subject:(NADH oxidase)

University of Rochester

1. Derr, Adam M. NADH Oxidase and Stress Responses in Streptococcus mutans: A Phenotypic and Regulatory Characterization.

Degree: PhD, 2012, University of Rochester

URL: http://hdl.handle.net/1802/25539

► Streptococcus mutans, an oral bacterium found on human tooth surfaces, is a primary causative agent of the disease dental caries. Dental caries is the result… (more)

▼ Streptococcus mutans, an oral bacterium found on human tooth surfaces, is a primary causative agent of the disease dental caries. Dental caries is the result of the demineralization of the tooth surface, partially due to the production of acid by oral bacteria through carbohydrate metabolism. Rapid sugar metabolism in S. mutans depends on the availability of reduced nicotinamide dinucleotides (NADH). A key enzyme for the regeneration of NADH is the flavin-containing NADH oxidase (Nox). This enzyme oxidizes NADH to NAD+, while reducing diatomic oxygen to H2O. In this study, we characterized the role of the NADH oxidase in the oxidative and acid stress responses of S. mutans, determined specific regulatory controls of NADH oxidase and described the global regulatory effects from the loss of nox. The nox mutant strain exhibited reduced ability to metabolize environmental oxygen present in chemostat-grown S. mutans cultures resulting in activation of the oxygen and acid-mediated stress responses, as demonstrated by elevated activity of superoxide dismutase and glutathione oxidoreductase, elevated transcription of DNA repair genes and altered membrane fatty acid composition, independent of external pH. An Spx recognition site was identified within the first 120 bp upstream of the translational start site of the nox-coding region. Measurements of transcription rates from the nox promoter showed that SpxA activates nox and that SpxB slightly inhibits nox, indicating that nox is part of the Spx global regulon. The global effects of the nox mutation and the impacts of oxygen were characterized using cDNA microarrays. Transcriptional patterns were similar between the nox mutant and parent strain, UA159, when exposed to elevated oxygen concentrations, with some exceptions. Notably, in the nox mutant strain, the global regulator Rex, responsible for regulation of oxygen homeostasis, sugar metabolism, and biofilm formation, was differentially regulated, suggesting that Nox and Rex participate in a redox-sensing and signaling pathway. In conclusion, nox is a major consumer of environmental oxygen in S. mutans and the loss of NADH oxidase, or an increase in environmental oxygen, leads to global transcriptional changes, allowing the organism to respond rapidly to stress at the expense of overall growth rate.

Subjects/Keywords: Streptococcus Mutans; NADH Oxidase; Oxygen

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APA (6^th Edition):

Derr, A. M. (2012). NADH Oxidase and Stress Responses in Streptococcus mutans: A Phenotypic and Regulatory Characterization. (Doctoral Dissertation). University of Rochester. Retrieved from http://hdl.handle.net/1802/25539

Chicago Manual of Style (16^th Edition):

Derr, Adam M. “NADH Oxidase and Stress Responses in Streptococcus mutans: A Phenotypic and Regulatory Characterization.” 2012. Doctoral Dissertation, University of Rochester. Accessed January 19, 2021. http://hdl.handle.net/1802/25539.

MLA Handbook (7^th Edition):

Derr, Adam M. “NADH Oxidase and Stress Responses in Streptococcus mutans: A Phenotypic and Regulatory Characterization.” 2012. Web. 19 Jan 2021.

Vancouver:

Derr AM. NADH Oxidase and Stress Responses in Streptococcus mutans: A Phenotypic and Regulatory Characterization. [Internet] [Doctoral dissertation]. University of Rochester; 2012. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/1802/25539.

Council of Science Editors:

Derr AM. NADH Oxidase and Stress Responses in Streptococcus mutans: A Phenotypic and Regulatory Characterization. [Doctoral Dissertation]. University of Rochester; 2012. Available from: http://hdl.handle.net/1802/25539

University of Georgia

2. Tomar, Atin. Production of pyruvate by Escherichia coli using metabolic engineering.

Degree: 2014, University of Georgia

URL: http://hdl.handle.net/10724/29445

► Pyruvate is a three-carbon (triose) ketoacid central to metabolism that could potentially be produced by fermentation. Previous studies observed pyruvate accumulation in strains having mutations… (more)

Subjects/Keywords: Pyruvate; Escherichia coli; Acetate mutants; Pyruvate Dehydrogenase complex; Phosphoenolpyruvate carboxylase; Pyruvate oxidase; NADH oxidase

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APA (6^th Edition):

Tomar, A. (2014). Production of pyruvate by Escherichia coli using metabolic engineering. (Thesis). University of Georgia. Retrieved from http://hdl.handle.net/10724/29445

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Tomar, Atin. “Production of pyruvate by Escherichia coli using metabolic engineering.” 2014. Thesis, University of Georgia. Accessed January 19, 2021. http://hdl.handle.net/10724/29445.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Tomar, Atin. “Production of pyruvate by Escherichia coli using metabolic engineering.” 2014. Web. 19 Jan 2021.

Vancouver:

Tomar A. Production of pyruvate by Escherichia coli using metabolic engineering. [Internet] [Thesis]. University of Georgia; 2014. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/10724/29445.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Tomar A. Production of pyruvate by Escherichia coli using metabolic engineering. [Thesis]. University of Georgia; 2014. Available from: http://hdl.handle.net/10724/29445

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Georgia

3. Vemuri, Goutham N. Systems biology of overflow metabolism.

Degree: 2014, University of Georgia

URL: http://hdl.handle.net/10724/24023

► The primary goal of this research is to elucidate the regulation of overflow metabolism in Escherichia coli and Saccharomyces cerevisiae. Insufficient capacity of the respiratory… (more)

Subjects/Keywords: Redox metabolism; Escherichia coli; Saccharomyces cerevisiae; Overflow metabolism; NADH oxidase; Alternate Oxidase; Metabolic engineering; Systems biology

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APA (6^th Edition):

Vemuri, G. N. (2014). Systems biology of overflow metabolism. (Thesis). University of Georgia. Retrieved from http://hdl.handle.net/10724/24023

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Vemuri, Goutham N. “Systems biology of overflow metabolism.” 2014. Thesis, University of Georgia. Accessed January 19, 2021. http://hdl.handle.net/10724/24023.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Vemuri, Goutham N. “Systems biology of overflow metabolism.” 2014. Web. 19 Jan 2021.

