Atomic force microscopy of spherical intermediates on the pathway to fibril formation of influenza A virus nuclear export protein

The nuclear export protein of the influenza A virus (NEP) is involved in many important processes of the virus life cycle. This makes it an attractive target for the treatment of a disease caused by a virus. Previously it has been shown, that recombinant variants of NEP are highly prone to aggregation in solution under various conditions with the formation of amyloid-like aggregates. In the present work, the amyloid nature of NEP aggregates was evidenced by Congo red binding assays. Atomic force microscopy has shown that NEP can form two types of spherical nanoparticles, which provide an alternative pathway for the formation of amyloid-like fibrils. Type I of these "fibrillogenic" spheres, formed under physiological conditions, represents the micelle-like particles with height 10-60 nm, which can generate worm-like flexible fibrils with the diameter 2.5-4.0 nm, length 20-500 nm and the Young's modulus ~73 MPa. Type II spherical aggregates with size of about 400-1000 nm, formed at elevated temperatures, includes fractions of drop-like and vesicle-like particles, generating more rigid amyloid-like fibrils with height of ~8 nm, and length of up to 2 μm. The hypothetical mechanism of fibril formation via nanospherical structures was suggested. RESEARCH HIGHLIGHTS: AFM has revealed two types of the influenza A virus nuclear export protein spherical aggregates. They provide an alternative pathway for the formation of amyloid-like fibrils. The mechanism of fibril formation via spherical structures is suggested.

Characterization of the mechanical properties of the cortex region of human hair fibers by multiparametric atomic force microscopy mapping

We show the benefit of the use of atomic force microscopy (AFM) in spectroscopy force mode (FV: force volume) for evaluation of the cosmetic active effectiveness in improving the mechanical properties of human hair fibers cortex region. For this, we characterized human hair fibers without and with chemical damage caused by bleaching process. Fiber and resin (embedding material) data were obtained simultaneously in the mapping in order to have the resin data as a reference to ensure a coherent comparison between data from the different fiber groups. Our AFM results, which were evaluated using statistical tests, demonstrated the degradation of fibers after bleaching, corroborating the findings of transmission electron microscopy analysis and the effectiveness of a cosmetic active ingredient in improving the Young's modulus (elastic modulus) (E) of the damaged fibers. We also found a radial decrease in the natural logarithm of Young's modulus ln(E) along the cross-section of the active group fiber, which is compatible with confocal Raman spectroscopy analysis by other authors, demonstrating variation of the active permeation with depth. We note that Young's modulus was also determined by a tensile tester (macro-scale technique), in which it was not possible to obtain statistically significant differences between the groups, evidencing the advantage of the FV-AFM analysis. We also found an increase in ln(E) accompanied by a decrease in maximum adhesion force between tip and sample (negative Pearson correlation coefficient). This result can be explained by the fact that structures composed of hydrophobic components have a higher Young's modulus than structures composed of hydrophilic components.

Fusion of amyloid beta with ferritin yields an isolated oligomeric beta-sheet-rich aggregate inside the ferritin cage

Alzheimer's disease is a severe brain condition caused by the formation of amyloid plaques composed of amyloid beta (Aβ) peptides. These peptides form oligomers, protofibrils, and fibrils before deposition into amyloid plaques. Among these intermediates, Aβ oligomers (AβOs) were found to be the most toxic and therefore an appealing target for drug development and understanding their role in the disease. However, precise isolation and characterization of AβOs have proven challenging because AβOs tend to aggregate and form heterogeneous mixtures in solution. As a solution, we genetically fused the Aβ peptide with a ferritin monomer. Such fusion allowed the encapsulation of precisely 24 Aβ peptides inside the 24-mer ferritin cage. Using high-speed atomic force microscopy (HS-AFM), we disassembled ferritin and directly visualized the Aβ core enclosed within the cage. The thioflavin-T assay (ThT) and attenuated total reflection infrared spectroscopy (ATR-IR) revealed the presence of a β-sheet structure in the encapsulated oligomeric aggregate. Gallic acid, an amyloid inhibitor, can inhibit the fluorescence of ThT bound AβOs. Our approach represents a significant advancement in the isolation and characterization of β-sheet rich AβOs and is expected to be useful for future studies of other disordered peptides such as α-synuclein and tau.

Antimicrobial effects of silver nanoparticle-microspots on the mechanical properties of single bacteria

Silver nanoparticles (AgNPs) conjugated with polymers are well-known for their powerful and effective antimicrobial properties. In particular, the incorporation of AgNPs in biocompatible catecholamine-based polymers, such as polydopamine (PDA), has recently shown promising antimicrobial activity, due to the synergistic effects of the AgNPs, silver(I) ions released and PDA. In this study, we generated AgNPs-PDA-patterned surfaces by localised electrochemical depositions, using a double potentiostatic method via scanning electrochemical cell microscopy (SECCM). This technique enabled the assessment of a wide parameter space in a high-throughput manner. The optimised electrodeposition process resulted in stable and homogeneously distributed AgNP-microspots, and their antimicrobial activity against Escherichia coli was assessed using atomic force microscopy (AFM)-based force spectroscopy, in terms of bacterial adhesion and cell elasticity. We observed that the bacterial outer membrane underwent significant structural changes, when in close proximity to the AgNPs, namely increased hydrophilicity and stiffness loss. The spatially varied antimicrobial effect found experimentally was rationalised by numerical simulations of silver(I) concentration profiles.

HIV-1 uncoating requires long double-stranded reverse transcription products

HIV-1 cores, which contain the viral genome and replication machinery, must disassemble (uncoat) during viral replication. However, the viral and host factors that trigger uncoating remain unidentified. Recent studies show that infectious cores enter the nucleus and uncoat near the site of integration. Here, we show that efficient uncoating of nuclear cores requires synthesis of a double-stranded DNA (dsDNA) genome >3.5 kb and that the efficiency of uncoating correlates with genome size. Core disruption by capsid inhibitors releases viral DNA, some of which integrates. However, most of the viral DNA is degraded, indicating that the intact core safeguards viral DNA. Atomic force microscopy and core content estimation reveal that synthesis of full-length genomic dsDNA induces substantial internal strain on the core to promote uncoating. We conclude that HIV-1 cores protect viral DNA from degradation by host factors and that synthesis of long double-stranded reverse transcription products is required to trigger efficient HIV-1 uncoating.

Toward the nanoscale chemical and physical probing of milk-derived extracellular vesicles using Raman and tip-enhanced Raman spectroscopy

Tip-enhanced Raman spectroscopy (TERS) is an advanced technique to perform local chemical analysis of the surface of a sample through the improvement of the sensitivity and the spatial resolution of Raman spectroscopy by plasmonic enhancement of the electromagnetic signal in correspondence with the nanometer-sized tip of an atomic force microscope (AFM). In this work, TERS is demonstrated to represent an innovative and powerful approach for studying extracellular vesicles, in particular bovine milk-derived extracellular vesicles (mEVs), which are nanostructures with considerable potential in drug delivery and therapeutic applications. Raman spectroscopy has been used to analyze mEVs at the micrometric and sub-micrometric scales to obtain a detailed Raman spectrum in order to identify the 'signature' of mEVs in terms of their characteristic molecular vibrations and, therefore, their chemical compositions. With the ability to improve lateral resolution, TERS has been used to study individual mEVs, demonstrating the possibility of investigating a single mEV selected on the surface of the sample and, moreover, analyzing specific locations on the selected mEV with nanometer lateral resolution. TERS potentially allows one to reveal local differences in the composition of mEVs providing new insights into their structure. Also, thanks to the intrinsic properties of TERS to acquire the signal from only the first few nanometers of the surface, chemical investigation of the lipid membrane in correspondence with the various locations of the selected mEV could be performed by analyzing the peaks of the Raman shift in the relevant range of the spectrum (2800-3000 cm-1). Despite being limited to mEVs, this work demonstrates the potential of TERS in the analysis of extracellular vesicles.

