDNA helicase. In this work, we employed quantitative pre-steady state kinetic techniques to establish the mechanisms responsible for the replication of the human mitochondrial DNA by Pol γ and explored the effects of point mutations that are observed in heritable diseases. With our biochemical characterization of mutants of Pol γ, we have shown unique characteristics that would lead to profound physiological consequences over time. Additionally, we have made significant progress towards reconstitution of the mitochondrial DNA replisome by monitoring DNA polymerization that is dependent on helicase unwinding of double stranded DNA. Overall, this work provides a better understanding of the mechanism of mtDNA replication and has important implications toward understanding the role of mitochondrial DNA replication in mitochondrial disease, ageing and cancer. In addition to the work on the mtDNA replisome, we have applied pre-steady state kinetic techniques to better understand the mechanism of RNA-dependent DNA polymerization by HIV reverse transcriptase (HIV-RT). This enzyme is responsible for the replication of the viral genome in HIV and is a common target for anti-HIV drugs. We have characterized the role of enzyme conformational changes in the kinetics of incorporation of correct nucleotide and the Nucleotide Reverse Transcriptase Inhibitor (NRTI) AZT by wild-type enzyme, as well as a mutant with clinical resistance to AZT. This work provides a better understanding of the complete mechanism of RNA-dependent DNA polymerization, the changes in the mechanism in the presence of inhibitor and the development of resistance to this nucleoside analog; and thereby this work contributes to the long-term goal of designing more effective drugs that can possibly deter resistance and be used successfully for treatment of HIV. Advisors/Committee Members: Johnson, Kenneth A. (Kenneth Allen) (advisor), Lambowitz, Alan M (committee member), Russell, Rick (committee member), Marcotte, Edward M (committee member), Dalby, Kevin (committee member).

Subjects/Keywords: DNA polymerase; Pre-steady state kinetics; HIV reverse transcriptase; Polymerase gamma

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APA (6^th Edition):

Ziehr, J. L. (2014). Kinetics and specificity of human mitochondrial DNA polymerase gamma and HIV-1 reverse transcriptase. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/31296

Chicago Manual of Style (16^th Edition):

Ziehr, Jessica Lea. “Kinetics and specificity of human mitochondrial DNA polymerase gamma and HIV-1 reverse transcriptase.” 2014. Doctoral Dissertation, University of Texas – Austin. Accessed March 03, 2021. http://hdl.handle.net/2152/31296.

MLA Handbook (7^th Edition):

Ziehr, Jessica Lea. “Kinetics and specificity of human mitochondrial DNA polymerase gamma and HIV-1 reverse transcriptase.” 2014. Web. 03 Mar 2021.

Vancouver:

Ziehr JL. Kinetics and specificity of human mitochondrial DNA polymerase gamma and HIV-1 reverse transcriptase. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2014. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/2152/31296.

Council of Science Editors:

Ziehr JL. Kinetics and specificity of human mitochondrial DNA polymerase gamma and HIV-1 reverse transcriptase. [Doctoral Dissertation]. University of Texas – Austin; 2014. Available from: http://hdl.handle.net/2152/31296

Brigham Young University

2. Brammer, Jeffrey M. Organellar DNA Polymerases Gamma I and II in Arabidopsis thaliana.

Degree: MS, 2010, Brigham Young University

URL: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=3533&context=etd

► Plants have two organelles outside the nucleus which carry their own DNA, mitochondria and chloroplasts. These organelles are descendants of bacteria that were engulfed… (more)

Subjects/Keywords: DNA polymerase; Arabidopsis; Arabidopsis thaliana; gamma polymerase; mitochondrion; mitochondria; chloroplast; plastid; DNA replication; Microbiology

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APA (6^th Edition):

Brammer, J. M. (2010). Organellar DNA Polymerases Gamma I and II in Arabidopsis thaliana. (Masters Thesis). Brigham Young University. Retrieved from https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=3533&context=etd

Chicago Manual of Style (16^th Edition):

Brammer, Jeffrey M. “Organellar DNA Polymerases Gamma I and II in Arabidopsis thaliana.” 2010. Masters Thesis, Brigham Young University. Accessed March 03, 2021. https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=3533&context=etd.

MLA Handbook (7^th Edition):

Brammer, Jeffrey M. “Organellar DNA Polymerases Gamma I and II in Arabidopsis thaliana.” 2010. Web. 03 Mar 2021.

Vancouver:

Brammer JM. Organellar DNA Polymerases Gamma I and II in Arabidopsis thaliana. [Internet] [Masters thesis]. Brigham Young University; 2010. [cited 2021 Mar 03]. Available from: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=3533&context=etd.

Council of Science Editors:

Brammer JM. Organellar DNA Polymerases Gamma I and II in Arabidopsis thaliana. [Masters Thesis]. Brigham Young University; 2010. Available from: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=3533&context=etd

Tampere University

3. Nurminen, Anssi. A Bioinformatics Approach to Analyzing the Pathogenicity of Mutations by Using Protein Structure Information : A Study on DNA Polymerase Gamma .

Degree: 2018, Tampere University

URL: https://trepo.tuni.fi/handle/10024/102657

► Geneettisen testauksen kustannusten laskiessa, pullonkaulaksi saatavilla olevan tiedon hyödyntämiseen on muodostumassa tietämyksemme eri geneettisten variaatioiden ja mutaatioden merkityksestä. Jokaisella henkilöllä on satoja, yksilöllisiä variaatioita perimässään… (more)

▼ Geneettisen testauksen kustannusten laskiessa, pullonkaulaksi saatavilla olevan tiedon hyödyntämiseen on muodostumassa tietämyksemme eri geneettisten variaatioiden ja mutaatioden merkityksestä. Jokaisella henkilöllä on satoja, yksilöllisiä variaatioita perimässään joiden vaikutuksia ei tunneta. Tilanteissa joissa perinöllisen sairauden syytä pyritään selvittämään geenitutkimuksen avulla nämä variaatiot pitää pystyä tunnistamaan joko merkityksettömiksi tai merkitysellisiksi taudin kannalta, jotta oikean diagnoosin tekeminen ja sopivien hoitometelmien valinta on mahdollista. Rakennebiologia ja bioinformatiikka tarjoavat monia keinoja mutaatioiden vaikutusten tarkasteluun. Tässä tutkimuksessa käytetään esimerkkinä DNA polymeraasi gammaa (Pol γ), joka on ainoa tunnettu entsyymi joka replikoi ja ylläpitää mitokondrionaalista DNA:ta. Pol γ tarjoaa uniikin tutkimuskohteen pistemutaatioiden vaikutuksille sen kriittisen toiminnalisuuden ja korvaavien mekanismien puuttumisen vuoksi. Pol γ:n tunnetun proteiinirakenteen, yli 700 hengen potilasaineiston ja mutaatioiden biokemiallisen karakterisoinnin avulla pystymme tuottamaan ennennäkemättömän tarkan kuvan mutaatioiden vaikutusmekanismeista ja ennustamaan sekä tunnettujen, että vielä tuntemattomien mutaatioiden vaikutusta taudin puhkeamiseen ja etenemiseen. Tämän tutkimuksen osana olemme kehittäneet uuden algoritmin proteiinien kolmiulotteisten rakenteiden tutkimukseen ja analysointiin, nimeltään StructureMapper. StructureMapper on skaalautuva, suurien aineistojen analysoitiin suunniteltu algoritmi, joka tarjoaa mahdollisuuksia analysoida esimerkikisi ennustusalgoritmien tulosten luotettavuutta, kokeellisen datan laatua, ja sitä voidaan hyödyntää myös mutaatioiden haitallisuuden ennustamisessa ja tutkimuksessa. Kaikkia tämän tutkimuksen osana tuotetuista menetelmistä ja työkaluista voidaan hyödyntää yleiskäyttöisesti proteiinien tutkimuksessa.; Genetic testing is becoming more and more prevalent in the field of medicine. The bottleneck in making a diagnosis based on genetic information has shifted from being able to acquire the required information by sequencing the genome of a patient, to understanding the effects of the detected, unique variations in the DNA. Mutations in the DNA can affect proteins and their structure on many levels. In a clinical setting, being able to separate the benign mutations from the pathogenic is of utmost importance. DNA polymerase gamma (Pol γ) offers an intriguing study subject in the world of structural biology. It is the sole enzyme responsible for replicating mitochondrial DNA. Defects in its functionality can manifest with a wide variety of symptoms that are often due to single point mutations that affect its structure in a deleterious way. Through analysis of the structure of Pol γ, combined with over 700 available patient case reports and biochemical characterization of some of the mutations, we have gained an unprecedented view to the reasons behind the mutations that lead to pathogenicity and altered biological functionality of…

Subjects/Keywords: DNA polymeraasi gamma ; POLG ; mutaatio ; proteiinirakenne ; patogeenisyys ; DNA polymerase gamma ; mutation ; protein structure ; pathogenicity

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

APA (6^th Edition):

Nurminen, A. (2018). A Bioinformatics Approach to Analyzing the Pathogenicity of Mutations by Using Protein Structure Information : A Study on DNA Polymerase Gamma . (Doctoral Dissertation). Tampere University. Retrieved from https://trepo.tuni.fi/handle/10024/102657

Chicago Manual of Style (16^th Edition):

Nurminen, Anssi. “A Bioinformatics Approach to Analyzing the Pathogenicity of Mutations by Using Protein Structure Information : A Study on DNA Polymerase Gamma .” 2018. Doctoral Dissertation, Tampere University. Accessed March 03, 2021. https://trepo.tuni.fi/handle/10024/102657.

MLA Handbook (7^th Edition):

Nurminen, Anssi. “A Bioinformatics Approach to Analyzing the Pathogenicity of Mutations by Using Protein Structure Information : A Study on DNA Polymerase Gamma .” 2018. Web. 03 Mar 2021.

Vancouver:

Nurminen A. A Bioinformatics Approach to Analyzing the Pathogenicity of Mutations by Using Protein Structure Information : A Study on DNA Polymerase Gamma . [Internet] [Doctoral dissertation]. Tampere University; 2018. [cited 2021 Mar 03]. Available from: https://trepo.tuni.fi/handle/10024/102657.

Council of Science Editors:

Nurminen A. A Bioinformatics Approach to Analyzing the Pathogenicity of Mutations by Using Protein Structure Information : A Study on DNA Polymerase Gamma . [Doctoral Dissertation]. Tampere University; 2018. Available from: https://trepo.tuni.fi/handle/10024/102657

4. Meng, Qingchao, master of arts in cell and molecular biology. Approaching the crystal structure of the polymerase γ catalytic complex: Approaching the crystal structure of the polymerase [gamma] catalytic complex.

Degree: MA, Cell and Molecular Biology, 2011, University of Texas – Austin

URL: http://hdl.handle.net/2152/ETD-UT-2011-08-4330

► In this thesis, a 4.7Å crystal structure of the human mitochondria DNA polymerase γ catalytic complex is reported. Though the DNA substrate-binding site is not… (more)

Subjects/Keywords: Pol γ; Crystal structure; Catalytic complex; Polymerase γ; Pol gamma; Polymerase gamma; Human mitochondria DNA polymerase gamma; DNA; DNA binding site; Human mitochondria DNA polymerase γ

…polymerase and exonuclease domains of the catalytic subunit of the Pol γ-DNA complex (red)… …nucleoside inhibitors of mitochondrial DNA polymerase gamma." Methods 51(4): 392-8… …laevis mitochondrial DNA polymerase gamma increases processivity of the catalytic subunit of… …human DNA polymerase gamma and is related to class II aminoacyl-tRNA synthetases." Mol… …x29;. "The accessory subunit B of DNA polymerase gamma is required for mitochondrial…

9 more images…

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APA (6^th Edition):

Meng, Qingchao, m. o. a. i. c. a. m. b. (2011). Approaching the crystal structure of the polymerase γ catalytic complex: Approaching the crystal structure of the polymerase [gamma] catalytic complex. (Masters Thesis). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/ETD-UT-2011-08-4330

Chicago Manual of Style (16^th Edition):

Meng, Qingchao, master of arts in cell and molecular biology. “Approaching the crystal structure of the polymerase γ catalytic complex: Approaching the crystal structure of the polymerase [gamma] catalytic complex.” 2011. Masters Thesis, University of Texas – Austin. Accessed March 03, 2021. http://hdl.handle.net/2152/ETD-UT-2011-08-4330.

