Recent progress in the application of atomic force microscopy imaging and force spectroscopy to microbiology

Nanomechanical Mapping of Three Dimensionally Printed Poly-ε-Caprolactone Single Microfibers at the Cell Scale for Bone Tissue Engineering Applications

Poly-ε-caprolactone (PCL) has been widely used in additive manufacturing for the construction of scaffolds for bone tissue engineering. However, its use is limited by its lack of bioactivity and inability to induce cell adhesion, hence limiting bone tissue regeneration. Biomimicry is strongly influenced by the dynamics of cell-substrate interaction. Thus, characterizing scaffolds at the cell scale could help to better understand the relationship between surface mechanics and biological response. We conducted atomic force microscopy-based nanoindentation on 3D-printed PCL fibers of ~300 µm thickness and mapped the near-surface Young's modulus at loading forces below 50 nN. In this non-disruptive regime, force mapping did not show clear patterns in the spatial distribution of moduli or a relationship with the topographic asperities within a given region. Remarkably, we found that the average modulus increased linearly with the logarithm of the strain rate. Finally, a dependence of the moduli on the history of nanoindentation was demonstrated on locations of repeated nanoindentations, likely due to creep phenomena capable of hindering viscoelasticity. Our findings can contribute to the rational design of scaffolds for bone regeneration that are capable of inducing cell adhesion and proliferation. The methodologies described are potentially applicable to various tissue-engineered biopolymers.

Structural studies of protein-nucleic acid complexes: A brief overview of the selected techniques

Protein-nucleic acid complexes are involved in all vital processes, including replication, transcription, translation, regulation of gene expression and cell metabolism. Knowledge of the biological functions and molecular mechanisms beyond the activity of the macromolecular complexes can be determined from their tertiary structures. Undoubtably, performing structural studies of protein-nucleic acid complexes is challenging, mainly because these types of complexes are often unstable. In addition, their individual components may display extremely different surface charges, causing the complexes to precipitate at higher concentrations used in many structural studies. Due to the variety of protein-nucleic acid complexes and their different biophysical properties, no simple and universal guideline exists that helps scientists chose a method to successfully determine the structure of a specific protein-nucleic acid complex. In this review, we provide a summary of the following experimental methods, which can be applied to study the structures of protein-nucleic acid complexes: X-ray and neutron crystallography, nuclear magnetic resonance (NMR) spectroscopy, cryogenic electron microscopy (cryo-EM), atomic force microscopy (AFM), small angle scattering (SAS) methods, circular dichroism (CD) and infrared (IR) spectroscopy. Each method is discussed regarding its historical context, advancements over the past decades and recent years, and weaknesses and strengths. When a single method does not provide satisfactory data on the selected protein-nucleic acid complex, a combination of several methods should be considered as a hybrid approach; thus, specific structural problems can be solved when studying protein-nucleic acid complexes.

Atomic Force Microscopy (AFM) As a Surface Mapping Tool in Microorganisms Resistant Toward Antimicrobials: A Mini-Review

The worldwide emergence of antimicrobial resistance (AMR) in pathogenic microorganisms, including bacteria and viruses due to a plethora of reasons, such as genetic mutation and indiscriminate use of antimicrobials, is a major challenge faced by the healthcare sector today. One of the issues at hand is to effectively screen and isolate resistant strains from sensitive ones. Utilizing the distinct nanomechanical properties (e.g., elasticity, intracellular turgor pressure, and Young’s modulus) of microbes can be an intriguing way to achieve this; while atomic force microscopy (AFM), with or without modification of the tips, presents an effective way to investigate such biophysical properties of microbial surfaces or an entire microbial cell. Additionally, advanced AFM instruments, apart from being compatible with aqueous environments—as often is the case for biological samples—can measure the adhesive forces acting between AFM tips/cantilevers (conjugated to bacterium/virion, substrates, and molecules) and target cells/surfaces to develop informative force-distance curves. Moreover, such force spectroscopies provide an idea of the nature of intercellular interactions (e.g., receptor-ligand) or propensity of microbes to aggregate into densely packed layers, that is, the formation of biofilms—a property of resistant strains (e.g., Staphylococcus aureus, Pseudomonas aeruginosa). This mini-review will revisit the use of single-cell force spectroscopy (SCFS) and single-molecule force spectroscopy (SMFS) that are emerging as powerful additions to the arsenal of researchers in the struggle against resistant microbes, identify their strengths and weakness and, finally, prioritize some future directions for research.

Influences of bioapatite mineral and fibril structure on the mechanical properties of chicken bone during the laying period

Laying hens suffer from osteoporosis during their laying period, which causes bone fragility and susceptibility to fracture. This study evaluated the changes of mechanical properties of their bones during the laying period (from 18 to 77 wk) by using nano-indentation, atomic force microscope, X-Ray diffraction, and Raman spectroscopy. Results indicated that the crystallite sizes of bioapatite in femur decreased significantly from 34.45 to 29.26 nm during aging from 18 to 49 wk. Then, the value increased to 37.79 nm at 77 wk. Despite the abundance in bone (usually >50 wt.%), bioapatite mineral content showed no continuous enhancement during aging. The fibrils demonstrated more regular and organized structure during the laying period. Meanwhile the elastic moduli (E) and hardness (H) of femur increased from 10.84 to 18.39 GPa and 43.79 to 97.21 Vickers respectively during this period. The changes in mechanical properties are hence tightly related to the structure of bone (composed of both collagen and mineral), rather than directly related to the mineralogical properties of bone bioapatite. This study addressed the importance of the interaction between collagen and bioapatite mineral during the laying period of hens by microscopic, physicochemical, and mechanical analysis.

