Host-pathogen metabolomics of Pseudomonas aeruginosa infection models:
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Abschlussarbeit Buch |
| Sprache: | English |
| Veröffentlicht: |
2013
|
| Schlagworte: | |
| Online-Zugang: | kostenfrei https://nbn-resolving.org/urn:nbn:de:bvb:91-diss-20130419-1127593-0-2 Inhaltsverzeichnis |
| Beschreibung: | XVIII, 179 S. Ill., graph. Darst. |
Internformat
MARC
| LEADER | 00000nam a2200000 c 4500 | ||
|---|---|---|---|
| 001 | BV041443297 | ||
| 003 | DE-604 | ||
| 005 | 20140110 | ||
| 007 | t | ||
| 008 | 131126s2013 ad|| m||| 00||| eng d | ||
| 035 | |a (OCoLC)864631284 | ||
| 035 | |a (DE-599)BVBBV041443297 | ||
| 040 | |a DE-604 |b ger |e rakwb | ||
| 041 | 0 | |a eng | |
| 049 | |a DE-384 |a DE-473 |a DE-703 |a DE-1051 |a DE-824 |a DE-29 |a DE-12 |a DE-91 |a DE-19 |a DE-1049 |a DE-92 |a DE-739 |a DE-898 |a DE-355 |a DE-706 |a DE-20 |a DE-1102 |a DE-M49 | ||
| 082 | 0 | |a 570 | |
| 084 | |a CHE 890d |2 stub | ||
| 084 | |a MED 730d |2 stub | ||
| 084 | |a MED 403d |2 stub | ||
| 084 | |a BIO 270d |2 stub | ||
| 084 | |a BIO 310d |2 stub | ||
| 084 | |a CHE 801d |2 stub | ||
| 100 | 1 | |a Witting, Michael |e Verfasser |4 aut | |
| 245 | 1 | 0 | |a Host-pathogen metabolomics of Pseudomonas aeruginosa infection models |c Michael Witting |
| 264 | 1 | |c 2013 | |
| 300 | |a XVIII, 179 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 502 | |a München, Techn. Univ., Diss., 2013 | ||
| 546 | |a Zsfassung in dt. Sprache | ||
| 655 | 7 | |0 (DE-588)4113937-9 |a Hochschulschrift |2 gnd-content | |
| 776 | 0 | 8 | |i Erscheint auch als |n Online-Ausgabe |o urn:nbn:de:bvb:91-diss-20130419-1127593-0-2 |
| 856 | 4 | 1 | |u http://mediatum.ub.tum.de/node?id=1127593 |x Verlag |z kostenfrei |3 Volltext |
| 856 | 4 | |u https://nbn-resolving.org/urn:nbn:de:bvb:91-diss-20130419-1127593-0-2 |x Resolving-System | |
| 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=026890016&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |3 Inhaltsverzeichnis |
| 912 | |a ebook | ||
| 999 | |a oai:aleph.bib-bvb.de:BVB01-026890016 | ||
Datensatz im Suchindex
| _version_ | 1804151563363549184 |
|---|---|
| adam_text | CONTENT
1. INTRODUCTION 1
ABSTRACT 1
1.1 METABOLOMICS - INTEGRATED STUDIES OF METABOLISM 2
1.1.1 LIFE, BIOCHEMISTRY, METABOLISM AND METABOLOMICS 2
1.1.2 METABOLOMICS AND OTHER OMICS -SCIENCE 5
1.1.3 NON-TARGETED AND TARGETED METABOLOMICS 8
1.1.4 LIPIDOMICS 8
1.2 ANALYTICAL APPROACHES - TOWARDS ULTRAHIGH RESOLUTION METABOLOMICS
AND
LIPIDOMICS 10
1.2.1 ION CYCLOTRON RESONANCE - FOURIER TRANSFORM MASS SPECTROMETRY
(ICR-FT/MS) 10
1.2.2 HYPHENATED ULTRAHIGH RESOLUTION TIME OF FLIGHT MASS SPECTROMETRY
13
1.2.3 NUCLEAR MAGNETIC RESONANCE (NMR) 15
1.2.4 COMPARISON OF THE SINGLE METHODS 17
1.3 PSEUDOMONAS AERUGINOSA - AN OPPORTUNISTIC HUMAN PATHOGEN 18
1.3.1 GENERAL OVERVIEW ON PSEUDOMONAS AERUGINOSA 18
1.3.2 PSEUDOMONAS AERUGINOSA VIRULENCE FACTORS 20
1.3.3 METABOLOMICS STUDIES ON PSEUDOMONAS 21
