Cell and molecular mechanics of biological materials

A Review on Investigating the Interactions between Nanoparticles and the Pulmonary Surfactant Monolayer with Coarse-Grained Molecular Dynamics Method

Pulmonary drug delivery has garnered significant attention due to its targeted local lung action, minimal toxic side effects, and high drug utilization. However, the physicochemical properties of inhaled nanoparticles (NPs) used as drug carriers can influence their interactions with the pulmonary surfactant (PS) monolayer, potentially altering the fate of the NPs and impairing the biophysical function of the PS monolayer. Thus, the objective of this review is to summarize how the physicochemical properties of NPs affect their interactions with the PS monolayer. Initially, the definition and properties of NPs, as well as the composition and characteristics of the PS monolayer, are introduced. Subsequently, the coarse-grained molecular dynamics (CGMD) simulation method for studying the interactions between NPs and the PS monolayer is presented. Finally, the implications of the hydrophobicity, size, shape, surface charge, surface modification, and aggregation of NPs on their interactions with the PS monolayer and on the composition of biomolecular corona are discussed. In conclusion, gaining a deeper understanding of the effects of the physicochemical properties of NPs on their interactions with the PS monolayer will contribute to the development of safer and more effective nanomedicines for pulmonary drug delivery.

Beyond stiffness: Multiscale viscoelastic features as biomechanical markers for assessing cell types and states

Cell mechanics are pivotal in regulating cellular activities, diseases progression, and cancer development. However, the understanding of how cellular viscoelastic properties vary in physiological and pathological stimuli remains scarce. Here, we develop a hybrid self-similar hierarchical theory-microrheology approach to accurately and efficiently characterize cellular viscoelasticity. Focusing on two key cell types associated with livers fibrosis-the capillarized liver sinusoidal endothelial cells and activated hepatic stellate cells-we uncover a universal two-stage power-law rheology characterized by two distinct exponents, αshort and αlong. The mechanical profiles derived from both exponents exhibit significant potential for discriminating among diverse cells. This finding suggests a potential common dynamic creep characteristic across biological systems, extending our earlier observations in soft tissues. Using a tailored hierarchical model for cellular mechanical structures, we discern significant variations in the viscoelastic properties and their distribution profiles across different cell types and states from the cytoplasm (elastic stiffness E1 and viscosity η), to a single cytoskeleton fiber (elastic stiffness E2), and then to the cell level (transverse expansion stiffness E3). Importantly, we construct a logistic-regression-based machine-learning model using the dynamic parameters that outperforms conventional cell-stiffness-based classifiers in assessing cell states, achieving an area under the curve of 97% vs. 78%. Our findings not only advance a robust framework for monitoring intricate cell dynamics but also highlight the crucial role of cellular viscoelasticity in discerning cell states across a spectrum of liver diseases and prognosis, offering new avenues for developing diagnostic and therapeutic strategies based on cellular viscoelasticity.

Robot-assisted chirality-tunable acoustic vortex tweezers for contactless, multifunctional, 4-DOF object manipulation

Robotic manipulation of small objects has shown great potential for engineering, biology, and chemistry research. However, existing robotic platforms have difficulty in achieving contactless, high-resolution, 4-degrees-of-freedom (4-DOF) manipulation of small objects, and noninvasive maneuvering of objects in regions shielded by tissue and bone barriers. Here, we present chirality-tunable acoustic vortex tweezers that can tune acoustic vortex chirality, transmit through biological barriers, trap single micro- to millimeter-sized objects, and control object rotation. Assisted by programmable robots, our acoustic systems further enable contactless, high-resolution translation of single objects. Our systems were demonstrated by tuning acoustic vortex chirality, controlling object rotation, and translating objects along arbitrary-shaped paths. Moreover, we used our systems to trap single objects in regions with tissue and skull barriers and translate an object inside a Y-shaped channel of a thick biomimetic phantom. In addition, we showed the function of ultrasound imaging-assisted acoustic manipulation by monitoring acoustic object manipulation via live ultrasound imaging.

Anisotropic power-law viscoelasticity of living cells is dominated by cytoskeletal network structure

During physiological and pathological processes, cells experience significant morphological alterations with the re-arrangement of cytoskeletal filaments, resulting in anisotropic viscoelasticity. Here, a structure-based cell model is proposed to study the anisotropic viscoelastic mechanical behaviors of living cells. We investigate how cell shape affects its creep responses in longitudinal and perpendicular directions. It is shown that cells exhibit power-law rheological behavior in both longitudinal and perpendicular directions under step stress, with a more solid-like behavior along the longitudinal direction. We reveal that the cell volume and cytoskeletal filament orientation, which have been neglected in most existing models, play a critical role in regulating cellular anisotropic viscoelasticity. The stiffness of the cell in both directions increases linearly with increasing its aspect ratio, due to the decrease of cell volume. Moreover, the increase in the cell's aspect ratio produces the aggregation of cytoskeletal filaments along the longitudinal direction, resulting in higher stiffness in this direction. It is also shown that the increase in cell's aspect ratio corresponds to a process of cellular ordering, which can be quantitatively characterized by the orientational entropy of cytoskeletal filaments. In addition, we present a simple yet robust method to establish the relationship between cell's aspect ratio and cell volume, thus providing a theoretical framework to capture the anisotropic viscoelastic behavior of cells. This study suggests that the structure-based cell models may be further developed to investigate cellular rheological responses to external mechanical stimuli and may be extended to the tissue scale. STATEMENT OF SIGNIFICANCE: The viscoelastic behaviors of cells hold significant importance in comprehending the roles of mechanical forces in embryo development, invasion, and metastasis of cancer cells. Here, a structure-based cell model is proposed to study the anisotropic viscoelastic mechanical behaviors of living cells. Our study highlights the crucial role of previously neglected factors, such as cell volume and cytoskeletal filament orientation, in regulating cellular anisotropic viscoelasticity. We further propose an orientational entropy of cytoskeletal filaments to quantitatively characterize the ordering process of cells with increasing aspect ratios. Moreover, we derived the analytical interrelationships between cell aspect ratio, cell stiffness, cell volume, and cytoskeletal fiber orientation. This study provides a theoretical framework to describe the anisotropic viscoelastic mechanical behavior of cells.

Towards an ion-channel-centric approach to ultrasound neuromodulation

Ultrasound neuromodulation is a promising technology that could revolutionize study and treatment of brain conditions ranging from mood disorders to Alzheimer's disease and stroke. An understanding of how ultrasound directly modulates specific ion channels could provide a roadmap for targeting specific neurological circuits and achieving desired neurophysiological outcomes. Although experimental challenges make it difficult to unambiguously identify which ion channels are sensitive to ultrasound in vivo, recent progress indicates that there are likely several different ion channels involved, including members of the K2P, Piezo, and TRP channel families. A recent result linking TRPM2 channels in the hypothalamus to induction of torpor by ultrasound in rodents demonstrates the feasibility of targeting a specific ion channel in a specific population of neurons.

Biomedical applications of stimuli-responsive "smart" interpenetrating polymer network hydrogels

In recent years, owing to the ongoing advancements in polymer materials, hydrogels have found increasing applications in the biomedical domain, notably in the realm of stimuli-responsive "smart" hydrogels. Nonetheless, conventional single-network stimuli-responsive "smart" hydrogels frequently exhibit deficiencies, including low mechanical strength, limited biocompatibility, and extended response times. In response, researchers have addressed these challenges by introducing a second network to create stimuli-responsive "smart" Interpenetrating Polymer Network (IPN) hydrogels. The mechanical strength of the material can be significantly improved due to the topological entanglement and physical interactions within the interpenetrating structure. Simultaneously, combining different network structures enhances the biocompatibility and stimulus responsiveness of the gel, endowing it with unique properties such as cell adhesion, conductivity, hemostasis/antioxidation, and color-changing capabilities. This article primarily aims to elucidate the stimulus-inducing factors in stimuli-responsive "smart" IPN hydrogels, the impact of the gels on cell behaviors and their biomedical application range. Additionally, we also offer an in-depth exposition of their categorization, mechanisms, performance characteristics, and related aspects. This review furnishes a comprehensive assessment and outlook for the advancement of stimuli-responsive "smart" IPN hydrogels within the biomedical arena. We believe that, as the biomedical field increasingly demands novel materials featuring improved mechanical properties, robust biocompatibility, and heightened stimulus responsiveness, stimuli-responsive "smart" IPN hydrogels will hold substantial promise for wide-ranging applications in this domain.

