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1
Stracker, Travis Hileman. "DNA virus interactions with host cell DNA replication and repair pathways /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2002. http://wwwlib.umi.com/cr/ucsd/fullcit?p3070999.
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Leavitt, Markley Carl. "Bacteriophage T5 DNA polymerase relationships of DNA polymerases." Diss., The University of Arizona, 1990. http://hdl.handle.net/10150/185335.
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T5 DNA polymerase, a highly processive single polypeptide enzyme, and PRD1 DNA polymerase, a protein-primed DNA polymerase, have been analyzed for their primary structural features. The amino acid sequence of T5 DNA polymerase reveals a high degree of homology with DNA polymerase I (Pol I) of Escherichia coli and retains many of the amino acid residues which have been implicated in the 3'-5' exonuclease and DNA polymerase activities of that enzyme. Alignment with sequences of polymerase I and T7 DNA polymerase (family A polymerases) was used to identify regions possibly involved in the high processivity of this enzyme. Further amino acid sequence comparisons of T5 DNA polymerase with a large group of DNA polymerases (family B) previously shown to exhibit little similarity to Pol I, indicate certain sequence segments are shared among distantly related DNA polymerases. These shared regions have been implicated in the 3'-5' exonuclease function of Pol I which suggests that the proofreading domains of all these enzymes may be related. Mutations in these segments in T5 DNA polymerase (family A) and PRD1 DNA polymerase (family B) greatly decrease the exonuclease activity of these enzymes but leave the polymerase activities intact. Additionally, an exonuclease deficient T5 DNA polymerase is used in DNA sequencing reactions and yields consistent results with low background contamination on autoradiographs of polyacrylamide/urea gels. PRD1 mutants defective in 3 regions which are highly conserved among family B DNA polymerases, are deficient in DNA polymerase activity but retain exonuclease activity.
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Mahajan, Preeti. "Academic Libraries in India: a Present-Day Scenario." Library Philosophy and Practice (LPP), 2005. http://hdl.handle.net/10150/106173.
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Education aims to impart knowledge and makes good citizens. Libraries are the repositories of knowledge and form an integral part of education. Libraries have a long history, starting with the chained and closed-access libraries of earlier times to the present-day hybrid, digital, and virtual libraries that use the latest technology for provision of information through various services. Accordingly, librarians have also changed from storekeepers who were concerned with protection of books against theft, mutilation, and pilferage, to that of information officers, navigators, and cybrarians who find themselves in the vast ocean of reading material and are busy in satisfying their clients who want anytime and anywhere information.
With the advent of computers, the nature of libraries has changed dramatically. Computers are being used in libraries to process, store, retrieve and disseminate information. As a result, the traditional concept of library is being redefined from a place to access books to one which houses the most advanced media including CD-ROM, Internet, and remote access to a wide range of resources. Libraries have now metamorphosed into digital institutions. Gone are the days when a library was judged by its quantitative resources. Today, libraries are surrounded by networked data that is connected to a vast ocean of Internet-based services. Moreover, electronic resources relevant to the professions are developing at an unprecedented pace.
Academic libraries are considered to be the nerve centres of academic institutions, and must support teaching, research, and other academic programmes. The situation in academic libraries of India is the same as that of academic libraries the world over; however, Indian libraries must provide maximum information with limited resources.
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Park, Frances E. "NF-kB DNA binding and transactivation /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2001. http://wwwlib.umi.com/cr/ucsd/fullcit?p3001261.
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You, Zhongsheng. "Sensing and responding to DNA replication /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2002. http://wwwlib.umi.com/cr/ucsd/fullcit?p3055806.
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Shanmuganatham, Karthik. "DNA binding specificity of Mu transcription factor C and crystallization of C : DNA Complex /." View the abstract Download the full-text PDF version (on campus access only), 2007. http://etd.utmem.edu/ABSTRACTS/2007-015-Shanmuganatham-Index.html.
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Thesis (Ph.D.)--University of Tennessee Health Science Center, 2007.Title from title page screen (viewed on June 19, 2008). Research advisor: Martha M. Howe, Ph.D. Document formatted into pages (xiv, 159 p. : ill.) Vita. Abstract. Includes bibliographical references (p.154-159).
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Van, Uden John Henry. "Immunostimulatory DNA and the host-pathogen relationship /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2001. http://wwwlib.umi.com/cr/ucsd/fullcit?p3013707.
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Hamlett, Anna. "Human trafficking : a modern day slavery." Honors in the Major Thesis, University of Central Florida, 2009. http://digital.library.ucf.edu/cdm/ref/collection/ETH/id/1270.
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This item is only available in print in the UCF Libraries. If this is your Honors Thesis, you can help us make it available online for use by researchers around the world by following the instructions on the distribution consent form at http://library.ucf.edu/Systems/DigitalInitiatives/DigitalCollections/InternetDistributionConsentAgreementForm.pdf You may also contact the project coordinator, Kerri Bottorff, at kerri.bottorff@ucf.edu for more information.Bachelors
Sciences
Political Science
9
Standish, Leisa Gaye. "The influence of quality day care on early academic achievement." CSUSB ScholarWorks, 1994. https://scholarworks.lib.csusb.edu/etd-project/969.
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Gunderson, Carl Wayne. "DNA repair is the target of novel antibiotics." Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2007. http://wwwlib.umi.com/cr/ucsd/fullcit?p3283892.
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Thesis (Ph. D.)--University of California, San Diego and San Diego State University, 2007.Title from first page of PDF file (viewed December 3, 2007). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 166-174).
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Galbraith, Evelyn Van, and University of Lethbridge Faculty of Arts and Science. "The eighth day : a novel with critical commentary." Thesis, Lethbridge, Alta : University of Lethbridge, Faculty of Arts and Science, 1994, 1994. http://hdl.handle.net/10133/25.
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This thesis contains two parts: a novel, The Eighth Day and its critical commentary. The novel sets the story of Olivia, a contemporary protagonist, into the Sumerian myth of Inanna: Queen of Heaven and Earth. Like Inanna, Olivia descends, removing her immortal vestments or metaphors of belief, in seven stages or gates that lead to the underworld where she will arrive naked and bowing low before her sister-self, Rahab. Because Olivia's ideology is rigidly bound by ethics framed in the Old Testament, both of these myths play a large part in the unfolding of her story. Livia's beliefs must be closely identified before she can dicard or amend them. The Inanna myth illuminates the spiral nature of life's journey from the blind innocence of a child descending down to a conscious innocence born of choice. The critical commentary that precedes the novel discusses the art and technique that plays part in all fiction and in the novel. The Eighth Day.xlv, 246 leaves : ill., [1] plate ; 29 cm
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Lee, Delphine Juihoa. ""Naked" plasmid DNA vaccines : cellular roles and applications /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 1999. http://wwwlib.umi.com/cr/ucsd/fullcit?p9944207.
