Education
The Experimental and Computational Plant Development research group participates in several courses of the Biology curriculum.
We participate in:
- Bachelor's courses in the first (Introduction in Biology, Plant Biology and Microorganisms), second (Food Forward, Plants in Context) and third (Plants Development and Environment) year. Bachelor's students can gain research expertise in our group by joining for research projects.
- An advanced course in the master program Environmental Biology (Plants in their Environment) and contributions to courses in the master programs Bioinspired Innovation and Molecular and Cellular Life Sciences. Master's students can gain practical research experience through a project of 6 to 9 months working on current topics of interest to the group.
- Project students are from Utrecht and other national and international universities.
- We lead the Environmental Biology Master's program.
- We coordinate the Plant Biology and the Genes to Organism tracks in the Environmental Biology and Molecular & Cellular Life Sciences Master's programmes respectively.
Educational projects
Tropic responses are directional growth responses of plants towards or away from stimuli. One of the most recently discovered tropisms in plants is halotropism, in which plant roots sense a gradient of detrimental salt and grow away from it.
Interestingly, higher salt levels result in stronger and more persistent bending away from the salt, while for lower salt levels at a certain point the roots seem to “give up” their halotropic response and grow back into the salt. Importantly, by growing away from the salt roots grow away from the gravity vector, which means that also gravitropism is being activated which serves to allow plants to return to the gravity vector. So, the root growth we observe is the net effect of a tug of war between halotropism and gravitropism.
In this project we will study the tug of war between these two tropisms. For this we will vary the salt concentration gradients, as well as introduce tilting of the plates on which the plants grow to vary the relative strength of these two tropisms. You will investigate the effects on root growth directions using root phenotyping. Additionally, given that gravitropism and halotropism arise from asymmetries in the plant hormone auxin, we will use microscopy to investigate the patterns of auxin and auxin transporting proteins over the course of the halotropic response.
Depending on the students’ interest and progress, the project could incorporate including the effect of light on root growth, incorporating mutant lines affected in gravitropism or salt sensing, or automating the root growth angle phenotyping as well as ideas put forward by the student.
Daily supervisors
As sessile organisms, plants face numerous challenges throughout their lives to which they must adapt in order to survive. One of the most pressing challenges in modern agriculture is the lack of nitrogen in the soil.
Nitrogen tends to leach into the lower layers of the soil, creating a heterogeneous environment in which root architecture develops. To cope with this nitrogen heterogeneity, plants have evolved various mechanisms to sense and respond to varying nitrogen concentrations. Initially, plants react to local nitrogen concentrations by activating a rapid metabolic response within the first few hours of exposure. Following this, a systemic response integrates the overall nitrogen status of the plant, allowing it to adapt more effectively to its environment. When plants are exposed to different nitrogen concentrations in different parts of the root system, they employ long-distance signaling pathways to communicate between root zones, ensuring an efficient response across the entire root environment.
This integration of local, systemic, and long-distance responses has been extensively studied, primarily through split-root experiments, where the plant’s root system is divided and exposed to both high and low nitrogen concentrations. These studies have demonstrated that plants preferentially grow roots in the nitrogen-rich zones (Figure 1). This behavior is mediated by at least two distinct pathways. First, cytokinin production (cKs) is triggered on the high nitrogen side of the root, which then signals the shoot to activate processes that are not yet fully understood9. Second, the production of C-terminally encoded peptides (CEPs) occurs on the low nitrogen side of the root, enabling root-to-shoot communication (Figure 2).
CEPs are known to be upregulated in roots under low nitrogen and high sucrose conditions, and are recognized by CEP receptors (CEPRs) in both roots and shoots, leading to the production of downstream signals (CEPD) that regulate systemic responses. While the role of CEPs in long-distance nitrogen signaling is not fully understood, previous studies have shown that CEPs can repress lateral root growth under certain conditions, while also being necessary for preferential root growth in nitrogen-rich patches.
In this project, we aim to clone various CEPs tagged with small fluorescent proteins to retain their mobility throughout the plant. This tool will allow us to investigate when and where these peptides are expressed in response to different nitrogen and carbon combinations, how their mobility is affected, and clarify their role in root system architecture. Through this research project, the student will acquire hands-on experience with a diverse range of advanced molecular techniques, including DNA isolation and purification, PCR amplification, and vector construction. The project will also involve essential transformation protocols and the application of cutting-edge methods in phenotyping and microscopy. These skills will provide a comprehensive foundation in molecular biology and plant genetics, equipping the student with both technical expertise and analytical insights.
