virology syllabus

7/29/2019 Virology Syllabus

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Syllabus (11 Weeks MOOC Certificate Course inVIROLOGY 1)

Learning Objectives

The basic thesis of the course is that all viruses adopt a common strategy. The strategy issimple:

1. Viral genomes are contained in metastable particles.2. Genomes encode gene products that promote an infectious cycle (mechanisms forgenomes to enter cells, replicate, and exit in particles).3. Infection patterns range from benign to lethal; infections can overcome or co-exist with hostdefenses.

Despite the apparent simplicity, the tactics evolved by particular virus families to survive andprosper are remarkable. This rich set of solutions to common problems in host/parasiteinteractions provides significant insight and powerful research tools. Virology has enabled amore detailed understanding of the structure and function of molecules, cells and organismsand has provided fundamental understanding of disease and virus evolution.

Course Structure and Grading Policy

The course consists of the following:

Videos. The lectures are delivered via video modules which will typically have aduration of anything from five minutes to twenty minutes. There will be an average ofapproximately two hours of video content per week but this number will vary. You may

watch the lecture videos at your convenience.

Reading. Suggestions for additional reading and/or listening (podcasts) will be

included in the syllabus. These are optional but will help to immerse you in the field ofvirology.

Slides. PDF files of all the lecture slides will be made available at the start of eachweek.

In-Module Quizzes. Most of the video modules will feature several "in-modulequizzes". Such a quiz consists of a short multiple choice question that appears at anappropriate time in the video to help emphasize an important concept. These "in-module quizzes" do not count towards your grade.

Discussion Forums. Participation in the discussion area is encouraged, but will not


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count towards a final grade.

Quizzes. There will be a quiz released every week that covers that weeks material andis intended to help you study for the final.

Final Exam. A required final exam will be given at the end of the course.

Grading Policy Quizzes - There will be a quiz released every week that covers that weeks material.

Starting in week 2, this quiz should be completed within 2 weeks of its release and willcount towards 30% of your final grade. You may re-take these quizzes up to 10 timesduring the that two week period and only the highest score will be counted. Quiz 1does not count towards your final grade.

A final exam is required. The final exam will be released in the last week of thecourse and must be completed within a two week period. Only two opportunities aregiven to achieve your desired grade on the final and this grade will count towards 70%of your final grade.

To receive a certificate of completion, students will need to earn an overall gradeaverage of 70% or above.

To receive a certificate of completion with distinction, students will need to earn anoverall grade average of 85% or above.

Discussion posts will not count towards the final average, but we encourage yourparticipation. Many ideas and solutions come out of the interaction that students have

with each other in the discussion area.

Schedule and Topics & Covered

Week 1 - August 4, 2013

S1: Welcome to virology

S2: What is a virus?

S3: Viruses then and now

Week 1 Reading

Flint vol. 1 chapter 1

Are viruses living?

What is a virus?

Are viruses alive? (take the poll)

The virus and the virion

Cell size and scale

TWiV 43: Virus classification

Week 2

S1: The infectious cycle

S2: Assay of viral infectivity
http://www.virology.ws/2004/06/09/are-viruses-living/http://www.virology.ws/2004/07/28/what-is-a-virus/http://www.virology.ws/are-viruses-alive/http://www.virology.ws/2010/07/22/the-virus-and-the-virion/http://learn.genetics.utah.edu/content/begin/cells/scale/http://www.twiv.tv/2009/08/02/twiv-43-virus-classification/http://www.virology.ws/2004/07/28/what-is-a-virus/http://www.virology.ws/are-viruses-alive/http://www.virology.ws/2010/07/22/the-virus-and-the-virion/http://learn.genetics.utah.edu/content/begin/cells/scale/http://www.twiv.tv/2009/08/02/twiv-43-virus-classification/http://www.virology.ws/2004/06/09/are-viruses-living/


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S3: Measurement of virions and their components

S4: Revolutionary methods

S5: One-step growth cycle

Week 2 Reading

Flint vol 1 chapter 2

Influenza virus growth in eggs

Influenza hemagglutination inhib ition assay

The amazing HeLa cells of Henrietta Lacks

Week 3

S1: The Baltimore scheme

S2: DNA virus genomes

S3: RNA virus genomes

S4: Viral geneticsWeek 3 Reading


Simplifying virus classification: The Baltimore system

Clinical benefit of lentiviral gene therapy in two patients with a rare neurological disease