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Zhu, Weiguo. "Structure-function analysis of DNA polymerase: Purification, characterization and in vitro mutagenesis of PRD1 DNA polymerase." Diss., The University of Arizona, 1993. http://hdl.handle.net/10150/186573.
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A small lipid-containing bacteriophage PRD1 encodes a DNA polymerase that utilizes a protein primer for the initiation of DNA replication. The purification of PRD1 DNA polymerase has been hampered by the insolubility of the overexpressed enzyme in E. coli cells. A simple and rapid procedure for purification of the overexpressed PRD1 DNA polymerase has been developed. This method is based on guanidine hydrochloride denaturation and renaturation of the insoluble PRD1 DNA polymerase overexpressed in E. coli containing recombinant plasmid pEJG. The purified DNA polymerase was extensively characterized and found to be indistinguishable from the normal soluble PRD1 DNA polymerase as judged by enzymatic properties. These properties include: protein-primed initiation of PRD1 DNA replication, strand-displacement DNA synthesis, DNA polymerase processivity, 3' to 5' exonuclease activity and filling-in repair type DNA synthesis. Furthermore, the kinetic parameters determined for dNTPs and primer-terminus were of the same order of magnitude. The availability of a simple purification procedure for PRD1 DNA polymerase should permit detailed structure-function analysis of this enzyme. All known family B DNA polymerases contain a conserved region of amino acids, KX₆₋₇YG, which appears to be correspond to the "finger" alpha helix O of the Klenow fragment of E. coli DNA polymerase I, a family A DNA polymerase. A site-directed mutagenesis study has been applied to access the functional role of the invariant amino acid lysine-340 of PRD1 DNA polymerase. Mutant DNA polymerases were overexpressed and purified to near homogeneity. The results showed that the modification of the lysine-340 of PRD1 DNA polymerase abolishes the polymerase activity without affecting the 3' to 5' exonuclease activity. Site-directed mutagenesis studies revealed that residues important for the 3' to 5' exonuclease activity, particularly metal binding ligands for the Klenow fragment, are all conserved in PRD1 DNA polymerase as well. Although PRD1 DNA polymerase has a smaller 3' to 5' exonuclease domain, active sites appear to be very similar to those of the Klenow fragment. Moreover, the metal binding ligands were also found to be important for the strand-displacement activity, a unique feature of PRD1 DNA polymerase.
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Lakdawala, Seema Sailesh. "Impact of DNA damage proteins on the adenoviral lifecycle." Diss., [La Jolla] : University of California, San Diego, 2009. http://wwwlib.umi.com/cr/ucsd/fullcit?p3373343.
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Thesis (Ph. D.)--University of California, San Diego, 2009.Title from first page of PDF file (viewed Oct. 19, 2009). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 172-200).
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Tabb, Juanita K. (Juanita Kay). "A Comparison of Academic Achievement of Boys and Girls from Full-Day and Half-Day Kindergartens." Thesis, North Texas State University, 1987. https://digital.library.unt.edu/ark:/67531/metadc331064/.
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The purpose of this study was to determine whether any differences in academic achievement existed between full-day and half-day kindergarten students at the end of their kindergarten and first-grade school years. Two public schools considered comparable in size, philosophy, and socioeconomic levels of a large school district in Texas participated in the study. One of the schools provided a full-day kindergarten program; the other school provided a half-day kindergarten program. Kindergarten students from each of the two schools were match-paired according to birthday and sex. The total sample size was fifty students. All students were tested in December, 1985, with the Metropolitan Achievement Test. Preprimer Level, and in May, 1986, the end of the kindergarten year, with the Primer Level of the Metropolitan Achievement Test. The Metropolitan Achievement Test. Primary I Level, was additionally administered to the subjects in April, 1987, at the end of their first-grade school year. During each testing period, the subjects were administered the Reading, Language, and Math subtests of the Metropolitan Achievement Test. The following supplemental data also were gathered on the students: The Metropolitan Readiness Test II scores and the TEAMS test scores. The data obtained from the testing batteries were statistically analyzed using the .05 level of significance to test each hypothesis. In analyzing the data of all of the academic achievement testing batteries, statistical conclusions revealed that there was no significant difference in the mean scores of children (boys or girls) attending the fullday kindergarten program and children attending the half-day kindergarten program in academic achievement at the end of the kindergarten year or at the end of the first-grade year. It is recommended that continued studies be conducted to investigate the academic achievement of students attending full-day and half-day kindergarten programs. It is also recommended that other variables rather than academic achievement be studied to determine their effects on full-day and half-day kindergarten students.
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RIVERA, ANNA LYDIA FISHER. "THE EFFECT OF HALF-DAY AND FULL-DAY SCHEDULES ON THE ACADEMIC ACHIEVEMENT OF KINDERGARTEN CHILDREN." Diss., The University of Arizona, 1985. http://hdl.handle.net/10150/184201.
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The purpose of the study was to determine whether a significant difference existed in the academic achievement of students as a function of attending half-day or full-day kindergartens. The hypothesis was students in full-day kindergartens will demonstrate more growth in academic achievement than students in half-day kindergartens as measured by the Head Start Measurements Battery (HSMB) in seven areas: language, math, nature/science, perception, reading, social development, and overall score. One hundred subjects were randomly selected from 158 qualified subjects that attended four Chapter 1 schools in a public school district in Southern Arizona. Four half-day and five full-day kindergartens participated. Five classes implemented a bilingual curriculum, one a Spanish curriculum, and three an English curriculum. Eventually, 74 subjects were pretested in November 1984 and posttested in May 1985. The majority of the subjects were Hispanics. Based on the literature review, the need to assess children in English/Spanish/bilingually, the need for an individually administered test of a manipulative nature, and the need for a psychometrically sound instrument, the Fall 1984 version of the Head Start Measures Battery was selected. It assesses the three-to-six-year-old child's cognitive development. The research design used was a quasi-experimental approach: the non-equivalent control group design. The independent variables were the schedules and the dependent variables were the seven areas measured by the HSMB. Mean gain scores were calculated in each of the seven areas. A t-test was used to analyze the data. The results indicated that there was a statistically significant difference (p<.05) between the mean gain scores of the half-day and full-day kindergartens (in favor of the full-day kindergartens) in language, math, and reading. The evidence failed to indicate a statistically significant difference in nature/science, perception, social development, and overall scores. In conclusion, the findings suggested that there was greater academic achievement in languages, math, and reading for full-day than for half-day kindergarten students. The findings failed to provide evidence of a difference in the academic achievement of half-day and full-day kindergarten students in nature/science, perception, social development, and overall scores.
