Directed assembly of living Pseudomonas aeruginosa bacteria on PEI patterns generated by nanoxerography for statistical AFM bioexperiments

Bacterial Patterning: A Promising Biofabrication Technique

Bacterial patterning has emerged as a pivotal biofabrication technique in the biomedical field. In the past 2 decades, a diverse array of bacterial patterning approaches have been developed to enable the precise manipulation of the spatial distribution of bacterial patterns for various applications. Despite the significance of these advancements, there is a deficiency of review articles providing an overview of bacterial patterning technologies. In this mini-review, we systematically summarize the progress of bacterial patterning over the past 2 decades. This review commences with an elucidation of the definition and fundamental principles of bacterial patterning. Subsequently, we introduce the established bacterial patterning strategies, accompanied by discussions about the advantages and limitations of each approach. Furthermore, we showcase the biomedical applications of these strategies, highlighting their efficacy in spatial control of biofilms, biosensing, and biointervention. Finally, this mini-review is concluded with a summary and an outlook on future challenges and opportunities. It is anticipated that this mini-review can serve as a concise guide for those who are interested in this exciting and rapidly evolving research area.

Patterning of Molecules/Ions via Reverse Micelle Vessels by Nanoxerography

Precise patterning of molecules/ions in the nanometer scale is a crucial but challenging technique for the fabrication of advanced functional nanodevices. We developed a robust method to print molecules/ions into arbitrarily defined patterns with sub-20 nm precision assisted by reverse micelles. The reverse micelle, serving as a nano-sized vessel, can load molecules/ions and then be patterned onto the predefined positions by electrostatic attraction. The number of molecules/ions on each spot, the spot spacing, and pattern shapes can be flexibly adjusted, reaching 10 nm position accuracy, 30 nm spot size, and 100 nm spot spacing (>250,000 DPI). Then, water-soluble dye molecules, protein molecules, and chloroaurate ions were loaded in the micelles and successfully patterned into nanoarrays, which provides an important platform for the convenient, flexible, and robust fabrication of functional molecule/ion-based nanodevices, such as biochips, for high-throughput and ultrasensitive analysis.

Stability of Charge Distributions in Electret Films on the nm-Scale

Electret materials find use in various applications, such as microphones or filter media. In recent years, electrets have been used also increasingly on the micrometer scale, for example, in MEMS or for nano-xerography. However, for these applications, it becomes more important to prepare defined charge structures with sub-micrometer features. On the macroscopic level, the technique of isothermal potential decay at elevated temperatures has been developed to study aging effects and charge retention capabilities in electret materials. Here, we extend this technique to the nm-level by means of AFM-based methods, such as contact charging by AFM and the Kelvin probe force microscopy. Defined charge distributions in polyetherimide (PEI) ULTEM 1000 thin-film electrets have been studied for the first time with a high lateral resolution on the nanometer scale. We found a linear correlation between externally applied contact charging potential on the AFM-tip and the resulting relative surface potential on the PEI film. Charge decay at elevated temperatures is independent from the length scale. The same time dependence as for macroscopic, homogenously charged films could be established. We observe a potential decay only at an elevated temperature of 120 °C and no significant lateral charge transport. Thus, we propose a thermally enhanced charge carrier release from surface traps and a subsequent charge migration to the back electrode as the dominant mechanism. This finding is in-line with the observation that potential decay can be reduced also on the nm-level by pre-annealing the film slightly below the glass transition temperature. In contrast to many polymeric or inorganic electrets, no lateral charge migration is observed. Therefore, the charge patterns are preserved for PEI ULTEM 1000 thin-film electrets, which makes it a good candidate as electret for applications in MEMS or similar applications.

Immobilization of Polyethyleneimine (PEI) on Flat Surfaces and Nanoparticles Affects Its Ability to Disrupt Bacterial Membranes

Interactions between a widely used polycationic polymer, polyethyleneimine (PEI), and a Gram-negative bacteria, E. coli, are investigated using atomic force microscopy (AFM) quantitative imaging. The effect of PEI, a known membrane permeabilizer, is characterized by probing both the structure and elasticity of the bacterial cell envelope. At low concentrations, PEI induced nanoscale membrane perturbations all over the bacterial surface. Despite these structural changes, no change in cellular mechanics (Young’s modulus) was detected and the growth of E. coli is barely affected. However, at high PEI concentrations, dramatic changes in both structure and cell mechanics are observed. When immobilized on a flat surface, the ability of PEI to alter the membrane structure and reduce bacterial elasticity is diminished. We further probe this immobilization-induced effect by covalently attaching the polymer to the surface of polydopamine nanoparticles (PDNP). The nanoparticle-immobilized PEI (PDNP-PEI), though not able to induce major structural changes on the outer membrane of E. coli (in contrast to the flat surface), was able to bind to and reduce the Young’s modulus of the bacteria. Taken together, our data demonstrate that the state of polycationic polymers, whether bound or free—which greatly dictates their overall configuration—plays a major role on how they interact with and disrupt bacterial membranes.

