Kooperativer Bibliotheksverbund

UID:

Format: 1 online resource (XX, 552 p.)

Edition: 1st ed. 2009.

ISBN: 1-60327-853-2

Series Statement: Methods in Molecular Biology, 532

Content: Horizontal gene transfer (HGT) events encompass processes as varied as the exchange of genetic material between microbes coexisting in the same environment, between symbiotic bacteria and their eukaryotic hosts, and the evolution of organelles by symbiosis, in which whole genomes are acquired. In Horizontal Gene Transfer: Genomes in Flux, expert researchers contribute an overview of HGT concepts as well as specific case histories that highlight the most current progress to inspire future work. Divided into three sections, the volume begins with an overview of terminology, concepts and the implications of HGT on current evolutionary thought and philosophy, and continues with methods involving computer and bioinformatics analyses of genomic data as well as molecular biology techniques for identifying, quantifying, and differentiating instances of HGT. A section of case studies follows, which provides detailed accounts of how HGT has shaped evolution across the diversity of organisms and organismal lineages. As a volume of the highly successful Methods in Molecular Biology™ series, this work provides the kind of detailed description and implementation advice that is crucial for getting optimal results. Cutting-edge and thoroughly detailed, Horizontal Gene Transfer: Genomes in Flux examines how HGT has contributed to genome evolution and how understanding HGT impacts our ability to accurately reconstruct and comprehend the web-like evolutionary history in order to aid scientists in furthering their own research.

Note: Bibliographic Level Mode of Issuance: Monograph , Gene Transfer: Who Benefits? -- Definitions, Philosophy, and Implications of HGT -- Defining the Mobilome -- The Interplay of Homologous Recombination and Horizontal Gene Transfer in Bacterial Speciation -- Epistemological Impacts of Horizontal Gene Transfer on Classification in Microbiology -- Persistence Mechanisms of Conjugative Plasmids -- The Integron/Gene Cassette System: An Active Player in Bacterial Adaptation -- Ancient Gene Transfer as a Tool in Phylogenetic Reconstruction -- The Tree of Life Viewed Through the Contents of Genomes -- Horizontal Gene Transfer and the Evolution of Methanogenic Pathways -- Genome Acquisition in Horizontal Gene Transfer: Symbiogenesis and Macromolecular Sequence Analysis -- Methods -- Detection and Quantitative Assessment of Horizontal Gene Transfer -- Composition-Based Methods to Identify Horizontal Gene Transfer -- Testing Phylogenetic Methods to Identify Horizontal Gene Transfer -- Untangling Hybrid Phylogenetic Signals: Horizontal Gene Transfer and Artifacts of Phylogenetic Reconstruction -- Construction and Use of Flow Cytometry Optimized Plasmid-Sensor Strains -- Experimental Evolution of an Essential Bacillus Gene in an E. coli Host -- Mass Action Models Describing Extant Horizontal Transfer of Plasmids: Inferences and Parameter Sensitivities -- Case Studies -- Interdomain Transfers of Sugar Transporters Overcome Barriers to Gene Expression -- The Role of Horizontal Gene Transfer in Photosynthesis, Oxygen Production, and Oxygen Tolerance -- Horizontal Gene Transfer in Cyanobacterial Signature Genes -- Population Genomics and the Bacterial Species Concept -- A Critique of Prokaryotic Species Concepts -- What Antimicrobial Resistance Has Taught Us About Horizontal Gene Transfer -- Potential for Horizontal Gene Transfer in Microbial Communities of the Terrestrial Subsurface -- Horizontal Gene Transfer and Mobile Genetic Elements in Marine Systems -- Horizontal Gene Transfer in Metal and Radionuclide Contaminated Soils -- Horizontal Gene Transfer Between Microbial Eukaryotes -- Horizontal Gene Transfer in Eukaryotic Parasites: A Case Study of Entamoeba histolytica and Trichomonas vaginalis -- Role of Horizontal Gene Transfer in the Evolution of Photosynthetic Eukaryotes and Their Plastids -- Role of Horizontal Gene Transfer in the Evolution of Plant Parasitism Among Nematodes. , English

Additional Edition: ISBN 1-60327-852-4

Language: English

DOI: 10.1007/978-1-60327-853-9

UID:

Format: 1 online resource (XX, 552 p.)

