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You searched for +publisher:"Dalhousie University" +contributor:("Dr Andrew Roger"). Showing records 1 – 3 of 3 total matches.

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Dalhousie University

1. Eveleigh, Robert. Being Aquifex aeolicus: Untangling a hyperthermophile's Checkered Past.

Degree: MS, Department of Computational Biology and Bioinformatics, 2012, Dalhousie University

Lateral gene transfer (LGT) is an important factor contributing to the evolution of prokaryotic genomes. The Aquificae are a hyperthermophilic bacterial group whose genes show affiliations to many other lineages, including the hyperthermophilic Thermotogae, the Proteobacteria, and the Archaea. Here I outline these scenarios and consider the fit of the available data, including two recently sequenced genomes from members of the Aquificae, to different sets of predictions. Evidence from phylogenetic profiles and trees suggests that the ?-Proteobacteria have the strongest affinities with the three Aquificae analyzed. However, this phylogenetic signal is by no means the dominant one, with the Archaea, many lineages of thermophilic bacteria, and members of genus Clostridium and class ?-Proteobacteria also showing strong connections to the Aquificae. The phylogenetic affiliations of different functional subsystems showed strong biases: as observed previously, most but not all genes implicated in the core translational apparatus tended to group Aquificae with Thermotogae, while a wide range of metabolic systems strongly supported the Aquificae - ?-Proteobacteria link. Given the breadth of support for this latter relationship, a scenario of ?-proteobacterial ancestry coupled with frequent exchange among thermophilic lineages is a plausible explanation for the emergence of the Aquificae. Advisors/Committee Members: Dr Andrew Roger (external-examiner), Dr. Christian Blouin (graduate-coordinator), Dr Andrew Roger (thesis-reader), Drs. Robert Beiko and John Archibald (thesis-supervisor), Not Applicable (ethics-approval), No (manuscripts), No (copyright-release).

Subjects/Keywords: Aquifex aeolicus; Thermotogae; phylogenomics; hyperthermophily; lateral gene transfer

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Eveleigh, R. (2012). Being Aquifex aeolicus: Untangling a hyperthermophile's Checkered Past. (Masters Thesis). Dalhousie University. Retrieved from http://hdl.handle.net/10222/14412

Chicago Manual of Style (16th Edition):

Eveleigh, Robert. “Being Aquifex aeolicus: Untangling a hyperthermophile's Checkered Past.” 2012. Masters Thesis, Dalhousie University. Accessed January 25, 2021. http://hdl.handle.net/10222/14412.

MLA Handbook (7th Edition):

Eveleigh, Robert. “Being Aquifex aeolicus: Untangling a hyperthermophile's Checkered Past.” 2012. Web. 25 Jan 2021.

Vancouver:

Eveleigh R. Being Aquifex aeolicus: Untangling a hyperthermophile's Checkered Past. [Internet] [Masters thesis]. Dalhousie University; 2012. [cited 2021 Jan 25]. Available from: http://hdl.handle.net/10222/14412.

Council of Science Editors:

Eveleigh R. Being Aquifex aeolicus: Untangling a hyperthermophile's Checkered Past. [Masters Thesis]. Dalhousie University; 2012. Available from: http://hdl.handle.net/10222/14412


Dalhousie University

2. Perry, Scott. Characterizing The Distinguishability Of Microbial Genomes.

Degree: MS, Faculty of Computer Science, 2010, Dalhousie University

The field of metagenomics has shown great promise in the ability to recover microbial DNA from communities whose members resist traditional cultivation techniques, although in most instances the recovered material comprises short anonymous genomic fragments rather than complete genome sequences. In order to effectively assess the microbial diversity and ecology represented in such samples, accurate methods for DNA classification capable of assigning metagenomic fragments into their most likely taxonomic unit are required. Existing DNA classification methods have shown high levels of accuracy in attempting to classify sequences derived from low-complexity communities, however genome distinguishability generally deteriorates for complex communities or those containing closely related organisms. The goal of this thesis was to identify factors both intrinsic or external to the genome that may lead to the improvement of existing DNA classification methods and to probe the fundamental limitations of composition-based genome distinguishability. To assess the suite of factors affecting the distinguishability of genomes, support vector machine classifiers were trained to discriminate between pairs of microbial genomes using the relative frequencies of oligonucleotide patterns calculated from orthologous genes or short genomic fragments, and the resulting classification accuracy scores used as the measure of genomic distinguishability. Models were generated in order to relate distinguishability to several measures of genomic and taxonomic similarity, and interesting outlier genome pairs were identified by large residuals to the fitted models. Examination of the outlier pairs identified numerous factors that influence genome distinguishability, including genome reduction, extreme G+C composition, lateral gene transfer, and habitat-induced genome convergence. Fragments containing multiple protein-coding and non-coding sequences showed an increased tendency for misclassification, except in cases where the genomes were very closely related. Analysis of the biological function annotations associated with each fragment demonstrated that certain functional role categories showed increased or decreased tendency for misclassification. The use of pre-processing steps including DNA recoding, unsupervised clustering, 'symmetrization' of oligonucleotide frequencies, and correction for G+C content did not improve distinguishability. Existing composition-based DNA classifiers will benefit from the results reported in this thesis. Sequence-segmentation approaches will improve genome distinguishability by decreasing fragment heterogeneity, while factors such as habitat, lifestyle, extreme G+C composition, genome reduction, and biological role annotations may be used to express confidence in the classification of individual fragments. Although genome distinguishability tends to be proportional to genomic and taxonomic relatedness, these trends can be violated for closely related genome pairs that have undergone rapid compositional divergence,… Advisors/Committee Members: N/A (external-examiner), Angie Bolivar (graduate-coordinator), Dr. Christian Blouin (thesis-reader), Dr. Andrew Roger (thesis-reader), Dr. Robert Beiko (thesis-supervisor), Not Applicable (ethics-approval), Not Applicable (manuscripts), Not Applicable (copyright-release).

