Recent advances in AFM-based biological characterization and applications at multiple levels

Design of Liquid Formulation Based on F127-Loaded Natural Dimeric Flavonoids as a New Perspective Treatment for Leishmaniasis

Infectious and Parasitic Diseases (IPD) remain a challenge for medicine due to several interconnected reasons, such as antimicrobial resistance (AMR). American tegumentary leishmaniasis (ATL) is an overlooked IPD causing persistent skin ulcers that are challenging to heal, resulting in disfiguring scars. Moreover, it has the potential to extend from the skin to the mucous membranes of the nose, mouth, and throat in both humans and various animals. Given the limited effectiveness and AMR of current drugs, the exploration of new substances has emerged as a promising alternative for ATL treatment. Arrabidaea brachypoda (DC). Bureau is a native Brazilian plant rich in dimeric flavonoids, including Brachydin (BRA), which displays antimicrobial activity, but still little has been explored regarding the development of therapeutic formulations. In this work, we present the design of a low-cost liquid formulation based on the use of Pluronic F127 for encapsulation of high BRA concentration (LF-B500). The characterization techniques revealed that BRA-loaded F127 micelles are well-stabilized in an unusual worm-like form. The in vitro cytotoxicity assay demonstrated that LF-B500 was non-toxic to macrophages but efficient in the inactivation of forms of Leishmania amazonensis promastigotes with IC50 of 16.06 µg/mL. The results demonstrated that LF-B500 opened a new perspective on the use of liquid formulation-based natural products for ATL treatment.

Hydrodynamic tearing of bacteria on nanotips for sustainable water disinfection

Water disinfection is conventionally achieved by oxidation or irradiation, which is often associated with a high carbon footprint and the formation of toxic byproducts. Here, we describe a nano-structured material that is highly effective at killing bacteria in water through a hydrodynamic mechanism. The material consists of carbon-coated, sharp Cu(OH)2 nanowires grown on a copper foam substrate. We show that mild water flow (e.g. driven from a storage tank) can efficiently tear up bacteria through a high dispersion force between the nanotip surface and the cell envelope. Bacterial cell rupture is due to tearing of the cell envelope rather than collisions. This mechanism produces rapid inactivation of bacteria in water, and achieved complete disinfection in a 30-day field test. Our approach exploits fluidic energy and does not require additional energy supply, thus offering an efficient and low-cost system that could potentially be incorporated in water treatment processes in wastewater facilities and rural communities.

The power of super-resolution microscopy in modern biomedical science

Super-resolution microscopy (SRM) technology that breaks the diffraction limit has revolutionized the field of cell biology since its appearance, which enables researchers to visualize cellular structures with nanometric resolution, multiple colors and single-molecule sensitivity. With the flourishing development of hardware and the availability of novel fluorescent probes, the impact of SRM has already gone beyond cell biology and extended to nanomedicine, material science and nanotechnology, and remarkably boosted important breakthroughs in these fields. In this review, we will mainly highlight the power of SRM in modern biomedical science, discussing how these SRM techniques revolutionize the way we understand cell structures, biomaterials assembly and how assembled biomaterials interact with cellular organelles, and finally their promotion to the clinical pre-diagnosis. Moreover, we also provide an outlook on the current technical challenges and future improvement direction of SRM. We hope this review can provide useful information, inspire new ideas and propel the development both from the perspective of SRM techniques and from the perspective of SRM's applications.

Targeting cell-matrix interface mechanobiology by integrating AFM with fluorescence microscopy

Mechanosensing at the interface of a cell and its surrounding microenvironment is an essential driving force of physiological processes. Understanding molecular activities at the cell-matrix interface has the potential to provide novel targets for improving tissue regeneration and early disease intervention. In the past few decades, the advancement of atomic force microscopy (AFM) has offered a unique platform for probing mechanobiology at this crucial microdomain. In this review, we describe key advances under this topic through the use of an integrated system of AFM (as a biomechanical testing tool) with complementary immunofluorescence (IF) imaging (as an in situ navigation system). We first describe the body of work investigating the micromechanics of the pericellular matrix (PCM), the immediate cell micro-niche, in healthy, diseased, and genetically modified tissues, with a focus on articular cartilage. We then summarize the key findings in understanding cellular biomechanics and mechanotransduction, in which, molecular mechanisms governing transmembrane ion channel-mediated mechanosensing, cytoskeleton remodeling, and nucleus remodeling have been studied in various cell and tissue types. Lastly, we provide an overview of major technical advances that have enabled more in-depth studies of mechanobiology, including the integration of AFM with a side-view microscope, multiple optomicroscopy, a fluorescence recovery after photobleaching (FRAP) module, and a tensile stretching device. The innovations described here have contributed greatly to advancing the fundamental knowledge of extracellular matrix biomechanics and cell mechanobiology for improved understanding, detection, and intervention of various diseases.