TWiV 49: Viral genomes

Week 4

S1: Structure

S2: The tools of structural virology

S3: Helical symmetry

S4: Icosahedral symmetry

S5: Enveloped virions

S6: Complex virions

Week 4 Reading


Structure of influenza virus

Virus images at ViperDB

TWiV 39: Virus structure

Week 5

S1: Attachment to cells

S2: Entry into cells

S3: Acid-catalyzed fusion
http://www.virology.ws/2009/12/10/influenza-virus-growth-in-eggs/http://www.virology.ws/2009/05/27/influenza-hemagglutination-inhibition-assay/http://www.virology.ws/2009/02/09/the-amazing-hela-cells-of-henrietta-lacks/http://www.virology.ws/2009/08/12/simplifying-virus-classification-the-baltimore-system/http://www.virology.ws/2009/11/25/clinical-benefit-of-lentiviral-gene-therapy-in-two-patients-with-a-rare-neurologic-disease/http://www.twiv.tv/2009/09/13/twiv-49-viral-genomes/http://www.virology.ws/2009/04/30/structure-of-influenza-virus/http://www.virology.ws/2009/03/06/virus-images-at-viperdb/http://www.twiv.tv/2009/07/05/twiv-39-virus-structure/http://www.virology.ws/2009/12/10/influenza-virus-growth-in-eggs/http://www.virology.ws/2009/05/27/influenza-hemagglutination-inhibition-assay/http://www.virology.ws/2009/02/09/the-amazing-hela-cells-of-henrietta-lacks/http://www.virology.ws/2009/08/12/simplifying-virus-classification-the-baltimore-system/http://www.virology.ws/2009/11/25/clinical-benefit-of-lentiviral-gene-therapy-in-two-patients-with-a-rare-neurologic-disease/http://www.twiv.tv/2009/09/13/twiv-49-viral-genomes/http://www.virology.ws/2009/04/30/structure-of-influenza-virus/http://www.virology.ws/2009/03/06/virus-images-at-viperdb/http://www.twiv.tv/2009/07/05/twiv-39-virus-structure/


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S4: A new paradigm for entry

S5: Entry of non-enveloped virions

S6: Entering the nucleus

Week 5 Reading

Flint Vol I Chapter 5

Influenza virus attachment to cells

Influenza virus attachment to cells: Role of different sialic acids

TWiV 46: Virus entry into cells

Week 6

S1: Viral RNA synthesis

S2: RNA polymerization

S3: Plus strand RNA synthesis

S4: Negative strand RNA synthesisS5: RNA synthesis of dsRNA genomes

S6: RNA synthesis as a source of diversity

Week 6 Reading


Influenza viral RNA synthesis

The error prone ways of RNA synthesis

TWiV 60: Making viral RNA

Week 7

Replication of DNA virus genomes

Week 7 Reading


TWiV 96: Making viral DNA I

TWiV 106: Making viral DNA II

Week 8

Transcription and RNA processing

Week 8 Reading

Flint Vol I Chapter 8 through page 277

TWiV 162: Transcription

TWiV 216: Processing viral RNA

Week 9

S1: Reverse transcriptase
http://www.virology.ws/2009/05/04/influenza-virus-attachment-to-cells/http://www.virology.ws/2009/05/05/influenza-virus-attachment-to-cells-role-of-different-sialic-acids/http://www.virology.ws/2009/05/05/influenza-virus-attachment-to-cells-role-of-different-sialic-acids/http://www.twiv.tv/2009/08/23/twiv-46-virus-entry-into-cells/http://www.virology.ws/2009/05/08/influenza-viral-rna-synthesis/http://www.virology.ws/2009/05/10/the-error-prone-ways-of-rna-synthesis/http://www.twiv.tv/2009/11/29/twiv-60-making-viral-rna/http://www.twiv.tv/2010/08/22/twiv-96-making-viral-dna/http://www.twiv.tv/2010/11/06/twiv-106-making-viral-dna-ii/http://www.twiv.tv/2010/11/06/twiv-106-making-viral-dna-ii/http://www.twiv.tv/2011/12/18/twiv-162-transcription/http://www.twiv.tv/2013/01/20/twiv-216-processing-viralguuaacaccagrna/http://www.virology.ws/2009/05/04/influenza-virus-attachment-to-cells/http://www.virology.ws/2009/05/05/influenza-virus-attachment-to-cells-role-of-different-sialic-acids/http://www.twiv.tv/2009/08/23/twiv-46-virus-entry-into-cells/http://www.virology.ws/2009/05/08/influenza-viral-rna-synthesis/http://www.virology.ws/2009/05/10/the-error-prone-ways-of-rna-synthesis/http://www.twiv.tv/2009/11/29/twiv-60-making-viral-rna/http://www.twiv.tv/2010/08/22/twiv-96-making-viral-dna/http://www.twiv.tv/2010/11/06/twiv-106-making-viral-dna-ii/http://www.twiv.tv/2011/12/18/twiv-162-transcription/http://www.twiv.tv/2013/01/20/twiv-216-processing-viralguuaacaccagrna/


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S2: Retroviruses

S3: Reverse transcription

S4: Integration

S5: The provirus

S6: Hepatitis B virus

Week 9 Reading


Museum pelts help date the koala retrovirus

Unexpected endogenous viruses

TWiV 66: Reverse transcription

Week 10

S1: End-dependent initiation of protein synthesis

S2: Other decoding mechanismsS3: One mRNA, one protein?

