Measuring microtubule dynamics

The interaction between KIF21A and KANK1 regulates dendritic morphology and synapse plasticity in neurons

JOURNAL/nrgr/04.03/01300535-202501000-00029/figure1/v/2024-05-14T021156Z/r/image-tiff Morphological alterations in dendritic spines have been linked to changes in functional communication between neurons that affect learning and memory. Kinesin-4 KIF21A helps organize the microtubule-actin network at the cell cortex by interacting with KANK1; however, whether KIF21A modulates dendritic structure and function in neurons remains unknown. In this study, we found that KIF21A was distributed in a subset of dendritic spines, and that these KIF21A-positive spines were larger and more structurally plastic than KIF21A-negative spines. Furthermore, the interaction between KIF21A and KANK1 was found to be critical for dendritic spine morphogenesis and synaptic plasticity. Knockdown of either KIF21A or KANK1 inhibited dendritic spine morphogenesis and dendritic branching, and these deficits were fully rescued by coexpressing full-length KIF21A or KANK1, but not by proteins with mutations disrupting direct binding between KIF21A and KANK1 or binding between KANK1 and talin1. Knocking down KIF21A in the hippocampus of rats inhibited the amplitudes of long-term potentiation induced by high-frequency stimulation and negatively impacted the animals' cognitive abilities. Taken together, our findings demonstrate the function of KIF21A in modulating spine morphology and provide insight into its role in synaptic function.

A circle of life: platelet and megakaryocyte cytoskeleton dynamics in health and disease

Platelets are blood cells derived from megakaryocytes that play a central role in regulating haemostasis and vascular integrity. The microtubule cytoskeleton of megakaryocytes undergoes a critical dynamic reorganization during cycles of endomitosis and platelet biogenesis. Quiescent platelets have a discoid shape maintained by a marginal band composed of microtubule bundles, which undergoes remarkable remodelling during platelet activation, driving shape change and platelet function. Disrupting or enhancing this process can cause platelet dysfunction such as bleeding disorders or thrombosis. However, little is known about the molecular mechanisms underlying the reorganization of the cytoskeleton in the platelet lineage. Recent studies indicate that the emergence of a unique platelet tubulin code and specific pathogenic tubulin mutations cause platelet defects and bleeding disorders. Frequently, these mutations exhibit dominant negative effects, offering valuable insights into both platelet disease mechanisms and the functioning of tubulins. This review will highlight our current understanding of the role of the microtubule cytoskeleton in the life and death of platelets, along with its relevance to platelet disorders.

Damage-repair events increase the instability of cortical microtubules in Arabidopsis

Microtubules rely on dynamic assembly and disassembly for their functions. Increasing evidences support that the damage-repair of microtubule lattices can affect microtubule dynamics in vitro and in animal cells. Here we successfully established a way for visualizing damage-repair sites on microtubule lattices in plant cells, via labeling the tubulin proteins with the photoconvertible fluorescent protein mEOS3.2. We observed that the crossovers of the microtubule lattice were more prone to be damaged and repaired, with the frequency of damage-repair events positively correlated with the crossing angle between microtubules. The microtubules with damage-repair events displayed shorter lifespans and significantly increased severing frequency compared with the undamaged microtubules. These observations suggested that the damage-repair events promoted instability of cortical microtubules in plant cells.

User-friendly oblique plane microscopy on a fully functional commercially available microscope base

In this work we present an oblique plane microscope designed to work seamlessly with a commercially available microscope base. To support all the functionality offered by the microscope base, where the position of the objective lens is not fixed, we adopted a two-mirror scanning geometry that can compensate for changes to the position of the objective lens during routine microscope operation. We showed that within a ± 1 mm displacement range of the 100X, 1.35 NA objective lens away from its designed position, the PSF size increased by <3% and <11% in the lateral and axial dimensions, respectively, while the error in magnification was <0.5% within volumes extending ± 10 µm about the focal plane. Compared to the more traditional scan-lens/galvo-mirror combination, the two-mirror scanning geometry offers higher light efficiency and a more compact footprint, which could be beneficial to all OPM designs regardless of the use of a commercial base or not.

Coherent light scattering from cellular dynamics in living tissues

This review examines the biological physics of intracellular transport probed by the coherent optics of dynamic light scattering from optically thick living tissues. Cells and their constituents are in constant motion, composed of a broad range of speeds spanning many orders of magnitude that reflect the wide array of functions and mechanisms that maintain cellular health. From the organelle scale of tens of nanometers and upward in size, the motion inside living tissue is actively driven rather than thermal, propelled by the hydrolysis of bioenergetic molecules and the forces of molecular motors. Active transport can mimic the random walks of thermal Brownian motion, but mean-squared displacements are far from thermal equilibrium and can display anomalous diffusion through Lévy or fractional Brownian walks. Despite the average isotropic three-dimensional environment of cells and tissues, active cellular or intracellular transport of single light-scattering objects is often pseudo-one-dimensional, for instance as organelle displacement persists along cytoskeletal tracks or as membranes displace along the normal to cell surfaces, albeit isotropically oriented in three dimensions. Coherent light scattering is a natural tool to characterize such tissue dynamics because persistent directed transport induces Doppler shifts in the scattered light. The many frequency-shifted partial waves from the complex and dynamic media interfere to produce dynamic speckle that reveals tissue-scale processes through speckle contrast imaging and fluctuation spectroscopy. Low-coherence interferometry, dynamic optical coherence tomography, diffusing-wave spectroscopy, diffuse-correlation spectroscopy, differential dynamic microscopy and digital holography offer coherent detection methods that shed light on intracellular processes. In health-care applications, altered states of cellular health and disease display altered cellular motions that imprint on the statistical fluctuations of the scattered light. For instance, the efficacy of medical therapeutics can be monitored by measuring the changes they induce in the Doppler spectra of livingex vivocancer biopsies.