Label-Free Techniques for Probing Biomolecular Condensates

Biomolecular condensates play important roles in a wide array of fundamental biological processes, such as cellular compartmentalization, cellular regulation, and other biochemical reactions. Since their discovery and first observations, an extensive and expansive library of tools has been developed to investigate various aspects and properties, encompassing structural and compositional information, material properties, and their evolution throughout the life cycle from formation to eventual dissolution. This Review presents an overview of the expanded set of tools and methods that researchers use to probe the properties of biomolecular condensates across diverse scales of length, concentration, stiffness, and time. In particular, we review recent years' exciting development of label-free techniques and methodologies. We broadly organize the set of tools into 3 categories: (1) imaging-based techniques, such as transmitted-light microscopy (TLM) and Brillouin microscopy (BM), (2) force spectroscopy techniques, such as atomic force microscopy (AFM) and the optical tweezer (OT), and (3) microfluidic platforms and emerging technologies. We point out the tools' key opportunities, challenges, and future perspectives and analyze their correlative potential as well as compatibility with other techniques. Additionally, we review emerging techniques, namely, differential dynamic microscopy (DDM) and interferometric scattering microscopy (iSCAT), that have huge potential for future applications in studying biomolecular condensates. Finally, we highlight how some of these techniques can be translated for diagnostics and therapy purposes. We hope this Review serves as a useful guide for new researchers in this field and aids in advancing the development of new biophysical tools to study biomolecular condensates.

Sluggish and Ion-Resilient Behavior of Interfacial Aqueous Layer on Single-Layer Graphene Oxide: Insights from In Situ Atomic Force Microscopy

Understanding interfacial interactions of graphene oxide (GO) is important to evaluate its colloidal behavior and environmental fate. Single-layer GO is the fundamental unit of GO colloids, and its interfacial aqueous layers critically dictate these interfacial interactions. However, conventional techniques like X-ray diffraction are limited to multilayer systems and are inapplicable to single-layer GO. Therefore, our study employed atomic force microscopy to precisely observe the in situ dynamic behaviors of interfacial aqueous layers on single-layer GO. The interfacial aqueous layer height was detected at the subnanometer level. In real-time monitoring, the single-layer height increased from 1.17 to 1.70 nm within 3 h immersion. This sluggish process is different from the rapid equilibration of multilayer GO in previous studies, underscoring a gradual transition in hydration kinetics. Ion strength exhibited negligible influence on the single-layer height, suggesting a resilient response of the interfacial aqueous layer to ion-related perturbations due to intricate ion interactions and electrical double-layer compression. Humic acid led to a substantial increase in the interfacial aqueous layers, improving the colloidal stability of GO and augmenting its potential for migration. These findings hold considerable significance regarding the environmental behaviors of the GO interfacial aqueous layer in ion- and organic-rich water and soil.

Rapid Silicification of a DNA Origami with Shape Fidelity

High-fidelity patterning of DNA origami nanostructures on various interfaces holds great potential for nanoelectronics and nanophotonics. However, distortion of a DNA origami often occurs due to the strong interface interactions, e.g., on two-dimensional (2D) materials. In this study, we discovered that the adsorption of silica precursors in rapid silicification can prevent the distortion caused by graphene and generates a high shape-fidelity DNA origami-silica composite on a graphene interface. We found that an incubation time of 1 min and silicification time of 16 h resulted in the formation of DNA origami-silica composites with the highest shape fidelity of 99%. By comparing the distortion of the DNA origami on the graphene interface with and without silicification, we observed that rapid silicification effectively preserved the integrity of the DNA origami. Statistical analysis of scanning electron microscopy data indicates that compared to bare DNA origami, the DNA origami-silica composite has an increased shape fidelity by more than two folds. Furthermore, molecular dynamics simulations revealed that rapid silicification effectively suppresses the distortion of the DNA origami through the interhelical insertion of silica precursors. Our strategy provides a simple yet effective solution to maintain the shape-fidelity DNA origami on interfaces that have strong interaction with DNA molecules, expanding the applicable interfaces for patterning 2D DNA origamis.

Controlling Solvent Polarity to Regulate Protein Self-Assembly Morphology and Its Universal Insight for Fibrillation Mechanism

The mechanism of ethanol-induced fibrillation of β-lactoglobulin (β-lg) in the acidic aqueous solution upon heating was investigated using various techniques, mainly thioflavin T fluorescence, atomic force microscopy, nonreducing electrophoresis, mass spectrometry, Fourier transform infrared spectroscopy, and circular dichroism spectroscopy. The results showed that fibrillation occurred with a heating time increase, but high ethanol content slowed down the process. At a low ethanol volume fraction, peptides existed after heating for 2 h, with long and straight fibrils formed after 4-6 h, while at a high ethanol volume fraction, the proteins aggregated with very few peptides appeared at the early stage of heating, and short and curved fibrils formed after heating for 8 h. Ethanol weakened the hydrophobic interactions between proteins in the aqueous solution; therefore the latter could not completely balance the electrostatic repulsion, and thus suppressing the fibrillation process. It is believed that the fibrillation of β-lg in the acidic solution upon heating is mainly dominated by the polypeptide model; however, ethanol inhibited the hydrolysis of proteins, and the self-assembly mechanism changed to the monomer model.

Rapid and Mechanically Robust Immobilization of Proteins on Silica Studied at the Single-Molecule Level by Force Spectroscopy and Verified at the Macroscopic Level

Typical methods for stable immobilization of proteins often involve time-consuming surface modification of silicon-based materials to enable specific binding, while the nonspecific adsorption method is faster but usually unstable. Herein, we fused a silica-binding protein, Si-tag, to target proteins so that the target proteins could attach directly to silica substrates in a single step, markedly streamlining the immobilization process. The adhesion force between the Si-tag and glass substrates was determined to be approximately 400-600 pN at the single-molecule level by atomic force microscopy, which is greater than the unfolding force of most proteins. The adhesion force of the Si-tag exhibits a slight increase when pulled from the C-terminus compared to that from the N-terminus. Furthermore, the Si-tag's adhesion force on a glass surface is marginally higher than that on a silicon nitride probe. The binding properties of the Si-tag are not obviously affected by environmental factors, including pH, salt concentration, and temperature. In addition, the macroscopic adhesion force between the Si-tag-coated hydrogel and glass substrates was ∼40 times higher than that of unmodified hydrogels. Therefore, the Si-tag, with its strong silica substrate binding ability, provides a useful tool as an excellent fusion tag for the rapid and mechanically robust immobilization of proteins on silica and for the surface coating of silica-binding materials.

Bacteriophage Engineering for Improved Copper Ion Binding

In this study, fd viruses are genetically modified to display seven cropped versions (H, HG, HGF, HGFA, HGFAN, HGFANV and HGFANVA) of the previously identified Cu(II) specific peptide (HGFANVA). Atomic force microscopy (AFM) imaging reveals the typical filamentous structures of recombinant phages with thicknesses of ≈2-5 nm in dry state. Scanning electron microscopy (SEM) imaging shows that HGFANVA viruses form larger elongated assemblies than H viruses that are deposited with a mineral layer after Cu(II) treatment. C and N peaks are detected for virus samples through Energy dispersive X-ray spectroscopy (EDX) analyses confirming the presence of phage organic material. Cu peak is only detected for engineered viruses after Cu(II) exposure. Enzyme-linked immunosorbent assay (ELISA) analyses show the selective Cu(II) binding of engineered phages. Agarose gel electrophoresis (AGE) and zeta potential analyses reveal negative surface charges of engineered viral constructs. Positively charged Cytopore beads are coated with bacteriophages and used for Cu(II) ion sorption studies. ICP-MS analyses clearly show the improved Cu(II) binding of engineered viruses with respect to wild-type fd phages. Such bottom-up constructed, genetically engineered virus-based biomaterials may be applied in bioremediation studies targeting metal species from environmental samples.