Atomic force microscopy in disease-related studies: Exploring tissue and cell mechanics

Despite significant progress in human medicine, certain diseases remain challenging to promptly diagnose and treat. Hence, the imperative lies in the development of more exhaustive criteria and tools. Tissue and cellular mechanics exhibit distinctive traits in both normal and pathological states, suggesting that "force" represents a promising and distinctive target for disease diagnosis and treatment. Atomic force microscopy (AFM) holds great promise as a prospective clinical medical device due to its capability to concurrently assess surface morphology and mechanical characteristics of biological specimens within a physiological setting. This review presents a comprehensive examination of the operational principles of AFM and diverse mechanical models, focusing on its applications in investigating tissue and cellular mechanics associated with prevalent diseases. The findings from these studies lay a solid groundwork for potential clinical implementations of AFM. RESEARCH HIGHLIGHTS: By examining the surface morphology and assessing tissue and cellular mechanics of biological specimens in a physiological setting, AFM shows promise as a clinical device to diagnose and treat challenging diseases.

Disruption of Fuz in mouse embryos generates hypoplastic hindbrain development and reduced cranial nerve ganglia

BACKGROUND

The brain and spinal cord formation is initiated in the earliest stages of mammalian pregnancy in a highly organized process known as neurulation. Environmental or genetic interferences can impair neurulation, resulting in clinically significant birth defects known collectively as neural tube defects. The Fuz gene encodes a subunit of the CPLANE complex, a macromolecular planar polarity effector required for ciliogenesis. Ablation of Fuz in mouse embryos results in exencephaly and spina bifida, including dysmorphic craniofacial structures due to defective cilia formation and impaired Sonic Hedgehog signaling.

RESULTS

We demonstrate that knocking Fuz out during embryonic mouse development results in a hypoplastic hindbrain phenotype, displaying abnormal rhombomeres with reduced length and width. This phenotype is associated with persistent reduction of ventral neuroepithelial stiffness in a notochord adjacent area at the level of the rhombomere 5. The formation of cranial and paravertebral ganglia is also impaired in these embryos.

CONCLUSIONS

This study reveals that hypoplastic hindbrain development, identified by abnormal rhombomere morphology and persistent loss of ventral neuroepithelial stiffness, precedes exencephaly in Fuz ablated murine mutants, indicating that the gene Fuz has a critical function sustaining normal neural tube development and neuronal differentiation.

Surface engineering of lipid nanoparticles: targeted nucleic acid delivery and beyond

Harnessing surface engineering strategies to functionalize nucleic acid-lipid nanoparticles (LNPs) for improved performance has been a hot research topic since the approval of the first siRNA drug, patisiran, and two mRNA-based COVID-19 vaccines, BNT162b2 and mRNA-1273. Currently, efforts have been mainly made to construct targeted LNPs for organ- or cell-type-specific delivery of nucleic acid drugs by conjugation with various types of ligands. In this review, we describe the surface engineering strategies for nucleic acid-LNPs, considering ligand types, conjugation chemistries, and incorporation methods. We then outline the general purification and characterization techniques that are frequently used following the engineering step and emphasize the specific techniques for certain types of ligands. Next, we comprehensively summarize the currently accessible organs and cell types, as well as the other applications of the engineered LNPs. Finally, we provide considerations for formulating targeted LNPs and discuss the challenges of successfully translating the "proof of concept" from the laboratory into the clinic. We believe that addressing these challenges could accelerate the development of surface-engineered LNPs for targeted nucleic acid delivery and beyond.

Disruption of Fuz in mouse embryos generates hypoplastic hindbrain development and reduced cranial nerve ganglia

The formation of the brain and spinal cord is initiated in the earliest stages of mammalian pregnancy in a highly organized process known as neurulation. Convergent and extension movements transforms a flat sheet of ectodermal cells into a narrow and elongated line of neuroepithelia, while a major source of Sonic Hedgehog signaling from the notochord induces the overlying neuroepithelial cells to form two apposed neural folds. Afterward, neural tube closure occurs by synchronized coordination of the surface ectoderm and adjacent neuroepithelial walls at specific axial regions known as neuropores. Environmental or genetic interferences can impair neurulation resulting in neural tube defects. The Fuz gene encodes a subunit of the CPLANE complex, which is a macromolecular planar polarity effector required for ciliogenesis. Ablation of Fuz in mouse embryos results in exencephaly and spina bifida, including dysmorphic craniofacial structures due to defective cilia formation and impaired Sonic Hedgehog signaling. In this work, we demonstrate that knocking Fuz out during embryonic mouse development results in a hypoplastic hindbrain phenotype, displaying abnormal rhombomeres with reduced length and width. This phenotype is associated with persistent loss of ventral neuroepithelial stiffness, in a notochord adjacent area at the level of the rhombomere 5, preceding the development of exencephaly in Fuz ablated mutants. The formation of cranial and paravertebral ganglia is also impaired in these embryos, indicating that Fuz has a critical function sustaining normal neural tube development and neuronal differentiation.

SIGNIFICANCE STATEMENT

Neural tube defects (NTDs) are a common cause of disability in children, representing the second most common congenital structural malformation in humans following only congenital cardiovascular malformations. NTDs affect approximately 1 to 2 pregnancies per 1000 births every year worldwide, when the mechanical forces folding the neural plate fails to close at specific neuropores located anteriorly (cranial) or posteriorly (caudal) along the neural tube, in a process known as neurulation, which happens throughout the third and fourth weeks of human pregnancy.

The Role of Membrane-Tethered Mucins in Axial Epithelial Adhesion in Controlled Normal Stress Environments

The collective adhesive behavior of epithelial cell layers mediated by complex macromolecular fluid environments plays a vital role in many biological processes. Mucins, a family of highly glycosylated proteins, are known to lubricate cell-on-cell contacts in the shear direction. However, the role of mucins mediating axial epithelial adhesion in the direction perpendicular to the plane of the cell sheet has received less attention. This article subjects cell-on-cell layers of live ocular epithelia that express mucins on their apical surfaces to compression/decompression cycles and tensile loading using a customized instrument. In addition to providing compressive moduli of native cell-on-cell layers, it is found that the mucin layer between the epithelia acts as a soft cushion between the epithelial cell layers. Decompression experiments reveal mucin layers act as soft, nonlinear springs in the axial direction. The cell-on-cell layers withstand decompression before fracturing by a cohesive failure within the mucin layer. When mucin deficiency is induced via a protease treatment, it is found that the axial adhesion between the cell layers is increased. The findings which correlate changes in biological factors with changes in mechanical properties might be of interest to challenges in ophthalmology, vision care, and mucus research.

Micro-mechanical response and power-law exponents from the longitudinal fluctuations of F-actin solutions

We investigate the local fluctuations of filamentous actin (F-actin), with a focus on the skeletal thin filament, using single-particle optical trapping interferometry. This experimental technique allows us to detect the Brownian motion of a tracer bead immersed in a complex fluid with nanometric resolution at the microsecond time-scale. The mean square displacement, loss modulus, and velocity autocorrelation function (VAF) of the trapped microprobes in the fluid follow power-law behaviors, whose exponents can be determined in the short-time/high-frequency regime over several decades. We obtain 7/8 subdiffusive power-law exponents for polystyrene depleted microtracers at low optical trapping forces. Microrheologically, the elastic modulus of these suspensions is observed to be constant up to the limit of high frequencies, confirming that the origin of this subdiffusive exponent is the local longitudinal fluctuations of the polymers. Deviations from this value are measured and discussed in relation to the characteristic length scales of these F-actin networks and probes' properties, and also in connection with the different power-law exponents detected in the VAFs. Finally, we observed that the thin filament, composed of tropomyosin (Tm) and troponin (Tn) coupled to F-actin in the presence of Ca2+, shows exponent values less dispersed than that of F-actin alone, which we interpret as a micro-measurement of the filament stabilization.

