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Queensland University of Technology
1.
Tsao, Theresa Tsun-Hui.
Towards the development of transgenic banana bunchy top virus (BBTV)-resistant banana plants : interference with replication.
Degree: 2008, Queensland University of Technology
URL: https://eprints.qut.edu.au/17031/
► Banana bunchy top virus (BBTV) causes one of the most devastating diseases of banana. Transgenic virus resistance is now considered one of the most promising…
(more)
▼ Banana bunchy top virus (BBTV) causes one of the most devastating diseases of banana. Transgenic virus resistance is now considered one of the most promising strategies to control BBTV. Pathogen-derived resistance (PDR) strategies have been applied successfully to generate plants that are resistant to numerous different viruses, primarily against those viruses with RNA genomes. BBTV is a circular, single-stranded (css) DNA virus of the family Nanoviridae, which is closely related to the family Geminiviridae. Although there are some successful examples of PDR against geminiviruses, PDR against the nanoviruses has not been reported. Therefore, the aim of this thesis was to investigate the potential of BBTV genes to interfere with virus replication when used as transgenes for engineering banana plants resistance to BBTV. The replication initiation protein (Rep) of nanoviruses is the only viral protein essential for viral replication and represents an ideal target for PDR. Therefore, this thesis focused on the effect of wild-type or mutated Rep genes from BBTV satellite DNAs or the BBTV integral genome on the replication of BBTV in banana embryogenic cell suspensions.
A new Rep-encoding satellite DNA, designated BBTV DNA-S4, was isolated from a Vietnamese BBTV isolate and characterised. When the effect of DNA-S4 on the replication of BBTV was examined, it was found that DNA-S4 enhanced the replication of BBTV. When the replicative capabilities of DNA-S4 and the previously characterised Rep-encoding BBTV satellite, DNA-S1, were compared, it was found that the amount of DNA-S4 accumulated to higher levels than DNA-S1. The interaction between BBTV and DNA-S1 was also examined. It was found that over-expression of the Rep encoded by DNA-S1 using ubi1 maize polyubiquitin promoter enhanced replication of BBTV. However, when the Rep-encoded by DNA-S1 was expressed by the native S1 promoter (in plasmid pBT1.1-S1), it suppressed the replication of BBTV. Based on this result, the use of DNA-S1 as a possible transgene to generate PDR against BBTV was investigated.
The roles of the Rep-encoding and U5 genes of BBTV DNA-R, and the effects of over-expression of these two genes on BBTV replication were also investigated. Three mutants of BBTV DNA-R were constructed; plasmid pUbi-RepOnly-nos contained the ubi1 promoter driving Rep expression from DNA-R, plasmid pUbi-IntOnly-nos contained the ubi1 promoter driving expression of the DNA-R internal gene product (U5), while plasmid pUbi-R.ORF-nos contained the ubi1 promoter driving the expression of both Rep and the internal U5 gene product. The replication of BBTV was found to be significantly suppressed by pUbi-RepOnly-nos, weakly suppressed by pUbi-IntOnly-nos, but strongly enhanced by pUbi-R.ORF-nos.
The effect of mutations in three conserved residues within the BBTV Rep on BBTV replication was also assessed. These mutations were all made in the regions in the ATPase motifs and resulted in changes from hydrophilic to hydrophobic residues (i.e. K187→M, D224→I and N268→L). None of…
Subjects/Keywords: banana bunchy top virus; nanoviruses; replication initiation protein (Rep); pathogen-derived resistance; BBTV DNA-R; BBTV DNA-S1; BBTV DNA-S3; BBTV DNA-S4; satellite DNA; ATPase; post-transcriptional gene silencing; RNA silencing suppressor
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APA (6th Edition):
Tsao, T. T. (2008). Towards the development of transgenic banana bunchy top virus (BBTV)-resistant banana plants : interference with replication. (Thesis). Queensland University of Technology. Retrieved from https://eprints.qut.edu.au/17031/
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Tsao, Theresa Tsun-Hui. “Towards the development of transgenic banana bunchy top virus (BBTV)-resistant banana plants : interference with replication.” 2008. Thesis, Queensland University of Technology. Accessed March 01, 2021.
https://eprints.qut.edu.au/17031/.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Tsao, Theresa Tsun-Hui. “Towards the development of transgenic banana bunchy top virus (BBTV)-resistant banana plants : interference with replication.” 2008. Web. 01 Mar 2021.
Vancouver:
Tsao TT. Towards the development of transgenic banana bunchy top virus (BBTV)-resistant banana plants : interference with replication. [Internet] [Thesis]. Queensland University of Technology; 2008. [cited 2021 Mar 01].
Available from: https://eprints.qut.edu.au/17031/.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Tsao TT. Towards the development of transgenic banana bunchy top virus (BBTV)-resistant banana plants : interference with replication. [Thesis]. Queensland University of Technology; 2008. Available from: https://eprints.qut.edu.au/17031/
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Queensland University of Technology
2.
Hafner, Gregory.
Replication of banana bunchy top virus : mechanisms and interference.
Degree: 1998, Queensland University of Technology
URL: http://eprints.qut.edu.au/36970/
Subjects/Keywords: Banana bunchy top disease; Bananas Diseases and pests; banana; bunchy top; virus; disease; transmission; movement; systemic spread; Pentalonia nigronervosa; genome; strand-initiation; self-priming; primer; Rep; replication; initiator; protein; nicking; joining; ribozyme; antisense; resistance; Musa; thesis; doctoral
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APA (6th Edition):
Hafner, G. (1998). Replication of banana bunchy top virus : mechanisms and interference. (Thesis). Queensland University of Technology. Retrieved from http://eprints.qut.edu.au/36970/
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Hafner, Gregory. “Replication of banana bunchy top virus : mechanisms and interference.” 1998. Thesis, Queensland University of Technology. Accessed March 01, 2021.
http://eprints.qut.edu.au/36970/.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Hafner, Gregory. “Replication of banana bunchy top virus : mechanisms and interference.” 1998. Web. 01 Mar 2021.
Vancouver:
Hafner G. Replication of banana bunchy top virus : mechanisms and interference. [Internet] [Thesis]. Queensland University of Technology; 1998. [cited 2021 Mar 01].
Available from: http://eprints.qut.edu.au/36970/.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Hafner G. Replication of banana bunchy top virus : mechanisms and interference. [Thesis]. Queensland University of Technology; 1998. Available from: http://eprints.qut.edu.au/36970/
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Queensland University of Technology
3.
Horser, Cathryn Louise.
Characterisation of the putative satellite DNAs associated with banana bunchy top virus.
Degree: 2000, Queensland University of Technology
URL: http://eprints.qut.edu.au/37078/
Subjects/Keywords: Banana bunchy top disease; Bananas Diseases and pests; banana bunchy top virus (BBTV); circular single-stranded DNA(cssDNA); nanovirus; geminivirus; replication initiation protein (Rep); BBTV-S1; BBTV-S2; BBTV-Y1; FBNYV; MDV; SCSV; CFDV; thesis; doctoral
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Horser, C. L. (2000). Characterisation of the putative satellite DNAs associated with banana bunchy top virus. (Thesis). Queensland University of Technology. Retrieved from http://eprints.qut.edu.au/37078/
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Horser, Cathryn Louise. “Characterisation of the putative satellite DNAs associated with banana bunchy top virus.” 2000. Thesis, Queensland University of Technology. Accessed March 01, 2021.
http://eprints.qut.edu.au/37078/.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Horser, Cathryn Louise. “Characterisation of the putative satellite DNAs associated with banana bunchy top virus.” 2000. Web. 01 Mar 2021.
Vancouver:
Horser CL. Characterisation of the putative satellite DNAs associated with banana bunchy top virus. [Internet] [Thesis]. Queensland University of Technology; 2000. [cited 2021 Mar 01].
Available from: http://eprints.qut.edu.au/37078/.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Horser CL. Characterisation of the putative satellite DNAs associated with banana bunchy top virus. [Thesis]. Queensland University of Technology; 2000. Available from: http://eprints.qut.edu.au/37078/
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Vanderbilt University
4.
Dhingra, Nalini.
Elucidating the role of Dpb11 in replication initiation.
Degree: PhD, Biological Sciences, 2015, Vanderbilt University
URL: http://hdl.handle.net/1803/12863
► Initiation of DNA Replication is a highly regulated process and is characterized by the conversion of inactive Mcm2-7 double hexamer around dsDNA to an active…
(more)
▼ Initiation of DNA
Replication is a highly regulated process and is characterized by the conversion of inactive Mcm2-7 double hexamer around dsDNA to an active helicase consisting of Mcm2-7 single hexamer which encircles ssDNA along with Cdc45 and GINS. This transition of inactive Mcm2-7 around dsDNA to the active helicase around ssDNA involves several unknown mechanisms. Many proteins like, Sld2, Sld3, Dpb11, Mcm10, have been reported to be essential for
replication initiation. Dpb11 is one of these essential proteins that functions in the
initiation of DNA
replication. Dpb11 binds to S-CDK phosphorylated Sld2 and Sld3 to form a ternary complex during S phase. These interactions are essential for the CDK-dependent activation of DNA
replication in budding yeast. Studies have also indicated that chromosomal
replication initiates by a fundamentally similar process in all eukaryotes, with Dpb11 being an evolutionary conserved
protein. Our studies using purified proteins from budding yeast show that Dpb11 alone binds to Mcm2-7, and Dpb11 also competes with GINS for binding to Mcm2-7. Furthermore, Dpb11 binds directly to single-stranded DNA (ssDNA), and ssDNA inhibits Dpb11 interaction with Mcm2-7. We also found that Dpb11 can recruit Cdc45 to Mcm2-7. We identified a mutant of the BRCT4 motif of Dpb11 that remains bound to Mcm2-7 in the presence of ssDNA (dpb11-m1,m2,m3,m5), and this mutant exhibits a DNA
replication defect when expressed in budding yeast cells. Expression of this mutant results in increased interaction between Dpb11 and Mcm2-7 during S phase, impaired GINS interaction with Mcm2-7 during S phase, and decreased RPA interaction with origin DNA during S phase. We propose a model wherein Dpb11 first recruits Cdc45 to Mcm2-7. Dpb11, while bound to Cdc45-Mcm2-7, can block the interaction between GINS and Mcm2-7. Upon the extrusion of ssDNA from the central channel of Mcm2-7, Dpb11 dissociates from Mcm2-7 and Dpb11 binds to ssDNA, thereby allowing GINS to bind to Cdc45-Mcm2-7. Finally, we propose that Dpb11 functions with Sld2 and Sld3 to help control the assembly of the
replication fork helicase.
Advisors/Committee Members: Dr. Todd Graham (Committee Chair).
Subjects/Keywords: initiation; replication fork; kinase; helicase; replication
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Dhingra, N. (2015). Elucidating the role of Dpb11 in replication initiation. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/12863
Chicago Manual of Style (16th Edition):
Dhingra, Nalini. “Elucidating the role of Dpb11 in replication initiation.” 2015. Doctoral Dissertation, Vanderbilt University. Accessed March 01, 2021.
http://hdl.handle.net/1803/12863.
MLA Handbook (7th Edition):
Dhingra, Nalini. “Elucidating the role of Dpb11 in replication initiation.” 2015. Web. 01 Mar 2021.
Vancouver:
Dhingra N. Elucidating the role of Dpb11 in replication initiation. [Internet] [Doctoral dissertation]. Vanderbilt University; 2015. [cited 2021 Mar 01].
Available from: http://hdl.handle.net/1803/12863.
Council of Science Editors:
Dhingra N. Elucidating the role of Dpb11 in replication initiation. [Doctoral Dissertation]. Vanderbilt University; 2015. Available from: http://hdl.handle.net/1803/12863

Queensland University of Technology
5.
Williams, Brett Robert.
Development of a novel rep-inducible tomato leaf curl virus expression system.
Degree: 2007, Queensland University of Technology
URL: https://eprints.qut.edu.au/16539/
► Pathogen-derived resistance (PDR) strategies, particularly those based on post-transcriptional gene silencing, have been used with great success for the generation of transgenic plants with resistance…
(more)
▼ Pathogen-derived resistance (PDR) strategies, particularly those based on post-transcriptional gene silencing, have been used with great success for the generation of transgenic plants with resistance to RNA viruses. In contrast, a suitable strategy for transgenic resistance to ssDNA plant viruses, including those viruses belonging to the Geminiviridae, has remained elusive. Further, there is no convincing evidence that either post-transcriptional gene silencing, or pathogen-derived resistance in general, would be broadly applicable to ssDNA plant viruses. Researchers at QUT have been developing a novel resistance strategy against ssDNA viruses based on virus-activated expression of a stably integrated suicide gene. The strategy, based on InPAct (In Plant Activation) technology, relies on a "split" suicide gene cassette being arranged in such a way that expression of a lethal ribonuclease (barnase) is dependent on the virus-encoded replication-associated protein (Rep). Upon infection, Rep mediates the release of the construct resulting in the reconstitution of a transcribable and translatable episomal suicide gene expression cassette. The research for this PhD describes the development of an InPAct vector designed to confer resistance to Tomato leaf curl begomovirus (ToLCV), a major cause of disease in Solanaceous crops in the tropics and subtropics.
