Single stranded RNA phages From molecular biology to nanotechnology 1st Edition by Paul Pumpens 0429671418 9780429671418

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ISBN-10 :  0429671418 

ISBN-13 :  9780429671418

Author:  Paul Pumpens 

This is a comprehensive guide to single-stranded RNA phages (family Leviviridae), first discovered in 1961. These phages played a unique role in early studies of molecular biology, the genetic code, translation, replication, suppression of mutations. Special attention is devoted to modern applications of the RNA phages and their products in nanotechnology, vaccinology, gene discovery, evolutionary and environmental studies. Included is an overview of the generation of novel vaccines, gene therapy vectors, drug delivery, and diagnostic tools exploring the role of RNA phage-derived products in the revolutionary progress of the protein tethering and bioimaging protocols. Key Features Presents the first full guide to single-stranded RNA phages Reviews the history of molecular biology summarizing the role RNA phages in the development of the life sciences Demonstrates how RNA phage-derived products have resulted in nanotechnological applications Presents an up-to-date account of the role played by RNA phages in evolutionary and environmental studies

Single-stranded RNA phages-From molecular biology to nanotechnology 1st table of contents:

Chapter 1: History and First Look
Classical Reviews
Male Specificity
RNA as the Genome
Growth Cycle
Coliphages
Worldwide
Non-Coli Phages
Diversity of Pili
Newcomers
Dangerous Similarity
Antibodies
Portraits of Icosahedra
Composition
Genome
Translation
Replication
Regulation
Reconstitution
Phage Tales
Chapter 2: Taxonomy and Grouping
Entries in Prestigious Books of Reference and Encyclopedias
Official ICTV Taxonomy
Relatedness to Other Taxa
NCBI Classification
Serogrouping
Affinities to Millipore Filters
Template Specificity of Replicases
Hybrid Particles
Physicochemical Parameters
Genogrouping
Metaviromics
Urgent Necessity for Improvements in the Taxonomy
Chapter 3: Pili and Hosts
Pili: Current Definition
F pili: Ascending to Clarity
How Pili Work
F Type Pili: R Factors
Genetics of F Pili
Chromosomal Mutations
F Pili in the Enterobacteriaceae Other Than E. coli
Conjugation and RNA Phages
Elimination of Sex Factors
Non-F-Encoded Pili
Incompatibility Groups: Definition
Incompatibility Groups and RNA Phages
Fine Mapping of F Pili
Fine Mapping of Polar Pili
Caulobacter and Acinetobacter Pili
Hosts
Enterobacteriaceae
Pseudomonadaceae
Caulobacteraceae
Moraxellaceae
Spheroplasts
Chapter 4: Physiology and Growth
Attachment or Adsorption
Ejection or Eclipse
Penetration
Replication Cycle
Crystalline Inclusions
Release
Plaque Assay
Phage Effect on Host
Host Mutants
Inhibition of Phage Growth
Rifamycin
Mixed Infections and Superinfections
Preparative Growth and Purification
Cell-Free Synthesis
Lysogeny
Chapter 5: Distribution
Geography
Sources
Human Beings
Enumeration
Chapter 6: Ecology
Measure of Pollution
Water Quality
Indicators of Fecal Pollution
Surveillance of Ground and Surface Waters
Water Surveillance
United States
Canada
Africa
New Zealand and Australia
Israel
Europe
Central and South America
Japan
China
India
Southeast Asia Countries
Antarctica
Different Survival in Water
Surrogates of Human Viruses
Inactivation
Ultraviolet Irradiation
Photocatalytic Disinfection
UV-LEDs
Photosensitizing Agents
Photosensitization of Fullerol Nanoparticles
Graphene and Carbon Nanomaterials
Other Nanoparticles
Ionizing Radiation
Plasma
Selective Photonic Disinfection
Metal Compounds
Nitrous Acid
Alkylating Agents
Bisulfite
Hydroxylamine
Chlorine, Iodine, and Bromine
Ammonia
Alkaline Stabilization
Peracetic Acid
Ozone
Other Inactivating Agents
Heat
Sunlight
High Pressure
Ultrasound
CO2
Desiccation, Humidity, and Aerosols
Biofilms
Dyed Phage Particles
Different Resistance to Inactivation
Adsorption and Coagulation
Fracture Flow and Transport
Filtration by Soil and Sand Columns
Membrane Filtration
Oysters and Mussels
Fruits and Vegetables
Food Total
Patient Care
Pseudomonaphage PP7
Chapter 7: Genome
Genetic Makeup
Full-Length Sequences
Peculiarities of the Genome
Similarities and Dissimilarities
Chapter 8: Genetics and Mutants
Conditionally Lethal Mutations
Polar Mutations
Gene Order