Ultrasensitivity of microtubule severing due to damage repair

Microtubule-based cytoskeletal structures aid in cell motility, cell polarization, and intracellular transport. These functions require a coordinated effort of regulatory proteins which interact with microtubule cytoskeleton distinctively. In-vitro experiments have shown that free tubulin can repair nanoscale damages of microtubules created by severing proteins. Based on this observation, we theoretically analyze microtubule severing as a competition between the processes of damage spreading and tubulin-induced repair. We demonstrate that this model is in quantitative agreement with in-vitro experiments and predict the existence of a critical tubulin concentration above which severing becomes rare, fast, and sensitive to concentration of free tubulin. We show that this sensitivity leads to a dramatic increase in the dynamic range of steady-state microtubule lengths when the free tubulin concentration is varied, and microtubule lengths are controlled by severing. Our work demonstrates how synergy between tubulin and microtubule-associated proteins can bring about specific dynamical properties of microtubules.

Quantification of cellular phototoxicity of organelle stains by the dynamics of microtubule polymerization

Being able to quantify the phototoxicity of dyes and drugs in live cells allows biologists to better understand cell responses to exogenous stimuli during imaging. This capability further helps to design fluorescent labels with lower phototoxicity and drugs with better efficacy. Conventional ways to evaluate cellular phototoxicity rely on late-stage measurements of individual or different populations of cells. Here, we developed a quantitative method using intracellular microtubule polymerization as a rapid and sensitive marker to quantify early-stage phototoxicity. Implementing this method, we assessed the photosensitization induced by organelle dyes illuminated with different excitation wavelengths. Notably, fluorescent markers targeting mitochondria, nuclei, and endoplasmic reticulum exhibited diverse levels of phototoxicity. Furthermore, leveraging a real-time precision opto-control technology allowed us to evaluate the synergistic effect of light and dyes on specific organelles. Studies in hypoxia revealed enhanced phototoxicity of Mito-Tracker Red CMXRos that is not correlated with the generation of reactive oxygen species but a different deleterious pathway in low oxygen conditions.

Teaser

Microtubule dynamics in live cells allow quantification of cellular phototoxicity of fluorescent dyes in various conditions.

Measuring Mitotic Spindle and Microtubule Dynamics in Marine Embryos and Non-model Organisms

During eukaryotic cell division a microtubule-based structure, the mitotic spindle, aligns and segregates chromosomes between daughter cells. Understanding how this cellular structure is assembled and coordinated in space and in time requires measuring microtubule dynamics and visualizing spindle assembly with high temporal and spatial resolution. Visualization is often achieved by the introduction and the detection of molecular probes and fluorescence microscopy. Microtubules and mitotic spindles are highly conserved across eukaryotes; however, several technical limitations have restricted these investigations to only a few species. The ability to monitor microtubule and chromosome choreography in a wide range of species is fundamental to reveal conserved mechanisms or unravel unconventional strategies that certain forms of life have developed to ensure faithful partitioning of chromosomes during cell division. Here, we describe a technique based on injection of purified proteins that enables the visualization of microtubules and chromosomes with a high contrast in several divergent marine embryos. We also provide analysis methods and tools to extract microtubule dynamics and monitor spindle assembly. These techniques can be adapted to a wide variety of species in order to measure microtubule dynamics and spindle assembly kinetics when genetic tools are not available or in parallel to the development of such techniques in non-model organisms.

Salactin, a dynamically unstable actin homolog in Haloarchaea

IMPORTANCE

Protein filaments play important roles in many biological processes. We discovered an actin homolog in halophilic archaea, which we call Salactin. Just like the filaments that segregate DNA in eukaryotes, Salactin grows out of the cell poles towards the middle, and then quickly depolymerizes, a behavior known as dynamic instability. Furthermore, we see that Salactin affects the distribution of DNA in daughter cells when cells are grown in low-phosphate media, suggesting Salactin filaments might be involved in segregating DNA when the cell has only a few copies of the chromosome.

A general model for the motion of multivalent cargo interacting with substrates

Multivalent interactions are common in biology at many different length scales, and can result in the directional motion of multivalent cargo along substrates. Here, a general analytical model has been developed that can describe the directional motion of multivalent cargo as a response to position dependence in the binding and unbinding rates exhibited by their interaction sites. Cargo exhibit both an effective velocity, which acts in the direction of increasing cargo-substrate binding rate and decreasing cargo-substrate unbinding rate, and an effective diffusivity. This model can reproduce previously published experimental findings using only the binding and unbinding rate distributions of cargo interaction sites, and without any further parameter fitting. Extension of the cargo binding model to two dimensions reveals an effective velocity with the same properties as that derived for the one-dimensional case.

Label-free drug response evaluation of human derived tumor spheroids using three-dimensional dynamic optical coherence tomography

This study aims at demonstrating label-free drug-response-patterns assessment of different tumor spheroids and drug types by dynamic optical coherence tomography (D-OCT). The study involved human breast cancer (MCF-7) and colon cancer (HT-29) spheroids. The MCF-7 and HT-29 spheroids were treated with paclitaxel (Taxol; PTX) and the active metabolite of irinotecan SN-38, respectively. The drugs were applied with 0 (control), 0.1, 1, and 10 μM concentrations and the treatment durations were 1, 3, and 6 days. A swept-source OCT microscope equipped with a repeated raster scanning protocol was used to scan the spheroids. Logarithmic intensity variance (LIV) and late OCT correlation decay speed (OCDS[Formula: see text]) algorithms were used to visualize the tumor spheroid dynamics. LIV and OCDS[Formula: see text] images visualized different response patterns of the two types of spheroids. In addition, spheroid morphology, LIV, and OCDS[Formula: see text] quantification showed different time-courses among the spheroid and drug types. These results may indicate different action mechanisms of the drugs. The results showed the feasibility of D-OCT for the evaluation of drug response patterns of different cell spheroids and drug types and suggest that D-OCT can perform anti-cancer drug testing.

