Course 2013


Virology – Biology W3310

Spring 2013

Click here for material from the 2012 virology course

viral video

This Columbia University virology course is offered each year in the spring semester. Below are the complete, archived course materials for the Spring 2013 version of this course. Materials for the 2014 virology course can be found at virology.ws/course.

Prerequisite: Two semesters of a rigorous, molecularly-oriented Introductory Biology course (such as C2005), or the Instructor’s permission (vrr1@columbia.edu).

Course Name: Virology
Sessions: M, W 4:10 – 5:25 PM
Start date: Wednesday, January 23, 2013
Points: 3
Location: Northwest Corner 501
Course #: Biology W3310.001 or W4310.001
Instructors: Prof. V. Racaniello, Prof. S. Silverstein

Description

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.

The course will emphasize the common reactions that must be completed by all viruses for successful reproduction within a host cell and survival and spread within a host population. The molecular basis of alternative reproductive cycles, the interactions of viruses with host organisms, and how these lead to disease are presented with examples drawn from a set of representative animal and human viruses, although selected bacterial viruses will be discussed.

Textbook

The recommended textbook is Principles of Virology. Vol I: Molecular Biology, Vol. II: Pathogenesis and Control (S.J. Flint et al., Third Edition, ASM Press 2009).

Other course resources

1. Students are expected to read Prof. Racaniello’s virology blog which will contain information relevant to the course.

2. Students are expected to listen to the weekly podcast “This Week in Virology”, produced by Prof. Racaniello, for additional material about viruses relevant to the course. You can subscribe to TWiV at iTunes or at the Zune Marketplace.

3. Lecture slides (pdf) will be posted at Courseworks and at this website before each class.

4. Videocasts of all lectures (slides plus audio) will be posted at Courseworks, at this website, and at iTunes University.

Click here for material from the 2012 virology course

Lecture Schedule, Spring 2013
Note: Several videocast file types are available – right-click and save as to download. Videos are also available at YouTube.

Date Topic Reading Lecturer Slides Videocast (right click, save as)
1/23 Lecture 1
What is a virus?
Flint vol 1 chapter 1

Are viruses living?

What is a virus?

Are viruses alive? (take the poll)

VRR pdf iPod
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1/28 Lecture 2
The infectious cycle
Flint vol 1 chapter 2

Influenza virus growth in eggs

Influenza hemagglutination inhibition assay

The amazing HeLa cells of Henrietta Lacks

VRR pdf iPod
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1/30 Lecture 3
Genomes and genetics
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

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2/04 Lecture 4
Structure of viruses
Flint vol 1 chapter 4

Structure of influenza virus

Virus images at ViperDB

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2/06 Lecture 5
Attachment & entry
Flint vol 1 chapter 5

Influenza virus attachment to cells

Influenza virus attachment to cells – Role of different sialic acids

VRR pdf mac
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2/11 Lecture 6
RNA-directed RNA synthesis
Flint vol 1 chapter 6

Influenza viral RNA synthesis

The error prone ways of RNA synthesis

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2/13 Lecture 7
Replication of DNA virus genomes
Flint vol 1 chapter 9
Making viral DNA I (TWiV)
Making viral DNA II (TWiV)
SJS pdf mac
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2/18 Exam I Lectures 1-7   Study questions (pdf)  
2/20 Lecture 8
Transcription and RNA processing
Flint vol 1 chapters 8, 10
Processing VIRALGUUAACACCAGRNA(TWiV)
Study questions (pdf)
SJS pdf mac
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2/25 Lecture 9
Reverse transcription and integration
Flint vol 1 chapter 7

Museum pelts help date the koala retrovirus

Unexpected endogenous viruses
Study questions (pdf)

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2/27 Lecture 10
Translation
Flint vol 1 chapter 11
Study questions (pdf)
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3/04 Lecture 11
Assembly
Flint vol 1 chapters 12, 13

Packaging of the segmented influenza RNA genome
Study questions (pdf)

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3/06 Lecture 12
Infection basics
Flint vol 2 chapters 1,2

Transmission of influenza
Slow motion sneezing
Chikungunya, an exotic virus on the move
Do the tropics have a flu season?
Study questions (pdf)

VRR pdf mac
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3/11 Lecture 13
Host defense
Flint vol 2 chapter 4

The inflammatory response

Natural antibody protects against viral infection
Study questions (pdf)

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3/13 Lecture 14
Virus-host interactions
Flint vol 2 chapters 3, 4
Immunopathology – Too much of a good thing
Severe cases of pandemic influenza
Antimicrobial peptides induced by herpesvirus enhance HIV-1 infection
Study questions (pdf)
VRR pdf mac
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3/18 – 3/22 Spring Recess
3/25 Lecture 15
Viral evasion strategies
Flint vol 2 chapters 3, 4
Study questions (pdf)
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3/27 Lecture 16
Persistent infections
Flint vol 2 chapter 5

Persistent viral infections
Study questions (pdf)

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4/01 Exam II Lectures 8-16  
4/03 Lecture 17
Acute infections
Flint vol 2 chapter 5

Acute viral infections

Chronology of an acute infection
Study questions (pdf)

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4/08 Lecture 18
HIV pathogenesis
Flint vol 2 chapter 6

TWiV 133: The HIV hideout
A tale of two viruses
Study questions (pdf)

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4/10 Lecture 19
Transformation and oncogenesis
Flint vol 2 chapter 7
TWiV 163: What Rous wrought
Study questions (pdf)
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4/15 Lecture 20
Vaccines
Flint vol 2 chapter 8

Influenza virus-like particle vaccine

Poliovirus vaccine safety
Study questions (pdf)

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4/17 Lecture 21
Antivirals
Flint vol 2 chapter 9

New hepatitis C virus antiviral drugs

An antiviral for enveloped viruses

TWiV 146: Draco’s potion
Study questions (pdf)

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4/22 Lecture 22
Evolution
Flint vol 2 chapter 10 pp 311-333

Virulence: A positive or negative trait for evolution?

Increased fidelity reduces viral fitness
Study questions (pdf)

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4/24 Lecture 23
Emerging viruses
Flint vol 2 chapter 10

Lujo virus, a new hemorrhagic fever virus from Southern Africa

The zoonotic pool
Study questions (pdf)

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4/29 Lecture 24
Unusual infectious agents
Flint vol 2 Appendix A

Virophages engineer the ecosystem
Study questions (pdf)

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5/01 Lecture 25
XMRV
Flint vol 1 chapter 7

Why John Coffin doesn’t sleep well

HIV in XMRV out

XMRV is a recombinant virus from mice
Study questions (pdf)

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5/06 Lecture 26
H5N1
TWiV 177: Live in Dublin

A bad day for science
Study questions (pdf)

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5/13 Exam III Lectures 17-26  

 

 

  • ahmed

    English subs?