Toward Precision Measurement and Manipulation of Single-Molecule Reactions by a Confined Space

All chemical reactions can be divided into a series of single molecule reactions (SMRs), the elementary steps that involve only isomerization of, dissociation from, and addition to an individual molecule. Analyzing SMRs is of paramount importance to identify the intrinsic molecular mechanism of a complex chemical reaction, which is otherwise implausible to reveal in an ensemble fashion, owing to the significant static and dynamic heterogeneity of real-world chemical systems. The single-molecule measurement and manipulation methods developed recently are playing an increasingly irreplaceable role to detect and recognize short-lived intermediates, visualize their transient existence, and determinate the kinetics and dynamics of single bond breaking and formation. Notably, none of the above SMRs characterizations can be realized without the aid of a confined space. Therefore, this Review aims to highlight the recent progress in the development of confined space enabled single-molecule sensing, imaging, and tuning methods to study chemical reactions. Future prospects of SMRs research are also included, including a push toward the physical limit on transduction of information to signals and vice versa, transmission and recording of signals, computational modeling and simulation, and rational design of a confined space for precise SMRs.

Characterization of Pseudomonas aeruginosa Films on Different Inorganic Surfaces before and after UV Light Exposure

The changes of the surface properties of Au, GaN, and SiO _x after UV light irradiation were used to actively influence the process of formation of Pseudomonas aeruginosa films. The interfacial properties of the substrates were characterized by X-ray photoelectron spectroscopy and atomic force microscopy. The changes in the P. aeruginosa film properties were accessed by analyzing adhesion force maps and quantifying the intracellular Ca²⁺ concentration. The collected analysis indicates that the alteration of the inorganic materials' surface chemistry can lead to differences in biofilm formation and variable response from P. aeruginosa cells.

Single-cell membrane drug delivery using porous pen nanodeposition

Delivering molecules onto the plasma membrane of single cells is still a challenging task in profiling cell signaling pathways with single cell resolution. We demonstrated that a large quantity of molecules could be targeted and released onto the membrane of individual cells to trigger signaling responses. This is achieved by a porous pen nanodeposition (PPN) method, in which a multilayer porous structure, serving as a reservoir for a large amount of molecules, is formed on an atomic force microscope (AFM) tip using layer-by-layer assembly and post processing. To demonstrate its capability for single cell membrane drug delivery, PPN was employed to induce a calcium flux triggered by the binding of released antibodies to membrane antigens in an autoimmune skin disease model. This calcium signal propagates from the target cell to its neighbors in a matter of seconds, proving the theory of intercellular communication through cell-cell junctions. Collectively, these results demonstrated the effectiveness of PPN in membrane drug delivery for single cells; to the best of our knowledge, this is the first technique that can perform the targeted transport and delivery in single cell resolution, paving the way for probing complex signaling interactions in multicellular settings.

Options and Limitations in Clinical Investigation of Bacterial Biofilms

Bacteria can form single- and multispecies biofilms exhibiting diverse features based upon the microbial composition of their community and microenvironment. The study of bacterial biofilm development has received great interest in the past 20 years and is motivated by the elegant complexity characteristic of these multicellular communities and their role in infectious diseases. Biofilms can thrive on virtually any surface and can be beneficial or detrimental based upon the community's interplay and the surface. Advances in the understanding of structural and functional variations and the roles that biofilms play in disease and host-pathogen interactions have been addressed through comprehensive literature searches. In this review article, a synopsis of the methodological landscape of biofilm analysis is provided, including an evaluation of the current trends in methodological research. We deem this worthwhile because a keyword-oriented bibliographical search reveals that less than 5% of the biofilm literature is devoted to methodology. In this report, we (i) summarize current methodologies for biofilm characterization, monitoring, and quantification; (ii) discuss advances in the discovery of effective imaging and sensing tools and modalities; (iii) provide an overview of tailored animal models that assess features of biofilm infections; and (iv) make recommendations defining the most appropriate methodological tools for clinical settings.

Atomic force microscopy studies of bioprocess engineering surfaces - imaging, interactions and mechanical properties mediating bacterial adhesion

The detrimental effect of bacterial biofilms on process engineering surfaces is well documented. Thus, interest in the early stages of bacterial biofilm formation; in particular bacterial adhesion and the production of anti-fouling coatings has grown exponentially as a field. During this time, Atomic force microscopy (AFM) has emerged as a critical tool for the evaluation of bacterial adhesion. Due to its versatility AFM offers not only insight into the topographical landscape and mechanical properties of the engineering surfaces, but elucidates, through direct quantification the topographical and biomechnical properties of the foulants The aim of this review is to collate the current research on bacterial adhesion, both theoretical and practical, and outline how AFM as a technique is uniquely equipped to provide further insight into the nanoscale world at the bioprocess engineering surface.