Edition: 1st ed. 2009.

ISBN: 1-60327-853-2

Series Statement: Methods in Molecular Biology, 532

Content: Horizontal gene transfer (HGT) events encompass processes as varied as the exchange of genetic material between microbes coexisting in the same environment, between symbiotic bacteria and their eukaryotic hosts, and the evolution of organelles by symbiosis, in which whole genomes are acquired. In Horizontal Gene Transfer: Genomes in Flux, expert researchers contribute an overview of HGT concepts as well as specific case histories that highlight the most current progress to inspire future work. Divided into three sections, the volume begins with an overview of terminology, concepts and the implications of HGT on current evolutionary thought and philosophy, and continues with methods involving computer and bioinformatics analyses of genomic data as well as molecular biology techniques for identifying, quantifying, and differentiating instances of HGT. A section of case studies follows, which provides detailed accounts of how HGT has shaped evolution across the diversity of organisms and organismal lineages. As a volume of the highly successful Methods in Molecular Biology™ series, this work provides the kind of detailed description and implementation advice that is crucial for getting optimal results. Cutting-edge and thoroughly detailed, Horizontal Gene Transfer: Genomes in Flux examines how HGT has contributed to genome evolution and how understanding HGT impacts our ability to accurately reconstruct and comprehend the web-like evolutionary history in order to aid scientists in furthering their own research.

Note: Bibliographic Level Mode of Issuance: Monograph , Gene Transfer: Who Benefits? -- Definitions, Philosophy, and Implications of HGT -- Defining the Mobilome -- The Interplay of Homologous Recombination and Horizontal Gene Transfer in Bacterial Speciation -- Epistemological Impacts of Horizontal Gene Transfer on Classification in Microbiology -- Persistence Mechanisms of Conjugative Plasmids -- The Integron/Gene Cassette System: An Active Player in Bacterial Adaptation -- Ancient Gene Transfer as a Tool in Phylogenetic Reconstruction -- The Tree of Life Viewed Through the Contents of Genomes -- Horizontal Gene Transfer and the Evolution of Methanogenic Pathways -- Genome Acquisition in Horizontal Gene Transfer: Symbiogenesis and Macromolecular Sequence Analysis -- Methods -- Detection and Quantitative Assessment of Horizontal Gene Transfer -- Composition-Based Methods to Identify Horizontal Gene Transfer -- Testing Phylogenetic Methods to Identify Horizontal Gene Transfer -- Untangling Hybrid Phylogenetic Signals: Horizontal Gene Transfer and Artifacts of Phylogenetic Reconstruction -- Construction and Use of Flow Cytometry Optimized Plasmid-Sensor Strains -- Experimental Evolution of an Essential Bacillus Gene in an E. coli Host -- Mass Action Models Describing Extant Horizontal Transfer of Plasmids: Inferences and Parameter Sensitivities -- Case Studies -- Interdomain Transfers of Sugar Transporters Overcome Barriers to Gene Expression -- The Role of Horizontal Gene Transfer in Photosynthesis, Oxygen Production, and Oxygen Tolerance -- Horizontal Gene Transfer in Cyanobacterial Signature Genes -- Population Genomics and the Bacterial Species Concept -- A Critique of Prokaryotic Species Concepts -- What Antimicrobial Resistance Has Taught Us About Horizontal Gene Transfer -- Potential for Horizontal Gene Transfer in Microbial Communities of the Terrestrial Subsurface -- Horizontal Gene Transfer and Mobile Genetic Elements in Marine Systems -- Horizontal Gene Transfer in Metal and Radionuclide Contaminated Soils -- Horizontal Gene Transfer Between Microbial Eukaryotes -- Horizontal Gene Transfer in Eukaryotic Parasites: A Case Study of Entamoeba histolytica and Trichomonas vaginalis -- Role of Horizontal Gene Transfer in the Evolution of Photosynthetic Eukaryotes and Their Plastids -- Role of Horizontal Gene Transfer in the Evolution of Plant Parasitism Among Nematodes. , English

Additional Edition: ISBN 1-60327-852-4

Language: English

DOI: 10.1007/978-1-60327-853-9

UID:

Format: 1 online resource (XX, 552 p.)

Edition: 1st ed. 2009.