Root system architecture of plant after 5 days of heterogeneous nitrogen treatment, where the left side is in low concentration of nitrogen, and the right side 
Graphic proposal of all the different molecular pathways being involved in the preferential growth of the arabidopsis plant in high nitrogen patches. Figure extracted from Poitout et al, (2018).
Daily supervisor
Plants exhibit remarkable adaptability to survive and thrive amidst different stresses. One notable mechanism is the development of a protective layer called the exodermis in plant roots when faced with abiotic stress.
The exodermis offers several advantages, such as enhanced water retention during drought, prevention or reduction of oxygen loss in flooded conditions, and increased uptake of ions and salts in response to salt stress. This beneficial trait holds great potential in safeguarding crops against the challenges posed by climate change. The exodermis is formed by the incorporation of two hydrophobic molecules, suberin and lignin, into the cell walls. However, it's important to note that the presence of exodermis varies among plant species, and different types of exodermis have been identified. Within the Poaceae family, which encompasses grasses, an extensive range of exodermis phenotypes exists, ranging from absent to present or even inducible. Some grass species exhibit multiple layers of exodermis. The Poaceae, grasses, as a family holds significant economic importance as it includes several crucial grain crops. By studying closely related species and their exodermis diversity, we can gain insights into the evolutionary history of this protective layer.
During this internship, you will learn about the screening techniques used to identify exodermis in various grass species, including important crop plants. This will involve utilizing plant hormones, conducting abiotic stress assays, and employing confocal imaging and fluorescent staining methods. Additionally, you will explore root anatomy and root system architecture to understand the effects of different treatments on root development. The primary goal of this internship is to deepen our understanding of how plant roots adapt to stress, specifically related to climate change. This knowledge will be instrumental in advancing future breeding programs aimed at developing resilient crops capable of withstanding environmental challenges.
Daily supervisor
Plants possess a wide array of adaptive strategies to thrive in their ever-changing environments. One such adaptation is the development of the exodermis, a specialized root barrier composed of suberin and lignin.
Incorporating these biopolymers into the outer cortex layer of the root provides plants with protection against various stresses, including drought, high salinity, and flooding. The legume family, Fabaceae, holds great diversity for this trait to study its development and evolution. By studying different exodermis types found in legume species, our goal is to unravel the mechanisms underlying exodermis development and evolution. Given the impact of climate change on crop productivity, it is vital to understand the mechanisms behind exodermis development and evolution.
During this internship, you will learn how to screen for exodermis using plant hormone and abiotic stress assays, as well as employing confocal imaging and fluorescent staining techniques. Additionally, you will delve into the study of root anatomy, root system architecture, and the response of roots to various treatments. Other opportunities validating our RNA-seq results, by for example generating hairy root cultures. The ultimate objective of this internship is to broaden our understanding of exodermis formation, equipping us with the knowledge to advance the cultivation of stress-tolerant crops.
Daily supervisor
Plants respond continuously to environmental changes, pathogen invasion, and insect attacks. One way to monitor these real-time responses is to introduce fluorescent molecules into plants and to quantify their early activity in response to stressors.
This fluorescent tool, called a biosensor, makes it easy to see how quickly plants can sense any environmental danger and activate defense mechanisms. Our research group has developed biosensors capable of quantifying changes in oxygen levels in plants at cellular resolution. This is crucial because plant growth and development depend heavily on oxygen, which acts as the final acceptor of aerobic respiration. Flooding caused by heavy rain can lead to limited oxygen diffusion, which is immediately detected by plants as a switch to anaerobic metabolism for adaptation. As soon as water moves away, plants can detect the presence of oxygen, switch to aerobic metabolism, and recover faster.
However, low oxygen levels (hypoxia) can also occur naturally in some plant tissues (shoot apical meristem, lateral root primordia etc.) and are considered physiologically necessary microenvironments. Engineering biosensors that can quantify oxygen is crucial for understanding the development and maintenance of endogenous low oxygen levels in plant tissues, as well as for identifying new hypoxic niches.
We developed several biosensors based on ideal fluorescent proteins that either depend strictly on or are completely independent of oxygen availability.
