Application of AFM in microbiology: a review

Biophysical, Molecular and Proteomic Profiling of Human Retinal Organoid-Derived Exosomes

PURPOSE

There is a growing interest in extracellular vesicles (EVs) for ocular applications as therapeutics, biomarkers, and drug delivery vehicles. EVs secreted from mesenchymal stem cells (MSCs) have shown to provide therapeutic benefits in ocular conditions. However, very little is known about the properties of bioreactor cultured-3D human retinal organoids secreted EVs. This study provides a comprehensive morphological, nanomechanical, molecular, and proteomic characterization of retinal organoid EVs and compares it with human umbilical cord (hUC) MSCs.

METHODS

The morphology and nanomechanical properties of retinal organoid EVs were assessed using Nanoparticle tracking analysis (NTA) and Atomic force microscopy (AFM). Gene expression analysis of exosome biogenesis of early and late retinal organoids were compared using qPCR. The protein profile of the EVs were analyzed with proteomic tools.

RESULTS

NTA indicated the average size of EV as 100-250 nm. A high expression of exosome biogenesis genes was observed in late retinal organoids EVs. Immunoblot analysis showed highly expressed exosomal markers in late retinal organoids EVs compared to early retinal organoids EVs. Protein profiling of retinal organoid EVs displayed a higher differential expression of retinal function-related proteins and EV biogenesis proteins than hUCMSC EVs, implicating that the use of retinal organoid EVs may have a superior therapeutic effect on retinal disorders.

CONCLUSION

This study provides supplementary knowledge on the properties of retinal organoid EVs and suggests their potential use in the diagnostic and therapeutic treatments for ocular diseases.

Novel combinatory method for surface and crystallinity analysis of crystalline materials

This work is dedicated to developing a method of combined surface morphology- and crystallographic analysis for crystalline silicon. To demonstrate the applicability of the method, a series of chemical operations, such as polishing and texturing, were applied to multi-crystalline silicon samples. The samples were pre- and post-analysed with WLI and Laue techniques, and the experimental data allowed construction of maps for crystal orientation to etching rate dependency. The study illustrates the strengths of the combinatory technique as an alternative to existing techniques such as atom force microscopy (AFM) and electron backscatter diffraction (EBSD).•Combination of LAUE tool and white light interferometry techniques.•Alternative time-effective method to EBSD.•Analysis of surface morphology and crystallographic properties for chemical processing.

Circulating Tumor Cells in Cancer Diagnostics and Prognostics by Single-Molecule and Single-Cell Characterization

Circulating tumor cells (CTCs) represent an interesting source of biomarkers for diagnosis, prognosis, and the prediction of cancer recurrence, yet while they are extensively studied in oncobiology research, their diagnostic utility has not yet been demonstrated and validated. Their scarcity in human biological fluids impedes the identification of dangerous CTC subpopulations that may promote metastatic dissemination. In this Perspective, we discuss promising techniques that could be used for the identification of these metastatic cells. We first describe methods for isolating patient-derived CTCs and then the use of 3D biomimetic matrixes in their amplification and analysis, followed by methods for further CTC analyses at the single-cell and single-molecule levels. Finally, we discuss how the elucidation of mechanical and morphological properties using techniques such as atomic force microscopy and molecular biomarker identification using nanopore-based detection could be combined in the future to provide patients and their healthcare providers with a more accurate diagnosis.

Oxidized Alginate Dopamine Conjugate: A Study to Gain Insight into Cell/Particle Interactions

Background: We had previously synthetized a macromolecular prodrug consisting of oxidized Alginate and dopamine (AlgOx-Da) for a potential application in Parkinson disease (PD). Methods: In the present work, we aimed at gaining an insight into the interactions occurring between AlgOx-Da and SH-SY5Y neuronal cell lines in view of further studies oriented towards PD treatment. With the scope of ascertaining changes in the external and internal structure of the cells, multiple methodologies were adopted. Firstly, fluorescently labeled AlgOx-Da conjugate was synthetized in the presence of fluorescein 5(6)-isothiocyanate (FITC), providing FITC-AlgOx-Da, which did not alter SH-SY5Y cell viability according to the sulforhodamine B test. Furthermore, the uptake of FITC-AlgOx-Da by the SH-SY5Y cells was studied using scanning near-field optical microscopy and assessments of cell morphology over time were carried out using atomic force microscopy. Results: Notably, the AFM methodology confirmed that no relevant damage occurred to the neuronal cells. Regarding the effects of DA on the intracellular reactive oxygen species (ROS) production, AlgOx-Da reduced them in comparison to free DA, while AlgOx did almost not influence ROS production. Conclusions: these findings seem promising for designing in vivo studies aiming at administering Oxidized Alginate Dopamine Conjugate for PD treatment.

