Introduction to Sanger sequencing and training for coral species identification.

June goals and daily notebook entries.

This post details WGCNA preliminary analysis for the E5 Deep Dive Project.

This post details the process I used to apply for a CITES export permit with the US Fish and Wildlife management authority.

May goals and daily notebook entries.

This post details the initial stable isotope metabolomics analysis for the Montipora capitata 2021 larval temperature exposure.

April goals and daily notebook entries.

This post details revisions to calculations for multivariate physiological plasticity analysis for the E5 Rules of Life project.

This post details analysis and bioinformatic steps to generate a gene count matrix from RNAseq data for the E5 Deep Dive Project.

This post details analysis of survival, settlement, physiology, and environmental data for the 2021 Montipora capitata larval temperature project.

March goals and daily notebook entries.

Workshop: Software Carpentry in R - Terminal, GitHub, and R

February goals and daily notebook entries.

Today, I attended a workshop through the UW eScience Data Science postdoc group for an introduction to DVC, a version-control platform.

This post is a running log of miscellaneous coding and TidyTuesday exercises!

January goals and daily notebook entries.

This post details integrative analysis and plotting for response variables in the Montipora capitata 2020 developmental time series.

This post details re-analyzing TagSeq data for the 2020 M. capitata developmental timeseries project to a more recent v3 genome with annotation.

This post shows newly revised figures and revisions to analysis for the 2020 Montipora capitata development project.

This post details recent updates to the Montipora capitata developmental time series 16S analysis.

Writing

1. Revise Montipora capitata 2020 time series figures
   • Conceptual
   • Metabolomic
   • Gene Expression
   • Physiology
   • Integration
2. Revise Montipora capitata 2020 time series text to PNAS short format
3. Work with Emma to revise results of E5 time series manuscript
4. Reanalyze TagSeq data to new M. capitata genome

This post details analysis of respirometry data for the Acropora pulchra larval metabolism experiment in Moorea in Oct 2022.

This post details alignment of TagSeq sequences from the Mcap2020 developmental time series project to the symbiont genome. We will evaluate the results of this alignment to see if we have enough sequences to analyze symbiont-specific gene expression.

This post details environmental measurements analysis for the 2022 Acropora larval metabolism experiment from the Moorea 2022 Field Expedition.

This post details the NCBI Sequence Read Archive upload for Ariana Huffmyer’s Montipora capitata 2020 early life history timeseries project.

This post includes the full notebook for Sept-Oct 2022 Acropora coral spawning and field expedition in Moorea, French Polynesia. These notebook posts by A. Huffmyer are updated in order of most recent to oldest.

Writing

1. Full draft of E5 results section for the 2020 time series project
2. Submit proofs for Pocillopora acuta diversity paper~
3. Revise Montipora capitata 2020 time series metabolomics and gene expression figures and associated text

Writing

1. First draft of E5 time series results section and outline of discussion section
2. Submit proofs for science education paper
3. Start Montipora capitata 2020 time series revisions

Writing

1. First draft of E5 time series results section and outline of discussion section
2. Submit revision for Pocillopora acuta genetic diversity paper
3. Go over Montipora capitata 2020 time series revisions with HP
4. Start Montipora capitata 2020 time series revisions

This post details multivariate physiological plasticity analysis for the E5 Rules of Life project.

Writing

1. Finish and send final draft of Montipora capitata ontogeny 2020 manuscript to co-authors
2. First draft of E5 time series manuscript by end of August with full results and outline of discussion section
3. Submit final revision for science education manuscript
4. Write methods and results section of Montipora capitata larval temperature exposure 2021 project
5. Submit revision for Pocillopora acuta genetic diversity paper

This protocol details the methods for collecting Montipora capitata bundles during spawning, fertilizing gametes, and rearing and settling larvae in Hawai’i during the summer months.

This protocol details the step-by-step process for incubations for stable isotope metabolomics for coral larvae.

This protocol details the step-by-step use of PreSens/Loligo Microplate respiration system for coral larvae.

Writing

1. Write results of Montipora capitata development manuscript
2. Draft results of E5 time series manuscript

Writing

1. Methods and results of Montipora capitata development manuscript
2. Submit final revision of science identity manuscript (delayed until August 2022)

This post details preliminary analyses of multi-omic datasets collected in the Montipora capitata early life history time series project.

This protocol describes the process for taking photographs of preserved coral larvae for measurement of larval size (volume, surface area, length, etc.).

This protocol details symbiont cell counts in coral larval tissue samples. This protocol is modified from the E5 cell counts protocol.

This protocol details metabolite extraction from coral larval samples labeled with stable isotopes (C13 bicarbonate) and control samples (C12 bicarbonate).

This protocol details quantification of soluble protein from coral larval samples. This protocol is modified from the E5 Protein Protocol.

This post details sample processing completed in April 2022 for the 2021 M. capitata larval thermal exposure experiment conducted in Hawaii.

This protocol details chlorophyll measurement in coral larval tissue samples. This protocol is modified from the E5 chlorophyll protocol.

This protocol details quantification of carbohydrate content in coral larvae in 96-well plates modified from the Bove Baumann protocol and the Putnam Lab carbohydrate protocol.