Microenvironments Matter: Advances in Brain-on-Chip

To highlight the particular needs with respect to modeling the unique and complex organization of the human brain structure, we reviewed the state-of-the-art in devising brain models with engineered instructive microenvironments. To acquire a better perspective on the brain's working mechanisms, we first summarize the importance of regional stiffness gradients in brain tissue, varying per layer and the cellular diversities of the layers. Through this, one can acquire an understanding of the essential parameters in emulating the brain in vitro. In addition to the brain's organizational architecture, we addressed also how the mechanical properties have an impact on neuronal cell responses. In this respect, advanced in vitro platforms emerged and profoundly changed the methods of brain modeling efforts from the past, mainly focusing on animal or cell line research. The main challenges in imitating features of the brain in a dish are with regard to composition and functionality. In neurobiological research, there are now methods that aim to cope with such challenges by the self-assembly of human-derived pluripotent stem cells (hPSCs), i.e., brainoids. Alternatively, these brainoids can be used stand-alone or in conjunction with Brain-on-Chip (BoC) platform technology, 3D-printed gels, and other types of engineered guidance features. Currently, advanced in vitro methods have made a giant leap forward regarding cost-effectiveness, ease-of-use, and availability. We bring these recent developments together into one review. We believe our conclusions will give a novel perspective towards advancing instructive microenvironments for BoCs and the understanding of the brain's cellular functions either in modeling healthy or diseased states of the brain.

Non-contact and label-free biomechanical imaging: Stimulated Brillouin microscopy and beyond

Brillouin microscopy based on spontaneous Brillouin scattering has emerged as a unique elastography technique because of its merit of non-contact, label-free, and high-resolution mechanical imaging of biological cell and tissue. Recently, several new optical modalities based on stimulated Brillouin scattering have been developed for biomechanical research. As the scattering efficiency of the stimulated process is much higher than its counterpart in the spontaneous process, stimulated Brillouin-based methods have the potential to significantly improve the speed and spectral resolution of existing Brillouin microscopy. Here, we review the ongoing technological advancements of three methods, including continuous wave stimulated Brillouin microscopy, impulsive stimulated Brillouin microscopy, and laser-induced picosecond ultrasonics. We describe the physical principle, the representative instrumentation, and biological application of each method. We further discuss the current limitations as well as the challenges for translating these methods into a visible biomedical instrument for biophysics and mechanobiology.

Stiffness Considerations for a MEMS-Based Weighing Cell

In this paper, a miniaturized weighing cell that is based on a micro-electro-mechanical-system (MEMS) is discussed. The MEMS-based weighing cell is inspired by macroscopic electromagnetic force compensation (EMFC) weighing cells and one of the crucial system parameters, the stiffness, is analyzed. The system stiffness in the direction of motion is first analytically evaluated using a rigid body approach and then also numerically modeled using the finite element method for comparison purposes. First prototypes of MEMS-based weighing cells were successfully microfabricated and the occurring fabrication-based system characteristics were considered in the overall system evaluation. The stiffness of the MEMS-based weighing cells was experimentally determined by using a static approach based on force-displacement measurements. Considering the geometry parameters of the microfabricated weighing cells, the measured stiffness values fit to the calculated stiffness values with a deviation from -6.7 to 3.8% depending on the microsystem under test. Based on our results, we demonstrate that MEMS-based weighing cells can be successfully fabricated with the proposed process and in principle be used for high-precision force measurements in the future. Nevertheless, improved system designs and read-out strategies are still required.

Rapid biomechanical imaging at low irradiation level via dual line-scanning Brillouin microscopy

Brillouin microscopy is a technique for mechanical characterization of biological material without contact at high three-dimensional resolution. Here, we introduce dual line-scanning Brillouin microscopy (dLSBM), which improves acquisition speed and reduces irradiation dose by more than one order of magnitude with selective illumination and single-shot analysis of hundreds of points along the incident beam axis. Using tumor spheroids, we demonstrate the ability to capture the sample response to rapid mechanical perturbations as well as the spatially resolved evolution of the mechanical properties in growing spheroids.

Atomic force microscopy-based assessment of multimechanical cellular properties for classification of graded bladder cancer cells and cancer early diagnosis using machine learning analysis

Cellular mechanical properties (CMPs) have been frequently reported as biomarkers for cell cancerization to assist objective cytology, compared to the current subjective method dependent on cytomorphology. However, single or dual CMPs cannot always successfully distinguish every kind of malignant cell from its benign counterpart. In this work, we extract 4 CMPs of four different graded bladder cancer (BC) cell lines by AFM (atomic force microscopy)-based nanoindentation to generate a CMP database, which is used to train a cancerization-grade classifier by machine learning. The classifier is tested on 4 categories of BC cells at different cancer grades. The classification shows split-independent robustness and an accuracy of 91.25% with an AUC-ROC (ROC stands for receiver operating characteristic, and ROC curve is a graphical plot which illustrates the performance of a binary classifier system as its discrimination threshold is varied) value of 97.98%. Finally, we also compare our proposed method with traditional invasive diagnosis and noninvasive cancer diagnosis relying on cytomorphology, in terms of accuracy, sensitivity and specificity. Unlike former studies focusing on the discrimination between normal and cancerous cells, our study fulfills the classification of 4 graded cell lines at different cancerization stages, and thus provides a potential method for early detection of cancerization. STATEMENT OF SIGNIFICANCE: We measured four cellular mechanical properties (CMPs) of 4 graded bladder cancer (BC) cell lines using AFM (atomic force microscopy). We found that single or dual CMPs cannot fulfill the task of BC cell classification. Instead, we employ MLA (Machine Learning Algorithm)-based analysis whose inputs are BC CMPs. Compared with traditional cytomorphology-based prognoses, the non-invasive method proposed in this study has higher accuracy but with many fewer cellular properties as inputs. The proposed non-invasive prognosis is characterized with high sensitivity and specificity, and thus provides a potential tumor-grading means to identify cancer cells with different metastatic potential. Moreover, our study proposes an objective grading method based on quantitative characteristics desirable for avoiding misdiagnosis induced by ambiguous subjectivity.

Artificial organelles for sustainable chemical energy conversion and production in artificial cells: Artificial mitochondrion and chloroplasts

Sustainable energy conversion modules are the main challenges for building complex reaction cascades in artificial cells. Recent advances in biotechnology have enabled this sustainable energy supply, especially the adenosine triphosphate (ATP), by mimicking the organelles, which are the core structures for energy conversion in living cells. Three components are mainly shared by the artificial organelles: the membrane compartment separating the inner and outer parts, membrane proteins for proton translocation, and the molecular rotary machine for ATP synthesis. Depending on the initiation factors, they are further categorized into artificial mitochondrion and artificial chloroplasts, which use chemical nutrients for oxidative phosphorylation and light for photosynthesis, respectively. In this review, we summarize the essential components needed for artificial organelles and then review the recent progress on two different artificial organelles. Recent strategies, purified and identified proteins, and working principles are discussed. With more study on the artificial mitochondrion and artificial chloroplasts, they are expected to be very powerful tools, allowing us to achieve complex cascading reactions in artificial cells, like the ones that happen in real cells.