Metal deposition and shape reproduction at biological temperatures on cell-level samples

The use of metal deposition has been limited to a limited number of applicable samples due to the increased temperature caused by accelerated electron impact on the substrate surface. The surfaces of various biological samples have a nanoscale structure with specific properties, which have been simulated in numerous studies. However, no examples of nano/microscale reproductions of biological surface features have used moulds. In this study, a mould that imitates the surface shape of a cellular-level biological material was fabricated, for the first time, and the shape was successfully reproduced using the mould. Al thin films were deposited on bovine sperm using magnetron sputtering without thermal denaturation with a cathode operating at a biological temperature. It is difficult to deposit films used as metal coatings on pre-treated biological materials at temperatures below 40 °C during evaporation. The Al thin film was peeled off and used as a mould to reproduce the shape of the sperm with high accuracy using a polymer. The results of this study represent a major innovation in reproducible biomimetic moulding technology, demonstrating biological temperature sputtering. We expect our non-destructive metal deposition and metal nano-moulding methods for biological samples to be the basis for the effective utilization of various biological structures.

Atomic Force Microscopy (AFM) on Biopolymers and Hydrogels for Biotechnological Applications-Possibilities and Limits

Atomic force microscopy (AFM) is one of the microscopic techniques with the highest lateral resolution. It can usually be applied in air or even in liquids, enabling the investigation of a broader range of samples than scanning electron microscopy (SEM), which is mostly performed in vacuum. Since it works by following the sample surface based on the force between the scanning tip and the sample, interactions have to be taken into account, making the AFM of irregular samples complicated, but on the other hand it allows measurements of more physical parameters than pure topography. This is especially important for biopolymers and hydrogels used in tissue engineering and other biotechnological applications, where elastic properties, surface charges and other parameters influence mammalian cell adhesion and growth as well as many other effects. This review gives an overview of AFM modes relevant for the investigations of biopolymers and hydrogels and shows several examples of recent applications, focusing on the polysaccharides chitosan, alginate, carrageenan and different hydrogels, but depicting also a broader spectrum of materials on which different AFM measurements are reported in the literature.

Atomic Force Microscopy for Tumor Research at Cell and Molecule Levels

Tumors have posed a serious threat to human life and health. Researchers can determine whether or not cells are cancerous, whether the cancer cells are invasive or metastatic, and what the effects of drugs are on cancer cells by the physical properties such as hardness, adhesion, and Young's modulus. The atomic force microscope (AFM) has emerged as a key important tool for biomechanics research on tumor cells due to its ability to image and collect force spectroscopy information of biological samples with nano-level spatial resolution and under near-physiological conditions. This article reviews the existing results of the study of cancer cells with AFM. The main foci are the operating principle of AFM and research advances in mechanical property measurement, ultra-microtopography, and molecular recognition of tumor cells, which allows us to outline what we do know it in a systematic way and to summarize and to discuss future directions.

Dual-Color Peak Force Infrared Microscopy

Peak force infrared (PFIR) microscopy achieves nanoscale infrared imaging at sub-10 nm spatial resolution through photothermal mechanical detection of atomic force microscopy (AFM). However, it suffers from a major limitation that only one infrared frequency can be scanned for an AFM frame at a time. To overcome this limitation, we report here dual-color PFIR microscopy that enables simultaneous imaging at two infrared frequencies. This dual-color PFIR microscopy bypasses the limitations of frame drift and distortion of AFM when comparing two images of different infrared frequencies. We benchmark the performance and spatial resolution of this method using structured polymers exhibiting phase separation. We further demonstrate the application of this technique in imaging biological samples by mapping the cell wall of Escherichia coli (E. coli) bacteria. The presence of a bacterial outer membrane was detected without extrinsic labels. This dual-color PFIR microscopy enables simultaneous nondestructive chemical nanoimaging of multiple chemical components and will be useful for potential applications such as in situ dual-channel monitoring of chemical reactions.

Comparison of nanostructure and nanomechanical properties of cast and air sides of polyimide films from different manufacturers

Polyimide films are widely applied in harsh environments because of their outstanding performance. High-quality polyimide films are often manufactured through a two-step process. The complicated procedure results in different properties on the two sides, i.e., the air side and cast side of the films, and the quality of products from different manufacturers varies notably. In the present work, polyimide films with two thicknesses (1 and 2 mm) from four manufacturers were investigated. Atomic force microscope and FT-IR spectrometer were employed to monitor morphology, roughness, nanomechanical properties, and corresponding relative imidization degree on the two sides of each film. Statistical tools were applied to analyze the data. T-test suggests that the two sides of the same film were significantly different in roughness, DMT modulus, and relative imidization degree (p < 0.05). The roughness on the air side was consistently smaller than that of the cast side. ANOVA was used to compare differences among the manufacturers. Manufacturer B provided the smoothest films with the highest DMT moduli and imidization degrees. A positive correlation was found between the DMT modulus and imidization degree (r = 0.7330). Nanostructure and nanomechanical properties could affect the quality of the film. Striped morphology and adhesion were found on the cast side of the 2-mm film from manufacturer D, which compromised the film tension in the direction perpendicular to the strips. Investigations of morphology and mechanical properties of polyimide film at the nanoscale would help us better characterize the film, assure its quality, and select suitable film and side for proper applications.

