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 55 for “"Sequence conservation"”.
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Identification of Deleterious and Disease Alleles in a General Population and Preterm Labor Patients
… genome by integrating functional evidences from sequence conservation, genome-wide association studies and the transcriptional regulatory network. However, even in protein-coding regions, it is not well understood how often and by what mechanism deleterious alleles disrupting strong sequence …
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Structure-based realignment of non-coding RNAs in multiple whole genome alignments
… have become a central tool in biological sequence analysis. A major application is the de novo prediction of non-coding RNAs (ncRNAs) from structural conservation visible in the alignment. However, current methods for constructing genome alignments do so by explicitly optimizing for …
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Developing a Contextual Annotation Framework for Short Linear Motifs in Proteins
… motifs (SLiMs) is challenging due to their low sequence complexity and high prevalence across the proteome. Many false positives—sequences that match the pattern of the SLiM but are not involved in the biological functions typically associated with SLiMs—complicate this task. Distinguishing …
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Integrating genomic conservation data with motif discovery
… formalize a probabilistic model of inter-species sequence conservation for motif discovery, and demonstrate that adding large-scale genomic conservation data to an existing motif discovery procedure improves the quality of that procedure's results. Existing motif discovery algorithms reveal …
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Folding patterns in protein sequences
… genome projects, a growing number of protein sequences remain uncharacterised. Generally, computational techniques have not been developed to distinguish between regions that are conserved in proteins owing to evolutionary pressures to maintain structure and those that are conserved in order …
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Genome-wide prediction of developmental enhancers and analysis of evolutionary plasticity in Drosophila
… binding to modular units of cis-regulatory DNA sequences. The transcription factors Bicoid (BCD), Caudal (CAD), Hunchback (HB), Kruppel (KR), and Knirps (KNI) are crucial in patterning the anterior-posterior axis of the embryo by acting at very early stages of Drosophila development. In prior …
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Cloning and regulation of rat and Xenopus laevis hepatic 3-hydroxy-3-methylglutaryl Coenzyme A reductase
… A (HMG-CoA) reductase have been cloned and sequenced. The rat liver HMG-CoA reductase cDNA clone contains one open reading frame coding for 887 amino acids. Its 106 nucleotide long 5$\sp\prime$-noncoding region contains no additional start codons. It does not contain a poly(A) tract at the …
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Developing bioinformatic tools for phosphorylation site co-regulation and correlation: The plant Cellulose Synthase Complex as a case study
… to directly visualize the number, frequency, and sequence conservation of phosphorylation sites within a given protein or network of proteins. Further comparison of the primary sequence flanking the phosphorylated residue will help identify motifs conserved across proteins within the network, …
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Interrogating the molecular mechanism of signal transduction in the TGF-β receptor superfamily
… ‘inside’ and ‘outside’ the cell. Here, I combine sequence conservation analysis, functional assays and structural approaches to try to build a picture of the molecular choreography of TGF-β signalling. These results lay the groundwork for future studies to unravel the molecular mechanisms of …
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Isolation and Characterization of D-Myo-Inositol-3-Phosphate Synthase Gene Family Members in Soybean
… and examination of MIPS-homologous soybean EST sequences suggested that GmMIPS1 is part of a multigene family of at least four similar members. The sequences of promoter and genomic regions of GmMIPS1 and GmMIPS2 revealed a high degree of sequence conservation. Northern and western blot analyses …
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Understanding the determinants for substrate recognition, regulation of enzymatic activity and the development of broad-spectrum inhibitors of coronavirus 3-chymotrypsin-like proteases
… is an attractive drug target. Moreover, high sequence conservation in the vicinity of active site among 3CLpro proteases from different coronavirus subclasses make them an excellent target for the development of broad-spectrum therapeutics for coronavirus infections. The overarching goal of …
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Tracing the evolution of lineage-specific transcription factor binding sites in a birth-death framework
… conserved sites, and rely heavily upon multiple sequence alignments. However, sequence conservation based approaches have limited ability to detect lineage-specific elements that could contribute to species-specific traits. In this thesis, we describe a novel framework that utilizes a birth-death …
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A survey of fly and nematode small RNAs by deep sequencing
… C. elegans, some of which exhibit patterns of sequence conservation suggesting important regulatory functions. Sequencing was performed across a time-course of D. melanogaster development, permitting refinement of preexisting miRNA annotations and providing insights into miRNA biogenesis and …
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Conserved Conformational Dynamics Control PTP1B Enzymatic Activity
… on intrinsic protein dynamics. Further, while sequence conservation is well-correlated with conservation of structure, it is unknown if sequence also conserves protein dynamics. To understand the role of dynamics, and its potential conservation, on enzyme function we studied Protein Tyrosine …
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Modulation of Nocturnin Phosphatase Activity through the Disordered Amino Terminus
… removal of the 2′-phosphate from NADP(H). High sequence conservation of the leucine zipper (LZ)-like motif, the only structural element in the amino terminus, highlights the potential importance of this domain in modulating phosphatase activity. I use in vitro biochemical and biophysical …
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Understanding co-expressed gene sets by identifying regulators and modeling genomic elements
… tools exist examining the non-coding, regulatory sequence of gene sets for evidence of a shared regulatory signature that may signal the involvement of important DNA-binding proteins called transcription factors (TFs). Here, we proposed and developed new computational methods for identifying major …
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Conserved recombination patterns across coronavirus subgenera
… both from controlled experiments and in genome sequences sampled from nature, that patterns of recombination in coronaviruses are nonrandom and that this is likely attributable to a combination of sequence features that favour the occurrence of recombination breakpoints at specific genomic …
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Contributions to the analysis of proteins
… and described in detail. Application of a sequence conservation analysis to the protein indicates highly conserved surface patches near the putative actin-binding domains of fascin. A novel conformational dynamics analysis suggests that these domains are coupled via an allosteric mechanism …
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Proton-coupled electron transfer in the Escherichia coli ribonucleotide reductase
… vitro and in vivo mutagenesis studies as well as sequence conservation, direct evidence for radical intermediates along this pathway has been masked by conformational gating. We have initiated R1 nucleotide reduction in the absence of R2, using a photoactive derivative of the R2 C-terminal …
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