Heterogeneity and Specificity of Nanoscale Adhesion Forces Measured between Self-Assembled Monolayers and Lignocellulosic Substrates: A Chemical Force Microscopy Study

Lack of fundamental understanding of cellulase interactions with different plant cell wall components during cellulose saccharification hinders progress toward achieving an economic production of biofuels from renewable plant biomass. Here, chemical force microscopy (CFM) was utilized to quantify the interactions between two surfaces that model either hydrophilic or hydrophobic functional groups of cellulases and a set of lignocellulosic substrates prepared through Kraft, sulfite, or organosolv pulping with defined chemical composition. The measured forces were then decoupled into specific and nonspecific components using the Poisson statistical approach. Heterogeneities in the distributions of forces as a function of the pretreatment method were mapped. Our results showed that hydrophobic domains and chemical moieties involved in hydrogen bonding and polar interactions were homogeneously distributed on all substrates but with distribution densities that varied with the type of the pretreatment method used to prepare substrates. In addition, we showed that increasing surface lignin coverage increased the heterogeneity of the substrates. When forces were decoupled, our results indicated that xylan reduced the strength of hydrogen bonding between the hydrophilic model surface and substrates. Permanent dipole-dipole interactions dominated the adhesion of the hydrophilic model surface to lignosulfonates, whereas hydrophobic interactions facilitated the adhesion of the hydrophobic model surface to Kraft lignin. We further showed that the structure of lignin determines the type of forces that dominate lignocellulosic interactions with other surfaces. Our findings suggest that nonproductive binding of cellulases to lignocellulosic biomass can be reduced by altering the hydrophobicity and/or chemical moieties involved in the polar interactions and by utilizing organosolv as a pretreatment method.

Single-virus force spectroscopy unravels molecular details of virus infection

Virus infection is a multistep process that has significant effects on the structure and function of both the virus and the host cell. The first steps of virus replication include cell binding, entry and release of the viral genome. Single-virus force spectroscopy (SVFS) has become a promising tool to understand the molecular details of those steps. SVFS data complemented by biochemical and biophysical, including theoretical modeling approaches provide valuable insights into molecular events that accompany virus infection. Properties of virus-cell interaction as well as structural alterations of the virus essential for infection can be investigated on a quantitative level. Here we review applications of SVFS to virus binding, structure and mechanics. We demonstrate that SVFS offers unexpected new insights not accessible by other methods.

Bacterial adhesion force quantification by fluidic force microscopy

Quantification of detachment forces between bacteria and substrates facilitates the understanding of the bacterial adhesion process that affects cell physiology and survival. Here, we present a method that allows for serial, single bacterial cell force spectroscopy by combining the force control of atomic force microscopy with microfluidics. Reversible bacterial cell immobilization under physiological conditions on the pyramidal tip of a microchanneled cantilever is achieved by underpressure. Using the fluidic force microscopy technology (FluidFM), we achieve immobilization forces greater than those of state-of-the-art cell-cantilever binding as demonstrated by the detachment of Escherichia coli from polydopamine with recorded forces between 4 and 8 nN for many cells. The contact time and setpoint dependence of the adhesion forces of E. coli and Streptococcus pyogenes, as well as the sequential detachment of bacteria out of a chain, are shown, revealing distinct force patterns in the detachment curves. This study demonstrates the potential of the FluidFM technology for quantitative bacterial adhesion measurements of cell-substrate and cell-cell interactions that are relevant in biofilms and infection biology.

Undifferentiated bronchial fibroblasts derived from asthmatic patients display higher elastic modulus than their non-asthmatic counterparts

During asthma development, differentiation of epithelial cells and fibroblasts towards the contractile phenotype is associated with bronchial wall remodeling and airway constriction. Pathological fibroblast-to-myofibroblast transition (FMT) can be triggered by local inflammation of bronchial walls. Recently, we have demonstrated that human bronchial fibroblasts (HBFs) derived from asthmatic patients display some inherent features which facilitate their FMT in vitro. In spite of intensive research efforts, these properties remain unknown. Importantly, the role of undifferentiated HBFs in the asthmatic process was systematically omitted. Specifically, biomechanical properties of undifferentiated HBFs have not been considered in either FMT or airway remodeling in vivo. Here, we combine atomic force spectroscopy with fluorescence microscopy to compare mechanical properties and actin cytoskeleton architecture of HBFs derived from asthmatic patients and non-asthmatic donors. Our results demonstrate that asthmatic HBFs form thick and aligned ‘ventral’ stress fibers accompanied by enlarged focal adhesions. The differences in cytoskeleton architecture between asthmatic and non-asthmatic cells correlate with higher elastic modulus of asthmatic HBFs and their increased predilection to TGF-β-induced FMT. Due to the obvious links between cytoskeleton architecture and mechanical equilibrium, our observations indicate that HBFs derived from asthmatic bronchi can develop considerably higher static tension than non-asthmatic HBFs. This previously unexplored property of asthmatic HBFs may be potentially important for their myofibroblastic differentiation and bronchial wall remodeling during asthma development.

