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2. 3′sialyllactose and 6′sialyllactose enhance performance in endurance‐type exercise through metabolic adaptation

Author

Arellano Spadaro, Jesus, primary, Hishida, Yukihiro, additional, Matsunaga, Yukihisa, additional, van Es‐Remers, Monique, additional, Korthout, Henrie, additional, Kim, Hye Kyong, additional, Poppelaars, Eefje, additional, Keizer, Hiskias, additional, Iliopoulou, Eva, additional, van Duijn, Bert, additional, Wildwater, Marjolein, additional, and van Rijnberk, Lotte, additional

Published
2023
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3. DARTpaths, an in silico platform to investigate molecular mechanisms of compounds

Author

Bhalla, Diksha, Steijaert, Marvin N, Poppelaars, Eefje S, Teunis, Marc, van der Voet, Monique, Corradi, Marie, Dévière, Elisabeth, Noothout, Luke, Tomassen, Wilco, Rooseboom, Martijn, Currie, Richard A, Krul, Cyrille, Pieters, Raymond, van Noort, Vera, Wildwater, Marjolein, Bhalla, Diksha, Steijaert, Marvin N, Poppelaars, Eefje S, Teunis, Marc, van der Voet, Monique, Corradi, Marie, Dévière, Elisabeth, Noothout, Luke, Tomassen, Wilco, Rooseboom, Martijn, Currie, Richard A, Krul, Cyrille, Pieters, Raymond, van Noort, Vera, and Wildwater, Marjolein

Abstract

SUMMARY: Xpaths is a collection of algorithms that allow for the prediction of compound-induced molecular mechanisms of action by integrating phenotypic endpoints of different species; and proposes follow-up tests for model organisms to validate these pathway predictions. The Xpaths algorithms are applied to predict developmental and reproductive toxicity (DART) and implemented into an in silico platform, called DARTpaths.AVAILABILITY AND IMPLEMENTATION: All code is available on GitHub https://github.com/Xpaths/dartpaths-app under Apache license 2.0, detailed overview with demo is available at https://www.vivaltes.com/dartpaths/.SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Published
2023

4. DARTpaths, an in silico platform to investigate molecular mechanisms of compounds

Author

IRAS OH Toxicology, Bhalla, Diksha, Steijaert, Marvin N, Poppelaars, Eefje S, Teunis, Marc, van der Voet, Monique, Corradi, Marie, Dévière, Elisabeth, Noothout, Luke, Tomassen, Wilco, Rooseboom, Martijn, Currie, Richard A, Krul, Cyrille, Pieters, Raymond, van Noort, Vera, Wildwater, Marjolein, IRAS OH Toxicology, Bhalla, Diksha, Steijaert, Marvin N, Poppelaars, Eefje S, Teunis, Marc, van der Voet, Monique, Corradi, Marie, Dévière, Elisabeth, Noothout, Luke, Tomassen, Wilco, Rooseboom, Martijn, Currie, Richard A, Krul, Cyrille, Pieters, Raymond, van Noort, Vera, and Wildwater, Marjolein

Published
2023

5. DARTpaths, an in silico platform to investigate molecular mechanisms of compounds

Author

Bhalla, Diksha, primary, Steijaert, Marvin N, additional, Poppelaars, Eefje S, additional, Teunis, Marc, additional, van der Voet, Monique, additional, Corradi, Marie, additional, Dévière, Elisabeth, additional, Noothout, Luke, additional, Tomassen, Wilco, additional, Rooseboom, Martijn, additional, Currie, Richard A, additional, Krul, Cyrille, additional, Pieters, Raymond, additional, van Noort, Vera, additional, and Wildwater, Marjolein, additional

Published
2022
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6. Additional file 10 of C. elegans as a test system to study relevant compounds that contribute to the specific health-related effects of different cannabis varieties

Author

van Es-Remers, Monique, Spadaro, Jesus Arellano, Poppelaars, Eefje, Kim, Hye Kyong, van Haaster, Marieke, de Wit, Marcel, ILiopoulou, Eva, Wildwater, Marjolein, and Korthout, Henrie

Abstract

Additional file 10: Additional file S10. Overview of the selected cannabis varieties used in this study and the effects as based on 25 years of human experiences. The effects were reported by surveys among 200 patients in the Netherlands using medicinal cannabis from MariPharms medicinal-cannabis breeding program. Varieties in green columns: Δ9 -tetrahydrocannabinol (THC)-rich; varieties in brown columns: cannabidiol (CBD)-rich varieties. √ indicates an reported effect, blank wells indicates an effect not reported by the patients.

