Science fair help

[seally]

I'm thinking about entering my county's science fair. I would like to investigate the genetics of long-living vs. short-living animals. I have some ideas for animals to compare like the grey squirrel and the fox squirrel or the African elephant and the Asian elephant. I am having trouble figuring out how to test this. I found out about Ensembl.org, but I have to figure out how to use that. I'm thinking about comparing genes like foxo3 and igf1. Are there any other ways to test my hypothesis that I'm not thinking of, or just any advice in general?

[akulk]

Hello!

Thank you for such a fascinating question!

Ensembl.org is a great resource for genome comparisons. I would also encourage you to explore NIH’s BLAST – where you can actually view the nucleotide sequence of your gene of choice in both animals (you will need a FASTA sequence as input, however, which Ensembl.org or the RCSB PDB database may help you generate).

Generally, if you want to compare genomes between two organisms, I would recommend looking at the base-pair-level – that is, identifying any point mutations (1 base pair changes) and corresponding amino acid changes due to those mutations. You can then observe the changes at a larger scale by analyzing what exactly those mutations/amino acid changes lead to – maybe a different folding of the resultant protein, maybe a pattern of aggregation of those proteins, etc.

Let us know if you have any more questions! This is such a fascinating project idea – excited to see where you will take this!

Anika

[seally]

Thank you so much! This really helped me get an idea of where to go from now. I just wanted to ask, I am not 100% sure but I will likely only have the capacity to compare two organisms. Would this still be considered a good research project if I didn't compare many organisms?

[akulk]

This would absolutely still be considered a good research project! I encourage you to instead explore different parameters of comparison between your two organisms – i.e. using more than 1 gene to explore the differences between the organisms (which you already have, as you mentioned foxo3 and igf1!). You can also try looking at specific amino acids resulting from any genetic differences – perhaps a certain amino acid correlates to a specific function of the resulting protein!

As always, let me know if you have more questions! Always happy to help.

[seally]

Hi, I got the BLAST to work after a while. For this search, I am using Blastp. It says that it is showing me the amino acids, but obviously, they are not in the standard amino acid format. I know that it is an amino acid substitution matrix, but I have no idea how to translate this to find the amino acids. I cannot add an image, but I will paste the output for one of the organisms here.
MNLSFFDQFTSPCLLGIPLILLSMLFPALLLPTPDNRWITNRFATLQLWLSHLITKQLMTPLNKAGHKWA
LILTSLMMFLLLINLLGLLPYTFTPTTQLSMNMALAFPLWLATLLTGLRNQPSASLGHLLPEGTPTPLIP
ALIMIETTSLLIRPLALGVRLTANLTAGHLLIQLISTATTALLPLIPAVSLLTTSILLLLTLLEVAVAMI
QAYVFVLLLSLYLQENI
Would you happen to know how to make sense of this?

[akulk]

Hi there!

Amino acids can have either 3-letter or 1-letter abbreviations! What you’re seeing here is a sequence of amino acids with their 1-letter abbreviations.

This link has a record of all 1-letter abbreviations corresponding to their full-form amino acids: https://i-base.info/ttfa/hiv-and-drug-r ... eviations/.

Here is a translation of the first 5 letters of your sequence: MNLSF.
M = Methionine
N = Asparagine
L = Leucine
S = Serine
F = Phenylalanine
So “MNLSF” is Methionine-Asparagine-Leucine-Serine-Phenylalanine!

Hope this helps!

Anika