1.4 MODEL SYSTEMS FOR HOST-PATHOGEN INTERACTIONS 22
1.4.1 HELA AND OTHER MAMMALIAN CELL CULTURE MODELS 22
1.4.2 METABOLOMICS RESEARCH IN MAMMALIAN CELL CULTURES 23
1.4.3 CAENORHABDITIS ELEGANS 23
1.4.4 METABOLOMICS RESEARCH ON C. ELEGANS 26
1.5 PATHOMICS PROJECT AIMS AND OBJECTIVES 28
1.6 THESIS STRUCTURE 30
2. DATA ANALYSIS TOOLS FOR HOST-PATHOGEN METABOLOMICS 33
ABSTRACT 33
2.1 BIO- AND CHEMOINFORMATICS TO ASSIST METABOLOMICS RESEARCH 34
2.1.1 REVIEW ON CHEMO AND BIOINFORMATICS RESEARCH IN METABOLOMICS 34
HTTP://D-NB.INFO/1046434381
2.2 MASSTRIX: A WEB-BASED METABOLITE ANNOTATION TOOL 36
2.2.1 ANNOTATION OF MASS SPECTROMETRIC DATA 36
2.2.2 ANALYSIS OF TRANSCRIPTOMIC DATA 37
2.2.3 VISUALIZATION OF METABOLOMICS AND TRANSCRIPTOMIC DATA ON KEGG
PATHWAYS 37
2.2.4 COMPARISON OF DIFFERENT JOBS 38
2.2.5 COMPARISON AGAINST OTHER EXISTING RESOURCES 40
2.3 METABOLIC RECONSTRUCTIONS AS BASIS FOR HOST-PATHOGEN METABOLOMICS 41
2.3.1 METABOLIC RECONSTRUCTION OF PSEUDOMONAS SPECIES 42
2.3.2 METABOLIC RECONSTRUCTION OF CAENORHABDITIS ELEGANS 45
2.3.3 METABOLIC RECONSTRUCTION OF HELA CELLS 46
2.3.4 IMPROVEMENTS OF RECONSTRUCTIONS 47
2.3.5 USE OF RECONSTRUCTIONS IN HOST-PATHOGEN METABOLOMICS 47
3. TAXONOMY BASED METABOLOMICS OF PSEUDOMONAS SPECIES 51
ABSTRACT 51
3.1 PHYLOGENETICS, BACTERIAL IDENTIFICATION AND METABOLOMICS 52
3.2 CULTIVATION AND EXTRACTION OF BACTERIA 54
3.2.1 BACTERIAL CULTIVATION AND EXTRACTION 54
3.3 RESULTS 55
3.3.1 STATISTICAL ANALYSIS 55
3.3.2 BACTERIAL STRAINS COMPARED ON A METABOLOMIC LEVEL 55
3.3.3 DIFFERENT GROWTH TEMPERATURES INFLUENCE THE METABOLOME 57
3.3.4 CORE AND PAN METABOLOME OF THE GENUS PSEUDOMONAS 58
3.3.5 COMPARISON AGAINST IN SILICO METABOLOMES 62
4. C. ELEGANS - P. AERUGINOSA INFECTION MODEL 65
ABSTRACT 65
4.1 C. ELEGANS INFECTION MODEL 66
4.2 KNOWN AND UNKNOWNS - FALSE POSITIVE FILTERING OF METABOLITE
ANNOTATIONS 67
4.2.1 PREDICTION OF CHEMICAL PROPERTIES TO BUILD RETENTION TIME MODELS
70
4.2.2 IDENTIFICATION OF FRAGMENTS, ADDUCTS AND ISOTOPES 78
4.2.3 LIPID IDENTIFICATION WITH AUTOMS AND IN SILICO FRAGMENTATION 79
4.2.4 MASS DIFFERENCE NETWORKING FOR IMPROVED METABOLITE ANNOTATION 84
4.2.5 ALIGNMENT OF ICR-FT/MS AND UHPLC-UHR-TOF-MS DATA 86
4.3 BIOLOGICAL INTERPRETATION OF THE C. ELEGANS INFECTION MODEL 88
4.3.1 STATISTICAL DATA ANALYSIS 88
4.3.2 SURVIVAL OF C. ELEGANS CHALLENGED WITH DIFFERENT PATHOGENS 89
4.3.3 ICR-FT/MS METABOLIC PROFILING SEPARATES DIFFERENT SAMPLE
CONDITIONS 90
4.3.4 INFECTION WITH P. AERUGINOSA LEADS TO INCREASED ^-OXIDATION 95
4.3.5 SYNTHESIS OF PHOSPHOLIPID SPECIES DURING PSEUDOMONAS INFECTION 98
4.3.6 METABOLIC MARKERS OF INCREASED AUTOPHAGY 100
4.3.7 RESISTANCE OF DAF-2 WORMS TO INFECTION 100
4.3.8 POTENTIAL INFECTION BIOMARKER 102
4.3.9 METABOLIC SIGNATURES IN LONG-LIVED C. ELEGANS 105
4.3.10 ROLE OF P. AERUGINOSA PEC7 DURING INFECTION 106
4.3.11 PROBIOTIC BACTERIA PROTECTS C. ELEGANS FROM P. AERUGINOSA
INFECTION 107
5. DEVELOPMENT OF EXTRACTION METHODS FOR NON-TARGETED METABOLOMICS OF
THE HELA-P.
