Biology subjects

Alric, B.

Publications and source records attributed to Alric, B..

11 recordsLinked to original sources

bioRxiv2026

Microfluidic Devices for Imaging and Biochemistry Analysis of Microbes Under Mechanical Pressure

Growth-induced pressure arises when proliferating cell populations are confined within rigid microenvironments and is increasingly recognized as a determinant of microbial physiology in soils, biofilms, and host tissues. We present two complementary microfluidic devices that confine microbes within polydimethylsiloxane (PDMS) chambers and apply defined, optically read-out growth-induced pressure of up to 1.5 MPa. The first, the self-closing (SC) chip, confines cells in multiple small chambers accommodating hundreds of cells; it provides excellent nutrient supply and rapid medium exchange, supports single-cell imaging, and allows multiplexing of cellular or chemical conditions. The second, the pressure-recovery (PR) chip, confines cells in a single 5 cm-long chamber accommodating hundreds of thousands of cells; a scalpel-cut step recovers live cells from the channel within minutes for bulk biochemical assays. The two devices share a single two-layer soft-lithography fabrication process and a common brightfield wall-displacement pressure readout. Together, they enable single-cell imaging and bulk biochemical analysis under matched, defined pressure conditions. We illustrate the protocol with two representative validations: rapid {beta}-estradiol-induced transcription in the SC chip, in which nascent transcription foci appear within 5 min independently of the applied pressure, and the PR chip, which produces uniform growth-induced pressure along the entire 5 cm channel and recovers between 0.1x10^6 and 1x10^6 cells per device in a pressure-tunable manner.

biophysics↗

bioRxiv2026

Uncovering aquatic toxicity as a specific stressor among multiple environmental drivers affecting the functional structure of French stream macroinvertebrate communities

O_LISince recent years, freshwater ecosystems such as rivers are subjected to increasing pressures from human-induced drivers of changes, including chemical contamination, warming and nutrient enrichment. Among those, toxic chemicals are particularly concerning, as aquatic contamination is strongly increasing but their effects on ecosystem structure and functioning remain poorly understood and difficult to predict. Yet, those are expected to impact freshwater ecological communities, notably through selecting species exhibiting particular biological traits. A growing literature tested predictions on the effects of multiple environmental drivers, including chemicals, on the functional structure of macroinvertebrate communities, but disentangling the respective influences of the different drivers on the observed patterns usually remains challenging. C_LIO_LIHere, we used multivariate analyses with variation partitioning to estimate the independent and combined effects of toxic contamination, water temperature and nutrient load on the species abundances and biological traits of macroinvertebrate communities in 76 French streams. Toxic contamination was quantified based on the Gammarus feeding inhibition indicator recorded during repeated in situ biotests. We then compared trait responses with expectations from a priori predictions derived from the literature, and looked at the link between taxon turnover and taxonomic and functional diversity metrics using linear models. C_LIO_LIOur results suggest that, when considered independently, each driver had specific impact on invertebrate taxa and biological traits, with different consequences on community composition and diversity. Notably, we showed significant changes in taxonomic composition linked to toxicity, associated with the reduction of both taxonomical and functional richness, but no significant effect on biological trait composition. In contrast, temperature and moreover nutrient load strongly effected traits, but with variables associations with diversity metrics depending on driver. Finally, when all three drivers were considered in combination, patterns were similar to those observed for temperature, suggesting dominance rather than additive effects between drivers. C_LIO_LIOur study reveals particular negative impacts of toxicity on macroinvertebrate communities in contrast with other drivers, which highlights the potential risk posed by contaminants for freshwater biodiversity. C_LI

ecology↗

bioRxiv2025

VEGF-A/C co-stimulation, without shear stress, triggers the polarization of lymphatic microvessels

The lymphatic system maintains interstitial fluid homeostasis and supports immune function through dynamic regulation of its architecture mediated by molecular signals--such as vascular endothelial growth factors (VEGFs)--and physical cues. While VEGFs are known to promote endothelial proliferation, their broader roles in tissue organization remain under investigation. Using a lymphatic vessel-on-a-chip platform, we examine how lymphatic endothelial cells (LECs) respond to VEGF-A, VEGF-C, or their combination. We find that co-stimulation synergistically enhances lymphangiogenic sprouting while preserving barrier integrity. Co-stimulation also induces axial polarization of the tissue along the vessel axis, even in the absence of external mechanical stimuli. This polarization requires activation of the VEGFR2/VEGFR3 heterodimer and is disrupted by inhibition of the Src-dependent mechanotransduction pathway. Further co-stimulation enhances LEC motility and triggers vessel contraction. Modeling suggests that the tubular geometry of the lymphatic monolayer imposes intrinsic mechanical anisotropy--softer in the circumferential than axial direction. This geometrically-encoded stiffness landscape directs cell migration along the stiffer axis, uncovering a form of durotaxis driven by curvature-induced anisotropy. These results highlight a previously unrecognized mechanism by which biochemical and biophysical cues direct lymphatic tissue polarization, offering new insight into how geometry and mechanosensing shape lymphatic function.

