Probing single-cell micromechanics in vivo: the microrheology of C. elegans developing embryos

The cell cycle controls spindle architecture in Arabidopsis by activating the augmin pathway

To ensure an even segregation of chromosomes during somatic cell division, eukaryotes rely on mitotic spindles. Here, we measured prime characteristics of the Arabidopsis mitotic spindle and built a three-dimensional dynamic model using Cytosim. We identified the cell-cycle regulator CYCLIN-DEPENDENT KINASE B1 (CDKB1) together with its cyclin partner CYCB3;1 as key regulators of spindle morphology in Arabidopsis. We found that the augmin component ENDOSPERM DEFECTIVE1 (EDE1) is a substrate of the CDKB1;1-CYCB3;1 complex. A non-phosphorylatable mutant rescue of ede1 resembled the spindle phenotypes of cycb3;1 and cdkb1 mutants and the protein associated less efficiently with spindle microtubules. Accordingly, reducing the level of augmin in simulations recapitulated the phenotypes observed in the mutants. Our findings emphasize the importance of cell-cycle-dependent phospho-control of the mitotic spindle in plant cells and support the validity of our model as a framework for the exploration of mechanisms controlling the organization of the eukaryotic spindle.

Quantifying surface tension and viscosity in biomolecular condensates by FRAP-ID

Many proteins with intrinsically disordered regions undergo liquid-liquid phase separation under specific conditions in vitro and in vivo. These complex biopolymers form a metastable phase with distinct mechanical properties defining the timescale of their biological functions. However, determining these properties is nontrivial, even in vitro, and often requires multiple techniques. Here we report the measurement of both viscosity and surface tension of biomolecular condensates via correlative fluorescence microscopy and atomic force microscopy (AFM) in a single experiment (fluorescence recovery after probe-induced dewetting, FRAP-ID). Upon surface tension evaluation via regular AFM-force spectroscopy, controlled AFM indentations induce dry spots in fluorescent condensates on a glass coverslip. The subsequent rewetting exhibits a contact line velocity that is used to quantify the condensed-phase viscosity. Therefore, in contrast with fluorescence recovery after photobleaching (FRAP), where molecular diffusion is observed, in FRAP-ID fluorescence recovery is obtained through fluid rewetting and the subsequent morphological relaxation. We show that the latter can be used to cross-validate viscosity values determined during the rewetting regime. Making use of fluid mechanics, FRAP-ID is a valuable tool to evaluate the mechanical properties that govern the dynamics of biomolecular condensates and determine how these properties impact the temporal aspects of condensate functionality.

Katanin, kinesin-13, and ataxin-2 inhibit premature interaction between maternal and paternal genomes in C. elegans zygotes

Fertilization occurs before the completion of oocyte meiosis in the majority of animal species and sperm contents move long distances within the zygotes of mouse and C. elegans. If incorporated into the meiotic spindle, paternal chromosomes could be expelled into a polar body resulting in lethal monosomy. Through live imaging of fertilization in C. elegans, we found that the microtubule disassembling enzymes, katanin and kinesin-13 limit long-range movement of sperm contents and that maternal ataxin-2 maintains paternal DNA and paternal mitochondria as a cohesive unit that moves together. Depletion of katanin or double depletion of kinesin-13 and ataxin-2 resulted in the capture of the sperm contents by the meiotic spindle. Thus limiting movement of sperm contents and maintaining cohesion of sperm contents within the zygote both contribute to preventing premature interaction between maternal and paternal genomes.

Katanin, kinesin-13 and ataxin-2 inhibit premature interaction between maternal and paternal genomes in C. elegans zygotes

Fertilization occurs before completion of oocyte meiosis in the majority of animal species and sperm contents move long distances within zygotes of mouse and C. elegans. If incorporated into the meiotic spindle, paternal chromosomes could be expelled into a polar body resulting in lethal monosomy. Through live imaging of fertilization in C. elegans, we found that the microtubule disassembling enzymes, katanin and kinesin-13 limit long range movement of sperm contents and that maternal ataxin-2 maintains paternal DNA and paternal mitochondria as a cohesive unit that moves together. Depletion of katanin or double depletion of kinesin-13 and ataxin-2 resulted in capture of the sperm contents by the meiotic spindle. Thus limiting movement of sperm contents and maintaining cohesion of sperm contents within the zygote both contribute to preventing premature interaction between maternal and paternal genomes.

Macromolecular crowding sensing during osmotic stress in plants

Osmotic stress conditions occur at multiple stages of plant life. Changes in water availability caused by osmotic stress induce alterations in the mechanical properties of the plasma membrane, its interaction with the cell wall, and the concentration of macromolecules in the cytoplasm. We summarize the reported players involved in the sensing mechanisms of osmotic stress in plants. We discuss how changes in macromolecular crowding are perceived intracellularly by intrinsically disordered regions (IDRs) in proteins. Finally, we review methods for dynamically monitoring macromolecular crowding in living cells and discuss why their implementation is required for the discovery of new plant osmosensors. Elucidating the osmosensing mechanisms will be essential for designing strategies to improve plant productivity in the face of climate change.

A surge in cytoplasmic viscosity triggers nuclear remodeling required for Dux silencing and pre-implantation embryo development

Embryonic genome activation (EGA) marks the transition from dependence on maternal transcripts to an embryonic transcriptional program. The precise temporal regulation of gene expression, specifically the silencing of the Dux/murine endogenous retrovirus type L (MERVL) program during late 2-cell interphase, is crucial for developmental progression in mouse embryos. How this finely tuned regulation is achieved within this specific window is poorly understood. Here, using particle-tracking microrheology throughout the mouse oocyte-to-embryo transition, we identify a surge in cytoplasmic viscosity specific to late 2-cell interphase brought about by high microtubule and endomembrane density. Importantly, preventing the rise in 2-cell viscosity severely impairs nuclear reorganization, resulting in a persistently open chromatin configuration and failure to silence Dux/MERVL. This, in turn, derails embryo development beyond the 2- and 4-cell stages. Our findings reveal a mechanical role of the cytoplasm in regulating Dux/MERVL repression via nuclear remodeling during a temporally confined period in late 2-cell interphase.