Atomic force microscopy as a biophysical tool for nanoscale forensic investigations

The atomic force microscope (AFM) has found its way to the arsenal of tools available to the forensic practitioner for the analysis of samples at the nano and microscales. As a non-destructive probing tool that requires minimal sample preparation, the AFM is very attractive, particularly in the case of minimal or precious sample. To date, the use of the AFM has primarily been in the arena of imaging where it has been complementary to other microscopic examination tools. Forensic applications in the visual examination of evidence such as blood stains, questioned documents, and hair samples have been reported. While a number of reviews have focused on the use of AFM as an imaging tool for forensic analyses, here we not only discuss these works, but also point to a versatile enhancement in the capabilities of this nanoscale tool - namely its use for force spectroscopy. In this mode, the AFM can determine elastic moduli, adhesion forces, energy dissipation, and the interaction forces between cognate ligands, that can be spatially mapped to provide a unique spatial visualization of properties. Our goals in this review are to provide a context for this capability of the AFM, explain its workings, cover some exemplary works pertaining to forensic sciences, and present a critical analysis on the advantages and disadvantages of this modality. Equipped with this high-resolution tool, imaging and biophysical analysis by the AFM can provide a unique complement to other tools available to the researcher for the analysis and characterization of forensic evidence.

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.

Near Simultaneous Laser Scanning Confocal and Atomic Force Microscopy (Conpokal) on Live Cells

Techniques available for micro- and nano-scale mechanical characterization have exploded in the last few decades. From further development of the scanning and transmission electron microscope, to the invention of atomic force microscopy, and advances in fluorescent imaging, there have been substantial gains in technologies that enable the study of small materials. Conpokal is a portmanteau that combines confocal microscopy with atomic force microscopy (AFM), where a probe "pokes" the surface. Although each technique is extremely effective for the qualitative and/or quantitative image collection on their own, Conpokal provides the capability to test with blended fluorescence imaging and mechanical characterization. Designed for near simultaneous confocal imaging and atomic force probing, Conpokal facilitates experimentation on live microbiological samples. The added insight from paired instrumentation provides co-localization of measured mechanical properties (e.g., elastic modulus, adhesion, surface roughness) by AFM with subcellular components or activity observable through confocal microscopy. This work provides a step by step protocol for the operation of laser scanning confocal and atomic force microscopy, simultaneously, to achieve same cell, same region, confocal imaging, and mechanical characterization.

Complementary SEM-AFM of Swelling Bi-Fe-O Film on HOPG Substrate

The objective of this work is to study the delamination of bismuth ferrite prepared by atomic layer deposition on highly oriented pyrolytic graphite (HOPG) substrate. The samples' structures and compositions are provided by XPS, secondary ion mass spectrometry (SIMS) and Raman spectroscopy. The resulting films demonstrate buckling and delamination from the substrates. The composition inside the resulting bubbles is in a gaseous state. It contains the reaction products captured on the surface during the deposition of the film. The topography of Bi-Fe-O thin films was studied in vacuum and under atmospheric conditions using simultaneous SEM and atomic force microscopy (AFM). Besides complementary advanced imaging, a correlative SEM-AFM analysis provides the possibility of testing the mechanical properties by using a variation of pressure. In this work, the possibility of studying the surface tension of the thin films using a joint SEM-AFM analysis is shown.

Biophysical analysis of lipidic nanoparticles

Biological nanoparticles include liposomes, extracellular vesicle and lipid-based discoidal systems. When studying such particles, there are several key parameters of interest, including particle size and concentration. Measuring these characteristics can be of particular importance in the research laboratory or when producing such particles as biotherapeutics. This article briefly describes the major types of lipid-containing nanoparticles and the techniques that can be used to study them. Such methodologies include electron microscopy, atomic force microscopy, dynamic light scattering, nanoparticle tracking analysis, flow cytometry, tunable resistive pulse sensing and microfluidic resistive pulse sensing. Whilst no technique is perfect for the analysis of all nanoparticles, this article provides advantages and disadvantages of each, highlighting the latest developments in the field. Finally, we demonstrate the use of microfluidic resistive pulse sensing for the analysis of biological nanoparticles.

Mapping the dielectric constant of a single bacterial cell at the nanoscale with scanning dielectric force volume microscopy

Mapping the dielectric constant at the nanoscale of samples showing a complex topography, such as non-planar nanocomposite materials or single cells, poses formidable challenges to existing nanoscale dielectric microscopy techniques. Here we overcome these limitations by introducing Scanning Dielectric Force Volume Microscopy. This scanning probe microscopy technique is based on the acquisition of electrostatic force approach curves at every point of a sample and its post-processing and quantification by using a computational model that incorporates the actual measured sample topography. The technique provides quantitative nanoscale images of the local dielectric constant of the sample with unparalleled accuracy, spatial resolution and statistical significance, irrespectively of the complexity of its topography. We illustrate the potential of the technique by presenting a nanoscale dielectric constant map of a single bacterial cell, including its small-scale appendages. The bacterial cell shows three characteristic equivalent dielectric constant values, namely, ε_r,bac1 = 2.6 ± 0.2, ε_r,bac2 = 3.6 ± 0.4 and ε_r,bac3 = 4.9 ± 0.5, which enable identifying different dielectric properties of the cell wall and of the cytoplasmatic region, as well as, the existence of variations in the dielectric constant along the bacterial cell wall itself. Scanning Dielectric Force Volume Microscopy is expected to have an important impact in Materials and Life Sciences where the mapping of the dielectric properties of samples showing complex nanoscale topographies is often needed.