Filament displacement image analytics tool for use in investigating dynamics of dense microtubule networks

The fate and motion of cells is influenced by a variety of physical characteristics of their microenvironments. Traditionally, mechanobiology focuses on external mechanical phenomena such as cell movement and environmental sensing. However, cells are inherently dynamic, where internal waves and internal oscillations are a hallmark of living cells observed under a microscope. We propose that these internal mechanical rhythms provide valuable information about cell health. Therefore, it is valuable to capture the rhythms inside cells and quantify how drugs or physical interventions affect a cell's internal dynamics. One of the key dynamical entities inside cells is the microtubule network. Typically, microtubule dynamics are measured by end-protein tracking. In contrast, this paper introduces an easy-to-implement approach to measure the lateral motion of the microtubule filaments embedded within dense networks with (at least) confocal resolution image sequences. Our tool couples the computer vision algorithm Optical Flow with an anisotropic, rotating Laplacian of Gaussian filtering to characterize the lateral motion of dense microtubule networks. We then showcase additional image analytics used to understand the effect of microtubule orientation and regional location on lateral motion. We argue that our tool and these additional metrics provide a fuller picture of the active forcing environment within cells.

Microtubule stabilization targeting regenerative chondrocyte cluster for cartilage regeneration

Purpose: Chondrocytes (CHs) in cartilage undergo several detrimental events during the development of osteoarthritis (OA). However, the mechanism underlying CHs regeneration involved in pathogenesis is largely unknown. The aim of this study was to explore the underlying mechanism of regeneration of CHs involved in the pathological condition and the potential therapeutic strategies of cartilage repair. Methods and Materials: CHs were isolated from human cartilage in different OA stages and the high-resolution cellular architecture of human osteoarthritis was examined by applying single-cell RNA sequencing. The analysis of gene differential expression and gene set enrichment was utilized to reveal the relationship of cartilage regeneration and microtubule stabilization. Microtubule destabilizer (nocodazole) and microtubule stabilizer (docetaxel) treated-human primary CHs and rats cartilage defect model were used to investing the effects and downstream signaling pathway of microtubule stabilization on cartilage regeneration. Results: CHs subpopulations were identified on the basis of their gene markers and the data indicated an imbalance caused by an increase in the degeneration and disruption of CHs regeneration in OA samples. Interestingly, the CHs subpopulation namely CHI3L1⁺ CHs, was characterized by the cell regenerative capacity, stem cell potency and the activated microtubule (MT) process. Furthermore, the data indicated that MT stabilization was effective in promoting cartilage regeneration in rats with cartilage injury model by inhibiting YAP activity. Conclusion: These findings lead to a new understanding of CHs regeneration in the OA pathophysiology context and suggest that MT stabilization is a promising therapeutic target for OA and cartilage injury.

Septum-associated microtubule organizing centers within conidia support infectious development by the blast fungus Magnaporthe oryzae

Cytoplasmic microtubule arrays play important and diverse roles within fungal cells, including serving as molecular highways for motor-driven organelle motility. While the dynamic plus ends of cytoplasmic microtubules are free to explore the cytoplasm through their stochastic growth and shrinkage, their minus ends are nucleated at discrete organizing centers, composed of large multi-subunit protein complexes. The location and composition of these microtubule organizing centers varies depending on genus, cell type, and in some instances cell-cycle stage. Despite their obvious importance, our understanding of the nature, diversity, and regulation of microtubule organizing centers in fungi remains incomplete. Here, using three-color fluorescence microscopy based live-cell imaging, we investigate the organization and dynamic behavior of the microtubule cytoskeleton within infection-related cell types of the filamentous fungus,Magnaporthe oryzae, a highly destructive pathogen of rice and wheat. We provide data to support the idea that cytoplasmic microtubules are nucleated at septa, rather than at nuclear spindle pole bodies, within the three-celled blast conidium, and provide new insight into remodeling of the microtubule cytoskeleton during nuclear division and inheritance. Lastly, we provide a more complete picture of the architecture and subcellular organization of the prototypical blast appressorium, a specialized pressure-generating cell type used to invade host tissue. Taken together, our study provides new insight into microtubule nucleation, organization, and dynamics in specialized and differentiated fungal cell types.

Dynamic microtubules slow down during their shrinkage phase

Microtubules are dynamic polymers that undergo stochastic transitions between growing and shrinking phases. The structural and chemical properties of these phases remain poorly understood. The transition from growth to shrinkage, termed catastrophe, is not a first-order reaction but rather a multistep process whose frequency increases with the growth time: the microtubule ages as the older microtubule tip becomes more unstable. Aging shows that the growing phase is not a single state but comprises several substates of increasing instability. To investigate whether the shrinking phase is also multistate, we characterized the kinetics of microtubule shrinkage following catastrophe using an in vitro reconstitution assay with purified tubulins. We found that the shrinkage speed is highly variable across microtubules and that the shrinkage speed of individual microtubules slows down over time by as much as several fold. The shrinkage slowdown was observed in both fluorescently labeled and unlabeled microtubules as well as in microtubules polymerized from tubulin purified from different species, suggesting that the shrinkage slowdown is a general property of microtubules. These results indicate that microtubule shrinkage, like catastrophe, is time dependent and that the shrinking microtubule tip passes through a succession of states of increasing stability. We hypothesize that the shrinkage slowdown is due to destabilizing events that took place during growth, which led to multistep catastrophe. This suggests that the aging associated with growth is also manifested during shrinkage, with the older, more unstable growing tip being associated with a faster depolymerizing shrinking tip.

