Biology subjects

Kotar, J.

Publications and source records attributed to Kotar, J..

18 recordsLinked to original sources

bioRxiv2026

Robust High-Throughput Flickering Spectroscopy for Measurements of Red Blood Cell Membrane Mechanics

The mechanical properties of red blood cell (RBC) membranes are critical to their function in oxygen delivery, and changes to these properties as RBCs age affect their journey around the circulatory system, including clearance by the spleen. Such changes can also have significant health effects,including in cardiovascular disease and on the interactions between RBCs and malaria parasites. The function of RBCs requires them to be very soft, which together with the small size of the cells brings the energy required for measurable deformation of the membrane into the range of typical thermal energies. Red Blood Cells can be observed to flicker under optical microscopy, and these shape fluctuations can be quantified and used to obtain key biophysical parameters such as the tension and bending modulus of the membrane. Typically the shape of the cell's equator is extracted, and the mean power spectrum is obtained by time-averaging the power present in the normal modes of the thermal fluctuations. Flickering spectroscopy has been used extensively on RBCs, but has so far been very low throughput and with some technical limitations. Here we address issues related to active versus passive fluctuations, focusing and optics, camera exposure and sampling, and fast contour detection. In combination with an automated imaging system it is possible to measure thousands of cells in one day, with no user input. We validate this new pipeline by chemical modification of RBC mechanics, and by comparison with simulated fluctuations including each confounding effect. The methods and codes for this robust flickering analysis will allow consistent measurements across labs.

biophysics↗

bioRxiv2025

Ionic environment and nutrients affect the cysB-dependent conditional susceptibility of E. coli to mecillinam

Antibiotic efficacy is influenced by environmental context. Urinary E. coli isolates lacking a functional cysB gene have been shown to be resistant to the {beta}-lactam antibiotic mecillinam under high-osmolarity conditions, suggesting that increased fluid intake might synergize with drug treatment. In this study, we further explore E. coli susceptibility to mecillinam across growth conditions. We show that while osmolarity has a mild protective effect on cysB knockout and reference strain, it is the presence of certain salts that leads to the resistant phenotype in the mutant. Such conditional resistance is specific to mecillinam and rapidly wanes when salts are removed. In agreement with our previous work showing that slow growing cells escape mecillinam-induced bursting by maintaining a small size, for both strains we observe low susceptibility to mecillinam in scarcely nutritious pooled human urine. As we supplement urine with nutrients, we observe a sharp transition to susceptibility when growth rate surpasses 0.6 h-1. Growth in the presence of salt or uncharged osmolites decreases cell size of both reference strain and cysB knockout offering a potential explanation to the observed mild protective effects of osmolarity. Our findings give insights into the mechanism of cysB dependent susceptibility to mecillinam and, due to the dual impact of nutrients and osmolites on treatment, allow us to reformulate ideas on potential diet recommendations. While increased fluid intake will decrease urine osmolarity, it will also reduce nutrient content, limiting mecillinam efficacy. We suggest instead that reducing sodium intake during mecillinam treatment might avoid this trade-off.

microbiology↗

bioRxiv2025

Microfluidic Platform for Automatic Quantification of Malaria Parasite Invasion Under Physiological Flow Conditions

Understanding the impact of forces generated by blood flow on biological processes in the circulatory system, such as the invasion of human red blood cells by malaria parasites, is currently limited by the lack of experimental systems that integrate them. Recent systematic quantification of the growth of Plasmodium falciparum, the species that causes the majority of malaria mortality, under a range of shaking conditions has shown that parasite invasion of erythrocytes is affected by the shear stress to which the interacting P. falciparum merozoites and their target red blood cells are exposed. Blood flow could similarly impact shear stress and therefore invasion in vivo, but there is currently no method to test the impact of flow-induced forces on parasite invasion. We have developed a microfluidic device with four channels, each with dimensions similar to those of a post-capillary venule, but with different flow velocities. Highly synchronised P. falciparum parasites are injected into the device, and parasite egress and invasion rates are quantified using newly developed custom video analysis, which fully automates cell type identification and trajectory tracking. The device was tested with both wild-type P. falciparum lines and lines in which genes encoding proteins involved in parasite invasion had been deleted. Deletion of Erythrocyte Binding Antigen 175 (PfEBA175) has a significant impact on invasion under flow, but not in static culture. These findings establish for the first time that flow conditions can critically affect parasite invasion in a genotype-dependent manner. The method can be applied to other biological processes affected by fluid motion, such as cell adhesion, migration, and mechanotransduction.

