What is life? What makes something alive? And how do viruses fit into those criteria?

In this episode, we'll explore the structure, diversity, and behavior of viruses. We'll also discuss the pathology of subviral particles like prions and viroids.

0:00 - Part 0: Introduction

2:29 - Part 1: The History of Viral Discovery

• Viral Size
• Adolf Mayer and the Tobacco Mosaic Virus
• Dmitri Ivanovsky and the Filter Experiment
• Martinus Beijerinck and the 'Contagium Vivum Fluidum'

8:40 - Part 2: Viral Structure

• Basic Virion Structure
• Structural Diversity
• Bacteriophage Structure

13:00 - Part 3: Bacteriophages

• Attachment and Penetration
• The Lytic Cycle
• Regulation of Infection Sequence
• The Lysogenic Cycle
• Lysogenic Conversion

28:06 - Part 4: Bacterial Defenses

• Bacterial Capsules
• Binding Failure
• Superinfection Exclusion
• Abortive Infection
• Restriction Enzymes
• The CRISPR/Cas9 System

37:44 - Part 5: Animal Viruses

• Variations in the Lytic Approach
• Variations in Lysogenic Terminology

42:38 - Part 6: Animal Virus Classification

• The ICTV System
• Baltimore Classification
• Retroviruses

53:26 - Part 7: Prions

• Protein Infections
• Transmissible Spongiform Encephalopathies

57:57 - Part 8: Viroids

• Viroid Structure
• Viroid Pathology

References + Further Reading

- Abedon, S. T. (2012). Bacterial ‘immunity’ against bacteriophages. Bacteriophage, 2(1), 50-54. https://doi.org/10.4161/bact.18609

- Bucher, M. J. & Czyż, D. M. (2024). Phage against the machine: The SIE-ence of superinfection exclusion. Viruses, 16(9), 1348. https://doi.org/10.3390/v16091348

- Cheng, C. & Kirkpatrick, M. (2021). Molecular evolution and the decline of purifying selection with age. Nature Communications, 12(2657). https://doi.org/10.1038/s41467-021-22981-9

- Clark, M. A., Douglas, M., & Choi, J. (2018). Biology 2e. OpenStax.

- Dutchen, S. (2022). The good that viruses do. Harvard Medicine. https://magazine.hms.harvard.edu/articles/good-viruses-do

- Elena, S. F., Dopazo, J., Flores, R., Diener, T. O., & Moya, A. (1991). Phylogeny of viroids, viroidlike satellite RNAs, and the viroidlike domain of hepatitis delta virus RNA. Proceedings of the National Academy of Sciences, 88(13), 5631-5634. https://doi.org/10.1073/pnas.88.13.5631

- Feiner, R., Argov, T., Rabinovich, L., Sigal, N., Borovok, I., & Herskovits, A. A. (2015). A new perspective on lysogeny: Pro-phages as active regulatory switches of bacteria. Nature Reviews Microbiology, 13, 641-650. https://doi.org/10.1038/nrmicro3527

- Gostimskaya, I. (2022). CRISPR-Cas9: A history of the discovery and ethical considerations of its use in genome editing. Biochemistry (Moscow), 87, 777-788. https://doi.org/10.1134/S0006297922080090

- Lopatina, A., Tal, N., & Sorek, R. (2020). Abortive infection: Bacterial suicide as an antiviral immune strategy. Annual Review of Virology, 7(1), 371-384. https://doi.org/10.1146/annurev-virology-011620-040628

- Pallin, D. J., & Wright, J. (2022). MCAT: Biology review (3rd ed.). The Princeton Review.

- Prussin, A. J., Garcia, E. B., & Marr, L. C. (2016). Total virus and bacteria concentrations in indoor and outdoor air. Environmental Science & Technology Letters, 2(4), 84-88. https://doi.org/10.1021/acs.estlett.5b00050

- Rostøl, J. T. & Marraffini, L. (2019). (Ph)ighting phages: How bacteria resist their parasites. Cell Host & Microbe, 25(2), 184-194. https://doi.org/10.1016/j.chom.2019.01.009

- Scheckel, C. & Aguzzi, A. (2018). Prions, prionoids and protein misfolding disorders. Nature Reviews Genetics, 19, 405-418. https://doi.org/10.1038/s41576-018-0011-4

- Urry, L. A., Cain, M. L., Wasserman, S. A., Minorsky, P. V., & Orr, R. B. (2021). Campbell: Biology (12th ed.). Pearson.

Correction

- At 16:55, Michael misspoke. He said "lysosome" but meant to say "lysozyme." Both these structures carry out reactions that degrade cellular components, but bacteriophages specifically mobilize the lysozyme (in this context) to degrade the bacterial cell wall.