Bi5050 Structural virology

Přírodovědecká fakulta
podzim 2018
Rozsah
3/0. 3 kr. (plus ukončení). Ukončení: zk.
Vyučující
doc. Mgr. Pavel Plevka, Ph.D. (přednášející)
Garance
doc. RNDr. Ivo Rudolf, Ph.D.
Ústav experimentální biologie – Biologická sekce – Přírodovědecká fakulta
Dodavatelské pracoviště: Ústav experimentální biologie – Biologická sekce – Přírodovědecká fakulta
Rozvrh
Po 1. 10. až Pá 14. 12. St 14:00–16:50 B11/335
Předpoklady
(Bi2060 Základy mikrobiologie, Bi4010 Základy molekulární biologie)
or
(Mikrobiologie Bi5710 a Molekularni biologie Bi4020)
This lecture series is intended for students of biology (general biology, molecular biology and genetics, specialised biology, biochemistry) and for other students interested in virology.
Omezení zápisu do předmětu
Předmět je otevřen studentům libovolného oboru.
Cíle předmětu
This course aims to provide an understanding of how viruses are built, how they infect and replicate in host cells, how they spread, evolve and cause disease. This is structural and molecular virology course with the aim to provide understanding of basic mechanisms controlling the virus life cycle. While it is focused primarily on human and animal viruses, it will also discuss bacteriophages. The course will explain important applications of virology, including: virus-based gene therapy; developments of virus-based vaccines; use of “oncolytic” viruses to treat cancers; ability bacteriophages to combat human and animal bacterial diseases. We will also discuss emerging viruses and potential bioterrorism agents.