MLA Handbook (7^th Edition):

Meng, Qingchao, master of arts in cell and molecular biology. “Approaching the crystal structure of the polymerase γ catalytic complex: Approaching the crystal structure of the polymerase [gamma] catalytic complex.” 2011. Web. 03 Mar 2021.

Vancouver:

Meng, Qingchao moaicamb. Approaching the crystal structure of the polymerase γ catalytic complex: Approaching the crystal structure of the polymerase [gamma] catalytic complex. [Internet] [Masters thesis]. University of Texas – Austin; 2011. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/2152/ETD-UT-2011-08-4330.

Council of Science Editors:

Meng, Qingchao moaicamb. Approaching the crystal structure of the polymerase γ catalytic complex: Approaching the crystal structure of the polymerase [gamma] catalytic complex. [Masters Thesis]. University of Texas – Austin; 2011. Available from: http://hdl.handle.net/2152/ETD-UT-2011-08-4330

Brigham Young University

5. Cupp, John D. Characterization of the Cellular and Organellar Dynamics that Occur with a Partial Depletion of Mitochondrial DNA when Arabidopsis Organellar DNA Polymerase IB is Mutated.

Degree: PhD, 2012, Brigham Young University

URL: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=4746&context=etd

► Plant mitochondrial genomes are large and complex, and the mechanisms for maintaining mitochondrial DNA (mtDNA) remain unclear. Arabidopsis thaliana has two DNA polymerase genes, polIA… (more)

Subjects/Keywords: polymerase gamma; PolIA; PolIB; TWINKLE; mitochondria; DNA replication; Microbiology

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APA (6^th Edition):

Cupp, J. D. (2012). Characterization of the Cellular and Organellar Dynamics that Occur with a Partial Depletion of Mitochondrial DNA when Arabidopsis Organellar DNA Polymerase IB is Mutated. (Doctoral Dissertation). Brigham Young University. Retrieved from https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=4746&context=etd

Chicago Manual of Style (16^th Edition):

Cupp, John D. “Characterization of the Cellular and Organellar Dynamics that Occur with a Partial Depletion of Mitochondrial DNA when Arabidopsis Organellar DNA Polymerase IB is Mutated.” 2012. Doctoral Dissertation, Brigham Young University. Accessed March 03, 2021. https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=4746&context=etd.

MLA Handbook (7^th Edition):

Cupp, John D. “Characterization of the Cellular and Organellar Dynamics that Occur with a Partial Depletion of Mitochondrial DNA when Arabidopsis Organellar DNA Polymerase IB is Mutated.” 2012. Web. 03 Mar 2021.

Vancouver:

Cupp JD. Characterization of the Cellular and Organellar Dynamics that Occur with a Partial Depletion of Mitochondrial DNA when Arabidopsis Organellar DNA Polymerase IB is Mutated. [Internet] [Doctoral dissertation]. Brigham Young University; 2012. [cited 2021 Mar 03]. Available from: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=4746&context=etd.

Council of Science Editors:

Cupp JD. Characterization of the Cellular and Organellar Dynamics that Occur with a Partial Depletion of Mitochondrial DNA when Arabidopsis Organellar DNA Polymerase IB is Mutated. [Doctoral Dissertation]. Brigham Young University; 2012. Available from: https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=4746&context=etd

Université Catholique de Louvain

6. Szczepanowska, Karolina. A cluster of pathogenic mutations in the 3'-5' exonuclease domain of DNA polymerase gamma defines a novel module coupling DNA synthesis and degradation.

Degree: 2011, Université Catholique de Louvain

URL: http://hdl.handle.net/2078.1/73438

►

DNA polymerase gamma (pol g in human, Mip1 in yeast) is the unique DNA replicase found in mitochondria. Pol g plays a key role in… (more)

Subjects/Keywords: Mitochondrial DNA polymerase gamma; Mitochondrial disorders; Mutations; Yeast

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APA (6^th Edition):

Szczepanowska, K. (2011). A cluster of pathogenic mutations in the 3'-5' exonuclease domain of DNA polymerase gamma defines a novel module coupling DNA synthesis and degradation. (Thesis). Université Catholique de Louvain. Retrieved from http://hdl.handle.net/2078.1/73438

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

Chicago Manual of Style (16^th Edition):

Szczepanowska, Karolina. “A cluster of pathogenic mutations in the 3'-5' exonuclease domain of DNA polymerase gamma defines a novel module coupling DNA synthesis and degradation.” 2011. Thesis, Université Catholique de Louvain. Accessed March 03, 2021. http://hdl.handle.net/2078.1/73438.

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

MLA Handbook (7^th Edition):

Szczepanowska, Karolina. “A cluster of pathogenic mutations in the 3'-5' exonuclease domain of DNA polymerase gamma defines a novel module coupling DNA synthesis and degradation.” 2011. Web. 03 Mar 2021.

Vancouver:

Szczepanowska K. A cluster of pathogenic mutations in the 3'-5' exonuclease domain of DNA polymerase gamma defines a novel module coupling DNA synthesis and degradation. [Internet] [Thesis]. Université Catholique de Louvain; 2011. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/2078.1/73438.

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

Council of Science Editors:

Szczepanowska K. A cluster of pathogenic mutations in the 3'-5' exonuclease domain of DNA polymerase gamma defines a novel module coupling DNA synthesis and degradation. [Thesis]. Université Catholique de Louvain; 2011. Available from: http://hdl.handle.net/2078.1/73438

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

University of Texas – Austin

7. Estep, Patricia Ann. The role of residue Y955 of mitochondrial DNA polymerase [gamma] in nucleotide binding and discrimination.

Degree: MA, Biochemistry, 2010, University of Texas – Austin

URL: http://hdl.handle.net/2152/ETD-UT-2010-12-2395

► The human mitochondrial polymerase (pol γ) is a nuclearly-encoded polymerase that is solely responsible for the faithful replication and repair of the mitochondrial genome. The… (more)

Subjects/Keywords: Pre-steady state kinetics; DNA polymerase gamma

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

APA (6^th Edition):

Estep, P. A. (2010). The role of residue Y955 of mitochondrial DNA polymerase [gamma] in nucleotide binding and discrimination. (Masters Thesis). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/ETD-UT-2010-12-2395

Chicago Manual of Style (16^th Edition):

Estep, Patricia Ann. “The role of residue Y955 of mitochondrial DNA polymerase [gamma] in nucleotide binding and discrimination.” 2010. Masters Thesis, University of Texas – Austin. Accessed March 03, 2021. http://hdl.handle.net/2152/ETD-UT-2010-12-2395.

MLA Handbook (7^th Edition):

Estep, Patricia Ann. “The role of residue Y955 of mitochondrial DNA polymerase [gamma] in nucleotide binding and discrimination.” 2010. Web. 03 Mar 2021.

Vancouver:

Estep PA. The role of residue Y955 of mitochondrial DNA polymerase [gamma] in nucleotide binding and discrimination. [Internet] [Masters thesis]. University of Texas – Austin; 2010. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/2152/ETD-UT-2010-12-2395.

Council of Science Editors:

Estep PA. The role of residue Y955 of mitochondrial DNA polymerase [gamma] in nucleotide binding and discrimination. [Masters Thesis]. University of Texas – Austin; 2010. Available from: http://hdl.handle.net/2152/ETD-UT-2010-12-2395

8. Sahashi, Ritsuko. Cell biological and genetical studies on DNA replication enzyme and protein modification enzyme in Drosophila : ショウジョウバエ DNA 複製酵素及びタンパク質修飾酵素の細胞生物学・遺伝学的解析.

Degree: 博士（学術）, 2014, Kyoto Institute of Technology / 京都工芸繊維大学

URL: http://hdl.handle.net/10212/2155

DNAポリメラーゼα,δ,そしてε（polα, polδ,polε）はゲノムのDNA合成を行う酵素である。polαがRNAプライマーとそれに引き続く20〜30塩基のDNAを合成し、その後、polαと置き換わったpolδ,polεが、それぞれ、ラギング鎖、リーディング鎖の合成を行うことがわかっている。先行研究によりpolαと相互作用する因子の１つとして、ヒストンH4の20番目のリジン残基（H4-K20）をモノメチル化する酵素であるPr-Set7が同定された。第1章において、私はDNA複製とヒストンH4-K20メチル化との関係及び、polαとPr-Set7の相互作用について注目をした。翅原基特異的にショウジョウバエpolαの触媒サブユニットであるpolα180kDaサブユニット（dpolαp180）をノックダウンすると成虫翅の萎縮（atrophied wing表現型）が見られdpolαp180とdPr-Set7のダブルノックダウン系統では、atrophied wing表現型の増強が見られた。また、dpolαp180ノックダウン系統の翅原基でのDNA合成をモニターするためBrdU incorporation assayを行なった結果、BrdU ポジティブな細胞数に減少がみられ、dpolαp180とdPr-Set7のダブルノックダウン系統では、BrdU ポジティブな細胞数は、さらに減少した。これらのことより、個体レベルでも両者の機能的関連が示唆され、dPr-Set7がdpolαとの相互作用を介してDNA複製の制御に関与することが示唆された。また、dpolαp180をノックダウンした翅原基における抗H4-K20モノメチル化抗体を用いた免疫染色法の結果、H4-K20モノメチル化のシグナルが減少するこを明らかにした。このことより、Pr-Set7のメチル化活性制御にdpolαが重要な働きを担っている可能性が示された。　2章では、ショウジョウバエpolεの58 kDサブユニット（dpolεp58）の機能解析を行った。polεはヘテロ4量体タンパク質であることが報告されているが、ショウジョウバエでは、現在のところ、触媒サブユニットである255 kD (dpolεp255)サブユニットと、2番目サブユニットのdpolεp58サブユニットが同定されている。dpolεp58変異系統は、蛹で致死となり、3齢幼虫の成虫原基や唾腺が野生型と比較して小型化していた。これらのことからdpolεp58が組織の成長、細胞増殖および生存に必須であると示唆された。dpolεp58変異系統3齢幼虫の複眼原基では、形態形成溝の後極側におけるBrdUの取り込みが減少し、通常は増殖が停止し、分化している後極側の細胞でM期のシグナルが増加していた。S期の遅延が引き起こされたため、後極側の細胞におけるM期のシグナルが増加したと考えられる。これらの結果より、dpolεp58がS期の進行に関与している事が明らかとなった。また、唾腺の核が野生型と比較して小型化している事が観察され、dpolεp58のendoreplicationへの関与も示唆された。さらに、変異系統を用いて他の複製関連因子の抗体でウエスタン免疫ブロットを行った結果、複製開始因子であるdOrc2レベルの顕著な減少が見られた。このことからdpolεp58とdOrc2が細胞内で相互作用する可能性が示めされ、これらのことよりpolεが複製開始に関与することが示唆された。第3章では、ショウジョウバエの発生において、私は、ショウジョウバエトランスグルタミナーゼ B（dTG-B）の働きを理解することを目的にdTG-B過剰発現系統を用いてその表現型の解析を行った。トランスグルタミナーゼ（TG）は、タンパク質間の架橋反応を触媒するタンパク質間翻訳後酵素で、様々な生物学的プロセスに関わっている。ショウジョウバエトランスグルタミナーゼの遺伝子は1種類で、A型とB型の2種類の転写産物が作られる。dTG-B過剰発現系統では、rough eye表現型と翅脈の過形成が観察された。これらの表現型は、先行研究により報告されているトランスグルタミナーゼA（dTG-A）の過剰発現系統において観察された表現型と同様であり、これらの結果からdTG-Aだけでなく、dTG-Bも複眼の形成と翅脈の形成において、その制御に関わっていることが示唆された。

Subjects/Keywords: DNA replication; DNA polymerase; Transglutaminase

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APA (6^th Edition):

Sahashi, R. (2014). Cell biological and genetical studies on DNA replication enzyme and protein modification enzyme in Drosophila : ショウジョウバエ DNA 複製酵素及びタンパク質修飾酵素の細胞生物学・遺伝学的解析. (Thesis). Kyoto Institute of Technology / 京都工芸繊維大学. Retrieved from http://hdl.handle.net/10212/2155

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

Chicago Manual of Style (16^th Edition):

Sahashi, Ritsuko. “Cell biological and genetical studies on DNA replication enzyme and protein modification enzyme in Drosophila : ショウジョウバエ DNA 複製酵素及びタンパク質修飾酵素の細胞生物学・遺伝学的解析.” 2014. Thesis, Kyoto Institute of Technology / 京都工芸繊維大学. Accessed March 03, 2021. http://hdl.handle.net/10212/2155.

