I, microbiologist: a discovery-based course in microbial ecology and molecular evolution
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Washington, DC
ASM Press
2010
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| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | Includes bibliographical references |
| Beschreibung: | XXX, 438 S. Ill., graph. Darst. |
| ISBN: | 9781555814700 |
Internformat
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| adam_text | IMAGE 1
I, MICROBIOLOGIST
A DISCOVERY-BASED COURSE IN MICROBIAL ECOLOGY AND MOLECULAR EVOLUTION
ERIN R. SANDERS AND JEFFREY H. MILLER DEPARTMENT OF MICROBIOLOGY,
IMMUNOLOGY, AND MOLECULAR GENETICS UNIVERSITY OF CALIFORNIA, LOS ANGELES
LOS ANGELES, CALIFORNIA
WITH CONTRIBUTIONS BY
CRAIG HERBOLD,KRYSTLEZIEBELL,ANCL KAREN FLUMMERFELT
A ASM PRESS WASHINGTON, DC
IMAGE 2
CONTENTS
PREFACE XI ABOUT THE AUTHORS AND CONTRIBUTORS XVII INTRODUCTION XIX
UNIT 1
SOIL COLLECTION AND COMPOSITIONAL ANALYSIS 1 SECTION 1.1 INTRODUCTION TO
MICROBIAL ECOLOGY IN THE RHIZOSPHERE 1 SECTION 1.2 ANALYSIS OF THE
PRIMARY LITERATURE: BIOGEOGRAPHY OF SOIL BACTERIAL COMMUNITIES 9
READING ASSESSMENT 18
EXPERIMENTAL OVERVIEW 21
EXPERIMENT 1.1 SOIL COLLECTION FROM THE RHIZOSPHERE 23
EXPERIMENT 1.2 STREAK PLATE PRACTICE 25
EXPERIMENT 1.3 DETERMINE THE WATER CONTENT OF SOIL BY DRY-WEIGHT
ANALYSIS 27
EXPERIMENT 1.4 DETERMINE THE PH OF SOIL 29
UNIT 2
CULTIVATION-DEPENDENT COMMUNITY ANALYSIS 31 SECTION 2.1 ENRICHMENT
STRATEGIES THAT TARGET THE MICROBIAL INHABITANTS OF THE RHIZOSPHERE 31
SECTION 2.2 ANALYSIS OF THE PRIMARY LITERATURE: OVERCOMING THE
MICROBIAL BOTTLENECK OF THE UNCULTIVATED MAJORITY 45
READING ASSESSMENT 51
EXPERIMENTAL OVERVIEW 55
EXPERIMENT 2.1 CULTIVATION OF SOIL MICROORGANISMS: FIRST ENRICHMENT 57
EXPERIMENT 2.2 CULTIVATION OF SOIL MICROORGANISMS: SECOND ENRICHMENT 61
VII
IMAGE 3
EXPERIMENT 2.3 PURIFICATION OF MICROBIAL ISOLATES 65
EXPERIMENT 2.4 PREPARATION OF CELL SAMPLES FOR STORAGE AT -80C 67
UNIT 3
MOLECULAR ANALYSIS OF CULTIVATED BACTERIAL COMMUNITIES 69 SECTION 3.1
PCR AND SEQUENCING OF THE 16S RRNA GENE 69 READING ASSESSMENT 83
EXPERIMENTAL OVERVIEW 85
EXPERIMENT 3.1 GENOMIC DNA ISOLATION 87
EXPERIMENT 3.2 PCR OF 16S RDNA 97
EXPERIMENT 3.3 GEL ELECTROPHORESIS OF AMPLICONS 101
EXPERIMENT 3.4 PURIFICATION OF PCR PRODUCTS 105
EXPERIMENT 3.5 QUANTIFICATION OF PURIFIED PCR PRODUCTS 107
EXPERIMENT 3.6 DNA SEQUENCING OF PURIFIED 16S RDNA AMPLICONS 109
UNIT 4
PHENOTYPIC CHARACTERIZATION OF BACTERIAL ISOLATES 113 SECTION 4.1
MICROBIAL PRODUCTION OF ANTIBIOTICS AND THE EMERGENT RESISTOME 113
READING ASSESSMENT 131
SECTION 4.2 MICROBIAL CONTRIBUTIONS TO THE PRODUCTION OF BIOMASS AND
BIOFUELS 133
READING ASSESSMENT 144
EXPERIMENTAL OVERVIEW 147
EXPERIMENT 4.1 MICROSCOPIC EXAMINATION AND CHARACTERIZATION OF ISOLATES
149
EXPERIMENT 4.2 WET MOUNT PREPARATION 159
EXPERIMENT 4.3 GRAM STAINS 161
EXPERIMENT 4.4 TESTING FOR ANTIBIOTIC PRODUCTION 165
EXPERIMENT 4.5 TESTING FOR ANTIBIOTIC RESISTANCE 169
EXPERIMENT 4.6 TESTING FOR CELLULASE ACTIVITY 173
UNIT 5
CULTIVATION-INDEPENDENT COMMUNITY ANALYSIS OF SOIL MICROBIOMES 177
SECTION 5.1 ACCESSING UNCULTIVATABLE MICROBIOMES BY USING METAGENOMIC
APPROACHES 177
SECTION 5.2 ANALYSIS OF THE PRIMARY LITERATURE: THE HUMAN GUT MICROBIOME
205
VIII CONTENTS
IMAGE 4
READING ASSESSMENT 217
EXPERIMENTAL OVERVIEW 221
EXPERIMENT 5.1 ISOLATION OF METAGENOMIC DNA DIRECTLY FROM SOIL 223
EXPERIMENT 5.2 PCR AMPLIFICATION OF 16S RDNA 229
EXPERIMENT 5.3 GEL ELECTROPHORESIS OF METAGENOMIC 16S RRNA GENES 233
EXPERIMENT 5.4 PURIFICATION OF METAGENOMIC 16S RRNA GENES 237
EXPERIMENT 5.5 QUANTIFICATION OF PURIFIED METAGENOMIC PCR PRODUCTS 241
EXPERIMENT 5.6 CLONING OF PCR PRODUCTS USING THE TA-TOPO KIT 243
EXPERIMENT^ 5.7 TOPO PLASMID DNA ISOLATION FROM TRANSFORMANTS 247
EXPERIMENT 5.8 SCREENING OF TOPO CLONES BY RESTRICTION ANALYSIS 251
EXPERIMENT 5.9 DNA SEQUENCING OF TOPO CLONES CONTAINING 16S RRNA GENES
253