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Fagenson, Alexander. "Gold (iii) macrocycles are dna intercalators that inhibit topoisomerase i and ii." Honors in the Major Thesis, University of Central Florida, 2012. http://digital.library.ucf.edu/cdm/ref/collection/ETH/id/1536.
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Human Topoisomerase IB (TOP1) and Topoisomerase II? (TOP2?) are essential nuclear enzymes that control DNA topology during DNA replication, gene transcription and cell division. These enzymes carry out their catalytic function by making transient single-strand (type I) or double-strand (type II) breaks in the DNA. In vivo, these complexes are short-lived but can be exploited by anti-cancer drugs to mechanistically kill cancer cells. Two general classes of compounds can kill cancer cells through a topo-targeted mechanism. Interfacial Poisons (IFPs) act at the enzyme-DNA interface to inhibit the religation reaction, resulting in the accumulation of DNA double-stand breaks (DSBs) in the genomic setting. Catalytic Inhibitor Compounds (CICs) act by interfering with other steps of the catalytic cycles such as DNA/protein binding or the cleavage reaction. In this work we identify new Au3+ macrocyclic gold complexes that act as CICs of both TOP1 and TOP2?. The complexes exhibit square planar geometry with an aromatic system that allows for DNA intercalation with binding affinities in the low micromolar range. A cytotoxicity screen across 60 human cancer cell lines performed by the National Cancer Institute (NCI, USA) reveals significant anti-tumor potential. Our lead compound (butyl gold(III) macrocycle, cmpd 3.) is currently undergoing further studies in animal models at the NCI. In vitro assays with purified DNA and enzyme reveal the Au3+ ion to be the quintessential switch that allows for DNA intercalation and subsequent inhibition of TOP1 and TOP2?.ID: 031908365; System requirements: World Wide Web browser and PDF reader.; Mode of access: World Wide Web.; Accepted in partial fulfillment of the requirements for honors in the major in DEPT HERE.; Thesis (B.A.)--University of Central Florida, 2012.; Includes bibliographical references.
B.S.
Bachelors
Burnett School of Biomedical Sciences
Molecular and Microbiology
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Shell, Scarlet Sara. "Mechanisms of initiation of DNA mismatch repair in Saccharomyces cerevisiae." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2008. http://wwwlib.umi.com/cr/ucsd/fullcit?p3307558.
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Thesis (Ph. D.)--University of California, San Diego, 2008.Title from first page of PDF file (viewed July 23, 2008). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references.
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Hua, Xuequn Helen. "Regulation of initiation of DNA replication in Xenopus egg extract /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 1997. http://wwwlib.umi.com/cr/ucsd/fullcit?p9814545.
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Sun, Li. "Studies of initiation of DNA replication using xenopus egg extracts /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2000. http://wwwlib.umi.com/cr/ucsd/fullcit?p9989761.
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Liang, Debbie T. "Multiple roles of fission yeast MCM proteins in DNA replication /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2001. http://wwwlib.umi.com/cr/ucsd/fullcit?p3041400.
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Hastings, Patsy-Ann Susan. "MITOCHONDRIAL DNA ANALYSIS BY PYROSEQUENCING." Master's thesis, University of Central Florida, 2004. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/4447.
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Mitochondrial DNA (deoxyribo nucleic acid) is typically used in forensic casework when small quantities of high molecular weight quality DNA is not expected to be present thus negating the chances of obtaining usable nuclear DNA. Typical samples that utilized mitochondrial DNA analysis are: hair, bones, teeth, ancient remains (samples or remains that are at least 100 years old) or very old samples (samples that are less than 100 but greater than 10 years old). The current method used to evaluate mitochondrial DNA is Sanger sequencing. Although robust, it is also time consuming and labor intensive, on the other hand pyrosequencing is a nonelectrophoretic, rapid, reliable, and sensitive sequencing method which can be easily automated. Therefore pyrosequencing could enable the widespread use of mitochondrial DNA in forensic casework and reduce the amount of time spent on each sample without compromising quality. The aim of this study is to evaluate the efficacy of pyrosequencing for forensic DNA applications, in particular mitochondrial DNA. Two dispensation orders, cyclic and directed, were examined to determine if there is any effect on the sequence generated. The accuracy of pyrosequencing was evaluated by sequencing samples of known sequence provided by the FBI. The sensitivity of pyrosequencing was evaluated by sequencing samples at different DNA concentrations and inputs. Experiments were conducted to determine the ability of pyrosequencing to detect mixtures and heteroplasmy. Additionally, the ability of pyrosequencing to sequence damaged/degraded DNA was evaluated using blood, semen, and saliva samples that were subjected to three different environmental conditions. A blind study will be conducted to confirm the accuracy of pyrosequencing. Finally, a comparison study will be conducted in which pyrosequencing will be compared to Sanger sequencing.M.S.
Department of Chemistry
Arts and Sciences
Chemistry
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Gadgil, William Himanshu S. "Advances in DNA Affinity Chromatography." View the abstract Download the full-text PDF version, 2001. http://etd.utmem.edu/ABSTRACTS/2001-001-gadgil-index.htm.
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Thesis (Ph.D.)--University of Tennessee Health Science Center, 2001.Title from title page screen (April 10, 2008). Research advisor: Harry W. Jarrett, Ph.D. Document formatted into pages (xv, 162 p. : ill.). Vita. Abstract. Includes bibliographical references (p. 152-162).
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Metzgar, David L. "Repetitive DNA, genome evolution, and the adaptive evolution of mutation rates /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2001. http://wwwlib.umi.com/cr/ucsd/fullcit?p3022205.
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Schwartz, Rachel Anna. "The intersection of degradation, replication, and DNA repair in virus-host interactions." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2008. http://wwwlib.umi.com/cr/ucsd/fullcit?p3307531.
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Thesis (Ph. D.)--University of California, San Diego, 2008.Title from first page of PDF file (viewed July 14, 2008). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 288-332).
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Chen, Sheng-hong. "Bottom up approach for the reconstitution and characterization of DNA replication checkpoint." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2008. http://wwwlib.umi.com/cr/ucsd/fullcit?p3331375.