Cytoplasm mechanics and cellular organization

As cells organize spatially or divide, they translocate many micron-scale organelles in their cytoplasm. These include endomembrane vesicles, nuclei, microtubule asters, mitotic spindles, or chromosomes. Organelle motion is powered by cytoskeleton forces but is opposed by viscoelastic forces imparted by the surrounding crowded cytoplasm medium. These resistive forces associated to cytoplasm physcial properties remain generally underappreciated, yet reach significant values to slow down organelle motion or even limit their displacement by springing them back towards their original position. The cytoplasm may also be itself organized in time and space, being for example stiffer or more fluid at certain locations or during particular cell cycle phases. Thus, cytoplasm mechanics may be viewed as a labile module that contributes to organize cells. We here review emerging methods, mechanisms, and concepts to study cytoplasm mechanical properties and their function in organelle positioning, cellular organization and division.

New tools reveal PCP-dependent polarized mechanics in the cortex and cytoplasm of single cells during convergent extension

Understanding biomechanics of biological systems is crucial for unraveling complex processes like tissue morphogenesis. However, current methods for studying cellular mechanics in vivo are limited by the need for specialized equipment and often provide limited spatiotemporal resolution. Here we introduce two new techniques, Tension by Transverse Fluctuation (TFlux) and in vivo microrheology, that overcome these limitations. They both offer time-resolved, subcellular biomechanical analysis using only fluorescent reporters and widely available microscopes. Employing these two techniques, we have revealed a planar cell polarity (PCP)-dependent mechanical gradient both in the cell cortex and the cytoplasm of individual cells engaged in convergent extension. Importantly, the non-invasive nature of these methods holds great promise for its application for uncovering subcellular mechanical variations across a wide array of biological contexts.

Summary

Non-invasive imaging-based techniques providing time-resolved biomechanical analysis at subcellular scales in developing vertebrate embryos.

How it feels in a cell

Life emerges from thousands of biochemical processes occurring within a shared intracellular environment. We have gained deep insights from in vitro reconstitution of isolated biochemical reactions. However, the reaction medium in test tubes is typically simple and diluted. The cell interior is far more complex: macromolecules occupy more than a third of the space, and energy-consuming processes agitate the cell interior. Here, we review how this crowded, active environment impacts the motion and assembly of macromolecules, with an emphasis on mesoscale particles (10-1000 nm diameter). We describe methods to probe and analyze the biophysical properties of cells and highlight how changes in these properties can impact physiology and signaling, and potentially contribute to aging, and diseases, including cancer and neurodegeneration.

Contractile ring composition dictates kinetics of in silico contractility

Constriction kinetics of the cytokinetic ring are expected to depend on dynamic adjustment of contractile ring composition, but the impact of ring component abundance dynamics on ring constriction is understudied. Computational models generally assume that contractile networks maintain constant total amounts of components, which is not always true. To test how compositional dynamics affect constriction kinetics, we first measured F-actin, non-muscle myosin II, septin, and anillin during Caenorhabditis elegans zygotic mitosis. A custom microfluidic device that positioned the cell with the division plane parallel to a light sheet allowed even illumination of the cytokinetic ring. Measured component abundances were implemented in a three-dimensional agent-based model of a membrane-associated contractile ring. With constant network component amounts, constriction completed with biologically unrealistic kinetics. However, imposing the measured changes in component quantities allowed this model to elicit realistic constriction kinetics. Simulated networks were more sensitive to changes in motor and filament amounts than those of crosslinkers and tethers. Our findings highlight the importance of network composition for actomyosin contraction kinetics.

Light-driven high-precision cell adhesion kinetics

Existing single-cell adhesion kinetics methods are performed under conditions highly unlike the physiological cell adhesion conditions. Now, researchers have developed a new optical technique for high-precision measurement of cell lateral adhesion kinetics in complex clinical samples.

Mechanical Characterization and Modelling of Subcellular Components of Oocytes

The early steps of embryogenesis are controlled exclusively by the quality of oocyte that linked closely to its mechanical properties. The mechanical properties of an oocyte were commonly characterized by assuming it was homogeneous such that the result deviated significantly from the true fact that it was composed of subcellular components. In this work, we accessed and characterized the subcellular components of the oocytes and developed a layered high-fidelity finite element model for describing the viscoelastic responses of an oocyte under loading. The zona pellucida (ZP) and cytoplasm were isolated from an oocyte using an in-house robotic micromanipulation platform and placed on AFM to separately characterizing their mechanical profiling by analyzing the creep behavior with the force clamping technique. The spring and damping parameters of a Kelvin–Voigt model were derived by fitting the creeping curve to the model, which were used to define the shear relaxation modulus and relaxation time of ZP or cytoplasm in the ZP and cytoplasm model. In the micropipette aspiration experiment, the model was accurate sufficiently to deliver the time-varying aspiration depth of the oocytes under the step negative pressure of a micropipette. In the micropipette microinjection experiment, the model accurately described the intracellular strain introduced by the penetration. The developed oocyte FEM model has implications for further investigating the viscoelastic responses of the oocytes under different loading settings.

Self-assembly of pericentriolar material in interphase cells lacking centrioles

The major microtubule-organizing center (MTOC) in animal cells, the centrosome, comprises a pair of centrioles surrounded by pericentriolar material (PCM), which nucleates and anchors microtubules. Centrosome assembly depends on PCM binding to centrioles, PCM self-association and dynein-mediated PCM transport, but the self-assembly properties of PCM components in interphase cells are poorly understood. Here, we used experiments and modeling to study centriole-independent features of interphase PCM assembly. We showed that when centrioles are lost due to PLK4 depletion or inhibition, dynein-based transport and self-clustering of PCM proteins are sufficient to form a single compact MTOC, which generates a dense radial microtubule array. Interphase self-assembly of PCM components depends on γ-tubulin, pericentrin, CDK5RAP2 and ninein, but not NEDD1, CEP152, or CEP192. Formation of a compact acentriolar MTOC is inhibited by AKAP450-dependent PCM recruitment to the Golgi or by randomly organized CAMSAP2-stabilized microtubules, which keep PCM mobile and prevent its coalescence. Linking of CAMSAP2 to a minus-end-directed motor leads to the formation of an MTOC, but MTOC compaction requires cooperation with pericentrin-containing self-clustering PCM. Our data reveal that interphase PCM contains a set of components that can self-assemble into a compact structure and organize microtubules, but PCM self-organization is sensitive to motor- and microtubule-based rearrangement.