ToLCV-based InPAct vectors were constructed based upon two ToLCV isolates from Australia and North Vietnam. Prior to the generation of InPAct cassettes, the entire ToLCV-[Au] and ToLCV-Vie intergenic regions (IRs) were embedded within the castorbean catalase intron of a β-glucuronidase expression vector to determine the effect of the IR upon transcript processing. Using transient reporter gene assays in tobacco NT-1 cells, it was demonstrated that the ToLCV IRs both contained cryptic intron splice sites which interfered with efficient transcript processing and GUS expression. A series of truncations to the IRs were subsequently made to identify the potential cryptic intron splice sites and/or interfering sequences in both the ToLCV-[Au] and ToLCV-Vie IRs. The final truncated IRs, which were used in the construction the InPAct cassettes, comprised approximately 100 bp and appeared to contain all the necessary cis-acting elements required for efficient rolling circle replication (RCR). Using histochemical GUS assays and Southern analyses, the InPAct cassettes were shown to be activated and replicated only in the presence of the cognate viral Rep. GUS expression levels were shown to be further enhanced in the presence of the ToLCV replication-enhancer protein (REn) and by the addition of the Tobacco yellow dwarf mastrevirus origin of second strand synthesis into the cassette. Under these conditions, Rep-activated GUS expression from the InPAct vectors was found to reach levels similar to that of the benchmark CaMV 35S promoter.
Fifteen independent transgenic lines containing the ToLCV-[Au] and -Vie InPAct-GUS cassettes were generated by…
Subjects/Keywords: pathogen-derived resistance (PDR); tomato leaf curl virus; replication-association protein (Rep); begomoviruses
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Williams, B. R. (2007). Development of a novel rep-inducible tomato leaf curl virus expression system. (Thesis). Queensland University of Technology. Retrieved from https://eprints.qut.edu.au/16539/
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Williams, Brett Robert. “Development of a novel rep-inducible tomato leaf curl virus expression system.” 2007. Thesis, Queensland University of Technology. Accessed March 01, 2021.
https://eprints.qut.edu.au/16539/.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Williams, Brett Robert. “Development of a novel rep-inducible tomato leaf curl virus expression system.” 2007. Web. 01 Mar 2021.
Vancouver:
Williams BR. Development of a novel rep-inducible tomato leaf curl virus expression system. [Internet] [Thesis]. Queensland University of Technology; 2007. [cited 2021 Mar 01].
Available from: https://eprints.qut.edu.au/16539/.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Williams BR. Development of a novel rep-inducible tomato leaf curl virus expression system. [Thesis]. Queensland University of Technology; 2007. Available from: https://eprints.qut.edu.au/16539/
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Queensland University of Technology
6.
Pirlo, Steven Dominic.
Identification of viral-based replicating vectors suitable for the development of a sugarcane bioreactor.
Degree: 2007, Queensland University of Technology
URL: https://eprints.qut.edu.au/16548/
► The circular, single-stranded (ss) DNA genomes of plant viruses in the families Geminiviridae and Nanoviridae are replicated within the nucleus of a host cell by…
(more)
▼ The circular, single-stranded (ss) DNA genomes of plant viruses in the families Geminiviridae and Nanoviridae are replicated within the nucleus of a host cell by a mechanism called rolling circle replication (RCR). Although this process relies almost exclusively on the replication machinery of the host cell, initiation occurs via the interaction of the viral replication initiation protein (Rep) with regulatory DNA sequences within the viral genome. The use of a virus-based episomal amplification technology as a plant bioreactor platform exploits the process of Rep-mediated RCR for the high-level amplification of virus-based episomes in plants and subsequent expression of heterologous proteins; such an approach offers advantages over existing gene expression technologies. This PhD thesis describes research towards the development of a virus-based episomal amplification system for use in sugarcane. Such a crop is ideally suited for a plant bioreactor system due to the efficient high-level production of plant biomass and the existence of established production, harvesting and processing infrastructure.
In order to rapidly assess the potential of a virus-based episomal amplification system in sugarcane, a transient assay system was established. Sugarcane callus was identified as the most suitable cell preparation; providing rapid cell regeneration, uniform experimental samples and upon isolation, total DNA suitable for Southern analysis. This assay system once established, proved effective in rapidly identifying virus-based episomes capable of undergoing RCR within sugarcane host cells.
This transient assay system was then used to test the functionality of a virus-based episomal amplification system based on the ssDNA virus, Banana bunchy top virus (BBTV) in sugarcane. BBTV-based episomal amplification vectors were constructed with a reporter gene expression cassette flanked by two copies of the BBTV regulatory DNA sequences. The episomal amplification vectors were bombarded into sugarcane and banana host cells in various combinations and evidence of RCR was assessed through Southern blot analysis. RCR products were identified in banana host cells bombarded with the BBTV-based episomal amplification vectors in combination with vectors encoding BBTV Master-Rep (M Rep). RCR products were not identified within sugarcane cells bombarded with the same construct combinations.
Integrated InPAct (In Plant Activation) episomal vectors based on BBTV were then employed to confirm the transient results, in addition, the functionality of an InPAct vector based on an alternate virus, Tobacco yellow dwarf virus (TYDV) was also assessed. InPAct vectors based on BBTV were constructed with an untranslatable expression cassette for integration within the sugarcane genome. Transient experiments were performed to assess the ability of BBTV M-Rep and TYDV Rep to initiate RCR of their respective InPAct vectors. Visual observation of GFP expression indicated that BBTV M-Rep was capable of initiating RCR of the BBTVbased InPAct vectors…
Subjects/Keywords: bioreactor; episomal; amplification; rolling circle replication; replication initiation protein; replication accessory protein; TYDV; BBTV; ToLCV-Au; CSMV; ssDNA plant virus
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
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Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Pirlo, S. D. (2007). Identification of viral-based replicating vectors suitable for the development of a sugarcane bioreactor. (Thesis). Queensland University of Technology. Retrieved from https://eprints.qut.edu.au/16548/
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Pirlo, Steven Dominic. “Identification of viral-based replicating vectors suitable for the development of a sugarcane bioreactor.” 2007. Thesis, Queensland University of Technology. Accessed March 01, 2021.
https://eprints.qut.edu.au/16548/.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Pirlo, Steven Dominic. “Identification of viral-based replicating vectors suitable for the development of a sugarcane bioreactor.” 2007. Web. 01 Mar 2021.
Vancouver:
Pirlo SD. Identification of viral-based replicating vectors suitable for the development of a sugarcane bioreactor. [Internet] [Thesis]. Queensland University of Technology; 2007. [cited 2021 Mar 01].
Available from: https://eprints.qut.edu.au/16548/.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Pirlo SD. Identification of viral-based replicating vectors suitable for the development of a sugarcane bioreactor. [Thesis]. Queensland University of Technology; 2007. Available from: https://eprints.qut.edu.au/16548/
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Temple University
7.
Cutrera, Jason Lewis.
Insights into the Structure and Function of PrgW and its Conserved Cysteines.
Degree: PhD, 2014, Temple University
URL: http://digital.library.temple.edu/u?/p245801coll10,299645
► Microbiology and Immunology
Enterococcus faecalis is a Gram-positive bacterial species that is typically a member of the human gastrointestinal tract microbiota. However, E. faecalis is…
(more)
▼ Microbiology and Immunology
Enterococcus faecalis is a Gram-positive bacterial species that is typically a member of the human gastrointestinal tract microbiota. However, E. faecalis is also a nosocomial pathogen, which is involved in urinary tract infections, soft tissue infections and endocarditis. In recent times, the occurrence of antibiotic resistance has complicated the treatment of these infections. One of the major differences between commensal and pathogenic strains of E. faecalis is that pathogens contain multiple mobile elements such as plasmids, transposons and integrative conjugative elements (ICE). These elements allow for the acquisition and transfer of virulence factors and resistance genes. Conjugative plasmids are a class of plasmids present in E. faecalis whose transfer to host cells is induced by a small pheromone peptide, cCF10 (LVTLVFV). This peptide is initially encoded as a 22-amino acid precursor (pre-cCF10) from the signal sequence of the chromosomal ccfA gene and is then proteolytically cleaved by signal peptidase II and Eep. Once pCF10 has been transferred a host E. faecalis cell, it is exceptionally stable. A replicon clone is maintained in greater than 85% of host cells over 100 generations in the absence of selection, suggesting the stability of pCF10 is intrinsic to the replicon. Three unique features of the replication initiation protein PrgW may contribute to this stability: (a) the interaction of PrgW with pre-cCF10, (b) disulfide bond formation at three conserved cysteines (C78, C275, and C307) in PrgW, and (c) processing of the nascent PrgW protein. Replication initiation proteins associated with theta replicons, such as pCF10, are often self-contained units. To initiate plasmid replication, the replication initiation protein (PrgW) binds to direct repeats (oriV) in its own coding sequence (prgW). In silico analysis of PrgW suggests the existence of three distinct domains within the protein. The first 122 amino acids are homologous to a conserved domain present in related replication initiation proteins, which includes a Helix-Turn-Helix (HTH) DNA binding domain. This suggests that this domain of PrgW has a DNA-binding function and binds to the oriV site in prgW. The following 61 amino acids are not similar to any known sequence, and are encoded by the DNA sequence containing the direct repeats in the oriV site. This domain may or may not have a distinct function. The remaining sequence forms a domain that contains cysteines C275 and C307, and is also similar to no known structure. It is hypothesized that this domain is related to the stability of pCF10. C307 appears to be critical, as previous experiments indicate that its mutation alone affects plasmid stability. Secondary structure analysis of this domain revealed the presence of multiple alpha-helices that contain distinct hydrophobic domains that possibly contribute to pre-cCF10 binding and PrgW tertiary structure. The positions of the conserved cysteines within these alpha-helices may stabilize a hydrophobic binding…
Advisors/Committee Members: Buttaro, Bettina A.;, Tsygankov, Alexander, Tukel, Cagla, Monestier, Marc, Grubmeyer, Charles;.
Subjects/Keywords: Microbiology;
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Cutrera, J. L. (2014). Insights into the Structure and Function of PrgW and its Conserved Cysteines. (Doctoral Dissertation). Temple University. Retrieved from http://digital.library.temple.edu/u?/p245801coll10,299645
Chicago Manual of Style (16th Edition):
Cutrera, Jason Lewis. “Insights into the Structure and Function of PrgW and its Conserved Cysteines.” 2014. Doctoral Dissertation, Temple University. Accessed March 01, 2021.
http://digital.library.temple.edu/u?/p245801coll10,299645.
MLA Handbook (7th Edition):
Cutrera, Jason Lewis. “Insights into the Structure and Function of PrgW and its Conserved Cysteines.” 2014. Web. 01 Mar 2021.
Vancouver:
Cutrera JL. Insights into the Structure and Function of PrgW and its Conserved Cysteines. [Internet] [Doctoral dissertation]. Temple University; 2014. [cited 2021 Mar 01].
Available from: http://digital.library.temple.edu/u?/p245801coll10,299645.
Council of Science Editors:
Cutrera JL. Insights into the Structure and Function of PrgW and its Conserved Cysteines. [Doctoral Dissertation]. Temple University; 2014. Available from: http://digital.library.temple.edu/u?/p245801coll10,299645

Universiteit Utrecht
8.
Breukelen, B. van.
The role of the adenovirus DNA binding protein in DNA replication and recombination.
Degree: 2003, Universiteit Utrecht
URL: http://dspace.library.uu.nl:8080/handle/1874/226
► Replication of adenovirus DNA in infected cells is an efficient process that, compared to cellular replication, has the use of a protein primer as a…
(more)
▼ Replication of adenovirus DNA in infected cells is an efficient process that, compared to cellular replication, has the use of a protein primer as a hallmark. The mechanism of this DNA replication process and especially the role of one of the replication proteins, the DNA binding protein DBP, is the main subject of this thesis.
Adenovirus DNA replication can be reconstituted in vitro, using three viral proteins, adenovirus DNA polymerase (pol), precursor terminal protein (pTP), and DBP. Optimal replication efficiency is obtained when two cellular transcription factors are added, nuclear factor I (NFI) and Oct-1. The adenoviral dsDNA genome contains two terminal proteins (TP) covalently linked to the 5. ends. The inverted terminal repeats contain the origins of replication. pTP and pol are tightly associated in solution. During initiation of replication pTP functions as a primer to which the first nucleotide, dCTP, is covalently coupled. Both NFI and Oct-1 stimulate the initiation by recruiting the pTP-pol complex to the origin of replication. Initiation starts opposite position 4 of the template strand. After formation of a pTP-trinucleotide (pTP-CAT), the complex jumps back and CAT becomes paired with template residues 1.3. Shortly after jumping back, the polymerase dissociates from pTP and elongation proceeds via strand displacement.
The adenovirus DNA binding protein is an important player in adenovirus DNA replication, where it serves multiple functions. In the first step of adenovirus DNA replication DBP stimulates the coupling of the first nucleotide to pTP. Also binding of NFI to the origin is stimulated by DBP. Subsequently, during elongation DBP unwinds the dsDNA ahead of pol and removes secondary structures. Adenovirus DBP binds with high affinity and cooperativity to ssDNA, whereas binding to dsDNA is non- cooperative and with lower affinity. These differences in binding affinity are the driving force for dsDNA unwinding which is required for processive DNA chain elongation by pol.
DBP is a 529 amino acids long protein with a molecular weight of 59 kD. The structure of adenovirus DBP possesses a remarkable feature; the C-terminal arm (aa. 512-529), which is important for the cooperative binding of DBP to another DBP molecule. In addition, the C-terminal arm is flexible and can rotate around a fixed point, called the hinge-region (aa. 512-515).
In Chapter 1, an introduction to the adenovirus DNA replication machinery and the role of several single stranded DNA binding proteins originating from different organisms is presented.
In Chapter 2 we present data on the function of the flexibility of the C-terminal arm of DBP and we discuss the implications of an altered flexibility on adenovirus DNA replication by mutating several aa in the hinge-region.