Dynamic response of red blood cells in health and disease

The viscoelastic response of the red blood cells (RBCs) affected by hematological disorders become severely impaired by the altered biophysical and morphological properties. These include traits like reduced deformability, increased membrane viscosity, and change in cell shape, causing substantial changes in the overall hemodynamics. RBCs, by virtue of their highly elastic membrane and low bending rigidity, exhibit complex dynamics when exposed to cyclic, transient forces in the microcirculation. Here, we employ mesoscopic numerical simulations based on the dissipative particle dynamics (DPD) framework to explore the dynamics of healthy, schizont stage malaria-infected and type 2 diabetes mellitus affected RBCs subjected to external time-dependent loads. The paper focuses on the imposition and cessation of external forcing on the cells of two different typologies, saw-tooth cyclic wave loading and sudden loads in the form of creep and relaxation phenomena. The effects of varying the rate of stress and the applied stress magnitude were investigated. Our simulations disclosed unique shape transitions of the hysteresis curves at varied loading rates. A careful analysis reveals a critical threshold of half cycle time of the from wherein the deformation of all cells observed, healthy or otherwise, falls under the nearly reversible deformation regime displaying minimal energy dissipation. Finally, we also examined the individual effects of the different constitutive and geometric characteristics attributed to the pathological cells and observed interesting recovery dynamics of spherocytes and cells having high shear moduli. The distinguished deformation behaviour of healthy and diseased cells could establish external force as a valuable initial biomarker.

Optical measurement of the picosecond fluid mechanics in simple liquids generated by vibrating nanoparticles: a review

Standard continuum assumptions commonly used to describe the fluid mechanics of simple liquids have the potential to break down when considering flows at the nanometer scale. Two common assumptions for simple molecular liquids are that (1) they exhibit a Newtonian response, where the viscosity uniquely specifies the linear relationship between the stress and strain rate, and (2) the liquid moves in tandem with the solid at any solid-liquid interface, known as the no-slip condition. However, even simple molecular liquids can exhibit a non-Newtonian, viscoelastic response at the picosecond time scales that are characteristic of the motion of many nanoscale objects; this viscoelasticity arises because these time scales can be comparable to those of molecular relaxation in the liquid. In addition, even liquids that wet solid surfaces can exhibit nanometer-scale slip at those surfaces. It has recently become possible to interrogate the viscoelastic response of simple liquids and associated nanoscale slip using optical measurements of the mechanical vibrations of metal nanoparticles. Plasmon resonances in metal nanoparticles provide strong optical signals that can be accessed by several spectroscopies, most notably ultrafast transient-absorption spectroscopy. These spectroscopies have been used to measure the frequency and damping rate of acoustic oscillations in the nanoparticles, providing quantitative information about mechanical coupling and exchange of mechanical energy between the solid particle and its surrounding liquid. This information, in turn, has been used to elucidate the rheology of viscoelastic simple liquids at the nanoscale in terms of their constitutive relations, taking into account separate viscoelastic responses for both shear and compressible flows. The nanoparticle vibrations have also been used to provide quantitative measurements of slip lengths on the single-nanometer scale. Viscoelasticity has been shown to amplify nanoscale slip, illustrating the interplay between different aspects of the unconventional fluid dynamics of simple liquids at nanometer length scales and picosecond time scales.

Multimodal microscale mechanical mapping of cancer cells in complex microenvironments

The mechanical phenotype of the cell is critical for survival following deformations due to confinement and fluid flow. One idea is that cancer cells are plastic and adopt different mechanical phenotypes under different geometries that aid in their survival. Thus, an attractive goal is to disrupt cancer cells' ability to adopt multiple mechanical states. To begin to address this question, we aimed to quantify the diversity of these mechanical states using in vitro biomimetics to mimic in vivo two-dimensional (2D) and 3D extracellular matrix environments. Here, we used two modalities Brillouin microscopy (∼GHz) and broadband frequency (7-15 kHz) optical tweezer microrheology to measure microscale cell mechanics. We measured the response of intracellular mechanics of cancer cells cultured in 2D and 3D environments where we modified substrate stiffness, dimensionality (2D versus 3D), and presence of fibrillar topography. We determined that there was good agreement between two modalities despite the difference in timescale of the two measurements. These findings on cell mechanical phenotype in different environments confirm a correlation between modalities that employ different mechanisms at different temporal scales (Hz-kHz versus GHz). We also determined that observed heterogeneity in cell shape is more closely linked to the cells' mechanical state. Moreover, individual cells in multicellular spheroids exhibit a lower degree of mechanical heterogeneity when compared with single cells cultured in monodisperse 3D cultures. The observed decreased heterogeneity among cells in spheroids suggested that there is mechanical cooperativity between cells that make up a single spheroid.

A method for generating dynamic compression shear coupled stress loading on living cells

Changes in the mechanical properties of single cells are related to the physiological state and fate of cells. The construction of cell constitutive equations is essential for understanding the material characteristics of single cells. With the help of atomic force microscopy, bio-image processing algorithms, and other technologies, research investigating the mechanical properties of cells during static/quasi-static processes has developed rapidly. A series of equivalent models, such as viscoelastic models, have been proposed to describe the constitutive behaviors of cells. The stress-strain relations under dynamic processes are essential to completing the constitutive equations of living cells. To explore the dynamic mechanical properties of cells, we propose a novel method to generate a controllable dynamical compression shear coupling stress on living cells. A CFD model was established to visualize this method and display the theories, as well as assess the scope of the application. As the requirements or limitations are met, researchers can adjust the details of this model according to their lab environment or experimental demands. This micro-flow channel-based method is a new tool for approaching the dynamic mechanical properties of cells.

The role of cellular traction forces in deciphering nuclear mechanics

Cellular forces exerted on the extracellular matrix (ECM) during adhesion and migration under physiological and pathological conditions regulate not only the overall cell morphology but also nuclear deformation. Nuclear deformation can alter gene expression, integrity of the nuclear envelope, nucleus-cytoskeletal connection, chromatin architecture, and, in some cases, DNA damage responses. Although nuclear deformation is caused by the transfer of forces from the ECM to the nucleus, the role of intracellular organelles in force transfer remains unclear and a challenging area of study. To elucidate nuclear mechanics, various factors such as appropriate biomaterial properties, processing route, cellular force measurement technique, and micromanipulation of nuclear forces must be understood. In the initial phase of this review, we focused on various engineered biomaterials (natural and synthetic extracellular matrices) and their manufacturing routes along with the properties required to mimic the tumor microenvironment. Furthermore, we discussed the principle of tools used to measure the cellular traction force generated during cell adhesion and migration, followed by recently developed techniques to gauge nuclear mechanics. In the last phase of this review, we outlined the principle of traction force microscopy (TFM), challenges in the remodeling of traction forces, microbead displacement tracking algorithm, data transformation from bead movement, and extension of 2-dimensional TFM to multiscale TFM.

Quantum-enhanced stimulated Brillouin scattering spectroscopy and imaging

Brillouin microscopy is an emerging label-free imaging technique used to assess local viscoelastic properties. Quantum-enhanced stimulated Brillouin scattering is demonstrated using low power continuous-wave lasers at 795 nm. A signal-to-noise ratio enhancement of 3.4 dB is reported by using two-mode intensity-difference squeezed light generated with the four-wave mixing process in atomic rubidium vapor. The low optical power and the excitation wavelengths in the water transparency window have the potential to provide a powerful bio-imaging technique for probing mechanical properties of biological samples prone to phototoxicity and thermal effects. The performance enhancement affordable through the use of quantum light may pave the way for significantly improved sensitivity that cannot be achieved classically. The proposed method for utilizing squeezed light for enhanced stimulated Brillouin scattering can be easily adapted for both spectroscopic and imaging applications in biology.