Project GOAL
As a student, you will use various oxygen-dependent fluorescent biosensors with different sensitivities, promoters, and hormone-inducible systems to visualize oxygen distribution in plant tissues. These biosensors will be assessed under different conditions such as hypoxia, darkness, flooding, respiratory inhibition, high temperature, stomatal closure stress etc. In addition, you will have the opportunity to perform other stress treatments of your choice and engineer new biosensors if you believe that it will advance research.
What can you learn?
Widefield and Confocal Microscopy, Image analysis, Hormone/chemical treatments, Hypoxia treatment, growing transgenic plants in sterile conditions and on soil, Cloning and Plant transformation.
Daily supervisor
Plants possess an extraordinary capacity for regeneration, allowing them to restore individual cells or even regrow the tip of damaged organs in a matter of days.
The ability of differentiated cells to regain pluripotency and restore the ability to divide has fascinated biologists for centuries. Plant regeneration is an important process to understand for improving genetic transformation of crops and for multiplication of rare or rarely flowering plants. Using root regeneration as a model system, we investigate the mechanisms behind this process through an experimental and computational approach. The removal of the tip of the root triggers a response where the cells remaining in the stump regain stemness, and gradually reconstitute the lost tissues through cell divisions and ordered changes in cell fate. Throughout this process some cells in the stump express WIP5, a key anaerobic response gene, suggesting that hypoxia signalling might play a role in root regeneration. Yet, we still do not know when and where this hypoxic response takes place, nor whether it is indispensable for the success of root regeneration.
Learning outcomes
In this project you will conduct an in-depth investigation into the so-far unexplored role oxygen-limited conditions in root regeneration. First, you will analyse the expression of WIP5 in root regeneration using qRT-PCR, and by constructing a transcriptional reporter to delineate its spatio-temporal pattern of expression in the regenerating root stump. Furthermore, you will use existing reporter lines to analyse hypoxia signalling at different timepoints in regeneration, and will evaluate the regeneration success of mutant and overexpressing lines of genes involved in hypoxic-stress signalling. Your results will be harnessed for the development of computational models of root regeneration in collaboration with modelers (Monica Garcia Gomez) in the Theoretical Biology.
Daily supervisor
Flooding is a major thread to the potato industry. One of the reasons potato plants die during flooding is the lack of access to oxygen.
Despite this necessity for oxygen, plants maintain certain tissues at very low oxygen concentrations, even in non-flooded times. Among these hypoxic tissues are the potato tuber and the shoot meristem, a tissue containing stem cells of the shoot. We investigate how plants manage these hypoxic niches and the impact of these niches on plant development. In the long run, this knowledge will aid us in the battle between potatoes and rising water levels.
Goals
The goal of this project is to gain a better understanding of oxygen distribution and signaling in potato plants. To achieve this, we will transform biosensors to potato via Agrobacterium mediated callus transformation. These biosensors are genetically encoded sensors that signal for oxygen concentrations. Using these biosensors, we will map out oxygen distributions throughout the potato plant. Additionally, you will be assisting me on a CRISPR-Cas9 project that is aimed at knocking out genes that are vital for oxygen signaling. The goal of this part of the research is to analyze the phenotypic responses in the plant after oxygen signaling is disrupted.
Learning outcomes
You will work with Agrobacterium based transformation of potato via callus regeneration and learn to work with plant tissue culture in a sterile environment. Transgenic lines will be analyzed with fluorescence microscopy. Additionally, you will gain experience with various molecular biology techniques, such as Golden Gate Cloning and CRISPR-Cas9 gene editing. Many of these skills are universal for the field of molecular (plant) biology and mastering these skills will be a great way to develop yourself as a scientist.
Daily supervisor
In recent decades, climate change has made plant survival more challenging, with flooding being a major agricultural disaster causing billions in crop losses.
When plants are submerged during flooding, oxygen levels in their environment decrease. Plants can sense this drop in oxygen levels through enzymes called Plant Cysteine Oxidases (PCOs), which then stabilize transcription factors that activate genes to respond to the low oxygen conditions. Furthermore, protein phosphorylation is the most abundant post-translational modification in eukaryotes, crucial for regulating enzyme activity. We found that PCOs contain a number of highly conserved phosphorylation sites (amino acid Serine) in their coding sequence, suggesting that these sites play a key role in enzyme function.
Goals
The overall aim of this project is to better understand how oxygen sensing by PCOs is regulated, and if plant tolerance to flooding could be improved.
