November 2023 goals and daily notebook entries.

Goals

STUDY FOR COMPREHENSIVE EXAMS – THIS IS THE PRIORITY

Writing and manuscripts

1. Full draft of dissertation proposal
2. Write full methods and results for Astrangia 2021 experiment
3. Intro outline for e5 ncRNA manuscript

Sample processing

1. RNA extractions for AH - HI 2023
2. Physiology processing for developmental time series 2023
   • Carbs
3. Initial cell counts for Astrangia 2021
   • Count 20 samples and see how variable they are after homogenizing 2x

Data analysis (if time)

1. E5 deep dive - lncRNA and miRNA
2. Astrangia mRNA analysis

Daily log

November 1

• Read Coles & Brown 2003
• Read Palumbi et al. 2014
• Met w/ Marta
• Met w/ Ben
• Made sure Fedex shipment went out

November 2

• Read Brown et al. 2000, 2002, 2014
• Read Gates & Edmunds 1999
• Read Brown & Cossins 2011
• Watched videos on cell signaling, protein phosphorylation, miRNA generation and action, NGS, etc
• E5 ncRNA meeting
• Meeting w/ Steven re comps topics

November 3

• Dentist appt
• E5 molec mechanisms meeting
• Lab meeting
• Read Drury 2020
• Read Barott et al. 2021

November 5

• Read chapter 5 in the flexible phenotype (chapter on phenotypic plasticity)
• Made ppt for acclimatization in corals

November 6

• Lead journal club discussion
• Read Goldberg et al. 2007
• Read Bird 2007
• Read Gibney & Nolan 2010
• Read Eirin-Lopez & Putnam 2019

November 7

• Read Ospelt 2022
• Read Murray et al. 2022
• Read Ding & Yang 2022
• Received Zymo stuff!
• Read Ding et al. 2020
• Read Deans & Maggert 2015
• Read Ashe et al. 2021
• Read about Illumina sequencing (specifically library prep)

November 8

• Read Ho & Burggren 2010
• Died from vaccines

November 9

• Read Kronholm et al. 2017
• Read Yao et al. 2019
  • This is a good review article about miRNAs and its interactions with other epigenetic mechanisms. It’s also a short and sweet paper
• Skimmed Dhanoa et al. 2018 & Liu et al. 2021 for info on lncRNA biogenesis and function
• Met w/ Shara (prospective student from UM)
• Reefbites meeting

November 10

• Lab meeting
• Podcast recording
• Read Bryne et al. 2019

November 11

• Went to Tomagouq museum

November 12

• Finished reading Bryne et al. 2019
• Read Eddy 2002
• Read Fu 2014
• Read Chao et al. 2022
• Read Kultz 2005
• Worked on sequencing info, primarily cluster generation and sequencing

November 13

• Worked on sequencing info, primarily data analysis and error rates
• Read Mittler et al. 2011
• Read Zhao et al. 2021
• Fed corals in BT 1/2 and cleaned BT 1/2 w/ Zoe
• Skimmed chapters 1 and 2 in thermal adaptation
• Watched videos on photosynthesis and cellular respiration
• Met w/ Sam Gurr re comps
• Typed up sequencing answer for JP exam

November 14

• Went to dentist
• Received Zymo switch free kit
• Helped Zoe w/ r script for wet lab
• Set up slack bot reminder for daily measurements in wet lab
• Organized text from PhD ideas google doc into my comps notes
• Read Taylor et al. 2015
• Read Li et al. 2015
• Read important parts of Baumgarten et al. 2017
• Read important parts of Moran et al. 2014
• Skimmed Harrison 2011
• Read gametogenesis parts of Harrison & Wallace 1990

November 15

• Read Leung & Sharp 2007
• Read Leung & Sharp 2010
• Read portions of Mendell & Olson 2012
• Read Emde & Hornstein 2014
• Skimmed ncRNA in cnidaria papers
  • Grimson et al. 2008
  • Krishna et al. 2013
  • Liew et al. 2014
  • Juliano et al. 2013
  • Lim et al. 2014
  • Modepalli & Moran 2017
  • Modepalli et al. 2018
  • Urbarova et al. 2018
  • Fridrich et al. 2023
  • Teefy et al. 2020

November 16

• Read Di Liegro et al. 2017
• Read Alvarez-Garcia & Miska 2005
• Read Acharya et al. 2017
• Read Hofmann 2017
• Read Duncan et al. 2014
• Read Fox et al. 2018
• Outlined some answers for potential comps questions
• Added threshold lines to daily measurement plots for wet lab

November 17

• Went to the dentist
• Started to organize terms to know document
• Molecular mechanisms meeting
• Lab meeting

November 19

• Worked on terms to know doc
• Read Shikina et al. 2013
• Read Shikina et al. 2012
• Read Shikina et al. 2018
• Read Chen et al. 2016
• Did an extraction for AH samples

November 20

• Ran a gel for AH samples
• Aliquoted out DNA and RNA for Nanodrop
  • Can’t find RNA tube for R105 in freezer, may need to re-extract
• Read Zuo et al. 2021
• Read Dellaert & Putnam 2023
• Read Van Etten et al. 2020
• Read Putnam 2021
• Read Chille et al. 2021
• Started on beyond gene expression manuscript

November 21

• Read Cavalli & Heard 2019
• Read Hackerott et al. 2023
• Read Putnam et al. 2020
• Read Gajigan & Conaco 2017
• Read Zhu et al. 2022
• Read Huang et al. 2019
• Did daily tasks for wet lab, cleaned BT 1/2 tank
• Read Beaman et al. 2016
• Read Tan et al. 2020

November 22

• Read Barshis et al. 2013
• Read Torda et al. 2017
• Read some of chapter 5 in Thermal Adaptation book

November 23

• Read Drury et al. 2021
• Read Hackerott et al. 2021

November 25

• Read the rest of the chapter 5 and some of chapter 3 in Thermal adaptation book

November 26

• Read Adrian-Kalchhauser et al. 2020
• Read some TEI papers but they were dense and my brain didn’t want to focus
• Read parts of Bonduriansky et al. 2011
• Read Fitz-James and Cavalli, 2022
• Skimmed Dimond & Roberts 2016, 2020
• Read Liew et al. 2018, 2020

November 27

• Did daily aquarium stuff
• Read about signaling cascades and their relation to DNA methylation
• Read Norouzitallab et al. 2019
• Outlined some potential questions
• Put key examples for specific topics in a doc

November 28

• Read Heard & Martienssen 2014
• Read parts of Gavery & Roberts 2017
• Outlined potential questions

November 29

• Read parts of Praher et al. 2021
• Outlining pathways w/ conserved miRNA pathways in cnidarians
• Reviewed lots of ncRNA papers
• Watched videos on cellular processes
• Looked through molec cell and epigenetics textbooks and marked relevant pages to reference during comps

November 30

• Reviewed computational methods for ncRNA analysis, specifically focusing on miRDeep2
• Mock oral exam w/ Danielle
• Outlined potential questions