May Goals:
rphil paper: This month we’re trying to get the rphil paper out. So wrapping up edits for that and getting a discussion in
outreach: Open house is this month, planning and prep for that
dont skip class: Just finished midterm! So just keep chuggin along with coursework
be a good TA: Get grades out to 370 students within reasonable timeframe & be prepared to help students with their methods
slight dream goal: run blast for my bivalves to get a gene list before summer
Daily Updates
May 1
447 lecture
Started grading gel writeups for 370 and run 370 lab
addressed remaining comments in rphil MS and updated tables/figures and reran enrichment with updated background
created clean GH repo for rphil work that excludes unused files and analyses
May 2
370 lecture & lab
Continued/finished grading gel writeups for 370 and run 370 lab
worked on some lit review for papers emma sent and started drafting part of discussion
May 7
370 lecture & office hours
continued lit review and discussion drafting
created folder for 2025 open house & updated activity
447 homework
May 8
447 homework
447 lecture
open house prep meeting + lab meeting
447 lab
May 9
370 lecture
meeting with mac and emma to discuss methods/results updates and discussion draft 1
started updated discussion outline
back to lit review
May 12
370 lecture & planning meeting
finished additional methods/results update
updated rphil figure / tables, and created/added supp table (GO info) to folder
finished (minus one sub section) updated discussion draft and added to MS
May 13
447 lecture
worked on addressing initial comments on updated discussion for rphil
personal errand which took a little bit of time (related to last months personal emergency situation)
short meeting with Andy to get everything squared away for open house / lobster tank
back to lit review
447 lab
May 14
370 lecture and extra planning meeting because course organization post week 7 is f****d with little to no documentation from previous quarters….
370 office hours – ran long. had ~7 students with long form questions. office hour? more like office 3 hour
sent out open house info
went back to lit review for last part of day to continue progress towards addressing Mac & Emmas discussion comments
May 15
gathered open house materials
447 lecture
brief follow up meeting with callum and andy on live clam ‘disposal’ instructions + ensuring access to aquarium roon
update lab notebook for the month so far (oopsies)
lab meeting
370 lab
rest of day: lit review & keep chippin away at discussion comments if time (not optimistic)
Who’s Lit is it Anyways?
This month has been a lot of paper hunting. Here’s a list of some of the papers from the last two weeks I’ve been digging through. A big thing I’ve been looking for is to get a general understanding of what might be typical differences in egg gene expression. Whether its as a results of parental priming to OA, spawn timing, immune system stimulation, etc. How much of an impact is parental contributions really having on egg expression?
A lot of the lit out there seems to be looking at priming within a generation, which seems to yield somewhat substantial differences between control and treatment groups (lots of DEGs). But when looking at eggs from treated vs control parents, there is less of a difference (few DEGs).
My shift now (5/15) is to find literature to continue fleshing out these different responses as a result of different life stages, different tissue types being analyzed, different types of stressors, etc. And also to dive deeper into the functional interpretation of the genes to see what kind of impact our DEGs have been having in other bivalves, and if they have been observed as DEGs in similar studies to ours.
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0172805
Yaamini - https://academic.oup.com/eep/article/10/1/dvae018/7764574#498950252
Func. groups (drosophila) - https://onlinelibrary.wiley.com/doi/epdf/10.1002/mrd.1080260310
Goby - https://link.springer.com/article/10.1186/s12862-018-1132-2#Sec3
Pco2 c. virginica - https://www.frontiersin.org/journals/marine-science/articles/10.3389/fmars.2020.566419/full
McNally EM, Downey-Wall AM, Titmuss FD et al. Parental exposure of Eastern oysters (Crassostrea virginica) to elevated pCO 2 mitigates its negative effects on early larval shell growth and morphology.
Strader. OA responses in bivalves review – https://frontiersinzoology.biomedcentral.com/articles/10.1186/s12983-020-0350-9
Gurr 2022 – single generation exposure, 429 DEGs @ 14 days
Kelly – Kelly MW, Padilla-Gamiño JL, Hofmann GE. High pCO 2 affects body size, but not gene expression in larvae of the California mussel (Mytilus californianus).
Transcriptomic features of Pecten maximus oocyte quality and maturation https://pmc.ncbi.nlm.nih.gov/articles/PMC5333834/
Growth – Differential gene expression identified by RNA-Seq and qPCR in two sizes of pearl oyster (Pinctada fucata) https://www.sciencedirect.com/science/article/pii/S0378111914000523
Maternal patterns of inheritance alter transcript expression in eggs https://pmc.ncbi.nlm.nih.gov/articles/PMC10084599/
Immune function – Priming European Sea Bass Female Broodstock Improves the Antimicrobial Immunity of Their Offspring https://pmc.ncbi.nlm.nih.gov/articles/PMC9913748/#sec3-animals-13-00415
Immune – Primed for success: Oyster parents treated with poly(I:C) produce offspring with enhanced protection against Ostreid herpesvirus type I infection https://www.sciencedirect.com/science/article/pii/S0161589016301754
Gene Expression and Phenotypic Assessment of Egg Quality across Developmental Stages of Atlantic Cod throughout the Spawning Season – https://pmc.ncbi.nlm.nih.gov/articles/PMC11242223/#sec2-ijms-25-07488
Epigenetics – Epigenetic considerations in aquaculture https://pmc.ncbi.nlm.nih.gov/articles/PMC5723431/