AERUGINOSA HOST-PATHOGEN MODEL ILL
ABSTRACT ILL
5.1 HELA CELLS AS HOST ORGANISM FOR P. AERUGINOSA INFECTION 112
5.2 SAMPLING AND SAMPLE PREPARATION 112
5.2.1 PREQUISITE FOR METABOLOMICS SAMPLES 112
5.2.2 QUENCHING OF METABOLISM 113
5.2.3 CELL LYSIS TECHNIQUES AND METABOLITE EXTRACTION 113
5.2.4 SOLID PHASE EXTRACTION AND SAMPLE CONCENTRATION 114
5.3 DEVELOPMENT OF AN EXTRACTION METHOD FOR A HELA CELL INFECTION MODEL
114
5.3.1 METABOLITE EXTRACTION FROM BACTERIAL PELLETS 114
5.3.2 METABOLITE EXTRACTION FROM CELL CULTURE MEDIUM CONTAINING HELA
CELLS 114
5.3.3 RESULTS 115
5.3.4 METABOLITE EXTRACTION FROM P. AERUGINOSA PELLETS 115
5.3.5 METABOLITE EXTRACTION FROM HELA CELLS 116
5.3.6 FINAL METHODS 117
5.4 INFECTION WITH P. AERUGINOSA AFFECTS THE HELA CELL LIPIDOME 118
5.5 EXOY
- A POTENT CELLULAR TOXIN 120
5.6 EFFECTS OF EXOY ON THE HELA CELL METABOLOME 121
6. CONCLUSION 127
ABSTRACT 127
6.1 METABOLOMICS - A FAST GROWING RESEARCH AREA 128
6.2 IMPROVED ANNOTATION AND DATA ANALYSIS METHODS 128
6.3 ULTRAHIGH RESOLUTION ANALYTICAL METHODS 129
6.4 METABOLOMICS BASED PHYLOGENY OF PSEUDOMONAS SPECIES 130
6.5 C. ELEGANS AS CONVENIENT MODEL FOR HOST-PATHOGEN RESEARCH 132
6.6 HELA CELL MODEL 137
6.7 COMPARISON OF THE INFECTION MODELS 137
LITERATURE 141
LIST OF FIGURES 156
LIST OF TABLES 159
LIST OF EQUATIONS 160
APPENDIX 161
USED INSTRUMENTS 162
ICR-FT/MS 162
U H PLC-U
HR-TOF-MS 162
GC-FID 162
OTHER INSTRUMENTS 162
USED CHEMICALS 163
SOLVENTS 163
BUFFER SALTS 163
CHEMICALS FOR SYNTHESIS 163
STANDARDS 163
COLUMNS 166
LC COLUMNS 166
GC COLUMNS 166
METHODS 167
CULTIVATION AND EXTRACTION OF C. ELEGANS 167
HELA INFECTION PROTOCOL 167
LIPID EXTRACTION FROM HELA CELLS 168
CULTIVATION AND EXTRACTION OF HELA CELLS EXPRESSING EXOY 168
METABOLIC PROFILING USING DI-ICR-FT/MS 168
DATA PROCESSING DI-ICR-FT/MS 169
METABOLIC PROFILING USING UHPLC-UHR-TOF-MS 169
LIPID PROFILING USING UHPLC-UHR-TOF-MS (C. ELEGANS) 170
LIPID PROFILING USING UHPLC-UHR-TOF-MS (HELA) 170
DATA PROCESSING UHPLC-UHR-TOF-MS 171
FATTY ACID PROFILING 172
DATA ANALYSIS SCRIPTS 173
ICR-FT/MS SPECTRA EXPORT 173
EXPORT OF MS/MS SPECTRA GENERATE BY AUTOMS 173
PERL SCRIPTS 174
ICR-FT/MS AND LC-MS ALIGNMENT 174
CONVERSION OF ASCII FILES TO METFRAG BATCHFILE 175
CONVERSION OF ASCII FILES TO LIBRARY 176
ALIGNMENT OF LC-MS AND LC-MS/MS FEATURES FROM AUTOMS 177
CURRICULUM VITAE 178
|
| any_adam_object | 1 |
| author | Witting, Michael |
| author_facet | Witting, Michael |
| author_role | aut |
| author_sort | Witting, Michael |
| author_variant | m w mw |
| building | Verbundindex |
| bvnumber | BV041443297 |
| classification_tum | CHE 890d MED 730d MED 403d BIO 270d BIO 310d CHE 801d |
| collection | ebook |
| ctrlnum | (OCoLC)864631284 (DE-599)BVBBV041443297 |
| dewey-full | 570 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 570 - Biology |
| dewey-raw | 570 |
| dewey-search | 570 |
| dewey-sort | 3570 |
| dewey-tens | 570 - Biology |
| discipline | Biologie Chemie Medizin |
| format | Thesis Book |
