Optimization based approaches for analyzing metabolic adjustment to changing environmental conditions:
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Abschlussarbeit Buch |
| Sprache: | English |
| Veröffentlicht: |
2014
|
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | Enth. Sonderabdr. |
| Beschreibung: | [IV], 130 S. graph. Darst. |
Internformat
MARC
| LEADER | 00000nam a2200000 c 4500 | ||
|---|---|---|---|
| 001 | BV042203284 | ||
| 003 | DE-604 | ||
| 005 | 20150217 | ||
| 007 | t | ||
| 008 | 141124s2014 d||| m||| 00||| eng d | ||
| 035 | |a (OCoLC)897405694 | ||
| 035 | |a (DE-599)GBV796851263 | ||
| 040 | |a DE-604 |b ger | ||
| 041 | 0 | |a eng | |
| 049 | |a DE-12 |a DE-188 | ||
| 082 | 0 | |a 571.75 |2 22/ger | |
| 100 | 1 | |a Töpfer, Nadine |e Verfasser |0 (DE-588)1067127208 |4 aut | |
| 245 | 1 | 0 | |a Optimization based approaches for analyzing metabolic adjustment to changing environmental conditions |c von Nadine Töpfer |
| 264 | 1 | |c 2014 | |
| 300 | |a [IV], 130 S. |b graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 500 | |a Enth. Sonderabdr. | ||
| 502 | |a Potsdam, Univ., Diss., 2014 | ||
| 650 | 0 | 7 | |a Anpassung |0 (DE-588)4128128-7 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Stoffwechsel |0 (DE-588)4057699-1 |2 gnd |9 rswk-swf |
| 655 | 7 | |0 (DE-588)4113937-9 |a Hochschulschrift |2 gnd-content | |
| 689 | 0 | 0 | |a Stoffwechsel |0 (DE-588)4057699-1 |D s |
| 689 | 0 | 1 | |a Anpassung |0 (DE-588)4128128-7 |D s |
| 689 | 0 | |5 DE-604 | |
| 856 | 4 | 2 | |m DNB Datenaustausch |q application/pdf |u http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=027642129&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |3 Inhaltsverzeichnis |
| 999 | |a oai:aleph.bib-bvb.de:BVB01-027642129 | ||
Datensatz im Suchindex
| _version_ | 1804152721529372672 |
|---|---|
| adam_text | CONTENTS
ACKNOWLEDGEMENT VIII
ABSTRACT I
ZUSAMMENFASSUNG I
TABLE OF CONTENTS IV
1 INTRODUCTION 1
1.1 WHAT IS METABOLISM? 2
1.2 A BRIEF REVIEW OF FORMALIZING METABOLISM 3
1.2.1 KINETIC MODELING 3
1.2.2 KINETIC MODELING FOR INVESTIGATING METABOLIC ADAPTATION . 5
1.2.3 STOICHIOMETRIC MODELING 7
1.2.4 THE ADVENT OF SYSTEMS BIOLOGY 8
1.2.5 GENOME-SCALE MODELS 10
1.2.6 GENOME-SCALE MODEL-GUIDED ANALYSIS 11
1.2.7 STOICHIOMETRIC GENOME-SCALE MODELING FOR INVESTIGATING
ADAPTATION 11
1.2.8 APPROACHES FOR BRIDGING KINETIC AND GENOME-SCALE MODE
LING 13
1.3 SYNOPSIS 14
LIST OF ABBREVIATIONS 1
2 STRESS-INDUCED METABOLIC ADAPTATION IN E. COLI 19
2.1 INTRODUCTION 21
2.2 METHODS 23
2.2.1 WEIGHTING OF REACTIONS 23
2.2.2 DATA-DRIVEN NETWORK REDUCTION*THE MIN-MAX PROBLEM . 25
2.2.3 FRACTIONAL APPEARANCE OF REACTIONS IN EFMS 27
I
HTTP://D-NB.INFO/1062574303
2.3 RESULTS 27
2.3.1 TIME- AND CONDITION-SPECIFIC MINIMAL OPERATING NETWORKS 27
2.3.2 COMPARISON TO NETWORKS EXTRACTED FROM MADE 27
2.3.3 EFM-BASED CHARACTERIZATION OF ADAPTABILITY 28
2.3.4 FRACTIONAL APPEARANCE OF REACTIONS IN EFMS DISCRIMINA
TES TWO TYPES OF REACTIONS 31
2.4 DISCUSSION 35
2.5 CONCLUSION 37
3 CARBON PARTITIONING UNDER NITROGEN-STARVATION IN THE GREEN
ALGAE H. PLUVIALIS 39
3.1 INTRODUCTION 41
3.2 EXPERIMENTAL PROCEDURES 43
3.2.1 ORGANISM AND GROWTH CONDITIONS 43
3.2.2 ALGEA CULTURES 44
3.2.3 MEASUREMENTS OF GROWTH PARAMETERS AND PIGMENT CONTENT 44
3.2.4 TOTAL SUGAR DETERMINATION 44