Foregut organ progenitors and their niche display distinct viscoelastic properties in vivo during early morphogenesis stages

Material properties of living matter play an important role for biological function and development. Yet, quantification of material properties of internal organs in vivo, without causing physiological damage, remains challenging. Here, we present a non-invasive approach based on modified optical tweezers for quantifying sub-cellular material properties deep inside living zebrafish embryos. Material properties of cells within the foregut region are quantified as deep as 150 µm into the biological tissue through measurements of the positions of an inert tracer. This yields an exponent, α, which characterizes the scaling behavior of the positional power spectra and the complex shear moduli. The measurements demonstrate differential mechanical properties: at the time when the developing organs undergo substantial displacements during morphogenesis, gut progenitors are more elastic (α = 0.57 ± 0.07) than the neighboring yolk (α = 0.73 ± 0.08), liver (α = 0.66 ± 0.06) and two mesodermal (α = 0.68 ± 0.06, α = 0.64 ± 0.06) progenitor cell populations. The higher elasticity of gut progenitors correlates with an increased cellular concentration of microtubules. The results infer a role of material properties during morphogenesis and the approach paves the way for quantitative material investigations in vivo of embryos, explants, or organoids.

Here, the authors present a method based on optical tweezers to measure mechanical properties of cells inside living zebrafish embryos. The measurement reveals spatiotemporally distinct mechanical properties, linking cell mechanics and morphogenesis.

Evolutionary divergence of anaphase spindle mechanics in nematode embryos constrained by antagonistic pulling and viscous forces

Cellular functions like cell division are remarkably conserved across phyla. However the evolutionary principles of cellular organization that drive it are less well explored. Thus, an essential question remains: to what extent cellular parameters evolve without altering the basic function they sustain? Here we have observed 6 different nematode species for which the mitotic spindle is positioned asymmetrically during the first embryonic division. Whereas the C. elegans spindle undergoes oscillations during its displacement, the spindle elongates without oscillations in other species. We asked which evolutionary changes in biophysical parameters could explain differences in spindle motion while maintaining a constant output. Using laser microsurgery of the spindle we revealed that all species are subjected to cortical pulling forces, of varying magnitudes. Using a viscoelastic model to fit the recoil trajectories and with an independent measurement of cytoplasmic viscosity, we extracted the values of cytoplasmic drag, cortical pulling forces and spindle elasticity for all species. We found large variations in cytoplasmic viscosity whereas cortical pulling forces and elasticity were often more constrained. In agreement with previous simulations, we found that increased viscosity correlates with decreased oscillation speeds across species. However, the absence of oscillations despite low viscosity in some species, can only be explained by smaller pulling forces. Consequently, we find that spindle mobility across the species analyzed here is characterized by a tradeoff between cytoplasmic viscosity and pulling forces normalized by the size of the embryo. Our work provides a framework for understanding mechanical constraints on evolutionary diversification of spindle mobility.

Optical tweezer measurements of asymptotic nonlinearities in complex fluids

This article presents micro-medium-amplitude oscillatory shear (μMAOS), a method to measure the frequency-dependent micromechanical properties of soft materials in the asymptotically nonlinear regime using optical tweezers. We have developed a theoretical framework to extract these nonlinear mechanical properties of the material from experimental measurements and also proposed a physical interpretation of the third-order nonlinearities measured in single-tone oscillatory tests. We validate the method using a well-characterized surfactant solution of wormlike micelles, and subsequently employ this technique to demonstrate that the cytoplasm of a living cell undergoes strain softening and shear thinning when locally subjected to weakly nonlinear oscillatory deformations.

Cytoskeletal control of early mammalian development

The cytoskeleton - comprising actin filaments, microtubules and intermediate filaments - serves instructive roles in regulating cell function and behaviour during development. However, a key challenge in cell and developmental biology is to dissect how these different structures function and interact in vivo to build complex tissues, with the ultimate aim to understand these processes in a mammalian organism. The preimplantation mouse embryo has emerged as a primary model system for tackling this challenge. Not only does the mouse embryo share many morphological similarities with the human embryo during its initial stages of life, it also permits the combination of genetic manipulations with live-imaging approaches to study cytoskeletal dynamics directly within an intact embryonic system. These advantages have led to the discovery of novel cytoskeletal structures and mechanisms controlling lineage specification, cell-cell communication and the establishment of the first forms of tissue architecture during development. Here we highlight the diverse organization and functions of each of the three cytoskeletal filaments during the key events that shape the early mammalian embryo, and discuss how they work together to perform key developmental tasks, including cell fate specification and morphogenesis of the blastocyst. Collectively, these findings are unveiling a new picture of how cells in the early embryo dynamically remodel their cytoskeleton with unique spatial and temporal precision to drive developmental processes in the rapidly changing in vivo environment.

Modelling Nuclear Morphology and Shape Transformation: A Review

As one of the most important cellular compartments, the nucleus contains genetic materials and separates them from the cytoplasm with the nuclear envelope (NE), a thin membrane that is susceptible to deformations caused by intracellular forces. Interestingly, accumulating evidence has also indicated that the morphology change of NE is tightly related to nuclear mechanotransduction and the pathogenesis of diseases such as cancer and Hutchinson–Gilford Progeria Syndrome. Theoretically, with the help of well-designed experiments, significant progress has been made in understanding the physical mechanisms behind nuclear shape transformation in different cellular processes as well as its biological implications. Here, we review different continuum-level (i.e., energy minimization, boundary integral and finite element-based) approaches that have been developed to predict the morphology and shape change of the cell nucleus. Essential gradients, relative advantages and limitations of each model will be discussed in detail, with the hope of sparking a greater research interest in this important topic in the future.

