AFM in cellular and molecular microbiology

Horizontal Distortion Correction of AFM Images Based on Automatic Labeling of Feature Graphics

The atomic force microscope (AFM) image will be inclined and bent due to the tilt angle between the probe and the sample surface. When the least squares fitting method is used to correct the horizontal distortion of the AFM image, the shape structure that is lower or higher than the sample base will affect the final fitting correction result. In view of the limitations of existing methods and the diversity of AFM images, an AFM image level distortion correction method based on automatic feature marking is proposed. The Canny edge detection algorithm with adaptive threshold is used to automatically detect and recognize the feature graphics, and the feature graphics are zeroed by the hole filling algorithm to automatically remove the feature graphics data from the line fitting data. After completing the least squares fitting correction of all the rows of data, the full AFM image data with eliminating horizontal distortion can be obtained. Finally, the corrected full image data are used for imaging. This method can be adapted to different types of AFM images and realize automatic fitting correction of the whole image, which improves the accuracy and efficiency of correction.

A hermetically closed sample chamber enables time-lapse nano-characterization of pathogenic microorganisms in vitro

Pathogenic microorganisms, such as pathogenic mycobacteria, pose a global health burden. Studying these organisms is crucial for gaining detailed knowledge about the pathogens and the diseases they cause. To handle pathogenic organisms, specific biosafety measures appropriate to the virulence of the organism must be fulfilled, most importantly ensuring that all manipulations of pathogenic material are performed within a confined environment. Atomic force microscopy (AFM) is a powerful technique to study biological samples at nanometer-scale resolution, yielding also mechanical properties, all while maintaining physiological conditions. However, standard AFM sample holders do not meet stringent biosafety requirements since they do not constitute a confined system. AFM imaging relies on direct contact between the cantilever and the sample and is sensitive to mechanical interference, rendering conventional containment systems for handling infectious substances inapplicable. Here, we introduce a hermetically sealed AFM sample chamber that meets biosafety demands while satisfying the mechanical and optical constraints of correlated optical microscopy and AFM. We imaged various pathogenic mycobacteria to demonstrate the chamber's versatility and effectiveness in containing biohazardous materials. This sample chamber enables high-resolution, time-lapse correlated imaging and biomechanical characterization of pathogenic microorganisms in vitro. It broadens the scope of research with pathogenic microorganisms under safe and controlled conditions.

Significant reduction of cell invasiveness in nanoneedle insertion into a living cell with an electron-beam-deposited probe: impacts of probe geometry, speed and vibration

Intracellular probing of living cells using atomic force microscopy (AFM) has advanced significantly, but it requires specially designed nanoprobes to achieve precision and minimize damage. The development of focused ion beam (FIB)-milled nanoprobes enabled this progress, allowing researchers to fabricate long, sharp probes that penetrate cell membranes with reduced force. Although these FIB-milled probes have been crucial in accessing the intracellular environment, they still cause considerable membrane deformation, limiting their effectiveness in detailed measurements. In response, we developed electron beam deposited (EBD) carbon nanoprobes with varying diameters to further reduce penetration force and resulting cell disturbance. Our study reveals that, for probes of the same diameter, EBD carbon nanoprobes inflict significantly less membrane deformation than FIB-milled ones, due to their sharper tip apex. Additionally, reducing the diameter of the EBD nanoprobes further decreased the penetration force and minimized cell disturbance. We also observed that, at similar speeds, EBD nanoprobes consistently caused less damage, emphasizing the importance of both tip geometry and penetration speed in reducing the impact on cells. Oscillating the cantilever during penetration further reduced friction with the membrane, significantly reducing damage. These findings advance the precision and gentleness of intracellular AFM measurements, offering improved methods for studying cellular mechanics while preserving cell viability.

Advancing High-Throughput Cellular Atomic Force Microscopy with Automation and Artificial Intelligence

Atomic force microscopy (AFM) has reached a significant level of maturity in biology, demonstrated by the diversity of modes for obtaining not only topographical images but also insightful mechanical and adhesion data by performing force measurements on delicate samples with a controlled environment (e.g., liquid, temperature, pH). Numerous studies have applied AFM to describe biological phenomena at the molecular and cellular scales, and even on tissues. Despite these advances, AFM is not established as a diagnostic tool in the biomedical field. This article describes the reasons for this gap, focusing on one of the main weaknesses of bio-AFM: its low data throughput. We review current efforts to improve the automation of AFM measurements in particular on living cells, as well as the developments in automating data analysis. For the latter, artificial intelligence (AI) is progressively employed to classify data to distinguish healthy and diseased cells or tissues. Finally, we propose a roadmap to foster the application of bio-AFM into medical diagnostics.

Altering the mechanical properties of self-assembled filaments through engineering of EspA bacterial protein

Protein-based biomaterials are in high demand due to their high biocompatibility, non-toxicity, and biodegradability. In this study, we explore the bacterial E. coli secreted protein A (EspA), which self-assembles into long extracellular filaments, as a potential building block for new protein-based biomaterials. We investigated the morphological and mechanical properties of EspA filaments and how protein engineering can modify them. Our study include three types of filaments: natural EspA filaments, full-length recombinant EspA filaments, and truncated recombinant EspA filaments lacking a third of the original codon region. The recombinant EspA proteins formed curly, thin filaments with higher longitudinal elasticity (shorter persistence length) compared to the natural, linear filaments. Additionally, the recombinant filaments had a radial elastic modulus about an order of magnitude lower than the natural filaments. The truncated recombinant filaments had a higher radial modulus than the full-length ones, and unlike the purely elastic natural filaments, recombinant filaments were less compliant with the applied force that penetrated them. These differences underscore the potential to modulate EspA filament properties through protein sequence mutations. Our findings suggest EspA as a fundamental element for developing a new biomaterial with a hierarchical structure, enabling the fabrication of macroscopic substances from self-assembled EspA-modulated filaments.