OBSERVER-BASED CONTROL OF A DUAL-STAGE PIEZOELECTRIC SCANNER

Despite its proven success in a wide variety of applications, the atomic force microscope (AFM) remains limited by its slow imaging rate. One approach to overcome this challenge is to rely on algorithmic approaches that reduce the imaging time not by scanning faster but by scanning less. Such schemes are particularly useful on older instruments as they can provide significant gains despite the existing (slow) hardware. At the same time, algorithms for sub-sampling can yield even greater improvements in imaging rate when combined with advanced scanners that can be retrofitted into the system. In this work, we focus on the use of a dual-stage piezoelectric scanner coupled with a particular scanning algorithm known as Local Circular Scan (LCS). LCS drives the tip of the AFM along a circular trajectory while using feedback to center that circle on a sample edge and to move the circle along the feature, thus reducing imaging time by concentrating the samples to the region of interest. Dual-stage systems are well-suited to LCS as the algorithm is naturally described in terms of a high-frequency, short range path (the scanning circle) and a slower, long range path (the track along the sample). However, control of the scanner is not straightforward as the system is multi-input, single-output. Here we establish controllability and observability of the scanning stage, allowing us to develop individual controllers for the long-range and short-range actuators through the principle of separation. We then use an internal model controller for the short range actuator to track a sinusoidal input (to generate the circular motion) and a state-space set-point tracking controller for the long range actuator. The results are demonstrated through simulation.

Customizable 3D printed diffusion chambers for studies of bacterial pathogen phenotypes in complex environments

Gaps in our understanding of the natural ecology and survival mechanisms of pathogenic bacteria in complex microenvironments such as soil typically occur due to the difficulty in characterizing biochemical profiles and morphological characteristics as they exist in environmental samples. Conversely, accurate simulation of the abiotic and biotic chemistries of soil habitats within the laboratory is often a significant challenge. Herein, we present the fabrication of customizable and precisely engineered 3D printed diffusion chambers that can be used to incubate bacterial cultures directly in soil matrices within a controlled laboratory experiment, and study the dynamics between bacterial cells and soil components. As part of the design process, different types of 3D printing materials were evaluated for ease of sterilization, structural integrity throughout the experiment, as well as cost/ease of production. To demonstrate potential applications for environmental studies, the diffusion chamber was used to incubate cultures of Bacillus cereus T-strain and Escherichia coli strain O157 directly in soil matrices. We show that the chamber facilitates diffusion of abiotic/biotic components of the soil with target cells without contamination from in situ microbial communities, while allowing for single cell and ensemble level phenotypic analyses of bacteria cultured with and without soil matrices.

Evaluation of resonance phenomena of mechanical oscillator by self-mixing solid-state laser Doppler vibrometry

We performed self-mixing laser Doppler vibrometry on a vibrating oscillator consisting of a rigid-body laser-light-scattering object attached to a piezoelectric element driven by low-frequency AC voltage to evaluate its motion. The sideband spectrum reflecting the motion of the oscillator is observed in the power spectrum of the modulated wave. The time dependence of the intensity of the sideband spectrum is explained by Newton's second law assuming that the oscillator has a mechanical resonance frequency and undergoes simple vibration under the driving force, which depends on the deformation velocity of the piezoelectric element. Our results indicate that the motion of a slowly moving target with sub-nanometer displacement, which is difficult to measure by general laser Doppler vibrometry, can be evaluated with high spatial and frequency resolutions by detecting the sideband signal, which changes periodically at the driving frequency of the piezoelectric element.

Identification of Genes Involved in Biogenesis of Outer Membrane Vesicles (OMVs) in Salmonella enterica Serovar Typhi

Outer membrane vesicles (OMVs) are nano-sized proteoliposomes discharged from the cell envelope of Gram-negative bacteria. OMVs normally contain toxins, enzymes and other factors, and are used as vehicles in a process that has been considered a generalized, evolutionarily conserved delivery system among bacteria. Furthermore, OMVs can be used in biotechnological applications that require delivery of biomolecules, such as vaccines, remarking the importance of their study. Although it is known that Salmonella enterica serovar Typhi (S. Typhi), the etiological agent of typhoid fever in humans, delivers toxins (e.g., HlyE) via OMVs, there are no reports identifying genetic determinants of the OMV biogenesis in this serovar. In the present work, and with the aim to identify genes participating in OMV biogenesis in S. Typhi, we screened 15,000 random insertion mutants for increased HlyE secretion. We found 9 S. Typhi genes (generically called zzz genes) determining an increased HlyE secretion that were also involved in OMV biogenesis. The genes corresponded to ompA, nlpI, and tolR (envelope stability), rfaE and waaC (LPS synthesis), yipP (envC), mrcB (synthesis and remodeling of peptidoglycan), degS (stress sensor serine endopeptidase) and hns (global transcriptional regulator). We found that S. Typhi Δzzz mutants were prone to secrete periplasmic, functional proteins with a relatively good envelope integrity. In addition, we showed that zzz genes participate in OMV biogenesis, modulating different properties such as OMV size distribution, OMV yield and OMV protein cargo.

