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1 Chapter 1Figure 1.1 A phylogenetic tree of selected species from the three domains of...Figure 1.2 A phylogenetic tree of selected eukaryotic and archaeal species a...

2 Chapter 2Figure 2.1 Dimensions and features of “typical” (a) animal, (b) plant, and (...Figure 2.2 The virus replication cycle. Most generally, virus replication ca...Figure 2.3 The pathogenesis of virus infection. Typically, infection is foll...Figure 2.4 Sites of virus entry in a human. These or similar sites apply to ...

3 Chapter 3Figure 3.1 Some transmission routes of specific viruses from their source (r...Figure 3.2 Occurrence of respiratory illness in an arctic community (Spitzbe...Figure 3.3 Fictionalized timeline of the spread of SARS virus following its ...Figure 3.4 The course of experimental poxvirus infection in laboratory mice....Figure 3.5 Visualization of rabies virus–infected neurons in experimentally ...Figure 3.6 Analysis of the establishment and maintenance of latent HSV infec...

4 Chapter 4Figure 4.1 Virus maintenance in small and large populations. (a) In a small ...Figure 4.2 Examples of virus infection of specific organs or organ systems. ...

5 Chapter 5Figure 5.1 A scale of dimensions for biologists. The wavelength of a photon ...Figure 5.2 The structure and relative sizes of a number of (a) DNA and (b) R...Figure 5.3 Crystallographic structure of a simple icosahedral virus. (a) The...Figure 5.4 The structure of a simple icosahedral virus. (a) A space‐filling ...Figure 5.5 The virosphere. Classification of a major portion of the currentl...

6 Chapter 6Figure 6.1 The surface of a “typical” animal cell. The lipid bilayer plasma ...Figure 6.2 Schematic of receptor‐mediated endocytosis utilized by rhinovirus...Figure 6.3 (a) The two basic modes of entry of an enveloped animal virus int...Figure 6.4 Entry of T4 bacteriophage DNA into an E. coli cell. Initial attac...Figure 6.5 Expression of a varicella zoster virus protein following transfec...Figure 6.6 Assembly of the helical tobacco mosaic virus (TMV). Steps in the ...Figure 6.7 Assembly of the phage P22 capsid and maturation by insertion of v...Figure 6.8 Insertion of glycoproteins into the cell's membrane structures an...Figure 6.9 Visualization of the budding of an enveloped virion from the plas...Figure 6.10 The envelopment and egress of herpesvirus. Electron micrographs ...

7 Chapter 7Figure 7.1 Schematic representation showing differences in the intensity and...Figure 7.2 The cascade of events leading to expression of interferon (IFN) a...Figure 7.3 The human lymphatic system. The lymphatic system is the principal...Figure 7.4 T and B cells in immunity. T lymphocytes play the central coordin...Figure 7.5 The antigenic structure of a protein. Specific groups of amino ac...Figure 7.6 The processing of a foreign antigen and stimulation of the immune...Figure 7.7 The clonal selection of B lymphocytes. Only the B lymphocytes rea...Figure 7.8 Immune memory. The first exposure to an antigen results in the pr...Figure 7.9 The maturational cascade of serum complement proteins upon bindin...Figure 7.10 An enzyme‐linked immunosorbent assay (ELISA): the method of usin...Figure 7.11 Antibody neutralization of virus infectivity. Specific types of ...Figure 7.12 The hemagglutination inhibition assay for measuring antibody aga...

8 Chapter 8Figure 8.1 The structure of some currently effective antiviral drugs.

9 Chapter 9Figure 9.1 A schematic comparison of light and electron microscopes. The pri...Figure 9.2 Shadowing specimens for viewing in the electron microscope. (a) A...Figure 9.3 Computer‐enhanced three‐dimensional reconstruction of viral capsi...Figure 9.4 Atomic force microscopy was used to visualize the protein capsid ...

