Biology subjects

Aristov, A.

Publications and source records attributed to Aristov, A..

4 recordsLinked to original sources

bioRxiv2025

Extending digital biology: bacterial survival and morphological heterogeneity under antibiotic stress

The morphology of bacteria is modified by antibiotic stress while also serving to survive the antibiotic. However associating morphological descriptors with quantitative measurements of cell survival remains elusive. Here we present a workflow to generate morphological signatures for the progeny of individual cells for 168 different antibiotic conditions. The workflow uses stationary microfluidic droplets, to encapsulate and grow bacteria, and confocal microscopy to image the contents of each droplet. A custom image analysis pipeline is developed to interact with the images in order to label of the morphologies within a subset of the images and train a neural network. The network yields a multidimensional morphological signature for 82000 droplets, showing the co-existence of different morphologies even for the progeny of individual cells. The morphological signatures are different for varying antibiotic type and concentration, thus providing a way to distinguish antibiotics by their mode of action. By combining these morphological signatures with the digital detection of survival within droplets, this workflow can serve to understand the emergence of antibiotic resistance or to identify antimicrobial activity of unknown substances.

bioengineering↗

bioRxiv2024

Culture of pluripotent stem cells in microscale droplets modulates differentiation and tissue patterning towards organoids on chip

1The differentiation of pluripotent stem cells (PSCs) and their self-organization into organoids are influenced by cell-cell interactions mediated by contacts and secreted molecules. These interactions are enhanced in microfluidic droplets due to confinement and small culture volumes. However, a comprehensive study on the culture of PSCs within droplets and the impact of this microenvironment has yet to be conducted. In this study, we present a droplet platform for the 3D culture of PSCs at various stages of cellular commitment. We demonstrate PSC differentiation into the three germ layers and the feasibility of organoid formation within droplets. Our findings reveal that culturing PSCs in confined volumes regulates cell fate decisions, promoting tissue patterning in gastruloids through the sequential induction of growth and migration of distinct differentiated cell populations, and facilitating the self-organization of cardiac organoids. This technological approach provides unique insights into the intrinsic factors regulating tissue self-patterning in vitro. 2 Highlights and eTOC blurbO_ST_ABSHighlightsC_ST_ABSO_LIDroplet microfluidics allows expansion and supports the pluripotency of 3D aggregates of PSCs. C_LIO_LIDroplet microfluidics supports and regulates spontaneous differentiation into embryoid bodies. C_LIO_LIDroplet promotes tissue patterning in gastruloids through the sequential induction of growth and migration of mesoderm followed by ectoderm. C_LIO_LIPerfused microfluidic droplets support long term culture and derivation of organoids on chip. C_LI Vertti-Quintero et al. introduces a microfluidic droplet platform for the 3D culture of pluripotent stem cells (PSCs) at various differentiation stages. The format supports the long term 3D culture and the differentiation of PSCs -either spontaneous or directed-. This "microscale culture" can regulate PSCs fate decision, while promoting tissue pattering -as demonstrated in gastruloids polarization- and allowing self-organization towards cardioids formation.

bioengineering↗

bioRxiv2023

Measuring single-cell susceptibility to antibiotics within monoclonal bacterial populations

Given the emergence of antimicrobial drug resistance, it is critical to understand the heterogeneity of response to an antibiotic within a population of cells. Since the drug can exert a selection pressure that leads to the emergence of resistant phenotypes. To date, neither bulk nor single-cell methods are able to link the heterogeneity of single-cell susceptibility to the population-scale response to antibiotics. Here we present a platform that measures the ability of individual E. coli cells to form small colonies at different ciprofloxacin concentrations, by using anchored microfluidic drops and an image and data analysis pipelines. The microfluidic results are benchmarked against classical microbiology measurements of antibiotic susceptibility, showing an agreement between the pooled microfluidic chip and replated bulk measurements. Further, the experimental likelihood of a single cell to form a colony is used to provide a probabilistic antibiotic susceptibility curve. In addition to the probabilistic viewpoint, the microfluidic format enables the characterization of morphological features over time for a large number of individual cells. This pipeline can be used to compare the response of different bacterial strains to antibiotics with different action mechanisms.

bioengineering↗

bioRxiv2019

Cell-wall synthases contribute to bacterial cell-envelope integrity by actively repairing defects

AbstracCell shape and cell-envelope integrity of bacteria are determined by the peptidoglycan cell wall. In rod-shaped Escherichia coli, two conserved sets of machinery are essential for cell-wall insertion in the cylindrical part of the cell, the Rod complex and the class-A penicillin-binding proteins (aPBPs). While the Rod complex governs rod-like cell shape, aPBP function is less well understood. aPBPs were previously hypothesized to either work in concert with the Rod complex or to independently repair cell-wall defects. First, we demonstrate through modulation of enzyme levels that class-A PBPs do not contribute to rod-like cell shape but are required for mechanical stability, supporting their independent activity. By combining measurements of cell-wall stiffness, cell-wall insertion, and PBP1b motion at the single-molecule level we then demonstrate that PBP1b, the major class-A PBP, contributes to cell-wall integrity by localizing and inserting peptidoglycan in direct response to local cell-wall defects.

microbiology↗