Raman, AFM and SNOM high resolution imaging of carotene crystals in a model carrot cell system

Three non-destructive and complementary techniques, Raman imaging, Atomic Force Microscopy and Scanning Near-field Optical Microscopy were used simultaneously to show for the first time chemical and structural differences of carotenoid crystals. Spectroscopic and microscopic scanning probe measurements were applied to the released crystals or to crystals accumulated in a unique, carotenoids rich callus tissue growing in vitro that is considered as a new model system for plant carotenoid research. Three distinct morphological crystal types of various carotenoid composition were identified, a needle-like, rhomboidal and helical. Raman imaging using 532 and 488 nm excitation lines provided evidence that the needle-like and rhomboidal crystals had similar carotenoid composition and that they were composed mainly of β-carotene accompanied by α-carotene. However, the presence of α-carotene was not identified in the helical crystals, which had the characteristic spatial structure. AFM measurements of crystals identified by Raman imaging revealed the crystal topography and showed the needle-like and rhomboidal crystals were planar but they differed in all three dimensions. Combining SNOM and Raman imaging enabled indication of carotenoid rich structures and visualised their distribution in the cell. The morphology of identified subcellular structures was characteristic for crystalline, membraneous and tubular chromoplasts that are plant organelles responsible for carotenoid accumulation in cells.

Ascent of atomic force microscopy as a nanoanalytical tool for exosomes and other extracellular vesicles

Over the last 30 years, atomic force microscopy (AFM) has made several significant contributions to the field of biology and medicine. In this review, we draw our attention to the recent applications and promise of AFM as a high-resolution imaging and force sensing technology for probing subcellular vesicles: exosomes and other extracellular vesicles. Exosomes are naturally occurring nanoparticles found in several body fluids such as blood, saliva, cerebrospinal fluid, amniotic fluid and urine. Exosomes mediate cell-cell communication, transport proteins and genetic content between distant cells, and are now known to play important roles in progression of diseases such as cancers, neurodegenerative disorders and infectious diseases. Because exosomes are smaller than 100 nm (about 30-120 nm), the structural and molecular characterization of these vesicles at the individual level has been challenging. AFM has revealed a new degree of complexity in these nanosized vesicles and generated growing interest as a nanoscale tool for characterizing the abundance, morphology, biomechanics, and biomolecular make-up of exosomes. With the recent interest in exosomes for diagnostic and therapeutic applications, AFM-based characterization promises to contribute towards improved understanding of these particles at the single vesicle and sub-vesicular levels. When coupled with complementary methods like optical super resolution STED and Raman, AFM could further unlock the potential of exosomes as disease biomarkers and as therapeutic agents.

Biophysical properties of cardiomyocyte surface explored by multiparametric AFM

PeakForce Quantitative Nanomechanical Mapping (PeakForce QNM) multiparametric AFM mode was adapted to qualitative and quantitative study of the lateral membrane of cardiomyocytes (CMs), extending this powerful mode to the study of soft cells. On living CM, PeakForce QNM depicted the crests and hollows periodic alternation of cell surface architecture previously described using AFM Force Volume (FV) mode. PeakForce QNM analysis provided better resolution in terms of pixel number compared to FV mode and reduced acquisition time, thus limiting the consequences of spontaneous living adult CM dedifferentiation once isolated from the cardiac tissue. PeakForce QNM mode on fixed CMs clearly visualized subsarcolemmal mitochondria (SSM) and their loss following formamide treatment, concomitant with the interfibrillar mitochondria climbing up and forming heaps at the cell surface. Interestingly, formamide-promoted SSM loss allowed visualization of the sarcomeric apparatus ultrastructure below the plasma membrane. High PeakForce QNM resolution led to better contrasted mechanical maps than FV mode and provided correlation between adhesion, dissipation, mechanical and topographical maps. Modified hydrophobic AFM tip enhanced contrast on adhesion and dissipation maps and suggested that CM surface crests and hollows exhibit distinct chemical properties. Finally, two-dimensional Fast Fourier Transform to objectively quantify AFM maps allowed characterization of periodicity of both sarcomeric Z-line and M-band. Overall, this study validated PeakForce QNM as a valuable and innovative mode for the exploration of living and fixed CMs. In the future, it could be applied to depict cell membrane architectural, mechanical and chemical defects as well as sarcomeric abnormalities associated with cardiac diseases.

Real-time single molecular study of a pretreated cellulose hydrolysis mode and individual enzyme movement

BACKGROUND

The main challenges of large-scale biochemical conversion involve the high costs of cellulolytic enzymes and the inefficiency in enzymatic deconstruction of polysaccharides embedded in the complex structure of the plant cell wall, leading to ongoing interests in studying the predominant mode of enzymatic hydrolysis. In this study, complete enzymatic hydrolysis of pretreated biomass substrates was visualized in situ and in real time by atomic force microscopy (AFM) topography and recognition imaging. Throughout the entire hydrolytic process, a hydrolysis mode for exoglucanase (CBH I) consisting of a peeling action, wherein cellulose microfibrils are peeled from sites on the pretreated cellulose substrate that have cracks sufficiently large for CBH I to immobilize.

