Posts Tagged ‘research’

Precise and scalable self-organization in mammalian pseudo-embryos

Mélody Merle, Leah Friedman, Corinne Chureau, Armin Shoushtarizadeh & Thomas Gregor.
Nature Structural & Molecular Biology, doi: 10.1038/s41594-024-01251-4 (2024)

Using physics to study life

My laboratory is interested in problems at the interface of physics and biology. The main thrust of our research is the design of new experimental approaches and performing high-precision physics-style measurements in living animals, such that our data allows for direct validation of mathematical models. This program is aimed at the generation of theories describing biological phenomena which are derived from general principles in the physics tradition. Currently, our primary interests lie in the self-organization and collective behaviors of eukaryotic cell aggregates, from microbes to embryonic tissue, and in how the control of gene expression in early fly embryos leads to the formation of an animal body plan. We are making experimental and theoretical progress on the biological questions in each of these areas but the long-term goal is to find theories inspired by experimental data that go beyond the specifics of the biological systems hoping to find in the living world new physics, which has been hidden and cannot quickly be revealed in the inanimate world. The approach outlined here extends the traditional physics approach, which my colleagues used to study the stars or inert matter on Earth, to the complex processes underlying the living world.

The laboratory is currently composed of two research facilities working on similar topics and questions. One at Princeton University, since 2009, and since recently (2018) a second laboratory at the Institut Pasteur in Paris (France). The laboratory in Princeton works with Drosophila melanogaster models for which we have developed many highly quantitative imaging technologies to perform precision measurements in living embryos. At the unit at Institut Pasteur, we implement derivatives of these technologies in mammalian model systems such as mouse embryonic stem cells and stem cell-derived embryoid cell aggregates (i.e. gastruloids). Once these perform at similar levels of precision to what we achieve with the fly system, we will assess physical concepts such as developmental precision and reproducibility, system size scaling, or self-organization phenomena across both model systems. 

Activities at Princeton will continue with the Drosophila model along the following directions: studying the flow of information from molecules to macroscopic patterns, where cells determine their identity by interpreting this information from a genetic network of interconnected transcription factors. With the gene regulatory sequence, the enhancer, still at the core of our investigation, we identified three central questions that we will continue to address during the next cycle:

1) How do individual enhancers read information from a genetic network of interconnected transcription factors?

2) How is this information transferred from the activated enhancer to its target promoter, often over large genomic distances?

3) How is information eventually transformed into a transcriptional output at the level of the promoter?

To answer these questions, several technologies are being developed, namely live single-molecule imaging and optogenetic perturbation of single cells and individual gene loci in living embryos.

A single-objective light-sheet microscope

We are developing a novel microscopy modality, a single-objective light-sheet microscope with a high numerical aperture. It is an entirely novel design for a light-sheet microscope that combines the convenience of conventional sample mounting with sensitive subcellular and super-resolution imaging of cells and tissues. This single objective light-sheet fluorescence microscope started acquiring from biological samples only a few months ago and already several researchers across campus claimed interest in obtaining their own version, and there are plans to build a clone of the microscope for the imaging facility.

In an OPM, a single primary objective is used to both create the excitation light sheet and capture emitted light from the sample. Excitation light enters the objective sideways, resulting in an oblique light sheet on the sample, with an angle between 30°–45°. Emitted light from the tilted plane is collected by the same objective and optically refocused to a secondary objective, without introducing any relevant aberrations. It is subsequently re-imaged by a tilted tertiary objective onto a camera. The beauty of this approach lies in having a single high NA objective close to the sample, allowing for traditional sample mounting geometry (microscope slides, glass-bottom dish), and leaving accessible space around the sample for other perturbations and manipulations, such as microfluidic devices or optogenetic light stimulation.

As a proof of concept, we acquired images of Drosophila embryos, mESCs, and mouse gastruloids in their optimal growth conditions, showing that we achieve diffraction-limited resolution that, e.g., allows us to discriminate sister chromatids, follow their dynamics over time, and measure how they are transcriptionally, spatially, and temporally correlated. Moreover, we achieve a combination of high resolution, high contrast, and high speed that enables us to identify and track single mRNA molecules as they are released at the transcription site. We are currently developing analysis tools that will allow us to extract quantitative data from these images, e.g., to measure the diffusion and reach of individual mRNA molecules.

Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome

David B. Brückner, Hongtao Chen, Lev Barinov, Benjamin Zoller, Thomas Gregor. Science 380, 1357-1362 (2023).

Eukaryotic gene regulation at equilibrium, or non?

Benjamin Zoller, Thomas Gregor, and Gasper Tkacik. Current Opinion in System Biology 31: 100435 (2022).

Temporally dynamic antagonism between transcription and chromatin compaction controls stochastic photoreceptor specification in flies

Lukas Voortman, Caitlin Anderson, Elizabeth Urban, Luorongxin Yuan, Sang Tran, Alexandra Neuhaus-Follini, Josh Derrick, Thomas Gregor, and Robert J. Johnston, Jr. Developmental Cell. 57(15), 1817–1832.E5 (2022).

Positions available for postdocs

We are currently looking for postdoctoral candidates interested in the following three general themes:

1. At the level of a genetic network, extract global properties and design principles from expression level measurements and analysis.

2. At the molecular level, develop mathematical models underlying the fundamental mechanisms of transcriptional regulation and test these using single molecule and live measurements of the transcriptional output.

3. At the level of the dynamics of the DNA polymer, link the nuclear architecture with actual transcriptional activity in terms of multiple enhancers recruiting the same promoter in a given cell.

Experimental and theoretical physicists (preferentially with experience in biological and/or soft-matter physics), engineers and materials scientists with experience in biology, and biologists interested and experienced in quantitative approaches are strongly encouraged to apply. Outstanding applicants in other fields (mathematics, computer science, chemistry, etc.) may also be considered. Experience with microscopy and image analysis is a plus.

Applicants should email me their CV and a brief description of research interests, as well as their motivation to join the lab.

The Impact of Space and Time on the Functional Output of the Genome

Marcello Nollmann, Isma Bennabi, Markus Götz, and Thomas Gregor (2021). Cold Spring Harb Perspect Biol.: a040378. doi: 10.1101/cshperspect.a040378.


Beyond D’Arcy Thompson: Future challenges for quantitative biology

Thomas Gregor. Mechanisms of Development 145: 10–12 (2017). (more…)

Easy pieces…

If you’re new to science and are curious to learn more about what our interests in the lab are, here are a couple of easy readings that professional science writers have written about our science. These pieces are meant to be accessible for everybody, no fancy science language nor any unnecessary jargon to pump up the jam…

Here is one on our amoebae work:
Scientists discover the molecular heart of collective behavior

And here is one on our fly work:
Fruit fly research may ‘clean up’ conventional impressions of biology

For other easy access writings please visit the media tab.