Serotype switching in Pseudomonas aeruginosa ST111 enhances adhesion and virulence

Evolution of the highly successful and multidrug resistant clone ST111 in Pseudomonas aeruginosa involves serotype switching from O-antigen O4 to O12. How expression of a different O-antigen serotype alters pathogen physiology to enable global dissemination of this high-risk clone-type is not understood. Here, we engineered isogenic laboratory and clinical P. aeruginosa strains that express the different O-antigen gene clusters to assess the correlation of structural differences of O4 and O12 O-antigens to pathogen-relevant phenotypic traits. We show that serotype O12 is associated with enhanced adhesion, type IV pili dependent twitching motility, and tolerance to host defense molecules and serum. Moreover, we find that serotype O4 is less virulent compared to O12 in an acute murine pneumonia infection in terms of both colonization and survival rate. Finally, we find that these O-antigen effects may be explained by specific biophysical properties of the serotype repeat unit found in O4 and O12, and by differences in membrane stability between O4 and O12 expressing cells. The results demonstrate that differences in O-antigen sugar composition can affect P. aeruginosa pathogenicity traits, and provide a better understanding of the potential selective advantages that underlie serotype switching and emergence of serotype O12 ST111.

Tuning stiffness of hyaluronan-cholesterol nanogels by mussel-inspired dopamine-Fe3+ coordination: Preparation and properties evaluation

In the evolving field of nanomedicine, tailoring the mechanical properties of nanogels to fine-tune their biological performance is a compelling avenue of research. This work investigates an innovative method for modulating the stiffness of hyaluronan-cholesterol (HACH) nanogels, an area that remains challenging. By grafting dopamine (DOPA) onto the HA backbone, characterized through UV, 1H NMR, and FT-IR analyses, we synthesized a novel polymer that spontaneously forms nanogels in aqueous environments. These HACH-DOPA nanogels are characterized by their small size (~170 nm), negative charge (around -32 mV), high stability, efficient drug encapsulation, and potent antioxidant activities (measured by ABTS test). Leveraging mussel-inspired metal coordination chemistry, the DOPA moieties enable stiffness modulation of the nanogels through catechol-Fe3+ interactions. This modification leads to increased crosslinking and, consequently, nanogels with a significantly increased stiffness, as measured by atomic force microscopy (AFM), with the formation of the HACH-DOPA@Fe3+ complex being pH-dependent and reversible. The cytocompatibility was evaluated via WST-1 cell proliferation assays on HUVEC and HDF cell lines, showing no evident cytotoxicity. Furthermore, the modified nanogels demonstrated enhanced cellular uptake, suggesting their substantial potential for intracellular drug delivery applications, a hypothesis supported by confocal microscopy assays. This work not only provides valuable insight into modulating nanogel stiffness but also advances new nanosystems for promising biomedical applications.

Direct investigations of interactions between nucleolins and aptamers on pancreatic cancer and normal cells by atomic force microscopy

Nucleolin is overexpressed on the surface of pancreatic cancer cells and are regarded as the remarkable therapeutic target. Aptamers are capable of binding the external domain of nucleolin on the cell surface with high affinity and specificity. But nucleolin has not been localized on pancreatic cancer cells at very high spatial resolution, and the interactions between nucleolin and aptamers have not been investigated at very high force resolution level. In this work, nucleolin was localized on pancreatic cancer and normal cells by aptamers (9FU-AS1411-NH2, AS1411-NH2 and CRONH2) in Single Molecule Recognition Imaging mode of Atomic Force Microscopy. There are plenty of nucleolin on the surfaces of pancreatic cancer cells (area percentage about 5 %), while there are little nucleolin on the surfaces of normal cells. The interactions between three types of aptamers and nucleolins on the surfaces of pancreatic cancer cells were investigated by Single Molecule Force Spectroscopy. The unbinding forces of nucleolins-(9FU-AS1411-NH2) are larger than nucleolins-(AS1411-NH2). The dissociation activation energy on nucleolin-(9FU-AS1411-NH2) is higher than nucleolin-(AS1411-NH2), which indicates that the former complex is more stable and harder to dissociate than the later complex. There are no unbinding forces between nucleolin and CRONH2. All these demonstrate that nucleolin was localized on pancreatic cancer and normal cells at single molecule level quantitatively, and the interactions (unbinding forces and kinetics) between nucleolin and aptamers were studied at picoNewton level. The approaches and results of this work will pave new ways in the investigations of nucleolin and aptamers, and will also be useful in the studies on other proteins and their corresponding aptamers.

Role of adhesion in the mechanics of pathogenic Listeria monocytogenes EGDe as a function of the pH of growth

Atomic force microscopy was utilized to estimate the adhesion strengths to silicon nitride as well as the cellular elasticities of pathogenic Listeria monocytogenes EGDe cells cultured in media adjusted to five different pH conditions of growth (5, 6, 7, 8, and 9) under water with 0.0027 fixed ionic strength. Particularly, the role of adhesion on the bacterial elastic properties was investigated. The nonadhesive Hertz model of contact mechanics was used to extract Young's moduli of elasticity of bacterial cells from the approach force-indentation data. Additionally, the adhesive models of contact mechanics: Johnson-Kendall-Roberts (JKR) and Derjaguin-Muller-Toporov (DMT) were used to estimate Young's moduli of elasticity of bacterial cells from the retraction force-indentation data. Our results indicated that adhesion to silicon nitride was the highest for cells cultured at a pH of 7. Similarly, bacterial cells cultured at pH 7 were characterized by the highest Young's moduli of elasticities compared to the lower or higher pH conditions of growth. Young's moduli of elasticities estimated from the Hertz model were stiffer than those estimated using JKR or DMT models. As the adhesion between bacterial cells and indenters increased, the difference between the Hertz model and JKR or DMT models estimates of Young's moduli of elasticity increased as well. Contradicting the current norm of using the Hertz model to quantify bacterial elasticity in the literature, our results highlight the extreme importance of utilizing contact mechanics models with adhesion components in them such as the JKR and DMT models to estimate bacterial elasticity.

