Cell Biophysics Research Articles

β-barrel proteins dictate the effect of core oligosaccharide composition on outer membrane mechanics.

The outer membrane is the defining cellular structure of Gram-negative bacteria, a group that contains many important pathogens like Escherichia coli , Vibrio cholerae , and Pseudomonas aeruginosa . One role of the outer membrane is to block the uptake of small molecules like antibiotics. However, it is becoming increasingly clear that it also functions as a structural exoskeleton that is critical for the cell's ability to cope with internal and external mechanical forces. Here, we carefully dissect the molecular basis for the load-bearing capacity of the outer membrane by screening a set of mutants with a new cell biophysics assay.

Endothelial protein disulfide isomerase A1 enhances membrane stiffness and platelet-endothelium interaction in hyperglycemia via SLC3A2 and LAMC1

BackgroundDiabetes carries an increased risk of cardiovascular disease and thromboembolic events. Upon endothelial dysfunction, platelets bind to endothelial cells to precipitate thrombus formation; however, it is unclear which surface proteins regulate platelet-endothelium interaction. We and others have shown that peri/epicellular protein disulfide isomerase A1 (pecPDI) influences the adhesion and migration of vascular cells. ObjectivesWe investigated whether pecPDI regulates adhesion-related molecules on the surface of endothelial cells and platelets that influence the binding of these cells in hyperglycemia. MethodsImmunofluorescence was used to assess platelet-endothelium interaction in vitro, cytoskeleton reorganization, and focal adhesions. Hydrogen peroxide production was assessed via Amplex Red assays (ThermoFisher Scientific). Cell biophysics was assessed using atomic force microscopy. Secreted proteins of interest were identified through proteomics (secretomics), and targets were knocked down using small interfering RNA. Protein disulfide isomerase A1 (PDI) contribution was assessed using whole-cell PDI or pecPDI inhibitors or small interfering RNA. ResultsPlatelets of healthy donors adhered more onto hyperglycemic human umbilical vein endothelial cells (HUVECs). Endothelial, but not platelet, pecPDI regulated this effect. Hyperglycemic HUVECs showed marked cytoskeleton reorganization, increased H2O2 production, and elongated focal adhesions. Indeed, hyperglycemic HUVECs were stiffer compared with normoglycemic cells. PDI and pecPDI inhibition reversed the abovementioned processes in hyperglycemic cells. A secretomics analysis revealed 8 proteins secreted in a PDI-dependent manner by hyperglycemic cells. Among these, we showed that genetic deletion of LAMC1 and SLC3A2 decreased platelet-endothelium interaction and did not potentiate the effects of PDI inhibitors. ConclusionEndothelial pecPDI regulates platelet-endothelium interaction in hyperglycemia through adhesion-related proteins and alterations in endothelial membrane biophysics.

Substrate stiffness alters layer architecture and biophysics of human induced pluripotent stem cells to modulate their differentiation potential

Lineage-specific differentiation of human induced pluripotent stem cells (hiPSCs) relies on complex interactions between biochemical and physical cues. Here we investigated the ability of hiPSCs to undergo lineage commitment in response to inductive signals and assessed how this competence is modulated by substrate stiffness. We showed that Activin A-induced hiPSC differentiation into mesendoderm and its derivative, definitive endoderm, is enhanced on gel-based substrates softer than glass. This correlated with changes in tight junction formation and extensive cytoskeletal remodeling. Further, live imaging and biophysical studies suggested changes in cell motility and interfacial contacts underlie hiPSC layer reshaping on soft substrates. Finally, we repurposed an ultra-soft silicone gel, which may provide a suitable substrate for culturing hiPSCs at physiological stiffnesses. Our results provide mechanistic insight into how epithelial mechanics dictate the hiPSC response to chemical signals and provide a tool for their efficient differentiation in emerging stem cell therapies.

High-Q WGM microcavity-based optofluidic sensor technologies for biological analysis.

High-quality-factor (Q) optical microcavities have attracted extensive interest due to their unique ability to confine light for resonant circulation at the micrometer scale. Particular attention has been paid to optical whispering-gallery mode (WGM) microcavities to harness their strong light-matter interactions for biological applications. Remarkably, the combination of high-Q optical WGM microcavities with microfluidic technologies can achieve a synergistic effect in the development of high-sensitivity optofluidic sensors for many emerging biological analysis applications, such as the detection of proteins, nucleic acids, viruses, and exosomes. They can also be utilized to investigate the behavior of living cells in human organisms, which may provide new technical solutions for studies in cell biology and biophysics. In this paper, we briefly review recent progress in high-Q microcavity-based optofluidic sensor technologies and their applications in biological analysis.

