Monthly Archives: August 2019

Domesticating the Wild Kelpie

By: Kelly DeWeese

Hi! My name is Kelly DeWeese, and I’m a second year graduate student in the Molecular Biology PhD program at USC. I research Macrocystis pyifera (giant kelp) in the Nuzhdin Lab, where we are working toward giant kelp domestication for growth in open ocean aquaculture. In our lab we nickname giant kelp “Kelpie”, like the fearsome Celtic sea monster made out of kelp featured in recent Harry Potter movies:

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Source: https://www.talenthouse.com/i/1521/submission/326356/e948dbdf

This summer I was awarded the USC Wrigley Summer Fellowship to do lab work and collect kelp on Catalina. My project is focused on using transcriptomic analyses to learn more about the genes involved in giant kelp reproductive pathways.

Transcriptomics uses data on mRNA (read: gene) expression to analyze which genes are being expressed in different conditions, at different times of day, etc. We are interested in the reproductive pathway because as part of the domestication process, our lab wants to sterilize (i.e. knock out the reproductive pathway of) the kelp that is farmed because it will be growing in the ocean, not in a controlled environment. A transcriptomic analysis that will help us understand the reproductive pathway is a differential expression analysis of both reproductive and nonreproductive giant kelp tissues. Comparing the genes that are differently expressed between each tissue type will highlight some candidate genes involved in reproduction that can be knocked out or selected for in domesticated giant kelp to sterilize the organism.

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Most days on the island, my undergrads, Ben and Jean, and I go out and collect sporophyte tissue growing near the ocean’s surface in the morning. Ben drives the boat, and Jean and I take punches of kelp blades and put them on in seawater, on dry ice or in preserving solution for transport back to the lab. Here some labmates and I are taking a Boston whaler to collect giant kelp off the coast of Catalina Island:

Screen Shot 2019-08-21 at 9.03.47 AMThen, Ben, Jean and I take the giant kelp samples back to the lab for homogenization and extraction of RNA. This summer we worked on optimizing a protocol to extract clean RNA in high concentrations, which is difficult because giant kelp has thick cell walls and cells full of macromolecules that contaminate RNA extractions. Last week, my undergrads presented on their research at the USC Wrigley REU Symposium to wrap up their time out on the island. Thanks for such a great summer and all your hard work, Ben and Jean!

Toward New Biofuels From the Sea

By: Jean Sabety

Hello from the island! I’m Jean Sabety, an undergraduate working with the Kelp Team in the Nuzhdin lab at USC.

Me collecting kelp samples for my projects.

Me collecting kelp samples for my projects.

We are working on improving open ocean kelp farming with the end goal of making an algae biofuel! I am working on two projects concurrently this summer:

I am working on the first project with Jose Diesel, we are looking at the effects that phytohormones (plant hormones) have on Giant Kelp (Macrocystis pyrifera) growth. Despite being morphologically similar, animals and fungi are more closely related than algae are to plants! Despite this fact, we are curious to see if plant hormones, which are commonly used to increase growth in agriculture, will improve kelp growth. If one of the hormones does have a positive effect on kelp growth, it could be used to decrease kelp hatchery time, the amount of time it takes for baby kelp to be strong enough to survive transfer into the ocean. This will make kelp farming faster and more efficient!

My lab partner Ben and I with our kelp before they were treated with hormones.

My lab partner Ben and I with our kelp before they were treated with hormones.

For my second project I am working with Kelly DeWeese and we are attempting to extract RNA from Giant Kelp. Kelp farms have an unfortunate history of invasiveness, but growing sterilized kelp would mitigate this problem. Giant Kelp has a unique life cycle, it alternates between a diploid sporophyte stage and a microscopic, haploid, gametophyte phase. Interestingly, only the sporophyte is reproductive. Gary Molano, a graduate student in the lab, came up with an idea to exploit this part of the life cycle and sterilize the kelp. If we can identify which genes allow for reproduction, we can farm kelp that has naturally occurring nonfunctional mutations in these genes. Identifying the reproductive genes can be done by comparing the genetic expression between the sporophyte and gametophyte, this is called differential expression analysis. In order to figure out which genes are being expressed, RNA needs to be extracted and sequenced. Unfortunately, it is extremely difficult to extract RNA from kelp tissue, so this summer I am working toward optimizing a protocol that allows for high quality RNA extraction.

When I’m not working in the lab, I spend my time swimming, hiking, kayaking, cliff jumping, and enjoying island life in general!

Sophia and I on our way back from nearby Two Harbors.

Sophia and I on our way back from nearby Two Harbors.