On costs and benefits of individual reactions in biochemical networks: a systems approach
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Abschlussarbeit Buch |
| Sprache: | English |
| Veröffentlicht: |
2014
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| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | Enth. 4 Zeitschr.aufsätze |
| Beschreibung: | IX, 156 S. graph. Darst. |
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Datensatz im Suchindex
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| adam_text | CONTENTS
ABSTRACT III
1 INTRODUCTION 1
1.1 BACKGROUND 1
1.1.1 IMPORTANCE OF INDIVIDUAL METABOLIC REACTIONS 2
1.1.2 CONTROL OF METABOLIC FUNCTION 3
1.1.3 METABOLIC COSTS 4
1.1.4 COST-BENEFIT ANALYSES OF METABOLISM 5
1.2 UTILIZED THEORIES 7
1.2.1 METABOLIC MODELING APPROACHES 7
1.2.2 COOPERATIVE GAME THEORY & THE SHAPLEY VALUE 8
1.3 THESIS STATEMENTS AND CONTRIBUTIONS 9
2 A NOVEL APPROACH FOR DETERMINING ENVIRONMENT-SPECIFIC PROTEIN COSTS:
THE CASE OF
ARABIDOPSIS THALIANA 11
2.1 INTRODUCTION 12
2.2 APPROACH 13
2.2.1 COST FROM PHYSICOCHEMICAL PROPERTIES 13
2.2.2 COST FROM SIMPLIFIED PATHWAYS 14
2.2.3 COST FROM GENOME-SCALE MODELS 14
2.2.4 OUR APPROACH 15
2.2.5 DATASETS 15
2.3 METHODS 15
2.3.1 GENOME-SCALE METABOLIC MODEL OF A. THALIANA 15
2.3.2 FLUX BALANCE ANALYSIS 16
2.3.3 NOVEL FBA-BASED COST MEASURE 17
2.4 RESULTS AND DISCUSSION 18
2.5 CONCLUSION 23
3 A NOVEL APPROACH FOR DETERMINING ENVIRONMENT-SPECIFIC PROTEIN COSTS:
THE CASE OF
ARABIDOPSIS THALIANA -
REVISION 25
3.1 ERRORS IN THE ANALYSIS AND SHORTCOMINGS OF THE COST MEASURE 25
3.2 CORRECTED PROOF OF PROPOSITION 2.3.1 26
4 EFFECTS OF VARYING NITROGEN SOURCES
ON AMINO
ACID COSTS IN
ARABIDOPSIS THALIANA
UNDER
DIFFERENT LIGHT AND
CARBON-SOURCE CONDITIONS 29
4.1 INTRODUCTION 30
4.1.1 COST ESTIMATION OF AMINO ACID SYNTHESIS 31
4.2 RESULTS AND DISCUSSION 32
HTTP://D-NB.INFO/106401688X
VIII CONTENTS
4.2.1 MODEL COMPARISON 32
4.2.2 COMPARISON OF DAY AND NIGHT SCENARIOS UNDER AUTOTROPHIC AND
HETEROTROPHIC
GROWTH CONDITIONS 34
4.2.3 EFFECTS OF DIFFERENT NITROGEN SOURCES 36
4.2.4 CONCLUSIONS AND IMPLICATIONS 38
4.3 METHODS 40
4.3.1 MODEL MODIFICATIONS 40
4.3.2 ENVIRONMENTAL AND CELLULAR SET-UP 41
4.3.3 AMINO ACID COST CALCULATION 43
5 RESTRICTED COOPERATIVE GAMES ON METABOLIC NETWORKS REVEAL FUNCTIONALLY
IMPORTANT
REACTIONS 47
5.1 INTRODUCTION 47
5.2 APPROACH 48
5.2.1 RELATION TO OTHER APPROACHES 50
5.2.2 FLUX BALANCE ANALYSIS 51
5.2.3 FBA AND COOPERATIVE GAMES 52
5.2.4 SHAPLEY VALUE OF FBA-BASED GAMES 53
5.2.5 CALCULATION OF THE SHAPLEY VALUE FOR RESTRICTED FBA-BASED GAMES 56
5.3 RESULTS & DISCUSSION 58
5.3.1 FUNCTIONALLY IMPORTANT REACTIONS IN A PARADIGMATIC NETWORK 58
5.3.2 GLYCOLYSIS & PENTOSE PHOSPHATE PATHWAY (GLYPPP) 62
5.4 CONCLUSION 66
6 STRUCTURAL CONTROL OF METABOLIC
FLUX 69
6.1 INTRODUCTION 70
6.2 RESULTS 72
6.2.1 EXAMINATION OF METABOLIC CONTROL 72
6.2.2 METABOLIC CONTROL ANALYSIS 72
6.2.3 STRUCTURAL METABOLIC CONTROL 73
6.2.4 APPROACHES RELATED TO STRUCTURAL METABOLIC CONTROL 74
6.2.5 ANALYSIS OF STRUCTURAL METABOLIC CONTROL 75
6.2.6 APPLICATION TO DATA 84
6.3 DISCUSSION 87
6.3.1 CONCLUDING REMARKS 89
6.4 METHODS 90
6.4.1 FLUX BALANCE ANALYSIS 90
6.4.2 FUNCTIONAL CENTRALITY 91
6.4.3 ESTIMATION OF FUNCTIONAL CENTRALITIES 93
6.4.4 ERROR CALCULATION OF ESTIMATED FUNCTIONAL CENTRALITY 95
6.4.5 CONTROL-EFFECTIVE FLUXES ., 97
6.4.6 MODEL 97
7 DISCUSSION 99
. 7.1 SUMMARY 99
7.2 METABOLIC COSTS 100
7.2.1 PROPERTIES OF METABOLIC COST CALCULATION 100
7.2.2 FUTURE DIRECTIONS 100
7.3 POTENTIAL APPLICATIONS AND MODIFICATIONS OF THE ROBUSTNESS MEASURE
101
7.4 FUNCTIONAL CENTRALITY 101
CONTENTS IX
