Thesis (Ph. D.)--Ohio State University, 2005. / Title from first page of PDF file. Document formatted into pages; contains xiv, 200 p.; also includes graphics (some col.). Includes bibliographical references (p. 167-197). Available online via OhioLINK's ETD Center

Thesis (Ph.D. in Molecular Biology) -- University of Colorado at Denver and Health Sciences Center, 2005. / Typescript. Includes bibliographical references (leaves 130-152). Free to UCDHSC affiliates. Online version available via ProQuest Digital Dissertations;

Thesis (Ph. D.)--University of Missouri-Columbia, 2007. / "May 2007" The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Vita. Includes bibliographical references.

Thesis (Ph. D)--University of Washington, 2000. / Vita. Includes bibliographical references (leaves 126-137).

Orientador: Sergio Roberto Peres Line / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Odontologia de Piracicaba / Made available in DSpace on 2018-08-15T00:52:49Z (GMT). No. of bitstreams: 1 Ramenzoni_LizaLima_D.pdf: 1680205 bytes, checksum: 6080ff087e6c9a65c1f6a082b0ad1d36 (MD5) Previous issue date: 2009 / Resumo: O gene PAX9, pertencente à família Pax, é amplamente expresso em vários tecidos craniofaciais durante o desenvolvimento. Sabe-se que mutações neste gene em humanos causam fenótipo de oligodontia, afetando os dentes molares e segundos pré-molares. Grande variedade de agentes fisiológicos e farmacológicos externos podem ter impacto relevante na regulação da atividade transcricional de genes modulando fatores de transcrição. A presente tese focaliza o estudo da região 5'do gene PAX9 humano e tem como objetivo analisar a influência da dexametasona, ácido retinóico e ergocalciferol (vitamina D2) na atividade transcricional de sua região promotora, utilizando construções em vetor plasmideano que dirige a transcrição do gene da luciferase de vagalume (Photinus pyralis, pGL3 basic vector). Para ensaios de transcrição, foram amplificados através de ensaios com transcriptase reversa, transcritos do gene PAX9 de células mamárias de adenocarcinoma MCF-7 e células odontoblastóides de camundongo MDPC23. Estes transcritos foram quantificados através de PCR quantitativo. Fragmentos da região promotora do gene PAX9 humano de 1198pb (-1106 - +92), 843pb (-751- +92) e 691bp (-1106 - +92 com deleção de 507pb nos sítios -645 e -138) foram recombinados com vetor de expressão pGL3Basic e denominados PAX9-pGL3B1, PAX9-pGL3B2 e PAX9-pGL3B3, respectivamente. As contruções foram transfectadas em cultura de células mamárias de adenocarcinoma MCF-7 e células odontoblastóides de camundongo MDPC23. Todas as placas de cultura foram submetidas à ação de três drogas: dexametasona (DEX), ácido retinóico (RE) e ergocalciferol (VITD2). Após lise das células, os níveis relativos de expressão da proteína luciferase foram analisados com o uso do kit Dual-Glo Luciferase em luminômetro. Os resultados referentes às células mamárias de adenocarcinoma MCF-7 mostraram que: 1) Altas concentrações de ácido retinóico aumentaram a síntese de RNA mensageiro transcrito. 2) Fragmentos do promotor PAX9 de 1198pb (PAX9-pGL3B1) e 843pb (PAX9-pGL3B2) foram ativados na presença de ácido retinóico mas suas transcrições desestimuladas na presença da dexametasona e ergocalciferol. 3) A atividade da luciferase na construção PAX9-pGL3B2 foi mais fraca que outras duas construções, indicando que a sequência -1106 and -751 ou 355pb era importante para a atividade transcricional. 4) Fragmento do promotor clivado nos sítios -645 e -138 com deleção de 507pb (PAX9-pGL3B3) foi ativado negativamente somente na presença do ergocaciferol, enquanto que com a dexametasona e ácido retinóico o mesmo não foi afetado. Quanto às células odontoblastóides de camundongo MDPC23, os resultados mostraram que: 1) Todas as concentrações de ergocalciferol influenciaram positivamente a síntese de RNA mensageiro transcrito. 2) A atividade promotora das construções PAX9-pGL3B1 e PAX9-pGL3B2 foi aumentada com baixa concentração de dexametasona e ergocaciferol enquanto que alta concentração diminuiu esta atividade. 