A Novel Step-T-Junction Microchannel for the Cell Encapsulation in Monodisperse Alginate-Gelatin Microspheres of Varying Mechanical Properties at High Throughput

Cell encapsulation has been widely employed in cell therapy, characterization, and analysis, as well as many other biomedical applications. While droplet-based microfluidic technology is advantageous in cell microencapsulation because of its modularity, controllability, mild conditions, and easy operation when compared to other state-of-art methods, it faces the dilemma between high throughput and monodispersity of generated cell-laden microdroplets. In addition, the lack of a biocompatible method of de-emulsification transferring cell-laden hydrogel from cytotoxic oil phase into cell culture medium also hurtles the practical application of microfluidic technology. Here, a novel step-T-junction microchannel was employed to encapsulate cells into monodisperse microspheres at the high-throughput jetting regime. An alginate–gelatin co-polymer system was employed to enable the microfluidic-based fabrication of cell-laden microgels with mild cross-linking conditions and great biocompatibility, notably for the process of de-emulsification. The mechanical properties of alginate-gelatin hydrogel, e.g., stiffness, stress–relaxation, and viscoelasticity, are fully adjustable in offering a 3D biomechanical microenvironment that is optimal for the specific encapsulated cell type. Finally, the encapsulation of HepG2 cells into monodisperse alginate–gelatin microgels with the novel microfluidic system and the subsequent cultivation proved the maintenance of the long-term viability, proliferation, and functionalities of encapsulated cells, indicating the promising potential of the as-designed system in tissue engineering and regenerative medicine.

Biomechanical Sensing Using Gas Bubbles Oscillations in Liquids and Adjacent Technologies: Theory and Practical Applications

Gas bubbles present in liquids underpin many natural phenomena and human-developed technologies that improve the quality of life. Since all living organisms are predominantly made of water, they may also contain bubbles—introduced both naturally and artificially—that can serve as biomechanical sensors operating in hard-to-reach places inside a living body and emitting signals that can be detected by common equipment used in ultrasound and photoacoustic imaging procedures. This kind of biosensor is the focus of the present article, where we critically review the emergent sensing technologies based on acoustically driven oscillations of bubbles in liquids and bodily fluids. This review is intended for a broad biosensing community and transdisciplinary researchers translating novel ideas from theory to experiment and then to practice. To this end, all discussions in this review are written in a language that is accessible to non-experts in specific fields of acoustics, fluid dynamics and acousto-optics.

From qualitative data to correlation using deep generative networks: Demonstrating the relation of nuclear position with the arrangement of actin filaments

The cell nucleus is a dynamic structure that changes locales during cellular processes such as proliferation, differentiation, or migration, and its mispositioning is a hallmark of several disorders. As with most mechanobiological activities of adherent cells, the repositioning and anchoring of the nucleus are presumed to be associated with the organization of the cytoskeleton, the network of protein filaments providing structural integrity to the cells. However, demonstrating this correlation between cytoskeleton organization and nuclear position requires the parameterization of the extraordinarily intricate cytoskeletal fiber arrangements. Here, we show that this parameterization and demonstration can be achieved outside the limits of human conceptualization, using generative network and raw microscope images, relying on machine-driven interpretation and selection of parameterizable features. The developed transformer-based architecture was able to generate high-quality, completed images of more than 8,000 cells, using only information on actin filaments, predicting the presence of a nucleus and its exact localization in more than 70 per cent of instances. Our results demonstrate one of the most basic principles of mechanobiology with a remarkable level of significance. They also highlight the role of deep learning as a powerful tool in biology beyond data augmentation and analysis, capable of interpreting—unconstrained by the principles of human reasoning—complex biological systems from qualitative data.

Influence of the mechanical and geometrical parameters on the cellular uptake of nanoparticles: A stochastic approach

Nanoparticles (NPs) are used for drug delivery with enhanced selectivity and reduced side-effect toxicity in cancer treatments. Based on the literature, the influence of the NPs mechanical and geometrical properties on their cellular uptake has been studied through experimental investigations. However, due to the difficulty to vary the parameters independently in such a complex system, it remains hard to efficiently conclude on the influence of each one of them on the cellular internalization of a NP. In this context, different mechanical / mathematical models for the cellular uptake of NPs have been developed. In this paper, we numerically investigate the influence of the NP's aspect ratio, the membrane tension and the cell-NP adhesion on the uptake of the NP using the model introduced in¹ coupled with a numerical stochastic scheme to measure the weight of each one of the aforementioned parameters. The results reveal that the aspect ratio of the particle is the most influential parameter on the wrapping of the particle by the cell membrane. Then the adhesion contributes twice as much as the membrane tension. Our numerical results match the previous experimental observations.

Mechanosurveillance: Tiptoeing T Cells

Efficient scanning of tissue that T cells encounter during their migratory life is pivotal to protective adaptive immunity. In fact, T cells can detect even a single antigenic peptide/MHC complex (pMHC) among thousands of structurally similar yet non-stimulatory endogenous pMHCs on the surface of antigen-presenting cells (APCs) or target cells. Of note, the glycocalyx of target cells, being composed of proteoglycans and bulky proteins, is bound to affect and even modulate antigen recognition by posing as a physical barrier. T cell-resident microvilli are actin-rich membrane protrusions that puncture through such barriers and thereby actively place the considerably smaller T-cell antigen receptors (TCRs) in close enough proximity to APC-presented pMHCs so that productive interactions may occur efficiently yet under force. We here review our current understanding of how the plasticity of T-cell microvilli and physicochemical properties of the glycocalyx may affect early events in T-cell activation. We assess insights gained from studies on T-cell plasma membrane ultrastructure and provide an update on current efforts to integrate biophysical aspects such as the amplitude and directionality of TCR-imposed mechanical forces and the distribution and lateral mobility of plasma membrane-resident signaling molecules into a more comprehensive view on sensitized T-cell antigen recognition.

Well-free agglomeration and on-demand three-dimensional cell cluster formation using guided surface acoustic waves through a couplant layer

Three-dimensional cell agglomerates are broadly useful in tissue engineering and drug testing. We report a well-free method to form large (1.4-mm) multicellular clusters using 100-MHz surface acoustic waves (SAW) without direct contact with the media or cells. A fluid couplant is used to transform the SAW into acoustic streaming in the cell-laden media held in a petri dish. The couplant transmits longitudinal sound waves, forming a Lamb wave in the petri dish that, in turn, produces longitudinal sound in the media. Due to recirculation, human embryonic kidney (HEK293) cells in the dish are carried to the center of the coupling location, forming a cluster in less than 10 min. A few minutes later, these clusters may then be translated and merged to form large agglomerations, and even repeatedly folded to produce a roughly spherical shape of over 1.4 mm in diameter for incubation—without damaging the existing intercellular bonds. Calcium ion signaling through these clusters and confocal images of multiprotein junctional complexes suggest a continuous tissue construct: intercellular communication. They may be formed at will, and the method is feasibly useful for formation of numerous agglomerates in a single petri dish.

Biophysics involved in the process of tumor immune escape

Much of the current research into immune escape from cancer is focused on molecular and cellular biology, an area of biophysics that is easily overlooked. A large number of immune drugs entering the clinic are not effective for all patients. Apart from the molecular heterogeneity of tumors, the biggest reason for this may be that knowledge of biophysics has not been considered, and therefore an exploration of biophysics may help to address this challenge. To help researchers better investigate the relationship between tumor immune escape and biophysics, this paper provides a brief overview on recent advances and challenges of the biophysical factors and strategies by which tumors acquire immune escape and a comprehensive analysis of the relevant forces acting on tumor cells during immune escape. These include tumor and stromal stiffness, fluid interstitial pressure, shear stress, and viscoelasticity. In addition, advances in biophysics cannot be made without the development of detection tools, and this paper also provides a comprehensive summary of the important detection tools available at this stage in the field of biophysics.

