Posts

Master’s Thesis Committee Meeting #3

Progress check-in on analyses

committee

presentations

Submitted NGS 16SrRNA sequences to NCBI SRA

Backing up raw sequences from mim_c

lab records

code

Watch this 10min video tutorial: How to Submit to SRA, A Beginner’s Guide

Backup your work

workflow

It’s good practice to have an active work server that you push code to GitHub, and a backup server that you’re not working in for the large files you generate. In case you…

Submitting NGS sequences to NCBI SRA

Backing up raw sequences from Azenta

learning journey

code

So you got an email from Azenta saying your files are ready for download! Exciting! It’s the moment we’ve been waiting for. What next??

Transfer data files from Azenta to a local server

Getting raw NGS fastq sequence files off Azenta Genewiz server to a local server using Command Line and SFTP

learning journey

code

Azenta will email you to notify you that your project is complete and is being uploaded to your account on the Azenta sFTP server, where it will be available for download…

Bioinformatics Pipeline Roadmap

Transcriptomics analysis of RNA-seq data from embryonic development of Montipora capitata rice corals exposed to PVC leachate

code

coral

We’ve extracted totalRNA and shipped it to Azenta for sequencing… so what happens next? How did we go from working with microcentrifuge tubes in the lab to large files on…

Summary of previous research on microplastic leachate exposure in marine invertebrate embryonic development

In sea urchin and mussel model organisms

learning journey

coral

(jimenez-guri2023?) either exposed adult sea urchins Paracentrotus lividus to excessively high¹ levels of PVC leachate or filtered seawater control for 2 weeks, and then…

Ontogenetic Development of Montipora capitata

learning journey

coral

Montipora capitata corals are taxonomically classified in the Domain Eukaryota, Kingdom Animalia, Phylum Cnidaria, Class Hexacorallia, Order Scleractinia, Family…

Grants & Fellowships

A running list of grants and fellowships to keep an eye on

stats

coral

Smithsonian fellowships are offered to individuals who design and develop proposals to conduct independent research.

Nikon scope pictures annotation & data collection

Annotating images of embryonic development of Montipora capitata rice corals exposed to PVC leachate

protocols

coral

This guide is meant to be a checklist for annotating categories of embryonic development in Montipora capitata using NIS-Elements BR.

Timeline & Goals Planning

committee

goals

This is a timeline of goals and progress made toward wrapping up my Master’s Thesis at UW SAFS.

Statistics for embryo scope data

Exploring data from embryonic development of Montipora capitata rice corals exposed to PVC leachate

stats

coral

What information can we get from looking at the Montipora capitata embryos that were exposed to varying levels of PVC leachate (High: 1mg/L, Mid: 0.1mg/L, Low: 0.01mg/L)?…

Nikon scope pictures & slide preservation protocol

For capturing embryonic development of Montipora capitata rice corals exposed to PVC leachate

protocols

Watch ’Mounting Your Specimen’ by Dr. Terry Bruce of Clemson University on YouTube

26-Aug-2024 Embryo RNA Extractions

lab records

8C9F, 9C9F = 89C9¹

23-Aug-2024 Embryo RNA Extractions

lab records

4L14F, 5CL14F, 6L14HF = 456L14

21-Aug-2024 Embryo RNA Extractions

lab records

1C14F, 2C14F, 3C14HF = 123C14

20-Aug-2024 Embryo RNA Extractions

lab records

1H9F, 2H9F, 3H9F = 123H9

19-Aug-2024 Embryo RNA Extractions

lab records

4H9F, 5H9F, 6H9F = 456H9

16-Aug-2024 Embryo RNA Extractions

lab records

1L4F, 2L4F, 3L4F = 123L4

15-Aug-2024 Embryo RNA Extractions

lab records

4C14F, 5C14F = 45C14

14-Aug-2024 Embryo RNA Extractions

lab records

1C4F, 2C4F, 3C4F = 123C4

13-Aug-2024 Embryo RNA Extractions

lab records

coral

1C9F, 2C9F, 3C9F = 123C9F

12-Aug-2024 Embryo RNA Extractions

lab records

6C14F (single sample ~10 embryos)

M. Capitata Embryo DNA/RNA Extractions Protocol

protocols

coral

For inspiration checkout:

Coral collections & tank acclimation protocol

For spawning of Montipora capitata rice corals

protocols

Describe the Montipora capitata coral colony collections under State of Hawai`i SAP2024-35 and tank acclimation prior to spawn night research activities in June & July of…

Spawn night protocol

For embryonic development of Montipora capitata rice corals

protocols

This spawn night checklist was used on July 5th, 6th and 7th 2024 at the Hawaiian Institute of Marine Biology (HIMB) on Moku o Loe in Kaneohe Bay, Oahu. The overarching goal…

Experiment Log

coral

Kat and Callum collected 10 distinct Montipora capitata colonies of approximately 30cm in diameter from Kaneohe Bay, Hawaii under permit

Extracting & measuring chlorophyll a & c2 concentrations

… from an anemone-hosted symbiotic dinoflagellate using a ThermoFischer Nanodrop 2000c

protocols

anemones

This protocol draws heavily (and almost exclusively!) from the awesome method paper, “Its What’s on the Inside That Counts: An Effective, Efficient, and Streamlined Method…

Single stressor leachate exposure summary

A 48 hour exposure to polyvinyl chloride (PVC) leachate and to aged polypropylene (PP) leachate

lab records

This summary serves as a broad overview and notes of the acute (48hour) single stressor polyvinyl chloride (PVC) and polypropylene (PP) leachate exposure to Anthopleura…

All about the aggregating anemone

What, where, who studies it, how, and why!

learning journey

anemones

Anthopleura elegantissima are clonal intertidal anemones that can form flexible symbiotic partnerships with different single-celled algae which provide supplemental sugars…

Anemone Leachate Heat Experiment Recipe

anemones

protocols

Collect anemones

How to make a custom respirometry chamber

protocols

anemones

I had to make some custom respirometry chambers for my experiment. Here’s the requirements I needed to meet, and how I did it!