Cell elasticity is an important indicator of the metastatic phenotype of melanoma cells

The relationship between melanin pigmentation and metastatic phenotype of melanoma cells is an intricate issue, which needs to be unambiguously determined to fully understand the process of metastasis of malignant melanoma. Despite significant research efforts undertaken to solve this problem, the outcomes are far from being satisfying. Importantly, none of the proposed explanations takes into consideration biophysical aspects of the phenomenon such as cell elasticity. Recently, we have demonstrated that melanin granules dramatically modify elastic properties of pigmented melanoma cells. This prompted us to examine the mechanical effects of melanosomes on the transmigration abilities of melanoma cells. Here, we show for the first time that melanin granules inhibit transmigration abilities of melanoma cells in a number of granules dependent manner. Moreover, we demonstrate that the inhibitory effect of melanosomes is mechanical in nature. Results obtained in this study demonstrate that cell elasticity may play a key role in the efficiency of melanoma cells spread in vivo. Our findings may also contribute to better understanding of the process of metastasis of malignant melanoma.

Unraveling microbial biofilms of importance for food microbiology

The presence of biofilms is a relevant risk factors in the food industry due to the potential contamination of food products with pathogenic and spoilage microorganisms. The majority of bacteria are able to adhere and to form biofilms, where they can persist and survive for days to weeks or even longer, depending on the microorganism and the environmental conditions. The biological cycle of biofilms includes several developmental phases such as: initial attachment, maturation, maintenance, and dispersal. Bacteria in biofilms are generally well protected against environmental stress, consequently, extremely difficult to eradicate and detect in food industry. In the present manuscript, some techniques and compounds used to control and to prevent the biofilm formation are presented and discussed. Moreover, a number of novel techniques have been recently employed to detect and evaluate bacteria attached to surfaces, including real-time polymerase chain reaction (PCR), DNA microarray and confocal laser scanning microscopy. Better knowledge on the architecture, physiology and molecular signaling in biofilms can contribute for preventing and controlling food-related spoilage and pathogenic bacteria. The present study highlights basic and applied concepts important for understanding the role of biofilms in bacterial survival, persistence and dissemination in food processing environments.

Nanoscale characterization of effect of L-arginine on Streptococcus mutans biofilm adhesion by atomic force microscopy

A major aetiological factor of dental caries is the pathology of the dental plaque biofilms. The amino acid L-arginine (Arg) is found naturally in saliva as a free molecule or as a part of salivary peptides and proteins. Plaque bacteria metabolize Arg to produce alkali and neutralize glycolytic acids, promoting a less cariogenous oral microbiome. Here, we explored an alternative and complementary mechanism of action of Arg using atomic force microscopy. The nanomechanical properties of Streptococcus mutans biofilm extracellular matrix were characterized under physiological buffer conditions. We report the effect of Arg on the adhesive behaviour and structural properties of extracellular polysaccharides in S. mutans biofilms. High-resolution imaging of biofilm surfaces can reveal additional structural information on bacterial cells embedded within the surrounding extracellular matrix. A dense extracellular matrix was observed in biofilms without Arg compared to those grown in the presence of Arg. S. mutans biofilms grown in the presence of Arg could influence the production and/or composition of extracellular membrane glucans and thereby affect their adhesion properties. Our results suggest that the presence of Arg in the oral cavity could influence the adhesion properties of S. mutans to the tooth surface.

Nanoscale adhesion forces between enamel pellicle proteins and hydroxyapatite

The acquired enamel pellicle (AEP) is important for minimizing the abrasion caused by parafunctional conditions as they occur, for instance, during bruxism. It is a remarkable feature of the AEP that a protein/peptide film can provide enough protection in normofunction to prevent teeth from abrasion and wear. Despite its obvious critical role in the protection of tooth surfaces, the essential adhesion features of AEP proteins on the enamel surface are poorly characterized. The objective of this study was to measure the adhesion force between histatin 5, a primary AEP component, and hydroxyapatite (HA) surfaces. Both biotinylated histatin 5 and biotinylated human serum albumin were allowed to adsorb to streptavidin-coated silica microspheres attached to atomic force microscope (AFM) cantilevers. A multimode AFM with a Nanoscope IIIa controller was used to measure the adhesion force between protein-functionalized silica microspheres attached to cantilever tips and the HA surface. The imaging was performed in tapping mode with a Si3N4 AFM cantilever, while the adhesion forces were measured in AFM contact mode. A collection of force-distance curves (~3,000/replicate) was obtained to generate histograms from which the adhesion forces between histatin 5 or albumin and the HA surface were measured. We found that histatin 5 exhibited stronger adhesion forces (90% >1.830 nN) to the HA surface than did albumin (90% > 0.282 nN). This study presents an objective approach to adhesion force measurements between histatin 5 and HA, and provides the experimental basis for measuring the same parameters for other AEP constituents. Such knowledge will help in the design of synthetic proteins and peptides with preventive and therapeutic benefits for tooth enamel.

Novel materials for biofilm reactors and their characterization

The application of adherently growing microorganisms for biotechnological production processes is established, but it is still a niche technology with only a small economic impact. However, novel approaches are under development for new types of biofilm reactors. In this context, increasingly more microstructured metal surfaces are being investigated, and they show positive effects on the bacterial growth and the biofilm establishment. However, for comparison of the data, the different surface materials have to correspond in their different characteristics, such as wettability and chemical composition. Also, new materials, such as plastic composite supports, were developed. To understand the interaction between these new materials and the biofilm-producing microorganisms, different surface science methods have to be applied to reveal a detailed knowledge of the surface characteristics. In conclusion, microstructured surfaces show a high potential for enhanced biofilm growth, probably accompanied by an enhanced productivity of the microorganisms.

The effect of alginate oligosaccharides on the mechanical properties of Gram-negative biofilms

The influence of a novel, safe antibiofilm therapy on the mechanical properties of Pseudomonas aeruginosa and Acinetobacter baumannii biofilms in vitro was characterized. A multiscale approach employing atomic force microscopy (AFM) and rheometry was used to quantify the mechanical disruption of the biofilms by a therapeutic polymer based on a low-molecular weight alginate oligosaccharide (OligoG). AFM demonstrated structural alterations in the biofilms exposed to OligoG, with significantly lower Young's moduli than the untreated biofilms, (149 MPa vs 242 MPa; p < 0.05), a decreased resistance to hydrodynamic shear and an increased surface irregularity (Ra) in the untreated controls (35.2 nm ± 7.6 vs 12.1 nm ± 5.4; p < 0.05). Rheology demonstrated that increasing clinically relevant concentrations of OligoG (<10%) were associated with an increasing phase angle (δ) over a wide range of frequencies (0.1-10 Hz). These results highlight the utility of these techniques for the study of three-dimensional biofilms and for quantifying novel disruption therapies in vitro.

Infection of orthopedic implants with emphasis on bacterial adhesion process and techniques used in studying bacterial-material interactions

Staphylococcus comprises up to two-thirds of all pathogens in orthopedic implant infections and they are the principal causative agents of two major types of infection affecting bone: septic arthritis and osteomyelitis, which involve the inflammatory destruction of joint and bone. Bacterial adhesion is the first and most important step in implant infection. It is a complex process influenced by environmental factors, bacterial properties, material surface properties and by the presence of serum or tissue proteins. Properties of the substrate, such as chemical composition of the material, surface charge, hydrophobicity, surface roughness and the presence of specific proteins at the surface, are all thought to be important in the initial cell attachment process. The biofilm mode of growth of infecting bacteria on an implant surface protects the organisms from the host immune system and antibiotic therapy. The research for novel therapeutic strategies is incited by the emergence of antibiotic-resistant bacteria. This work will provide an overview of the mechanisms and factors involved in bacterial adhesion, the techniques that are currently being used studying bacterial-material interactions as well as provide insight into future directions in the field.

Advances in research on structural characterisation of agricultural products using atomic force microscopy

Atomic force microscopy (AFM) has many unique features compared with other conventional microscopies, such as high magnification with high resolution, minimal sample preparation, acquiring 2D and 3D images at the same time, observing ongoing processes directly, the possibility of manipulating macromolecules, etc. As a nanotechnology tool, AFM has been used to investigate the nanostructure of materials in many fields. This mini-review focuses mainly on its latest application to characterise the macromolecular nanostructure and surface topography of agricultural products. First the fundamentals of AFM are briefly explained. Then the macromolecular nanostructure information on agricultural products from AFM images is introduced by exploring the structure-function relationship in three aspects: agricultural product processing, agricultural product ripening and storage, and genetic and environmental factors. The surface topography characterisation of agricultural products using AFM is also discussed. The results reveal that AFM could be a powerful nanotechnology tool to acquire a deeper understanding of the mechanisms of structure and quality variations of agricultural products, which could be instructive in improving processing and storage technologies, and AFM is also helpful to reveal the essential nature of a product at nanoscale.

Atomic force microscopy: a tool to analyze the structural organization of pathogenic protozoa

The fine structure of parasitic protozoa has been the subject of intense investigation with the use of electron microscopy. The recent development of atomic force microscopy (AFM) and all of the techniques associated with AFM has created new ways to further analyze the structure of cells. In this review, the various, presently-available modalities of AFM are discussed, as well as the results obtained in analysis of: (i) the structure of intact and detergent-extracted protozoa; (ii) the surface of infected cells; (iii) the structure of parasite macromolecules; (iv) the measurement of surface potential; and (v) force spectroscopy, the measurement of elasticity and ligand-receptor interactions.

Short time-scale bacterial adhesion dynamics

In natural conditions many bacterial populations are found as surface-attached communities exhibiting features distinct from those of planktonic cells. We focus here on the question of initial adhesion, the mechanisms of which are still far from being fully understood. Recently, the frontier between microbiologists and physicists has become increasingly permeable, boosting implementation of new methodological approaches for better elucidating the intricate aspects of initial bacterial adhesion. After discussing briefly the main sources of complexity that confuse the understanding of the early steps of cell-surface attachment, we present a selection of physical methods enabling real-time measurement of early adhesion kinetics in live cells. We also discuss the limitations and pitfalls that might appear when applying such methodologies - initially designed for studying physically ideal systems - to analysis of these, more complex, living systems. We address mainly on the use of dispersed-surfaces flow cytometry (DS-FCM), quartz microbalance (QCM) and surface plasmon resonance (SPR) approaches, and give a brief survey of new perspectives in optical microscopy. We conclude that the use of combined and multiparametric technical approaches will lead to significant advances in providing a comprehensive understanding of the early events in bacterial adhesion.

Multiscale observation of biological interactions of nanocarriers: from nano to macro

Microscopic observations have played a key role in recent advancements in nanotechnology-based biomedical sciences. In particular, multiscale observation is necessary to fully understand the nano-bio interfaces where a large amount of unprecedented phenomena have been reported. This review describes how to address the physicochemical and biological interactions of nanocarriers within the biological environments using microscopic tools. The imaging techniques are categorized based on the size scale of detection. For observation of the nanoscale biological interactions of nanocarriers, we discuss atomic force microscopy (AFM), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). For the micro to macro-scale (in vitro and in vivo) observation, we focus on confocal laser scanning microscopy (CLSM) as well as in vivo imaging systems such as magnetic resonance imaging (MRI), superconducting quantum interference devices, and IVIS. Additionally, recently developed combined techniques such as AFM-CLSM, correlative light and electron microscopy (CLEM), and SEM spectroscopy are also discussed. In this review, we describe how each technique helps elucidate certain physicochemical and biological activities of nanocarriers such as dendrimers, polymers, liposomes, and polymeric/inorganic nanoparticles, thus providing a toolbox for bioengineers, pharmaceutical scientists, biologists, and research clinicians.

Characterization of cell surface and extracellular matrix remodeling of Azospirillum brasilense chemotaxis-like 1 signal transduction pathway mutants by atomic force microscopy

To compete in complex microbial communities, bacteria must sense environmental changes and adjust cellular functions for optimal growth. Chemotaxis-like signal transduction pathways are implicated in the regulation of multiple behaviors in response to changes in the environment, including motility patterns, exopolysaccharide production, and cell-to-cell interactions. In Azospirillum brasilense, cell surface properties, including exopolysaccharide production, are thought to play a direct role in promoting flocculation. Recently, the Che1 chemotaxis-like pathway from A. brasilense was shown to modulate flocculation, suggesting an associated modulation of cell surface properties. Using atomic force microscopy, distinct changes in the surface morphology of flocculating A. brasilense Che1 mutant strains were detected. Whereas the wild-type strain produces a smooth mucosal extracellular matrix after 24 h, the flocculating Che1 mutant strains produce distinctive extracellular fibril structures. Further analyses using flocculation inhibition, lectin-binding assays, and comparison of lipopolysaccharides profiles suggest that the extracellular matrix differs between the cheA1 and the cheY1 mutants, despite an apparent similarity in the macroscopic floc structures. Collectively, these data indicate that disruption of the Che1 pathway is correlated with distinctive changes in the extracellular matrix, which likely result from changes in surface polysaccharides structure and/or composition.

Measuring the influence of solution chemistry on the adhesion of au nanoparticles to mica using colloid probe atomic force microscopy

Engineered nanoparticles are used increasingly in numerous commercial products, leading to concerns over their environmental fate and ecotoxicity. We report the adaptation of colloid probe atomic force microscopy (AFM) to quantitatively determine the adhesive behavior of gold nanoparticles (Au NPs) with mica, chosen as a model for sand, in various water chemistries. Au NP-covered polystyrene (PS) beads were prepared by a combined swelling-heteroaggregation (CSH) technique prior to attachment to tipless AFM cantilevers. Force measurements were performed over a range of solution conditions (pH, ionic strength (IS), and natural organic matter (NOM) content). Plain PS beads with no Au NPs were used as controls. In general, adhesion of Au NP-PS beads to mica were found to increase as IS increased while a rise in pH led to a decrease in adhesion. Plain PS beads were not observed to adhere to mica in any of the experimental solution conditions, and the PS force curves were unaffected by changes in the pH and electrolyte concentrations. In the presence of NOM, pull-off forces for Au NP-PS beads increased in magnitude when NaCl was added. In addition, the experimental approach force curves were not successfully described by the classical Derjaguin-Landau-Verwey-Overbeek (DLVO) theory of colloidal stability. To reconcile the discrepancy between theory and experiment, an extended DLVO (xDLVO) empirical model was used to account for the contribution of non-DLVO interactions (known collectively as structural forces) between the Au NPs and mica surfaces.

Virus' (MS2, phiX174, and Aichi) attachment on sand measured by atomic force microscopy and their transport through sand columns

Atomic force microscopy (AFM) was used to study the attachment of phiX174, MS2, and Aichi viruses on sands of different surface properties: oxide-removed (clean), goethite-coated, and aluminum oxide-coated. Interaction forces between viruses and sand surfaces were measured by contact mode AFM using tips coated with particles of each virus. Column experiments were conducted to quantify the macroscopic transport and retention of the viruses in sand. The average adhesion force measured with AFM was highest between aluminum oxide-coated sand and all three viruses, followed by goethite-coated sand, and was significantly lower on oxide-removed sand. Among the viruses, adhesion on goethite-coated and aluminum oxide-coated sands followed the order of MS2 > Aichi > phiX174, and on oxide-removed sand it was phiX174 > Aichi > MS2. Column breakthrough results revealed the same retention trend, which was completely consistent with AFM force measurements. Strong electrostatic attraction and, to a lesser extent, hydrophobic interactions are responsible for the much greater removal of all three viruses observed in the oxide-coated sands compared to the oxide-removed sand. Mass recovery data indicate that the removal of phiX174, MS2, and Aichi was largely reversible when eluted with 3% beef extract solution at pH 9.5. The Derjaguin-Landau-Verwey-Overbeek (DLVO) and extended DLVO theories provided correct qualitative predictions on the deposition trend observed in the experiments. This study, to the best of our knowledge, was the first to employ AFM to directly measure interaction forces between viruses and solid surfaces; and it was the first to evaluate the retention and transport behavior of Aichi virus, a human pathogen.

The effects of copper additives on the quantity and cell viability of adherent Staphylococcus epidermidis in silicone implants

This in vitro study evaluated the antibacterial effect of copper additives in silicone implants. Specimens of a standard silicone material used in breast augmentation and modified copper-loaded silicone specimens were prepared and incubated in a Staphylococcus epidermidis suspension (2 h, 37 degrees C). After the quantification of adhering staphylococci using a biofluorescence assay (Resazurin), the viability of the adhering bacterial cells was quantified by live or dead cell labeling in combination with fluorescence microscopy. In the Resazurin fluorometric quantification, a higher amount of adhering S. epidermidis cells was detected on pure silicone (4612 [2319/7540] relative fluorescence units [rfu]) than on silicone with copper additives (2701 [2158/4153] rfu). Additionally, a significantly higher amount of adhering bacterial cells (5.07% [2.03%/8.93%]) was found for pure silicone than for silicone with copper additives (1.72% [1.26%/2.32%]); (p < 0.001). Calculations from live or dead staining showed that the percentage of dead S. epidermidis cells adhered on pure silicone (52.1%) was significantly lower than on silicone with copper additives (79.7%); (p < 0.001). In vitro, silicone material with copper additives showed antibacterial effects against S. epidermidis. Copper-loaded silicone may prevent bacterial colonization, resulting in lower infection rates of silicone implants.

Application of AFM in microbiology: a review

Atomic force microscopy (AFM) is a powerful tool for microbiological investigation. This versatile technique cannot only image cellular surfaces at high resolution, but also measure many forms of fundamental interactions over scales ranging from molecules to cells. In this work, we review the recent development of AFM applications in the microbial area. We discuss several approaches for using AFM scanning images to investigate morphological characteristics of microbes and the use of force-distance curves to investigate interaction of microbial samples at the nanometer and cellular levels. Complementary techniques used in combination with AFM for study of microbes are also discussed.

Characterization of ragweed pollen adhesion to polyamides and polystyrene using atomic force microscopy

Pollen is a leading contributor to asthma and allergies, yet pollen adhesion to common indoor surfaces is not well understood. We report the adhesive behavior of short ragweed (A. artemisiifolia) pollen grains with Nylon 6 (N6) and Nylon 6,6 (N66), chosen due to their use in synthetic carpet, and three control surfaces: polyamide 12 (PA12), polystyrene (PS), and silicon. The forces were measured by using atomic force microscopy (AFM) under controlled humidity, where single pollen grains were attached to tipless AFM cantilevers. Pollen grains had an average adhesion of 10 +/- 3 nN with the surfaces, independent of surface type or relative humidity from 20% to 60%. van der Waals forces are the primary molecular attraction driving pollen adhesion to these surfaces. The results also indicate that ragweed pollen contacts the polymer surface via its exine surface spikes, and the total adhesion force scales with the number of contacts. The pollen surface spikes are strong, resisting fracture and compliance up to a load of 0.5 GPa.

Surface rigidity change of Escherichia coli after filamentous bacteriophage infection

In this study, the feasibility using atomic force microscopy (AFM) to study the interaction between bacteriophages (phages) and bacteria in situ was demonstrated here. Filamentous phage M13 specifically infects the male Escherichia coli, which expresses F-pili. After infection, E. coli become fragile and grows at a slower rate. AFM provides a powerful tool for investigating these changes in a near-physiological environment. Using high-resolution AFM in phosphate-buffered saline, the damage to the lipopolysaccharide (LPS) layer on the outer membrane of the M13 phage-infected E. coli was observed. The membrane became smoother and more featureless compared to those that were not infected. Besides, the force-distance (f-d) curves were measured to reveal the surface rigidity change in E. coli after M13 phage infection. The effective spring constant and Young's modulus of E. coli decreased after M13 phage infection. Furthermore, the AFM tip was pressed against E. coli to study the response of E. coli under load before and after M13 phage infection. The results showed that after infection E. coli became less rigid and the membrane was also damaged. However, the stiffness changes, including the spring constant and Young's modulus of E. coli, are negligible after M13 phage infection compared with those in previous reports, which may be one of the reasons that E. coli still can maintain its viability after filamentous phage infection.

Atomic force microscopy (AFM)

The atomic force microscope (AFM) is an important tool for studying biological samples due to its ability to image surfaces under liquids. The AFM operates by physical interaction of a cantilever tip with the molecules on the cell surface. Adhesion forces between the tip and cell surface molecules are detected as cantilever deflections. Thus, the cantilever tip can be used to image live cells with atomic resolution and to probe single molecular events in living cells under physiological conditions. Currently, this is the only technique available that directly provides structural, mechanical, and functional information at high resolution. This unit presents the basic AFM components, modes of operation, useful tips for sample preparation, and a short review of AFM applications in microbiology.

