Biophysical journal最新文献

{"title":"Computing whole embryo strain maps during gastrulation.","authors":"David Denberg, Xiaoxuan Zhang, Tomer Stern, Eric Wieschaus, Krishna Garikipati, Stanislav Y Shvartsman","doi":"10.1016/j.bpj.2024.10.003","DOIUrl":"10.1016/j.bpj.2024.10.003","url":null,"abstract":"<p><p>Gastrulation is a critical process during embryonic development that transforms a single-layered blastula into a multilayered embryo with distinct germ layers, which eventually give rise to all the tissues and organs of the organism. Studies across species have uncovered the mechanisms underlying the building blocks of gastrulation movements, such as localized in-plane and out-of-plane epithelial deformations. The next challenge is to understand dynamics on the scale of the embryo: this requires quantifying strain tensors, which rigorously describe the differences between the deformed configurations taken on by local clusters of cells at time instants of observation and their reference configuration at an initial time. We present a systematic strategy for computing such tensors from the local dynamics of cell clusters, which are chosen across the embryo from several regions whose morphogenetic fate is central to viable gastrulation. As an application of our approach, we demonstrate a strategy of identifying distinct Drosophila morphological domains using strain tensors.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"3911-3922"},"PeriodicalIF":3.2,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11617634/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142387631","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unexpected asymmetric distribution of cholesterol and phospholipids in equilibrium model membranes.","authors":"Yuli Zhu, Lionel Porcar, Thirupathi Ravula, Krishna C Batchu, Tera L Lavoie, Ying Liu, Ursula Perez-Salas","doi":"10.1016/j.bpj.2024.10.004","DOIUrl":"10.1016/j.bpj.2024.10.004","url":null,"abstract":"<p><p>Lipid compositional asymmetry across the leaflets of the plasma membrane is an ubiquitous feature in eukaryotic cells. How this asymmetry is maintained is thought to be primarily controlled by active transport of lipids between leaflets. This strategy is facilitated by the fact that long-tail phospholipids and sphingolipids diffuse through the lipid bilayer slowly-taking many hours or days. However, a lipid like cholesterol-which is the most abundant lipid in the plasma membrane of animal cells-has been harder to pinpoint in terms of its favored side. In this work we show that, when a saturated lipid is added to a mix of the unsaturated lipid palmitoyl-oleoyl-phosphatidylcholine (POPC) and cholesterol, both cholesterol and the long-tail phospholipids organize asymmetrically across the membrane's leaflets naturally. In these extruded unilamellar vesicles, most cholesterol as well as the saturated lipid-dipalmitoylphosphatidylcholine or sphingomyelin-segregated to the inner leaflet while POPC preferentially localized in the outer leaflet. This asymmetric arrangement generated a slight phospholipid number imbalance favoring the outer leaflet and thus opposite to where cholesterol and the saturated lipids preferentially partitioned. These results were obtained using magic-angle spinning nuclear magnetic resonance (MAS NMR) in combination with small-angle neutron scattering (SANS) using isotope labeling to differentiate lipid species. We suggest that sidedness in membranes can be driven by thermodynamic processes. In addition, our MAS NMR results show that the lower bound for cholesterol's flip-flop half-time at 45°C is 10 ms, which is at least two orders of magnitude slower than current MD simulations predict. This result stands in stark contrast to previous work that suggested that cholesterol's flip-flop half-time at 37°C has an upper bound of 10 ms.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"3923-3934"},"PeriodicalIF":3.2,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11617633/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142399238","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcribing RNA polymerases: Dynamics of twin supercoiled domains.","authors":"Marc Joyeux","doi":"10.1016/j.bpj.2024.10.002","DOIUrl":"10.1016/j.bpj.2024.10.002","url":null,"abstract":"<p><p>Gene transcription by an RNA polymerase (RNAP) enzyme requires that double-stranded DNA be locally and transiently opened, which results in an increase of DNA supercoiling downstream of the RNAP and a decrease of supercoiling upstream of it. When the DNA is initially torsionally relaxed and the RNAP experiences sufficiently large rotational drag, these variations lead to positively supercoiled plectonemes ahead of the RNAPs and negatively supercoiled ones behind it, a feature known as \"twin supercoiled domain\" (TSD). This work aims at deciphering into some more detail the torsional dynamics of circular DNA molecules being transcribed by RNAP enzymes. To this end, we performed Brownian dynamics simulations with a specially designed coarse-grained model. Depending on the superhelical density of the DNA molecule and the ratio of RNAP's twist injection rate and rotational relaxation speed, simulations reveal a rich panel of behaviors, which sometimes differ markedly from the crude TSD picture. In particular, for sufficiently slow rotational relaxation speed, positively supercoiled plectonemes never form ahead of an RNAP that transcribes a DNA molecule with physiological negative supercoiling. Rather, negatively supercoiled plectonemes form almost periodically at the upstream side of the RNAP and grow up to a certain length before detaching from the RNAP and destabilizing rapidly. The extent to which topological barriers hinder the dynamics of TSDs is also discussed.