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

MLA Handbook (7^th Edition):

Sahashi, Ritsuko. “Cell biological and genetical studies on DNA replication enzyme and protein modification enzyme in Drosophila : ショウジョウバエ DNA 複製酵素及びタンパク質修飾酵素の細胞生物学・遺伝学的解析.” 2014. Web. 03 Mar 2021.

Vancouver:

Sahashi R. Cell biological and genetical studies on DNA replication enzyme and protein modification enzyme in Drosophila : ショウジョウバエ DNA 複製酵素及びタンパク質修飾酵素の細胞生物学・遺伝学的解析. [Internet] [Thesis]. Kyoto Institute of Technology / 京都工芸繊維大学; 2014. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/10212/2155.

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

Council of Science Editors:

Sahashi R. Cell biological and genetical studies on DNA replication enzyme and protein modification enzyme in Drosophila : ショウジョウバエ DNA 複製酵素及びタンパク質修飾酵素の細胞生物学・遺伝学的解析. [Thesis]. Kyoto Institute of Technology / 京都工芸繊維大学; 2014. Available from: http://hdl.handle.net/10212/2155

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

9. Jatsenko, Tatjana. Role of translesion DNA polymerases in mutagenesis and DNA damage tolerance in Pseudomonads .

Degree: 2018, Tartu University

URL: http://hdl.handle.net/10062/61278

► Kahjustused DNA-s, mis tekivad kas rakkude normaalse elutegevuse käigus või erinevate keskonnategurite mõjul (näiteks UV-kiirgus, DNA-d kahjustavad kemikaalid), pärsivad genoomi replikatsiooni, takistades replikatiivse DNA polümeraasi… (more)

Subjects/Keywords: mutations; DNA damage; DNA polymerase; DNA repair

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APA (6^th Edition):

Jatsenko, T. (2018). Role of translesion DNA polymerases in mutagenesis and DNA damage tolerance in Pseudomonads . (Thesis). Tartu University. Retrieved from http://hdl.handle.net/10062/61278

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

Chicago Manual of Style (16^th Edition):

Jatsenko, Tatjana. “Role of translesion DNA polymerases in mutagenesis and DNA damage tolerance in Pseudomonads .” 2018. Thesis, Tartu University. Accessed March 03, 2021. http://hdl.handle.net/10062/61278.

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

MLA Handbook (7^th Edition):

Jatsenko, Tatjana. “Role of translesion DNA polymerases in mutagenesis and DNA damage tolerance in Pseudomonads .” 2018. Web. 03 Mar 2021.

Vancouver:

Jatsenko T. Role of translesion DNA polymerases in mutagenesis and DNA damage tolerance in Pseudomonads . [Internet] [Thesis]. Tartu University; 2018. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/10062/61278.

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

Council of Science Editors:

Jatsenko T. Role of translesion DNA polymerases in mutagenesis and DNA damage tolerance in Pseudomonads . [Thesis]. Tartu University; 2018. Available from: http://hdl.handle.net/10062/61278

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

University of Texas – Austin

10. -8850-5086. Structural analysis of hypoxanthine mutagenicity using DNA polymerase β and η: Structural analysis of hypoxanthine mutagenicity using DNA polymerase [beta] and [eta].

Degree: MA, Cell and Molecular Biology, 2019, University of Texas – Austin

URL: http://hdl.handle.net/2152/72726

► Cellular life is precarious. Dangers abound for a cell’s DNA, from both external and internal factors, and maintaining genomic integrity is crucial for cell survival.… (more)

Subjects/Keywords: DNA polymerase beta; DNA polymerase eta; Hypoxanthine; DNA repair; Mutation

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APA (6^th Edition):

-8850-5086. (2019). Structural analysis of hypoxanthine mutagenicity using DNA polymerase β and η: Structural analysis of hypoxanthine mutagenicity using DNA polymerase [beta] and [eta]. (Masters Thesis). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/72726

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Chicago Manual of Style (16^th Edition):

-8850-5086. “Structural analysis of hypoxanthine mutagenicity using DNA polymerase β and η: Structural analysis of hypoxanthine mutagenicity using DNA polymerase [beta] and [eta].” 2019. Masters Thesis, University of Texas – Austin. Accessed March 03, 2021. http://hdl.handle.net/2152/72726.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

MLA Handbook (7^th Edition):

-8850-5086. “Structural analysis of hypoxanthine mutagenicity using DNA polymerase β and η: Structural analysis of hypoxanthine mutagenicity using DNA polymerase [beta] and [eta].” 2019. Web. 03 Mar 2021.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Vancouver:

-8850-5086. Structural analysis of hypoxanthine mutagenicity using DNA polymerase β and η: Structural analysis of hypoxanthine mutagenicity using DNA polymerase [beta] and [eta]. [Internet] [Masters thesis]. University of Texas – Austin; 2019. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/2152/72726.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Council of Science Editors:

-8850-5086. Structural analysis of hypoxanthine mutagenicity using DNA polymerase β and η: Structural analysis of hypoxanthine mutagenicity using DNA polymerase [beta] and [eta]. [Masters Thesis]. University of Texas – Austin; 2019. Available from: http://hdl.handle.net/2152/72726

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

11. 山本, 崇史. 大腸菌DNA polymerase I の細胞内機能におけるβ-clampの役割 : Roles of β-clamp in cellular function of DNA polymerase I of Escherichia coli; ダイチョウキン DNA polymerase I ノサイボウナイキノウニオケル β-clamp ノヤクワリ.

Degree: 博士(バイオサイエンス), 2016, Nara Institute of Science and Technology / 奈良先端科学技術大学院大学

URL: http://hdl.handle.net/10061/10991

Subjects/Keywords: DNA polymerase

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APA (6^th Edition):

山本, �. (2016). 大腸菌DNA polymerase I の細胞内機能におけるβ-clampの役割 : Roles of β-clamp in cellular function of DNA polymerase I of Escherichia coli; ダイチョウキン DNA polymerase I ノサイボウナイキノウニオケル β-clamp ノヤクワリ. (Thesis). Nara Institute of Science and Technology / 奈良先端科学技術大学院大学. Retrieved from http://hdl.handle.net/10061/10991

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

Chicago Manual of Style (16^th Edition):

山本, 崇史. “大腸菌DNA polymerase I の細胞内機能におけるβ-clampの役割 : Roles of β-clamp in cellular function of DNA polymerase I of Escherichia coli; ダイチョウキン DNA polymerase I ノサイボウナイキノウニオケル β-clamp ノヤクワリ.” 2016. Thesis, Nara Institute of Science and Technology / 奈良先端科学技術大学院大学. Accessed March 03, 2021. http://hdl.handle.net/10061/10991.

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

MLA Handbook (7^th Edition):

山本, 崇史. “大腸菌DNA polymerase I の細胞内機能におけるβ-clampの役割 : Roles of β-clamp in cellular function of DNA polymerase I of Escherichia coli; ダイチョウキン DNA polymerase I ノサイボウナイキノウニオケル β-clamp ノヤクワリ.” 2016. Web. 03 Mar 2021.

Vancouver:

山本 �. 大腸菌DNA polymerase I の細胞内機能におけるβ-clampの役割 : Roles of β-clamp in cellular function of DNA polymerase I of Escherichia coli; ダイチョウキン DNA polymerase I ノサイボウナイキノウニオケル β-clamp ノヤクワリ. [Internet] [Thesis]. Nara Institute of Science and Technology / 奈良先端科学技術大学院大学; 2016. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/10061/10991.

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

Council of Science Editors:

山本 �. 大腸菌DNA polymerase I の細胞内機能におけるβ-clampの役割 : Roles of β-clamp in cellular function of DNA polymerase I of Escherichia coli; ダイチョウキン DNA polymerase I ノサイボウナイキノウニオケル β-clamp ノヤクワリ. [Thesis]. Nara Institute of Science and Technology / 奈良先端科学技術大学院大学; 2016. Available from: http://hdl.handle.net/10061/10991

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

University of Pretoria

12. [No author]. Efficacy of different DNA polymerase enzymes in PCR amplification of forensic bovine DNA .

Degree: 2012, University of Pretoria

URL: http://upetd.up.ac.za/thesis/available/etd-08062012-144315/

► DNA profiling of exhibits that originate from forensic stock theft cases is routinely used as a tool to link suspects to the crime or scene.… (more)

Subjects/Keywords: Dna polymerase enzymes; Forensic bovine dna; UCTD

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APA (6^th Edition):

author], [. (2012). Efficacy of different DNA polymerase enzymes in PCR amplification of forensic bovine DNA . (Masters Thesis). University of Pretoria. Retrieved from http://upetd.up.ac.za/thesis/available/etd-08062012-144315/

Chicago Manual of Style (16^th Edition):

author], [No. “Efficacy of different DNA polymerase enzymes in PCR amplification of forensic bovine DNA .” 2012. Masters Thesis, University of Pretoria. Accessed March 03, 2021. http://upetd.up.ac.za/thesis/available/etd-08062012-144315/.

MLA Handbook (7^th Edition):

author], [No. “Efficacy of different DNA polymerase enzymes in PCR amplification of forensic bovine DNA .” 2012. Web. 03 Mar 2021.

Vancouver:

author] [. Efficacy of different DNA polymerase enzymes in PCR amplification of forensic bovine DNA . [Internet] [Masters thesis]. University of Pretoria; 2012. [cited 2021 Mar 03]. Available from: http://upetd.up.ac.za/thesis/available/etd-08062012-144315/.

Council of Science Editors:

author] [. Efficacy of different DNA polymerase enzymes in PCR amplification of forensic bovine DNA . [Masters Thesis]. University of Pretoria; 2012. Available from: http://upetd.up.ac.za/thesis/available/etd-08062012-144315/

University of Pretoria

13. Nemakonde, Avhashoni Agnes. Efficacy of different DNA polymerase enzymes in PCR amplification of forensic bovine DNA.

Degree: Animal and Wildlife Sciences, 2012, University of Pretoria

URL: http://hdl.handle.net/2263/27077

► DNA profiling of exhibits that originate from forensic stock theft cases is routinely used as a tool to link suspects to the crime or scene.… (more)

Subjects/Keywords: Dna polymerase enzymes; Forensic bovine dna; UCTD

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APA (6^th Edition):

Nemakonde, A. (2012). Efficacy of different DNA polymerase enzymes in PCR amplification of forensic bovine DNA. (Masters Thesis). University of Pretoria. Retrieved from http://hdl.handle.net/2263/27077

Chicago Manual of Style (16^th Edition):

Nemakonde, Avhashoni. “Efficacy of different DNA polymerase enzymes in PCR amplification of forensic bovine DNA.” 2012. Masters Thesis, University of Pretoria. Accessed March 03, 2021. http://hdl.handle.net/2263/27077.

MLA Handbook (7^th Edition):

Nemakonde, Avhashoni. “Efficacy of different DNA polymerase enzymes in PCR amplification of forensic bovine DNA.” 2012. Web. 03 Mar 2021.

