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 409 for “"Codon"”.
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DNA Phonology: Investigating the Codon Space
… thesis is concerned with large-scale studies of codon usage in completely sequenced genomes. A new compositional analysis scheme is presented, complete with a number of computation and visualisation tools. The thesis addresses the benefits of this very general scheme, named codon profiling, with …
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Information and the evolution of codon bias
… a case study of the genetic code (specifically, codon bias) and the translation system from the perspective of information. The codon biases of 831 Bacteria and Archeae are analyzed and modeled as points in a 64-dimensional statistical space. The major results are that (1) codon bias evolution …
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Engineering exclusively-quadruplet codon translation in vivo
… universally encode amino acids with three-base codons specifying the twenty canonical amino acids. A genetic code entirely based on four-base codons would answer many questions about the origin of life and have profound implications for expanding the genetic code to include novel amino acids. …
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Codon: A Framework for Pythonic Domain-Specific Languages
… lower performance. In this thesis, we propose Codon, a framework for implementing high-performance DSLs based on Python. Whereas previously achieving high-performance in dynamic languages has been difficult, often requiring separate compiled libraries, we provide a robust base for analysis and …
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KRAS Codon 12 and Codon 13 Mutations in Relation to Overall Survival among Colorectal Cancer Patients: A Systematic Review and Meta-Analysis
Oncogenic mutations in KRAS codon 12 and codon 13 within exon 2 are frequently occurring mutations in colorectal cancer (CRC). However, the existing published data on the association of KRAS codon 12 and codon 13 mutations on the survival of CRC patients remains inconclusive. To address this, we …
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Computational Targeted Codon Optimization and Translation with Deep Learning
Codon optimization—the task of recoding a protein’s underlying DNA sequence to maximize expression in a target organism—is a complicated biological optimization problem. Each gene brings a dynamic combination of local and long-range dependencies along with globally imposed constraints specific to …
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Oligonucleotide design and codon optimization for PCR-based gene synthesis
… If the primary concern is a protein sequence, codons can be changed to synonymous codons with little consequence, making it possible to remove problematic repetitive elements. We show that our algorithm can theoretically be extended and used with constraint optimization algorithms to solve the …
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The Role of Codon Usage in Regulating Protein Expression, Structure and Function
Codon usage bias has been observed in the genomes of almost all organisms and is thought to result from selection for efficient translation of highly expressed genes. Many genes, however, exhibit little codon usage bias. It's not clear whether the lack of codon bias for a gene is due to lack of …
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Modulating Avidity of H8F4-Car By Regulation of Expression Via Codon Modification
… studies using the genetic code and its inherent codon bias. This was done by altering serine and arginine residues within the non-variable regions of h8F4-CAR from their endogenous codons into the rare codon isoforms TCG and CGT for serine and arginine, respectively. Synonymous codon modification …
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Evaluation of Altered Kras Codon Bias and NOS Inhibition During Lung Tumorigenesis
… <italic>RAS proto-oncogenes exhibit divergent codon usage. Of the three isoforms, <italic>KRAS contains the most rare codons resulting in lower levels of KRAS protein expression relative to <italic>HRAS and <italic>NRAS. To determine the consequences of rare codon bias during <italic>de …
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How codon choice determines evolvability and evolutionary robustness in short linear motifs
… that is defined from the nucleotide and codon levels. Simulations using this methodology suggested that different codons have varying propensities to evolve into amino acids within a linear motif. In other words, some sequences have higher motif evolvability. The simulations also …
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Design and screening of degenerate-codon-based protein ensembles with M13 bacteriophage
A billion years of evolution has crafted a diverse set of proteins capable of complex and varied functionalities. Within recent decades, scientists have applied both rational design and directed evolution to accelerate development of high-value proteins, including biotherapeutics. While …
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Identifying protein-coding genes and synonymous constraint elements using phylogenetic codon models
… of protein-coding genes using phylogenetic codon models, in pursuit of two main lines of biological investigation: First, we develop PhyloCSF, an algorithm based on empirical phylogenetic codon models to distinguish protein-coding and non-coding regions in multi-species genome alignments. We …
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Gene finding and the evaluation of synonymous codon usage features in microbial genomes
… sich mit der Evaluierung des synonymen Codongebrauchs in den Kodierregionen prokaryotischer Genome. Zur Klassifikation anhand von Eigenschaften des Codongebrauchs wird ein neues, auf log-odds ratio scores basierendes Verfahren eingeführt, welches einige vorteilhafte Eigenschaften …
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The Roles of Codon Usage in Translational and Transcriptional Regulation on Gene Expression
Codon usage bias refers to the universal feature of genome that synonymous codons are used at different frequency. Codon usage plays critical roles in determining gene expression levels through impacting multiple fundamental cellular processes. Although the correlation between codon usage and gene …
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A Stress-Induced TRNA Depletion Response Mediates Codon-Based Translational Repression and Growth Suppression
… of proteins enriched in its cognate tyrosine codons, comprising growth and metabolic genes. Consistent with these affected pathways, depletion of tyrosyl tRNAGUA or its downstream targets, EPCAM, SCD, or USP3, repressed growth—revealing a tRNA-dependent growth suppressive pathway for oxidative …
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Codon Usage Biases Differ Between Tissues and Can Confer Tissue-Specific Gene Expression in Drosophila
<p>Codon usage bias is a fundamental aspect of the genetic code. For many years synonymous mutations to a coding sequence were considered to be functionally “silent.” We now appreciate that is not the case and that synonymous codon choice can have drastic implications for gene expression and …
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