1 / 18

Lateral Gene Transfer: Using Bioinformatics in Allied Health Microbiology

Lateral Gene Transfer: Using Bioinformatics in Allied Health Microbiology. Ruth Wrightsman Flathead Valley Community College Kalispell, MT Cynthia Brame Centenary College Shreveport, LA. Q&A.

aladdin-reese
Download Presentation

Lateral Gene Transfer: Using Bioinformatics in Allied Health Microbiology

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Lateral Gene Transfer: Using Bioinformatics in Allied Health Microbiology Ruth Wrightsman Flathead Valley Community College Kalispell, MT Cynthia Brame Centenary College Shreveport, LA

  2. Q&A E. coli is found naturally in the human large intestine, and there it is beneficial. However, the strain designated E. coli O157:H7 produces Shiga toxin. How did E. coli acquire this gene from Shigella? From Tortora et al. 10th ed.

  3. The Challenge: Students have problems understanding lateral gene transfer • Assume that all changes are “mutations” • Have trouble understanding “how do we know this?”

  4. Not the first time this problem has been noted………….. • ASM/JGI Bioinformatics Institute 2010 • Presentation: E. coli O157:H7Where Did the Toxin Gene Come From? • Hypothesis testing: • Mutation vs. Gene Transfer

  5. Solution: A bioinformatics approach to study lateral gene transfer Learning Goals: • Learn to use and interpret results from IMG genome comparison • Identify genes associated with pathogenicity • Identify genes associated with lateral gene transfer • Use Pfam to identify protein function

  6. Step 1: Set up the Genome Comparison • Use IMG – Integrated Microbial Genomes • http://img.jgi.doe.gov/cgi-bin/w/main.cgi • Go to “Find Genes” • Choose Phylogenetic Profiler • Choose Single Genes

  7. IMG – Phylogenetic Profiler http://img.jgi.doe.gov/cgi-bin/w/main.cgi

  8. Phylogenetic Comparison • Look for genes that ARE found in: • E. coli O157:H7 EDL 933 (EHEC) • Shigelladysenteriae SD197 • And genes that ARE NOT found in • E. coli DH 1 • Note to self……the strains chosen DO matter!

  9. The Results……….. 93 genes is a reasonable number to examine.

  10. Step 2. Choose some genes to examine. • Students may need some background on pathogenicity mechanisms • References to textbook or CDC reports • May also need some reminders about how gene transfer may occur • References for genetic mechanisms

  11. Here are a few of the gene results.

  12. Step 3: Choose an interesting gene • See where gene is located • Examine environment around gene • See if Pfam has information on protein

  13. Look what’s next to the Stx1A gene!

  14. Information from Pfam

  15. More information from Pfam

  16. And more information from Pfam

  17. Step 4: Extend this process….. • Examine lateral gene transfer in other E. coli strains • Use MUSCLE to align and compare protein sequences • Overlay with solved structure • (Get a pretty picture of the molecule!) • Examine lateral gene transfer in other pathogens • Diphtheria • Cholera

More Related