Syllabus (11 Weeks MOOC Certificate Course in VIROLOGY 1)

Learning Objectives
The basic thesis of the course is that all viruses adopt a common strategy. The strategy is simple: 1. Viral genomes are contained in metastable particles. 2. Genomes encode gene products that promote an infectious cycle (mechanisms for genomes to enter cells, replicate, and exit in particles). 3. Infection patterns range from benign to lethal; infections can overcome or co-exist with host defenses. Despite the apparent simplicity, the tactics evolved by particular virus families to survive and prosper are remarkable. This rich set of solutions to common problems in host/parasite interactions provides significant insight and powerful research tools. Virology has enabled a more detailed understanding of the structure and function of molecules, cells and organisms and 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 a duration of anything from five minutes to twenty minutes. There will be an average of approximately 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 of virology. Slides. PDF files of all the lecture slides will be made available at the start of each week. In-Module Quizzes. Most of the video modules will feature several "in-module quizzes". Such a quiz consists of a short multiple choice question that appears at an appropriate time in the video to help emphasize an important concept. These "inmodule quizzes" do not count towards your grade. Discussion Forums. Participation in the discussion area is encouraged, but will not

count towards a final grade. Quizzes. There will be a quiz released every week that covers that weeks material and is 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 will count towards 30% of your final grade. You may re-take these quizzes up to 10 times during the that two week period and only the highest score will be counted. Quiz 1 does not count towards your final grade. A final exam is required. The final exam will be released in the last week of the course and must be completed within a two week period. Only two opportunities are given 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 grade average of 70% or above. To receive a certificate of completion with distinction , students will need to earn an overall grade average of 85% or above. Discussion posts will not count towards the final average, but we encourage your participation. 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

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 inhibition assay The amazing HeLa cells of Henrietta Lacks Week 3 S1: The Baltimore scheme S2: DNA virus genomes S3: RNA virus genomes S4: Viral genetics Week 3 Reading Flint vol 1 chapter 3 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 Flint vol 1 chapter 4 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

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 synthesis S5: RNA synthesis of dsRNA genomes S6: RNA synthesis as a source of diversity Week 6 Reading Flint Vol I Chapter 6 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 Flint Vol I Chapter 9 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

S2: Retroviruses S3: Reverse transcription S4: Integration S5: The provirus S6: Hepatitis B virus Week 9 Reading Flint vol 1 chapter 7 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 mechanisms S3: 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 Flint vol 1 chapter 11 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 segmented influenza RNA genome TWiV 238: Lost in translation

LECTURER

Vincent Racaniello, Professor of Microbiology & Immunology in the College of Physicians and Surgeons of Columbia University, has done laboratory research on viruses for 37 years. Dr. Racaniello has a Ph.D. in Biomedical Sciences from Mt. Sinai School of Medicine of the City University of New York, where his thesis research was focussed on influenza viruses. In 1982 he joined the faculty in the Department of Microbiology at Columbia University 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 years he 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 by Ph.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 the CCNMTL once again, Dr. Racaniello is excited to deliver this course to the masses through Coursera. Ashlee Bennett decided to pursue a career in science after graduating from Drexel University in 2007. While working as a research technician full-time under Dr. Ian Lipkin at the Center for Infection and Immunity, Ashlee honed her research interests and decided to pursue a 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 doctoral research is currently focused upon understanding the anti-rhinoviral mechanism of metal compounds. In addition to research, Ashlee is passionate about science education and cultivating public science literacy. Through her experience podcasting, tutoring and working as a teaching assistant at Columbia University, Ashlee has enjoyed the opportunity to share her enthusiasm for virology and develop teaching strategies that make science education accessible and entertaining. 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 the park. The Columbia Center for New Media Teaching and Learning (CCNMTL) was founded at Columbia University in 1999 to enhance teaching and learning through the purposeful use of new media and technology. In partnership with faculty, the Center supports efforts ranging from basic course website management to advanced project development. CCNMTL is committed 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 of education for the digital age. CCNMTL are committed to ongoing evaluation of the efficacy of our work within the University. Staff members Stephanie Ogden, Ellen Maleszewski, and Michael Cennamo will be providing technical support, helping Vincent and Ashlee create the best learning experience possible.