Synergistic stabilization of microtubules by BUB-1, HCP-1, and CLS-2 controls microtubule pausing and meiotic spindle assembly

During cell division, chromosome segregation is orchestrated by a microtubule-based spindle. Interaction between spindle microtubules and kinetochores is central to the bi-orientation of chromosomes. Initially dynamic to allow spindle assembly and kinetochore attachments, which is essential for chromosome alignment, microtubules are eventually stabilized for efficient segregation of sister chromatids and homologous chromosomes during mitosis and meiosis I, respectively. Therefore, the precise control of microtubule dynamics is of utmost importance during mitosis and meiosis. Here, we study the assembly and role of a kinetochore module, comprised of the kinase BUB-1, the two redundant CENP-F orthologs HCP-1/2, and the CLASP family member CLS-2 (hereafter termed the BHC module), in the control of microtubule dynamics in Caenorhabditis elegans oocytes. Using a combination of in vivo structure-function analyses of BHC components and in vitro microtubule-based assays, we show that BHC components stabilize microtubules, which is essential for meiotic spindle formation and accurate chromosome segregation. Overall, our results show that BUB-1 and HCP-1/2 do not only act as targeting components for CLS-2 at kinetochores, but also synergistically control kinetochore-microtubule dynamics by promoting microtubule pause. Together, our results suggest that BUB-1 and HCP-1/2 actively participate in the control of kinetochore-microtubule dynamics in the context of an intact BHC module to promote spindle assembly and accurate chromosome segregation in meiosis.

Effect of the Rho-Kinase/ROCK Signaling Pathway on Cytoskeleton Components

The mechanical properties of cells are important in tissue homeostasis and enable cell growth, division, migration and the epithelial-mesenchymal transition. Mechanical properties are determined to a large extent by the cytoskeleton. The cytoskeleton is a complex and dynamic network composed of microfilaments, intermediate filaments and microtubules. These cellular structures confer both cell shape and mechanical properties. The architecture of the networks formed by the cytoskeleton is regulated by several pathways, a key one being the Rho-kinase/ROCK signaling pathway. This review describes the role of ROCK (Rho-associated coiled-coil forming kinase) and how it mediates effects on the key components of the cytoskeleton that are critical for cell behaviour.

Discovery of potent microtubule-destabilizing agents targeting for colchicine site by virtual screening, biological evaluation, and molecular dynamics simulation

Microtubule has been considered as attractive therapeutic target for various cancers. Although numerous of chemically diverse compounds targeting to colchicine site have been reported, none of them was approved by Food and Drug Administration. In this investigation, the virtual screening methods, including pharmacophore model, molecular docking, and interaction molecular fingerprints similarity, were applied to discover novel microtubule-destabilizing agents from database with 324,474 compounds. 22 compounds with novel scaffolds were identified as microtubule-destabilizing agents, and then submitted to the biological evaluation. Among these 22 hits, hit4 with novel scaffold represents the best anti-proliferative activity with IC₅₀ ranging from 4.51 to 14.81 μM on four cancer cell lines. The in vitro assays reveal that hit4 can effectively inhibit tubulin assembly, and disrupt the microtubule network in MCF-7 cell at a concentration-dependent manner. Finally, the molecular dynamics simulation analysis exhibits that hit4 can stably bind to colchicine site, interact with key residues, and induce αT5 and βT7 regions changes. The values of ΔG_bind for the tubulin-colchicine and tubulin-hit4 are -172.9±10.5 and -166.0±12.6 kJ·mol^-1, respectively. The above results indicate that the hit4 is a novel microtubule destabilizing agent targeting to colchicine-binding site, which could be developed as a promising tubulin polymerization inhibitor with higher activity for cancer therapy.

Graphene 2D platform is safe and cytocompatibile for HaCaT cells growing under static and dynamic conditions

The study concerns the influence of graphene monolayer, as a 2 D platform, on cell viability, cytoskeleton, adhesions sites andmorphology of mitochondria of keratinocytes (HaCaT) under static conditions. Based on quantitative and immunofluorescent analysis, it could be stated that graphene substrate does not cause any damage to membrane or disruption of other monitored parameters. Spindle poles and cytokinesis bridges indicating proliferation of cells on this graphene substrate were detected. Moreover, the keratinocyte migration rate on the graphene substrate was comparable to control glass substrate when the created wound was completely closed after 38 hours. HaCaT morphology and viability were also assessed under dynamic conditions (lab on a chip - micro scale). For this purpose, microfluidic graphene system was designed and constructed. No differences as well as no anomalies were observed during cultivation of these cells on the graphene or glass substrates in relation to cultivation conditions: static (macro scale) and dynamic (micro scale). Only natural percentage of dead cells was determined using different methods, which proved that the graphene as the 2 D platform is cytocompatible with keratinocytes. The obtained results encourage the use of the designed lab on a chip system in toxicity testing of graphene also on other cells and further research on the use of graphene monolayers to produce bio-bandages for skin wounds in animal tests.

