Atomic Force Microscopy: An Introduction

Chlamydia psittaci infected cell studies by 4Pi Raman and atomic force microscopy

Chlamydia psittaci is an avian bacterial pathogen that can cause atypical pneumonia in humans via zoonotic transmission. It is a Gram-negative intracellular bacterium that proliferates inside membrane bound inclusions in the cytoplasm of living eukaryotic cells. The study of such cells with C. psittaci inside without destroying them poses a significant challenge. We demonstrated in this work the utility of a combined multitool approach to analyze such complex samples. Atomic force microscopy was applied to obtain high-resolution images of the surface of infected cells upon entrance of bacteria. Atomic force microscopy scans revealed the morphological changes of the cell membrane of Chlamydia infected cells such as changes in roughness of cell membrane and the presence of micro vesicles. 4Pi Raman microscopy was used to image and probe the molecular composition of intracellular bacteria inside intact cells. Information about the structure of the inclusion produced by C. psittaci was obtained and it was found to have a similar molecular fingerprint as that of an intracellular lipid droplet but with less proteins and unsaturated lipids. The presented approach demonstrates complementarity of various microscopy-based approaches and might be useful for characterization of intracellular bacteria.

Atypical cofilin signaling drives dendritic cell migration through the extracellular matrix via nuclear deformation

To mount an adaptive immune response, dendritic cells must migrate to lymph nodes to present antigens to T cells. Critical to 3D migration is the nucleus, which is the size-limiting barrier for migration through the extracellular matrix. Here, we show that inflammatory activation of dendritic cells leads to the nucleus becoming spherically deformed and enables dendritic cells to overcome the typical 2- to 3-μm diameter limit for 3D migration through gaps in the extracellular matrix. We show that the nuclear shape change is partially attained through reduced cell adhesion, whereas improved 3D migration is achieved through reprogramming of the actin cytoskeleton. Specifically, our data point to a model whereby the phosphorylation of cofilin-1 at serine 41 drives the assembly of a cofilin-actomyosin ring proximal to the nucleus and enhances migration through 3D collagen gels. In summary, these data describe signaling events through which dendritic cells deform their nucleus and enhance their migratory capacity.

Quartz crystal microbalance and atomic force microscopy to characterize mimetic systems based on supported lipids bilayer

Quartz Crystal Microbalance (QCM) with dissipation and Atomic Force Microscopy (AFM) are two characterization techniques that allow describing processes taking place at solid-liquid interfaces. Both are label-free and, when used in combination, provide kinetic, thermodynamic and structural information at the nanometer scale of events taking place at surfaces. Here we describe the basic operation principles of both techniques, addressing a non-specialized audience, and provide some examples of their use for describing biological events taking place at supported lipid bilayers (SLBs). The aim is to illustrate current strengths and limitations of the techniques and to show their potential as biophysical characterization techniques.

Study of Amyloid Fibers Using Atomic Force Microscopy

Atomic force microscopy (AFM) provides high-resolution images of the topography of amyloid fibers adsorbed on surfaces. This information is very useful to study their molecular assembly under various conditions. This chapter describes the basic protocols required to deposit fibers on flat surfaces and discusses some of the practical issues required to operate a good commercial microscope setup to obtain appropriate high-resolution AFM topographic images of amyloid fibers.

Effect of different polishing systems on the surface roughness of various bulk-fill and nano-filled resin-based composites: An atomic force microscopy and scanning electron microscopy study

The aim of the study was to evaluate the effects of different polishing systems on the surface roughness of various bulk-fill and nano-filled resin-based composites using different methods. For the study, a total of 192 disc-shaped samples (10-mm wide and 2-mm thick) were prepared from four different bulk-fill composites (Filtek Bulk Fill, X-tra fil, Beautifil-Bulk Restorative and Fill Up) and two nano-filled resin-based composites (Ceram.x SphereTEC and Filtek Z550). The samples in each composite group were divided into four subgroups according to the polishing system to be used (n = 8). Four different polishing systems (Sof-Lex Diamond, Clearfil Twist Dia, HiLuster Plus, OptiDisc) were applied. Then, surface roughness measurements were carried out using a contact-type profilometer. One sample from each group was subjected to atomic force microscopy (AFM) and scanning electron microscope (SEM) examinations. Surface roughness (Ra) values were statistically analyzed in terms of composites and polishing systems using the two-way analysis of variance (ANOVA) and comparisons among groups were performed using the Tukey test (α = .05). Surface roughness values differed significantly in relation to the composite and polishing system used (p < .05). Among all composites, the lowest surface roughness values were obtained in the groups treated with the OptiDisc polishing system (except Beautifil-Bulk Restorative), whereas the highest roughness values were observed in the group polished with Clearfil Twist Dia (except Filtek Z550). X-tra fil showed the highest roughness value with all polishing systems tested. The findings of AFM analyses were consistent with profilometric measurements. The nano-filled resin-based composites showed smoother surface than bulk-fill composites and the type of the polishing systems was found to affect surface roughness.