microbiology↗

bioRxiv2025

Cilia dynamics creates a dynamic barrier to penetration of the periciliary layer in human airway epithelia

The ciliated epithelium of the human respiratory tract is covered by the airway surface liquid (ASL), a protective fluid consisting of two layers: the periciliary layer (PCL), where motile cilia reside and generate fluid flow, and an overlying mucus layer. The complex structure and stratified nature of the PCL complicate both the prediction and quantification of fluid flow at the scale of individual or small groups of cilia, making it difficult to connect microscopic flows to macroscopic clearance. To tackle this challenge, we developed a novel methodology that involves un-caging a fluorescent compound to trace the flow field within the PCL. Fluorescence is activated at micrometric spots within the cilia layer, and displacement vectors and diffusion are recorded using high-speed video. Our experiments reveal a complex fluid transport pattern, with displacement velocity along the epithelial surface varying due to a non-uniform vertical flow field. Additionally, we observed that cilia expel fluid at their tips, a mechanism likely aimed at preventing pathogen access to the epithelium. Simulations, where cilia are modeled as arrays of rigid rods with length asymmetry, support these findings and offer new insights into the dynamics of fluid transport in the respiratory tract and the critical role of cilia coordination. Significance StatementThis study introduces an experimental pipeline to investigate fluid velocity and diffusion within the PCL of the human respiratory tract. By integrating experimental data with simulations of ciliary motion, we offer a robust framework to understand how cilia, depending on their collective beating properties, propel periciliary fluid in this structurally and dynamically complex environment. Our findings significantly expand the understanding of ciliary function, revealing that when cilia are beating coherently near cilia tips fluid is actively driven away from the epithelial surface. This suggests that coordinated cilia movement not only plays a key role in maintaining respiratory health by clearing mucus, but may also provide a dynamic barrier against pathogen entry.

biophysics↗

bioRxiv2025

Hyphal growth determines spatial organization and coexistence in a pathogenic polymicrobial community within alveoli-like geometries

The bodies of macroorganisms host microbes living in multi-species communities. Sequencing approaches have revealed that different organs host different microbiota and tend to be infected by different pathogens, drawing correlations between environmental parameters at the organ level and microbial composition. However, less is known about the microscale dimension of microbial ecology, particularly during infection. In this study, we focus on the role of microscale spatial structure, studying its influence on the ecology of a polymicrobial infection of P. aeruginosa, S. aureus and C. albicans. Although these pathogens are commonly found together in the lungs of chronically ill patients, it is unclear whether they coexist or compete and segregate in different niches. We find that, while P. aeruginosa quickly outcompetes C. albicans and S. aureus on large surfaces, robust spatial organization and coexistence emerges in microfluidic microchambers that mimic the spatial characteristics of alveoli. In these microenvironments, slowly growing C. albicans is able to leverage fast eccentric hyphal growth to conquer boundary spaces, where it establishes itself excluding the other pathogens. We show that the emerging spatial patterning is robust to changes in the virulence of the community, enabling coexistence and potentially determining infection severity and outcomes. Our findings reveal a previously unrecognized role of mechanical forces in shaping infection dynamics, suggesting that microenvironmental structure is a critical determinant of pathogen coexistence, virulence, and treatment outcomes. Because adaptations, such as changes in morphology, are widespread among microbes, these results are generalizable to other ecologies and environments.