Quantification of Microtubule Stutters: Dynamic Instability Behaviors that are Strongly Associated with Catastrophe

Microtubules (MTs) are cytoskeletal fibers that undergo dynamic instability (DI), a remarkable process involving phases of growth and shortening separated by stochastic transitions called catastrophe and rescue. Dissecting DI mechanism(s) requires first characterizing and quantifying these dynamics, a subjective process that often ignores complexity in MT behavior. We present a Statistical Tool for Automated Dynamic Instability Analysis (STADIA) that identifies and quantifies not only growth and shortening, but also a category of intermediate behaviors that we term “stutters.” During stutters, the rate of MT length change tends to be smaller in magnitude than during typical growth or shortening phases. Quantifying stutters and other behaviors with STADIA demonstrates that stutters precede most catastrophes in our in vitro experiments and dimer-scale MT simulations, suggesting that stutters are mechanistically involved in catastrophes. Related to this idea, we show that the anticatastrophe factor CLASP2γ works by promoting the return of stuttering MTs to growth. STADIA enables more comprehensive and data-driven analysis of MT dynamics compared with previous methods. The treatment of stutters as distinct and quantifiable DI behaviors provides new opportunities for analyzing mechanisms of MT dynamics and their regulation by binding proteins.

Effects of random hydrolysis on biofilament length distributions in a shared subunit pool

The sizes of filamentous structures in a cell are often regulated for many physiological processes. A key question in cell biology is how such size control is achieved. Here, we theoretically study the length distributions of multiple filaments, growing by stochastic assembly and disassembly of subunits from a limiting subunit pool. Importantly, we consider a chemical switching of subunits (hydrolysis) prevalent in many biofilaments like microtubules (MTs). We show by simulations of different models that hydrolysis leads to a skewed unimodal length distribution for a single MT. In contrast, hydrolysis can lead to bimodal distributions of individual lengths for two MTs, where individual filaments toggle stochastically between bigger and smaller sizes. For more than two MTs, length distributions are also bimodal, although the bimodality becomes less prominent. We further show that this collective phenomenon is connected with the nonequilibrium nature of hydrolysis, and the bimodality disappears for reversible dynamics. Consistent with earlier theoretical studies, a homogeneous subunit pool, without hydrolysis, cannot control filament lengths. We thus elucidate the role of hydrolysis as a control mechanism on MT length diversity.

Stochastic model of T Cell repolarization during target elimination (II)

Cytotoxic T lymphocytes (T cells) and natural killer cells form a tight contact, the immunological synapse (IS), with target cells, where they release their lytic granules containing perforin/granzyme and cytokine-containing vesicles. During this process the cell repolarizes and moves the microtubule organizing center (MTOC) toward the IS. In the first part of our work we developed a computational model for the molecular-motor-driven motion of the microtubule cytoskeleton during T cell polarization and analyzed the effects of cortical-sliding and capture-shrinkage mechanisms. Here we use this model to analyze the dynamics of the MTOC repositioning in situations in which 1) the IS is in an arbitrary position with respect to the initial position of the MTOC and 2) the T cell has two IS at two arbitrary positions. In the case of one IS, we found that the initial position determines which mechanism is dominant and that the time of repositioning does not rise monotonously with the MTOC-IS distance. In the case of two IS, we observe several scenarios that have also been reported experimentally: the MTOC alternates stochastically (but with a well-defined average transition time) between the two IS; it wiggles in between the two IS without transiting to one of the two; or it is at some point pulled to one of the two IS and stays there. Our model allows one to predict which scenario emerges in dependency of the mechanisms in action and the number of dyneins present. We report that the presence of capture-shrinkage mechanism in at least one IS is necessary to assure the transitions in every cell configuration. Moreover, the frequency of transitions does not decrease with the distance between the two IS and is the highest when both mechanisms are present in both IS.

Nucleus-cytoskeleton communication impacts on OCT4-chromatin interactions in embryonic stem cells

BACKGROUND

The cytoskeleton is a key component of the system responsible for transmitting mechanical cues from the cellular environment to the nucleus, where they trigger downstream responses. This communication is particularly relevant in embryonic stem (ES) cells since forces can regulate cell fate and guide developmental processes. However, little is known regarding cytoskeleton organization in ES cells, and thus, relevant aspects of nuclear-cytoskeletal interactions remain elusive.

RESULTS

We explored the three-dimensional distribution of the cytoskeleton in live ES cells and show that these filaments affect the shape of the nucleus. Next, we evaluated if cytoskeletal components indirectly modulate the binding of the pluripotency transcription factor OCT4 to chromatin targets. We show that actin depolymerization triggers OCT4 binding to chromatin sites whereas vimentin disruption produces the opposite effect. In contrast to actin, vimentin contributes to the preservation of OCT4-chromatin interactions and, consequently, may have a pro-stemness role.

CONCLUSIONS

Our results suggest roles of components of the cytoskeleton in shaping the nucleus of ES cells, influencing the interactions of the transcription factor OCT4 with the chromatin and potentially affecting pluripotency and cell fate.

Nanoscale characterization of drug-induced microtubule filament dysfunction using super-resolution microscopy

BACKGROUND

The integrity of microtubule filament networks is essential for the roles in diverse cellular functions, and disruption of its structure or dynamics has been explored as a therapeutic approach to tackle diseases such as cancer. Microtubule-interacting drugs, sometimes referred to as antimitotics, are used in cancer therapy to target and disrupt microtubules. However, due to associated side effects on healthy cells, there is a need to develop safer drug regimens that still retain clinical efficacy. Currently, many questions remain open regarding the extent of effects on cellular physiology of microtubule-interacting drugs at clinically relevant and low doses. Here, we use super-resolution microscopies (single-molecule localization and optical fluctuation based) to reveal the initial microtubule dysfunctions caused by nanomolar concentrations of colcemid.

RESULTS

We identify previously undetected microtubule (MT) damage caused by clinically relevant doses of colcemid. Short exposure to 30-80 nM colcemid results in aberrant microtubule curvature, with a trend of increased curvature associated to increased doses, and curvatures greater than 2 rad/μm, a value associated with MT breakage. Microtubule fragmentation was detected upon treatment with ≥ 100 nM colcemid. Remarkably, lower doses (< 20 nM after 5 h) led to subtle but significant microtubule architecture remodelling characterized by increased curvature and suppression of microtubule dynamics.

