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 39 for “"codon usage"”.
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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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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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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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Improvements in codon usage analysis for a more detailed understanding of genome content and horizontal gene transfer
… amino acids to be encoded by multiple synonymous codons. Genes can vary in their utilization of synonymous codons, and this provides a basis of comparison for studying the compositional histories and evolution of genomes. The original goal of this dissertation work was to study the effects of …
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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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Increased genome sampling reveals novel insights into vertebrate molecular evolution
… and polar bear. It is known that synonymous codon usage is governed by a combination of selective and neutral processes. Currently, it is thought that primarily neutral processes govern synonymous codon usage in vertebrates, possibly due to their lower long-term effective population sizes. …
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Attempt to express the Xerophyta viscose stress-responsive gene, Xvcor, in yeast with view to functional analysis
… of recombinant protein. A computer search for codon usage showed that the codon usage bias in Xvcor was low compared with that of highly expressed genes of S. cerevisiae. Together, these results suggest that the codon usage in Xvcor could influence its expression in yeast.
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Genome Signatures Reveal the Importance of Context Dependent Codon Bias In A Range of Bacterial Genomes
… species was investigated for all four and six codon families to identify the role of context dependency on synonymous codon usage. Genome signatures of four nucleotide words were used to identify the distribution, magnitude and nucleotide contextual patterns.</p>
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Collective Evolution of Biological and Physical Systems
… genome biases. Selection on translation leads to codon usage bias; selection on transcription or replication leads to nucleotide composition biases such as the GC content. These biases result from the generic tradeoffs inherent to template-directed synthesis and occur even in the absence of biased …
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Genome evolutionary studies of the Salmonella enterica serovars: implications for the dynamics of horizontal gene transfer, the pangenome concept, and bacterial and archaeal taxonomy
… loss processes. Chapters 2 and 3 describe the codon usage studies of the horizontally acquired genes of S .enterica. Chapter 2 provides the first known quantitative evidence that some groups of closely related, but traditionally distinct species derive the plurality of their recently …
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DIRECT REPEATS AND DELETIONS IN MITOCHONDRIAL DNA: CASUAL AND EVOLUTIONARY ASPECTS
… of DRs revealed that the bias in synonymous codon usage within protein coding genes was the most important determinant of mtDNA DR count. Analysis of deletion breakpoints using a theoretical model based on thermodynamic principles of DNA hybridization indicated that age-related mtDNA …
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A multiplexed approach for quantitative profiling of the translatome using bioorthogonal non-canonical amino acids
… genes. These genes also demonstrated a unique codon bias compared to the average codon usage of the genome. An analysis of codon frequency revealed changes in global codon usage over time following EGF stimulation. Changes in chemical modifications of tRNA isoacceptors were also observed which …
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Expression of HIV-1 subtype C nef in E. coli and Nicotiana benthamiana : development of plant-based vaccines for HIV
… anti Nef antiserum raised in sheep. The role of codon optimization in expression of Nef in benthamiana was investigated. A synthetic nef gene was constructed based on the codon usage of benthamiana. The plant codon optimized gene and the wild type nef genes were inserted into the TMV -based …
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PCR-based Synthesis of Codon Optimized cry2Aa Gene for Production of Shoot and Fruit Borer (Leucinodes orbonalis) Resistant Eggplant (Solanum melongena L.) Cultivars
… was to develop eggplant cultivars that express a codon-optimized cry2Aa gene, the sequence of which is based on that of an Indian isolate of Bt, with the eventual goal of producing fully resistant cultivars. The cry2Aa gene was modified for optimal expression in eggplant using the codon usage …
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Improvement and establishment of the tTA-dependent inducible system in the mouse brain
… of the htTA was altered concerning mammalian codon usage, putative splicing signals, CG dinucleotide content, and toxicity of the transactivation domain VP16. These sequence changes on tTA resulted in the three-fold increase of the inducible activity in transiently transfected HeLa cells, …
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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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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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Comparative and Functional Analysis of Gene Expression in Ophiostoma Species
… EST datasets were also investigated to determine codon usage and to identify the presence of genes predicted to encode proteases. Both are important factors in recombinant protein expression. Protease production can severely inhibit the production of recombinant protein in fungal hosts. Based on …
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