Morphological and Biophysical Study of S100A9 Protein Fibrils by Atomic Force Microscopy Imaging and Nanomechanical Analysis

Atomic force microscopy (AFM) imaging enables the visualization of protein molecules with high resolution, providing insights into their shape, size, and surface topography. Here, we use AFM to study the aggregation process of protein S100A9 in physiological conditions, in the presence of calcium at a molar ratio 4Ca2+:S100A9. We find that S100A9 readily assembles into a worm-like fibril, with a period dimension along the fibril axis of 11.5 nm. The fibril's chain length extends up to 136 periods after an incubation time of 144 h. At room temperature, the fibril's bending stiffness was found to be 2.95×10-28 Nm2, indicating that the fibrils are relatively flexible. Additionally, the values obtained for the Young's modulus (Ex=6.96×105 Pa and Ey=3.37×105 Pa) are four orders of magnitude lower than those typically reported for canonical amyloid fibrils. Our findings suggest that, under the investigated conditions, a distinct aggregation mechanism may be in place in the presence of calcium. Therefore, the findings reported here could have implications for the field of biomedicine, particularly with regard to Alzheimer's disease.

Aptamer Screening: Current Methods and Future Trend towards Non-SELEX Approach

Aptamers are nucleic acid sequences that specifically bind with target molecules and are vital to applications such as biosensing, drug development, disease diagnostics, etc. The traditional selection procedure of aptamers is based on the Systematic Evolution of Ligands by an Exponential Enrichment (SELEX) process, which relies on repeating cycles of screening and amplification. With the rapid development of aptamer applications, RNA and XNA aptamers draw more attention than before. But their selection is troublesome due to the necessary reverse transcription and transcription process (RNA) or low efficiency and accuracy of enzymes for amplification (XNA). In light of this, we review the recent advances in aptamer selection methods and give an outlook on future development in a non-SELEX approach, which simplifies the procedure and reduces the experimental costs. We first provide an overview of the traditional SELEX methods mostly designed for screening DNA aptamers to introduce the common tools and methods. Then a section on the current screening methods for RNA and XNA is prepared to demonstrate the efforts put into screening these aptamers and the current difficulties. We further predict that the future trend of aptamer selection lies in non-SELEX methods that do not require nucleic acid amplification. We divide non-SELEX methods into an immobilized format and non-immobilized format and discuss how high-resolution partitioning methods could facilitate the further improvement of selection efficiency and accuracy.

Direct investigations of the effects of nicardipine on calcium channels of astrocytes by Atomic Force Microscopy

Calcium channel blockers (CCB) of astrocytes can blockade the calcium ions entry through the voltage gated calcium channels (VGCC), and is widely used in the diseases related with VGCC of astrocytes. But many aspects of the interaction mechanisms between the CCB and VGCC of astrocytes still remain unclear due to the limited resolution of the approaches. Herein the effects of the nicardipine (a type of CCB) on VGCC of astrocytes were investigated at very high spatial, force and electrical resolution by multiple modes of Atomic Force Microscopy (AFM) directly. The results reveal that after the addition of nicardipine, the recognition signals of VGCC disappeared; the specific unbinding forces vanished; the conductivity of the astrocytes decreased (the current decreased about 2.9 pA and the capacitance was doubled); the surface potential of the astrocytes reduced about 14.2 mV. The results of electrical properties investigations are consistent with the simulation experiments. The relations between these biophysical and biochemical properties of VGCC have been discussed. All these demonstrate that the interactions between nicardipine and VGCC have been studied at nanometer spatial resolution, at picoNewton force resolution and very high electrical signal resolution (pA in current, pF in capacitance and 0.1 mV in surface potential) level. The approaches are considered to be high resolution and high sensitivity, and will be helpful and useful in the further investigations of the effects of other types of CCB on ion channels, and will also be helpful in the investigations of mechanisms and therapy of ion channelopathies.

Size Matters: Rethinking Hertz Model Interpretation for Cell Mechanics Using AFM

Cell mechanics are a biophysical indicator of cell state, such as cancer metastasis, leukocyte activation, and cell cycle progression. Atomic force microscopy (AFM) is a widely used technique to measure cell mechanics, where the Young modulus of a cell is usually derived from the Hertz contact model. However, the Hertz model assumes that the cell is an elastic, isotropic, and homogeneous material and that the indentation is small compared to the cell size. These assumptions neglect the effects of the cytoskeleton, cell size and shape, and cell environment on cell deformation. In this study, we investigated the influence of cell size on the estimated Young's modulus using liposomes as cell models. Liposomes were prepared with different sizes and filled with phosphate buffered saline (PBS) or hyaluronic acid (HA) to mimic the cytoplasm. AFM was used to obtain the force indentation curves and fit them to the Hertz model. We found that the larger the liposome, the lower the estimated Young's modulus for both PBS-filled and HA-filled liposomes. This suggests that the Young modulus obtained from the Hertz model is not only a property of the cell material but also depends on the cell dimensions. Therefore, when comparing or interpreting cell mechanics using the Hertz model, it is essential to account for cell size.