RESULTS

We quantitatively monitored the complete hydrolytic process on pretreated cellulose. The synergetic effect among the different enzymes can accelerate the cellulose hydrolysis rate dramatically. However, the combination of CBH I and β-glucosidases (β-G) exhibited a similar degradation capacity as did whole enzyme (contains the cellobiohydrolases and endoglucanase as its major enzyme components). We developed a comprehensive dynamic analysis for individual cellulase acting on single pretreated cellulose through use of functional AFM topography and recognition imaging. The single crystalline cellulose was divided into different regions based on the cracks on the substrate surface and was observed to either depolymerize or to peel away by the jammed enzyme molecules. After the exfoliation of one region, new cracks were produced for the enzyme molecules to immobilize. The fiber width may have a relationship with the peeling mode of the fibers. We performed a statistical height measure of the generated peaks of the peeled fibers. The height values range from 11 to 24 nm. We assume that the CBH I enzymes stop progressing along the cellulose microfibril when the peeled microfibril height exceeds 11 nm.

CONCLUSION

The combination of CBH I and β-G can achieve an effective hydrolysis of the pretreated biomass substrates. The single-molecule study of the complete hydrolytic process indicates that the hydrolytic mode involves the peeling of the microfibrils and progressive depolymerization, which depend on the size of the cracks on the surface of the pretreated cellulose microfibrils.

In vitro biophysical, microspectroscopic and cytotoxic evaluation of metastatic and non-metastatic cancer cells in responses to anti-cancer drug

The Breast Cancer Metastasis Suppressor 1 (BRMS1) is a nucleo-cytoplasmic protein that suppresses cancer metastasis without affecting the growth of the primary tumor. Previous work has shown that it decreases the expression of protein mediators involved in chemoresistance. This study measured the biomechanical and biochemical changes in BRMS1 expression and the responses of BRMS1 to drug treatments on cancer cells in vitro. The results show that BRMS1 expression affects biomechanical properties by decreasing the Young's modulus and adhesion force of breast cancer cells after doxorubicin (DOX) exposure. Raman spectral bands corresponding to DNA/RNA, lipids and proteins were similar for all cells after DOX treatment. The expression of cytokines were similar for cancer cells after DOX exposure, although BRMS1 expression had different effects on the secretion of cytokines for breast cancer cells. The absence of significant changes on apoptosis, reactive oxygen species (ROS) expression and cell viability after BRMS1 expression shows that BRMS1 has little effect on cellular chemoresistance. Analyzing cancer protein expression is critical in evaluating therapeutics. Our study may provide evidence of the benefit of metastatic suppressor expression before chemotherapy.

A comparison of reconstruction methods for undersampled atomic force microscopy images

Non-raster scanning and undersampling of atomic force microscopy (AFM) images is a technique for improving imaging rate and reducing the amount of tip-sample interaction needed to produce an image. Generation of the final image can be done using a variety of image processing techniques based on interpolation or optimization. The choice of reconstruction method has a large impact on the quality of the recovered image and the proper choice depends on the sample under study. In this work we compare interpolation through the use of inpainting algorithms with reconstruction based on optimization through the use of the basis pursuit algorithm commonly used for signal recovery in compressive sensing. Using four different sampling patterns found in non-raster AFM, namely row subsampling, spiral scanning, Lissajous scanning, and random scanning, we subsample data from existing images and compare reconstruction performance against the original image. The results illustrate that inpainting generally produces superior results when the image contains primarily low frequency content while basis pursuit is better when the images have mixed, but sparse, frequency content. Using support vector machines, we then classify images based on their frequency content and sparsity and, from this classification, develop a fast decision strategy to select a reconstruction algorithm to be used on subsampled data. The performance of the classification and decision test are demonstrated on test AFM images.

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.

Analysis of cell surface alterations in Legionella pneumophila cells treated with human apolipoprotein E

Binding of human apolipoprotein E (apoE) to Legionella pneumophila lipopolysaccharide was analysed at the molecular level by Fourier-transform infrared spectroscopy, thereby providing biophysical evidence for apoE-L. pneumophila lipopolysaccharide interaction. Atomic force microscopy imaging of apoE-exposed L. pneumophila cells revealed alterations in the bacterial cell surface topography and nanomechanical properties in comparison with control bacteria. The changes induced by apoE binding to lipopolysaccharide on the surface of L. pneumophila cells may participate in: (1) impeding the penetration of host cells by the bacteria; (2) suppression of pathogen intracellular growth and eventually; and (3) inhibition of the development of infection.