Mechanisms of Action in FLASH Radiotherapy: A Comprehensive Review of Physicochemical and Biological Processes on Cancerous and Normal Cells.

The advent of FLASH radiotherapy (FLASH-RT) has brought forth a paradigm shift in cancer treatment, showcasing remarkable normal cell sparing effects with ultra-high dose rates (>40 Gy/s). This review delves into the multifaceted mechanisms underpinning the efficacy of FLASH effect, examining both physicochemical and biological hypotheses in cell biophysics. The physicochemical process encompasses oxygen depletion, reactive oxygen species, and free radical recombination. In parallel, the biological process explores the FLASH effect on the immune system and on blood vessels in treatment sites such as the brain, lung, gastrointestinal tract, skin, and subcutaneous tissue. This review investigated the selective targeting of cancer cells and the modulation of the tumor microenvironment through FLASH-RT. Examining these mechanisms, we explore the implications and challenges of integrating FLASH-RT into cancer treatment. The potential to spare normal cells, boost the immune response, and modify the tumor vasculature offers new therapeutic strategies. Despite progress in understanding FLASH-RT, this review highlights knowledge gaps, emphasizing the need for further research to optimize its clinical applications. The synthesis of physicochemical and biological insights serves as a comprehensive resource for cell biology, molecular biology, and biophysics researchers and clinicians navigating the evolution of FLASH-RT in cancer therapy.

Machine learning approach for recognition and morphological analysis of isolated astrocytes in phase contrast microscopy

Astrocytes are glycolytically active cells in the central nervous system playing a crucial role in various brain processes from homeostasis to neurotransmission. Astrocytes possess a complex branched morphology, frequently examined by fluorescent microscopy. However, staining and fixation may impact the properties of astrocytes, thereby affecting the accuracy of the experimental data of astrocytes dynamics and morphology. On the other hand, phase contrast microscopy can be used to study astrocytes morphology without affecting them, but the post-processing of the resulting low-contrast images is challenging. The main result of this work is a novel approach for recognition and morphological analysis of unstained astrocytes based on machine-learning recognition of microscopic images. We conducted a series of experiments involving the cultivation of isolated astrocytes from the rat brain cortex followed by microscopy. Using the proposed approach, we tracked the temporal evolution of the average total length of branches, branching, and area per astrocyte in our experiments. We believe that the proposed approach and the obtained experimental data will be of interest and benefit to the scientific communities in cell biology, biophysics, and machine learning.

Some fall to sleep slowly: cell biophysics and metabolism of quiescence in diatom resting cells.

Some fall to sleep slowly: cell biophysics and metabolism of quiescence in diatom resting cells.

Frequency-dependent membrane polarization across neocortical cell types and subcellular elements by transcranial alternating current stimulation.

Objective.Transcranial alternating current stimulation (tACS) is a non-invasive brain stimulation technique that directly interacts with ongoing brain oscillations in a frequency-dependent manner. However, it remains largely unclear how the cellular effects of tACS vary between cell types and subcellular elements.Approach.In this study, we use a set of morphologically realistic models of neocortical neurons to simulate the cellular response to uniform oscillating electric fields (EFs). We systematically characterize the membrane polarization in the soma, axons, and dendrites with varying field directions, intensities, and frequencies.Main results.Pyramidal cells are more sensitive to axial EF that is roughly parallel to the cortical column, while interneurons are sensitive to axial EF and transverse EF that is tangent to the cortical surface. Membrane polarization in each subcellular element increases linearly with EF intensity, and its slope, i.e. polarization length, highly depends on the stimulation frequency. At each frequency, pyramidal cells are more polarized than interneurons. Axons usually experience the highest polarization, followed by the dendrites and soma. Moreover, a visible frequency resonance presents in the apical dendrites of pyramidal cells, while the other subcellular elements primarily exhibit low-pass filtering properties. In contrast, each subcellular element of interneurons exhibits complex frequency-dependent polarization. Polarization phase in each subcellular element of cortical neurons lags that of field and exhibits high-pass filtering properties. These results demonstrate that the membrane polarization is not only frequency-dependent, but also cell type- and subcellular element-specific. Through relating effective length and ion mechanism with polarization, we emphasize the crucial role of cell morphology and biophysics in determining the frequency-dependent membrane polarization.Significance.Our findings highlight the diverse polarization patterns across cell types as well as subcellular elements, which provide some insights into the tACS cellular effects and should be considered when understanding the neural spiking activity by tACS.