Vancouver:

Vemuri GN. Systems biology of overflow metabolism. [Internet] [Thesis]. University of Georgia; 2014. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/10724/24023.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Vemuri GN. Systems biology of overflow metabolism. [Thesis]. University of Georgia; 2014. Available from: http://hdl.handle.net/10724/24023

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Georgia

4. Yang, Fei. Production of pyruvate by Escherichia coli using metabolic engineering.

Degree: 2014, University of Georgia

URL: http://hdl.handle.net/10724/22034

► Pyruvate is a three-carbon ketoacid produced at the end of glycolysis. This research involves the metabolic engineering of the bacterium Escherichia coli in order to… (more)

Subjects/Keywords: Pyruvate; Escherichia coli; Pyruvate dehydrogenase complex, Phosphoenolpyruvate carboxylase; Pyruvate oxidase; NADH oxidase; 2,4-dinitrophenol, Plackett-Burman design

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APA (6^th Edition):

Yang, F. (2014). Production of pyruvate by Escherichia coli using metabolic engineering. (Thesis). University of Georgia. Retrieved from http://hdl.handle.net/10724/22034

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Yang, Fei. “Production of pyruvate by Escherichia coli using metabolic engineering.” 2014. Thesis, University of Georgia. Accessed January 19, 2021. http://hdl.handle.net/10724/22034.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Yang, Fei. “Production of pyruvate by Escherichia coli using metabolic engineering.” 2014. Web. 19 Jan 2021.

Vancouver:

Yang F. Production of pyruvate by Escherichia coli using metabolic engineering. [Internet] [Thesis]. University of Georgia; 2014. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/10724/22034.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Yang F. Production of pyruvate by Escherichia coli using metabolic engineering. [Thesis]. University of Georgia; 2014. Available from: http://hdl.handle.net/10724/22034

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Georgia

5. Han, Qi. Reducing degradation of intracellular cofactors to improve bioconversion to oxidized chemicals and production of recombinant proteins by escherichia coli.

Degree: 2019, University of Georgia

URL: http://hdl.handle.net/10724/38600

► Microorganisms are widely used to synthesize chemicals. One set of microbial conversions involves the transfer of electron from a starting material to a microbial electron… (more)

▼ Microorganisms are widely used to synthesize chemicals. One set of microbial conversions involves the transfer of electron from a starting material to a microbial electron carrier (such as NAD+): A + NAD+ to B + NADH. L-xylulose formation is a good example of this microbial conversion, which is a rare sugar generated from xylitol by an NAD+-dependent xylitol 4-dehydrogenase (XDH) from Pantoea ananatis. Since the general conversion of A to B (or the specific example of xylitol to L-xylulose) involves the utilization of NAD+ and the formation of NADH, the continued presence of NAD+ is necessary to drive the process. Two fundamental challenges exist, however. First, to drive the reaction forward at a fast rate toward the product, a relatively high ratio of NAD+/NADH is required. Second, microbes continually degrade both NAD+ and NADH as part of biochemical recycling that occurs in living systems, which will lead essentially to a loss of NAD(H) availability. Using the conversion of xylitol to L-xylulose as a model system, we co-expressed water-forming NADH oxidase (NOX) from Streptococcus pneumoniae with XDH to regenerate NAD+, and also modified the biochemical pathways involved in NAD(H) degradation. Controlled batch process demonstrated that the final equilibrium L-xylulose/xylitol ratio was correlated to an elevated ratio of NAD+/NADH. The E. coli strain (MEC697) with deletions of the nadR nudC mazG genes in the degradation pathway of NAD(H) increased the total amount of NAD(H) and delayed the degradation of this cofactor, further improving the conversion of xylitol to L-xylulose. As a potential platform for enhancing formation of the oxidized biochemical product, MEC697 also successfully improved the conversion of galactitol to L-tagatose, with almost a 60% increase in the final product. In addition, MEC697 reduced the acetate formation when grown on glucose and improved galactosidase production. Using steady-state cultures, we demonstrated the enhanced total NAD(H) in MEC697 delayed the threshold growth rate for acetate formation to beyond 0.27 h-1. At the 1 liter scale, a batch process with 10 g/L glucose, MEC697 as the host strain for recombinant protein production reduced acetate by about 50% and doubled the formation of galactosidase.

Subjects/Keywords: Escherichia coli; Rare sugars; Recombinant protein; NAD+/NADH; Xylitol 4-dehydrogenase; NADH oxidase; galactosidase; Glucose; Glycerol; Xylitol; L-xylulose; Acetate; Batch process; Chemostat

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APA (6^th Edition):

Han, Q. (2019). Reducing degradation of intracellular cofactors to improve bioconversion to oxidized chemicals and production of recombinant proteins by escherichia coli. (Thesis). University of Georgia. Retrieved from http://hdl.handle.net/10724/38600

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Han, Qi. “Reducing degradation of intracellular cofactors to improve bioconversion to oxidized chemicals and production of recombinant proteins by escherichia coli.” 2019. Thesis, University of Georgia. Accessed January 19, 2021. http://hdl.handle.net/10724/38600.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Han, Qi. “Reducing degradation of intracellular cofactors to improve bioconversion to oxidized chemicals and production of recombinant proteins by escherichia coli.” 2019. Web. 19 Jan 2021.

Vancouver:

Han Q. Reducing degradation of intracellular cofactors to improve bioconversion to oxidized chemicals and production of recombinant proteins by escherichia coli. [Internet] [Thesis]. University of Georgia; 2019. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/10724/38600.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Han Q. Reducing degradation of intracellular cofactors to improve bioconversion to oxidized chemicals and production of recombinant proteins by escherichia coli. [Thesis]. University of Georgia; 2019. Available from: http://hdl.handle.net/10724/38600

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Georgia Tech

6. Jiang, Rongrong. Oxidative Biocatalysis with Novel NADH Oxidases.

Degree: PhD, Chemical Engineering, 2006, Georgia Tech

URL: http://hdl.handle.net/1853/11533

► Many oxidoreductases need nicotinamide cofactors for their reactions. The big obstacle of using these syntheses in industry is the high cost of these nicotinamide cofactors.… (more)

Subjects/Keywords: NADH oxidase; Cofactor regeneration; Flavoprotein; Oxidases; Enzymes

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APA (6^th Edition):

Jiang, R. (2006). Oxidative Biocatalysis with Novel NADH Oxidases. (Doctoral Dissertation). Georgia Tech. Retrieved from http://hdl.handle.net/1853/11533

Chicago Manual of Style (16^th Edition):

Jiang, Rongrong. “Oxidative Biocatalysis with Novel NADH Oxidases.” 2006. Doctoral Dissertation, Georgia Tech. Accessed January 19, 2021. http://hdl.handle.net/1853/11533.