CONCLUSIONS

Our results support the emerging hypothesis that microtubule-interacting drugs induce non-mitotic effects in cells, and establish a multi-modal imaging assay for detecting and measuring nanoscale microtubule dysfunction. The sub-diffraction visualization of these less severe precursor perturbations compared to the established antimitotic effects of microtubule-interacting drugs offers potential for improved understanding and design of anticancer agents.

In vivo Assessment of Microtubule Dynamics and Orientation in Caenorhabditis elegans Neurons

In neurons, microtubule orientation has been a key assessor to identify axons that have plus-end out microtubules and dendrites that generally have mixed orientation. Here we describe methods to label, image, and analyze the microtubule dynamics and growth during the development and regeneration of touch neurons in C. elegans. Using genetically encoded fluorescent reporters of microtubule tips, we imaged the axonal microtubules. The local changes in microtubule behavior that initiates axon regeneration following axotomy can be quantified using this protocol. This assay is adaptable to other neurons and genetic backgrounds to investigate the regulation of microtubule dynamics in various cellular processes.

The Microtubule Minus-End Binding Protein Patronin Is Required for the Epithelial Remodeling in the Drosophila Abdomen

In the developing Drosophila abdomen, the epithelial tissue displays extensive cytoskeletal remodeling. In stark contrast to the spatio-temporal control of the actin cytoskeleton, the regulation of microtubule architecture during epithelial morphogenesis has remained opaque. In particular, its role in cell motility remains unclear. Here, we show that minus-end binding protein Patronin is required for organizing microtubule arrays in histoblast cells that form the Drosophila abdomen. Loss of Patronin results in a dorsal cleft, indicating the compromised function of histoblasts. We further show that Patronin is polarized in these cells and is required for the formation of highly dynamic non-centrosomal microtubules in the migrating histoblasts. Thus, our study demonstrates that regulation of microtubule cytoskeleton through Patronin mediates epithelium remodeling.

Growth rate-dependent flexural rigidity of microtubules influences pattern formation in collective motion

Background

Microtubules (MTs) are highly dynamic tubular cytoskeleton filaments that are essential for cellular morphology and intracellular transport. In vivo, the flexural rigidity of MTs can be dynamically regulated depending on their intracellular function. In the in vitro reconstructed MT-motor system, flexural rigidity affects MT gliding behaviors and trajectories. Despite the importance of flexural rigidity for both biological functions and in vitro applications, there is no clear interpretation of the regulation of MT flexural rigidity, and the results of many studies are contradictory. These discrepancies impede our understanding of the regulation of MT flexural rigidity, thereby challenging its precise manipulation.

Results

Here, plausible explanations for these discrepancies are provided and a new method to evaluate the MT rigidity is developed. Moreover, a new relationship of the dynamic and mechanic of MTs is revealed that MT flexural rigidity decreases through three phases with the growth rate increases, which offers a method of designing MT flexural rigidity by regulating its growth rate. To test the validity of this method, the gliding performances of MTs with different flexural rigidities polymerized at different growth rates are examined. The growth rate-dependent flexural rigidity of MTs is experimentally found to influence the pattern formation in collective motion using gliding motility assay, which is further validated using machine learning.

Conclusion

Our study establishes a robust quantitative method for measurement and design of MT flexural rigidity to study its influences on MT gliding assays, collective motion, and other biological activities in vitro. The new relationship about the growth rate and rigidity of MTs updates current concepts on the dynamics and mechanics of MTs and provides comparable data for investigating the regulation mechanism of MT rigidity in vivo in the future.

Graphic Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s12951-021-00960-y.

Neuroinflammation decreased hippocampal microtubule dynamics in the acute behavioral deficits induced by intracerebroventricular injection of lipopolysaccharide in male adult rats

Neuroinflammation plays a vital role in the pathology of depression. Microtubule dynamics produces an immediate response to stress, but the effect of microtubule dynamics in the rats with acute behavioral deficits following a central immune challenge remains elusive. Adult male Sprague-Dawley rats were subjected to the intracerebroventricular (icv) injection of lipopolysaccharide (. Behavioral tests, including bodyweight, sucrose preference test (SPT), forced swimming test (FST) and open field test (OFT), were performed to evaluate anxiety-like and depressive-like phenotypes at 24 h after injection, and some neuroinflammation biomarkers and microtubule dynamics in the hippocampus were detected. Lipopolysaccharide decreased the bodyweight, sucrose preference in SPT (depressive-like behavior), spontaneous activity in OFT (anxiety-like behavior) and increased the immobility time in FST (depressive-like behavior). Besides, lipopolysaccharide increased the mRNA levels of hippocampal CD11b and ionized calcium binding adaptor molecule (Iba1), which suggest microglial activation, and also upregulated hippocampal NLR Family Pyrin Domain Containing 3 inflammasome/interleukin-18/nuclear factor kappa-B mRNA. Lipopolysaccharide injection(icv) reduced the ratio of Tyr-/Acet-tubulin, an important marker of microtubule dynamics, in the acute behavioral deficit rats. Specifically, a decrease in Tyr-tubulin and an increase in the expression of Acet-tubulin were observed, indicating weakened microtubule dynamics. Pearson correlation analysis further showed that there was a significant negative correlation between hippocampal microtubule dynamics and neuroinflammatory activity. This study confirmed that hippocampal microtubule dynamics was decreased in the rats with acute behavioral deficits following a central immune challenge.

