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1
Durand, Alexandre. "Structural study of the transcriptional co-activator SAGA." Thesis, Strasbourg, 2014. http://www.theses.fr/2014STRAJ051/document.
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Le complexe SAGA (Spt-Ada-Gcn5 acetyl transferase) est un co-activateur transcriptionel, conservé chez les eucaryotes, qui participent à la transcription d’environ 10% des gènes chez la levure, où il fait le lien entre les composants du complexe de pré-initiation, tel que la TATA-box Binding Protein (TBP) et des activateurs, et modifie les histones dans le contexte de la chromatine (acétylation et déubiquitination). Ces travaux de thèse ont permis de décrire l’architecture moléculaire du complexe observée par microscopie électronique. Nous avons pu (i) localiser le module de déubiquitination au sein du complexe entier et ainsi (ii) définir une zone d’interaction avec le nucléosome ; (iii) montrer la présence de deux sites d’interaction avec la protéine TBP situé au niveau d’une « pince »moléculaire ; (iv) observer un lien fonctionnel entre le module de déubiquitination, en particulier de la protéine Sgf73, et les conformations adoptées par cette pinceThe SAGA complex (Spt-Ada-Gcn5 acetyl transferase) is a transcriptional coactivator, highly conserved in eukaryotes, involved in the transcription of 10% of the genes in yeast, where it bridges the components of the pre-initiation complex such as the TATA-box Binding Protein (TBP) and activators, as well as modifies histones in the chromatin template (acetylation and deubiquitination). This work has revealed the molecular architecture of the complex observed by electron microscopy. We could (i) localize the deubiquitination module within the whole complex and thus (ii) define the interaction surface with the nucleosome; (iii) reveal the presence of two TBP-interacting surfaces localized at the tips of a molecular clamp; (iv) observe a functional link between the deubiquitination module, in particular the Sgf73 protein, and the conformation adopted by this clamp
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Ameur, Adam. "A Bioinformatics Study of Human Transcriptional Regulation." Doctoral thesis, Uppsala universitet, Centrum för bioinformatik, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-9346.
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Regulation of transcription is a central mechanism in all living cells that now can be investigated with high-throughput technologies. Data produced from such experiments give new insights to how transcription factors (TFs) coordinate the gene transcription and thereby regulate the amounts of proteins produced. These studies are also important from a medical perspective since TF proteins are often involved in disease. To learn more about transcriptional regulation, we have developed strategies for analysis of data from microarray and massively parallel sequencing (MPS) experiments. Our computational results consist of methods to handle the steadily increasing amount of data from high-throughput technologies. Microarray data analysis tools have been assembled in the LCB-Data Warehouse (LCB-DWH) (paper I), and other analysis strategies have been developed for MPS data (paper V). We have also developed a de novo motif search algorithm called BCRANK (paper IV). The analysis has lead to interesting biological findings in human liver cells (papers II-V). The investigated TFs appeared to bind at several thousand sites in the genome, that we have identified at base pair resolution. The investigated histone modifications are mainly found downstream of transcription start sites, and correlated to transcriptional activity. These histone marks are frequently found for pairs of genes in a bidirectional conformation. Our results suggest that a TF can bind in the shared promoter of two genes and regulate both of them. From a medical perspective, the genes bound by the investigated TFs are candidates to be involved in metabolic disorders. Moreover, we have developed a new strategy to detect single nucleotide polymorphisms (SNPs) that disrupt the binding of a TF (paper IV). We further demonstrated that SNPs can affect transcription in the immediate vicinity. Ultimately, our method may prove helpful to find disease-causing regulatory SNPs.
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Koch, Frédéric. "From enhancer transcription to initiation and elongation : a study of eukaryotic transcriptional regulation during lymphocyte development." Thesis, Aix-Marseille 2, 2011. http://www.theses.fr/2011AIX22097.
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La régulation transcriptionnelle des eucaryotes supérieurs est un processus hautement contrôlé du point de vue spatial et temporel lors du développement, ou en réaction à l’environnement. La transcription ciblée des gènes codant requiert l’assemblage d’un complexe de pré-initiation (PIC) aux promoteurs comprenant l’ARN Polymérase (Pol) II et les facteurs généraux de transcription (GTFs) et dépend de la médiation d’un signal par les facteurs activateurs de transcription (TFs). Les années récentes ont montré que la transition de l’initiation vers l’élongation productive de la transcription représente une étape clé de la régulation de l’expression des gènes. Ce processus est également contrôlé par la structure de la chromatine, les modifications d’histones et par la présence d’éléments cis-régulateurs tels que les ‘enhancers’ ou les ‘silencers’. Au cours de ma thèse, nous avons entrepris de décrypter les mécanismes de régulation transcriptionnelle impliqués dans les étapes du développement lymphocytaire. Nous avons essentiellement travaillé sur des thymocytes primaires murins isolés au stade de différenciation double positif (DP, CD4+/CD8+) pour lequel de nombreuses séquences de type ‘enhancers’ ont été caractérisées dans la littérature scientifique. Nous avons également utilisé des lymphocytes B humains (Raji) immortalisés pour certaines des expériences impliquant des manipulation génétiques complexes permettant l’étude de mutants du domaine carboxy-terminal (CTD) de Pol II. En couplant des approches d’analyse à l’échelle du génome au séquençage à haut-débit, nous avons établi des cartographies fines de la localisation de Pol II, des GTFs, des TFs,de modifications d’histones (ChIP-Seq) et de nucléosomes (MNase-seq) ainsi que la caractérisation de populations variées d’ARN par RNA-seq. Nos principaux résultats ont révélé (i) l’assemblage du PIC et la transcription des enhancers tissus-spécifiques, (ii) l’existence de plateforme d’initiation de la transcription (TIPs) aux enhancers et aux promoteurs tissus-spécifique, (ii) que le contenu en GC représente l’un des principaux éléments promoteurs mammifères en permettant une ouverture transcription-indépendante de la chromatine, (iv) l’importance d’une nouvelle modification post-traductionnelle du domaine CTD de Pol II pour la progression de l’enzyme en élongation et finalement (v) que la modification de l’histone H3 sur le résidu K36 methylé corrèle avec l’épissage des transcrits Pol II. Globalement, les résultats les plus important de ce manuscrit consistent dans la mise en évidence de la transcription des enhancers comme caractérisant l’expression des gènes tissus-spécifiques et dans l’importance des ilots CpG comme éléments promoteurs mammifères permettant la formation d’une structure ouverte de la chromatineTranscriptional regulation in higher eukaryotes resembles a tightly controlled temporal and spatial process, as exemplified during development or an organism’s response to environmental stimuli. Directed transcription requires the assembly of the preinitiation complex (PIC) at the promoter of protein-coding genes, including RNA Polymerase (Pol) II and the general transcription factors (GTFs), mediated by activating transcription factors (TFs). Several rate-limiting steps further control the progression of Pol II initiation to productive elongation of the gene. This process is further controlled by chromatin structure, histone modifications as well as cis-regulatory elements, such as enhancers or silencers. We set out to decipher some of these regulatory mechanisms during the tightly controlled process of lymphocyte development. Our work primarily made use of primary mouse thymocytes in CD4+/CD8+ double positive (DP, CD4+/CD8+) stage during T-cell development. To our advantage, many developmentally important cis-regulatory regions are well characterized in this cell population. For genetic manipulations, we made use of the Raji B-cell lymphoma cell-line. Using high throughput genome-wide approaches based on next generation sequencing (NGS), we performed both localization studies of Pol II, GTFs, TFs, histone modifying enzymes, histone modifications and nucleosomes as well as deep-sequencing of different RNA transcript populations. In summary, we find that (i) PICs assemble at tissue-specific enhancers leading to local transcription, (ii) large transcription initiation platforms (TIPs) at tissue-specific promoters and enhancers exist, which correlate with high CG-content of the DNA and transcription factor binding sites (TFBS), (iii) GC-content regulates the nucleosomal structure and initiation, including directionality, at promoters, (iv) Pol II is phosphorylated at a new residue of it C-terminal domain (CTD) in the 3’ regions of genes and (v) splicing events can influence the chromatin structure. Altogether, these results show that PIC formation at and transcription of enhancers are important for the regulation of T-cell target genes, that CpG islands represent important if not the major regulatory promoter element in mammals guiding tissue-specific gene expression and nucleosome structure, as well as novel mechanisms of Pol II elongation and the effect on chromatin structure
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Liu, Ching-Ti. "Study on transcriptional regulation of protein complexes in Saccharomyces cerevisiae." Diss., Restricted to subscribing institutions, 2006. http://proquest.umi.com/pqdweb?did=1276392271&sid=1&Fmt=2&clientId=1564&RQT=309&VName=PQD.
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Mandke, Pooja P. "Study of MicroRNA-34a mediated post transcriptional regulation of MDM4." Wright State University / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=wright1347648257.
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Watanabe, Satoshi. "Structural study of the oxidative-stress sensing SoxR transcriptional activator." 京都大学 (Kyoto University), 2007. http://hdl.handle.net/2433/136799.
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Lin, Ling. "Genetic Approaches to Study Transcriptional Activation and Tumor Suppression: A Dissertation." eScholarship@UMMS, 2012. https://escholarship.umassmed.edu/gsbs_diss/610.
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The development of methods and techniques is the driving force of scientific research. In this work, we described two large-scale screens in studying transcriptional activation and tumor suppression.