A simple agent-based hybrid model to simulate the biophysics of glioblastoma multiforme cells and the concomitant evolution of the oxygen field

Background and objectives: Glioblastoma multiforme (GBM) is one of the most aggressive cancers of the central nervous system. It is characterized by a high mitotic activity and an infiltrative ability of the glioma cells, neovascularization and necrosis. GBM evolution entails the continuous interplay between heterogeneous cell populations, chemotaxis, and physical cues through different scales. In this work, an agent-based hybrid model is proposed to simulate the coupling of the multiscale biological events involved in the GBM invasion, specifically the individual and collective migration of GBM cells and the concurrent evolution of the oxygen field and phenotypic plasticity. An asset of the formulation is that it is conceptually and computationally simple but allows to reproduce the complexity and the progression of the GBM micro-environment at cell and tissue scales simultaneously. Methods: The migration is reproduced as the result of the interaction between every single cell and its micro-environment. The behavior of each individual cell is formulated through genotypic variables whereas the cell micro-environment is modeled in terms of the oxygen concentration and the cell density surrounding each cell. The collective behavior is formulated at a cellular scale through a flocking model. The phenotypic plasticity of the cells is induced by the micro-environment conditions, considering five phenotypes. Results: The model has been contrasted by benchmark problems and experimental tests showing the ability to reproduce different scenarios of glioma cell migration. In all cases, the individual and collective cell migration and the coupled evolution of both the oxygen field and phenotypic plasticity have been properly simulated. This simple formulation allows to mimic the formation of relevant hallmarks of glioblastoma multiforme, such as the necrotic cores, and to reproduce experimental evidences related to the mitotic activity in pseudopalisades. Conclusions: In the collective migration, the survival of the clusters prevails at the expense of cell mitosis, regardless of the size of the groups, which delays the formation of necrotic foci and reduces the rate of oxygen consumption.

Fluorescence-based multifunctional light sheet imaging flow cytometry for high-throughput optical interrogation of live cells

Multifunctional light sheet imaging flow cytometry of a large population of live cells at high throughput is challenging and requires new technological advancement. Existing cytometry techniques are limited due to point-based illumination that does not allow volume interrogation and biophysical parameter estimation on the go. Here, we propose a multifunctional (multichannel, multisheet and multicolor) imaging cytometry (M3IC) system that employs vertically-aligned multi-sheet array (VAMSA) illumination for interrogating cells flowing simultaneously through multiple microfluidic channels. We studied cancer cells (volume interrogation with organelle-level resolution and high signal-to-background-ratio(SBR)) at high throughput (~2500 nl/min). M3IC system demonstrates organelle-level resolution with a SBR comparable to that of confocal, especially at low flow rates. In addition, the multicolor imaging capability of the system facilitates multi-organelle investigation, determination of critical biophysical parameters, and drug (Paclitaxel) treatment studies on cancer cells. M3IC system is expected to advance the field of fluorescence microscopy, cell biophysics, disease biology and optical physics.

Biological Applications of Thermoplasmonics.

Thermoplasmonics has emerged as an extraordinarily versatile tool with profound applications across various biological domains ranging from medical science to cell biology and biophysics. The key feature of nanoscale plasmonic heating involves remote activation of heating by applying laser irradiation to plasmonic nanostructures that are designed to optimally convert light into heat. This unique capability paves the way for a diverse array of applications, facilitating the exploration of critical biological processes such as cell differentiation, repair, signaling, and protein functionality, and the advancement of biosensing techniques. Of particular significance is the rapid heat cycling that can be achieved through thermoplasmonics, which has ushered in remarkable technical innovations such as accelerated amplification of DNA through quantitative reverse transcription polymerase chain reaction. Finally, medical applications of photothermal therapy have recently completed clinical trials with remarkable results in prostate cancer, which will inevitably lead to the implementation of photothermal therapy for a number of diseases in the future. Within this review, we offer a survey of the latest advancements in the burgeoning field of thermoplasmonics, with a keen emphasis on its transformative applications within the realm of biosciences.

