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https://www.nwo-i.nl/vacature/phd-position-single-cell-dynamics-within-lung-organoids/

Geprint op :
21 november 2017
15:10:42

Research
The ‘Quantitative Developmental Biology’ research group will use a quantitative, physics-inspired approach to study problems in developmental biology, focusing on the small roundworm C. elegans. The aim of the research is to elucidate how living organisms can reliably build their bodies during development, despite the considerable underlying variability on the molecular level. Organoids are miniature organs that can be grown in-vitro from adult stem cells. We have recently found that cells within lung organoids become surprisingly motile upon infection by the RSV virus, resulting in a dramatic, collective rotation of the entire spherical organoid. The aim of this project is to uncover the responsible mechanisms, which has implication for understanding the fundamentals of coordinated cellular motion in tissues and its role in viral infections. We will study these questions using confocal and light-sheet microscopy, cellular tracking analysis, and mathematical modelling. We will use fluorescent labeling to follow cell movement in space and time, both on the cellular and sub-cellular level. These highly quantitative data will provide a unique insight into the dynamic response of the lung epitheleum to viral infection and collective cell moltility in general. This is a joint project between the Tans and van Zon labs at AMOLF Amsterdam and is in collaboration with the Clevers lab at the Hubrecht institute, and the HUB institute in Utrecht. The 'Biophysics research group' focusses on three themes:
1. Folding pathways are traditionally studied for proteins in isolation, even though chaperones are critical to achieving native folds. Consequently, the mechanisms by which chaperones act remains poorly understood. We address this question with a single-molecule approach, using optical tweezers, protein constructs, and computer modelling (Science 2007).
2. The stochastic nature of gene expression is increasingly understood, but how it impacts growth and fitness remains unclear. We investigate this issue using genetic engineering, microfabricated flow-cells, single-cell time-lapse fluorescence microscopy (EMBO rep. 2009).
3. Evolutionary processes are typically studied in constant environments, and a descriptive manner. As a result, the evolutionary dynamics in variable environments has been barely addressed, even though this is considered central to the evolution of complex biological functions. Using synthetic biology and mathematical modelling, we aim to bring a more predictive approach to these fascinating issues (Nature 2007). Past research topics include single-molecule studies on DNA packaging by bacterial viruses, and carbon nanotube-based electronics.

Job description
Organoids are miniature organs that can be grown in-vitro from adult stem cells. We have recently found that cells within lung organoids become surprisingly motile upon infection by the RSV virus, resulting in a dramatic, collective rotation of the entire spherical organoid. The aim of this project is to uncover the responsible mechanisms, which has implication for understanding the fundamentals of coordinated cellular motion in tissues and its role in viral infections. We will study these questions using confocal and light-sheet microscopy, cellular tracking analysis, and mathematical modelling. We will use fluorescent labeling to follow cell movement in space and time, both on the cellular and sub-cellular level. These highly quantitative data will provide a unique insight into the dynamic response of the lung epitheleum to viral infection and collective cell moltility in general. This is a joint project between the Tans and van Zon labs at AMOLF Amsterdam and is in collaboration with the Clevers lab at the Hubrecht institute, and the HUB institute in Utrecht.

Location
AMOLF initiates and performs leading fundamental research on the physics of complex forms of matter, and creates new functional materials, in partnership with academia and industry. AMOLF is located at the Amsterdam Science Park, The Netherlands, and engages approximately 140 scientists and 70 support staff. See also www.amolf.nl

Job requirements
We are looking for an outstanding experimental physicist, chemist, or biologist with skills in handling complex data and an interest in fundamental questions about development, and a strong drive to excel in a competitive international environment. Prior experience with quantitative (light-sheet) microscopy, organoid/tissue culture or quantitative analysis of single-cell behavior is not required, but is considered a plus.

Conditions of employment
When fulfilling a PhD position at NWO-I, the Institutes Organisation of NWO, you will get the status of junior scientist. 
You will have an employee status and can participate in all the employee benefits NWO-I offers. You will get a contract for four years. Your salary will be up to a maximum of 2,834 euro gross per month. The salary is supplemented with a holiday allowance of 8 percent and an end-of-year bonus of 8.33 percent. 
You are supposed to have a thesis finished at the end of your four year term with NWO-I. 
A training programme is part of the agreement. You and your supervisor will make up a plan for the additional education and supervising that you specifically need. This plan also defines which teaching activities you will be responsible (up to a maximum of ten percent of your time). The conditions of employment of NWO-I are laid down in the Collective Labour Agreement for Research Centres (Cao-Onderzoekinstellingen), more exclusive information is available at this website under Personeelsinformatie (in Dutch) or under Personnel (in English).
General information about working at NWO-I can be found in the English part of this website under Personnel. The 'Job interview code' applies to this position.

Contact
Prof.dr.ir Sander Tans (Group leader Biophysics) and Dr. Jeroen van Zon (Group leader Quantitative Developmental Biology). Phone: +31 (0)20-754 7100.

Website

Address
Please go to the AMOLF website, choose this job ad and use the button 'Apply for this position' at the bottom of that advertisement.