In Chapter 3, we present data on the function of DBP in the stimulation of initiation. In contrast to a direct protein-protein interaction of DBP with pol we demonstrate that DBP stimulates the binding of pol to the dsDNA origin. We assume that the…
Subjects/Keywords: Biologie; adenovirus; DBP; unwinding; replication; recombination; initiation; elongation; protein-interaction; DNA
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Breukelen, B. v. (2003). The role of the adenovirus DNA binding protein in DNA replication and recombination. (Doctoral Dissertation). Universiteit Utrecht. Retrieved from http://dspace.library.uu.nl:8080/handle/1874/226
Chicago Manual of Style (16th Edition):
Breukelen, B van. “The role of the adenovirus DNA binding protein in DNA replication and recombination.” 2003. Doctoral Dissertation, Universiteit Utrecht. Accessed March 01, 2021.
http://dspace.library.uu.nl:8080/handle/1874/226.
MLA Handbook (7th Edition):
Breukelen, B van. “The role of the adenovirus DNA binding protein in DNA replication and recombination.” 2003. Web. 01 Mar 2021.
Vancouver:
Breukelen Bv. The role of the adenovirus DNA binding protein in DNA replication and recombination. [Internet] [Doctoral dissertation]. Universiteit Utrecht; 2003. [cited 2021 Mar 01].
Available from: http://dspace.library.uu.nl:8080/handle/1874/226.
Council of Science Editors:
Breukelen Bv. The role of the adenovirus DNA binding protein in DNA replication and recombination. [Doctoral Dissertation]. Universiteit Utrecht; 2003. Available from: http://dspace.library.uu.nl:8080/handle/1874/226

University of Saskatchewan
9.
Horbay, Monique Adelle.
Inhibition phenotype specific for orië replication-dependent phage growth, and a reappraisal of the Influence of ë P expression on escherichia coli cell metabolism : p-interference phenotype.
Degree: 2005, University of Saskatchewan
URL: http://hdl.handle.net/10388/etd-12222005-145257
► Bacteriophage ë has been used as a model replicon system for forty years. While the basic ë replication initiation scheme has been elucidated for several…
(more)
▼ Bacteriophage ë has been used as a model replicon system for forty years. While the basic ë
replication initiation scheme has been elucidated for several decades, many aspects of the mechanisms are unclear. I wished to study two unanswered issues in ë
replication initiation.
Replication initiation of E. coli and ë each depend upon a
protein generally called a licensing factor, which brings the DnaB helicase
protein to the origin site to begin DNA synthesis. The licensing factors are the products of host gene dnaC and ë gene P. The synthesis of P from ë DNA in an E. coli cell can competitively interfere with DnaC activity needed for E. coli
replication initiation. I wished to learn more about what happens to a host cell when exposed to extended P expression. Previous studies in this laboratory suggested that i) the continuous expression of P was tolerated by a subset of exposed cells and that ii) host defects mapping to dnaB could suppress the effect of extended P expression (P-lethality). I used DNA sequencing to determine if these suppressor mutations were within dnaB. I screened known host mutations for their influence on P-lethality. In summary: E. coli strains with GrpD55 and GrpA80 defects were found to each have two point mutations within their dnaB genes. I was unable to isolate mutations within P that suppressed P-lethality and instead obtained regulatory mutations preventing wild type P expression. Two of these sequenced mutations showed that a cI[Ts] lambda repressor was reverted to cI wild type, blocking P expression at all assay temperatures. P-lethality was reversible in cells exposed to P for up to five hours, causing me to suggest that P-Interference be used in place of the term P-lethality. A non-inducible allele of lexA prevented P-mediated cellular filamentation and enhanced P-Interference. This suggests that induction of the SOS response helps cells to tolerate extended P expression. A host strain containing a defective ClpXP protease significantly enhanced cellular sensitivity to P-Interference. This suggests an important role for the ClpXP chaperone-protease complex in degradation of P and cellular resistance to P expression. I present models to explain the P-Interference Phenotype.Recent reports have re-opened the possibility that the tO-oop-pO element influences ë DNA
replication initiation. I have also been investigating this possibility. I found that a plasmid with tO-oop-pO (the terminator, nucleotide sequence and promoter for OOP RNA) and orië DNA sequence was inhibitory to the development of repë phages, and designated this the Inhibition Phenotype (IP). In pursuing the mechanism for this inhibition, I mutated the tO-oop-pO and orië elements. I found that the expression of the 77nt OOP RNA transcript and the presence of four 18 base pair repeats (iterons) within orië were required for the IP. I isolated spontaneous phage mutants, resistant to the IP. I determined that singly infected cells were sensitive to the IP but that multiply infected cells escaped the IP. I…
Advisors/Committee Members: Hayes, Sidney, Xiao, Wei, Loh, Lambert, Howard, S. Peter, Goldie, Hughes, Cupples, Claire, Bull, Harold.
Subjects/Keywords: OOP RNA; DNA replication initiation; lambda P protein; bacteriophage lambda
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Horbay, M. A. (2005). Inhibition phenotype specific for orië replication-dependent phage growth, and a reappraisal of the Influence of ë P expression on escherichia coli cell metabolism : p-interference phenotype. (Thesis). University of Saskatchewan. Retrieved from http://hdl.handle.net/10388/etd-12222005-145257
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Horbay, Monique Adelle. “Inhibition phenotype specific for orië replication-dependent phage growth, and a reappraisal of the Influence of ë P expression on escherichia coli cell metabolism : p-interference phenotype.” 2005. Thesis, University of Saskatchewan. Accessed March 01, 2021.
http://hdl.handle.net/10388/etd-12222005-145257.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Horbay, Monique Adelle. “Inhibition phenotype specific for orië replication-dependent phage growth, and a reappraisal of the Influence of ë P expression on escherichia coli cell metabolism : p-interference phenotype.” 2005. Web. 01 Mar 2021.
Vancouver:
Horbay MA. Inhibition phenotype specific for orië replication-dependent phage growth, and a reappraisal of the Influence of ë P expression on escherichia coli cell metabolism : p-interference phenotype. [Internet] [Thesis]. University of Saskatchewan; 2005. [cited 2021 Mar 01].
Available from: http://hdl.handle.net/10388/etd-12222005-145257.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Horbay MA. Inhibition phenotype specific for orië replication-dependent phage growth, and a reappraisal of the Influence of ë P expression on escherichia coli cell metabolism : p-interference phenotype. [Thesis]. University of Saskatchewan; 2005. Available from: http://hdl.handle.net/10388/etd-12222005-145257
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Gothenburg / Göteborgs Universitet
10.
Simonsson, Stina 1969-.
Initiation of herpes simplex virus DNA replication.
Degree: 2000, University of Gothenburg / Göteborgs Universitet
URL: http://hdl.handle.net/2077/14135
► During virus infection multiple new copies of the virus genome are made by a DNA synthesis machinery. Initiation of DNA replication involves the recognition of…
(more)
▼ During virus infection multiple new copies of the virus genome are made by a DNA synthesis machinery. Initiation of DNA replication involves the recognition of origins of DNA replication by an initiator protein. The genome of Herpes simplex virus type-1, HSV-1, contains three largely homologous origins of replication: one copy of oriL and two copies of oriS. The origins of DNA replication are activated by the HSV-1 origin binding protein OBP, which is the product of the UL9 gene. A virus specific replication machinery consisting of six proteins is then assembled at the origins. It consists of a heterodimeric DNA polymerase, a single-strand DNA-binding protein and a heterotrimeric helicase-primase complex.This thesis focuses on interactions between oriS and OBP. We have examined the stoichiometry of complexes formed between the DNA binding domain of OBP and its recognition sequence, GTTCGCAC, and established that a 1:1 complex forms. We have identified phosphates and methyl groups in DNA that are involved in the sequence specific recognition of oriS. The results show that OBP primarily recognizes its target sequence through major groove interactions. Interestingly, we find that single-stranded versions of HSV-1 oriS can adopt a novel conformation referred to as oriS*, which forms a stable and specific complex with OBP. Genetic experiments suggest that oriS* is formed as an intermediate during initiation of HSV-1 DNA replication. On the basis of these results a model for initiation of DNA replication that may be applicable also for other organisms is discussed.
Subjects/Keywords: initiation of DNA replication; origin binding protein; Herpes Simplex Virus
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Simonsson, S. 1. (2000). Initiation of herpes simplex virus DNA replication. (Thesis). University of Gothenburg / Göteborgs Universitet. Retrieved from http://hdl.handle.net/2077/14135
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Simonsson, Stina 1969-. “Initiation of herpes simplex virus DNA replication.” 2000. Thesis, University of Gothenburg / Göteborgs Universitet. Accessed March 01, 2021.
http://hdl.handle.net/2077/14135.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Simonsson, Stina 1969-. “Initiation of herpes simplex virus DNA replication.” 2000. Web. 01 Mar 2021.
Vancouver:
Simonsson S1. Initiation of herpes simplex virus DNA replication. [Internet] [Thesis]. University of Gothenburg / Göteborgs Universitet; 2000. [cited 2021 Mar 01].
Available from: http://hdl.handle.net/2077/14135.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Simonsson S1. Initiation of herpes simplex virus DNA replication. [Thesis]. University of Gothenburg / Göteborgs Universitet; 2000. Available from: http://hdl.handle.net/2077/14135
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
11.
Brenkman, A.B. (Arjan Bernard).
Molecular architecture and function of adenovirus DNA polymerase.
Degree: 2002, University Utrecht
URL: https://dspace.library.uu.nl/handle/1874/462
;
URN:NBN:NL:UI:10-1874-462
;
URN:NBN:NL:UI:10-1874-462
;
https://dspace.library.uu.nl/handle/1874/462
► Central to this thesis is the role of adenovirus DNA polymerase (Ad pol) in adenovirus DNA replication. Ad pol is a member of the family…
(more)
▼ Central to this thesis is the role of adenovirus DNA polymerase (Ad pol) in adenovirus DNA replication. Ad pol is a member of the family B DNA polymerases but belongs to a distinct subclass of polymerases that use a protein as primer. As Ad pol catalyses both the initiation and elongation phases and needs to accomodate both DNA and protein as a primer, it is not surprising that a large number of protein-protein and protein-DNA interactions are involved in efficient replication. Indeed, Ad pol is known to interact with pTP, NFI and DNA, although our understanding of these interactions is limited. In this thesis, these interactions have been studied in greater detail. After an introductory chapter on DNA dependent DNA polymerases and Ad replication, the jumping back mechanism that characterizes the change from initiation to elongation is extensively reviewed in chapter 2. In chapter 3, the highly conserved (I/Y)XGG motif of Ad pol is studied. In chapter 4, the interaction between Ad pol and DNA is further studied by the use of biotinylated oligo-nucleotides with a bulky streptavidin block. Chapter 5 examines the termination of Ad pol on the native TP-containing viral DNA. Finally, in chapter 6 the recruitment of the pTP-pol complex via a direct interaction between Ad pol and NFI is studied in detail.
Subjects/Keywords: protein priming; DNA polymerase; replication; NFI; transcription factor; adenovirus; termination; initiation; pTP; origin
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Record Details
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Brenkman, A. B. (. B. (2002). Molecular architecture and function of adenovirus DNA polymerase. (Doctoral Dissertation). University Utrecht. Retrieved from https://dspace.library.uu.nl/handle/1874/462 ; URN:NBN:NL:UI:10-1874-462 ; URN:NBN:NL:UI:10-1874-462 ; https://dspace.library.uu.nl/handle/1874/462
Chicago Manual of Style (16th Edition):
Brenkman, A B (Arjan Bernard). “Molecular architecture and function of adenovirus DNA polymerase.” 2002. Doctoral Dissertation, University Utrecht. Accessed March 01, 2021.
https://dspace.library.uu.nl/handle/1874/462 ; URN:NBN:NL:UI:10-1874-462 ; URN:NBN:NL:UI:10-1874-462 ; https://dspace.library.uu.nl/handle/1874/462.
MLA Handbook (7th Edition):
Brenkman, A B (Arjan Bernard). “Molecular architecture and function of adenovirus DNA polymerase.” 2002. Web. 01 Mar 2021.
Vancouver:
Brenkman AB(B. Molecular architecture and function of adenovirus DNA polymerase. [Internet] [Doctoral dissertation]. University Utrecht; 2002. [cited 2021 Mar 01].
Available from: https://dspace.library.uu.nl/handle/1874/462 ; URN:NBN:NL:UI:10-1874-462 ; URN:NBN:NL:UI:10-1874-462 ; https://dspace.library.uu.nl/handle/1874/462.
Council of Science Editors:
Brenkman AB(B. Molecular architecture and function of adenovirus DNA polymerase. [Doctoral Dissertation]. University Utrecht; 2002. Available from: https://dspace.library.uu.nl/handle/1874/462 ; URN:NBN:NL:UI:10-1874-462 ; URN:NBN:NL:UI:10-1874-462 ; https://dspace.library.uu.nl/handle/1874/462
12.
Breukelen, B. van.
The role of the adenovirus DNA binding protein in DNA replication and recombination.
Degree: 2003, University Utrecht
URL: https://dspace.library.uu.nl/handle/1874/226
;
URN:NBN:NL:UI:10-1874-226
;
1874/226
;
URN:NBN:NL:UI:10-1874-226
;
https://dspace.library.uu.nl/handle/1874/226
► Replication of adenovirus DNA in infected cells is an efficient process that, compared to cellular replication, has the use of a protein primer as a…
(more)
▼ Replication of adenovirus DNA in infected cells is an efficient process that, compared to cellular replication, has the use of a protein primer as a hallmark. The mechanism of this DNA replication process and especially the role of one of the replication proteins, the DNA binding protein DBP, is the main subject of this thesis.