Strengthen oriented poly (L-lactic acid) monofilaments via mechanical training

Polymer materials have found extensive applications in the clinical and medical domains due to their exceptional biocompatibility and biodegradability. Compared to metallic counterparts, polymers, particularly Poly (L-lactic acid) (PLLA), are more suitable for fabricating biodegradable stents. As a viscoelastic material, PLLA monofilaments exhibit a creep phenomenon under sustained tensile stress. This study explores the use of creep to enhance the mechanical attributes of PLLA monofilaments. By subjecting the highly oriented monofilaments to controlled, constant force stretching, we achieved notable improvements in their mechanical characteristics. The results, as confirmed by tensile testing and dynamic mechanical analysis, revealed a remarkable 67 % increase in total elongation and over a 20 % rise in storage modulus post-mechanical training. Further microscopic analyses, including Atomic Force Microscopy (AFM) and Scanning Electron Microscopy (SEM), revealed enhanced spacing and cavity formation. These mechanical advancements are attributed to the unraveling and a more orderly arrangement of molecular chains in the amorphous regions. This investigation offers a promising approach for augmenting the mechanical properties of PLLA monofilaments, potentially benefiting their application in biomedical engineering.

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.

Understanding the Retention of Vaping Additives in the Lungs: Model Lung Surfactant Membrane Perturbation by Vitamin E and Vitamin E Acetate

Deviations from the normal physicochemical and functional properties of pulmonary surfactants are associated with the incidence of lung injury and other respiratory disorders. This study aims to evaluate the alteration of the 2D molecular organization and morphology of pulmonary surfactant model membranes by the electronic cigarette additives α-tocopherol (vitamin E) and α-tocopherol acetate (vitamin E acetate), which have been associated with lung injury, termed e-cigarette or vaping-use-associated lung injury (EVALI). The model membranes used contained a 7:3 molar ratio of DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) and POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol) to which α-tocopherol and α-tocopherol acetate were added to form mixtures of up to 20 mol % additive. The properties of the neat tocopherol additives and DPPC/POPG (7:3) mixtures with increasing molar proportions of additive were evaluated by surface pressure-area isotherms, excess area calculations, Brewster angle microscopy, grazing incidence X-ray diffraction, X-ray reflectivity, and atomic force microscopy. The addition of either additive alters the essential phase balance of the model pulmonary surfactant membrane by generating a greater proportion of the fluid phase. Despite this net fluidization, both tocopherol additives have space-filling effects on the liquid-expanded and condensed phases, yielding negative excess areas in the liquid-expanded phase and reduced tilt angles in the condensed phase. Both tocopherol additives alter the stability of the fluid phase, pushing the eventual collapse of this phase to higher surface pressures than the model membrane in the absence of an additive.

Protocol for localized macrophage stimulation with small-molecule TLR agonist via fluidic force microscopy

Here, we present a protocol to deliver nanoliter volumes of Toll-like receptor (TLR) agonist onto a culture of nuclear factor κB (NF-κB) reporter macrophages using fluidic force microscopy and a micron-scale probe. We describe steps for quantifying the dose of agonist by modeling their diffusion with experimental inputs. We then detail procedures for quantifying and categorizing macrophage responses to individual and varied doses and combining agonist concentration and macrophage response to analyze the NF-κB response to localized TLR stimulation. For complete details on the use and execution of this protocol, please refer to Mulder et al. (2024).1.

Multiscale elasticity mapping of biological samples in 3D at optical resolution

The mechanical properties of biological tissues have emerged as an integral determinant of tissue function in health and disease. Nonetheless, characterizing the elasticity of biological samples in 3D and at high resolution remains challenging. Here, we present a µElastography platform: a scalable elastography system that maps the elastic properties of tissues from cellular to organ scales. The platform leverages the use of a biocompatible, thermo-responsive hydrogel to deliver compressive stress to a biological sample and track its resulting deformation. By surrounding the specimen with a reference hydrogel of known Young's modulus, we are able to map the absolute values of elastic properties in biological samples. We validate the experimental and computational components of the platform using a hydrogel phantom and verify the system's ability to detect internal mechanical heterogeneities. We then apply the platform to map the elasticity of multicellular spheroids and the murine lymph node. With these applications, we demonstrate the platform's ability to map tissue elasticity at internal planes of interest, as well as capture mechanical heterogeneities neglected by most macroscale characterization techniques. The µElastography platform, designed to be implementable in any biology lab with access to 3D microscopy (e.g., confocal, multiphoton, or optical coherence microscopy), will provide the capability to characterize the mechanical properties of biological samples to labs across the large community of biological sciences by eliminating the need of specialized instruments such as atomic force microscopy. STATEMENT OF SIGNIFICANCE: Understanding the elasticity of biological tissues is of great importance, but characterizing these properties typically requires highly specialized equipment. Utilizing stimulus-responsive hydrogels, we present a scalable, hydrogel-based elastography method that uses readily available reagents and imaging modalities to generate resolved maps of internal elasticity within biomaterials and biological samples at optical resolution. This new approach is capable of detecting internal stiffness heterogeneities within the 3D bulk of samples and is highly scalable across both imaging modalities and biological length scales. Thus, it will have significant impact on the measurement capabilities of labs studying engineered biomaterials, mechanobiology, disease progression, and tissue engineering and development.

Microrheological comparison of melanoma cells by atomic force microscopy

Melanoma is one of the most severe cancers due to its great potential to form metastasis. Recent studies showed the importance of mechanical property assessment in metastasis formation which depends on the cytoskeleton dynamics and cell migration. Although cells are considered purely elastic, they are viscoelastic entities. Microrheology atomic force microscopy (AFM) enables the assessment of elasticity and viscous properties, which are relevant to cell behavior regulation. The current work compares the mechanical properties of human neonatal primary melanocytes (HNPMs) with two melanoma cell lines (WM793B and 1205LU cells), using microrheology AFM. Immunocytochemistry of F-actin filaments and phosphorylated focal adhesion kinase (p-FAK) and cell migration assays were performed to understand the differences found in microrheology AFM regarding the tumor cell lines tested. AFM revealed that HNPMs and tumor cell lines had distinct mechanical properties. HNPMs were softer, less viscous, presenting a higher power-law than melanoma cells. Immunostaining showed that metastatic 1205LU cells expressed more p-FAK than WM793B cells. Melanoma cell migration assays showed that WM73B did not close the gap, in contrast to 1205LU cells, which closed the gap at the end of 23 h. These data seem to corroborate the high migratory behavior of 1205LU cells. Microrheology AFM applied to HNPMs and melanoma cells allowed the quantification of elasticity, viscous properties, glassy phase, and power-law properties, which have an impact in cell migration and metastasis formation. AFM study is important since it can be used as a biomarker of the different stages of the disease in melanoma.