| fullrecord | <?xml version="1.0" encoding="UTF-8"?><collection xmlns="http://www.loc.gov/MARC21/slim"><record><leader>01735nam a2200421 c 4500</leader><controlfield tag="001">BV041443297</controlfield><controlfield tag="003">DE-604</controlfield><controlfield tag="005">20140110 </controlfield><controlfield tag="007">t</controlfield><controlfield tag="008">131126s2013 ad|| m||| 00||| eng d</controlfield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(OCoLC)864631284</subfield></datafield><datafield tag="035" ind1=" " ind2=" "><subfield code="a">(DE-599)BVBBV041443297</subfield></datafield><datafield tag="040" ind1=" " ind2=" "><subfield code="a">DE-604</subfield><subfield code="b">ger</subfield><subfield code="e">rakwb</subfield></datafield><datafield tag="041" ind1="0" ind2=" "><subfield code="a">eng</subfield></datafield><datafield tag="049" ind1=" " ind2=" "><subfield code="a">DE-384</subfield><subfield code="a">DE-473</subfield><subfield code="a">DE-703</subfield><subfield code="a">DE-1051</subfield><subfield code="a">DE-824</subfield><subfield code="a">DE-29</subfield><subfield code="a">DE-12</subfield><subfield code="a">DE-91</subfield><subfield code="a">DE-19</subfield><subfield code="a">DE-1049</subfield><subfield code="a">DE-92</subfield><subfield code="a">DE-739</subfield><subfield code="a">DE-898</subfield><subfield code="a">DE-355</subfield><subfield code="a">DE-706</subfield><subfield code="a">DE-20</subfield><subfield code="a">DE-1102</subfield><subfield code="a">DE-M49</subfield></datafield><datafield tag="082" ind1="0" ind2=" "><subfield code="a">570</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">CHE 890d</subfield><subfield code="2">stub</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">MED 730d</subfield><subfield code="2">stub</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">MED 403d</subfield><subfield code="2">stub</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">BIO 270d</subfield><subfield code="2">stub</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">BIO 310d</subfield><subfield code="2">stub</subfield></datafield><datafield tag="084" ind1=" " ind2=" "><subfield code="a">CHE 801d</subfield><subfield code="2">stub</subfield></datafield><datafield tag="100" ind1="1" ind2=" "><subfield code="a">Witting, Michael</subfield><subfield code="e">Verfasser</subfield><subfield code="4">aut</subfield></datafield><datafield tag="245" ind1="1" ind2="0"><subfield code="a">Host-pathogen metabolomics of Pseudomonas aeruginosa infection models</subfield><subfield code="c">Michael Witting</subfield></datafield><datafield tag="264" ind1=" " ind2="1"><subfield code="c">2013</subfield></datafield><datafield tag="300" ind1=" " ind2=" "><subfield code="a">XVIII, 179 S.</subfield><subfield code="b">Ill., 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="502" ind1=" " ind2=" "><subfield code="a">München, Techn. Univ., Diss., 2013</subfield></datafield><datafield tag="546" ind1=" " ind2=" "><subfield code="a">Zsfassung in dt. Sprache</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="776" ind1="0" ind2="8"><subfield code="i">Erscheint auch als</subfield><subfield code="n">Online-Ausgabe</subfield><subfield code="o">urn:nbn:de:bvb:91-diss-20130419-1127593-0-2</subfield></datafield><datafield tag="856" ind1="4" ind2="1"><subfield code="u">http://mediatum.ub.tum.de/node?id=1127593</subfield><subfield code="x">Verlag</subfield><subfield code="z">kostenfrei</subfield><subfield code="3">Volltext</subfield></datafield><datafield tag="856" ind1="4" ind2=" "><subfield