Surface characterization of an ultra-soft contact lens material using an atomic force microscopy nanoindentation method

As new ultra-soft materials are being developed for medical devices and biomedical applications, the comprehensive characterization of their physical and mechanical properties is both critical and challenging. To characterize the very low surface modulus of the novel biomimetic lehfilcon A silicone hydrogel contact lens coated with a layer of a branched polymer brush structure, an improved atomic force microscopy (AFM) nanoindentation method has been applied. This technique allows for precise contact-point determination without the effects of viscous squeeze-out upon approaching the branched polymer. Additionally, it allows individual brush elements to be mechanically characterized in the absence of poroelastic effects. This was accomplished by selecting an AFM probe with a design (tip size, geometry, and spring constant) that was especially suited to measuring the properties of soft materials and biological samples. The enhanced sensitivity and accuracy of this method allows for the precise measurement of the very soft lehfilcon A material, which has an extremely low elastic modulus in the surface region (as low as 2 kPa) and extremely high elasticity (nearly 100%) in an aqueous environment. The surface-characterization results not only reveal the ultra-soft nature of the lehfilcon A lens surface but also demonstrate that the elastic modulus exhibits a 30 kPa/200 nm gradient with depth due to the disparity between the modulus of the branched polymer brushes and the SiHy substrate. This surface-characterization methodology may be applied to other ultra-soft materials and medical devices.

Thin head atomic force microscope for integration with optical microscope

We present a novel thin head atomic force microscope (AFM) that can be easily integrated with an upright optical microscope (OM). The optical beam detection unit in the AFM used an obliquely incident laser beam onto the cantilever, reducing the AFM head's effective thickness to 7.3 mm. That allows an open space above the cantilever probe to accommodate the objective lens up to 0.6 numerical aperture (N.A.) without obstruction. A multi-function digital controller was developed to control the AFM and reserved interfaces to communicate with the OM. To assess the performance of the developed AFM, we first measured the noise level and bandwidths of the AFM system. Then, the imaging quality of the AFM was evaluated by both calibration grids and two-dimensional materials. Finally, the thin head AFM was integrated into a homemade white light interferometer as a demonstration of combined use with an advanced optical system. The experimental results demonstrated that our developed AFM is suitable for integration under upright OM and brings AFM high-resolution advantages to the existing OM system.

Surface aspects and multifractal features of 3D spatial patterns of low-cost Amazon açaí-loaded kefir microbial films

In this study, açaí-loaded kefir microbial films obtained in solutions containing demerara sugar, a low-cost and relatively organic sugar, were prepared. Environmental scanning electron microscopy (ESEM), atomic force microscopy (AFM), stereometric and multifractal analyses were applied to study the influence of the concentration of açaí over the surface morphology as well as its multifractal nature. The ESEM and AFM images showed that low concentrations of acai berry form surface covered by bacteria, while higher concentrations promote yeast growth. The autocorrelation function suggested that the degree of surface anisotropy changes as the concentration of açaí increases, while the Minkowski Functionals confirmed that the sample with the highest content has a different morphology than the samples containing 10-40 ml. The multifractal analysis revealed that the surfaces have a strong multifractal behavior, where the multifractal singularity strength was higher in the sample containing the highest concentration of açaí. The sample with the highest concentration was then mapped to have a greater vertical growth of its spatial patterns. These results prove that image analysis using mathematical tools can be very useful for the characterization of biological-based systems for application in the biomedicine field. We characterized the micromorphology of the 3D surface of the kefir biofilms associated with Acai extract. The 3D surface analysis of the samples was performed using by environmental scanning electron microscope and atomic force microscopy. We determined the multifractal and Minkowski Functionals of the analyzed samples.