MLA Handbook (7^th Edition):

Jiang, Rongrong. “Oxidative Biocatalysis with Novel NADH Oxidases.” 2006. Web. 19 Jan 2021.

Vancouver:

Jiang R. Oxidative Biocatalysis with Novel NADH Oxidases. [Internet] [Doctoral dissertation]. Georgia Tech; 2006. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/1853/11533.

Council of Science Editors:

Jiang R. Oxidative Biocatalysis with Novel NADH Oxidases. [Doctoral Dissertation]. Georgia Tech; 2006. Available from: http://hdl.handle.net/1853/11533

7. Vaillant, Francois. Effectors of the mammalian plasma membrane NADH-oxidoreductase system. Short-chain ubiquinone analogues as potent stimulators.

Degree: 1996, Australian Catholic University

URL: 10.1007/BF02110443 ; https://researchbank.acu.edu.au/psp/24

► In the presence of effectors variations in the two recognized activities of the plasma membrane NADH-oxidoreductase system were studied in separate, specificin vitro assays.… (more)

Subjects/Keywords: Zoology; Plasma membrane NADH-oxidoreductase; NADH-oxidase; NADH∶ferricyanide reductase; ubiquinone analogues; ρ0 cells

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APA (6^th Edition):

Vaillant, F. (1996). Effectors of the mammalian plasma membrane NADH-oxidoreductase system. Short-chain ubiquinone analogues as potent stimulators. (Thesis). Australian Catholic University. Retrieved from 10.1007/BF02110443 ; https://researchbank.acu.edu.au/psp/24

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Vaillant, Francois. “Effectors of the mammalian plasma membrane NADH-oxidoreductase system. Short-chain ubiquinone analogues as potent stimulators.” 1996. Thesis, Australian Catholic University. Accessed January 19, 2021. 10.1007/BF02110443 ; https://researchbank.acu.edu.au/psp/24.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Vaillant, Francois. “Effectors of the mammalian plasma membrane NADH-oxidoreductase system. Short-chain ubiquinone analogues as potent stimulators.” 1996. Web. 19 Jan 2021.

Vancouver:

Vaillant F. Effectors of the mammalian plasma membrane NADH-oxidoreductase system. Short-chain ubiquinone analogues as potent stimulators. [Internet] [Thesis]. Australian Catholic University; 1996. [cited 2021 Jan 19]. Available from: 10.1007/BF02110443 ; https://researchbank.acu.edu.au/psp/24.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Vaillant F. Effectors of the mammalian plasma membrane NADH-oxidoreductase system. Short-chain ubiquinone analogues as potent stimulators. [Thesis]. Australian Catholic University; 1996. Available from: 10.1007/BF02110443 ; https://researchbank.acu.edu.au/psp/24

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

8. Ellis, Melissa L. (Melissa Lynn). Modulation of capsule production in serotype 3 Streptococcus pneumoniae.

Degree: PhD, 2012, University of Alabama – Birmingham

URL: http://contentdm.mhsl.uab.edu/u?/etd,1141

►

Streptococcus pneumoniae is a Gram-positive pathogen and an important cause of community-acquired pneumonia and meningitis, and it can also cause otitis media and bacteremia. A… (more)

▼

Streptococcus pneumoniae is a Gram-positive pathogen and an important cause of community-acquired pneumonia and meningitis, and it can also cause otitis media and bacteremia. A major virulence factor of S. pneumoniae is its polysaccharide capsule which functions to prevent complement-mediated opsonophagocytosis. At least 93 dis-tinct serotypes that vary in sugar composition and structure exist. S. pneumoniae can asymptomatically colonize the nasopharynx and transition to other body sites such as the lungs and blood causing invasive disease. The ability to regulate capsule production in these vastly different environments is critical for survival as low levels of capsule are necessary for colonization, while high levels of capsule are needed to prevent comple-ment-mediated opsonophagocytosis. In serotype 3 S. pneumoniae, [-4)-β-D-Glc-(1-3)-β-D-GlcUA-(1-], capsule is synthesized by the type 3 synthase, encoded by cps3S, using the UDP-glucose (UDP-Glc) and UDP-glucuronic acid (UDP-GlcUA) sugar precursors on a phosphatidylglycerol membrane anchor. The polysaccharide capsule may remain anchored to the membrane or released from the cell. Previous work has shown that [UDP-GlcUA] plays a critical role in modulating capsule production, but little is known how the concentration of this nucleotide sugar is regulated within the cell. In this study, we found that increased NADH/NAD+ ratios inhibited in vitro activity of purified Cps3D, the type 3 UDP-Glc dehydrogenase that catalyzes the NAD+-dependent oxidation of UDP-Glc to UDP-GlcUA. Analysis of conditions with altered capsule production corre-lated with increased NADH/NAD+ ratios, suggesting that the NADH/NAD+ ratio may alter Cps3D activity. Shortened capsule chain-length in some of the conditions with al-tered capsule production was also observed, suggesting that Cps3D activity was altered by the NADH/NAD+ ratio. An NADH oxidase mutant was constructed and found to have significantly increased NADH/NAD+ ratio that also correlated with reduced capsule pro-duction and shortened chain-lengths. The data presented here suggest a metabolic model where the NADH/NAD+ ratio alters Cps3D activity, the enzyme responsible for synthe-sizing UDP-GlcUA, and alterations in Cps3D activity ultimately lead to changes in cap-sule production. Another aspect of serotype 3 capsule synthesis: release of capsule from the cell was examined. We characterized released capsule from the cell and found that it was of similar size to cell-associated capsule. In addition, capsule release was found to occur steadily over time. However, we were unable to determine the exact mechanism of capsule release.

1 online resource (ix, 91 p.) : ill., digital, PDF file.

Microbiology;

Joint Health Sciences;

NADH/NAD+ ratio UDP-Glc dehydrogenase UDP-GlcUA capsule NADH oxidase

UNRESTRICTED

Advisors/Committee Members: Yother, Janet L., Dybvig, Kevin<br>, Niederweis, Michael E.<br>, Prevelige, Peter E.<br>, Pritchard, David G..