3.2.5 ANALYSIS OF FA COMPOSITION AND CONTENT 44
3.2.6 ENZYME ACTIVITY MEASUREMENTS 45
3.2.7 SAMPLE EXTRACTION FOR METABOLITE PROFILING 45
3.2.8 DERIVATIZATION AND ANALYSIS OF PRIMARY METABOLITES USING
GC-MS 46
3.2.9 MULTIVARIATE AND STATISTICAL ANALYSES 46
3.2.10 COMPUTATIONAL APPROACH 47
3.3 RESULTS 50
3.3.1 CHANGES IN METABOLIC STATUS CAUSED BY N STARVATION UN
DER HL 50
3.3.2 INTEGRATED CLUSTER ANALYSIS OF THE ENZYME ACTIVITY AND
METABOLITE DATA 56
3.3.3 MODEL DEVELOPMENT AND CONSTRAINT-BASED DATA INTEGRATION 57
3.3.4 FLUX VARIABILITY 60
3.3.5 MODEL-BASED HYPOTHESIS TESTING: C REDISTRIBUTION FROM
STARCH TO FAS 60
3.3.6 MODEL-BASED HYPOTHESIS TESTING: C REDISTRIBUTION FROM
THE TCA CYCLE TO FA BIOSYNTHESIS 63
3.4 DISCUSSION 65
METABOLIC FUNCTIONS IN ARABIDOPSIS^S
LIGHT AND TEMPERATURE
ACCLIMATION 69
4.1 INTRODUCTION 71
4.2 RESULTS AND DISCUSSION 75
4.2.1 MAXIMIZATION OF METABOLIC FUNCTIONS UNDER A NULL MODEL
FOR DISTRIBUTION OF TRANSCRIPTS 75
4.2.2 DIFFERENTIAL METABOLIC FUNCTIONS ACT AS EITHER MODULATORS
OR SUSTAINERS 77
4.2.3 CONDITION-INDEPENDENT MODULATORS AND SUSTAINERS .... 78
4.2.4 CONDITION-SPECIFIC MODULATORS AND SUSTAINERS 81
4.2.5 OPTIMIZATION-BASED INDICES FOR COMPARISON OF METABOLIC
FUNCTIONS 83
4.2.6 OPTIMIZATION-BASED INDICES REVEAL TEMPORAL DIFFERENCES
BETWEEN METABOLIC FUNCTIONS 85
4.2.7 OPTIMIZATION-BASED INDICES FOR MODULATORS AND SUSTAINERS 87
4.2.8 COMPARATIVE ANALYSIS OF CONDITIONS BASED ON THE INDICES . 89
4.2.9 FUTURE CHALLENGES 92
4.3 MATERIALS AND METHODS 93
4.3.1 TRANSCRIPTOMICS DATA INTEGRATION 95
4.3.2 METABOLIC FUNCTIONS 95
4.3.3 STATISTICAL ANALYSIS 96
4.3.4 SOFTWARE 96
INSIGHTS INTO ARABIDOPSIS S LIGHT AND TEMPERATURE ACCLIMATION 97
5.1 ADDENDUM 99
VARIABILITY OF METABOLITE LEVELS IN ARABIDOPSIS S LIGHT AND TEM
PERATURE ACCLIMATION 103
6.1 INTRODUCTION 105
6.2 RESULTS 107
6.2.1 DATA INTEGRATION IN A CONSTRAINT-BASED MODEL TO PREDICT
CONDITION-SPECIFIC DIFFERENTIAL METABOLIC FUNCTIONS .... 107
6.2.2 RELATIONS BETWEEN SUSTAINERS/MODULATORS AND
METABOLITE VARIATION 109
6.2.3 VARIABILITY OF SUBSTRATES IN DIFFERENTIALLY BEHAVING
FUNCTIONS
ILL
6.2.4 INITIAL SUBSTRATES IN DIFFERENTIALLY BEHAVING FUNCTIONS . . .115
6.3 DISCUSSION 116
6.3.1 COMPARISON TO RELATED STUDIES 116
6.3.2 THE ROLE OF SUBSTRATES AS SYSTEMS INPUT IN TERMS OF NUM
BER AND VARIABILITY 117
6.3.3 FURTHER BIOLOGICAL IMPLICATIONS 118
6.4 MATERIALS AND METHODS 119
6.4.1 DATA 119
6.4.2 MAPPING OF HIGH-THROUGHPUT DATA ONTO THE MODEL . . . .119
6.4.3 STATISTICAL METHODS 119
7 DISCUSSION & OUTLOOK 121
7.1 SUMMARY 121
7.2 GENERAL DISCUSSION 123
7.2.1 ASPECTS CRUCIAL FOR THE STUDIES PRESENTED HERE 123
7.2.2 ASPECTS CRUCIAL FOR NETWORK RECONSTRUCTION AND DATA IN
TEGRATION 126
7.2.3 FUTURE PROSPECTIVE FOR MODELING METABOLIC ADJUSTMENT . 129
7.3 CONCLUSION 130
APPENDIX - SUPPLEMENTARY INFORMATION 131
BIBLIOGRAPHY 168
AUTHOR S CONTRIBUTIONS 169
SELBSTANDIGKEITSERKLARUNG
171
|
| any_adam_object | 1 |
| author | Töpfer, Nadine |
| author_GND | (DE-588)1067127208 |
| author_facet | Töpfer, Nadine |
| author_role | aut |
| author_sort | Töpfer, Nadine |
| author_variant | n t nt |
| building | Verbundindex |
| bvnumber | BV042203284 |
| ctrlnum | (OCoLC)897405694 (DE-599)GBV796851263 |
| dewey-full | 571.75 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 571 - Physiology & related subjects |
| dewey-raw | 571.75 |