ISBN: 1-60327-853-2

Series Statement: Methods in Molecular Biology, 532

Content: Horizontal gene transfer (HGT) events encompass processes as varied as the exchange of genetic material between microbes coexisting in the same environment, between symbiotic bacteria and their eukaryotic hosts, and the evolution of organelles by symbiosis, in which whole genomes are acquired. In Horizontal Gene Transfer: Genomes in Flux, expert researchers contribute an overview of HGT concepts as well as specific case histories that highlight the most current progress to inspire future work. Divided into three sections, the volume begins with an overview of terminology, concepts and the implications of HGT on current evolutionary thought and philosophy, and continues with methods involving computer and bioinformatics analyses of genomic data as well as molecular biology techniques for identifying, quantifying, and differentiating instances of HGT. A section of case studies follows, which provides detailed accounts of how HGT has shaped evolution across the diversity of organisms and organismal lineages. As a volume of the highly successful Methods in Molecular Biology™ series, this work provides the kind of detailed description and implementation advice that is crucial for getting optimal results. Cutting-edge and thoroughly detailed, Horizontal Gene Transfer: Genomes in Flux examines how HGT has contributed to genome evolution and how understanding HGT impacts our ability to accurately reconstruct and comprehend the web-like evolutionary history in order to aid scientists in furthering their own research.

Note: Bibliographic Level Mode of Issuance: Monograph , Gene Transfer: Who Benefits? -- Definitions, Philosophy, and Implications of HGT -- Defining the Mobilome -- The Interplay of Homologous Recombination and Horizontal Gene Transfer in Bacterial Speciation -- Epistemological Impacts of Horizontal Gene Transfer on Classification in Microbiology -- Persistence Mechanisms of Conjugative Plasmids -- The Integron/Gene Cassette System: An Active Player in Bacterial Adaptation -- Ancient Gene Transfer as a Tool in Phylogenetic Reconstruction -- The Tree of Life Viewed Through the Contents of Genomes -- Horizontal Gene Transfer and the Evolution of Methanogenic Pathways -- Genome Acquisition in Horizontal Gene Transfer: Symbiogenesis and Macromolecular Sequence Analysis -- Methods -- Detection and Quantitative Assessment of Horizontal Gene Transfer -- Composition-Based Methods to Identify Horizontal Gene Transfer -- Testing Phylogenetic Methods to Identify Horizontal Gene Transfer -- Untangling Hybrid Phylogenetic Signals: Horizontal Gene Transfer and Artifacts of Phylogenetic Reconstruction -- Construction and Use of Flow Cytometry Optimized Plasmid-Sensor Strains -- Experimental Evolution of an Essential Bacillus Gene in an E. coli Host -- Mass Action Models Describing Extant Horizontal Transfer of Plasmids: Inferences and Parameter Sensitivities -- Case Studies -- Interdomain Transfers of Sugar Transporters Overcome Barriers to Gene Expression -- The Role of Horizontal Gene Transfer in Photosynthesis, Oxygen Production, and Oxygen Tolerance -- Horizontal Gene Transfer in Cyanobacterial Signature Genes -- Population Genomics and the Bacterial Species Concept -- A Critique of Prokaryotic Species Concepts -- What Antimicrobial Resistance Has Taught Us About Horizontal Gene Transfer -- Potential for Horizontal Gene Transfer in Microbial Communities of the Terrestrial Subsurface -- Horizontal Gene Transfer and Mobile Genetic Elements in Marine Systems -- Horizontal Gene Transfer in Metal and Radionuclide Contaminated Soils -- Horizontal Gene Transfer Between Microbial Eukaryotes -- Horizontal Gene Transfer in Eukaryotic Parasites: A Case Study of Entamoeba histolytica and Trichomonas vaginalis -- Role of Horizontal Gene Transfer in the Evolution of Photosynthetic Eukaryotes and Their Plastids -- Role of Horizontal Gene Transfer in the Evolution of Plant Parasitism Among Nematodes. , English

Additional Edition: ISBN 1-60327-852-4

Language: English

DOI: 10.1007/978-1-60327-853-9

UID:

Format: 1 online resource (494 p.)