Adenovirus DNA replication can be reconstituted in vitro, using three viral proteins, adenovirus DNA polymerase (pol), precursor terminal protein (pTP), and DBP. Optimal replication efficiency is obtained when two cellular transcription factors are added, nuclear factor I (NFI) and Oct-1. The adenoviral dsDNA genome contains two terminal proteins (TP) covalently linked to the 5. ends. The inverted terminal repeats contain the origins of replication. pTP and pol are tightly associated in solution. During initiation of replication pTP functions as a primer to which the first nucleotide, dCTP, is covalently coupled. Both NFI and Oct-1 stimulate the initiation by recruiting the pTP-pol complex to the origin of replication. Initiation starts opposite position 4 of the template strand. After formation of a pTP-trinucleotide (pTP-CAT), the complex jumps back and CAT becomes paired with template residues 1.3. Shortly after jumping back, the polymerase dissociates from pTP and elongation proceeds via strand displacement.
The adenovirus DNA binding protein is an important player in adenovirus DNA replication, where it serves multiple functions. In the first step of adenovirus DNA replication DBP stimulates the coupling of the first nucleotide to pTP. Also binding of NFI to the origin is stimulated by DBP. Subsequently, during elongation DBP unwinds the dsDNA ahead of pol and removes secondary structures. Adenovirus DBP binds with high affinity and cooperativity to ssDNA, whereas binding to dsDNA is non- cooperative and with lower affinity. These differences in binding affinity are the driving force for dsDNA unwinding which is required for processive DNA chain elongation by pol.
DBP is a 529 amino acids long protein with a molecular weight of 59 kD. The structure of adenovirus DBP possesses a remarkable feature; the C-terminal arm (aa. 512-529), which is important for the cooperative binding of DBP to another DBP molecule. In addition, the C-terminal arm is flexible and can rotate around a fixed point, called the hinge-region (aa. 512-515).
In Chapter 1, an introduction to the adenovirus DNA replication machinery and the role of several single stranded DNA binding proteins originating from different organisms is presented.
In Chapter 2 we present data on the function of the flexibility of the C-terminal arm of DBP and we discuss the implications of an altered flexibility on adenovirus DNA replication by mutating several aa in the hinge-region.
In Chapter 3, we present data on the function of DBP in the stimulation of initiation. In contrast to a direct protein-protein interaction of DBP with pol we demonstrate that DBP stimulates the binding of pol to the dsDNA origin. We assume that the…
Subjects/Keywords: adenovirus; DBP; unwinding; replication; recombination; initiation; elongation; protein-interaction; DNA
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Record Details
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Breukelen, B. v. (2003). The role of the adenovirus DNA binding protein in DNA replication and recombination. (Doctoral Dissertation). University Utrecht. Retrieved from https://dspace.library.uu.nl/handle/1874/226 ; URN:NBN:NL:UI:10-1874-226 ; 1874/226 ; URN:NBN:NL:UI:10-1874-226 ; https://dspace.library.uu.nl/handle/1874/226
Chicago Manual of Style (16th Edition):
Breukelen, B van. “The role of the adenovirus DNA binding protein in DNA replication and recombination.” 2003. Doctoral Dissertation, University Utrecht. Accessed March 01, 2021.
https://dspace.library.uu.nl/handle/1874/226 ; URN:NBN:NL:UI:10-1874-226 ; 1874/226 ; URN:NBN:NL:UI:10-1874-226 ; https://dspace.library.uu.nl/handle/1874/226.
MLA Handbook (7th Edition):
Breukelen, B van. “The role of the adenovirus DNA binding protein in DNA replication and recombination.” 2003. Web. 01 Mar 2021.
Vancouver:
Breukelen Bv. The role of the adenovirus DNA binding protein in DNA replication and recombination. [Internet] [Doctoral dissertation]. University Utrecht; 2003. [cited 2021 Mar 01].
Available from: https://dspace.library.uu.nl/handle/1874/226 ; URN:NBN:NL:UI:10-1874-226 ; 1874/226 ; URN:NBN:NL:UI:10-1874-226 ; https://dspace.library.uu.nl/handle/1874/226.
Council of Science Editors:
Breukelen Bv. The role of the adenovirus DNA binding protein in DNA replication and recombination. [Doctoral Dissertation]. University Utrecht; 2003. Available from: https://dspace.library.uu.nl/handle/1874/226 ; URN:NBN:NL:UI:10-1874-226 ; 1874/226 ; URN:NBN:NL:UI:10-1874-226 ; https://dspace.library.uu.nl/handle/1874/226
13.
Brenkman, A.B. (Arjan Bernard).
Molecular architecture and function of adenovirus DNA polymerase.
Degree: 2002, University Utrecht
URL: https://dspace.library.uu.nl/handle/1874/462
;
URN:NBN:NL:UI:10-1874-462
;
1874/462
;
URN:NBN:NL:UI:10-1874-462
;
https://dspace.library.uu.nl/handle/1874/462
► Central to this thesis is the role of adenovirus DNA polymerase (Ad pol) in adenovirus DNA replication. Ad pol is a member of the family…
(more)
▼ Central to this thesis is the role of adenovirus DNA polymerase (Ad pol) in adenovirus DNA replication. Ad pol is a member of the family B DNA polymerases but belongs to a distinct subclass of polymerases that use a protein as primer. As Ad pol catalyses both the initiation and elongation phases and needs to accomodate both DNA and protein as a primer, it is not surprising that a large number of protein-protein and protein-DNA interactions are involved in efficient replication. Indeed, Ad pol is known to interact with pTP, NFI and DNA, although our understanding of these interactions is limited. In this thesis, these interactions have been studied in greater detail. After an introductory chapter on DNA dependent DNA polymerases and Ad replication, the jumping back mechanism that characterizes the change from initiation to elongation is extensively reviewed in chapter 2. In chapter 3, the highly conserved (I/Y)XGG motif of Ad pol is studied. In chapter 4, the interaction between Ad pol and DNA is further studied by the use of biotinylated oligo-nucleotides with a bulky streptavidin block. Chapter 5 examines the termination of Ad pol on the native TP-containing viral DNA. Finally, in chapter 6 the recruitment of the pTP-pol complex via a direct interaction between Ad pol and NFI is studied in detail.
Subjects/Keywords: protein priming; DNA polymerase; replication; NFI; transcription factor; adenovirus; termination; initiation; pTP; origin
Record Details
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Record Details
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Brenkman, A. B. (. B. (2002). Molecular architecture and function of adenovirus DNA polymerase. (Doctoral Dissertation). University Utrecht. Retrieved from https://dspace.library.uu.nl/handle/1874/462 ; URN:NBN:NL:UI:10-1874-462 ; 1874/462 ; URN:NBN:NL:UI:10-1874-462 ; https://dspace.library.uu.nl/handle/1874/462
Chicago Manual of Style (16th Edition):
Brenkman, A B (Arjan Bernard). “Molecular architecture and function of adenovirus DNA polymerase.” 2002. Doctoral Dissertation, University Utrecht. Accessed March 01, 2021.
https://dspace.library.uu.nl/handle/1874/462 ; URN:NBN:NL:UI:10-1874-462 ; 1874/462 ; URN:NBN:NL:UI:10-1874-462 ; https://dspace.library.uu.nl/handle/1874/462.
MLA Handbook (7th Edition):
Brenkman, A B (Arjan Bernard). “Molecular architecture and function of adenovirus DNA polymerase.” 2002. Web. 01 Mar 2021.
Vancouver:
Brenkman AB(B. Molecular architecture and function of adenovirus DNA polymerase. [Internet] [Doctoral dissertation]. University Utrecht; 2002. [cited 2021 Mar 01].
Available from: https://dspace.library.uu.nl/handle/1874/462 ; URN:NBN:NL:UI:10-1874-462 ; 1874/462 ; URN:NBN:NL:UI:10-1874-462 ; https://dspace.library.uu.nl/handle/1874/462.
Council of Science Editors:
Brenkman AB(B. Molecular architecture and function of adenovirus DNA polymerase. [Doctoral Dissertation]. University Utrecht; 2002. Available from: https://dspace.library.uu.nl/handle/1874/462 ; URN:NBN:NL:UI:10-1874-462 ; 1874/462 ; URN:NBN:NL:UI:10-1874-462 ; https://dspace.library.uu.nl/handle/1874/462

Queensland University of Technology
14.
Hastie, Marcus Lachlan.
In vitro activities of BBTV-REP.
Degree: 2001, Queensland University of Technology
URL: http://eprints.qut.edu.au/37077/
Subjects/Keywords: Banana bunchy top disease; Bananas Diseases and pests; REP; replication associated protein; replication initiator protein; banana bunchy top virus; nanovirus; geminivirus; rolling circle replication; topoisomerase; ATPase; thesis; doctoral
Record Details
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Record Details
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Hastie, M. L. (2001). In vitro activities of BBTV-REP. (Thesis). Queensland University of Technology. Retrieved from http://eprints.qut.edu.au/37077/
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Hastie, Marcus Lachlan. “In vitro activities of BBTV-REP.” 2001. Thesis, Queensland University of Technology. Accessed March 01, 2021.
http://eprints.qut.edu.au/37077/.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Hastie, Marcus Lachlan. “In vitro activities of BBTV-REP.” 2001. Web. 01 Mar 2021.
Vancouver:
Hastie ML. In vitro activities of BBTV-REP. [Internet] [Thesis]. Queensland University of Technology; 2001. [cited 2021 Mar 01].
Available from: http://eprints.qut.edu.au/37077/.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Hastie ML. In vitro activities of BBTV-REP. [Thesis]. Queensland University of Technology; 2001. Available from: http://eprints.qut.edu.au/37077/
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Hong Kong University of Science and Technology
15.
Huang, Yining.
The role of hIpi3 in human DNA replication.
Degree: 2013, Hong Kong University of Science and Technology
URL: http://repository.ust.hk/ir/Record/1783.1-62314
;
https://doi.org/10.14711/thesis-b1254380
;
http://repository.ust.hk/ir/bitstream/1783.1-62314/1/th_redirect.html
► Ipi3 is required for cell viability in Saccharomyces cerevisiae. Yeast Ipi3 has been reported to be an essential component of the Rix1 complex (Rix1-Ipi1-Ipi3) that…
(more)
▼ Ipi3 is required for cell viability in Saccharomyces cerevisiae. Yeast Ipi3 has been reported to be an essential component of the Rix1 complex (Rix1-Ipi1-Ipi3) that is required for the processing of ITS2 sequences from 35S pre-rRNA in pre-60S ribosomal particles and for the initiation of DNA replication by interacting with ORC, MCM, Cdt1 and Cdc6. It has also been suggested that that human Ipi3 homolog plays a role in the assembly of the large ribosomal subunit in a computational analysis of large-scale protein-protein interactions. Human Ipi3 is WDR18 (WD repeat domain 18), which is a member of the WD repeat protein family, and it shares significant homology with the yeast Ipi3; the identity is 22% and similarity is 40%. Since yeast Ipi3 has an important role in the initiation of DNA replication, it is possibly that hIpi3 also functions in the initiation of DNA replication in human cells. We performed several experiments to support the hypothesis that hIpi3 is involved in the control of human DNA replication. First, knockdown of hIpi3 inhibited DNA replication, resulting in defective cell cycle progression. Second, the mRNA and protein levels of hIpi3 fluctuate in the cell cycle, just as some other pre-replicative (pre-RC) proteins do. Third, HA-tagged hIpi3 has been used to perform co-IP assay to identify hIpi3 interacting proteins. The results showed that hMcm7 interacted with hIpi3. Forth, hMcm7 and hCdc6 were reduced from chromatin after hIpi3 silencing, suggesting that hIpi3 is required for the chromatin association of the MCM complex. These results support that hIpi3 plays an important role in DNA replication in human cells.
Subjects/Keywords: DNA replication
; DNA-protein interactions
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APA ·
Chicago ·
MLA ·
Vancouver ·
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Export
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APA (6th Edition):
Huang, Y. (2013). The role of hIpi3 in human DNA replication. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-62314 ; https://doi.org/10.14711/thesis-b1254380 ; http://repository.ust.hk/ir/bitstream/1783.1-62314/1/th_redirect.html
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Huang, Yining. “The role of hIpi3 in human DNA replication.” 2013. Thesis, Hong Kong University of Science and Technology. Accessed March 01, 2021.
http://repository.ust.hk/ir/Record/1783.1-62314 ; https://doi.org/10.14711/thesis-b1254380 ; http://repository.ust.hk/ir/bitstream/1783.1-62314/1/th_redirect.html.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Huang, Yining. “The role of hIpi3 in human DNA replication.” 2013. Web. 01 Mar 2021.
Vancouver:
Huang Y. The role of hIpi3 in human DNA replication. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2013. [cited 2021 Mar 01].
Available from: http://repository.ust.hk/ir/Record/1783.1-62314 ; https://doi.org/10.14711/thesis-b1254380 ; http://repository.ust.hk/ir/bitstream/1783.1-62314/1/th_redirect.html.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Huang Y. The role of hIpi3 in human DNA replication. [Thesis]. Hong Kong University of Science and Technology; 2013. Available from: http://repository.ust.hk/ir/Record/1783.1-62314 ; https://doi.org/10.14711/thesis-b1254380 ; http://repository.ust.hk/ir/bitstream/1783.1-62314/1/th_redirect.html
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Université Paris-Sud – Paris XI
16.
Saïfi, Boubekeur.
Caractérisation de cycC, un nouveau gène impliqué dans le programme de réplication d'Escherichia coli : Characterization of cycC, a new gene involved in the replication program of Escherichia coli.