Subjects/Keywords: Bacterial Capsules<; br>; NADH oxidase<; br>; Serotyping<; br>; Streptococcus pneumoniae<; br>; UDP-N-acetylglucosamine dehydrogenase

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APA (6^th Edition):

Ellis, M. L. (. L. (2012). Modulation of capsule production in serotype 3 Streptococcus pneumoniae. (Doctoral Dissertation). University of Alabama – Birmingham. Retrieved from http://contentdm.mhsl.uab.edu/u?/etd,1141

Chicago Manual of Style (16^th Edition):

Ellis, Melissa L (Melissa Lynn). “Modulation of capsule production in serotype 3 Streptococcus pneumoniae.” 2012. Doctoral Dissertation, University of Alabama – Birmingham. Accessed January 19, 2021. http://contentdm.mhsl.uab.edu/u?/etd,1141.

MLA Handbook (7^th Edition):

Ellis, Melissa L (Melissa Lynn). “Modulation of capsule production in serotype 3 Streptococcus pneumoniae.” 2012. Web. 19 Jan 2021.

Vancouver:

Ellis ML(L. Modulation of capsule production in serotype 3 Streptococcus pneumoniae. [Internet] [Doctoral dissertation]. University of Alabama – Birmingham; 2012. [cited 2021 Jan 19]. Available from: http://contentdm.mhsl.uab.edu/u?/etd,1141.

Council of Science Editors:

Ellis ML(L. Modulation of capsule production in serotype 3 Streptococcus pneumoniae. [Doctoral Dissertation]. University of Alabama – Birmingham; 2012. Available from: http://contentdm.mhsl.uab.edu/u?/etd,1141

9. 三好, 徹. 海洋細菌および大腸菌に存在する呼吸鎖の比較生化学的研究 : Comparative and biochemical study of respiratory chains in a marine bacterium and Escherichia coli.

Degree: Chiba University / 千葉大学

URL: http://opac.ll.chiba-u.jp/da/curator/900022568/

研究科: 千葉大学大学院薬学研究科

学位:千大院薬博甲第67号

Subjects/Keywords: NADH:quinone oxidereductase; guinol oxidase; NADH:キノン酸化還元酵素; キノールオキシダーゼ

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APA (6^th Edition):

三好, �. (n.d.). 海洋細菌および大腸菌に存在する呼吸鎖の比較生化学的研究 : Comparative and biochemical study of respiratory chains in a marine bacterium and Escherichia coli. (Thesis). Chiba University / 千葉大学. Retrieved from http://opac.ll.chiba-u.jp/da/curator/900022568/

Note: this citation may be lacking information needed for this citation format:
No year of publication.
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

三好, 徹. “海洋細菌および大腸菌に存在する呼吸鎖の比較生化学的研究 : Comparative and biochemical study of respiratory chains in a marine bacterium and Escherichia coli.” Thesis, Chiba University / 千葉大学. Accessed January 19, 2021. http://opac.ll.chiba-u.jp/da/curator/900022568/.

Note: this citation may be lacking information needed for this citation format:
No year of publication.
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

三好, 徹. “海洋細菌および大腸菌に存在する呼吸鎖の比較生化学的研究 : Comparative and biochemical study of respiratory chains in a marine bacterium and Escherichia coli.” Web. 19 Jan 2021.

Note: this citation may be lacking information needed for this citation format:
No year of publication.

Vancouver:

三好 �. 海洋細菌および大腸菌に存在する呼吸鎖の比較生化学的研究 : Comparative and biochemical study of respiratory chains in a marine bacterium and Escherichia coli. [Internet] [Thesis]. Chiba University / 千葉大学; [cited 2021 Jan 19]. Available from: http://opac.ll.chiba-u.jp/da/curator/900022568/.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
No year of publication.

Council of Science Editors:

三好 �. 海洋細菌および大腸菌に存在する呼吸鎖の比較生化学的研究 : Comparative and biochemical study of respiratory chains in a marine bacterium and Escherichia coli. [Thesis]. Chiba University / 千葉大学; Available from: http://opac.ll.chiba-u.jp/da/curator/900022568/

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
No year of publication.

University of Georgia

10. Zhu, Yihui. Production of pyruvate and lactate by metabolically engineering Escherichia coli.

Degree: 2014, University of Georgia

URL: http://hdl.handle.net/10724/25106

► Pyruvic acid and lactic acid have a wide range of applications in the food, chemical, and pharmaceutical industries. The primary goal of this research is… (more)

▼ Pyruvic acid and lactic acid have a wide range of applications in the food, chemical, and pharmaceutical industries. The primary goal of this research is to improve pyruvate and lactate production through bacterial strain engineering and fermentation process development. Lactate production was studied using E. coli strain YYC202 (aceEF pfl poxB pps), whichgenerated 90 g/L lactate in a two-phase fermentation (aerobic growth phase followed by anaerobic phase for lactate production). This process also generated over 7 g/L succinate. Ca(OH)2 was found to be superior to NaOH for pH control. Strain ALS961 (YYC202 ppc) prevented succinate accumulation but growth was very poor. Strain ALS974 (YYC202 13frdABCD) reduced succinate formation by 70% to less than 3 g/L.C-NMR using uniformly labeled acetate demonstrated that succinate formation by ALS974 was biochemically derived from acetate in the medium. The two-phase process with ALS974 achieved 138 g/L lactate (1.55 M, 97% of carbon products) with a yield of 0.99 g/g and productivity of 6.3 g/L·h during the anaerobic phase. By using the dissolved oxygen (DO) during the initial cell-growth phase to monitor residual acetate, and timing the switch to the anaerobic production phase with acetate depletion, succinate production was reduced to less than 1 g/L, and ethanol production was eliminated. Furthermore, by using a cell-recycle fermentation with ultrafiltration, the anaerobic lactate production phase was prolonged from 22 h to 34 h, and an overall lactate productivity of 4.2 g/L·h was achieved. The productivity of this process was nearly 20% greater than the productivity of the fed-batch process.Pyruvate was studied using E. coli strain ALS929 (pflB aceEF poxB pps ldhA). First, a series of steady-state (chemostat) experiments were conducted to evaluate pyruvate formationunder four different nutrient-limited conditions: glucose, acetate, nitrogen (ammonia), and phosphorus (phosphate). The greatest specific glucose consumption rate of 1.60 g/g·h and specific pyruvate formation rate of 1.10 g/g·h were found under conditions of acetate-limited growth. The specific glucose consumption rate and therefore pyruvate productivity were further increased to 2.67 g/g·h and 2.01 g/g·h respectively by introducing ATP synthase knockout (atpFH), an arcA knockout and introducing heterologous NADH oxidase. A fed-batch process at -1a constant specific growth rate of 0.15 h using ALS1059 (pflB aceEF poxB pps ldhA atpFH arcA) resulted in the highest pyruvate yield and productivity. In a defined medium with 5mM betaine, a final pyruvate concentration of 89.7 g/L, a yield of 0.68 g/g and a productivity of 2.04 g/L·h were achieved.