UNIT 6
BIOINFORMATICS ANALYSIS OF 16S RRNA GENES 257 SECTION 6.1 MATHEMATICAL
ALGORITHMS AS THE BUILDING BLOCKS OF DNA SEQUENCE ALIGNMENTS 257
SECTION 6.2 DNA SEQUENCE ALIGNMENTS IN A BLAST SEARCH 269
SECTION 6.3 MODEL-BASED ALIGNMENT TOOLS FOR 16S RRNA 283
SECTION 6.4 MULTIPLE SEQUENCE ALIGNMENTS 289
READING ASSESSMENT 297
EXPERIMENTAL OVERVIEW 301
EXPERIMENT 6.1 ASSEMBLY OF CONSENSUS DNA SEQUENCES 303
EXPERIMENT 6.2 NUCLEOTIDE BLAST SEARCH TO IDENTIFY MICROORGANISMS 309
EXPERIMENT 6.3 APPROXIMATION OF TAXONOMIC ASSIGNMENTS USING THE
RIBOSOMAL
DATABASE PROJECT 317 ,
UNIT 7
MOLECULAR EVOLUTION: PHYLOGENETIC ANALYSIS OF 16S RRNA GENES 325 SECTION
7.1 DEPICTING EVOLUTIONARY RELATIONSHIPS WITH PHYLOGENETIC TREES 325
SECTION 7.2 STATISTICAL TESTS: CONFIDENCE AND BIAS 339
SECTION 7.3 METHODS OF EVOLUTIONARY ANALYSIS 349
READING ASSESSMENT (SECTIONS 7.1 TO 7.3) 361
SECTION 7.4 RECONCILING BACTERIAL TAXONOMY: AN EVOLVING LEXICON FOR THE
21ST-CENTURY MICROBIOLOGIST 365
READING ASSESSMENT (SECTION 7.4) 392
EXPERIMENTAL OVERVIEW 393
CONTENTS IX
IMAGE 5
EXPERIMENT 7.1 TREE CONSTRUCTION USING THE RIBOSOMAL DATABASE PROJECT
395
EXPERIMENT 7.2 BUILDING PHYLOGENETIC TREES WITH MEGA 403
APPENDIX: MEDIA, SUPPLIES, AND EQUIPMENT 421
INDEX 429
CONTENTS
|
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| dewey-ones | 579 - Microorganisms, fungi & algae |
| dewey-raw | 579/.17 |
| dewey-search | 579/.17 |
| dewey-sort | 3579 217 |
| dewey-tens | 570 - Biology |
| discipline | Biologie |
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| id | DE-604.BV037214715 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T22:53:33Z |
| institution | BVB |
| isbn | 9781555814700 |
| language | English |
| lccn | 2009026843 |
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| physical | XXX, 438 S. Ill., graph. Darst. |
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| publisher | ASM Press |
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| spelling | Sanders, Erin R. Verfasser aut I, microbiologist a discovery-based course in microbial ecology and molecular evolution Erin R. Sanders and Jeffrey H. Miller Washington, DC ASM Press 2010 XXX, 438 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Includes bibliographical references Microbial ecology Textbooks Molecular evolution Textbooks Miller, Jeffrey H. Sonstige oth HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=021128707&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Sanders, Erin R. I, microbiologist a discovery-based course in microbial ecology and molecular evolution Microbial ecology Textbooks Molecular evolution Textbooks |
| title | I, microbiologist a discovery-based course in microbial ecology and molecular evolution |
| title_auth | I, microbiologist a discovery-based course in microbial ecology and molecular evolution |
| title_exact_search | I, microbiologist a discovery-based course in microbial ecology and molecular evolution |
| title_full | I, microbiologist a discovery-based course in microbial ecology and molecular evolution Erin R. Sanders and Jeffrey H. Miller |
| title_fullStr | I, microbiologist a discovery-based course in microbial ecology and molecular evolution Erin R. Sanders and Jeffrey H. Miller |
| title_full_unstemmed | I, microbiologist a discovery-based course in microbial ecology and molecular evolution Erin R. Sanders and Jeffrey H. Miller |
| title_short | I, microbiologist |
| title_sort | i microbiologist a discovery based course in microbial ecology and molecular evolution |
| title_sub | a discovery-based course in microbial ecology and molecular evolution |
| topic | Microbial ecology Textbooks Molecular evolution Textbooks |
| topic_facet | Microbial ecology Textbooks Molecular evolution Textbooks |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=021128707&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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