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"3898-3910"},"PeriodicalIF":3.2,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11617637/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142375033","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Accurate drift-invariant single-molecule force calibration using the Hadamard variance.","authors":"Stefanie D Pritzl, Alptuğ Ulugöl, Caroline Körösy, Laura Filion, Jan Lipfert","doi":"10.1016/j.bpj.2024.10.008","DOIUrl":"10.1016/j.bpj.2024.10.008","url":null,"abstract":"<p><p>Single-molecule force spectroscopy (SMFS) techniques play a pivotal role in unraveling the mechanics and conformational transitions of biological macromolecules under external forces. Among these techniques, multiplexed magnetic tweezers (MT) are particularly well suited to probe very small forces, ≤1 pN, critical for studying noncovalent interactions and regulatory conformational changes at the single-molecule level. However, to apply and measure such small forces, a reliable and accurate force-calibration procedure is crucial. Here, we introduce a new approach to calibrate MT based on thermal motion using the Hadamard variance (HV). To test our method, we perform bead-tether Brownian dynamics simulations that mimic our experimental system and compare the performance of the HV method against two established techniques: power spectral density (PSD) and Allan variance (AV) analyses. Our analysis includes an assessment of each method's ability to mitigate common sources of additive noise, such as white and pink noise, as well as drift, which often complicate experimental data analysis. We find that the HV method exhibits overall similar or higher precision and accuracy, yielding lower force estimation errors across a wide range of signal-to-noise ratios (SNRs) and drift speeds compared with the PSD and AV methods. Notably, the HV method remains robust against drift, maintaining consistent uncertainty levels across the entire studied SNR and drift speed spectrum. We also explore the HV method using experimental MT data, where we find overall smaller force estimation errors compared with PSD and AV approaches. Overall, the HV method offers a robust method for achieving sub-pN resolution and precision in multiplexed MT measurements. Its potential extends to other SMFS techniques, presenting exciting opportunities for advancing our understanding of mechanosensitivity and force generation in biological systems. To make our methods widely accessible to the research community, we provide a well-documented Python implementation of the HV method as an extension to the Tweezepy package.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"3964-3976"},"PeriodicalIF":3.2,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11617635/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142543437","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characteristic frequencies of localized stress relaxation in scaling-law rheology of living cells.","authors":"Jiu-Tao Hang, Huajian Gao, Guang-Kui Xu","doi":"10.1016/j.bpj.2024.11.015","DOIUrl":"10.1016/j.bpj.2024.11.015","url":null,"abstract":"<p><p>Living cells are known to exhibit power-law viscoelastic responses and localized stress relaxation behaviors in the frequency spectrum. However, the precise interplay between molecular-scale cytoskeletal dynamics and macroscale dynamical rheological responses remains elusive. Here, we propose a mechanism-based general theoretical model showing that cytoskeleton dissociation generates a peak in the loss modulus as a function of frequency, while the cytoplasmic viscosity promotes its recovery, producing a subsequent trough. We define two characteristic frequencies (ω_c1 and ω_c2) related to the dissociation rate of crosslinkers and the viscosity of the cytoplasm, where the loss modulus 1) exhibits peak and trough values for ω_c1<ω_c2 and 2) monotonically increases with frequency for ω_c1>ω_c2. Furthermore, the characteristic frequency ω_c1 exhibits a biphasic stress-dependent behavior, with a local minimum at sufficiently high stress due to the stress-dependent dissociation rate. Moreover, the characteristic frequency ω_c2 evolves with age, following a power-law relationship. The predictions of the dissociation-based multiscale theoretical mechanical model align well with experimental observations. Our model provides a comprehensive description of the dynamical viscoelastic behaviors of cells and cell-like materials.