Tooth Wear and Tribological Investigations in Dentistry

Dental or tooth wear is a physiological process in the life cycle of teeth. Loss of the occlusal surface may cause excessive tooth wear. Several factors may contribute to tooth wear with different intensities and duration in the oral cavity. The oral cavity is generally compared to a tribological system to determine the various types of wear between teeth and restorative materials and assess the amount of dental wear. However, it is challenging to investigate in vitro and in vivo wear owing to the complexity of tooth wear; thus, a clear correlation between in vitro and in vivo data could not be established. This review is aimed at providing an insight into the etiology of tooth wear and tribological investigations in dentistry.

A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices

Single-molecule techniques have shifted the paradigm of biological measurements from ensemble measurements to probing individual molecules and propelled a rapid revolution in related fields. Compared to ensemble measurements of biomolecules, single-molecule techniques provide a breadth of information with a high spatial and temporal resolution at the molecular level. Usually, optical and electrical methods are two commonly employed methods for probing single molecules, and some platforms even offer the integration of these two methods such as optofluidics. The recent spark in technological advancement and the tremendous leap in fabrication techniques, microfluidics, and integrated optofluidics are paving the way toward low cost, chip-scale, portable, and point-of-care diagnostic and single-molecule analysis tools. This review provides the fundamentals and overview of commonly employed single-molecule methods including optical methods, electrical methods, force-based methods, combinatorial integrated methods, etc. In most single-molecule experiments, the ability to manipulate and exercise precise control over individual molecules plays a vital role, which sometimes defines the capabilities and limits of the operation. This review discusses different manipulation techniques including sorting and trapping individual particles. An insight into the control of single molecules is provided that mainly discusses the recent development of electrical control over single molecules. Overall, this review is designed to provide the fundamentals and recent advancements in different single-molecule techniques and their applications, with a special focus on the detection, manipulation, and control of single molecules on chip-scale devices.

What makes carbon nanoparticle a potent material for biological application?

Carbon materials are generally utilized in the form of carbon allotropes and their characteristics are exploited as such or for improving the thermal, electrical, optical, and mechanical properties of other biomaterials. This has now found a broader share in conventional biomaterial space with the generation of nanodiamond, carbon dot, carbon nanoparticles (CNPs), and so forth. With properties of better biocompatibility, intrinsic optical emission, aqueous suspendability, and easier surface conjugation possibilities made CNPs as one of the fore most choice for biological applications especially for use in intracellular spaces. There are various reports available presenting methods of preparing, characterizing, and using CNPs for various biological applications but a collection of information on what makes CNP a suitable biomaterial to achieve those biological activities is yet to be provided in a significant way. Herein, a series of correlations among synthesis, characterization, and mode of utilization of CNP have been incorporated along with the variations in its use as agent for sensing, imaging, and therapy of different diseases or conditions. It is ensembled that how simplified and optimized methods of synthesis is correlated with specific characteristics of CNPs which were found to be suitable in the specific biological applications. These comparisons and correlations among various CNPs, will surely provide a platform to generate new edition of this nanomaterial with improvised applications and newer methods of evaluating structural, physical, and functional properties. This may ensure the eventual use of CNPs for human being for specific need in near future. This article is categorized under: Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Diagnostic Tools > Biosensing Diagnostic Tools > In Vitro Nanoparticle-Based Sensing Therapeutic Approaches and Drug Discovery > Emerging Technologies.

Determining the Stoichiometry of Amyloid Oligomers by Single-Molecule Photobleaching

Small oligomers are the initial intermediates in the pathway to amyloid fibril formation. They have a distinct identity from the monomers as well as from the protofibrils and the fibrils, both in their structure and in their properties. In many cases, they play a crucial biological role. However, due to their transient nature, they are difficult to characterize. "Oligomer" is a diffuse definition, encompassing aggregates of many different sizes, and this lack of precise definition causes much confusion and disagreement between different research groups. Here, we define the small oligomers as "n"-mers with n < 10, which is the size range in which the amyloid proteins typically exist at the initial phase of the aggregation process. Since the oligomers dynamically interconvert into each other, a solution of aggregating amyloid proteins will contain a distribution of sizes. A precise characterization of an oligomeric solution will, therefore, require quantification of the relative population of each size. Size-based separation methods, such as size-exclusion chromatography, are typically used to characterize this distribution. However, if the interconversion between oligomers of different sizes is fast, this would not yield reliable results. Single-molecule photobleaching (smPB) is a direct method to evaluate this size distribution in a heterogeneous solution without separation. In addition, understanding the mechanism of action of amyloid oligomers requires knowing the affinity of each oligomer type to different cellular components, such as the cell membrane. These measurements are also amenable to smPB. Here we show how to perform smPB, both for oligomers in solution and for oligomers attached to the membrane.

