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 27 for “"protein-DNA binding"”.
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Protein-DNA Binding: Discovering Motifs and Distinguishing Direct from Indirect Interactions
… in the eukaryotic cell, gene transcription and DNA replication, is regulated largely through interactions between proteins or protein complexes and DNA. Although a lot is known about the interacting proteins and their role in regulating transcription and replication, the specific DNA binding …
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Inferring regulatory networks from multiple sources of genomic data
… algorithm to identify the regulatory models from protein-DNA binding and gene expression data. These models to a large extent agree with the knowledge of gene regulation pertaining to the corresponding regulators. The three works in this thesis provide a framework of modeling gene regulatory …
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High-Throughput Screening Development Using Photonic-Crystal Optical Biosensor
Protein-DNA interactions are essential for fundamental cellular processes such as transcription, DNA damage repair, and apoptosis. As such, small molecule disruptors of these interactions could be powerful tools for investigation of these biological processes, and such compounds would have great …
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Inferring interactions, expression programs and regulatory networks from high throughput biological data
… complementary large-scale expression and protein-DNA binding data to discover co-regulated modules of genes. This algorithm is extended so that it can infer sub-networks for specific systems in the cell. Finally, I present an algorithm which combines some of the above methods to …
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Characterization of Aryl Hydrocarbon receptor and Kruppel-Like-Factor-6 interaction
… (ARNT). The canonical AhR-ARNT complex binds to DNA regions known as Xenobiotic Response Elements (XRE), inducing the transcription of target genes. Our previous results demonstrated that the AhR is also involved in a novel protein-DNA complex with the Kruppel Like Factor 6 (KLF6), a zinc finger …
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Methods for identifying regulatory grammars
… study the mechanisms of gene regulation, such as protein-DNA binding, at greater resolution and on a greater scale than was previously possible. We present an expectation-maximization learning algorithm that identifies enriched spatial relationships between motifs in sets of DNA sequences. For …
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A bioinformatic study of the 5' upstream region of the human gene
… and representation of regulatory motifs. DNA generally avoids flexible dinucleotide steps. In the upstream sequence the DNA becomes even less flexible towards the start site of transcription. In contrast there is an increase in bistable steps in this direction. It is concluded that these …
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Development of Extrachromosomal Genetic Technologies for Persistent and Tunable Expression of Therapeutic Payloads
… through genomic integration of transgenic DNA via genome editing (e.g., CRISPR\Cas9) or integrating viral vectors (e.g., retrovirus, lentivirus). Integration-based approaches risk insertional mutagenesis and oncogene activation, yielding unpredictable, irreversible consequences. Inspired by …
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Zero-Inflated Models to Identify Transcription Factor Binding Sites in ChIP-seq Experiments
<p>It is essential to determine the protein-DNA binding sites to understand many biological processes. A transcription factor is a particular type of protein that binds to DNA and controls gene regulation in living organisms. Chromatin immunoprecipitation followed by highthroughput sequencing …
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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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Using photonic crystal biosensors for pharmaceutical screening
… ongoing project involving the screening of plant protein samples from Pakistan is then presented. In further work, the description of the photonic crystal biosensor used for a protein macromolecule binding assay is presented. A high-throughput screen aimed at identifying small molecule disrupters …
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Exploring Genome Structure and Gene Regulation Related to Virulence in Fungal Phytopathogens Using Next Generation Sequencing Techniques
… entire transcriptome (RNA-Seq), and detection of protein-DNA binding sites (ChIP-Seq). The cost of sequencing a fungal genome, for example, has decreased from more than one hundred thousand dollars to currently only three thousand dollars. With the development of the applications and the …
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Understanding and improving the anticancer activity of cisplatin
… human malignancies. It is widely accepted that DNA is the cellular target for cisplatin. Prior to this work, several structures of duplex DNA modified by cisplatin revealed the distinctive distortions caused by cisplatin-DNA adducts. High mobility group (HMG) domain proteins are DNA binding …
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Assessing effects of symmetry on motif finding
Identifying protein DNA binding sites like transcription factor binding sites is a key component of gene regulatory networks. The challenging task of predicting and identifying DNA binding sites both experimentally, and computationally suffers from high false positive due to various contributing …
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Computational analysis of cis-regulatory mechanisms underlying cellular response to drug perturbations
… on the presence/absence of a (c) finite set of protein regulators binding to the (d) genes immediate upstream DNA sequence, but rather, that the span of regulators ranges from protein DNA binding factors to other such nuclear factors (including the DNA itself) up and through various signaling …
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Computational Dissection of Composite Molecular Signatures and Transcriptional Modules
… moves from gene module level down to DNA sequence level to identify gene regulatory programs by integrating gene expression data and protein-DNA binding data. A sparse hidden component model is first developed for this problem, taking into account a well-known biological principle, …
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Subunit Interactions of Recombinant HIV-1 Reverse Transcriptase With Mutations at L289
… active; therefore, identification of subunit binding sites could lead to potential targets for antiviral therapy. In order to identify where subunit binding of RT occurs, mutations were made at leucine (L) 289, a residue believed to be involved in dimerization through hydrophobic interactions …
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Structural basis for the function of the transcriptional regulator KstR from Mycobacterium tuberculosis
… 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 assays have demonstrated that the …
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Development of a Gram-type Specific Method for Detection of Bovine Mastitis Pathogens by Combining Loop-mediated Isothermal Amplification (LAMP) and Split Trehalase Technologies
… bacteria and (ii) use a modified amplicon binding split trehalase assay (ABSTA) to detect this amplification by a specific protein-DNA binding and the complementation of split trehalase. To do this, split trehalase fusion proteins HisTreA-C-SpoIIID and HisTreA-N-SpoIIID were purified, and …
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Structural and biochemical studies of plant inositol phosphate kinases
… and StIPKα, along with two inositol Phosphate binding proteins: COI1 and TIR1, were cloned with the aim of fully characterising each. The research became centered around AtIPK1, although AtITPK4 was also investigated as a novel ITPK family member. X-ray crystallographic structures of AtIPK1XHis …
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