Vancouver:

Nemakonde A. Efficacy of different DNA polymerase enzymes in PCR amplification of forensic bovine DNA. [Internet] [Masters thesis]. University of Pretoria; 2012. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/2263/27077.

Council of Science Editors:

Nemakonde A. Efficacy of different DNA polymerase enzymes in PCR amplification of forensic bovine DNA. [Masters Thesis]. University of Pretoria; 2012. Available from: http://hdl.handle.net/2263/27077

University of New South Wales

14. Gautam, Shweta Dutta. The sequence specificity of bleomycin and gamma radiation-induced damage in systematically altered DNA sequences.

Degree: Biotechnology & Biomolecular Sciences, 2018, University of New South Wales

URL: http://handle.unsw.edu.au/1959.4/60202 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:51297/SOURCE2?view=true

► Bleomycin is an anti-tumour agent that is clinically used to treat several types of cancers. Bleomycin cleaves DNA at specific DNA sequences and recent genome-wide… (more)

Subjects/Keywords: Gamma radiation; Bleomycin; DNA sequences

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APA (6^th Edition):

Gautam, S. D. (2018). The sequence specificity of bleomycin and gamma radiation-induced damage in systematically altered DNA sequences. (Doctoral Dissertation). University of New South Wales. Retrieved from http://handle.unsw.edu.au/1959.4/60202 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:51297/SOURCE2?view=true

Chicago Manual of Style (16^th Edition):

Gautam, Shweta Dutta. “The sequence specificity of bleomycin and gamma radiation-induced damage in systematically altered DNA sequences.” 2018. Doctoral Dissertation, University of New South Wales. Accessed March 03, 2021. http://handle.unsw.edu.au/1959.4/60202 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:51297/SOURCE2?view=true.

MLA Handbook (7^th Edition):

Gautam, Shweta Dutta. “The sequence specificity of bleomycin and gamma radiation-induced damage in systematically altered DNA sequences.” 2018. Web. 03 Mar 2021.

Vancouver:

Gautam SD. The sequence specificity of bleomycin and gamma radiation-induced damage in systematically altered DNA sequences. [Internet] [Doctoral dissertation]. University of New South Wales; 2018. [cited 2021 Mar 03]. Available from: http://handle.unsw.edu.au/1959.4/60202 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:51297/SOURCE2?view=true.

Council of Science Editors:

Gautam SD. The sequence specificity of bleomycin and gamma radiation-induced damage in systematically altered DNA sequences. [Doctoral Dissertation]. University of New South Wales; 2018. Available from: http://handle.unsw.edu.au/1959.4/60202 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:51297/SOURCE2?view=true

15. Aquino, Simone. Efeitos da radiação gama no crescimento de aspergillus flavus produtor de aflatoxinas e no emprego da técnica da reação em cadeia da polimerase (PCR) em amostras de grãos de milho inoculadas artificialmente.

Degree: Mestrado, Tecnologia Nuclear - Aplicações, 2004, University of São Paulo

URL: http://www.teses.usp.br/teses/disponiveis/85/85131/tde-16042012-105910/ ;

►

O presente trabalho teve como objetivos verificar os efeitos da radiação gama em grãos de milho contaminados artificialmente com Aspergillus flavus Link produtor de aflatoxinas;… (more)

▼

O presente trabalho teve como objetivos verificar os efeitos da radiação gama em grãos de milho contaminados artificialmente com Aspergillus flavus Link produtor de aflatoxinas; demonstrar a aplicação da técnica da Reação em Cadeia da Polimerase (PCR) no diagnóstico de A. flavus, bem como verificar o efeito da radiação no perfil das bandas de DNA. Vinte amostras de grãos de milho com 200 g cada foram irradiadas individualmente com 20 kGy, para eliminar a contaminação microbiana. Em seguida, as amostras foram inoculadas com A. flavus toxigênico (1 x 106 esporos / ml), incubadas por 15 dias a 25 °C em ambiente com umidade relativa ao redor de 97,5% e irradiadas com 0; 2; 5 e 10 kGy. As amostras, 5 para cada dose de irradiação, foram analisadas individualmente quanto ao número de células fúngicas, atividade de água, teste de viabilidade (diacetato de fluoresceína e brometo de etídio), PCR e detecção de aflatoxinas (AFB). Os resultados demonstraram que as doses utilizadas foram efetivas na redução do número de Unidades Formadoras de Colônias (UFC/g), principalmente as doses de 5 e 10 kGy. Em adição, o teste de viabilidade mostrou uma diminuição de células viáveis com o aumento das doses de irradiação. A redução de AFB1 e AFB2 foi mais eficiente com o emprego de 2 kGy, comparativamente à dose de 5 kGy, enquanto a dose de 10 kGy degradou totalmente as aflatoxinas. Além disso, observou-se que AFB2 apresentou-se mais radiosensível. O emprego da técnica de PCR revelou a presença de bandas de DNA em todas as amostras.

The aim of this present study was to verify the effects of gamma radiation on the growth of Aspergillus flavus Link aflatoxins producer; to demonstrate the application of Polymerase Chain Reaction (PCR) technique in the diagnostic of A. Flavus, as well to verify the effect of radiation in the profile of DNA bands. Twenty samples of grains maize with 200 g each were individually irradiated with 20 kGy, to eliminate the microbial contamination. In following, the samples were inoculated with an toxigenic A. flavus (1x106 spores/ml), incubated for 15 days at 25 °C with a relative humidity of around 97,5% and irradiated with 0; 2; 5 and 10 kGy. The samples, 5 to each dose of irradiation, were individually analyzed for the number of fungal cells, water activity, viability test (fluorescein diacetate and ethidium bromide), PCR and aflatoxins (AFB) detection. The results showed that the doses used were effectives in reducing the number of Colony Forming Units (CFU/g) mainly the doses of 5 and 10 kGy. In addition, the viability test showed a decrease of viable cells with increase of irradiation doses. The reduction of AFB1 and AFB2, was more efficient with the use of 2 kGy in comparison with the dose of 5 kGy, while the dose of 10 kGy, degraded the aflatoxins. Thereby, it was observed that AFB2 showed to be more radiosensitive. The use of PCR technique showed the presence of DNA bands, in all samples

Advisors/Committee Members: Villavicencio, Anna Lucia Casañas Haasis.

Subjects/Keywords: aflatoxinas; aflatoxins; Aspergillus; Aspergillus; biological radiation effects; DNA; DNA; gamma radiation; maize; polymerase chain reaction; radiação gama; seeds

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APA (6^th Edition):

Aquino, S. (2004). Efeitos da radiação gama no crescimento de aspergillus flavus produtor de aflatoxinas e no emprego da técnica da reação em cadeia da polimerase (PCR) em amostras de grãos de milho inoculadas artificialmente. (Masters Thesis). University of São Paulo. Retrieved from http://www.teses.usp.br/teses/disponiveis/85/85131/tde-16042012-105910/ ;

Chicago Manual of Style (16^th Edition):

Aquino, Simone. “Efeitos da radiação gama no crescimento de aspergillus flavus produtor de aflatoxinas e no emprego da técnica da reação em cadeia da polimerase (PCR) em amostras de grãos de milho inoculadas artificialmente.” 2004. Masters Thesis, University of São Paulo. Accessed March 03, 2021. http://www.teses.usp.br/teses/disponiveis/85/85131/tde-16042012-105910/ ;.

MLA Handbook (7^th Edition):

Aquino, Simone. “Efeitos da radiação gama no crescimento de aspergillus flavus produtor de aflatoxinas e no emprego da técnica da reação em cadeia da polimerase (PCR) em amostras de grãos de milho inoculadas artificialmente.” 2004. Web. 03 Mar 2021.

Vancouver:

Aquino S. Efeitos da radiação gama no crescimento de aspergillus flavus produtor de aflatoxinas e no emprego da técnica da reação em cadeia da polimerase (PCR) em amostras de grãos de milho inoculadas artificialmente. [Internet] [Masters thesis]. University of São Paulo; 2004. [cited 2021 Mar 03]. Available from: http://www.teses.usp.br/teses/disponiveis/85/85131/tde-16042012-105910/ ;.

Council of Science Editors:

Aquino S. Efeitos da radiação gama no crescimento de aspergillus flavus produtor de aflatoxinas e no emprego da técnica da reação em cadeia da polimerase (PCR) em amostras de grãos de milho inoculadas artificialmente. [Masters Thesis]. University of São Paulo; 2004. Available from: http://www.teses.usp.br/teses/disponiveis/85/85131/tde-16042012-105910/ ;

16. Lee, Young-Sam. Structural and functional studies of the human mitochondrial DNA polymerase.

Degree: PhD, Cell and Molecular Biology, 2010, University of Texas – Austin

URL: http://hdl.handle.net/2152/ETD-UT-2010-08-1798

► The human mitochondrial DNA polymerase (Pol γ) catalyzes mitochondrial DNA synthesis, and thus is essential for the integrity of the organelle. Mutations of Pol γ… (more)

▼ The human mitochondrial DNA polymerase (Pol γ) catalyzes mitochondrial DNA synthesis, and thus is essential for the integrity of the organelle. Mutations of Pol γ have been implicated in more than 150 human diseases. Reduced Pol γ activity caused by inhibition of anti-HIV drugs targeted to HIV reverse transcriptase confers major drug toxicity. To illustrate the structural basis for mtDNA replication and facilitate rational design of antiviral drugs, I have determined the crystal structure of human Pol γ holoenzyme. The structure reveals heterotrimer architecture of Pol γ holoenzyme with a monomeric catalytic subunit Pol γA, and a dimeric processivity factor Pol γB. While the polymerase and exonuclease domains in Pol γA present high structural homology with the other members of the DNA Pol I family, the spacer between the two functional domains shows a unique fold, and constitutes the subunit interface. The structure suggests a novel mechanism for Pol γ’s high processivity of DNA replication. Furthermore, the structure reveals dissimilarity in the active sites between Pol γ and HIV RT, thereby indicating an exploitable space for design of less toxic anti-HIV drugs. Interestingly, the structure shows an asymmetric subunit interaction, that is, one monomer of dimeric Pol γB primarily participates in interactions with Pol γA. To understand the roles of each Pol γB monomer, I generated a monomeric human Pol γB variant by disrupting the dimeric interface of the subunit. Comparative studies of this variant and dimeric wild-type Pol γB reveal that each monomer in the dimeric Pol γB makes a distinct contribution to processivity: one monomer (proximal to Pol γA) increases DNA binding affinity whereas the other monomer (distal to Pol γA) enhances the rate of polymerization. The pol γ holoenzyme structure also gives a rationale to establish the genotypic-phenotypic relationship of many disease-implicated mutations, especially for those located outside of the conserved pol or exo domains. Using the structure as a guide, I characterized a substitution of Pol γA residue R232 that is located at the subunit interface but far from either active sites. Kinetic analyses reveal that the mutation has no effect on intrinsic Pol γA activity, but shows functional defects in the holoenzyme, including decreased polymerase activity and increased exonuclease activity, as well as reduced discrimination between mismatched and corrected base pair. Results provide a molecular rationale for the Pol γA-R232 substitution mediated mitochondrial diseases. Advisors/Committee Members: Yin, Yuhui Whitney (advisor), Molineux, Ian J. (committee member), Johnson, Kenneth A. (committee member), Paull, Tanya T. (committee member), Robertus, Jon D. (committee member).

Subjects/Keywords: Mitochondrial DNA polymerase; DNA replication; Mitochondrial disease; Drug toxicity; AIDS; mtDNA; Pol gamma holoenzyme

…polymerase (Pol γ) catalyzes mitochondrial DNA synthesis, and thus is essential for the… …1 Mitochondrial DNA polymerase (Pol γ)… …103 xiii Chapter 1: Introduction MITOCHONDRIAL DNA POLYMERASE (POL γ) DNA… …mitochondria. Because Pol γ is the sole DNA polymerase in mitochondria, mutations in Pol γ can cause… …Studies of the Human Mitochondrial DNA Polymerase Committee: Whitney Yin, Supervisor Ian…

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APA (6^th Edition):

Lee, Y. (2010). Structural and functional studies of the human mitochondrial DNA polymerase. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/ETD-UT-2010-08-1798

Chicago Manual of Style (16^th Edition):

Lee, Young-Sam. “Structural and functional studies of the human mitochondrial DNA polymerase.” 2010. Doctoral Dissertation, University of Texas – Austin. Accessed March 03, 2021. http://hdl.handle.net/2152/ETD-UT-2010-08-1798.