Preparation and characterization of sulfated nanocellulose: From hydrogels to highly transparent films

This study focuses on the production of sulfated cellulose microfibers and nanocellulose hydrogels from native cellulose microfibers (CMF). The process involves using a combination of H2SO4 and urea, resulting in highly sulfated cellulose microfiber hydrogel (SC) with notable properties such as a sulfur content of 7.5 %, a degree of sulfation of 0.49, a surface charge content of 2.2 mmol. g-1, and a high yield of 81 %. The SC hydrogel can be easily fibrillated into sulfated nanocellulose hydrogel (S-NC) with elongated nanocellulose structures having an average diameter of 6.85 ± 3.11 nm, as determined using atomic force microscopy (AFM). X-ray photoelectron spectroscopy (XPS) analysis confirms the presence of sulfate groups on the surface of the nanocellulose material. Transparent films with good mechanical properties can be produced from both cellulose microfiber and nanocellulose hydrogels. The sulfate functionality gives the hydrogel attractive rheological properties and makes S-NC re-dispersible in water, which can be beneficial for various applications. This study demonstrates the potential of this process to address previous challenges related to nanocellulose materials production.

Atomic force microscope kymograph analysis: A case study of two membrane proteins

Kymograph analysis is employed across the biological atomic force microscopy (AFM) community to boost temporal resolution. The method is well suited for revealing protein dynamics at the single molecule level in near-native conditions. Yet, kymograph analysis comes with limitations that depend on several factors including protein geometry and instrumental drift. This work focuses on conformational dynamics of difficult-to-study sparse distributions of membrane proteins. We compare and contrast AFM kymograph analysis for two proteins, one of which (SecDF) exhibits conformational dynamics primarily in the vertical direction (normal to the membrane surface) and the other (Pgp) exhibits a combination of lateral dynamics and vertical motion. Common experimental issues are analyzed including translational and rotational drift. Conformational transition detection is evaluated via kymograph simulations followed by state detection algorithms. We find that kymograph analysis is largely robust to lateral drift. Displacement of the AFM line scan trajectory away from the protein center of mass by a few nanometers, roughly half of the molecule diameter, does not significantly affect transition detection nor generate undue dwell time errors. On the other hand, for proteins like Pgp that exhibit significant azimuthal maximum height dependence, rotational drift can potentially produce artifactual transitions. Measuring the height of a membrane protein protrusion is generally superior to measurement of width, confirming intuition based on vertical resolution superiority. In low signal-to-noise scenarios, common state detection algorithms struggle with transition detection as opposed to infinite hidden Markov models. AFM kymography represents a valuable addition to the membrane biophysics toolkit; continued hardware and software improvements are poised to expand the method's impact in the field.

Structure of Amyloid Peptide Ribbons Characterized by Electron Microscopy, Atomic Force Microscopy, and Solid-State Nuclear Magnetic Resonance

Polypeptides often self-assemble to form amyloid fibrils, which contain cross-β structural motifs and are typically 5-15 nm in width and micrometers in length. In many cases, short segments of longer amyloid-forming protein or peptide sequences also form cross-β assemblies but with distinctive ribbon-like morphologies that are characterized by a well-defined thickness (on the order of 5 nm) in one lateral dimension and a variable width (typically 10-100 nm) in the other. Here, we use a novel combination of data from solid-state nuclear magnetic resonance (ssNMR), dark-field transmission electron microscopy (TEM), atomic force microscopy (AFM), and cryogenic electron microscopy (cryoEM) to investigate the structures within amyloid ribbons formed by residues 14-23 and residues 11-25 of the Alzheimer's disease-associated amyloid-β peptide (Aβ14-23 and Aβ11-25). The ssNMR data indicate antiparallel β-sheets with specific registries of intermolecular hydrogen bonds. Mass-per-area values are derived from dark-field TEM data. The ribbon thickness is determined from AFM images. For Aβ14-23 ribbons, averaged cryoEM images show a periodic spacing of β-sheets. The combined data support structures in which the amyloid ribbon growth direction is the direction of intermolecular hydrogen bonds between β-strands, the ribbon thickness corresponds to the width of one β-sheet (i.e., approximately the length of one molecule), and the variable ribbon width is a variable multiple of the thickness of one β-sheet (i.e., a multiple of the repeat distance in a stack of β-sheets). This architecture for a cross-β assembly may generally exist within amyloid ribbons.

Quantitative Analysis of Resistance to Deformation of the DNA Origami Framework Supported by Struts

Nanostructures with controlled shapes are of particular interest due to their consistent physical and chemical properties and their potential for assembly into complex superstructures. The use of supporting struts has proven to be effective in the construction of precise DNA polyhedra. However, the influence of struts on the structure of DNA origami frameworks on the nanoscale remains unclear. In this study, we developed a flexible square DNA origami (SDO) framework and enhanced its structural stability by incorporating interarm supporting struts (SDO-s). Comparing the framework with and without such struts, we found that SDO-s demonstrated a significantly improved resistance to deformation. We assessed the deformability of these two DNA origami structures through the statistical analysis of interior angles of polygons based on atomic force microscopy and transmission electron microscopy data. Our results showed that SDO-s exhibited more centralized interior angle distributions compared to SDO, reducing from 30-150° to 60-120°. Furthermore, molecular dynamics simulations indicated that supporting struts significantly decreased the thermodynamic fluctuations of the SDO-s, as described by the root-mean-square fluctuation parameter. Finally, we experimentally demonstrated that the 2D arrays assembled from SDO-s exhibited significantly higher quality than those assembled from SDO. These quantitative analyses provide an understanding of how supporting struts can enhance the structural integrity of DNA origami frameworks.

Maturation-dependent changes in the size, structure and seeding capacity of Aβ42 amyloid fibrils

Many proteins self-assemble to form amyloid fibrils, which are highly organized structures stabilized by a characteristic cross-β network of hydrogen bonds. This process underlies a variety of human diseases and can be exploited to develop versatile functional biomaterials. Thus, protein self-assembly has been widely studied to shed light on the properties of fibrils and their intermediates. A still open question in the field concerns the microscopic processes that underlie the long-time behaviour and properties of amyloid fibrillar assemblies. Here, we use atomic force microscopy with angstrom-sensitivity to observe that amyloid fibrils undergo a maturation process, associated with an increase in both fibril length and thickness, leading to a decrease of their density, and to a change in their cross-β sheet content. These changes affect the ability of the fibrils to catalyse the formation of new aggregates. The identification of these changes helps us understand the fibril maturation processes, facilitate the targeting of amyloid fibrils in drug discovery, and offer insight into the development of biocompatible and sustainable protein-based materials.

Observing Dynamic Conformational Changes within the Coiled-Coil Domain of Different Laminin Isoforms Using High-Speed Atomic Force Microscopy

Laminins are trimeric glycoproteins with important roles in cell-matrix adhesion and tissue organization. The laminin α, ß, and γ-chains have short N-terminal arms, while their C-termini are connected via a triple coiled-coil domain, giving the laminin molecule a well-characterized cross-shaped morphology as a result. The C-terminus of laminin alpha chains contains additional globular laminin G-like (LG) domains with important roles in mediating cell adhesion. Dynamic conformational changes of different laminin domains have been implicated in regulating laminin function, but so far have not been analyzed at the single-molecule level. High-speed atomic force microscopy (HS-AFM) is a unique tool for visualizing such dynamic conformational changes under physiological conditions at sub-second temporal resolution. After optimizing surface immobilization and imaging conditions, we characterized the ultrastructure of laminin-111 and laminin-332 using HS-AFM timelapse imaging. While laminin-111 features a stable S-shaped coiled-coil domain displaying little conformational rearrangement, laminin-332 coiled-coil domains undergo rapid switching between straight and bent conformations around a defined central molecular hinge. Complementing the experimental AFM data with AlphaFold-based coiled-coil structure prediction enabled us to pinpoint the position of the hinge region, as well as to identify potential molecular rearrangement processes permitting hinge flexibility. Coarse-grained molecular dynamics simulations provide further support for a spatially defined kinking mechanism in the laminin-332 coiled-coil domain. Finally, we observed the dynamic rearrangement of the C-terminal LG domains of laminin-111 and laminin-332, switching them between compact and open conformations. Thus, HS-AFM can directly visualize molecular rearrangement processes within different laminin isoforms and provide dynamic structural insight not available from other microscopy techniques.

