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SARS: A Multidisciplinary Exploration

SARS: A Multidisciplinary Exploration. Nitya Jacob Doug Graham Eloise Carter Manish Chakrabarti. Teaching with an Epidemic. SARS as a topic to introduce problem solving in biology, medical epidemiology and bioinformatics Diverse sources of information on SARS used to introduce the topic

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SARS: A Multidisciplinary Exploration

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  1. SARS: A Multidisciplinary Exploration Nitya Jacob Doug Graham Eloise Carter Manish Chakrabarti

  2. Teaching with an Epidemic • SARS as a topic to introduce problem solving in biology, medical epidemiology and bioinformatics • Diverse sources of information on SARS used to introduce the topic • Platform for developing questions that engage students • Use of existing data/information to develop analysis skills for future projects

  3. SARS – Severe Acute Respiratory Syndrome • Coronovirus – SARS CoV • Global epidemic 2003 • 8,000 cases, 24 countries • Spread by respiratory droplets

  4. SARS - Symptoms • High fever > 100oC • Headaches • Body aches and pains • All pneumonia

  5. SARS – Integrating Topics • Biogeography • Epidemiology/Biology • Detection and Diagnosis • Time Line • Genome • Phylogeny • Bioinformatic Tools • Public Health – Quarantine, Education, etc. • Vaccine Development

  6. Questions to Explore • Evolution/variation of sequences encoding specific proteins (Orf 1ab vs. spike) • Differences between Coronaviruses • Differences between strains from China and Taiwan vs. strains transmitted to North America

  7. SARS Sequences Available FULL GENOME SEQUENCES • TOR2 • SIN2500, SIN2748, SIN2774, SIN2677, SIN2679 • URBANI • HKU39849 • BJO1 • HKU39849 • CUHKUW1, CUHK-Su10 • LLJ-2004 • HSR1 – Italy • Frankfurt 1 • Sino1-11 • GD01 www.ncbi.nlm.nih.gov Salemi et al, 2004

  8. SARS Protein Sequences • Spike glycoprotein (S) • Replicase polyprotein (Orf1ab) • Nucleocapsid (N) • Membrane protein (M) www.ncbi.nlm.nih.gov

  9. Epidemiology • Origin of SARS coronavirus? • Case definition • Factors (biological/cultural) contributing to global spread

  10. Bioinformatics Target Audience: Computer Science, Math and Statistics students. Exploration Ideas: • Search NCBI for the complete SARS Co-v genome (Accession number: NC_004718) • Download the entire sequence in FASTA format (goal: learn about FASTA) • Now download the sequence in XML format (learn about the different XML formats such as GBSeqXML, TinySeqXM, etc.) • Play with the NCBI Protein Viewer (Cn3D) to explore the structure of Nsp9 Protein From Sars-Coronavirus.

  11. SARS Resources • Epidemic! The Natural History of Disease at the San Diego Natural History Museum www.sdnhm.org/exhibits/epidemic/resources.html • Useful site for additional web links and info http://microvet.arizona.edu/Courses/MIC438/collectjc04.html (images above) • CDC information http://www.cdc.gov/ncidod/EID/vol5no2/snacken.htm • Maps and photos http://www.geo.arizona.edu/Antevs/nats104/00lect24sars.html (images above)

  12. Resources for Evolution and Phylogeny • Salemi et al. 2004. “Severe Acute Respiratory Syndrome Coronavirus sequence characteristics and evolutionary rate estimate from maximum likelihood analysis”. J of Virology 78:1602-1603. • Chinese SARS Molecular Epidemiology Consortium. 2004. “Molecular evolution of the SARS coronavirus during the course of the SARS epidemic in China.” Science 303:1666-1669. • Lan et al. 2005. “Phylogenetic analysis and sequence comparison of structural and non-structural SARS coronavirus proteins in Taiwan.” Infect. Genet. Evol. 5:261-9

  13. Resources for Bioinformatics Complete SARS Genome • Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage - Snijder,E.J at al, J. Mol. Biol. 331 (5), 991-1004 (2003) PUBMED 12927536

  14. Conclusions • This approach could be used in other areas of study • Epidemic diseases capture interest and integrate diverse skills and concepts • Meaningful connection of bioinformatics to timely and engaging problems • Find your favorite disease!

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