microbiology↗

bioRxiv2024

Antibiotics change the growth rate heterogeneity and morphology of bacteria

A better understanding of the system-level effects of antibiotics is necessary to fight the rise of antibiotic resistance. Utilising the Multipad Agarose Plate (MAP), we monitor the growth rate and cell morphology of three clinically relevant species (E.coli, S.aureus and P.aeruginosa) after exposure to 11 different concentrations of 13 antibiotics (for a total of 24 microbe-antibiotic combinations). As the drug dose approaches the MIC and regardless of the mode of action, our results show a consistent increase in growth rate heterogeneity. Remarkably, drugs that affect protein synthesis consistently show the opposite trend, reducing heterogeneity. We hypothesize that growth rate heterogeneity under antibiotic treatment might therefore depend on the functional distance of the target from ribosomal activity, which is key in determining growth rate. Low heterogeneity is desirable from a clinical perspective, as the opposite is often associated to persistence and antibiotic survival. For all of the antibiotics and species tested, we also find a striking and non-trivial correlation between morphological alterations and growth inhibition. This observation allows us to introduce a new morphological parameter, MOR50, that enables the estimation of minimum inhibitory concentration (MIC) for antibiotic susceptibility testing (AST) with a single snapshot after 2.5 hours of incubation. In addition to introducing a novel, resource-efficient, rapid AST method, our findings shed new light on the effects of antibiotic perturbations on bacteria at the system level that might inform treatment design.

microbiology↗

bioRxiv2024

Combined thermodynamic and time-resolved structural analysis of interactions between AP2 and biomimetic plasma membranes provides insights into clathrin-mediated endocytosis

Clathrin mediated endocytosis (CME) is the main mechanism for swift and selective uptake of proteins into eukaryotic cells. CME is initiated by recruitment to the plasma membrane (PM) of the adaptor protein AP2, which recognizes the PM-associated lipid PtdIns(4,5)P2, as well as the protein cargo to be internalized. Nonetheless, many aspects of this process remain unclear due to their in vivo complexity. Here, a thermodynamic and time-resolved structural analysis of AP2 binding to different biomimetic PM was undertaken under physiological conditions using a combination of neutron reflectometry, interfacial tensiometry and rheology, and atomic force microscopy. The resultant in vitro data replicated previous in vivo observations, as well as yielded biophysical insights into normal and aborted CME. The presence of cargo may not be pivotal for the "activating" conformational change of AP2. However, the presence of cargo extends AP2s residence time on the membrane surface, due to slower on- and off-rates, thereby tentatively giving sufficient time for CME to proceed fully. Moreover, upon interaction with AP2, phospholipid lateral diffusion decreases markedly, inducing a gel phase attributed to creating a percolated network involving AP2 on the membrane, which could potentially serve as a mechanism for modulating subsequent clathrin binding.

biophysics↗

bioRxiv2024

Optical tweezers reveal that PfEBA and PfRH ligands, not PfMSP1, play a central role in Plasmodium-falciparum merozoite-erythrocyte attachment

Malaria pathogenesis and parasite multiplication both depend on the ability of Plasmodium falciparum merozoites to invade human erythrocytes. Invasion is a complex multi-step process that is known to involve multiple P. falciparum proteins but dissecting the precise role of individual proteins has to date been limited by the availability of quantifiable phenotypic assays. In this study, we apply a new approach to assigning function to invasion proteins by using optical tweezers to directly manipulate recently egressed merozoites and erythrocytes and quantify the strength of attachment between them, as well as the frequency with which such attachments occur. Using a range of inhibitors, antibodies, and genetically modified P. falciparum strains, we quantitated the contribution of individual P. falciparum proteins to these merozoite-erythrocyte attachment phenotypes for the first time. Most of the interactions investigated did not affect the force needed to pull merozoites and erythrocytes apart, including loss of the major P. falciparum merozoite surface protein PfMSP1 and PfGAP45, part of the glideosome actinomyosin motor complex. The only factors that significantly reduced the strength of merozoite-erythrocyte attachment were ones that disrupted the function of members of the EBA-175 like Antigen (PfEBA) family and Reticulocyte Binding Protein Homologue (PfRH) invasion ligand families. While these assays also reinforced the known redundancy within these families, with the deletion of some ligands not impacting detachment force, it appears that the PfEBA/PfRH families play a central role in merozoite attachment, not the major merozoite surface protein PfMSP1. Author summaryMalaria is a devastating disease caused by a parasitic infection. The deadliest species is Plasmodium falciparum, which causes more than 600,000 deaths annually. The parasites life cycle is complex, but all the symptoms of malaria are caused when the parasites replicate in human red blood cells. Replication depends on the invasion of the red blood cells by the parasites which is a complex process involving multiple molecular interactions and multiple steps. Invasion begins with the attachment of the parasite to the red blood cell, making this step of particular interest in the development of new therapeutics. We assessed which interactions are key to the strength of attachment using an optical tweezer assay, which allowed us to directly measure the binding force between individual parasites and red blood cells whilst using a range of molecular and genetic tools that target specific interactions known to have a role in invasion. This showed that loss of a protein commonly thought to be critical to the early stages of binding (PfMSP1) had no effect on attachment strength, whereas disruptions of several members from two families of proteins (the Erythrocyte Binding Like protein family and the reticulocyte binding-like protein family) affect attachment strength.