In Part I, we studied transcriptional activation mechanisms by deriving and characterizing activation defective mutants. Promoter-specific transcriptional activators stimulate transcription through direct interactions with one or more components of the transcription machinery, termed the “target.” The identification of direct in vivo targets of activators has been a major challenge. We perform a large-scale genetic screen to derive and characterize tra1 alleles that are selectively defective for interaction with Gal4 in vivo. Utilizing these mutants, we demonstrated that Tra is an essential target for Gal4 activation, Gal4 and Tra1 bind cooperatively at the promoter and the Gal4–Tra1 interaction occurs predominantly on the promoter. In addition, we demonstrated that the Gal4-interaction site on Tra1 is highly selective.
In Part II, we described a functional genomics approach to discover new tumor suppressor genes. A goal of contemporary cancer research is to identify the genes responsible for neoplastic transformation. Cells that are immortalized but non-tumorigenic were stably transduced with pools of short hairpin RNAs (shRNAs) and tested for their ability to form tumors in mice. ShRNAs in any resulting tumors were identified by sequencing to reveal candidate TSGs, which were then validated both experimentally and clinically by analysis of human tumor samples. Using this approach, we identified and validated 33 candidate TSGs. We found that most candidate TSGs were down-regulated in >70% of human lung squamous cell carcinoma (hLSCC) samples, and 17 candidate TSGs negatively regulate FGFR signalling pathway, and their ectopic expression inhibited growth of hLSCC xenografts. Furthermore, we suggest that by examining at the expression level of TSGs in lung cancer patients, we can predict their drug responsiveness to FGFR inhibitors. In conclusion, we have identified many new lung squamous cell cancer TSGs, using an experimental strategy that can be broadly applied to find TSGs in other tumor types.
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Cridland, Nigel A. "A study of cellular factors interacting with the Xenopus laevis vitellogenin B2 gene promoter." Thesis, University of Oxford, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.276525.
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Edwards, Helen Jane. "Transcriptional and post-transcriptional regulation of MDR1 expression during oxidative stress and recovery : a spatial and temporal study of MDR1 mRNA localization." Thesis, Imperial College London, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.438197.
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Romanish, Mark Taras. "Regulatory elements within repeated elements : a case study of NAIP transcriptional innovation." Thesis, University of British Columbia, 2009. http://hdl.handle.net/2429/12271.
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Neuronal Apoptosis Inhibitory Protein (NAIP, also known as BIRC1) is a member of the conserved Inhibitor of Apoptosis Protein (IAP) family. However, it is no longer principally considered an apoptosis inhibitor since its domain structure and functions in innate immunity also warrant inclusion in the Nod-Like Receptor (NLR) superfamily. Lineage-specific rearrangement and expansion of this locus have yielded different copy numbers among primates and rodents, providing an interesting case study in which to study transcriptional regulatory changes by a rapidly evolving gene.
In the first stage of my thesis, I show that NAIP has multiple promoters sharing no similarity between human and rodents. Moreover, I demonstrate that multiple, domesticated long terminal repeats (LTRs) of endogenous retroviral (ERV) elements provide NAIP promoter function in human, mouse and rat. In human, an LTR serves as a tissue-specific promoter active primarily in testis. However, in rodents, our evidence indicates that an ancestral LTR common to all rodent genes is the major, constitutive promoter for these genes and that a second LTR found in two of the mouse genes is a minor promoter. Thus, independently acquired LTRs have assumed regulatory roles for orthologous genes, a remarkable evolutionary scenario. It is also demonstrated that 5’ flanking regions of IAP family genes as a group, in both human and mouse, are enriched for LTR insertions compared to average genes.
In the second stage of my thesis, I demonstrate that several of the human NAIP paralogues are expressed, and that novel transcripts arise from both internal and upstream transcription start sites. Remarkably, two internal start sites initiate within Alu short interspersed element (SINE) retrotransposons, and a third novel transcription start site exists within the final intron of the GUSBP1 gene, upstream of only two NAIP copies. One Alu functions alone as a promoter in transient assays, while the other likely combines with upstream L1 sequences to form a composite promoter. The novel transcripts encode shortened open reading frames and I show that corresponding proteins are translated in a number of cell lines and primary tissues, in some cases above the level of full length NAIP. Interestingly, some NAIP isoforms lack their caspase-sequestering motifs, indicating that they have novel functions.
My results support an important role for transposable elements in NAIP evolution, particularly as transcriptional regulatory modules, and illustrate a fascinating example of regulatory innovations adopted by a rapidly evolving gene.
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Fu, Dechen. "The study of multiple mechanisms that regulate the transcriptional activity of Bicoid /." Cincinnati, Ohio University of Cincinnati, 2004. http://www.ohiolink.edu/etd/view.cgi?acc%5Fnum=ucin1100790435.
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Zheng, Dongling. "Studies of Escherichia coli promoters : mutational study and in vitro transcriptional profiling." Thesis, University of Birmingham, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.403445.
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Thurlow, Jane Anne. "A study of the transcriptional regulation of fibroblast growth factor-3 gene." Thesis, King's College London (University of London), 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.405575.
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Cavalli, Florence Marie Géraldine. "A computational study of transcriptional regulation in eukaryotes on a genomic scale." Thesis, University of Cambridge, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.609725.
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FU, DECHEN. "THE STUDY OF MULTIPLE MECHANISMS THAT REGULATE THE TRANSCRIPTIONAL ACTIVITY OF BICOID." University of Cincinnati / OhioLINK, 2004. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1100790435.
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Kolar-Znika, Lorena. "Study of the organisation and the transcriptional activity of mouse major satellites." Thesis, Paris 6, 2015. http://www.theses.fr/2015PA066156/document.
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Dans les cellules de souris, l'hétérochromatine péricentromérique, caractérisée par les répétitions des satellites majeurs et une signature épigénétique spécifique, la triméthylation de l'histone H3 sur la lysine 9 (H3K9me3), est organisée en structures nucléaires particulières appelées chromocentres. Cette région est transcriptionnellement active, produisant des ARN non-codants. Pour caractériser le profil transcriptionnel des satellites majeurs, nous avons utilisé des oligonucléotides LNA séquence spécifiques, pour des expériences de northern blot. Nous avons mis en évidence un profil de transcription complexe, révélé avec les sondes conçues pour cibler les deux brins des répétitions des satellites majeurs. Ce profil est modulé en réponse au choc thermique, condition dans laquelle un court ARN transcrit par l'ARN polymérase III, est surexprimé. Cependant, des problèmes de spécificité inhérents à l'utilisation de ces sondes LNA, ne nous ont pas permis de confirmer que les transcrits détectés ont pour origine les satellites majeurs. La seconde partie de ce travail a consisté en l'étude de l'impact de la modification ciblée de H3K9me3 aux satellites majeurs par une protéine TALE fusionnée à l'histone déméthylase mJMJD2D. Nous avons montré que le signal H3K9me3 est aboli dans les cellules transfectées avec cette protéine TALE. La déméthylation provoque des changements morphologiques des chromocentres, tels que l'augmentation de la taille des foci de satellites majeurs, accompagnés par la diminution de leur nombre, suggérant la fusion de plusieurs chromocentresIn mouse cells, pericentromeric heterochromatin, characterized by major satellite repeats and a specific epigenetic signature, the trimethylation of the histone H3 at lysine 9 (H3K9me3) is organised in particular nuclear structures called chromocenters. This region is actively transcribed, producing non-coding RNA. To investigate the transcriptional profile of major satellites, we made used of the sequence specific LNA modified oligonucleotides in northern blot experiments. We have shown that a complex transcriptional pattern is revealed with the probes designed to target both strands of the major satellite repeat. This pattern is modified in response to heat shock, in which we reveal that a short, RNA polymerase III-transcribed RNA is overexpressed. However, specificity problems encountered with the use of these LNA probes inabled us to confirm with certainty the major satellite origin of the detected transcripts. The second part of this work consisted in the studying of the impact of the targeted modification of the H3K9me3 at the major satellites by a TALE protein fused to a histone demethylase, mJMJD2D. We have shown that the H3K9me3 signal is abolished in the cells transfected with this TALE protein. The demethylation triggers morphological changes of the chromocenters such as the increase of the major satellite foci size, that are accompanied by the decrease in the foci number, suggesting the merging of several chromocenters
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Lamb, Alastair David Gordon. "A study of Hes6 as a transcriptional regulator in castrate resistant prostate cancer." Thesis, University of Cambridge, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.610562.
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Federation, Alexander Joel. "The Development of Chemical and Computational Tools to Study Transcriptional Regulation in Cancer." Thesis, Harvard University, 2015. http://nrs.harvard.edu/urn-3:HUL.InstRepos:17463980.
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Eukaryotic gene regulation is a complex process requiring the action of many multicomponent complexes in the cell. Specific inhibitors of chromatin-associated factors allow the functional study of protein domains without genetic removal of the entire protein. Here, two small molecule probes were used to study the role of DOT1L and BET proteins in cancer biology.
DOT1L is a histone methyltransferase with activity correlating with positive regulation of transcription. In MLL-rearranged leukemia, DOT1L is recruited aberrantly to early developmental transcription factors, leading to their inappropriate expression and leukemia maintenance. The development of an assay platform for DOT1L allowed the investigation of many small molecule DOT1L inhibitors, leading to compounds with improved potency and pharmacokinetics.
Studying the action of BET bromodomain inhibitors led to the identification of super enhancers, large tissue-specific regulatory elements driving the expression of genes critical for the function of the cell. Super enhancers are often found in oncogenic translocation events, especially in B cell malignancies. This study identified a subset of super enhancers that promote off-target DNA damage from the B cell antibody diversity enzyme AID, leading to double strand break events and translocations.