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Thesis (Ph. D.)--University of California, San Diego, 2008.Title from first page of PDF file (viewed Dec. 16, 2008). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 81-89).
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De, las Alas Maida M. "The identification of functional domains of the DNA mismatch repair protien hMSH2 /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 1999. http://wwwlib.umi.com/cr/ucsd/fullcit?p9961760.
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James, McConnell Michael. "An impaired DNA damage response alters neural aneuploidy : implications for ataxia-telangiectasia /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2004. http://wwwlib.umi.com/cr/ucsd/fullcit?p3144329.
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Calloway, Richard J. "Homologous pairing through DNA driven harmonics-- a simulation investigation." Doctoral diss., University of Central Florida, 2011. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/4744.
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The objective of this research is to determine if a better understanding of the “molecule of life”, deoxyribonucleic acid or DNA can be obtained through Molecular Dynamics (MD) modeling and simulation (MandS) using contemporary MD MandS. It is difficult to overstate the significance of the DNA molecule. The now-completed Human Genome Project stands out as the most significant testimony yet to the importance of understanding DNA. The Human Genome Project (HGP) enumerated many areas of application of genomic research including molecular medicine, energy sources, environmental applications, agriculture and livestock breeding to name just a few. (Science, 2008) In addition to the fact that DNA contains the informational blueprints for all life, it also exhibits other remarkable characteristics most of which are either poorly understood or remain complete mysteries. One of those completely mysterious characteristics is the ability of DNA molecules to spontaneously segregate with other DNA molecules of similar sequence. This ability has been observed for years in living organisms and is known as “homologous pairing.” It is completely reproducible in a laboratory and defies explanation. What is the underlying mechanism that facilitates long-range attraction between 2 double-helix DNA molecules containing similar nucleotide sequences? The fact that we cannot answer this question indicates we are missing a fundamental piece of information concerning the DNA bio-molecule. The research proposed herein investigated using the Nano-scale Molecular Dynamics NAMD (Phillips et al., 2005) simulator the following hypotheses: H(Simulate Observed Closure NULL) : = Current MD force field models when used to model DNA molecule segments, contain sufficient variable terms and parameters to describe and reproduce directed segregating movement (closure of the segments) as previously observed by the Imperial College team between two Phi X 174 DNA molecules. H(Resonance NULL) : = Current MD force field models when used to model DNA molecule segments in a condensed phased solvent contain sufficient variable terms and parameters to reproduce theorized molecular resonation in the form of frequency content found in water between the segments. H(Harmonized Resonance NULL) : = Current MD force field models of DNA molecule segments in a condensed phase solvent produce theorized molecular resonation in the form of frequency content above and beyond the expected normal frequency levels found in water between the segments. H(Sequence Relationship NULL): = The specific frequencies and amplitudes of the harmonized resonance postulated in H(Harmonized Resonance NULL) are a direct function of DNA nucleotide sequence. H(Resonance Causes Closure NULL) : = Interacting harmonized resonation produces an aggregate force between the 2 macro-molecule segments resulting in simulation of the same directed motion and segment closure as observed by the Imperial College team between two Phi X 174 DNA molecules. After nearly six months of molecular dynamic simulation for H(Simulate Observed Closure NULL) and H(Resonance Causes Closure NULL) no evidence of closure between two similar sequenced DNA segments was found. There exist several contributing factors that potentially affected this result that are described in detail in the Results section. Simulations investigating H( Resonance NULL), H(Harmonized Resonance NULL) and the emergent hypothesis H(Sequence Relationship NULL) on the other hand, revealed a rich selection of periodic pressure variation occurring in the solvent between simulated DNA molecules. About 20% of the power in Fourier coefficients returned by Fast Fourier Transforms performed on the pressure data was characterized as statistically significant and was located in less than 2% of the coefficients by count. This unexpected result occurred consistently in 5 different system configurations with considerable system-to-system variation in both frequency and magnitude. After careful analysis given the extent of our experiments the data was found to be in support of H( Resonance NULL), and H(Harmonized Resonance NULL) . Regarding the emergent hypothesis H(Sequence Relationship NULL), further analysis was done on the aggregate data set looking for correlation between nucleotide sequence and frequency/magnitude. Some of the results may be related to sequence but were insufficient to prove it. Overall the conflicting results were inconclusive so the hypothesis was neither accepted nor rejected. Of particular interest to future researchers it was noted that the computational simulations performed herein were NOT able to reproduce what we know actually happens in a laboratory environment. DNA segregation known to occur in-vitro during the Imperial College investigation did not occur in our simulation. Until this discrepancy is resolved MM simulation should not as yet be considered a suitable tool for further investigation of Homologous Chromosome Pairing. In Chapter 5 specific follow on research is described in priority of need addressing several new questions.ID: 031001514; System requirements: World Wide Web browser and PDF reader.; Mode of access: World Wide Web.; Title from PDF title page (viewed August 8, 2013).; Thesis (Ph.D.)--University of Central Florida, 2011.; Includes bibliographical references (p. 212-215).
Ph.D.
Doctorate
Industrial Engineering and Management Systems
Engineering and Computer Science
Modeling and Simulation
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Perez, Gerardo Legrama. "Transport of phage P22 DNA into the cytoplasm of salmonella enterica serovar Typhimurium." Diss., [La Jolla] : [San Diego] : University of California, San Diego ; San Diego State University, 2008. http://wwwlib.umi.com/cr/ucsd/fullcit?p3319845.
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Thesis (Ph. D.)--University of California, San Diego and San Diego State University, 2008.Title from first page of PDF file (viewed Sept. 9, 2008). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 169-187).
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Cornett, Evan M. "Light-activated binary nucleotide reagent for inactivation of DNA polymerase." Master's thesis, University of Central Florida, 2012. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/5172.
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This work explores a binary reagent approach to increase the specificity of covalent inhibitors. In this approach, two ligand analogs equipped with inert pre-reactive groups specifically bind a target biopolymer. The binding event brings the pre-reactive groups in proximity with each other. The two groups react, generating active chemical intermediates that covalently modify and inactivate the target. In the present study we compare the new approach with the traditional single-component reagent strategy using DNA polymerase from bacteriophage T4 as a model target biopolymer. We report the design and synthesis of two analogs of deoxythymidine triphosphate, a natural DNA polymerase substrate. Together, the analogs function as a binary nucleotide reagent which is activated by light with wavelengths 365 nm and longer. However, the active analog functions as a traditional single component reagent when activated by light with wavelengths at 300 nm and longer. The traditional single-component reagent efficiently inactivated DNA polymerase. However, in the presence of non-target protein the inactivation efficiency is greatly diminished. Under the same conditions, the binary nucleotide reagent also inactivated DNA polymerase, and the inactivation efficiency is not affected by the presence of the non-target protein. Our results validate that a binary approach can be employed to design highly specific covalent inhibitors. The binary reagent strategy might be useful as a research tool for investigation of ligand-protein interactions in complex biological systems and for drug design.ID: 031001303; System requirements: World Wide Web browser and PDF reader.; Mode of access: World Wide Web.; Title from PDF title page (viewed March 15, 2013).; Thesis (M.S.)--University of Central Florida, 2012.; Includes bibliographical references (p. 26-29).