Physics of viral dynamics

Viral capsids are often regarded as inert structural units, but in actuality they display fascinating dynamics during different stages of their life cycle. With the advent of single-particle approaches and high-resolution techniques, it is now possible to scrutinize viral dynamics during and after their assembly and during the subsequent development pathway into infectious viruses. In this Review, the focus is on the dynamical properties of viruses, the different physical virology techniques that are being used to study them, and the physical concepts that have been developed to describe viral dynamics.

The effect of various asthma medications on surface roughness of pediatric dental restorative materials: An atomic force microscopy and scanning electron microscopy study

The aim of the study is to examine and compare the effects of various inhaled asthma medications (IAMs) on the surface roughness of dental restorative materials (DRMs). In total, 192 samples were prepared including 32 samples for the each material group from six different DRMs [Nanohybrid composite (Filtek Z550), Nanofilled flowable composite (Filtek Ultimate), Compomer (Dyract XP), Conventional glass ionomer (Fuji IX Fast), Resin-modified glass ionomer (Fuji II LC), Self-adhering flowable composite (Fusio Liquid Dentin)]. Each group, were divided into four subgroups (n = 8) according to four different IAMs. Surface roughness values (Ra) were obtained by atomic force microscopy (AFM). After the initial roughness of DRMs was analyzed by using AFM and scanning electron microscopy (SEM), each samples were exposed to the same IAMs for 21 days and all analysis were repeated on the 7th and 21st day. Ras increased in all DRMs and higher Ras were recorded through the long-term IAMs administrations. For all IAMs, Fuji II LC had the highest Ra and Filtek Z550 had the lowest Ra. The combined IAM created the highest roughness change on the 7th and 21st day compared to other IAMs. As a result, in in vitro conditions IAMs significantly increased the surface roughness of DRMs.

Mechanical Characterization of Liposomes and Extracellular Vesicles, a Protocol

Both natural as well as artificial vesicles are of tremendous interest in biology and nanomedicine. Small vesicles (<200 nm) perform essential functions in cell biology and artificial vesicles (liposomes) are used as drug delivery vehicles. Atomic Force Microscopy (AFM) is a powerful technique to study the structural properties of these vesicles. AFM is a well-established technique for imaging at nanometer resolution and for mechanical measurements under physiological conditions. Here, we describe the procedure of AFM imaging and force spectroscopy on small vesicles. We discuss how to image vesicles with minimal structural disturbance, and how to analyze the data for accurate size and shape measurements. In addition, we describe the procedure for performing nanoindentations on vesicles and the subsequent data analysis including mechanical models used for data interpretation.

De novo rational design of a freestanding, supercharged polypeptide, proton-conducting membrane

Proton translocation enables important processes in nature and man-made technologies. However, controlling proton conduction and fabrication of devices exploiting biomaterials remains a challenge. Even more difficult is the design of protein-based bulk materials without any functional starting scaffold for further optimization. Here, we show the rational design of proton-conducting, protein materials exceeding reported proteinaceous systems. The carboxylic acid-rich structures were evolved step by step by exploring various sequences from intrinsically disordered coils over supercharged nanobarrels to hierarchically spider β sheet containing protein-supercharged polypeptide chimeras. The latter material is characterized by interconnected β sheet nanodomains decorated on their surface by carboxylic acid groups, forming self-supportive membranes and allowing for proton conduction in the hydrated state. The membranes showed an extraordinary proton conductivity of 18.5 ± 5 mS/cm at RH = 90%, one magnitude higher than other protein devices. This design paradigm offers great potential for bioprotonic device fabrication interfacing artificial and biological systems.

Cancer-ID: Toward Identification of Cancer by Tumor-Derived Extracellular Vesicles in Blood

Extracellular vesicles (EVs) have great potential as biomarkers since their composition and concentration in biofluids are disease state dependent and their cargo can contain disease-related information. Large tumor-derived EVs (tdEVs, >1 μm) in blood from cancer patients are associated with poor outcome, and changes in their number can be used to monitor therapy effectiveness. Whereas, small tumor-derived EVs (<1 μm) are likely to outnumber their larger counterparts, thereby offering better statistical significance, identification and quantification of small tdEVs are more challenging. In the blood of cancer patients, a subpopulation of EVs originate from tumor cells, but these EVs are outnumbered by non-EV particles and EVs from other origin. In the Dutch NWO Perspectief Cancer-ID program, we developed and evaluated detection and characterization techniques to distinguish EVs from non-EV particles and other EVs. Despite low signal amplitudes, we identified characteristics of these small tdEVs that may enable the enumeration of small tdEVs and extract relevant information. The insights obtained from Cancer-ID can help to explore the full potential of tdEVs in the clinic.

