Biology subjects

Ben Meriem, Z.

Publications and source records attributed to Ben Meriem, Z..

6 recordsLinked to original sources

bioRxiv2025

Proportional modulation of proliferation and motility under 2D compressive stress depends on mesenchymal phenotype

Tumor development is accompanied by strong physico-chemical modifications. Among them, compressive stress can emerge in both the epithelial and stromal compartments. Using a simple two-dimensional compression assay which consisted in placing an agarose weight on top of adherent cells, we studied the impact of compressive stress on cell proliferation and motility in different pancreatic cancer cell lines. We observed a proportional reduction of both proliferation and motility in all tested cell types, with genotypes displaying a more "mesenchymal" phenotype (high velocity-to-proliferation ratio) and others related to a more "epithelial" phenotype (low velocity-to-proliferation ratio). Moreover, "mesenchymal" cells seemed more sensitive to compression, a result that was further suggested by a TGF{beta}1 induction of epithelial-to-mesenchymal transition. Finally, we measured that the change in cell proliferation was associated with a change in intracellular macromolecular crowding, which could modulate a plethora of biochemical reactions. Our results together suggest a mechanism in which all biochemical reactions related to proliferation and motility can be modulated by a change in macromolecular crowding, itself depending on the phenotype, leading to differential sensitivity to pressure.

biophysics↗

bioRxiv2023

Mechanical characterization of regenerating Hydra tissue spheres

Hydra vulgaris, long known for its remarkable regenerative capabilities, is also a longstanding source of inspiration for models of spontaneous patterning. Recently, it became clear that early patterning during Hydra regeneration is an integrated mechano-chemical process where morphogen dynamics is influenced by tissue mechanics. One roadblock to understand Hydra self-organization is our lack of knowledge about the mechanical properties of these organisms. In this paper, we combined microfluidic developments to perform parallelized microaspiration rheological experiments and numerical simulations to characterize these mechanical properties. We found three different behaviors depending on the applied stresses: an elastic response, a visco-elastic one and tissue rupture. Using models of deformable shells, we quantify their Youngs modulus, shear viscosity as well as the critical stresses required to switch between behaviors. Based on these experimental results, we propose a description of the tissue mechanics during normal regeneration. Our results provide a first step towards the development of original mechano-chemical models of patterning grounded in quantitative, experimental data. Statement of significanceHydra vulgaris is a remarkable organism thanks to its regenerative abilities. One can cut this animal into several pieces which will reform a full Hydra in a few days. In this process, the pieces have to define a new organizing axis. Recently, researchers have shown that this axis definition is under mechanical control. One roadblock to understand the relationship between tissue mechanics and Hydra biology is our lack of knowledge about the mechanical state of this organism. Here, we perform a mechanical characterization using a combination of microaspiration setups and numerical simulations. We finally propose a description of what happens at the mechanical level during Hydra regeneration, allowing quantitative approaches questioning the role of mechanical cues in axis definition.

biophysics↗

bioRxiv2023

An easy-to-use microfluidic mechano-chemostat for tissues and organisms reveals that confined growth is accompanied with increased macromolecular crowding

Conventional culture conditions are oftentimes insufficient to study tissues, organisms, or 3D multicellular assemblies. They lack both dynamic chemical and mechanical control over the microenvironment. While specific microfluidic devices have been developed to address chemical control, they are often hard to use and do not allow the control of compressive forces. Here, we present a set of microfluidic devices which all rely on the use of sliding elements consisting of microfabricated rods that can be inserted inside a microfluidic device. Sliding elements enable the creation of reconfigurable sealed culture chambers for the study of whole organisms or model micro-tissues. By confining the micro-tissues, we studied the biophysical impact of growth-induced pressure and showed that this mechanical stress is associated with an increase in macromolecular crowding, shedding light on this understudied type of mechanical stress. Our mechano-chemostat is an easy-to-use microfluidic device that allows the long-term culture of biological samples and can be used to study both the impact of specific conditions as well as the consequences of mechanical compression.

biophysics↗

bioRxiv2019

The memory of hyperosmotic stress response in yeast is modulated by gene-positioning

Cellular memory is a critical ability displayed by microorganisms in order to adapt to potentially detrimental environmental fluctuations. In the unicellular eukaryote S. cerevisiae cellular memory can take the form of a faster or a decreased response following repeated stresses in cell population. Using microfluidics and fluorescence time-lapse microscopy, we studied how yeasts respond to short-pulsed hyperosmotic stresses at the single-cell level by analyzing the dynamical behavior of the stress responsive STL1 promoter fused to a fluorescent reporter. We established that pSTL1 shows variability in its successive activations following two repeated short stresses. Despite this variability, most cells displayed a memory of past stresses through a decreased activity of pSTL1 upon repeated stress. Notably, we showed that genomic location is important for the memory effect since promoter displacement to a pericentromeric chromatin domain leads to a decreased transcriptional strength of pSTL1 and to the loss of memory. This study provides a quantitative description of a cellular memory that includes single-cell variability and points towards the contribution of the chromatin structure in stress memory.

genetics↗

bioRxiv2019

Rational programming of history-dependent logic in cellular populations.

Genetic programs operating in an history-dependent fashion are ubiquitous in nature and govern sophisticated processes such as development and differentiation. The ability to systematically and predictably encode such programs would advance the engineering of synthetic organisms and ecosystems with rich signal processing abilities. Here we implement robust, scalable history-dependent programs by distributing the computational labor across a cellular population. Our design is based on recombinase-driven DNA scaffolds expressing different genes according to the order of occurrence of inputs. These multicellular computing systems are highly modular and any program can be built by differential composition of strains containing well-characterized logic scaffolds. We developed an automated workflow that researchers can use to streamline program design and optimization. We anticipate that the history-dependent programs presented here will support many applications using cellular populations for material engineering, biomanufacturing and healthcare.\n\nOne Sentence SummarySystematic and automated frameworks for implementing robust history-dependent genetic programs in cellular populations.

synthetic biology↗

bioRxiv2019

Isolation of persisters enabled by ss-lactam-induced filamentation reveals their single-cell awakening characteristics

When exposed to lethal doses of antibiotics, bacterial populations are most often not completely eradicated. A small number of phenotypic variants, defined as persisters, are refractory to antibiotics and survive treatment. Despite their involvement in relapsing infections caused by major pathogens, processes determining phenotypic switches from and to the persister state largely remain elusive. This is mainly due to the low frequency of persisters in a population and the lack of reliable persistence markers, both hampering studies of persistence at the single-cell level. Problematically, existing methods to enrich for persisters result in samples with very low persister densities and/or a too high abundance of other cell types. Here we present a novel and highly effective persister isolation method involving cephalexin, an antibiotic that induces extensive filamentation of susceptible cells. We show that antibiotic-tolerant cells can easily be separated by size after a short cephalexin treatment, and that the isolated cells are genuine persisters. We used our isolation method to monitor persister outgrowth at the single-cell level in a microfluidic device, thereby conclusively demonstrating that awakening is a stochastic phenomenon. We anticipate that our novel approach can have far-reaching consequences in the persistence field, by allowing single-cell studies at a much higher throughput than previously reported.

microbiology↗