10 Chapter 10Figure 10.1 Generating a primary cell culture. Tissue is surgically removed ...Figure 10.2 The progression of cells in culture from primary to transformed ...Figure 10.3 Apoptosis versus necrosis in cell death.Figure 10.4 HSV‐induced changes in the properties of actin microfilaments of...Figure 10.5 Visualization of virus plaques. Under appropriate conditions, vi...Figure 10.6 Rabbitpox virus pocks on the chorioallantoic membrane (CAM) of a...Figure 10.7 Some representative morphologies of rat fibroblast cells (F‐111)...Figure 10.8 Serial 10‐fold dilutions of HSV to determine the titer of virus ...Figure 10.9 Quantal (endpoint dilution) assay of HSV in tissue culture wells...Figure 10.10 Graphic analysis of the data from Figure 10.8. The percentage o...

11 Chapter 11Figure 11.1 Equilibrium density gradient centrifugation of virus‐infected ce...Figure 11.2 Differential centrifugation to purify virions. Infected cells ar...Figure 11.3 Denaturing gel electrophoresis of proteins. If proteins are gent...Figure 11.4 Electrophoretic fractionation of the capsid proteins isolated fr...Figure 11.5 Electrophoretic fractionation of the capsid proteins isolated fr...Figure 11.6 The famous Kleinschmidt electron micrograph of phage T4 DNA extr...Figure 11.7 Enzymatic sequencing of DNA. The generation of overlapping oligo...Figure 11.8 High‐throughput sequencing (HTS) of DNA. Several different...Figure 11.9 Amplification of DNA with the polymerase chain reaction (PCR). (...Figure 11.10 Real‐time PCR amplification of globin DNA in blood macrophages....

12 Chapter 12Figure 12.1 Changes in the proteins synthesized in virus‐infected cells with...Figure 12.2 The structure of an antibody molecule, IgG. This molecule is mad...Figure 12.3 Generation of monoclonal antibodies by making hybridoma cells by...Figure 12.4 Outline of immunofluorescence as a means of detecting and locali...Figure 12.5 Confocal microscopy to detect co‐localization of antigens. (a) T...Figure 12.6 Human thymocytes in organ culture were mock infected or infected...Figure 12.7 Detection and isolation of proteins reactive with a specific ant...Figure 12.8 Use of immunoaffinity chromatography to isolate HSV envelope pro...Figure 12.9 Saliva from recently HIV‐infected people, individuals with long‐...Figure 12.10 Different viral mRNA molecules are encoded by different regions...Figure 12.11 In situ hybridization of human neurons latently infected with H...Figure 12.12 In situ hybridization of sections of suckling mice infected wit...Figure 12.13 Characterization of isolated viral mRNA by in vitro translationFigure 12.14 The application of microarrays or the study of viral products p...

13 Chapter 13Figure 13.1 The enzymes and other proteins associated with DNA around a grow...Figure 13.2 Initiation of HSV DNA replication. This process is virtually ide...Figure 13.3 The E. coli lac operon. The promoter is always “on,” but normall...Figure 13.4 The bacterial RNA polymerase molecule. The enzyme is made up of ...Figure 13.5 The multistep process of transcription initiation at a eukaryoti...Figure 13.6 The flexibility of DNA allows transcription factors to bind at s...Figure 13.7 Control of eukaryotic transcription. (a) The availability of the...Figure 13.8 Steps involved in transcription and posttranscriptional modifica...Figure 13.9 A “high‐resolution” example of mRNA processing. The sequence of ...Figure 13.10 Some splicing patterns seen in the generation of eukaryotic vir...Figure 13.11 Posttranscriptional regulation of eukaryotic mRNA. Once transcr...Figure 13.12 Initiation of eukaryotic translation. Note the initiation compl...Figure 13.13 Initiation of translation of a prokaryotic mRNA. This can occur...