Late Changes in the Extracellular Matrix of the Bladder after Radiation Therapy for Pelvic Tumors

Radiation therapy is one of the cardinal approaches in the treatment of malignant tumors of the pelvis. It leads to the development of radiation-induced complications in the normal tissues. Thus, the evaluation of radiation-induced changes in the extracellular matrix of the normal tissue is deemed urgent, since connective tissue stroma degradation plays a crucial role in the development of Grade 3-4 adverse effects (hemorrhage, necrosis, and fistula). Such adverse effects not only drastically reduce the patients' quality of life but can also become life-threatening. The aim of this study is to quantitatively analyze the bladder collagen state in patients who underwent radiation therapy for cervical and endometrial cancer and in patients with chronic bacterial cystitis and compare them to the normal bladder extracellular matrix.

MATERIALS AND METHODS

One hundred and five patients with Grade 2-4 of radiation cystitis, 67 patients with bacterial chronic cystitis, and 20 volunteers without bladder pathology were enrolled. Collagen changes were evaluated depending on its hierarchical level: fibrils and fibers level by atomic force microscopy; fibers and bundles level by two-photon microscopy in the second harmonic generation (SHG) mode; general collagen architectonics by cross-polarization optical coherence tomography (CP OCT).

RESULTS

The main sign of the radiation-induced damage of collagen fibrils and fibers was the loss of the ordered "basket-weave" packing and a significant increase in the total area of ruptures deeper than 1 µm compared to the intact sample. The numerical analysis of SHG images detected that a decrease in the SHG signal intensity of collagen is correlated with the increase in the grade of radiation cystitis. The OCT signal brightness in cross-polarization images demonstrated a gradual decrease compared to the intact bladder depending on the grade of the adverse event.

CONCLUSIONS

The observed correspondence between the extracellular matrix changes at the microscopic level and at the level of the general organ architectonics allows for the consideration of CP OCT as a method of "optical biopsy" in the grading of radiation-induced collagen damage.

Unlocking the secret of lignin-enzyme interactions: Recent advances in developing state-of-the-art analytical techniques

Bioconversion of renewable lignocellulosics to produce liquid fuels and chemicals is one of the most effective ways to solve the problem of fossil resource shortage, energy security, and environmental challenges. Among the many biorefinery pathways, hydrolysis of lignocellulosics to fermentable monosaccharides by cellulase is arguably the most critical step of lignocellulose bioconversion. In the process of enzymatic hydrolysis, the direct physical contact between enzymes and cellulose is an essential prerequisite for the hydrolysis to occur. However, lignin is considered one of the most recalcitrant factors hindering the accessibility of cellulose by binding to cellulase unproductively, which reduces the saccharification rate and yield of sugars. This results in high costs for the saccharification of carbohydrates. The various interactions between enzymes and lignin have been explored from different perspectives in literature, and a basic lignin inhibition mechanism has been proposed. However, the exact interaction between lignin and enzyme as well as the recently reported promotion of some types of lignin on enzymatic hydrolysis is still unclear at the molecular level. Multiple analytical techniques have been developed, and fully unlocking the secret of lignin-enzyme interactions would require a continuous improvement of the currently available analytical techniques. This review summarizes the current commonly used advanced research analytical techniques for investigating the interaction between lignin and enzyme, including quartz crystal microbalance with dissipation (QCM-D), surface plasmon resonance (SPR), attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy, atomic force microscopy (AFM), nuclear magnetic resonance (NMR) spectroscopy, fluorescence spectroscopy (FLS), and molecular dynamics (MD) simulations. Interdisciplinary integration of these analytical methods is pursued to provide new insight into the interactions between lignin and enzymes. This review will serve as a resource for future research seeking to develop new methodologies for a better understanding of the basic mechanism of lignin-enzyme binding during the critical hydrolysis process.