Biopolymer Patterning-Directed Secretion in Mucoid and Nonmucoid Strains of Pseudomonas aeruginosa Revealed by Multimodal Chemical Imaging

Quinolone, pyocyanin, and rhamnolipid production were studied in Pseudomonas aeruginosa by spatially patterning mucin, a glycoprotein important to infection of lung epithelia. Mass spectrometric imaging and confocal Raman microscopy are combined to probe P. aeruginosa biofilms from mucoid and nonmucoid strains grown on lithographically defined patterns. Quinolone signatures from biofilms on patterned vs unpatterned and mucin vs mercaptoundecanoic acid (MUA) surfaces were compared. Microbial attachment is accompanied by secretion of 2-alkyl-4-quinolones as well as rhamnolipids from the mucoid and nonmucoid strains. Pyocyanin was also detected both in the biofilm and in the supernatant in the mucoid strain only. Significant differences in the spatiotemporal distributions of secreted factors are observed between strains and among different surface patterning conditions. The mucoid strain is sensitive to composition and patterning while the nonmucoid strain is not, and in promoting community development in the mucoid strain, nonpatterned surfaces are better than patterned, and mucin is better than MUA. Also, the mucoid strain secretes the virulence factor pyocyanin in a way that correlates with distress. A change in the relative abundance for two rhamnolipids is observed in the mucoid strain during exposure to mucin, whereas minimal variation is observed in the nonmucoid strain. Differences between mucoid and nonmucoid strains are consistent with their strain-specific phenology, in which the mucoid strain develops highly protected and withdrawn biofilms that achieve Pseudomonas quinolone signal production under limited conditions.

Arbitrary Gold Nanoparticle Arrays Fabricated through AFM Nanoxerography and Interfacial Seeded Growth

Based on arrays of Au seeds fabricated with atomic force microscopy (AFM) nanoxerography, the seeded growth of gold nanoparticles (Au NPs) on surface is achieved. The size evolution of Au NPs in each spot is tracked by in situ AFM and SEM images because each spot can be easily localized in the array system. The extinction microspectra extracted in real time with enhanced signals and red-shift can further monitor the increasing size of Au NPs. As a powerful platform, AFM nanoxerography makes it easy to tune the spot size and the intervals among spots in the Au NP arrays without preparing a template. It also allows for fabricating arbitrary patterns including various symbols and graphs. More interestingly, the in situ growth of Au NPs offers an approach to decreasing the interparticle distance, and thus forming closely interconnected Au nanowire assembly, exhibiting immense potential in the nanoelectronic system.

Automated multi-sample acquisition and analysis using atomic force microscopy for biomedical applications

In the last 20 years, atomic force microscopy (AFM) has emerged as a ubiquitous technique in biological research, allowing the analysis of biological samples under near-physiological conditions from single molecules to living cells. Despite its growing use, the low process throughput remains a major drawback. Here, we propose a solution validated on a device allowing a fully automated, multi-sample analysis. Our approach is mainly designed to study samples in fluid and biological cells. As a proof of concept, we demonstrate its feasibility applied to detect and scan both fixed and living bacteria before completion of data processing. The effect of two distinct treatments (i.e. gentamicin and heating) is then evidenced on physical parameters of fixed Yersinia pseudotuberculosis bacteria. The multi-sample analysis presented allows an increase in the number of scanned samples while limiting the user's input. Importantly, cantilever cleaning and control steps are performed regularly-as part of the automated process-to ensure consistent scanning quality. We discuss how such an approach is paving the way to AFM developments in medical and clinical fields, in which statistical significance of results is a prerequisite.

