LESSON 3: Using Bioinformatics to Study Evolutionary Relationships PowerPoint slides to accompany...
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LESSON 3: Using Bioinformatics to Study Evolutionary Relationships
PowerPoint slides to accompany
Using Bioinformatics: Genetic Research
MicrobiologistLalita 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 SequenceAA
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.
TomatoWatermelon
PapayaGrape Look for changes
relative to each other
A T G G T G CA T G C T G CA T G C A G CA T G G A C A
Reference BRCA1 Sequence Query Sequence(s): Patient 1 Look for mutations or changes
relative to Reference SequenceAA
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: ATGGTGCCGGrape: ATGCTGCCG
Papaya : ATGGTGCCGTomato: ATGCAGCCG
Grape : ATGCTGCCGWatermelon: ATGGACACG
Tomato : ATGCAGCCGWatermelon: ATGGACACG
Papaya: ATGGTGCCGWatermelon: ATGGACACG
Grape : ATGGTGCCGTomato: ATGGTGAAG
Number of Nucleotide Differences:
Papaya Grape Tomato WatermelonPapaya 0 1 2 3Grape 1 0 2 4Tomato 2 2 0 3Watermelon 3 4 3 0
Image Source: Wikimedia Commons.
Phylogenetic Trees Reflect Evolution
Internal Nodes(Common Ancestors)
External Nodes
Image Source: Wikimedia Commons.
Phylogenetic Trees: The CarnivoresRelatedness of Major Carnivores
Internal Nodes(Common Ancestors)
Domestic CatFelis catus
Gray WolfCanis lupus
RaccoonProcyon lotor
Spotted HyenaCrocuta crocuta
Cats
Civets
Mongooses
Hyenas
Canids
Bears
Red PandasSkunksWeaselsRaccoons
SealsFur SealsSea Lions
Walruses
Dog/Bear Branch
Cat Branch
Adapted from : “WhoZoo: Images and Information about Animals at the Fort Worth Zoo.” http://www.whozoo.org/mammals/Carnivores/carnivorephylogeny.htm. 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): 8151-8156. Images Source includes Wikimedia Commons.
Phylogenetic Trees: Infectious Disease Pandemic H1N1 Influenza (“bird flu”)
Internal Nodes(Common Ancestors)
‘Spanish Flu’ H1N1 1918Pandemic H1N1 2009
California/7/2009California/4/2009Mexico/4/2009
New York/1/1918South Carolina/1/1918
Puerto Rico/8/1934Denver/1/1957
Brisbane/57/2007Solomon 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): e11601. doi:10.1371/journal.pone.0011601.
Phylogenetic Trees with an Outgroup Provide a Point of Reference
Laminaria (brown algae)
Outgroup:
Tomato
Grape
Papaya
Watermelon
Image Source: Wikimedia Commons.
MicrobiologistLalita 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