Sunday, November 20, 2011

Bio380 Human Evolution Genes and Genomes Bioinformatics Practical


I have a bioinformatics practical class tomorrow and rather than hide it away, I thought I might as well share it with the world via this blog. Happy to receive comments on any mistakes or suggestions for improvements or additional reading.


Bio380 Human Evolution Bioinformatics Practical 2011

Follow this link to the entry for the FOXP2 chimpanzee protein:
http://www.uniprot.org/uniprot/Q8MJA0
Take a minute to explore the information on the page.
  • Q. What is the evidence that this gene is functional in the chimpanzee?
  • Q. Why is this entry called FOXP2_PANTR
  • Q. What does the Forkhead domain do?
Scroll down to the sequence at the bottom of the page
  • Q. What is unusual about the first third of the protein sequence?
Click on the pop-up Fasta view button
  • Q. What is a FASTA sequence?
Select the sequence that pops up and copy it to the clipboard. Then return to the previous window.

Open in a new tab and go to http://www.ncbi.nlm.nih.gov/BLAST/
Select “protein blast”
  • Q. What is BLAST?
Paste the FoxP2 FASTA sequence into the search box. Click on the algorithm parameters link, then tick the box indicating Filter low complexity regions
  • Q. What does this do?
Start the Blast search. The Blast search may take some time, so open a fresh tab and go to http://www.uniprot.org/
Search for “foxp2_human”
Spend some time exploring the information therein, while you wait for the Blast search to finish.

Return to the Blast search result. Scroll through the results. In the segment of the query spanning residues 241-698, how many differences does the chimp protein show from the following:
Orang utan (Pongo pygmaeus) Gorilla (Gorilla gorilla)
Lar gibbon (Hylobytes lar) Macaque (Macaca mulatta)
Horse (Equus cabellus) Mouse (Mus musculus)
Humans (Homo sapiens)
PS: use the sequence with header "FoxP2_Human"
  • Q. What differences do you find?
  • Q. How conservative or radical are the changes in amino-acid properties?
Go to http://www.nature.com/nature/journal/v418/n6900/full/nature01025.html
This paper suggests that the human sequence undergoes an additional post-translational modification compare to the chimp sequence
  • Q. What is this difference and how significant is likely to be?
Go to http://www.ncbi.nlm.nih.gov/omim
Search for FoxP2, then click on the first entry and explore the information therein, particularly that under the Evolution heading.
  • Q. Does this confirm or deny any of your previous conclusions?
Follow the link to this recent paper:
http://dx.doi.org/10.1016/j.jhevol.2007.07.006
Speed-read the abstract and introduction
  • Q. On the basis of this, would you expect Neandertals to be able to speak?
  • Q. What would you expect their FoxP2 gene to look like?
Follow this link to another recent paper
http://www.cell.com/current-biology/abstract/S0960-9822(07)02065-9
  • Q. What do you conclude?
Now read these blog entries
  • Q. Do your conclusions change?
  • Q. Are blogs are useful source of scientific information?

The genome of James Watson, Nobel laureate and co-discoverer of the structure of DNA can be found here: http://jimwatsonsequence.cshl.edu/

  • Q. Is Jim Watson a black man?
And, finally, is Watson’s recent gaffe on race more likely to be due to:
  1. A single gene disorder (the “butt-head racist gene”?)
  2. A polygenic disoder (the “butt-head racist gene complex”?)
  3. The racist culture in which he grew up?
Posted by at
Labels: , , , , ,