Phd In Biophysics: Single-Cell Tracking In Organoids

Work Activities

Summary – In this project, you will use advanced 3D imaging and AI-driven cell tracking to reveal the remarkable self-organization of cells within intestinal organoids. Using a biophysics approach, you will study how stem cells move, grow, divide, and differentiate into specific functional cell types, and hence reveal how functional miniature organs are formed. Specifically, you will for the first time reveal how this spatio-temporal program is affected by key molecular signals from the immune system. You will work in a vibrant and supportive team of PhD students and postdocs with physics and biology backgrounds within the Tans and van Zon labs in the AMOLF institute in Amsterdam, and collaborate with leading groups in organoid biology.

Questions – According to the textbooks, organs like the intestine continuously regenerate new functional cells from stem cells. However, current methods like antibody staining and RNA sequencing are ill suited to address the inherent underlying spatio-temporal dynamics. These dynamics are arguably even more important to understand the interplay with immune signals, which are thought to affect the organ regeneration process. They are in turn central to the major and growing societal challenge of chronic inflammatory diseases such as intestinal bowel disease and Crohn’s disease. Many fascinating fundamental questions of broad relevance are therefore unresolved: Do signals like interleukins increase the stem cell pool or stimulate differentiation rates to boost renewal? Do they target specific cell types, or impact movement or position of cells? Do they cause cells within the intestine to signal to each other? Given the novelty of the AI-driven cell tracking approach, you will have a unique chance to address such questions first. In addition, the organoid field is currently undergoing a massive expansion yet generally lacks the physics-inspired dynamic methodology that you will help advance.

Approach – Central to the approach is 3D imaging with advanced confocal microscopy, and AI-driven cell tracking, but also organoid growth protocols, antibody staining, and genetic engineering of fluorescent markers, which you will do in collaboration with other PhD students and technical staff. This approach allows you to follow each cell, and hence analyze diverse features including lineage relations between cells of different type or within a specific spatial region, and how they correlate with the expression of key differentiation markers – and how these features are affected by molecular signals that are normally emitted by immune cells but that you add in controlled manner. These advances will allow you to push the boundaries of AI-enabled analysis of single-cell dynamics, which will be more generally relevant both to fundamental science and applications. This first has great potential to reveal a host of unexpected phenomena. More generally, you will develop new experimental schemes, perform cutting-edge experiments, analyze the complex spatio-temporal data, come up with new mechanistic models, and describe your findings in high-level scientific papers.

Qualifications

We are looking for outstanding experimental physicists, chemists, or biologists with demonstratable interest in quantitative biophysics questions, experience in programming and/or machine learning, handling of complex data, and who thrives in a diverse, collaborative, and supportive environment. Excellent verbal and written English skills are essential. You meet the requirements for an MSc-degree to ensure eligibility for a Dutch PhD examination.

Work environment

AMOLF is a part of NWO-I and initiate and performs leading fundamental research on the physics of complex forms of matter, and to create new functional materials, in partnership with academia and industry. The institute is located at Amsterdam Science Park and currently employs about 140 researchers and 80 support employees. www.amolf.nl

Our group - We form a lively and close-knit research group of about 10 PhD students and postdocs, which work together in small teams on various projects in a highly supportive and social atmosphere that extends to the other research groups at the AMOLF institute, which is housed in a modern building in the east of Amsterdam.

Tans group: https://www.sandertanslab.nl

Van Zon group: https://amolf.nl/research-groups/quantitative-developmental-biology

Working conditions

• The working atmosphere at the institute is largely determined by young, enthusiastic, mostly foreign employees. Communication is informal and runs through short lines of communication.
• The position is intended as full-time (40 hours / week, 12 months / year) appointment in the service of the Netherlands Foundation of Scientific Research Institutes (NWO-I) for the duration of four years
• The starting salary is 2.781 Euro’s gross per month and a range of employment benefits.
• After successful completion of the PhD research a PhD degree will be granted at Delft University of Technology.
• Several courses are offered, specially developed for PhD-students.
• Funding is available to attend regularly international conferences.
• AMOLF assists any new foreign PhD-student with housing and visa applications and compensates their transport costs and furnishing expenses.

More information?

For further information:
Prof. dr. ir. Sander Tans
tans@amolf.nl

Dr. Jeroen van Zon

J.v.Zon@amolf.nl

Application

You can respond to this vacancy online via the button below.

Please annex your:
– Resume;
– Motivation on why you want to join the group (max. 1 page).

It is important to us to know why you want to join our team. Hence, we will only consider your application if it contains your motivation letter.

Applications will be evaluated on a rolling basis and as soon as an excellent match is made, the position will be filled.

Online screening may be part of the selection.

Diversity code

AMOLF is highly committed to an inclusive and diverse work environment: we want to develop talent and creativity by bringing together people from different backgrounds and cultures. We recruit and select on the basis of competencies and talents. We strongly encourage anyone with the right qualifications to apply for the vacancy, regardless of age, gender, origin, sexual orientation or physical ability.

AMOLF has won the NNV Diversity Award 2022, which is awarded every two years by the Netherlands Physical Society for demonstrating the most successful implementation of equality, diversity and inclusion (EDI).

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