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You searched for subject:(Thermotogae). 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


University of Alberta

2. Pollo, Stephen MJ. Insights into temperature adaptation in the Thermotogae gained through transcriptomics and comparative genomics.

Degree: MS, Department of Biological Sciences, 2014, University of Alberta

Thermophilic microbes are extremophiles that live at high temperatures. In order to survive and maintain function of their biological molecules, they have a suite of characteristics not found in organisms that grow at moderate temperatures (mesophiles) that range from the cellular to the protein level. These fundamental differences presumably present a barrier to transitioning between the two lifestyles, yet many lineages are thought to have transitioned between thermophily and mesophily at least once. Studying groups of closely related thermophilic and mesophilic organisms can provide insight into these transitions. The bacterial phylum Thermotogae comprises hyperthermophiles (growing up to 90°C), thermophiles (50-70°C) and mesophiles (<45°C), thus presenting an excellent opportunity to study bacterial temperature adaptation. One Thermotogae species, Kosmotoga olearia, grows optimally at 65°C but grows over an extraordinarily broad temperature range of ~25 - 79°C. To investigate how this bacterium can tolerate such an enormous temperature range, RNA-seq experiments were performed on cultures grown across its permissive temperature range. Multivariate analyses of the resulting transcriptomes showed that the temperature treatments separated into three groups: heat-stressed (77°C), intermediate (65°C and 40°C), and cold-stressed (30°C and 25°C). Among the genes differentially expressed, unsurprisingly, were genes with known temperature responses like chaperones, proteases, cold-shock proteins, and helicases. Intriguingly however, increased expression of genes involved in carbohydrate metabolism and transport at supra-optimal temperature, contrasted with increased expression of genes involved in amino acid metabolism and transport at sub-optimal temperature suggests global metabolism is changed by growth temperature. This may allow K. olearia to play distinct roles across a range of thermal environments. Among the differentially expressed genes in K. olearia are genes shared with mesophilic Mesotoga spp. but none of the other thermophilic Thermotogae. Many of these genes have inferred regulatory functions implying that large regulatory changes accompany low temperature growth. In agreement with this, more genes were found to be differentially expressed at low temperatures compared to optimal than at high temperatures compared to optimal in K. olearia. Further genomic comparisons between K. olearia and the related K. arenicorallina, which has a narrower growth temperature range of 35 - 70°C, identified 243 genes that could be important for the wide temperature range of K. olearia. Clarifying mechanisms by which Bacteria adapt to temperature changes in isolation can inform studies of complex microbial communities in environments that experience fluctuations in temperature as well as provide a starting place to predict the responses of microbial communities to long term temperature change.

Subjects/Keywords: Comparative genomics; Bacteria; Thermophile; Thermotogae; Kosmotoga olearia; RNA-Seq; Mesophile; Temperature adaptation; Transcriptomics

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

APA (6th Edition):

Pollo, S. M. (2014). Insights into temperature adaptation in the Thermotogae gained through transcriptomics and comparative genomics. (Masters Thesis). University of Alberta. Retrieved from https://era.library.ualberta.ca/files/hd76s071t

Chicago Manual of Style (16th Edition):

Pollo, Stephen MJ. “Insights into temperature adaptation in the Thermotogae gained through transcriptomics and comparative genomics.” 2014. Masters Thesis, University of Alberta. Accessed January 25, 2021. https://era.library.ualberta.ca/files/hd76s071t.

MLA Handbook (7th Edition):

Pollo, Stephen MJ. “Insights into temperature adaptation in the Thermotogae gained through transcriptomics and comparative genomics.” 2014. Web. 25 Jan 2021.

Vancouver:

Pollo SM. Insights into temperature adaptation in the Thermotogae gained through transcriptomics and comparative genomics. [Internet] [Masters thesis]. University of Alberta; 2014. [cited 2021 Jan 25]. Available from: https://era.library.ualberta.ca/files/hd76s071t.

