To Örebro University

oru.seÖrebro University Publications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
New Approaches for Daphnia magna Toxicity Assessment
Örebro University, School of Science and Technology.ORCID iD: 0000-0002-2299-5024
2023 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Risk assessment plays a crucial role in evaluating and managing the potential hazards and health effects associated with exposure to substances. In recent decades, the field of risk assessment has undergone significant expansion, embracing innovative approaches and methodologies. Despite these advancements, it's noteworthy that the standards governing experimental setups have remained largely unchanged. This thesis focuses on enhancing environmental risk assessment methodologies, particularly in the context of exposure protocols, by incorporating toxicogenomics and machine learning approaches as well as suggestions for improved toxicity testing setup. The main objectives of the Paper I was to assess the sensitivity differences and shared responses of different animal models to exposure settings. Seven different organisms were tested with varying metal concentrations. Paper II investigated the effects of altering exposure media parameters, particularly water hardness. Paper III utilized computational advancements in toxicogenomics for gene ranking and exposure prediction. Paper IV investigated a larger number of genes by utilizing transcriptomics to discover novel biomarkers and molecular functions affected by metal exposures at the boundaries of Zn and Cu homeostasis. The research findings revealed that traditional toxicity assessment setups may not fully provide a base to capture the complexity of occurring toxicity. Therefore, the study proposes deviations from standard test protocols and emphasizes the need for holistic models that consider multiple factors to accurately assess toxicity risks in aquatic environments.

Place, publisher, year, edition, pages
Örebro: Örebro University , 2023. , p. 74
Series
Örebro Studies in Life Science, ISSN 1653-3100 ; 20
Keywords [en]
Risk assessment, toxicogenomics, zinc, copper, machine learning
National Category
Other Biological Topics
Identifiers
URN: urn:nbn:se:oru:diva-106168ISBN: 9789175295183 (print)ISBN: 9789175295190 (electronic)OAI: oai:DiVA.org:oru-106168DiVA, id: diva2:1761323
Public defence
2023-09-15, Örebro universitet, Långhuset, Hörsal L2, Fakultetsgatan 1, Örebro, 09:15 (English)
Opponent
Supervisors
Available from: 2023-06-01 Created: 2023-06-01 Last updated: 2023-09-06Bibliographically approved
List of papers
1. Assessing organism differences in mixed metal sensitivity
Open this publication in new window or tab >>Assessing organism differences in mixed metal sensitivity
Show others...
(English)Manuscript (preprint) (Other academic)
National Category
Other Biological Topics
Identifiers
urn:nbn:se:oru:diva-107800 (URN)
Available from: 2023-08-22 Created: 2023-08-22 Last updated: 2023-08-22Bibliographically approved
2. Influence of water hardness on zinc toxicity in Daphnia magna
Open this publication in new window or tab >>Influence of water hardness on zinc toxicity in Daphnia magna
Show others...
2022 (English)In: Journal of Applied Toxicology, ISSN 0260-437X, E-ISSN 1099-1263, Vol. 42, no 9, p. 1510-1523Article in journal (Refereed) Published
Abstract [en]

Zinc is an essential trace metal required for the maintenance of multiple physiological functions. Due to this, organisms can experience both zinc deficiency and toxicity. Hardness is recognized as one of the main modifying physiochemical factors regulating zinc bioavailability. Therefore, the present study analyzed the effect of hardness on zinc toxicity using Daphnia magna. Endpoint parameters were acute-toxicity, development, reproduction, and expression data for genes involved in metal regulation and oxidative stress. In addition, the temporal expression profiles of genes during the initiation of reproduction and molting were investigated. Water hardness influenced the survival in response to exposures to zinc. A zinc concentration of 50μg/L in soft water (50 mg CaCO3 /L) caused 73% mortality after 96h exposure, whereas the same zinc concentration in the hardest water did not cause any significant mortality. Moreover, increasing water hardness from 100 to 200mg CaCO3 /L resulted in a reduced number of offspring. Fecundity was higher at first brood for groups exposed to higher Zn concentrations. The survival data was used to assess the precision of the bioavailability models (Bio-met) and the geochemical model (Visual MINTEQ). As the Bio-met risk predictions overestimated the Zn toxicity, a competition-based model to describe the effects of hardness on zinc toxicity is proposed. This approach can be used to minimize differences in setting environmental quality standards. Moreover, gene expression data showed that using the toxicogenomic approach was more sensitive than the physiological endpoints. Therefore, data presented in the study can be used to improve risk assessment for zinc toxicity.

