April Goals
Revise methods and results for r.phil MS
Finish first draft of intro/disc. for r.phil chapter
Get gametogenesis gene list for bivalve species of interest
Recap of March
I didn’t really (at all, actually) in March. Here’s generally what went down:
March 5-11 was at the Aquaculture 2025 conference. Was great to see what up and coming research is happening and was a good experience presenting my findings (and forced me to actually finish my findings….)
March 12 was my one day in town before leaving for a personal trip. Held extended office hours for any questions about the final lab project for 270. I was also asked a little bit ago by Luke if I could help out one of his undergrads who is starting a stable isotope project, just with some light training on tissue collection and sample prep stuff, so we had a little tissue collecting party in the fish collection this day as well.
March 13-23 was technically “out of town” – had a snowboarding/climb trip, but got rained out for the climbing part of it. Most of this week was finishing and finalizing lab grades for 270 to get them to jose before grades need to be submitted.
March 24 had a planning meeting with the 370 teaching team and trained some folks from SEAS on how to do salmon dissections for science fairs, classroom/lab visits, etc.
March 25-28. There was a personal emergency at home. I was largely indisposed, occupied, distracted, whatever you wish to call it. (Things are more or less OK now, slightly too soon to fully tell, but everyone is hangin in there). Found some time within the craziness to update the functional annotation sheet for all GO terms (not just the 16 BP-first listed ones) and do some lit review where needed on those, as well as add the methods and results to the shared M.S.
March 31 was first day of the quarter – had 370 lecture, 370 teaching team meeting, and 370 lab prep for the week (fin clipping and DNeasy kit prep).
April!
April 1
447 lecture & lab
There’s this researcher, Li Yixuan, from Hong Kong I’ve been emailing with who has a paper (hot off the press!) using ultraconserved elements (UCEs) to generate a bivalve phylogeny. It includes many species, but only 6 of the 16 I’m interested in. If I could get a fasta file for some of the UCEs used, I can generate my own phylogeny using the 16 species, which is key to trait mapping the gametogenesis genes for my ch.1. Had a meeting with Luke to discuss this, and we were able to work with Yixuan to get the files.
some light lit review for r.phil intro/discussion – Gurr 2022
April 2
370 lecture
office hours
additional lit review for r.phil – Xu et a. 2024 ,Zhao et al. 2020
met with Mac to go over needed revisions for results and methods in MS as well as next steps / key things in lit to look out for
April 3
447 lecture
emails
update lab notebook
lab meeting
370 lab one
maybe TGIT seminar ? we’ll see how I feel :P
April 4
370 lecture, lab prep & lab
emails
April 7
370 lecture & planning meeting
reviewed GRFP update slides sent out to fellows
brief meeting with luke about phylo stuff
bivalve gametogenesis (BG) stuff:
created repo on GH
pulled the cds files for all the refseq annotated genomes
made the blast DB for the GO term of interest – GO:007276 Gamete Generation. Next steps I want to find a way to loop the query file / actual blast steps now that I have a sub directory containing all my genomes (cds) of interest.
April 8
447 lecture and lab – lab went 1h45m over time…. BUT learned some pretty siic stuff about hydrology and estimating flood event probabilities.
April 9
370 lecture
office hours
April 10
447 lecture
370 lab prep & lab
April 11
370 lecture
addressed comments in clam MS
370 lab
April 14
370 lecture & planning meeting
some admin-type work (emails, mostly) and preparing handouts for 370 week 3 labs
April 15
447 lecture & field day – went to several spots along Taylor Creek – very fun and informative case study on the impacts of altering geomorphological processes and the journey towards restoring them.
Also updated my functional annotation sheet for clam stuff and revisited a couple of the comments / mac’s suggestions.
April 16
370 class, office hours, and lab prep
did enzyme comparison for lipid metabolism enzymes in a paper Emma sent vs. DEG functional annotation list. None of the enzymes were shared explicitly, but other genes associated with lipid metabolism are on our list including none of the enzymes in those sections are on the DEG list, but we do have some DEGs associated with lipid metabolism: acyl-CoA dehydrogenase family member 10-like (LOC132737163), phospholipase D1-like (LOC132746792).
light lit review that really pushed my memory of biochem.
Anticipated 4/17-4/30
4/17: 447 class, lab meeting, 370 lab, lit review
4/18: 370 lecture and lab, lit review
4/19: grading
4/21: lecture, planning meeting. I need to do my GRFP AAR and declaration. Depending on how long GRFP stuff takes, would like to do some more lit review / revisit methods and results (goal is to revise these sections this weekish in such a way that is consistent with other literature in terms of phrasing, detail, etc)
4/22: 447 lecture and lab, continue on clam stuff
4/23: 370 lecture, office hours, lab prep, more clam stuff & check on code for gametogenesis workflow. Last week I got it to the point where I could run blast with variables, but I want to see if I can set it up as a loop in a way that is worth overcoming the initial work of learning/setting that up. Perhaps I’ll make a debut appearance at science hour depending on how this goes.
4/24: 447 lecture, lab meeting, 370 lab, lit review if brain is not mush
4/25: 370 lecture and lab, science hour (?), more reading :D
4/28: same stuff. lecture, planning meeting, lit review and addressing any of the MS comments.
4/29: 447 lecture and lab. See where I’m at with clam revisions, work on those if still more, if not, go back to code for gametogenesis and pushing that forward.
4/30: 370 lecture, office hours, and lab prep. Suppose I should change those clam intro and discussion bullet points to paragraphs at some point….