Degree: Docteur es, Aspects moléculaires et cellulaires de la biologie, 2012, Université Paris-Sud – Paris XI
URL: http://www.theses.fr/2012PA112211
► Dans Escherichia coli la Dam Methyl Transferase (DamMT) est responsable du transfert d’un groupement méthyle sur les adénosines situés au cœur du tétranucléotide GATC; il…
(more)
▼ Dans Escherichia coli la Dam Methyl Transferase (DamMT) est responsable du transfert d’un groupement méthyle sur les adénosines situés au cœur du tétranucléotide GATC; il s’agit donc d’une activité post réplicative. Ainsi, après le passage de la fourche de réplication, le brin d’ADN nouvellement synthétisé est non méthylé – l’ADN est dit hémimethylé. L’ADN reste hémimethylé pendent une brève période - de l’ordre de la minute - avant d’être reméthylé par la DamMT. L’hypothèse de l’implication de la méthylation de l’ADN dans le contrôle général du programme de maintenance de l’ADN repose essentiellement sur cette observation, puisque l’ADN hemimethyle – exception faite de l’origine de réplication et de la région promotrice du gène dnaA – est diagnostique du passage récent de la fourche de réplication. Cette hypothèse, et le criblage phylogénomique qui en a découlé a conduit a l’identification de plusieurs gènes dont les produits sont supposes être impliqués dans la maintenance de l’ADN. yjaG est l’un de ces gènes. Il a été renomme cycC en raison des dérèglements de la progression du cycle cellulaire associés a un mutant nul de ce gène. L’étude effectuée au cours de ma thèse s’attachera à expliquer l’état actuel de nos connaissances sur la protéine CycC et de son implication dans le processus de réplication de l’ADN. Nos résultats montrent que la protéine CycC est impliquée dans la processivité de la réplication lorsqu’il y a un dommage au niveau de l’ADN. CycC spécifie une activité qui conduit à freiner les fourches de réplication, afin de prévenir des avortements des réplisomes. La surexpression de CycC bloque l’initiation de la réplication entre l’ouverture de la molécule d’ADN et le chargement de l’hélicase réplicative. Nous proposons que CycC interagisse avec le complexe réplicative et ralentit les fourches de réplication. Ce ralentissement prévient de nouvelles collisions lorsque les cellules sont dans des conditions de stress-qui cause des arrêts de la réplication.
In Escherichia coli the Dam Methyl Transferase (DamMT) is responsible for the transfer of a methyl group on the adenosine located in tetranucleotide GATC, so this is a post-replicative activity. Thus, after the passage of the replication fork, the newly synthesized DNA strand is unmethylated - DNA is called hemimethylated. DNA remains hemimethylated in a brief period - about a minute - before being reméthylé by DamMT. The hypothesis of the involvement of DNA methylation in the general control of the maintenance program of the DNA is essentially on this observation, since the hemimethylated DNA - except the origin of replication and the region dnaA gene promoter - is diagnostic of the recent passage of the replication fork. This assumption and phylogenomics screening has led to the identification of several genes whose protein are supposed to be involved in the maintenance of DNA. yjaG is one of these genes. It was renamed cycC, the cell cycle progression is deregulated with a null mutant of this gene. The study in my thesis will focus on explaining…
Advisors/Committee Members: Ferat, Jean-Luc (thesis director).
Subjects/Keywords: Initiation de la réplication; Réactivation des fourches; Processivité de la réplication; Initiation of replication; Forks reactivation; Processivity of replication
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Saïfi, B. (2012). Caractérisation de cycC, un nouveau gène impliqué dans le programme de réplication d'Escherichia coli : Characterization of cycC, a new gene involved in the replication program of Escherichia coli. (Doctoral Dissertation). Université Paris-Sud – Paris XI. Retrieved from http://www.theses.fr/2012PA112211
Chicago Manual of Style (16th Edition):
Saïfi, Boubekeur. “Caractérisation de cycC, un nouveau gène impliqué dans le programme de réplication d'Escherichia coli : Characterization of cycC, a new gene involved in the replication program of Escherichia coli.” 2012. Doctoral Dissertation, Université Paris-Sud – Paris XI. Accessed March 01, 2021.
http://www.theses.fr/2012PA112211.
MLA Handbook (7th Edition):
Saïfi, Boubekeur. “Caractérisation de cycC, un nouveau gène impliqué dans le programme de réplication d'Escherichia coli : Characterization of cycC, a new gene involved in the replication program of Escherichia coli.” 2012. Web. 01 Mar 2021.
Vancouver:
Saïfi B. Caractérisation de cycC, un nouveau gène impliqué dans le programme de réplication d'Escherichia coli : Characterization of cycC, a new gene involved in the replication program of Escherichia coli. [Internet] [Doctoral dissertation]. Université Paris-Sud – Paris XI; 2012. [cited 2021 Mar 01].
Available from: http://www.theses.fr/2012PA112211.
Council of Science Editors:
Saïfi B. Caractérisation de cycC, un nouveau gène impliqué dans le programme de réplication d'Escherichia coli : Characterization of cycC, a new gene involved in the replication program of Escherichia coli. [Doctoral Dissertation]. Université Paris-Sud – Paris XI; 2012. Available from: http://www.theses.fr/2012PA112211

University of Minnesota
17.
Lovendahl, Klaus.
Adaptation of HUH endonucleases for protein-DNA conjugation.
Degree: PhD, Biochemistry, Molecular Bio, and Biophysics, 2018, University of Minnesota
URL: http://hdl.handle.net/11299/201685
► The conjugation of proteins to DNA is a useful technique for basic research and medicine. Current methods for conjugation are limited in both specificity and…
(more)
▼ The conjugation of proteins to DNA is a useful technique for basic research and medicine. Current methods for conjugation are limited in both specificity and efficiency, as they generally depend on nonspecific exogenous chemical crosslinkers or reversible DNA-binding proteins. In this work we have adapted a natural protein domain, known as the HUH domain, which targets DNA and forms a covalent phosphotyrosine adduct with the DNA backbone. We show that HUH domains react efficiently with specific sequences of unmodified single-stranded DNA, and we have identified five proteins which react orthogonally with distinct DNA sequences. We demonstrate a number of applications for this technology. HUH fusion proteins can be use to label proteins both in vitro and in cultured mammalian cells with excellent specificity. Fusing an HUH domain to the gene-editing Cas9 protein enhances the integration of a single-stranded donor DNA template in mammalian cells. Surface-adhered HUH protein can be used to tether DNA molecules for sensitive measurements in a single- molecule magnetic tweezer. Additionally, we show that an HUH domain protein can be rationally mutated to increase its stability and reactivity. This work presents a novel technology with wide applicability and presents several avenues for future work.
Subjects/Keywords: dna barcoding; huh; magnetic tweezers; protein-dna conjugation; relaxase; rep; replicase
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Lovendahl, K. (2018). Adaptation of HUH endonucleases for protein-DNA conjugation. (Doctoral Dissertation). University of Minnesota. Retrieved from http://hdl.handle.net/11299/201685
Chicago Manual of Style (16th Edition):
Lovendahl, Klaus. “Adaptation of HUH endonucleases for protein-DNA conjugation.” 2018. Doctoral Dissertation, University of Minnesota. Accessed March 01, 2021.
http://hdl.handle.net/11299/201685.
MLA Handbook (7th Edition):
Lovendahl, Klaus. “Adaptation of HUH endonucleases for protein-DNA conjugation.” 2018. Web. 01 Mar 2021.
Vancouver:
Lovendahl K. Adaptation of HUH endonucleases for protein-DNA conjugation. [Internet] [Doctoral dissertation]. University of Minnesota; 2018. [cited 2021 Mar 01].
Available from: http://hdl.handle.net/11299/201685.
Council of Science Editors:
Lovendahl K. Adaptation of HUH endonucleases for protein-DNA conjugation. [Doctoral Dissertation]. University of Minnesota; 2018. Available from: http://hdl.handle.net/11299/201685

University of California – San Diego
18.
Li, Dongyang.
DNA replication and cell size control in Escherichia coli.
Degree: Biology, 2018, University of California – San Diego
URL: http://www.escholarship.org/uc/item/5tt038j7
► The defining feature of living organisms is their capacity to reproduce and pass on the genetic information so that their progeny can flourish. For bacteria,…
(more)
▼ The defining feature of living organisms is their capacity to reproduce and pass on the genetic information so that their progeny can flourish. For bacteria, reproduction is a feat by itself – Escherichia coli cells cultured in optimal conditions grow rapidly and divide about every 20 minutes. In other words, the cell has to replicate all cellular contents, and be ready to divide evenly into two daughter cells within this 20 minutes. Biosynthesis of new cellular materials, e.g. proteins, nucleic acis, lipids and other metabolites accumulate and roughly doubles after every generation. Notably, the deoxyribonucleic acid (DNA) encodes genetic informationand needs to be duplicated in order to faithfully pass on this information to the progeny. This process of DNA replication in the cell needs to dynamically adapt to fluctuation in growth condition and cellular physiology. Such coordination is controlled at the first step of replcation – the initiation of replication. In this thesis, I presented the development of methods for measuring DNA replication duration (replication period), the quantitative relationship between DNA replication and cell size as well as the mechanism of replication initiation. DNA replication measurement laid the foundation of studying the quantitative relationship between cell size and DNA replication. A general growth law was proposed to describe cell size regulation in light of three physiological variables including biosynthesis rate, cell cycle progression and replicaiton initiation. Of the three variables, the mass when cell initiates replication (initiation mass) remains invariant despite a wide spectrum of antibiotics or growth limitation challenge. This invariant initiation mass called into question about the mechanism of initiation to achieve such constancy. We proposed a simple threshold model to explain how cells can maintain a invariant initiation mass by regulating the expression of initiation regulators (initiators). The initiaiton mass is inversely proportional to the initiator levels, which is held constant. Experimental evidence was provided to test our model prediction.
Subjects/Keywords: Biology; Microbiology; Biophysics; bacterial physiology; cell size; DNA replication; Escherichia coli; replication initiation
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Li, D. (2018). DNA replication and cell size control in Escherichia coli. (Thesis). University of California – San Diego. Retrieved from http://www.escholarship.org/uc/item/5tt038j7
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Li, Dongyang. “DNA replication and cell size control in Escherichia coli.” 2018. Thesis, University of California – San Diego. Accessed March 01, 2021.
http://www.escholarship.org/uc/item/5tt038j7.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Li, Dongyang. “DNA replication and cell size control in Escherichia coli.” 2018. Web. 01 Mar 2021.
Vancouver:
Li D. DNA replication and cell size control in Escherichia coli. [Internet] [Thesis]. University of California – San Diego; 2018. [cited 2021 Mar 01].
Available from: http://www.escholarship.org/uc/item/5tt038j7.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Li D. DNA replication and cell size control in Escherichia coli. [Thesis]. University of California – San Diego; 2018. Available from: http://www.escholarship.org/uc/item/5tt038j7
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Cambridge
19.
Jatikusumo, Vincentius Aji.
Treslin and its role in the assembly of the replicative DNA helicase.
Degree: PhD, 2020, University of Cambridge
URL: https://www.repository.cam.ac.uk/handle/1810/301381
► DNA replication is an essential biochemical process that underlies genetic inheritance. In eukaryotic cells, this process is carried out by a multi-subunit protein complex called…
(more)
▼ DNA replication is an essential biochemical process that underlies genetic inheritance.
In eukaryotic cells, this process is carried out by a multi-subunit protein complex called
replisome. The core of replisome is made up of six-subunit protein ring Mcm2–7, which
contains weak DNA helicase activity. In order to fully activate the helicase activity, protein
co-activators of Cdc45 and GINS have to be recruited to assemble a replicative DNA helicase
called the CMG (Cdc45-Mcm2–7-GINS) complex. The active CMG subsequently unwinds
the parental DNA duplex to provide single-stranded DNA templates for replicative DNA
polymerases. The precise mechanism for CMG assembly and activation is still poorly
understood. Recent studies using model organisms suggested the importance of protein
called Sld3/Treslin for CMG assembly.
The aim of the project was to understand in detail how human Treslin participates in
the assembly of the CMG helicase. The interactions of Treslin with Cdc45, Mcm2–7, and
DNA were characterised by a series of biochemical, biophysical, and structural biology
experiments.
Cdc45–Treslin interaction was shown to be conserved from budding yeast to human, in
which it is mediated by a domain called Sld3/Treslin Homology Domain (SHD). However,
human Treslin contains an additional Cdc45-binding site—next to the C-terminus of SHD—
in an intrinsically disordered region referred to as Treslin ’extension’ (Treslinext). Treslinext
was also demonstrated to interact with Mcm2–7 ring and DNA. S-phase Cyclin-Dependent
Kinase (S-CDK) appeared to regulate Treslin’s interaction with Cdc45 and Mcm2–7, in
which it targets a number of potential S-CDK phosphorylation sites present in Treslinext.
As a part of this project, low-resolution Cdc45–Treslin and medium-resolution of MCM
single hexamer 3D maps were obtained through single-particle cryo-electron microscopy
(cryo-EM) analyses.
The results provide molecular basis for Treslin’s role in the assembly of the CMG
complex. Treslin acts as a molecular chaperone for Cdc45 recruitment to the DNA-bound
Mcm2-7 ring. Treslin’s role during CMG assembly may involve its binding ability to the
Mcm2–7 and DNA. Furthermore, the regulatory role of S-CDK in Treslin’s interactions with
Cdc45 and Mcm2–7 suggests a link of the CMG assembly control to the cell cycle in human.
Subjects/Keywords: Treslin; DNA replication; CryoEM; Biochemistry; CMG Helicase; MCM; Cdc45; DNA replication initiation; Replisome
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Jatikusumo, V. A. (2020). Treslin and its role in the assembly of the replicative DNA helicase. (Doctoral Dissertation). University of Cambridge. Retrieved from https://www.repository.cam.ac.uk/handle/1810/301381
Chicago Manual of Style (16th Edition):
Jatikusumo, Vincentius Aji. “Treslin and its role in the assembly of the replicative DNA helicase.” 2020. Doctoral Dissertation, University of Cambridge. Accessed March 01, 2021.
https://www.repository.cam.ac.uk/handle/1810/301381.
