Stephen Depuydt
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View article: Coumarin Promotes Hypocotyl Elongation in Light-grown Arabidopsis thaliana Seedlings by Enhancing Brassinosteroid Signalling in an Auxin-Dependent Manner
Coumarin Promotes Hypocotyl Elongation in Light-grown Arabidopsis thaliana Seedlings by Enhancing Brassinosteroid Signalling in an Auxin-Dependent Manner Open
View article: Correction to: Harnessing green tide Ulva biomass for carbon dioxide sequestration
Correction to: Harnessing green tide Ulva biomass for carbon dioxide sequestration Open
View article: Harnessing green tide Ulva biomass for carbon dioxide sequestration
Harnessing green tide Ulva biomass for carbon dioxide sequestration Open
Green tides, characterised by massive blooms of the seaweed Ulva, pose a significant threat to coastal economies and marine ecosystems. This review explores the potential repurposing of harmful Ulva blooms for carbon sequestration, address…
View article: Assessing the reliability of point mutation as data augmentation for deep learning with genomic data
Assessing the reliability of point mutation as data augmentation for deep learning with genomic data Open
View article: Harnessing the power of tidal flat diatoms to combat climate change
Harnessing the power of tidal flat diatoms to combat climate change Open
In approximately one decade, global temperatures will likely exceed a warming level that a United Nations Intergovernmental Panel on Climate Change report considers a "red alert for humanity". We propose exploring tidal flat diatoms to add…
View article: Interactive Effects of Blue Light and Water Turbulence on the Growth of the Green Macroalga Ulva australis (Chlorophyta)
Interactive Effects of Blue Light and Water Turbulence on the Growth of the Green Macroalga Ulva australis (Chlorophyta) Open
Macroalgal growth and yield are key to sustainable aquaculture. Although light and water turbulence are two important factors that affect algal productivity, research on their interaction is limited. Therefore, in this study, we investigat…
View article: Giant Duckweed (Spirodela polyrhiza) Root Growth as a Simple and Sensitive Indicator of Copper and Chromium Contamination
Giant Duckweed (Spirodela polyrhiza) Root Growth as a Simple and Sensitive Indicator of Copper and Chromium Contamination Open
Aquatic environment are often contaminated with heavy metals from various industrial sources. However, physicochemical techniques for pollutant detection are limited, thus prompting the need for additional bioassays. We investigated the us…
View article: How to make sense of 3D representations for plant phenotyping: a compendium of processing and analysis techniques
How to make sense of 3D representations for plant phenotyping: a compendium of processing and analysis techniques Open
View article: Metal Toxicity across Different Thallus Sections of the Green Macroalga, Ulva australis
Metal Toxicity across Different Thallus Sections of the Green Macroalga, Ulva australis Open
We aimed to identify functional differences between different sections of the thallus of Ulva australis and develop tissue-endpoint combinations to assess the toxicity of six metals (i.e., Ag, As, Cd, Cr, Cu, and Ni). EC50 values for these…
View article: Mutate and observe: utilizing deep neural networks to investigate the impact of mutations on translation initiation
Mutate and observe: utilizing deep neural networks to investigate the impact of mutations on translation initiation Open
Motivation The primary regulatory step for protein synthesis is translation initiation, which makes it one of the fundamental steps in the central dogma of molecular biology. In recent years, a number of approaches relying on deep neural n…
View article: Evaluating ecotoxicological assays for comprehensive risk assessment of toxic metals present in industrial wastewaters in the Republic of Korea
Evaluating ecotoxicological assays for comprehensive risk assessment of toxic metals present in industrial wastewaters in the Republic of Korea Open
View article: Utilizing Mutations to Evaluate Interpretability of Neural Networks on Genomic Data
Utilizing Mutations to Evaluate Interpretability of Neural Networks on Genomic Data Open
Even though deep neural networks (DNNs) achieve state-of-the-art results for a number of problems involving genomic data, getting DNNs to explain their decision-making process has been a major challenge due to their black-box nature. One w…
View article: IMPLANT: a new technique for transgene copy number estimation in plants using a single end-point PCR reaction
IMPLANT: a new technique for transgene copy number estimation in plants using a single end-point PCR reaction Open
View article: Opposing effects of <i>trans</i>‐ and <i>cis</i>‐cinnamic acid during rice coleoptile elongation
Opposing effects of <i>trans</i>‐ and <i>cis</i>‐cinnamic acid during rice coleoptile elongation Open
The phenylpropanoid cinnamic acid (CA) is a plant metabolite that can occur under a trans ‐ or cis ‐form. In contrast to the proven bioactivity of the cis ‐form ( c ‐CA), the activity of trans ‐CA ( t ‐CA) is still a matter of debate. We t…
View article: A Ten-Minute Bioassay to Test Metal Toxicity with the Freshwater Flagellate Euglena agilis
A Ten-Minute Bioassay to Test Metal Toxicity with the Freshwater Flagellate Euglena agilis Open
A chemical analysis of water quality cannot detect some toxicants due to time constraints, high costs, and limited interactions for detection. Bioassays would offer a complementary means to assess pollution levels in water. Euglena is a fl…