Acquiring structural and mechanical information of a fibrous network through deep learning

Fibrous networks play an essential role in the structure and properties of a variety of biological and engineered materials, such as cytoskeletons, protein filament-based hydrogels, and entangled or crosslinked polymer chains. Therefore, insight into the structural features of these fibrous networks and their constituent filaments is critical for discovering the structure-property-function relationships of these material systems. In this paper, a fibrous network-deep learning system (FN-DLS) is established to extract fibrous network structure information from atomic force microscopy images. FN-DLS accurately assesses the structural and mechanical characteristics of fibrous networks, such as contour length, number of nodes, persistence length, mesh size and fractal dimension. As an open-source system, FN-DLS is expected to serve a vast community of scientists working on very diverse disciplines and pave the way for new approaches on the study of biological and synthetic polymer and filament networks found in current applied and fundamental sciences.

Effects of heat stress on cyto(chemo)kine and inflammasome gene expression and mechanical properties in isolated red and white blood cells from 4 commercial broiler lines and their ancestor jungle fowl

Commercial broilers have been selected for high growth rate and productivity; however, this has negatively impacted their susceptibility to heat stress (HS). Insight into the molecular mechanisms underlying this vulnerability can help design targeted strategies for improvement of HS tolerance. Red blood cells (RBC) and white blood cells (WBC) were isolated from red jungle fowl and 4 lines of commercial modern broilers. Lines A and B are considered standard-yielding lines, whereas Lines C and D are high-yielding. Cells were cultured at either 37°C or 45°C for 2 h to induce heat stress (HS). Gene expression of cytokines, chemokines, and inflammasome components were measured. Heat shock proteins 27 and 70 (HSPs) in RBC were significantly affected by line (P < 0.05), whereas HSP27 and 60 were affected by temperature (P < 0.05). In WBC, there was a significant line effect on HSP gene expression (P < 0.05), and a significant increase (P < 0.05) in HSP90 in Line D in HS compared to TN conditions. In RBC, there was a main effect of HS on TNFα, CCL4, and CCLL4 (P < 0.05). HS significantly increased IL-8L1 (>30-fold, P < 0.0001) in Line C. Inflammasome genes (NLRP3, NLRC5 and NLRC3) were significantly affected by the line studied (P < 0.05). In WBC, the effect of line was significant for all cytokines, chemokines, and inflammasome components studied (P < 0.05). To examine the mechanical properties of isolated RBC from the 4 commercial lines and jungle fowl, RBC were placed into nematic liquid crystals, where Lines B and D were the most strained, and Line A and the jungle fowl were the least strained. Together, these findings indicate not only the dynamic nature of circulating cells, but the differences in the stress and inflammatory response among commercially available lines and their common ancestor. These profiles have the potential to serve as a future marker for stress responses in broilers, though further study is warranted.

Smart biomaterial platforms: Controlling and being controlled by cells

Across diverse research and application areas, dynamic functionality-such as programmable changes in biochemical property, in mechanical property, or in microscopic or macroscopic architecture-is an increasingly common biomaterials design criterion, joining long-studied criteria such as cytocompatibility and biocompatibility, drug release kinetics, and controlled degradability or long-term stability in vivo. Despite tremendous effort, achieving dynamic functionality while simultaneously maintaining other desired design criteria remains a significant challenge. Reversible dynamic functionality, rather than one-time or one-way dynamic functionality, is of particular interest but has proven especially challenging. Such reversible functionality could enable studies that address the current gap between the dynamic nature of in vivo biological and biomechanical processes, such as cell traction, cell-extracellular matrix (ECM) interactions, and cell-mediated ECM remodeling, and the static nature of the substrates and ECM constructs used to study the processes. This review assesses dynamic materials that have traditionally been used to control cell activity and static biomaterial constructs, experimental and computational techniques, with features that may inform continued advances in reversible dynamic materials. Taken together, this review presents a perspective on combining the reversibility of smart materials and the in-depth dynamic cell behavior probed by static polymers to design smart bi-directional ECM platforms that can reversibly and repeatedly communicate with cells.

Viscoelasticity, Like Forces, Plays a Role in Mechanotransduction

Viscoelasticity and its alteration in time and space has turned out to act as a key element in fundamental biological processes in living systems, such as morphogenesis and motility. Based on experimental and theoretical findings it can be proposed that viscoelasticity of cells, spheroids and tissues seems to be a collective characteristic that demands macromolecular, intracellular component and intercellular interactions. A major challenge is to couple the alterations in the macroscopic structural or material characteristics of cells, spheroids and tissues, such as cell and tissue phase transitions, to the microscopic interferences of their elements. Therefore, the biophysical technologies need to be improved, advanced and connected to classical biological assays. In this review, the viscoelastic nature of cytoskeletal, extracellular and cellular networks is presented and discussed. Viscoelasticity is conceptualized as a major contributor to cell migration and invasion and it is discussed whether it can serve as a biomarker for the cells’ migratory capacity in several biological contexts. It can be hypothesized that the statistical mechanics of intra- and extracellular networks may be applied in the future as a powerful tool to explore quantitatively the biomechanical foundation of viscoelasticity over a broad range of time and length scales. Finally, the importance of the cellular viscoelasticity is illustrated in identifying and characterizing multiple disorders, such as cancer, tissue injuries, acute or chronic inflammations or fibrotic diseases.

High Doses of Silica Nanoparticles Obtained by Microemulsion and Green Routes Compromise Human Alveolar Cells Morphology and Stiffness Differently

Among all the inorganic nanomaterials used in commercial products, industry, and medicine, the amorphous silica nanoparticles (SiO2 NPs) appeared to be often tolerated in living organisms. However, despite several toxicity studies, some concerns about the exposure to high doses of SiO2 NPs with different sizes were raised. Then, we used the microemulsion method to obtain stable SiO2 NPs having different sizes (110 nm, 50 nm, and 25 nm). In addition, a new one-pot green synthetic route using leaves extract of Laurus nobilis was performed, obtaining monodispersed ultrasmall SiO2 NPs without the use of dangerous chemicals. The NPs achieved by microemulsion were further functionalized with amino groups making the NPs surface positively charged. Then, high doses of SiO2 NPs (1 mg/mL and 3 mg/mL) achieved from the two routes, having different sizes and surface charges, were used to assess their impact on human alveolar cells (A549), being the best cell model mimicking the inhalation route. Cell viability and caspase-3 induction were analyzed as well as the cellular uptake, obtaining that the smallest (25 nm) and positive-charged NPs were more able to induce cytotoxicity, reaching values of about 60% of cell death. Surprisingly, cells incubated with green SiO2 NPs did not show strong toxicity, and 70% of them remained vital. This result was unusual for ultrasmall nanoobjects, generally highly toxic. The actin reorganization, nuclear morphology alteration, and cell membrane elasticity analyses confirmed the trend achieved from the biological assays. The obtained data demonstrate that the increase in cellular softness, i.e., the decrease in Young’s modulus, could be associated with the smaller and positive NPs, recording values of about 3 kPa. On the contrary, green NPs triggered a slight decrease of stiffness values (c.a. 6 kPa) compared to the untreated cells (c.a. 8 kPa). As the softer cells were implicated in cancer progression and metastasization, this evidence strongly supported the idea of a link between the cell elasticity and physicochemical properties of NPs that, in turn, influenced the interaction with the cell membrane. Thus, the green SiO2 NPs compromised cells to a lesser extent than the other SiO2 NPs types. In this scenario, the elasticity evaluation could be an interesting tool to understand the toxicity of NPs with the aim of predicting some pathological phenomena associated with their exposure.