Super enhancers also regulate the expression of master transcription factors (TFs) in a given cell type. Using the topology of the super enhancer, the sites of master TF binding can be predicted, allowing the construction of network models for transcriptional regulation. These models were built in a large number of healthy and diseased cell types, including the pediatric malignancy medulloblastoma. In medulloblastoma, a network motif was identified that matches an expression pattern seen in a transient cell population in the developing cerebellum, providing evidence for the previously unknown cell of origin for Group 4 medulloblastoma.Chemical Biology
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Casanovas, Palau Sònia [Verfasser]. "The Rbfox1 gene: expression analysis and study of the transcriptional regulation / Sònia Casanovas Palau." Mainz : Universitätsbibliothek Mainz, 2019. http://d-nb.info/1183163940/34.
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Moore, Andrew Douglas. "A study of effects on MMP14 transcriptional regulation and angiogenesis by hypoxia and statins." Thesis, Queen Mary, University of London, 2014. http://qmro.qmul.ac.uk/xmlui/handle/123456789/8802.
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Atheromas contain hypoxic areas which upregulate HIF1α expression, promoting angiogenesis and unstable lesion formation. Simvastatin stabilises atheromas through preventing rupture and neovascularisation. Atheromas express matrix metalloproteinase 14 (MMP14) which degrades matrix proteins and promotes neovascularisation. MMP14 is upregulated by hypoxia and contains Hypoxic-Inducible Factor (HIF) recognition sequences (5’-RCGTG-3’). My project sought to investigate if HIF1α interacts with the MMP14 promoter to enhance MMP14 expression, and whether simvastatin attenuates this effect, inhibiting angiogenesis. Immunostaining of atheromas identified MMP14 and HIF1α localisation. Protein-DNA binding assays were performed on human umbilical vein endothelial cells (HUVECs) and showed HIF1α bound to the MMP14 promoter in hypoxia, which was significantly decreased by simvastatin. To assess gene regulation, a human MMP14 promoter-firefly luciferase reporter construct was transfected into C166 endothelial cells alongside HIF-overexpression plasmids and mutations of the MMP14 promoter region at HIF recognition sequences. Overexpression of HIF1α and HIF1β increased MMP14 activity which was abolished by introducing the mutations and diminished by simvastatin in a HIF-dependent manner. Immunoblots, flow cytometry, scratch assays and bromodeoxyuridine incorporation showed HIF1α knockdown and simvastatin significantly attenuated hypoxia upregulated MMP14 expression, migration and proliferation in a HIF1α-dependent manner. Angiogenesis was assessed using in vivo sponge angiogenesis assays and ex vivo aortic ring assays cultured in hypoxia or normoxia, with or without 0.1μM simvastatin, and MMP14 inhibitor, utilising HIF1αfl/flTie1Cre+ and wildtype littermates. Simvastatin perturbed angiogenesis through decreasing MMP14 expression in a HIF1α-dependent manner. The results show hypoxia upregulates MMP14 through HIF1α interaction with the MMP14 promoter. Simvastatin attenuates MMP14 upregulation which reduces HIF1α:MMP14 promoter interaction. HIF1α knockdown and simvastatin treated HUVECs show less migration and proliferation, equivalent to that of MMP14 inhibition. Simvastatin inhibits neovascularisation in a HIF1α-dependent manner. These results suggest simvastatin may stabilise atheromas through inhibiting MMP14 driven angiogenesis which may have further implications in the treatment of atherosclerosis.
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Dey, Heena T. "Functional Study of the Threonine Phosphorylation and the Transcriptional Coactivator Role of P68 RNA Helicase." Digital Archive @ GSU, 2012. http://digitalarchive.gsu.edu/biology_diss/123.
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P68 RNA helicase is a RNA helicase and an ATPase belonging to the DEAD-box family. It is important for the growth of normal cells, and is implicated in diverse functions ranging from pre-mRNA splicing, transcriptional activation to cell proliferation, and early organ development. The protein is documented to be phosphorylated at several amino-acid residues. It was previously demonstrated in several cancer cell-lines that p68 gets phosphorylated at threonine residues during treatments with TNF-α and TRAIL. In this study, the role of threonine phosphorylation of p68 under the treatment of anti-cancer drug, oxaliplatin in the colon cancer cells is characterized. Oxaliplatin treatment activates p38 MAP-kinase, which subsequently phosphorylates p68 at T564 and/or T446. P68 phosphorylation, at least partially, influences the role of the drug on apoptosis induction. This study shows an important mechanism of action of the anti-cancer drug which could be used for improving cancer treatment.
This study also shows that p68 is an important transcriptional regulator regulating transcription of the cytoskeletal gene TPPP/p25. Previous analyses revealed that p68 RNA helicase could regulate expression of genes responsible for controlling stability and dynamics of different cytoskeletons. P68 is found to regulate TPPP/p25 gene transcription by associating with the TPPP/p25 gene promoter. Expression of TPPP/p25 plays an important role in cellular differentiation while the involvement of p68 in the regulation of TPPP/p25 expression is an important event for neurite outgrowth. Loss of TPPP expression contributes to the development and progression of gliomas. Thus, our studies further enhance our understanding of the multiple cellular functions of p68 and its regulation of the cellular processes.
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Chong, Shasha. "Detection of Single-Molecule Optical Absorption at Room Temperature and Mechanistic Study of Transcriptional Bursting." Thesis, Harvard University, 2014. http://dissertations.umi.com/gsas.harvard:11501.
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Advances in optical imaging techniques have allowed quantitative studies of many biological systems. This dissertation elaborates on our efforts in both developing novel imaging modalities based on detection of optical absorption and applying high-sensitivity fluorescence microscopy to the study of biology.Chemistry and Chemical Biology
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Hansen, Clinton Hugh. "Allele-specific detection of single mRNA molecules in situ and the study of transcriptional regulation." Thesis, Harvard University, 2014. http://nrs.harvard.edu/urn-3:HUL.InstRepos:13064969.
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We developed a method for fluorescence in situ identification of individual mRNA molecules, allowing quantitative and accurate measurement, in single cells, of allele-specific transcripts that differ by only a few nucleotides. By using a combination of allele-specific and non-allele-specific probe libraries, we achieved >95% detection accuracy. We used this technique to investigate the allele-specific stochastic expression of Nanog, which encodes a pluripotency factor, in murine embryonic stem cells. We find that Nanog does not switch between monoallelic and biallelic expression when culture conditions are altered.
We next worked towards adapting our allele-specific single molecule mRNA fluorescent in situ hybridization technique to detect early expression of the immunoglobulin kappa gene in Pre-B cells. Mature B cells only express a single allele of the immunoglobulin kappa gene, and assaying allele-specific expression in single cells will allow the study of the mechanism behind this choice.
We also developed a theoretical model of cell specification in the mammalian inner ear using single-molecule mRNA expression data. During mammalian hair cell development, prosensory cells acquire a spatial pattern of distinct cellular fates. This process is dependent upon the expression of the transcription factor Atoh1, and is mediated by Notch signaling between neighboring cells. We find that both the Notch ligand and transcription factor Atoh1 are expressed in an extended region before turning off in non-hair cells. Our model reveals that this extended pattern creates a system that can suppress extraneous expression over a large region and is robust to movement of prosensory cells as the cochlea extends, especially in the case of a limited time window for specification. Our model can also explain the two types of expression patterns of Atoh1 that are observed.
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Zaugg, Judith Barbara. "A computational study of promoter structure and transcriptional regulation in yeast on a genomic scale." Thesis, University of Cambridge, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.609838.
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Bolinger, Cheryl Giles. "Study of translation control by a RNA helicase A-responsive post-transcriptional control element in Retroviridae." The Ohio State University, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=osu1226513076.
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Pereira, Mário. "The use of site-directed integration to study genomic and transcriptional stability of recombinant promoters in CHO cells." Thesis, University of Manchester, 2016. https://www.research.manchester.ac.uk/portal/en/theses/the-use-of-sitedirected-integration-to-study-genomic-and-transcriptional-stability-of-recombinant-promoters-in-cho-cells(5b7e28fc-38e6-47b4-be9e-aa96265ac9ba).html.
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Transcriptional regulation is a determinant of stability of recombinant protein production in CHO cells. Fundamental studies of recombinant gene transcription in relation to chromatin environment and promoter regulation are important for CHO cell line development and selection. This study has developed a methodology based on a cell/vector system to study recombinant transcription and expression stability of different promoters and/or proteins in the similar genomic environment. The CHO-FRT mini-pools developed in this project were mini-pools of CHO-S cell lines containing Flp Recombination Target (FRT) sites with ß-galactosidase gene, under the influence of a SV40 promoter. Continuous culture of these mini-pools for 8 weeks using a robotic system demonstrated that 20% of the mini-pools studied revealed an unstable profile (with 30% loss of protein expression). Two of these mini-pools with different characteristics, CHO-FRT 1 (low producer/unstable) and CHO-FRT 108 (high producer/stable), were selected to be used on the study of influence of SV40 and CMV promoters in long-term recombinant expression. Genes encoding fluorescent proteins were integrated in a site-directed manner under the influence of SV40 or CMV promoters. A sub-clonal population of the top 10% yellow fluorescent protein (YFP) expressing cells of each mini-pool/promoter combination was selected by cell sorting and cultured for 4 weeks. During this period protein expression was monitored by flow cytometry and compared between both promoters. The results revealed that both SV40 and CMV promoters had an unstable expression with different degrees of instability and long-term expressing behaviours. For CMV, instability was considerably high displaying a long-term logarithmic loss of 50-80% of productivity while for SV40 the loss of productivity observed was only 40-45% with a linear behaviour during long-term culture. The vector system generated contained an MS2-RNA tag sequence cloned 3'- of the recombinant gene to track the recombinant mRNA by using the MS2/MCP-GFP system. This study showed the development of a protocol to measure the transcriptional output of recombinant promoters in CHO cells. The results showed background signal in CHO cells that requires further optimisation studies to allow the direct live cell image quantification of the transcriptional activity of recombinant promoters. Although not yet optimised, the successful combination of site-directed integration with recombinant mRNA tagging method has the potential to become a valuable tool to study the mechanisms of transcriptional activity and stability of transcription driven by different promoters in CHO cells.