By the end of this course, students should be able to do the following:
• Understand what is a virus. Have your own opinion as to whether viruses are alive or not.
• Understand basic concepts in virology related to strategies of virus cell entry, replication, particle assembly, release of virions from cells, and virus structure.
• Describe how the simplicity of viruses enabled groundbreaking discoveries of fundamental concepts in biology such as:
o Demonstration that genes are composed of DNA
o Discovery of Internal Ribosomal Entry Site (IRES)
o Discovery of transcription enhancers
o Discovery of translation factors
• Critically analyze what you read in scientific journals.
• Have a general overview of virus taxonomy. Be familiar with viruses that cause severe diseases in humans or are economically important pathogens of agricultural animals and plants.
The gained knowledge and skills will be useful for basic and applied virology research. The critical analysis of published research may be useful for any field of research enterprise.
Osnova
  • Week 1
  • Introduction
  • - viruses and their importance
  • - methods used in virology
  • - introduction to virus structure
  • • Read chapters 1-2 in the textbook.
  • • Lecture reading: Caspar D. L. D. and Klug A. (1962) Physical principles in the construction of regular viruses. Cold Spring Harbor Symposia Quantitative Biology, 27, 1–24
  • Week 2
  • Virus structure (continued), virus transmission
  • - Icosahedral viruses and quasi-equivalence (Caspar Klug theory)
  • - Enveloped viruses and viruses with complex structures
  • • Read chapters 3 and 4 from the textbook.
  • • Lecture reading: Rossmann M. G. et al. (2005) Combining X-ray crystallography and electron microscopy. Structure, 13, 355–362
  • Week 3
  • Attachment and entry of viruses into cells; virus transcription, translation and transport of virus macromolecules within a cell
  • - Cell entry of enveloped viruses
  • - Cell entry of naked viruses
  • - Various methods that viruses use to ensure translation of their genes
  • • Read chapters 5 and 6 from the textbook.
  • • Lecture reading: Crick F. (1970) Central dogma of molecular biology. Nature, 227, 561–563
  • Week 4
  • Virus genome replication, impact of virus infection of cell architecture; assembly and exit of virions from cells
  • - Locations within cells where replication takes place
  • - Reverse transcription
  • - Roles of host and virus proteins in replication
  • - Assembly mechanisms of virus capsids
  • - Mechanisms by which viruses exit the cells
  • - Origins of membranes that are components of virions
  • • Read chapters 7 and 8 from the textbook.
  • • Lecture reading: Steven A. C. et al. (2005) Virus maturation: dynamics and mechanism of a stabilizing structural transition that leads to infectivity. Current Opinion in Structural Biology, 15, 227–236
  • Week 5
  • Outcomes of infection for the host; immune response; classification and nomenclature of viruses; Herpesviruses
  • - Components of innate and adaptive immunity in vertegrates
  • - Immunity at cellular level
  • - Baltimore classification of viruses
  • - Structure of HSV virion, genome, and replication cycle
  • - Herpesvirus persistence
  • • Read chapters 9-11 from the textbook.
  • • Lecture reading: Mettenleiter T. C., Klupp B. G. and Granzow H. (2006) Herpesvirus assembly: a tale of two membranes. Current Opinion in Microbiology, 9, 423–429
  • • First research assignment is due
  • Week 6
  • Parvoviruses, Reoviruses
  • - Structure of parvovirus virions, main features of parvovirus genomes and replication
  • - Differences between autonomous and defective parvoviruses
  • - Structure of rotavirus virions, genome, and mechanism of replication
  • - How rotaviruses cause disease.
  • • Read chapters 12 and 13 from the textbook.
  • • Lecture reading: Hueffer K. and Parrish C. R. (2003) Parvovirus host range, cell tropism and evolution. Current Opinion in Microbiology, 6, 392–398
  • Week 7
  • Picornaviruses; Rhabdoviruses
  • - Structure of picornavirus virion, genome and, determinants of picornavirus replication
  • - Picornavirus recombination, experimental systems for picornavirus studies
  • - Structure of rhabdovirus virions, genome, and mechanism of replication.
  • - Use of rhabdovirus reverse genetics.
  • • Read chapters 14 and 15 from the textbook.
  • • Lecture reading: Xing L. et al. (2003) Structural analysis of human rhinovirus complexed with ICAM-1 reveals the dynamics of receptor-mediated virus uncoating. Journal of Virology, 77, 6101–6107
  • Week 8
  • Retroviruses + HIV; Hepadnaviruses
  • - Structure of retrovirus virion, genome and, mechanism of retrovirus replication
  • - Endogenous retroviruses
  • - Effects of HIV infection on the host, methods for HIV prevention
  • - Hepadnavirus virion, genome, and mechanism of replication.
  • - Methods for HBV prevention
  • • Read chapters 16, 17 and, 18 from the textbook.
  • • Lecture reading: Zhu P. et al. (2006) Distribution and three-dimensional structure of AIDS virus envelope spikes. Nature, 441, 847–852
  • Week 9
  • Bacteriophages
  • - Replication cycle and gene expression control of coliphages
  • - Virion structure and infection process of dsRNA phages
  • - Virion structure and replication cycle of T4 and T7 phages
  • - Regulation of switching between lytic cycle and lysogeny
  • - Use of phages in medicine and biotechnology
  • • Read chapter 19 from the textbook.
  • • Lecture reading: Leiman P.G. et al. (2003) Structure and morphogenesis of bacteriophage T4. Cellular and Molecular Life Sciences, 60, 2356–2370
  • • Second research assignment is due
  • Week 10
  • Origins and evolution of viruses; emerging viruses; bioterorism
  • - Basic theories on the origins of viruses
  • - Virus evolution through mutation, recombination and, reassortment
  • - Co-evolution of viruses and their hosts
  • - What is emerging virus?
  • - Measures that can be taken to prevent and contain outbreaks of infectious diseases.
  • • Read chapters 20 and 21 from the textbook.
  • • Lecture reading: Froissart R. et al. (2005) Recombination every day: abundant recombination in a virus during a single multi-cellular host infection. PLoS Biology, 3, e89
  • Week 11
  • Viruses and cancer; virus persistence; vaccines
  • - Characteristics of viruses that are associated with cancers
  • - Mechanisms for virus induction of cancer
  • - Examples of physical and chemical agents that affect virus survival
  • - Reasons to preserve and destroy viruses
  • - How vaccination helps to control virus diseases
  • - Types of vaccines
  • - Virus-based vaccines against non-viral disorders
  • • Read chapters 22, 23 and 24 from the textbook.
  • • Lecture reading: Longworth M. S. and Laimins L. A. (2004) Pathogenesis of human papillomaviruses in differentiating epithelia. Microbiology and Molecular Biology Reviews, 68, 362–372
  • Week 12
  • Anti-viral drugs; satellite viruses, viroids, virusoids, satellite virophages, prions
  • - Modes of action of antiviral drugs
  • - Origins of virus resistance to drugs
  • - Description and charactirization of sub-viral infectious agents
  • • Read chapters 25 and 26 from the textbook.
  • • Lecture reading: Plevka P. et al. (2013) Structure of human enterovirus 71 in complex with a capsid-binding inhibitor. Proc Natl Acad Sci USA. 110(14):5463-7
Literatura
    doporučená literatura
  • • John Carter and Venetia Saunders. (2007) “Virology : principles and applications”, 2nd edition; ISBN: 978-0-470-02386-0 (HB); John Wiley & Sons Ltd, The Atrium, Southern Gate, Chichester, West Sussex PO19 8SQ, England
Výukové metody
The course will be presented as a series of lectures presented with the aid of PowerPoint slides.
Metody hodnocení
Final grade will be calculated according to Table 1 based on following performance indicators:

Two Mini-Research Assignments (each of them is worth 10% of your final grade).
The assignments will take a form of short papers. Detailed instructions explaining the assignments will be posted on www in the “Mini-Research Assignments” section. All Mini-Research Assignments will be due at 10:30am on the day listed in the Course outline section of this syllabus. Taking off 1% for each day the assignment is late will penalize late work. Mini-Research Assignments should be submitted in electronic form only.

Final exam (90% of your grade).
The final exam will be a mixture of multiple choice and essay questions.

Table 1. Grading scale.
A 100-91%; B 90-81%; C 80-71%; D 70-61%; E 60-51%; F 50-0%
Vyučovací jazyk
Angličtina
Informace učitele
Academic Integrity
You are required to adhere to the following the rules of academic integrity (as described in „Disciplinární řád pro studenty”). You are prohibited from (among other things): cheating, lying, stealing, and deceit in any of their diverse forms (such as use of ghost-written papers, the use of substitutes for taking examinations, the use of illegal cribs, plagiarism, and copying during examinations).
Violations of academic integrity will result in sanctions. These sanctions range from taking off points from the particular part of the grade to assigning „Failed“ as the final grade in the class. The decision about the sanction for academic dishonesty is entirely at the discretion of the instructor. All cases of academic dishonesty will be reported to the „Disciplinární komise PřF MU“ (disciplinary commitee).

Course Format
In this course, you will be acquiring knowledge in two main ways: in the lectures and by home study (which means by reading the assigned materials and working on assignments and homeworks). Reading the material will give you a base of factual knowledge. It will also introduce you to the main theoretical points. The lectures then will reinforce your understanding of the material. The lectures will also introduce you to concepts and theories that are not covered by the readings. Class sessions will also be a space for discussions.

Class rules
Before coming to class, please turn off anything that beeps or rings.
Please, help create a nice learning environment for yourself and your classmates. Reading any material that is not related to the class, texting, or checking the internet during the class is rude and will not be tolerated.
Please refrain from eating during class. Having something to drink is fine.
If you have any question regarding the material being discussed in class, do not hesitate to ask. If you ask such question, it will help to clarify the issue not only for you but for your peers as well!
In class discussions, be respectful of other students' opinions. You have the right to hold and express whatever opinion on the discussed topic, no matter how unacceptable they may seem to your classmates. They can disagree with you by they must respect your right to hold your opinion. Likewise, you must respect their right to express their views freely.
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Předmět je vyučován každoročně.
Předmět je zařazen také v obdobích podzim 2014.
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