molecular biology↗

bioRxiv2024

Multipad Agarose Plate (MAP): A Rapid and High-Throughput Approach for Antibiotic Susceptibility Testing

We describe a phenotypic antibiotic susceptibility testing (AST) method that can provide an eightfold speedup in turnaround time compared to the current clinical standard by leveraging advances in microscopy and single-cell imaging. A newly developed growth plate containing 96 agarose pads, termed the Multipad Agarose Plate (MAP), can be assembled at low costs. Pads can be prepared with dilution series of antibiotics. Bacteria are seeded on the pads and automatically imaged using brightfield microscopy, with a fully automated segmentation pipeline quantifying microcolony formation and growth rate. Using a test set of nine antibiotics with very different targets, we demonstrate that accurate minimum inhibitory concentration (MIC) measurements can be performed based on the growth rate of microcolonies within three hours of incubation with the antibiotic. Faster, reliable and high throughput methods for AST, such as MAP, could improve patient care by expediting treatment initiation and alleviating the burden of antimicrobial resistance.

microbiology↗

bioRxiv2023

Surface crosslinking of virus-like particles increases resistance to proteases, low pH and mechanical stress for mucosal applications

AbstractVirus-like particles (VLPs) are emerging as nano-scaffolds in a variety of biomedical applications including the delivery of vaccine antigens to mucosal surfaces. These soft, colloidal, and proteinaceous structures (capsids) are nevertheless susceptible to mucosal environmental factors which limit their usefulness. We addressed this issue by crosslinking multiple capsid surface reactive residues using polyethylene glycol tethers. Surface crosslinking enhanced the colloidal stability and mechanical strength of VLPs against low pH, proteases, and mechanical agitation, while it did not interfere with function as vaccine. Chemical crosslinking thus offers a viable means to enhance the resilience of VLPs in mucosal applications.

biophysics↗

bioRxiv2023

Assessing motile cilia coverage and beat frequency in mammalian in-vitro cell culture tissues

Cilia density, distribution and beating frequency are important parameters lung tissues, for example in diagnostics of Primary Ciliary Dyskinesia, and in the study of in vitro models, e.g. derived from induced Pluripotent Stem Cells. Video microscopy can be used to characterise these parameters, but most tools available at the moment are limited in the type of information they can provide, usually only describing the ciliary beat frequency of very small areas, while requiring human intervention and training for their use. We propose a novel and open source method to fully characterise cilia beating frequency and motile cilia coverage in an automated fashion without user intervention. We demonstrate the ability to differentiate between different coverage densities, identifying even small patches of cilia in a larger field of view, and to fully characterise the cilia beating frequency of all moving areas. We also show that the method can be used to combine multiple fields of view to better describe a sample without relying on small pre-selected regions of interest. This is released with a simple graphical user interface for file handling, enabling a full analysis of individual fields of view in a few minutes on a typical personal computer.

biophysics↗

bioRxiv2023

A synthetic signalling network imitating the action of immune cells in response to bacterial metabolism

