Microbiology KU Medical Center

Molecular and Pathogenesis (MICR 812) Fall, 2016 Syllabus

Location of Classes: 1006 Orr‐Major A. Contact Information

Jianming Qiu, Ph.D. 4004 Hixon 588‐4329 [email protected]

B. Purpose of this Course

This Virology course is aimed at graduate students who pursue master degree in science in the Department of Microbiology. It provides a contemporary understanding of how are built, how they infect and replicate in cells, how they spread and evolve, how they interact with host cells, how they eventually cause diseases, and how of a host can be prevented.

This course will provide a balanced approach to Virology, combining the molecular and pathogenesis aspects of Virology. While it is focused primarily on human viruses, it will also discuss animal viruses, as human viruses often are evolved from animal viruses.

In addition to traditional topics, this course will explain new “hot” trends in Virology, including: ‐based vector in human gene therapy; modern advances in vaccinology; “oncolytic” viruses to treat cancers; emerging viruses and potential bioterrorism agents (influenza virus, coronavirus, and filoviruses).

C. Intended Course Outcomes

By the end of this course, students should be able to: 1. Describe virus taxonomy, virus structure and virus entry, trafficking and egress.

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2. Describe the basics of the viral gene expression, including , transcription, post‐transcriptional regulation, translation and post‐translational regulation of virus genes. 3. Apply techniques used in modern virology and design experiments to test novel hypotheses in virology. 4. Distinguish diverse characteristics of viruses – host range, target tissues, replication strategy, transmission, etc., in particular, of these emerging/reemerging viruses, e.g., influenza and viruses, and medical important viruses, e.g., HIV. 5. Describe the principle of virus infection and the host immune defense, viral ontogenesis innovative approaches to the development of antiviral drugs and . 6. Relate the principle of virus infection, the host immune response and viral ontogenesis to innovative approaches to the development of antiviral drugs and vaccines.

D. Text/Reference Book: Textbook: S. J. Flint, et al: Principles of Virology: , Pathogenesis, and Control of Animal Viruses (2 Volume Set, 3rd Edition) ASM press.

Reference book: D. M. Knipe, et al: Fields Virology (6 edition, 2011) Lippincott Williams & Wilkins.

E. Organization of the Course

This course is designed as a set of interactive lectures. Students must read the relevant chapters in the textbook before each class. The course sessions will generally begin with readiness quiz and a lecture on a given topic, with questions to facilitate discussion. This will be followed by a quiz at the end of the session.

F. Expectations of Participants

We will meet an hour each Wednesday and Friday morning throughout the semester. You are required to complete the pre‐class assignment, attend the learning sessions, participate in the class activities and submit quizzes.

Grades will be determined based on students meeting the attendance requirements, participating in a respectful and collegial manner in class, submitting quizzes, and completing the midterm and final exams.

H. Assessments

Learning will be assessed by oral and written assignments, including low‐stakes “readiness quizzes” during class time. Some of your graded projects will be undertaken in teams of learners. Grades will be determined by the following formula:

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20% assignments/readiness quizzes/classroom participation 20% session assessments (see calendar of sessions) 30% team‐based learning projects 30% final project presentations Grading Scale: 86 – 100% = A 71 – 85% = B 60 – 70 % = C <60% = F

I. Schedule 10:00 – 10:50 AM, Monday and Wednesday You MUST read the relevant textbook chapter BEFORE the scheduled lecture.