Subjects/Keywords: genome signature; genome composition; metagenomics; support vector machine

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Perry, S. (2010). Characterizing The Distinguishability Of Microbial Genomes. (Masters Thesis). Dalhousie University. Retrieved from http://hdl.handle.net/10222/12809

Chicago Manual of Style (16th Edition):

Perry, Scott. “Characterizing The Distinguishability Of Microbial Genomes.” 2010. Masters Thesis, Dalhousie University. Accessed January 25, 2021. http://hdl.handle.net/10222/12809.

MLA Handbook (7th Edition):

Perry, Scott. “Characterizing The Distinguishability Of Microbial Genomes.” 2010. Web. 25 Jan 2021.

Vancouver:

Perry S. Characterizing The Distinguishability Of Microbial Genomes. [Internet] [Masters thesis]. Dalhousie University; 2010. [cited 2021 Jan 25]. Available from: http://hdl.handle.net/10222/12809.

Council of Science Editors:

Perry S. Characterizing The Distinguishability Of Microbial Genomes. [Masters Thesis]. Dalhousie University; 2010. Available from: http://hdl.handle.net/10222/12809


Dalhousie University

3. Bay, Rachael. Analysis of Functional Constraint and Recombination in Gene Sequences of the Cyanobacteria Prochlorococcus.

Degree: MS, Department of Biology, 2010, Dalhousie University

Lineages of the cyanobacteria Prochlorococcus marinus have diverged into two genetically distinct ‘ecotypes,’ high-light adapted (HL) and low-light adapted (LL), which thrive under different environmental conditions. This type of niche differentiation in prokaryotes is often accompanied by genetic and genomic divergence. Differential selection pressure associated with ecotype divergence can be analyzed using models of codon evolution. However, some characteristics of the Prochlorococcus genome violate underlying assumptions of these models. For example, high levels of recombination between bacterial strains are known to cause false positives for codon models. Therefore, it is important that statistical methods for detecting recombination be reliable. In Chapter 2, I evaluate a set of recombination detection methods under four different scenarios related to functional divergence: 1) varying tree shape, 2) positive selection, 3) non-stationary evolution, and 4) varying levels of recombination and divergence. Advisors/Committee Members: Dr. Jonathan Wright (external-examiner), Dr. Hal Whitehead (graduate-coordinator), Dr. Katherine Dunn (thesis-reader), Dr. Andrew Roger (thesis-reader), Dr. Joseph Bielawski (thesis-supervisor), Not Applicable (ethics-approval), Not Applicable (manuscripts), Not Applicable (copyright-release).

Subjects/Keywords: Cyanobacteria; Recombination; Natural Selection

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Bay, R. (2010). Analysis of Functional Constraint and Recombination in Gene Sequences of the Cyanobacteria Prochlorococcus. (Masters Thesis). Dalhousie University. Retrieved from http://hdl.handle.net/10222/13021

Chicago Manual of Style (16th Edition):

Bay, Rachael. “Analysis of Functional Constraint and Recombination in Gene Sequences of the Cyanobacteria Prochlorococcus.” 2010. Masters Thesis, Dalhousie University. Accessed January 25, 2021. http://hdl.handle.net/10222/13021.

MLA Handbook (7th Edition):

Bay, Rachael. “Analysis of Functional Constraint and Recombination in Gene Sequences of the Cyanobacteria Prochlorococcus.” 2010. Web. 25 Jan 2021.

Vancouver:

Bay R. Analysis of Functional Constraint and Recombination in Gene Sequences of the Cyanobacteria Prochlorococcus. [Internet] [Masters thesis]. Dalhousie University; 2010. [cited 2021 Jan 25]. Available from: http://hdl.handle.net/10222/13021.

Council of Science Editors:

Bay R. Analysis of Functional Constraint and Recombination in Gene Sequences of the Cyanobacteria Prochlorococcus. [Masters Thesis]. Dalhousie University; 2010. Available from: http://hdl.handle.net/10222/13021

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