Accompanying data for the PhD thesis 'Nanomaterial safety for microbially-colonized hosts'

These files include all data presented in chapter 6 of the dissertation:

"Nanomaterial safety for microbially-colonized hosts: microbiota-mediated physisorption interactions and particle-specific toxicity" by Bregje Brinkmann (2022).

The data presented in chapters 2-5 have previously been published elsewhere:

Chapter 2: Zenodo (DOI: 10.5281/zenodo.6800734).

Chapter 3: Mendeley Data (DOI: 10.17632/2d4hcr5cb5.1)

Chapter 4: Figshare (DOI: 10.6084/m9.figshare.c.4923261)

Chapter 5: Mendeley Data (DOI: 10.17632/4nfg69v8hy.1)

1. Data presented in Figure 6.1: Survival_CFU_(...)
Tab-delimited file with zebrafish larvae survival, and the number of colony-forming units (CFUs) associated with zebrafish larvae, following exposure to silver nanoparticles (nAg) from 3-5 days-post fertilization (dpf):

Concentration: Nominal exposure concentration (mg nAg·L-1).

Date: The date at which the mortality was scored (Format: DD/MM/YYYY). 

Family: A code referring to the aquarium of wildtype zebrafish (ABxTL) that were crossed to obtain the larvae for the experiment.  

Survival: Percentage of larvae that had survived the treatment.

CFU: Number of colony-forming units that was isolated per larva

The methodology for toxicity tests and the procedures to determine CFU counts, have been published in Nanotoxicology:

Brinkmann BW, Koch BEV, Spaink HP, Peijnenburg WJGM, Vijver MG. 2020. Colonizing microbiota protect zebrafish larvae against silver nanoparticle toxicity. Nanotoxicology. 14: 725-739. DOI: 10.1080/17435390.2020.1755469

2. Data presented in Figure 6.2: ABs_DoseResponses_(...)
Tab-delimited file with zebrafish larvae mortality following a pretreatment of 0, 6 or 72 hours with an antibiotic and antifungal cocktail, and subsequent exposure to nAg from 3-5 dpf:

Concentration: Nominal exposure concentration (mg nAg·L-1). 

Mortality: Percentage of larvae that had died.

Date: The date at which the mortality was scored (Format: DD/MM/YYYY).

Family: A code referring to the aquarium of wildtype zebrafish (ABxTL) that were crossed to obtain the larvae for the experiment.  

ABs: Duration of the antibiotic/ antifungal pretreatment, either 0, 6 or 72 hours.

3. Data presented in Figure 6.3: il1beta_eGFP_(...)
Three folders comprising fluorescence microscopy images (TIFF format) of il1beta:eGFP reporter zebrafish larvae at 5 dpf:

(...)_replicates1_20200226: images for the first experimental replicate.

(...)_replicates2_20200304: images for the second experimental replicate.

(...)_replicates3_20200318: images for the third experimental replicate.

For each of the replicates, the following images were acquired:

nZnO_GFP: GFP signal for larvae exposed to nZnO.

Znion_GFP: GFP signal for larvae exposed to zinc ions.

nZnO_trans: transmitted light images for larvae exposed to nZnO. 

Znion_trans: transmitted light images for larvae exposed to zinc ions.

Additionally, the following images  have previously been deposited to Mendeley Data (DOI: 10.17632/4nfg69v8hy.1):

nAg_GFP: GFP signal for larvae exposed to nAg.

nAg_trans: transmitted light images for larvae exposed to nAg.

Agion_GFP: GFP signal for larvae exposed to silver ions.

Agion_trans: transmitted light images for larvae exposed to silver ions.

control_GFP: GFP signal for control larvae that had not been exposed to silver ions or nAg

control_trans: transmitted light images for control larvae that had not been exposed to silver ions or nAg.

All image processing steps have been published in Ecotoxicology and Environmental Safety:

Brinkmann BW, Koch BEV, Peijnenburg WJGM, Vijver MG. 2022. Microbiota-dependent TLR2 signaling reduces silver nanoparticle toxicity to zebrafish larvae. Ecotox Environ Saf. 237: 113522. DOI: 10.1016/j.ecoenv.2022.113522

Abbreviations:

ABs: antibiotics

CFU: colony-forming units

dpf: days post-fertilization

il1beta: interleukin-1beta

nAg: silver nanoparticles (NM-300 K)

nZnO: zinc oxide nanoparticles (NM-110)