3) Na construção PAX9-pGL3B3, todas concentrações de ergocaciferol influenciaram a transcrição do promotor negativamente, enquanto que com a dexametasona e ácido retinóico, a mesma não foi afetada. Concluímos que as drogas dexametasona, ácido retinóico e ergocalciferol podem modular a expressão do gene PAX9. A região de 507pb deletada do promotor do gene PAX9 humano pode conter sítios de ligação para receptores do ácido retinóico e dexametasona. / Abstract: PAX9, member of the family homeobox, has important functions in embryogenesis and it is widely expressed in various craniofacial tissues during development. PAX9 mutations in human families cause autosomal dominant oligodontia, characterized by the absence of permanent molars and pre-molars. A great variety of physiological or pharmacological environmental factors may have impact on downstream signaling cascades and transcriptional regulation of gene modulating transcription factors. This work focused on the analysis on the 5'-flanking region of the PAX9 gene studying the influence of retinoic acid, dexamethasone and vitamin D on the expression of PAX9 by expression constructs that carry the reporter gene luciferase (Photinus pyralis, pGL3 basic vector). In the present study, we have PCR amplified cDNAs encoding mouse Pax9 from Mouse Odontoblast Cell-Like-23 (MDPC23) and PAX9 from Human breast adenocarcinoma (MCF-7) and quantified by Quantitative PCR. We examined the transcriptional activity of human PAX9 promoter from constructions: 1) PAX9-pGL3B1 construct clone PAX9 gene promoter 1198bp from -1106 upstream to +92 downstream of translation start site (ATG). 2) PAX9-pGL3B2 construct clone PAX9 gene promoter 843bp from -751 upstream of translation start site (ATG) to +92 downstream of translation start site (ATG). 3) PAX9-pGLB3 construct clone PAX9 gene promoter 691bp from -1106 upstream of translation start site (ATG) to +92 downstream of translation start site (ATG) using deletion of 507bp in restriction sites (-645 and -138) of ApaI enzyme. These constructions were transfected into Mouse Odontoblast Cell-Like-23 (MDPC23) and PAX9 from Human breast adenocarcinoma (MCF-7). Cell cultures were all submitted to selective regulation of tree drugs: dexamethasone (DEX), retinoic acid (RE) and ergocalciferol (VITD2). Relative luciferase expression units were obtained by dual luciferase assay kit. The results in Human breast adenocarcinoma (MCF-7) showed that retinoic acid and dexamethasone influenced negatively the expression of PAX9 promoter. PAX9-pGL3B1 and PAX9-pGL3B2 promoter was inhibited under the treatment of dexamethasone and ergocalciferol. Retinoic acid and dexamethasone did not altered PAX9-pGL3B3 (-1106 to +92, 507bp deleted with ApaI digest) behavior. Luciferase activity in plasmid PAX9-pGL3B2 was always weaker than the other two constructions indicating that sequence present between -1106 and -751 or 355bb were important for the transcriptional activity of PAX9 promoter. The results in Mouse Odontoblast Cell-Like-23 (MDPC23) showed that it PAX9-pGL3B1 and PAX9-pGL3B2 promoter activity was increased by the treatment of lower concentration of dexamethasone and ergocalciferol, whereas higher concentration of the same drugs decreased this activity. The effect of the retinoic acid in the luciferase activity of PAX9-pGL3B1 has the same pattern but for the PAX9-pGL3B2, all concentrations increased the promoter activity. For the PAX9-pGL3B3 construction, concentrations of ergocalciferol had a statistically significance decreasing the activity of the promoter and no effect of the activity was observed in the dexamethasone and retinoic acid treatment. In conclusion, dexamethasone, retinoic acid and ergocalciferol may bind to PAX9 gene promoter and up or down-regulate PAX9 transcriptional activity. A 507bp region (-645 and -138) within PAX9 promoter may harbor biding sites for dexamethasone and retinoic acid since none of concentrations of these reagents influenced changes in promoter activity. / Doutorado / Histologia e Embriologia / Doutor em Biologia Buco-Dental

The initiation of transcription by the Bacillus subtilis sigma-M3 RNA polymerase at two Bacillus phage ɸ29 promoters and the effect of the delta subunit on initiation have been investigated by an in vitro kinetic analysis. The templates for the analysis were plasmids which carried the ɸ29 A2 or G2 promoter. The cloning and localization of the A2 promoter are reported here. The kinetics of RNA synthesis initiation were examined using a single-round run-off transcription assay in which multiple initiation events at a single promoter were inhibited with heparin. It was observed that the formation of heparin-resistant complexes at the A2 promoter required the presence of the initiating nucleotides, while the RNA polymerase alone was able to form heparin-resistant, non-initiated complexes at the G2 promoter. The G2 promoter was also shown by a competition assay to be a stronger promoter than A2. The effect of the delta subunit on complex formation at the two promoters was investigated with the single-round transcription assay. Delta had no effect on the formation of initiation complexes at the G2 promoter but lowered the rate and extent of complex formation at the A2 promoter. The effect of delta on the kinetic parameters of complex formation at the A2 promoter was also investigated. The data suggested that delta affects the efficiency with which the enzyme/promoter complexes undergo the transition(s) to a complex from which RNA synthesis can be initiated, although other interpretations were possible. A model for the effect of delta is proposed, in which it is postulated that the release of delta from the enzyme/promoter complex is essential for initiation. Enzyme which is associated with delta can interact with both the A2 and G2 promoters but complexes at the weaker A2 promoter do not efficiently release delta, thus slowing the formation of initiation complexes. / Science, Faculty of / Microbiology and Immunology, Department of / Graduate

Rhodobacter capsulatus is a Gram negative bacterium that exhibits a variety of growth modes, including chemoheterotrophic growth and photoheterotrophic growth. Upon a shift of cultures from high to low oxygen concentrations the photosynthetic apparatus is synthesized and incorporated into the inner membrane. The puf operon contains genes that encode structural proteins found in the light-harvesting and reaction center complexes. In a preliminary attempt to pinpoint the location of the puf promoter R. capsulatus RNA polymerase was purified by standard techniques and used in in vitro runoff transcription assays. It was found that the polymerase was capable of specific transcription with linearized pUC13 DNA but no specific transcription could be obtained with K capsulatus DNA. It was concluded that some factor or condition necessary for specific transcription with R capsulatus DNA was absent from these assays. The location of the puf promoter was subsequently found through a series of deletions and oligonucleotide-directed mutations in the 5' region of the puf operon. Fragments that contained these mutations were placed translationally in-frame with the lacZ gene of Escherichia coli in plasmids that could be conjugated into K capsulatus. Assays of beta-galactosidase activities under low and high oxygen conditions resulted in localization of the promoter to a position approximately 540 basepairs upstream of what was previously believed to be the first gene of the operon, the pufB gene. RNA 5' end-mapping experiments showed that the quantity of RNA transcripts obtained were comparable to the lacZ activities. The existence of multiple low abundance RNA 5' ends prompted the theory that the primary transcript has a short half-life, and is rapidly processed to yield a more stable transcript with a 5' end that maps just upstream of the pufB gene. It was found that only the 5' end nearest to the promoter could be capped by guanylyl transferase, and this could only be detected when the putative processing sites were deleted. The DNA sequence between the promoter and the pufB gene contains a new gene of the puf operon, the pufO gene. Deletion of this gene showed that it plays an essential role in the formation of mature light-harvesting and reaction center complexes. / Science, Faculty of / Microbiology and Immunology, Department of / Graduate

Transcriptional analysis was used to investigate the molecular mechanisms which effect cellulase gene expression in the gram-positive bacterium Cellulomonas fimi strain ATCC 484 and the gram-negative bacterium Agrobacterium sp. strain ATCC 21400. The cenA, cex and cenB genes of C. fimi encoding the extracellular β-1,4-endoglucanase, EngA (EC 3.2.1.4; Mr 48,700), the extracellular β-1, 4-exoglucanase, Exg (EC 3.2.1.91; Mr 47,300) and the extracellular β-1,4-endoglucanase EngB (EC 3.2.1.4; Mr 110,000) respectively, were characterised. By northern blot analysis, cenA mRNA was detected in C. fimi RNA prepared from glycerol- and carboxymethylcellulose (CMC)-grown cells but not in RNA from glucose-grown cells. The cex mRNA was found only in RNA from CMC-grown cells. The cenB mRNA was found in all three preparations of RNA. Therefore, the expression of these genes is subject to regulation by the carbon source provided to C. fimi. High resolution nuclease SI protection studies with unique 5'-labeled DNA probes and C. fimi RNA isolated in vivo, were used to map the 5' termini of cenA and cex mRNAs. Two cenA mRNA 5' ends, 11 bases apart, mapped 51 and 62 bases upstream of the cenA start codon, suggesting that in vivo, cenA transcription was directed from two promoters in tandem. The cex mRNA 5' end was found to map 28 bases upstream of the cex start codon. Using SI mapping with unlabeled DNA probes and C. fimi RNA which had been isolatedin vivo but which had been 5'-labeled in vitro with vaccinia virus capping enzyme confirmed that true transcription initiation sites for cenA and cex mRNA had been identified. The SI mapping revealed mRNA 3' termini 1,438, 1,449, and 1, 464 bases from the major cenA start site, and one 3' terminus 1,564 bases from the major cex mRNA start site, in good agreement with the northern blot data. High resolution SI studies were also used to show that abundant mRNA 5' ends mapped upstream of the cenB start codon in RNA prepared from CMC-grown cells, while less-abundant species mapped 52 bases closer to the ATG codon in RNA prepared from C. fimi grown on any one of the three substrates. These results seem to indicate a tandem promoter arrangement with an ATG-proximal promoter directing low-level constitutive cenB transcription and a more distal promoter directing higher levels of cenB transcription as a result of C. fimi growth on cellulosic substrate. Steady- state levels were determined for cenA, cex and cenB mRNAs with RNA prepared from glycerol-, glucose-, and CMC-grown cultures of C. fimi in slot-blot hybridisations with radiolabeled oligodeoxyribonucleotide probes. A cex-linked gene (clg) was identified by sequence inspection and SI mapping. Transcripts of the abg gene encoding the β-glucosidase (Abg, EC 3.2.2.21/ Mr 50,000) of Agrobacterium sp. strain ATCC 21400 were also characterised. Northern blot analysis of Agrobacterium RNA revealed the size of the in vivo abgmRNA was approximately 1,500 bases in length. High resolution SI mapping determined abg mRNA 5' ends 22 bases upstream of the abg ATG codon and 3' ends 71 bases downstream of the abg stop codon. / Science, Faculty of / Microbiology and Immunology, Department of / Graduate

L1-type cell adhesion molecule (L1CAM) plays an essential role in the development of nervous system and is also highly relevant for the progression of diseases such as Alzheimer’s disease, stroke and cancers, some of the leading causes of human mortality. In addition to its canonical role as a plasma membrane protein organizing the cytoskeleton, recent in vitro studies have revealed that transmembrane as well as cytosolic fragments of proteolytically cleaved vertebrate L1CAM translocate to the nucleus and regulate expression of genes involved in DNA post-replication repair, cell cycle control, migration and differentiation. However, little is known about the in vivo function of L1CAM in the adult nervous system. This dissertation research focuses on studying in vivo nuclear translocation and function of L1CAM. Using the Drosophila model system, we first show that the sole Drosophila L1CAM homolog, Neuroglian (Nrg), is proteolytically cleaved by Alzheimer’s associated secretases, similar to L1CAM, and is also translocated to the nucleus in the adult nervous system. Subsequently, we have shown that the deletion of highly conserved Ankyrin binding domain or FIGQY motif disrupts nuclear import. Further experiments have revealed that the nuclear translocation of Nrg is in fact regulated by the phosphorylation of the FIGQY motif. Importantly, our studies also show transgenic expression of full-length Nrg or the intracellular domain of Nrg resulted in increased myc expression, which is associated with increased sensitivity to oxidative stress and reduced life span. On the other hand, deletion of the FIGQY motif or mutations preventing its phosphorylation led to decrease in myc expression. In summary, we have identified a novel role for the highly conserved Ankyrin binding domain in nuclear translocation and transcriptional regulation of the Drosophila myc oncogene, which is of high relevance to neurodegenerative diseases and cancer associated with oxidative stress. / Includes bibliography. / Dissertation (Ph.D.)--Florida Atlantic University, 2018. / FAU Electronic Theses and Dissertations Collection