Advantages of integrating Brillouin microscopy in multimodal mechanical mapping of cells and tissues

Recent research has highlighted the growing significance of the mechanical properties of cells and tissues in the proper execution of physiological functions within an organism; alterations to these properties can potentially result in various diseases. These mechanical properties can be assessed using various techniques that vary in spatial and temporal resolutions as well as applications. Due to the wide range of mechanical behaviors exhibited by cells and tissues, a singular mapping technique may be insufficient in capturing their complexity and nuance. Consequently, by utilizing a combination of methods-multimodal mechanical mapping-researchers can achieve a more comprehensive characterization of mechanical properties, encompassing factors such as stiffness, modulus, viscoelasticity, and forces. Furthermore, different mapping techniques can provide complementary information and enable the exploration of spatial and temporal variations to enhance our understanding of cellular dynamics and tissue mechanics. By capitalizing on the unique strengths of each method while mitigating their respective limitations, a more precise and holistic understanding of cellular and tissue mechanics can be obtained. Here, we spotlight Brillouin microscopy (BM) as a noncontact, noninvasive, and label-free mechanical mapping modality to be coutilized alongside established mechanical probing methods. This review summarizes some of the most widely adopted individual mechanical mapping techniques and highlights several recent multimodal approaches demonstrating their utility. We envision that future studies aim to adopt multimodal techniques to drive advancements in the broader realm of mechanobiology.

The Contribution of Scanning Force Microscopy on Dental Research: A Narrative Review

Scanning force microscopy (SFM) is one of the most widely used techniques in biomaterials research. In addition to imaging the materials of interest, SFM enables the mapping of mechanical properties and biological responses with sub-nanometer resolution and piconewton sensitivity. This review aims to give an overview of using the scanning force microscope (SFM) for investigations on dental materials. In particular, SFM-derived methods such as force-distance curves (scanning force spectroscopy), lateral force spectroscopy, and applications of the FluidFM® will be presented. In addition to the properties of dental materials, this paper reports the development of the pellicle by the interaction of biopolymers such as proteins and polysaccharides, as well as the interaction of bacteria with dental materials.

Probing the expression and adhesion of glycans involved in Helicobacter pylori infection

Helicobacter pylori infects approximately half the human population and has an unusual infective niche of the human stomach. Helicobacter pylori is a major cause of gastritis and has been classified as a group 1 carcinogen by the WHO. Treatment involves triple or quadruple antibiotic therapy, but antibiotic resistance is becoming increasingly prevalent. Helicobacter pylori expresses certain blood group related antigens (Lewis system) as a part of its lipopolysaccharide (LPS), which is thought to assist in immune evasion. Additionally, H. pylori LPS participates in adhesion to host cells alongside several adhesion proteins. This study profiled the carbohydrates of H. pylori reference strains (SS1 and 26695) using monoclonal antibodies (mAbs) and lectins, identifying interactions between two carbohydrate-targeting mAbs and multiple lectins. Atomic force microscopy (AFM) scans were used to probe lectin and antibody interactions with the bacterial surfaces. The selected mAb and lectins displayed an increased adhesive force over the surface of the curved H. pylori rods. Furthermore, this study demonstrates the ability of anti-carbohydrate antibodies to reduce the adhesion of H. pylori 26695 to human gastric adenocarcinoma cells via AFM. Targeting bacterial carbohydrates to disrupt crucial adhesion and immune evasion mechanisms represents a promising strategy for combating H. pylori infection.

Holotomography and atomic force microscopy: a powerful combination to enhance cancer, microbiology and nanotoxicology research

Modern imaging strategies are paramount to studying living systems such as cells, bacteria, and fungi and their response to pathogens, toxicants, and nanomaterials (NMs) as modulated by exposure and environmental factors. The need to understand the processes and mechanisms of damage, healing, and cell survivability of living systems continues to motivate the development of alternative imaging strategies. Of particular interest is the use of label-free techniques (microscopy procedures that do not require sample staining) that minimize interference of biological processes by foreign marking substances and reduce intense light exposure and potential photo-toxicity effects. This review focuses on the synergic capabilities of atomic force microscopy (AFM) as a well-developed and robust imaging strategy with demonstrated applications to unravel intimate details in biomedical applications, with the label-free, fast, and enduring Holotomographic Microscopy (HTM) strategy. HTM is a technique that combines holography and tomography using a low intensity continuous illumination laser to investigate (quantitatively and non-invasively) cells, microorganisms, and thin tissue by generating three-dimensional (3D) images and monitoring in real-time inner morphological changes. We first review the operating principles that form the basis for the complementary details provided by these techniques regarding the surface and internal information provided by HTM and AFM, which are essential and complimentary for the development of several biomedical areas studying the interaction mechanisms of NMs with living organisms. First, AFM can provide superb resolution on surface morphology and biomechanical characterization. Second, the quantitative phase capabilities of HTM enable superb modeling and quantification of the volume, surface area, protein content, and mass density of the main components of cells and microorganisms, including the morphology of cells in microbiological systems. These capabilities result from directly quantifying refractive index changes without requiring fluorescent markers or chemicals. As such, HTM is ideal for long-term monitoring of living organisms in conditions close to their natural settings. We present a case-based review of the principal uses of both techniques and their essential contributions to nanomedicine and nanotoxicology (study of the harmful effects of NMs in living organisms), emphasizing cancer and infectious disease control. The synergic impact of the sequential use of these complementary strategies provides a clear drive for adopting these techniques as interdependent fundamental tools.

Characterization of a unique attachment organelle: Single-cell force spectroscopy of Giardia duodenalis trophozoites

The unicellular parasite Giardia duodenalis is the causative agent of giardiasis, a gastrointestinal disease with global spread. In its trophozoite form, G. duodenalis can adhere to the human intestinal epithelium and a variety of other, artificial surfaces. Its attachment is facilitated by a unique microtubule-based attachment organelle, the so-called ventral disc. The mechanical function of the ventral disc, however, is still debated. Earlier studies postulated that a dynamic negative pressure under the ventral disc, generated by persistently beating flagella, mediates the attachment. Later studies suggested a suction model based on structural changes of the ventral discs, substrate clutching or grasping, or unspecific contact forces. In this study, we aim to contribute to the understanding of G. duodenalis attachment by investigating detachment characteristics and determining adhesion forces of single trophozoites on a smooth glass surface (RMS = 1.1 ± 0.2 nm) by fluidic force microscopy (FluidFM)-based single-cell force spectroscopy (SCFS). Briefly, viable adherent trophozoites were approached with a FluidFM micropipette, immobilized to the micropipette aperture by negative pressure, and detached from the surface by micropipette retraction while retract force curves were recorded. These force curves displayed novel and so far undescribed characteristics for a microorganism, namely, gradual force increase on the pulled trophozoite, with localization of adhesion force shortly before cell detachment length. Respective adhesion forces reached 7.7 ± 4.2 nN at 1 μm s-1 pulling speed. Importantly, this unique force pattern was different from that of other eukaryotic cells such as Candida albicans or oral keratinocytes, considered for comparison in this study. The latter both displayed a force pattern with force peaks of different values or force plateaus (for keratinocytes) indicative of breakage of molecular bonds of cell-anchored classes of adhesion molecules or membrane components. Furthermore, the attachment mode of G. duodenalis trophozoites was mechanically resilient to tensile forces, when the pulling speeds were raised up to 10 μm s-1 and adhesion forces increased to 28.7 ± 10.5 nN. Taken together, comparative SCSF revealed novel and unique retract force curve characteristics for attached G. duodenalis, suggesting a ligand-independent suction mechanism, that differ from those of other well described eukaryotes.

The intricate link between membrane lipid structure and composition and membrane structural properties in bacterial membranes

It is now evident that the cell manipulates lipid composition to regulate different processes such as membrane protein insertion, assembly and function. Moreover, changes in membrane structure and properties, lipid homeostasis during growth and differentiation with associated changes in cell size and shape, and responses to external stress have been related to drug resistance across mammalian species and a range of microorganisms. While it is well known that the biomembrane is a fluid self-assembled nanostructure, the link between the lipid components and the structural properties of the lipid bilayer are not well understood. This perspective aims to address this topic with a view to a more detailed understanding of the factors that regulate bilayer structure and flexibility. We describe a selection of recent studies that address the dynamic nature of bacterial lipid diversity and membrane properties in response to stress conditions. This emerging area has important implications for a broad range of cellular processes and may open new avenues of drug design for selective cell targeting.

Preventing E. coli Biofilm Formation with Antimicrobial Peptide-Functionalized Surface Coatings: Recognizing the Dependence on the Bacterial Binding Mode Using Live-Cell Microscopy

Antimicrobial peptides (AMPs) can kill bacteria by destabilizing their membranes, yet translating these molecules' properties into a covalently attached antibacterial coating is challenging. Rational design efforts are obstructed by the fact that standard microbiology methods are ill-designed for the evaluation of coatings, disclosing few details about why grafted AMPs function or do not function. It is particularly difficult to distinguish the influence of the AMP's molecular structure from other factors controlling the total exposure, including which type of bonds are formed between bacteria and the coating and how persistent these contacts are. Here, we combine label-free live-cell microscopy, microfluidics, and automated image analysis to study the response of surface-bound Escherichia coli challenged by the same small AMP either in solution or grafted to the surface through click chemistry. Initially after binding, the grafted AMPs inhibited bacterial growth more efficiently than did AMPs in solution. Yet, after 1 h, E. coli on the coated surfaces increased their expression of type-1 fimbriae, leading to a change in their binding mode, which diminished the coating's impact. The wealth of information obtained from continuously monitoring the growth, shape, and movements of single bacterial cells allowed us to elucidate and quantify the different factors determining the antibacterial efficacy of the grafted AMPs. We expect this approach to aid the design of elaborate antibacterial material coatings working by specific and selective actions, not limited to contact-killing. This technology is needed to support health care and food production in the postantibiotic era.

Antimicrobial mechanisms of nanopatterned surfaces-a developing story

Whilst it is now well recognized that some natural surfaces such as seemingly fragile insect wings possess extraordinary antimicrobial properties, a quest to engineer similar nanopatterned surfaces (NPSs) is ongoing. The stake is high as biofouling impacts critical infrastructure leading to massive social and economic burden with an antimicrobial resistance (AMR) issue at the forefront. AMR is one of the most imminent health challenges the world is facing today. Here, in the effort to find more sustainable solutions, the NPSs are proposed as highly promising technology as their antimicrobial activity arises from the topographical features, which could be realized on multiple material surfaces. To fully exploit these potentials however, it is crucial to mechanistically understand the underlying killing pathways. Thus far, several mechanisms have been proposed, yet they all have one thing in common. The antimicrobial process is initiated with bacteria contacting nanopatterns, which then imposes mechanical stress onto bacterial cell wall. Hence, the activity is called "mechano-bactericidal". From this point on, however, the suggested mechanisms start to diverge partly due to our limited understanding of force interactions at the interface. The aim of this mini review is to analyze the state-of-the-art in proposed killing mechanisms by categorizing them based on the characteristics of their driving force. We also highlight the current gaps and possible future directions in investigating the mechanisms, particularly by shifting towards quantification of forces at play and more elaborated biochemical assays, which can aid validating the current hypotheses.