Subjects/Keywords: Pyruvate; Lactate; Escherichia coli; Fumarate reductase; Glyoxylate shunt; Succinate; Ultrafiltration; Dissolved oxygen; Glycolysis; F1F0(H+)-ATP synthase; NADH oxidase; arcA; Betaine; Chemostat; Fed-batch

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APA (6^th Edition):

Zhu, Y. (2014). Production of pyruvate and lactate by metabolically engineering Escherichia coli. (Thesis). University of Georgia. Retrieved from http://hdl.handle.net/10724/25106

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Zhu, Yihui. “Production of pyruvate and lactate by metabolically engineering Escherichia coli.” 2014. Thesis, University of Georgia. Accessed January 19, 2021. http://hdl.handle.net/10724/25106.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Zhu, Yihui. “Production of pyruvate and lactate by metabolically engineering Escherichia coli.” 2014. Web. 19 Jan 2021.

Vancouver:

Zhu Y. Production of pyruvate and lactate by metabolically engineering Escherichia coli. [Internet] [Thesis]. University of Georgia; 2014. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/10724/25106.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Zhu Y. Production of pyruvate and lactate by metabolically engineering Escherichia coli. [Thesis]. University of Georgia; 2014. Available from: http://hdl.handle.net/10724/25106

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Lund

11. Sabet Azad, Ramin. Microbial production of 3-hydroxypropionic acid and poly(3-hydroxypropionate): Investigation of Lactobacillus reuteri propanediol utilization pathway enzymes.

Degree: 2015, University of Lund

URL: https://lup.lub.lu.se/record/5265772 ; https://portal.research.lu.se/ws/files/5992852/5265801.pdf

► Concerns regarding environmental issues such as greenhouse gas emissions and climate change have led to a shift within the research community and chemical and energy… (more)

▼ Concerns regarding environmental issues such as greenhouse gas emissions and climate change have led to a shift within the research community and chemical and energy industry sectors for finding sustainable routes for producing fuels and chemicals from renewable resources, thereby minimizing our dependence on petroleum. The C3-chemical 3-hydroxypropionic acid has been identifed as a top candidate for the biobased chemical industry. This platform chemical is a β-hydroxy acid containing two functional groups (hydroxyl and carboxyl) enabling its conversion into value-added chemicals such as 1,3-propanediol, acrolein, malonic acid, acrylamide and acrylic acid, which can be used in resins, coatings, paints, adhesives, lubricants, and in the textile industry as anti-static agent. Polymerized 3- HP, poly(3-hydroxypropionate) (poly(3-HP)), is a biodegradable and stable polymer which, besides its potential role as a biomaterial, can be degraded to 3-HP monomer. In recent years, a dramatic increase in the interest for microbial production of 3-HP and poly(3-HP) has been observed. Metabolic engineering and recombinant expression of various enzymatic pathways in a number of bacterial strains have been suggested and implemented, with mainly renewable glucose and glycerol as substrates. This thesis presents a novel pathway called the propanediol utilization pathway present in Lactobacillus reuteri that catalyzes dehydration of glycerol to 3- hydroxypropionaldehyde (3-HPA) and further to 3-HP by a series of reactions catalyzed by propionaldehyde dehydrogenase (PduP), phosphotransacylase (PduL) and propionate kinase (PduW). Through structural modeling and kinetic characterization of PduP, its 3-HPA consuming ability was confirmed and catalytic mechanism proposed. PduP, PduL and PduW-mediated conversion of 3-HPA to 3- HP was confirmed through their recombinant expression in Escherichia coli. 3-HPA produced from glycerol by L. reuteri was used as a substrate for conversion to 3-HP by the recombinant E. coli. A yield of 1 mol/mol was reached with a titer of 12 mM 3-HP. Depletion of the cofactor NAD+ required for the catalysis of 3-HP to 3-HPCoA, was deemed responsible for the low titer. Regeneration of NAD+, used up in PduP catalyzed reaction, was achieved by recombinant expression of NADH oxidase (Nox) from L. reuteri in E. coli expressing PduP, PduL and PduW. The final 3-HP titer by this recombinant strain was at least twice that of E. coli carrying solely PduP, PduL and PduW. For the production of poly(3-HP), PduL and PduW in the recombinant strain were replaced by polyhydroxyalkanoate synthase of Chromobacterium sp. that converts 3- HP-CoA to poly(3-HP). A poly(3-HP) content of up to 40% (w/w) cell dry weight was reached in an efficient and cheap process requring no additivies or expensive cofactors.

Subjects/Keywords: Industrial Biotechnology; Platform chemicals; biopolymers; 3-hydroxypropionic acid; 3-hydroxypropionaldehyde; glycerol; poly(3-hydroxypropionate); polyhydroxyalkanoates; Escherichia coli; Lactobacillus reuteri; propanediol utilization pathway; propionaldehyde dehydrogenase; biotransformation; cofactor regeneration; NADH oxidase

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

APA (6^th Edition):

Sabet Azad, R. (2015). Microbial production of 3-hydroxypropionic acid and poly(3-hydroxypropionate): Investigation of Lactobacillus reuteri propanediol utilization pathway enzymes. (Doctoral Dissertation). University of Lund. Retrieved from https://lup.lub.lu.se/record/5265772 ; https://portal.research.lu.se/ws/files/5992852/5265801.pdf

Chicago Manual of Style (16^th Edition):

Sabet Azad, Ramin. “Microbial production of 3-hydroxypropionic acid and poly(3-hydroxypropionate): Investigation of Lactobacillus reuteri propanediol utilization pathway enzymes.” 2015. Doctoral Dissertation, University of Lund. Accessed January 19, 2021. https://lup.lub.lu.se/record/5265772 ; https://portal.research.lu.se/ws/files/5992852/5265801.pdf.

MLA Handbook (7^th Edition):

Sabet Azad, Ramin. “Microbial production of 3-hydroxypropionic acid and poly(3-hydroxypropionate): Investigation of Lactobacillus reuteri propanediol utilization pathway enzymes.” 2015. Web. 19 Jan 2021.

Vancouver:

Sabet Azad R. Microbial production of 3-hydroxypropionic acid and poly(3-hydroxypropionate): Investigation of Lactobacillus reuteri propanediol utilization pathway enzymes. [Internet] [Doctoral dissertation]. University of Lund; 2015. [cited 2021 Jan 19]. Available from: https://lup.lub.lu.se/record/5265772 ; https://portal.research.lu.se/ws/files/5992852/5265801.pdf.