MLA Handbook (7th Edition):
Jatikusumo, Vincentius Aji. “Treslin and its role in the assembly of the replicative DNA helicase.” 2020. Web. 01 Mar 2021.
Vancouver:
Jatikusumo VA. Treslin and its role in the assembly of the replicative DNA helicase. [Internet] [Doctoral dissertation]. University of Cambridge; 2020. [cited 2021 Mar 01].
Available from: https://www.repository.cam.ac.uk/handle/1810/301381.
Council of Science Editors:
Jatikusumo VA. Treslin and its role in the assembly of the replicative DNA helicase. [Doctoral Dissertation]. University of Cambridge; 2020. Available from: https://www.repository.cam.ac.uk/handle/1810/301381

University of Cambridge
20.
Jatikusumo, Vincentius Aji.
Treslin and its role in the assembly of the replicative DNA helicase.
Degree: PhD, 2020, University of Cambridge
URL: https://doi.org/10.17863/CAM.48462
;
https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.801694
► DNA replication is an essential biochemical process that underlies genetic inheritance. In eukaryotic cells, this process is carried out by a multi-subunit protein complex called…
(more)
▼ DNA replication is an essential biochemical process that underlies genetic inheritance. In eukaryotic cells, this process is carried out by a multi-subunit protein complex called replisome. The core of replisome is made up of six-subunit protein ring Mcm2–7, which contains weak DNA helicase activity. In order to fully activate the helicase activity, protein co-activators of Cdc45 and GINS have to be recruited to assemble a replicative DNA helicase called the CMG (Cdc45-Mcm2–7-GINS) complex. The active CMG subsequently unwinds the parental DNA duplex to provide single-stranded DNA templates for replicative DNA polymerases. The precise mechanism for CMG assembly and activation is still poorly understood. Recent studies using model organisms suggested the importance of protein called Sld3/Treslin for CMG assembly. The aim of the project was to understand in detail how human Treslin participates in the assembly of the CMG helicase. The interactions of Treslin with Cdc45, Mcm2–7, and DNA were characterised by a series of biochemical, biophysical, and structural biology experiments. Cdc45–Treslin interaction was shown to be conserved from budding yeast to human, in which it is mediated by a domain called Sld3/Treslin Homology Domain (SHD). However, human Treslin contains an additional Cdc45-binding site—next to the C-terminus of SHD— in an intrinsically disordered region referred to as Treslin ’extension’ (Treslinext). Treslinext was also demonstrated to interact with Mcm2–7 ring and DNA. S-phase Cyclin-Dependent Kinase (S-CDK) appeared to regulate Treslin’s interaction with Cdc45 and Mcm2–7, in which it targets a number of potential S-CDK phosphorylation sites present in Treslinext. As a part of this project, low-resolution Cdc45–Treslin and medium-resolution of MCM single hexamer 3D maps were obtained through single-particle cryo-electron microscopy (cryo-EM) analyses. The results provide molecular basis for Treslin’s role in the assembly of the CMG complex. Treslin acts as a molecular chaperone for Cdc45 recruitment to the DNA-bound Mcm2-7 ring. Treslin’s role during CMG assembly may involve its binding ability to the Mcm2–7 and DNA. Furthermore, the regulatory role of S-CDK in Treslin’s interactions with Cdc45 and Mcm2–7 suggests a link of the CMG assembly control to the cell cycle in human.
Subjects/Keywords: Treslin; DNA replication; CryoEM; Biochemistry; CMG Helicase; MCM; Cdc45; DNA replication initiation; Replisome
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Record Details
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Jatikusumo, V. A. (2020). Treslin and its role in the assembly of the replicative DNA helicase. (Doctoral Dissertation). University of Cambridge. Retrieved from https://doi.org/10.17863/CAM.48462 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.801694
Chicago Manual of Style (16th Edition):
Jatikusumo, Vincentius Aji. “Treslin and its role in the assembly of the replicative DNA helicase.” 2020. Doctoral Dissertation, University of Cambridge. Accessed March 01, 2021.
https://doi.org/10.17863/CAM.48462 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.801694.
MLA Handbook (7th Edition):
Jatikusumo, Vincentius Aji. “Treslin and its role in the assembly of the replicative DNA helicase.” 2020. Web. 01 Mar 2021.
Vancouver:
Jatikusumo VA. Treslin and its role in the assembly of the replicative DNA helicase. [Internet] [Doctoral dissertation]. University of Cambridge; 2020. [cited 2021 Mar 01].
Available from: https://doi.org/10.17863/CAM.48462 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.801694.
Council of Science Editors:
Jatikusumo VA. Treslin and its role in the assembly of the replicative DNA helicase. [Doctoral Dissertation]. University of Cambridge; 2020. Available from: https://doi.org/10.17863/CAM.48462 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.801694

University of Waterloo
21.
Ramer, Matthew.
Characterization of the association of Dbf4 and Cdc7 with Mcm2-7 and chromatin in Saccharomyces cerevisiae.
Degree: 2012, University of Waterloo
URL: http://hdl.handle.net/10012/6429
► Initiation of DNA replication requires the action of the Dbf4/Cdc7 kinase complex (DDK) which is also a phosphorylation target of Rad53 kinase in the S-phase…
(more)
▼ Initiation of DNA replication requires the action of the Dbf4/Cdc7 kinase complex (DDK) which is also a phosphorylation target of Rad53 kinase in the S-phase checkpoint. DDK is thought to trigger DNA replication by phosphorylating members of the Mcm2-7 complex present at origins of replication. While DDK phosphorylation sites have been identified on Mcm2-7, the contributions made by Dbf4 and Cdc7 to the targeting of the complex have not been established. DDK has also been implicated in the S-phase checkpoint response since it is removed from chromatin in a Rad53-dependent manner.
The interaction of Dbf4 and Cdc7 with each of the Mcm2-7 subunits was assessed and showed an interaction between Dbf4 and Mcm2 and Mcm6, while interactions between Cdc7 and Mcm4 and Mcm5 were observed. Mutations in Mcm2 and Mcm4 that disrupt the interactions with Dbf4 or Cdc7 showed modest growth impairment and compromised DNA replication, while simultaneous abrogation of both interactions resulted in lethality. Strains overexpressing Mcm2 or Mcm4 were sensitive to genotoxic agents, while overexpression of Mcm2 in a Mcm4Δ175-333 strain background resulted in a severe growth impairment as well as sensitivity to genotoxic stress. ChIP analysis revealed the possibility of Dbf4/Cdc7 localization to origin flanking regions through most of S-phase, which may redistribute to origins at the time of firing.
Fluorescence microscopy of Mcm2 and Dbf4 in S-phase seem to show a punctate pattern of staining, consistent with these factors’ localization to ‘replication factories.’ By using a Dbf4ΔN mutant, the N-motif was shown to be required for the Rad53-mediated removal of Dbf4 from chromatin under checkpoint conditions. Initial optimization of a DNA combing protocol was also performed, which along with Dbf4ΔN mutant and the fluorescently-epitope tagged strains, will be useful tools for evaluating a role for DDK in the S-phase checkpoint response.
Altered levels of DNA replication factors have been implicated in many human cancers. The data presented in this study provide novel insight into the normal process of the initiation of DNA replication which can be applied to research involving higher eukaryotes, including humans, and can serve as a benchmark for comparison with the cancer phenotype.
Subjects/Keywords: Cell cycle; Initiation of DNA Replication; S-phase checkpoint
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Ramer, M. (2012). Characterization of the association of Dbf4 and Cdc7 with Mcm2-7 and chromatin in Saccharomyces cerevisiae. (Thesis). University of Waterloo. Retrieved from http://hdl.handle.net/10012/6429
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Ramer, Matthew. “Characterization of the association of Dbf4 and Cdc7 with Mcm2-7 and chromatin in Saccharomyces cerevisiae.” 2012. Thesis, University of Waterloo. Accessed March 01, 2021.
http://hdl.handle.net/10012/6429.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Ramer, Matthew. “Characterization of the association of Dbf4 and Cdc7 with Mcm2-7 and chromatin in Saccharomyces cerevisiae.” 2012. Web. 01 Mar 2021.
Vancouver:
Ramer M. Characterization of the association of Dbf4 and Cdc7 with Mcm2-7 and chromatin in Saccharomyces cerevisiae. [Internet] [Thesis]. University of Waterloo; 2012. [cited 2021 Mar 01].
Available from: http://hdl.handle.net/10012/6429.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Ramer M. Characterization of the association of Dbf4 and Cdc7 with Mcm2-7 and chromatin in Saccharomyces cerevisiae. [Thesis]. University of Waterloo; 2012. Available from: http://hdl.handle.net/10012/6429
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Universiteit Utrecht
22.
Brenkman, A.B. (Arjan Bernard).
Molecular architecture and function of adenovirus DNA polymerase.
Degree: 2002, Universiteit Utrecht
URL: http://dspace.library.uu.nl:8080/handle/1874/462
► Central to this thesis is the role of adenovirus DNA polymerase (Ad pol) in adenovirus DNA replication. Ad pol is a member of the family…
(more)
▼ Central to this thesis is the role of adenovirus DNA polymerase (Ad pol) in adenovirus DNA replication. Ad pol is a member of the family B DNA polymerases but belongs to a distinct subclass of polymerases that use a protein as primer. As Ad pol catalyses both the initiation and elongation phases and needs to accomodate both DNA and protein as a primer, it is not surprising that a large number of protein-protein and protein-DNA interactions are involved in efficient replication. Indeed, Ad pol is known to interact with pTP, NFI and DNA, although our understanding of these interactions is limited. In this thesis, these interactions have been studied in greater detail. After an introductory chapter on DNA dependent DNA polymerases and Ad replication, the jumping back mechanism that characterizes the change from initiation to elongation is extensively reviewed in chapter 2. In chapter 3, the highly conserved (I/Y)XGG motif of Ad pol is studied. In chapter 4, the interaction between Ad pol and DNA is further studied by the use of biotinylated oligo-nucleotides with a bulky streptavidin block. Chapter 5 examines the termination of Ad pol on the native TP-containing viral DNA. Finally, in chapter 6 the recruitment of the pTP-pol complex via a direct interaction between Ad pol and NFI is studied in detail.
Subjects/Keywords: Geneeskunde; protein priming; DNA polymerase; replication; NFI; transcription factor; adenovirus; termination; initiation; pTP; origin
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APA ·
Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
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APA (6th Edition):
Brenkman, A. B. (. B. (2002). Molecular architecture and function of adenovirus DNA polymerase. (Doctoral Dissertation). Universiteit Utrecht. Retrieved from http://dspace.library.uu.nl:8080/handle/1874/462
Chicago Manual of Style (16th Edition):
Brenkman, A B (Arjan Bernard). “Molecular architecture and function of adenovirus DNA polymerase.” 2002. Doctoral Dissertation, Universiteit Utrecht. Accessed March 01, 2021.
http://dspace.library.uu.nl:8080/handle/1874/462.
MLA Handbook (7th Edition):
Brenkman, A B (Arjan Bernard). “Molecular architecture and function of adenovirus DNA polymerase.” 2002. Web. 01 Mar 2021.
Vancouver:
Brenkman AB(B. Molecular architecture and function of adenovirus DNA polymerase. [Internet] [Doctoral dissertation]. Universiteit Utrecht; 2002. [cited 2021 Mar 01].
Available from: http://dspace.library.uu.nl:8080/handle/1874/462.
Council of Science Editors:
Brenkman AB(B. Molecular architecture and function of adenovirus DNA polymerase. [Doctoral Dissertation]. Universiteit Utrecht; 2002. Available from: http://dspace.library.uu.nl:8080/handle/1874/462

Vanderbilt University
23.
Guler, Gulfem Dilek.
Human DNA helicase B in replication fork surveillance and replication stress recovery.
Degree: PhD, Biological Sciences, 2012, Vanderbilt University
URL: http://hdl.handle.net/1803/15350
► Correct and faithful genome duplication is crucial for preserving genomic integrity. Genome duplication is, therefore, highly regulated through a complex network of proteins that accomplish…
(more)
▼ Correct and faithful genome duplication is crucial for preserving genomic integrity. Genome duplication is, therefore, highly regulated through a complex network of proteins that accomplish DNA
replication in addition to DNA repair, as needed. Human DNA helicase B (HDHB) was previously proposed to function in DNA
replication and DNA damage response. Work presented in this dissertation aimed to gain insight into the cellular pathway(s) HDHB participates in, particularly in response to
replication stress. Contrary to previous studies where helicase-dead DHB inhibited DNA
replication, we did not observe any cell cycle or DNA
replication defect in HDHB silenced cells, suggesting that HDHB activity in DNA
replication can be compensated by other proteins in the absence of HDHB. On the other hand, HDHB silencing disrupted efficient recovery from
replication stress. HDHB silenced cells were capable of activating checkpoint signaling, suggesting a checkpoint-independent or downstream pathway for HDHB function. Consistent with a role in
replication stress response, HDHB accumulated on chromatin upon UV, hydroxyurea and camptothecin exposure in a time- and dose-dependent manner. We found that genotoxin-induced HDHB accumulation on chromatin is RPA-dependent. Biophysical and biochemical characterization revealed a direct physical interaction between RPA70N basic cleft and a conserved acidic motif in HDHB helicase domain. The interaction interface between HDHB and RPA70N is strikingly similar to the previously reported interaction interfaces of RPA70N and p53, ATRIP, Rad9 or Mre11. Site-directed mutagenesis of the HDHB-RPA70N interaction interface demonstrated its contribution to HDHB recruitment to chromatin upon genotoxin exposure. These results altogether implicate HDHB in
replication stress response.