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Ciarallo, Anthony. "A study of the transcriptional regulation of the mouse Indian Hedgehog gene in ATDC5 and COS7 cells /." Thesis, McGill University, 2005. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=81613.
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The signaling peptide Indian Hedgehog (Ihh) is secreted by prehypertrophic chondrocytes of the growth plate, the growth center of long bones. It functions to negatively regulate differentiation and positively regulate proliferation of chondrocytes. Thus, Ihh ultimately controls the rate of bone growth.The transcriptional regulation of the Ihh gene, however, remains uncharacterized. In order to study the gene's regulation, the genomic Ihh sequences from several species were aligned to identify conserved regions that may contain regulatory sites. Two putative Stat transcription factor binding sites were identified, one of which is conserved across all species studied while the other is rodent-specific.
In addition, an in vitro system was established to test the upstream region of the gene for transcriptional activity. ATDC5 chondrogenic cells were stably transfected with a plasmid containing 5kb of sequence located upstream of Ihh as well as a luciferase reporter gene. The presence of the Ihh sequence induced expression of the luciferase reporter 50 fold above expression from a control plasmid. COS7 and ATDC5 cells transiently transfected with similar Ihh-luciferase constructs resulted in unique induction patterns. Thus, the Ihh upstream genomic region contains sequences that regulate expression in a tissue-specific fashion.
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Righetti, Karima Maria. "Study of Rsm/Gac post-transcriptional regulation by quorum sensing, extracellular and intracellular signals in Pseugomonas aeruginosa." Thesis, University of Nottingham, 2011. http://eprints.nottingham.ac.uk/13853/.
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Bacteria have evolved ways to sense and respond to changes in their population density through quorum sensing (QS) systems, and to adapt to changes in the extracellular environment through two component systems (TCS). In Pseudomonas aeruginosa, QS and the GacS/GacA TCS are global regulatory systems that modulate the expression of virulence genes at the transcriptional and post-transcriptional level, respectively. Although in P. aeruginosa the QS network has been extensively characterized, the way the Gac/Rsm global regulatory system is regulated is still unclear. The study of QS and Gac/Rsm networks is crucial for the development of new drugs able to interfere with these regulatory systems. This thesis is dedicated to the study of the Gac/Rsm global regulatory system and its interaction with the QS network. An introduction to these systems is presented in Chapter 1. The materials and methods used in this study are described in Chapter 2. In Chapter 3 the methods to detect and identify the extracellular signals modulating Gac/Rsm system are investigated. This analysis led to the identification of the Pseudomonas Quinolone Signal (PQS) molecule, which is responsible for the activation of the gene coding for the small RNA RsmZ. RsmZ (in synergy with RsmY) antagonises by titration the effects of the global post-transcriptional regulator RsmA, a small RNA-binding protein which targets specific mRNAs. Since the discovery of QS, there have been many studies showing the importance of this type of regulatory mechanism in the global transcriptional control of gene expression. However, there has been no clear evidence to attribute to QS a key role in post-transcriptional regulation of terminal gene targets. In Chapter 4, the importance of PQS in the control of lecA is demonstrated. lecA encodes for the PA-I galactophilic lectin protein whose translation rates is modulated by the activity of the regulatory small RNA rsmZ in concert with RsmA. These results demonstrate that QS not only controls terminal target gene expression at the transcriptional level, but also at the translational level. Using a genetic bank, a transposon mutagenesis and a promoter pull-down approach, new regulators were identified together with regulatory networks involved in the modulation of the global Gac/Rsm system. These results are described in Chapter 5. Chapter 6 is focused on the effect of a library of compounds available in our laboratory, for their QS-inhibiting potential. The conclusions and future directions are presented in Chapter 7.
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Gristwood, T. "A study of transcriptional regulators involved in the control of secondary metabolism in Serratia sp. ATCC 39006." Thesis, University of Cambridge, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.599747.
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Serratia sp. ATCC 39006 (Serratia 39006) is a Gram-negative member of the Enterobacteriaceae that synthesises several secondary metabolites, including the red tripyrrole antibiotic, prodigiosin (Pig; 2-methyl-3-pentyl-6-methoxyprodigiosin) and the β-lactam antibiotic, carbapenem (Car; 1-carbapen-2-em-3-carboxylic acid). Pig is of clinical interest as it has been shown to have anticancer and immunosuppressive properties. However, the natural physiological role of Pig I the producing organisms is unclear. This study investigates the mechanism by which three transcriptional regulators (PigZ, PigS and PhoB) modulate secondary metabolism in Serratia 39006. PigZ, a TetR-family transcriptional repressor, is shown to differentially modulate Pig and Car production via the transcriptional regulation of an unusual four-component RND-family efflux pump. The putative ArsR/SmtB family regulator, PigS, which is linked to the Pig biosynthetic cluster, is also shown to be a transcriptional repressor that modulates Pig production via repression of novel target genes. Finally, this study investigates the mechanism by which the transcriptional activator, PhoB, upregulates secondary metabolism in response to phosphate limitation, via multiple inter-linked pathways. In conclusion, this study has furthered our understanding of the regulation of secondary metabolism in Serratia 39006 and a model is presented in which this additional information has been integrated into the previously proposed regulatory network.
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Sazinas, Pavelas. "The application of high-throughput sequencing to study the genome composition and transcriptional response of Haemophilus influenzae." Thesis, University of Warwick, 2016. http://wrap.warwick.ac.uk/89145/.
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Haemophilus influenzae is an important human pathogen, responsible for respiratory infections, such as otitis media, bronchitis and epiglottitis, as well as invasive disease. Despite being the first free-‐living organism to have its whole genome sequenced, there have been only a few published studies investigating its transcriptional profile using next-‐generation sequencing (NGS). The work presented in this thesis aimed to use NGS to improve the understanding of how H. influenzae behaves during natural infection and to identify novel RNA structures with potentially important roles in pathogenesis. The whole transcriptome of H. influenzae during infection-‐relevant conditions was analysed using high-‐throughput RNA sequencing. For the first time, the transcriptional profile of H. influenzae during stationary phase and nutritional stress was determined on a whole-‐genome scale. Differential gene expression analysis of an invasive strain, R2866, and a laboratory strain, Rd KW20, revealed differences in their transcriptional response, particularly during oxidative stress and iron starvation. Importantly, a new systematic and robust bioinformatic tool, "toRNAdo", was developed to identify non-‐coding RNA elements from the bacterial transcriptomic data. It enabled discovery of a repertoire of novel putative intergenic and antisense non-‐coding RNAs in H. influenzae. In addition, the first fully sequenced genome of a free-‐living organism, the Rd KW20 strain of H. influenzae, was re-‐sequenced and re-‐ annotated for the first time. This enabled identification of multiple nucleotide-‐ level differences between original and re-‐sequenced genomes of Rd KW20. The work presented here facilitates future characterisation of novel RNA elements, with potentially important regulatory roles in pathogenesis in H. influenzae, and has implications for defining a model bacterial strain. Importantly, the findings present significant insight into the pathogenic lifestyle of H. influenzae. They provide the basis for further work, where novel vaccine and antibiotic targets may get developed.
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Cheng, Xiwen. "The Functional Study of Transcriptional Corepressor G-Protein Suppressor 2 (GPS2) and Tumor Suppressor Promyelocytic Leukemia (PML)." Case Western Reserve University School of Graduate Studies / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=case1277741995.
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Delorey, Toni Marie. "Host-fungal pathogen interactions: A study of Candida albicans and mammalian macrophage and epithelial cells at the transcriptional level." Digital WPI, 2019. https://digitalcommons.wpi.edu/etd-dissertations/548.
