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The evolution and emergence of RNA viruses / / Edward C. Holmes
| The evolution and emergence of RNA viruses / / Edward C. Holmes |
| Autore | Holmes Edward C. |
| Pubbl/distr/stampa | Oxford, England : , : Oxford University Press, , 2009 |
| Descrizione fisica | 1 online resource (267 p.) |
| Disciplina | 579.25 |
| Collana | Oxford Series in Ecology and Evolution |
| Soggetto topico |
RNA viruses
Viruses - Evolution Viral genetics Virus diseases |
| ISBN | 0-19-154941-X |
| Formato | Materiale a stampa  |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Contents; 1 Introduction; 1.1 Why study RNA virus evolution?; 1.1.1 Ways to study viral evolution; 1.1.2 The scope of this book; 1.2 RNA viruses and evolutionary biology; 1.2.1 The RNA virus world; 1.3 The basics of viral biology; 1.3.1 A cursory history of virology; 1.3.2 Virology 101; 1.3.3 Exploring the virosphere; 2 The origins of RNA viruses; 2.1 Introduction; 2.1.1 The perils of deep viral phylogeny; 2.2 Theories for the origin of RNA viruses; 2.2.1 The regressive origin theory; 2.2.2 RNA viruses as escaped genes; 2.2.3 RNA viruses and the RNA world; 2.2.4 Eigen's paradox
2.2.5 The taxonomic distribution of RNA viruses2.2.6 Conserved protein structures; 2.3 Deep phylogenetic relationships among RNA viruses; 2.3.1 The 'higher-order' relationships of RNA viruses; 2.3.2 Phylogenies based on genome organization; 2.3.3 Phylogenies based on protein structure; 2.4 RNA viruses and the evolution of the genetic code; 3 The mechanisms of RNA virus evolution; 3.1 The evolutionary dynamics of RNA viruses; 3.1.1 Mutation rates in RNA viruses and their determinants; 3.1.2 A comparison of substitution rates in viruses; 3.1.3 Differences in viral generation time 3.1.4 Slowly evolving RNA viruses?3.1.5 Rapidly evolving ssDNA viruses; 3.1.6 What sets the rate of RNA virus evolution?; 3.1.7 Trade-offs and the evolution of mutation rates; 3.1.8 Mutation rates and mutational loads; 3.1.9 Are RNA viruses trapped by high mutation rates?; 3.2 Recombination and reassortment in RNA virus evolution; 3.2.1 Recombination frequency in RNA viruses; 3.2.2 Detecting recombination in RNA viruses; 3.2.3 What determines the rate of recombination in RNA viruses?; 3.2.4 Recombination and deleterious mutation 3.3 Natural selection, genetic drift, and the genetics of adaptation3.3.1 Effective population sizes in viral evolution; 3.3.2 Transmission bottlenecks; 3.3.3 The dynamics of allele fixation: estimating selection coefficients; 3.3.4 The importance of hitch-hiking; 3.3.5 Patterns of synonymous and nonsynonymous evolution; 3.3.6 Natural selection and transmission mode; 3.3.7 Escape from intrinsic immunity; 3.3.8 Strictly neutral evolution in RNA viruses?; 3.3.9 Determinants of codon bias (and nucleotide composition) in RNA viruses; 3.4 Deleterious mutation and RNA virus evolution 3.4.1 Deleterious mutation and intra-host genetic diversity3.4.2 The importance of defective interfering particles and complementation; 3.4.3 Complementation may be commonplace in RNA viruses; 3.5 Epistasis in RNA virus evolution; 3.5.1 Epistasis and robustness; 3.5.2 The importance of RNA secondary structure; 3.5.3 Convergence and pleiotropy; 3.6 The importance of intra-host viral diversity; 4 The RNA virus quasispecies; 4.1 What is a quasispecies?; 4.2 The great quasispecies debate; 4.2.1 What's in a name: quasispecies or polymorphism? 4.2.2 Is quasispecies theory different from 'classical' population genetics? |
| Record Nr. | UNINA-9910798280503321 |
Holmes Edward C.