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142674954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High-fidelity predictions of diffusion in the brain microenvironment.","authors":"Nels Schimek, Thomas R Wood, David A C Beck, Michael McKenna, Ali Toghani, Elizabeth Nance","doi":"10.1016/j.bpj.2024.10.005","DOIUrl":"10.1016/j.bpj.2024.10.005","url":null,"abstract":"<p><p>Multiple-particle tracking (MPT) is a microscopy technique capable of simultaneously tracking hundreds to thousands of nanoparticles in a biological sample and has been used extensively to characterize biological microenvironments, including the brain extracellular space (ECS). Machine learning techniques have been applied to MPT data sets to predict the diffusion mode of nanoparticle trajectories as well as more complex biological variables, such as biological age. In this study, we develop a machine learning pipeline to predict and investigate changes to the brain ECS due to injury using supervised classification and feature importance calculations. We first validate the pipeline on three related but distinct MPT data sets from the living brain ECS-age differences, region differences, and enzymatic degradation of ECS structure. We predict three ages with 86% accuracy, three regions with 90% accuracy, and healthy versus enzyme-treated tissue with 69% accuracy. Since injury across groups is normally compared with traditional statistical approaches, we first used linear mixed effects models to compare features between healthy control conditions and injury induced by two different oxygen glucose deprivation exposure times. We then used machine learning to predict injury state using MPT features. We show that the pipeline predicts between the healthy control, 0.5 h OGD treatment, and 1.5 h OGD treatment with 59% accuracy in the cortex and 66% in the striatum, and identifies nonlinear relationships between trajectory features that were not evident from traditional linear models. Our work demonstrates that machine learning applied to MPT data is effective across multiple experimental conditions and can find unique biologically relevant features of nanoparticle diffusion.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"3935-3950"},"PeriodicalIF":3.2,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11617630/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142399236","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ovarian cancer cells exhibit diverse migration strategies on stiff collagenous substrata.","authors":"Madhumitha Suresh, Ramray Bhat","doi":"10.1016/j.bpj.2024.10.014","DOIUrl":"10.1016/j.bpj.2024.10.014","url":null,"abstract":"<p><p>In homoeostasis, the shape and sessility of untransformed epithelial cells are intricately linked together. Variations of this relationship in migrating cancer cells as they encounter different microenvironments are as yet ill understood. Here, we explore the interdependency of such traits in two morphologically distinct invasive ovarian cancer cell lines (OVCAR-3 and SK-OV-3) under mechanically variant contexts. We first established a metric toolkit that assessed traits associated with cell motion and shape, and rigorously measured their dynamical variation across trajectories of migration using a Shannon entropic distribution. Two stiffness conditions on polymerized collagen I with Young's moduli of 0.5 kPa (soft) and 20 kPa (stiff) were chosen. Both the epithelioid OVCAR-3 and mesenchymal SK-OV-3 cells on soft substrata exhibited slow and undirected migration. On stiff substrata, SK-OV-3 showed faster persistent directed motion. Surprisingly, OVCAR-3 cells on stiffer substrata moved even faster than SK-OV-3 cells but showed a distinct angular motion. The polarity of SK-OV-3 cells on stiff substrata was well correlated with their movement, whereas, for OVCAR-3, we observed an unusual \"slip\" behavior, wherein the axes of cell shape and movement were poorly correlated. Whereas SK-OV-3 and OVCAR-3 showed greater mean deformation on stiffer substrata, the latter was anticorrelated with variation in angular motion or the mean deviation between shape and motility axis for SK-OV-3 but poorly correlated for OVCAR-3. Moreover, on softer substrata OVCAR-3 and SK-OV-3 were relatively rigid but showed greater shape variation (with OVCAR-3 showing a higher fold change) on stiffer substrata. Our findings suggest that greater deformability on stiffer milieu allow epithelioid cells to overcome constraints on the congruence in axis of shape and motion seen for mesenchymal cells and display distinct motile behaviors across this phenotypic spectrum.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"4009-4021"},"PeriodicalIF":3.2,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11617636/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142494168","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structure and function of skin barrier lipids: Effects of hydration and natural moisturizers in vitro.","authors":"Irene Sagrafena, Maxim Morin, Georgios Paraskevopoulos, Emelie J Nilsson, Iva Hrdinová, Andrej Kováčik, Sebastian Björklund, Kateřina Vávrová","doi":"10.1016/j.bpj.2024.10.006","DOIUrl":"10.1016/j.bpj.2024.10.006","url":null,"abstract":"<p><p>Lipid membranes play a crucial role in regulating the body's water balance by adjusting their properties in response to hydration. The intercellular lipid matrix of the stratum corneum (SC), the outermost skin layer, serves as the body's primary defense against environmental factors. Osmolytes, including urocanic acid (UCA) and glycerol, are key components of the natural moisturizing factor that help the SC resist osmotic stress from dry environments. This study examines the effects of UCA and glycerol (each at 5 mol %) on isolated human SC lipids. For this, different techniques were employed, offering complementary information of the system's multiscale characteristics, including humidity-scanning quartz crystal microbalance with dissipation monitoring, infrared spectroscopy, x-ray diffraction, electrical impedance spectroscopy, and studies of water loss and permeability. Our results show that UCA increases water sorption and makes lipid films more liquid-like at high relative humidity, without significantly altering the lipid lamellar structure, chain order, or orthorhombic chain packing. Lipid films containing UCA exhibited higher water loss and significantly higher model drug permeability compared to lipid films without UCA. Further, incorporation of UCA resulted in kinetically faster changes in electrical properties upon contact with aqueous solution compared with control lipids. These observations suggest that UCA reduces lipid cohesion in regions other than the acyl chain-rich leaflets, which may impact SC desquamation. In contrast, glycerol did not influence the hydration or permeability of the SC lipid matrix. However, it increased the proportion of orthorhombic domains at high humidities and slowed the kinetics of the hydration process, as evidenced by slower changes in the dielectric properties of the lipid film. These findings suggest that glycerol enhances lipid cohesion rather than increasing water uptake, which is typically the expected function of humectants. Consequently, UCA and glycerol appear to have distinct roles in maintaining epidermal homeostasis.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"3951-3963"},"PeriodicalIF":3.2,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11617626/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142399237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Contact area and tissue growth dynamics shape synthetic juxtacrine signaling patterns.","authors":"Jonathan E Dawson, Abby Bryant, Breana Walton, Simran Bhikot, Shawn Macon, Amber Ajamu-Johnson, Trevor Jordan, Paul D Langridge, Abdul N Malmi-Kakkada","doi":"10.1016/j.bpj.2024.11.007","DOIUrl":"10.1016/j.bpj.2024.11.007","url":null,"abstract":"<p><p>Cell-cell communication through direct contact, or juxtacrine signaling, is important in development, disease, and many areas of physiology. Synthetic forms of juxtacrine signaling can be precisely controlled and operate orthogonally to native processes, making them a powerful reductionist tool with which to address fundamental questions in cell-cell communication in vivo. Here, we investigate how cell-cell contact length and tissue growth dynamics affect juxtacrine signal responses through implementing a custom synthetic gene circuit in Drosophila wing imaginal discs alongside mathematical modeling to determine synthetic Notch (synNotch) activation patterns. We find that the area of contact between cells largely determines the extent of synNotch activation, leading to the prediction that the shape of the interface between signal-sending and signal-receiving cells will impact the magnitude of the synNotch response. Notably, synNotch outputs form a graded spatial profile that extends several cell diameters from the signal source, providing evidence that the response to juxtacrine signals can persist in cells as they proliferate away from source cells, or that cells remain able to communicate directly over several cell diameters. Our model suggests that the former mechanism may be sufficient, since it predicts graded outputs without diffusion or long-range cell-cell communication. Overall, we identify that cell-cell contact area together with output synthesis and decay rates likely govern the pattern of synNotch outputs in both space and time during tissue growth, insights that may have broader implications for juxtacrine signaling in general.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643354","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Initiation of epithelial wound closure by an active instability at the purse string.","authors":"Vita Movrin, Matej Krajnc","doi":"10.1016/j.bpj.2024.11.008","DOIUrl":"10.1016/j.bpj.2024.11.008","url":null,"abstract":"<p><p>The ability of biological systems to withstand and recover from various disruptions, such as spontaneous genetic mutations and environmental damage, largely relies on intricate feedback mechanisms. We theoretically study the mechanical response of an epithelial tissue facing damage in the form of a circular wound. Our model describes a feedback loop between the generation of active forces in the actomyosin and tissue mechanics, described by the vertex model. While the exact dynamics of wound closure may be influenced by several biophysical mechanisms that interplay in a nontrivial way, our findings suggest that the closure may initiate as an active instability, triggered by a reduced myosin turnover rate at the wound's perimeter. We explore the interplay between myosin dynamics and the elastic properties of the tissue, elucidating their collective role in determining a wound's loss of stability, leading to the initiation of the closure process.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142614032","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}