The coordination of spindle-positioning forces during the asymmetric division of the Caenorhabditis elegans zygote

In Caenorhabditis elegans zygote, astral microtubules generate forces essential to position the mitotic spindle, by pushing against and pulling from the cortex. Measuring microtubule dynamics there, we revealed the presence of two populations, corresponding to pulling and pushing events. It offers a unique opportunity to study, under physiological conditions, the variations of both spindle-positioning forces along space and time. We propose a threefold control of pulling force, by polarity, spindle position and mitotic progression. We showed that the sole anteroposterior asymmetry in dynein on-rate, encoding pulling force imbalance, is sufficient to cause posterior spindle displacement. The positional regulation, reflecting the number of microtubule contacts in the posterior-most region, reinforces this imbalance only in late anaphase. Furthermore, we exhibited the first direct proof that dynein processivity increases along mitosis. It reflects the temporal control of pulling forces, which strengthens at anaphase onset following mitotic progression and independently from chromatid separation. In contrast, the pushing force remains constant and symmetric and contributes to maintaining the spindle at the cell centre during metaphase.

Principles and Applications of Single Particle Tracking in Cell Research

It is a tough challenge for many decades to decipher the complex relationships between cell behaviors and cellular physical properties. Single particle tracking (SPT) with high spatial and temporal resolution has been applied extensively in cell research to understand physicochemical properties of cells and their bio-functions by tracking endogenous or exogenous probes. This review describes the fundamental principles of SPT as well as its applications in intracellular mechanics, membrane dynamics, organelles distribution, and processes of internalization and transport. Finally, challenges and future directions of SPT are also discussed.

Force balancing ACT-IN the tumor microenvironment: Cytoskeletal modifications in cancer and stromal cells to promote malignancy

The tumor microenvironment is a complex milieu that dictates the growth, invasion, and metastasis of cancer cells. Both cancer and stromal cells in the tumor tissue encounter and adapt to a variety of extracellular factors, and subsequently contribute and drive the progression of the disease to more advanced stages. As the disease progresses, a small population of cancer cells becomes more invasive through a complex process known as epithelial-mesenchymal transition, and nearby stromal cells assume a carcinoma associated fibroblast phenotype characterized by enhanced migration, cell contractility, and matrix secretion with the ability to reorganize extracellular matrices. As cells transition into more malignant phenotypes their biophysical properties, controlled by the organization of cytoskeletal proteins, are altered. Actin and its associated proteins are essential modulators and facilitators of these changes. As the cells respond to the cues in the microenvironment, actin driven mechanical forces inside and outside the cells also evolve. Recent advances in biophysical techniques have enabled us to probe these actin driven changes in cancer and stromal cells and demarcate their role in driving changes in the microenvironment. Understanding the underlying biophysical mechanisms that drive cancer progression could provide critical insight on novel therapeutic approaches in the fight against cancer.

Keratins are asymmetrically inherited fate determinants in the mammalian embryo

To implant in the uterus, the mammalian embryo first specifies two cell lineages: the pluripotent inner cell mass that forms the fetus, and the outer trophectoderm layer that forms the placenta1. In many organisms, asymmetrically inherited fate determinants drive lineage specification2, but this is not thought to be the case during early mammalian development. Here we show that intermediate filaments assembled by keratins function as asymmetrically inherited fate determinants in the mammalian embryo. Unlike F-actin or microtubules, keratins are the first major components of the cytoskeleton that display prominent cell-to-cell variability, triggered by heterogeneities in the BAF chromatin-remodelling complex. Live-embryo imaging shows that keratins become asymmetrically inherited by outer daughter cells during cell division, where they stabilize the cortex to promote apical polarization and YAP-dependent expression of CDX2, thereby specifying the first trophectoderm cells of the embryo. Together, our data reveal a mechanism by which cell-to-cell heterogeneities that appear before the segregation of the trophectoderm and the inner cell mass influence lineage fate, via differential keratin regulation, and identify an early function for intermediate filaments in development.

Probing Intracellular Dynamics Using Fluorescent Carbon Dots Produced by Femtosecond Laser In Situ

Fluorescent particle tracking is a powerful technique for studying intracellular transport and microrheological properties within living cells, which in most cases employs exogenous fluorescent tracer particles delivered into cells or fluorescent staining of cell organelles. Herein, we propose an alternative strategy, which is based on the generation of fluorescent species in situ with ultrashort laser pulses. Using mouse germinal vesicle oocytes as a model object, we demonstrate that femtosecond laser irradiation produces compact dense areas in the intracellular material containing fluorescent carbon dots synthesized from biological molecules. These dots have tunable persistent and excitation-dependent emission, which is highly advantageous for fluorescent imaging. We further show that tight focusing and tuning of irradiation parameters allow precise control of the location and size of fluorescently labeled areas and minimization of damage inflicted to cells. Pieces of the intracellular material down to the submicrometer size can be labeled with laser-produced fluorescent dots in real time and then employed as probes for detecting intracellular motion activity via fluorescent tracking. Analyzing their diffusion in the oocyte cytoplasm, we arrive to realistic characteristics of active forces generated within the cell and frequency-dependent shear modulus of the cytoplasm. We also quantitatively characterize the level of metabolic activity and density of the cytoskeleton meshwork. Our findings establish a new technique for probing intracellular mechanical properties and also promise applications in tracking individual cells in population or studies of spatiotemporal cell organization.

Bond Type and Discretization of Nonmuscle Myosin II Are Critical for Simulated Contractile Dynamics

Molecular motors drive cytoskeletal rearrangements to change cell shape. Myosins are the motors that move, cross-link, and modify the actin cytoskeleton. The primary force generator in contractile actomyosin networks is nonmuscle myosin II (NMMII), a molecular motor that assembles into ensembles that bind, slide, and cross-link actin filaments (F-actin). The multivalence of NMMII ensembles and their multiple roles have confounded the resolution of crucial questions, including how the number of NMMII subunits affects dynamics and what affects the relative contribution of ensembles' cross-linking versus motoring activities. Because biophysical measurements of ensembles are sparse, modeling of actomyosin networks has aided in discovering the complex behaviors of NMMII ensembles. Myosin ensembles have been modeled via several strategies with variable discretization or coarse graining and unbinding dynamics, and although general assumptions that simplify motor ensembles result in global contractile behaviors, it remains unclear which strategies most accurately depict cellular activity. Here, we used an agent-based platform, Cytosim, to implement several models of NMMII ensembles. Comparing the effects of bond type, we found that ensembles of catch-slip and catch motors were the best force generators and binders of filaments. Slip motor ensembles were capable of generating force but unbound frequently, resulting in slower contractile rates of contractile networks. Coarse graining of these ensemble types from two sets of 16 motors on opposite ends of a stiff rod to two binders, each representing 16 motors, reduced force generation, contractility, and the total connectivity of filament networks for all ensemble types. A parallel cluster model, previously used to describe ensemble dynamics via statistical mechanics, allowed better contractility with coarse graining, though connectivity was still markedly reduced for this ensemble type with coarse graining. Together, our results reveal substantial tradeoffs associated with the process of coarse graining NMMII ensembles and highlight the robustness of discretized catch-slip ensembles in modeling actomyosin networks.

Spherical spindle shape promotes perpendicular cortical orientation by preventing isometric cortical pulling on both spindle poles during C. elegans female meiosis

Meiotic spindles are positioned perpendicular to the oocyte cortex to facilitate segregation of chromosomes into a large egg and a tiny polar body. In C. elegans, spindles are initially ellipsoid and parallel to the cortex before shortening to a near-spherical shape with flattened poles and then rotating to the perpendicular orientation by dynein-driven cortical pulling. The mechanistic connection between spindle shape and rotation has remained elusive. Here, we have used three different genetic backgrounds to manipulate spindle shape without eliminating dynein-dependent movement or dynein localization. Ellipsoid spindles with flattened or pointed poles became trapped in either a diagonal or a parallel orientation. Mathematical models that recapitulated the shape dependence of rotation indicated that the lower viscous drag experienced by spherical spindles prevented recapture of the cortex by astral microtubules emanating from the pole pivoting away from the cortex. In addition, maximizing contact between pole dynein and cortical dynein stabilizes flattened poles in a perpendicular orientation, and spindle rigidity prevents spindle bending that can lock both poles at the cortex. Spindle shape can thus promote perpendicular orientation by three distinct mechanisms.

A Molecular Sensor Reveals Differences in Macromolecular Crowding between the Cytoplasm and Nucleoplasm

We describe a molecular sensor that reports, using fluorescence resonance energy transfer (FRET), on the degree of macromolecular crowding in different cellular compartments. The oligonucleotide-based sensor is sensitive to changes in the volume fraction of macromolecules over a wide range in vitro and, when introduced in cells, rapidly distributes and shows a striking contrast between the cytosol and the nucleus. This contrast can be modulated by osmotic stress or by using a number of drugs that alter chromatin organization within the nucleus. These findings suggest that the sensor can be used as a tool to probe chromosome organization. Further, our finding that the cell maintains different degrees of macromolecular crowding in the cytoplasm and nucleoplasm has implications on molecular mechanisms since crowding can alter protein conformations, binding rates, reaction kinetics, and therefore protein function.

Single-Crystal Rutile TiO2 Nanocylinders are Highly Effective Transducers of Optical Force and Torque

Optical trapping of (sub)micron-sized particles is broadly employed in nanoscience and engineering. The materials commonly employed for these particles, however, have physical properties that limit the transfer of linear or angular momentum (or both). This reduces the magnitude of forces and torques, and the spatiotemporal resolution, achievable in linear and angular traps. Here, we overcome these limitations through the use of single-crystal rutile TiO₂, which has an exceptionally large optical birefringence, a high index of refraction, good chemical stability, and is amenable to geometric control at the nanoscale. We show that rutile TiO₂ nanocylinders form powerful joint force and torque transducers in aqueous environments by using only moderate laser powers to apply nN·nm torques at kHz rotational frequencies to tightly trapped particles. In doing so, we demonstrate how rutile TiO₂ nanocylinders outperform other materials and offer unprecedented opportunities to expand the control of optical force and torque at the nanoscale.

Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes

Segregation of maternal determinants within the oocyte constitutes the first step in embryo patterning. In zebrafish oocytes, extensive ooplasmic streaming leads to the segregation of ooplasm from yolk granules along the animal-vegetal axis of the oocyte. Here, we show that this process does not rely on cortical actin reorganization, as previously thought, but instead on a cell-cycle-dependent bulk actin polymerization wave traveling from the animal to the vegetal pole of the oocyte. This wave functions in segregation by both pulling ooplasm animally and pushing yolk granules vegetally. Using biophysical experimentation and theory, we show that ooplasm pulling is mediated by bulk actin network flows exerting friction forces on the ooplasm, while yolk granule pushing is achieved by a mechanism closely resembling actin comet formation on yolk granules. Our study defines a novel role of cell-cycle-controlled bulk actin polymerization waves in oocyte polarization via ooplasmic segregation.

Role of mechanical flow for actin network organization

The major cytoskeletal protein actin forms complex networks to provide structural support and perform vital functions in cells. In vitro studies have revealed that the structure of the higher-order actin network is determined primarily by the type of actin binding protein (ABP). By comparison, there are far fewer studies about the role of the mechanical environment for the organization of the actin network. In particular, the duration over which cells reorganize their shape in response to functional demands is relatively short compared to the in vitro protein polymerization time, suggesting that such changes can influence the actin network formation. We hypothesize that mechanical flows in the cytoplasm generated by exogenous and endogenous stimulation play a key role in the spatiotemporal regulation of the actin architecture. To mimic cytoplasmic streaming, we generated a circulating flow using surface acoustic wave in a microfluidic channel and investigated its effect on the formation of networks by actin and ABPs. We found that the mechanical flow affected the orientation and thickness of actin bundles, depending on the type and concentration of ABPs. Our computational model shows that the extent of alignment and thickness of actin bundle are determined by the balance between flow-induced drag forces and the tendency of ABPs to crosslink actin filaments at given angles. These results suggest that local intracellular flows can affect the assembly dynamics and morphology of the actin cytoskeleton. STATEMENT OF SIGNIFICANCE: Spatiotemporal regulation of actin cytoskeleton structure is essential in many cellular functions. It has been shown that mechanical cues including an applied force and geometric boundary can alter the structural characteristics of actin network. However, even though the cytoplasm accounts for a large portion of the cell volume, the effect of the cytoplasmic streaming flow produced during cell dynamics on actin network organization has not been reported. In this study, we demonstrated that the mechanical flow exerted during actin network organization play an important role in determining the orientation and dimension of actin bundle network. Our result will be beneficial in understanding the mechanism of the actin network reorganization occurred during physiological and pathological processes.