S4: Maximizing coding capacity of the viral genome

S5: Regulation of translation: eIF2alpha

S6: How viruses regulate cell translation

S7: MicroRNAs

Week 10 Reading


Week 11

S1: Principles of virion assembly

S2: Getting to the right place

S3: Making sub-assemblies

S4: Concerted assembly: Budding

S5: Genome packaging

S6: Acquistion of an envelope and egress

Week 11 Reading

Flint vol 1 chapters 12, 13

Packaging of the segment ed influenza RNA genome

TWiV 238: Lost in translation

LECTURER
http://www.virology.ws/2012/10/11/museum-pelts-help-date-the-koala-retrovirus/http://www.virology.ws/2010/12/10/unexpected-endogenous-viruses/http://www.twiv.tv/2010/01/17/twiv-66-reverse-transcription/http://www.virology.ws/2009/06/26/packaging-of-the-segmented-influenza-rna-genome/http://www.twiv.tv/2013/06/23/twiv-238-lost-in-translation/http://www.virology.ws/2012/10/11/museum-pelts-help-date-the-koala-retrovirus/http://www.virology.ws/2010/12/10/unexpected-endogenous-viruses/http://www.twiv.tv/2010/01/17/twiv-66-reverse-transcription/http://www.virology.ws/2009/06/26/packaging-of-the-segmented-influenza-rna-genome/http://www.twiv.tv/2013/06/23/twiv-238-lost-in-translation/


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Vincent Racaniello, Professor of Microbiology & Immunology in the College ofPhysicians and Surgeons of Columbia University, has done laboratory research on viruses for37 years. Dr. Racaniello has a Ph.D. in Biomedical Sciences from Mt. Sinai School ofMedicine of the City University of New York, where his thesis research was focussed oninfluenza viruses. In 1982 he joined the faculty in the Department of Microbiology at ColumbiaUniversity College of Physicians & Surgeons in New York City. There he established a

laboratory to study viruses, and to train other scientists to become virologists. Over the yearshe have studied a variety of viruses including poliovirus, echovirus, enterovirus 70, rhinovirus,and hepatitis C virus. As principal investigator he oversees the research that is carried out byPh.D. students and postdoctoral fellows. He also teaches virology to graduate students, as

well as medical, dental, and nursing students.

Dr. Racaniello has partnered with Columbia's Center for New Media Teaching and Learning(CCNMTL) to educate as many people as he can about viruses. Utilizing iTunes U, Dr.Racaniello delivered his Virology lectures to over 90,000 subscribers. Partnering with theCCNMTL once again, Dr. Racaniello is excited to deliver this course to the masses throughCoursera.

Ashlee Bennett decided to pursue a career in science after graduating from DrexelUniversity in 2007. While working as a research technician full-time under Dr. Ian Lipkin at theCenter for Infection and Immunity, Ashlee honed her research interests and decided to pursuea doctoral degree in the department of Microbiology and Immunology at Columbia University.Now, as a PhD student under the supervision of Dr. Vincent Racaniello, Ashlees doctoralresearch is currently focused upon understanding the anti-rhinoviral mechanism of metalcompounds.

In addition to research, Ashlee is passionate about science education and cultivating publicscience literacy. Through her experience podcasting, tutoring and working as a teachingassistant at Columbia University, Ashlee has enjoyed the opportunity to share her enthusiasm

for virology and develop teaching strategies that make science education accessible andentertaining. When Ashlee's not nerding-out in the laboratory, she enjoys running, swimming,rock-climbing, cycling around NYC and taking her pet tortoise for [very slow] walks in thepark.

The Columbia Center for New Media Teaching and Learning (CCNMTL) was founded atColumbia University in 1999 to enhance teaching and learning through the purposeful use ofnew media and technology. In partnership with faculty, the Center supports efforts rangingfrom basic course website management to advanced project development. CCNMTL iscommitted to remaining a leader in the field of new media teaching and learning, engaging

faculty, educators, librarians, partner institutions, and the community in the reinvention ofeducation for the digital age. CCNMTL are committed to ongoing evaluation of the efficacy ofour work within the University. Staff members Stephanie Ogden, Ellen Maleszewski, andMichael Cennamo will be providing technical support, helping Vincent and Ashlee create thebest learning experience possible.

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