Hi everyone 😊, I’m writing this post a day late since it was a bank holiday in Ireland yesterday and I went on a nice trip to the Sealife aquarium! There were certain fish species there who ate frogs and I shunned them in solidarity with my amphibian friends, but I have a newfound appreciation for manta rays, they are incredibly elegant creatures! Also to highlight getting in some rest days is very important during research! You do your best work when you are refreshed and energised.
Last week, I finally completed a sequence alignment for the dataset I collected for numerous amphibian species based on a reference FASTA amino acid sequence from Rana yavapaiensis, the Lowland Leopard frog of Mexico and the US. FASTA is just a shorthand format of the sequence, either as nucleotide or amino acid sequences, where they are represented using single-letter codes. For example, displaying a nucleotide sequence as ATCGCGTA or amino acid sequence as ADQY. This is a very handy way to organise the sequences when comparing hundreds of them!
Following a meeting with my supervisor and fellow lab members, I was advised to use macse as the alignment tool as it aligns by codon instead of individual nucleotide. Since a codon (a triplet of nucleotides) is used to form one amino acid and many different codons code for the one amino acid due to genetic code redundancy, it is preferable to align based on codons to obtain an idea on the amino acid differences/similarities between the samples. The specific amino acids which promote chytridiomycosis resistance are known and can be easily accounted for in this alignment.
After creating my alignment, I used Seaview to visualise the data as each amino acid was given a specific colour, creating a rainbow effect, and allowing for differences to be easily seen across the species, corresponding to a single base position. This week, I am going to continue from here and take account of the amino acids at positions of interest across the amphibians to deduce whether there is a definitive pattern of expression for these chytridiomycosis resistance-promoting proteins across a large range of amphibian species.
That’s all from me! I hope everyone had a lovely weekend, thanks for reading, and have an amazing week 😊