Puget Sound Microplastics

learning journey

What are the commonly measured concentrations of microplastics in Puget Sound, Washington? This goal of this objective is to understand the environmentally relevant range of…

Field collection at Constellation Park, Alki, West Seattle

anemones

lab records

On Saturday, March 30th, 2024 Kip and I collected Anthopleura elegantissima from Constellation Park near Alki in West Seattle, Washington under WDFW scientific collection…

Leachate preparation & dilution protocol

Modified from the lab protocol of Dr. Francesco Saliu and Valerio Isa

protocols

In order to study the effects of microplastic leachate we have to be able to re-create it in a controlled and defined way. For this, I partnered with Dr. Francesco Saliu and…

Field collection at Owens Beach, Point Defiance Park, Tacoma

anemones

lab records

On Monday, March 18th, 2024 we collected Anthopleura elegantissima from Owen’s Beach at Point Defiance Park in Tacoma, Washington under WDFW scientific collection permit Tanj…

Daily Lab Log

Enter at your peril; This one is for me, not you

daily log

Received confirmation that RNA is in line for QAQC

Experimental tank setup

protocols

anemones

Hydra 32HD manual

Measuring photosynthesis

Understanding & Operating the Walz Diving-PAM-II

learning journey

anemones

Photosynthesis is magic. Four proteins embedded in a delicate lipid membrane turn light into sugar. It’s energy transformation! The process by which light energy is…

Tides & WX Station Data

How to use the rnoaa package

learning journey

“Air temperature and tide data Air temperature and tide level data was obtained from various sources depending on the location. Hourly temperature and tide data for Toke…

Anemone Project Planning

anemones

The objective of this study is to examine the combined effects of thermal stress and marine microplastic leachate on photosynthetic efficiency, microbiome community, and…

Pseudoreplication & Control

How to design a manipulation experiment

learning journey

“the use of inferential statistics to test for treatment effects with data from experiments where either treatments are not replicated (though samples may be) or replicates…

How I created & maintain my open lab notebook using Quarto, Git & RStudio

code

learning journey

follow happy git for the useR

Phthalates around the World

learning journey

What are the common concentrations (ug/L) of phthalates measured in seawater around the world? This goal of this objective is to understand the environmentally relevant…

Master’s Thesis Committee Meeting #2

Options for addressing the need for a solvent control

committee

Introduce issue with lack of solvent control in experimental design - 5 mins

Master’s Thesis Progress

learning journey

committee

SAFS Masters Thesis Milestones are laid out here

Making PAE treatments and controls

protocols

I used the EPA 506 phthalate esters mix 1, which comes as a 1mL ampule vial with a glass break-off cap. It includes 6 common phthalates each at a concentration of \(500\mu…

Workflow with Git

For all the times I accidentally commit a file that is too big

workflow

.gitignore cannot filter files by size — it only filters by path patterns, like filenames, extensions, or directory names. It doesn’t support dynamic criteria like file…

Dual DNA & RNA Extraction Protocol

protocols

The aim of this protocol is to take coral fragments that have been snap-frozen in liquid nitrogen and extract both DNA for downstream archaea & bacteria microbiome 16S…

The RNA Inhibitors

A tragic saga of continued troubles

lab records

After shipping 20 samples to the University of Texas at Austin GSAF for TagSeq on June 7th 2023, I got a message back from them on June 28th 2023:

Getting Started with `QIIME2` and `Jupyter Lab`

Working from a Windows OS and connecting via VPN to a remote server

code

learning journey

Sometimes it seems the hardest part about developing a new workflow is deciding where to put it! As I start working on analyzing my microbiome data, I need to have a Linux…

Target Journals for Submitting Manuscripts

learning journey

Impact Factor 8.9

Phthalate exposure to coral embryos methods

M. capitata embryo development and EPA 506 pthalate mix 1 acute exposure experimental methods

lab records

protocols

Plasticizers are a suite of chemicals added to plastic consumer products to increase flexibily. The most widely used plasticizers are phthalate acid esters (PAEs). PAE’s are…

Choosing 16S Primers for M. capitata microbiome

learning journey

” Indeed Cruaud et al. (2014) and Fouhy et al. (2016) show that primer choice has a far deeper influence on microbial community than extraction method, although they did…

DNA/RNA Extractions Overview

lab records

Qubit RNA BR Assay Kit The Qubit RNA BR (Broad-Range) Assay Kit, when used with the Qubit Fluorometer, provides an accurate and selective method for the quantitation of RNA…

Environmental Landscape of an Intertidal Heat Wave

Using NOAA National Data Buoy Center (NDBC) to map air and water temperatures in Commencement Bay, Tacoma, WA, during the June 2021 Puget Sound heat wave

I searched the NDBC map for the stations closest to my collection site at Owens Beach, Point Defiance Park in Commencement Bay, Tacoma.

Dual DNA & RNA Extractions for Montipora capitata coral

lab records

These lab extractions follow the Dual DNA & RNA Extraction Protocol with any deviations, exceptions, or notes explained in detail.

Master’s Thesis Committee Meeting #1

committee

Introduction - 5 mins

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