MLA Handbook (7^th Edition):

Lee, Young-Sam. “Structural and functional studies of the human mitochondrial DNA polymerase.” 2010. Web. 03 Mar 2021.

Vancouver:

Lee Y. Structural and functional studies of the human mitochondrial DNA polymerase. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2010. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/2152/ETD-UT-2010-08-1798.

Council of Science Editors:

Lee Y. Structural and functional studies of the human mitochondrial DNA polymerase. [Doctoral Dissertation]. University of Texas – Austin; 2010. Available from: http://hdl.handle.net/2152/ETD-UT-2010-08-1798

University of Alberta

17. Gammon, Donald Brad. Vaccinia virus DNA polymerase and ribonucleotide reductase: their role in replication, recombination and drug resistance.

Degree: PhD, Department of Medical Microbiology and Immunology, 2009, University of Alberta

URL: https://era.library.ualberta.ca/files/1g05fd17k

► Despite the eradication of smallpox, poxviruses continue to cause human disease around the world. At the core of poxvirus replication is the efficient and accurate… (more)

▼ Despite the eradication of smallpox, poxviruses continue to cause human disease around the world. At the core of poxvirus replication is the efficient and accurate synthesis and repair of the viral genome. The viral DNA polymerase is critical for these processes. Acyclic nucleoside phosphonate (ANP) compounds that target the viral polymerase are effective inhibitors of poxvirus replication and pathogenesis. Cidofovir (CDV) is an ANP that inhibits vaccinia virus (VAC) DNA polymerase (E9) DNA synthesis and 3’-to-5’ exonuclease (proofreading) activities. We determined that point mutations in the DNA polymerase genes of ANP-resistant (ANPR) VAC strains were responsible for CDV resistance and resistance to the related compound, HPMPDAP. Although these resistant strains replicated as well as wild-type VAC in culture, they were highly attenuated in mice. The generation of ANPR VAC strains, in combination with our knowledge of how CDV inhibits E9 activities, allowed us to study the hypothesized role of E9 in catalyzing double-strand break repair through homologous recombination. We provide evidence that VAC uses E9 proofreading activity to catalyze genetic recombination through single-strand annealing reactions (SSA) in infected cells. Both the polarity of end resection of recombinant intermediates and the involvement of polymerase proofreading activity establish these poxviral SSA reactions as unique among homologous recombination schemes. Furthermore, we identified roles for the VAC single-stranded DNA-binding (SSB) protein and nucleotide pools in regulating these reactions. During these later studies we uncovered a differential requirement for the large and small subunits of the VAC ribonucleotide reductase (RR) in viral replication and pathogenesis. Our studies suggest that poxviral RR small subunits form functional complexes with host large RR subunits to provide sufficient nucleotide pools to support DNA replication. We present a model whereby interaction of VAC SSB and RR proteins at replication forks allows for modulation of E9 activity through local nucleotide pool changes, which serves to maximize replication rates while still allowing for recombinational repair.

Subjects/Keywords: recombination; DNA polymerase; vaccinia virus; ribonucleotide reductase

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APA (6^th Edition):

Gammon, D. B. (2009). Vaccinia virus DNA polymerase and ribonucleotide reductase: their role in replication, recombination and drug resistance. (Doctoral Dissertation). University of Alberta. Retrieved from https://era.library.ualberta.ca/files/1g05fd17k

Chicago Manual of Style (16^th Edition):

Gammon, Donald Brad. “Vaccinia virus DNA polymerase and ribonucleotide reductase: their role in replication, recombination and drug resistance.” 2009. Doctoral Dissertation, University of Alberta. Accessed March 03, 2021. https://era.library.ualberta.ca/files/1g05fd17k.

MLA Handbook (7^th Edition):

Gammon, Donald Brad. “Vaccinia virus DNA polymerase and ribonucleotide reductase: their role in replication, recombination and drug resistance.” 2009. Web. 03 Mar 2021.

Vancouver:

Gammon DB. Vaccinia virus DNA polymerase and ribonucleotide reductase: their role in replication, recombination and drug resistance. [Internet] [Doctoral dissertation]. University of Alberta; 2009. [cited 2021 Mar 03]. Available from: https://era.library.ualberta.ca/files/1g05fd17k.

Council of Science Editors:

Gammon DB. Vaccinia virus DNA polymerase and ribonucleotide reductase: their role in replication, recombination and drug resistance. [Doctoral Dissertation]. University of Alberta; 2009. Available from: https://era.library.ualberta.ca/files/1g05fd17k

18. Nayak, Shreenath. Cloning sequence analysis and characterization of DNA polymerase from Geobacillus sp. WBI.

Degree: Botany, 2014, Visva Bharti University

URL: http://shodhganga.inflibnet.ac.in/handle/10603/19542

►

A thermostable DNA polymerase gene (DNA pol) was isolated from the genomic DNA of Geobacillus sp.WBI by polymerase chain reaction (PCR). PCR amplification with the… (more)

Subjects/Keywords: Geobacillus; Sequence analysis; Thermostable DNA polymerase

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APA (6^th Edition):

Nayak, S. (2014). Cloning sequence analysis and characterization of DNA polymerase from Geobacillus sp. WBI. (Thesis). Visva Bharti University. Retrieved from http://shodhganga.inflibnet.ac.in/handle/10603/19542

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

Chicago Manual of Style (16^th Edition):

Nayak, Shreenath. “Cloning sequence analysis and characterization of DNA polymerase from Geobacillus sp. WBI.” 2014. Thesis, Visva Bharti University. Accessed March 03, 2021. http://shodhganga.inflibnet.ac.in/handle/10603/19542.

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

MLA Handbook (7^th Edition):

Nayak, Shreenath. “Cloning sequence analysis and characterization of DNA polymerase from Geobacillus sp. WBI.” 2014. Web. 03 Mar 2021.

Vancouver:

Nayak S. Cloning sequence analysis and characterization of DNA polymerase from Geobacillus sp. WBI. [Internet] [Thesis]. Visva Bharti University; 2014. [cited 2021 Mar 03]. Available from: http://shodhganga.inflibnet.ac.in/handle/10603/19542.

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

Council of Science Editors:

Nayak S. Cloning sequence analysis and characterization of DNA polymerase from Geobacillus sp. WBI. [Thesis]. Visva Bharti University; 2014. Available from: http://shodhganga.inflibnet.ac.in/handle/10603/19542

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

Penn State University

19. Almishwat, Mohammad Ali. Time-resolved X-ray crystallography of DNA polymerases: A platform for studies in structural and mechanistic enzymology.

Degree: 2013, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/19024

► DNA-dependent DNA polymerase is the enzyme responsible for carrying out DNA replication. DNA polymerase regulates the faithful transmission of an organism’s genetic material, and performs… (more)

Subjects/Keywords: DNA polymerase; X-ray crystallography; Time-reolved

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APA (6^th Edition):

Almishwat, M. A. (2013). Time-resolved X-ray crystallography of DNA polymerases: A platform for studies in structural and mechanistic enzymology. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/19024

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

Chicago Manual of Style (16^th Edition):

Almishwat, Mohammad Ali. “Time-resolved X-ray crystallography of DNA polymerases: A platform for studies in structural and mechanistic enzymology.” 2013. Thesis, Penn State University. Accessed March 03, 2021. https://submit-etda.libraries.psu.edu/catalog/19024.

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

MLA Handbook (7^th Edition):

Almishwat, Mohammad Ali. “Time-resolved X-ray crystallography of DNA polymerases: A platform for studies in structural and mechanistic enzymology.” 2013. Web. 03 Mar 2021.

Vancouver:

Almishwat MA. Time-resolved X-ray crystallography of DNA polymerases: A platform for studies in structural and mechanistic enzymology. [Internet] [Thesis]. Penn State University; 2013. [cited 2021 Mar 03]. Available from: https://submit-etda.libraries.psu.edu/catalog/19024.

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

Council of Science Editors:

Almishwat MA. Time-resolved X-ray crystallography of DNA polymerases: A platform for studies in structural and mechanistic enzymology. [Thesis]. Penn State University; 2013. Available from: https://submit-etda.libraries.psu.edu/catalog/19024

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

Penn State University

20. Barnes, Ryan Patrick. The Roles and Regulation of Specialized DNA Polymerases in Mitigating Replication Stress and Replicating Common Fragile Sites.

Degree: 2017, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/14528rpb180

► Replicative DNA polymerases serve as the essential enzymes that duplicate our genome with high fidelity and efficiency. This function is compromised however, when repetitive DNA… (more)

▼ Replicative DNA polymerases serve as the essential enzymes that duplicate our genome with high fidelity and efficiency. This function is compromised however, when repetitive DNA sequences adopt a structure differing from the Watson-Crick B-form or during conditions of replicative stress. However, cells also possess specialized DNA polymerases that can compensate for the replicative polymerases when they are inhibited. The goals of this thesis were to investigate how the specialized DNA polymerases (Pols) eta (η) and kappa (κ) 1) cooperate with the replicative polymerase delta (δ) in the synthesis of repetitive DNA derived from chromosomal fragile sites, and 2) understand how these enzymes function during cellular replication stress. Common fragile sites (CFSs) are genomic loci that display recurrent instability in cells experiencing replication stress. Replication stress, defined as the slowing or stalling of replication forks, occurs when cells are treated with agents that inhibit DNA synthesis or are deficient in DNA repair/replication enzymes. CFSs are sensitive to replication stress, and one rationale for this is their enrichment in repetitive DNA sequences that can adopt a non-B DNA structure. Previous work in the Eckert lab has shown that all three replicative, human DNA polymerases are inhibited by repetitive CFS sequences in vitro whereas polymerases η and κ can replicate the same sequences with high efficiency. In chapter 3, I test the hypothesis that Pols η and κ can cooperate with Pol δ in CFS sequence replication in vitro. To investigate this, I developed a model of lagging strand synthesis using primed ssDNA templates containing RFC-loaded PCNA, the processivity factor of Pol δ. This system was designed to allow RFC and Pols δ, η, and κ to function optimally in the same reaction conditions. Using this system, I found that Pols η and κ can indeed rescue the Pol δ holoenzyme (Pol δ/ RFC-loaded PCNA; Pol δHE) stalled at CFS sequences containing different repetitive DNA motifs. I found this polymerase cooperativity was not mediated by PCNA however, as reactions where RFC was omitted displayed no defect in replication rescue. Moreover, using this system I did not observe any enhancement of cooperativity between Pol δ and Pols η and κ using mono-ubiquitinated PCNA (Ub-PCNA), a post-translational modification thought to regulate polymerase exchange at DNA lesions. Finally, by modeling replication stress in vitro using Aph, a drug that directly inhibits replicative polymerases, I found that Pols η and κ become indispensable for repetitive CFS sequence replication. In total, the data in this chapter advances our understanding of human DNA polymerase exchange, and how repetitive DNA replication is accomplished by multiple polymerases. While the relationship between CFS stability and Pol η has been characterized by work in the Eckert lab and others, we did not know how Pol η might impact the cell cycle and checkpoint signaling in replication stressed cells. To study this, I employed several models of… Advisors/Committee Members: Kristin Ann Eckert, Dissertation Advisor/Co-Advisor, Kristin Ann Eckert, Committee Chair/Co-Chair, George Lucian Moldovan, Committee Member, James Riley Broach, Committee Member, Edward Joseph Gunther, Outside Member, Sergei A Grigoryev, Committee Member.