Caenorhabditis elegans as a complete model organism for biosafety assessments of nanoparticles

The number of biosafety evaluation studies of nanoparticles (NPs) using different biological models is increasing with the rapid development of nanotechnology. Thus far, nematode Caenorhabditis elegans (C. elegans), as a complete model organism, has become an important in vivo alternative assay system to assess the risk of NPs, especially at the environmental level. According to results of qualitative and quantitative analyses, it can be concluded that studies of nanoscientific research using C. elegans is persistently growing. However, the comprehensive conclusion and analysis of toxic effects of NPs in C. elegans are limited and chaotic. This review focused on the effects, especially sublethal ones, induced by NPs in C. elegans, including the development, intestinal function, immune response, neuronal function, and reproduction, as well as the underlying mechanisms of NPs causing these effects, including oxidative stress and alterations of several signaling pathways. Furthermore, we presented some factors that influence the toxic effects of NPs in C. elegans. The advantages and limitations of using nematodes in the nanotoxicology study were also discussed. Finally, we predicted that the application of C. elegans to assess long-term impacts of metal oxide NPs in the ecosystem would become a vital part of the nanoscientific research field, which provided an insight for further study.

Separating the contributions of zona pellucida and cytoplasm in the viscoelastic response of human oocytes

The successful characterization of the mechanical properties of human oocytes and young embryos is of crucial relevance to reduce the risk of pregnancy arrest in in-vitro fertilization processes. Unfortunately, current study has been hindered by the lack of accuracy in describing the mechanical contributions of each structure (zona pellucida, cytoplasm) due to its high heterogeneity. In this work, we present a novel approach to model the oocyte response taking into account the effect of both zona and cytoplasm, as well as different loading conditions. The model is then applied to develop an experimental protocol capable of accurately separating the viscoelastic contribution of zona and cytoplasm by simply varying the loading condition. This new protocol has the potential to open the door to improving our understanding the mechanical properties of oocytes at different stages, and provide a quantitative predictive ability to the evaluation of oocyte quality. STATEMENT OF SIGNIFICANCE: Assisted reproductive technologies, such as in vitro fertilization, often rely on identifying high quality oocytes or female egg cells. The viscoelastic properties of these cells, such as stiffness and stress relaxation time, have been identified as potential objective indicators of cell quality. However, their characterization has proven difficult due to the structural heterogeneity of the cell and inconsistent loading conditions. This paper presents a new model that, although simple, addresses the above difficulties to provide accurate estimations of the cell's mechanical properties. Learning from this model, we then propose a novel non-invasive testing protocol to allow oocyte characterization with increased accuracy. We believe this effort would improve consistency in measurements and enhance our knowledge on the mechanics of oocytes.

Using Microinjection to Generate Genetically Modified Caenorhabditis elegans by CRISPR/Cas9 Editing

In this chapter, we describe the procedure for generating genetically modified Caenorhabditis elegans using microinjection via the Cas9-mediated Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) editing technique. Specifically, we describe the detailed method of performing CRISPR editing by microinjection using the Cloning-free Co-CRISPR method described by the Seydoux lab. This microinjection protocol can also be used for CRISPR editing with protocols from other labs as well as for a variety of other editing techniques including Mos1-mediated single-copy transgene insertions (MosSCI), transcriptional activator-like nucleases (TALENs), and zinc-finger nucleases (ZFNs). Further, this microinjection protocol can also be used for injecting plasmid DNA to generate heritable extrachromosomal arrays for gene expression and mosaic analysis, performing RNAi by injection and delivering RNA, dyes or other molecules into the C. elegans germline.

Unite to divide - how models and biological experimentation have come together to reveal mechanisms of cytokinesis

Cytokinesis is the fundamental and ancient cellular process by which one cell physically divides into two. Cytokinesis in animal and fungal cells is achieved by contraction of an actomyosin cytoskeletal ring assembled in the cell cortex, typically at the cell equator. Cytokinesis is essential for the development of fertilized eggs into multicellular organisms and for homeostatic replenishment of cells. Correct execution of cytokinesis is also necessary for genome stability and the evasion of diseases including cancer. Cytokinesis has fascinated scientists for well over a century, but its speed and dynamics make experiments challenging to perform and interpret. The presence of redundant mechanisms is also a challenge to understand cytokinesis, leaving many fundamental questions unresolved. For example, how does a disordered cytoskeletal network transform into a coherent ring? What are the long-distance effects of localized contractility? Here, we provide a general introduction to 'modeling for biologists', and review how agent-based modeling and continuum mechanics modeling have helped to address these questions.

Tissue biomechanics during cranial neural tube closure measured by Brillouin microscopy and optical coherence tomography

BACKGROUND

Embryonic development involves the interplay of driving forces that shape the tissue and the mechanical resistance that the tissue offers in response. While increasing evidence has suggested the crucial role of physical mechanisms underlying embryo development, tissue biomechanics is not well understood because of the lack of techniques that can quantify the stiffness of tissue in situ with 3D high-resolution and in a noncontact manner.

METHODS

We used two all-optical techniques, optical coherence tomography (OCT) and Brillouin microscopy, to map the longitudinal modulus of the tissue from mouse embryos in situ.

RESULTS

We acquired 2D mechanical maps of the neural tube region of embryos at embryonic day (E) 8.5 (n = 2) and E9.5 (n = 2) with submicron spatial resolution. We found the modulus of tissue varied distinctly within the neural tube region of the same embryo and between embryos at different development stages, suggesting our technique has enough sensitivity and spatial resolution to monitor the tissue mechanics during embryonic development in a noncontact and noninvasive manner.

