Viruses and Computer Scientists

Courtney D. CorleyComputational Epidemiology Research Laboratory

Department of Computer Science

University of North Texas

Department of Biostatistics

UNT Health Science Center

Motivation

Why is a computer scientist looking at viruses?

Current Research in Comp Epi

• Graph-based data mining (SUBDUE)

• Dynamic social networks (STD transmission dynamics)

• Models and tools to facilitate public health strategy evaluation

• Global Stochastic Field Simulation

• Agent-based Models

Herpes Simplex type-1

Herpes Simplex type-1

Smallpox

Smallpox

Overview

• Motivation

• Etymology

• Epistemology

• Living Cells

• Virus definition

• Viral diversity

• Conclusion

Etymology

• Derived from Latin: virulentus poisonous

• 1392 -- first used in English.

• 1728 – “agent that causes infectious diseases”

• 1972 – biological virus and metaphor for other parasitically reproducing things.

Virus

A subcellular parasite with genes of DNA or RNA and which replicates inside the host cell upon which it relies for energy and protein synthesis.

In addition, it has an extra-cellular form in which the virus genes are contained inside a protective coat

Epistemology part 1

Are viruses “GOOD” or “BAD”?

• Biological Knowledgebase

• Viro-therapy

• Vectors

• Nanotechnology – the golden thread

Epistemology part 2

Is a virus “ALIVE” or “DEAD”

?

Living Cells

Which of the following apply to a living cell?

a) It contains genetic information (DNA)

b) It uses RNA as a genetic messenger

c) It is capable of making its own proteins

d) It generates its own energy

e) It is surrounded by a cell membrane

Living Cell

A Virus Flunks the “Living Cell” test

c) It is capable of making its own proteins

d) It generates its own energy

Is the following true?

e) It is surrounded by a cell membrane

What defines a “VIRUS”

• Cannot multiply without a host cell• Intracellular parasites• Two forms

– Viron – inert particle that survives out of the host cell

– Active intracellular phase

• Capsid – Protein surrounding a length of nucleic acid (DNA or RNA) which caries the virus genes.

• Viral Genome

Virus Lifecycle

a) Attachment to the correct host cell

b) Entry of the virus genome

c) Replication of the virus genome

d) Manufacture of the virus proteins

e) Assembly of new virus particles

f) Release of new virus particles from the host cell

Retrovirus: Infection and Replication

Thief

Many animal viruses have an extra envelope outside the protein shell.

This membrane is STOLEN from the previous host cell into which viruses have been stuck.

Now, the virus encoded proteins function to detect and bind to the next target cell

Animal VirusWhen an enveloped virus enters a new cell, its

envelope layer merges with the cell membrane and the inner protein shell containing the nucleic acid enters.

Once inside, the protein shell disassembles exposing the genome

Bacterial VirusCell wall protects cell membrane – so

Bacteriophages do not bother with an outer envelope.

After binding to cell surface, they inject their genome into the bacterial cell and leave the protein shell behind

Summary

• Viral Philosophy

• Living Cells

• Great Diversity– Animal– Bacteria

Thanks!References:

“Molecular Biology Made Simple and Fun” Clark and Russell

http://science.nhmccd.edu/biol/bio1int.htm#virushttp://www.whfreeman.com/kuby/content/anm/kb03an01.htmhttp://www.hhmi.org/biointeractive/animations/anim_index.htm http://www.hhmi.org/biointeractive/animations/subunit/sub_frames.htmhttp://www.hhmi.org/biointeractive/animations/infection/inf_frames.htm http://pathmicro.med.sc.edu/weaver/testflash-1.htm http://highered.mcgraw-hill.com/sites/0072437316/student_view0/

chapter26/animations.html