Genes identified by SAGE may serve as potential prognostic marker or therapeutic target. 14-3-3 sigma is a putative tumor suppressor and can be induced in response to DNA damage following irradiation, leading to cell cycle arrest in G2/M in human cancer cells. Our SAGE results revealed that 14-3-3 sigma expression is significantly downregulated in C666-1 cells. The study of 72 primary NPCs showed that an increased expression of 14-3-3 sigma was associated with a poorer clinical outcome in terms of shorter overall survival (OS; p=0.0297) and shorter disease free survival (DFS; p=0.042) using univariate analysis. Hence, 14-3-3 sigma may be used as an independent prognostic marker for NPC patients. / In conclusion, a NPC transcription profile has been successfully generated and several candidate NPC-associated genes have been identified by Serial Analysis of Gene Expression (SAGE) and NPC transcriptome map. These novel findings lead to better understanding of the molecular basis of NPC development and provide a foundation for discovery of new therapeutic strategies. / Nasopharyngeal carcinoma (NPC) is one of the most prevalent cancers among Southern Chinese. To better understand the genetic basis of this disease, Serial Analysis of Gene Expression (SAGE) was performed to investigate the transcriptional profiles of an EBV-positive NPC cell line (C666-1) and a normal NP outgrowth (NP4). A total of 102,059 SAGE tags were extracted in both libraries and 250 genes with 10-fold or more differential expression were found in NPC cells compared to normal NP cells. Eleven differentially expressed genes identified by SAGE were selected for confirmation using real time RT-PCR. The transcripts for 5 of the 11 genes, CD 74, Transcriptional intermediary factor 1, Ferritin 1, Claudin 4, and fatty acid synthase were overexpressed in NPC cells. Conversely, the remaining transcripts including Keratin 17, Keratin 5, S100 calcium-binding A2, Cystatin A, 14-3-3 sigma and Caveolin 1 were underexpressed in NPC cells. The aberrant expression of CD74, Claudin 4, Fatty acid synthase, 14-3-3 sigma, Caveolin 1 were further validated by immunohistochemistry on 20 NPC patients. / On the other hand, fatty acid synthase (FASN), a key enzyme for de novo lipogenesis, is a putative therapeutic target in treating NPC. Immunohistochemical studies showed upregulation of FASN in 20.8% (15/72) of the NPC cases compared with the adjacent normal NP epithelium. In addition, FASN expression also had prognostic significance in predicting the outcome of patients after radiotherapy, as high levels of FASN expression were associated with worse overall survival (OS, p=0.032) and disease free survival (DFS, p=0.002) in NPC patients. FASN inhibitors, such as C75 which inhibit cell growth via cell cycle arrest in G2/M phase, are potential chemotherapeutic agents in treating NPC. / The genome-wide quantitative analysis of gene expression by SAGE with matched chromosomal positions enables the construction of a transcriptome map of NPC. A total of 8 and 29 overexpressed and underexpressed gene clusters were observed, respectively. Some novel regions that have never been illustrated in previous reports such as amplification regions at 2p11.2-p25.1, 2q33-q37, 9q22-q34, 17p11.2-p13.2 and deletion regions at 1p12-p31.2, 1q25-q42.12, 2q21.3-q33, 8p21.1-p22, 9q33-q34.3, 10q23.3-q26.3, 12p13, 16p13, 17q23.2-q25, 19p13, 19q12-q13.2, 20p11-p13, 22q13, Xp11.2-p11.4, and Xq26-q28 were also identified. A candidate tumor suppressor gene named MEG3 has been found within an underexpressed region at 14q32.2 in the NPC transcriptome map. Our FISH analysis revealed that chromosome loss at 14q32 is associated with hypermethylation of MEG3 promoter region in 9/13 (75%) of NPC patients. Loss of imprinting is the major mechanism that governs the MEG3 expression. Moreover, transient transfection of one of the MEG3 isoforms (accession no. AF119863) could obviously inhibit cell colony formation of NPC cells. Taken together, MEG3 gene on chromosome 14q32.2 might act as a tumor suppressor in NPC. / Chan, Yat Yee. / "March 2008." / Adviser: Lo Kwok Wai. / Source: Dissertation Abstracts International, Volume: 70-03, Section: B, page: 1605. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2008. / Includes bibliographical references (p. 196-225). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstracts in English and Chinese. / School code: 1307.