M.S.
Masters
Molecular Biology and Microbiology
Medicine
Biotechnology
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Coccia, Marco Anthony. "Identification and cloning of amplified DNA sequences by a modified-in-gel renaturation technique: Isolation of an amplified DNA sequence from a human sarcoma." Diss., The University of Arizona, 1991. http://hdl.handle.net/10150/185368.
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A modified in gel renaturation technique has been developed which detects DNA sequence amplifications of ≥10-fold without prior identification of the target gene. In order to determine the sensitivity of detection and applicability of modified in gel renaturation, primary human tumor cultures and drug resistant human cell lines with identified cellular gene amplifications were assayed. The modified in gel renaturation technique was then used to screen 71 human tumor cell lines and direct tumor biopsies for amplified sequences. Particular emphasis was placed on screening cell lines derived from human melanoma and direct tumor samples from adult sarcomas. Four of 55 cell lines tested had amplification ≥10-fold of previously known cellular oncogenes. None of the 25 melanoma short term cultures tested positive by this assay. One of 16 adult sarcoma samples (a malignant fibrous histiocytoma (MFH)) tested positive for DNA sequence amplification >10-fold. The amplified DNA present in this MFH, (termed ST-23987), was not identified by Southern blot analysis with a panel of oncogene probes previously reported as amplified in other human malignancies. In order to further characterize the amplified DNA in ST-23987, DNA was subjected to in gel renaturation cloning procedures followed by PCR modified cloning. Of 55 clones isolated and analyzed, four cloned inserts (termed pMAC895, pMAC15, pMAC20, and pMAC30) were amplified between 10-to-15-fold in ST-23987DNA. Several other adult sarcomas were probed with these four clones and three other instances of amplification were identified by Southern blot analysis with probes generated from pMAC15 and pMAC30 (found in tumors ST-24609, 870141 and ST-23493). A bacteriophage lambda genomic library was constructed from DNA isolated from a ST-23493. Four clones representing ∼34 kb of the amplified domain (designated 493.1, 493.2, 493.4, and 493.5) were isolated using clones pMAC15 and pMAC30 as probes. Plasmid subclones generated from the EcoRI fragments of the amplified bacteriophage lambda clones (termed p10.5, p6.0, p5.2, p5.0, p4.7, p2.8, and p0.5) were used as probes against Northern blots of sarcoma mRNA in an attempt to identify transcribed sequences within the cloned regions of the amplification unit. The hypothesized target gene carried within the amplification unit will likely be important to the progression, diagnosis and treatment of adult sarcoma, irrespective of the target gene identity.
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York, William A. "Re-examining subfamily classifications for the alu family of repeated dna sequences." Master's thesis, University of Central Florida, 1994. http://digital.library.ucf.edu/cdm/ref/collection/RTD/id/24455.
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University of Central Florida College of Arts and Sciences ThesisThe primate Alu family of repetitive elements has been wedely characterized. This ubiquitous class of retroposons has been found to occupy some 5% of the human genome. This hetergenous group of Short Interspersed Nucleic acid Elements (SINEs) has been theorized to possess an identifiable subfamily structure between and within various taxonomic levels in promates. It has been postulated that humans possess up to 6 Alu sequences and found evidence supporting the amplification/fixation theory in 5 subfamilies. The research presented in this thesis posits that Quentin's method of alignment used in the correspondence analysis is questionable. A reexamination using an alternative, perhaps more tenable, alignment of the Alu sequences may allow for a more lucid and accurate identification of Alu subfamily structure in the human genome.
M.S.;
Biology;
Arts and Sciences;
Biology;
65 p.
viii, 65 leaves, bound : ill. ; 28 cm.
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Peck, Vickie Marie. "DNA replication in Drosophila embryos: Proteins at the fork." Diss., The University of Arizona, 1992. http://hdl.handle.net/10150/185786.
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Drosophila embryos provide a rich source of replicative enzymes. Also, the duration of 2 hour embryo DNA synthesis phase of the cell cycle is approximately 6-fold shorter than the more regulated 9 hour embryo S phase. Thus, Drosophila embryos are a good system in which to explore the mechanisms and regulation of DNA replication. Early stage, 2 hour embryos contain at least two distinct DNA polymerases, DNA polymerase α and δ, as determined by associated enzymatic activities (DNA primase and 3'-5' exonuclease), inhibitor studies, immunologic reactivity, and processivity measurements. The observation that a δ-type enzyme with an inherent 3'-5' exonuclease activity is present in Drosophila embryos is a novel observation, and may have important implications for maintaining the fidelity of embryonic DNA synthesis. Both 2 hour and 9 hour embryos contained similar replicative activities. The enzymes which copurified with 2 hour and 9 hour DNA polymerases include a DNA primase activity with DNA polymerase α; and a 3'-5' exonuclease, 5'-3' exonuclease, and DNA ligase activities with DNA polymerase δ. The association of these activities suggests that DNA polymerase α-associated enzymes may initiate Okazaki fragments, which would then be elongated and ligated by the DNA polymerase δ-associated group.
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Rossetti, Emili Adami. "Divulga??o cient?fica para empoderamento institucional: o discurso da revista Darcy e a midiatiza??o da academia." Universidade Federal do Rio Grande do Norte, 2015. http://repositorio.ufrn.br/handle/123456789/20063.
