LESSON 3: Using Bioinformatics to Study Evolutionary Relationships PowerPoint slides to accompany Using Bioinformatics : Genetic Research

Microbiologist Lalita Ramakrishnan, MD, PhD Place of Employment: University of Washington Type of Research: Tuberculosis infection Model Organism: Zebrafish Zebrafish are naturally susceptible to tuberculosis. Because their genes are fairly easy to manipulate, we can create some zebrafish that are susceptible to TB and some that are resistant to TB. Zebrafish are also good model organisms because they are transparent, so we can watch the infection process develop.

Comparing DNA Sequences Reference BRCA1 Sequence Query Sequence(s): Patient 1 Look for mutations or changes relative to Reference Sequence A A C A T A G C T G Example: Genetic Testing using BLAST Patient 2 Patient 3

Comparing DNA Sequences Example: Genetic Testing using BLAST Example: Multiple Sequence Alignments Using JalView and ClustalW The amount of change among the sequences reflects the evolutionary relatedness of the organisms. Tomato Watermelon Papaya Grape Look for changes relative to each other A T G G T G C A T G C T G C A T G C A G C A T G G A C A Reference BRCA1 Sequence Query Sequence(s): Patient 1 Look for mutations or changes relative to Reference Sequence A A C A T A G C T G Patient 2 Patient 3 Image Source: Wikimedia Commons.

Pairs of Sequences are Compared to Each Other Papaya: ATGGTGCCG Grape: ATGCTGCCG Papaya : ATGGTGCCG Tomato: ATGCAGCCG Grape : ATGCTGCCG Watermelon: ATGGACACG Tomato : ATGCAGCCG Watermelon: ATGGACACG Papaya: ATGGTGCCG Watermelon: ATGGACACG Grape : ATGGTGCCG Tomato: ATGGTGAAG Number of Nucleotide Differences: PapayaGrape TomatoWatermelon Papaya0123 Grape1024 Tomato2203 Watermelon3430 Image Source: Wikimedia Commons.

Phylogenetic Trees Reflect Evolution Internal Nodes (Common Ancestors) External Nodes Image Source: Wikimedia Commons.

Phylogenetic Trees: The Carnivores Relatedness of Major Carnivores Internal Nodes (Common Ancestors) Domestic Cat Felis catus Gray Wolf Canis lupus Raccoon Procyon lotor Spotted Hyena Crocuta crocuta Cats Civets Mongooses Hyenas Canids Bears Red Pandas Skunks Weasels Raccoons Seals Fur Seals Sea Lions Walruses Dog/Bear Branch Cat Branch Adapted from : “WhoZoo: Images and Information about Animals at the Fort Worth Zoo.” Developed in part from mitochondrial sequence data from Arnason, et al. Mammalian mitogenomic relationships and the root of the eutherian tree. PNAS 99 (June 11, 2002): Images Source includes Wikimedia Commons.

Phylogenetic Trees: Infectious Disease Pandemic H1N1 Influenza (“bird flu”) Internal Nodes (Common Ancestors) ‘Spanish Flu’ H1N Pandemic H1N California/7/2009 California/4/2009 Mexico/4/2009 New York/1/1918 South Carolina/1/1918 Puerto Rico/8/1934 Denver/1/1957 Brisbane/57/2007 Solomon Islands/3/2006 New Caledonia/20/1999 ‘Seasonal Flu’ H1N1 0.08% different Scale: Influenza Image Source: Wikimedia Commons. Adapted from: Zimmerman SM, Crevar CJ, Carter DM, Stark JH, Giles BM, et al. (2010). Seroprevalence Following the Second Wave of Pandemic 2009 H1N1 Influenza in Pittsburgh, PA, USA. PLoS ONE 5(7): e doi: /journal.pone

Phylogenetic Trees with an Outgroup Provide a Point of Reference Laminaria (brown algae) Outgroup: Tomato Grape Papaya Watermelon Image Source: Wikimedia Commons.

Microbiologist Lalita Ramakrishnan, MD, PhD Place of Employment: University of Washington Type of Research: Tuberculosis infection Model Organism: Zebrafish Zebrafish are naturally susceptible to tuberculosis. Because their genes are fairly easy to manipulate, we can create some zebrafish that are susceptible to TB and some that are resistant to TB. Zebrafish are also good model organisms because they are transparent, so we can watch the infection process develop.

CAREERS IN SPOTLIGHT: Microbiologist What do they do? Microbiologists study microbes: bacteria, viruses, fungi, and protists. Dr. Ramakrishnan is an expert in tuberculosis, a type of bacteria that infects almost a third of humanity worldwide. She also studies immunology, including the body’s reaction to or defense from microbes. What kind of training is involved? Most Microbiologists who run their own lab have a Bachelor’s degree and a PhD (which is usually 5–6 years of research training). However, each lab often employs scientists with diverse backgrounds, including people with Associate’s, Bachelor’s, and Master’s degrees. What is a typical salary for a Microbiologist? Associate’s degree: $35,000/year ($17.50/hour) PhD, Full Professor: $100,000/year or more ($48.00/hour) Source: Bureau of Labor and Statistics