Place, publisher, year, edition, pages
John Wiley & Sons, 2022
Keywords
BLM, Bioavailability, Gene expression, Risk assessment, Toxicogenomics
National Category
Pharmacology and Toxicology
Identifiers
urn:nbn:se:oru:diva-98053 (URN)10.1002/jat.4319 (DOI)000771229300001 ()35285959 (PubMedID)2-s2.0-85126766109 (Scopus ID)
Funder
Knowledge Foundation, 20170118 20180027
Note

Funding agency:

Örebro University NT3042 NT3061

Available from: 2022-03-15 Created: 2022-03-15 Last updated: 2024-01-02Bibliographically approved
3. Utilization of Computer Classification Methods for Exposure Prediction and Gene Selection in Daphnia magna Toxicogenomics
Open this publication in new window or tab >>Utilization of Computer Classification Methods for Exposure Prediction and Gene Selection in Daphnia magna Toxicogenomics
2023 (English)In: Biology, E-ISSN 2079-7737, Vol. 12, no 5, article id 692Article in journal (Refereed) Published
Abstract [en]

Zinc (Zn) is an essential element that influences many cellular functions. Depending on bioavailability, Zn can cause both deficiency and toxicity. Zn bioavailability is influenced by water hardness. Therefore, water quality analysis for health-risk assessment should consider both Zn concentration and water hardness. However, exposure media selection for traditional toxicology tests are set to defined hardness levels and do not represent the diverse water chemistry compositions observed in nature. Moreover, these tests commonly use whole organism endpoints, such as survival and reproduction, which require high numbers of test animals and are labor intensive. Gene expression stands out as a promising alternative to provide insight into molecular events that can be used for risk assessment. In this work, we apply machine learning techniques to classify the Zn concentrations and water hardness from Daphnia magna gene expression by using quantitative PCR. A method for gene ranking was explored using techniques from game theory, namely, Shapley values. The results show that standard machine learning classifiers can classify both Zn concentration and water hardness simultaneously, and that Shapley values are a versatile and useful alternative for gene ranking that can provide insight about the importance of individual genes.

Place, publisher, year, edition, pages
MDPI, 2023
Keywords
Zn, bioavailability, biomarker, machine learning, water hardness
National Category
Water Engineering
Identifiers
urn:nbn:se:oru:diva-106096 (URN)10.3390/biology12050692 (DOI)000995573200001 ()37237504 (PubMedID)2-s2.0-85160308477 (Scopus ID)
Funder
Knowledge Foundation, 20180027Örebro University, 1214-NT3060
Available from: 2023-05-29 Created: 2023-05-29 Last updated: 2024-01-02Bibliographically approved
4. Transcriptional responses of Daphnia magna to sublethal Cu and Zn exposures
Open this publication in new window or tab >>Transcriptional responses of Daphnia magna to sublethal Cu and Zn exposures
Show others...
(English)Manuscript (preprint) (Other academic)
National Category
Other Biological Topics
Identifiers
urn:nbn:se:oru:diva-107801 (URN)
Available from: 2023-08-22 Created: 2023-08-22 Last updated: 2023-08-22Bibliographically approved

Open Access in DiVA

Cover(141 kB)47 downloads
File information
File name COVER01.pdfFile size 141 kBChecksum SHA-512
7db2d5ca9b19835006deb8a5c8b7702ec69c8b9790a00e7dafcdd8fe2ea11bfaf3f633cee326c5767942df5e8b6b3b032f30cb181c3378b821243f834b46187f
Type coverMimetype application/pdf
Spikblad(95 kB)41 downloads
File information
File name SPIKBLAD01.pdfFile size 95 kBChecksum SHA-512
db36f06756bde4f39c5595ae01da7d602798087a14c342fd8dcf9fd941914fc19fd07a610df4dfbe71363e1242a9eba31f18e83b31533af534dda8828ec9273c
Type spikbladMimetype application/pdf

Authority records

Paylar, Berkay

Search in DiVA

By author/editor
Paylar, Berkay
By organisation
School of Science and Technology
Other Biological Topics

Search outside of DiVA

GoogleGoogle Scholar
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

isbn
urn-nbn

Altmetric score

isbn
urn-nbn
Total: 1407 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf