High-resolution mapping of intracellular fluctuations using carbon nanotubes

Heterogeneities Shape Passive Intracellular Transport

A living cell's interior is one of the most complex and intrinsically dynamic systems, providing an elaborate interplay between cytosolic crowding and ATP-driven motion that controls cellular functionality. Here, we investigated two distinct fundamental features of the merely passive, non-biomotor-shuttled material transport within the cytoplasm of Dictyostelium discoideum cells: the anomalous non-linear scaling of the mean-squared displacement of a 150-nm-diameter particle and non-Gaussian distribution of increments. Relying on single-particle tracking data of 320,000 data points, we performed a systematic analysis of four possible origins for non-Gaussian transport: 1) sample-based variability, 2) rarely occurring strong motion events, 3) ergodicity breaking/aging, and 4) spatiotemporal heterogeneities of the intracellular medium. After excluding the first three reasons, we investigated the remaining hypothesis of a heterogeneous cytoplasm as cause for non-Gaussian transport. A, to our knowledge, novel fit model with randomly distributed diffusivities implementing medium heterogeneities suits the experimental data. Strikingly, the non-Gaussian feature is independent of the cytoskeleton condition and lag time. This reveals that efficiency and consistency of passive intracellular transport and the related anomalous scaling of the mean-squared displacement are regulated by cytoskeleton components, whereas cytoplasmic heterogeneities are responsible for the generic, non-Gaussian distribution of increments.

Advanced nanostructures for cell membrane poration

Nanostructured devices are able to foster the technology for cell membrane poration. With the size smaller than a cell, nanostructures allow efficient poration on the cell membrane. Emerging nanostructures with various physical transduction have been demonstrated to accommodate effective intracellular delivery. Aside from improving poration and intracellular delivery performance, nanostructured devices also allow for the discovery of novel physiochemical phenomena and the biological response of the cell. This article provides a brief introduction to the principles of nanostructured devices for cell poration and outlines the intracellular delivery capability of the technology. In the future, we envision more exploration on new nanostructure designs and creative applications in biomedical fields.

Scaling behavior of nonequilibrium measures in internally driven elastic assemblies

Detecting and quantifying nonequilibrium activity is essential for studying internally driven assemblies, including synthetic active matter and complex living systems such as cells or tissue. We discuss a noninvasive approach of measuring nonequilibrium behavior based on the breaking of detailed balance. We focus on "cycling frequencies"-the average frequency with which the trajectories of pairs of degrees of freedom revolve in phase space-and explain their connection with other nonequilibrium measures, including the area enclosing rate and the entropy production rate. We test our approach on simple toy models composed of elastic networks immersed in a viscous fluid with site-dependent internal driving. We prove both numerically and analytically that the cycling frequencies obey a power law as a function of distance between the tracked degrees of freedom. Importantly, the behavior of the cycling frequencies contains information about the dimensionality of the system and the amplitude of active noise. The mapping we use in our analytical approach thus offers a convenient framework for predicting the behavior of two-point nonequilibrium measures for a given activity distribution in the network.

Local actin nucleation tunes centrosomal microtubule nucleation during passage through mitosis

Cells going through mitosis undergo precisely timed changes in cell shape and organisation, which serve to ensure the fair partitioning of cellular components into the two daughter cells. These structural changes are driven by changes in actin filament and microtubule dynamics and organisation. While most evidence suggests that the two cytoskeletal systems are remodelled in parallel during mitosis, recent work in interphase cells has implicated the centrosome in both microtubule and actin nucleation, suggesting the potential for regulatory crosstalk between the two systems. Here, by using both in vitro and in vivo assays to study centrosomal actin nucleation as cells pass through mitosis, we show that mitotic exit is accompanied by a burst in cytoplasmic actin filament formation that depends on WASH and the Arp2/3 complex. This leads to the accumulation of actin around centrosomes as cells enter anaphase and to a corresponding reduction in the density of centrosomal microtubules. Taken together, these data suggest that the mitotic regulation of centrosomal WASH and the Arp2/3 complex controls local actin nucleation, which may function to tune the levels of centrosomal microtubules during passage through mitosis.

Quantifying dissipation using fluctuating currents

Systems coupled to multiple thermodynamic reservoirs can exhibit nonequilibrium dynamics, breaking detailed balance to generate currents. To power these currents, the entropy of the reservoirs increases. The rate of entropy production, or dissipation, is a measure of the statistical irreversibility of the nonequilibrium process. By measuring this irreversibility in several biological systems, recent experiments have detected that particular systems are not in equilibrium. Here we discuss three strategies to replace binary classification (equilibrium versus nonequilibrium) with a quantification of the entropy production rate. To illustrate, we generate time-series data for the evolution of an analytically tractable bead-spring model. Probability currents can be inferred and utilized to indirectly quantify the entropy production rate, but this approach requires prohibitive amounts of data in high-dimensional systems. This curse of dimensionality can be partially mitigated by using the thermodynamic uncertainty relation to bound the entropy production rate using statistical fluctuations in the probability currents.

The determination of entropy production from experimental data is a challenge but a recently introduced theoretical tool, the thermodynamic uncertainty relation, allows one to infer a lower bound on entropy production. Here the authors provide a critical assessment of the practical implementation of this tool.

Active Mechanics Reveal Molecular-Scale Force Kinetics in Living Oocytes

Active diffusion of intracellular components is emerging as an important process in cell biology. This process is mediated by complex assemblies of molecular motors and cytoskeletal filaments that drive force generation in the cytoplasm and facilitate enhanced motion. The kinetics of molecular motors have been precisely characterized in vitro by single molecule approaches, but their in vivo behavior remains elusive. Here, we study the active diffusion of vesicles in mouse oocytes, where this process plays a key role in nuclear positioning during development, and combine an experimental and theoretical framework to extract molecular-scale force kinetics (force, power stroke, and velocity) of the in vivo active process. Assuming a single dominant process, we find that the nonequilibrium activity induces rapid kicks of duration τ ∼ 300 μs resulting in an average force of F ∼ 0.4 pN on vesicles in in vivo oocytes, remarkably similar to the kinetics of in vitro myosin-V. Our results reveal that measuring in vivo active fluctuations allows extraction of the molecular-scale activity in agreement with single-molecule studies and demonstrates a mesoscopic framework to access force kinetics.

Actin filaments regulate microtubule growth at the centrosome

The centrosome is the main microtubule-organizing centre. It also organizes a local network of actin filaments. However, the precise function of the actin network at the centrosome is not well understood. Here, we show that increasing densities of actin filaments at the centrosome of lymphocytes are correlated with reduced amounts of microtubules. Furthermore, lymphocyte activation resulted in disassembly of centrosomal actin and an increase in microtubule number. To further investigate the direct crosstalk between actin and microtubules at the centrosome, we performed in vitro reconstitution assays based on (i) purified centrosomes and (ii) on the co-micropatterning of microtubule seeds and actin filaments. These two assays demonstrated that actin filaments constitute a physical barrier blocking elongation of nascent microtubules. Finally, we showed that cell adhesion and cell spreading lead to lower densities of centrosomal actin, thus resulting in higher microtubule growth. We therefore propose a novel mechanism, by which the number of centrosomal microtubules is regulated by cell adhesion and actin-network architecture.

Characterization and Biodistribution Analysis of Oxygen-Doped Single-Walled Carbon Nanotubes Used as in Vivo Fluorescence Imaging Probes

Single-walled carbon nanotubes (SWCNTs) show strong fluorescence in the 1000-1700 nm second near-infrared (NIR-II) wavelength range and are considered promising candidates for angiographic imaging probes. Oxygen-doped SWCNTs coated with phospholipid-polyethylene glycol (o-SWCNT-PEG) show exceptional potential, as they emit fluorescence at ∼1300 nm through excitation with 980 nm light. Here, with the aim of putting o-SWCNTs to practical use as an angiographic agent in animal experiments, the retention time after intravenous administration in the vasculature of mice and the biodistribution were studied. To provide bio affinity, the o-SWCNTs were coated with phospholipid polyethylene glycol. The intravenously injected o-SWCNT-PEG circulated within the vasculature for 3 h and cleared within 1 day. There was prominent fluorescence and Raman signals from the SWCNTs in the liver and spleen early in the experiment; the signals remained for 1 month. No apparent abnormalities in weight or appearance were observed after 2 months, suggesting low toxicity of o-SWCNT-PEG. These characteristics of o-SWCNT-PEG would make it useful as an angiographic imaging probe in the NIR-II wavelength range.

Recent advances in optical microscopic methods for single-particle tracking in biological samples

With the rapid development of optical microscopic techniques, explorations on the chemical and biological properties of target objects in biological samples at single-molecule/particle level have received great attention recently. In the past decades, various powerful techniques have been developed for single-particle tracking (SPT) in biological samples. In this review, we summarize the commonly used optical microscopic methods for SPT, such as total internal reflection fluorescence microscopy (TIRFM), super-resolution fluorescence microscopy (SRM), dark-field optical microscopy (DFM), total internal reflection scattering microscopy (TIRSM), and differential interference contrast microscopy (DICM). We then discuss the image processing and data analysis methods, including particle localization, trajectory reconstruction, and diffusion behavior analysis. The application of SPT on the cell membrane, within the cell, and the cellular invading process of viruses are introduced. Finally, the challenges and prospects of optical microscopic technologies for SPT are delineated.

Mechanistic three-dimensional model to study centrosome positioning in the interphase cell

During the interphase in mammalian cells, the position of the centrosome is actively maintained at a small but finite distance away from the nucleus. The perinuclear positioning of the centrosome is crucial for cellular trafficking and progression into mitosis. Although the literature suggests that the contributions of the microtubule-associated forces bring the centrosome to the center of the cell, the position of the centrosome was merely investigated in the absence of the nucleus. Upon performing a coarse-grained simulation study with mathematical analysis, we show that the combined effect of the forces due to the cell cortex and the nucleus facilitate the centrosome positioning. Our study also demonstrates that in the absence of nucleus-based forces, the centrosome collapses on the nucleus due to cortical forces. Depending upon the magnitudes of the cortical forces and the nucleus-based forces, the centrosome appears to stay at various distances away from the nucleus. Such null force regions are found to be stable as well as unstable fixed points. This study uncovers a set of redundant schemes that the cell may adopt to produce the required cortical and nucleus-based forces stabilizing the centrosome at a finite distance away from the nucleus.

DNA Sequence Mediates Apparent Length Distribution in Single-Walled Carbon Nanotubes

Single-walled carbon nanotubes (SWCNTs) functionalized with short single-stranded DNA have been extensively studied within the last decade for biomedical applications due to the high dispersion efficiency and intrinsic biocompatibility of DNA as well as the photostable and tunable fluorescence of SWCNTs. Characterization of their physical properties, particularly their length distribution, is of great importance regarding their application as a bioengineered research tool and clinical diagnostic agent. Conventionally, atomic force microscopy (AFM) has been used to quantify the length of DNA-SWCNTs by depositing the hybrids onto an electrostatically charged flat surface. Here, we demonstrate that hybrids of DNA-SWCNTs with different oligomeric DNA sequences ((GT)₆ and (GT)₃₀) differentially deposit on the AFM substrate, resulting in significant inaccuracies in the reported length distributions of the parent solutions. Using a solution-based surfactant exchange technique, we placed both samples into a common surfactant wrapping and found identical SWCNT length distributions upon surface deposition. Additionally, by spin-coating the surfactant-wrapped SWCNTs onto a substrate, thus mitigating effects of electrostatic interactions, we found length distributions that did not depend on DNA sequence but were significantly longer than electrostatic deposition methods, illuminating the inherent bias of the surface deposition method. Quantifying the coverage of DNA molecules on each SWCNT through both absorbance spectroscopy and direct observation, we found that the density of DNA per SWCNT was significantly higher in short (GT)₆-SWCNTs (length < 100 nm) compared to long (GT)₆-SWCNTs (length > 100 nm). In contrast, we found no dependence of the DNA density on SWCNT length in (GT)₃₀-SWCNT hybrids. Thus, we attribute differences in the observed length distributions of DNA-SWCNTs to variations in electrostatic repulsion induced by sequence-dependent DNA density.

Anisotropic mechanics and dynamics of a living mammalian cytoplasm

During physiological processes, cells can undergo morphological changes that can result in a significant redistribution of the cytoskeleton causing anisotropic behavior. Evidence of anisotropy in cells under mechanical stimuli exists; however, the role of cytoskeletal restructuring resulting from changes in cell shape in mechanical anisotropy and its effects remain unclear. In the present study, we examine the role of cell morphology in inducing anisotropy in both intracellular mechanics and dynamics. We change the aspect ratio of cells by confining the cell width and measuring the mechanical properties of the cytoplasm using optical tweezers in both the longitudinal and transverse directions to quantify the degree of mechanical anisotropy. These active microrheology measurements are then combined with intracellular movement to calculate the intracellular force spectrum using force spectrum microscopy (FSM), from which the degree of anisotropy in dynamics and force can be quantified. We find that unrestricted cells with aspect ratio (AR) ∼1 are isotropic; however, when cells break symmetry, they exhibit significant anisotropy in cytoplasmic mechanics and dynamics.

Intracellular transport is accelerated in early apoptotic cells

Intracellular transport of cellular proteins and organelles is critical for establishing and maintaining intracellular organization and cell physiology. Apoptosis is a process of programmed cell death with dramatic changes in cell morphology and organization, during which signaling molecules are transported between different organelles within the cells. However, how the intracellular transport changes in cells undergoing apoptosis remains unknown. Here, we study the dynamics of intracellular transport by using the single-particle tracking method and find that both directed and diffusive motions of endocytic vesicles are accelerated in early apoptotic cells. With careful elimination of other factors involved in the intracellular transport, the reason for the acceleration is attributed to the elevation of adenosine triphosphate (ATP) concentration. More importantly, we show that the accelerated intracellular transport is critical for apoptosis, and apoptosis is delayed when the dynamics of intracellular transport is regulated back to the normal level. Our results demonstrate the important role of transport dynamics in apoptosis and shed light on the apoptosis mechanism from a physical perspective.

Analytical and Quantitative in Vivo Monitoring of Brain Neurochemistry by Electrochemical and Imaging Approaches

Quantitative monitoring of brain neurochemistry is aimed at an accurate measurement of chemical basal levels and dynamics defining neuronal activities. Analytical tools must be endowed with high selectivity, sensitivity, and spatiotemporal resolution to tackle this task. On one hand, in vivo electroanalysis combined with miniature electrodes has evolved into a minimally invasive method for probing transient events during neural communication and metabolism. On the other hand, noninvasive imaging techniques have been widely adopted in visualizing the neural structure and processes within a population of neurons in two or three dimensions. This perspective will give a concise review of the inspiring frontiers at the interface of neurochemistry and electrochemistry (microvoltammetry, nanoamperometry, galvanic redox potentiometry and ion transport-based sensing) or imaging (super-resolution single nanotube tracking, deep multiphoton microscopy, and free animal imaging). Potential opportunities with these methods and their combinations for multimodal brain analysis will be discussed, intending to draw a brief picture for future neuroscience research.

Unveiling the Extracellular Space of the Brain: From Super-resolved Microstructure to In Vivo Function

The extracellular space occupies approximately one-fifth of brain volume, molding a spider web of gaps filled with interstitial fluid and extracellular matrix where neurons and glial cells perform in concert. Yet, very little is known about the spatial organization and dynamics of the extracellular space, let alone its influence on brain function, owing to a lack of appropriate techniques (and a traditional bias toward the inside of cells, not the spaces in between). At the same time, it is clear that understanding fundamental brain functions, such as synaptic transmission, memory, sleep, and recovery from disease, calls for more focused research on the extracellular space of the brain. This review article highlights several key research areas, covering recent methodological and conceptual progress that illuminates this understudied, yet critically important, brain compartment, providing insights into the opportunities and challenges of this nascent field.

Carbon Nanomaterials in Optical Detection

Owing to their unique optical, electronic, mechanical, and chemical properties, flexible chemical modification, large surface coverage and ready cellular uptake, various carbon nanomaterials such as carbon nanotubes (CNTs), graphene and its derivatives, carbon dots (CDs), graphene quantum dots, fullerenes, carbon nanohorns (CNHs) and carbon nano-onions (CNOs), have been widely explored for use in optical detection. Most of them are based on fluorescence changes. In this chapter, we will focus on carbon nanomaterials-based optical detection applications, mainly including fluorescence sensing and bio-imaging. Moreover, perspectives on future exploration of carbon nanomaterials for optical detection are also given.

Small-scale displacement fluctuations of vesicles in fibroblasts

The intracellular environment is a dynamic space filled with various organelles moving in all directions. Included in this diverse group of organelles are vesicles, which are involved in transport of molecular cargo throughout the cell. Vesicles move in either a directed or non-directed fashion, often depending on interactions with cytoskeletal proteins such as microtubules, actin filaments, and molecular motors. How these proteins affect the local fluctuations of vesicles in the cytoplasm is not clear since they have the potential to both facilitate and impede movement. Here we show that vesicle mobility is significantly affected by myosin-II, even though it is not a cargo transport motor. We find that myosin-II activity increases the effective diffusivity of vesicles and its inhibition facilitates longer states of non-directed motion. Our study suggests that altering myosin-II activity in the cytoplasm of cells can modulate the mobility of vesicles, providing a possible mechanism for cells to dynamically tune the cytoplasmic environment in space and time.

Quantitative analysis of cell shape and the cytoskeleton in developmental biology

Computational approaches that enable quantification of microscopy data have revolutionized the field of developmental biology. Due to its inherent complexity, elucidating mechanisms of development requires sophisticated analysis of the structure, shape, and kinetics of cellular processes. This need has prompted the creation of numerous techniques to visualize, quantify, and merge microscopy data. These approaches have defined the order and structure of developmental events, thus, providing insight into the mechanisms that drive them. This review describes current computational approaches that are being used to answer developmental questions related to morphogenesis and describe how these approaches have impacted the field. Our intent is not to comprehensively review techniques, but to highlight examples of how different approaches have impacted our understanding of development. Specifically, we focus on methods to quantify cell shape and cytoskeleton structure and dynamics in developing tissues. Finally, we speculate on where the future of computational analysis in developmental biology might be headed. This article is categorized under: Technologies > Analysis of Cell, Tissue, and Animal Phenotypes Early Embryonic Development > Gastrulation and Neurulation Early Embryonic Development > Development to the Basic Body Plan.

Hydroxide Ions Stabilize Open Carbon Nanotubes in Degassed Water

The main hurdle preventing the widespread use of single-walled carbon nanotubes remains the lack of methods with which to produce formulations of pristine, unshortened, unfunctionalized, individualized single-walled carbon nanotubes, thus preserving their extraordinary properties. In particular, sonication leads to shortening, which is detrimental to percolation properties (electrical, thermal, mechanical, etc.). Using reductive dissolution and transfer into degassed water, open-ended, water-filled nanotubes can be dispersed as individualized nanotubes in water-dimethyl sulfoxide mixtures, avoiding the use of sonication and surfactant. Closed nanotubes, however, aggregate immediately upon contact with water. Photoluminescence and absorption spectroscopy both point out a very high degree of individualization while retaining lengths of several microns. The resulting transparent conducting films are 1 order of magnitude more conductive than surfactant-based blanks at equal transmittance.

Intracellular Delivery by Membrane Disruption: Mechanisms, Strategies, and Concepts

Intracellular delivery is a key step in biological research and has enabled decades of biomedical discoveries. It is also becoming increasingly important in industrial and medical applications ranging from biomanufacture to cell-based therapies. Here, we review techniques for membrane disruption-based intracellular delivery from 1911 until the present. These methods achieve rapid, direct, and universal delivery of almost any cargo molecule or material that can be dispersed in solution. We start by covering the motivations for intracellular delivery and the challenges associated with the different cargo types-small molecules, proteins/peptides, nucleic acids, synthetic nanomaterials, and large cargo. The review then presents a broad comparison of delivery strategies followed by an analysis of membrane disruption mechanisms and the biology of the cell response. We cover mechanical, electrical, thermal, optical, and chemical strategies of membrane disruption with a particular emphasis on their applications and challenges to implementation. Throughout, we highlight specific mechanisms of membrane disruption and suggest areas in need of further experimentation. We hope the concepts discussed in our review inspire scientists and engineers with further ideas to improve intracellular delivery.

Nonequilibrium Scaling Behavior in Driven Soft Biological Assemblies

Measuring and quantifying nonequilibrium dynamics in active biological systems is a major challenge because of their intrinsic stochastic nature and the limited number of variables accessible in any real experiment. We investigate what nonequilibrium information can be extracted from noninvasive measurements using a stochastic model of soft elastic networks with a heterogeneous distribution of activities, representing enzymatic force generation. In particular, we use this model to study how the nonequilibrium activity, detected by tracking two probes in the network, scales as a function of the distance between the probes. We quantify the nonequilibrium dynamics through the cycling frequencies, a simple measure of circulating currents in the phase space of the probes. We find that these cycling frequencies exhibit power-law scaling behavior with the distance between probes. In addition, we show that this scaling behavior governs the entropy production rate that can be recovered from the two traced probes. Our results provide insight into how internal enzymatic driving generates nonequilibrium dynamics on different scales in soft biological assemblies.

Microrheology, advances in methods and insights

Microrheology is an emerging technique that probes mechanical response of soft material at micro-scale. Generally, microrheology technique can be divided into active and passive versions. During last two decades, extensive efforts have been paid to improve both the experiment techniques and data analysis methods, especially about how to link consequential particle positions into trajectories. We review the recent advances in microrheology, including improvements in labeling, imaging, data acquiring, data processing and data interpretation. Some of the recent insights in soft matter and living systems gained by using this technique are given. Before these, we also give a very brief description of the basic principles of both active and passive microrheology techniques, and some details about optical particle tracking and DWS.

Self-organized stress patterns drive state transitions in actin cortices

Biological functions rely on ordered structures and intricately controlled collective dynamics. This order in living systems is typically established and sustained by continuous dissipation of energy. The emergence of collective patterns of motion is unique to nonequilibrium systems and is a manifestation of dynamic steady states. Mechanical resilience of animal cells is largely controlled by the actomyosin cortex. The cortex provides stability but is, at the same time, highly adaptable due to rapid turnover of its components. Dynamic functions involve regulated transitions between different steady states of the cortex. We find that model actomyosin cortices, constructed to maintain turnover, self-organize into distinct nonequilibrium steady states when we vary cross-link density. The feedback between actin network structure and organization of stress-generating myosin motors defines the symmetries of the dynamic steady states. A marginally cross-linked state displays divergence-free long-range flow patterns. Higher cross-link density causes structural symmetry breaking, resulting in a stationary converging flow pattern. We track the flow patterns in the model actomyosin cortices using fluorescent single-walled carbon nanotubes as novel probes. The self-organization of stress patterns we have observed in a model system can have direct implications for biological functions.

Broken detailed balance and non-equilibrium dynamics in living systems: a review

Living systems operate far from thermodynamic equilibrium. Enzymatic activity can induce broken detailed balance at the molecular scale. This molecular scale breaking of detailed balance is crucial to achieve biological functions such as high-fidelity transcription and translation, sensing, adaptation, biochemical patterning, and force generation. While biological systems such as motor enzymes violate detailed balance at the molecular scale, it remains unclear how non-equilibrium dynamics manifests at the mesoscale in systems that are driven through the collective activity of many motors. Indeed, in several cellular systems the presence of non-equilibrium dynamics is not always evident at large scales. For example, in the cytoskeleton or in chromosomes one can observe stationary stochastic processes that appear at first glance thermally driven. This raises the question how non-equilibrium fluctuations can be discerned from thermal noise. We discuss approaches that have recently been developed to address this question, including methods based on measuring the extent to which the system violates the fluctuation-dissipation theorem. We also review applications of this approach to reconstituted cytoskeletal networks, the cytoplasm of living cells, and cell membranes. Furthermore, we discuss a more recent approach to detect actively driven dynamics, which is based on inferring broken detailed balance. This constitutes a non-invasive method that uses time-lapse microscopy data, and can be applied to a broad range of systems in cells and tissue. We discuss the ideas underlying this method and its application to several examples including flagella, primary cilia, and cytoskeletal networks. Finally, we briefly discuss recent developments in stochastic thermodynamics and non-equilibrium statistical mechanics, which offer new perspectives to understand the physics of living systems.

Active transport of cytoophidia in Schizosaccharomyces pombe

The metabolic enzyme cytidine triphosphate synthase has recently been found to form micrometer-sized filamentous structures termed cytoophidia, which are evolutionarily conserved across prokaryotes and eukaryotes. The cytoophidium represents a novel type of membraneless organelle and behaves dynamically inside the cell. The question of how cytoophidia transport is mediated, however, remains unanswered. For the first time, we detected in this study the active transport of cytoophidia, taking advantage of the fission yeast Schizosaccharomyces pombe as an excellent model for studying membraneless organelles. We demonstrated that actin filaments, not microtubules, are responsible for this transport. Furthermore, we determined that Myo52, a type of myosin V, is required for the active transport of cytoophidia. These results reveal the major players critical to the dynamics of cytoophidia and extend our understanding of intracellular transport of membraneless organelles.—Li, H., Ye, F., Ren, J.-Y., Wang, P.-Y., Du, L.-L., Liu, J.-L. Active transport of cytoophidia in Schizosaccharomyces pombe.

Motion of kinesin in a viscoelastic medium

Kinesin is a molecular motor that transports cargo along microtubules. The results of many in vitro experiments on kinesin-1 are described by kinetic models in which one transition corresponds to the forward motion and subsequent binding of the tethered motor head. We argue that in a viscoelastic medium like the cytosol of a cell this step is not Markov and has to be described by a nonexponential waiting time distribution. We introduce a semi-Markov kinetic model for kinesin that takes this effect into account. We calculate, for arbitrary waiting time distributions, the moment generating function of the number of steps made, and determine from this the average velocity and the diffusion constant of the motor. We illustrate our results for the case of a waiting time distribution that is Weibull. We find that for realistic parameter values, viscoelasticity decreases the velocity and the diffusion constant, but increases the randomness (or Fano factor).

Active and passive transport of cargo in a corrugated channel: A lattice model study

Inside cells, cargos such as vesicles and organelles are transported by molecular motors to their correct locations via active motion on cytoskeletal tracks and passive, Brownian diffusion. During the transportation of cargos, motor-cargo complexes (MCCs) navigate the confining and crowded environment of the cytoskeletal network and other macromolecules. Motivated by this, we study a minimal two-state model of motor-driven cargo transport in confinement and predict transport properties that can be tested in experiments. We assume that the motion of the MCC is directly affected by the entropic barrier due to confinement if it is in the passive, unbound state but not in the active, bound state where it moves with a constant bound velocity. We construct a lattice model based on a Fokker Planck description of the two-state system, study it using a kinetic Monte Carlo method and compare our numerical results with analytical expressions for a mean field limit. We find that the effect of confinement strongly depends on the bound velocity and the binding kinetics of the MCC. Confinement effectively reduces the effective diffusivity and average velocity, except when it results in an enhanced average binding rate and thereby leads to a larger average velocity than when unconfined.

Dynamics of networks in a viscoelastic and active environment

We investigate the dynamics of fractals and other networks in a viscoelastic and active environment. The viscoelastic dynamics is modeled based on the generalized Langevin equation, where the activity is introduced to it by means of the exponentially correlated noise. The intramolecular interactions are taken into account by the bead-spring picture. The microscopic connectivity (studied in the form of Vicsek fractals, of dual Sierpiński gaskets, of NT_D trees, and of a family of deterministic small-world networks) reveals itself in the multiscale monomeric dynamics, which shows vastly different behaviors in the active and passive baths. In particular, the dynamics under active forces leads to a swelling that is characterized through power laws which are not present in the passive case. In all cases, the dynamics reflects the broad scaling behavior of the density of states and not necessarily the maximal relaxation time of the structures in a passive bath, as it is exemplified on the NT_D trees.

Controlling Polyelectrolyte Adsorption onto Carbon Nanotubes by Tuning Ion-Image Interactions

Understanding and controlling polyelectrolyte adsorption onto carbon nanotubes is a fundamental challenge in nanotechnology. Polyelectrolytes have been shown to stabilize nanotube suspensions through adsorbing onto the nanotube surface, and polyelectrolyte-coated nanotubes are emerging as building blocks for complex and addressable self-assembly. Conventional wisdom suggests that polyelectrolyte adsorption onto nanotubes is driven by specific chemical or van der Waals interactions. We develop a simple mean-field model and show that ion-image attraction significantly effects adsorption onto conducting nanotubes at low salt concentrations. Our theory suggests a simple strategy to selectively and reversibly functionalize carbon nanotubes on the basis of their electronic structures, which in turn modify the ion-image attraction.

Immotile Active Matter: Activity from Death and Reproduction

Unlike equilibrium atomic solids, biofilms-soft solids composed of bacterial cells-do not experience significant thermal fluctuations at the constituent level. However, living cells stochastically reproduce and die, provoking a mechanical response. We investigate the mechanical consequences of cellular death and reproduction by measuring surface-height fluctuations of biofilms containing two mutually antagonistic strains of Vibrio cholerae that kill one another on contact via the type VI secretion system. While studies of active matter typically focus on activity via constituent mobility, here, activity is mediated by reproduction and death events in otherwise immobilized cells. Biofilm surface topography is measured in the nearly homeostatic limit via white light interferometry. Although biofilms are far from equilibrium systems, measured surface-height fluctuation spectra resemble the spectra of thermal permeable membranes but with an activity-mediated effective temperature, as predicted by Risler, Peilloux, and Prost [Phys. Rev. Lett. 115, 258104 (2015)PRLTAO0031-900710.1103/PhysRevLett.115.258104]. By comparing the activity of killer strains of V. cholerae with that of genetically modified strains that cannot kill each other and validating with individual-based simulations, we demonstrate that extracted effective temperatures increase with the amount of death and reproduction and that death and reproduction can fluidize biofilms. Together, these observations demonstrate the unique physical consequences of activity mediated by death and reproduction events.

Cellular and Nuclear Forces: An Overview

Biological cells sample their surrounding microenvironments using nanoscale force sensors on the cell surfaces. These surface-based force and stress sensors generate physical and chemical responses inside the cell. The inherently well-connected cytoskeleton and its physical contacts with the force elements on the nuclear membrane lead these physicochemical responses to cascade all the way inside the cell nucleus, physically altering the nuclear state. These physical alterations of the cell nucleus, through yet-unknown complex steps elicit physical and functional response from the chromatin in the form of altered gene expression profiles. This mechanism of force/stress sensing by the cell and then its nuclear response has been shown to play a vital role in maintaining robust cellular homeostasis, controlling gene expression profiles during developmental phases as well as cell differentiation. Over the last few years, there has been appreciable progress toward identification of the molecular players responsible for force sensing. However, the actual sensing mechanism of cell surface bound force sensors and more importantly cascading of the signals, both physical (via cytosolic force sensing elements such as microtubule and actin framework) and chemical (cascade of biochemical signaling from cell surface to nuclear surface and further to the chromatin), inside the cell is poorly understood. In this chapter, we present a review of the currently known molecular players in cellular as well as nuclear force sensing repertoire and their possible mechanistic aspects. We also introduce various biophysical concepts that are used to describe the force/stress sensing and response of a cell. We hope this will help asking clearer questions and designing pointed experiments for better understanding of the force-dependent design principles of the cell surface, nuclear surface, and gene expression.

Single-Walled Carbon Nanotubes Probed with Insulator-Based Dielectrophoresis

Single-walled carbon nanotubes (SWNTs) offer unique electrical and optical properties. Common synthesis processes yield SWNTs with large length polydispersity (several tens of nanometers up to centimeters) and heterogeneous electrical and optical properties. Applications often require suitable selection and purification. Dielectrophoresis is one manipulation method for separating SWNTs based on dielectric properties and geometry. Here, we present a study of surfactant and single-stranded DNA-wrapped SWNTs suspended in aqueous solutions manipulated by insulator-based dielectrophoresis (iDEP). This method allows us to manipulate SWNTs with the help of arrays of insulating posts in a microfluidic device around which electric field gradients are created by the application of an electric potential to the extremities of the device. Semiconducting SWNTs were imaged during dielectrophoretic manipulation with fluorescence microscopy making use of their fluorescence emission in the near IR. We demonstrate SWNT trapping at low-frequency alternating current (AC) electric fields with applied potentials not exceeding 1000 V. Interestingly, suspended SWNTs showed both positive and negative dielectrophoresis, which we attribute to their ζ potential and the suspension properties. Such behavior agrees with common theoretical models for nanoparticle dielectrophoresis. We further show that the measured ζ potentials and suspension properties are in excellent agreement with a numerical model predicting the trapping locations in the iDEP device. This study is fundamental for the future application of low-frequency AC iDEP for technological applications of SWNTs.

Cytoplasmic Flow and Mixing Due to Deformation of Motile Cells

The cytoplasm of a living cell is a dynamic environment through which intracellular components must move and mix. In motile, rapidly deforming cells such as human neutrophils, bulk cytoplasmic flow couples cell deformation to the transport and dispersion of cytoplasmic particles. Using particle-tracking measurements in live neutrophil-like cells, we demonstrate that fluid flow associated with the cell deformation contributes to the motion of small acidic organelles, dominating over diffusion on timescales above a few seconds. We then use a general physical model of particle dispersion in a deforming fluid domain to show that transport of organelle-sized particles between the cell periphery and the bulk can be enhanced by dynamic deformation comparable to that observed in neutrophils. Our results implicate an important mechanism contributing to organelle transport in these motile cells: cytoplasmic flow driven by cell shape deformation.

Evaluation of Different Single-Walled Carbon Nanotube Surface Coatings for Single-Particle Tracking Applications in Biological Environments

Fluorescence imaging of biological systems down to the single-molecule level has generated many advances in cellular biology. For applications within intact tissue, single-walled carbon nanotubes (SWCNTs) are emerging as distinctive single-molecule nanoprobes, due to their near-infrared photoluminescence properties. For this, SWCNT surfaces must be coated using adequate molecular moieties. Yet, the choice of the suspension agent is critical since it influences both the chemical and emission properties of the SWCNTs within their environment. Here, we compare the most commonly used surface coatings for encapsulating photoluminescent SWCNTs in the context of bio-imaging applications. To be applied as single-molecule nanoprobes, encapsulated nanotubes should display low cytotoxicity, and minimal unspecific interactions with cells while still being highly luminescent so as to be imaged and tracked down to the single nanotube level for long periods of time. We tested the cell proliferation and cellular viability of each surface coating and evaluated the impact of the biocompatible surface coatings on nanotube photoluminescence brightness. Our study establishes that phospholipid-polyethylene glycol-coated carbon nanotube is the best current choice for single nanotube tracking experiments in live biological samples.

Active diffusion and advection in Drosophila oocytes result from the interplay of actin and microtubules

Transport in cells occurs via a delicate interplay of passive and active processes, including diffusion, directed transport and advection. Despite progress in super-resolution microscopy, discriminating and quantifying these processes is a challenge, requiring tracking of rapidly moving, sub-diffraction objects in a crowded, noisy environment. Here we use differential dynamic microscopy with different contrast mechanisms to provide a thorough characterization of the dynamics in the Drosophila oocyte. We study the movement of vesicles and the elusive motion of a cytoplasmic F-actin mesh, a known regulator of cytoplasmic flows. We find that cytoplasmic motility constitutes a combination of directed motion and random diffusion. While advection is mainly attributed to microtubules, we find that active diffusion is driven by the actin cytoskeleton, although it is also enhanced by the flow. We also find that an important dynamic link exists between vesicles and cytoplasmic F-actin motion, as recently suggested in mouse oocytes.

Intracellular transport is facilitated by a combination of processes including directed transport, advection and diffusion. Here the authors microscopically characterise the dynamics of the Drosophila oocyte and find distinct contributions of cytoskeletal components to advection and active diffusion.

Topography on a subcellular scale modulates cellular adhesions and actin stress fiber dynamics in tumor associated fibroblasts

Cells can sense and adapt to mechanical properties of their environment. The local geometry of the extracellular matrix, such as its topography, has been shown to modulate cell morphology, migration, and proliferation. Here we investigate the effect of micro/nanotopography on the morphology and cytoskeletal dynamics of human pancreatic tumor-associated fibroblast cells (TAFs). We use arrays of parallel nanoridges with variable spacings on a subcellular scale to investigate the response of TAFs to the topography of their environment. We find that cell shape and stress fiber organization both align along the direction of the nanoridges. Our analysis reveals a strong bimodal relationship between the degree of alignment and the spacing of the nanoridges. Furthermore, focal adhesions align along ridges and form preferentially on top of the ridges. Tracking actin stress fiber movement reveals enhanced dynamics of stress fibers on topographically patterned surfaces. We find that components of the actin cytoskeleton move preferentially along the ridges with a significantly higher velocity along the ridges than on a flat surface. Our results suggest that a complex interplay between the actin cytoskeleton and focal adhesions coordinates the cellular response to micro/nanotopography.

Mapping Cell Membrane Fluctuations Reveals Their Active Regulation and Transient Heterogeneities

Shape fluctuations of the plasma membrane occur in all cells, are incessant, and are proposed to affect membrane functioning. Although studies show how membrane fluctuations are affected by cellular activity in adherent cells, their spatial regulation and the corresponding change in membrane mechanics remain unclear. In this article, we study how ATP-driven activities and actomyosin cytoskeleton impact basal membrane fluctuations in adherent cells. Using interference imaging, we map height fluctuations within single cells and compare the temporal spectra with existing theoretical models to gain insights about the underlying membrane mechanics. We find that ATP-dependent activities enhance the nanoscale z fluctuations but stretch out the membrane laterally. Although actin polymerization or myosin-II activity individually enhances fluctuations, the cortex in unperturbed cells stretches out the membrane and dampens fluctuations. Fitting with models suggest this dampening to be due to confinement by the cortex. However, reduced fluctuations on mitosis or on ATP-depletion/stabilization of cortex correlate with increased tension. Both maps of fluctuations and local temporal autocorrelation functions reveal ATP-dependent transient short-range (<2 μm) heterogeneities. Together, our results show how various ATP-driven processes differently affect membrane mechanics and hence fluctuations, while creating distinct local environments whose functional role needs future investigation.

The effect of antibiotics on protein diffusion in the Escherichia coli cytoplasmic membrane

Accumulating evidence suggests that molecular motors contribute to the apparent diffusion of molecules in cells. However, current literature lacks evidence for an active process that drives diffusive-like motion in the bacterial membrane. One possible mechanism is cell wall synthesis, which involves the movement of protein complexes in the cell membrane circumferentially around the cell envelope and may generate currents in the lipid bilayer that advectively transport other transmembrane proteins. We test this hypothesis in Escherichia coli using drug treatments that slow cell wall synthesis and measure their effect on the diffusion of the transmembrane protein mannitol permease using fluorescence recovery after photobleaching. We found no clear decrease in diffusion in response to vancomycin and no decrease in response to mecillinam treatment. These results suggest that cell wall synthesis is not an active contributor to mobility in the cytoplasmic membrane.

