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)
May 16
370 lecture
finalized open house prep (got clams!)
370 lab
continued lit review to address rphil MS comments
May 17
field trip for 447 (watershed ecology) —
May 19
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.
| author | year | title | link |
| Pauletto | 2017 | Transcriptomic features of Pecten maximus oocyte quality and maturation | https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0172805 |
| Cheung | 2019 | What makes a bad egg? Egg transcriptome reveals dysregulation of translational machinery and novel fertility genes important for fertilization |
https://pubmed.ncbi.nlm.nih.gov/31307377/ |
| Venkataraman | 2024 | DNA methylation correlates with transcriptional noise in response to elevated pCO2 in the eastern oyster (Crassostrea virginica) | https://academic.oup.com/eep/article/10/1/dvae018/7764574#498950252 |
| Adrian-Kalchhauser | 2018 | RNA sequencing of early round goby embryos reveals that maternal experiences can shape the maternal RNA contribution in a wild vertebrate | https://link.springer.com/article/10.1186/s12862-018-1132-2#Sec3 |
| Downey-Wall | 2020 | Ocean Acidification Induces Subtle Shifts in Gene Expression and DNA Methylation in Mantle Tissue of the Eastern Oyster (Crassostrea virginica) | |
| McNally | 2022 | Parental exposure of Eastern oysters (Crassostrea virginica) to elevated pCO 2 mitigates its negative effects on early larval shell growth and morphology | https://aslopubs.onlinelibrary.wiley.com/doi/10.1002/lno.12162 |
| Strader | 2020 | Ocean acidification promotes broad transcriptomic responses in marine metazoans: a literature survey | https://frontiersinzoology.biomedcentral.com/articles/10.1186/s12983-020-0350-9 |
| Gurr | 2022 | Acclimatory gene expression of primed clams enhances robustness to elevated pCO2 | https://pubmed.ncbi.nlm.nih.gov/35947503/ |
| Kelly | 2016 | High pCO2 affects body size, but not gene expression in larvae of the California mussel (Mytilus californianus) | https://academic.oup.com/icesjms/article/73/3/962/2458759 |
| Barbosa | 2022 | A Transcriptomic Analysis of Phenotypic Plasticity in Crassostrea virginica Larvae under Experimental Acidification | https://pubmed.ncbi.nlm.nih.gov/36140697/ |
| Kim | 2020 | Transcriptome Analysis of Maternal Gene Transcripts in Unfertilized Eggs of Misgurnus anguillicaudatus and Identification of Immune-Related Maternal Genes | https://pmc.ncbi.nlm.nih.gov/articles/PMC7312655/ |
| Skimmed / not yet annotated | |||
| Shi | 2014 | Differential gene expression identified by RNA-Seq and qPCR in two sizes of pearl oyster (Pinctada fucata) | |
| Waite | 2025 | Characteristics of positive parental effects under exposure to climate change in marine invertebrates | https://link.springer.com/article/10.1007/s10452-025-10177-y |
| Zhang | 2022 | Comparative transcriptomic analysis revealed dynamic changes of distinct classes of genes during development of the Manila clam (Ruditapes philippinarum) | https://pmc.ncbi.nlm.nih.gov/articles/PMC9524096/#Sec17 |
| Zhao | 2018 | Transgenerational acclimation to seawater acidification in the Manila clam Ruditapes philippinarum: Preferential uptake of metabolic carbon | |
| Castets | 2012 | Combined analysis of Perca fluviatilis reproductive performance and oocyte proteomic profile | https://www.sciencedirect.com/science/article/abs/pii/S0093691X12001331 |
| Harry | 2023 | Maternal patterns of inheritance alter transcript expression in eggs | https://pmc.ncbi.nlm.nih.gov/articles/PMC10084599/ |
| Valero | 2023 | 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 |
| Green | 2016 | 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/abs/pii/S0161589016301754 |
| Miguez | 2024 | Gene Expression and Phenotypic Assessment of Egg Quality across Developmental Stages of Atlantic Cod throughout the Spawning Season | |
| Vihtakari | 2016 | Variable Individual- and Population- Level Responses to Ocean Acidification | https://www.frontiersin.org/journals/marine-science/articles/10.3389/fmars.2016.00051/full |
| Padilla-Gamino | 2022 | Ocean acidification does not overlook sex: Review of understudied effects and implications of low pH on marine invertebrate sexual reproduction | |
| Lymbery | 2019 | Ocean acidification during prefertilization chemical communication affects sperm success | https://onlinelibrary.wiley.com/doi/10.1002/ece3.5720 |