Positions available

PhD and Postdoc positions

Ph.D. position in the Berger group is available on the project “Self-organization principles of complex microtubule networks”

Ph.D. position in the Berger group is available on the project “Connecting intracellular transport patterns to molecular principles”

PhD position in the Farías group is available on the project “Polarized sorting of proteins in neurons”

Postdoc position in the Farías group is available on the project “Organelle contacts in neurons”

Postdoctoral position in the Akhmanova group is available on the analysis of complex cytoskeletal networks.

PhD position on Cell Biology in the Akhmanova group on the project “Microtubule organisation and membrane trafficking in metastatic cancer”

PhD position in Biology, Virology and Pharmacy available in the Oliveira group.
 


 

Berger group

In the lab of Florian Berger for theoretical biophysics, a Ph.D. position (4 years) is available.
To apply, please send an email to f.m.berger@uu.nl

Self-organization principles of complex microtubule networks

The shape and internal organization of cells largely depend on the dynamics of the microtubule (MT) cytoskeleton and associated proteins such as motor molecules. These motors transport cargos along MTs in a directed manner, can slide MTs, and influence their polymerization dynamics. In turn, the spatial organization of the MT network dictates where these motor proteins function. This mutual regulation results in complex MT networks and organizations. For example, the axon and dendrites are functionally distinct compartments of neurons and display unique MT organizations. How these different MT networks can be generated and maintained in the same cell at different locations is largely unknown. In this project, we aim to find fundamental principles that govern the organization of complex MT networks by using biophysical models either with analytical approaches or with computer simulations. In collaboration with the Kapitein lab, we are in an exceptional position to validate our findings and conceptualize the latest experimental results within our framework.
The ideal candidate is eager to use mathematical descriptions for biological systems, improve their programming skills, and feel comfortable working at the intersection of physics and cell biology. A background in a quantitative field such as physics, mathematics, or theoretical biology is advantageous, but not required.

In the lab of Florian Berger for theoretical biophysics, a Ph.D. position (4 years) is available.
To apply, please send an email to f.m.berger@uu.nl

Connecting intracellular transport patterns to molecular principles

The internal organization of cells depends to a large extent on active transport of cargos by molecular motors. Although this transport is essential for cells to maintain a constant flow of material, only little is known about how these systems operate as a whole and function on a cellular level. Strikingly, different cargos display distinct transport behaviors characterized by different velocities and switching statistics resulting in robust patterns. How these patterns are generated, why they are cargo-specific, and how they are regulated on a cellular level is unknown. In this project, we aim to develop a “bottom-down” approach by first analyze the movement of intracellular cargos, preferable automatically with machine-learning methods. Subsequently, we will explore possible molecular mechanisms that are consistent with the observed transport behavior using biophysical models. From our collaboration with the Kapitein lab, we have access to high-quality imaging data and more importantly, our experimental colleagues can locally perturb transport patterns in a reversible way with optogenetic tools. The systematic analysis of data from such perturbation-response experiments may reveal the organizational principles underlying the dynamical transport patterns.
The ideal candidate is eager to use mathematical descriptions for biological systems, improve their programming skills to dive into image analysis and machine learning methods. They also feel comfortable working at the intersection of physics and cell biology. A background in a quantitative field such as physics, mathematics, computer science, or theoretical biology is advantageous, but not required.

 


 

Farías group

In the lab of Ginny Farías, 1 PhD position (4 years) is available.
Polarized sorting of proteins in neurons.
Neurons are highly polarized cells with two morphologically and functionally distinct domains, the somatodendritic and axonal domains. Sorting of transmembrane proteins into the correct compartment is essential for neuronal function. However, the secretion routes required for polarized sorting in neurons remain largely unknown. By using biochemical and imaging approaches combined with innovative protein-protein interaction tools and the use of microfluidic devices, this project aims to identify novel players and routes for the polarized sorting of proteins in neurons. The applicant should hold a master’s degree in Biology, Biochemistry, Biomedical Sciences, Biophysics, Neuroscience or a related field in Life Sciences. Knowledge and experience with protein-protein interaction tools and/or proteomic data analysis is desirable. The candidate should be fluent in English and have good communication skills. To apply, please send your CV, contact for references and a motivation letter to Dr. Ginny Farías (g.c.fariasgaldames@uu.nl).

In the lab of Ginny Farías, 1 postdoc position (2 years) is available.
Organelle contacts in neurons.
Cell function relies on the compartmentalization of different processes. The formation of discrete organelles ensures the segregation of incompatible processes, but at the same time they must be coordinated to ensure proper cellular function. In highly polarized cells such as neurons, this organelle coordination is much more complex because of the highly asymmetric architecture of these cells. By using biochemical and imaging approaches in neurons, this project aims to identify novel players involved in organelle contacts and elucidate their contribution to neuronal function. Experience in protein-protein interaction tools and/or proteomics data analysis is required. To apply, please send your CV and a motivation letter to Dr. Ginny Farías (g.c.fariasgaldames@uu.nl).

 


 

Akhmanova group

In the lab of Anna Akhmanova, 1 postdoc position (3 years) is available.
To apply, please send an email to A.Akhmanova@uu.nl

Multifactorial control of microtubule dynamics in vitro and in cells

Microtubule dynamics are regulated by a plethora of factors, the individual activities of which are known. However, it is still poorly understood how these factors work together and how their collective activity is modulated by physical barriers and interactions with other cytoskeletal structures such as actin. The aim of this project is to address these questions by combining cell biological experiments, multicomponent in vitro reconstitution assays and the use of microfabricated devices. This project is in collaboration with the groups of Marileen Dogterom at TU Delft, Gijsje Koenderink at AMOLF and Lukas Kapitein at Utrecht University.

In the lab of Anna Akhmanova, a PhD position (4 years) is available.
To apply, please send an email to A.Akhmanova@uu.nl

Microtubule organisation and membrane trafficking in metastatic cancer

Metastasis is the major cause of cancer-related mortality. It depends on the ability of cancer cells to migrate away from the primary tumour and invade distant organs. Cancer cell motility has been extensively investigated in conventional two-dimensional cell culture systems. However, recent studies firmly established that cancer cell behaviour and architecture is best studied in three-dimensional (3D) matrices, which more closely mimic the 3D physiological tumour microenvironment. In this project, we propose to investigate how microtubule dynamics and microtubule-based membrane trafficking contribute to cancer cell motility in 3D and to metastasis in mice. The project is a collaboration with the laboratories of Judith Klumperman and Patrick Derksen at UMC Utrecht.

 


 

Oliveira group

PhD position in Biology, Virology and Pharmacy (1.0 FTE)

We are looking for a highly motivated PhD candidate who will develop nanobodies binding to conserved epitopes on viral proteins from corona and influenza viruses. After thorough characterization of their binding properties, these nanobodies will subsequently be explored for application in diagnosis, protection, and treatment of viral infection.

This project is a collaboration between Cell Biology, Neurobiology and Biophysics (Department of Biology, Faculty of Science), Pharmaceutics (Department of Pharmaceutical Sciences, Faculty of Science), and Virology (Faculty of Veterinary Medicine).

https://www.academictransfer.com/nl/288747/phd-position-in-biology-virology-and-pharmacy-10-fte/