Frequencies of Mutations
Complementation
Function of Mutant Genes
Azure Mutants
Op-3 Mutant
Streptomycin Suppression
Mutants of the Phage f2
Mutants of the Phage MS2
Mutants of the Phage fr
Mutants of the Phage R17
Mutants of the Phage GA
Mutants of the Phages Qβ, SP, and FI
Mutants of the Phage PP7
Chapter 9: Particles
Molecular Mass
Size
Composition
Symmetry
Morphology
Coat-RNA Contact
Defective Particles
Reconstitution
Monitoring
Aggregation
Standards and Internal Controls
Chapter 10: RNA
Biophysics
Gel Electrophoresis
General Properties
Hybridization
Preparations for Sequencing
MS2 Sequencing: Walter Fiers’ Team
MS2 Sequencing: Other Groups
By-Products and Direct Consequences of the MS2 Sequencing
R17 Sequencing
f2 Sequencing
Qβ Sequencing
Sequencing of Other Phage RNAs
Electron Microscopy
Secondary Structure: Jan van Duin’s Team
Secondary Structure: Further Inquiry
MS2 RNA and Programmed Cell Death
MS2 RNA as a Substrate and Interaction Probe
MS2 RNA as a Control
Chapter 11: Maturation Protein
Mutant Allusions
Gel Electrophoresis
Isolation
Chemical Studies
Fate of the Maturation Protein
Sequencing
Homology
Spatial Structure
Lysis
Chapter 12: Coat Protein
Composition and Sequencing
N-Terminal Modification
Isolation
Aggregation
Physical Properties
Homology
Spatial Structure
Lysis
Readthrough Protein
Chapter 13: Replicase
Activity
Replicase Subunit
Homology
Qβ Replicase
Subunits of the Qβ Replicase
EF Tu-Ts
Ribosomal Protein S1
Fine Structure of the Qβ Replicase
Host Factors
Host Factor I, or HF, or Hfq
The hfq Gene
Fine Structure of the Hfq
Some Special Features of the Qβ Replicase Enzyme
Non-Allolevivirus Replicases
f2 Replicase
MS2 Replicase
GA Replicase
R17 Replicase
Chapter 14: Lysis Protein
Discovery
Homology
Natural Expression of the Lysis Gene
Lysis Mechanism
Protein Antibiotics
Other Applications
Chapter 15: Immunology
Serological Criteria
Serogrouping
Immunoglobulins
Phylogeny of Antibodies
Target of Antibodies
Mapping
Immunodetection
Chapter 16: Translation
The Essentials
Translation In Vivo
Translation In Vitro
Heterologous Translation In Vitro
Polarity
Nascent Chains
Initiation
Initiation Sites
Shine-Dalgarno
Elongation
Termination
Intergenic Sequences
RNA Fragments as Messengers
Miscellaneous by the in Vitro Translation
Secondary and Tertiary Structure
Ribosomal Frameshifting
Reinitiation
Large-Scale Translation
Genetic Code
Non-Coliphages
Repressor Complex I
Repressor Complex I: f2
Repressor Complex I: R17
Repressor Complex I: MS2
Repressor Complex I: fr
Repressor Complex I: GA
Repressor Complex I: Qβ
Repressor Complex I: PP7
Repressor Complex I: PRR1
Repressor Complex II
Chapter 17: Replication
The Essentials
Early Studies
Replicative Intermediate
Regulation of the Replication Cycle
Induction of Interferon
Larifan
Chapter 18: Evolution
Darwinian Experiments
6S RNA
MDV-1: A Midi-Variant
Micro- and Nanovariants
De Novo Synthesis?
Molecular Parasites
Molecular Colonies
Autocatalytic Synthesis of Heterologous RNAs
RQ Variants
Mapping of Qβ Replicase
Diagnostics
Mutagenesis System
Coupled Replication-Translation
RNA World
Phylogeny
RNA-Dependent Polymerases
Recombination
Quasispecies and Evolution
Chapter 19: Expression
Era of Gene Engineering
Generation of Mutants
Chimeric Phages
Maturation Gene
Lysis Gene
Replicase Gene
Replicase Fusions
Coat Gene
Chapter 20: Chimeric VLPs
Protein Engineering and VLP Nanotechnology
Genetic Fusions of Coats
fr
MS2
Qβ
PP7
AP205
GA
Peptide Display
Chemical Coupling
Martin F. Bachmann’s Team
Bryce Chackerian and David S. Peabody
Functionalization
MS2
Qβ
Plug-and-Display: AP205
Stability
Packaging
Chapter 21: 3D Particles
Viruses and/or VLPs?
RNA Aptamers
Packing of Genomic RNA
Maturation Protein
Self-Assembly
Lattices
AP205
Chimeric VLPs
Chapter 22: VLP Vaccines
General
Basic Immunology
Genetic Fusions
Chemical Coupling
Chimeric Phages
Chapter 23: Non-Vaccine VLPs
Armored RNA
Nanocontainers: Drug Delivery
Nanomaterials and Imaging
Nanoreactors
Chapter 24: Non-VLPs
Gene Therapy
Tethering
Imaging
New Challenge: PP7
CRISPR-Cas9
Chapter 25: Epilogue
Statistics
Goal Achievements
Virome
Novel VLP Models
Three-Dimensional Structure
Immediate Future
Bacterial Immunity
Phage Therapy
PHAGE: Therapy, Applications, and Research
Author Index
Subject Index

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