7.4.1 POTENTIAL MODIFICATIONS 101
7.4.2 ON THE COMPUTATIONAL AND MATHEMATICAL PROPERTIES 102
7.4.3 FUNCTIONAL CENTRALITY AND CONTROLLABILITY 104
7.4.4 FUTURE DIRECTIONS 104
7.5 PERSPECTIVE ON COST-BENEFIT ANALYSIS 106
7.6 OUTLOOK 106
APPENDIX A A NOVEL APPROACH FOR DETERMINING ENVIRONMENT-SPECIFIC PROTEIN
COSTS: THE
CASEOTARABIDOPSISTHALIANA
109
APPENDIX B EFFECTS OF VARYING NITROGEN SOURCES ON AMINO ACID COSTS IN
ARABIDOPSIS
THALIANA
UNDER DIFFERENT LIGHT AND CARBON-SOURCE CONDITIONS 111
APPENDIX C AXIOMATIZATION OF FUNCTIONAL CENTRALITIES 115
APPENDIX D SHAPLEY VALUE OF ENZYME
SUBSETS IN FBA-BASED
GAMES 117
D.L UNRESTRICTED GAMES 117
D.2 RESTRICTED GAMES 118
APPENDIX E STRUCTURAL CONTROL OF METABOLIC FLUX 121
E.L ERROR CALCULATION FOR KO-REDUCED FUNCTIONALITY IN THE MULTIPLE
KNOCKOUT STUDY . . 139
BIBLIOGRAPHY 141
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| any_adam_object | 1 |
| author | Sajitz-Hermstein, Max |
| author_GND | (DE-588)1066388032 |
| author_facet | Sajitz-Hermstein, Max |
| author_role | aut |
| author_sort | Sajitz-Hermstein, Max |
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| building | Verbundindex |
| bvnumber | BV042288618 |
| ctrlnum | (OCoLC)900734467 (DE-599)GBV806997206 |
| dewey-full | 570.285 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 570 - Biology |
| dewey-raw | 570.285 |
| dewey-search | 570.285 |
| dewey-sort | 3570.285 |
| dewey-tens | 570 - Biology |
| discipline | Biologie |
| format | Thesis Book |
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| spelling | Sajitz-Hermstein, Max Verfasser (DE-588)1066388032 aut On costs and benefits of individual reactions in biochemical networks a systems approach von Max Sajitz-Hermstein 2014 IX, 156 S. graph. Darst. txt rdacontent n rdamedia nc rdacarrier Enth. 4 Zeitschr.aufsätze Potsdam, Univ., Diss., 2014 Biochemische Reaktion (DE-588)4145593-9 gnd rswk-swf Stoffwechsel (DE-588)4057699-1 gnd rswk-swf (DE-588)4113937-9 Hochschulschrift gnd-content Biochemische Reaktion (DE-588)4145593-9 s Stoffwechsel (DE-588)4057699-1 s DE-604 DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=027725834&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Sajitz-Hermstein, Max On costs and benefits of individual reactions in biochemical networks a systems approach Biochemische Reaktion (DE-588)4145593-9 gnd Stoffwechsel (DE-588)4057699-1 gnd |
| subject_GND | (DE-588)4145593-9 (DE-588)4057699-1 (DE-588)4113937-9 |
| title | On costs and benefits of individual reactions in biochemical networks a systems approach |
| title_auth | On costs and benefits of individual reactions in biochemical networks a systems approach |
| title_exact_search | On costs and benefits of individual reactions in biochemical networks a systems approach |
| title_full | On costs and benefits of individual reactions in biochemical networks a systems approach von Max Sajitz-Hermstein |
| title_fullStr | On costs and benefits of individual reactions in biochemical networks a systems approach von Max Sajitz-Hermstein |
| title_full_unstemmed | On costs and benefits of individual reactions in biochemical networks a systems approach von Max Sajitz-Hermstein |
| title_short | On costs and benefits of individual reactions in biochemical networks |
| title_sort | on costs and benefits of individual reactions in biochemical networks a systems approach |
| title_sub | a systems approach |
| topic | Biochemische Reaktion (DE-588)4145593-9 gnd Stoffwechsel (DE-588)4057699-1 gnd |
| topic_facet | Biochemische Reaktion Stoffwechsel Hochschulschrift |
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