14 Chapter 14Figure 14.1 Some general features of viruses containing RNA genomes that use...Figure 14.2 (a) Poliovirus, a typical picornavirus. The 30‐nm‐diameter icosa...Figure 14.3 The poliovirus replication cycle. The schematic representation i...Figure 14.4 The steps in the assembly of the poliovirus virion. Precursor pr...Figure 14.5 The yellow fever virus (a flavivirus) and its genome. This flavi...Figure 14.6 Sindbis virus – a typical togavirus. The virion (60–70 nm in dia...Figure 14.7 The early stages of Sindbis virus infection. (a) The first step ...Figure 14.8 (a) The replication of Sindbis virus genome, and generation of t...Figure 14.9 A schematic representation of the coronavirus virion. This is th...Figure 14.10 The replication cycle of a coronavirus. Replication is entirely...Figure 14.11 The approximately 25‐nm‐diameter icosahedral capsid of positive...Figure 14.12 Coupled transcription–translation of bacteriophage Qβ RNA resul...

15 Chapter 15Figure 15.1 The vesicular stomatitis virus (VSV) virion. All rhabdoviruses h...Figure 15.2 The VSV replication cycle. (a) Early events in infection begin w...Figure 15.3 A higher‐resolution schematic of the generation of positive‐sens...Figure 15.4 The genetic map and virion structure of Sendai virus, a typical ...Figure 15.5 The structure of influenza virus A. The virion is about 120 nm i...Figure 15.6 An outline of the replication cycle of influenza. Following viru...Figure 15.7 Antigenic changes in the surface glycoproteins of influenza A vi...Figure 15.8 The bunyavirus virion. The three ribonucleoprotein (RNP) segment...Figure 15.9 The ambisense strategy of gene expression exhibited by some buny...Figure 15.10 The 60‐nm‐diameter human reovirus with its double shell. The 10...Figure 15.11 The reovirus replication cycle. Virus attachment is followed by...Figure 15.12 The potato spindle tuber viroid genome. Various pathogenic stra...Figure 15.13 Prion‐specific protein.

16 Chapter 16Figure 16.1 Polyomavirus and the genetic and transcript map of SV40 virus. (...Figure 16.2 The replication cycle of SV40 virus in a permissive cell. The re...Figure 16.3 The replication of SV40 DNA. The closed circular DNA has no end ...Figure 16.4 Representation of the two steps in transformation of a nonpermis...Figure 16.5 The human papillomavirus 16 (HPV‐16) genome. The 7‐kb circular g...Figure 16.6 The formation of a wart by cell proliferation caused by infectio...Figure 16.7 The genetic and transcription map of the 30‐kb adenovirus genome...Figure 16.8 Adenovirus DNA replication. The 5′ ends of the viral genome have...Figure 16.9 The 5000‐nucleotide (nt) linear genome of adeno‐associated virus...Figure 16.10 The capsid structure and compressed genome of bacteriophage ΦX1...

17 Chapter 17Figure 17.1 Electron micrograph of an enveloped HSV‐1 virion revealing speci...Figure 17.2 The HSV‐1 genetic and transcription map. Specific features of th...Figure 17.3 The programmed cascade of HSV transcription at different stages ...Figure 17.4 The entry of HSV‐1 into a cell for the initiation of infection. ...Figure 17.5 The HSV‐1 productive and latent infection cycles. In productive ...Figure 17.6 Replication and encapsidation of viral genomes. (a) HSV DNA init...Figure 17.7 Immune fluorescence analysis of the rearrangement of nuclear str...Figure 17.8 Maturation of the HSV capsid and its envelopment by tegument and...Figure 17.9 The “decision” made by HSV upon infection of epidermal tissue en...Figure 17.10 The expression of HSV transcripts during latent infection and r...Figure 17.11 The Epstein–Barr virus (EBV) genome and the latency transcripts...

18 Chapter 18Figure 18.1 The vaccinia virus virion. The structure of poxviruses is the mo...Figure 18.2 The replication cycle of vaccinia virus. Following viral attachm...Figure 18.3 Replication of poxvirus DNA. The covalently closed, circular gen...Figure 18.4 The structure and genetic map of T7 bacteriophage. (a) The 40‐kb...Figure 18.5 The genetic map and structure of bacteriophage T4. By convention...Figure 18.6 Rolling circle replication and packaging of phage T4 DNA. The pr...Figure 18.7 Time of appearance of various functions encoded by T4 bacterioph...Figure 18.8 The assembly of T4 bacteriophage. Note that assembly of the phag...Figure 18.9 The bacteriophage λ genetic map. Specific clustered functions ar...Figure 18.10 The earliest events in the infection of a bacteria by phage λ. ...Figure 18.11 A phylogenetic tree of selected large‐DNA‐containing virus fami...

