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Published byCorey Allison Modified over 9 years ago
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While hiking, a student decided to collect and eat berries from the plants he came across on the AT trail. Unfortunately, he became very ill and had to be taken to the hospital with the following symptoms: pain in mouth and throat, severe upset stomach, vomiting, bloody diarrhea.
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As a class, we collected eleven plants from the Appalachian trail We used genetic techniques to find out each of the plants DNA sequences in their MatK region The MatK region is in the chloroplast genomes of all plants and is often used to build evolutionary trees of plants
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Identify three unknown plant samples each Determine which plant made the student sick Present findings in mini presentation Look at the relationship among the unknown plant samples Each INDIVIDUAL does all these steps, except for presenting with partner or group
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Each student is assigned a number This number corresponds to a plant (there are eleven plants altogether)
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Merges biology, computer science and information technology Aims to find new insights about biological systems Often applied to molecular data NEW AND EXCITING FIELD OF BIOLOGY!
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Basic Local Alignment Search Tool Compares nucleotide or amino acid sequences Looks for areas of similarity and calculates the statistical significance of the matches (http://blast.ncbi.nlm.nih.gov/Blast.cgi)
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COPY AND PASTE YOUR SEQUENCE HERE
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Closer the E-value is to zero the better the match Click accession number of first search result
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Length of geneType of data Description of gene
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gene information Encoded Protein DNA sequence
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Common name Poisonous? Symptoms Other interesting information Prepare 5-minute presentation with partner or group; each person must speak
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Go to http://www.uniprot.org/http://www.uniprot.org/ Enter the genus and gene name here
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Find and click on the accession for your gene and species
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Click here to get more information about your gene
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Find information on the structure and function of protein with Pfam. When finished with that, begin next exercise. Copy and paste all 11 sequences into the Clustal Omega site as is, numbers and ‘<‘s’ and all http://www.ebi.ac.uk/Tools/msa/clustalo/ http://www.ebi.ac.uk/Tools/msa/clustalo/
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Phylogram: shows common ancestry and branch lengths indicate amount of evolutionary change Cladogram: shows only common ancestry
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1. Hemerocallis fulva (orange daylily) 2. Chenopodium album (lambsquarters) 3. Fragaria virginiana (Virginia strawberry) 4. Gleditsia triacanthos (honeylocust) 7. Rumex obtusifolius (bitter dock) 9. *Phytolacca americana (American pokeweed) 10. Vaccinium parvifolium (red huckleberry) 11. Vaccinium pallidum (Blue Ridge blueberry)
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