Effects of Methyl, Ester, and Amine Surface Groups on Microbial Activity and Communities in Nitrifying Biofilms

The objective of this study was to determine how different attachment surface chemistries affected the initial and long-term performance and microbial populations of nitrifying biofilms under well-controlled hydrodynamic mixing conditions. While much previous research has focused on the effects of surface properties such as hydrophobicity on bacterial attachment in pure cultures, this study evaluated the effects of specific functional groups on mixed culture composition and functional behavior. Three surfaces with varying hydrophobicity and charge were evaluated for biofilm community development and performance: unmodified poly(dimethylsiloxane) (PDMS), which included terminal methyl groups and was relatively hydrophobic (P-Methyl), PDMS silanized with ester groups (P-Ester), which was uncharged and relatively hydrophilic, and PDMS modified with amine groups (P-Amine), which possessed a positive charge and was the most hydrophilic. The surface chemistries of the three attachment surfaces were characterized by contact angle goniometry, Fourier transform infrared (FTIR) spectroscopy, and X-ray photoelectron spectroscopy (XPS). These surfaces were inoculated with dilute activated sludge, and biofilms were grown in rotating annular bioreactors for 80 days, with experimental triplicates. Nitrification rates increased most rapidly in P-Amine biofilm reactors, and their biofilm communities contained significantly more Nitrosomonas (p < 0.05) than those on the other surfaces in early growth stages (days 40-50). From days 50-60, the P-Amine surface biofilm had significantly higher nitrate production rates than the P-Methyl and P-Ester biofilms. The biofilms grown on the P-Amine and P-Methyl surfaces were significantly (p < 0.05) more diverse than the P-Ester biofilms, containing higher relative abundances of the order Rhizobiales, including a significantly higher abundance of the nitrifying genus Nitrobacter (p < 0.05), which coincided with higher rates of nitrate generation. Conversely, biofilms grown on the uncharged hydrophilic P-Ester surface were consistently less productive and had lower diversity than biofilms on the other surfaces. These results indicate that surface chemistry may be a useful design parameter to improve the performance of nitrifying biofilm systems for wastewater treatment and that surface chemistry affects mixed biofilm community composition.

Single-molecule analysis of genome-wide DNA methylation by fiber FISH coupled with atomic force microscopy

A straightforward single-molecule approach was developed for identifying whole-genome DNA methylation through fiber-FISH coupled with AFM. This method has advantages of low DNA input, reproduction, long reads and low cost.

Viscoelasticity Acts as a Marker for Tumor Extracellular Matrix Characteristics

Biological materials such as extracellular matrix scaffolds, cancer cells, and tissues are often assumed to respond elastically for simplicity; the viscoelastic response is quite commonly ignored. Extracellular matrix mechanics including the viscoelasticity has turned out to be a key feature of cellular behavior and the entire shape and function of healthy and diseased tissues, such as cancer. The interference of cells with their local microenvironment and the interaction among different cell types relies both on the mechanical phenotype of each involved element. However, there is still not yet clearly understood how viscoelasticity alters the functional phenotype of the tumor extracellular matrix environment. Especially the biophysical technologies are still under ongoing improvement and further development. In addition, the effect of matrix mechanics in the progression of cancer is the subject of discussion. Hence, the topic of this review is especially attractive to collect the existing endeavors to characterize the viscoelastic features of tumor extracellular matrices and to briefly highlight the present frontiers in cancer progression and escape of cancers from therapy. Finally, this review article illustrates the importance of the tumor extracellular matrix mechano-phenotype, including the phenomenon viscoelasticity in identifying, characterizing, and treating specific cancer types.

Cancer-Cell Deep-Learning Classification by Integrating Quantitative-Phase Spatial and Temporal Fluctuations

We present a new classification approach for live cells, integrating together the spatial and temporal fluctuation maps and the quantitative optical thickness map of the cell, as acquired by common-path quantitative-phase dynamic imaging and processed with a deep-learning framework. We demonstrate this approach by classifying between two types of cancer cell lines of different metastatic potential originating from the same patient. It is based on the fact that both the cancer-cell morphology and its mechanical properties, as indicated by the cell temporal and spatial fluctuations, change over the disease progression. We tested different fusion methods for inputting both the morphological optical thickness maps and the coinciding spatio-temporal fluctuation maps of the cells to the classifying network framework. We show that the proposed integrated triple-path deep-learning architecture improves over deep-learning classification that is based only on the cell morphological evaluation via its quantitative optical thickness map, demonstrating the benefit in the acquisition of the cells over time and in extracting their spatio-temporal fluctuation maps, to be used as an input to the classifying deep neural network.

Contact guidance via heterogeneity of substrate elasticity

Contact guidance, the widely-known phenomenon of cell alignment, is an essential step in the organization of adherent cells. This guidance is known to occur by, amongst other things, anisotropic features in the environment including elastic heterogeneity. To understand the origins of this guidance we employed a novel statistical thermodynamics framework, which recognises the non-thermal fluctuations in the cellular response, for modelling the response of the cells seeded on substrates with alternating soft and stiff stripes. Consistent with observations, the modelling framework predicts the existence of three regimes of cell guidance: (i) in regime I for stripe widths much larger than the cell size guidance is primarily entropic; (ii) for stripe widths on the order of the cell size in regime II guidance is biochemically mediated and accompanied by changes to the cell morphology while (iii) in regime III for stripe widths much less than the cell size there is no guidance as cells cannot sense the substrate heterogeneity. Guidance in regimes I and II is due to "molli-avoidance" with cells primarily residing on the stiff stripes. While the molli-avoidance tendency is not lost with decreasing density of collagen coating the substrate, the reduced focal adhesion formation with decreasing collagen density tends to inhibit contact guidance. Our results provide clear physical insights into the interplay between cell mechano-sensitivity and substrate elastic heterogeneity that ultimately leads to the contact guidance of cells in heterogeneous tissues. STATEMENT OF SIGNIFICANCE: Cellular morphology and organization play a crucial role in the micro-architecture of tissues and dictates their biological and mechanical functioning. Despite the importance of cellular organization in all facets of tissue biology, the fundamental question of how a cell organizes itself in an anisotropic environment is still poorly understood. We employ a novel statistical thermodynamics framework which recognises the non-thermal fluctuations in the cellular response to investigate cell guidance on substrates with alternating soft and stiff stripes. The propensity of cells to primarily reside on stiff stripes results in strong guidance when the period of the stripes is larger than the cell size. For smaller stripe periods, cells sense a homogeneous substrate and guidance is lost.

Nanoscale structural and mechanical characterization of thin bicontinuous cubic phase lipid films

The mechanical response of lipid membranes to nanoscale deformations is of fundamental importance for understanding how these interfaces behave in multiple biological processes; in particular, the nanoscale mechanics of non-lamellar membranes represents a largely unexplored research field. Among these mesophases, inverse bicontinuous cubic phase Q_II membranes have been found to spontaneously occur in stressed or virally infected cells and to play a role in fundamental processes, such as cell fusion and food digestion. We herein report on the fabrication of thin ( ̴150 nm) supported Q_II cubic phase lipid films (SQ_IIFs) and on their characterization via multiple techniques including Small Angle X-Ray Scattering (SAXS), Ellipsometry and Atomic Force Microscopy (AFM). Moreover, we present the first nanomechanical characterization of a cubic phase lipid membrane, through AFM-based Force Spectroscopy (AFM-FS). Our analysis reveals that the mechanical response of these architectures is strictly related to their topology and structure. The observed properties are strikingly similar to those of macroscopic 3D printed cubic structures when subjected to compression tests in material science; suggesting that this behaviour depends on the 3D organisation, rather than on the length-scale of the architecture. We also show for the first time that AFM-FS can be used for characterizing the structure of non-lamellar mesophases, obtaining lattice parameters in agreement with SAXS data. In contrast to classical rheological studies, which can only probe bulk cubic phase solutions, our AFM-FS analysis allows probing the response of cubic membranes to deformations occurring at length and force scales similar to those found in biological interactions.

A mini-review on peptide-based self-assemblies and their biological applications

Peptide-based supramolecular self-assembly from peptide monomers into well-organized nanostructures, has attracted extensive attentions towards biomedical and biotechnological applications in recent decades. This spontaneous and reversible assembly process involving non-covalent bonding interactions can be artificially regulated. In this review, we have elaborated different strategies to modulate the peptide self-assembly through tuning the physicochemical and environmental conditions, includingpH, light, temperature, solvent, and enzyme. Detailed introduction of biological applications and future potential of the peptide-based nano-assemblies will also be given.