State-of-the-art bottom-up synthetic biology allows us to replicate many basic biological functions in artificial cell-like devices. To mimic more complex behaviours, however, artificial cells would need to perform many of these functions in a synergistic and coordinated fashion, which remains elusive. Here we considered a sophisticated biological response, namely the capture and deactivation of pathogens by neutrophil immune cells, through the process of netosis. We designed a consortium consisting of two synthetic agents - responsive DNA-based particles and antibiotic-loaded lipid vesicles - whose coordinated action mimics the sought immune-like response when triggered by bacterial metabolism. The artificial netosis-like response emerges from a series of interlinked sensing and communication pathways between the live and synthetic agents, and translates into both physical and chemical antimicrobial actions, namely bacteria immobilisation and exposure to antibiotics. Our results demonstrate how advanced life-like responses can be prescribed with a relatively small number of synthetic molecular components, and outlines a new strategy for artificial-cell-based antimicrobial solutions.

synthetic biology↗

bioRxiv2022

Reaction-diffusion patterning of DNA-based artificial cells

Biological cells display complex internal architectures, with distinct micro environments that establish the chemical heterogeneity needed to sustain cellular functions. The continued efforts to create advanced cell mimics - artificial cells - demands strategies to construct similarly heterogeneous structures with localized functionalities. Here, we introduce a platform for constructing membrane-less artificial cells from the self-assembly of synthetic DNA nanostructures, in which internal domains can be established thanks to prescribed reaction-diffusion waves. The method, rationalized through numerical modeling, enables the formation of up to five distinct, concentric environments, in which functional moieties can be localized. As a proof-of-concept, we apply this platform to build DNA-based artificial cells in which a prototypical nucleus synthesizes fluorescent RNA aptamers, which then accumulate in a surrounding storage shell, thus demonstrating spatial segregation of functionalities reminiscent of that observed in biological cells.

synthetic biology↗

bioRxiv2019

Diurnal variations in the motility of algal populations

The motility of microalgae has been studied extensively, particularly in model microorganisms such as Chlamy-domonas reinhardtii. For this and other microalgal species, diurnal cycles are well-known to control the metabolism, growth and cell division. Diurnal variations, however, have been largely neglected in quantitative studies of motility. Here, we demonstrate using tracking microscopy how the motility statistics of C. reinhardtii are modulated by diurnal cycles. We discovered that the mean swimming speed is greater during the dark period of a diurnal cycle. From this measurement, using a hydrodynamic power balance, we conjecture that this is a result of the mean flagellar beat frequency being modulated by the flagellar ATP. Our measurements also quantify the diurnal variations of the orientational and gravitactic transport of C. reinhardtii. We discuss the implications of our frequency results in the context of cellular bioenergetics. Further, we explore the population-level consequences of diurnal variations of motility statistics by evaluating a prediction for how the gravitactic steady state changes with time during a diurnal cycle. SIGNIFICANCEWe report tracking microscopy measurements which demonstrate that the mean swimming speed of C. reinhardtii is significantly greater during the dark period of a diurnal cycle. Using hydrodynamic (low Reynolds number) power balance, we also inferred the mean flagellar beat frequency from the swimming speed, hypothesising that the observed variations in this frequency correlate with the diurnal regulation of flagellar ATP. Diurnal variations of the orientational and gravitactic transport of C. reinhardtii were also quantified and used in a continuum model to predict that, at the population scale, the steady state vertical distribution of C. reinhardtii is broader during the dark period. Our findings could have significant implications for microalgal biotechnologies, e.g. microalgal harvesting, and plankton migration in the ocean.

biophysics↗

bioRxiv2019

Synchronization of mammalian motile cilia in the brain with hydrodynamic forces

Motile cilia are widespread across the animal and plant kingdoms, displaying complex collective dynamics central to their physiology. Their coordination mechanism is not generally understood, with pre-vious work mainly focusing on algae and protists. We study here the synchronization of cilia beat in multiciliated cells from brain ven-tricles. The response to controlled oscillatory external flows shows that strong flows at a similar frequency to the actively beating cilia can entrain cilia oscillations. We find that the hydrodynamic forces required for this entrainment strongly depend on the number of cilia per cell. Cells with few cilia (up to five) can be entrained at flows comparable to the cilia-driven flows reported in vivo. Simulations of a minimal model of cilia interacting hydrodynamically show the same trends observed in cilia. Our results suggest that hydrody-namic forces between cilia are sufficient to be the mechanism behind the synchronization of mammalian brain cilia dynamics.\n\nSignificance StatementIt is shown experimentally, and also reproducing key qualitative results in a minimal mechanistic model simulated numerically, that in the motile cilia of the brain hydrodynamic forces of the magnitude that cilia themselves can generate are sufficient to establish the coordination of dynamics which is so crucial phys-iologically. This is the first experiment of its kind on multicilated cells, the key result is the unexpected importance of cilia num-ber per cell, with cells with fewer cilia much more susceptible to external flows. This finding changes the way in which we think about the question of collective cilia beating - it is not correct to simply examine isolated cilia and draw conclusions about the behaviour of cilia assemblies in multiciliated cells.