Improved bounds on entropy production in living systems

Living systems maintain or increase local order by working against the second law of thermodynamics. Thermodynamic consistency is restored as they consume free energy, thereby increasing the net entropy of their environment. Recently introduced estimators for the entropy production rate have provided major insights into the efficiency of important cellular processes. In experiments, however, many degrees of freedom typically remain hidden to the observer, and, in these cases, existing methods are not optimal. Here, by reformulating the problem within an optimization framework, we are able to infer improved bounds on the rate of entropy production from partial measurements of biological systems. Our approach yields provably optimal estimates given certain measurable transition statistics. In contrast to prevailing methods, the improved estimator reveals nonzero entropy production rates even when nonequilibrium processes appear time symmetric and therefore may pretend to obey detailed balance. We demonstrate the broad applicability of this framework by providing improved bounds on the energy consumption rates in a diverse range of biological systems including bacterial flagella motors, growing microtubules, and calcium oscillations within human embryonic kidney cells.

Genetically encoded live-cell sensor for tyrosinated microtubules

Microtubule cytoskeleton exists in various biochemical forms in different cells due to tubulin posttranslational modifications (PTMs). Tubulin PTMs are known to affect microtubule stability, dynamics, and interaction with MAPs and motors in a specific manner, widely known as tubulin code hypothesis. At present, there exists no tool that can specifically mark tubulin PTMs in living cells, thus severely limiting our understanding of their dynamics and cellular functions. Using a yeast display library, we identified a binder against terminal tyrosine of α-tubulin, a unique PTM site. Extensive characterization validates the robustness and nonperturbing nature of our binder as tyrosination sensor, a live-cell tubulin nanobody specific towards tyrosinated microtubules. Using this sensor, we followed nocodazole-, colchicine-, and vincristine-induced depolymerization events of tyrosinated microtubules in real time and found each distinctly perturbs the microtubule polymer. Together, our work describes a novel tyrosination sensor and its potential applications to study the dynamics of microtubule and their PTM processes in living cells.

Live-Cell Fluorescence Imaging of Microtubules by Using a Tau-Derived Peptide

Microtubules (MTs) are important targets for imaging in living cells because of their vital roles in cellular processes. The dynamics (polymerization/depolymerization) of MTs has been imaged in living cells by utilizing MT-targeted drugs as scaffolds. We previously developed a unique MT-binding motif derived from a MT-associated protein, Tau. The Tau-derived peptide (TP) binds to the inner surface of MTs without inhibiting the dynamics of MTs. We introduce a new protocol for live-cell imaging of MTs by using fluorescently labeled TP. We exemplify that tetramethylrhodamine (TMR)-labeled TP (TP-TMR) is spontaneously internalized into HepG2 cells and binds to intracellular MTs, enabling visualization of MTs in living cells. TP-TMR shows no apparent effects on polymerization/depolymerization of MTs and no cytotoxicity. Thus, the peptide-based approach is useful for long-term imaging of MTs.

Ultrastructural aspects of spermatogenesis in Calyptogena pacifica Dall 1891 (Vesicomyidae; Bivalvia)

The process of spermatogenesis and spermatozoon morphology was characterized from a deep-sea bivalve, Calyptogena pacifica (Vesicomyidae, Pliocardiinae), a member of the superfamily Glossoidea, using light and electron microscopy. Spermatogenesis in C. pacifica is generally similar to that in shallow-water bivalves but, the development of spermatogenic cells in this species has also some distinguishing features. First proacrosomal vesicles are observed in early spermatocytes I. Although, early appearance of proacrosomal vesicles is well known for bivalves, in C. pacifica, these vesicles are associated with electron-dense material, which is located outside the limiting membrane of the proacrosomal vesicles and disappears in late spermatids. Another feature of spermatogenesis in C. pacifica is the localization of the axoneme and flagellum development. Early spermatogenic cells lack typical flagellum, while in spermatogonia, spermatocytes, and early spermatids, the axoneme is observed in the cytoplasm. In late spermatids, the axoneme is located along the nucleus, and the flagellum is oriented anteriorly. During sperm maturation, the bent flagellum is transformed into the typical posteriorly oriented tail. Spermatozoa of C. pacifica are of ect-aqua sperm type with a bullet-like head of about 5.8 μm in length and 1.8 μm in width, consisting of a well-developed dome-shaped acrosomal complex, an elongated barrel-shaped nucleus filled with granular chromatin, and a midpiece with mainly four rounded mitochondria. A comparative analysis has shown a number of common traits in C. pacifica and Neotrapezium sublaevigatum.

Bioinformatics analysis of the biological changes involved in the osteogenic differentiation of human mesenchymal stem cells

The mechanisms underlying the osteogenic differentiation of human bone marrow mesenchymal stem cells (hBMSCs) remain unclear. In the present study, we aimed to identify the key biological processes during osteogenic differentiation. To this end, we downloaded three microarray data sets from the Gene Expression Omnibus (GEO) database: GSE12266, GSE18043 and GSE37558. Differentially expressed genes (DEGs) were screened using the limma package, and enrichment analysis was performed. Protein-protein interaction network (PPI) analysis and visualization analysis were performed with STRING and Cytoscape. A total of 240 DEGs were identified, including 147 up-regulated genes and 93 down-regulated genes. Functional enrichment and pathways of the present DEGs include extracellular matrix organization, ossification, cell division, spindle and microtubule. Functional enrichment analysis of 10 hub genes showed that these genes are mainly enriched in microtubule-related biological changes, that is sister chromatid segregation, microtubule cytoskeleton organization involved in mitosis, and spindle microtubule. Moreover, immunofluorescence and Western blotting revealed dramatic quantitative and morphological changes in the microtubules during the osteogenic differentiation of human adipose-derived stem cells. In summary, the present results provide novel insights into the microtubule- and cytoskeleton-related biological process changes, identifying candidates for the further study of osteogenic differentiation of the mesenchymal stem cells.

