This document outlines the laboratory procedure for identifying the clade of Zooxanthellae (symbiotic algae, primarily Symbiodiniaceae) associated with coral tissue. The protocol involves gDNA extraction using the ISOLATE II Plant DNA Kit, followed by PCR amplification of the ITS2 region, and visualization via Agarose Gel Electrophoresis.

Updated 10-11-2025 by: Rachel Bober

Updated 11-07-2024 by: Rachel Bober

updated 26.6.24

Click here for Technical Specifications

Israeli supplier: Lumitron

Power switch: top right

Screen type: Touch Screen

Drainage: make sure the water hose is not kinked and the water drains and collects in a bucket.

Alert system:

You can connect a communication cable that enables receiving incoming notifications signals from your alarm system however make sure there is someone receiving them.

As the power switch is turned on, a green light will appear on the screen, you must wait a bit and only then can you program the stability chamber.

Programing:

1. It is mandatory to make sure that the clock of the stability chamber is set, but if it is not, make sure to set according to the instructions in the device’s manual.

2. It is recommended to read the detailed instructions for programming in the device’s manual on page 39 to 45.

The following parameters can be adjusted:

temperature

humidity

illumination

ventilation

gas concentration in ppm.

How do you program?

On the touch screen: ‘stop 1 program’

Up and down arrows -

you can select ‘edit’ for editing the desired program and move between the segments.

Right and left arrows -

secondary screen of the segment, for selecting the parameters within the segment.

Programming example:

We are working with program #3

For instance, for one interested in setting a program that will activate 12 hours of light and 12 hours of darkness and will run for two to three months:

We will use arrows and set the constant parameters:

Temp - 22 °C

humidity - 70%

ventilation - 60%

It is also possible to determine the concentration of CO2 in ppm

Selecting light/dark conditions:

Illumination - 10% of the illumination capacity

300 minutes - be aware ‘300 minutes’ means that the setting is for 5 hours until dark.

Change in illumination conditions:

If a gradual transition from dark to light is desired, then choose ‘Ramp’ ON

By finishing programming, one must select the number of repetitions in which the program will repeat itself.

To do this, click on the loop icon and Choose ‘Repeat’

Do not forget to enter a number, for example: 99 - that is, 99 days will pass until the program is stopped.

#Respirometer Manual

Walk-though of Forking and Modifying this Notebook Site

All steps that can be done through the terminal instead of a GUI will be written for doing in the terminal because it is good practice to use the shell

Written by Maggie Schedl

This protocol details the step-by-step use of the PreSens/Loligo Microplate respiration system for measuring respiration and photosynthesis of coral planulae.

Using the DMEM no glucose and antibiotic-antimycotics

These instructions allow to quantitatively assess coral physiological parameters, i.e. tissue biomass (protein concentration), algal density and chlorophyll concentration.

These instructions cover two ways to get algal cell counts using Fiji, one manual and one automated. A fluorescence microscope (Nikon Eclipse Ti, Japan) was used to image symbiotic algae (isolated from coral tissue) both in brightfield and in fluorescent light using 440 nm emission, to identify chlorophyll and to ensure counting of symbiont cells only.

📖 Project Overview

This repository documents the molecular identification of fire worms (Hermodice carunculata and Eurythoe complanata) using DNA extraction, PCR amplification, gel electrophoresis, and sequencing.
The goal is to:

• Establish reliable gDNA extraction protocols for polychaetes.
• Test Folmer and Geller COI primers for amplification efficiency.
• Sequence PCR products and confirm species identity via BLAST analysis.
• Provide reproducible lab notes and results for future reference.

Fixation

1. 1.5 ml FSW (0.2 µm filtered seawater) in a 15 ml tube (for small fragments).
2. Cut the sample into approximately 2 cm fragments and place them in the tube.
3. Leave the fragments in the tube with the FSW for 10 min before adding 1M MgCl₂.
4. Add 0.3 ml of 1M MgCl₂ to a single tube, and cover the plate with aluminum foil for 10 min.
5. Remove the FSW from the tube.
6. Add 4% formaldehyde solution into the tube.
   Second option: leave the 1.8 ml of FSW and 1M MgCl₂ solution in the tube and add 0.5 ml of 16% formaldehyde to the tube for a final concentration of 4%.
7. Leave at 4°C overnight or 1–2 hours at room temperature.
8. Wash ×3 with sterile PBS solution.
9. For extended storage, store in 70% sterile ethanol, or leave in PBS for short storage of 2–3 days.