Nanoscale chemical characterization of secondary protein structure of F-Actin using mid-infrared photoinduced force microscopy (PiF-IR)

The recently developed photoinduced force microscopy for mid-infrared (PiF-IR) offers high spectral resolution in combination with surface sensitivity and a spatial resolution in the range of a few nanometers. Although PiF-IR has primarily been applied to polymer materials, this technology presents significant potential for the chemical characterization of cellular structures approaching single-molecule sensitivity. We applied PiF-IR to differently polymerized F-Actin samples finding general agreement with FTIR spectra from the same samples. Single PiF-IR spectra of F-Actin show variations in the amide I band spectral region, which is related to secondary protein structure. Local variations are also seen in PiF-IR hyperspectra in this region. Such high sensitivity is a necessary requirement for discriminating Actin organization into bundles and other networks in cells and tissue. We applied PiF-IR to mouse liver tissue ex vivo. Single-frequency PiF-IR scans at three different IR frequencies show significant variations in local contrast. However, the presence of other proteins and the unique spatial resolution of PiF-IR pose a challenge to interpreting and validating such data. Careful design of model systems and further theoretical understanding of PiF-IR data far from bulk averages are needed to fully unfold the potential of PiF-IR for high-resolution chemical investigation in the Life Sciences.

Characterization of transient and progressive pulmonary fibrosis by spatially correlated phase contrast microCT, classical histopathology and atomic force microscopy

Pulmonary fibrosis (PF) is a severe and progressive condition in which the lung becomes scarred over time resulting in pulmonary function impairment. Classical histopathology remains an important tool for micro-structural tissue assessment in the diagnosis of PF. A novel workflow based on spatial correlated propagation-based phase-contrast micro computed tomography (PBI-microCT), atomic force microscopy (AFM) and histopathology was developed and applied to two different preclinical mouse models of PF - the commonly used and well characterized Bleomycin-induced PF and a novel mouse model for progressive PF caused by conditional Nedd4-2 KO. The aim was to integrate structural and mechanical features from hallmarks of fibrotic lung tissue remodeling. PBI-microCT was used to assess structural alteration in whole fixed and paraffin embedded lungs, allowing for identification of fibrotic foci within the 3D context of the entire organ and facilitating targeted microtome sectioning of planes of interest for subsequent histopathology. Subsequently, these sections of interest were subjected to AFM to assess changes in the local tissue stiffness of previously identified structures of interest. 3D whole organ analysis showed clear morphological differences in 3D tissue porosity between transient and progressive PF and control lungs. By integrating the results obtained from targeted AFM analysis, it was possible to discriminate between the Bleomycin model and the novel conditional Nedd4-2 KO model using agglomerative cluster analysis. As our workflow for 3D spatial correlation of PBI, targeted histopathology and subsequent AFM is tailored around the standard procedure of formalin-fixed paraffin-embedded (FFPE) tissue specimens, it may be a powerful tool for the comprehensive tissue assessment beyond the scope of PF and preclinical research.

Effect of curcumin on malignant hepatocytes and mitochondria studied using atomic force microscopy

Mitochondria are emerging as potential targets for the cancer treatment. In this study, the effects of curcumin on the activity, migration, and mitochondrial membrane potential (MMP) of malignant hepatocytes (SMMC-7721 cells) were determined using cell viability, migration, and MMP assays. Changes in the morphology and biomechanics of SMMC-7721 cells and their mitochondria were studied using both optical microscopy and atomic force microscopy (AFM). The cell survival rate, migration and MMP depended on the concentration of curcumin. Optical microscopy studies showed that curcumin altered the cell morphology. AFM studies showed that the changes in the morphology and nanomechanics of SMMC-7721 cells and their mitochondria, were induced by curcumin. As the concentration of curcumin increased, the cell length, width, and adhesion decreased, but the height, roughness and Young's modulus increased. In contrast, the mitochondrial length, width, height and roughness increased, but the adhesion and Young's modulus decreased. There was a close relationship between mitochondria and cells in terms of function, morphology and biomechanics. This study shows the effects of curcumin on SMMC-7721 cells and their mitochondria from biology and biophysics perspectives. The findings aid in comprehensively understanding the interactions between mitochondria and malignant hepatocytes.

Nanorheology and Nanoindentation Revealed a Softening and an Increased Viscous Fluidity of Adherent Mammalian Cells upon Increasing the Frequency

The nanomechanical response of a cell depends on the frequency at which the cell is probed. The components of the cell that contribute to this property and their interplay are not well understood. Here, two force microscopy methods are integrated to characterize the frequency and/or the velocity-dependent properties of living cells. It is shown on HeLa and fibroblasts, that cells soften and fluidize upon increasing the frequency or the velocity of the deformation. This property was independent of the type and values (25 or 1000 nm) of the deformation. At low frequencies (2-10 Hz) or velocities (1-10 µm s-1 ), the response is dominated by the mechanical properties of the cell surface. At higher frequencies (>10 Hz) or velocities (>10 µm s-1 ), the response is dominated by the hydrodynamic drag of the cytosol. Softening and fluidization does not seem to involve any structural remodeling. It reflects a redistribution of the applied stress between the solid and liquid-like elements of the cell as the frequency or the velocity is changed. The data indicates that the quasistatic mechanical properties of a cell featuring a cytoskeleton pathology might be mimicked by the response of a non-pathological cell which is probed at a high frequency.

Virtual indentation of the empty capsid of the minute virus of mice using a minimal coarse-grained model

A minimal coarse-grained model for T=1 viral capsids assembled from 20 protein rigid trimers has been designed by extending a previously proposed form of the interaction energy written as a sum of anisotropic pairwise interactions between the trimeric capsomers. The extension of the model has been performed to properly account for the coupling between two internal coordinates: the one that measures the intercapsomer distance and the other that gives the intercapsomer dihedral angle. The model has been able to fit with less than a 10% error the atomic force microscopy (AFM) indentation experimental data for the empty capsid of the minute virus of mice (MVM), providing in this way an admissible picture of the main mechanisms behind the capsid deformations. In this scenario, the bending of the intercapsomer dihedral angle is the angular internal coordinate that can support larger deformations away from its equilibrium values, determining important features of the AFM indentation experiments as the elastic constants along the three symmetry axes of the capsid and the critical indentations. From the value of one of the parameters of our model, we conclude that trimers in the MVM must be quite oblate tops, in excellent agreement with their known structure. The transition from the linear to the nonlinear regimes sampled in the indentation process appears to be an interesting topic for future research in physical virology.

Insight into the hydration friction of lipid bilayers

Hydration layers formed on charged sites play crucial roles in many hydration lubrication systems in aqueous media. However, the underlying molecular mechanism is not well understood. Herein, we explored the hydration friction of lipid bilayers with different charged headgroups at the nanoscale through a combination of frequency-modulation atomic force microscopy and friction force microscopy. The nanoscale friction experiments showed that the hydration friction coefficient and frictional energy dissipation of a cationic lipid (DPTAP) were much lower than those of zwitterionic (DPPE) and anionic (DPPG) lipids. The hydration layer probing at the surfaces of different lipid bilayers clearly revealed the relationship between the charged lipid headgroups and hydration layer structures. Our detailed analysis demonstrated that the cationic lipid had the largest hydration force in comparison with zwitterionic and anionic lipids. These friction and hydration force results indicated that the difference of the lipid headgroup charge resulted in different hydration strengths which led to the difference of hydration friction behaviors. The findings in this study provide molecular insights into the hydration friction of lipid bilayers, which has potential implications for the development of efficient hydration lubrication systems with boundary lipid bilayers in aqueous media.

