DecaPod | bittercrab.science

This episode was initially recorded in April 2020… and is now finally being shared with you! In this episode, I interviewed Laura Slater, a Crab Research Biologist at the Alaska Department of Fish and Game in the Division of Commercial Fisheries, and a PhD student at the University of Alaska, Fairbanks.

We discuss her work, her PhD project: understanding mating dynamics of snow crab in the Bering Sea, and SO much more!

http://owl.fish.washington.edu/scaphapoda/grace/Crab-project/DecaPod/S2E6-LauraSlater-interview.mp3

DecaPod | bittercrab.science is made with Jetpack Podcast. Full show notes and every episode at https://bittercrab.wordpress.com/

In this episode, we go over our three month plan (grant ends in March) for finishing sample processing and analyses. We also talk about some things I’ll add to my talk for the Alaska Marine Science Symposium 2020 conference, and finally Pam identifies a strange frilly crab tissue from samples she gave us!

http://owl.fish.washington.edu/scaphapoda/grace/Crab-project/DecaPod/S2E5-january-crab-mtg.mp3

DecaPod | bittercrab.science is made with Jetpack Podcast. Full show notes and every episode at https://bittercrab.wordpress.com/

In this episode, we talk about the process leading up to having 6 new libraries ready for sequencing. The 6 libraries are (note: Day 9 is before temperature treatment):

http://owl.fish.washington.edu/scaphapoda/grace/Crab-project/DecaPod/S2E4-crabmtg-november2019-progress.mp3

DecaPod | bittercrab.science is made with Jetpack Podcast. Full show notes and every episode at https://bittercrab.wordpress.com/

In this episode, we have a special guest, Shanelle Haughton! She is a PhD student at the University of Maryland, Eastern Shore. We talk about her path to graduate school, her upcoming research on Hematodinium spp. infection in Eastern Bering Sea, Alaskan Tanner crabs, and imposter syndrome and finding ways to work through it by making time for self care, and building community.

http://owl.fish.washington.edu/scaphapoda/grace/Crab-project/DecaPod/S2E3-shanelle-interview.mp3

DecaPod | bittercrab.science is made with Jetpack Podcast. Full show notes and every episode at https://bittercrab.wordpress.com/

In this week’s episode, we give an update on our libraries being prepped and sequenced by NWGC: libraries accounting for sampling day and infection statuses. Additionally, we talk about the plan for when sequence data arrives in August/September.

http://owl.fish.washington.edu/scaphapoda/grace/Crab-project/DecaPod/S2E2-daylibraries-update-complete.mp3

DecaPod | bittercrab.science is made with Jetpack Podcast. Full show notes and every episode at https://bittercrab.wordpress.com/

In this episode, we go through Grace’s GitHub repository for one of her classes in which she made some figures using BLAST results from our first assembled crab transcriptome against the swissprot/uniprot protein database, and against the nucleotide taxonomy database. Follow along as we discuss the README.md of this repository: https://github.com/fish546-2018/grace-Cbairdi-transcriptome

http://owl.fish.washington.edu/scaphapoda/grace/Crab-project/DecaPod/S2E1-Crab-Meeting-BLAST-results.mp3

DecaPod | bittercrab.science is made with Jetpack Podcast. Full show notes and every episode at https://bittercrab.wordpress.com/

This week, I talk with Madison (Madi) Shipley.

She is a graduate student (MS) in the School of Aquatic and Fishery Sciences, at the University of Washington. We talk about her thesis work of developing a management strategy evaluation for Tanner crab in the Eastern Bering Sea, her job with the Natural Resources Consultants Incorporated, how she got into the crab world, and her plans after receiving her degree. She also shares some of her at-sea experience with surveying in the Bering Sea.

http://owl.fish.washington.edu/scaphapoda/grace/Crab-project/DecaPod/S1E13-Interview-Madi-Shipley.mp3

DecaPod | bittercrab.science is made with Jetpack Podcast. Full show notes and every episode at https://bittercrab.wordpress.com/

This week we talk about transcriptome assembly (with our new RNAseq data from NWGC!!) and next steps. Also, we decide that Qiagen RNeasy Kit works pretty well for extracting RNA, and will be used to create the remaining libraries for the project.

http://owl.fish.washington.edu/scaphapoda/grace/Crab-project/DecaPod/S1E12-Crab-Mtg-6.mp3

DecaPod | bittercrab.science is made with Jetpack Podcast. Full show notes and every episode at https://bittercrab.wordpress.com/

This week Pam tells us about her recent experience on a survey on the Bering Sea, and we discuss our new plan.

The original RNA extraction method using RNAzol RT resulted in low RNA yields, as well as contaminated samples, likely due to excess salts. We have submitted a pooled sample to the NWGC for library prep and sequencing. The pooled sample consists of samples from day 26 (samples were taken in triplicate) from cold and ambient infected and uninfected treatments. This library will be used for gene discovery.

As we continue investigating better methods for RNA extraction, we will create libraries that will be used for comparison between treatment groups.

http://owl.fish.washington.edu/scaphapoda/grace/Crab-project/DecaPod/S1Ep11-Crab-Mtg-5.mp3

DecaPod | bittercrab.science is made with Jetpack Podcast. Full show notes and every episode at https://bittercrab.wordpress.com/

This week we discuss our plan of having three pools sequenced and next steps going forward. Three pools for the current three libraries are as follows:

http://owl.fish.washington.edu/scaphapoda/grace/Crab-project/DecaPod/S1E10-crab-mtg-4.mp3

DecaPod | bittercrab.science is made with Jetpack Podcast. Full show notes and every episode at https://bittercrab.wordpress.com/