|
||
| Oxford, England : , : Oxford University Press, , 2009 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
The evolution and emergence of RNA viruses / / Edward C. Holmes
| The evolution and emergence of RNA viruses / / Edward C. Holmes |
| Autore | Holmes Edward C. |
| Pubbl/distr/stampa | Oxford, England : , : Oxford University Press, , 2009 |
| Descrizione fisica | 1 online resource (267 p.) |
| Disciplina | 579.25 |
| Collana | Oxford Series in Ecology and Evolution |
| Soggetto topico |
RNA viruses
Viruses - Evolution Viral genetics Virus diseases |
| ISBN | 0-19-154941-X |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Contents; 1 Introduction; 1.1 Why study RNA virus evolution?; 1.1.1 Ways to study viral evolution; 1.1.2 The scope of this book; 1.2 RNA viruses and evolutionary biology; 1.2.1 The RNA virus world; 1.3 The basics of viral biology; 1.3.1 A cursory history of virology; 1.3.2 Virology 101; 1.3.3 Exploring the virosphere; 2 The origins of RNA viruses; 2.1 Introduction; 2.1.1 The perils of deep viral phylogeny; 2.2 Theories for the origin of RNA viruses; 2.2.1 The regressive origin theory; 2.2.2 RNA viruses as escaped genes; 2.2.3 RNA viruses and the RNA world; 2.2.4 Eigen's paradox
2.2.5 The taxonomic distribution of RNA viruses2.2.6 Conserved protein structures; 2.3 Deep phylogenetic relationships among RNA viruses; 2.3.1 The 'higher-order' relationships of RNA viruses; 2.3.2 Phylogenies based on genome organization; 2.3.3 Phylogenies based on protein structure; 2.4 RNA viruses and the evolution of the genetic code; 3 The mechanisms of RNA virus evolution; 3.1 The evolutionary dynamics of RNA viruses; 3.1.1 Mutation rates in RNA viruses and their determinants; 3.1.2 A comparison of substitution rates in viruses; 3.1.3 Differences in viral generation time 3.1.4 Slowly evolving RNA viruses?3.1.5 Rapidly evolving ssDNA viruses; 3.1.6 What sets the rate of RNA virus evolution?; 3.1.7 Trade-offs and the evolution of mutation rates; 3.1.8 Mutation rates and mutational loads; 3.1.9 Are RNA viruses trapped by high mutation rates?; 3.2 Recombination and reassortment in RNA virus evolution; 3.2.1 Recombination frequency in RNA viruses; 3.2.2 Detecting recombination in RNA viruses; 3.2.3 What determines the rate of recombination in RNA viruses?; 3.2.4 Recombination and deleterious mutation 3.3 Natural selection, genetic drift, and the genetics of adaptation3.3.1 Effective population sizes in viral evolution; 3.3.2 Transmission bottlenecks; 3.3.3 The dynamics of allele fixation: estimating selection coefficients; 3.3.4 The importance of hitch-hiking; 3.3.5 Patterns of synonymous and nonsynonymous evolution; 3.3.6 Natural selection and transmission mode; 3.3.7 Escape from intrinsic immunity; 3.3.8 Strictly neutral evolution in RNA viruses?; 3.3.9 Determinants of codon bias (and nucleotide composition) in RNA viruses; 3.4 Deleterious mutation and RNA virus evolution 3.4.1 Deleterious mutation and intra-host genetic diversity3.4.2 The importance of defective interfering particles and complementation; 3.4.3 Complementation may be commonplace in RNA viruses; 3.5 Epistasis in RNA virus evolution; 3.5.1 Epistasis and robustness; 3.5.2 The importance of RNA secondary structure; 3.5.3 Convergence and pleiotropy; 3.6 The importance of intra-host viral diversity; 4 The RNA virus quasispecies; 4.1 What is a quasispecies?; 4.2 The great quasispecies debate; 4.2.1 What's in a name: quasispecies or polymorphism? 4.2.2 Is quasispecies theory different from 'classical' population genetics? |
| Record Nr. | UNINA-9910814101303321 |
|
Holmes Edward C.
|
||
| Oxford, England : , : Oxford University Press, , 2009 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Genes & development
| Genes & development |
| Pubbl/distr/stampa | [Cold Spring Harbor, New York] : , : Cold Spring Harbor Laboratory Press in association with the Genetical Society of Great Britain |
| Disciplina | 575 |
| Soggetto topico |
Genetics
Eukaryotic cells Viral genetics Cytogenetics Gene Expression Regulation Génétique du développement Génétique Génétique virale Cytogénétique |
| Soggetto genere / forma |
Periodicals.