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A ci?ncia tem se mantido em posi??o hegem?nica entre as diversas formas de conhecimento que possibilitam perceber nosso entorno. Ap?s um movimento de introvers?o do campo cient?fico, que oportunizou o empoderamento da academia, ? crescente a discuss?o, na atualidade, sobre a necessidade de se divulgar o conhecimento da ?rea para a sociedade. Nosso estudo se prop?e a observar o discurso de divulga??o cient?fica institucional, levando em considera??o as condi??es hist?ricas que possibilitaram a emerg?ncia da ci?ncia como leg?tima observa??o da natureza e do homem, bem como a outorga de credibilidade ? m?dia. Para tanto, temos como objeto de estudo os textos de editoriais da revista Darcy, de divulga??o cient?fica e cultural da Universidade de Bras?lia. Voltamo-nos para a observa??o do discurso de compartilhamento de saber pela m?dia, abordando, para tal, os conceitos de campo, de Bourdieu, e de ?profana??o?, de Agamben, em conson?ncia com no??es da ?rea de comunica??o organizacional. Al?m deles, os conceitos de dispositivo, discurso e saber-poder empregados t?m como base os estudos da escola francesa que os associam ? necessidade de se pensar o poder como rela??o entre o discursivo e o n?odiscursivo, tendo Michel Foucault como importante expoente deste pensamento. A pesquisa, apoiada da An?lise do Discurso de escola francesa, leva-nos a perceber um processo de m?tua valida??o dos discursos cient?fico e jornal?stico, que se associam ao fortalecimento da pr?pria institui??o e do pr?prio campo cient?fico, em textos que t?m como pano de fundo o fortalecimento da imagem e da reputa??o institucionais.
Science has remained in hegemonic position among the various forms of knowledge that enable us perceive our surroundings. After a growing movement of introversion of the scientific field, which enabled the empowerment of the academy, it is growing today the discussion about the need to spread knowledge of this area to society. Our study aims to observe the discourse of institutional science communication, taking into account the historical conditions that made possible the emergence of science as legitimate observation of nature and of man and also the credibility granted to the media. Therefore, we have as our study object the editorials of the Darcy magazine, for scientific and cultural journalism of the University of Brasilia. We focused on observing the discourse of knowledge sharing by the media, using the concepts of field, from Bourdieu?s work, and Agamben?s "profanation" together with notions from the organizational communication area. Also, the concepts of dispositive, discourse and knowledge-power used are based on the studies from the French school which associate them to the need of thinking power as a relation between what is and what is not said, having Michel Foucault as an important exponent of this area. The research, which uses as a method the Discourse Analysis, shows us a process of mutual validation of the scientific and journalistic discourses, which contribute to the strengthening of the institution itself as well as the scientific field, in texts which have as a backdrop the institutional image and reputation.
36
Daniel, Amber J. S. "Faculty/Student Perceptions Of Their Relationship In A Cross-Cultural Academic Mentoring Dyad." Wright State University / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=wright1468934836.
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Knoepfler, Paul S. "Analysis of cooperative DNA binding of Pbx proteins and its importance for transformation by HoxB8 /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 1998. http://wwwlib.umi.com/cr/ucsd/fullcit?p9834970.
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Lau, Patrick J. "Characterization of the proliferating cell nuclear antigen (PCNA) in the context of DNA mismatch repair /." Diss., Connect to a 24 p. preview or request complete full text in PDF formate. Access restricted to UC campuses, 2002. http://wwwlib.umi.com/cr/ucsd/fullcit?p3071043.
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Samuels, Scott. "Phosphorylation of DNA topoisomerase I: Role in mammalian cell signal transduction." Diss., The University of Arizona, 1991. http://hdl.handle.net/10150/185373.
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The tumor promoter 12-O-tetradecanoylphorbol-13-acetate (TPA) induces an altered program of gene expression, followed by DNA synthesis and cell division, in quiescent murine fibroblasts. The phosphorylation of DNA topoisomerase I, a nuclear enzyme involved in transcription and replication, was characterized in quiescent 3T3-L1 cells treated with TPA. An anti-DNA topoisomerase I antibody from sera of patients with the autoimmune disease diffuse scleroderma was used to isolate phosphorylated DNA topoisomerase I. Phosphorylation was stimulated slightly within 10 min and 6-fold by 2 h of TPA treatment; TPA at 100 ng/ml maximally enhanced phosphorylation. DNA topoisomerase I was modified primarily on serine, with a minor phosphothreonine component. The half-life of incorporated phosphate on DNA topoisomerase I was approximately 40 min in both TPA-treated and control cells, suggesting that stimulation of a kinase was the mechanism for increased phosphorylation. In addition, the phosphorylation of DNA topoisomerase I was enhanced in rat H-35 hepatoma cells treated with insulin as well as Swiss/3T3 fibroblasts treated with epidermal growth factor. DNA topoisomerase I phosphorylation in vitro by protein kinase C, the cellular receptor for TPA, was also characterized. DNA topoisomerase I from HeLa cells was purified to apparent homogeneity and was phosphorylated in a Ca²⁺ and phospholipid-dependent fashion by type III protein kinase C, purified 860-fold from mouse brain; the reaction was stimulated by TPA. Approximately 1.3 moles of phosphate were incorporated per mole of substrate, predominantly on a tryptic peptide that comigrated with the major in vivo phosphopeptide, although other sites were phosphorylated to a lesser extent. Serine was the primary amino acid modified, however phosphothreonine was also detected. The incorporation of phosphate into DNA topoisomerase I was linear in the range of time and protein kinase C examined. The apparent K(m) and V(max) for the reaction were 0.4 μM and 0.7 μmol phosphate per min per mg, respectively. Thus, phosphorylation, possibly mediated by protein kinase C, was postulated to be a physiologically significant means of regulating DNA topoisomerase I during mammalian cell proliferation.
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Boyer, Angelique Sun. "Purification and characterization of a chloroplast DNA-dependent soluble RNA polymerase from pea." Diss., The University of Arizona, 1994. http://hdl.handle.net/10150/186651.
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A chloroplast DNA-dependent RNA polymerase has been purified 350,000-fold from pea. The purification procedure includes the following steps: 100,000 x g centrifugation, DE-52 ion exchange chromatography, ammonium sulfate precipitation, Sephacryl S-300 gel filtration and two sequential Mono-Q columns. The purified protein preparation was resolved into a predominant protein complex at 669 kDa by non-denaturing gel electrophoresis. Based on gel filtration chromatography the native molecular weight of the purified enzyme is approximately 620,000. Using SDS-PAGE the purified enzyme is separated into ten polypeptides of 120, 110, 95, 84, 81, 75, 54, 51, 42, and 35 kDa. The enzyme is completely dependent on an exogenous DNA template for activity. The 110 kDa polypeptide binds nucleotide triphosphates. The 42 kDa polypeptide cross-reacts with antiserum raised to the plastid encoded α-subunit protein. The enzymatic properties of the soluble RNA polymerase from pea chloroplasts were determined. The apparent energy of activation for the incorporation of UMP into RNA is 34 kcal/mole. The apparent Km value is 0.1 mM for GTP and the Vmax is 200 pmol/min/mg. The optimal conditions for maximum enzyme activity were 2 mM KCl, 15 mM MgCl₂ (or MnCl₂), 40°C and pH 7.9. The soluble enzyme activity is inhibited by (NH₄)₂SO₄, tagetitoxin and heparin. The bacterial RNA polymerase inhibitor rifampicin inhibits chloroplast RNA polymerase enzyme activity completely at high concentration (1 mg/ml). Slot blot hybridization, S1 nuclease protection, and in vitro transcription assays were employed to demonstrate that the purified RNA polymerase selectively initiates transcription from higher plant psbA and rbcL promoters and the Euglena tRNAᴾʰᵉ promoter. Transcription occurs from supercoiled DNA templates but not from linear DNA templates. The soluble RNA polymerase does not transcribe from the higher plant 16S rRNA or tRNA promoter, and does not recognize the threonine attenuator (thra).
