Bi5050 Structural virology

Faculty of Science
Autumn 2018
Extent and Intensity
3/0. 3 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).
Teacher(s)
doc. Mgr. Pavel Plevka, Ph.D. (lecturer)
Guaranteed by
doc. RNDr. Ivo Rudolf, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Timetable
Mon 1. 10. to Fri 14. 12. Wed 14:00–16:50 B11/335
Prerequisites
(Bi2060 Základy mikrobiologie, Bi4010 Základy molekulární biologie)
nebo
(Mikrobiologie Bi5710 a Molekularni biologie Bi4020)
Přednáška je určena studujícím biologických oborů (obecná biologie, molekulární biologie a genetika, speciální biologie), případně dalším potenciálním zájemcům o virologii.
Course Enrolment Limitations
The course is offered to students of any study field.
Course objectives
Cílem předmětu je seznámit studenty se strukturou virů, způsoby doručení virového genomu do buněk, replikací genomu, šíření virů mezi organismy, virovou evolucí a způsoby jak viry způsobují onemocnění. Tento kurz je zaměřen na strukturní a molekulární aspekty virologie. Po jeho abslovování budou studenti rozumět základním mechanismům zajišťujícím úspěšný průběh virového replikačního cyklu. Kurz je zaměřen primárně na lidské a zvířecí viry, ale zběžně se věnuje také bakteriofágům. Studenti se také seznámí s důležitými aplikacemi virologie zahrnujícími využití virů v genové terapii, vývoj protivirových vakcín, použití „onkolytických“ virů k léčbě nádorových onemocnění a použití bakteriofágů v boji proti bakteriálním onemocněním. Budeme se také zabývat možnostmi vzniku nových virů a potenciálním využitím virů v bioterorismu.

Studenti budou mít na konci kurzu následující znalosti a dovednosti:
• Pochopení, co je to virus. Budou mít vlastní názor na to, jestli jsou viry živé, nebo ne.
• Pochopení základních virologických konceptů spojených s mechanismy vstupu virů do buněk, replikace, sestavování virových partikulí, uvolnění dceřinných virionů z buněk a virové struktury.
• Budou schopni popsat, jak jednoduchost virů umožnila zásadní objevy v biologii jako například:
o objev, že geny jsou tvořeny DNA
o identifikaci “vnitřního místa pro vstup ribozomu” (internal ribosome entry site – IRES
o objev zesilovačů transkripce (transcription enhancers)
o objev transkripčních faktorů (transcription factors)
• Budou umět kriticky analyzovat obsah vědeckých článků.
• Budou mít základní přehled v taxonomii virů. Budou znát viry, které způsobují závažná lidská onemocnění a viry, které jsou původci onemocnění hospodářských zvířat a rostlin.
Syllabus
  • 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
Literature
    recommended literature
  • • 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
Teaching methods
The course will be presented as a series of lectures presented with the aid of PowerPoint slides.
Assessment methods
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%
Language of instruction
English
Further comments (probably available only in Czech)
Study Materials
The course is taught annually.
The course is also listed under the following terms Autumn 2014.
  • Enrolment Statistics (recent)
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