Advances in extracellular vesicles analysis

Extracellular vesicles (EVs) play an important role in intercellular communication in normal cellular process and pathological conditions by facilitating the transport of cellular content from one cell to another. EVs as conveyors of various biological molecules with their ability to redirect effects on a target cell physiological function in cell type-specific manner makes EVs an excellent candidate for drug delivery vehicle in disease therapy. Moreover, unique characteristics and contents of EVs which differ depends on cellular origin and physiological state make them a valuable source of diagnostic biomarker. Herein, we review the current progress in extracellular vesicle (EV) analysis, its transition from biomedical research to advancing therapy, and recent pioneered approaches to characterize and quantify EVs' subclasses with an emphasis on the integration of advanced technologies for both qualitative and quantitative analysis of EVs in different clinical tissue/body fluid samples.

Active probing of the mechanical properties of biological and synthetic vesicles

BACKGROUND

The interest in mechanics of synthetic and biological vesicles has been continuously growing during the last decades. Liposomes serve as model systems for investigating fundamental membrane processes and properties. More recently, extracellular vesicles (EVs) have been investigated mechanically as well. EVs are widely studied in fundamental and applied sciences, but their material properties remained elusive until recently. Elucidating the mechanical properties of vesicles is essential to unveil the mechanisms behind a variety of biological processes, e.g. budding, vesiculation and cellular uptake mechanisms.

SCOPE OF REVIEW

The importance of mechanobiology for studies of vesicles and membranes is discussed, as well as the different available techniques to probe their mechanical properties. In particular, the mechanics of vesicles and membranes as obtained by nanoindentation, micropipette aspiration, optical tweezers, electrodeformation and electroporation experiments is addressed.

MAJOR CONCLUSIONS

EVs and liposomes possess an astonishing rich, diverse behavior. To better understand their properties, and for optimization of their applications in nanotechnology, an improved understanding of their mechanical properties is needed. Depending on the size of the vesicles and the specific scientific question, different techniques can be chosen for their mechanical characterization.

GENERAL SIGNIFICANCE

Understanding the mechanical properties of vesicles is necessary to gain deeper insight in the fundamental biological mechanisms involved in vesicle generation and cellular uptake. This furthermore facilitates technological applications such as using vesicles as targeted drug delivery vehicles. Liposome studies provide insight into fundamental membrane processes and properties, whereas the role and functioning of EVs in biology and medicine are increasingly elucidated.

The role of VPS4 in ESCRT-III polymer remodeling

The endosomal sorting complex required for transport-III (ESCRT-III) and VPS4 catalyze a variety of membrane-remodeling processes in eukaryotes and archaea. Common to these processes is the dynamic recruitment of ESCRT-III proteins from the cytosol to the inner face of a membrane neck structure, their activation and filament formation inside or at the membrane neck and the subsequent or concomitant recruitment of the AAA-type ATPase VPS4. The dynamic assembly of ESCRT-III filaments and VPS4 on cellular membranes induces constriction of membrane necks with large diameters such as the cytokinetic midbody and necks with small diameters such as those of intraluminal vesicles or enveloped viruses. The two processes seem to use different sets of ESCRT-III filaments. Constriction is then thought to set the stage for membrane fission. Here, we review recent progress in understanding the structural transitions of ESCRT-III proteins required for filament formation, the functional role of VPS4 in dynamic ESCRT-III assembly and its active role in filament constriction. The recent data will be discussed in the context of different mechanistic models for inside-out membrane fission.

Dissection of structural dynamics of chromatin fibers by single-molecule magnetic tweezers

The accessibility of genomic DNA, as a key determinant of gene-related processes, is dependent on the packing density and structural dynamics of chromatin fiber. However, due to the highly dynamic and heterogeneous properties of chromatin fiber, it is technically challenging to study these properties of chromatin. Here, we report a strategy for dissecting the dynamics of chromatin fibers based on single-molecule magnetic tweezers. Using magnetic tweezers, we can manipulate the chromatin fiber and trace its extension during the folding and unfolding process under tension to investigate the dynamic structural transitions at single-molecule level. The highly accurate and reliable in vitro single-molecule strategy provides a new research platform to dissect the structural dynamics of chromatin fiber and its regulation by different epigenetic factors during gene expression.