Quantitative Developmental Biology

We currently have openings for PhD and postdoc positions!

Development is the process by which the fertilized egg, a single cell, transforms into a fully functional multicellular organism. During this transformation, all basic cellular processes – from the cycle of each cell division to the formation of individual organs – need to be precisely coordinated in time and space. Our team is interested in how this is achieved. Our research is driven by the conviction that mathematical and physical concepts are indispensable for a deeper understanding of how the collective action of gene networks and environmental factors drives the emergence of biological shapes and patterns. Ultimately, we would like to reveal evolutionary conserved principles of patterning in metazoan development and expose novel mechanisms underlying developmental precision and robustness.

 C elegans

Long-term high-resolution imaging of C. elegans larvae with microfluidics. A C. elegans animal immobilized at various post-embryonic stages from L1 (upper left) to L4 (lower right), showing dynamic expression of the miRNA mir-47. Scale bar, 100 um.

We use an interdisciplinary strategy at the interface between physics and biology, employing both experimental and theoretical approaches. Our model organism is the small roundworm Caenorhabditis elegans (C. elegans), a simple multicellular organism with ~1000 cells.  On one end, we develop novel techniques to improve our ability to obtain quantitative high-resolution dynamic data on C. elegans development (live imaging with microfluidics, on-chip perturbations of development, software for automated phenotypic analyses of 4D microscopy data etc.). At the same time, we study a variety of paradigmatic developmental patterning problems in the worm for which high-resolution dynamic imaging data can really transform our understanding of the underlying mechanisms. Finally, we develop theoretical approaches to conceptualize these mechanisms and uncover general principles of development.

Oscillatory expression dynamics of the microRNA lin-4, a key gene regulating developmental timing and temporal cell identity in C. elegans.

image 3

(A) Live Nomarksi and fluorescence microscopy of the first two cell divisions during the development of the C. elegans egg-laying organ. YFP visualizes the dynamics of Notch target gene (lst-5) expression (yellow). (B) Fluorescence intensity (lst-5pro::YFP) as a function of time in the precursor cells of the organ.

Our approach relies on a combination of areas of expertise of the group:

(i) Large scale quantitative live-imaging capturing relevant gene expression and protein dynamics as well as developmental phenotypes (i.e. cell-lineages) during C. elegans development

(ii) Cutting-edge microfluidics technologies for high-resolution long-term live-imaging as well as for delivering precise spatiotemporal perturbations of development on-chip;

(iii) State-of-the-art genome editing tools to generate live reporter strains and mutants

(iv) Software tools for automated high-throughput analyses of developmental phenotypes, including, e.g. tracking of cell divisions, gene expression in C. elegans;

(v) Mathematical modeling of gene expression dynamics and cell-fate decisions processes, making quantitative predictions that are testable in experiments.