Council of Science Editors:

Sabet Azad R. Microbial production of 3-hydroxypropionic acid and poly(3-hydroxypropionate): Investigation of Lactobacillus reuteri propanediol utilization pathway enzymes. [Doctoral Dissertation]. University of Lund; 2015. Available from: https://lup.lub.lu.se/record/5265772 ; https://portal.research.lu.se/ws/files/5992852/5265801.pdf

NSYSU

12. Wang, Jen-Ya. Application of Sol-Gel Derived Silica Particulates as Enzyme and Reagent Immobilization Support in Electrochemiluminescence-Based Flow Injection Analysis.

Degree: PhD, Chemistry, 2004, NSYSU

URL: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0624104-171241

► Based on the linear relationship between concentration of H2O2 and the decrease of electrochemiluminescence (ECL) intensity in a Ru(bpy)32+/TPA system, procedures for the indirect determination… (more)

▼ Based on the linear relationship between concentration of H2O2 and the decrease of electrochemiluminescence (ECL) intensity in a Ru(bpy)32+/TPA system, procedures for the indirect determination of glucose with a flow injection analysis were developed. By passing solutions of glucose through a FIA system containing a glucose oxidase (GOx) immobilized sol-gel column and an ECL system of Ru(bpy)32+ and TPA, glucose can be determined optimally with a detection limit of 1.0 Î¼M in a linear dynamic range of 1.0 â 200.0 Î¼M. A repetitive injection of glucose (100 Î¼M) and human serum solutions gave satisfactory reproducibility with relative standard deviations of 1.3 (N=31) and 3.9 % (N=42) respectively. Interference due to the presence of ascorbic acid, uric acid or other reducible agents in solution can be corrected by passing sample solutions through another sol-gel column that contained no GOx. From the agreement between the contents of glucose in human serum and soft drink analyzed by the developed method and those obtained by the spectroscopy method based glucose assay kit and satisfactory recovery of glucose from interferent containing solutions, the feasibility of the developed method for real sample analysis was confirmed. One of the major purposes of this study was to develop new immobilization approaches and flow cell designs for the fabrication of regenerable ECL-based sensors with improved sensitivity, convenience and long-term stability. Silica particulates were used as immobilization support in ECL sensors for TPA and NAD(P)H and in biosensors for glucose and glucose-6-phosphateï¼G6Pï¼. The first ECL flow cell was fabricated from a glass tube, and a platinum wire was used as working electrode held at +1.3 V. The volume of the flow cell was about 50 Î¼L. An Ag/AgCl electrode and a piece of Pt wire were used as the reference and counter electrode respectively and placed downstream of the working electrode. Ru(bpy)32+ immobilized silica particulates with 1/3 silica sol content showed the best performance for TPA determination, and the sensitivity of TPA determination was dependent upon the amount of Ru(bpy)32+ immobilized in silica particulates. The lowest level of analyte detected for TPA was 0.02Î¼M, and linear range was from 0.02Î¼M to 5Î¼M. Up to a certain concentration level, it was found that Ru(bpy)32+ was tightly held in silica particulates and did not leach out into aqueous solutions, even with continuous flow for up to ten hours. Ru(bpy)32+ immobilized silica particulates were characterized of well activity and high stability; that stored at 0â exhibited its original activity for up to one year. The second ECL flow cell was fabricated from a piece of epoxy block supported Pt electrode (1 Ã 2 cm) as counter electrode, a piece glass window and a polyethylene spacer with 78 Î¼L cell volume, two 2.0-cm length of 0.6-mm diameter platinum wires were used as working electrodes held at +1.1 V, and an Ag/AgCl electrode as reference electrode. All three electrodes were incorporated within the main body of the… Advisors/Committee Members: Jentaie Shiea (chair), S.-J. Jiang (chair), H. L. Wu (chair), C.-M. Chiang (chair), H.J. Huang (committee member).

Subjects/Keywords: Ru(bpy)32+; inhibition effect; sol-gel column; NADPH; TPA; dehydrogenase; glucose oxidase; electrochemiluminescence; H2O2; NADH; regenerable sensors.; reagentless

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

APA (6^th Edition):

Wang, J. (2004). Application of Sol-Gel Derived Silica Particulates as Enzyme and Reagent Immobilization Support in Electrochemiluminescence-Based Flow Injection Analysis. (Doctoral Dissertation). NSYSU. Retrieved from http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0624104-171241

Chicago Manual of Style (16^th Edition):

Wang, Jen-Ya. “Application of Sol-Gel Derived Silica Particulates as Enzyme and Reagent Immobilization Support in Electrochemiluminescence-Based Flow Injection Analysis.” 2004. Doctoral Dissertation, NSYSU. Accessed January 19, 2021. http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0624104-171241.

MLA Handbook (7^th Edition):

Wang, Jen-Ya. “Application of Sol-Gel Derived Silica Particulates as Enzyme and Reagent Immobilization Support in Electrochemiluminescence-Based Flow Injection Analysis.” 2004. Web. 19 Jan 2021.

Vancouver:

Wang J. Application of Sol-Gel Derived Silica Particulates as Enzyme and Reagent Immobilization Support in Electrochemiluminescence-Based Flow Injection Analysis. [Internet] [Doctoral dissertation]. NSYSU; 2004. [cited 2021 Jan 19]. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0624104-171241.

Council of Science Editors:

Wang J. Application of Sol-Gel Derived Silica Particulates as Enzyme and Reagent Immobilization Support in Electrochemiluminescence-Based Flow Injection Analysis. [Doctoral Dissertation]. NSYSU; 2004. Available from: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/view_etd?URN=etd-0624104-171241

13. Johnson, Lisa Anne 1991-. Detection and characterization of pathogenic and non-pathogenic Brachyspira.

Degree: 2017, University of Saskatchewan

URL: http://hdl.handle.net/10388/8212

► Brachyspira is associated with mucohaemorrhagic diarrhea in pigs, though the pathogenesis and virulence factors behind the disease are not currently understood. This thesis aimed to… (more)