Study on antibacterial mechanism of copper-bearing austenitic antibacterial stainless steel by atomic force microscopy

A study was made on the antibacterial mechanism of copper-bearing austenitic antibacterial stainless steel by a series of methods such as atomic force microscopy (AFM) observation, force-distance curves and inductively coupled plasma mass spectrometer test. It was observed by AFM that the structure of the outer cell membrane responsible for the cell permeability was substantially changed for the bacteria after contacting with the antibacterial stainless steel, showing that cell walls were seriously damaged and a lot of contents in the cells leaked. It was also found that the adhesion force of bacteria to antibacterial stainless steel was considerably greater than that to the contrast steel, indicating that the electrostatic forces by Cu(2+ )being an important factor for killing bacteria.

Bond strengthening in oral bacterial adhesion to salivary conditioning films

Transition from reversible to irreversible bacterial adhesion is a highly relevant but poorly understood step in initial biofilm formation. We hypothesize that in oral biofilm formation, irreversible adhesion is caused by bond strengthening due to specific bacterial interactions with salivary conditioning films. Here, we compared the initial adhesion of six oral bacterial strains to salivary conditioning films with their adhesion to a bovine serum albumin (BSA) coating and related their adhesion to the strengthening of the binding forces measured with bacteria-coated atomic force microscopy cantilevers. All strains adhered in higher numbers to salivary conditioning films than to BSA coatings, and specific bacterial interactions with salivary conditioning films were accompanied by stronger initial adhesion forces. Bond strengthening occurred on a time scale of several tens of seconds and was slower for actinomyces than for streptococci. Nonspecific interactions between bacteria and BSA coatings strengthened twofold faster than their specific interactions with salivary conditioning films, likely because specific interactions require a closer approach of interacting surfaces with the removal of interfacial water and a more extensive rearrangement of surface structures. After bond strengthening, bacterial adhesion forces with a salivary conditioning film remained stronger than those with BSA coatings.

Nanorheology of viscoelastic shells: applications to viral capsids

We study the microrheology of nanoparticle shells [A. D. Dinsmore, Science 298, 1006 (2002)] and viral capsids [I. L. Ivanovska, Proc. Natl. Acad. Sci. U.S.A. 101, 7600 (2004)] by computing the mechanical response function and thermal fluctuation spectrum of a viscoelastic spherical shell that is permeable to the surrounding solvent. We determine analytically the damped dynamics of bend and compression modes of the shell coupled to the solvent both inside and outside the sphere in the zero Reynolds number limit. We identify fundamental length and time scales in the system, and compute the thermal correlation function of displacements of antipodal points on the sphere and the mechanical response to pinching forces applied at these points. We describe how such a frequency-dependent antipodal correlation and/or response function, which should be measurable in new AFM-based microrheology experiments, can probe the viscoelasticity of these synthetic and biological shells constructed of nanoparticles.

The influence of ionic strength, nutrients and pH on bacterial adhesion to metals

Bacteria-metal interactions in aqueous solutions are important in biofilm formation, biofouling and biocorrosion problems in the natural environment and engineered systems. In this study, the adhesion forces of two anaerobes (Desulfovibrio desulfuricans and Desulfovibrio singaporenus) and an aerobe (Pseudomonas sp.) to stainless steel 316 in various aqueous systems were quantified using atomic force microscopy (AFM) with a cell probe. Results show that the nutrient and ionic strength of the solutions influence the bacteria-metal interactions. The bacteria-metal adhesion force was reduced in the presence of the nutrients in the solution, because a trace organic film was formed and thus decreased the metal surface wettability. Stronger ionic strength in the solution results in a larger bacteria-metal adhesion force, which is due to the stronger electrostatic attraction force between the positively charged metal surface and negatively charged bacterial surface. Solution pH also influences the interaction between the bacterial cells and the metal surface; the bacteria-metal adhesion force reached its highest value when the pH of the solution was near the isoelectric point of the bacteria, i.e. at the zero point charge. The adhesion forces at pH 9 were higher than at pH 7 due to the increase in the attraction between Fe ions and negative carboxylate groups.

Measurement of polyamide and polystyrene adhesion with coated-tip atomic force microscopy

This work presents atomic force microscopy (AFM) measurements of adhesion forces between polyamides, polystyrene and AFM tips coated with the same materials. The polymers employed were polyamide 6 (PA6), PA66, PA12 and polystyrene (PS). All adhesion forces between the various unmodified or modified AFM tips and the polymer surfaces were in the range -1.5 to -8 nN. The weakest force was observed for an unmodified AFM tip with a PS surface and the strongest was between a PS-coated tip and PS surface. The results point to both the benefits and drawbacks of coated-tip AFM force-distance measurements. Adhesion forces between the two most dissimilar (PA6-PS and PA66-PS) materials were significantly asymmetric, e.g., the forces were different depending on the relative placement of each polymer on the AFM tip or substrate. Materials with similar chemistry and intermolecular interactions yielded forces in close agreement regardless of placement on tip or substrate. Using experimental forces, we calculated the contact radii via four models: Derjaguin, Muller, and Toporov; Johnson, Kendall, and Roberts; parametric tip-force-distance relation; and a square pyramid-flat surface (SPFS) model developed herein. The SPFS model gave the most reasonable contact tip radius estimate. Hamaker constants calculated from the SPFS model using this radius agreed in both magnitude and trends with experiment and Lifshitz theory.