Characterization and analysis of the Oenothera plastome mutant collection:
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Abschlussarbeit Buch |
| Sprache: | English |
| Veröffentlicht: |
2014
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| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | V, 94 S. Ill., graph. Darst. |
Internformat
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| 100 | 1 | |a Massouh, Amid |e Verfasser |0 (DE-588)1067987541 |4 aut | |
| 245 | 1 | 0 | |a Characterization and analysis of the Oenothera plastome mutant collection |c by Amid Massouh |
| 264 | 1 | |c 2014 | |
| 300 | |a V, 94 S. |b Ill., graph. Darst. | ||
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| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 502 | |a Potsdam, Univ., Diss., 2014 | ||
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| 650 | 0 | 7 | |a Plastom |0 (DE-588)4357429-4 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Mutation |0 (DE-588)4170883-0 |2 gnd |9 rswk-swf |
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Datensatz im Suchindex
| _version_ | 1804152995367092224 |
|---|---|
| adam_text | INDEX
INDEX : I
ACKNOWLEDGMENTS IV
LIST OF ABBREVIATIONS V
ABSTRACT 1
1. INTRODUCTION 2
1.1 PLASTIDS AND THEIR GENOMES 2
1.1.1
PLASTIDS 2
1.1.2 CHLOROPLAST GENOME 2
1.2 REPEATS IN PLASTID GENOMES 4
1.3 REPLICATION SLIPPAGE IN PLASTID GENOME 5
1.4 HOMOLOGOUS RECOMBINATION IN PLASTIDS 6
1.5 HOT SPOTS FOR RECOMBINATION IN ORGANELLE GENOMES 7
1.6 PLASTID GENETICS AND THE UTILIZATION OF PLASTOME MUTANTS 9
1.7 ORIGIN OF PLASTOME MUTANTS 12
1.7.1 SPONTANEOUSLY OCCURRING PLASTOME MUTANTS 12
1.7.2 CHEMICALLY INDUCED MUTANTS 12
1.7.3 PHYSICALLY
INDUCED MUTANTS BY RADIATION 12
1.7.4 MUTANTS INDUCED BY NUCLEAR GENE-MEDIATED MUTAGENESIS 13
1.8 PHENOTYPES OF PLASTOME MUTANTS PRIMERILY OR SECONDARILY AFFECTED IN
PHOTOSYNTHESIS 13
1.8.1 HERBICIDE RESISTANCE 14
1.8.2 ANTIBIOTIC RESISTANCE 14
1.9 PLASTOME MUTANTS IN OENOTHERA 15
1.9.1 PLASTOME MUTANT COLLECTION IN OENOTHERA 15
1.10
THE PLASTOME MUTANT L-IOTA 16
1.10.1 PROGRAMMED RIBOSOMAL FRAMESHITING (PRF) 17
1.10.2 TRANSCRIPT SLIPPAGE 19
1.11 AIM OF THE THESIS 20
2. MATERIAL AND METHODS 22
2.1
MATERIALS 22
2.1.1
CHEMICALS 22
2.1.2 OLIGONUCLEOTIDES 22
2.1.3 ANTIBODIES 22
2.1.4
OENOTHERA STRAINS 23
2.1.4.1
OENOTHERA WILD TYPE STRAINS 23
2.1.4.2 OENOTHERA PLASTOME MUTANTS 23
2.1.4.2.1 PHENOTYPES 23
2.1.5 BACTERIAL STRAINS 27
2.2 METHODS 27
2.2.1.
