PhD position in Molecular control of growth-immunity trade-offs in Arabidopsis

18 May 2024
Job Information

Organisation/Company

Utrecht University

Research Field

Physics

Researcher Profile

First Stage Researcher (R1)

Country

Netherlands

Application Deadline

17 Jun 2024 - 21:59 (UTC)

Type of Contract

Permanent

Job Status

Not Applicable

Hours Per Week

40.0

Is the job funded through the EU Research Framework Programme?

Not funded by an EU programme

Is the Job related to staff position within a Research Infrastructure?

No

Offer Description

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 how plants control their growth during and after an immune response. This research is embedded in the CropXR work package on growth-resilience trade-offs and combines digital phenotyping and molecular omics technologies.
Your job
Current projections show that the incidence of diseases on crops will increase in the coming decades, and thus, new strategies, beyond strengthening the immune system, are needed to ensure the resilience of future crops to diseases. 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 PhD project embedded in CropXR, you uncover the genetic and molecular basis of plant growth during and after an immune response. With this knowledge, we aim to develop solutions for resistance that do not compromise crop growth.
Your project is a part of the CropXR research programme. CropXR develops innovative breeding methods for making crops more resilient, sustainable, and climate-adapted. With a budget of 96 million euros for the next ten years, CropXR focuses on creating eXtra Resilient (XR), sustainable, and climate adaptive crops. By combining plant biology, simulation modelling, and artificial intelligence we aim to develop ‘smart breeding and cultivation’ methods. Thus, we try to speed up the breeding of complex resilience traits for several crops in different growing systems. This collaborative effort involves four universities and numerous companies. It encompasses scientific research, data collection and sharing, education, and practical applications in agriculture and plant breeding.
Your project is embedded in the CropXR work package C4 that brings together expertise on biotic and abiotic stress tolerance, proteomics, and molecular biology to decipher the molecular-genetic networks that plants use to regulate trade-offs between growth and stress resilience. You will work closely with other PhD candidates in this and other CropXR work packages.
The project comprises three phases:

• In the first phase of the project, you will perform high-throughput digital phenotyping of Arabidopsis thaliana mutant population grown with or without administered immunity-activating treatments in the Netherlands Plant Ecophenotyping Center (NPEC) . You will utilise modelling, genetic mapping, and machine learning techniques to identify genes controlling the growth during and after an immune response.
• In the second phase of the project, validation of the genetic leads will be performed using CRISPR-Cas gene editing and alteration of gene expression.
• In the final phase, you will perform time-course experiments using quantitative proteomics (proximity labeling) and RNAseq methods for selected targets to gain insights into the protein complexes driving growth during and after an immune response. You will also have an option to explore possibilities to translate obtained knowledge into applications.

As a PhD candidate, you will be responsible for designing and conducting experiments behind the computer and in the laboratory. You will interact with other PhD candidates and researchers involved in experimental research, bioinformatics and/or modelling at Utrecht University, Wageningen University and Research, University of Amsterdam, and TU Delft, as well as with experts from breeding companies within CropXR. You will also be involved in supervising students and, occasionally, sharing your expertise in the classroom with Bachelor's students. This second part of the job will help you learn about teaching and open additional perspectives for the next career steps.
A supervision team of 2-3 people will support your professional development as a researcher. Our research group and the CropXR consortium provide all the needed expertise. 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.

Requirements
Specific Requirements

We are looking for a collaborative, enthusiastic, and curious colleague who:

• has a completed MSc degree or is about to get an MSc degree in molecular and/or computational biology;
• has an affinity with 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.

Additional Information
Benefits

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 .

Selection process

As Utrecht University, we want to be a home for everyone. We value staff with diverse backgrounds, perspectives and identities, including cultural, religious or ethnic background, gender, sexual orientation, disability or age. We strive to create a safe and inclusive environment in which everyone can flourish and contribute.
If you are enthusiastic about this position, just apply via the 'Apply now' button! Please enclose:

• your letter of motivation;
• your curriculum vitae;
• contact information of at least two references;
• optional: your record of academic transcripts.

If this specific opportunity isn’t for you, but you know someone else who may be interested, please forward this vacancy to them.
Some connections are fundamental – Be one of them
#FundamentalConnection

Additional comments

For more information, please contact Dmitry Lapin at [email protected]
Do you have a question about the application procedure? Please send an email to [email protected] .

Website for additional job details

https://www.academictransfer.com/341704/

Work Location(s)

Number of offers available

1

Company/Institute

Universiteit Utrecht

Country

Netherlands

City

Utrecht

Postal Code

3584CH

Street

Padualaan 8

Geofield

Where to apply

Website

https://www.academictransfer.com/en/341704/phd-position-in-molecular-control-of…

Contact

City

Utrecht

Website

http://www.uu.nl/

Street

Domplein 29

Postal Code

3512 JE

STATUS: EXPIRED