Single-bacterium nanomechanics in biomedicine: unravelling the dynamics of bacterial cells

The use of the atomic force microscope (AFM) in microbiology has progressed significantly throughout the years since its first application as a high-resolution imaging instrument. Modern AFM setups are capable of characterizing the nanomechanical behaviour of bacterial cells at both the cellular and molecular levels, where elastic properties and adhesion forces of single bacterium cells can be examined under different experimental conditions. Considering that bacterial and biofilm-mediated infections continue to challenge the biomedical field, it is important to understand the biophysical events leading towards bacterial adhesion and colonization on both biological and non-biological substrates. The purpose of this review is to present the latest findings concerning the field of single-bacterium nanomechanics, and discuss future trends and applications of nanoindentation and single-cell force spectroscopy techniques in biomedicine.

Integrated compositional and nanomechanical analysis of a polyurethane surface modified with a fluorous oxetane siliceous-network hybrid

Investigating the surface characteristics of heterogeneous polymer systems is important for understanding how to better tailor surfaces and engineering specific reactions and desirable properties. Here we report on the surface properties for a blend consisting of a major component, a linear polyurethane or thermoplastic elastomer (TPU), and a minor component that is a hybrid network. The hybrid network consists of a fluorous polyoxetane soft block and a hydrolysis/condensation inorganic (HyCoin) network. Phase separation during coating formation results in surface concentration of the minor fluorous hybrid domain. The TPU is H12MDI/BD(50)-PTMO-1000 derived from bis(cyclohexylmethylene)-diisocyanate and butane diol (50 wt %) and poly(tetramethylene oxide). Surface modification results from a novel network-forming hybrid composed of poly(trifluoroethoxymethyl-methyl oxetane) diol) (3F) as the fluorous moiety end-capped with 3-isocyanatopropylriethoxysilane and bis(triethoxysilyl)ethane (BTESE) as a siliceous stabilizer. We use an integrated approach that combines elemental analysis of the near surface via X-ray photoelectron microscopy with surface mapping using atomic force microscopy that presents topographical and phase imaging along with nanomechanical properties. Overall, this versatile, high-resolution approach enabled unique insight into surface composition and morphology that led to a model of heterogeneous surfaces containing a range of constituents and properties.

Atomic Force Microscopy and pharmacology: from microbiology to cancerology

BACKGROUND

Atomic Force Microscopy (AFM) has been extensively used to study biological samples. Researchers take advantage of its ability to image living samples to increase our fundamental knowledge (biophysical properties/biochemical behavior) on living cell surface properties, at the nano-scale.

SCOPE OF REVIEW

AFM, in the imaging modes, can probe cells morphological modifications induced by drugs. In the force spectroscopy mode, it is possible to follow the nanomechanical properties of a cell and to probe the mechanical modifications induced by drugs. AFM can be used to map single molecule distribution at the cell surface. We will focus on a collection of results aiming at evaluating the nano-scale effects of drugs, by AFM. Studies on yeast, bacteria and mammal cells will illustrate our discussion. Especially, we will show how AFM can help in getting a better understanding of drug mechanism of action.

MAJOR CONCLUSIONS

This review demonstrates that AFM is a versatile tool, useful in pharmacology. In microbiology, it has been used to study the drugs fighting Candida albicans or Pseudomonas aeruginosa. The major conclusions are a better understanding of the microbes' cell wall and of the drugs mechanism of action. In cancerology, AFM has been used to explore the effects of cytotoxic drugs or as an innovative diagnostic technology. AFM has provided original results on cultured cells, cells extracted from patient and directly on patient biopsies.

GENERAL SIGNIFICANCE

This review enhances the interest of AFM technologies for pharmacology. The applications reviewed range from microbiology to cancerology.

Atomic force microscopy recognition of protein A on Staphylococcus aureus cell surfaces by labelling with IgG-Au conjugates

The labelling of functional molecules on the surface of bacterial cells is one way to recognize the bacteria. In this work, we have developed a method for the selective labelling of protein A on the cell surfaces of Staphylococcus aureus by using nanosized immunogold conjugates as cell-surface markers for atomic force microscopy (AFM). The use of 30-nm size Au nanoparticles conjugated with immunoglobulin G (IgG) allowed the visualization, localization and distribution of protein A-IgG complexes on the surface of S. aureus. The selectivity of the labelling method was confirmed in mixtures of S. aureus with Bacillus licheniformis cells, which differed by size and shape and had no IgG receptors on the surface. A preferential binding of the IgG-Au conjugates to S. aureus was obtained. Thus, this novel approach allows the identification of protein A and other IgG receptor-bearing bacteria, which is useful for AFM indication of pathogenic microorganisms in poly-component associations.

Imaging living cells surface and quantifying its properties at high resolution using AFM in QI™ mode

Since the last 10 years, AFM has become a powerful tool to study biological samples. However, the classical modes offered (imaging or tapping mode) often damage sample that are too soft or loosely immobilized. If imaging and mechanical properties are required, it requests long recording time as two different experiments must be conducted independently. In this study we compare the new QI™ mode against contact imaging mode and force volume mode, and we point out its benefit in the new challenges in biology on six different models: Escherichia coli, Candida albicans, Aspergillus fumigatus, Chinese hamster ovary cells and their isolated nuclei, and human colorectal tumor cells.

