Development of a cell flux model and its application to nitrogen fixers
Thesis: Ph. D., Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences, 2016.
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| Format: | Thesis |
| Language: | eng |
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Massachusetts Institute of Technology
2017
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| Online Access: | http://hdl.handle.net/1721.1/107105 |
| _version_ | 1826210912423378944 |
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| author | Inomura, Keisuke |
| author2 | Michael J. Follows. |
| author_facet | Michael J. Follows. Inomura, Keisuke |
| author_sort | Inomura, Keisuke |
| collection | MIT |
| description | Thesis: Ph. D., Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences, 2016. |
| first_indexed | 2024-09-23T14:57:45Z |
| format | Thesis |
| id | mit-1721.1/107105 |
| institution | Massachusetts Institute of Technology |
| language | eng |
| last_indexed | 2024-09-23T14:57:45Z |
| publishDate | 2017 |
| publisher | Massachusetts Institute of Technology |
| record_format | dspace |
| spelling | mit-1721.1/1071052019-04-12T21:41:27Z Development of a cell flux model and its application to nitrogen fixers Inomura, Keisuke Michael J. Follows. Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences. Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences. Earth, Atmospheric, and Planetary Sciences. Thesis: Ph. D., Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences, 2016. Cataloged from PDF version of thesis. Includes bibliographical references. .Quantifying and modeling the macroscopic ecological and biogeochemical effects of cellular physiology and metabolism is a challenge: most quantitative "systems biology" models are focused at the metabolic and individual scale. In this study, we develop and apply a simplified metabolic model at the individual scale, which we call "the cell flux model", in order to quantify costs and benefits of nitrogen fixers. In Chapter 2, we develop the cell flux model for heterotrophic nitrogen fixers in order to examine and quantify the direct and indirect energy costs of nitrogen fixation. We have tested the model using data from Azotobacter vinelandii grown in continuous culture. The model indicates that the direct energy cost of nitrogen fixation is relatively small, whereas oxygen management to protect nitrogenase becomes dominant as the oxygen concentration increases. In Chapter 3, we have adapted the cell flux model of Azotobacter vinelandii to consider the organisms' response to the presence of ammonium in the environment. The model shows that even under high oxygen concentrations and with high ambient concentrations of fixed nitrogen, nitrogen fixation occurs if there is sufficient carbohydrate resource available to fully consume intracellular oxygen. Most nitrogen fixers in the ocean are photoautotrophic. Thus, in Chapter 4, we extend the cell flux model to resolve phototrophy and use it simulate and study light and nutrient colimitation of Synechococcus spp. as observed in published continuous culture studies. In order to capture the observed variations in elemental composition with light and resource availability, we resolve the macromolecular composition of the cells. The highly simplified model is able to simulate key aspects of the laboratory cultures including explicit prediction of the average elemental composition and maximum growth rates under different environmental limitations. In Chapter 5, we have applied the cell flux model to simulate laboratory studies, and interpreted the ecological costs for the photoautotrophic nitrogen fixer Crocosphaera watsonii. Our model suggests that these organism also utilize multiple oxygen protection strategies, including scavenging oxygen with excess respiration, changing their size, and using extracellular polymeric substances as a barrier to the invasion of oxygen into the cell. by Keisuke Inomura. Ph. D. 2017-02-22T19:03:46Z 2017-02-22T19:03:46Z 2016 2016 Thesis http://hdl.handle.net/1721.1/107105 971494590 eng MIT theses are protected by copyright. They may be viewed, downloaded, or printed from this source but further reproduction or distribution in any format is prohibited without written permission. http://dspace.mit.edu/handle/1721.1/7582 233 pages application/pdf Massachusetts Institute of Technology |
| spellingShingle | Earth, Atmospheric, and Planetary Sciences. Inomura, Keisuke Development of a cell flux model and its application to nitrogen fixers |
| title | Development of a cell flux model and its application to nitrogen fixers |
| title_full | Development of a cell flux model and its application to nitrogen fixers |
| title_fullStr | Development of a cell flux model and its application to nitrogen fixers |
| title_full_unstemmed | Development of a cell flux model and its application to nitrogen fixers |
| title_short | Development of a cell flux model and its application to nitrogen fixers |
| title_sort | development of a cell flux model and its application to nitrogen fixers |
| topic | Earth, Atmospheric, and Planetary Sciences. |
| url | http://hdl.handle.net/1721.1/107105 |
| work_keys_str_mv | AT inomurakeisuke developmentofacellfluxmodelanditsapplicationtonitrogenfixers |