Blanchard, O. | bioRxiv Science

bioRxiv2024

Substrate Rigidity Modulates Segmentation Clock Dynamics in Isolated Presomitic Mesoderm Cells

The segmentation clock, a genetic oscillator in the presomitic mesoderm (PSM), is known to be influenced by biochemical signals, yet its potential regulation by mechanical cues remains unclear. The complex PSM microenvironment has made it challenging to isolate the effects of mechanical signals on clock behavior. Here we investigated how mechanical stimuli affect clock oscillations by culturing zebrafish PSM cells on bioengineered elastic substrates (PDMS micropost arrays) with tunable rigidities ranging from 0.6 to 1,200 kPa. We observed an inverse sigmoidal relationship between substrate rigidity and the percentage of oscillating PSM cells, with a switching rigidity threshold between 3-6 kPa. The oscillation periods of oscillating PSM cells showed a consistently broad distribution across the substrate rigidity conditions tested. Moreover, these oscillatory PSM cells exhibited distinct biophysical properties, including reduced motility, contractility, and sustained circularity, compared to non-oscillating ones. These findings highlight a role of cell-substrate interactions in regulating segmentation clock behavior, providing insights into the mechanobiology of somitogenesis. HighlightsO_LIOscillatory behaviors of single PSM cells respond to substrate rigidity in a switch-like manner, transitioning from an oscillatory state to a quiescent state at a critical rigidity threshold between 2.9 kPa and 6 kPa. C_LIO_LIIncreased substrate rigidity significantly suppresses the percentage of oscillating PSM cells, while oscillation period and cycle number show no consistent rigidity-dependent trend. C_LIO_LINon-oscillating PSM cells exhibit distinct biophysical properties compared to oscillating ones, including reduced circularity, a polarized and elongated morphology, greater motility, and increased contractility. C_LIO_LIAggregates of PSM cells exhibit similar trends in response to substrate rigidity changes, except for increased oscillation percentages across different rigidity conditions, suggesting a potential interplay between cell-cell and cell-matrix communications in influencing clock oscillation behavior. C_LI

developmental biology↗

bioRxiv2021

An open-source tool to assess the carbon footprint of research

The scrutiny over the carbon footprint of academics has increased rapidly in the last few years. This has resulted in a series of publications providing various estimates of the carbon footprint of one or several research activities, principally at the scale of a university or a research center or, more recently, a field of research. The variety of tools or methodologies - on which these estimates rely - unfortunately prevents from any direct comparison because of the sensitivity of carbon footprint assessments to variations in the scope and to key parameters such as emission factors. In an effort to enabling a robust comparison of research carbon footprints across institutions, contexts or disciplines, we present an open-source web application, GES 1point5 designed to estimate the carbon footprint of a department, research lab or team in any country of the world with a transparent and common methodology. The current version of GES 1point5, open-source and freely available, takes into account the most common and often predominant emission sources in research labs: buildings, digital devices, commuting, and professional travel. GES 1point5 is developed by an interdisciplinary team of scientists from several public research institutions in France as part of the Labos 1point5 project. GES 1point5 is therefore presently tailored for the French context but can be adjusted to any national contexts by adjusting the values of emission factors. The versatility and usability of the software have been empirically validated by its adoption by several hundred research labs in France over the last 18 months. In addition to enabling the estimation and monitoring of greenhouse gas (GHG) emissions at the scale of a research lab, GES 1point5 is designed to aggregate the data entered by the labs and the corresponding GHG emissions estimates into a comprehensive database. GES 1point5 can therefore allow to (i) identify robust determinants of the carbon footprint of research activities across a network of research labs (ii) estimate the carbon footprint of research at the national scale. A preliminary analysis of the carbon footprint of more than one hundred laboratories is presented to illustrate the potential of the approach. While assessments of carbon footprints are often externalized onto extension services and proprietary softwares, GES 1point5 is designed as a hands-on, pedagogic and transparent tool for research labs to monitor and reduce their own carbon footprint. This internalization has strong positive co-benefits for academics in terms of awareness and empowerment. We further expect that international dissemination of GES 1point5 will contribute to establishing a global understanding of the drivers of the research carbon footprint worldwide and an identification of the levers to decrease it. Availability and implementationGES 1point5 is available online at http://labos1point5.org/ges-1point5 and its source code can be downloaded from the GitLab platform at https://framagit.org/labos1point5/l1p5-vuejs.

scientific communication and education↗