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It is estimated that fungal infections kill greater than 1.6 million people annually, a number that is comparable to the number of deaths associated with tuberculosis. Candida species are the fourth leading cause of hospital-acquired blood infections and Candida albicans is the most common cause of these fungal blood infections (known as candidemia). Immunocompromised individuals, such as those who have HIV/AIDS, those undergoing chemotherapy treatments, or those on broad-spectrum antibiotics, are most likely to develop candidemia. Candidemia is associated with a 20-40% mortality rate. However, when patient treatment for candidemia is delayed for over 48 hours, associated mortality rates increase to 78%. Blood infections can disseminate Candida albicans throughout the body, eventually leading to infection in vital organs like the liver, kidney and brain. Optimal patient outcomes are achieved if antifungal therapy is given within 12 hours after a blood sample is obtained for culture and testing. However, current blood tests cannot reliably detect Candida this early and thus antifungals are not routinely given to patients in this time frame. Counterintuitively, it is believed that some fungi, like many bacteria, are non-harmful residents in small intestines of most adults and this hypothesis is supported by the fact that the most common fungal species in the human gut is Candida albicans. However, intestinal overgrowth of C. albicans is linked to Crohn's disease, and disease-causing forms of C. albicans can arise from commensal strains that once resided in the patient’s gastrointestinal tract. The specific molecular mechanisms by which C. albicans interacts with host immune cells versus intestinal cells, and those that trigger Candida pathogenicity remain unknown. Many strains of Candida albicans have developed resistance to azoles, the major class of drugs used to treat both superficial and systemic infections. In order to develop new treatments, we must better understand host-fungal pathogen biology to determine novel antifungal targets or therapeutics to fight fungal infections at the early stages of infection. In this work, we developed a novel tool that allows us to measure which genes are important to both the host and Candida albicans simultaneously, in specific infection states. We have applied this tool to measure gene expression in Candida albicans interacting with mammalian macrophages and small intestine epithelial cells– at both the population and single cell levels. When examining populations of sorted infection samples, we found that host immune cells both exposed to and infected with fungal cells exhibit similar expression patterns. In contrast, phagocytosed C. albicans exhibit unique expression patterns compared to those merely exposed to macrophages. We found that immune response genes in single, Candida infected macrophages exhibited bimodal expression patterns for some immune response genes. We also observed examples of expression bimodality in live Candida inside of single macrophages. Both Candida albicans and host small intestine epithelial cells demonstrate distinct patterns of expression when exposed to each other at the population level, compared to unexposed controls. However, the magnitude of these differences is dependent on the multiplicity of infection. Some expression programs overlapped with those observed in populations of Candida cells interacting with macrophages, with key differences. We also observed expression bimodality among epithelial cells infected with C. albicans. We believe the information obtained using this technique could be used when considering new antifungal or therapeutics targets; if uniform and high expression of particular in genes in Candida populations phagocytosed by macrophages or invading epithelial cells leads to high and early protein production, these proteins may be effective antifungal targets. Similarly, if some host immune response genes are not expressed in a population of Candida infected macrophages as uniformly and highly as expected, these genes or proteins could be target of a therapeutic for patients with Candida infections that are resistant to azoles.
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Serroukh, Yasmina. "Transcriptional and epigenetic regulation of human CD4 T cell cytotoxic function: Molecular study of human cytotoxic CD4 T cells." Doctoral thesis, Universite Libre de Bruxelles, 2017. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/245998.
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Cytotoxicity is the capacity for immune cells to kill infected or malignant cells in order to eliminate pathogens and tumours through different mechanisms including the exocytosis of perforin-containing cytosolic granules. This crucial property is usually restricted to specialized innate and adaptive lymphocytes such as natural killer (NK) cells and CD8 T cells. T lymphocytes differentiate in the thymus and are delivered to the peripheral blood as naive T cells committed to either the CD8 or the CD4 lineage. CD8 T cells are programmed to acquire cytotoxic effector functions under the control of the transcription factor (TF) Runx3. The fate of CD4 T cells is to acquire multiple helper functions through the action of the TF ThPOK that promotes CD4 helper functions and restricts the CD8 cytotoxic program. However, this restriction is not absolute as cytotoxic CD4 (CD4CTX) T cells differentiate in vivo, indicating that the multipotency of human naive CD4 T cells includes the ability to acquire perforin expression and potent cytotoxicity in vitro and ex vivo. This cytotoxic potential correlates with outcome in human pathology and mediates protection against viral challenge and tumour eradication in murine models. CD4CTX T cells are terminally differentiated effector memory T cells that accumulate during cytomegalovirus chronic infection and ageing. They are phenotypically and functionally related to T helper type 1 (Th1)-effector memory cells. However, whether they belong to the Th1 pathway or constitute a separate specialized helper T cell subset is unknown. In this work, we show that CD4CTX T cell differentiation is an integral part of the Th1 pathway. Indeed, CD4 T cells acquire cytotoxic potential early in the memory differentiation process as central memory Th1 but not Th2 and Th17 cells are epigenetically primed to develop a cytotoxic program. The expression of perforin and other cytotoxic genes present a stepwise increase profile that is specific of the Th1 differentiation pathway. This profile has been recapitulated in an in vitro model of effector CD4 T cell differentiation in which naive CD4 T cells acquire cytotoxicity one to two weeks after polyclonal stimulation when cultured in presence of Th1 cytokines. The molecular regulation of CD4CTX T cells is poorly understood and most available data have been generated in mice. These data include the observation of intraepithelial CD4CTX T cells in the mouse gut after loss of ThPOK expression and subsequent up-regulation of a Runx3-dependent cytotoxic program. Other candidate regulators of CD4 T cell cytotoxic function include the TF regulating Th1 and CD8CTX T cells differentiation such as Runx3, T-bet and Eomesodermin (Eomes). We show that the transcriptional program of human CD4CTX T cells is enriched in CD8-lineage genes. However, by contrast to CD4CTX T cells from the mouse intestine, human circulating CD4CTX T cells maintain the expression of ThPOK and even up-regulate this TF upon differentiation from naive CD4 T cells. Surprisingly, this sustained expression of ThPOK was compatible with the establishment of a T-bet- and Runx3-dependent cytotoxic transcriptional program. The specific knockdown of T-bet or Runx3 but not Eomes resulted in impaired cytotoxic differentiation whereas ThPOK knockdown enhanced perforin expression and cytotoxicity. We propose that CD4CTX T cells constitute the terminal stage of Th1 memory differentiation and that ThPOK, Runx3 and T-bet co-regulate this process by instructing a cytotoxic transcriptional network largely shared with CD8CTX T cells. The modulation of this network is a potential target for novel immunotherapeutic strategies in viral infections and cancer.Doctorat en Sciences médicales (Médecine)
info:eu-repo/semantics/nonPublished
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Despuig, i. Busquet Albert. "The Study of Human Tuberculosis Lesions: circulant and transcriptional biomarkers in a cohort of tuberculosis patients undergoing therapeutic surgery." Doctoral thesis, Universitat Autònoma de Barcelona, 2020. http://hdl.handle.net/10803/671081.
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La tuberculosi (TB), és la major causant de morts associades a malalties infeccioses al món. La cirurgia terapèutica segueix sent una eina essencial en els casos més complicats de TB, per exemple, si el pacient mostra persistència de lesions cavitàries malgrat bona adherència als antibiòtics. Avui dia, la recerca en TB està centrada en identificar factors clínics-epidemiològics que condueixen al pacient a evolucionar negativament durant el tractament i identificar biomarcadors que puguin predir l’estat de salut i una mala prognosi. Aquestes estratègies no reflecteixen la malaltia pulmonar in situ, i per tant, la resposta local de l’hostatger al patogen no està representada. En aquesta tesi doctoral vàrem hipotetizar que l’estudi de la resposta immunològica local i sistèmica de pacients que rebran cirurgia terapèutica per la seva TB pulmonar podria ajudar a determinar nous biomarcadors així com informació essencial respecte els mecanismes de resposta de l’hostatger en la generació de les lesions tuberculoses. Es van analitzar retrospectivament dades clínic-epidemiològiques considerant les característiques macroscòpiques de les lesions obtingudes en una cohort de 137 pacients tuberculosos sotmesos a cirurgia. En una nova cohort de 40 pacients sotmesos a cirurgia terapèutica, vam avaluar els nivells de marcadors immunològics circulants i vam realitzar RNA-seq en biòpsies fresques de granuloma tuberculós humà, per ser correlacionades amb el perfil fisiopatològic dels participants juntament amb les característiques macroscòpiques de les lesions extirpades. Vam detectar persistència del Mycobacterium tuberculosis en biòpsies de lesions malgrat negativitat microbiològica en cultiu. El sexe i hàbits tòxics son factors importants que podrien determinar l’evolució de la TB. Biomarcadors circulants correlacionen amb la mida de la lesió, formes multi-resistents i factors considerats de mal pronòstic. Es va detectar un efecte immunosupressor induït per la presència de les lesions, suggerit per marcadors immunològics i el transcriptoma de la lesió tuberculosa. Vam generar una signatura de 6056 gens del granuloma tuberculós humà i una llista de gens d’interès que aglomeren l’expressió gènica de les característiques fisiopatològiques de la cohort. La plataforma de biomarcadors circulants i els gens haurien de ser validats i avaluats en altres pacients amb TB i confirmar la seva potencial utilitat com a eina de prognosi.La tuberculosis (TB), es la mayor causante de muertes asociadas a enfermedades infecciosas en el mundo. La cirugía terapéutica sigue siendo una herramienta esencial en los casos más complicados de TB, por ejemplo, si el paciente muestra persistencia de lesiones cavitarias a pesar de probar una buena adherencia a los antibióticos. Hoy en día, la investigación en TB está centrada en identificar factores clínicos-epidemiológicos que conducen al paciente a evolucionar negativamente durante el tratamiento e identificar biomarcadores que puedan predecir el estado de salud y un mal pronóstico. Estas estrategias no reflejan la enfermedad pulmonar in situ y, por tanto, la respuesta local del huésped al patógeno no está representada. En esta tesis doctoral hipotetizamos que el estudio de la respuesta inmunológica local y sistémica de pacientes que recibirán cirugía terapéutica por su TB pulmonar podría ayudar a determinar nuevos biomarcadores así como información esencial respecto a los mecanismos de respuesta del huésped en la generación de las lesiones tuberculosas. Se analizaron retrospectivamente datos clínico-epidemiológicos considerando las características macroscópicas de las lesiones obtenidas en una cohorte de 137 pacientes tuberculosos sometidos a cirugía. En una nueva cohorte de 40 pacientes sometidos a cirugía terapéutica, evaluamos los niveles de marcadores inmunológicos circulantes y realizamos RNA-seq en biopsias frescas de granuloma tuberculoso humano, para ser correlacionadas con el perfil fisiopatológico de los participantes junto con las características macroscópicas de las lesiones extirpadas. Detectamos persistencia de Mycobacterium tuberculosis en biopsias de lesiones a pesar de mostrar negatividad microbiológica en cultivo. El sexo y los hábitos tóxicos son factores importantes que podrían determinar la evolución de la TB. Biomarcadores circulantes correlacionan con el tamaño de la lesión, formas multi-resistentes y factores considerados de mal pronóstico. Se detectó un efecto inmunosupresor inducido por la presencia de las lesiones, sugerido por marcadores inmunológicos y el transcriptoma de la lesión tuberculosa. Generamos una firma de 6056 genes del granuloma tuberculoso humano y una lista de genes de interés que aglomeran la expresión génica de las características fisiopatológicas de la cohorte. La plataforma de biomarcadores circulantes y los genes deberían ser validados y evaluados en otros pacientes con TB y confirmar su potencial utilidad como herramienta de prognosis de los pacientes con TB.
Tuberculosis (TB) is the worldwide leading cause of death among infectious diseases. Therapeutic surgery is still an invaluable tool to resolve the most complicated TB cases, for instance, if the patient is experiencing persistent lung cavities despite good adherence to chemotherapy. Scientific efforts are focused on identifying which clinical-epidemiological factors lead a patient to evolve poorly during treatment and to identify biomarkers that can predict the treatment response, health status, and fatal outcomes. Nonetheless, these strategies are not reflecting the in situ lung pathology, and therefore, the local host-to-pathogen response is misrepresented. We hypothesized that the study of the local and systemic immune responses from patients undergoing therapeutic surgery for their pulmonary TB could help us to identify potential TB biomarkers and essential information regarding the role of the host in the mechanisms associated to the generation of the TB lesions. Clinical-epidemiological data of a cohort of 137 patients undergoing therapeutic surgery for pulmonary TB were retrospectively analyzed according to the macroscopic features of the removed TB lesions. Next, in a new cohort of 40 patients also receiving therapeutic surgery, we assessed the levels of circulating immune markers and we performed RNA-seq upon the fresh human TB granuloma biopsies, to be correlated with the pathophysiological phenotype of the participants together with the macroscopic lesions’ characteristics. We found the persistence of Mycobacterium tuberculosis in surgical TB cavitary biopsies despite microbiological clearance in culture. Sex and toxic habits are important factors that may determine the evolution of the disease. Circulant biomarkers correlated with the size of the lesion, with multi-drug resistant forms, and factors considered to indicate the worst disease outcomes. We noted an immunosuppressive effect exerted by the presence of the TB lesions, suggested by the immune-markers and the human TB granuloma transcriptome. Finally, we generated a 6056-gene signature of the human TB granuloma and a list of genes of interest gathering the total-RNA expression of the main pathophysiological traits of the cohort. The proposed platform of circulant biomarkers and its genes should be further validated and assessed in other active TB patients to confirm the potential use as a prognostic tool.
Universitat Autònoma de Barcelona. Programa de Doctorat en Microbiologia
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Fill, Mary-Margaret Anne. "Establishment of a tRNA over-expression system in Trypanosoma brucei to study the role of post-transcriptional modifications on function." Connect to resource, 2007. http://hdl.handle.net/1811/28390.
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Thesis (Honors)--Ohio State University, 2007.Title from first page of PDF file. Document formatted into pages: contains x, 25 p.; also includes graphics. Includes bibliographical references (p. 24-25). Available online via Ohio State University's Knowledge Bank.
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Ciolli, Mattioli Camilla. "Post-transcriptional mechanisms contributing to RNA and protein localization: study of local translation and alternative 3′UTRs in induced neurons." Doctoral thesis, Humboldt-Universität zu Berlin, 2019. http://dx.doi.org/10.18452/20702.
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Die asymmetrische Verteilung von mRNA und Proteinen innerhalb einer Zelle definiert die Polarität. Dies ermöglicht eine strikte Regulierung der Genexpression in Raum und Zeit. Ich habe in dieser Arbeit untersucht, wie das Soma und die Neuriten in induzierten Neuronen sich hinsichtlich ihres Transkriptoms und Translatoms unterscheiden. Eine räumliche ribosomale Profilanalyse ergab, dass die Hälfte des lokalen Proteoms durch die mRNA-Lokalisierung und der lokalen Translation definiert wird. Dies sind Prozesse, die durch die synergistische Aktivität von trans- und cis-agierenden Elementen durchgeführt werden. In dieser Arbeit konzentrierte ich mich auf MOV10 als trans-agierendes Element und die alternativen 3′UTRs als cis-agierende Elemente, um ihre Rolle in der Asymmetrie zu untersuchen. MOV10 ist eine RNA-Helikase, welche an vielen Aspekten des RNA-Metabolismus beteiligt ist. Mit den Methoden RIP und PAR-CLIP konnte ich zeigen, dass sowohl MOV10-Ziele als auch MOV10 selbst in den Neuriten lokalisiert sind. Aus ̈erdem ist MOV10 möglicherweise an der translationalen Repression mitinvolviert.
In der Tat konnte ich unter den MOV10-Protein-Interaktoren mehrere Proteine identifizieren, welche an der translationalen Repression beteiligt sind, wie z.Bsp. AGO2, FMR1, und TRIM71. Für die Identifizierung der cis-agierenden Elemente führte ich das "Mapping" von alternativen 3′UTRs durch. Diese Analyse zeigte mehrere Gene, die differentiell lokalisierte 3′UTR-Isoformen exprimieren. Insbesondere habe ich mich auf Cdc42 konzentriert. Ich konnte beweisen, dass die beiden Isoformen von Cdc42 auf mRNA-Ebene unterschiedlich lokalisiert sind und dass die 3′UTR der entscheidende Faktor für die mRNA- und Proteinlokalisierung ist. Darüber hinaus habe ich mehrere RBPs identifiziert, die an der Cdc42-Lokalisierung beteiligt sind. Diese Analyse zeigt, dass für die differenzierte Lokalisierung von funktional unterschiedlichen alternativen Protein-Isoformen die Verwendung von alternativen 3′UTR Isoformen als neu-entdeckter Mechanismus eine entscheidende Rolle spielt.Asymmetric distribution of mRNA and proteins inside a cell defines polarity, which allow tight regulation of gene expression in space and time. In this thesis I investigated how asymmetric distribution characterizes the somatic and neuritic compartments of in induced neurons, in terms of transcriptome and translatome. Spatial ribosome profiling analysis revealed that half of the local proteome is defined by mRNA localization and local translation. These, are processes accomplished by the synergistic activity of trans- and cis-acting elements. I focused on MOV10 as trans-acting element, and on alternative 3′UTRs as cis-elements, to investigate their role in asymmetry. MOV10 is an RNA helicase which participates to many aspects of RNA metabolism. With RIP and PAR-CLIP I showed that MOV10 targets are localized to the neurites, consistently with MOV10-neuritic localization, and that MOV10 might be involved in translational repression. Indeed, among MOV10 protein interactors, I identified several proteins involved in translational repression, i.e. AGO2, FMR1, and TRIM71. On the side of cis-elements, I performed mapping of alternative 3′UTRs. This analysis identified several genes expressing differentially localized 3′UTR isoforms. In particular, I focused on Cdc42. I showed that the two isoforms of Cdc42 are differentially localized at mRNA level, and that the 3′UTR is the driver of mRNA and protein localization. Moreover, I identified several RBPs that might be involved in Cdc42 localization. This analysis points to usage of alternative 3′UTR isoforms as a novel mechanism to provide for differential localization of functionally diverse alternative protein isoforms.
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Calvo, Arnedo María Isabel 1983. "Study of the role of Pap1 as a sensor of H2O2 and as a transcriptional activator of stress responses in Schizosaccharimyces pombe." Doctoral thesis, Universitat Pompeu Fabra, 2012. http://hdl.handle.net/10803/128679.
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En el laboratorio se utiliza como sistema modelo la levadura Schizosaccaromyces pombe para poder estudiar la respuesta a estrés oxidativo. Las dos rutas principales de respuesta a estrés oxidativo son las del factor de transcripción Pap1 y la de la MAP quinasa Sty1. Cuando aplicamos a la célula bajas dosis de H2O2, Pap1 que se encuentra en el citoplasma en estado reducido, sufre un cambio conformacional, se oxida, y activo viaja al núcleo, donde se une a diferentes promotores para activar su transcripción.
La caracterización de Pap1 como sensor de H2O2 y como factor de transcripción centran el trabajo de esta tesis. Respecto al mecanismo molecular de activación de Pap1, esta proteína necesita de varias cisteínas que son esenciales para su activación. Así como intentar averiguar qué papel juegan las diferentes proteínas que componen el sistema tiorredoxina en la activación-inactivación de Pap1.
Con respecto al estudio de Pap1 como factor de transcripción, se ha visto que la expresión de genes Pap1 dependientes tiene diferentes requerimientos dependiendo de la localización y el estado de oxidación de Pap1, dando lugar a dos grupos de genes; antioxidantes y de resistencia a drogas. Para activar el primer grupo de genes, se necesita a Pap1 reducido y además la actividad conjunta con otra proteína, Prr1. Ambas necesitan de la presencia de la otra para llevar a cabo correctamente su función. Por el contrario, para activar los genes de resistencia a drogas es sólo suficiente con la localización nuclear de Pap1.In our laboratory we used as a model the fission yeast S. pombe; which has specific sensors for oxidative stress, such as the transcription factor Pap1 (pombe AP-1-like). At the beginning of this project, it was known that the activation of Pap1, which is reduced and in the cytosol before stress, occurs mainly at low hydrogen peroxide (H2O2) concentrations, in a thioredoxin peroxidase (Tpx1)-dependent manner. With this work we have characterized Pap1 as a sensor of H2O2 and as a transcriptor factor. Regarding its role as a sensor of H2O2, we studied the molecular mechanism for its activation, the role of its different cysteine residues, and the participation of Tpx1, Trx1 and Trr1 in the activation and inactivation of Pap1-dependent manner. Secondly, we have studied the Pap1-dependent gene expression program. The expression of some Pap1-induced genes have different requirements regarding Pap1 activity/subcellular localization/oxidation state leading to two subsets of genes: the antioxidant and the drug resistance genes. Oxidized Pap1 forms a heterodimer with the constitutively nuclear transcription factor Prr1 to induce the antioxidant response. The ability of Pap1 to bind and activate drug tolerance promoters is independent on Prr1, whereas its ability to bind to the antioxidant promoters is significantly enhanced upon association with Prr1. Prr1 is recruited to promoters in an oxidized Pap1-dependent manner.
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De, Nisco Nicole J. "Global analysis of the transcriptional regulation of Sinorhizobium meliloti cell cycle progression and study of cell cycle regulation during symbiosis with Medicago sativa." Thesis, Massachusetts Institute of Technology, 2013. http://hdl.handle.net/1721.1/83636.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2013.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references.
The complex [alpha]-proteobacterial cell cycle regulatory network is essential not only for faithful replication and segregation of the genome, but also to coordinate unique cellular differentiation events that have evolved as adaptations to the different lifestyles of this diverse group of bacteria. The soil-dwelling [alpha]-proteobacterium, Sinorhizobium meliloti, not only has to accurately coordinate the replication of its tripartite genome, but also must undergo a dramatic cellular differentiation in order to form an effective symbiosis with the legume Medicago sativa. Preliminary analyses have indicated that plasticity in the S. meliloti cell cycle regulatory network may be essential to symbiosis, but cell cycle research in S. meliloti has been hindered largely by lack of a method to obtain synchronous populations of S. meliloti. In this thesis, I present the first method to generate synchronous cultures of S. meliloti. I performed microarray gene expression analysis on synchronous populations of S. meliloti to gain a global view of transcriptional regulation of cell cycle events. This represents the first work of this kind done in an [alpha]-proteobacterium besides Caulobacter crescentus, which is the current model for [alpha]-proteobacterial cell cycle studies. The importance of transcriptional regulation of cell cycle progression was first discovered in C. crescentus and the work presented in this thesis highlights the conservation of cell cycle regulated gene expression in S. meliloti. I identified 462 cell cycle regulated transcripts in S. meliloti, which included genes involved in vital cell processes such as cell division, flagella biogenesis, replication and segregation of its tripartite genome as well as several putative cell cycle regulators. I compared the set of genes with cell cycle regulated transcripts identified in my analysis with the set identified in C. crescentus to generate a core set of 128 conserved genes demonstrating cell cycle regulated gene expression in both species. To determine which of the S. meliloti genes with cell cycle regulated transcripts might be part of the CtrA and DnaA regulons in S. meiloti, I performed CtrA and DnaA binding motif analysis. To understand the evolutionary significance of these CtrA and DnaA binding motifs, I looked at conservation of these motifs in homologous genes from several related [alpha]-proteobacteria. The results indicated that the putative CtrA regulon might be more evolutionarily constrained than the putative DnaA regulon. Organisms more closely related to S. meliloti or with more similar lifestyles demonstrated a much greater conservation of the CtrA binding motifs identified in S. meliloti. The CtrA binding motifs in S. meliloti identified by my analysis were not at all well conserved in C. crescentus, which was the most distantly related [alpha]-proteobacteria surveyed. These differences in cell cycle regulated transcription and the putative CtrA regulon between S. meliloti and C. crescentus thus appear to represent specific adaptations to the distinctive genome and unique intracellular symbiotic lifestyle of S. meliloti and illustrate the importance of S. meliloti as a model for cell cycle regulation in [alpha]-proteobacteria with similar intracellular lifestyles. The work presented in this thesis also describes the importance of CtrA regulation in S. meliloti during symbiosis with M. sativa. A crucial part of this symbiosis is a striking cellular differentiation (termed bacteroid differentiation), which includes changes in membrane permeability, cell elongation and branching, endoreduplication of the genome and loss of reproductive capacity and therefore a significant deviation from the free-living cell cycle program. Endoreduplication of the genome requires a decoupling of DNA replication and cell division, which could be achieved by down-regulation of the essential master cell cycle regulator CtrA. I tested the effects of CtrA depletion in S. meliloti and found that CtrA depletion induces a bacteroid-like state characterized by elongated and branched cells and highly elevated DNA content. I also show that S. meliloti CtrA has a comparable half-life to C. crescentus CtrA, but regulated proteolysis of CtrA may be different in the two species since we found CtrA proteolysis to be essential in S. meliloti. In addition, I demonstrate that the promoter and coding regions of C. crescentus ctrA cannot complement an S. meliloti ctrA chromosomal deletion during symbiosis even though they can do so in the free-living state. My attempts to identify the defects in the function C. cresentus ctrA promoter or coding region within M. sativa gave surprising results since S. melioti strains expressing C. crescentus CtrA from the S. meliloti ctrA promoter region and vice versa were able to establish an effective symbiosis with M. sativa. I discuss several possibilities to explain this apparent paradox, but further study is required to fully clarify this observation. Taken as a whole, my thesis work represents a significant advancement to the field of cell cycle research in S. meliloti and [alpha]-proteobacteria as a whole. The cell synchronization method I developed will greatly facilitate more comprehensive analysis of cell cycle regulation in S. meliloti. My microarray gene expression analysis provides a global view of cell cycle regulated transcription in S. meliloti, which can be used in more in-depth explorations of specific mechanisms of transcriptional regulation of cell cycle events in S. meliloti. Lastly, my study of CtrA function in S. meliloti establishes the importance of CtrA regulation during symbiosis with M. sativa.
by Nicole J. De Nisco.
Ph.D.
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Davis, Lynn Marie Carleton University Dissertation Biology. "An ultrastructural, immunocytochemical and biochemical study of the effects of the transcriptional inhibitor DRB on nuclei and nuclear matrices of concanavalin A-stimulated lymphocytes." Ottawa, 1993.
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Raja, Priya. "Methylation of Geminivirus Genomes: Investigating its role as a host defense and evaluating its efficacy as a model to study chromatin methylation in plants." The Ohio State University, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=osu1274728228.
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Abdelzaher, Ahmed F. "Identifying Parameters for Robust Network Growth using Attachment Kernels: A case study on directed and undirected networks." VCU Scholars Compass, 2016. http://scholarscompass.vcu.edu/etd/4481.
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Network growing mechanisms are used to construct random networks that have structural behaviors similar to existing networks such as genetic networks, in efforts of understanding the evolution of complex topologies. Popular mechanisms, such as preferential attachment, are capable of preserving network features such as the degree distribution. However, little is known about such randomly grown structures regarding robustness to disturbances (e.g., edge deletions). Moreover, preferential attachment does not target optimizing the network's functionality, such as information flow. Here, we consider a network to be optimal if it's natural functionality is relatively high in addition to possessing some degree of robustness to disturbances. Specifically, a robust network would continue to (1) transmit information, (2) preserve it's connectivity and (3) preserve internal clusters post failures. In efforts to pinpoint features that would possibly replace or collaborate with the degree of a node as criteria for preferential attachment, we present a case study on both; undirected and directed networks. For undirected networks, we make a case study on wireless sensor networks in which we outline a strategy using Support Vector Regression. For Directed networks, we formulate an Integer Linear Program to gauge the exact transcriptional regulatory network optimal structures, from there on we can identify variations in structural features post optimization.
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Ohler, Uwe [Gutachter], Florian [Gutachter] Heyd, and Chakrabarti [Gutachter] Sutapa. "Post-transcriptional mechanisms contributing to RNA and protein localization: study of local translation and alternative 3′UTRs in induced neurons / Gutachter: Uwe Ohler, Florian Heyd, Chakrabarti Sutapa." Berlin : Humboldt-Universität zu Berlin, 2019. http://d-nb.info/1199930695/34.
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Naughton, Bartholomew J. IV. "Brain Region and Cell Type Specific Approaches to Study Drug Abuse." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1314715486.
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Hoermann, Astrid 1981. "A Systems-level study of giant regulation in Drosophila melanogaster." Doctoral thesis, Universitat Pompeu Fabra, 2014. http://hdl.handle.net/10803/286075.