Advisors/Committee Members: Ellen Fanning (committee member), Daniel Kaplan (committee member), David Cortez (committee member), Walter J. Chazin (committee member), James G. Patton (Committee Chair).
Subjects/Keywords: Replication protein A; RPA; DNA helicase; DNA replication; DNA repair; replication stress; HelB; HDHB
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Guler, G. D. (2012). Human DNA helicase B in replication fork surveillance and replication stress recovery. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/15350
Chicago Manual of Style (16th Edition):
Guler, Gulfem Dilek. “Human DNA helicase B in replication fork surveillance and replication stress recovery.” 2012. Doctoral Dissertation, Vanderbilt University. Accessed March 01, 2021.
http://hdl.handle.net/1803/15350.
MLA Handbook (7th Edition):
Guler, Gulfem Dilek. “Human DNA helicase B in replication fork surveillance and replication stress recovery.” 2012. Web. 01 Mar 2021.
Vancouver:
Guler GD. Human DNA helicase B in replication fork surveillance and replication stress recovery. [Internet] [Doctoral dissertation]. Vanderbilt University; 2012. [cited 2021 Mar 01].
Available from: http://hdl.handle.net/1803/15350.
Council of Science Editors:
Guler GD. Human DNA helicase B in replication fork surveillance and replication stress recovery. [Doctoral Dissertation]. Vanderbilt University; 2012. Available from: http://hdl.handle.net/1803/15350

Queensland University of Technology
24.
Chanson, Aurelie Heitiare.
Recombinant protein production using a Tobacco yellow dwarf virus-based episomal expression vector : control of Rep activity.
Degree: 2009, Queensland University of Technology
URL: https://eprints.qut.edu.au/30290/
► Over the past decade, plants have been used as expression hosts for the production of pharmaceutically important and commercially valuable proteins. Plants offer many advantages…
(more)
▼ Over the past decade, plants have been used as expression hosts for the production of pharmaceutically important and commercially valuable proteins. Plants offer many advantages over other expression systems such as lower production costs, rapid scale up of production, similar post-translational modification as animals and the low likelihood of contamination with animal pathogens, microbial toxins or oncogenic sequences. However, improving recombinant protein yield remains one of the greatest challenges to molecular farming. In-Plant Activation (InPAct) is a newly developed technology that offers activatable and high-level expression of heterologous proteins in plants. InPAct vectors contain the geminivirus cis elements essential for rolling circle replication (RCR) and are arranged such that the gene of interest is only expressed in the presence of the cognate viral replication-associated protein (Rep). The expression of Rep in planta may be controlled by a tissue-specific, developmentally regulated or chemically inducible promoter such that heterologous protein accumulation can be spatially and temporally controlled. One of the challenges for the successful exploitation of InPAct technology is the control of Rep expression as even very low levels of this protein can reduce transformation efficiency, cause abnormal phenotypes and premature activation of the InPAct vector in regenerated plants. Tight regulation over transgene expression is also essential if expressing cytotoxic products. Unfortunately, many tissue-specific and inducible promoters are unsuitable for controlling expression of Rep due to low basal activity in the absence of inducer or in tissues other than the target tissue. This PhD aimed to control Rep activity through the production of single chain variable fragments (scFvs) specific to the motif III of Tobacco yellow dwarf virus (TbYDV) Rep. Due to the important role played by the conserved motif III in the RCR, it was postulated that such scFvs can be used to neutralise the activity of the low amount of Rep expressed from a “leaky” inducible promoter, thus preventing activation of the TbYDV-based InPAct vector until intentional induction. Such scFvs could also offer the potential to confer partial or complete resistance to TbYDV, and possibly heterologous viruses as motif III is conserved between geminiviruses. Studies were first undertaken to determine the levels of TbYDV Rep and TbYDV replication-associated protein A (RepA) required for optimal transgene expression from a TbYDV-based InPAct vector. Transient assays in a non-regenerable Nicotiana tabacum (NT-1) cell line were undertaken using a TbYDV-based InPAct vector containing the uidA reporter gene (encoding GUS) in combination with TbYDV Rep and RepA under the control of promoters with high (CaMV 35S) or low (Banana bunchy top virus DNA-R, BT1) activity. The replication enhancer protein of Tomato leaf curl begomovirus (ToLCV), REn, was also used in some co-bombardment experiments to examine whether RepA could be substituted by a replication…
Subjects/Keywords: recombinant protein production; tobacco yellow dwarf virus; episomal expression vector; Rep activity
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Chanson, A. H. (2009). Recombinant protein production using a Tobacco yellow dwarf virus-based episomal expression vector : control of Rep activity. (Thesis). Queensland University of Technology. Retrieved from https://eprints.qut.edu.au/30290/
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Chanson, Aurelie Heitiare. “Recombinant protein production using a Tobacco yellow dwarf virus-based episomal expression vector : control of Rep activity.” 2009. Thesis, Queensland University of Technology. Accessed March 01, 2021.
https://eprints.qut.edu.au/30290/.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Chanson, Aurelie Heitiare. “Recombinant protein production using a Tobacco yellow dwarf virus-based episomal expression vector : control of Rep activity.” 2009. Web. 01 Mar 2021.
Vancouver:
Chanson AH. Recombinant protein production using a Tobacco yellow dwarf virus-based episomal expression vector : control of Rep activity. [Internet] [Thesis]. Queensland University of Technology; 2009. [cited 2021 Mar 01].
Available from: https://eprints.qut.edu.au/30290/.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Chanson AH. Recombinant protein production using a Tobacco yellow dwarf virus-based episomal expression vector : control of Rep activity. [Thesis]. Queensland University of Technology; 2009. Available from: https://eprints.qut.edu.au/30290/
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Université Paris-Sud – Paris XI
25.
Graindorge, Dany.
Effets du rayonnement ultraviolet a sur la réplication de l’adn chez les eucaryotes supérieurs : Effects of ultraviolet radiation on the replication of DNA in higher eukaryotes.
Degree: Docteur es, Biologie cellulaire et moléculaire, 2012, Université Paris-Sud – Paris XI
URL: http://www.theses.fr/2012PA11T056
► Le rayonnement ultraviolet (UV) émis par le soleil et qui atteint la peau de chaque individu est composé majoritairement de photons UVA (λ de 315…
(more)
▼ Le rayonnement ultraviolet (UV) émis par le soleil et qui atteint la peau de chaque individu est composé majoritairement de photons UVA (λ de 315 à 400 nm), le reste (5 à 10 %) étant composé d’UVB les plus longs (λ de 300 à 315 nm), car les radiations de longueur d’onde 300nm, c’est-à-dire les plus toxiques en terme de santé humaine, sont absorbées par la couche d’ozone stratosphérique. Contrairement aux UVB, les radiations UVA sont faiblement absorbées par l’ADN et de fait, génèrent peu de dimères cyclobutaniques de pyrimidines. Néanmoins, un des problèmes majeurs posés par une exposition aux UVA tient à ce que ce rayonnement excite certains composés endogènes photosensibles, inducteurs de la production d’espèces réactives de l’oxygène (ROS) qui peuvent alors endommager les composants cellulaires tels que les lipides,les acides nucléiques et les protéines. De ce fait, si les UVB restent le facteur étiologique majeur contribuant à la cancérogenèse cutanée photoinduite, un rôle des UVA, via la production de ROS, semble également émerger. Des précédents travaux obtenus au laboratoire ont montré que le rayonnement UVA ralentit la réplication de l’ADN, indépendamment de l’activation des points de contrôle du cycle cellulaire. Les auteurs ont émis l’hypothèse que les UVA, via l’oxydation des protéines, pouvaient altérer la machinerie de réplication. Mon travail de thèse a donc consisté à tenter de préciser le mécanisme qui gouverne ce retard de la réplication de l’ADN induit par les UVA dans les cellules de mammifères.Pour étudier au niveau moléculaire les effets des UVA sur la réplication, nous avons tout d’abord mis en place et utilisé au laboratoire la technique du peignage moléculaire (DNA combing) qui permet de mesurer divers paramètres de la réplication. Ainsi, nous montrons que le rayonnement UVA inhibe immédiatement et transitoirement les vitesses de fourches alors que l’inhibition sur l’
initiation des origines est plus prolongée. Dans le cadre d’une collaboration, nous montrons également que les radiations UVA induisent une diminution modeste et transitoire du pool de dNTPs intracellulaires. La complémentation en ribonucléosides ne semble pas suffisante pour restaurer une vélocité normale de fourches immédiatement après UVA, ni la réplication dans sa totalité. En parallèle, nous observons l’oxydation réversible de la sous-unité R1 de la ribonucléotide réductase impliquée dans la biosynthèse des dNTPs. Bien que cette oxydation ne puisse expliquer la baisse transitoire du pool de nucléotides après UVA, nous ne pouvons pas exclure que d’autres formes d’oxydation de la RNR puissent affecter son activité.La présence d’azide de sodium (NaN3) au cours de l’irradiation UVA prévient le retard réplicatif, limite l’oxydation de la sous-unité R1 et la diminution du pool de dNTPs, ce qui démontre que ce retard de réplication est totalement dépendant des ROS, principalement de l’oxygène singulet généré pendant l’irradiation.L’ensemble de nos résultats indiquent que les UVA affectent le processus de réplication en modifiant non…
Advisors/Committee Members: Sage, Evelyne (thesis director).
Subjects/Keywords: UVA; Stress oxydant; Réplication; Élongation; Initiation,; DNTPs; Ribonucléotide réductase; UVA; Oxidative stress; DNA replication; Elongation; Initiation; DNTPs; RRibonucleotide reductase.
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Graindorge, D. (2012). Effets du rayonnement ultraviolet a sur la réplication de l’adn chez les eucaryotes supérieurs : Effects of ultraviolet radiation on the replication of DNA in higher eukaryotes. (Doctoral Dissertation). Université Paris-Sud – Paris XI. Retrieved from http://www.theses.fr/2012PA11T056
Chicago Manual of Style (16th Edition):
Graindorge, Dany. “Effets du rayonnement ultraviolet a sur la réplication de l’adn chez les eucaryotes supérieurs : Effects of ultraviolet radiation on the replication of DNA in higher eukaryotes.” 2012. Doctoral Dissertation, Université Paris-Sud – Paris XI. Accessed March 01, 2021.
http://www.theses.fr/2012PA11T056.
MLA Handbook (7th Edition):
Graindorge, Dany. “Effets du rayonnement ultraviolet a sur la réplication de l’adn chez les eucaryotes supérieurs : Effects of ultraviolet radiation on the replication of DNA in higher eukaryotes.” 2012. Web. 01 Mar 2021.
Vancouver:
Graindorge D. Effets du rayonnement ultraviolet a sur la réplication de l’adn chez les eucaryotes supérieurs : Effects of ultraviolet radiation on the replication of DNA in higher eukaryotes. [Internet] [Doctoral dissertation]. Université Paris-Sud – Paris XI; 2012. [cited 2021 Mar 01].
Available from: http://www.theses.fr/2012PA11T056.
Council of Science Editors:
Graindorge D. Effets du rayonnement ultraviolet a sur la réplication de l’adn chez les eucaryotes supérieurs : Effects of ultraviolet radiation on the replication of DNA in higher eukaryotes. [Doctoral Dissertation]. Université Paris-Sud – Paris XI; 2012. Available from: http://www.theses.fr/2012PA11T056

Hong Kong University of Science and Technology
26.
Amin, Aftab.
Studies of human and budding yeast DNA replication initiation proteins.
Degree: 2016, Hong Kong University of Science and Technology
URL: http://repository.ust.hk/ir/Record/1783.1-86342
;
https://doi.org/10.14711/thesis-b1610639
;
http://repository.ust.hk/ir/bitstream/1783.1-86342/1/th_redirect.html
► DNA replication is a stringently regulated cellular process. In proliferating normal cells, replication initiation proteins (RIPs) are sequentially loaded on to origins of replication during…
(more)
▼ DNA replication is a stringently regulated cellular process. In proliferating normal cells, replication initiation proteins (RIPs) are sequentially loaded on to origins of replication during the M-to-G1 transition to form the pre-replication complex (pre-RC), in a process known as replication licensing. Critically, RIPs ensure chromosomal DNA is replicated only once per cell cycle, following origin activation. RIPs (Noc3p, Ipi3p, Cdt1p, Cdc6p, Mcm2-7p) are recruited by the origin recognition complex (ORC), which binds and marks replication origins throughout the cell cycle to form the pre-RC. The detailed mechanism(s) and regulation of the pre-RC and its architecture still remain unclear. In this study, 146 combinations of pairwise protein-protein interactions among 16 human pre-RC proteins were systematically and comprehensively examined for the first time. The yeast two-hybrid assay identified 72 positive interactions, of which 41 were previously unknown. hNOC3 and hIPI3 proteins had interactions with several RIPs, suggesting a role in DNA replication, similar to that found in the budding yeast homologs. The self-interactions of hORC2, -4, -5 and hNOC3 proteins were also of particular interest. Critically this study may provide a foundation for understanding the architecture(s) and function(s) of the human pre-RC. ORC self-interaction in the budding yeast was also examined to verify the Orc1p, -2p, -5p and -6p self-interactions. Subsequent experiments further supported the ORC dimerization mechanism. According to this model, ORC components self-interact to form dimer complexes (double-hexamers), at replication origins, prior to pre-RC formation. Following replication initiation, at origins in S phase, ORC double-hexamers dissociate into single-hexamers, which bind to the duplicated origins until late M phase, prior to replication-licensing. During the M-to-G1 transition, the double-hexamers, completing a semi-conservative, cell cycle dependent ORC 'dimerization cycle'. Depletion of non-chromatin bound ORC from the nucleus during the M-to-G1 transition abrogates ORC self-interactions, pre-RC formation and DNA replication. Three different yeast NOC3 temperature sensitive mutants were also examined in relation to DNA replication (ORC dimerization, pre-RC formation and maintenance, and cell cycle progression) and ribosome biogenesis in budding yeast to conclude that the functions of Noc3p in DNA replication and ribosome biogenesis are separable. Inactivation of Noc3p results in the failure of ORC dimerization, and MCM loading at the M-to-G1 transition and maintenance in G1 phase. Noc3p is the only non-ORC/MCM RIP that possesses self-interaction and potential dimerization. Noc3p and its self-interaction may be a prerequisite for ORC dimerization and eventual MCM double-hexamer loading. The 'ORC dimerization' model provides a symmetric platform to load the symmetric pre-RCs and guards against origin re-licensing within the same cell cycle by marking and protecting the nascent sister…
Subjects/Keywords: DNA replication
; DNA-protein interactions
; Protein-protein interactions
; Yeast
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Amin, A. (2016). Studies of human and budding yeast DNA replication initiation proteins. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-86342 ; https://doi.org/10.14711/thesis-b1610639 ; http://repository.ust.hk/ir/bitstream/1783.1-86342/1/th_redirect.html
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Amin, Aftab. “Studies of human and budding yeast DNA replication initiation proteins.” 2016. Thesis, Hong Kong University of Science and Technology. Accessed March 01, 2021.
http://repository.ust.hk/ir/Record/1783.1-86342 ; https://doi.org/10.14711/thesis-b1610639 ; http://repository.ust.hk/ir/bitstream/1783.1-86342/1/th_redirect.html.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Amin, Aftab. “Studies of human and budding yeast DNA replication initiation proteins.” 2016. Web. 01 Mar 2021.
