Self-organization of biological structures
Previous and Current Research
Our lab combines biophysics, cell biology and soft matter physics to study the underlying principles of self-organization in biological structures. We currently use the mitotic spindle and the nucleus in Xenopus laevis egg extract and zebrafish Danio rerio embryos as model systems to study how the large-scale patterns and behaviors of biological structures emerge from the collective behaviors of molecules. To this end, we design new multi-scale quantitative methods that can resolve the local dynamics of soluble proteins, dissect the architecture of cellular structures, and characterize the mechanical properties and dynamics at large scales.
Dynamics of chromatin organization in the nucleus
The spatio-temporal organization of chromatin in the nucleus is emerging as a fundamental factor regulating gene expression. Recent studies have started to map the gene-wide chromatin interactions in the interphase nucleus, revealing some principles of chromosome organization into territories, and dramatic changes of chromatin organization and interactions during differentiation and lineage specification. These studies are typically based on chromosome capture techniques that require many nuclei and provide a static picture of the chromosome organization in the nucleus. Therefore, the dynamics of chromatin organization are still poorly understood. In this new research line, we initially will study how transcription factors, RNA polymerases, and other molecules are partitioned in the nucleoplasm, and how they contribute to the establishment of structures such as transcription factories, chromosome territories or chromatin states. To this end, we are developing a new multi-scale live imaging approach to characterize nuclear organization dynamics at the single cell level based on the simultaneous characterization of both the local dynamics of RNA polymerases and transcription factors and the large scale behavior of chromatin.
Design of new quantitative microscopy methods
The spatial and temporal regulation of signaling controls a variety of biological phenomena ranging from the self-organization of cellular structures to the development of embryos and tissue formation. These processes arise ultimately from the combination of local molecular activities, interactions, and diffusion processes. Although some of the key molecular components involved in the formation of cellular structures and tissue formation are known, we currently lack a bottoms up understanding of how the behavior of these molecules gives rise to the formation of large structures, partly because of the lack of tools for both studying the spatial regulation of soluble proteins and biophysically characterizing the behavior of large structures and tissues. We are developing several new methods to characterize the microscopic behavior of molecules and the biophysics of large scale structures. These include custom-built light sheet microscopy for single molecule and whole embryo measurements, laser ablation to perturb and dissect the architecture of microtubule structures, quantitative polarization microscopy, and new fluorescence correlation spectroscopy approaches.
Spindle morphology and scaling
It has been known for a long time that there is a correlation between the size of a cell and the size of its organelles, including the spindle and the nucleus. This relationship is perhaps most striking during the first stages of embryogenesis, when cells change in size and shape several fold in the absence of growth. During this process, in order to accurately segregate chromosomes over a wide range of length scales, the spindle adapts its size and shape. These changes in size and shape ultimately relate to chromosome and cleavage plane positioning and are therefore crucial for the proper development of the embryo. Despite its importance the mechanisms that regulate spindle scaling, microtubule nucleation and force generation remain elusive. To gain insight into these questions, we combine mathematical modelling, biophysics and quantitative measurements of spindles during the early development of the zebrafish Danio rerio and in Xenopus laevis egg extract.
Future Projects and Goals
For this selection we are looking to recruit a student under the highly competitive ELBE PhD program together with the Jochen Guck lab. In this project we want to unravel how nuclei integrate external mechanical cues and how these affect chromatin organization and gene expression. It has been proposed that the nucleus acts a mechanosensor, where nuclear deformations lead to chromatin reorganization and changes in gene expression, but the exact mechanism of how this reorganization works is still mysterious. Moreover, from the mechanical point of view, the nucleus has been thought to simply be a blob of chromatin held together by nuclear lamina. This view has been challenged by recent findings showing that nuclei can display very exotic mechanical properties, such as auxeticity and negative Poisson ratio (volume increase under uniaxial stress), a feature only very few materials in nature display. The nucleus may exploit these unusual behaviors to control gene regulation by decondensing and reorganizing chromatin when mechanically perturbed (increase of volume). A physical understanding of the mechanical origin of the nucleus could therefore lead to an understanding of how cells integrate mechanical stimuli and activate genetic programs accordingly. The nucleus is, however, a very complex organelle and studying its mechanosensing role in-vivo is challenging. Our goal here is to reduce the complexity of the nucleus to test basic mechanisms. We propose a systems biology approach to create an artificial nucleus capable of recapitulating its most salient mechanical properties that is also transcriptionally active.
Methodological and Technical Expertise
- Fluorescence spinning disk microscopy
- LC-Polscope (quantitative polarization microscopy)
- Femto-second laser ablation
- DIC microscopy
- Xenopus Laevis extract preparation
- Spindle assembly and biochemistry
- Fluorescence Correlation Spectroscopy
- Single molecule imaging
- Mathematical modeling
- Image processing
- Numerical simulation and analysis
Decker, Franziska; Brugués, Jan
Dissecting microtubule structures by laser ablation
Methods Mol Biol, 125, pp. 61–75, (2015)
Brugués, Jan, Needleman, Daniel
Physical basis of spindle self-organization.
Proc. Natl. Acad. Sci. U.S.A., 111, no. 52, pp. 18496-18500 (2014)
Brugués, J, Nuzzo, V, Mazur, E, and Needleman, D J.
Nucleation and Transport Organize Microtubules in the Spindle.
Cell, 149, 554-564 (2012)
Brugués, J, Maugis, B, Casademunt, J, Nassoy, P, Amblard, F, and Sens, P.
Dynamical Organization of the Cytoskeletal Cortex Probed by Micropipette Aspiration.
Proceedings of the National Academy of Sciences, 107, 15415-20 (2010)
Brugués, J, and Casademunt, J.
Self-Organization and Cooperativity of Weakly Coupled Molecular Motors under Unequal Loading.
Physical Review Letters, 102, 118104 (2009)