code="u">https://nbn-resolving.org/urn:nbn:de:bvb:91-diss-20130419-1127593-0-2</subfield><subfield code="x">Resolving-System</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=026890016&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA</subfield><subfield code="3">Inhaltsverzeichnis</subfield></datafield><datafield tag="912" ind1=" " ind2=" "><subfield code="a">ebook</subfield></datafield><datafield tag="999" ind1=" " ind2=" "><subfield code="a">oai:aleph.bib-bvb.de:BVB01-026890016</subfield></datafield></record></collection> |
| genre | (DE-588)4113937-9 Hochschulschrift gnd-content |
| genre_facet | Hochschulschrift |
| id | DE-604.BV041443297 |
| illustrated | Illustrated |
| indexdate | 2024-07-10T00:56:48Z |
| institution | BVB |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-026890016 |
| oclc_num | 864631284 |
| open_access_boolean | 1 |
| owner | DE-384 DE-473 DE-BY-UBG DE-703 DE-1051 DE-824 DE-29 DE-12 DE-91 DE-BY-TUM DE-19 DE-BY-UBM DE-1049 DE-92 DE-739 DE-898 DE-BY-UBR DE-355 DE-BY-UBR DE-706 DE-20 DE-1102 DE-M49 DE-BY-TUM |
| owner_facet | DE-384 DE-473 DE-BY-UBG DE-703 DE-1051 DE-824 DE-29 DE-12 DE-91 DE-BY-TUM DE-19 DE-BY-UBM DE-1049 DE-92 DE-739 DE-898 DE-BY-UBR DE-355 DE-BY-UBR DE-706 DE-20 DE-1102 DE-M49 DE-BY-TUM |
| physical | XVIII, 179 S. Ill., graph. Darst. |
| psigel | ebook |
| publishDate | 2013 |
| publishDateSearch | 2013 |
| publishDateSort | 2013 |
| record_format | marc |
| spelling | Witting, Michael Verfasser aut Host-pathogen metabolomics of Pseudomonas aeruginosa infection models Michael Witting 2013 XVIII, 179 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier München, Techn. Univ., Diss., 2013 Zsfassung in dt. Sprache (DE-588)4113937-9 Hochschulschrift gnd-content Erscheint auch als Online-Ausgabe urn:nbn:de:bvb:91-diss-20130419-1127593-0-2 http://mediatum.ub.tum.de/node?id=1127593 Verlag kostenfrei Volltext https://nbn-resolving.org/urn:nbn:de:bvb:91-diss-20130419-1127593-0-2 Resolving-System DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=026890016&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Witting, Michael Host-pathogen metabolomics of Pseudomonas aeruginosa infection models |
| subject_GND | (DE-588)4113937-9 |
| title | Host-pathogen metabolomics of Pseudomonas aeruginosa infection models |
| title_auth | Host-pathogen metabolomics of Pseudomonas aeruginosa infection models |
| title_exact_search | Host-pathogen metabolomics of Pseudomonas aeruginosa infection models |
| title_full | Host-pathogen metabolomics of Pseudomonas aeruginosa infection models Michael Witting |
| title_fullStr | Host-pathogen metabolomics of Pseudomonas aeruginosa infection models Michael Witting |
| title_full_unstemmed | Host-pathogen metabolomics of Pseudomonas aeruginosa infection models Michael Witting |
| title_short | Host-pathogen metabolomics of Pseudomonas aeruginosa infection models |
| title_sort | host pathogen metabolomics of pseudomonas aeruginosa infection models |
| topic_facet | Hochschulschrift |
| url | http://mediatum.ub.tum.de/node?id=1127593 https://nbn-resolving.org/urn:nbn:de:bvb:91-diss-20130419-1127593-0-2 http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=026890016&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT wittingmichael hostpathogenmetabolomicsofpseudomonasaeruginosainfectionmodels |