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BLAST Lab

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by

Anna Groebner

on 1 March 2013

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Transcript of BLAST Lab

by: Joey Hock and Anna Groebner BLAST: MidKine and Pleiotrophin Fossil Specimen Questions Results Observations:
-long tail
-a body and a vertebrae
-two limbs (probably legs) can be seen towards the back
-part of a head (with a rather large eye)
-has what seem to be mouthparts
-no fur or feather impressions are visible
-no palatal valve, opposable thumbs, or specialized incisors -our classmates all agree about the placement of this species on the cladogram
-there are 198 genomes available to compare to gene sequences with BLAST, this is a significant limitation for us because it is an extremely small sample of the millions of genomes that exist - we probably aren't seeing all of the most similar sequences due this limited resource
-other information we could obtain from this fossil include: the age of the specimen through examination of the rock layers it was found in (or possibly through radio carbon dating), the bone structure of the specimen, and possibly the specimen's habitat through investigation of the environment in which it was found Fossil Specimen "Evaluating Results" Question:
What are the functions of midkine and pleiotrophin in humans? What other organisms have midkine and pleiotrophin? What is their evolutionary relationship? Hypothesis:
-we thought that both midkine and pleiotrophin would be most similar to genes in chimpanzees and other primates; overall, we assumed they would appear in many of the same genomes and be evolutionarily related to each other Midkine:
most similar to humans-
-Gorilla gorilla gorilla (Western Lowland Gorilla), 100%
-Nomascus leucogenys (White-Cheeked Crested Gibbon), 100%
-Pan troglodytes (Common Chimpanzee), 99%

Pleiotrophin:
most similar to humans:
-Pan troglodytes (Common Chimpanzee), 100%
-Pan paniscus (Bonobo), 99%
-Gorilla gorilla gorilla (Western Lowland Gorilla), 99% Hypothesis:
-we believe that this species should be categorized as a vertebrae, somewhere before the crocodilians
-we decided this based on the fact that it has exposed mouthparts, two limbs, and a vertebrae, but no visible palatal valve, feather impressions, fur impressions, opposable thumbs, or specialized incisors

Classification:
-after further research, we decided that this species should be placed near the bird branch of the cladogram because of the reasons we stated above, and the fact that its genes are similar to those of species in this general area (genes 1 and 3 were extremely similar, some even identical, to those found in species of birds) Fossil Specimen Cladogram Gene 1:
-most similar gene sequence - Gallus gallus (tropical pheasant)
-similarity - 100% similar
-next most similar - Meleagris gallopavo (trukey), 97% similar Gene 2:
- most similar gene sequence - Drosophila melanogaster (common fruit fly)
-similarity: 100% similar
-next most similar - Drosophila simulans (same melanogaster species), 99% Gene 3:
-most similar gene sequence - Taeniopygia guttata (zebra finch)
-similarity: 100% similar
-next most similar - Alethe castanea (fire crested Alethe), 96% similar = hypothesis = gene 1 = gene 2 = gene 3 = actual classification Self-Designed BLAST Investigation Procedure:
1. made a hypothesis
2. searched "human midkine" on the Entrez Gene website
3. clicked on first link and scrolled down to "NCBI Reference Sequences"
4. clicked on the first file under "mRNA and Proteins"
5. clicked on "FASTA"
6. copied the whole sequence that is displayed
7. went to the BLAST homepage and clicked on "nucleotide blast" under the Basic BLAST menu
8. pasted the sequence into the box that says "Enter Query Sequence"
9. selected to search all genomes available under "Choose Search Set"
10. chose to search for highly similar sequences under "Program Selection"
11. repeated for pleiotrophin Midkine:
-also known as neurite growth-promoting factor 2
-basic heparin-binding growth factor
-developmentally important gene
-product strongly induced in mid-gestation
-restricted mainly to specific tissues in a normal adult
-also strongly induced in tissue repair
-expression has been found to be elevated in many types of cancers Pleiotrophin:
-also known as neurite growth-promoting factor 1 or herapin-binding growth factor 8
-structurally related to Midkine
-expressed in the central peripheral nervous system and other non-neural tissues during embryonic and postnatal development
-also expressed in tumors Conclusions Bonobo Western Lowland Gorilla Common Chimpanzee White-Cheeked Crested Gibbon As we hypothesized from the beginning, human midkine and human pleiotropin have very similar evolutionary histories, and these gene sequences in humans are extremely similar to those in primates. We were able to make these conclusions because the human midkine and pleiotrophin gene sequences both had a very high similarity those found in the Western Lowland Gorilla and the Common Chimpanzee. We can also see their relatedness in their functions. Both are neurite growth-promoting factors, and are expressed in development as well as in tumors.
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