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Mendillo, Marc Laurence. "The MutS and MutL protein families and their role in the initiation of DNA mismatch repair." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2007. http://wwwlib.umi.com/cr/ucsd/fullcit?p3273476.
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Thesis (Ph. D.)--University of California, San Diego, 2007.Title from first page of PDF file (viewed April 9, 2008). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references.
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Chan, Shing Fai. "ATM phosphorylates and activates the transcription factor MEF2D for neuronal survival in response to DNA damage." Diss., [La Jolla] : University of California, San Diego, 2009. http://wwwlib.umi.com/cr/ucsd/fullcit?p3359980.
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Thesis (Ph. D.)--University of California, San Diego, 2009.Title from first page of PDF file (viewed July 22, 2009). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 73-92).
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Goldstein, Eric D. "Analysis of the repair of topoisomerase II DNA damage." Honors in the Major Thesis, University of Central Florida, 2011. http://digital.library.ucf.edu/cdm/ref/collection/ETH/id/385.
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A large number of anti-cancer chemotherapeutics target DNA topoisomerases. Etoposide is a specific topoisomerase II poison which causes reversible double strand DNA breaks. The focus of this project is to analyze the repair of DNA damage induced by etoposide.. Double strand DNA break repair is mediated by through either non-homologous end joining (NHEJ) or homologous recombination. NHEJ repairs through direct ligation of a double stranded break while homologous recombination utilizes a homologous template to recover the wild type sequence. A reporter cassette, RYDR-GFP, has been stably integrated into HeLa cells. This reporter contains an ultra-high affinity topoisomerase II cleavage site (RY) placed in the middle of a mutant GFP sequence. Flanking this sequence is a corresponding stretch of wild type GFP that is used as template to repair the break and restore gene function yielding GFP positive cells. Titrations with etoposide have shown that a logarithmic increase in drug concentration yields a corresponding increase in repair through homologous recombination (HR). This result demonstrates that topoisomerase II mediated damage is efficiently repaired by the process of HR. To examine NHEJ repair, a doxycycline inducible, stably integrated NHEJ HeLa cell reporter cassette was also evaluated. The data indicates that repair of topoisomerase II mediated DNA damage occurs more efficiently through the HR pathway. Collectively, the data suggests that tumor cells proficient in HR repair may effectively elude treatment by topoisomerase II targeting drugs.B.S.
Bachelors
Medicine
Molecular Biology and Microbiology
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Raymond, Amy Conroy. "Structure and function of human tyrosyl-DNA phosphodiesterase I /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2004. http://wwwlib.umi.com/cr/ucsd/fullcit?p3141930.
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Hyman, Paul Lawrence. "The genetics of bacteriophage T4 DNA repair during infection." Diss., The University of Arizona, 1991. http://hdl.handle.net/10150/185380.
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Recombinational repair is a widespread mechanism for dealing with DNA damage. It is found in both prokaryotes and eukaryotes which implies that it is an ancient process which arose early in the evolutionary history of life on Earth. In addition, it has been implicated as a driving force in the evolution of sexual reproduction. In this dissertation I report experimental results which clarify the role of recombinational repair in bacteriophage (phage) T4. The Luria-Latarjet effect is an increase in resistance to DNA damage by phage T4 during infection. It has often been assumed to involve recombinational repair, but this has never been actually demonstrated. Using eleven phage T4 mutants, I have obtained evidence that the Luria-Latarjet effect is due to three repair pathways--excision repair, post-replication-recombinational-repair (PRRR) and multiplicity reactivation (MR), a form of recombinational repair. My results show that the Luria-Latarjet effect develops in two stages. The first stage starts soon after infection. Damage which occurs during the first stage can be repaired by excision repair or PRRR. The second stage appears to start after the first round of DNA replication is complete. Damage which occurs during this stage can apparently be repaired by MR as well as the other two repair pathways. I have also transferred the yeast RAD50 gene, which is required for recombinational repair, into an E. coli expression vector. After demonstrating expression of the protein, I used this construct to test for complementation by the RAD50 gene of E. coli and phage T4 mutants defective in recombinational repair. I was unable to demonstrate complementation in five different assays. Based on the results discussed above and what is known about the phage T4 life cycle, I propose a model for the Luria-Latarjet effect in phage T4. Further, I propose that recombinational repair has been selected to ensure progeny phage genomes are packaged with minimum damage. Since numerous other viruses also show a Luria-Latarjet effect type resistance to DNA damage, I suggest that the conclusions from this phage T4 study may have wide applicability to other viruses.
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Torres, Gabriella. "An exploratory study : romanticism in modern day men and women." Honors in the Major Thesis, University of Central Florida, 2010. http://digital.library.ucf.edu/cdm/ref/collection/ETH/id/1509.
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This item is only available in print in the UCF Libraries. If this is your Honors Thesis, you can help us make it available online for use by researchers around the world by following the instructions on the distribution consent form at http://library.ucf.edu/Systems/DigitalInitiatives/DigitalCollections/InternetDistributionConsentAgreementForm.pdf You may also contact the project coordinator, Kerri Bottorff, at kerri.bottorff@ucf.edu for more information.Bachelors
Sciences
Psychology
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Bodnovich, Kara Lynn. "The relationship between preschoolers academic self-esteem and the quality of their child care center." Morgantown, W. Va. : [West Virginia University Libraries], 2002. http://etd.wvu.edu/templates/showETD.cfm?recnum=2331.
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Thesis (M.S.)--West Virginia University, 2002.Title from document title page. Document formatted into pages; contains vi, 49 p. Vita. Includes abstract. Includes bibliographical references (p. 36-37).