Protein-Ligand Binding Molecular Details Revealed by Terahertz Optical Kerr Spectroscopy: A Simulation Study

Picosecond fast motions and their involvement in the biochemical processes such as protein-ligand binding has engaged significant attention. Terahertz optical Kerr spectroscopy (OKE) has the superior potential to probe these fast motions directly. Application of OKE in protein-ligand binding study is, however, limited by the difficulty of quantitative atomistic interpretation, and the calculation of Kerr spectrum for entire solvated protein complex was considered not yet feasible, due to the lack of one consistent polarizable model for both configuration sampling and polarizability calculation. Here, we analyzed the biochemical relevance of OKE to the lysozyme-triacetylchitotriose binding based on the first OKE simulation using one consistent Drude polarizable model. An analytical multipole and induced dipole scheme was employed to calculate the off-diagonal Drude polarizability more efficiently and accurately. Further theoretical analysis revealed how the subtle twisting and stiffening of aromatic protein residues' spatial arrangement as well as the confinement of small water clusters between ligand and protein cavity due to the ligand binding can be examined using Kerr spectroscopy. Comparison between the signals of bound complex and that of uncorrelated protein/ligand demonstrated that binding action alone has reflection in the OKE spectrum. Our study indicated OKE as a powerful terahertz probe for protein-ligand binding chemistry and dynamics.

Hydration Dynamics in Biological Membranes: Emerging Applications of Terahertz Spectroscopy

Water drives the spontaneous self-assembly of lipids and proteins into quasi two-dimensional biological membranes that act as catalytic scaffolds for numerous processes central to life. However, the functional relevance of hydration in membrane biology is only beginning to be addressed, predominantly because of challenges associated with direct measurements of hydration microstructure and dynamics in a biological milieu. Our recent work on the novel interplay of membrane electrostatics and crowding in shaping membrane hydration dynamics utilizing terahertz (THz) spectroscopy represents an important step in this context. In this Perspective, we provide a glimpse into the ever-broadening functional landscape of hydration dynamics in biological membranes in the backdrop of the unique physical chemistry of water molecules. We further highlight the immense (and largely untapped) potential of the THz toolbox in addressing contemporary problems in membrane biology, while emphasizing the adaptability of the analytical framework reported recently by us to such studies.

Engineered Extracellular Matrices with Integrated Wireless Microactuators to Study Mechanobiology

Mechanobiology explores how forces regulate cell behaviors and what molecular machinery are responsible for the sensing, transduction, and modulation of mechanical cues. To this end, probing of cells cultured on planar substrates has served as a primary experimental setting for many decades. However, native extracellular matrices (ECMs) consist of fibrous protein assemblies where the physical properties spanning from the individual fiber to the network architecture can influence the transmission of forces to and from the cells. Here, a robotic manipulation platform that allows wireless, localized, and programmable deformation of an engineered fibrous ECM is introduced. A finite-element-based digital twin of the fiber network calibrated against measured local and global parameters enables the calculation of deformations and stresses generated by different magnetic actuation schemes across a range of network properties. Physiologically relevant mechanical forces are applied to cells cultured on the fiber network, statically or dynamically, revealing insights into the effects of matrix-borne forces and deformations as well as force-mediated matrix remodeling on cell migration and intracellular signaling. These capabilities are not matched by any existing approach, and this versatile platform has the potential to uncover fundamental mechanisms of mechanobiology in settings with greater relevance to living tissues.

External cues to drive B cell function towards immunotherapy

Immunotherapy stands out as a powerful and promising therapeutic strategy in the treatment of cancer, infections, and autoimmune diseases. Adoptive immune therapies are usually centered on modified T cells and their specific expansion towards antigen-specific T cells against cancer and other diseases. However, despite their unmatched features, the potential of B cells in immunotherapy is just beginning to be explored. The main role of B cells in the immune response is to secrete antigen-specific antibodies and provide long-term protection against foreign pathogens. They further function as antigen-presenting cells (APCs) and secrete pro- and anti-inflammatory cytokines and thus exert positive and negative regulatory stimuli on other cells involved in the immune response such as T cells. Therefore, while hyperactivation of B cells can cause autoimmunity, their dysfunctions lead to severe immunodeficiencies. Only suitably activated B cells can play an active role in the treatment of cancers, infections, and autoimmune diseases. As a result, studies have focused on B cell-targeted immunotherapies in recent years. For this, the development, functions, interactions with the microenvironment, and clinical importance of B cells should be well understood. In this review, we summarize the main events during B cell activation. From the viewpoint of mechanobiology we discuss the translation of external cues such as surface topology, substrate stiffness, and biochemical signaling into B cell functions. We further dive into current B cell-targeted therapy strategies and their clinical applications. STATEMENT OF SIGNIFICANCE: B cells are proving as a promising tool in the field of immunotherapy. B cells exhibit various functions such as antibody production, antigen presentation or secretion of immune-regulatory factors which can be utilized in the fight against oncological or immunological disorders. In this review we discuss the importance of external mechanobiological cues such as surface topology, substrate stiffness, and biochemical signaling on B cell function. We further summarize B cell-targeted therapy strategies and their clinical applications, as in the context of anti-tumor responses and autoimmune diseases.

Visualizing the Invisible: Advanced Optical Microscopy as a Tool to Measure Biomechanical Forces

The importance of mechanical force in biology is evident across diverse length scales, ranging from tissue morphogenesis during embryo development to mechanotransduction across single adhesion proteins at the cell surface. Consequently, many force measurement techniques rely on optical microscopy to measure forces being applied by cells on their environment, to visualize specimen deformations due to external forces, or even to directly apply a physical perturbation to the sample via photoablation or optogenetic tools. Recent developments in advanced microscopy offer improved approaches to enhance spatiotemporal resolution, imaging depth, and sample viability. These advances can be coupled with already existing force measurement methods to improve sensitivity, duration and speed, amongst other parameters. However, gaining access to advanced microscopy instrumentation and the expertise necessary to extract meaningful insights from these techniques is an unavoidable hurdle. In this Live Cell Imaging special issue Review, we survey common microscopy-based force measurement techniques and examine how they can be bolstered by emerging microscopy methods. We further explore challenges related to the accompanying data analysis in biomechanical studies and discuss the various resources available to tackle the global issue of technology dissemination, an important avenue for biologists to gain access to pre-commercial instruments that can be leveraged for biomechanical studies.

Fatty acid synthase as a feasible biomarker for triple negative breast cancer stem cell subpopulation cultured on electrospun scaffolds

There is no targeted therapy for triple negative breast cancer (TNBC), which presents an aggressive profile and poor prognosis. Recent studies noticed the feasibility of breast cancer stem cells (BCSCs), a small population responsible for tumor initiation and relapse, to become a novel target for TNBC treatments. However, new cell culture supports need to be standardized since traditional two-dimensional (2D) surfaces do not maintain the stemness state of cells. Hence, three-dimensional (3D) scaffolds represent an alternative to study in vitro cell behavior without inducing cell differentiation. In this work, electrospun polycaprolactone scaffolds were used to enrich BCSC subpopulation of MDA-MB-231 and MDA-MB-468 TNBC cells, confirmed by the upregulation of several stemness markers and the existence of an epithelial-to-mesenchymal transition within 3D culture. Moreover, 3D-cultured cells displayed a shift from MAPK to PI3K/AKT/mTOR signaling pathways, accompanied by an enhanced EGFR and HER2 activation, especially at early cell culture times. Lastly, the fatty acid synthase (FASN), a lipogenic enzyme overexpressed in several carcinomas, was found to be hyperactivated in stemness-enriched samples. Its pharmacological inhibition led to stemness diminishment, overcoming the BCSC expansion achieved in 3D culture. Therefore, FASN may represent a novel target for BCSC niche in TNBC samples.