Ressource Internet (Descripteur de forme) Périodique électronique (Descripteur de forme) |
| ISSN | 1549-5477 |
| Formato | Materiale a stampa |
| Livello bibliografico | Periodico |
| Lingua di pubblicazione | eng |
| Altri titoli varianti | Genes and development |
| Record Nr. | UNISA-996203108503316 |
| [Cold Spring Harbor, New York] : , : Cold Spring Harbor Laboratory Press in association with the Genetical Society of Great Britain | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. di Salerno | ||
| ||
Genes & development
| Genes & development |
| Pubbl/distr/stampa | [Cold Spring Harbor, N.Y.], : Cold Spring Harbor Laboratory Press in association with the Genetical Society of Great Britain |
| Disciplina | 575 |
| Soggetto topico |
Genetics
Eukaryotic cells Viral genetics Cytogenetics Gene Expression Regulation Prokaryotes - Genetics Génétique du développement Génétique Eucaryote Génétique virale Cytogénétique |
| Soggetto genere / forma | Periodicals. |
| ISSN | 1549-5477 |
| Formato | Materiale a stampa |
| Livello bibliografico | Periodico |
| Lingua di pubblicazione | eng |
| Altri titoli varianti | Genes and development |
| Record Nr. | UNINA-9910145872403321 |
| [Cold Spring Harbor, N.Y.], : Cold Spring Harbor Laboratory Press in association with the Genetical Society of Great Britain | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
HIV sequence compendium
| HIV sequence compendium |
| Pubbl/distr/stampa | Los Alamos, N.M., : Theoretical Biology and Biophysics Group T-10, Los Alamos National Laboratory, [2001?-] |
| Soggetto topico |
HIV (Viruses) - Molecular genetics
HIV (Viruses) - Genome mapping Nucleotide sequence Amino acid sequence Viral genomes Viral genetics Retroviruses - Genetics HIV (Viruses) HIV - genetics Base Sequence Molecular Sequence Data Simian Immunodeficiency Virus - genetics Virus de l'immunodéficience humaine Séquence nucléotidique Séquence des acides aminés Génétique virale Virus de l'immunodéficience humaine - Génétique moléculaire Virus de l'immunodéficience humaine - Cartes chromosomiques Génomes viraux Rétrovirus - Génétique |
| Soggetto genere / forma |
Periodical
periodicals. Periodicals. Périodiques. |
| Formato | Materiale a stampa |
| Livello bibliografico | Periodico |
| Lingua di pubblicazione | eng |
| Altri titoli varianti |
Human immunodeficiency virus sequence compendium
HIV sequence database |
| Record Nr. | UNINA-9910895663503321 |
| Los Alamos, N.M., : Theoretical Biology and Biophysics Group T-10, Los Alamos National Laboratory, [2001?-] | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Methods in bioengineering : systems analysis of biological networks / / Arul Jayaraman, Juergen Hahn, editors
| Methods in bioengineering : systems analysis of biological networks / / Arul Jayaraman, Juergen Hahn, editors |
| Pubbl/distr/stampa | Boston [Mass.] : , : Artech House, , ©2009 |
| Descrizione fisica | 1 online resource (328 p.) |
| Disciplina |
610.28
660.6 |
| Altri autori (Persone) |
JayaramanArul
HahnJuergen |
| Collana | Artech House methods in bioengineering series |
| Soggetto topico |
Bacterial genetics
Cytology - Technique Viral genetics |
| Soggetto genere / forma | Electronic books. |
| ISBN | 1-59693-407-7 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Methods in Bioengineering: Systems Analysis of Biological Networks; Contents; Chapter 1 Quantitative Immunofluorescence for Measuring Spatial Compartmentation of Covalently Modified Signaling Proteins; 1.1 Introduction; 1.2 Experimental Design; 1.3 Materials; 1.3.1 Cell culture; 1.3.2 Buffers/reagents; 1.3.3 Immunofluorescence reagents; 1.4 Methods; 1.4.1 Cell culture and stimulation for phospho-ERK measurements; 1.4.2 Antibody labeling of phosphorylated ERK (ppERK); 1.4.3 Fluorescence microscopy imaging of ppERK and automated imageanalysis