Experiments in micro-patterned model membranes support the narrow escape theory

The narrow escape theory (NET) predicts the escape time distribution of Brownian particles confined to a domain with reflecting borders except for one small window. Applications include molecular activation events in cell biology and biophysics. Specifically, the mean first passage time bar{tau } can be analytically calculated from the size of the domain, the escape window, and the diffusion coefficient of the particles. In this study, we systematically tested the NET in a disc by variation of the escape opening. Our model system consisted of micro-patterned lipid bilayers. For the measurement of bar{tau }, we imaged diffusing fluorescently-labeled lipids using single-molecule fluorescence microscopy. We overcame the lifetime limitation of fluorescent probes by re-scaling the measured time with the fraction of escaped particles. Experiments were complemented by matching stochastic numerical simulations. To conclude, we confirmed the NET prediction in vitro and in silico for the disc geometry in the limit of small escape openings, and we provide a straightforward solution to determine bar{tau } from incomplete experimental traces.

Dual mechanical impact of β-escin on model lipid membranes

Understanding the mechanical behavior of biological membranes is of paramount importance in cell biophysics and in developing new biomaterials for medicine. In this study, we delve into the mechanical impact of β-escin, commonly referred to as escin, a naturally occurring biosurfactant derived from the seeds of the horse chestnut tree. To examine the modulable interaction between escin and dimyristoylphosphatidylcholine (DMPC), which is an archetypical fluid phospholipid and an essential constituent of the cellular fluid membrane, we have used artificial models based on the liquid crystal structure, such as bilayer vesicles and Langmuir monolayers. We have focused on the energetic and kinetic aspects of escin insertion when transversally adsorbed or longitudinally integrated within these model membranes. By employing surface microscopies of epifluorescence and Brewster angle reflectivity, we have elucidated the structural phase behavior of hybrid escin–phospholipid membranes, which exhibit dual mechanical properties characterized by high rigidity and reduced fluidity. Notably, at low temperatures, we observe a soft, glassy rheological behavior reminiscent of liquid crystalline ordered phases, which turns into a fluid-like viscoelasticity resembling more disordered phases at physiological temperatures. The hybrid membranes behave in one way or another as both are driven by an adsorption potential well imposed by escin cohesivity. These intriguing findings are discussed from a physicochemical perspective, highlighting their potential for future pharmacological designs and biomedical applications that exploit the dual mechanical impact of escin on biological membranes.

Nonextensive realizations in interacting ion channels: Implications for mechano-electrical transducer mechanisms

We propose a theoretical model to investigate the thermodynamics of single and coupled two-state ion channels, associated with mechanoelectrical transduction (MET) and hair cell biophysics. The modeling was based on the Tsallis nonextensive statistical mechanics. The choice for a nonextensive framework in modeling ion channels is encouraged on the fact that we take into account the presence of interactions or long-range correlations in the dynamics of single and coupled ion channels. However, the basic assumptions that support Boltzmann–Gibbs statistics, traditionally used to model ion channel dynamics, state that the system is formed by independent or weakly interacting elements. Despite being well studied in many biological systems, the literature has not yet addressed the study of both entropy and mutual information related to isolated or physically interacting pairs of MET channels. Inspired by hair cell biophysics, we show how the presence of nonextensivity, or subadditivity and superadditivity modulates the nonextensive entropy and mutual information as functions of stereocilia displacements. We also observe that the magnitude of the interaction between the two channels, given by a nonextensive parameter, influences the amplitude of the nonextensive joint entropy and mutual information as functions of the hair cell displacements. Finally, we show how nonextensivity regulates the current versus displacement curve for a single and a pair of interacting two-state channels. The present findings shed light on the thermodynamic process involved in the molecular mechanisms of the auditory system.