CONCLUSIONS

We demonstrated the capability of OCT-guided Brillouin microscopy to quantify tissue longitudinal modulus of mouse embryos in situ, and observed distinct change in the modulus during the closure of cranial neural tube. Although this preliminary work cannot provide definitive conclusions on biomechanics of neural tube closure yet as a result of the limited number of samples, it provides an approach of quantifying the tissue mechanics during embryo development in situ, thus could be helpful in investigating the role of tissue biomechanics in the regulation of embryonic development. Our next study involving more embryo samples will investigate systematic changes in tissue mechanics during embryonic development.

mTORC1 Controls Phase Separation and the Biophysical Properties of the Cytoplasm by Tuning Crowding

Macromolecular crowding has a profound impact on reaction rates and the physical properties of the cell interior, but the mechanisms that regulate crowding are poorly understood. We developed genetically encoded multimeric nanoparticles (GEMs) to dissect these mechanisms. GEMs are homomultimeric scaffolds fused to a fluorescent protein that self-assemble into bright, stable particles of defined size and shape. By combining tracking of GEMs with genetic and pharmacological approaches, we discovered that the mTORC1 pathway can modulate the effective diffusion coefficient of particles ≥20 nm in diameter more than 2-fold by tuning ribosome concentration, without any discernable effect on the motion of molecules ≤5 nm. This change in ribosome concentration affected phase separation both in vitro and in vivo. Together, these results establish a role for mTORC1 in controlling both the mesoscale biophysical properties of the cytoplasm and biomolecular condensation.

The importance of mechanical constraints for proper polarization and psuedo-cleavage furrow generation in the early Caenorhabditis elegans embryo

Intracellular polarization, where a cell specifies a spatial axis by segregation of specific factors, is a fundamental biological process. In the early embryo of the nematode worm Caenorhabditis elegans (C. elegans), polarization is often accompanied by deformations of the cortex, a highly contractile structure consisting of actin filaments cross-linked by the motor protein myosin (actomyosin). It has been suggested that the eggshell surrounding the early embryo plays a role in polarization although its function is not understood. Here we develop a mathematical model which couples a reaction-diffusion model of actomyosin dynamics with a phase field model of the cell cortex to implicitly track cell shape changes in the early C. elegans embryo. We investigate the potential rigidity effect of the geometric constraint imposed by the presence and size of the eggshell on polarization dynamics. Our model suggests that the geometric constraint of the eggshell is essential for proper polarization and the size of the eggshell also affects the dynamics of polarization. Therefore, we conclude that geometric constraint on a cell might affect the dynamics of a biochemical process.

Polarization, whereby molecules and proteins are asymmetrically distributed throughout the cell, is a vital process for many cellular functions. In the early C. elegans embryo the asymmetric distribution of cell cytoskeleton during the initiation of polarization leads to asymmetric contractions which are higher in the anterior and lower in the posterior of a cell. The C. elegans embryo is surrounded by a rigid body, the eggshell, which functions in numerous cell processes. We investigate the structural support of eggshell during the establishment phase by tracking the moving cell surface. We incorporate protein dynamics involved in polarization into the membrane evolution. We conclude that eggshell might have a role in cell polarization by preventing the distortion of cell surface.

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.

mTORC1 Controls Phase Separation and the Biophysical Properties of the Cytoplasm by Tuning Crowding

Macromolecular crowding has a profound impact on reaction rates and the physical properties of the cell interior, but the mechanisms that regulate crowding are poorly understood. We developed genetically encoded multimeric nanoparticles (GEMs) to dissect these mechanisms. GEMs are homomultimeric scaffolds fused to a fluorescent protein that self-assemble into bright, stable particles of defined size and shape. By combining tracking of GEMs with genetic and pharmacological approaches, we discovered that the mTORC1 pathway can modulate the effective diffusion coefficient of particles ≥20 nm in diameter more than 2-fold by tuning ribosome concentration, without any discernable effect on the motion of molecules ≤5 nm. This change in ribosome concentration affected phase separation both in vitro and in vivo. Together, these results establish a role for mTORC1 in controlling both the mesoscale biophysical properties of the cytoplasm and biomolecular condensation.

How Do We Know when Single-Molecule Force Spectroscopy Really Tests Single Bonds?

Single-molecule force spectroscopy makes it possible to measure the mechanical strength of single noncovalent receptor-ligand-type bonds. A major challenge in this technique is to ensure that measurements reflect bonds between single biomolecules because the molecules cannot be directly observed. This perspective evaluates different methodologies for identifying and reducing the contribution of multiple molecule interactions to single-molecule measurements to help the reader design experiments or assess publications in the single-molecule force spectroscopy field. We apply our analysis to the large body of literature that purports to measure the strength of single bonds between biotin and streptavidin as a demonstration that measurements are only reproducible when the most reliable methods for ensuring single molecules are used.

Magnetic tweezers optimized to exert high forces over extended distances from the magnet in multicellular systems

Magnetic tweezers are mainly divided into two classes depending on the ability of applying torque or forces to the magnetic probe. We focused on the second category and designed a device composed by a single electromagnet equipped with a core having a special asymmetric profile to exert forces as large as 230 pN-2.8 μm Dynabeads at distances in excess of 100 μm from the magnetic tip. Compared to existing solutions our magnetic tweezers overcome important limitations, opening new experimental paths for the study of a wide range of materials in a variety of biophysical research settings. We discuss the benefits and drawbacks of different magnet core characteristics, which led us to design the current core profile. To demonstrate the usefulness of our magnetic tweezers, we determined the microrheological properties inside embryos of Drosophila melanogaster during the syncytial stage. Measurements in different locations along the dorsal-ventral axis of the embryos showed little variation, with a slight increase in cytoplasm viscosity at the periphery of the embryos. The mean cytoplasm viscosity we obtain by active force exertion inside the embryos is comparable to that determined passively using high-speed video microrheology.

A multiplexed magnetic tweezer with precision particle tracking and bi-directional force control

Background

In the past two decades, methods have been developed to measure the mechanical properties of single biomolecules. One of these methods, Magnetic tweezers, is amenable to aquisition of data on many single molecules simultaneously, but to take full advantage of this "multiplexing" ability, it is necessary to simultaneously incorprorate many capabilities that ahve been only demonstrated separately.