1.5 Data Acquisition, Anticipated Results, and Interpretation1.6 Statistical Guidelines; 1.7 Discussion and Commentary; 1.8 Application Notes; 1.9 Summary Points; Acknowledgments; References; Chapter 2 Development of Green Fluorescent Protein-Based Reporter Cell Lines for Dynamic Profiling of Transcription Factor and Kinase Activation; 2.1 Introduction; 2.2 Materials; 2.2.1 Cell and bacterial culture; 2.2.2 Buffers and reagents; 2.2.3 Cloning; 2.2.4 Microscopy; 2.3 Methods; 2.3.1 3T3-L1 cell culture; 2.3.2 Transcription factor reporter development; 2.3.3 Kinase reporter development 2.4 Application Notes2.4.1 Electroporation of TF reporter plasmids into 3T3-L1 preadipocytes; 2.4.2 Monitoring activation of ERK in HepG2 cells; 2.5 Data Acquisition, Anticipated Results, and Interpretation; 2.6 Discussion and Commentary; 2.7 Summary Points; Acknowledgments; References; Chapter 3 Comparison of Algorithms for Analyzing Fluorescent Microscopy Images and Computation of Transcription Factor Profiles; 3.1 Introduction; 3.2 Preliminaries; 3.2.1 Principles of GFP reporter systems; 3.2.2 Wavelets; 3.2.3 K-means clustering; 3.2.4 Principal component analysis 3.2.5 Mathematical description of digital images and image analysis3.3 Methods; 3.3.1 Image analysis based on wavelets and a bidirectional search; 3.3.2 Image analysis based on K-means clustering and PCA; 3.3.3 Determining fluorescence intensity of an image; 3.3.4 Comparison of the two image analysis procedures; 3.4 Data Acquisition, Anticipated Results, and Interpretation; 3.4.1 Developing a model describing the relationship between the transcription factor concentration and the observed fluorescence intensity 3.4.2 Solution of an inverse problem for determining transcription factor concentrations3.5 Application Notes; 3.6 Summary and Conclusions; Acknowledgments; References; Chapter 4 Data-Driven, Mechanistic Modeling of Biochemical Reaction Networks; 4.1 Introduction; 4.2 Principles of Data-Driven Modeling; 4.2.1 Types of experimental data; 4.2.2 Data processing and normalization; 4.2.3 Suitability of models used in conjunction with quantitative data; 4.2.4 Issues related to parameter specification and estimation; 4.3 Examples of Data-Driven Modeling 4.3.1 Example 1: Systematic analysis of crosstalk in the PDGF receptor signaling network |
| Altri titoli varianti | Systems analysis of biological networks |
| Record Nr. | UNINA-9910456668503321 |
| Boston [Mass.] : , : Artech House, , ©2009 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Methods in bioengineering : systems analysis of biological networks / / Arul Jayaraman, Juergen Hahn, editors
| Methods in bioengineering : systems analysis of biological networks / / Arul Jayaraman, Juergen Hahn, editors |
| Pubbl/distr/stampa | Boston [Mass.] : , : Artech House, , ©2009 |
| Descrizione fisica | 1 online resource (328 p.) |
| Disciplina |
610.28
660.6 |
| Altri autori (Persone) |
JayaramanArul
HahnJuergen |
| Collana | Artech House methods in bioengineering series |
| Soggetto topico |
Bacterial genetics
Cytology - Technique Viral genetics |
| ISBN |
1-5231-4635-4
1-59693-407-7 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Methods in Bioengineering: Systems Analysis of Biological Networks; Contents; Chapter 1 Quantitative Immunofluorescence for Measuring Spatial Compartmentation of Covalently Modified Signaling Proteins; 1.1 Introduction; 1.2 Experimental Design; 1.3 Materials; 1.3.1 Cell culture; 1.3.2 Buffers/reagents; 1.3.3 Immunofluorescence reagents; 1.4 Methods; 1.4.1 Cell culture and stimulation for phospho-ERK measurements; 1.4.2 Antibody labeling of phosphorylated ERK (ppERK); 1.4.3 Fluorescence microscopy imaging of ppERK and automated imageanalysis
1.5 Data Acquisition, Anticipated Results, and Interpretation1.6 Statistical Guidelines; 1.7 Discussion and Commentary; 1.8 Application Notes; 1.9 Summary Points; Acknowledgments; References; Chapter 2 Development of Green Fluorescent Protein-Based Reporter Cell Lines for Dynamic Profiling of Transcription Factor and Kinase Activation; 2.1 Introduction; 2.2 Materials; 2.2.1 Cell and bacterial culture; 2.2.2 Buffers and reagents; 2.2.3 Cloning; 2.2.4 Microscopy; 2.3 Methods; 2.3.1 3T3-L1 cell culture; 2.3.2 Transcription factor reporter development; 2.3.3 Kinase reporter development 2.4 Application Notes2.4.1 Electroporation of TF reporter plasmids into 3T3-L1 preadipocytes; 2.4.2 Monitoring activation of ERK in HepG2 cells; 2.5 Data Acquisition, Anticipated Results, and Interpretation; 2.6 Discussion and Commentary; 2.7 Summary Points; Acknowledgments; References; Chapter 3 Comparison of Algorithms for Analyzing Fluorescent Microscopy Images and Computation of Transcription Factor Profiles; 3.1 