View article: <i>MAX2</i>-dependent competence for callus formation and shoot regeneration from <i>Arabidopsis thaliana</i> root explants
<i>MAX2</i>-dependent competence for callus formation and shoot regeneration from <i>Arabidopsis thaliana</i> root explants Open
Although the division of the pericycle cells initiates both lateral root development and root-derived callus formation, these developmental processes are affected differently in the strigolactone and karrikin/KARRIKIN INSENSITIVE 2 (KAI2) …
View article: Commercial Potential of the Cyanobacterium Arthrospira maxima: Physiological and Biochemical Traits and the Purification of Phycocyanin
Commercial Potential of the Cyanobacterium Arthrospira maxima: Physiological and Biochemical Traits and the Purification of Phycocyanin Open
Arthrospira maxima is a natural source of fine chemicals for multiple biotechnological applications. We determined the optimal environmental conditions for A. maxima by measuring its relative growth rate (RGR), pigment yield, and photosynt…
View article: IMPLANT: a new technique for transgene copy number estimation in plants using a single end-point PCR reaction
IMPLANT: a new technique for transgene copy number estimation in plants using a single end-point PCR reaction Open
Background Copy number determination is one of the first steps in the characterization of transgenic plant lines. The classical approach to this, Southern blotting, is time-consuming, expensive and requires massive amounts of high-quality …
View article: Evaluating Ecotoxicological Assays for Comprehensive Risk Assessment of Industrial Wastewaters in Republic of Korea
Evaluating Ecotoxicological Assays for Comprehensive Risk Assessment of Industrial Wastewaters in Republic of Korea Open
View article: Interlaboratory Validation of Toxicity Testing Using the Duckweed Lemna minor Root-Regrowth Test
Interlaboratory Validation of Toxicity Testing Using the Duckweed Lemna minor Root-Regrowth Test Open
The common duckweed (Lemna minor), a freshwater monocot that floats on the surfaces of slow-moving streams and ponds, is commonly used in toxicity testing. The novel Lemna root- regrowth test is a toxicity test performed in replicate test …
View article: Assessment of Various Toxicity Endpoints in Duckweed (Lemna minor) at the Physiological, Biochemical, and Molecular Levels as a Measure of Diuron Stress
Assessment of Various Toxicity Endpoints in Duckweed (Lemna minor) at the Physiological, Biochemical, and Molecular Levels as a Measure of Diuron Stress Open
The common, broad-spectrum herbicide diuron poses some risks to the environment due to its long persistence and high toxicity. Therefore, the effective monitoring of diuron residues will inform efforts to assess its impacts on ecosystems. …
View article: Unraveling the MAX2 Protein Network in Arabidopsis thaliana: Identification of the Protein Phosphatase PAPP5 as a Novel MAX2 Interactor
Unraveling the MAX2 Protein Network in Arabidopsis thaliana: Identification of the Protein Phosphatase PAPP5 as a Novel MAX2 Interactor Open
View article: Agrobacterium strains and strain improvement: Present and outlook
Agrobacterium strains and strain improvement: Present and outlook Open
Almost 40 years ago the first transgenic plant was generated through Agrobacterium tumefaciens-mediated transformation, which, until now, remains the method of choice for gene delivery into plants. Ever since, optimized Agrobacterium strai…
View article: Development of a novel and rapid phenotype-based screening method to assess rice seedling growth
Development of a novel and rapid phenotype-based screening method to assess rice seedling growth Open
View article: Application of a programmed semi-automated Ulva pertusa bioassay for testing single toxicants and stream water quality
Application of a programmed semi-automated Ulva pertusa bioassay for testing single toxicants and stream water quality Open
A toxicity test based on inhibition of reproduction in the green macroalga Ulva pertusa involves quantifying the change in thallus color as reproduction progresses. However, interpretation of this color change is reliant on the skill level…
View article: Toward the molecular understanding of the action mechanism of Ascophyllum nodosum extracts on plants
Toward the molecular understanding of the action mechanism of Ascophyllum nodosum extracts on plants Open
The importance of biostimulants, defined as plant growth-promoting agents that differ notably from fertilizers, is increasing steadily because of their potential contribution to a worldwide strategy for securing food production without bur…
View article: Towards a multi-bioassay-based index for toxicity assessment of fluvial waters
Towards a multi-bioassay-based index for toxicity assessment of fluvial waters Open
View article: Reappraisal of the toxicity test method using the green alga Ulva pertusa Kjellman (Chlorophyta)
Reappraisal of the toxicity test method using the green alga Ulva pertusa Kjellman (Chlorophyta) Open
View article: How to make sense of 3D representations for plant phenotyping: a compendium of processing and analysis techniques
How to make sense of 3D representations for plant phenotyping: a compendium of processing and analysis techniques Open
Machine vision technology is moving more and more towards a three-dimensional approach, and plant phenotyping is following this trend. However, despite its potential, the complexity of the analysis of 3D representations has been the main b…
View article: Testing the toxicity of metals, phenol, effluents, and receiving waters by root elongation in Lactuca sativa L.
Testing the toxicity of metals, phenol, effluents, and receiving waters by root elongation in Lactuca sativa L. Open