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Esta tesis revela la regulación transcripcional del gen gap giant (gt) en el embrión blastodermal de Drosophila por ingeniería inversa: un modelo matemático infiere los mecanismos subyacentes de datos cuantitativos de expresión recopilados en un fondo genético silvestre. El modelo se amolda a mRNA reportero controlado por elementos reguladores en cis (CRE) de gt. Es una herramienta potente para investigar cómo se forma el patrón a nivel molecular por los sitios de unión de factores de transcripción y permite predecir la expresión en cepas mutantes. La presente tesis esclarece la regulación diferencial de dos CRE adyacentes de gt y presenta la primera evidencia experimental de auto-activación de gt mediante mutagénesis de sus elementos reguladores. Tras la optimización de los parámetros en un fondo de tipo silvestre, el modelo predice correctamente los cambios observados en mutantes de Krüppel y tailless. Otras contribuciones reglamentarias sugeridas por el modelo son confirmadas por la evaluación sistemática de los CREs en mutantesThis thesis unravels the transcriptional regulation of the gap gene giant (gt) in the Drosophila blastoderm embryo via a reverse-engineering approach: a mathematical model infers the underlying mechanisms from quantitative expression data collected in the wild-type background. The model is fit to reporter mRNA driven by cis-regulatory elements (CRE) of gt. It is a powerful tool to investigate how the pattern is formed at the molecular level from transcription factor binding sites and it gives us the ability to predict the expression in mutants. This thesis elucidates the differential regulation of two adjacent gt CREs and presents the first experimental evidence for Gt auto-activation via site-directed mutagenesis of its enhancers. After optimizing the parameters in the wild-type background, the model correctly predicts the observed changes in Krüppel and tailless mutants. Other regulatory contributions suggested by the model are confirmed by systematic evaluation of the CREs in mutants
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Matthaei, Peter E. "Automatic music transcription : an exploratory study." Thesis, Stellenbosch : Stellenbosch University, 2004. http://hdl.handle.net/10019.1/53727.
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Thesis (MScEng) -- University of Stellenbosch, 2004.ENGLISH ABSTRACT: In a pioneering project for the University of Stellenbosch, and indeed South Africa, an automatic music transcription system was designed to explore the underlying theory, concepts and problematies of polyphonic music transcription. Automatic music transcription involves knowledge from the fields of acoustics, music theory, digital signal processing and information theory. The key concepts from these contributing fields as they relate to transcription systems are described in overview. A transcription system is then developed which includes components for FFT-based multipitch estimation, basic post-processing, estimation of the degree of polyphony, key determination, note duration quantisation and score output. The operation of the system is explained and tested at the hand of a synthetic polyphonic signal. The system produced usable transcriptions of real monophonic input signals to scores with standard notational symbols. The success of the system (as are the successes of all published polyphonic transcription systems) was limited for real polyphonic music signals. Nonetheless, the initial results are encouraging and indicate that the current implementation can serve as a platform for a more sophisticated and accurate system.
AFRIKAANSE OPSOMMING: In 'n baanbrekersprojek vir die Universiteit van Stellenbosch (en die breër Suid-Afrika) is 'n outomatiese musiek transkripsie stelselontwerp om die onderliggende teorie, konsepte en problematiek van polifoniese musiek transkripsie te ondersoek. Outomatiese musiek transkripsie kombineer kennis uit die navorsingsvelde van akoestiek, musiekteorie, syferseinverwerking en informasieteorie. Die sluitelkonsepte van elkeen van hierdie velde word kortliks weergegee soos dit van toepassing is op transkripsie stelsels. 'n Transkripsie stelsel met modules vir FFT-gebaseerde afskatting van polifoniese toonhoogtes, basiese naverwerking, afskatting van die graad van polifonie, bepaling van die sleutel, nootlengte kwantisering en bladmusiek notasie word aansluitend ontwikkel. Die werkswyse van die stelsel word aan hand van 'n sintetiese polifoniese sein verduidelik en getoets. Die stelsel lewer bruikbare transkripsies van enkelstemmige intreeseine na bladmusiek met standaard musieksimbole. Die sukses van die stelsel is beperk vir polifoniese musiek, soos ook die algemene geval is vir ander gepubliseerde meerstemmige transkripsie stelsels. Tog is die aanvanklike resultate belowend, met aanduidings dat die huidige implementering kan dien as 'n beginpunt vir die ontwikkeling van 'n meer gesofistikeerde en akkurate stelsel.
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Wiggins, Alison. "Guy of Warwick : study and transcription." Thesis, University of Sheffield, 2000. http://etheses.whiterose.ac.uk/6039/.
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The purpose of this thesis is to provide a detailed study of the texts and manuscripts of the Middle English Guy of Warwick, such as is not presently available. The agenda of this investigation is essentially interdisciplinary. Each chapter considers a different set of evidence (literary, historical, manuscript and linguistic). In addition to which, this study benefits from the opportunities offered by new media, incorporating the results of exhaustive and highly accurate computer-enabled searches of a range of late medieval texts. Through this approach it has been possible to integrate and identify links between different areas of research in a way which has been crucial to dispelling various myths and misconceptions which have, in the past, dominated the critical perception of Guy of Warwick. This thesis encourages a view which emphasises the complexity of the textual tradition of Guy of Warwick and rejects past assumptions which over simplify the circumstances of its production and circulation. Chapter 1 considers the place of Guy of Warwick in late medieval literature and culture, assembling the evidence for sources, relations, transmission and reception. This chapter emphasises the protean nature of the romance, its adaptation and regeneration for different contexts and the evidence for a range of responses. Chapter 2 provides, for the first time, a comprehensive account of all of the Guy of Warwick manuscripts, including full codicological descriptions and giving special consideration to the presentation of Guy of Warwick in each. By combining this codicological data with the linguistic findings of Chapter 3, it has here been possible to review and reject a number of theories, most notably concerning the Auchinleck MS, which misinterpret the significance of the manuscript presentation of Guy of Warwick. Chapter 3 uses linguistic data to clarify the relationship between the manuscript texts and the different versions of Guy of Warwick. Traditional dialect analysis is combined with computer-enabled searches to provide detailed information which establishes the origin and circulation of the texts and their literary and stylistic affiliations, including evidence which rejects the traditional Warwickshire origin for the A-version. The thesis is supplemented on CD ROM by new, accurate transcriptions of all the complete texts of Guy of Warwick and a review of Zupitza's 1875-91 edition, including a list of errors.
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Brunkhorst, Adrian. "A study on the TFIID subunit TAF4 /." Stockholm, 2005. http://diss.kib.ki.se/2005/91-7140-206-3/.
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Garnier, France. "Study of transcription regulation of the gene mdr1." Thesis, McGill University, 1992. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=56986.
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In order to characterize cis-acting sequences and trans-acting factors important in regulating the expression of the mouse mdr1 gene, in vitro DNAsel footprinting experiments were carried out on a mdr1 promoter segment between positions $-$245 and +84, using nuclear protein extracts prepared from cell lines expressing different endogenous amounts of mdr1 mRNAs. Three footprinted sequences were detected on the non-coding strand of the $-$245 to +84 mdr1 promoter fragment (between -77 to -56, between -46 to -24, and between +5 and +15) with nuclear extracts from mdr1 expressing cells (CMT-93, LTA, and Y-1 cells). In addition, a specific footprinted sequence ($-$14 to +5) was detected on both strands only with nuclear extracts from the mdr1 non-expressing cell line (RAG cells) suggesting the presence and binding of a putative negative regulatory factor in these cells. However, replacement of this sequence in the mdr1 basal promoter ($-$93 to +84) by a heterologous, although similar positioned SV40 sequence did not restore promoter activity in RAG cells. The basal mdr1 promoter was further characterized in bidirectional deletion mutants, in order to identify cis-acting elements important for general transcriptional regulation. These studies further localized the mdr1 basal promoter between positions $-$74 and +84, and also suggested the presence of possible positive and negative cis-acting sequence elements modulating the activity of this basal promoter.
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Afzal, Muhammad A. "A study of the transcription of mumps virus." Thesis, Queen's University Belfast, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.335323.
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Re, Adrien Marcus. "The role of transcription in jazz improvisation : examining the aural-imitative approach in jazz pedagogy." Virtual Press, 2004. http://liblink.bsu.edu/uhtbin/catkey/1285406.
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Jazz musicians traditionally learned jazz improvisation by transcribing other musicians they admired in order to absorb, assimilate and retain important stylistic elements of jazz. Indeed, many famous jazz musicians have testified to the importance of transcribing as part of their jazz education. By the latel960's, jazz increasingly gained acceptance as a legitimate American genre within academia. As jazz studies programs became more formalized in colleges and universities, a plethora of methods and materials have followed suit. Lately, critics of these programs claim that many of the procedures, methods and materials used have abandoned the aural-imitative tradition. This study examines the current use of and the viability of future jazz education methods based primarily on aural-imitative procedures.Forty-one jazz faculty from universities and colleges throughout the United States participated in an interview process. An open-ended questionnaire survey was used to elicit responses. Each was asked a series of questions directly related to transcribing. The responses were recorded via cassette and were transcribed verbatim. In addition, four music teachers at schools at four schools for the blind were asked a similar series of questions. Their interviews responses were analyzed for similarities and differences.The results suggest that current methods do not contain adequate aural representations and that transcription could be a viable alternative to current methods. A practical system based on the transcription paradigm could and should be developed. Current digital technologies and Internet developments may help facilitate an all-transcription based methodology. Certain recordings and solos have become recognized as `masterpieces' that deserve to be transcribed and studied. The insights gained from school for the blind suggest that certain musical aspects may be beet gained from an aural-centric perspective.School of Music