▼ Brachyspira is associated with mucohaemorrhagic diarrhea in pigs, though the pathogenesis and virulence factors behind the disease are not currently understood. This thesis aimed to identify putative virulence factors of Brachyspira through a comparative genomics approach, and to determine the frequency of the occurrence of mixed Brachyspira species infections within clinical case material. “B. hampsonii” strain 30446 was originally isolated from colon contents of a pig with mucohaemorrhagic diarrhea, and through inoculation trials has been demonstrated to be pathogenic in swine. “B. hampsonii” strain KL-180 was isolated from a Lesser Snow Goose, and is remarkably genetically similar to strain 30446. However, inoculation trials indicate “B. hampsonii” strain KL-180 is not pathogenic in swine. Their differing pathogenicity, despite their genetic similarity, allows comparison to identify gene content differences, which may correspond to putative virulence factors. Genome sequences for each strain were available, and were annotated. The basic genome features of strain 30446 and strain KL-180 were similar, with an average nucleotide identity (ANI) of 97%. Comparison of the annotated genomes revealed genes unique to each strain. Any gene differences could be important to disease outcome, including hypothetical proteins. “B. hampsonii” strain 30446, contained a set of genes absent in strain KL-180 which correspond to the Streptolysin S (sag) operon. The presence of this operon was confirmed with PCR and primers designed for each gene. The presence of this operon in pathogenic Brachyspira species, and absence in the non-pathogenic “B. hampsonii” strain KL-180 supports the possibility of the operon being a virulence factor and contributing to disease outcome. Current diagnostic methods implemented on clinical case material often indicate the presence of more than one Brachyspira species. It is not currently known if co-infection with multiple species is common, or if the presence of multiple species contributes to Brachyspira pathogenesis. To investigate the frequency of the occurrence of multiple species in Brachyspira clinical cases, deep sequencing of the nox gene target was used on clinical case material from Western Canada, Mexico and Brazil. Synthetically created communities were also sequenced, to provide insight as to what levels of Brachyspira can be detected through this method. Pigs with clinical disease were very frequently colonized by multiple species of Brachyspira. “B. hampsonii” was detected in pigs from both Mexico and Brazil, though often at very low levels. Canadian clinical cases were more diverse than those from Mexico and Brazil, and were dominated by a range of Brachyspira species. Sequencing of the synthetic communities revealed a negative primer bias towards “B. hampsonii” strain 30599 (Clade I). Strain 30599 may therefore be present at higher levels and be more widely distributed than demonstrated by current diagnostic methods based on PCR of the nox gene. The results of this thesis demonstrate… Advisors/Committee Members: Hill, Janet E, White, Aaron, Luby, Chris, Misra, Vikram.

Subjects/Keywords: Swine dysentery; comparative genomics; virulence; diagnostics; sequencing; polymerase chain reaction; NADH-oxidase; Brachyspira

…x29;. Using the NADH-oxidase (nox) gene target, sequencing of partial nox gene PCR… …given it is a quick method to provide results. The NADH-oxidase (nox) gene is a… …Another important resistance mechanism to oxygen toxicity is NADH-oxidase (nox), which…

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

APA (6^th Edition):

Johnson, L. A. 1. (2017). Detection and characterization of pathogenic and non-pathogenic Brachyspira. (Thesis). University of Saskatchewan. Retrieved from http://hdl.handle.net/10388/8212

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Johnson, Lisa Anne 1991-. “Detection and characterization of pathogenic and non-pathogenic Brachyspira.” 2017. Thesis, University of Saskatchewan. Accessed January 19, 2021. http://hdl.handle.net/10388/8212.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Johnson, Lisa Anne 1991-. “Detection and characterization of pathogenic and non-pathogenic Brachyspira.” 2017. Web. 19 Jan 2021.

Vancouver:

Johnson LA1. Detection and characterization of pathogenic and non-pathogenic Brachyspira. [Internet] [Thesis]. University of Saskatchewan; 2017. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/10388/8212.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Johnson LA1. Detection and characterization of pathogenic and non-pathogenic Brachyspira. [Thesis]. University of Saskatchewan; 2017. Available from: http://hdl.handle.net/10388/8212

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

University of Maryland

14. Watson, Jr, James Ambrose. Insight into the Structure and Mechanism of Iodotyrosine Deiodinase, the First Mammalian Member of the NADH Oxidase / Flavin Reductase Superfamily.

Degree: Chemistry, 2006, University of Maryland

URL: http://hdl.handle.net/1903/3794

► Iodotyrosine deiodinase (IYD) has remained poorly characterized for nearly 50 years in spite of its function as an iodine salvage pathway and its role in… (more)

▼ Iodotyrosine deiodinase (IYD) has remained poorly characterized for nearly 50 years in spite of its function as an iodine salvage pathway and its role in regulation of mammalian basal metabolism. IYD catalyzes the reductive deiodination of both mono- and diiodotyrosine, the iodinated side-products of thyroid hormone production. The Rokita lab previously purified IYD from porcine thyroids and identified a putative dehalogenase cDNA. The work in this dissertation confirms the identity of the cDNA that encodes IYD through expression in HEK293 cells (KM = 4.4 ± 1.7 μM and Vmax = 12 ± 1 nmol hr-1 g-1) and, furthermore, identifies IYD as the first mammalian member of the NADH oxidase/flavin reductase superfamily, a protein fold previously found only in bacteria. In addition, a three-dimensional model of the NADH oxidase/flavin reductase domain of IYD was constructed based on the x-ray crystal structure coordinates (Protein Data Bank code 1ICR) of the minor nitroreductase from Escherichia coli. The model also predicts structural features of IYD, including interactions between the flavin bound to IYD and one of three conserved cysteines. To investigate the role of the NADH oxidase/flavin reductase domain plays in electron transfer, two truncation mutants were generated: IYD-NR (residues 81-285) and IYD-ΔTM (residues 34-285) encoding transmembrane-domain deleted IYD. The two mutants were expressed in HEK293 cells and their catalytic properties were measured. IYD-NR did not promote deiodination (Vmax = 0.0 ± 0.4 nmol hr-1 ug-1) of diiodotyrosine in a literature-derived iodide release assay. However, IYD-ΔTM was catalytically active toward DIT (KM = 4.6 ± 1.3 μM and Vmax = 7.0 ± 0.5 nmol hr-1 g-1) when the chemical reductant dithionite was used but did not promote NADPH-responsive deiodination. The subcellular location for both mutants was determined by ultracentrifugation. IYD-NR was observed in the insoluble fraction after centrifugation at 100,000 x g. However, IYD-ΔTM remained in the supernatant after centrifugation at 100,000 x g for 1 hour. Advisors/Committee Members: Rokita, Steven E (advisor).