Assessment of the nano-mechanical properties of healthy and atherosclerotic coronary arteries by atomic force microscopy

Nano-indentation techniques might be better equipped to assess the heterogeneous material properties of plaques than macroscopic methods but there are no bespoke protocols for this kind of material testing for coronary arteries. Therefore, we developed a measurement protocol to extract mechanical properties from healthy and atherosclerotic coronary artery tissue sections. Young's modulus was derived from force-indentation data. Metrics of collagen fibre density were extracted from the same tissue, and the local material properties were co-registered to the local collagen microstructure with a robust framework. The locations of the indentation were retrospectively classified by histological category (healthy, plaque, lipid-rich, fibrous cap) according to Picrosirius Red stain and adjacent Hematoxylin & Eosin and Oil-Red-O stains. Plaque tissue was softer (p < 0.001) than the healthy coronary wall. Areas rich in collagen within the plaque (fibrous cap) were significantly (p < 0.001) stiffer than areas poor in collagen/lipid-rich, but less than half as stiff as the healthy coronary media. Young's moduli correlated (Pearson's ρ = 0.53, p < 0.05) with collagen content. Atomic force microscopy (AFM) is capable of detecting tissue stiffness changes related to collagen density in healthy and diseased cardiovascular tissue. Mechanical characterization of atherosclerotic plaques with nano-indentation techniques could refine constitutive models for computational modelling.

Nanopore-related cellular death through cytoskeleton depolymerization by drug-induced ROS

Prostate cancer (PCa) is a malignant tumor with a very high incidence which ranks second after lung cancer. Although there are many drugs available for the treatment of PCa, their effectiveness and anti-cancer mechanisms still need to be explored. Atomic force microscopy (AFM) could characterize minor morphological changes on cell surfaces, which provides an effective method to explore the interaction between drugs and cells at the nanometer level and further investigate the mechanisms for treating PCa. In our research, AFM visualized pore-like structures in the PC3M cell membrane after treatment with the eminent anticancer agent paclitaxel (PTX). The diameter, depth and number of these pores were in a concentration and time-dependent manner. Reactive oxygen species (ROS) was shown to depolymerize the actin cytoskeleton and make the membrane more sensitive to oxidative damage, thus inducing pore information. After pretreatment with a ROS scavenger, pore formation was prevented. AFM imaging technology provides a new evaluation method for drug-targeted therapy for cancer.

The biophysical and compositional properties of human basement membranes

Basement membranes are among the most widespread, non-cellular functional materials in metazoan organisms. Despite this ubiquity, the links between their compositional and biophysical properties are often difficult to establish due to their thin and delicate nature. In this article, we examine these features on a molecular level by combining results from proteomics, elastic, and nanomechanical analyses across a selection of human basement membranes. Comparing results between these different membranes connects certain compositional attributes to distinct nanomechanical signatures and further demonstrates to what extent water defines these properties. In all, these data underline BMs as stiff yet highly elastic connective tissue layers and highlight how the interplay between composition, mechanics and hydration yields such exceptionally adaptable materials.

Dense Monolayer Network Structures of Double Hydrophilic Hyperbranched Copolymers at the Air/Water Interface

Influences of subphase pH and temperature on the interfacial aggregation behavior of two double hydrophilic hyperbranched copolymers of poly[oligo(ethylene glycol) methacrylate-co-(2-diisopropylamino)ethyl methacrylate] (P(OEGMA-co-DIPAEMA)) at the air/water interface are studied by the Langmuir film balance technique. Morphologies of their Langmuir-Blodgett (LB) films are characterized by atomic force microscopy (AFM). At the interface, P(OEGMA-co-DIPAEMA) copolymers tend to form a dense network structure of circular micelles composed of branching agent-connected carbon backbone cores and mixed shells of OEGMA and DIPAEMA segments (pendant groups). This network structure containing many honeycomb-like holes with diameters of 6-8 nm is identified for the first time and clearly observed in the enlarged AFM images of their LB films. Under acidic conditions, surface pressure versus molecular area isotherms of the two copolymers in the low-pressure region show larger mean molecular area than those under neutral and alkaline conditions due to the lack of impediment from DIPAEMA segments. Upon further compression, each isotherm exhibits a wide pseudo-plateau, which corresponds to OEGMA segments being pressed into the subphase. Furthermore, the isotherms under neutral and alkaline conditions exhibit the lower critical solution temperature behavior of OEGMA segments, and the critical temperature is lower when the hyperbranched copolymer contains higher OEGMA content.

Quantitative Analysis of Therapeutic Antibody Interactions with Fcγ Receptors Using High-Speed Atomic Force Microscopy

This study employed high-speed atomic force microscopy to quantitatively analyze the interactions between therapeutic antibodies and Fcγ receptors (FcγRs). Antibodies are essential components of the immune system and are integral to biopharmaceuticals. The focus of this study was on immunoglobulin G molecules, which are crucial for antigen binding via the Fab segments and cytotoxic functions through their Fc portions. We conducted real-time, label-free observations of the interactions of rituximab and mogamulizumab with the recombinant FcγRIIIa and FcγRIIa. The dwell times of FcγR binding were measured at the single-molecule level, which revealed an extended interaction duration of mogamulizumab with FcγRIIIa compared with that of rituximab. This is linked to enhanced antibody-dependent cellular cytotoxicity that is attributed to the absence of the core fucosylation of Fc-linked N-glycan. This study also emphasizes the crucial role of the Fab segments in the interaction with FcγRIIa as well as that with FcγRIIIa. This approach provided quantitative insight into therapeutic antibody interactions and exemplified kinetic proofreading, where cellular discrimination relies on ligand residence times. Observing the dwell times of antibodies on the effector molecules has emerged as a robust indicator of therapeutic antibody efficacy. Ultimately, these findings pave the way for the development of refined therapeutic antibodies with tailored interactions with specific FcγRs. This research contributes to the advancement of biopharmaceutical antibody design and optimizing antibody-based treatments for enhanced efficacy and precision.

Y-Shaped Backbone-Rigidified DNA Tiles for the Construction of Supersized Nondeformable Tetrahedrons for Precise Cancer Therapies

While engineered DNA nanoframeworks have been extensively exploited for delivery of diagnostic and therapeutic regents, DNA tiling-based DNA frameworks amenable to applications in living systems lag much behind. In this contribution, by developing a Y-shaped backbone-based DNA tiling technique, we assemble Y-shaped backbone-rigidified supersized DNA tetrahedrons (RDT) with 100% efficiency for precisely targeted tumor therapy. RDT displays unparalleled rigidness and unmatched resistance to nuclease degradation so that it almost does not deform under the force exerted by the atomic force microscopy tip, and the residual amount is not less than 90% upon incubating in biological media for 24 h, displaying at least 11.6 times enhanced degradation resistance. Without any targeting ligand, RDT enters the cancer cell in a targeted manner, and internalization specificity is up to 15.8. Moreover, 77% of RDT objects remain intact within living cells for 14 h. The drug loading content of RDT is improved by 4-8 times, and RDT almost 100% eliminates the unintended drug leakage in a stimulated physiological medium. Once systemically administrated into HeLa tumor-bearing mouse models, doxorubicin-loaded RDTs preferentially accumulate in tumor sites and efficiently suppress tumor growth without detectable off-target toxicity. The Y-DNA tiling technique offers invaluable insights into the development of structural DNA nanotechnology for precise medicine.