Introduction; 3.2 Preliminaries; 3.2.1 Principles of GFP reporter systems; 3.2.2 Wavelets; 3.2.3 K-means clustering; 3.2.4 Principal component analysis 3.2.5 Mathematical description of digital images and image analysis3.3 Methods; 3.3.1 Image analysis based on wavelets and a bidirectional search; 3.3.2 Image analysis based on K-means clustering and PCA; 3.3.3 Determining fluorescence intensity of an image; 3.3.4 Comparison of the two image analysis procedures; 3.4 Data Acquisition, Anticipated Results, and Interpretation; 3.4.1 Developing a model describing the relationship between the transcription factor concentration and the observed fluorescence intensity 3.4.2 Solution of an inverse problem for determining transcription factor concentrations3.5 Application Notes; 3.6 Summary and Conclusions; Acknowledgments; References; Chapter 4 Data-Driven, Mechanistic Modeling of Biochemical Reaction Networks; 4.1 Introduction; 4.2 Principles of Data-Driven Modeling; 4.2.1 Types of experimental data; 4.2.2 Data processing and normalization; 4.2.3 Suitability of models used in conjunction with quantitative data; 4.2.4 Issues related to parameter specification and estimation; 4.3 Examples of Data-Driven Modeling 4.3.1 Example 1: Systematic analysis of crosstalk in the PDGF receptor signaling network |
| Altri titoli varianti | Systems analysis of biological networks |
| Record Nr. | UNINA-9910780809003321 |
| Boston [Mass.] : , : Artech House, , ©2009 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
RNA viruses [[electronic resource] ] : host gene responses to infections / / edited by Decheng Yang
| RNA viruses [[electronic resource] ] : host gene responses to infections / / edited by Decheng Yang |
| Pubbl/distr/stampa | Hackensack, NJ, : World Scientific, c2009 |
| Descrizione fisica | 1 online resource (722 p.) |
| Disciplina | 579.2/5 |
| Altri autori (Persone) | YangDecheng |
| Soggetto topico |
RNA viruses
Viral genetics |
| Soggetto genere / forma | Electronic books. |
| ISBN |
1-282-44115-9
9786612441158 981-283-380-3 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Contents; Contributors; Preface; Section I Retrovirus; Section II Negative Single-Stranded RNA Virus; Section III Positive Single-Stranded RNA Virus; Section IV Double-Stranded RNA Virus; Index |
| Record Nr. | UNINA-9910456582703321 |
| Hackensack, NJ, : World Scientific, c2009 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
RNA viruses [[electronic resource] ] : host gene responses to infections / / edited by Decheng Yang
| RNA viruses [[electronic resource] ] : host gene responses to infections / / edited by Decheng Yang |
| Pubbl/distr/stampa | Hackensack, NJ, : World Scientific, c2009 |
| Descrizione fisica | 1 online resource (722 p.) |
| Disciplina | 579.2/5 |
| Altri autori (Persone) | YangDecheng |
| Soggetto topico |
RNA viruses
Viral genetics |
| ISBN |
1-282-44115-9
9786612441158 981-283-380-3 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Contents; Contributors; Preface; Section I Retrovirus; Section II Negative Single-Stranded RNA Virus; Section III Positive Single-Stranded RNA Virus; Section IV Double-Stranded RNA Virus; Index |
| Record Nr. | UNINA-9910780928403321 |
| Hackensack, NJ, : World Scientific, c2009 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
RNA viruses : host gene responses to infections / / edited by Decheng Yang
| RNA viruses : host gene responses to infections / / edited by Decheng Yang |
| Edizione | [1st ed.] |
| Pubbl/distr/stampa | Hackensack, NJ, : World Scientific, c2009 |
| Descrizione fisica | 1 online resource (722 p.) |
| Disciplina | 579.2/5 |
| Altri autori (Persone) | YangDecheng |
| Soggetto topico |
RNA viruses
Viral genetics |
| ISBN |
1-282-44115-9
9786612441158 981-283-380-3 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Contents; Contributors; Preface; Section I Retrovirus; Section II Negative Single-Stranded RNA Virus; Section III Positive Single-Stranded RNA Virus; Section IV Double-Stranded RNA Virus; Index |
| Record Nr. | UNINA-9910825008103321 |
| Hackensack, NJ, : World Scientific, c2009 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Soggetto topico
-
Viral genetics
(27)
- Génétique virale (5)
- RNA viruses (5)
- Viruses - Evolution (4)
- Bacterial genetics (3)