Quantifying the polymerization dynamics of plant cortical microtubules using kymograph analysis

The plant cortical microtubule array is a dynamic structure that confers cell shape and enables plants to alter their growth and development in response to internal and external cues. Cells use a variety of microtubule regulatory proteins to spatially and temporally modulate the intrinsic polymerization dynamics of cortical microtubules to arrange them into specific configurations and to reshape arrays to adapt to changing conditions. To obtain mechanistic insight into how particular microtubule regulatory proteins mediate the dynamic (re)structuring of cortical microtubule arrays, we need to measure their effect on the dynamics of cortical microtubules. In this chapter, we describe new ImageJ plugins to generate kymographs from time-lapse images and to analyze them to measure the parameters that quantitatively describe cortical microtubule dynamics.

During mitosis ZEB1 "switches" from being a chromatin-bound epithelial gene repressor, to become a microtubule-associated protein

Microtubules are polymers of α/β-tubulin, with microtubule organization being regulated by microtubule-associated proteins (MAPs). Herein, we describe a novel role for the epithelial gene repressor, zinc finger E-box-binding homeobox 1 (ZEB1), that "switches" from a chromatin-associated protein during interphase, to a MAP that associates with α-, β- and γ-tubulin during mitosis. Additionally, ZEB1 was also demonstrated to associate with γ-tubulin at the microtubule organizing center (MTOC). Using confocal microscopy, ZEB1 localization was predominantly nuclear during interphase, with α/β-tubulin being primarily cytoplasmic and the association between these proteins being minimal. However, during the stages of mitosis, ZEB1 co-localization with α-, β-, and γ-tubulin was significantly increased, with the association commonly peaking during metaphase in multiple tumor cell-types. ZEB1 was also observed to accumulate in the cleavage furrow during cytokinesis. The increased interaction between ZEB1 and α-tubulin during mitosis was also confirmed using the proximity ligation assay. In contrast to ZEB1, its paralog ZEB2, was mainly perinuclear and cytoplasmic during interphase, showing some co-localization with α-tubulin during mitosis. Considering the association between ZEB1 with α/β/γ-tubulin during mitosis, studies investigated ZEB1's role in the cell cycle. Silencing ZEB1 resulted in a G₂-M arrest, which could be mediated by the up-regulation of p21^Waf1/Cip1 and p27^Kip1 that are known downstream targets repressed by ZEB1. However, it cannot be excluded the G₂/M arrest observed after ZEB1 silencing is not due to its roles as a MAP. Collectively, ZEB1 plays a role as a MAP during mitosis and could be functionally involved in this process.

Studying Tau-Microtubule Interaction Using Single-Molecule TIRF Microscopy

Microtubule architecture depends on a complex network of microtubule-associated proteins (MAPs) that act in concert to modulate microtubule assembly/disassembly and spatial arrangement. In vitro reconstitution of cytoskeleton dynamics coupled to single-molecule fluorescence assays has opened new perspectives to quantify the interaction of MAPs with microtubules. Here, we present a Total Internal Reflection Fluorescence (TIRF) microscopy-based assay enabling the characterization of Tau interaction with dynamic microtubules at the single-molecule level. We describe protein sample preparation in flow cells, single-molecule acquisitions by TIRF microscopy, and quantitative analysis of Tau oligomerization states and dwell time on microtubules.

Fluorescent Tau-derived Peptide for Monitoring Microtubules in Living Cells

Microtubules (MTs) are key cytoskeletal components that modulate various cellular activities with their dynamic structural changes, including polymerization and depolymerization. To monitor the dynamics of MTs in living cells, many drug-based fluorescent probes have been developed; however, these also potentially disturb the polymerization/depolymerization of MTs. Here, we report nondrug, peptide-based fluorescent probes to monitor MTs in living cells. We employed a Tau-derived peptide (TP) that has been shown to bind MTs without inhibiting polymerization/depolymerization in vitro. We show that a tetramethylrhodamine (TMR)-labeled TP (TP-TMR) is internalized into HepG2 cells and binds to intracellular MTs, enabling visualization of MTs as clear, fibrous structures. The binding of TP-TMR shows no apparent effects on polymerization/depolymerization of MTs induced by MT-targeted drugs and temperature change. The main uptake mechanism of TP-TMR was elucidated as endocytosis, and partial endosomal escape resulted in the binding of TP-TMR to MTs. TP-TMR exhibited no cytotoxicity compared with MT-targeted drug scaffolds. These results indicate that TP scaffolds can be exploited as useful MT-targeted tools in living cells, such as in long-term imaging of MTs.

LSPR Biosensing Approach for the Detection of Microtubule Nucleation

Microtubules are dynamic protein filaments that are involved in a number of cellular processes. Here, we report the development of a novel localized surface plasmon resonance (LSPR) biosensing approach for investigating one aspect of microtubule dynamics that is not well understood, namely, nucleation. Using a modified Mie theory with radially variable refractive index, we construct a theoretical model to describe the optical response of gold nanoparticles when microtubules form around them. The model predicts that the extinction maximum wavelength is sensitive to a change in the local refractive index induced by microtubule nucleation within a few tens of nanometers from the nanoparticle surface, but insensitive to a change in the refractive index outside this region caused by microtubule elongation. As a proof of concept to demonstrate that LSPR can be used for detecting microtubule nucleation experimentally, we induce spontaneous microtubule formation around gold nanoparticles by immobilizing tubulin subunits on the nanoparticles. We find that, consistent with the theoretical model, there is a redshift in the extinction maximum wavelength upon the formation of short microtubules around the nanoparticles, but no significant change in maximum wavelength when the microtubules are elongated. We also perform kinetic experiments and demonstrate that the maximum wavelength is sensitive to the microtubule nuclei assembly even when microtubules are too small to be detected from an optical density measurement.