GROWTH OF BIOLOGICAL MATERIAL 27
2.2.1.1
GROWTH CONDITIONS OF OENOTHERA PLANTS AND BREEDING 27
2.2.1.1.1 GROWTH OF OENOTHERA PLASTOME MUTANTS AND WILD TYPE PLANTS IN
SOIL 27
2.2.1.1.2 CROSSING
EXPERIMENT AND SEED STORAGE 28
2.2.1.1.3 PLANT MATERIAL CULTIVATION AND MAINTENANCE OF OENOTHERA
PLASTOME MUTANTS 28
2.2.1.2 BACTERIAL GROWTH CONDITIONS 28
HTTP://D-NB.INFO/1066258104
INDEX
2.2.2 ORGANELLE ANALYSIS 28
2.2.2.1 CHLOROPLAST ISOLATION FROM OENOTHERA 28
2.2.2.2 ISOLATION OF THYLAKOIDS 29
2.2.2.3 MICROSCOPY 30
2.2.3 ANALYSIS OF NUCLEIC ACIDS 30
2.2.3.1 ISOLATION OF NUCLEIC ACID 30
2.2.3.1.1 ISOLATION OF CHLOROPLAST DNA 30
2.2.3.1.2 ISOLATION OF TOTAL DNA (QIAGEN-KIT) 30
2.2.3.1.3 ISOLATION OF TOTAL DNA (CTAB/IGEPAL METHOD) 31
2.2.3.1.4 ISOLATION OF PLASMID DNA 31
2.2.3.1.5 ISOLATION OF RNA 31
2.2.3.2 PURIFICATION OF NUCLEIC ACID 32
2.2.3.2.1 RNA PURIFICATION 32
2.2.3.2.2 DNA PURIFICATION 32
2.2.3.3 AGAROSE GEL
ELECTROPHORESIS 32
2.2.3.4 CDNA SYNTHESIS 32
2.2.3.5 PCR REACTIONS 32
2.2.3.5.1 STANDARD PCR 32
2.2.3.6 TRANSFORMATION OF COLI 33
2.2.3.6.1
ELECTROTRANSFORMATION 33
2.2.3.6.2 HEAT SHOCK
TRANSFORMATION 33
2.2.4.
PROTEIN ANALYSIS 33
2.2.4.1 BRADFORD PROTEIN ASSAY 33
2.2.4.2 AMIDOBLACK PROTEIN ASSAY 33
2.2.4.3 TRIS-TRICINE SDS POLYACRYLAMIDE GEL
ELECTROPHORESIS (TRIS-TRICINE SDS-PAGE) 34
2.2.4.4 SILVER
STAINING 34
2.2.4.5 TRIS-GLYCINE ELECTROBLOTTING 34
2.2.4.6 WESTERN BLOTTING 35
2.2.4.7 FILM EXPOSURE 35
2.2.4.8 SAMPLE PREPARATION FOR LC-MS/MS ANALYSIS 35
2.2.4.8.1 IN SOLUTION DIGEST 35
2.2.4.8.2. PEPTIDES ISOLATION (STAGETIPS) 36
2.2.4.9 LIQUID CHROMATOGRAPHY LINKED TO TANDEM MASS SPECTROMETRY
(LC-MS/MS) 36
2.2.4.9.1 PROTEIN AND PEPTIDE ANALYSIS 36
2.3 DNA-SEQUENCING
APPROACHES 38
2.3.1
SANGER SEQUENCING 38
2.3.1.1 SEQUENCING
OF PCR PRODUCTS
AND PLASMID VECTORS 38
2.3.2 NEXT GENERATION SEQUENCING 38
2.3.2.1454 SEQUENCING 38
2.3.2.2 LLLUMINA SEQUENCING 38
2.3.2 PREDICTION OF MRNA SECONDARY STRUCTURES 38
3. RESULTS 39
3.1
CHARACTERIZATION OF OENOTHERA PLASTOME MUTANT COLLECTION 39
3.1.1
ESTABLISHMENT OF AN IMPROVED CHLOROPLAST ISOLATION PROTOCOL FOR
OENOTHERA 39
3.1.2 PURITY OF ISOLATED CHLOROPLASTS AND ENRICHMENT OF PTDNA 41
3.1.3 DETERMINATION OF REFERENCE SEQUENCE PLASTOMES 42
II
INDEX
3.1.3.1
ESTABLISHMENT OF ASSEMBLY AND ANNOTATION PIPELINE FOR WILD TYPE
REFERENCE PLASTOMES 42
3.1.3.1.1 DE NOVO 454 ASSEMBLIES OF THE WILD TYPE REFERENCES 42
3.1.3.1.2 RE-SEQUENCING
OF 454 ASSEMBLIES BY A REFERENCE-GUIDED ASSEMBLY OF LLLUMINA READS 43
3.1.3.2 ANALYSIS OF THE NEW WILD TYPE PLASTID REFERENCE GENOMES 44
3.1.3.2.1 GENE COMPOSITION AND ORGANIZATION OF OENOTHERA PLASTID
CHROMOSOME 44
3.1.4
DETERMINATION OF PLASTOME MUTANT ALLELS 46
3.1.4.1 MAPPING PLASTOME MUTANTS BY ASSEMBLING
TO WILD TYPE REFERENCE GENOMES 46
3.1.4.1.1 STATISTICS OF THE DE NOVO ASSEMBLIES FROM 454 SEQUENCING 47
3.1.4.1.2 STATISTICS OF THE MAPPED ASSEMBLIES FROM LLLUMINA SEQUENCING
47
3.1.4.2 MUTATION DETECTION IN PLASTID GENOME OF ANALYZED PLASTOME
MUTANTS 48
