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You searched for subject:(flavobacteria). Showing records 1 – 2 of 2 total matches.

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University of Guelph

1. Fan, Ying. SPECTROSCOPIC STUDIES OF NOVEL MICROBIAL RHODOPSINS FROM FUNGI AND BACTERIA.

Degree: PhD, Department of Physics, 2011, University of Guelph

Microbial rhodopsins are widespread bacteriorhodopsin-like proteins found in many prokaryotes and lower eukaryotic groups. They serve as photosensors, light-driven ion pumps, and light-gated channels. The main goal of this thesis was to spectroscopically characterize a new subgroup of fungal rhodopsins (so-called auxiliary group) and a new type of rhodopsin found in flavobacteria. Towards the first goal, products of two known rhodopsin genes from the fungal wheat pathogen, Phaeosphaeria nodorum, were investigated. The two yeast-expressed Phaeosphaeria rhodopsins were spectroscopically characterized by Raman, time-resolved visible and Fourier transform infrared (FTIR) spectroscopy and shown many similarities: absorption spectra, conformation of the retinal chromophore, fast photocycling, and carboxylic acid protonation changes. It is likely that both Phaeosphaeria rhodopsins are proton-pumping, at least in vitro. We suggest that auxiliary rhodopsins have separated from their ancestors fairly recently and have acquired the ability to interact with as yet unidentified transducers, performing a photosensory function without changing their spectral properties and basic photochemistry. In the second project, we studied a flavobacterial rhodopsin with highly unusual sequence, which was functionally expressed in E.coli by our collaborators and produced light-induced pH changes in the spheroplast suspensions, suggesting an inward H+ transport. Using time-resolved visible spectroscopy, we revealed that its photochemical reaction cycle was fast and strongly dependent on cations. Analysis of the sequence alignments, combined with visible and FTIR spectroscopic studies of the wild-type and mutant flavobacterial rhodopsin, provided the clues for the mechanism of binding metal ions and origin of the observed light-induced pH changes. Finally, isotope labeling protocol, previously used for soluble secreted proteins, was successfully implemented and optimized to produce homogeneous samples of eukaryotic rhodopsin from Leptosphaeria in methylotrophic yeast. Isotope-labeling extent and functionality were verified by FTIR spectroscopy, and obtained samples gave high-resolution ssNMR spectra suitable for structural studies. This protocol for overexpression of isotope-labeled multi-spanning eukaryotic membrane proteins in Pichia pastoris can be adopted for challenging mammalian targets, which often resist characterization by other structural methods. Advisors/Committee Members: Brown, Leonid (advisor).

Subjects/Keywords: microbial rhodopsin; fungal; flavobacteria; spectroscopy

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

APA (6th Edition):

Fan, Y. (2011). SPECTROSCOPIC STUDIES OF NOVEL MICROBIAL RHODOPSINS FROM FUNGI AND BACTERIA. (Doctoral Dissertation). University of Guelph. Retrieved from https://atrium.lib.uoguelph.ca/xmlui/handle/10214/2924

Chicago Manual of Style (16th Edition):

Fan, Ying. “SPECTROSCOPIC STUDIES OF NOVEL MICROBIAL RHODOPSINS FROM FUNGI AND BACTERIA.” 2011. Doctoral Dissertation, University of Guelph. Accessed October 31, 2020. https://atrium.lib.uoguelph.ca/xmlui/handle/10214/2924.

MLA Handbook (7th Edition):

Fan, Ying. “SPECTROSCOPIC STUDIES OF NOVEL MICROBIAL RHODOPSINS FROM FUNGI AND BACTERIA.” 2011. Web. 31 Oct 2020.

Vancouver:

Fan Y. SPECTROSCOPIC STUDIES OF NOVEL MICROBIAL RHODOPSINS FROM FUNGI AND BACTERIA. [Internet] [Doctoral dissertation]. University of Guelph; 2011. [cited 2020 Oct 31]. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/2924.

Council of Science Editors:

Fan Y. SPECTROSCOPIC STUDIES OF NOVEL MICROBIAL RHODOPSINS FROM FUNGI AND BACTERIA. [Doctoral Dissertation]. University of Guelph; 2011. Available from: https://atrium.lib.uoguelph.ca/xmlui/handle/10214/2924


University of Southern California

2. Tully, Benjamin J. Using sequencing techniques to explore the microbial communities associated with ferromanganese nodules and sediment from the South Pacific gyre.

Degree: PhD, Marine and Environmental Biology, 2013, University of Southern California

The formation and maintenance of deep-sea ferromanganese/polymetallic nodules still remains a mystery 140 years after their discovery. The wealth of rare metals concentrated in these nodules has spurred global interest in exploring the mining potential of these resources. The prevailing theory of abiotic formation has been called into question and the role of microbial metabolisms in nodule development is now an area of active research. To understand the community structure of microbes associated with nodules and their surrounding sediment, we performed targeted sequencing of the V4 hypervariable region of the 16S rRNA gene from three nodules collected from the central South Pacific. Results have shown that the microbial communities of the nodules are significantly distinct from the communities in the surrounding sediments, and that the interiors of the nodules harbor communities different from the exterior. This suggests not only differences in potential metabolisms between the nodule and sediment communities, but also differences in the dominant metabolisms of interior and exterior communities. We identified several operational taxonomic units (OTUs) unique to both the nodule and sediment environments. The identified OTUs were assigned putative taxonomic identifications, including two OTUs only found associated with the nodules, which were assigned to the Alpha-Proteobacteria. Finally, we explored the diversity of the most assigned taxonomic group, the Thaumarchaea MG-1, which revealed novel OTUs compared to previous research from the region and suggests a potential role as a source of fixed carbon for ammonia oxidizing archaea in the environment. ❧ Oligotrophic ocean gyres compose ~50% of the marine environment. The South Pacific Gyre (SPG) is the most oligotrophic of all the central gyres. The oligotrophic surface waters directly correlate to deep-sea sediment with low organic carbon content. Low microbial biomass ( Advisors/Committee Members: Heidelberg, John F. (Committee Chair), Nealson, Kenneth H. (Committee Member), Berelson, William M. (Committee Member).

Subjects/Keywords: microbial ecology; metagenomics; nodules; Gulf of Maine; Thaumarchaea; Flavobacteria; amplicon

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

APA (6th Edition):

Tully, B. J. (2013). Using sequencing techniques to explore the microbial communities associated with ferromanganese nodules and sediment from the South Pacific gyre. (Doctoral Dissertation). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/317866/rec/7776

Chicago Manual of Style (16th Edition):

Tully, Benjamin J. “Using sequencing techniques to explore the microbial communities associated with ferromanganese nodules and sediment from the South Pacific gyre.” 2013. Doctoral Dissertation, University of Southern California. Accessed October 31, 2020. http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/317866/rec/7776.

MLA Handbook (7th Edition):

Tully, Benjamin J. “Using sequencing techniques to explore the microbial communities associated with ferromanganese nodules and sediment from the South Pacific gyre.” 2013. Web. 31 Oct 2020.

Vancouver:

Tully BJ. Using sequencing techniques to explore the microbial communities associated with ferromanganese nodules and sediment from the South Pacific gyre. [Internet] [Doctoral dissertation]. University of Southern California; 2013. [cited 2020 Oct 31]. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/317866/rec/7776.

Council of Science Editors:

Tully BJ. Using sequencing techniques to explore the microbial communities associated with ferromanganese nodules and sediment from the South Pacific gyre. [Doctoral Dissertation]. University of Southern California; 2013. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/317866/rec/7776

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