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!
DecaPod S2E4: November Progress update – 6 new libraries ready for RNAseq!
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
DecaPod S2E3: Interview with Shanelle Haughton
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.
DecaPod S2E2: Status update on libraries being sequenced
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.
DecaPod S2E1: Discussing preliminary BLAST results and figures from our first assembled C. bairdi transcriptome
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
Poster: Effects of temperature and Hematodinium-sp. infection on Southeast Alaskan Tanner Crabs
Check our new poster!
This poster was given at a Graduate Student Symposium at the School of Aquatic and Fishery Sciences. It encompasses the overall project outline and goals, as well as some data from our first assembled transcriptome. More information on the project and updates can be found at our website (bittercrab.science) or our podcast (DecaPod) that is now available on iTunes.
180 SE Alaskan Tanner crabs (Chionoecetes bairdi) were brought into the NOAA, Juneau lab in the fall of 2017. Their initial infection status with Hematodinium -sp. (Bitter crab disease) was determined using a conventional PCR assay.
The crabs were then placed in 9 tanks (10 infected and 10 uninfected in each tank). Three tanks were brought up to warm temperature (10C), three at ambient (6C), and three at cold (4C). The hemolymph was sampled three times over the course of a few weeks.
FUNDING
North Pacific Research Board, Project No. 1705.
Direct link to poster
DecaPod S1E13: Interview with Madi Shipley
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.
DecaPod S1E12: Crab Meeting #6
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.
BLAST with bad Trinity fasta, R plan for adding Qubit data, and Testing out RNeasy Plus Mirco Kit – Grace’s Lab Notebook
Today I ran BLAST with the bad fasta from the Trinity run from last weekend. Will look more at the notebook Steven sent me to do the BLAST stats, goslim, contigs, go slim tables, etc. I also have been getting some input from Sam as to how best to manage adding new Qubit data to a master file consisting of all the hemolymph sampling data joined with the Qubit data results. Finally, I tested out the RNeasy Plus Micro Kit on 4 samples from Day 26, and ran the Qubit.
DecaPod S1E11: Crab Meeting #5
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.
