Transparency. Rigor. Reproducibility.
PRJ002 aims to reduce the microbiome of Exaiptasia pallida. We tested and compared 2 antibiotic solutions plus a control population. This post serves to establish the sampling protocol used across all our sampling timepoints following the initial Start point. See T0 Notes
To test and setup up sampling procedures for Flow cytometry to obtain symbiodiniacae counts and potentially also live and dead bacteria counts.
This is the third round of experimentation on this project with the goal of further improving the method of extraction on marine sediments with high humic contents.
To optimize PCR conditions for the Sequencing primers for 16s rRNA amplification using the Q5 mastermix Kit from NEB
To optimize PCR conditions for the Sequencing primers for 16s rRNA amplification using the Q5 mastermix Kit from NEB
## Objective: Sample individuals that have been treated in ABS, or ABS 2 without the priming for one week , then allowed to recover in Filtered Sewater for a further week in order to determine the the susceptibility of anemones to conditions and test if knockdown remains after one week of ir bacterial abundance increases within that time period
## Objective: Sample individuals that have been treated in ABS, or ABS 2 without the priming for one week in order to determine the the susceptibility of anemones to conditions and test the if concentrations used were appropriate.
This is the second use of the ZymoBiomics DNA/RNA Prep minikit. After the first experimental concentrations and 260/280 values were less than optimal, the aim is to test the kit using bulk samples directly frozen on dry ice
To optimize PCR conditions for the Sequencing primers for 16s rRNA amplification using the Q5 mastermix Kit from NEB
Objective: Experimental Setup of microbial Knockdown project.
This project will monitor the success of microbial knockdown under two seperate Antibiotic solutions being treated fro 7 days, and will also monitor the duration for which the microbiome stays reduced. Initial sample priming will involve the reduction of the microbiome through keeping the organisms in Seawater filtered with a .22 micron filtered, and feeding with Artemia that have had their microbiome knocked down through the use of antibiotics.
Initial priming: individuals will be kept in 12 well plates for 1 month, in Artificial seawater which has been filtered through a 0.22 micron filter (FSW) and fed twice weekly with Artemia treated with ABS 1 ( see entry on antibiotic preparations)
Objective: The objective of today’s experiment is twofold. 1. Test and confirm the extraction protocol modifications made using the Zymo kit. 2. compare lysis matrices in the bead beater to see which one returns a more optimal
Objective: Experimental Setup of microbial Knockdown project.
This project will monitor the success of microbial knockdown under two seperate Antibiotic solutions being treated fro 7 days, and will also monitor the duration for which the microbiome stays reduced. Initial sample priming will involve the reduction of the microbiome through keeping the organisms in Seawater filtered with a .22 micron filtered, and feeding with Artemia that have had their microbiome knocked down through the use of antibiotics.
Objective: This is the third round of experimentation on this project with the goal of further improving the method of extraction on marine sediments with high humic contents. first round data can be found in the post from Sept. 14th
The samples used here were part of the initial sample collection from the scouting trip to Bodega bay in late july. successful optimization of this protocol will allow us to simultaneously collect DNA and RNA from a single sample to be used in multiple downstream analyses such as simultaneous metagenomics and metabolomics
This Protocol aims to establish a standard Protocol for the sampling of Anemones for the Microbiome Manipulation Experiment , which we will standardize across timepoints.
Objective: This is the second round of experimentation on this project with the goal of further improving the method of extraction on marine sediments with high humic contents. first round data can be found in the post from Sept. 14th
The samples used here were part of the initial sample collection from the scouting trip to Bodega bay in late july. successful optimization of this protocol will allow us to simultaneously collect DNA and RNA from a single sample to be used in multiple downstream analyses such as simultaneous metagenomics and metabolomics
This Protocol aims to establish a standard Protocol for the sampling of Anemones for the Microbiome Manipulation Experiment , which we will standardize across timepoints.
This is the first use of the ZymoBiomics DNA/RNA Prep minikit. We are hoping this kit will prove to be a more efficient alternative for Sediment extractions that we can use for metagenomic analyses and metabolomics. the purpose of this experiment was to test the protocol per the manufacturers instructions on our marine sediment samples collected in Bodega Bay
Objective: The objective of this experiment is to optimize an extraction protocol for marine seagrass associated sediment microbial communities. This is a 2 day (September 13th and 14th) process part of a larger multi-day experiment which will work to adjust this protocol to maximize Nucleic acid output. It is adapted from Lever et. al 2015.
Objective: The purpose of this entry is to set precedent for what I’d like my Notebook to look like going forward and to create a means of organization that is clear and easy to follow.
PRJ003-Aiptasia-STB’s primary objective is to monitor and establish patterns for the variability acrross four strains (CC7-Endo, CC7-SSB01, CC7-Apo, and H2-Endo)