Posts Tagged ‘dynamics’

Functional analysis of the Drosophila eve locus in response to non-canonical combinations of gap gene expression levels

Netta Haroush, Michal Levo, Eric Wieschaus, Thomas Gregor. Developmental Cell 58 (23), 2789-2801.e5 (2023).


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).

Growth produces coordination trade-offs in Trichoplax adhaerens, an animal lacking a central nervous system

Mircea R. Davidescu, Pavel Romanczuk, Thomas Gregor, Iain D. Cousin. Proc Natl Acad Sci (USA) 120 (11) e2206163120 (2023).


Structured foraging of soil predators unveils functional responses to bacterial defenses

Fernando W. Rossine, Gabriel Vercelli, Corina Tarnita, and Thomas Gregor. Proceedings of the National Academy of Science (USA) 119(52): e2210995119 (2022).


Eukaryotic gene regulation at equilibrium, or non?

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

Latent space of a small genetic network: Geometry of dynamics and information

Rabea Seyboldt, Juliette Lavoie, Adrien Henry, Jules Vanaret, Mariela D. Petkova, Thomas Gregor, and Paul François. Proceedings of the National Academy of Science 119 (26): e2113651119 (2022).

Transcriptional coupling of distant regulatory genes in living embryos

Michal Levo, João Raimundo, Xin Yang Bing, Zachary Sisco, Philippe J. Batut, Sergey Ryabichko, Thomas Gregor & Michael S. Levine (2022). Nature 605, 754–760 (2022).

Optogenetic control of the Bicoid morphogen reveals fast and slow modes of gap gene regulation

Anand P. Singh, Ping Wu, Sergey Ryabichko, Joao Raimundo, Michael Swan, Eric Wieschaus,
Thomas Gregor, and Jared E. Toettcher (2022). Cell Reports 38, 110543.

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.


Diverse spatial expression patterns emerge from unified kinetics of transcriptional bursting

Benjamin Zoller, Shawn C. Little, and Thomas Gregor. Cell 175(3), 835–847 (2018). (more…)

Dynamic interplay between enhancer-promoter topology and gene activity

Hongtao Chen, Michal Levo, Lev Barinov, Miki Fujioka, James B. Jaynes and Thomas Gregor. Nature Genetics 50, 1296–1303 (2018). (more…)

Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo

Jacques Bothma, Hernan Garcia, Samuel Ng, Michael W. Perry, Thomas Gregor, and Michael S. Levine. eLife 2015; 4:e07956 (2015). (more…)

Dynamic Regulation of Eve Stripe 2 Expression Reveals Transcriptional Bursts in Living Drosophila Embryos

Jacques P. Bothma, Hernan G. Garcia, Emilia Esposito, Gavin Schlissel, Thomas Gregor, Michael S. Levine. PNAS 111 (29): 10598–10603 (2014).

Quantitative imaging of transcription in living Drosophila embryos links polymerase activity to patterning

Hernan G. Garcia, Mikhail Tikhonov, Albert Lin and Thomas Gregor. Current Biology 23, 2140–2145 (2013).

Dynamic interpretation of maternal inputs by the Drosophila segmentation gene network

Feng Liu, Alexander H. Morrison and Thomas Gregor, PNAS 110: 6724–6729 (2013).

Accurate measurements of dynamics and reproducibility in small genetic networks

Julien O. Dubuis, Reba Samanta and Thomas Gregor, Molecular Systems Biology 9: 639 (2013).

The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized mRNA.

Shawn Little, Gašper Tkačik, Thomas Kneeland, Eric Wieschaus and Thomas Gregor, PLoS Biology 9(3): e1000596 (2011).

Abstracts from contributions to recent international Dictyostelium meeting in Tsukuba/Japan

Currently, I am in the process of finishing up my work on amoeba signaling and aggregation in Tokyo. This work is in collaboration with and in the laboratory of Satoshi Sawai at the University of Tokyo. We also collaborate with Koichi Fujimoto, a theorist at the same institution. While no papers have been published yet, as a preview pasted below are three abstracts of contributions to a recent international Dictyostelium meeting held in Tsukuba/Japan. (more…)

Stability and nuclear dynamics of the Bicoid morphogen gradient.

T. Gregor, E. F. Wieschaus, A. P. McGregor, W. Bialek, D. W. Tank, Cell 130, 141-152 (2007).