Published
2022
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7. Towards a reporting guideline for developmental and reproductive toxicology testing in C. elegans and other nematodes

Author

van der Voet, Monique, primary, Teunis, Marc, additional, Louter-van de Haar, Johanna, additional, Stigter, Nienke, additional, Bhalla, Diksha, additional, Rooseboom, Martijn, additional, Wever, Kimberley E, additional, Krul, Cyrille, additional, Pieters, Raymond, additional, Wildwater, Marjolein, additional, and van Noort, Vera, additional

Published
2021
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8. Serum Metabolomic Analysis of Coronary Heart Disease Patients with Stable Angina Pectoris Subtyped by Traditional Chinese Medicine Diagnostics Reveals Biomarkers Relevant to Personalized Treatments

Author

Guo, Na, primary, Wang, Peili, additional, Yang, Jiaying, additional, Yang, Xiaofang, additional, van der Voet, Monique, additional, Wildwater, Marjolein, additional, Wei, Junying, additional, Tang, Xuan, additional, Wang, Mei, additional, and Yang, Hongjun, additional

Published
2021
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9. Towards a reporting guideline for developmental and reproductive toxicology testing in C. elegans and other nematodes

Author

van der Voet, Monique, Teunis, Marc, Louter-van de Haar, Johanna, Stigter, Nienke, Bhalla, Diksha, Rooseboom, Martijn, Wever, Kimberley E, Krul, Cyrille, Pieters, Raymond, Wildwater, Marjolein, van Noort, Vera, van der Voet, Monique, Teunis, Marc, Louter-van de Haar, Johanna, Stigter, Nienke, Bhalla, Diksha, Rooseboom, Martijn, Wever, Kimberley E, Krul, Cyrille, Pieters, Raymond, Wildwater, Marjolein, and van Noort, Vera

Abstract

Implementation of reliable methodologies allowing Reduction, Refinement, and Replacement (3Rs) of animal testing is a process that takes several decades and is still not complete. Reliable methods are essential for regulatory hazard assessment of chemicals where differences in test protocol can influence the test outcomes and thus affect the confidence in the predictive value of the organisms used as an alternative for mammals. Although test guidelines are common for mammalian studies, they are scarce for non-vertebrate organisms that would allow for the 3Rs of animal testing. Here, we present a set of 30 reporting criteria as the basis for such a guideline for Developmental and Reproductive Toxicology (DART) testing in the nematode Caenorhabditis elegans. Small organisms like C. elegans are upcoming in new approach methodologies for hazard assessment; thus, reliable and robust test protocols are urgently needed. A literature assessment of the fulfilment of the reporting criteria demonstrates that although studies describe methodological details, essential information such as compound purity and lot/batch number or type of container is often not reported. The formulated set of reporting criteria for C. elegans testing can be used by (i) researchers to describe essential experimental details (ii) data scientists that aggregate information to assess data quality and include data in aggregated databases (iii) regulators to assess study data for inclusion in regulatory hazard assessment of chemicals.

Published
2021

10. Towards a reporting guideline for developmental and reproductive toxicology testing in C. elegans and other nematodes

Author

Voet, Monique van der, Teunis, Marc, Louter-van de Haar, Johanna, Stigter, Nienke, Bhalla, Diksha, Rooseboom, Martijn, Wever, K.E., Wildwater, Marjolein, Noort, Vera van, Voet, Monique van der, Teunis, Marc, Louter-van de Haar, Johanna, Stigter, Nienke, Bhalla, Diksha, Rooseboom, Martijn, Wever, K.E., Wildwater, Marjolein, and Noort, Vera van

Abstract

Item does not contain fulltext

Published
2021

11. Towards a reporting guideline for developmental and reproductive toxicology testing in C. elegans and other nematodes

Author

IRAS OH Toxicology, dIRAS RA-1, van der Voet, Monique, Teunis, Marc, Louter-van de Haar, Johanna, Stigter, Nienke, Bhalla, Diksha, Rooseboom, Martijn, Wever, Kimberley E, Krul, Cyrille, Pieters, Raymond, Wildwater, Marjolein, van Noort, Vera, IRAS OH Toxicology, dIRAS RA-1, van der Voet, Monique, Teunis, Marc, Louter-van de Haar, Johanna, Stigter, Nienke, Bhalla, Diksha, Rooseboom, Martijn, Wever, Kimberley E, Krul, Cyrille, Pieters, Raymond, Wildwater, Marjolein, and van Noort, Vera

