PhD Position Evolutionary Robustness of Cell Polarity

Unraveling the genetic pathways of evolutionary resilience by exploring how yeast adapts to polarity gene loss through experimental evolution and quantitative genomics

Job description

Cells are often viewed as intricate machines, in which specific proteins work together in a tightly coordinated fashion to give rise to cellular functions. Surprisingly however, some proteins that are essential for core cellular functions in one species are absent in closely related species, while the core function itself is maintained. How this robustness is achieved, while the underlying molecular networks dramatically diversify during evolution is currently not understood. Previous work showed that the polarity network in yeast can evolutionarily adapt to the loss of an important protein by losing three more proteins. The Laan lab showed that these losses repair polarity through a collective adaptive response, affecting many cellular processes rather than only a few proteins. So, how do intricate cellular networks collectively achieve such evolutionary robustness?

Within the ERC project "PolarRobustness" you willl, as part of a team within the Laan Lab work on this problem. You role will be to investigate the genetics of how cells maintain cell polarity after the loss of key polarity genes using experimental evolution in budding yeast. You will generate and analyze a library of evolved yeast strains, each compensating for different deleted polarity genes, and track adaptive mutations through whole-genome sequencing. Using transposon sequencing, you will identify genes crucial for fitness before and after evolution, constructing dynamic genetic interaction networks. You will explore how adaptive mutations reshape cellular processes, using bioinformatics tools like Markov clustering and STRING analysis to uncover fundamental principles of cellular resilience.

The PolarRobustness team will include another PhD student and a Post Doc that will analyse the evolved strains with live cell microscopy, mass spectrometry and multiscale modeling in collaboration with the theoretical phyicisist dr. Jos Zwanikken and the bioinformatician dr Nikolina Sostaric. A yeast genetics technician will help with strain construction and prepare samples for sequencing. The team together will dissect how molecular changes collectively propagate through the polarity network to achieve evolutionary robustness.

Job requirements

We are looking for an experimentalist, with a background in (bio)physics, nanobiology or quantitative biology, who is eager to combine wetlab work with big data analysis and bioinformatics and has a keen interest in unraveling cellular resilience. We are a highly collaborative research group that likes to work on challenging and ambitious fundamental problems, that typically combine experiments with computational work. We expect the candidate to be a team-player, to have an independent and well-organized work style, to be communicative and creative, and to contribute to our open, interactive, and social lab culture.

TU Delft (Delft University of Technology)

Delft University of Technology is built on strong foundations. As creators of the world-famous Dutch waterworks and pioneers in biotech, TU Delft is a top international university combining science, engineering and design. It delivers world class results in education, research and innovation to address challenges in the areas of energy, climate, mobility, health and digital society. For generations, our engineers have proven to be entrepreneurial problem-solvers, both in business and in a social context.

At TU Delft we embrace diversity as one of our core values and we actively engage to be a university where you feel at home and can flourish. We value different perspectives and qualities. We believe this makes our work more innovative, the TU Delft community more vibrant and the world more just. Together, we imagine, invent and create solutions using technology to have a positive impact on a global scale. That is why we invite you to apply. Your application will receive fair consideration.

Challenge. Change. Impact!

Faculty Applied Sciences

With more than 1,100 employees, including 150 pioneering principal investigators, as well as a population of about 3,600 passionate students, the Faculty of Applied Sciences is an inspiring scientific ecosystem. Focusing on key enabling technologies, such as quantum- and nanotechnology, photonics, biotechnology, synthetic biology and materials for energy storage and conversion, our faculty aims to provide solutions to important problems of the 21st century. To that end, we educate innovative students in broad Bachelor's and specialist Master's programmes with a strong research component. Our scientists conduct ground-breaking fundamental and applied research in the fields of Life and Health Science & Technology, Nanoscience, Chemical Engineering, Radiation Science & Technology, and Engineering Physics. We are also training the next generation of high school teachers.

Conditions of employment

Doctoral candidates will be offered a 4-year period of employment in principle, but in the form of 2 employment contracts. An initial 1,5 year contract with an official go/no go progress assessment within 15 months. Followed by an additional contract for the remaining 2,5 years assuming everything goes well and performance requirements are met.

Salary and benefits are in accordance with the Collective Labour Agreement for Dutch Universities, increasing from € 2872 per month in the first year to € 3670 in the fourth year. As a PhD candidate you will be enrolled in the TU Delft Graduate School. The TU Delft Graduate School provides an inspiring research environment with an excellent team of supervisors, academic staff and a mentor. The Doctoral Education Programme is aimed at developing your transferable, discipline-related and research skills.

The TU Delft offers a customisable compensation package, discounts on health insurance, and a monthly work costs contribution. Flexible work schedules can be arranged.

Will you need to relocate to the Netherlands for this job? TU Delft is committed to make your move as smooth as possible! The HR unit, Coming to Delft Service, offers information on their website to help you prepare your relocation. In addition, Coming to Delft Service organises events to help you settle in the Netherlands, and expand your (social) network in Delft. A Dual Career Programme is available, to support your accompanying partner with their job search in the Netherlands.