Quantum-enhanced diamond molecular tension microscopy for quantifying cellular forces

The constant interplay and information exchange between cells and the microenvironment are essential to their survival and ability to execute biological functions. To date, a few leading technologies such as traction force microscopy, optical/magnetic tweezers, and molecular tension-based fluorescence microscopy are broadly used in measuring cellular forces. However, the considerable limitations, regarding the sensitivity and ambiguities in data interpretation, are hindering our thorough understanding of mechanobiology. Here, we propose an innovative approach, namely, quantum-enhanced diamond molecular tension microscopy (QDMTM), to precisely quantify the integrin-based cell adhesive forces. Specifically, we construct a force-sensing platform by conjugating the magnetic nanotags labeled, force-responsive polymer to the surface of a diamond membrane containing nitrogen-vacancy centers. Notably, the cellular forces will be converted into detectable magnetic variations in QDMTM. After careful validation, we achieved the quantitative cellular force mapping by correlating measurement with the established theoretical model. We anticipate our method can be routinely used in studies like cell-cell or cell-material interactions and mechanotransduction.

Bimodal DNA self-origami material with nucleic acid function enhancement

BACKGROUND

The design of DNA materials with specific nanostructures for biomedical tissue engineering applications remains a challenge. High-dimensional DNA nanomaterials are difficult to prepare and are unstable; moreover, their synthesis relies on heavy metal ions. Herein, we developed a bimodal DNA self-origami material with good biocompatibility and differing functions using a simple synthesis method. We simulated and characterized this material using a combination of oxDNA, freeze-fracture electron microscopy, and atomic force microscopy. Subsequently, we optimized the synthesis procedure to fix the morphology of this material.

RESULTS

Using molecular dynamics simulation, we found that the bimodal DNA self-origami material exhibited properties of spontaneous stretching and curling and could be fixed in a single morphology via synthesis control. The application of different functional nucleic acids enabled the achievement of various biological functions, and the performance of functional nucleic acids was significantly enhanced in the material. Consequently, leveraging the various functional nucleic acids enhanced by this material will facilitate the attainment of diverse biological functions.

CONCLUSION

The developed design can comprehensively reveal the morphology and dynamics of DNA materials. We thus report a novel strategy for the construction of high-dimensional DNA materials and the application of functional nucleic acid-enhancing materials.

Sub-Tip-Radius Near-Field Interactions in Nano-FTIR Vibrational Spectroscopy on Single Proteins

Tip-enhanced vibrational spectroscopy has advanced to routinely attain nanoscale spatial resolution, with tip-enhanced Raman spectroscopy even achieving atomic-scale and submolecular sensitivity. Tip-enhanced infrared spectroscopy techniques, such as nano-FTIR and AFM-IR spectroscopy, have also enabled the nanoscale chemical analysis of molecular monolayers, inorganic nanoparticles, and protein complexes. However, fundamental limits of infrared nanospectroscopy in terms of spatial resolution and sensitivity have remained elusive, calling for a quantitative understanding of the near-field interactions in infrared nanocavities. Here, we demonstrate the application of nano-FTIR spectroscopy to probe the amide-I vibration of a single protein consisting of ∼500 amino acid residues. Detection with higher tip tapping demodulation harmonics up to the seventh order leads to pronounced enhancement in the peak amplitude of the vibrational resonance, originating from sub-tip-radius geometrical effects beyond dipole approximations. This quantitative characterization of single-nanometer near-field interactions opens the path toward employing infrared vibrational spectroscopy at the subnanoscale and single-molecule levels.

Evidence of collective influence in innate sensing using fluidic force microscopy

The innate immune system initiates early response to infection by sensing molecular patterns of infection through pattern-recognition receptors (PRRs). Previous work on PRR stimulation of macrophages revealed significant heterogeneity in single cell responses, suggesting the importance of individual macrophage stimulation. Current methods either isolate individual macrophages or stimulate a whole culture and measure individual readouts. We probed single cell NF-κB responses to localized stimuli within a naïve culture with Fluidic Force Microscopy (FluidFM). Individual cells stimulated in naïve culture were more sensitive compared to individual cells in uniformly stimulated cultures. In cluster stimulation, NF-κB activation decreased with increased cell density or decreased stimulation time. Our results support the growing body of evidence for cell-to-cell communication in macrophage activation, and limit potential mechanisms. Such a mechanism might be manipulated to tune macrophage sensitivity, and the density-dependent modulation of sensitivity to PRR signals could have relevance to biological situations where macrophage density increases.

Molecular Adhesion of a Pilus-Derived Peptide Involved in Pseudomonas aeruginosa Biofilm Formation on Non-Polar ZnO-Surfaces

Bacterial colonization and biofilm formation on abiotic surfaces are initiated by the adhesion of peptides and proteins. Understanding the adhesion of such peptides and proteins at a molecular level thus represents an important step toward controlling and suppressing biofilm formation on technological and medical materials. This study investigates the molecular adhesion of a pilus-derived peptide that facilitates biofilm formation of Pseudomonas aeruginosa, a multidrug-resistant opportunistic pathogen frequently encountered in healthcare settings. Single-molecule force spectroscopy (SMFS) was performed on chemically etched ZnO11 2 ‾ 0 ${\left(11\bar{2}0\right)}$ surfaces to gather insights about peptide adsorption force and its kinetics. Metal-free click chemistry for the fabrication of peptide-terminated SMFS cantilevers was performed on amine-terminated gold cantilevers and verified by X-ray photoelectron spectroscopy (XPS) and polarization-modulated infrared reflection absorption spectroscopy (PM-IRRAS). Atomic force microscopy (AFM) and XPS analyses reveal stable topographies and surface chemistries of the substrates that are not affected by SMFS. Rupture events described by the worm-like chain model (WLC) up to 600 pN were detected for the non-polar ZnO surfaces. The dissociation barrier energy at zero force ΔG(0), the transition state distance xb and bound-unbound dissociation rate at zero force koff (0) for the single crystalline substrate indicate that coordination and hydrogen bonds dominate the peptide/surface interaction.

Ligand-Mediated Mechanical Enhancement in Protein Complexes at Nano- and Macro-Scale

Protein self-assembly plays a vital role in a myriad of biological functions and in the construction of biomaterials. Although the physical association underlying these assemblies offers high specificity, the advantage often compromises the overall durability of protein complexes. To address this challenge, we propose a novel strategy that reinforces the molecular self-assembly of protein complexes mediated by their ligand. Known for their robust noncovalent interactions with biotin, streptavidin (SAv) tetramers are examined to understand how the ligand influences the mechanical strength of protein complexes at the nanoscale and macroscale, employing atomic force microscopy-based single-molecule force spectroscopy, rheology, and bioerosion analysis. Our study reveals that biotin binding enhances the mechanical strength of individual SAv tetramers at the nanoscale. This enhancement translates into improved shear elasticity and reduced bioerosion rates when SAv tetramers are utilized as cross-linking junctions within hydrogel. This approach, which enhances the mechanical strength of protein-based materials without compromising specificity, is expected to open new avenues for advanced biotechnological applications, including self-assembled, robust biomimetic scaffolds and soft robotics.

Mechanical Characterization of Murine Oocytes by Atomic Force Microscopy

The quality of murine and human oocytes correlates to their mechanical properties, which are tightly regulated to reach the blastocyst stage after fertilization. Oocytes are nonadherent spherical cells with a diameter over 80 μm. Their mechanical properties have been studied in our lab and others using the micropipette aspiration technique, particularly to obtain the oocyte cortical tension. Micropipette aspiration is affordable but has a low throughput and induces cell-scale deformation. Here we present a step-by-step protocol to characterize the mechanical properties of oocytes using atomic force microscopy (AFM), which is minimally invasive and has a much higher throughput. We used electron microscopy grids to immobilize oocytes. This allowed us to obtain local and reproducible measurements of the cortical tension of murine oocytes during their meiotic divisions. Cortical tension values obtained by AFM are in agreement with the ones previously obtained by micropipette aspiration. Our protocol could help characterize the biophysical properties of oocytes or other types of large nonadherent samples in fundamental and medical research.