This post details 16S analysis of the Putnam Lab oyster project using the Mothur pipeline based on A. Huffmyer’s pipeline here.

Writing

1. Write results of Montipora capitata development manuscript
2. Start discussion of Montipora capitata development manuscript

This post details analysis of TagSeq data from previous alignment to M. capitata version 1 assembly and version 2 assembly.

Writing

1. Finish methods of Montipora capitata development manuscript
2. Write results of Montipora capitata development manuscript
3. Start discussion of Montipora capitata development manuscript

This post details QC and filtering steps that were done in both Mothur and QIIME2 to compare the sequence QC results.

This post details analyzing relative abundance and diversity metrics in R output from mothur analysis of 16S data for the 2020 early life history Montipora capitata time series.

This post details continued analysis of metabolomics data for the 2020 M. capitata developmental time series with WGCNA.

This post details 16S data analysis using the Mothur pipeline for the 2020 Montipora capitata developmental time series.

Publications

1. Revise and submit intraspecific diversity paper
2. Write methods for Pocillopora acuta thermal exposure paper
3. Outline revisions for Life History energetics perspective paper
4. Outline results section of E5 timeseries manuscript
5. Finish methods and write results of Montipora capitata development manuscript

This post details QC and QIIME analysis for the 16S analysis adapted from the pipeline developed by Emma Strand.

This post details SymPortal analysis for the ITS2 analysis pipeline modified from Kevin Wong pipeline.

This post details MultiQC for the ITS2 analysis pipeline. 16S files are analyzed in a separate post.

This post details QC and QIIME analysis for the 16S analysis adapted from the pipeline developed by Emma Strand.

This post details MultiQC for the 16S analysis pipeline adapted from the pipeline developed by Emma Strand. In this post there is information for moving/managing ITS2 sequences, but this post details preliminary analysis of 16S. ITS2 files will be analyzed in a separate post.

This post details all activities in Moorea in December 2021 for Symbiont Integration project for the study species Pocillopora acuta.

This posts describes extraction protocols for ITS2 and 16s sequencing for the 2020 Montipora capitata developmental time series.

Publications

1. Revise and submit intraspecific diversity paper
2. Finish revisions and submit larval thermal conditioning paper
3. Outline revisions for Life History energetics perspective paper

Environmental data analysis for the E5 Rules of Life Project continued.

This posts describes the QC process from November 2021 for the E5 Rules of Life timeseries data.

This post continues analysis of environmental time series data for the E5 Rules of Life Project.

This post details environmental time series QC and plotting for the E5 Rules of Life project.

This posts describes weighted gene co-expression analysis (WGCNA) applied to metabolmoics data from the 2020 Montipora capitata early life history developmental time series.

Proposals and applications

1. Submit education paper revisions to CBE - Life Sciences Education (November 9)
2. Submit Science Incubator proposal (November 10)
3. Submit NSF OCE proposal (November 12)
4. Prepare E5 time series talk for Moorea LTER Annual Meeting in early December

Post describing Pocillopora larval collection for collaborative projects with Carneige and Rutgers in June 2021.

Post detailing larval settlement and maintenance in June 2021 for M. capitata spawning.

Post detailing stable isotope time series data collection for methods optimization and development for coral larvae in collaboration with Rutgers University.

Post detailing temperature exposure and experimental design for M. capitata larval temperature experiment in June 2021.

Post detailing survival measurements and experimental maintenance in larval temperature experiment with M. capitata in June 2021.

Collection, fertilization, and rearing of Montipora capitata spawned gametes during the June 2021 spawning at the Hawaii Institute of Marine Biology.

Post details sampling and data collection for M. capitata larval temperature exposure experiment in June 2021.

Post detailing tank and experimental set up for Montipora capitata coral spawning in Hawaii in June 2021.

Post detailing culture maintenance of embryos of Montipora capitata during June 2021 larval temperature experiment and spawning.

Post detailing sampling of Mcapitata larvae collected as baseline samples prior to temperature experiment in June 2021.

This entry details sample processing for Mcapitata 2020 early life history samples for metabolomics, larval size and symbiont cell densitites, and RNA excxtraction for TagSeq.

This entry describes the sampling and respirometry data collection for Acropora hyacinthus in Moorea, French Polynesia at CRIOBE and Gump Research Stations.

This entry lists the runs and data collection for early life history respirometry (photosynthesis and respiration) in early life stages (larvae, recruits, and juveniles) of Montipora capitata in July 2020.

This notebook entry details methods for larval rearing and settlement for Montipora capitata early life history in July 2020. Sampling of these life stages is described in additional notebook entries.

This entry details the sampling and collection of embryos, larvae, and recruits of Montipora capitata during July-Aug 2020 spawning period.

This entry describes the protocol for measuring photosynthesis and respiration in early life history stages of Montipora capitata.

This protocol provides an overview of sampling early life history stages for Montipora capitata in July-August 2020.

Collection, fertilization, and rearing of Montipora capitata spawned gametes during the July 2020 spawning at the Hawaii Institute of Marine Biology in collaboration with C. Drury and J. Hancock in the Gates Coral Lab.