In this project, you will be altering the individual phosphorylation sites of the PCO enzymes using site-directed mutagenesis. This has the potential to make the PCOs more or less active, which can affect tolerance. Then, by using laser confocal microscopy, you will observe any changes in enzyme subcellular localization. Later, you will conduct transactivation assays to test each mutated enzyme's activity and whether flooding tolerance could be improved.
Techniques you will learn
Site-directed mutagenesis, PCR, Golden Gate molecular cloning, agroinfiltration, laser scanning confocal microscopy, Arabidopsis protoplast isolation, transactivation assays, submergence experiments
Daily supervisor
The Kawa team is affiliated both with Plant Stress Resilience and Experimental and Computational Plant Development.
Plant roots exhibit an enormous level of developmental plasticity allowing a plant to adapt to the challenges of its surroundings.
For example, deposition of suberin in specific root cell type layers, endodermis and/or exodermis, protects the plant from drought, and flooding and forms a barrier for several pathogens. Engineering of suberin-enhanced protective layers offers an exciting avenue to enhance plant resilience to a broad spectrum of environmental stresses.
We recently identified bacterial species able to increase the level of suberization of sorghum endodermis and exodermis. Microbe-based solutions provide an exciting alternative to strengthen plant's environmental resilience in addition to breeding efforts. This is particularly attractive for plant species staple for regions with extreme climate events, for which breeding solutions are not always efficient or available for all farmers. (i.e. sorghum).
To verify whether previously identified Suberin-Inducing Microbes (SIMs) have the potential for future agricultural application, it is essential to understand the mechanism of SIMs’ action and how robust their effect is to environmental changes.
We offer several MSc projects. Depending on your interest you can choose to:
- Characterize the spatiotemporal dynamics of Arthrobacter-induced suberization;
- Study the robustness of Arthrobacter-induced suberization to environmental perturbations;
- Identify molecular modules elicited in plant roots by SIM species that govern microbe-induced suberization.
- the impact of SIMs on plant stress resilience.
- Study the conservation of SIMs action between various plant species
Students are also welcome to come up with their own questions.
We are particularly interested in cereal crops, and our favorite plant in the lab is sorghum. This internship will combine plant cultivation, molecular lab work, and bioinformatics analysis. You will learn how to study root responses to microbes and test the effect of changes in the environment on their interactions. You will focus on root cellular anatomy, plant responses to external factors, and associated changes in gene expression. You will get an opportunity to become an expert in plant inoculation with microbes, plant histology techniques, confocal microscopy, and transcriptome analysis. Your work will be essential to understand the potential of Arthrobacter species to strengthen plant stress resilience in agricultural settings!
Daily supervisors
This is a joint project with the Microbiology group
Plant roots are the primary point of contact with the dense and diverse populations of soil bacteria. In a process of exudation, roots release to the soil a wide range of chemical compounds that act as signaling molecules to influence bacterial behavior.
While several studies have assessed the impact of root exudates on the growth and chemotactic behavior of bacteria, the influence of these exudates on bacterial conjugation remains largely unexplored.
Bacterial conjugation, often described as "bacterial mating", is the process through which one bacterial cell horizontally transfers its genetic material to another via direct contact. This bacterial behavior is cornerstone for the spread of genes encoding antibiotic resistance among (pathogenic) bacteria, contributing significantly to the global health crisis of antibiotic resistance. Therefore, identifying chemical compounds that can inhibit bacterial conjugation could play a key role in combating this crisis. However, research efforts to identify such inhibitors have been very limited, and, as a result, no bacterial conjugation inhibitors have been discovered so far.
To change this, we will explore the untapped potential of root exudates to identify inhibitors of bacterial conjugation. Specifically, during this multidisciplinary project, we aim to collect root exudates from a broad panel of model and crop species and assess their potential to inhibit bacterial conjugation using fluorescent/luminescent-based conjugation assays. The composition of the exudates with inhibitory potential and the responsible compound will be assessed using untargeted and targeted metabolomics.
For this multidisciplinary internship, you will be hosted in the Kawa lab (Experimental and Computational Plant Development & Stress Resilience) and the Liakopoulos lab (Microbiology). You will benefit from their complementary expertise, which is essential for this specific project, and will get the opportunity to master bacterial and plant cultivation techniques, bacterial and/or plant genetic engineering, root exudate collection techniques, high-throughput bacterial conjugation assays and metabolite profiling.
Daily supervisor
Does low oxygen help plants regrow a missing end?
A shared project with Daan Wiets' team.