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Constructing Evolutionary Lineages Using DNA BLAST

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Hannah Williams

on 13 January 2013

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Transcript of Constructing Evolutionary Lineages Using DNA BLAST

7. Add four additional dots representing the four researched genes(use their sequence number) on the cladogram created in procedure 1
8.Use Google to research the proteins function and types of organisms the protein is expressed.

a. If the types of organisms aren’t available online, the Distance Tree option can be used to obtain results.
9. Using the Google Data rank the importance of the 4 genes from most important to least.
10. Using the ranking, attain the most closely related organism of the fossil by viewing the genes that occur the most in one type organism. Srijaa Kannan
Nikita Paturu
Hannah Williams Exploring DNA Sequencing
with Cladograms Primary Question Where would the fossil specimen be placed on
the following cladogram? Background Context Hypothesis We hypothesized that the fossil would be placed on the rodent branch of the cladogram because it had a vertebrae. From the fossil only, we were unsure if it had feathers or fur. Abstract Evolutionary relationships can be shown through cladograms. These diagrams plot inherited traits in order to help to show which organisms are related to which. In the experiment, a fossil and cladogram were given to find where the fossil belongs on the cladogram. Four genes from the fossil were also given to compare to the genes of other animals in the cladogram. A series of databases, including BLAST, were used to figure out the identity of the genes, their functions, and in which organisms they exist. Conclusions and
Interpretations of Results It was found that the fossil was most closely related to a bird. From the nucleotide sequences entered, the following proteins were found (ordered from most to least important): ubiquitin-conjugating enzyme E2Q (coded for T. Guttata), collagen alpha-I (V), chain precursor (which coded for the organism G. Gallus), NADH dehydrogenase subunit 1 (coded for A. Sinesis), and F102063 or shaker (coded for the Drosophila). G.Gallus was a chicken, T. Guttata was a zebra finch (or a bird), A.Sinesis was a chinese alligator, and Drosophila was a fruit fly. It was concluded from the results that the animal would have to be closely related to a bird. The Zebra Finch is a bird, so it seems to be the most likely choice as similar to the organism in the fossil. The chicken is closely related to the organism because the gene sequences found coded for the characteristics of bird-like creatures; however, it isn't as close as the zebra finch. A chinese alligator is also related to birds; however, it isn't as closely related since they aren't actual birds. Last but not least the fruit fly was not as important as the protein it coded for the fossil since, although they can fly, they do not have a vertebrae and therefore aren't closely related. Literature Cited Results Methodology and Experimental Design 1. Sketch the given Cladogram and mark where the fossil would probably go.
2.Form an hypothesis of where the fossil would be placed in the cladogram
3.Go to http://blogging4biology.edublogs.org/2010/08/28/college-board-lab-files/ to download the 4 gene files.
4. Go to BLAST’s homepage: http://blast.ncbi.nlm.nih.gov/
a. Saved Strategies, Click Browse and select the downloaded gene file
b. Click view
c. Don’t change any of the settings and click BLAST
5. Once at the results scroll down to results and pick the gene that has(for closer alignment):
a. the highest max score
b. and a low e value close to zero
6. Use Gen Bank to fill out: Blast Data Results: Sequence #1:
Protein produced by the sequence: Collagen alpha-I (V), chain precursor
Presumed function of the protein: assembly of small diameter fibrils observed in the cornea
Types of organisms present in: G. Gallus- birds
Sequence #2:
Protein produced by the sequence: F102063 (shaker)
Presumed function of the protein: Sodium Potassium channel
Types of organisms present in: Drosophila (flies)
Sequence #3:
Protein produced by sequence: ubiquitin-conjugating enzyme E2Q
Presumed function of the protein: catalyzes the covalent attachment of ubiquitin to other proteins
Organism which the protein is expressed in: zebra birds (T. Guttata), and even mice (mus musculus)
Sequence #4:
Protein produced by sequence: NADH dehydrogenase subunit 1
Presumed function of the protein: accessory subunit of mitochondrial membrane respiratory chain, transfers electrons from NADH to respiratory chain (known as a housekeeping gene)
Organism found in: alligators, crocodiles, birds 1. T. Guttata 2. G. gallus 3. A. sinensis 4. D. melanogaster Scientists have been working for a very long time trying to identify and map the plethora of genes that define human beings. Through the discovery of many different fossils, some of unknown organisms, it is possible to conclude what the unknown organism is by understanding and figuring out what omnipresent and well-known organisms it is most similar to. Bioinformatics is a field that is used to analyze biological data, using the BLAST tool, which can compute and provide results for many different animals that are possibly related or that possibly contain the specific gene searched up. Cladograms are further used to show a visualization of the evolutionary relatedness of the species of different animals. With these, we are able to see how animals evolved and how they are similar by plotting the similar traits or genes that pertain to a specific animal and the animals it is related to. Birds, 5 leaves Alethe castanea Taenopygia guttata Crocodiles, 7 leaves A. Sinensis Taenopygia guttata Taeniopygia guttata Meleogris gallopara Gallus gallus Birds, 5 leaves Alethe castanea Taenopygia guttata Birds, 5 leaves Gallus Gallus Drosophila melanogaster "Basic Local Alignment Search Tool." BLAST:. N.p., n.d. Web. 12 Jan. 2013.
"Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST." CollegeBoard, n.d. Web. 11 Jan. 2013. <http://media.collegeboard.com/digitalServices/pdf/ap/bio-manual/CB_Bio_Lab_03_WEB_1_24_12.pdf>.
"Ubiquitin-conjugating Enzyme E2Q-like Protein 1 - Mus Musculus (Mouse)." Ubiquitin-conjugating Enzyme E2Q-like Protein 1 - Mus Musculus (Mouse). N.p., n.d. Web. 11 Jan. 2013.
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