Vancouver:
Amin A. Studies of human and budding yeast DNA replication initiation proteins. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2016. [cited 2021 Mar 01].
Available from: http://repository.ust.hk/ir/Record/1783.1-86342 ; https://doi.org/10.14711/thesis-b1610639 ; http://repository.ust.hk/ir/bitstream/1783.1-86342/1/th_redirect.html.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Amin A. Studies of human and budding yeast DNA replication initiation proteins. [Thesis]. Hong Kong University of Science and Technology; 2016. Available from: http://repository.ust.hk/ir/Record/1783.1-86342 ; https://doi.org/10.14711/thesis-b1610639 ; http://repository.ust.hk/ir/bitstream/1783.1-86342/1/th_redirect.html
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Vanderbilt University
27.
Zamora Vargas, Paula Francisca.
Functions of the nonstructural protein σNS in reovirus replication.
Degree: PhD, Microbiology and Immunology, 2018, Vanderbilt University
URL: http://hdl.handle.net/1803/12735
► Viral nonstructural proteins, which are not packaged into virions, are essential for the replication of most viruses. Reovirus, a nonenveloped, double-stranded RNA (dsRNA) virus, encodes…
(more)
▼ Viral nonstructural proteins, which are not packaged into virions, are essential for the
replication of most viruses. Reovirus, a nonenveloped, double-stranded RNA (dsRNA) virus, encodes three nonstructural proteins that are required for viral
replication and dissemination in the host. The reovirus nonstructural
protein σNS is a single-stranded RNA (ssRNA)-binding
protein that must be expressed in infected cells for production of viral progeny. However, the activities of σNS during individual steps of the reovirus
replication cycle are poorly understood. We explored the function of σNS by disrupting its expression during infection using cells expressing a small interfering RNA (siRNA) targeting the σNS-encoding S3 gene and found that σNS is required for viral genome
replication. Using complementary biochemical assays, we determined that σNS forms complexes with viral and nonviral RNAs. We also discovered, using in vitro and cell-based RNA degradation experiments, that σNS increases the RNA half-life. Cryo-electron microscopy revealed that σNS and ssRNAs organize into long, filamentous structures. High-resolution optical and electron microscopy showed that reovirus
replication organelles are membranous networks and that σNS appears to facilitate the recruitment of endoplasmic reticulum membranes to these structures. Collectively, our findings indicate that σNS functions as an RNA-binding
protein that increases viral RNA half-life and facilitates construction of
replication organelles. These results suggest that σNS forms RNA-
protein complexes in preparation for genome
replication.
Advisors/Committee Members: Larry Swift (committee member), Todd Graham (committee member), Anne Kenworthy (committee member), Terence Dermody (committee member), Kristen Ogden (committee member), Earl Ruley (Committee Chair).
Subjects/Keywords: reovirus; dsRNA replication; RNA-binding protein; σNS
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Zamora Vargas, P. F. (2018). Functions of the nonstructural protein σNS in reovirus replication. (Doctoral Dissertation). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/12735
Chicago Manual of Style (16th Edition):
Zamora Vargas, Paula Francisca. “Functions of the nonstructural protein σNS in reovirus replication.” 2018. Doctoral Dissertation, Vanderbilt University. Accessed March 01, 2021.
http://hdl.handle.net/1803/12735.
MLA Handbook (7th Edition):
Zamora Vargas, Paula Francisca. “Functions of the nonstructural protein σNS in reovirus replication.” 2018. Web. 01 Mar 2021.
Vancouver:
Zamora Vargas PF. Functions of the nonstructural protein σNS in reovirus replication. [Internet] [Doctoral dissertation]. Vanderbilt University; 2018. [cited 2021 Mar 01].
Available from: http://hdl.handle.net/1803/12735.
Council of Science Editors:
Zamora Vargas PF. Functions of the nonstructural protein σNS in reovirus replication. [Doctoral Dissertation]. Vanderbilt University; 2018. Available from: http://hdl.handle.net/1803/12735

Vanderbilt University
28.
Alers Rivera, Ileana.
NMR analysis of the RPA dimer core RPA32D/14.
Degree: MS, Chemical and Physical Biology, 2011, Vanderbilt University
URL: http://hdl.handle.net/1803/13061
► CHEMICAL AND PHYSICAL BIOLOGY NMR STUDIES OF THE RPA DIMER CORE RPA32D/14 ILEANA ALERS RIVERA Thesis under the direction of Professor Walter J. Chazin Replication…
(more)
▼ CHEMICAL AND PHYSICAL BIOLOGY
NMR STUDIES OF THE RPA DIMER CORE RPA32D/14
ILEANA ALERS RIVERA
Thesis under the direction of Professor Walter J. Chazin
Replication protein A (RPA) is the primary eukaryotic single-stranded DNA binding
protein. RPA is an essential factor for DNA transactions including
replication, repair and telomere maintenance, when the DNA is unwound for processing. Binding of RPA protects ssDNA from nucleases, formation of secondary structures and reannealing of the two strands. RPA also serves as a scaffold that orchestrates the assembly and disassembly of DNA processing machinery. RPA is a heterotrimer of subunits RPA70, RPA32 and RPA14, which together contain six OB-fold, one winged-helix and one disordered domain. Characterization by NMR of the structure and dynamics of RPA and the effect of interactions with DNA and DNA processing proteins is being used to understand the physical basis for RPA function. Recently, RPA was shown to bind DNA G-quadruplexes found at the end of telomeres and to disrupt these structures. This activity has been mapped to the RPA32/14 dimer. To enable NMR analysis of this system, we have undertaken a series of three-dimensional triple resonance NMR experiments acquired with TROSY enhancement at 800 MHz to assign the backbone resonances of RPA32D/14. Assignments were made for approximately 60% of the 149 residues of RPA32D/14 from these data and about half were confirmed in a NOESY experiment. These resonance assignments lay a foundation for characterizing the interaction of RPA32D/14 with G-quadruplex structures, and will facilitate future NMR analysis of the RPA trimer core and the full-length
protein.
Approved: Date:
Advisors/Committee Members: Albert H. Beth (committee member), Borden D. Lacy (committee member), Walter J. Chazin (Committee Chair).
Subjects/Keywords: telomeres; Replication Protein A; G-quadruplex
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MLA ·
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to Zotero / EndNote / Reference
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APA (6th Edition):
Alers Rivera, I. (2011). NMR analysis of the RPA dimer core RPA32D/14. (Thesis). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/13061
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Alers Rivera, Ileana. “NMR analysis of the RPA dimer core RPA32D/14.” 2011. Thesis, Vanderbilt University. Accessed March 01, 2021.
http://hdl.handle.net/1803/13061.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Alers Rivera, Ileana. “NMR analysis of the RPA dimer core RPA32D/14.” 2011. Web. 01 Mar 2021.
Vancouver:
Alers Rivera I. NMR analysis of the RPA dimer core RPA32D/14. [Internet] [Thesis]. Vanderbilt University; 2011. [cited 2021 Mar 01].
Available from: http://hdl.handle.net/1803/13061.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Alers Rivera I. NMR analysis of the RPA dimer core RPA32D/14. [Thesis]. Vanderbilt University; 2011. Available from: http://hdl.handle.net/1803/13061
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Vanderbilt University
29.
Riddle, Abigail Leigh.
Characterizing the role of the Est1 protein in stimulating the recruitment of the Est3 protein to the yeast telomerase complex.
Degree: MS, Biological Sciences, 2012, Vanderbilt University
URL: http://hdl.handle.net/1803/12435
► Telomeres are protective protein/DNA complexes that cap the ends of linear chromosomes. The repetitive, TG-rich telomeric sequences are elongated by the telomerase ribonucleoprotein. In Saccharomyces…
(more)
▼ Telomeres are protective
protein/DNA complexes that cap the ends of linear chromosomes. The repetitive, TG-rich telomeric sequences are elongated by the telomerase ribonucleoprotein. In Saccharomyces cerevisiae, the catalytic core of telomerase consists of the reverse transcriptase Est2p and the TLC1 RNA, which contains the template for nucleotide addition. The Est1 and Est3 proteins serve regulatory roles in vivo but are dispensable for in vitro telomerase activity. The mechanism through which Est3p assembles with the holoenzyme is debated within the field, specifically concerning Est1p’s role in Est3p recruitment. Based on evidence demonstrating that Est1p is not absolutely required to recruit Est3p, I hypothesize that Est1p stimulates Est3p recruitment. To identify residues of the Est1
protein responsible for this function, I used a combination of in vivo and in vitro experiments and two genetic screens. Using an in vivo assembly assay, I determined that a putative Est3p recruitment domain lies between amino acids 499 and 563 of Est1p and optimized the protocol for analyzing point mutations within this region. Additionally, I have designed two genetic screens to isolate alleles of EST1 specifically disrupted for stimulating Est3p recruitment. The first uses an Est2-Est3 fusion
protein predicted to bypass only the Est3p recruitment function of Est1p. The second utilizes a galactose-inducible allele of EST3 to screen for Est1p mutants rescued by over-expression of Est3p. Identification of separation-of-function alleles of EST1 with these tools will clarify the precise mechanisms of yeast telomerase complex assembly and potentially provide insight into the interactions of human telomerase components.
Advisors/Committee Members: Katherine Friedman (committee member), Brandt Eichman (Committee Chair).
Subjects/Keywords: DNA replication; protein complex; assembly; cancer
Record Details
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Record Details
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Riddle, A. L. (2012). Characterizing the role of the Est1 protein in stimulating the recruitment of the Est3 protein to the yeast telomerase complex. (Thesis). Vanderbilt University. Retrieved from http://hdl.handle.net/1803/12435
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Riddle, Abigail Leigh. “Characterizing the role of the Est1 protein in stimulating the recruitment of the Est3 protein to the yeast telomerase complex.” 2012. Thesis, Vanderbilt University. Accessed March 01, 2021.
http://hdl.handle.net/1803/12435.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Riddle, Abigail Leigh. “Characterizing the role of the Est1 protein in stimulating the recruitment of the Est3 protein to the yeast telomerase complex.” 2012. Web. 01 Mar 2021.
Vancouver:
Riddle AL. Characterizing the role of the Est1 protein in stimulating the recruitment of the Est3 protein to the yeast telomerase complex. [Internet] [Thesis]. Vanderbilt University; 2012. [cited 2021 Mar 01].
Available from: http://hdl.handle.net/1803/12435.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Riddle AL. Characterizing the role of the Est1 protein in stimulating the recruitment of the Est3 protein to the yeast telomerase complex. [Thesis]. Vanderbilt University; 2012. Available from: http://hdl.handle.net/1803/12435
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Jawaharlal Nehru University
30.
Mehra, Parul.
Functional characterization of plasmodium falciparum
replication initiation proteins; -.
Degree: Biology, 2007, Jawaharlal Nehru University
URL: http://shodhganga.inflibnet.ac.in/handle/10603/17572
Subjects/Keywords: Molecular Biology; Replication; plasmodium; falciparum; initiation
Record Details
Similar Records
Cite
Share »
Record Details
Similar Records
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Mehra, P. (2007). Functional characterization of plasmodium falciparum
replication initiation proteins; -. (Thesis). Jawaharlal Nehru University. Retrieved from http://shodhganga.inflibnet.ac.in/handle/10603/17572
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Mehra, Parul. “Functional characterization of plasmodium falciparum
replication initiation proteins; -.” 2007. Thesis, Jawaharlal Nehru University. Accessed March 01, 2021.
http://shodhganga.inflibnet.ac.in/handle/10603/17572.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Mehra, Parul. “Functional characterization of plasmodium falciparum
replication initiation proteins; -.” 2007. Web. 01 Mar 2021.
Vancouver:
Mehra P. Functional characterization of plasmodium falciparum
replication initiation proteins; -. [Internet] [Thesis]. Jawaharlal Nehru University; 2007. [cited 2021 Mar 01].
Available from: http://shodhganga.inflibnet.ac.in/handle/10603/17572.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Mehra P. Functional characterization of plasmodium falciparum
replication initiation proteins; -. [Thesis]. Jawaharlal Nehru University; 2007. Available from: http://shodhganga.inflibnet.ac.in/handle/10603/17572
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
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