bioengineering↗

bioRxiv2025

Intraluminal pressure triggers a rapid and persistent reinforcement of endothelial barriers

In response to mechanical cues, endothelial cells elicit highly sensitive cellular response pathways that contribute to the regulation of the physiology and disorders of the vascular system. However, it remains relatively unexplored how endothelial tissues process and integrate the intraluminal pressure, and in turn regulate the permeation flow across the vessel wall. Leveraging a tissue engineering approach to create microvessels (MVs), we measured real-time permeation flow induced by intraluminal pressures ranging from 0.1 to 2.0 kPa. Our findings reveal that mechanically stimulated MVs strengthen their barrier function within seconds of exposure to pressures below 1 kPa, with this enhanced barrier function persisting for 30 minutes. We demonstrate that this barrier reinforcement is linked to the closure of paracellular gaps. Additionally, we observe that it is associated with, and depends on, actin cytoskeleton reorganization, including the accumulation of stress fibers near intercellular junctions and the broadening of adherence junction protein localization. These findings provide insights into the ability of endothelial tissues to regulate interstitial fluid flow in response to sudden increases in blood pressure.

biophysics↗

bioRxiv2024

Bacterial growth under confinement requires transcriptional adaptation to resist metabolite-induced turgor pressure build-up

Bacterial proliferation often occurs in confined spaces, during biofilm formation, within host cells, or in specific niches during infection, creating mechanical constraints. We investigated how spatial confinement and growth-induced mechanical pressure affect bacterial physiology. Here, we found that, when proliferating in a confining microfluidic-based device with access to nutrients, Escherichia coli cells generate forces in the hundreds of kPa range. This pressure decouples growth and division, producing shorter bacteria with higher protein concentrations. This leads to cytoplasmic crowding, which ultimately arrests division and stalls protein synthesis. In this arrested state, the pressure produced by bacteria keeps increasing. A minimal theoretical model of bacterial growth predicts this novel regime of steady pressure increase in the absence of protein production, that we named overpressurization. In this regime, the Rcs pathway is activated and that abnormal shapes appear in rcs mutant populations only when they reach the overpressurized state. A uropathogenic strain of E. coli displayed the same confined growth phenotypes in vitro and requirement for Rcs in a mice model of urinary tract infection, suggesting that these pressurized regimes are relevant to understand the physiopathology of bacterial infections.

microbiology↗

bioRxiv2024

Intracellular dry mass density increases under growth-induced pressure

Cells that proliferate in confined environments develop mechanical compressive stress, referred to as growth-induced pressure, which inhibits growth and division across various organisms. Recent studies have shown that in these confined spaces, the diffusivity of intracellular nanoparticles decreases. However, the physical mechanisms behind this reduction remain unclear. In this study, we use quantitative phase imaging to measure the refractive index and dry mass density of Saccharomyces cerevisiae cells proliferating under confinement in a microfluidic bioreactor. Our results indicate that the observed decrease in diffusivity can be at least attributed to the intracellular accumulation of macromolecules. Furthermore, the linear scaling between cell content and growth-induced pressure suggests that the concentrations of macromolecules and osmolytes are maintained proportionally under such pressure in S. cerevisiae.

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↗

bioRxiv2022

Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies

The ever-increasing number of available microbial genomes and metagenomes provide new opportunities to investigate the links between niche partitioning and genome evolution in the ocean, notably for the abundant and ubiquitous marine picocyanobacteria Prochlorococcus and Synechococcus. Here, by combining metagenome analyses of the Tara Oceans dataset with comparative genomics, including phyletic patterns and genomic context of individual genes from 256 reference genomes, we first showed that picocyanobacterial communities thriving in different niches possess distinct gene repertoires. We then managed to identify clusters of adjacent genes that display specific distribution patterns in the field (CAGs) and are thus potentially involved in the adaptation to particular environmental niches. Several CAGs are likely involved in the uptake or incorporation of complex organic forms of nutrients, such as guanidine, cyanate, cyanide, pyrimidine or phosphonates, which might be either directly used by cells, for e.g. the biosynthesis of proteins or DNA, or degraded into inorganic nitrogen and/or phosphorus forms. We also highlight the frequent presence of CAGs involved in polysaccharide capsule biosynthesis in Synechococcus populations thriving in both nitrogen- and phosphorus-depleted areas, which are absent in low-iron regions, suggesting that the complexes they encode may be too energy-consuming for picocyanobacteria thriving in these areas. In contrast, Prochlorococcus populations thriving in iron-depleted areas specifically possess an alternative respiratory terminal oxidase, potentially involved in the reduction of Fe(III) into Fe(II). Together, this study provides insights into how these key members of the phytoplankton community might behave in response to ongoing global change. Significance StatementPicocyanobacteria face various environmental conditions in the ocean and numerous studies have shown that genetically distinct ecotypes colonize different niches. Yet the functional basis of their adaptation remains poorly known, essentially due to the large number of genes of yet unknown function, many of which have little or no beneficial effect on fitness. Here, by combining comparative genomics and metagenomics approaches, we have identified not only single genes but also entire gene clusters, potentially involved in niche adaptation. Although being sometimes present in only one or a few sequenced strains, they occur in a large part of the population in specific ecological niches and thus constitute precious targets for elucidating the biochemical function of yet unknown niche-related genes.