Subjects/Keywords: DNA polymerase; replication stress; genome stability

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APA (6^th Edition):

Barnes, R. P. (2017). The Roles and Regulation of Specialized DNA Polymerases in Mitigating Replication Stress and Replicating Common Fragile Sites. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/14528rpb180

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

Chicago Manual of Style (16^th Edition):

Barnes, Ryan Patrick. “The Roles and Regulation of Specialized DNA Polymerases in Mitigating Replication Stress and Replicating Common Fragile Sites.” 2017. Thesis, Penn State University. Accessed March 03, 2021. https://submit-etda.libraries.psu.edu/catalog/14528rpb180.

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

MLA Handbook (7^th Edition):

Barnes, Ryan Patrick. “The Roles and Regulation of Specialized DNA Polymerases in Mitigating Replication Stress and Replicating Common Fragile Sites.” 2017. Web. 03 Mar 2021.

Vancouver:

Barnes RP. The Roles and Regulation of Specialized DNA Polymerases in Mitigating Replication Stress and Replicating Common Fragile Sites. [Internet] [Thesis]. Penn State University; 2017. [cited 2021 Mar 03]. Available from: https://submit-etda.libraries.psu.edu/catalog/14528rpb180.

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

Council of Science Editors:

Barnes RP. The Roles and Regulation of Specialized DNA Polymerases in Mitigating Replication Stress and Replicating Common Fragile Sites. [Thesis]. Penn State University; 2017. Available from: https://submit-etda.libraries.psu.edu/catalog/14528rpb180

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

21. Thanh, Le Thi. Biochemical analysis revealing the molecular actions of Escherichia coli DNA polymerase III and IV at the replication fork : 大腸菌損傷乗り越え型DNAポリメラーゼⅣによる複製フォークでの複製型DNAポリメラーゼⅢとの交換機構の生化学的解析; ダイチョウキンソンショウノリコエガタ DNA ポリメラーゼ Ⅳ ニヨルフクセイフォークデノフクセイガタ DNA ポリメラーゼ Ⅲ トノコウカンキコウノセイカガクテキカイセキ.

Degree: 博士(バイオサイエンス), 2017, Nara Institute of Science and Technology / 奈良先端科学技術大学院大学

URL: http://hdl.handle.net/10061/11737

Subjects/Keywords: DNA polymerase switching

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APA (6^th Edition):

Thanh, L. T. (2017). Biochemical analysis revealing the molecular actions of Escherichia coli DNA polymerase III and IV at the replication fork : 大腸菌損傷乗り越え型DNAポリメラーゼⅣによる複製フォークでの複製型DNAポリメラーゼⅢとの交換機構の生化学的解析; ダイチョウキンソンショウノリコエガタ DNA ポリメラーゼ Ⅳ ニヨルフクセイフォークデノフクセイガタ DNA ポリメラーゼ Ⅲ トノコウカンキコウノセイカガクテキカイセキ. (Thesis). Nara Institute of Science and Technology / 奈良先端科学技術大学院大学. Retrieved from http://hdl.handle.net/10061/11737

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

Chicago Manual of Style (16^th Edition):

Thanh, Le Thi. “Biochemical analysis revealing the molecular actions of Escherichia coli DNA polymerase III and IV at the replication fork : 大腸菌損傷乗り越え型DNAポリメラーゼⅣによる複製フォークでの複製型DNAポリメラーゼⅢとの交換機構の生化学的解析; ダイチョウキンソンショウノリコエガタ DNA ポリメラーゼ Ⅳ ニヨルフクセイフォークデノフクセイガタ DNA ポリメラーゼ Ⅲ トノコウカンキコウノセイカガクテキカイセキ.” 2017. Thesis, Nara Institute of Science and Technology / 奈良先端科学技術大学院大学. Accessed March 03, 2021. http://hdl.handle.net/10061/11737.

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

MLA Handbook (7^th Edition):

Thanh, Le Thi. “Biochemical analysis revealing the molecular actions of Escherichia coli DNA polymerase III and IV at the replication fork : 大腸菌損傷乗り越え型DNAポリメラーゼⅣによる複製フォークでの複製型DNAポリメラーゼⅢとの交換機構の生化学的解析; ダイチョウキンソンショウノリコエガタ DNA ポリメラーゼ Ⅳ ニヨルフクセイフォークデノフクセイガタ DNA ポリメラーゼ Ⅲ トノコウカンキコウノセイカガクテキカイセキ.” 2017. Web. 03 Mar 2021.

Vancouver:

Thanh LT. Biochemical analysis revealing the molecular actions of Escherichia coli DNA polymerase III and IV at the replication fork : 大腸菌損傷乗り越え型DNAポリメラーゼⅣによる複製フォークでの複製型DNAポリメラーゼⅢとの交換機構の生化学的解析; ダイチョウキンソンショウノリコエガタ DNA ポリメラーゼ Ⅳ ニヨルフクセイフォークデノフクセイガタ DNA ポリメラーゼ Ⅲ トノコウカンキコウノセイカガクテキカイセキ. [Internet] [Thesis]. Nara Institute of Science and Technology / 奈良先端科学技術大学院大学; 2017. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/10061/11737.

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

Council of Science Editors:

Thanh LT. Biochemical analysis revealing the molecular actions of Escherichia coli DNA polymerase III and IV at the replication fork : 大腸菌損傷乗り越え型DNAポリメラーゼⅣによる複製フォークでの複製型DNAポリメラーゼⅢとの交換機構の生化学的解析; ダイチョウキンソンショウノリコエガタ DNA ポリメラーゼ Ⅳ ニヨルフクセイフォークデノフクセイガタ DNA ポリメラーゼ Ⅲ トノコウカンキコウノセイカガクテキカイセキ. [Thesis]. Nara Institute of Science and Technology / 奈良先端科学技術大学院大学; 2017. Available from: http://hdl.handle.net/10061/11737

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

Northeastern University

22. Ippoliti, Paul Joseph. DNA damage specificity of Escherichia coli DNA polymerase DinB.

Degree: MS, Department of Chemistry and Chemical Biology, 2012, Northeastern University

URL: http://hdl.handle.net/2047/d20002749

► Exogenous and endogenous DNA damaging agents such as UV light cause lesions in DNA, which halt the progress of DNA replication. Microbes such as E.… (more)

▼ Exogenous and endogenous DNA damaging agents such as UV light cause lesions in DNA, which halt the progress of DNA replication. Microbes such as E. coli have a response mechanism known as the SOS response which is initiated upon DNA damage. The SOS response ultimately results in the expression of the Y-family DNA polymerases which catalyze translesion synthesis to copy damaged DNA (Walsh 2011). Y-family polymerases specifically bypass certain types of DNA lesions. Understanding DNA damage specificity of Y-family polymerases is necessary due to their mutagenic nature. They lack proofreading ability which removes incorrectly inserted nucleotides, and can therefore be error-prone (Jarosz 2007). Eventually, the insertion of the incorrect base can lead to mutations that confer a selective advantage in the cell, such as antibiotic resistance. In E. coli, there are two Y-family polymerases known as polymerase IV and polymerase V. Polymerase V, also known as UmuD'2C , is capable of bypassing lesions caused by UV light exposure namely thymine-thymine cyclobutane pyrimidine dimers and T-T (6-4) photoproducts (Tang 2000). Polymerase IV, otherwise known as DinB, is capable of bypassing N2-dG adducts4 (among others), but not T-T CPDs or (6-4) photoproducts (Tang 2000; Jarosz 2006). The goal of this study is to understand how DinB is able to bypass certain types of lesions, but not others. In this study, directed evolution methods are used to mutate the DinB gene and acquire variants that confer UV resistance. Characterization of these variants will help to understand which regions on the DinB protein allow for the specificity of lesion bypass. In addition, primer extension assays are used to study the lesion bypass efficiency of DinB variants in the Loop 1 region of the protein.; References; Jarosz, D. F., P. J. Beuning, S. E. Cohen and G. C. Walker (2007). "Y-family DNA polymerases in Escherichia coli." Trends in Microbiology 15(2): 70-77.; Jarosz, D. F., V. G. Godoy, J. C. Delaney, J. M. Essigmann and G. C. Walker (2006). "A single amino acid governs enhanced activity of DinB DNA polymerases on damaged templates." Nature 439(7073): 225-228.; Tang, M. J., P. Pham, X. Shen, J. S. Taylor, M. O'Donnell, R. Woodgate and M. F. Goodman (2000). "Roles of E-coli DNA polymerases IV and V in lesion-targeted and untargeted SOS mutagenesis." Nature 404(6781): 1014-1018.; Walsh, J. M., L. A. Hawver and P. J. Beuning (2011). "Escherichia coli Y family DNA polymerases." Frontiers in Bioscience-Landmark 16: 3164-3182.

Subjects/Keywords: DinB; DNA; Escherichia coli; Polymerase; UmuC; Biochemistry

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APA (6^th Edition):

Ippoliti, P. J. (2012). DNA damage specificity of Escherichia coli DNA polymerase DinB. (Masters Thesis). Northeastern University. Retrieved from http://hdl.handle.net/2047/d20002749

Chicago Manual of Style (16^th Edition):

Ippoliti, Paul Joseph. “DNA damage specificity of Escherichia coli DNA polymerase DinB.” 2012. Masters Thesis, Northeastern University. Accessed March 03, 2021. http://hdl.handle.net/2047/d20002749.

MLA Handbook (7^th Edition):

Ippoliti, Paul Joseph. “DNA damage specificity of Escherichia coli DNA polymerase DinB.” 2012. Web. 03 Mar 2021.

Vancouver:

Ippoliti PJ. DNA damage specificity of Escherichia coli DNA polymerase DinB. [Internet] [Masters thesis]. Northeastern University; 2012. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/2047/d20002749.

Council of Science Editors:

Ippoliti PJ. DNA damage specificity of Escherichia coli DNA polymerase DinB. [Masters Thesis]. Northeastern University; 2012. Available from: http://hdl.handle.net/2047/d20002749

University of Oregon

23. Mostales, Joshua Calixterio. Investigating the Physiological Effects of Mutations in the Proposed Backtrack Site of Yeast RNA Polymerase II.

Degree: 2019, University of Oregon

URL: https://scholarsbank.uoregon.edu/xmlui/handle/1794/25046

► Transcription, the first step of gene expression, is a process fundamental to all known forms of life. In eukaryotic cells, the enzyme RNA polymerase II… (more)

Subjects/Keywords: Biochemistry; RNA Polymerase; Transcription; DNA; Mutations; Backtracking

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APA (6^th Edition):

Mostales, J. C. (2019). Investigating the Physiological Effects of Mutations in the Proposed Backtrack Site of Yeast RNA Polymerase II. (Thesis). University of Oregon. Retrieved from https://scholarsbank.uoregon.edu/xmlui/handle/1794/25046

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

Chicago Manual of Style (16^th Edition):

Mostales, Joshua Calixterio. “Investigating the Physiological Effects of Mutations in the Proposed Backtrack Site of Yeast RNA Polymerase II.” 2019. Thesis, University of Oregon. Accessed March 03, 2021. https://scholarsbank.uoregon.edu/xmlui/handle/1794/25046.

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

MLA Handbook (7^th Edition):

Mostales, Joshua Calixterio. “Investigating the Physiological Effects of Mutations in the Proposed Backtrack Site of Yeast RNA Polymerase II.” 2019. Web. 03 Mar 2021.

Vancouver:

Mostales JC. Investigating the Physiological Effects of Mutations in the Proposed Backtrack Site of Yeast RNA Polymerase II. [Internet] [Thesis]. University of Oregon; 2019. [cited 2021 Mar 03]. Available from: https://scholarsbank.uoregon.edu/xmlui/handle/1794/25046.