Subjects/Keywords: Chemistry, Biochemistry; Chemistry, Organic; iodotyrosine deiodinase; reductive dehalogenation; NADH oxidase/flavin reductase; flavoprotein; iodine metabolism; thyroid

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

APA (6^th Edition):

Watson, Jr, J. A. (2006). Insight into the Structure and Mechanism of Iodotyrosine Deiodinase, the First Mammalian Member of the NADH Oxidase / Flavin Reductase Superfamily. (Thesis). University of Maryland. Retrieved from http://hdl.handle.net/1903/3794

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Watson, Jr, James Ambrose. “Insight into the Structure and Mechanism of Iodotyrosine Deiodinase, the First Mammalian Member of the NADH Oxidase / Flavin Reductase Superfamily.” 2006. Thesis, University of Maryland. Accessed January 19, 2021. http://hdl.handle.net/1903/3794.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Watson, Jr, James Ambrose. “Insight into the Structure and Mechanism of Iodotyrosine Deiodinase, the First Mammalian Member of the NADH Oxidase / Flavin Reductase Superfamily.” 2006. Web. 19 Jan 2021.

Vancouver:

Watson, Jr JA. Insight into the Structure and Mechanism of Iodotyrosine Deiodinase, the First Mammalian Member of the NADH Oxidase / Flavin Reductase Superfamily. [Internet] [Thesis]. University of Maryland; 2006. [cited 2021 Jan 19]. Available from: http://hdl.handle.net/1903/3794.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Watson, Jr JA. Insight into the Structure and Mechanism of Iodotyrosine Deiodinase, the First Mammalian Member of the NADH Oxidase / Flavin Reductase Superfamily. [Thesis]. University of Maryland; 2006. Available from: http://hdl.handle.net/1903/3794

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

15. Shymansky, Christopher Michael. Application of 2-Scale 13C Metabolic Flux Analysis to Growth Phenotypes in S. cerevisiae.

Degree: Chemical Engineering, 2015, University of California – Berkeley

URL: http://www.escholarship.org/uc/item/99j5w5q9

► Fluxes are useful because they are the most phenotypically relevant output we can infer. The dominant methods of obtaining these profiles, FBA and 13C MFA,… (more)

▼ Fluxes are useful because they are the most phenotypically relevant output we can infer. The dominant methods of obtaining these profiles, FBA and 13C MFA, have advantages and disadvantages. 2S-13C MFA combines the advantages of both to obtain more reliable genome-scale flux profiles that are self-consistent with both the carbon transition model and data used to infer them. This makes them a better basis for troubleshooting phenotypic changes and for making predictions.We do not fully understand the role of Sip1 in glucose repression systems. A better understanding of it and the general phenomenon of carbon catabolite-repression could result in better ways to engineer cells and utilize various feedstocks. Previous work in our lab re- sulted in an unreported growth phenotype upon knockout of SIP1 in mixed glucose/galactose medium. To better understand the relative roles of galactose and knockout of SIP1, we constructed base and sip1∆ mutant strains in a CEN.PK113-7D ura3∆ gal1∆ background and compared their 2S-13C MFA-derived flux profiles in both glucose-only and mixed glu- cose/galactose media. Our original hypothesis, that deletion of SIP1 was necessary to see an effect from the presence of galactose, was incorrect. The presence of galactose was nec- essary to see a phenotypic difference in growth rate upon knockout of SIP1. Both the base and mutant strains exhibited, upon addition of galactose, increases in specific growth rate, decrease of PPP pathway activity to 1/100 of its initial value, shift from use of NAD- to NADP-dependent malic enzyme, and redistribution of flux towards branched-chain amino acid biosynthesis. Despite the expected lack of change in growth rate upon knockout of SIP1 in glucose repressing conditions, extracellular ethanol flux decreased, mitochondrial flow completely shut down, and flow was directed toward a part of the network involving arginine and threonine biosynthesis. Regardless of the noted differences, all strain/condition pairs were accompanied by certain normal glucose-repressing phenotypes (i.e. ethanol pro- duction and repression of TCA/glyoxylate cycle activity). Additionally, a cycle from cytosolic pyruvate through cytosolic malate and the mitochondria back to cytosolic pyruvate through NAD-dependent malic enzyme occurred. Clearly, glucose repression and the role of Sip1 is more complicated than we realized. Recent work makes it plausible that galactose enters the cell at the galactose/glucose ratio in this study. The more-reliable and self-consistent flux12profiles generated by 2S-13C MFA were instrumental in studying this problem at unprece- dented detail. However, more work is necessary to fully elucidate the role of Sip1 in carbon catabolite-repressing conditions.Carbon lost to non-target metabolites (e.g. ethanol) represents a missed opportunity. It might be possible to redirect this lost flux towards biomass and/or target-molecule produc- tion. Additionally, the question of whether we can use an NADH oxidase to correct cofactor imbalances is an interesting one. We…

Subjects/Keywords: Chemical engineering; Bioinformatics; Molecular biology; 13C metabolic flux analysis; adh1; glucose repression; NADH oxidase; semidefinite relaxation; sip1

…three NADH oxidases, and one TEF1 terminator in a pRS416 Ura-plasmid backbone Averaged maximum… …rebalance it using expression of heterologous NADH oxidases. Chapter 4 describes our attempt to…

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APA (6^th Edition):

Shymansky, C. M. (2015). Application of 2-Scale 13C Metabolic Flux Analysis to Growth Phenotypes in S. cerevisiae. (Thesis). University of California – Berkeley. Retrieved from http://www.escholarship.org/uc/item/99j5w5q9

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Shymansky, Christopher Michael. “Application of 2-Scale 13C Metabolic Flux Analysis to Growth Phenotypes in S. cerevisiae.” 2015. Thesis, University of California – Berkeley. Accessed January 19, 2021. http://www.escholarship.org/uc/item/99j5w5q9.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Shymansky, Christopher Michael. “Application of 2-Scale 13C Metabolic Flux Analysis to Growth Phenotypes in S. cerevisiae.” 2015. Web. 19 Jan 2021.

Vancouver:

Shymansky CM. Application of 2-Scale 13C Metabolic Flux Analysis to Growth Phenotypes in S. cerevisiae. [Internet] [Thesis]. University of California – Berkeley; 2015. [cited 2021 Jan 19]. Available from: http://www.escholarship.org/uc/item/99j5w5q9.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Shymansky CM. Application of 2-Scale 13C Metabolic Flux Analysis to Growth Phenotypes in S. cerevisiae. [Thesis]. University of California – Berkeley; 2015. Available from: http://www.escholarship.org/uc/item/99j5w5q9

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

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Open Access Theses and Dissertations