19 Chapter 19Figure 19.1 The structures of an oncornavirus and a mature lentivirus. Virio...Figure 19.2 Genetic maps of various retroviruses. Specific examples are disc...Figure 19.3 The replication cycle of a typical retrovirus. (1) Adsorption an...Figure 19.4 The detailed mechanism for formation of retroviral cDNA from vir...Figure 19.5 Splicing patterns of various retrovirus RNAs to generate subgeno...Figure 19.6 Cell division and oncogenes. (a) In the normal cell, division is...Figure 19.7 The genomic structure of yeast Ty1. The similarity to a retrovir...

20 Chapter 20Figure 20.1 The HIV‐1 genome, viral particle, and transcripts. The figure sh...Figure 20.2 HIV‐1 entry in detail. HIV‐1 binds cell surface CD4 via its surf...Figure 20.3 The HIV‐1 life cycle. After receptor‐mediated membrane fusion at...Figure 20.4 Vif and APOBEC action. In the absence of effective HIV‐1 Vif pro...Figure 20.5 Tat activation of HIV‐1 transcription. A tripartite complex cons...Figure 20.6 Rev binds to the Rev response element (RRE) to mediate nuclear e...Figure 20.7 HIV‐1 Vpu protein blocks the antiviral effect of tetherin. In th...Figure 20.8 Nef and Vpu downregulate CD4 expression and Nef downregulates MH...Figure 20.9 The pathogenesis of HIV infection leading to AIDS. Acute infecti...Figure 20.10 Triphasic decay of HIV‐1 in plasma following initiation of effe...

21 Chapter 21Figure 21.1 A diagram of the virion structure and a genomic and genetic map ...Figure 21.2 The three RNAs of hepatitis delta virus found in infected liver ...Figure 21.3 The genome of cauliflower mosaic virus. The three breaks in the ...

22 Chapter 22Figure 22.1 The impact of molecular understanding of viral and host genes on...Figure 22.2 Complementation. Neither of two mutant viruses shown can replica...Figure 22.3 Replica plating of virus plaques to distinguish genotypes produc...Figure 22.4 Mapping restriction endonuclease cleavage sites on a viral genom...Figure 22.5 Three widely used cloning plasmids that replicate in E. coli. Th...Figure 22.6 Isolation of a specific restriction fragment of viral DNA cloned...Figure 22.7 A togavirus expression vector. Semliki Forest virus (a togavirus...Figure 22.8 Directed mutagenesis of viral DNA. (a) Single‐stranded DNA conta...Figure 22.9 Generating and isolating recombinant viruses. (a) As outlined in...Figure 22.10 Generating a recombinant virus using CRISPR‐Cas gene editing. I...

23 Chapter 23Figure 23.1 Construction of a transgenic mouse. The desired DNA (here, the h...Figure 23.2 Use of SCID‐hu mice to study HIV pathogenesis. Human thymus–live...Figure 23.3 Use of ß‐galactosidase (ß‐gal) as a report...Figure 23.4 (a) MRI images of a mouse infected with HSV‐1 10 days post infec...Figure 23.5 Use of a protein microarray to assay patient antibody reactivity...

24 Chapter 24Figure 24.1 Growth of the genomic databases. Data displayed here are taken f...Figure 24.2 Results of a BLAST Search for a Nucleotide Sequence. (a) Initial...Figure 24.3 Random versus scale‐free networks. (a) A random network, in whic...Figure 24.4 Yeast two‐hybrid detection system. Transformation vectors are cr...Figure 24.5 Protein interaction map (PIM) for the round worm, Caenorhabditis...Figure 24.6 Host–virus protein interaction map of hepatitis C virus (HCV): t...

25 Chapter 25Figure 25.1 Mortality from infectious diseases in the United States between ...