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THÔNG TIN TÀI LIỆU
Cấu trúc
Chapter 1
1.1. Introduction
1.2. Aims of this thesis
1.3. Thesis overview
Chapter 2
Review: Proteomic Analysis of Saccharomyces cerevisiae and Bioethanol Fermentation
2.1. Abstract
2.2. Literature review of Saccharomyces cerevisiae proteomic analysis
2.2.1. The importance of proteomic investigations in Saccharomyces cerevisiae
2.2.2. Proteomics as a tool for the identification and quantitation of S. cerevisiae proteins
2.2.2.1. Introduction
2.2.2.2. Comparison of methods
2.2.3. The identification and quantitation of S. cerevisiae proteins in proteomics experiments
2.2.3.1. How tandem mass spectrometry and protein identification work?
2.2.3.2. Number of publication
2.2.3.3. Identification of the S. cerevisiae proteomes
2.2.3.4. Localization of proteins
2.2.3.5. The quantitative proteome of S. cerevisiae
2.2.4. Proteomics in the study of S. cerevisiae networks
2.2.5. Proteomic analysis of S. cerevisiae protein modifications
2.2.6. Discussion
2.2.7. The outlook of S. cerevisiae proteomics analysis
2.3. Bioethanol fermentation process and methods to improve this process
2.3.1. Bioethanol fermentation process
2.3.2. Methods (techniques) to improve bioethanol fermentation
2.3.2.1. Technical Processes
2.3.2.2. Improvement of media quality
2.3.2.3. Metabolic engineering
Chapter 3
3.1. Abstract
3.2. Introduction
3.3. Materials and Methods
3.3.1. Sample preparation
3.3.2. Protein preparation
3.3.3. Experimental design
3.3.4. Isobaric peptide labeling
3.3.5. Strong cation exchange fractionation
3.3.6. Mass spectrometric analysis
3.3.7. Data analysis
3.4. Results and discussion
3.4.1. Multiple injections(
3.4.1.1. Database search strategy
3.4.1.2. Multiple injections effect at the protein level
3.4.1.3. Multiple injections effect at the peptide level
3.4.1.4. Coefficient of variation (CV)
3.4.2. Technical variation(
3.5. Conclusions
Chapter 4
4.1. Abstract
4.2. Introduction
4.3. Materials and methods
4.3.1. Fermentation conditions
4.3.2. Measurements of fermentation parameters
4.3.3. Cell extraction, labeling, mass spectrometry and data analysis
4.4. Results and discussion
4.4.1. Ethanol fermentation as a function of glucose concentration
4.4.2. Relative protein expression under different glucose concentrations
4.4.3. The glycolysis pathway
4.4.4. Storage carbohydrates
4.4.5. The requirement for redox balance led to secondary products generation
4.4.6. Tricarboxylic acid cycle (TCA cycle)
4.4.7. Amino acids metabolism
4.4.8. Proteins involved in eIF (eukaryotic initiation factor), and heat-shock proteins
4.5. Conclusions
Chapter 5
5.1. Abstract
5.2. Introduction
5.3. Materials and methods
5.3.1. Growth conditions
5.3.2. Measurements of fermentation parameters
5.3.3. Cell viability determination
5.3.4. Dry weight determination
5.3.5. Glycogen and trehalose determination
5.3.6. Intracellular amino acids determination
5.3.7. Labeling, mass spectrometry and data analysis
5.4. Results and discussion
5.4.1. The cell growth during lag phase under stress condition
5.4.2. The fluctuations in intracellular amino acids concentrations
5.4.3. The identification and classification of detected proteins
5.4.4. The expression of proteins related to the biosynthesis of amino acids
5.4.5. Response of heat-shock proteins to VHG conditions with amino acid supplementation
5.4.6. The expression of proteins related to translation processes (aminoacyl-tRNA biosynthesis) and yeast growth
5.4.7. The expression of proteins related to cell division, cycle, and homeostasis
5.4.8. The expression of proteins related to the stress condition, trehalose and glycogen biosynthesis
5.4.9. The expression of proteins related to ethanol fermentation
5.4.10. The expression of proteins relating to energy metabolism and nucleotide metabolism
5.4.11. Comparison of ethanol fermentation process
5.5. Conclusions
Chapter 6
6.1. Abstract
6.2. Introduction
6.3. Materials and methods
6.3.1. Cell growth conditions and immobilization
6.3.2. Measurement of fermentation parameters
6.3.3. Immobilized cell extraction
6.3.4. Labeling, mass spectrometry and data analysis
6.4. Results and discussion
6.4.1. The behaviour of immobilized cells, and the kinetic fermentation parameters
6.4.2. The identification and quantitation of protein expression
6.4.3. The Ras/cAMP pathway
6.4.4. The glycolysis pathway
6.4.5. Utilization of ATP, and the synthesis of trehalose and glycogen
6.4.6. Differential expression of ribosomal proteins
6.4.7. Proteins essential for viability
6.4.8. Proteins related to de novo biosynthesis of amino acids and aminoacyl-tRNA biosynthesis
6.4.9. Heat-shock proteins
6.4.10. Comparison of ethanol fermentation processes
6.5. Conclusions
Chapter 7
7.1. Abstract
7.2. Introduction
7.3. Materials and methods
7.3.1. Fermentation system
7.3.2. Cell growth conditions, immobilization, measurements of fermentation parameters, and proteomic analysis
7.3.3. ATP and ADP measurements
7.3.4. Ethanol yield determination
7.4. Results and discussion
7.4.1. The fluctuation of parameters
7.4.1.1. Glucose fluctuations
7.4.1.2. Ethanol fluctuations
7.4.1.3. Glycerol fluctuations
7.4.1.4. Biomass fluctuations
7.4.1.5. Mixing of the system
7.4.2. Ethanol yield oscillations
7.4.3. The rhythm of oscillations
7.4.4. Expression of proteins in generating the rhythm of the oscillations
7.4.4.1. The regulation of ATP during continuous fermentation under VHG conditions
7.4.4.2. The expression fluctuations of proteins relating to oxidative phosphorylation
7.4.4.3. The regulation of NADH during continuous fermentation under VHG conditions
7.4.5. Comparison of ethanol fermentation process
7.5. Conclusions
Chapter 8
8.1. Conclusions
8.2. Recommendations
Nội dung
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