| dewey-search | 571.75 |
| dewey-sort | 3571.75 |
| dewey-tens | 570 - Biology |
| discipline | Biologie |
| format | Thesis Book |
| fullrecord | <?xml version="1.0" encoding="UTF-8"?><collection xmlns="http://www.loc.gov/MARC21/slim"><record><leader>01392nam a2200361 c 4500</leader><controlfield tag="001">BV042203284</controlfield><controlfield tag="003">DE-604</controlfield><controlfield tag="005">20150217 </controlfield><controlfield tag="007">t</controlfield><controlfield tag="008">141124s2014 d||| m||| 00||| eng d</controlfield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(OCoLC)897405694</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(DE-599)GBV796851263</subfield></datafield><datafield tag="040" ind1=" " ind2=" "><subfield code="a">DE-604</subfield><subfield code="b">ger</subfield></datafield><datafield tag="041" ind1="0" ind2=" "><subfield code="a">eng</subfield></datafield><datafield tag="049" ind1=" " ind2=" "><subfield code="a">DE-12</subfield><subfield code="a">DE-188</subfield></datafield><datafield tag="082" ind1="0" ind2=" "><subfield code="a">571.75</subfield><subfield code="2">22/ger</subfield></datafield><datafield tag="100" ind1="1" ind2=" "><subfield code="a">Töpfer, Nadine</subfield><subfield code="e">Verfasser</subfield><subfield code="0">(DE-588)1067127208</subfield><subfield code="4">aut</subfield></datafield><datafield tag="245" ind1="1" ind2="0"><subfield code="a">Optimization based approaches for analyzing metabolic adjustment to changing environmental conditions</subfield><subfield code="c">von Nadine Töpfer</subfield></datafield><datafield tag="264" ind1=" " ind2="1"><subfield code="c">2014</subfield></datafield><datafield tag="300" ind1=" " ind2=" "><subfield code="a">[IV], 130 S.</subfield><subfield code="b">graph. Darst.</subfield></datafield><datafield tag="336" ind1=" " ind2=" "><subfield code="b">txt</subfield><subfield code="2">rdacontent</subfield></datafield><datafield tag="337" ind1=" " ind2=" "><subfield code="b">n</subfield><subfield code="2">rdamedia</subfield></datafield><datafield tag="338" ind1=" " ind2=" "><subfield code="b">nc</subfield><subfield code="2">rdacarrier</subfield></datafield><datafield tag="500" ind1=" " ind2=" "><subfield code="a">Enth. Sonderabdr.</subfield></datafield><datafield tag="502" ind1=" " ind2=" "><subfield code="a">Potsdam, Univ., Diss., 2014</subfield></datafield><datafield tag="650" ind1="0" ind2="7"><subfield code="a">Anpassung</subfield><subfield code="0">(DE-588)4128128-7</subfield><subfield code="2">gnd</subfield><subfield code="9">rswk-swf</subfield></datafield><datafield tag="650" ind1="0" ind2="7"><subfield code="a">Stoffwechsel</subfield><subfield code="0">(DE-588)4057699-1</subfield><subfield code="2">gnd</subfield><subfield code="9">rswk-swf</subfield></datafield><datafield tag="655" ind1=" " ind2="7"><subfield code="0">(DE-588)4113937-9</subfield><subfield code="a">Hochschulschrift</subfield><subfield code="2">gnd-content</subfield></datafield><datafield tag="689" ind1="0" ind2="0"><subfield code="a">Stoffwechsel</subfield><subfield code="0">(DE-588)4057699-1</subfield><subfield code="D">s</subfield></datafield><datafield tag="689" ind1="0" ind2="1"><subfield code="a">Anpassung</subfield><subfield code="0">(DE-588)4128128-7</subfield><subfield code="D">s</subfield></datafield><datafield