zenodoopen

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: <ul> <li>Chapter 2: Zenodo (DOI: <a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.5281%2Fzenodo.6800734&data=05%7C01%7Cb.w.brinkmann%40cml.leidenuniv.nl%7Cb5837fcc5a1b4cb5e88008da7615fe87%7Cca2a7f76dbd74ec091086b3d524fb7c8%7C0%7C0%7C637952134073527979%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=z4LB7Ziyiy%2BLXe0SllX67AJ%2F9zhfARBXp8QNzZsVg%2B4%3D&reserved=0">10.5281/zenodo.6800734</a>).</li> <li>Chapter 3: Mendeley Data (DOI: <a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.17632%2F2d4hcr5cb5.1&data=05%7C01%7Cb.w.brinkmann%40cml.leidenuniv.nl%7Cb5837fcc5a1b4cb5e88008da7615fe87%7Cca2a7f76dbd74ec091086b3d524fb7c8%7C0%7C0%7C637952134073527979%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=x7LFz2OgiJ20%2BD18QlwR9qIwGH%2BCbju4BKqkUaqIoXs%3D&reserved=0">10.17632/2d4hcr5cb5.1</a>)</li> <li>Chapter 4: Figshare (DOI: <a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.6084%2Fm9.figshare.c.4923261&data=05%7C01%7Cb.w.brinkmann%40cml.leidenuniv.nl%7Cb5837fcc5a1b4cb5e88008da7615fe87%7Cca2a7f76dbd74ec091086b3d524fb7c8%7C0%7C0%7C637952134073527979%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=n3wegOuHzKihCO%2FKbZhClnYHPyxWI0cALApBgLkUHnQ%3D&reserved=0">10.6084/m9.figshare.c.4923261</a>)</li> <li>Chapter 5: Mendeley Data (DOI: <a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.17632%2F4nfg69v8hy.1&data=05%7C01%7Cb.w.brinkmann%40cml.leidenuniv.nl%7Cb5837fcc5a1b4cb5e88008da7615fe87%7Cca2a7f76dbd74ec091086b3d524fb7c8%7C0%7C0%7C637952134073527979%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=0A0ktYDmgfxwc7U%2BgzHzQUj8Q5wixi%2BUzoSzMctlbso%3D&reserved=0">10.17632/4nfg69v8hy.1</a>)</li> </ul> 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): <ul> <li>Concentration: Nominal exposure concentration (mg nAg·L-1).</li> <li>Date: The date at which the mortality was scored (Format: DD/MM/YYYY). </li> <li>Family: A code referring to the aquarium of wildtype zebrafish (ABxTL) that were crossed to obtain the larvae for the experiment.  </li> <li>Survival: Percentage of larvae that had survived the treatment.</li> <li>CFU: Number of colony-forming units that was isolated per larva</li> </ul> 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: <a href="http://doi.org/10.1080/17435390.2020.1755469">10.1080/17435390.2020.1755469</a>   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: <ul> <li>Concentration: Nominal exposure concentration (mg nAg·L-1). </li> <li>Mortality: Percentage of larvae that had died.</li> <li>Date: The date at which the mortality was scored (Format: DD/MM/YYYY).</li> <li>Family: A code referring to the aquarium of wildtype zebrafish (ABxTL) that were crossed to obtain the larvae for the experiment.  </li> <li>ABs: Duration of the antibiotic/ antifungal pretreatment, either 0, 6 or 72 hours.</li> </ul>   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: <ul> <li>(...)_replicates1_20200226: images for the first experimental replicate.</li> <li>(...)_replicates2_20200304: images for the second experimental replicate.</li> <li>(...)_replicates3_20200318: images for the third experimental replicate.</li> </ul> For each of the replicates, the following images were acquired: <ul> <li>nZnO_GFP: GFP signal for larvae exposed to nZnO.</li> <li>Znion_GFP: GFP signal for larvae exposed to zinc ions.</li> <li>nZnO_trans: transmitted light images for larvae exposed to nZnO. </li> <li>Znion_trans: transmitted light images for larvae exposed to zinc ions.</li> </ul> Additionally, the following images  have previously been deposited to Mendeley Data (DOI: <a href="http://doi.org/10.1016/j.ecoenv.2022.113522">10.17632/4nfg69v8hy.1</a>): <ul> <li>nAg_GFP: GFP signal for larvae exposed to nAg.</li> <li>nAg_trans: transmitted light images for larvae exposed to nAg.</li> <li>Agion_GFP: GFP signal for larvae exposed to silver ions.</li> <li>Agion_trans: transmitted light images for larvae exposed to silver ions.</li> <li>control_GFP: GFP signal for control larvae that had not been exposed to silver ions or nAg</li> <li>control_trans: transmitted light images for control larvae that had not been exposed to silver ions or nAg.</li> </ul> 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: <a href="http://doi.org/10.1016/j.ecoenv.2022.113522">10.1016/j.ecoenv.2022.113522</a>   Abbreviations: <ul> <li>ABs: antibiotics</li> <li>CFU: colony-forming units</li> <li>dpf: days post-fertilization</li> <li>il1beta: interleukin-1beta</li> <li>nAg: silver nanoparticles (NM-300 K)</li> <li>nZnO: zinc oxide nanoparticles (NM-110)</li> </ul>

ShareScore

48/100

Overall dataset sharing score

Score breakdown

These five areas show where the dataset supports — or may limit — practical reuse.

Stewardship: 8
Harmonization: 8
Access: 20
Reuse readiness: 8
Engagement: 4

Topics

Nanomaterials Nanoparticles Silver NM-300K Zinc oxide NM-110 Zebrafish Microbiota Immunotoxicity Antibiotics