Feedback-tracking microrheology in living cells

Living cells are composed of active materials, in which forces are generated by the energy derived from metabolism. Forces and structures self-organize to shape the cell and drive its dynamic functions. Understanding the out-of-equilibrium mechanics is challenging because constituent materials, the cytoskeleton and the cytosol, are extraordinarily heterogeneous, and their physical properties are strongly affected by the internally generated forces. We have analyzed dynamics inside two types of eukaryotic cells, fibroblasts and epithelial-like HeLa cells, with simultaneous active and passive microrheology using laser interferometry and optical trapping technology. We developed a method to track microscopic probes stably in cells in the presence of vigorous cytoplasmic fluctuations, by using smooth three-dimensional (3D) feedback of a piezo-actuated sample stage. To interpret the data, we present a theory that adapts the fluctuation-dissipation theorem (FDT) to out-of-equilibrium systems that are subjected to positional feedback, which introduces an additional nonequilibrium effect. We discuss the interplay between material properties and nonthermal force fluctuations in the living cells that we quantify through the violations of the FDT. In adherent fibroblasts, we observed a well-known polymer network viscoelastic response where the complex shear modulus scales as G* ∝ (-iω)3/4. In the more 3D confluent epithelial cells, we found glassy mechanics with G* ∝ (-iω)1/2 that we attribute to glassy dynamics in the cytosol. The glassy state in living cells shows characteristics that appear distinct from classical glasses and unique to nonequilibrium materials that are activated by molecular motors.

Force percolation of contractile active gels

Living systems provide a paradigmatic example of active soft matter. Cells and tissues comprise viscoelastic materials that exert forces and can actively change shape. This strikingly autonomous behavior is powered by the cytoskeleton, an active gel of semiflexible filaments, crosslinks, and molecular motors inside cells. Although individual motors are only a few nm in size and exert minute forces of a few pN, cells spatially integrate the activity of an ensemble of motors to produce larger contractile forces (∼nN and greater) on cellular, tissue, and organismal length scales. Here we review experimental and theoretical studies on contractile active gels composed of actin filaments and myosin motors. Unlike other active soft matter systems, which tend to form ordered patterns, actin-myosin systems exhibit a generic tendency to contract. Experimental studies of reconstituted actin-myosin model systems have long suggested that a mechanical interplay between motor activity and the network's connectivity governs this contractile behavior. Recent theoretical models indicate that this interplay can be understood in terms of percolation models, extended to include effects of motor activity on the network connectivity. Based on concepts from percolation theory, we propose a state diagram that unites a large body of experimental observations. This framework provides valuable insights into the mechanisms that drive cellular shape changes and also provides design principles for synthetic active materials.

Nonequilibrium dynamics of probe filaments in actin-myosin networks

Active dynamic processes of cells are largely driven by the cytoskeleton, a complex and adaptable semiflexible polymer network, motorized by mechanoenzymes. Small dimensions, confined geometries, and hierarchical structures make it challenging to probe dynamics and mechanical response of such networks. Embedded semiflexible probe polymers can serve as nonperturbing multiscale probes to detect force distributions in active polymer networks. We show here that motor-induced forces transmitted to the probe polymers are reflected in nonequilibrium bending dynamics, which we analyze in terms of spatial eigenmodes of an elastic beam under steady-state conditions. We demonstrate how these active forces induce correlations among the mode amplitudes, which furthermore break time-reversal symmetry. This leads to a breaking of detailed balance in this mode space. We derive analytical predictions for the magnitude of resulting probability currents in mode space in the white-noise limit of motor activity. We relate the structure of these currents to the spatial profile of motor-induced forces along the probe polymers and provide a general relation for observable currents on two-dimensional hyperplanes.

Mode Selection in Compressible Active Flow Networks

Coherent, large-scale dynamics in many nonequilibrium physical, biological, or information transport networks are driven by small-scale local energy input. Here, we introduce and explore an analytically tractable nonlinear model for compressible active flow networks. In contrast to thermally driven systems, we find that active friction selects discrete states with a limited number of oscillation modes activated at distinct fixed amplitudes. Using perturbation theory, we systematically predict the stationary states of noisy networks and find good agreement with a Bayesian state estimation based on a hidden Markov model applied to simulated time series data. Our results suggest that the macroscopic response of active network structures, from actomyosin force networks to cytoplasmic flows, can be dominated by a significantly reduced number of modes, in contrast to energy equipartition in thermal equilibrium. The model is also well suited to study topological sound modes and spectral band gaps in active matter.

Segmentation of 3D Trajectories Acquired by TSUNAMI Microscope: An Application to EGFR Trafficking

Whereas important discoveries made by single-particle tracking have changed our view of the plasma membrane organization and motor protein dynamics in the past three decades, experimental studies of intracellular processes using single-particle tracking are rather scarce because of the lack of three-dimensional (3D) tracking capacity. In this study we use a newly developed 3D single-particle tracking method termed TSUNAMI (Tracking of Single particles Using Nonlinear And Multiplexed Illumination) to investigate epidermal growth factor receptor (EGFR) trafficking dynamics in live cells at 16/43 nm (xy/z) spatial resolution, with track duration ranging from 2 to 10 min and vertical tracking depth up to tens of microns. To analyze the long 3D trajectories generated by the TSUNAMI microscope, we developed a trajectory analysis algorithm, which reaches 81% segment classification accuracy in control experiments (termed simulated movement experiments). When analyzing 95 EGF-stimulated EGFR trajectories acquired in live skin cancer cells, we find that these trajectories can be separated into three groups-immobilization (24.2%), membrane diffusion only (51.6%), and transport from membrane to cytoplasm (24.2%). When EGFRs are membrane-bound, they show an interchange of Brownian diffusion and confined diffusion. When EGFRs are internalized, transitions from confined diffusion to directed diffusion and from directed diffusion back to confined diffusion are clearly seen. This observation agrees well with the model of clathrin-mediated endocytosis.