tag="689" ind1="0" ind2=" "><subfield code="5">DE-604</subfield></datafield><datafield tag="856" ind1="4" ind2="2"><subfield code="m">DNB Datenaustausch</subfield><subfield code="q">application/pdf</subfield><subfield code="u">http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=027642129&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA</subfield><subfield code="3">Inhaltsverzeichnis</subfield></datafield><datafield tag="999" ind1=" " ind2=" "><subfield code="a">oai:aleph.bib-bvb.de:BVB01-027642129</subfield></datafield></record></collection> |
| genre | (DE-588)4113937-9 Hochschulschrift gnd-content |
| genre_facet | Hochschulschrift |
| id | DE-604.BV042203284 |
| illustrated | Illustrated |
| indexdate | 2024-07-10T01:15:13Z |
| institution | BVB |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-027642129 |
| oclc_num | 897405694 |
| open_access_boolean | |
| owner | DE-12 DE-188 |
| owner_facet | DE-12 DE-188 |
| physical | [IV], 130 S. graph. Darst. |
| publishDate | 2014 |
| publishDateSearch | 2014 |
| publishDateSort | 2014 |
| record_format | marc |
| spelling | Töpfer, Nadine Verfasser (DE-588)1067127208 aut Optimization based approaches for analyzing metabolic adjustment to changing environmental conditions von Nadine Töpfer 2014 [IV], 130 S. graph. Darst. txt rdacontent n rdamedia nc rdacarrier Enth. Sonderabdr. Potsdam, Univ., Diss., 2014 Anpassung (DE-588)4128128-7 gnd rswk-swf Stoffwechsel (DE-588)4057699-1 gnd rswk-swf (DE-588)4113937-9 Hochschulschrift gnd-content Stoffwechsel (DE-588)4057699-1 s Anpassung (DE-588)4128128-7 s DE-604 DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=027642129&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Töpfer, Nadine Optimization based approaches for analyzing metabolic adjustment to changing environmental conditions Anpassung (DE-588)4128128-7 gnd Stoffwechsel (DE-588)4057699-1 gnd |
| subject_GND | (DE-588)4128128-7 (DE-588)4057699-1 (DE-588)4113937-9 |
| title | Optimization based approaches for analyzing metabolic adjustment to changing environmental conditions |
| title_auth | Optimization based approaches for analyzing metabolic adjustment to changing environmental conditions |
| title_exact_search | Optimization based approaches for analyzing metabolic adjustment to changing environmental conditions |
| title_full | Optimization based approaches for analyzing metabolic adjustment to changing environmental conditions von Nadine Töpfer |
| title_fullStr | Optimization based approaches for analyzing metabolic adjustment to changing environmental conditions von Nadine Töpfer |
| title_full_unstemmed | Optimization based approaches for analyzing metabolic adjustment to changing environmental conditions von Nadine Töpfer |
| title_short | Optimization based approaches for analyzing metabolic adjustment to changing environmental conditions |
| title_sort | optimization based approaches for analyzing metabolic adjustment to changing environmental conditions |
| topic | Anpassung (DE-588)4128128-7 gnd Stoffwechsel (DE-588)4057699-1 gnd |
| topic_facet | Anpassung Stoffwechsel Hochschulschrift |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=027642129&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT topfernadine optimizationbasedapproachesforanalyzingmetabolicadjustmenttochangingenvironmentalconditions |