Project Outline

Background and scientific rationale

Embryonic tissues and organs are shaped and patterned by complex genetic, molecular and cellular mechanisms that regulate essential processes during development [1]. Dissecting such mechanisms remains challenging as the formation of tissues is controlled on different levels including genes that regulate cell-fate decisions, biochemical signalling pathways and mechanical (physical) forces that act within and between cells to define 3D form and function. Our group aims to understand how these complex processes on multiple scales are linked using the zebrafish embryo as a model system – from tissue to cells, from the cell membrane to the nucleus, and on transcriptional/genomic level. This requires an interdisciplinary approach where we combine approaches from molecular and cell biology, state-of-the-art microscopy, organoids, biophysics tools, computational image analysis, transcriptomics and theoretical modelling.

In particular, the lab is interested in processes during development such as cell movements, cell divisions, cell shape changes, cell adhesion and cell fate specification that require feedback between biochemical and mechanical signals [2]. It is now well recognised that cells for example push and pull on each other and thereby triggering profound changes in cell and tissue behaviour that are essential to drive many developmental programmes [1]. However, the precise molecular and cellular mechanisms involved are not well explored. We aim to gain mechanistic insights into how tissues get their shape, how cells migrate directionally, how cells communicate via cell-cell adhesions and how cells change their identity or state.

Project Outlines

Below are examples of potential projects available that highlight the broad scope of topics and technologies the lab:

1 - Feedback between cell fate specification and tissue morphogenesis

This project investigates how progenitor cells organise into different territories and establish sharp boundaries during tissue formation in the early embryo [3].

Objective

Unravelling how cellular and tissue dynamics contribute to establishing different territories in the early brain with distinct cell fates.

Methods

Live imaging and immunofluorescence of zebrafish embryos, quantitative image analysis of cellular morphodynamics (movement, shape) and molecules involved in cell fate specification (transcription factors, morphogens). Biophysical characterisation of isolated cells in vivo and ex vivo.

2 - Cellular force sensing and response

Cells can sense mechanical stimuli from the microenvironment. [4]. Yet, it is still unclear how embryonic stem (ES) cells respond to specific forces to activate specific cell and developmental programmes

Objective

Identifying how ES cells sense and respond to mechanical signals and regulate essential processes including cell division or cell fate specification.

Methods

Live cell imaging and immunofluorescence of cells in the embryo and isolated cells ex vivo, cell confiner, atomic force microscopy (AFM), computational image analysis of cell and molecule dynamics. Characterisation of nuclear mechanics and response.

3 - Self-organisation of early brain development

Recent stem cell models (gastruloids, organoids) highlight the remarkable potential to recapitulate early embryonic development through self-organisation and patterning in vitro [5].

Objective

Establishing cell culture conditions mirroring early embryonic brain development and investigating the role of biomechanics in cell fate patterning.

Methods

Generation of ES cell-derived aggregates in tissue culture. Live imaging and immunofluorescence (confocal, multiphoton), micropatterning, chemical and physical perturbations, computational image analyses of cell morphodynamics (movements, shapes) and tissue patterning.

References

[1] Gilmour D. et al. Nature. 2017

[2] Heisenberg CP. and Bellaiche Y. Cell. 2013

[3] Dahman C. et al. Nat Rev Genet. 2011

[4] Inman A. and Smutny M. Semin Cell Dev Biol. 2021

[5] Shahbazi MN. et al. Science. 2019

Techniques

• Zebrafish embryo as model system: genetics (genome editing), transgenic lines.
• Stem cell culture assays (ex vivo isolated cells, organoids), micropatterning.
• Microscopy (live & fixed specimen): confocal and multiphoton microscopy, selective plane illumination (light sheet) microscopy
• Optogenetics
• Computational image analysis and statistics (Fiji, Matlab, R) of biological and physical processes (cell tracking; cell shape changes; protein and membrane dynamics; tissue, cell and nuclear mechanics).
• Biophysical tools: cell confiner, atomic force microscopy, magnetic tweezer