Scientific Internship/Master thesis project: Development of microfluidic device for detecting immune cell interactions for combating antimicrobial resistance

Date posted June 16, 2020
Type Scientific Internships

Representative models of host-pathogen interactions during the course of infection require studying in vitro (e.g., cell culture) or in vivo (e.g., serum, blood) systems, leading to complex samples consisting of pathogen cells and various host cell types. This heterogeneity makes defining changes to host and pathogen genes, transcripts, proteins, or metabolites challenging, as analysis will be dominated by the properties of the most abundant cell types in the sample. To substantially advance our understanding of host-pathogen interactions on the systems biology level, and to reveal novel mechanisms to combat antimicrobial resistance, it will therefore be key to separate different types of immune cells and pathogens at different time points after infection and study these groups in isolation.

More about the project

The goal of this project is to develop a new microfluidic chip to separate individual cell types based on their size, shape, and electrical properties . Established methods to purify cell samples are flow cytometric and magnetic sorting. However, these require the a priori knowledge of cellular markers, are sensitive to changes in surface antigens (that may be induced during infection), and require high-cost equipment (FACS machines, antibodies). In your Master project in the Ganzinger group, you will therefore develop a microdevice that does not rely on binding of probes to specific surface molecules but uses the biophysical properties of cells for their separation by applied flow or in an electric field.

Thereby, cells can be efficiently and reliably sorted into different chip outlets from which a pipetting robot can transfer the cells for further processing in a 96-well plate format for subsequent mass spec analysis. This project is a close collaboration with the Geddes-McAlister lab at University of Guelph, Canada, and towards the end of the project, you will be expected to spend some weeks in her lab to help with the knowledge transfer.

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T. A. Douglas, J. Cemazar, N. Balani, D. C. Sweeney, E. M. Schmelz and R. V. Davalos, Electrophoresis, 2017, 38, 1507–1514.


About the group

Our group focuses specifically on processes that are critical to communication in the immune system. We address these questions mainly by reconstituting signaling processes in model-membrane systems (“artificial cells”), combining this synthetic biology approach with tools from single-molecule biophysics and microfabrication (Nat Commun 2018, bioRxiv 791459). In this project, we will build on our expertise in microfluidics to contribute to a multi-OMICs platform for studying communication between immune cells in cultures across multiple levels (e.g., DNA, RNA, protein, metabolite) in a single experiment.


  • You already have a Bachelor’s degree in physics, (biomedical) engineering or a related discipline and now participate in a Master study in one of these areas.
  • Some experience with microfluidics, CAD design or electronics design would be an advantage
  • You should like the idea of working in a collaborative, ambitious and international environment.
  • Formalities: the internship has to be a mandatory part of your curriculum. You have a nationality of an EU-member state and/or you are a student at a Dutch University. You must be available for at least 6 months.
  • Ideal starting time would be October 2020 – January 2021.

Terms of employment

In the beginning of your placement, along with your supervisor at AMOLF and Dr Jennifer Geddes-McAlister, you will make a step-by-step plan in which working conditions and supervision will be agreed on.

Contact info

dr. Kristina Ganzinger
Group leader Physics of Cellular Interactions
Phone: +31 (0)20-754 7100

You can respond to this vacancy online via the button below.
Please annex your:
–  Resume;
–  List of followed courses plus grades.
–  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. This means that we will only consider your application if it entails your motivation letter.

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