Changes in nanomechanical properties and adhesion dynamics of algal cells during their growth

Nanomechanical and structural characterisations of algal cells are of key importance for understanding their adhesion behaviour at interfaces in the aquatic environment. We examine here the nanomechanical properties and adhesion dynamics of the algal cells during two phases of their growth using complementary surface methods and the mathematical modelling. Mechanical properties of motile cells are hard to assess while keeping cells viable, and studies to date have been limited. Immobilisation of negatively charged cells to a positively charged substrate enables high-resolution AFM imaging and nanomechanical measurements. Cells were stiffer and more hydrophobic in the exponential than in the stationary phase, suggesting molecular modification of the cell envelope during aging. The corresponding properties of algal cells were in agreement with the increase of critical interfacial tensions of adhesion, determined amperometrically. Cells in exponential phase possessed a larger cell volume, in agreement with the large amount of amperometrically measured displaced charge at the interface. Differences in the kinetics of adhesion and spreading of cells at the interface were attributed to their various volumes and nanomechanical properties that varied during cell aging. Our findings contribute to the present body of knowledge on the biophysics of algal cells on a fundamental level.

Algal cell response to laboratory-induced cadmium stress: a multimethod approach

We examined the response of algal cells to laboratory-induced cadmium stress in terms of physiological activity, autonomous features (motility and fluorescence), adhesion dynamics, nanomechanical properties, and protein expression by employing a multimethod approach. We develop a methodology based on the generalized mathematical model to predict free cadmium concentrations in culture. We used algal cells of Dunaliella tertiolecta, which are widespread in marine and freshwater systems, as a model organism. Cell adaptation to cadmium stress is manifested through cell shape deterioration, slower motility, and an increase of physiological activity. No significant change in growth dynamics showed how cells adapt to stress by increasing active surface area against toxic cadmium in the culture. It was accompanied by an increase in green fluorescence (most likely associated with cadmium vesicular transport and/or beta-carotene production), while no change was observed in the red endogenous fluorescence (associated with chlorophyll). To maintain the same rate of chlorophyll emission, the cell adaptation response was manifested through increased expression of the identified chlorophyll-binding protein(s) that are important for photosynthesis. Since production of these proteins represents cell defence mechanisms, they may also signal the presence of toxic metal in seawater. Protein expression affects the cell surface properties and, therefore, the dynamics of the adhesion process. Cells behave stiffer under stress with cadmium, and thus, the initial attachment and deformation are slower. Physicochemical and structural characterizations of algal cell surfaces are of key importance to interpret, rationalize, and predict the behaviour and fate of the cell under stress in vivo.

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

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

Methods of Micropatterning and Manipulation of Cells for Biomedical Applications

Micropatterning and manipulation of mammalian and bacterial cells are important in biomedical studies to perform in vitro assays and to evaluate biochemical processes accurately, establishing the basis for implementing biomedical microelectromechanical systems (bioMEMS), point-of-care (POC) devices, or organs-on-chips (OOC), which impact on neurological, oncological, dermatologic, or tissue engineering issues as part of personalized medicine. Cell patterning represents a crucial step in fundamental and applied biological studies in vitro, hence today there are a myriad of materials and techniques that allow one to immobilize and manipulate cells, imitating the 3D in vivo milieu. This review focuses on current physical cell patterning, plus chemical and a combination of them both that utilizes different materials and cutting-edge micro-nanofabrication methodologies.

Cell biology of microbes and pharmacology of antimicrobial drugs explored by Atomic Force Microscopy

Antimicrobial molecules have been used for more than 50 years now and are the basis of modern medicine. No surgery can nowdays be imagined to be performed without antibiotics; dreadful diseases like tuberculosis, leprosis, siphilys, and more broadly all microbial induced diseases, can be cured only through the use of antimicrobial treatments. However, the situation is becoming more and more complex because of the ability of microbes to adapt, develop, acquire, and share mechanisms of resistance to antimicrobial agents. We choose to introduce this review by briefly drawing the panorama of antimicrobial discovery and development, but also of the emergence of microbial resistance. Then we describe how Atomic Force Microscopy (AFM) can be used to provide a better understanding of the mechanisms of action of these drugs at the nanoscale level on microbial interfaces. In this section, we will address these questions: (1) how does drug treatment affect the morphology of single microbes?; (2) do antimicrobial molecules modify the nanomechanical properties of microbes, or do the nanomechanical properties of microbes play a role in antimicrobial activity and efficiency?; and (3) how are the adhesive abilitites of microbes affected by antimicrobial drugs treatment? Finally, in a second part of this review we focus on recent studies aimed at changing the paradigm of the single molecule/cell technology that AFM typically represents. Recent work dealing with the creation of a microbe array which can be explored by AFM will be presented, as these developments constitute the first steps toward transforming AFM into a higher throughput technology. We also discuss papers using AFM as NanoMechnanicalSensors (NEMS), and demonstrate the interest of such approaches in clinical microbiology to detect quickly and with high accuracy microbial resistance.