Simulating biological surface dynamics in high-speed atomic force microscopy experiments

High-speed atomic force microscopy (HSAFM) is an important tool for studying the dynamic behavior of large biomolecular assemblies at surfaces. However, unlike light microscopy techniques, which visualize each point in the field of view at the same time, in HSAFM, the surface is literally imaged pixel-by-pixel with a variable extent of time separation existing between recordings made at one pixel and all others within the surface image. Such "temporal asynchronicity" in the recording of the spatial information can introduce distortions into the image when the surface components move at a rate comparable to that at which the surface is imaged. This Letter describes recently released software developments that are able to predict the likely form of these distortions and estimate confidence levels when assigning the identity of observed structures. These described approaches may facilitate both the design and optimization of future HSAFM experimental protocols. Further to this, they may assist in the interpretation of results from already published HSAFM studies.

Cancer Development in Hepatocytes by Long-Term Induction of Hypoxic Hepatocellular Carcinoma Cell (HCC)-Derived Exosomes In Vivo and In Vitro

Hypoxic tumor cell-derived exosomes play a key role in the occurrence, development, and metastasis of tumors. However, the mechanism of hypoxia-mediated metastasis remains unclear. In this study, hypoxic hepatocellular carcinoma cell (HCC-LM3)-derived exosomes (H-LM3-exos) were used to induce hepatocytes (HL-7702) over a long term (40 passages in 120 days). A nude mouse experiment further verified the effect of H-LM3-exos on tumor growth and metastasis. The process of cancer development in hepatocytes induced by H-LM3-exos was analyzed using both biological and physical techniques, and the results showed that the proliferation and soft agar growth abilities of the transformed cells were enhanced. The concentration of tumor markers secreted by transformed cells was increased, the cytoskeleton was disordered, and the migration ability was enhanced and was accompanied by epithelial-mesenchymal transition (EMT). Transcriptome results showed that differentially expressed genes between transformed cells and hepatocytes were enriched in cancer-related signaling pathways. The degree of cancer development in transformed cells was enhanced by an increase in H-LM3-exos-induced passages. Nude mice treated with different concentrations of H-LM3-exos showed different degrees of tumor growth and liver lesions. The physical properties of the cells were characterized by atomic force microscopy. Compared with the hepatocytes, the height and roughness of the transformed cells were increased, while the adhesion and elastic modulus were decreased. The changes in physical properties of primary tumor cells and hepatocytes in nude mice were consistent with this trend. Our study linking omics with the physical properties of cells provides a new direction for studying the mechanisms of cancer development and metastasis.

Multi-faceted analysis of bacterial transformation of nitrofurantoin

Excessive presence of antibiotics and their residues can be dangerous to the natural environment. To reduce this negative effect, efficient strategies to remove them from the ecosystem are required. This study aimed to explore the potential of bacterial strains to degrade nitrofurantoin (NFT). Single strains isolated from contaminated areas, namely Stenotrophomonas acidaminiphila N0B, Pseudomonas indoloxydans WB, and Serratia marcescens ODW152 were employed in this study. Degradation efficiency and dynamic changes within the cells during NFT biodegradation were investigated. For this purpose, atomic force microscopy, flow cytometry, zeta potential, and particle size distribution measurements were applied. Serratia marcescens ODW152 showed the highest performance in removal of NFT (96 % in 28 days). The AFM images revealed modifications of cell shape and surface structure induced by NFT. Zeta potential showed significant variations during biodegradation. Cultures exposed to NFT had a broader size distribution than the control cultures due to increased cells agglomeration or aggregation. 1-Aminohydantoin and semicarbazide were detected as nitrofurantoin biotransformation products. They showed increased cytotoxicity toward bacteria as determined by spectroscopy and flow cytometry. Results of this study suggest that nitrofurantoin biodegradation leads to formation of stable transformation products that significantly affect the physiology and structure of bacterial cells.

Surveying membrane landscapes: a new look at the bacterial cell surface

Recent studies applying advanced imaging techniques are changing the way we understand bacterial cell surfaces, bringing new knowledge on everything from single-cell heterogeneity in bacterial populations to their drug sensitivity and mechanisms of antimicrobial resistance. In both Gram-positive and Gram-negative bacteria, the outermost surface of the bacterial cell is being imaged at nanoscale; as a result, topographical maps of bacterial cell surfaces can be constructed, revealing distinct zones and specific features that might uniquely identify each cell in a population. Functionally defined assembly precincts for protein insertion into the membrane have been mapped at nanoscale, and equivalent lipid-assembly precincts are suggested from discrete lipopolysaccharide patches. As we review here, particularly for Gram-negative bacteria, the applications of various modalities of nanoscale imaging are reawakening our curiosity about what is conceptually a 3D cell surface landscape: what it looks like, how it is made and how it provides resilience to respond to environmental impacts.

Quantifying the Mechanical Properties of Yeast Candida albicans Using Atomic Force Microscopy-based Force Spectroscopy

Fungi can adapt to a wide range of environmental stresses in the wild and host milieu by employing their plastic genome and great diversity in morphology. Among different adaptive strategies, mechanical stimuli, such as changes in osmotic pressure, surface remodeling, hyphal formation, and cell divisions, could guide the physical cues into physiological responses through a complex signaling network. While fungal pathogens require a pressure-driven force to expand and penetrate host tissues, quantitatively studying the biophysical properties at the host-fungal interface is critical to understand the development of fungal diseases. Microscopy-based techniques have enabled researchers to monitor the dynamic mechanics on fungal cell surface in responses to the host stress and antifungal drugs. Here, we describe a label-free, high-resolution method based on atomic force microscopy, with a step-by-step protocol to measure the physical properties in human fungal pathogen Candida albicans.

