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 125 for “"protein-coding genes"”.
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Identifying protein-coding genes and synonymous constraint elements using phylogenetic codon models
… methods for comparative genomics analysis 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 …
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THE ROLE OF INTEGRATOR SUBUNIT 11 IN PROMOTOR-PROXIMAL ATTENUATION OF PROTEIN CODING GENES
The Integrator complex is a 14-subunit protein complex that interacts with RNA polymerase II (RNAPII) in metazoans during transcription of multiple forms of coding and non-coding RNA. Originally described as being responsible for the 3’ cleavage and termination of uridine-rich small nuclear RNA, …
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Characterization of two Bacillus subtilis penicillin-binding protein-coding genes, ykuA (pbpH) and yrrR (pbpI)
Penicillin-binding proteins (PBPs) are required in the synthesis of the cell wall of bacteria. In Bacillus subtilis, PBPs play important roles in the life cycle, including both vegetative growth and sporulation, and contribute to the formation of the different structures of vegetative cell wall and …
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Gene prediction with conditional random fields
The accurate annotation of an organism's protein-coding genes is crucial for subsequent genomic analysis. The rapid advance of sequencing technology has created a gap between genomic sequences and their annotations. Automated annotation methods are needed to bridge this gap, but existing solutions …
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Evolutionary Fitness of Non-Coding Genetic Elements
Proper protein structure and function are integral to cellular homeostasis. The wide array of known natural protein sequences are a product of millions of years of evolutionary pressure maintaining physical stability and biological function. The evolutionary process occurs via random instances of …
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Regulation of the Kcnq1ot1 Imprinting Domain in Mouse
… the Kcnq1ot1 ncRNA, and maternally expressed protein-coding genes. Truncation of the Kcnq1ot1 ncRNA or deletion of the Kcnq1ot1 ICR, including the Kcnq1ot1 ncRNA promoter results in biallelic expression of normally paternally silent protein-coding genes in postimplantation, suggesting the …
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Transcriptional profiles of cumulus-oocyte complexes related to developmental competence in bovine oocytes
During folliculogenesis, oocytes and cumulus cells undergo many morphological and physiological changes. Transcriptome data were produced from single oocytes and corresponding cumulus cells (CC) to infer the differences in the transcript abundance from fully grown versus growing phase oocytes and …
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Discovering Conserved cis-Regulatory Elements That Regulate Expression in Caenorhabditis elegans
… motifs with instances in about half of the protein-coding genes. This initial first step was valuable as it recovered some known elements and cis-regulatory modules. Yet the results had a lot of redundant motifs and sites, and the approach was not efficiently scalable to the entire regulome …
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Computational comparative genomics : genes, regulation, evolution
… the genome contains the blueprint of all protein-coding genes and the regulatory motifs used to coordinate the expression of these genes. Comparative genome analysis of related species provides a general approach for identifying these functional elements, by virtue of their stronger …
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Dicer deletion and short RNA expression analysis in mouse embryonic stem cells
… in length, guide the various effector proteins of RNAi to silence fully or partially complementary targets. The sequencing of endogenously expressed short RNA species coupled with genetic studies in various experimental organisms has revealed a role for RNAi in the silencing of …
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Complex evolution of mitochondrial genomes: lessons from salamanders
… experience weaker purifying selection on protein-coding sequences than do frogs, a comparable amphibian clade with higher metabolic rates. In contrast, there is no evidence for weaker selection against mitochondrial genome expansion in salamanders. Together, these results suggest that …
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Genetic Determinants of Salmonella and Campylobacter Required for In Vitro Fitness
… overlapping set of 339 conditionally essential genes (CEGs) required by S. Typhimurium to overcome these host stressors. In Chapter 3, we screened of S. Typhimurium Tn5 library for desiccation survival. Salmonella spp. is the most notable and frequent cause of contamination in low-water activity …
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Targeting and function of mammalian microRNAs
… 2-8 at the 5' end of the microRNA. We show that protein-coding genes preferentially expressed at the same time and place as a highly expressed microRNA have evolved their 3' UTR sequence to specifically avoid seed sites matching that microRNA. In contrast, conserved sites appear to be …
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TOWARDS AN UNDERSTANDING OF GENETIC SELECTION IN BREAST CANCER
… cell lines. Stable regions contained 9,463 protein coding genes, of which expression of 7,489 were analyzed. We found 78% (5804/7489) of genes had both stable copy number and expression. The breast cancer genome preferentially preserves functions that include cellular metabolic processes, …
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Comparative gene identification in mammalian, fly, and fungal genomes
… interpretation is the accurate identification of protein-coding genes. One approach to gene identification is comparative analysis of the genomes of several related species, to find genes that have been conserved by natural selection over millions of years of evolution. I develop general …
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Multiplexed Crispr Libraries For Cancer Functional Genomics
… targeting efficiency. We optimized the AsCpf1 protein for functional genomics use and demonstrated that an AsCpf1-based multiplexed library outperforms its monocistronic CRISPR/Cas9 library counterpart with a greatly reduced library size. With this strategy, we constructed the smallest …
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DIRECT REPEATS AND DELETIONS IN MITOCHONDRIAL DNA: CASUAL AND EVOLUTIONARY ASPECTS
… in mitochondrial DNA (mtDNA) deletion mutagenesis. Meta-analysis of age-related deletion breakpoints indicated that in human and rhesus monkey but not in mouse and rat, the average distance observed between a mtDNA breakpoint and its nearest direct repeat (DR) motif was significantly …
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Genome scale metabolic reconstruction and hypothesis testing in the methanogenic archaeon Methanosarcina acetivorans C2A
… iMB744, accounting for 744 of the 4540 predicted protein coding genes (16%) in the M. acetivorans genome. The reconstruction effort has identified key knowledge gaps and differences in the peripheral metabolism and central metabolism between methanogenic species. Using flux balance analysis, the …
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Computational Tools and Analyses for Improved Inference of Variant Effects
… all possible missense variants in selected protein targets, while computational methods seek to infer missense variant impacts using statistical modelling. Here I describe work to assist and exploit both MAVE and computational studies.To assist in planning and to promote collaboration and …
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Alternative Splicing Expands Spatiotemporal Expression Complexity of Arthropod N -Cadherin
… expands genomics, the small number of protein-coding genes in metazoan genomes is insufficient to account for their cellular diversity within organisms. Alternative splicing, producing more than one transcript from a single gene, provides a way to generate complexity with limited amount …
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