The immune system helps plants resist pathogen infections and has been well studied. However, it becomes increasingly clear that enhancing defense comes at a cost, as plants slow down growth even if the infection is successfully combatted. In this project, you will investigate the poorly understood process of how plants control their growth during and after an immune response. You will capitalise on the available extensive lettuce gene expression and high-throughput phenotyping datasets.

Your job
Current projections show that the incidence of diseases on crops will increase in the coming decades, and thus, conceptually new strategies, beyond strengthening the immune system, are needed to ensure the resilience of future crops. It turns out that plants slow down their growth during and after an immune response regardless of the disease intensity. However, how these growth processes are regulated in plants is unclear. In this curiosity-driven PhD project, you will uncover the genetic and molecular basis of plant growth during and after an immune response. With this knowledge, one could develop approaches that reduce this tradeoff in crop growth. You will primarily work with lettuce (Lactuca sativa), but conservation of the deduced concepts can be investigated in other plant species, such as Arabidopsis thaliana.

Your project will capitalise on two types of datasets generated during the LettuceKnow programme. The first dataset includes large and dense time-course RNAseq experiments, where we activated the lettuce immune system and tracked the transcriptome changes over several hours. The second dataset includes high-throughput digital phenotyping data for the growth of ~180 lettuce varieties in the presence of defense hormones and after their removal (the recovery phase). This dataset was obtained with the Netherlands Plant Ecophenotyping Center (NPEC).

In the first phase of the project, you will utilise bioinformatics, genome-wide association mapping (GWAS), and machine learning techniques to identify new players of plant growth during and after an immune response. You will validate the genetic leads, such as transcription factors (TFs), identified in our earlier research. In the second phase of the project, you will work on the functional validation and characterization of the identified regulators of immunity-conditioned growth (e.g., TFs) using CRISPR-Cas gene editing and alteration of gene expression in lettuce and Arabidopsis. For selected targets, you will use quantitative proteomics and chromatin-protein interaction assays to gain insights into the activity of protein complexes driving growth during and after an immune response. Similarly, high-throughput digital phenotyping of mutants and overexpression lines in NPEC can be used to investigate their impact on inferred regulatory pathways.

As a PhD candidate, you will be responsible for designing and conducting experiments behind the computer and in the laboratory. You will also be involved partially in supervising BSc and MSc students and, occasionally, sharing your expertise in BSc courses. This will help you learn about supervision and teaching and open additional perspectives for the next career steps.

Your professional development as a researcher will be supported by a supervision team of 2-3 people. All needed expertise is present in our research group or through the collaborators. At the start of the project, you will work together with an experienced PhD candidate and postdoc, that will give you a productive start. Although there are no industry partners involved in the project, you will have opportunities to discuss your professional development and future career steps with a mentor from an industry or other area of your choice.

We currently have another PhD position on growth-immunity tradeoffs available in Dmitry Lapin’s team. For more information about this position, check out our website.

We are looking for a collaborative, enthusiastic, and curiosity-driven colleague who:

• has a completed MSc degree or is about to get an MSc degree in molecular and/or computational biology;
• has an affinity to experimental (plant) biology research;
• has demonstrated skills in either or both computational and molecular biology research;
• wants to learn, deploy, or even develop new methods of computational and molecular biology research.

• We offer:
• a position for 4 years;
• a gross monthly salary between €2,770 and €3,539 in the case of full-time employment (salary scale P under the Collective Labour Agreement for Dutch Universities (CAO NU);
• 8% holiday pay and 8.3% year-end bonus;
• a pension scheme, partially paid parental leave and flexible terms of employment based on the CAO NU.

In addition to the terms of employment laid down in the CAO NU, Utrecht University has a number of schemes and facilities of its own for employees. This includes schemes facilitating professional development, leave schemes and schemes for sports and cultural activities, as well as discounts on software and other IT products. We also offer access to additional employee benefits through our Terms of Employment Options Model. In this way, we encourage our employees to continue to invest in their growth. For more information, please visit Working at Utrecht University.

Universiteit Utrecht

A better future for everyone. This ambition motivates our scientists in executing their leading research and inspiring teaching. At Utrecht University, the various disciplines collaborate intensively towards major strategic themes. Our focus is on Dynamics of Youth, Institutions for Open Societies, Life Sciences and Pathways to Sustainability. Sharing science, shaping tomorrow.

At the Faculty of Science there are 6 departments to make a fundamental connection with: Biology, Chemistry, Information and Computing Sciences, Mathematics, Pharmaceutical Sciences and Physics. Each of these is made up of distinct institutes that work together to focus on answering some of humanity’s most pressing challenges. More fundamental still are the individual research groups – the building blocks of our ambitious scientific projects.

The department of Biology consists of an Education Institute and 12 chair groups with a total of 350 staff members. The chair groups are organised within the Institute of Environmental Biology and the Institute for Biodynamics and Biocomplexity. The department is responsible for the Bachelor's programme in Biology, where we annually welcome over 400 students. This means we educate over 30% of biology students in the Netherlands. Additionally, staff members of the department also teach in the Utrecht Bachelor's programme in Biomedical Sciences and the Bachelor's program of University College Utrecht. In addition to bachelor education, our staff also provide teaching in various master's programmes. The department of Biology is successful in attracting international and Dutch research funding (CropXR, GreenTE, grants from European Research Council, etc.).

You will join Dmitry Lapin’s team (5-10 team members) in the Translational Plant Biology (TPB) group. The TPB group includes four principal investigators with expertise in different aspects of plant-microbe interactions, plant development, and epigenetics. We exchange expertise to understand the principles of plant biology better and translate this knowledge into technologies that improve the sustainability of agriculture. To ensure that the researchers benefit from each other’s expertise in real-time the team and TPB have regular work-together sessions such as hackathons for data analysis, writing retreats, and thematic meetings.

In the Lapin team, we answer fundamental questions about plant immunity and growth in collaboration with industry partners. For that, we use cutting-edge technologies in high-throughput phenotyping (NPEC), machine learning, and omics analyses; the focus is not on technology development but on fascinating genetic and molecular principles of plant biology. The team is an active contributor to the research programmes LettuceKnow and CropXR. High-quality supervision and guidance are among the core values of the Lapin team, with a dedicated PhD supervision team of 2-3 members ensuring timely project guidance. You will also have opportunities to find a mentor in the plant breeding industry or public sector to enhance your career prospects after finishing the PhD research. The Graduate School of Life Sciences (GSLS) and the Graduate School of Experimental Plant Sciences (EPS), which you will be a part of, further guarantee the quality of supervision. The Lapin team, as a part of the TPB group, has monthly social events, annual retreats and goes for daily short walks in the University Botanical Gardens. We respect each other’s working hours and strive together to maintain a healthy working environment.

For more information, please contact Dmitry Lapin at d.lapin@uu.nl

Do you have a question about the application procedure? Please send an email to science.recruitment@uu.nl.