biophysics↗

bioRxiv2019

A How-To guide to: Quantitative high-speed video profiling to discriminate between variants of primary ciliary dyskinesia

This document presents detailed steps to analysing the waveforms of beating cilia, measured in high speed video microscopy. We show that in the case of PCD caused by mutations in DNAH11 and HYDIN the classification by a handful of parameters describing ciliary dynamics allows to distinguish the genotype, as well as (much more easily) distinguishing healthy from PCD samples. This document is intended to complement the brief highlight (1) and presents the details of the datasets used in that letter.

cell biology↗

bioRxiv2018

Red blood cell tension controls Plasmodium falciparum invasion and protects against severe malaria in the Dantu blood group

Malaria has had a major effect on the human genome, with many protective polymorphisms such as sickle cell trait having been selected to high frequencies in malaria endemic regions1, 2. Recently, we showed that a novel blood group variant, Dantu, provides 74% protection against all forms of severe malaria in homozygous individuals3-5. This is a similar degree of protection to sickle cell trait and considerably greater than the most advanced malaria vaccine, but until now the mechanism of protection has been unknown. In the current study, we demonstrate a significant impact of Dantu on the ability of Plasmodium falciparum merozoites to invade RBCs. The Dantu variant was associated with extensive changes to the RBC surface protein repertoire, but unexpectedly the malaria protective effect did not correlate with specific RBC-parasite receptor-ligand interactions. By following invasion using video microscopy, we found a strong link between RBC tension and parasite invasion and, even in non-Dantu RBCs, identified a tension threshold above which RBC invasion did not occur. Dantu RBCs had higher average tension, meaning that a higher proportion of Dantu RBCs could not be invaded. These findings not only provide an explanation for the protective effect of Dantu against severe malaria, but also provide fresh insights into the essential process of P. falciparum parasite invasion, and how invasion efficiency varies across the heterogenous populations of RBCs that are present both within and between individuals.

genetics↗

bioRxiv2017

Phenotyping ciliary dynamics and coordination in response to CFTR-modulators in Cystic Fibrosis respiratory epithelial cells

The diagnosis and treatment of respiratory disorders are challenging and would benefit from new approaches to systematically assess ciliary beating dynamics and to test new drugs. A novel approach based on multiscale differential dynamic microscopy (multi-DDM) is shown to quantitatively assess collective beating of cilia in a non-biased automated manner, in human airway epithelial cells (HAECs) derived from subjects with cystic fibrosis (CF) and grown in 2D air-liquid interface culture. Multi-DDM can readily detect changes in both ciliary beat frequency (CBF) and cilia coordination that result from perturbations to the mucosal layer. The efficacy of three CFTR-modulating treatments is investigated: ivacaftor (VX-770) with lumacaftor (VX-809), VX-809 alone and Thymosin alpha 1 (T1) alone. All three treatments restore coordination of cilia beating in the CF cells, albeit to varying degrees. We argue cilia are affected by these treatments through the physical properties of the mucus. Phenotyping cilia dynamics through multi-DDM provides novel insight into the response of ciliary beating following treatment with drugs, and has application in the broader context of respiratory disease and for drug screening.\n\nOne sentence summaryA semi-automated and unbiased assay based on multiscale differential dynamic microscopy (multi-DDM) detects changes in the coordination and frequency of ciliary beating in F508del/F508del primary human airway cells under different conditions and in response to CFTR-modulating compounds.

physiology↗