Correlating viscosity and molecular crowding with fluorescent nanobeads and molecular probes: in vitro and in vivo

In eukaryotes, intracellular physico-chemical properties like macromolecular crowding and cytoplasmic viscoelasticity influence key processes such as metabolic activities, molecular diffusion and protein folding. However, mapping crowding and viscoelasticity in living cells remains challenging. One approach uses passive rheology in which diffusion of exogenous fluorescent particles internalized in cells is tracked and physico-chemical properties inferred from derived mean square displacement relations. Recently, the crGE2.3 Förster resonance energy transfer biosensor was developed to quantify crowding in cells, though it is unclear how this readout depends on viscoelasticity and the molecular weight of the crowder. Here, we present correlative, multi-dimensional data to explore diffusion and molecular crowding characteristics of molecular crowding agents using super-resolved fluorescence microscopy and ensemble time-resolved spectroscopy. We firstly characterize in vitro and then apply these insights to live cells of budding yeast Saccharomyces cerevisiae. It is to our knowledge the first time this has been attempted. We demonstrate that these are usable both in vitro and in the case of endogenously expressed sensors in live cells. Finally, we present a method to internalize fluorescent beads as in situ viscoelasticity markers in the cytoplasm of live yeast cells and discuss limitations of this approach including impairment of cellular function.

The staphylococcal biofilm protein Aap mediates cell-cell adhesion through mechanically distinct homophilic and lectin interactions

The accumulation phase of staphylococcal biofilms relies on both the production of an extracellular polysaccharide matrix and the expression of bacterial surface proteins. A prototypical example of such adhesive proteins is the long multidomain protein Aap (accumulation-associated protein) from Staphylococcus epidermidis, which mediates zinc-dependent homophilic interactions between Aap B-repeat regions through molecular forces that have not been investigated yet. Here, we unravel the remarkable mechanical strength of single Aap-Aap homophilic bonds between living bacteria and we demonstrate that intercellular adhesion also involves sugar binding through the lectin domain of the Aap A region. We find that the mechanical force needed to unfold individual β-sheet-rich G5-E domains from the Aap B-repeat regions is very high, ranging from 300 up to 1,000 pN at high loading rates, indicating these are extremely stable. This high mechanostability provides a means to the cells to form highly adhesive and cohesive biofilms capable of sustaining high physiological shear stress. Importantly, we identify a previously undescribed role of Aap in bacterial-bacterial adhesion, that is, heterophilic sugar binding by a specific lectin domain located in the N-terminal A region, which might be important to establish initial contacts between cells before strong homophilic bonds come into play. This study emphasizes the remarkable mechanical and binding properties of Aap as well as its wide diversity of adhesive functions.

Studies of probe tip materials by atomic force microscopy: a review

As a tool that can test insulators' surface morphology and properties, the performance index of atomic force microscope (AFM) probes is the most critical factor in determining the resolution of microscopy, and the performance of probes varies in various modes and application requirements. This paper reviews the latest research results in metal, carbon nanotube, and colloidal probes and reviews their related methods and techniques, analyses the advantages and disadvantages of the improved probes compared with ordinary probes by comparing the differences in spatial resolution, sensitivity, imaging, and other performance aspects, and finally provides an outlook on the future development of AFM probes. This paper promotes the development of AFM probes in the direction of new probes and further promotes the broader and deeper application of scanning probe microscope (SPM).

Interaction of the Staphylococcus aureus Surface Protein FnBPB with Corneodesmosin Involves Two Distinct, Extremely Strong Bonds

Attachment of Staphylococcus aureus to human skin corneocyte cells plays a critical role in exacerbating the severity of atopic dermatitis (AD). Pathogen-skin adhesion is mediated by bacterial cell-surface proteins called adhesins, including fibronectin-binding protein B (FnBPB). FnBPB binds to corneodesmosin (CDSN), a glycoprotein exposed on AD patient corneocytes. Using single-molecule experiments, we demonstrate that CDSN binding by FnBPB relies on a sophisticated two-site mechanism. Both sites form extremely strong bonds with binding forces of ∼1 and ∼2.5 nN albeit with faster dissociation rates than those reported for homologues of the adhesin. This previously unidentified two-binding site interaction in FnBPB illustrates its remarkable variety of adhesive functions and is of biological significance as the high strength and short bond lifetime will favor efficient skin colonization by the pathogen.

Nanomechanical and Molecular Characterization of Aging in Dentinal Collagen

Methylglyoxal (MGO) is an important molecule derived from glucose metabolism with the capacity of attaching to collagen and generating advanced glycation end products (AGEs), which accumulate in tissues over time and are associated with aging and diseases. However, the accumulation of MGO-derived AGEs in dentin and their effect on the nanomechanical properties of dentinal collagen remain unknown. Thus, the aim of the present study was to quantify MGO-based AGEs in the organic matrix of human dentin as a function of age and associate these changes with alterations in the nanomechanical and ultrastructural properties of dentinal collagen. For this, 12 healthy teeth from <26-y-old and >50-y-old patients were collected and prepared to obtain crown and root dentin discs. Following demineralization, MGO-derived AGEs were quantified with a competitive ELISA. In addition, atomic force microscopy nanoindentation was utilized to measure changes in elastic modulus in peritubular and intertubular collagen fibrils. Finally, principal component analysis was carried out to determine aging profiles for crown and root dentin. Results showed an increased presence of MGO AGEs in the organic matrix of dentin in the >50-y-old specimens as compared with the <26-y-old specimens in crown and root. Furthermore, an increase in peritubular and intertubular collagen elasticity was observed in the >50-y-old group associated with ultrastructural changes in the organic matrix as determined by atomic force microscopy analysis. Furthermore, principal component analysis loading plots suggested different "aging profiles" in crown and root dentin, which could have important therapeutic implications in restorative and adhesive dentistry approaches. Overall, these results demonstrate that the organic matrix of human dentin undergoes aging-related changes due to MGO-derived AGEs with important changes in the nanomechanical behavior of collagen that may affect diagnostic and restorative procedures in older people.