Methods

Our custom built magnetic tweezer combines high multiplexing, precision bead tracking, and bi-directional force control into a flexible and stable platform for examining single molecule behavior. This was accomplished using electromagnets, which provide high temporal control of force while achieving force levels similar to permanent magnets via large paramagnetic beads.

Results

Here we describe the instrument and its ability to apply 2–260 pN of force on up to 120 beads simultaneously, with a maximum spatial precision of 12 nm using a variety of bead sizes and experimental techniques. We also demonstrate a novel method for increasing the precision of force estimations on heterogeneous paramagnetic beads using a combination of density separation and bi-directional force correlation which reduces the coefficient of variation of force from 27% to 6%. We then use the instrument to examine the force dependence of uncoiling and recoiling velocity of type 1 fimbriae from Eschericia coli (E. coli) bacteria, and see similar results to previous studies.

Conclusion

This platform provides a simple, effective, and flexible method for efficiently gathering single molecule force spectroscopy measurements.

AFM and Microrheology in the Zebrafish Embryo Yolk Cell

Elucidating the factors that direct the spatio-temporal organization of evolving tissues is one of the primary purposes in the study of development. Various propositions claim to have been important contributions to the understanding of the mechanical properties of cells and tissues in their spatiotemporal organization in different developmental and morphogenetic processes. However, due to the lack of reliable and accessible tools to measure material properties and tensional parameters in vivo, validating these hypotheses has been difficult. Here we present methods employing atomic force microscopy (AFM) and particle tracking with the aim of quantifying the mechanical properties of the intact zebrafish embryo yolk cell during epiboly. Epiboly is an early conserved developmental process whose study is facilitated by the transparency of the embryo. These methods are simple to implement, reliable, and widely applicable since they overcome intrusive interventions that could affect tissue mechanics. A simple strategy was applied for the mounting of specimens, AFM recording, and nanoparticle injections and tracking. This approach makes these methods easily adaptable to other developmental times or organisms.

Quantification of Lipid Metabolism in Living Cells through the Dynamics of Lipid Droplets Measured by Stimulated Raman Scattering Imaging

Dysregulation of lipid metabolism is associated with many diseases including cancer. Lipid droplet (LD), a ubiquitous organelle in mammalian cells, serves as a hub for lipid metabolism. Conventional assays on the measurement of lipid metabolism rely on the quantification of the lipid composition or amount. Such methods cannot distinguish LDs having different biofunctionalities in living cells, and thus could be inaccurate in measuring the instantaneous lipogenesis of the living cells. We applied label-free stimulated Raman scattering microscopy to quantify the LDs' spatial-temporal dynamics, which showed direct links to cellular lipid metabolisms and can separate LDs involved in different metabolic events. In human cancer cells, we found that changes in the maximum displacement of LDs reflected variations in cellular lipogenic activity, and changes in the average speed of LDs revealed alterations in LD size. The LD dynamics analysis allowed for more accurate measurement in the lipogenesis and LD dimensions, and can break the optical diffraction limit to detect small variation in lipid metabolism that was conventionally undetectable. By this method, we revealed changes in the lipogenic activity and LD sizes during glucose starvation of HeLa cells and transforming growth factor beta-induced epithelial-to-mesenchymal transition of SKOV-3 cells. This method opens a way to quantify lipid metabolism in living cells during cellular development and transition.

In Vivo Multiscale and Spatially-Dependent Biomechanics Reveals Differential Strain Transfer Hierarchy in Skeletal Muscle

Biological tissues have a complex hierarchical architecture that spans organ to subcellular scales and comprises interconnected biophysical and biochemical machinery. Mechanotransduction, gene regulation, gene protection, and structure-function relationships in tissues depend on how force and strain are modulated from macro to micro scales, and vice versa. Traditionally, computational and experimental techniques have been used in common model systems (e.g., embryos) and simple strain measures were applied. But the hierarchical transfer of mechanical parameters like strain in mammalian systems is largely unexplored in vivo. Here, we experimentally probed complex strain transfer processes in mammalian skeletal muscle tissue over multiple biological scales using complementary in vivo ultrasound and optical imaging approaches. An iterative hyperelastic warping technique quantified the spatially-dependent strain distributions in tissue, matrix, and subcellular (nuclear) structures, and revealed a surprising increase in strain magnitude and heterogeneity in active muscle as the spatial scale also increased. The multiscale strain heterogeneity indicates tight regulation of mechanical signals to the nuclei of individual cells in active muscle, and an emergent behavior appearing at larger (e.g. tissue) scales characterized by dramatically increased strain complexity.

Disentangling Random Motion and Flow in a Complex Medium

We describe a technique for deconvolving the stochastic motion of particles from large-scale fluid flow in a dynamic environment such as that found in living cells. The method leverages the separation of timescales to subtract out the persistent component of motion from single-particle trajectories. The mean-squared displacement of the resulting trajectories is rescaled so as to enable robust extraction of the diffusion coefficient and subdiffusive scaling exponent of the stochastic motion. We demonstrate the applicability of the method for characterizing both diffusive and fractional Brownian motion overlaid by flow and analytically calculate the accuracy of the method in different parameter regimes. This technique is employed to analyze the motion of lysosomes in motile neutrophil-like cells, showing that the cytoplasm of these cells behaves as a viscous fluid at the timescales examined.

Polarized cortical tension drives zebrafish epiboly movements

The principles underlying the biomechanics of morphogenesis are largely unknown. Epiboly is an essential embryonic event in which three tissues coordinate to direct the expansion of the blastoderm. How and where forces are generated during epiboly, and how these are globally coupled remains elusive. Here we developed a method, hydrodynamic regression (HR), to infer 3D pressure fields, mechanical power, and cortical surface tension profiles. HR is based on velocity measurements retrieved from 2D+T microscopy and their hydrodynamic modeling. We applied HR to identify biomechanically active structures and changes in cortex local tension during epiboly in zebrafish. Based on our results, we propose a novel physical description for epiboly, where tissue movements are directed by a polarized gradient of cortical tension. We found that this gradient relies on local contractile forces at the cortex, differences in elastic properties between cortex components and the passive transmission of forces within the yolk cell. All in all, our work identifies a novel way to physically regulate concerted cellular movements that might be instrumental for the mechanical control of many morphogenetic processes.