Visualization of Gram-positive bacterial pili

Pili or fimbriae are recognized as essential virulence determinants assembled on the bacterial surface. Gram-positive bacteria produce covalently linked pilus structures that are distinct from gram-negative counterparts. In this chapter, we describe three commonly used techniques to extract, detect, and visualize pili from gram-positive bacteria: (1) Western blot analysis, (2) Immuno-Electron Microscopy, and (3) Atomic Force Microscopy.

Surface topographical factors influencing bacterial attachment

Substratum surface roughness is known to be one of the key factors in determining the extent of bacterial colonization. Understanding the way by which the substratum topography, especially at the nanoscale, mediates bacterial attachment remains ambiguous at best, despite the volume of work available on the topic. This is because the vast majority of bacterial attachment studies do not perform comprehensive topographical characterization analyses, and typically consider roughness parameters that describe only one aspect of the surface topography. The most commonly reported surface roughness parameters are average and root mean square (RMS) roughness (R(a) and R(q) respectively), which are both measures of the typical height variation of the surface. They offer no insights into the spatial distribution or shape of the surface features. Here, a brief overview of the current state of research on topography-mediated bacterial adhesion is presented, as well as an outline of the suite of roughness characterization parameters that are available for the comprehensive description of the surface architecture of a substratum. Finally, a set of topographical parameters is proposed as a new standard for surface roughness characterization in bacterial adhesion studies to improve the likelihood of identifying direct relationships between substratum topography and the extent of bacterial adhesion.

Nanoscale analysis of the effects of antibiotics and CX1 on a Pseudomonas aeruginosa multidrug-resistant strain

Drug resistance is a challenge that can be addressed using nanotechnology. We focused on the resistance of the bacteria Pseudomonas aeruginosa and investigated, using Atomic Force Microscopy (AFM), the behavior of a reference strain and of a multidrug resistant clinical strain, submitted to two antibiotics and to an innovative antibacterial drug (CX1). We measured the morphology, surface roughness and elasticity of the bacteria under physiological conditions and exposed to the antibacterial molecules. To go further in the molecules action mechanism, we explored the bacterial cell wall nanoscale organization using functionalized AFM tips. We have demonstrated that affected cells have a molecularly disorganized cell wall; surprisingly long molecules being pulled off from the cell wall by a lectin probe. Finally, we have elucidated the mechanism of action of CX1: it destroys the outer membrane of the bacteria as demonstrated by the results on artificial phospholipidic membranes and on the resistant strain.

Investigating fibrillar aggregates of Tau protein by atomic force microscopy

Atomic force microscopy (AFM) has been used in numerous studies to visualize and analyze the structure and conformation of biological samples, from single molecules to biopolymers to cells. The possibility to analyze native samples without fixation, staining and in physiological buffer conditions, combined with the sub-nanometer resolution, makes AFM a versatile tool for the analysis of protein aggregation and amyloid structures. Here, we describe the application of AFM to study fibrillar Tau protein aggregates.

Morphology and mechanics of chondroid cells from human adipose-derived Stem cells detected by atomic force microscopy

Chondroid cell from human adipose-derived stem cells (ADSCs) has emerged as an alternative treatment option for articular cartilage defects. Herein, we successfully compared ADSCs, normal chondrocytes, and chondroid cells. The comparative study of ADSCs and chondroid cells revealed type II collagen (COL II) and glycosaminoglycans expression of chondroid cells were similar to those in normal chondrocytes, and much higher than ADSCs. Using atomic force microscope (AFM) and laser confocal scanning microscopy (LCSM), we compared the differences in morphology, mechanical properties, and F-actin distribution between chondroid cells and normal chondrocytes. Our results showed no differences observed between these two types of cells regarding morphology, stiffness, and F-actin distribution. However, found that the adhesion force in chondroid cells was lower than that in normal chondrocytes. Taken together, our AFM and LCSM analyses suggest that the lower adhesion force in chondroid cells may contribute to the dedifferentiation of ADSC-derived chondroid cells. Future examination of surface adhesion force-related protein expression will likely provide new insight into the molecular mechanisms underlying the dedifferentiation of ADSC-derived chondroid cells.

Assembly of live micro-organisms on microstructured PDMS stamps by convective/capillary deposition for AFM bio-experiments

Immobilization of live micro-organisms on solid substrates is an important prerequisite for atomic force microscopy (AFM) bio-experiments. The method employed must immobilize the cells firmly enough to enable them to withstand the lateral friction forces exerted by the tip during scanning but without denaturing the cell interface. In this work, a generic method for the assembly of living cells on specific areas of substrates is proposed. It consists in assembling the living cells within the patterns of microstructured, functionalized poly-dimethylsiloxane (PDMS) stamps using convective/capillary deposition. This versatile approach is validated by applying it to two systems of foremost importance in biotechnology and medicine: Saccharomyces cerevisiae yeasts and Aspergillus fumigatus fungal spores. We show that this method allows multiplexing AFM nanomechanical measurements by force spectroscopy on S. cerevisiae yeasts and high-resolution AFM imaging of germinated Aspergillus conidia in buffer medium. These two examples clearly demonstrate the immense potential of micro-organism assembly on functionalized, microstructured PDMS stamps by convective/capillary deposition for performing rigorous AFM bio-experiments on living cells.