Surface characteristics of 3D printed PEEK polymer using atomic force microscopy

High-performance polymer three-dimensional printing is becoming more popular for producing unique parts suitable for different applications. It has been utilized extensively in biomedical applications such as dental prosthetics, surgical equipment, and implants. However, the performance of the material is significantly influenced by its surface qualities, particularly in aspects of its adhesion and biocompatibility. This study involves the fabrication of PEEK specimens S1, S2, S3, and S4 with different printing parameters such as layer height of 0.10 and 0.15 mm and printing speed of 20 and 25 mm/s using a fused deposition modeling process. The surface roughness of the fabricated specimens is measured using atomic force microscopy. The results showed that the printing parameters significantly impact the surface roughness of the PEEK specimens. The surface roughness of specimen S3, printed at a layer height of 0.15 mm and a speed of 20 mm/s, has a low roughness value of 0.017 μm, which is considerable in comparison to the other specimens. In addition to the measurement of surface roughness from roughness profile, the force curve separation graph was plotted and the adhesion force values were calculated for all the specimens to determine the interlayer bonding strength.

Effect of a demineralization model on the microhardness, surface roughness and topography of giomers: An in vitro study

The purpose of this study is to compare the effect of a demineralization model on the microhardness, surface roughness, and topography of giomers.Seventy-two discs of six different dental materials in three different presentations (pit and fissure sealant (PFS), flowable and restorative materials) were divided into six groups (n = 12 p/g). Three experimental groups (giomers) consisted of BeautiSealant, Beautifil Flow Plus, and Beautifil II, and three control groups (resin-based materials) were formed using ClinproTM, FiltekTM Z350 XT Flow, and Filtek™ Bulk Fill materials. Vickers microhardness, surface roughness, and topographic analysis with atomic force microscopy were measured at the beginning (0) after four (1) and 7 days (2) of immersion in a demineralizing model. Statistical analysis was performed using One-way and Repeated Measures ANOVA and Pearson's correlation coefficient (p ≤ .05). The microhardness values showed significant variations, except for the G_RM group. All the groups presented significant increases in roughness through the experiment stages, except for RB_PFS in the Ra parameter. The topographic analysis showed variations in the micromorphology, especially in the experimental group at the end of the demineralization model. Finally, there was no correlation between microhardness and surface roughness. The demineralization model decreased the microhardness, with the lowest reductions in the giomers groups. The effect of the demineralizing model on the surface roughness and topography showed an increase in specific patterns for the experimental and control groups. Therefore, their clinical use is recommended. RESEARCH HIGHLIGHTS: The demineralization model decreased the microhardness property of the evaluated materials, with better performance for the giomer groups. The effect of the demineralizing model on surface roughness showed an increase with specific patterns for the experimental and control groups. Although the materials presented changes in their microhardness, roughness, and topography, their clinical use is recommended.

Pattern recognition in the nucleation kinetics of non-equilibrium self-assembly

Inspired by biology's most sophisticated computer, the brain, neural networks constitute a profound reformulation of computational principles1-3. Analogous high-dimensional, highly interconnected computational architectures also arise within information-processing molecular systems inside living cells, such as signal transduction cascades and genetic regulatory networks4-7. Might collective modes analogous to neural computation be found more broadly in other physical and chemical processes, even those that ostensibly play non-information-processing roles? Here we examine nucleation during self-assembly of multicomponent structures, showing that high-dimensional patterns of concentrations can be discriminated and classified in a manner similar to neural network computation. Specifically, we design a set of 917 DNA tiles that can self-assemble in three alternative ways such that competitive nucleation depends sensitively on the extent of colocalization of high-concentration tiles within the three structures. The system was trained in silico to classify a set of 18 grayscale 30 × 30 pixel images into three categories. Experimentally, fluorescence and atomic force microscopy measurements during and after a 150 hour anneal established that all trained images were correctly classified, whereas a test set of image variations probed the robustness of the results. Although slow compared to previous biochemical neural networks, our approach is compact, robust and scalable. Our findings suggest that ubiquitous physical phenomena, such as nucleation, may hold powerful information-processing capabilities when they occur within high-dimensional multicomponent systems.

Characterization of Cancer Cell Mechanics by Measuring Active Deformation Behavior

Active deformation behavior reflects cell structural dynamics adapting to varying environmental constraints during malignancy progression. In most cases, cell mechanics is characterized by modeling using static equilibrium systems, which fails to comprehend cell deformation behavior leading to inaccuracies in distinguishing cancer cells from normal cells. Here, a method is introduced to measure the active deformation behavior of cancer cells using atomic force microscopy (AFM) and the newly developed deformation behavior cytometry (DBC). During the measurement, cells are deformed and allows a long timescale relaxation (≈5 s). Two parameters are derived to represent deformation behavior: apparent Poisson's ratio for adherent cells, which is measured with AFM and refers to the ratio of the lateral strain to the longitudinal strain of the cell, and shape recovery for suspended cells, which is measured with DBC. Active deformation behavior defines cancer cell mechanics better than traditional mechanical parameters (e.g., stiffness, diffusion, and viscosity). Additionally, aquaporins are essential for promoting the deformation behavior, while the actin cytoskeleton acts as a downstream effector. Therefore, the potential application of the cancer cell active deformation behavior as a biomechanical marker or therapeutic target in cancer treatment should be evaluated.

Mechanical Characterization of Mucus on Intestinal Tissues by Atomic Force Microscopy

Mucus is part of the innate immune system that defends the mucosa against microbiota and other infectious threats. The mechanical characteristics of mucus, such as viscosity, elasticity, and lubricity, are critically involved in its barrier function. However, assessing the mechanical properties of mucus remains challenging because of technical limitations. Thus, a new approach that characterizes the mechanical properties of mucus on colonic tissues needs to be developed. Here, we describe a novel strategy to characterize the ex vivo mechanical properties of mucus on colonic tissues using atomic force microscopy. This description includes the preparation of the mouse colon sample, AFM calibration, and determining the elasticity (Young's modulus, E [kPa]) of the mucus layer in the colon.

Pericellular Matrix Formation and Atomic Force Microscopy of Single Primary Human Chondrocytes Cultured in Alginate Microgels

One of the main components of articular cartilage is the chondrocyte's pericellular matrix (PCM), which is critical for regulating mechanotransduction, biochemical cues, and healthy cartilage development. Here, individual primary human chondrocytes (PHC) are encapsulated and cultured in 50 µm diameter alginate microgels using drop-based microfluidics. This unique culturing method enables PCM formation and manipulation of individual cells. Over ten days, matrix formation is observed using autofluorescence imaging, and the elastic moduli of isolated cells are measured using AFM. Matrix production and elastic modulus increase are observed for the chondrons cultured in microgels. Furthermore, the elastic modulus of cells grown in microgels increases ≈ten-fold over ten days, nearly reaching the elastic modulus of in vivo PCM. The AFM data is further analyzed using a Gaussian mixture model and shows that the population of PHCs grown in microgels exhibit two distinct populations with elastic moduli averaging 9.0 and 38.0 kPa. Overall, this work shows that microgels provide an excellent culture platform for the growth and isolation of PHCs, enabling PCM formation that is mechanically similar to native PCM. The microgel culture platform presented here has the potential to revolutionize cartilage regeneration procedures through the inclusion of in vitro developed PCM.