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, … Continue reading DecaPod S2E6: Interview with Laura Slater

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!

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): Day 9, infected Day 9, uninfected Day 12, cold, infected Day 12, cold, uninfected Day 12, warm, infected Day 12, warm, uninfected

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 … Continue reading DecaPod S2E3: Interview with Shanelle Haughton

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.

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

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, … Continue reading DecaPod S1E13: Interview with Madi Shipley

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.

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 … Continue reading DecaPod S1E11: Crab Meeting #5

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: uninfected from Day 9 (before temperature treatment began) infected from Day 9 (before temperature treatment began) “MasterPool” : 10 samples. One sample per each of the following treatments: uninfected, … Continue reading DecaPod S1E10: Crab Meeting #4