Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 24 for “"Protein-DNA Interaction"”.
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Protein-DNA interaction, random walks and polymer statistics
… physical framework describing the kinetics of protein- DNA interaction is developed. Recognition and binding of specific sites on DNA by proteins is central for many cellular functions such as transcription, replication, and recombination. In the process of recognition, a protein rapidly …
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SWI/SNF-NUCLEOSOME INTERACTIONS AND DISASSEMBLY OF NUCLEOSOMES: NOVEL METHODOLOGIES FOR MAPPING PROTEIN-PROTEIN AND PROTEIN-DNA INTERACTION
… University Carbondale. TITLE: SWI/SNF-NUCLEOSOME INTERACTIONS AND DISASSEMBLY OF NUCLEOSOMES: NOVEL METHODOLOGIES FOR MAPPING PROTEIN-PROTEIN AND PROTEIN-DNA INTERACTION MAJOR PROFESSOR: Dr. Blaine Bartholomew The SWI/SNF complex disrupts and mobilizes chromatin in an ATP-dependent manner. A …
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Computational Inference of Genome-Wide Protein-DNA Interactions Using High-Throughput Genomic Data
… One important aspect of this regulation is the interaction between regulatory proteins, such as transcription factors (TF) and nucleosomes, and the genome. Different high-throughput techniques have been invented to map these interactions genome-wide, including ChIP-based methods (ChIP-chip, …
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Structural Studies of DNA Replication Machinery in Archaea
DNA replication is a fundamental process present in all living organisms. It is the means by which organisms transfer their genetic information to their offspring to ensure the propagation of their lineage. One of the essential features of DNA replication is to separate the DNA double helix to …
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Comparative analysis of the promoters of the CyI-CyIIa-CyIIb actin gene cluster in the sea urchin Strongylocentrotus purpuratus
… are linked in the genome and encode very similar proteins. However, their spatial and temporal expression patterns are differentially regulated. The region of CyIIa upstream of the ATG and putative transcription start site was subcloned and sequenced. Sites of protein-DNA interaction were …
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Systematic determination of a transcription factor/binding site functional interaction landscape
… factors are a major class of regulatory proteins that specifically bind DNA to modulate the expression of targeted genes. While they have been extensively studied, major questions remain about the protein-DNA interaction underlying this hub of regulation. What binding site sequences …
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A Statistical Model to Determine Multiple Binding Sites of a Transcription Factor on DNA Using ChIP-seq Data
<p>Protein-DNA interaction is vital to many biological processes in cells such as cell division, embryo development and regulating gene expression. Chromatin Immunoprecipitation followed by massively parallel sequencing (ChIP-seq) is a new technology that can reveal protein binding sites in genome …
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Investigation of mass spectrometry approaches for aiding fragment-based drug discovery
… mass spectrometry (MS)-based techniques to study protein structure dynamics is a relatively new field, with seminal developments such as nanoelectrospray ionization (nano-ESI) and traveling-wave ion mobility-mass spectrometry (TWIM-MS) MS being introduced only around twenty-five and fifteen years …
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Tissue-Specific Expression and Steroid Hormone Regulation of Human Gonadotropin -Releasing Hormone (hGnRH) Gene in Placental Cells (JEG -3 cells)
… to be functionally active in JEG-3 cells. The DNA sequence responsible for functioning of the upstream promoter in JEG-3 cells is narrowed to a region between –1048 bp and –730 bp. This DNA fragment contains four elements, which can bind with nuclear extract from JEG-3 cells (but not from GT1-7 …
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From network to pathway: integrative network analysis of genomic data
… we dissect the molecular pathway into two parts: protein-DNA interaction network and protein-protein interaction network. Several novel approaches are proposed to integrate gene expression data with various forms of biological knowledge, such as protein-DNA interaction and protein-protein …
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Resolving the Role of POU1F1 in Human Growth Hormone Locus Activation
… LCR/hGH-N domain. A series of in vitro DNA binding experiments revealed that POU1F1 binds to multiple sites at HSII, consistent with a direct role in HSII function. These observations clarify the function of HSII, expanding the role of POU1F1 in hGH LCR activity, and provide insight on …
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Simultaneous computational discovery of DNA regulatory motifs and transcription factor binding constraints at high spatial resolution
… methods to address the challenge of identifying protein-DNA interactions at high spatial resolution from noisy ChIP-Seq data. I first present the genome positioning system (GPS) algorithm which predicts protein-DNA interaction events from ChIP-Seq data using a single-base resolution generative …
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Characterization of signaling pathways underlying key growth and development processes in Populus trichocarpa
… This led to the characterization of 165 protein-protein interactions and 20 protein-DNA interaction which constitute numerous woody tissue related subnetworks. One such network, centered on the DIVARACATA and RADIALIS INTERACTING FACTOR (PtrDRIF), identified PtrWOX13c as an interacting …
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Structural basis for the function of the transcriptional regulator KstR from Mycobacterium tuberculosis
… targeting the cholesterol metabolism in Mtb. The interactions between KstR and cognate DNA or ligands have been investigated by multiple biochemical techniques (i.e. electrophoretic mobility shift assay, surface plasmon resonance and intrinsic fluorescence quenching assay). Protein-DNA binding …
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Cloning and characterization of a single-stranded DNA-binding protein of Leishmania major
… referred to as leishmaniasis. The major surface protein on all species of Leishmania is a highly abundant 63 kDa glycoprotein referred to as GP63. GP63 has been characterized as a cell surface protease, however, its exact role in the Leishmania life cycle is not clear. The genes encoding GP63 are …
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Structural and Functional Evolution of Human Heat Shock Transcription Factors
… the expression of numerous genes involved in protein folding, protein degradation, and cellular survival. The studies presented here utilize a diverse array of techniques including yeast genetics, recombinant protein expression and purification, biochemical analysis of protein-DNA …
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Integrative Modeling and Analysis of High-throughput Biological Data
… data, including microarray gene expression data, protein-DNA interaction data and protein-protein interaction data. These methods will help improve our understanding of biological systems. First, we propose a knowledge-guided multi-scale independent component analysis (ICA) method for biomarker …
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Discovery of New Protein-DNA and Protein-Protein Interactions Associated With Wood Development in Populus trichocarpa
… biomass yield. Transcription factors (TFs) are DNA-binding regulatory proteins capable of either activation or repression by binding to a specific region of DNA, normally located in the 5-prime upstream promoter region of the gene. In the first section of this work, six DNA promoters from wood …
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Theoretical investigation of protein search for targets on DNA
Protein-DNA interactions activate many biochemical transitions used by living systems for successful functioning. The starting point in this process is a protein search and recognition of specific target sequences on DNA among millions of non-specific sites. One of the most striking observations is …
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DNA Binding Specificity of Mu Transcription Factor C and Crystallization of C : DNA Complex
… of early, middle and late transcription. The Mor protein is an activator of the middle promoter Pm and is encoded by the last gene of the early transcript. The C protein is an activator of the four late promoters Plys, PI, PP, and Pmom and is expressed from the middle transcript. Both Mor and C …
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