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

Council of Science Editors:

Mostales JC. Investigating the Physiological Effects of Mutations in the Proposed Backtrack Site of Yeast RNA Polymerase II. [Thesis]. University of Oregon; 2019. Available from: https://scholarsbank.uoregon.edu/xmlui/handle/1794/25046

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

Louisiana State University

24. Zhu, Xinji. Salt Dependence of Thermodynamic Stability of a Cold-Active DNA Polymerase I Fragment.

Degree: PhD, Biochemistry, Biophysics, and Structural Biology, 2020, Louisiana State University

URL: https://digitalcommons.lsu.edu/gradschool_dissertations/5389

► P. ingrahamii is a halo-psychrophilic bacterium isolated from Arctic sea ice. We have cloned and purified the large fragment of the cold-active DNA polymerase… (more)

▼ P. ingrahamii is a halo-psychrophilic bacterium isolated from Arctic sea ice. We have cloned and purified the large fragment of the cold-active DNA polymerase I from P. ingrahamii, named Klenpin. The objective of this project is to directly compare the thermodynamic stability of Klenpin, and the salt dependence of that stability, with Klenow and Klentaq; two homologous polymerases from a mesophile (E. coli) and a thermophile (Thermus aquaticus). We first examined the effects of salts on the thermal stability (Tm) of Klenpin and Klenow across the Hofmeister series. Significantly different trends were observed on the melting temperature changes for Klenpin versus Klenow, even in chaotropic salts such as guanidine hydrochloride at low concentrations. Klenow responded to Hofmeister stabilizing salts and destabilizing salts as expected, while Klenpin was stabilized by all salts, even those that normally destabilize proteins. We further examined the salt effect on the structure of Klenpin and Klenow using CD spectra, Trp fluorescence quenching, and dynamic light scattering. The results show that salt alters the structure of Klenpin to a more compact conformation, whereas no significant influence is observed in Klenow. Salt also alters the unfolding process of Klenpin. In chemical denaturation, an intermediate is observed in the presence of salt, whereas Klenpin folds following a two-state model without salt. An increase in free energy of unfolding of Klenpin is also seen upon the addition of NaCl, and this improvement is mainly from the additional unfolding transition introduced due to the intermediate. We hypothesize that non-specific screening of unfavorable electrostatic interactions on the surface of Klenpin may be responsible for many of the observed salt effects and several computational comparisons were conducted to test this hypothesis. Unlike those typically found for archaebacterial halophilic proteins, no significant difference is observed in the comparison of amino acid preference between Klenpin and Klenow. But the electrostatic surface potential maps of Klenpin, Klenow, and Klentaq show larger clusters of acidic and basic residues on the Klenpin surface, supporting our hypothesis that salts modify Klenpin through the nonspecific screening of unfavorable electrostatic interactions on the surface.

Subjects/Keywords: DNA Polymerase; Psychrophile; Thermodynamic stability; Salt dependence

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

APA (6^th Edition):

Zhu, X. (2020). Salt Dependence of Thermodynamic Stability of a Cold-Active DNA Polymerase I Fragment. (Doctoral Dissertation). Louisiana State University. Retrieved from https://digitalcommons.lsu.edu/gradschool_dissertations/5389

Chicago Manual of Style (16^th Edition):

Zhu, Xinji. “Salt Dependence of Thermodynamic Stability of a Cold-Active DNA Polymerase I Fragment.” 2020. Doctoral Dissertation, Louisiana State University. Accessed March 03, 2021. https://digitalcommons.lsu.edu/gradschool_dissertations/5389.

MLA Handbook (7^th Edition):

Zhu, Xinji. “Salt Dependence of Thermodynamic Stability of a Cold-Active DNA Polymerase I Fragment.” 2020. Web. 03 Mar 2021.

Vancouver:

Zhu X. Salt Dependence of Thermodynamic Stability of a Cold-Active DNA Polymerase I Fragment. [Internet] [Doctoral dissertation]. Louisiana State University; 2020. [cited 2021 Mar 03]. Available from: https://digitalcommons.lsu.edu/gradschool_dissertations/5389.

Council of Science Editors:

Zhu X. Salt Dependence of Thermodynamic Stability of a Cold-Active DNA Polymerase I Fragment. [Doctoral Dissertation]. Louisiana State University; 2020. Available from: https://digitalcommons.lsu.edu/gradschool_dissertations/5389

25. Trujillo, Joshua T. The Origin and Evolution of Plant-Specific RNA Polymerases and Genes Involved in RNA-Directed DNA Methylation .

Degree: 2019, University of Arizona

URL: http://hdl.handle.net/10150/632985

► Gene evolution is one of the most significant contributors to the extensive number and diversity of organisms that have arisen on planet Earth. Gene duplication… (more)

▼ Gene evolution is one of the most significant contributors to the extensive number and diversity of organisms that have arisen on planet Earth. Gene duplication is a major driving force in gene evolution by allowing the development of novel functions and the creation of new pathways. Every gene within an organism’s genome has been retained through numerous duplication events and has a unique evolutionary history that dictates structure and function. As organisms retain increasing numbers of related genes, more complex pathways evolve. Whole genome duplications have occurred numerous times within the land plant lineage and are a contributing factor in the complexity of plant genomes. The plant-specific epigenetic pathway of RNA-directed DNA Methylation (RdDM) arose through evolution of specialized genes following gene duplications in the ancestor of plants. RdDM is responsible for de novo methylation associated with transcriptional gene silencing of transposons and other repetitive sequences. Evolution of RdDM components is dynamic and ongoing with many lineage specific paralogs, leading to further complexity of the pathway. Understanding the evolutionary history and relationship among gene families can drive the formation of hypotheses regarding the molecular necessity of related genes. RdDM requires the cooperative activity of plant-specific DNA-dependent RNA polymerases (Pol) IV and V, which evolved from RNA Pol II subunits. Although many subunits are shared among the polymerases, the largest subunit of Pol IV and V are unique and harbor distinct carboxyl terminal domains. In addition to separate largest subunits, Pol IV and V possess other specialized subunits and interacting partners that influence their functions. The evolutionary origin of these subunit and interacting proteins is unclear and requires further investigation. Determining the origin and evolutionary history of these proteins will be valuable for translating research from model organisms to other species, such as crops which are economically and agronomically important. Additionally, investigating ongoing evolution of these proteins will not only improve our current models and understanding of RdDM, but the mechanisms by which multi-subunit complex can evolve. This dissertation is the culmination of three studies investigating the evolution of genes involved in the RdDM pathway, in particular the plant-specific DNA-dependent RNA polymerases IV and V. In Chapter 1, I elucidate the evolutionary origin of Pol IV and V subunits in Charophytic Green Algae and describe early Pol evolution. In Appendix A, my coauthors and I describe a recent duplication and retention of distinct Pol subunits and associated proteins in the grass (Poaceae) lineage of monocots. The results of this study led us to generate a hypothesis for the existence of a distinct, Pol VI complex within grasses. Lastly in Appendix B, I analyzed a highly variable region within the carboxyl terminal domain of the Pol V largest subunit to better understand the molecular function and… Advisors/Committee Members: Mosher, Rebecca A (advisor), Beilstein, Mark A. (committeemember), Tax, Frans E. (committeemember), Buchan, John R. (committeemember), McMahon, Michelle M. (committeemember).

Subjects/Keywords: RNA-directed DNA Methylation; RNA polymerase

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

APA (6^th Edition):

Trujillo, J. T. (2019). The Origin and Evolution of Plant-Specific RNA Polymerases and Genes Involved in RNA-Directed DNA Methylation . (Doctoral Dissertation). University of Arizona. Retrieved from http://hdl.handle.net/10150/632985

Chicago Manual of Style (16^th Edition):

Trujillo, Joshua T. “The Origin and Evolution of Plant-Specific RNA Polymerases and Genes Involved in RNA-Directed DNA Methylation .” 2019. Doctoral Dissertation, University of Arizona. Accessed March 03, 2021. http://hdl.handle.net/10150/632985.

MLA Handbook (7^th Edition):

Trujillo, Joshua T. “The Origin and Evolution of Plant-Specific RNA Polymerases and Genes Involved in RNA-Directed DNA Methylation .” 2019. Web. 03 Mar 2021.

Vancouver:

Trujillo JT. The Origin and Evolution of Plant-Specific RNA Polymerases and Genes Involved in RNA-Directed DNA Methylation . [Internet] [Doctoral dissertation]. University of Arizona; 2019. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/10150/632985.

Council of Science Editors:

Trujillo JT. The Origin and Evolution of Plant-Specific RNA Polymerases and Genes Involved in RNA-Directed DNA Methylation . [Doctoral Dissertation]. University of Arizona; 2019. Available from: http://hdl.handle.net/10150/632985

University of Southern California

26. Corzett, Christopher Hale. Physiological roles and evolutionary implications of alternative DNA polymerases in Escherichia coli.

Degree: PhD, Molecular Biology, 2012, University of Southern California

URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/110357/rec/5048

► Escherichia coli DNA polymerases II, IV and V serve dual roles within cells by facilitating efficient replication past potentially lethal DNA damage while simultaneously introducing… (more)

Subjects/Keywords: alternative DNA polymerase; error-prone DNA polymerase; microbial evolution; SOS response; stationary phase; translesion synthesis

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APA (6^th Edition):

Corzett, C. H. (2012). Physiological roles and evolutionary implications of alternative DNA polymerases in Escherichia coli. (Doctoral Dissertation). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/110357/rec/5048

Chicago Manual of Style (16^th Edition):

Corzett, Christopher Hale. “Physiological roles and evolutionary implications of alternative DNA polymerases in Escherichia coli.” 2012. Doctoral Dissertation, University of Southern California. Accessed March 03, 2021. http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/110357/rec/5048.

MLA Handbook (7^th Edition):

Corzett, Christopher Hale. “Physiological roles and evolutionary implications of alternative DNA polymerases in Escherichia coli.” 2012. Web. 03 Mar 2021.

Vancouver:

Corzett CH. Physiological roles and evolutionary implications of alternative DNA polymerases in Escherichia coli. [Internet] [Doctoral dissertation]. University of Southern California; 2012. [cited 2021 Mar 03]. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/110357/rec/5048.

Council of Science Editors:

Corzett CH. Physiological roles and evolutionary implications of alternative DNA polymerases in Escherichia coli. [Doctoral Dissertation]. University of Southern California; 2012. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/110357/rec/5048

27. Λογοθέτη, Στυλιανή. Μελέτη του ρόλου των p73 ισομορφών στον καρκίνο του πνεύμονα.

Degree: 2011, University of Crete (UOC); Πανεπιστήμιο Κρήτης

URL: http://hdl.handle.net/10442/hedi/24877

►

The p73 gene possesses an extrinsic P1 promoter and an intrinsic P2 promoter, resulting in synthesis of the full-length TAp73 and the N-terminal-truncated ΔNp73 isoforms,… (more)

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The p73 gene possesses an extrinsic P1 promoter and an intrinsic P2 promoter, resulting in synthesis of the full-length TAp73 and the N-terminal-truncated ΔNp73 isoforms, respectively. The ultimate effect of p73 in oncogenesis is thought to depend on the apoptotic TAp73 to the antiapoptotic ΔNp73 isoforms’ ratio. The selective activation of p73 promoters could trigger the expression of either the apoptotic or the antiapoptotic p73 isoforms, thus shifting the ΔN/ΤΑ ratio towards an oncogenic or an oncosuppression direction. Therefore, the epigenetic and transcription factors that differentially activate P1 and P2 promoters are crucial deterninants of the role of p73 in cancer, since they can alter the ΔN/ΤΑ ratio. This study was aimed at identifying novel epigenetic and transcription factors that affect both TAp73 and ΔNp73 isoform synthesis in the context of lung cancer, where both TAp73 and ΔNp73 isoforms have been previously found overexpressed. First, we investigated the DNA methylation status of both promoters as a means of epigenetic transcriptional control of their corresponding isoforms in 102 primary non-small cell lung carcinomas (NSCLCs). We demonstrated that while P1 hypermethylation-associated reduction of TAp73 mRNA levels is rare, the P2 hypomethylation-associated overexpression of ΔNp73 mRNA is a frequent event, particularly among squamous cell carcinomas. P1 promoter remained essentially unmethylated in the majority of lung cancer carcinomas. On the other hand, P2 hypomethylation strongly correlated with the hypomethylation of LINE-1 transposon, a marker of global DNA hypomethylation, indicating that ΔNp73 overexpression may be a passive consequence of global DNA hypomethylation. Since overexpression of TAp73 isoforms could not be attributed to change in the methylation status of P1 promoter, we plausibly hypothesized that it could potentially be caused by deregulated activity of specific transcription factor(s) . In the light of this notion, we then searched for novel transcription factors that could activate P1 promoter and result to TAp73 overexpression in lung cancer. With the use of bioinformatics tools, in vitro binding assays, and chromatin immunoprecipitation analysis, a region extending -233 to -204 bps upstream of the transcription start site of the human p73 P1 promoter, containing conserved Sp1 binding sites, was characterized. Treatment of cells with Sp1 RNAi and Sp1 inhibitor functionally suppresses TAp73 expression, indicating positive regulation of P1 by the Sp1 protein. Notably Sp1 inhibition or silencing also reduces ΔΝp73 protein levels. Therefore, Sp1 directly regulates TAp73 transcription and affects ΔΝp73 levels in lung cancer. TAp73γ was shown to be the only TA isoform overexpressed in several lung cancer cell lines and in 26 non-small cell lung cancers, consistent with Sp1 overexpression, thereby questioning the apoptotic role of this specific p73 isoform in lung cancer.