3.1.4.2.1 MUTANT LOCI PRESENT IN THE COLLECTION 52
3.1.5 CHARACTERIZATION OF L-IOTA MUTANT 60
3.1.5.1 PHENOTYPE 60
3.1.5.2 GENETIC BACKGROUND 60
3.1.5.3 OVERLAPPING CODING FRAMES OF ATPB/ATPE 62
3.1.5.4 FUSION BETWEEN ATPB AND ATPE
SUBUNITS OF ATP SYNTHASE 62
3.1.5.5 MUTATED ALLELE IN ATPB GENE 63
3.1.5.6 IMPACT OF SINGLE BASE PAIR
INSERTION ON ATP SYNTHASE PROTEIN LEVEL 64
3.1.5.7 SAMPLE
PURITY VALIDATION BY TARGETED PROTEOMIC APPROACH 69
3.1.5.8 INVESTIGATION OF ATPB GENE SEQUENCE
IN THE REGION OF L-IOTA MUTATION 71
3.1.5.8.1 SECONDARY STRUCTURES OF MRNA 72
3.1.5.8.2 IMPACT OF SINGLE ADENINE INSERTION IN POLYA TRACT ON THE LEVEL
OF TRANSCRIPTION 73
4. DISCUSSION 75
4.1
MUTATIONS IN OENOTHERA PLASTOME MUTANTS CHLOROPLAST GENOMES 75
4.2 L-IOTA PLASTOME MUTANT 79
5. REFERENCES 84
6. PUBLICATIONS
AND CONFERENCES 94
III
|
| any_adam_object | 1 |
| author | Massouh, Amid |
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| spelling | Massouh, Amid Verfasser (DE-588)1067987541 aut Characterization and analysis of the Oenothera plastome mutant collection by Amid Massouh 2014 V, 94 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Potsdam, Univ., Diss., 2014 Nachtkerze Gattung (DE-588)4171051-4 gnd rswk-swf Plastom (DE-588)4357429-4 gnd rswk-swf Mutation (DE-588)4170883-0 gnd rswk-swf (DE-588)4113937-9 Hochschulschrift gnd-content Nachtkerze Gattung (DE-588)4171051-4 s Plastom (DE-588)4357429-4 s Mutation (DE-588)4170883-0 s DE-188 DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=027799534&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Massouh, Amid Characterization and analysis of the Oenothera plastome mutant collection Nachtkerze Gattung (DE-588)4171051-4 gnd Plastom (DE-588)4357429-4 gnd Mutation (DE-588)4170883-0 gnd |
| subject_GND | (DE-588)4171051-4 (DE-588)4357429-4 (DE-588)4170883-0 (DE-588)4113937-9 |
| title | Characterization and analysis of the Oenothera plastome mutant collection |
| title_auth | Characterization and analysis of the Oenothera plastome mutant collection |
| title_exact_search | Characterization and analysis of the Oenothera plastome mutant collection |
| title_full | Characterization and analysis of the Oenothera plastome mutant collection by Amid Massouh |
| title_fullStr | Characterization and analysis of the Oenothera plastome mutant collection by Amid Massouh |
| title_full_unstemmed | Characterization and analysis of the Oenothera plastome mutant collection by Amid Massouh |
| title_short | Characterization and analysis of the Oenothera plastome mutant collection |
| title_sort | characterization and analysis of the oenothera plastome mutant collection |
| topic | Nachtkerze Gattung (DE-588)4171051-4 gnd Plastom (DE-588)4357429-4 gnd Mutation (DE-588)4170883-0 gnd |
| topic_facet | Nachtkerze Gattung Plastom Mutation Hochschulschrift |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=027799534&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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