Force measurements of Myosin II waves at the yolk surface during Drosophila dorsal closure

The mechanical properties and the forces involved during tissue morphogenesis have been the focus of much research in the last years. Absolute values of forces during tissue closure events have not yet been measured. This is also true for a common force-producing mechanism involving Myosin II waves that results in pulsed cell surface contractions. Our patented magnetic tweezer, CAARMA, integrated into a spinning disk confocal microscope, provides a powerful explorative tool for quantitatively measuring forces during tissue morphogenesis. Here, we used this tool to quantify the in vivo force production of Myosin II waves that we observed at the dorsal surface of the yolk cell in stage 13 Drosophila melanogaster embryos. In addition to providing for the first time to our knowledge quantitative values on an active Myosin-driven force, we elucidated the dynamics of the Myosin II waves by measuring their periodicity in both absence and presence of external perturbations, and we characterized the mechanical properties of the dorsal yolk cell surface.

Structural dynamics of a DNA-binding protein analyzed using diffracted X-ray tracking

Diffracted X-ray tracking (DXT) is one of methods for the real-time evaluation of protein structural dynamics by detecting the movement of a gold-nanocrystal attached to a target protein. However, one of the technical concerns is the size of the gold-nanocrystals, which are larger than the protein. In our previous results of mean square angular displacement curves in DXT analysis, dynamical movements of the DNA-binding protein, c-Myb R2R3, were observed in only one population in either DNA-unbound or -bound state, and was found to decrease upon DNA binding. In this study, c-Myb R2R3 dynamical movements were re-evaluated with a low density of the protein immobilized on the DXT substrate, to decrease the possibility that the gold-nanocrystals attached to more than one R2R3 molecule. We observed two dynamical moving populations in the DNA-bound state, which could be classified due to electrostatic attraction and repulsion between the DNA-protein complexes, and determined the apparent angular diffusion constant, which was similar to the value calculated in our previous study. We showed more real movement of the protein could be observed by lowering the immobilization density of the protein.

Movements of Mycoplasma mobile Gliding Machinery Detected by High-Speed Atomic Force Microscopy

Mycoplasma mobile, a parasitic bacterium, glides on solid surfaces, such as animal cells and glass, by a special mechanism. This process is driven by the force generated through ATP hydrolysis on an internal structure. However, the spatial and temporal behaviors of the internal structures in living cells are unclear. In this study, we detected the movements of the internal structure by scanning cells immobilized on a glass substrate using high-speed atomic force microscopy (HS-AFM). By scanning the surface of a cell, we succeeded in visualizing particles, 2 nm in height and aligned mostly along the cell axis with a pitch of 31.5 nm, consistent with previously reported features based on electron microscopy. Movements of individual particles were then analyzed by HS-AFM. In the presence of sodium azide, the average speed of particle movements was reduced, suggesting that movement is linked to ATP hydrolysis. Partial inhibition of the reaction by sodium azide enabled us to analyze particle behavior in detail, showing that the particles move 9 nm right, relative to the gliding direction, and 2 nm into the cell interior in 330 ms and then return to their original position, based on ATP hydrolysis.

Force-Induced Changes of PilY1 Drive Surface Sensing by Pseudomonas aeruginosa

During biofilm formation, the opportunistic pathogen Pseudomonas aeruginosa uses its type IV pili (TFP) to sense a surface, eliciting increased second-messenger production and regulating target pathways required to adapt to a surface lifestyle. The mechanisms whereby TFP detect surface contact are still poorly understood, although mechanosensing is often invoked, with few data supporting this claim. Using a combination of molecular genetics and single-cell analysis, with biophysical, biochemical, and genomics techniques, we show that force-induced changes mediated by the von Willebrand A (vWA) domain-containing, TFP tip-associated protein PilY1 are required for surface sensing. Atomic force microscopy shows that TFP/PilY1 can undergo force-induced, sustained conformational changes akin to those observed for mechanosensitive proteins like titin. We show that mutation of a single cysteine residue in the vWA domain of PilY1 results in modestly lower surface adhesion forces, reduced sustained conformational changes, and increased nanospring-like properties, as well as reduced c-di-GMP signaling and biofilm formation. Mutating this cysteine has allowed us to genetically separate a role for TFP in twitching motility from surface-sensing signaling. The conservation of this Cys residue in all P. aeruginosa PA14 strains and its absence in the ∼720 sequenced strains of P. aeruginosa PAO1 may contribute to explaining the observed differences in surface colonization strategies observed for PA14 versus PAO1. IMPORTANCE Most bacteria live on abiotic and biotic surfaces in surface-attached communities known as biofilms. Surface sensing and increased levels of the second-messenger molecule c-di-GMP are crucial to the transition from planktonic to biofilm growth. The mechanism(s) underlying TFP-mediated surface detection that triggers this c-di-GMP signaling cascade is unclear. Here, we provide key insight into this question; we show that the eukaryote-like vWA domain of the TFP tip-associated protein PilY1 responds to mechanical force, which in turn drives the production of a key second messenger needed to regulate surface behaviors. Our studies highlight a potential mechanism that may account for differing surface colonization strategies.