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Lee, Bongyong. "Epigenetic Control Mechanisms in Somatic Cells Mediated by DNA Methyltransferase 1." Master's thesis, University of Central Florida, 2009. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/6228.
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DNA methylation regulates gene expression through a complex network of protein/protein and protein/DNA interactions in chromatin. The maintenance methylase, DNA methyltransferase 1 (DNMT1), is a prominent enzyme in the process that is linked to DNA replication and drives the heritable nature of epigenetic modifications in somatic cells. The mechanistic details that explain how DNMT1 catalytic action is directed in a chromatin setting are not well understood. We hypothesize that post translational modifications and a variety of protein-protein interactions processes are key regulatory elements that set the methylation of CpG elements essential for normal growth behavior in somatic cells. These fundamental processes can be disrupted by DNA damage leading to inappropriate gene silencing and loss of growth control in somatic cells. First, we show that DNMT1 is post-translationally modified by sumoylation and we have mapped these sumoylation sites by defined mutations. Sumoylated DNMT1 is catalytically active on genomic DNA in vivo and substantially increases the enzymatic activity of DNMT1 both in vitro and in chromatin. These data establish that sumoylation modulates the endogenous activity of a prominent epigenetic maintenance pathway in cells. Second, we investigated novel mechanisms whereby somatic cells can erase then reset DNA methylation events in somatic cells. In this study, the relationship between DNA damage and gene silencing was explored. To this end, we generated a HeLa cell line containing a specialized GFP reporter cassette (DRGFP) containing two mutated GFP genes and a unique I-SceI restriction endonuclease site. These cells do not express GFP. A unique double strand break is then delivered by transfecting in the gene for I-SceI. About 4% of the cells produced a functional GFP by gene conversion and homologous recombination (HR); however roughly half of the GFP recombinants expressed the gene poorly and this was attributed to gene silencing. Silencing of the GFP expressing cell clones was due to DNA methylation and could be reversed using a drug that inhibits global methylation (5-aza-2'-deoxycytidine). Approximately half of the repaired genes were heavily methylated, and half were hypomethylated. That is, a key intermediate methylation state after HR repair is hemimethylated DNA, defined as methylation limited to one strand. Evidence is given that DNMT1 is acting as a de novo methylase at the HR repair patches in cells. Moreover, the DNA damage inducible protein, GADD45 [alpha], interacts specifically with the catalytic domain of DNMT1 and GADD45 [alpha] binds with extremely high affinity to hemimethylated DNA sites. Thus, GADD45 [alpha] is a key regulatory element in silencing of HR repaired DNA segments and appears to inhibit the activity of DNMT1. Consistent with these results, we found that GADD45 [alpha] increased the expression of recombinant GFP following HR repair, further suggesting its role in orchestrating strand specific DNA methylation by DNMT1. Since these experiments were performed in live cells, there is strong physiological relevance. We propose that DS DNA damage and the resulting HR process involves precise, strand selected DNA methylation mediated by the prominent methylase enzyme, DNMT1. Moreover, DS DNA break repair through HR and gene conversion, may potentially erase and reset DNA methylation patterns and therefore alter the expression of repaired genes. The overall process is tightly regulated by the DNA damage inducible protein GADD45 [alpha], which may coordinate strand specific methylation by recruiting DNMT1 to HR repair templates. The ability of GADD45 [alpha] to modulate DNMT1 catalytic activity may explain its role as a passive mediator of demethylation that has been reported by other groups. The overall process of silencing post DNA repair is a strong evolutionary force that may predispose cells to malignant transformation.Ph.D.
Doctorate
Burnett School of Biomedical Sciences
Biomedical Sciences
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Hart, Jennifer A. "An analysis of the primordial soup hypothesis with respect to DNA structure and the genetic code." Lynchburg, Va. : Liberty University, 1995. http://digitalcommons.liberty.edu.
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Kim, Baek. "Biochemical and genetic analyses on DNA binding and cleavage of LexA repressor." Diss., The University of Arizona, 1993. http://hdl.handle.net/10150/186221.
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LexA is an Escherichia coli repressor that controls the expression of about 20 SOS target genes in response to DNA damage. Two biological activities of LexA, DNA binding and proteolytic self-cleavage, play important roles in regulation of SOS response. Upon DNA damage, the repressor function of LexA is inactivated by the cleavage reaction, and the expression of the SOS target genes is derepressed, which results in DNA damage repair. LexA binds to sites with dyad symmetry. However, unlike most repressors, LexA dimerizes very poorly in solution. This poor dimerization could be a disadvantage for tight binding to DNA if the DNA binding species of LexA is a dimer form as observed in phage λ repressor. An alternative DNA binding pathway, the monomer binding pathway, was tested. In this pathway, two LexA monomers bind individually to DNA and then dimerize on the DNA. This monomer binding pathway predicts that LexA should bind to a half-site of the symmetric recA operator sequence. Since binding of LexA monomer to a half-site operator was observed, the monomer binding pathway was favored for the LexA DNA binding pathway. The calculated degree of cooperativity between two LexA monomers was 10⁶. This high degree of cooperativity is generated by protein-protein interaction in the C-terminal potential dimerization domain. The second part of the study focused on the cleavage of LexA. In the course of a screen for defective repressor mutants, an Indˢ mutant, LP89, was isolated. This mutant protein autodigested about 50 times faster than wild-type LexA under physiological conditions in vitro. A LexA combination mutant that contains three Indˢ mutations can undergo the self-cleavage extremely rapidly under these conditions in vivo (t₁/₂ = ≈ 10 second). This multiple mutant, LP89-QW92-EA152, was suggested to overcome most of the rate-limiting steps of the cleavage reaction. Finally, an intermolecular trans-cleavage reaction was developed. In this reaction one molecule of LexA C-terminal fragment containing the active site could cleave many molecules of a LexA substrate containing the cleavage site. This trans-cleavage reaction was used to investigate several aspects of the self-cleavage mechanism of not only LexA but also phage λ CI repressor. First, possible functional roles of three Indˢ mutations were assessed by this trans-cleavage reaction. Second, demonstration of various types of trans-cleavage reaction suggested that both cleavage site and active site of LexA are exposed to the surface of the protein. Third, this reaction was used to study how phage λ CI autodigests much slower than LexA. Since the active sites of both proteins have the same enzymatic activity and substrate specificity, it was strongly suggested that E. coli LexA and phage λ CI repressor have evolved such different cleavage rates by modulating the interaction between their cleavage site and active site.