ISBN: 1-86094-983-5

Series Statement: Series on advances in bioinformatics and computational biology, v. 7

Content: Over 500 prokaryotic genomes have been sequenced to date, and thousands more have been planned for the next few years. While these genomic sequence data provide unprecedented opportunities for biologists to study the world of prokaryotes, they also raise extremely challenging issues such as how to decode the rich information encoded in these genomes. This comprehensive volume includes a collection of cohesively written chapters on prokaryotic genomes, their organization and evolution, the information they encode, and the computational approaches needed to derive such information. A comparative

Note: Description based upon print version of record. , Preface; CONTENTS; List of Contributors; Acknowledgments; 1. General Characteristics of Prokaryotic Genomes Jan Mr ́azek and Anne O. Summers; 1. Introduction; 1.1. The Replicon Concept and Classification of Replicons; 1.2. Physical Organization of Replicons in the Cell; 2. Overall Properties of Prokaryotic Chromosomes; 2.1. Size and Gene Content; 2.2. Why Are Prokaryotic Chromosomes Small?; 2.3. G+C Content; 2.4. Oligonucleotide Composition and Genome Signature; 2.5. Amino Acid Composition and Adaptation to Growth at High Temperatures; 3. Heterogeneity of Prokaryotic Chromosomes , 3.1. Intrachromosomal Variance of Nucleotide and Oligonucleotide Composition3.2. Synonymous Codon Usage; 3.3. Identification of Genomic Islands and Lateral Gene Transfer Events; 3.4. G-C Skew; 4. Repeats in Prokaryotic Genomes; 4.1. Large Repeats and Duplications; 4.2. Transposons and Insertion Sequences; 4.3. Integrons; 4.4. Chimeric Mobile Elements: Conjugative Transposons, ICEs, Plasmid-Prophages, Transposon-Prophages, Genomic Islands, and Genetic Litter; 4.5. Retrons; 4.6. Short Dispersed Repeats; 4.7. Simple Sequence Repeats; 4.8. CRISPR Repeats; 5. Further Reading; Acknowledgments , 2. Genes in Prokaryotic Genomes and Their Computational Prediction Rajeev K. Azad1. Introduction; 2. Inhomogeneous Markov Models; 2.1. The GeneMark Program; 3. Interpolated Markov Models; 3.1. The Glimmer Program; 3.2. Using Deleted Interpolation in Gene Prediction; 4. Hidden Markov Models; 4.1. The Forward-Backward Algorithm; 4.2. The Viterbi Algorithm; 4.3. HMM Training; 4.4. The ECOPARSE Program; 4.5. The GeneHacker Program; 4.6. HMM Versions of the GeneMark Program; 5. Fourier Transform Methods; 5.1. The GeneScan Program; 5.2. The Lengthen-Shu.e Program; 6. Self-Organizing Maps , 6.1. The RescueNet Program7. Directed Acyclic Graphs; 7.1. The FrameD Program; 8. Linear Discriminant Function; 8.1. The ZCURVE Program; 9. Unsupervised Model Training: The Self-Learning Algorithms; 9.1. The GeneMark-Genesis Program; 9.2. The GeneMarkS Program; 9.3. The MED Program; 10. Using Similarity Search in Gene Prediction; 10.1. The ORPHEUS Program; 10.2. The CRITICA Program; 10.3. The BDGF Program; 10.4. The EasyGene Program; 10.5. The GISMO Program; 11. Gene Start Prediction; 12. Resolving Overlapping Genes; 13. Non-coding RNA Gene Prediction; 14. Assessing Gene Prediction Programs , 15. Discussion16. Further Reading; Acknowledgments; 3. Evolution of the Genetic Code: Computational Methods and Inferences Greg Fournier; 1. Introduction; 1.1. The Amino Acids; 1.2. Codon Designations; 1.3. Transfer RNA; 1.4. Aminoacyl-tRNA Synthetases; 2. Major Methods and Algorithms: Variations of the Genetic Code; 2.1. Non-canonical Codes; 2.2. Selenocysteine; 2.3. Pyrrolysine; 2.4. The Sep System; 2.5. Asparagine and Glutamine; 2.6. Evolutionary Considerations; 2.7. Nanoarchaeal tRNA; 3. Major Methods and Algorithms: Models of Genetic Code Evolution; 3.1. Overview , 3.2. Physiochemical Models , English

Additional Edition: ISBN 1-86094-982-7

Language: English