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 50 for “"bacterial genomes"”.
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Computational Techniques Applied to RNA Structures and Bacterial Genomes
Modern molecular biology studies increasingly require customized computation support. This is especially true for studies associated with atomic resolution structures and/or NextGen sequencing. In this dissertation, three separate studies are described in which modern computational methodologies …
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Genome Signatures Reveal the Importance of Context Dependent Codon Bias In A Range of Bacterial Genomes
… context on fifteen evolutionarily distinct bacterial 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 …
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Efficient Synergistic De Novo Co-Assembly Of Bacterial Genomes From Single Cells Using Colored De Bruijn Graph
… has made it possible to sequence and assemble bacterial</p> <p>genomes from a single cell. However, the quality of single cell genome assembly has</p> <p>not yet reached the quality of normal multi-cell genome assembly due to the coverage</p> <p>bias (including uneven depth of coverage and …
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OperomeDB: database of condition specific transcription in prokaryotic genomes and genomic insights of convergent transcription in bacterial genomes
… using high-throughput sequencing datasets for bacterial genomes. 2) Genomics and mechanistic insights of convergent transcription in bacterial genomes. In the first project we developed a database for the prediction of operons for bacterial genomes using RNA-seq datasets, we predicted operons …
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Exploring the boundaries of shallow phylogeny in the YESS group and the dynamics of gene cluster and operon formation in bacterial genomes
… this thesis I look at two different problems in bacterial genomic analysis. The first involves reconstructing the evolutionary history between a group of closely related bacteria. I addressed whether or not it is possible to separate such genomes into different genera, species and strains. …
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Characterization of microbial primary and secondary metabolism in the marine realm
… tool for predicting the metabolic potential of bacterial genomes. This tool addresses the lack of computational pipelines for pathway reconstruction that predict the presence of KEGG modules in highly incomplete prokaryotic genomes. MetaPathPredict made robust predictions in highly incomplete …
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The Sequence Landscape of Bacterial Genes is Shaped by Long-Range mRNA Folding
… has led to discernable sequence patterns in bacterial genomes observed in nature. Such patterns result from gene regulatory strategies that leverage sequence-dependent interactions with key cellular machineries and regulatory molecules. While numerous regulatory strategies that shape …
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Characterization of Microbial Primary and Secondary Metabolism in the Marine Realm
… tool for predicting the metabolic potential of bacterial genomes. This tool addresses the lack of computational pipelines for pathway reconstruction that predict the presence of KEGG modules in highly incomplete prokaryotic genomes. MetaPathPredict made robust predictions in highly incomplete …
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Extracellular Contractile Injection Systems (eCIS) - Characterization of Conserved Phage Tail-like Structures in Streptomyces
… a comprehensive analysis of eCIS across bacterial genomes. I show that all eCIS are comprised of nine core protein families and are closely related to contractile phage tails, a relationship emphasized by the discovery of rare eCIS-like prophages that are the likely evolutionary link …
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BIOLOGICAL CHARACTERIZATION OF TWO PUTATIVE DNA METABOLISM ENZYMES IN DEINOCOCCUS RADIODURANS
… superfamily of P-loop ATPases. FtsK is a bacterial protein that translocates double-stranded DNA during cell division. In archaea, herA is an essential gene that encodes an enzyme believed to be important for recombinational DNA repair. It is typically found in an operon with a gene that …
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Understanding Voltage -Gated Ion Channels via Molecular Archeology
… potassium channel auxiliary subunits in bacterial genomes. Novel calcium channel auxiliary subunits from insects were also identified. Auxiliary subunits of voltage-gated ion channels have been implicated as potential drug targets for epilepsy. In addition, we here report results of …
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Examining bacterial variation with genome graphs and Nanopore sequencing
A bacterial species' genetic content can be remarkably fluid. The collection of genes found within a given species is called the pan-genome and is generally much larger than the gene repertoire of a single cell. A consequence of this pan-genome is that bacterial genomes are highly adaptable and …
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Discovery of novel CRISPR enzymes for transcriptome engineering and human health
… and manipulate RNA are limited. Recently, the bacterial adaptive immune system, CRISPR, has revolutionized our ability to manipulate DNA, but no known RNA-targeting versions exist. To discover parallel bacterial RNA-targeting systems that could be used for transcriptome engineering, we …
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Microfluidic gene synthesis
… of novel proteins to the complete re-writing of bacterial genomes. However, the current cost of de novo synthesis--driven largely by reagent and handling costs-is a significant barrier to the widespread availability of such technology. The use of microfluidic technology greatly reduces reaction …
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Gene transfer agents promote survival and DNA repair during stationary phase for Caulobacter crescentus
… (GTAs) are prophage-like entities found in many bacterial genomes that cannot propagate themselves and instead package ~5-15 kbp fragments of the host genome that can then be transferred to related recipient cells. Although suggested to facilitate horizontal gene transfer in the wild, no clear …
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Suitability of RelBE and MazEF toxin-antitoxin systems as antibacterial targets
… via post-segregational killing of the bacterial host. The genes encoding TA systems also exist on bacterial chromosomes, and it has been speculated that these are involved in a variety of cellular processes. Interest in TA systems has increased dramatically over the past five years as …
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Host and pathogen genetics associated with pneumococcal meningitis
… (GWAS) in bacteria, which can find variation in bacterial genomes associated with bacterial traits such as antibiotic resistance and virulence. I then applied this method to longitudinal samples from asymptomatic carriage, and found lineages and specific variants associated with altered duration …
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Evolution-Inspired Design of Bacterial Biosensors
Bacterial signal transduction systems are critical tools for synthetic biology. However, while hundreds of thousands of systems have been identified in bacterial genomes, only a small subset have been characterized. In this work, we develop tools for scalable interrogation of bacterial signal …
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Computational discovery and modelling of tandem domain repeats in proteins
… tools across large datasets of proteins and bacterial genomes to survey the prevalence and distribution of tan- dem domain repeats across organisms and domain families. Next, I computation- ally analyse and compare structures of domains found as tandem repeats, several of which have been …
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