News from Alyssa

The past few weeks sure have flown by! I have been hard at work, continuing with my feeding assays  (today marks seaweed 45!)  while also trying to get back into the molecular side of things. I do still need to finish up my trait assays on the last couple of seaweeds before I have my final results, but trying to generate DNA sequences is currently at the top of my priority list. As of the last time I did molecular work, I had successfully isolated and amplified DNA from 26 seaweeds. So I re-extracted DNA from the 9 seaweeds that didn’t work last time and then also extracted DNA from the 17 seaweeds that were sent to us this summer. I then attempted to amplify the DNA in those seaweeds using PCR and all but 8 seaweeds worked (we can tell success based on gel electrophoresis). For the seaweeds that still were not successfully amplifying, I began troubleshooting the PCR reaction, first by increasing the amount of DNA in the PCR and then by diluting the amount of DNA in the PCR. I tried increasing the amount of DNA in case the DNA extracted was a very low concentration, in which case an increase in amount added to the PCR reactions would allow for better amplification. I also tried diluting the DNA in my brown seaweeds that didn’t work because brown seaweeds are known to have properties that can inhibit amplification if the DNA is too concentrated. Increasing the DNA amount led to successful PCR in 3 of the 5 reds while diluting the DNA led to success with the 3 brown seaweeds. Now there are just 2 seaweeds left to try re-extracting and amplifying again which I will try to do this week.



While we have had success with our PCR, we still need to see if it produces good DNA sequences. Before sending all of our PCR products for sequencing, we decided to send a subsample of 8 seaweeds for sequencing. I am aiming to get that done this week as well, so fingers crossed that we get good sequences back and then we can send the rest of our seaweeds for sequencing. The goal again is to get DNA sequences for all of our seaweeds so we can then construct a phylogenetic tree (a tree based on related ancestry- so think family tree). This tree will be used subsequently to look at the effect of phylogeny on the various seaweed traits and the overall palatability of those seaweeds to herbivores.