Published
2021

12. The RETINOBLASTOMA-RELATED gene regulates stem cell maintenance in Arabidopsis roots

Author

Wildwater, Marjolein, Mariconti, Luisa, Campilho, Ana, Chatterjee, Jayanta, Perez-Perez, Jose Manuel, Gruissem, Wilhelm, Heidstra, Renze, Korthout, Henrie, and Blilou, Ikram

Subjects
Arabidopsis -- Genetic aspects, Gene expression -- Research, Cell cycle -- Research, Stem cells -- Research, Genetic research, Biological sciences
Abstract

The local reduction of expression of the RETINOBLASTOMA-RELATED (RBR) gene in Arabidopsis roots increases the amount of stem cells without affecting cell cycle duration in mitotically active cells. Expression analysis and genetic interactions position RBR-mediated regulation of the stem cell state downstream of the patterning gene SCARECROW.

Published
2005

13. The PIN auxin efflux facilitator network controls growth and patterning in Arabidopsis roots

Author

Blilou, Ikram, Xu, Jian, Wildwater, Marjolein, Willemsen, Viola, Paponov, Ivan, Friml, Jiři, Heidstra, Renze, Aida, Mitsuhiro, Palme, Klaus, and Scheres, Ben

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Ikram Blilou [1]; Jian Xu [1, 4]; Marjolein Wildwater [1, 4]; Viola Willemsen [1, 4]; Ivan Paponov [2]; Jiří Friml [3]; Renze Heidstra [1]; Mitsuhiro Aida [1]; Klaus Palme [...]

Published
2005
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14. Towards a reporting guideline for developmental and reproductive toxicology testing in C. elegansand other nematodes

Author

van der Voet, Monique, Teunis, Marc, Louter-van de Haar, Johanna, Stigter, Nienke, Bhalla, Diksha, Rooseboom, Martijn, Wever, Kimberley E, Krul, Cyrille, Pieters, Raymond, Wildwater, Marjolein, and van Noort, Vera

Abstract

Implementation of reliable methodologies allowing Reduction, Refinement, and Replacement (3Rs) of animal testing is a process that takes several decades and is still not complete. Reliable methods are essential for regulatory hazard assessment of chemicals where differences in test protocol can influence the test outcomes and thus affect the confidence in the predictive value of the organisms used as an alternative for mammals. Although test guidelines are common for mammalian studies, they are scarce for non-vertebrate organisms that would allow for the 3Rs of animal testing.Here, we present a set of 30 reporting criteria as the basis for such a guideline for Developmental and Reproductive Toxicology (DART) testing in the nematode Caenorhabditis elegans. Small organisms like C. elegansare upcoming in new approach methodologies for hazard assessment; thus, reliable and robust test protocols are urgently needed. A literature assessment of the fulfilment of the reporting criteria demonstrates that although studies describe methodological details, essential information such as compound purity and lot/batch number or type of container is often not reported. The formulated set of reporting criteria for C. eleganstesting can be used by (i) researchers to describe essential experimental details (ii) data scientists that aggregate information to assess data quality and include data in aggregated databases (iii) regulators to assess study data for inclusion in regulatory hazard assessment of chemicals.

Published
2021
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16. SCARECROW is involved in positioning the stem cell niche in the Arabidopsis root meristem

Author

Sabatini, Sabrina, Heidstra, Renze, Wildwater, Marjolein, and Scheres, Ben

Subjects
Genetic research -- Analysis, Stem cells -- Genetic aspects, Arabidopsis -- Genetic aspects, Meristem -- Genetic aspects, Genetic regulation -- Analysis, Biological sciences
Abstract

Research has been conducted on stem cells. The authors report that the Arobidopsis root meristem has stem cell population depending on cells' central group, quiescent center, which positions the stem cell niche and regulates stem cell fate.

Published
2003

19. DARTpaths, an in silico platform to investigate molecular mechanisms of compounds.

Author

Bhalla D, Steijaert MN, Poppelaars ES, Teunis M, van der Voet M, Corradi M, Dévière E, Noothout L, Tomassen W, Rooseboom M, Currie RA, Krul C, Pieters R, van Noort V, and Wildwater M

Subjects
Software, Algorithms
Abstract

Summary: Xpaths is a collection of algorithms that allow for the prediction of compound-induced molecular mechanisms of action by integrating phenotypic endpoints of different species; and proposes follow-up tests for model organisms to validate these pathway predictions. The Xpaths algorithms are applied to predict developmental and reproductive toxicity (DART) and implemented into an in silico platform, called DARTpaths., Availability and Implementation: All code is available on GitHub https://github.com/Xpaths/dartpaths-app under Apache license 2.0, detailed overview with demo is available at https://www.vivaltes.com/dartpaths/., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2022. Published by Oxford University Press.)

Published
2023
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