Proteomic characterization of the cellulolytic enzyme system expressed by the extremely thermophilic bacteria Caldicellulosiruptor spp.:
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Abschlussarbeit Buch |
| Sprache: | English |
| Veröffentlicht: |
Berlin
mbv, Mensch-und-Buch-Verl.
2011
|
| Schriftenreihe: | Biological science
|
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | IX, 209 S. Ill., graph. Darst. |
| ISBN: | 9783863870829 |
Internformat
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| 100 | 1 | |a Lochner, Adriane |d 1982- |e Verfasser |0 (DE-588)1021185817 |4 aut | |
| 245 | 1 | 0 | |a Proteomic characterization of the cellulolytic enzyme system expressed by the extremely thermophilic bacteria Caldicellulosiruptor spp. |c von Adriane Lochner |
| 264 | 1 | |a Berlin |b mbv, Mensch-und-Buch-Verl. |c 2011 | |
| 300 | |a IX, 209 S. |b Ill., graph. Darst. | ||
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| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 490 | 0 | |a Biological science | |
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Datensatz im Suchindex
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|---|---|
| adam_text | IMAGE 1
CONTENTS
1 INTRODUCTION 1
1.1 BIOCONVERSION CONCEPTS FOR LIGNOCELLULOSIC BIOFUEL PRODUCTION 1
1.2 PLANT CELL WALL STRUCTURE A N D MICROBIAL DECONSTRUCTION STRATEGIES
4
1.2.1 CELLULOSE STRUCTURE A N D DECONSTRUCTION 4
1.2.2 HEMICELLULOSE STRUCTURE A N D DECONSTRUCTION 6
1.2.3 SUBSTRATES F O R THE STUDY O F BIOMASS DEGRADING MICROBES 8
1.3 ADVANTAGES O F A HIGH-TEMPERATURE BIOCONVERSION PROCESS 9
1.4 T H E POTENTIAL O F CALDICEUULOSIRAPTOR SPP. FOR THE BIOCONVERSION O
F LIGNOCELLULOSE 11
1.5 BASIC CONCEPTS O F PROTEOMICS FOR CELLULAR CHARACTERIZATIONS 12
1.5.1 T H E ROLE O F PROTEOMICS IN SYSTEMS BIOLOGY 12
1.5.2 LIQUID CHROMATOGRAPHY TANDEM MASS SPECTROMETRY ( L C - M S / M S )
13
1.5.3 QUANTITATIVE PROTEOMIC STUDIES O F MICROBIAL B I O M A S S
DECONSTRUCTION SYSTEMS 16
1.6 OBJECTIVES O F THIS DISSERTATION 17
2 MATERIALS A N D METHODS 18
2.1 MICROBIOLOGICAL METHODS 18
2.1.1 CULTIVATION O F CALDICE/LULOSIRUPTOR SPP. A N D SAMPLING 18
2.1.1.1 C. BESCII A N D C. OBSIDIANSIS SIMULTANEOUS FERMENTATIONS 18
2.1.1.2 C. OBSIDIANSIS CULTIVATION O N VARIOUS CARBON SOURCES 2 0
2.1.2 DETERMINATION O F GROWTH RATES 23
2.1.3 PREPARATION O F GLYCEROL STOCKS 2 3
2.1.4 LIVE/DEAD STAINING 2 3
2.1.5 MICROSCOPY 2 4
2.2 PREPARATION A N D QUALITY CONTROL O F C. OBSIDIANSIS GENOMIC D N A
2 4
2.2.1 ISOLATION O F GENOMIC D N A 2 4
2.2.2 AGAROSE GEL ELECTROPHORESIS 2 4
2.3 METABOLOMICS 2 5
2.3.1 DETERMINATION O F REDUCING SUGARS IN CULTURE SUPERNATANTS 2 5
2.3.2 O T H E R ANALYTICAL METHODS 2 5
2.4 PROTEIN BIOCHEMICAL METHODS 2 6
2.4.1 PROTEIN CONCENTRATION DETERMINATION 2 6
2.4.2 CONCENTRATION O F PROTEIN SOLUTIONS VIA TANGENTIAL F L O W
FILTRATION 2 6
2.4.3 GLYCOSIDE HYDROLASE ENRICHMENT VIA AFFINITY DIGEST 2 6
HTTP://D-NB.INFO/1018816461
IMAGE 2
2.4.4 CELLULASE ASSAYS 2 7
2.4.5 POLYACRYLAMIDE GEL ELECTROPHORESIS A N D Z Y M O G R A M 2 7
2.4.6 REDUCING SUGAR ASSAY FOR CELLULASE ACTIVITY IN SOLUTIONS 2 7
2.4.7 VISIBLE FILTER P A P E R DEGRADATION TEST F O R CELL-FREE CULTURE
SUPERNATANTS 2 9
2.5 PROTEOMICS METHODS 2 9
2.5.1 SAMPLE PREPARATION 2 9
2.5.1.1 PROTEIN DENATURATION WITH SODIUM DODECYL SULFATE 2 9
2.5.1.2 PROTEIN DENATURATION WITH GUANIDINIUM 3 0
2.5.2 L C - M S / M S ANALYSIS 3 0
2.5.2.1 METHOD F O R C. BESCII AND C. OBSIDIANSIS SECRETOME COMPARISON 3
0
2.5.2.2 M E T H O D FOR C. OBSIDIANSIS PROTEOME COMPARISON ACROSS CARBON
SOURCES 31
2.6 BIOINFORMATICS 31
2.6.1 EVALUATION O F MASS SPECTROMETRY DATA FOR QUANTITATIVE PROTEOMICS
31
2.6.1.1 M S DATA ANALYSIS F O R C. BESCII A N D C. OBSIDIANSIS SECRETOME
COMPARISON 31
2.6.1.2 M S DATA ANALYSIS FOR C. OBSIDIANSIS PROTEOME COMPARISON ACROSS
SUBSTRATES 3 2
2.6.2 PROTEIN D O M A I N A N D ACTIVITY PREDICTION 3 5
2.6.3 PREDICTION O F SECRETION SIGNAL SEQUENCES 3 5
3 RESULTS 3 6
3.1 MICROSCOPY IMAGES O F C. BESCII A N D C. OBSIDIANSIS CELLS O N
INSOLUBLE SUBSTRATES 3 6
3.2 VISIBLE FILTER P A P E R DEGRADATION B Y CELL-FREE CULTURE
SUPERNATANT 3 8
3.3 D N A PREPARATION FOR W H O L E G E N O M E SEQUENCING 3 9
3.3.1 QUALITY CONTROL A N D CONCENTRATION ESTIMATION 3 9
3.3.2 SEQUENCING 4 0
3.4 SECRETOME COMPARISON BETWEEN C. BESCII AND C. OBSIDIANSIS 4 0
3.4.1 GROWTH CHARACTERIZATION 4 0
3.4.2 EXTRACELLULAR PROTEOME CHARACTERIZATION 4 1
3.4.3 STATISTICAL ANALYSIS FOR SIGNIFICANTLY CHANGING PROTEINS O V E R
TIME 4 2
3.4.4 GLYCOSIDE HYDROLASE ABUNDANCE A N D D O M A I N COMPOSITION 4 5
3.4.5 CORRELATION O F CELLULASE ACTIVITY WITH M S DATA 4 8
3.4.6 SELECTIVE CELLULASE ENRICHMENT 4 9
3.4.7 S D S - P A G E ANALYSIS A N D Z Y M O G R A M 5 0
3.4.8 PROTEOMIC ANALYSIS O F THE CELLULASE-ENRICHED FRACTIONS 51
3.4.9 BIOCHEMICAL CHARACTERIZATION O F THE CELLULASE-ENRICHED FRACTIONS
5 2
3.5 CALDICELLULOSIRUPTOR METABOLOMICS 5 4
IMAGE 3
3.5.1 COMPARATIVE C. BESCII AND C. OBSIDIANSIS METABOLOMICS 5 4
3.5.1.1 ACETATE A N D LACTATE CONCENTRATIONS IN CULTURE SUPERNATANTS O V
E R TIME 54
3.5.1.2 SMALL MOLECULE CONCENTRATIONS IN STATIONARY P H A S E CULTURE
SUPERNATANTS 5 6
3.5.1.3 OLIGOSACCHARIDE CONCENTRATIONS IN CULTURE SUPERNATANTS O V E R
TIME 57
3.5.2 REDUCING SUGAR CONCENTRATIONS IN C. OBSIDIANSIS CULTURE
SUPERNATANTS O V E R TIME 59
3.6 C. OBSIDIANSIS PROTEOME COMPARISON ACROSS DIFFERENT CARBON SOURCES 6
0
3.6.1 GROWTH CHARACTERIZATION 6 0
3.6.2 PROTEIN IDENTIFICATION ACROSS SUBSTRATES A N D FRACTIONS 61
3.6.3 DATA PROCESSING A N D STATISTICAL ANALYSIS 63
3.6.4 IDENTIFICATION O F SIGNIFICANTLY CHANGING PROTEINS 6 5
3.6.5 IDENTIFICATION O F THE M O S T ABUNDANT PROTEINS ACROSS THE
SUBSTRATES 67
3.6.6 PROTEIN ABUNDANCE VARIATION O N DIFFERENT CARBON SOURCES 6 9
4 DISCUSSION 7 4
4.1 C. BESCII A N D C. OBSIDIANSIS SUBSTRATE ATTACHMENT AND GROWTH
QUANTITATION 74
4.2 CALDICELLULOSIRUPTOR G E N O M E COMPARISON 7 5
4.3 SECRETOME COMPARISON BETWEEN C. BESCII A N D C. OBSIDIANSIS 77
4.4 CALDICELLULOSIRUPTOR CELLULOSE HYDROLYSIS PRODUCTS A N D METABOLITES
84
4.5 HYDROLYSATE UTILIZATION B Y C. OBSIDIANSIS BIOFILMS 87
4.6 C. OBSIDIANSIS PROTEOME COMPARISON ACROSS DIFFERENT CARBON SOURCES
88
4.6.1 CELLOBIOSE VERSUS CRYSTALLINE CELLULOSE 88
4.6.2 AVICEL VERSUS FILTER P A P E R 9 2
4.6.3 SWITCHGRASS VERSUS CRYSTALLINE CELLULOSE 9 3
4.6.4 HIGHLY ABUNDANT PROTEINS ACROSS ALL SUBSTRATES 9 5
5 S U M M A R Y 100
6 ZUSAMMENFASSUNG 102
7 REFERENCES 104
|
| any_adam_object | 1 |
| author | Lochner, Adriane 1982- |
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| bvnumber | BV040808360 |
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| dewey-full | 572.75629364 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 572 - Biochemistry |
| dewey-raw | 572.75629364 |
| dewey-search | 572.75629364 |
| dewey-sort | 3572.75629364 |
| dewey-tens | 570 - Biology |
| discipline | Biologie |
| format | Thesis Book |
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| indexdate | 2024-07-10T00:34:20Z |
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| isbn | 9783863870829 |
| language | English |
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| spelling | Lochner, Adriane 1982- Verfasser (DE-588)1021185817 aut Proteomic characterization of the cellulolytic enzyme system expressed by the extremely thermophilic bacteria Caldicellulosiruptor spp. von Adriane Lochner Berlin mbv, Mensch-und-Buch-Verl. 2011 IX, 209 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Biological science Zugl.: Hamburg, Techn. Univ., Diss., 2011 Caldicellulosiruptor (DE-588)1028608675 gnd rswk-swf Proteomanalyse (DE-588)4596545-6 gnd rswk-swf Glykosidasen (DE-588)4299582-6 gnd rswk-swf (DE-588)4113937-9 Hochschulschrift gnd-content Caldicellulosiruptor (DE-588)1028608675 s Glykosidasen (DE-588)4299582-6 s Proteomanalyse (DE-588)4596545-6 s DE-604 DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025788272&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Lochner, Adriane 1982- Proteomic characterization of the cellulolytic enzyme system expressed by the extremely thermophilic bacteria Caldicellulosiruptor spp. Caldicellulosiruptor (DE-588)1028608675 gnd Proteomanalyse (DE-588)4596545-6 gnd Glykosidasen (DE-588)4299582-6 gnd |
| subject_GND | (DE-588)1028608675 (DE-588)4596545-6 (DE-588)4299582-6 (DE-588)4113937-9 |
| title | Proteomic characterization of the cellulolytic enzyme system expressed by the extremely thermophilic bacteria Caldicellulosiruptor spp. |
| title_auth | Proteomic characterization of the cellulolytic enzyme system expressed by the extremely thermophilic bacteria Caldicellulosiruptor spp. |
| title_exact_search | Proteomic characterization of the cellulolytic enzyme system expressed by the extremely thermophilic bacteria Caldicellulosiruptor spp. |
| title_full | Proteomic characterization of the cellulolytic enzyme system expressed by the extremely thermophilic bacteria Caldicellulosiruptor spp. von Adriane Lochner |
| title_fullStr | Proteomic characterization of the cellulolytic enzyme system expressed by the extremely thermophilic bacteria Caldicellulosiruptor spp. von Adriane Lochner |
| title_full_unstemmed | Proteomic characterization of the cellulolytic enzyme system expressed by the extremely thermophilic bacteria Caldicellulosiruptor spp. von Adriane Lochner |
| title_short | Proteomic characterization of the cellulolytic enzyme system expressed by the extremely thermophilic bacteria Caldicellulosiruptor spp. |
| title_sort | proteomic characterization of the cellulolytic enzyme system expressed by the extremely thermophilic bacteria caldicellulosiruptor spp |
| topic | Caldicellulosiruptor (DE-588)1028608675 gnd Proteomanalyse (DE-588)4596545-6 gnd Glykosidasen (DE-588)4299582-6 gnd |
| topic_facet | Caldicellulosiruptor Proteomanalyse Glykosidasen Hochschulschrift |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025788272&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT lochneradriane proteomiccharacterizationofthecellulolyticenzymesystemexpressedbytheextremelythermophilicbacteriacaldicellulosiruptorspp |