VII congress of biophysicists of Russia

The problems and results of research in biophysics, which were devoted to the VII Congress of Biophysicists of Russia (Krasnodar, April 17-23, 2023, http://rusbiophysics.ru/db/conf.pl), are discussed. The results of fundamental and applied research in the field of molecular biophysics, cell biophysics, biophysics of complex multicomponent systems were presented at plenary, sectional and poster sessions. The structure and dynamics of biopolymers, the fundamental mechanisms underlying the impact of physicochemical factors on biological systems, membrane and transport processes were actively discussed. Much attention was paid to new experimental methods of biophysical research, methods of bioinformatics, computer and mathematical modeling as essential research tools at all levels of organization of living systems. Along with the fundamental problems of studying the biophysical mechanisms of regulation of processes at the molecular, subcellular and cellular levels, much attention was paid to applied research in the field of biotechnology and environmental monitoring. Works in the field of medical biophysics were especially widely represented. During the Congress, the National Council for Biophysics was formed.

Measuring cell deformation by microfluidics.

Microfluidics is an increasingly popular method for studying cell deformation, with various applications in fields such as cell biology, biophysics, and medical research. Characterizing cell deformation offers insights into fundamental cell processes, such as migration, division, and signaling. This review summarizes recent advances in microfluidic techniques for measuring cellular deformation, including the different types of microfluidic devices and methods used to induce cell deformation. Recent applications of microfluidics-based approaches for studying cell deformation are highlighted. Compared to traditional methods, microfluidic chips can control the direction and velocity of cell flow by establishing microfluidic channels and microcolumn arrays, enabling the measurement of cell shape changes. Overall, microfluidics-based approaches provide a powerful platform for studying cell deformation. It is expected that future developments will lead to more intelligent and diverse microfluidic chips, further promoting the application of microfluidics-based methods in biomedical research, providing more effective tools for disease diagnosis, drug screening, and treatment.

Cells and Materials for Cardiac Repair and Regeneration.

After more than 20 years following the introduction of regenerative medicine to address the problem of cardiac diseases, still questions arise as to the best cell types and materials to use to obtain effective clinical translation. Now that it is definitively clear that the heart does not have a consistent reservoir of stem cells that could give rise to new myocytes, and that there are cells that could contribute, at most, with their pro-angiogenic or immunomodulatory potential, there is fierce debate on what will emerge as the winning strategy. In this regard, new developments in somatic cells' reprogramming, material science and cell biophysics may be of help, not only for protecting the heart from the deleterious consequences of aging, ischemia and metabolic disorders, but also to boost an endogenous regeneration potential that seems to be lost in the adulthood of the human heart.

First person – Olivera Mitevska

ABSTRACT First Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping researchers promote themselves alongside their papers. Olivera Mitevska is first author on ‘ Lis1–dynein drives corona compaction and limits erroneous microtubule attachment at kinetochores’, published in JCS. Olivera conducted the research described in this article while an Undergraduate Research Fellow in Dr Philip Auckland's lab at Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK. She is now a Placement student in the lab of Prof. Zameel Cader at Nuffield Department of Clinical Neurosciences, University of Oxford, UK. She has broad interests in cell and molecular biology; currently she is working on elucidating circadian biology in the CNS as part of a professional placement on the MSci Pharmacology with Professional Placement Year course at King's College London.

First person – Lilian Sluimer

ABSTRACT First Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping researchers promote themselves alongside their papers. Lilian Sluimer is first author on ‘ SKOR1 mediates FER kinase-dependent invasive growth of breast cancer cells’, published in JCS. Lilian conducted the research described in this article while working on this research as a first-year master's student and continued working on this project as a research technician for a year in Patrick Derksen's lab at UMC Utrecht, The Netherlands. She is now a PhD student in the lab of Anna Akhmanova at the Division of Cell Biology, Neurobiology and Biophysics, Utrecht University, The Netherlands, investigating the organization and dynamics of cytoskeletal microtubule networks in different cellular systems.

First person – Sherman Foo

ABSTRACT First Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping researchers promote themselves alongside their papers. Sherman Foo is first author on ‘ Diacylglycerol at the inner nuclear membrane fuels nuclear envelope expansion in closed mitosis’, published in JCS. Sherman conducted the research described in this article while a PhD student in the labs of Snezhana Oliferenko (The Francis Crick Institute, London, UK, and Randall Centre for Cell and Molecular Biophysics, King's College London, UK) and Markus R. Wenk (Singapore Lipidomics Incubator, National University of Singapore). He is now a postdoc in the lab of Buzz Baum at Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK, where he is currently studying cellular organization of hyperthermophilic archaea, with a particular focus on the surface layer and cell cycle of Sulfolobus acidocaldarius.