microbiology↗

bioRxiv2022

Insight into diatoms diversity at two European coastal sites (LTER-MC in the Mediterranean Sea and SOMLIT-Astan in the Western English Channel) using a DNA metabarcoding approach

Diatoms are among the most successful marine eukaryotic phytoplankton groups. Their diversity has been investigated in the worlds oceans through expeditions and observations carried out from the equator to the poles. Traditionally, diatom species have been distinguished based on morphological characters of their frustules, but high-throughput sequencing offers new, high-resolution data that can be used to re-examine spatial and/or temporal patterns of diversity. Here we investigated diatoms genetic diversity using metabarcoding (18S V4 rRNA gene) obtained along the years 2011 to 2013 at two coastal time series stations (SOMLIT-Astan and LTER-MareChiara) installed respectively off Roscoff in the Western English Channel and in the Gulf of Naples in the Mediterranean Sea. Diatom species pools detected were different, which fitted with previous observations and with our expectations, since these stations are installed in two contrasted pelagic habitats (permanently-mixed versus stratified in summer). However, this analysis also shows a pool of common ASVs among which some are persistent and dominant in both sites. The observed synchronous variations in relative read abundances of shared ASVs assigned to Chaetoceros socialis, C. tenuissimus, Cyclotella, Mediolabrus comicus and Leptocylindrus aporus at the two geographically distant sites could indicate that internal controls of growth rate and sexual reproduction, rather that external environmental parameters are at work.

ecology↗

bioRxiv2021

Macromolecular crowding limits growth under pressure

Cells that grow in confined spaces eventually build up mechanical compressive stress. This growth-induced pressure (GIP) decreases cell growth. GIP is important in a multitude of contexts from cancer[1-3], to microbial infections[4], to biofouling, yet our understanding of its origin and molecular consequences remains limited. Here, we combine microfluidic confinement of the yeast Saccha-romyces cerevisiae[5],with rheological measurements using genetically encoded multimeric nanoparticles (GEMs)[6] to reveal that growth-induced pressure is accompanied with an increase in a key cellular physical property: macromolecular crowding. We develop a fully calibrated model that predicts how increased macromolecular crowding hinders protein expression and thus diminishes cell growth. This model is sufficient to explain the coupling of growth rate to pressure without the need for specific molecular sensors or signaling cascades. As molecular crowding is similar across all domains of life, this could be a deeply conserved mechanism of biomechanical feedback that allows environmental sensing originating from the fundamental physical properties of cells.

biophysics↗

bioRxiv2021

Microwell array-based opto-electrochemical detections revealing co-adaptation of rheological properties and oxygen metabolism in budding yeast

Microdevices composed of microwell arrays integrating nanoelectrodes (OptoElecWell) were developed to achieve dual high-resolution optical and electrochemical detections on single Saccharomyces cerevisiae budding yeast cells. Each array consists in 1.6 x 105 microwells of 8 {micro}m diameter and 5 {micro}m height, with a platinum nanoring electrode for in-situ electrochemistry, all integrated on a transparent thin wafer for further high-resolution live-cell imaging. After optimizing the filling rate, 32% of cells were effectively trapped within microwells. This allowed to analyse S. cerevisiae metabolisms associated with basal respiration while simultaneously measuring optically other cellular parameters. In this study, we focused on the impact of glucose concentration on respiration and intracellular rheology. We found that while oxygen uptake rate decreased with increasing glucose concentration, diffusion of tracer nanoparticles increased. Our OptoElecWell based respiration methodology provided similar results compared to the commercial gold-standard Seahorse XF analyser, while using 20 times lesser biological samples, paving the way to achieve single cell metabolomics. In addition, it facilitates an optical route to monitor the contents within single cells. The proposed device, in combination with the dual detection analysis, opens up new avenues for measuring cellular metabolism, and relating it to various cellular physiological and rheological indicators at single cell level.

biophysics↗