Το γονίδιο p73 διαθέτει έναν εξωτερικό υποκινητή (P1) και έναν εσωτερικό υποκινητή (P2), από τους οποίους…

Subjects/Keywords: Μεθυλίωση DNA; Καρκίνος πνεύμονα; ΔΝp73; p73; Sp1; DNA methylation; Lung cancer; TAp73 γ

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APA (6^th Edition):

Λογοθέτη, . �. (2011). Μελέτη του ρόλου των p73 ισομορφών στον καρκίνο του πνεύμονα. (Thesis). University of Crete (UOC); Πανεπιστήμιο Κρήτης. Retrieved from http://hdl.handle.net/10442/hedi/24877

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

Chicago Manual of Style (16^th Edition):

Λογοθέτη, Στυλιανή. “Μελέτη του ρόλου των p73 ισομορφών στον καρκίνο του πνεύμονα.” 2011. Thesis, University of Crete (UOC); Πανεπιστήμιο Κρήτης. Accessed March 03, 2021. http://hdl.handle.net/10442/hedi/24877.

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

MLA Handbook (7^th Edition):

Λογοθέτη, Στυλιανή. “Μελέτη του ρόλου των p73 ισομορφών στον καρκίνο του πνεύμονα.” 2011. Web. 03 Mar 2021.

Vancouver:

Λογοθέτη �. Μελέτη του ρόλου των p73 ισομορφών στον καρκίνο του πνεύμονα. [Internet] [Thesis]. University of Crete (UOC); Πανεπιστήμιο Κρήτης; 2011. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/10442/hedi/24877.

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

Council of Science Editors:

Λογοθέτη �. Μελέτη του ρόλου των p73 ισομορφών στον καρκίνο του πνεύμονα. [Thesis]. University of Crete (UOC); Πανεπιστήμιο Κρήτης; 2011. Available from: http://hdl.handle.net/10442/hedi/24877

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

Wayne State University

28. Arrabi, Amanda Lynn. Effect Of Folate Deficiency And Aging On Mtor Signaling Network In The Liver Of Dna Polymerase B Haploinsufficient Mice.

Degree: MS, Nutrition and Food Science, 2013, Wayne State University

URL: https://digitalcommons.wayne.edu/oa_theses/258

► EFFECT OF FOLATE DEFICIENCY AND AGING ON mTOR SIGNALING NETWORK IN THE LIVER OF DNA POLYMERASE B HAPLOINSUFFICIENT MICE by AMANDA ARRABI August 2013… (more)

Subjects/Keywords: Apoptosis; Beta polymerase; Cancer; DNA POLYMERASE B; DNA POLYMERASE B HAPLOINSUFFICIENT MICE; Folate Deficiency; Molecular Biology; Nutrition

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APA (6^th Edition):

Arrabi, A. L. (2013). Effect Of Folate Deficiency And Aging On Mtor Signaling Network In The Liver Of Dna Polymerase B Haploinsufficient Mice. (Masters Thesis). Wayne State University. Retrieved from https://digitalcommons.wayne.edu/oa_theses/258

Chicago Manual of Style (16^th Edition):

Arrabi, Amanda Lynn. “Effect Of Folate Deficiency And Aging On Mtor Signaling Network In The Liver Of Dna Polymerase B Haploinsufficient Mice.” 2013. Masters Thesis, Wayne State University. Accessed March 03, 2021. https://digitalcommons.wayne.edu/oa_theses/258.

MLA Handbook (7^th Edition):

Arrabi, Amanda Lynn. “Effect Of Folate Deficiency And Aging On Mtor Signaling Network In The Liver Of Dna Polymerase B Haploinsufficient Mice.” 2013. Web. 03 Mar 2021.

Vancouver:

Arrabi AL. Effect Of Folate Deficiency And Aging On Mtor Signaling Network In The Liver Of Dna Polymerase B Haploinsufficient Mice. [Internet] [Masters thesis]. Wayne State University; 2013. [cited 2021 Mar 03]. Available from: https://digitalcommons.wayne.edu/oa_theses/258.

Council of Science Editors:

Arrabi AL. Effect Of Folate Deficiency And Aging On Mtor Signaling Network In The Liver Of Dna Polymerase B Haploinsufficient Mice. [Masters Thesis]. Wayne State University; 2013. Available from: https://digitalcommons.wayne.edu/oa_theses/258

Vanderbilt University

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

Degree: PhD, Human Genetics, 2012, Vanderbilt University

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

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

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

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

APA (6^th Edition):

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

Chicago Manual of Style (16^th Edition):

Song, Zhuo. “Stochastic modeling of mitochondrial polymerase gamma replication and novel algorithms to enrich rare disease alleles and detect tumor somatic mutations in deep sequencing data.” 2012. Doctoral Dissertation, Vanderbilt University. Accessed March 03, 2021. http://hdl.handle.net/1803/10702.

MLA Handbook (7^th Edition):

Song, Zhuo. “Stochastic modeling of mitochondrial polymerase gamma replication and novel algorithms to enrich rare disease alleles and detect tumor somatic mutations in deep sequencing data.” 2012. Web. 03 Mar 2021.

Vancouver:

Song Z. Stochastic modeling of mitochondrial polymerase gamma replication and novel algorithms to enrich rare disease alleles and detect tumor somatic mutations in deep sequencing data. [Internet] [Doctoral dissertation]. Vanderbilt University; 2012. [cited 2021 Mar 03]. Available from: http://hdl.handle.net/1803/10702.

Council of Science Editors:

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

30. Aubry, Valentin. Étude de la régulation de l'expression des gènes tardifs du virus d'Epstein-Barr : Study of the regulation of late Epstein-Barr virus genes expression.

Degree: Docteur es, Sciences de la Vie, 2016, Lyon

URL: http://www.theses.fr/2016LYSEN029

►

Le virus d’Epstein-Barr (EBV) est un Herpesvirus humain appartenant à la sous-famille des γ-Herpesvirinae. L’expression des gènes d’EBV est régulée très finement, de manière séquentielle… (more)

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Le virus d’Epstein-Barr (EBV) est un Herpesvirus humain appartenant à la sous-famille des γ-Herpesvirinae. L’expression des gènes d’EBV est régulée très finement, de manière séquentielle et débute par l’expression des gènes immédiats précoces dont les produits contrôlent l’expression des gènes précoces. Les produits de ces derniers permettent la réplication de l’ADN viral et la synthèse des gènes tardifs. Les mécanismes contrôlant l’expression des gènes immédiats précoces et précoces sont assez bien compris, à contrario de ceux qui contrôlent l’expression des gènes tardifs. En effet, il est connu que ces derniers ne sont exprimés qu’après réplication de l’ADN viral. Par ailleurs, les promoteurs des gènes tardifs présentent une structure différente des promoteurs de gènes immédiats précoces, précoces ou des gènes cellulaires. Ils sont essentiellement caractérisés par la présence d’une boîte TATT à la place de la TATA-box canonique. EBV a la particularité de coder pour une TBP-like, la protéine BcRF1 qui est essentielle mais pas suffisante pour l’expression des gènes viraux tardifs et qui se fixe spécifiquement sur la séquence TATT des promoteurs viraux tardifs. Notre objectif était principalement d’identifier l’ensemble des protéines virales nécessaires à l’expression des gènes tardifs d’EBV. Nous avons ainsi démontré qu’en plus de la protéine BcRF1, EBV code pour cinq autres protéines nécessaires à l’expression des gènes viraux tardifs : BFRF2, BGLF3, BVLF1, BDLF4 et BDLF3.5. Ces six protéines virales forment un complexe qui permet le recrutement de l’ARN polymérase II sur les promoteurs des gènes viraux tardifs. Nous avons nommé ce complexe vPIC (viral Pre-Initiation Complex), par analogie avec le complexe d’initiation de la transcription cellulaire formé autour de la TATA-Binding Protein (TBP). Le vPIC est conservé chez les herpesvirus des sous familles β et γ, mais est absent chez les herpesvirus de la sous famille des α. Par ailleurs, nos résultats suggèrent que le complexe vPIC interagit avec le complexe de réplication viral ce qui peut expliquer la liaison entre réplication de l’ADN viral et transcription des gènes viraux tardifs. Ces résultats permettent ainsi de mieux comprendre les mécanismes de régulation de l’expression des gènes tardifs d’EBV et serviront de base pour la recherche de nouveaux antiviraux.

The Epstein-Barr virus (EBV) is a human Herpersvirus belonging to the subfamily of γ-Herpesvirinae. EBV genes expression is tightly regulated, in a sequential manner and begins with the expression of immediate early genes whose products control the expression of early genes. Products of these allow the viral DNA synthesis and late genes expression. Mechanisms controlling immediate early and early genes expression are well documented, in contrast to those controlling late genes expression. Indeed, it is known that late genes are expressed after viral DNA replication. Furthermore, late genes promoters have a different structure of those of immediate early, early and cellular genes. They are essentially…

Advisors/Committee Members: Gruffat, Henri (thesis director).

Subjects/Keywords: Γ-Herpesvirinae; Gènes tardifs; Transcription; VPIC; Réplication de l’ADN viral; Γ-Herpesvirinae; Late genes; Transcription; VPIC; Viral DNA replication

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

APA (6^th Edition):

Aubry, V. (2016). Étude de la régulation de l'expression des gènes tardifs du virus d'Epstein-Barr : Study of the regulation of late Epstein-Barr virus genes expression. (Doctoral Dissertation). Lyon. Retrieved from http://www.theses.fr/2016LYSEN029

Chicago Manual of Style (16^th Edition):

Aubry, Valentin. “Étude de la régulation de l'expression des gènes tardifs du virus d'Epstein-Barr : Study of the regulation of late Epstein-Barr virus genes expression.” 2016. Doctoral Dissertation, Lyon. Accessed March 03, 2021. http://www.theses.fr/2016LYSEN029.

MLA Handbook (7^th Edition):

Aubry, Valentin. “Étude de la régulation de l'expression des gènes tardifs du virus d'Epstein-Barr : Study of the regulation of late Epstein-Barr virus genes expression.” 2016. Web. 03 Mar 2021.

Vancouver:

Aubry V. Étude de la régulation de l'expression des gènes tardifs du virus d'Epstein-Barr : Study of the regulation of late Epstein-Barr virus genes expression. [Internet] [Doctoral dissertation]. Lyon; 2016. [cited 2021 Mar 03]. Available from: http://www.theses.fr/2016LYSEN029.

Council of Science Editors:

Aubry V. Étude de la régulation de l'expression des gènes tardifs du virus d'Epstein-Barr : Study of the regulation of late Epstein-Barr virus genes expression. [Doctoral Dissertation]. Lyon; 2016. Available from: http://www.theses.fr/2016LYSEN029

Open Access Theses and Dissertations