This past week consisted of massive amounts of DNA extractions and PCRs!
I have been working with undergraduates, Sarah Shainker and Connon Thomas.
Sarah Shainker continued optimizing her restriction enzyme digest (see Sarah's research page for more information about restriction enzymes!) and now has the method nailed down. She started processing Gracilaria vermiculophylla samples from the native range in Japan, Korea and China and samples from our trip to the DelMarVa peninsula. So far, results are quite interesting with very clear patterns differentiating native and non-native ranges! Stay tuned for more about her research!
Connon Thomas continued his G. vermiculophylla growth experiments manipulating salinity for several South Carolina populations. He also got his feet wet doing high-throughput (high throughput means 96 or more samples processed at once as opposed to 5 or 6 samples) microsatellite genotyping on all his algal individuals.
I spent this past week doing PCRs with Sarah and Connon plus continuing with the samples we collected this summer along the DelMarVa peninsula and in South Carolina. Samples are now being run on the capillary sequencer (see the equipment page to learn more about the capillary sequencer). This week also saw installment 7 of my monthly phenology sampling of the DNR mudflat here at Fort Johnson. Though we found 1 male, all other individual G. vermiculophylla fragments were sporophytes or vegetative (meaning they were not yet reproductive).
I have been hard at work helping our high school student Hannah work through traits on Gracilaria. She is looking at how the amount of organic material, protein content, surface area to volume ratio, and palatability (how yummy it is) varies between males, females, and sporophytes. Males and Females are haploid so they only have one set of genetic material (DNA, chromosomes, etc) while sporophytes are diploid meaning they have two sets of genetic material--one from mom and one from dad.
I am continuing to do feeding assays with the urchins and crabs. I also spent some time this week collecting more amphipods (and one local type of isopod). I ran a choice assay with three different amphipod species and the isopod to see which animals would behave best for our experiment. While all of the animals behaved and consumed food from the feeding strips, we ultimately decided to continue on with Ampithoe valida since it is the most abundant species around Grice Marine Lab.
Courtney, Meredith, and I also collected some Diopatra from the mudflat and brought them into the lab in order to run an experiment with the Gracilaria chemistry we extracted last week. We are currently keeping an eye on the worms to make sure that they are happy and eating before running the experiment.
Sarah Shainker, an undergrad working in the lab, will be continuing extracting DNA and genotyping native and non-native populations.
Connon Thomas, a REU student, will continue his salinity experiments with material we collected last week from Myrtle Beach south to Beaufort.
I will be continuing to fill in genotypes from our massive microsatellite effort from the winter and early spring as well as continuing with analyses of the DelMarVa samples and new SC samples. As well, I will be doing some more phenology work at the end of the week.
I just finished setting up my experiment with lots of help from Alyssa and Meredith. I am now continuing working on a survey of amphipod abundance and amphipod predation on the Fort Johnson mudflat.
This past week I continued running feeding assays with the urchins and crabs. I also helped Courtney set up her field experiment and worked with our former high school student (Jess) to extract the secondary metabolites from Gracilaria vermiculophylla. Now that we have the secondary metabolites, we can confirm that Gracilaria is deterrent to consumption by Diopatra and work with our collaborators in Florida to identify what compounds are present that act as deterrents.
"An undergrad, Sarah Shainker, who is in the lab for the summer on a HHMI fellowship, and I just returned from a 9 day, 2500 mile and 25 site collection trip in VA, MD and DE. We are now processing all the seaweeds we collected, meaning we are beginning to extract DNA and then Sarah and I will be embarking on a joint effort. Sarah will be sequencing a single gene marker called cox 1 as well as doing some restriction enzyme work (basically chopping up the DNA into smaller pieces in which some samples get chopped one way and other samples get chopped another way). I will be tackling the genotyping of all the specimens with microsatellite markers (the same markers used in forensics and paternity cases in humans). My immediate goals will be to round up all the worldwide samples we have to finish off their genotyping and then get cracking on the new samples!
Next week another undergrad, Connon Thomas, and I will be headed as far south as Beaufort and as far north as Myrtle Beach to sample more Gracilaria for his Research Experience for Undergraduate summer project!"
"I am currently in the process of conducting choice feeding assays on the urchins and crabs. So far I have tested four temperate seaweeds, one antarctic seaweed, and one tropical seaweed. I have a total of 35 seaweeds in house and one of our collaborators (Dr. Mark Hay at Georgia Tech) is going to be sending us approximately 10 more Fijian seaweeds soon which is exciting!
I also spent some time this past week learning how to distinguish between amphipod species so I can collect enough of one kind to do feeding assays with them as well.
Additionally, I have been helping Hannah (our high school student) learn how to determine ash-free dry mass and protein content in Gracilaria vermiculophylla as part of her summer project."
Nicole has finished up her master's degree, meaning her research at the Sotka Lab has come to an end. She is moving on to her next scientific journey and we wish her the best of luck!
"I am setting up my experiment again. So, I have been going out into the field and collecting Gracilaria and then bringing it back to the lab to removing all the epiphytes (plants) and epifauna (animals) that are on it. Then I am breaking it into equal weight pieces and stringing it on to ropes so that I can redeploy the algae and not lose it!"
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Stay updated with what the Sotka Lab scientists have been up to with their blog posts.
Patriots Point Naval and Maritime Museum
40 Patriots Point Rd.
Mt. Pleasant, SC 29464
40 Patriots Point Rd.
Mt. Pleasant, SC 29464