Lecture Date Lecturer Topic Subtopics number 1 Mon, Aug 22 Jianming Qiu Virus Taxonomy Classification of animal viruses Vol. I, Chapter 1) Viral genomes 2 Wed, Aug 24 Jianming Qiu Virology Methods Virus culture, detection, (Vol. I, Chapter 2) diagnostics and genetics 3 Mon, Aug 29 Severin Virus Entry Virus attachment, receptors, Gudima (Vol. I, Chapter 5) and intracellular trafficking 4 Wed, Aug 31 Severin RNA Virus Replication Negative stranded RNA viruses Gudima (Vol. I, Chapter 6) Positive stranded RNA viruses Double stranded RNA viruses Mon, Sept 5 LABOR DAY NO CLASSES 5 Wed, Sept 7 Jianming Qiu Viral DNA Transcription Transcription initiation (Vol. I, Chapter 8) complexes Viral transactivators 6 Mon, Sept 12 Severin Reverse Transcription & HIV& hepatitis B Gudima (Vol. I, Chapter 7) virus 7 Wed, Sept 14 Jianming Qiu DNA Virus Replication ds DNA viruses (Vol. I, Chapter 9) ssDNA viruses Viral DNA replication 8 Mon, Sept 19 Jianming Qiu Viral RNA processing RNA splicing, polyadenylation, (Vol. I, Chapter 10) and RNA export 9 Wed, Sept 21 Jianming Qiu Viral mRNA translation Mechanism of translation (Vol. I, Chapter 11) 10 Mon, Sept 26 Jianming Qiu ASSESSMENT #1 11 Wed, Sept 28 Severin Virus Assembly Virus assembly, maturation, and Gudima (Vol. I, Chapter 13) release 12 Mon, Oct 3 Jianming Qiu Vaccine development and the (Vol. II, Chapter 8) challenges 13 Wed Oct 5 Maria Principles of virus Infection of a host, infection of Kalamvoki infection populations (Vol. II, Chapter 1&2) 14 Mon, Oct 10 Maria Host defense I Innate immune response Kalamvoki (Vol. II, Chapter 4) against DNA viruses

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15 Wed, Oct 12 Maria Host defense II Innate immune response Kalamvoki (Vol. II, Chapter 4) against RNA viruses 16 Mon, Oct 17 Maria Infection patterns I Lytic, latent infection, and slow Kalamvoki (Vol. II, Chapter 5) 17 Wed, Oct 19 Maria ASSESSMENT #2 Kalamvoki 18 Mon, Oct 24 Severin Infection patterns II Transformation and Gudima (Vol. II, Chapter 7) oncogenesis 19 Wed, Oct 26 Severin Antiviral drugs I Principle of antiviral drug Gudima (Vol. II, Chapter 9) development 20 Mon, Oct 31 Severin Antiviral drugs II Antiviral drug development, Gudima (Vol. II, Chapter 9) and anti‐HIV and anti‐HCV drugs 21 Wed, Nov 2 Severin Emerging viruses I Ebola virus Gudima (A chapter in a reference book, TBD) 22 Mon, Nov 7 Maria Emerging viruses II Coronavirus Kalamvoki (A chapter in a reference book, TBD) 23 Wed, Nov 9 Severin ASSESSMENT #3 Gudima 24 Mon, Nov 14 Jianming Qiu Emerging viruses III Influenza virus (A chapter in a reference book, TBD) 25 Wed, Nov 16 Jianming Qiu Viral Vector I DNA virus vectors (Ad, AAV, and (A chapter in a reference HSV) book, TBD) 26 Mon, Nov 21 Jianming Qiu Viral Vector II RNA virus vectors (A chapter in a reference (Retroviral/lentiviral Vector, book, TBD) and others) Wed, Nov 23 Thanksgiving Holiday NO CLASSES 27 Mon, Nov 28 Maria Topics in virology I HIV pathogenesis Kalamvoki (Vol. II, Chapter 6) 28 Wed, Nov. 30 Severin Topics in virology II HBV, HCV, HEV and HDV Gudima (A chapter in a reference book, TBD)

29 Mon, Dec 5 Maria Topics in virology III DNA viruses Kalamvoki (A chapter in a reference book, TBD) 30 Wed, Dec 7 Jianming Qiu ASSESSMENT #4 31 Mon, Dec 14 Jianming Qiu Final exam Final project presentations

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