Council of Science Editors:

Pollo SM. Insights into temperature adaptation in the Thermotogae gained through transcriptomics and comparative genomics. [Masters Thesis]. University of Alberta; 2014. Available from: https://era.library.ualberta.ca/files/hd76s071t

3. Bhandari, Vaibhav. COMPARATIVE ANALYSES OF MICROBIAL GENOMES TO IDENTIFY MOLECULAR MARKERS FOR DIFFERENT GROUPS OF PROKARYOTES.

Degree: MSc, 2013, McMaster University

Currently centered on molecular data, bacterial and archaeal relationships are often based on their relative branching in 16S rRNA based phylogenetic trees. The availability of numerous bacterial genome sequences over the past two decades has provided new information for insights previously inaccessible to the field of taxonomy. Through utilization of comparative genomics, numerous molecular markers in the form of insertions and deletions within conserved regions of proteins, also known as Conserved Signature Indels or CSIs, have been discovered for various prokaryotic taxa. Using these techniques, we have analyzed relationships among the bacterial phyla of Thermotogae and Synergistetes and the conglomeration of bacterial organisms known as the PVC super-phylum. Through identification of large numbers of CSIs we have described the phyla Thermotogae and Synergistetes, and their sub-groups, in molecular terms for the first time. The identified molecular markers support a reconstruction of the current taxonomic divisions of these phyla. Similarly, previously only observed to group in phylogenetic trees, we have identified molecular markers for the PVC clade of bacterial phyla which are indicative of their shared ancestry. Further, in response to recent suggestions of extensive lateral gene transfer masking evolutionary relationships, an argument in favour of Darwinian mode of evolution for prokaryotic organisms is made using the identified molecular markers identified here along with markers previously identified in similar studies. Due to their taxonomic specificity, the markers that we have discovered provide useful tools for biochemical tests aiming for an understanding of the unique characteristics of the bacterial groups to which they are specific.

Master of Science (MSc)

Advisors/Committee Members: Gupta, Radhey S., Murray Junop, Herbert E. Schellhorn, Biochemistry.

Subjects/Keywords: conserved indels; signature proteins; lateral gene transfer; phylogeny; taxonomy; thermotogae; synergistetes; PVC; Bioinformatics; Biology; Evolution; Genomics; Bioinformatics

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

APA (6th Edition):

Bhandari, V. (2013). COMPARATIVE ANALYSES OF MICROBIAL GENOMES TO IDENTIFY MOLECULAR MARKERS FOR DIFFERENT GROUPS OF PROKARYOTES. (Masters Thesis). McMaster University. Retrieved from http://hdl.handle.net/11375/12951

Chicago Manual of Style (16th Edition):

Bhandari, Vaibhav. “COMPARATIVE ANALYSES OF MICROBIAL GENOMES TO IDENTIFY MOLECULAR MARKERS FOR DIFFERENT GROUPS OF PROKARYOTES.” 2013. Masters Thesis, McMaster University. Accessed January 25, 2021. http://hdl.handle.net/11375/12951.

MLA Handbook (7th Edition):

Bhandari, Vaibhav. “COMPARATIVE ANALYSES OF MICROBIAL GENOMES TO IDENTIFY MOLECULAR MARKERS FOR DIFFERENT GROUPS OF PROKARYOTES.” 2013. Web. 25 Jan 2021.

Vancouver:

Bhandari V. COMPARATIVE ANALYSES OF MICROBIAL GENOMES TO IDENTIFY MOLECULAR MARKERS FOR DIFFERENT GROUPS OF PROKARYOTES. [Internet] [Masters thesis]. McMaster University; 2013. [cited 2021 Jan 25]. Available from: http://hdl.handle.net/11375/12951.

Council of Science Editors:

Bhandari V. COMPARATIVE ANALYSES OF MICROBIAL GENOMES TO IDENTIFY MOLECULAR MARKERS FOR DIFFERENT GROUPS OF PROKARYOTES. [Masters Thesis]. McMaster University; 2013. Available from: http://hdl.handle.net/11375/12951

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