Development of a flexure-based nano-actuator for high-frequency high-resolution directional sensing with atomic force microscopy

Scanning probe microscopies typically rely on the high-precision positioning of a nanoscale probe in order to gain local information about the properties of a sample. At a given location, the probe is used to interrogate a minute region of the sample, often relying on dynamical sensing for improved accuracy. This is the case for most force-based measurements in atomic force microscopy (AFM) where sensing occurs with a tip oscillating vertically, typically in the kHz to MHz frequency regime. While this approach is ideal for many applications, restricting dynamical sensing to only one direction (vertical) can become a serious limitation when aiming to quantify the properties of inherently three-dimensional systems, such as a liquid near a wall. Here, we present the design, fabrication, and calibration of a miniature high-speed scanner able to apply controlled fast and directional in-plane vibrations with sub-nanometer precision. The scanner has a resonance frequency of ∼35 kHz and is used in conjunction with a traditional AFM to augment the measurement capabilities. We illustrate its capabilities at a solid-liquid interface where we use it to quantify the preferred lateral flow direction of the liquid around every sample location. The AFM can simultaneously acquire high-resolution images of the interface, which can be superimposed with the directional measurements. Examples of sub-nanometer measurements conducted with the new scanner are also presented.

AFM-Based Correlative Microscopy Illuminates Human Pathogens

Microbes have an arsenal of virulence factors that contribute to their pathogenicity. A number of challenges remain to fully understand disease transmission, fitness landscape, antimicrobial resistance and host heterogeneity. A variety of tools have been used to address diverse aspects of pathogenicity, from molecular host-pathogen interactions to the mechanisms of disease acquisition and transmission. Current gaps in our knowledge include a more direct understanding of host-pathogen interactions, including signaling at interfaces, and direct phenotypic confirmation of pathogenicity. Correlative microscopy has been gaining traction to address the many challenges currently faced in biomedicine, in particular the combination of optical and atomic force microscopy (AFM). AFM, generates high-resolution surface topographical images, and quantifies mechanical properties at the pN scale under physiologically relevant conditions. When combined with optical microscopy, AFM probes pathogen surfaces and their physical and molecular interaction with host cells, while the various modes of optical microscopy view internal cellular responses of the pathogen and host. Here we review the most recent advances in our understanding of pathogens, recent applications of AFM to the field, how correlative AFM-optical microspectroscopy and microscopy have been used to illuminate pathogenicity and how these methods can reach their full potential for studying host-pathogen interactions.

Non-invasive acquisition of mechanical properties of cells via passive microfluidic mechanisms: A review

The demand to understand the mechanical properties of cells from biomedical, bioengineering, and clinical diagnostic fields has given rise to a variety of research studies. In this context, how to use lab-on-a-chip devices to achieve accurate, high-throughput, and non-invasive acquisition of the mechanical properties of cells has become the focus of many studies. Accordingly, we present a comprehensive review of the development of the measurement of mechanical properties of cells using passive microfluidic mechanisms, including constriction channel-based, fluid-induced, and micropipette aspiration-based mechanisms. This review discusses how these mechanisms work to determine the mechanical properties of the cell as well as their advantages and disadvantages. A detailed discussion is also presented on a series of typical applications of these three mechanisms to measure the mechanical properties of cells. At the end of this article, the current challenges and future prospects of these mechanisms are demonstrated, which will help guide researchers who are interested to get into this area of research. Our conclusion is that these passive microfluidic mechanisms will offer more preferences for the development of lab-on-a-chip technologies and hold great potential for advancing biomedical and bioengineering research studies.

In-Situ Investigation on Nanoscopic Biomechanics of Streptococcus mutans at Low pH Citric Acid Environments Using an AFM Fluid Cell

Streptococcus mutans (S. mutans) is widely regarded as the main cause of human dental caries via three main virulence factors: adhesion, acidogenicity, and aciduricity. Citric acid is one of the antibiotic agents that can inhibit the virulence capabilities of S. mutans. A full understanding of the acidic resistance mechanisms (ARMs) causing bacteria to thrive in citrate transport is still elusive. We propose atomic force microscopy (AFM) equipped with a fluid cell to study the S. mutans ARMs via surface nanomechanical properties at citric acid pH 3.3, 2.3, and 1.8. Among these treatments, at pH 1.8, the effect of the citric acid shock in cells is demonstrated through a significantly low number of high adhesion zones, and a noticeable reduction in adhesion forces. Consequently, this study paves the way to understand that S. mutans ARMs are associated with the variation of the number of adhesion zones on the cell surface, which is influenced by citrate and proton transport. The results are expected to be useful in developing antibiotics or drugs involving citric acid for dental plaque treatment.