Our Experimental Design

We propose to test our hypothesis, that trees which survived the radiation exposure have genetically adapted to this radiation. These adaptations should be detected through sequence analysis of exposed trees, and their comparison to non-exposed trees.

First, we will look for an increase in the number of mutations for trees that have been exposed. Mutations come in many forms, including Single Nucleotide Polymorphisms (SNPs). The SNP listed below is called a Missense mutation, because it changed the amino acid that was coded for from the original sequence.

Example 1.

Example 2. We will also look for chromosomal inversions

-----C A T C A T C A T C A T C A T C A T C A T C A T ------

That get changed to

----C A T C A T T A C T A C C A T C A T C A T C A T ------

Example 3. We will also look for chromosomal duplications

------C A T C A T C A T C A T C A T C A T C A T C A T ------

That get changed to

------C A T CCC A T C A T C A T C A T C A T C A T C A T ------

Initially we will be specifically looking for and counting the new mutations, and using that to infer mutation rates when compared to trees outside of the exclusion zone. Historically, this has been shown in many radiation studies for exposed plants as well as animals.

We also plan to translate these mutations to the amino acid level (shown above in example 1) as well as potential adaptive genetic changes that may allow the trees to survive the harsh conditions of this radiation. Such adaptive genetic changes have been shown to happen to plants in other stressful conditions, and will likely be detected in our samples as well.

Because we do not know exactly where these changes will happen in the genome, we plan to use what is called next generation sequencing, whereby we sequence the entire genome for our samples. This will allow us to detect any changes throughout the genomes, anything from SNPs (single nucleotide polymorphisms) to inversions (flipped parts of the chromosomes) to insertions and deletions. Once we have accumulated the genetic change data, we plan to translate the proteins that are coded for by these genes (known as the proteome) and see if we can detect any that may help the trees survive such extreme increases in radiation.